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Bibliography on: The Denisovans, Another Human Ancestor



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The Denisovans, Another Human Ancestor

Wikipedia: The Denisovans are an extinct species or subspecies of human in the genus Homo. In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female who lived about 41,000 years ago, found in the remote Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans. Two teeth belonging to different members of the same population have since been reported. In November 2015, a tooth fossil containing DNA was reported to have been found and studied. A bone needle dated to 50,000 years ago was discovered at the archaeological site in 2016 and is described as the most ancient needle known. Analysis of the mitochondrial DNA (mtDNA) of the finger bone showed it to be genetically distinct from the mtDNAs of Neanderthals and modern humans. Subsequent study of the nuclear genome from this specimen suggests that Denisovans shared a common origin with Neanderthals, that they ranged from Siberia to Southeast Asia, and that they lived among and interbred with the ancestors of some modern humans. A comparison with the genome of a Neanderthal from the same cave revealed significant local interbreeding with local Neanderthal DNA representing 17% of the Denisovan genome, while evidence was also detected of interbreeding with an as yet unidentified ancient human lineage.

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Citations The Papers (from PubMed®)

RevDate: 2019-04-16

Jones M, Denisova A, Mitchell S, et al (2019)

Acceptability of a Plasticity-Focused Serious Game Intervention for Posttraumatic Stress Disorder: User Requirements Analysis.

JMIR serious games, 7(2):e11909 pii:v7i2e11909.

BACKGROUND: Trauma-focused cognitive behavioral therapy (TF-CBT) is a first-line treatment for posttraumatic stress disorder (PTSD). Despite a solid evidence base, TF-CBT response and attrition rates vary considerably. Plasticity-focused interventions, including the use of serious games, have the potential to improve TF-CBT response and treatment retention.

OBJECTIVE: The aim of this study was to assess the acceptability of a mobile phone-delivered plasticity-focused serious game to improve response to TF-CBT for PTSD, and carry out a user requirements analysis should the development of a prototype be warranted.

METHODS: We conducted 2 one-to-one interviews (n=2), one focus group involving service users who had received a diagnosis of PTSD (n=3) and one focus group involving psychological trauma service clinicians (n=4).

RESULTS: We found that the concept of a plasticity-focused mobile phone intervention for PTSD is acceptable to patients and clinicians. Service users and clinicians both believed that the usage should be guided by a therapist, and both contributed useful inputs regarding the audiovisual aspects of the proposed serious game. It was accepted that the game would not be suitable for all patients and that clinicians would need to appropriately prescribe the usage of the game.

CONCLUSIONS: The findings highlight the acceptability of the proposed serious game and clarify the user requirements for such an intervention. It is the intention of the authors to carry out a user experience evaluation using a prototype serious game in a clinical population.

RevDate: 2019-04-16

Ragino YI, Shcherbakova LV, Denisova DV, et al (2019)

[Blood lipids and angina pectoris (by epidemiological cardiological Rose questionnaire) in the population of 25-45 years of Novosibirsk].

Kardiologiia, 59(3S):30-35.

The aim of the study was to investigate the prevalence of angina pectoris (AP) according to the standardized epidemiological questionnaire of Rose in the population of 25-45 years of Novosibirsk and to identify its association with some lipid and non-lipid risk factors for coronary heart disease (CHD).

MATERIAL AND METHODS: Cross-sectional survey of the population aged 25-45 in Novosibirsk was carried out. The study included 1439 people (656 men and 783 women). Within the framework of the complex survey program, the standardized epidemiological questionnaire of Rose (WHO, 1984) was used. Blood levels of total cholesterol (total C), triglycerides (TG), low and high density lipoprotein cholesterol (LDL-C, HDL-C) were determinate by biochemical methods.

RESULTS: For all lipid indicators, significant differences were found between men and women. The levels of total C, TG and LDL-C were significantly higher, and the level of HDL-C was lower in men, than in women. According to the Rose questionnaire, out of 1439 people included in the study, 12 patients (0.8%) had AP (75% women). In persons with AP, blood levels of TG were 1.8 times higher, and the levels of HDL-C in blood was 1.2 times lower compared to persons without AP. Univariate analysis of associations of AP with CHD risk factors showed that the chance of developing angina pectoris in the population of 25-45 years was significantly increased in individuals with high blood TG levels (OR 3,515, DI 1,106-11,168, p = 0.039) and low HDL-C (OR 1,203, DI 1,054-1,372, p = 0.006). A natural, although statistically not significant (OR 3,165, p=0,055, due to the small number of groups with AP) increasing in the chance of developing AP in hypertension was detected.

CONCLUSION: In the young population of 25-45 years in Novosibirsk, elevated blood levels of TG, reduced levels of HDL-C, and hypertension were associated with AP, according to Rosecardiological questionnaire, which underlines the importance of conducting screening surveys of the young population to improve effective prevention and treatment of diseases.

RevDate: 2019-04-16

Kuznetsov AA, Tsvetkova EE, Denisova DV, et al (2019)

[Central Aortic Pressure: Reference and Diagnostic Values].

Kardiologiia, 59(3):11-17.

OBJECTIVE: Practical application of central aortic pressure (CAP) parameters is limited by the absence of generally recognized reference and threshold diagnostic indices. The purpose of this work is to establish their values in the general population of Novosibirsk. Materials and Methods. A total of 327 people were examined: 155 men and 172 women aged 25-44 years from a representative sample from the general population of Novosibirsk. Applanation tonometry of the radial artery was performed by the SphygmoCor system. The reference values of CAP parameters were obtained by a nonparametric method according to the Clinical and Laboratory Standards Institute (CLSI) recommendations (95 % percentile interval with 2.5 % and 97.5 % cut-off points and their 90 % confidence intervals). Diagnostic thresholds and categories of CAP were determined as mean values depending on the categories of brachial arterial pressure (BP) and on the basis of risk estimates, as well as sensitivity and specificity values for left ventricular hypertrophy similar to risk and sensitivity and specificity values of threshold levels (categories) of brachial BP.

RESULTS: The reference values of the parameters of the CAP were: 18-43 mm Hg for pulse pressure; 5-24 mm Hg for the amplification of pulse pressure; - 8.8-40 % for the augmentation index. Diagnostic categories of CAP were determined to be: optimal - less than 110 / 80, normal - 110 / 80-114 / 84, high normal - 115 / 85-124 / 89, hypertension - more than 125 / 90 mm Hg.

CONCLUSION: The reference values, diagnostic thresholds and categories of parameters of CAP in the general population of Novosibirsk aged 25-44 years have been determined. It is expedient to further study them.

RevDate: 2019-04-14

Jacobs GS, Hudjashov G, Saag L, et al (2019)

Multiple Deeply Divergent Denisovan Ancestries in Papuans.

Cell pii:S0092-8674(19)30218-1 [Epub ahead of print].


RevDate: 2019-04-03

Harris DN, Ruczinski I, Yanek LR, et al (2019)

Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.

Genome biology and evolution pii:5426762 [Epub ahead of print].

The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (> 20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.

RevDate: 2019-03-19

Vyas DN, CJ Mulligan (2019)

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history.

American journal of physical anthropology [Epub ahead of print].

OBJECTIVES: Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history.

MATERIALS AND METHODS: We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes.

RESULTS: We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes.

DISCUSSION: We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.

RevDate: 2019-03-19

Alexeeva E, Dvoryakovskaya T, Denisova R, et al (2019)

Dynamics of concomitant therapy in children with juvenile idiopathic arthritis treated with etanercept and methotrexate.

Pediatrics and neonatology pii:S1875-9572(18)30396-6 [Epub ahead of print].

BACKGROUND: Both the steroid- and NSAID-sparing effects of biologics in juvenile idiopathic arthritis (JIA) treatment are key aspects of the dynamics of patient's condition. The proper selection of biologics enables maximum treatment effectiveness and reduction of the dosage of concomitant therapy. Our aim was to study the dynamics of concomitant therapy during etanercept (ETA) and methotrexate (MTX) treatment in patients with JIA.

METHODS: This analysis included 215 JIA patients (63.3% females) showing sufficient response to main therapy. One hundred patients received MTX as main therapy, 24 received ETA monotherapy, and 91 received ETA þ MTX combination therapy. The dynamics of concomitant therapy were analyzed after 1 month, every 3 months during the first year, and every 6 months during the long-term follow-up (up to 5 years).

RESULTS: At the baseline, 24 (11.2%) patients received concomitant oral glucocorticoids (orGCs) and NSAIDs; the remaining 191 (88.8%) patients were treated with concomitant NSAIDs only. Within 1-year treatment, NSAIDs were discontinued in 162 (75.3%) patients. There were no significant differences in the dynamics of withdrawal of NSAIDs in patients who received and did not receive concomitant MTX. However, the percentage of treatment discontinuation in the MTX group was significantly lower compared to the other two groups (p < 0.001). Oral GCs were discontinued completely in 4 children (16.7%), and the dose of oral GCs was reduced in another 4 patients (16.7%). By the end of the follow-up period, 44 of 115 patients (38.3%) treated with ETA in combination with any concomitant therapy could switch to ETA monotherapy.

CONCLUSION: Therapy with ETA makes it possible to reduce the dosage or completely discontinue most concomitant medications (orGCs, NSAIDs, MTX) in a significant percentage of patients. This reduces the risk of development of NSAID- and GC-induced pathological conditions, while the effectiveness of therapy of the underlying condition remains high.

RevDate: 2019-03-23

Kovalkova NA, Ragino YI, Hudyakovа AD, et al (2019)


Kardiologiia, 59(2):32-37.

PURPOSE: to study blood pressure levels and the prevalence of hypertension in persons aged 25-45 years in Novosibirsk.

MATERIALS AND METHODS: A cross-sectional population study in one of typical areas of Novosibirsk was performed in 2013-2016. The study included 479 men and 612 women aged 25-45 years. Arterial hypertension was defined as blood pressure (BP) ≥140 / 90 mmHg according to Russian recommendations (2004). For analysis two age groups were distinguished: 25-34 years and 35-45 years.

RESULTS: Mean values of systolic and diastolic BP were significantly lower in women than in men in age groups. In men and women, the analyzed indicators were significantly higher in the older than in the younger age group. Mean values of pulse pressure in men were significantly higher than in women in both age groups, there were no differences in the analyzed index between age groups in either men or women. Optimal BP was more often recorded among women than among men in both age groups. The proportion of persons with normal BP among men was grate than among women in both age groups. In the age group 35-45 years compared with the younger group, in men there was a decrease in incidence of category with BP<140 / 90 mmHg, an increase of the proportion of persons with hypertension grades 1 and 2, the appearance of persons with grade 3 hypertension; in women - an increase of the proportion of individuals with normal, high-normal BP, and with grade 1 hypertension, appearance of individuals with grades 2 and 3 hypertension. Frequency of BP categories ≥140 / 90 mmHg in age group 25-34 years among men was 17.6 %, among women 3.1 % (p<0.0001); in age group 35-45 years among men - 34.7 %, among women - 12.5 % (p<0.0001).

CONCLUSIONS: Prevalence of hypertension in men was 28 %, in women - 9 %. Favorable tendencies of BP indicators in both sexes were revealed over a 30-year period, while gender differences did not change.

RevDate: 2019-02-18

Buttura RV, Ramalho J, Lima THA, et al (2019)

HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels.

Human immunology, 80(2):112-119.

HLA-F is one of the most conserved loci among the HLA gene family. The exact function of HLA-F is still under investigation. HLA-F might present tolerogenic features, participate in the stabilization of HLA molecules in open conformation, and also participate in the recycling of HLA molecules. Here we evaluate the variability and haplotype structure of the HLA-F distal promoter segment (from -1893 to -943) and how this segment is correlated with the coding region. Variability at the promoter segment was surveyed in 196 Brazilian samples using second-generation sequencing. The HLA-F promoter region presents two major haplotype lineages. Most of the variable sites are in perfect linkage and associated with a single promoter haplotype, here named F∗distal-C. This haplotype is associated with F∗01:01:02 alleles, while alleles from the F∗01:01:01 or F∗01:03 groups present closely related promoter sequences. F∗distal-C is quite frequent in Brazil and in worldwide populations, with frequencies ranging from 8.41% at the Iberian Population in Spain to 34.34% in Vietnam. F∗distal-C is also present in Neanderthal and Denisovan samples. In silico analyses demonstrated that F∗distal-C presents a different transcription factor binding profile compared with other HLA-F promoters. Moreover, individuals carrying this haplotype present higher HLA-F mRNA expression levels. Functional studies are required to define the exact mechanism underlying this higher HLA-F mRNA expression level associated with F∗distal-C and F∗01:01:02 alleles.

RevDate: 2019-02-17

James WPT, Johnson RJ, Speakman JR, et al (2019)

Nutrition and its role in human evolution.

Journal of internal medicine [Epub ahead of print].

Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300 000 years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50 000-100 000 years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.

RevDate: 2019-02-14

Denisova EI, Korolev AA, Nikitenko EI, et al (2018)

[Hygienic assessment of indoles in the diet of medical students].

Voprosy pitaniia, 87(6):22-27.

A number of studies have shown the relationship between the regular consumption of cruciferous vegetables and the risk of malignant tumors in certain localizations, the activation of mechanisms of alimentary adaptation of the organism under conditions of alien loads, by inducing enzymes of the biotransformation system of xenobiotics. The cruciferous vegetables are distinguished by the presence of minor components, such as indole-3-carbinol, formed during the hydrolysis of glucosinolates. The aim of the investigation was a retrospective study of the content of indoles in students' diet with subsequent quantitative analysis in different comparison groups. The study involved 250 students from a medical university aged 21 to 27 years. To assess the actual nutrition, the developed questionnaires were used, which included the most common products in the Moscow region, sources of indole glucosinolates. It was found that 44% of the respondents didn't include cruciferous vegetables in the diet, and of those who consumed sources of indoles (56% of respondents), only about half received them in the recommended amount. It should also be noted that as in men, in women the most commonly used in the diet product as a source of indoles was cabbage, it was included in the diet of 68% of the respondents who used cruciferous vegetables, rarely pekin cabbage was used (16.3%) and broccoli (16.3%). Cauliflower, radishes, Kale and horseradish was included in the diet of 7.8-14.9% of the students. Less often turnip was consumed - only by 2.1% of the students. No significant differences in the consumption of indoles in the student with deficient, normal or overweight was revealed. Also, there was no correlation between excess weight and the consumption of various indoles sources. The obtained results testify to the extremely low level of alimentary intake of indole-3-carbinol.

RevDate: 2019-02-14

Gringolts ML, Denisova YI, Finkelshtein ES, et al (2019)

Olefin metathesis in multiblock copolymer synthesis.

Beilstein journal of organic chemistry, 15:218-235.

Multiblock copolymers constitute a basis for an emerging class of nanomaterials that combine various functional properties with durability and enhanced mechanical characteristics. Our mini-review addresses synthetic approaches to the design of multiblock copolymers from unsaturated monomers and polymers using olefin metathesis reactions and other ways of chemical modification across double C=C bonds. The main techniques, actively developed during the last decade and discussed here, are the coupling of end-functionalized blocks, sequential ring-opening metathesis polymerization, and cross metathesis between unsaturated polymers, or macromolecular cross metathesis. The last topic attracts special interest due to its relative simplicity and broad opportunities to tailor the structure and hence the properties of the copolymer products. Whenever possible, we analyze the structure-property relations for multiblock copolymers and point to their possible practical applications.

RevDate: 2019-03-23

Bulynko SA, Denisova OA, Soldatsky YL, et al (2018)

[The observation of two cases of isolated parapharyngeal abscess in a single child].

Vestnik otorinolaringologii, 83(6):44-45.

This article reports a rare observation of the simultaneous appearance of two isolated parapharyngeal abscesses in a 3 year-old child.

RevDate: 2019-02-15
CmpDate: 2019-02-12

Dennell R (2019)

Dating of hominin discoveries at Denisova.

Nature, 565(7741):571-572.

RevDate: 2019-02-11

Douka K, Slon V, Jacobs Z, et al (2019)

Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave.

Nature, 565(7741):640-644.

Denisova Cave in the Siberian Altai (Russia) is a key site for understanding the complex relationships between hominin groups that inhabited Eurasia in the Middle and Late Pleistocene epoch. DNA sequenced from human remains found at this site has revealed the presence of a hitherto unknown hominin group, the Denisovans1,2, and high-coverage genomes from both Neanderthal and Denisovan fossils provide evidence for admixture between these two populations3. Determining the age of these fossils is important if we are to understand the nature of hominin interaction, and aspects of their cultural and subsistence adaptations. Here we present 50 radiocarbon determinations from the late Middle and Upper Palaeolithic layers of the site. We also report three direct dates for hominin fragments and obtain a mitochondrial DNA sequence for one of them. We apply a Bayesian age modelling approach that combines chronometric (radiocarbon, uranium series and optical ages), stratigraphic and genetic data to calculate probabilistically the age of the human fossils at the site. Our modelled estimate for the age of the oldest Denisovan fossil suggests that this group was present at the site as early as 195,000 years ago (at 95.4% probability). All Neanderthal fossils-as well as Denisova 11, the daughter of a Neanderthal and a Denisovan4-date to between 80,000 and 140,000 years ago. The youngest Denisovan dates to 52,000-76,000 years ago. Direct radiocarbon dating of Upper Palaeolithic tooth pendants and bone points yielded the earliest evidence for the production of these artefacts in northern Eurasia, between 43,000 and 49,000 calibrated years before present (taken as AD 1950). On the basis of current archaeological evidence, it may be assumed that these artefacts are associated with the Denisovan population. It is not currently possible to determine whether anatomically modern humans were involved in their production, as modern-human fossil and genetic evidence of such antiquity has not yet been identified in the Altai region.

RevDate: 2019-02-11

Jacobs Z, Li B, Shunkov MV, et al (2019)

Timing of archaic hominin occupation of Denisova Cave in southern Siberia.

Nature, 565(7741):594-599.

The Altai region of Siberia was inhabited for parts of the Pleistocene by at least two groups of archaic hominins-Denisovans and Neanderthals. Denisova Cave, uniquely, contains stratified deposits that preserve skeletal and genetic evidence of both hominins, artefacts made from stone and other materials, and a range of animal and plant remains. The previous site chronology is based largely on radiocarbon ages for fragments of bone and charcoal that are up to 50,000 years old; older ages of equivocal reliability have been estimated from thermoluminescence and palaeomagnetic analyses of sediments, and genetic analyses of hominin DNA. Here we describe the stratigraphic sequences in Denisova Cave, establish a chronology for the Pleistocene deposits and associated remains from optical dating of the cave sediments, and reconstruct the environmental context of hominin occupation of the site from around 300,000 to 20,000 years ago.

RevDate: 2019-01-23

Henry JP (2019)

[Genetics and origin of Homo sapiens].

Medecine sciences : M/S, 35(1):39-45.

Usually, paleoanthropology studies remains and artefacts. However, more recently, genetics offer new avenues. Information on humanisation mechanisms has been obtained from comparison with primate or archaic Homo DNA sequences. Likewise, the 1 000 Genomes Project has characterized the geographic spectrum of human genetic variation offering a basis for a genomic study of Homo sapiens phylogeny. From these studies, a model, Out of Africa, was derived. His origin is Africa, where he lived 200 000 years ago. A small fraction of the population left Africa between 50 and 100 000 years ago that have populated the rest of the world, to Europe, coastal Asia to Australia and mainland Asia to Behring Land Bridge and America. The model is supported by the decrease of genetic diversity with the distance to Eastern Africa (serial founder effect). In Europe and Asia, Homo sapiens met archaic Homo neanderthalis and H denisova. The presence of 1-3% neanderthalis sequences in modern Homo ADN indicates admixtures between these groups. Some archaic sequences are on positive selection pressure, thus suggesting that the extinct hominins might have facilitated the adaptation of H sapiens to new environments.

RevDate: 2019-02-15
CmpDate: 2019-02-01

Mondal M, Bertranpetit J, O Lao (2019)


Nature communications, 10(1):246 pii:10.1038/s41467-018-08089-7.

Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.

RevDate: 2018-12-28

Kirpichenkova EV, Korolev AA, Onishchenko GG, et al (2018)

[Study of lutein and zeaxanthin content in the diet with the assessment of the relationship between the level of alimentary intake of non-vitamin carotenoids and the density of the macular region of the retina at a young age].

Voprosy pitaniia, 87(5):20-26.

Lutein and zeaxanthin are carotenoid pigments that affect the function of the visual analyzer. They selectively accumulate in the yellow spot of the retina, form macular pigment and determine the density of the retina macula. Lutein and zeaxanthin slow down the progression of age-related macular degeneration, a leading cause of senior-age blindness. The main food sources of non-vitamin carotenoids are green leafy vegetables, zucchini, pumpkin, green peas, broccoli. The aim of the study is a retrospective assessment of the levels and sources of alimentary intake of lutein and zeaxanthin in young people and research of the effect of lutein and zeaxanthin in the diet on macula density. A specially designed questionnaire was used to quantify the content of lutein and zeaxanthin in the diet, reflecting the amount of consumption of the main sources of these carotenoids on the day preceding the survey. A non-invasive non-contact method of optical coherence tomography of the retina was used to determine the density of the macula. The study involved 96 students of Sechenov University at the age of 21-27 years. The study found that only 6.25% of the respondents had daily intake of lutein and zeaxanthin of 6 mg or more, 8.33% had 4.6-5.9 mg, 8.33% had 3.0-4.5 mg, in 18.75% - 1.5-2.9 mg, in 45.83% <1.4 mg. 12.5% of respondents didn't include sources of lutein and zeaxanthin in the diet. The more common sources of lutein and zeaxanthin in the diet were eggs and fresh tomatoes. Retinal density indices corresponded to the age standards in the majority of the examined. In 8.3% surveyed the thickness of the retina was decreased, and 4.2% had higher thickness of the retina in comparison with the standards. Significant differences in the Central subfield thickness in men and women were revealed. There was no dependence of the levels of lutein and zeaxanthin coming from food sources on the retina thickness indicators.

RevDate: 2018-12-28

Martinchik AN, Baeva VS, Peskova EV, et al (2018)

[Actual liquid consumption by highly qualified athletes in the mode of the training process].

Voprosy pitaniia, 87(3):36-44.

The purpose of the study was to evaluate the actual intake of fluids by athletes of various sports during the day with one and two training sessions before, during and after workout. The dietary intake, including consumption of various types of liquid foods and beverages, was evaluated by the method of 24-hour recall in 280 athletes of high qualification (candidates for masters and masters of sports) of both gender of various sports during the training period. It has been established that the main drink of rehydration was drinking bottled water. Bottled water was consumed on average by 86% of athletes. It was consumed by 95-96% of sportsmen from the group of single combats and power kinds, whereas in other groups the share of water consumers was less - 67-79%. In second place in terms of percentage of consuming was tea. Consumption of sports drinks was observed only during training by athletes from the group of cyclic sports (31%) and single combat (11%). Calculating the per capita fluid intake of athletes who had 2 workouts a day showed that athletes from the martial arts group consumed the largest volumes of fluid in the mode of both training sessions as compared to representatives of other sports. Athletes of other sports consumed on average less liquid in the 2nd training mode compared to the 1st one. The total fluid intake during two training sessions was maximum in the group of martial arts and was minimum in the group of complex coordination sports. It should be specially noted a small proportion of athletes who consumed specialized sports drinks - only 17% of athletes and more than half of them - cyclical sportsmen. Consumption of liquid food outside training has been observed in 76% of athletes. The mean volume of consumed liquid products varied by the user from 382 and 437 ml in complex coordination and game sports up to 504-553 ml in other sports. The daily fluid intake was maximum (2326 ml) in athletes engaged in martial arts, minimum (1009 ml) - in athletes of complex coordination sports.

RevDate: 2019-04-12
CmpDate: 2019-04-12

Reher D, Key FM, Andrés AM, et al (2019)

Immune Gene Diversity in Archaic and Present-day Humans.

Genome biology and evolution, 11(1):232-241 pii:5253179.

Genome-wide analyses of two Neandertals and a Denisovan have shown that these archaic humans had lower genetic heterozygosity than present-day people. A similar reduction in genetic diversity of protein-coding genes (gene diversity) was found in exome sequences of three Neandertals. Reduced gene diversity, particularly in genes involved in immunity, may have important functional consequences. In fact, it has been suggested that reduced diversity in immune genes may have contributed to Neandertal extinction. We therefore explored gene diversity in different human groups, and at different time points on the Neandertal lineage, with a particular focus on the diversity of genes involved in innate immunity and genes of the Major Histocompatibility Complex (MHC).We find that the two Neandertals and a Denisovan have similar gene diversity, all significantly lower than any present-day human. This is true across gene categories, with no gene set showing an excess decrease in diversity compared with the genome-wide average. Innate immune-related genes show a similar reduction in diversity to other genes, both in present-day and archaic humans. There is also no observable decrease in gene diversity over time in Neandertals, suggesting that there may have been no ongoing reduction in gene diversity in later Neandertals, although this needs confirmation with a larger sample size. In both archaic and present-day humans, genes with the highest levels of diversity are enriched for MHC-related functions. In fact, in archaic humans the MHC genes show evidence of having retained more diversity than genes involved only in the innate immune system.

RevDate: 2019-04-09

Starshinova A, Zinchenko Y, Filatov M, et al (2018)

Specific features of immune complexes in patients with sarcoidosis and pulmonary tuberculosis.

Immunologic research, 66(6):737-743.

Clinical and radiological features of tuberculosis and sarcoidosis are quite overlapping, and therefore, a diagnostic dilemma often persists. There are no commonly accepted criteria for the diagnosis of sarcoidosis due to the lack of data on the etiology of the disease. The exclusion of tuberculosis in every patient with suspected sarcoidosis is a mandatory stage of diagnosis, especially in countries with a high burden of tuberculosis. A prospective study was conducted with two groups of patients: group I (n = 50)-patients with pulmonary sarcoidosis established according to standard criteria; group II (n = 28)-patients with pulmonary tuberculosis with bacterial excretion. The control group (n = 24) was presented by healthy subjects. The examination complex included x-ray, bacteriological, immunological (Mantoux test with 2 TE, TB.SPOT test), and histological methods. All patients and healthy subjects were assessed for immune complexes with the use of the dynamic light scattering (DLS) method and adding of "healthy lung tissue extract" antigens and specific tuberculosis antigens ESAT-6 and SFP-10 in vitro. Significant differences were found in determining specific immune complexes in patients with pulmonary sarcoidosis and pulmonary tuberculosis. Registration of specific immune complex formation with "healthy lung tissue extract" in 100% cases may indicate the autoimmune nature of sarcoidosis. The absence of the immune complex formation in response to ESAT-6/SFP-10 antigens can be used for the differential diagnosis of two diseases. The diagnostic significance of the DLS method was 100% for sarcoidosis and 92.2% for tuberculosis. The data obtained in the study allows not only understanding the etiology of sarcoidosis, but also obtaining new criteria for the differential diagnosis of tuberculosis and pulmonary sarcoidosis.

RevDate: 2018-12-17

Pol JG, Acuna SA, Yadollahi B, et al (2019)

Preclinical evaluation of a MAGE-A3 vaccination utilizing the oncolytic Maraba virus currently in first-in-human trials.

Oncoimmunology, 8(1):e1512329.

Multiple immunotherapeutics have been approved for cancer patients, however advanced solid tumors are frequently refractory to treatment. We evaluated the safety and immunogenicity of a vaccination approach with multimodal oncolytic potential in non-human primates (NHP) (Macaca fascicularis). Primates received a replication-deficient adenoviral prime, boosted by the oncolytic Maraba MG1 rhabdovirus. Both vectors expressed the human MAGE-A3. No severe adverse events were observed. Boosting with MG1-MAGEA3 induced an expansion of hMAGE-A3-specific CD4+ and CD8+ T-cells with the latter peaking at remarkable levels and persisting for several months. T-cells reacting against epitopes fully conserved between simian and human MAGE-A3 were identified. Humoral immunity was demonstrated by the detection of circulating MAGE-A3 antibodies. These preclinical data establish the capacity for the Ad:MG1 vaccination to engage multiple effector immune cell populations without causing significant toxicity in outbred NHPs. Clinical investigations utilizing this program for the treatment of MAGE-A3-positive solid malignancies are underway (NCT02285816, NCT02879760).

RevDate: 2019-04-03
CmpDate: 2019-04-03

Denisova TG, Gerasimova LI, Pakhmutova NL, et al (2018)

Individualized Homeopathic Therapy in a Case of Obesity, Dysfunctional Uterine Bleeding, and Autonomic Dystonia.

The American journal of case reports, 19:1474-1479 pii:913328.

BACKGROUND Obesity is one of the leading causes of morbidity and mortality globally and challenging to treat because of the multifactorial etiology and presentation. Individualized homeopathy takes into account factors that led to a patient's health condition and hence may have a role in the treatment of obesity and related co-morbidities; co-morbidities that may arising from the same etiology may respond as a whole to homeopathy treatment. CASE REPORT A 39-year-old Russian female who developed multiple problems after severe emotional stress was treated with individualized classical homeopathic therapy. Obesity, dysfunctional uterine bleeding, and dysautonomia were pathologies that showed improvement. CONCLUSIONS The response in this patient's case, supports the need for further investigation on the relevance of individualized homeopathy in these related conditions.

RevDate: 2018-11-19

Safronova EI, Dydykin SS, Grigorevskiy ED, et al (2018)

Experimental animal model for assessment of tracheal epithelium regeneration.

The Laryngoscope [Epub ahead of print].

OBJECTIVES/HYPOTHESIS: To develop an experimental model in rabbits for assessment of tracheal epithelium regeneration through application of either natural or artificial polymer scaffolds.

STUDY DESIGN: First, we identified the size of full-thickness mucosal defect, which does not allow self-healing (a "critical defect"), thus representing an adequate experimental model for regenerative therapy of tracheal epithelium damage. Then, two methods of polymer scaffold fixation at the site of the epithelium defect were compared: suturing and fixation with a stent. This was done through: 1) formation of a full-thickness anterolateral mucosal defect by tracheal mucosa excision; and 2) fixation of the scaffold at the site of the tracheal epithelium defect using sutures (through a tracheal wall "window") or a vascular stent (through a small tracheal incision).

RESULTS: The dimension of a critical anterolateral mucosal defect of the trachea for rabbits was found to be 1.5 cm in length and more than 50% of the tracheal circumference. Fixation of the scaffold with a stent proved to be more efficient due to a uniform distribution of the pressure over the entire surface of the scaffold, whereas the suturing of the scaffold provided unsatisfactory results. In addition, fixation of the scaffold by suturing required formation of a large "window" in the tracheal wall. Thus, using the stent appeared to be technically less complicated and much less traumatic as compared to suturing.

CONCLUSION: We present an experimental in vivo animal model of tracheal epithelium injury and recovery. It can be effectively used with certain further modifications as a basis for routine testing of bioengineered constructs.

LEVEL OF EVIDENCE: NA. Laryngoscope, 2018.

RevDate: 2019-03-07
CmpDate: 2019-03-07

Malinova LI, Furman NV, Dolotovskaya PV, et al (2018)

[ADP-Induced Recalcified Blood Clotting Time as a Marker of Rethrombosis Risk and Effectiveness of Antiplatelet Therapy in Acute Coronary Syndrome].

Kardiologiia, 58(6):5-12.

PURPOSE: to assess the possibility of the use of ADP induced blood-clotting time measurement in clinical practice prognostication of the course of acute coronary syndrome (ACS) and assessment of effectiveness of antiplatelet therapy (APT).

MATERIALS AND METHODS: We enrolled in the study 163 male patients admitted to the coronary unit for acute coronary syndrome (ACS) and 38 male practically healthy volunteers (PHV). ADP induced blood-clotting time (ADP BCT) was measured as time (sec) between addition of ADP (10 μcmol) to recalcificated sample of citrate blood and clot formation. In healthy volunteers ADP BCT was determined before and 45 minutes after oral administration of acetylsalicylic acid (ASA, 250 mg). Risk of cardiovascular death was calculated using the GRACE score. Platelet function tests were performed by optical aggregometry. Follow-up period for patients with ACS was 24 months. The primary end point (PEP) was the composite of cardiovascular death and rehospitalization.

RESULTS: In ACS patients ADP BCT was significantly lower than in PHV: 134.8 (109.9; 161.3) vs 85.7 (60.5; 108.7) sec, p=0.015. In PHV ASA increased ADP BCT - 103.2 (95.1; 130.7) vs 133.1 (102.8; 154.3) sec, p=0.041. ADP BCT correlated with age in both PHV and patients (R= -0.431, p.

RevDate: 2019-02-04

Johannessen TC, Hasan-Olive MM, Zhu H, et al (2019)

Thioridazine inhibits autophagy and sensitizes glioblastoma cells to temozolomide.

International journal of cancer, 144(7):1735-1745.

Glioblastoma multiforme (GBM) has a poor prognosis with an overall survival of 14-15 months after surgery, radiation and chemotherapy using temozolomide (TMZ). A major problem is that the tumors acquire resistance to therapy. In an effort to improve the therapeutic efficacy of TMZ, we performed a genome-wide RNA interference (RNAi) synthetic lethality screen to establish a functional gene signature for TMZ sensitivity in human GBM cells. We then queried the Connectivity Map database to search for drugs that would induce corresponding changes in gene expression. By this approach we identified several potential pharmacological sensitizers to TMZ, where the most potent drug was the established antipsychotic agent Thioridazine, which significantly improved TMZ sensitivity while not demonstrating any significant toxicity alone. Mechanistically, we show that the specific chemosensitizing effect of Thioridazine is mediated by impairing autophagy, thereby preventing adaptive metabolic alterations associated with TMZ resistance. Moreover, we demonstrate that Thioridazine inhibits late-stage autophagy by impairing fusion between autophagosomes and lysosomes. Finally, Thioridazine in combination with TMZ significantly inhibits brain tumor growth in vivo, demonstrating the potential clinical benefits of compounds targeting the autophagy-lysosome pathway. Our study emphasizes the feasibility of exploiting drug repurposing for the design of novel therapeutic strategies for GBM.

RevDate: 2019-03-14
CmpDate: 2019-03-14

Hoover KC (2018)

Intragenus (Homo) variation in a chemokine receptor gene (CCR5).

PloS one, 13(10):e0204989.

Humans have a comparatively higher rate of more polymorphisms in regulatory regions of the primate CCR5 gene, an immune system gene with both general and specific functions. This has been interpreted as allowing flexibility and diversity of gene expression in response to varying disease loads. A broad expression repertoire is useful to humans-the only globally distributed primate-due to our unique adaptive pattern that increased pathogen exposure and disease loads (e.g., sedentism, subsistence practices). The main objective of the study was to determine if the previously observed human pattern of increased variation extended to other members of our genus, Homo. The data for this study are mined from the published genomes of extinct hominins (four Neandertals and two Denisovans), an ancient human (Ust'-Ishim), and modern humans (1000 Genomes). An average of 15 polymorphisms per individual were found in human populations (with a total of 262 polymorphisms). There were 94 polymorphisms identified across extinct Homo (an average of 13 per individual) with 41 previously observed in modern humans and 53 novel polymorphisms (32 in Denisova and 21 in Neandertal). Neither the frequency nor distribution of polymorphisms across gene regions exhibit significant differences within the genus Homo. Thus, humans are not unique with regards to the increased frequency of regulatory polymorphisms and the evolution of variation patterns across CCR5 gene appears to have originated within the genus. A broader evolutionary perspective on regulatory flexibility may be that it provided an advantage during the transition to confrontational foraging (and later hunting) that altered human-environment interaction as well as during migration to Eurasia and encounters with novel pathogens.

RevDate: 2019-01-16
CmpDate: 2019-01-16

Skov L, Hui R, Shchur V, et al (2018)

Detecting archaic introgression using an unadmixed outgroup.

PLoS genetics, 14(9):e1007641.

Human populations outside of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a low rate of false detection, given data from a suitable outgroup population is available, without the archaic introgression but containing a majority of the variation that arose since initial separation from the archaic lineage. Furthermore our approach is able to infer admixture proportions and the times both of admixture and of initial divergence between the human and archaic populations. We apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan admixture than previous studies and find a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time. Furthermore, we identify small amounts of Denisova ancestry in South East Asians and South Asians.

RevDate: 2018-10-24

Clyde D (2018)

The girl with Neanderthal and Denisovan parents.

Nature reviews. Genetics, 19(11):668-669.

RevDate: 2018-11-14
CmpDate: 2018-11-12

Dergunova LV, Filippenkov IB, Stavchansky VV, et al (2018)

Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model.

BMC genomics, 19(1):655.

BACKGROUND: The transient middle cerebral artery occlusion (tMCAO) model is used for studying the molecular mechanisms of ischemic damage and neuroprotection. Numerous studies have demonstrated the role of individual genes and associated signaling pathways in the pathogenesis of ischemic stroke. Here, the tMCAO model was used to investigate the genome-wide response of the transcriptome of rat brain tissues to the damaging effect of ischemia and subsequent reperfusion.

RESULTS: Magnetic resonance imaging and histological examination showed that the model of focal ischemia based on endovascular occlusion of the right middle cerebral artery for 90 min using a monofilament, followed by restoration of the blood flow, led to reproducible localization of ischemic damage in the subcortical structures of the brain. High-throughput RNA sequencing (RNA-Seq) revealed the presence of differentially expressed genes (DEGs) in subcortical structures of rat brains resulting from hemisphere damage by ischemia after tMCAO, as well as in the corresponding parts of the brains of sham-operated animals. Real-time reverse transcription polymerase chain reaction expression analysis of 20 genes confirmed the RNA-Seq results. We identified 469 and 1939 genes that exhibited changes in expression of > 1.5-fold at 4.5 and 24 h after tMCAO, respectively. Interestingly, we found 2741 and 752 DEGs under ischemia-reperfusion and sham-operation conditions at 24 h vs. 4.5 h after tMCAO, respectively. The activation of a large number of genes involved in inflammatory, immune and stress responses, apoptosis, ribosome function, DNA replication and other processes was observed in ischemia-reperfusion conditions. Simultaneously, massive down-regulation of the mRNA levels of genes involved in the functioning of neurotransmitter systems was recorded. A Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that dozens of signaling pathways were associated with DEGs in ischemia-reperfusion conditions.

CONCLUSIONS: The data obtained revealed a global profile of gene expression in the rat brain sub-cortex under tMCAO conditions that can be used to identify potential therapeutic targets in the development of new strategies for the prevention and treatment of ischemic stroke.

RevDate: 2018-08-28

Alexeeva E, Dvoryakovskaya T, Denisova R, et al (2018)

Comparative Analysis of the Etanercept Efficacy in Children with Juvenile Idiopathic Arthritis Under the Age of 4 Years and Children of Older Age Groups Using the Propensity Score Matching Method.

Modern rheumatology [Epub ahead of print].

OBJECTIVE: The study aim was to analyze the efficacy and safety of etanercept (ETA) in children with juvenile idiopathic arthritis (JIA) under the age of 4 years and to compare the data with those for older age groups.

METHODS: Three groups comprising 34 patients each (the total number, 102 patients) were selected using the PSM method. The study group (patients under the age of 4 years; the Junior group (JNR)) were compared with patients of the older age groups adjusted for gender, JIA category, JIA severity, and either age at disease onset (the RAO group) or disease duration (the RDD group).

RESULTS: All three groups showed good response to ETA therapy. During the follow-up period, only 4 (3.9%) patients failed to reach ACR50. In the JNR group, 82.4% of patients achieved ACR90 within median time 3 months (IQR, 3 - 6 months), which was a better result compared to the other two groups: 61.8% (RAO group) and 58.8% (RDD group) of patients achieved ACR90 within 6 (IQR, 3 - 9) months (p = 0.028). Three (9%) patients in the JNR group and none of the RDD and RAO groups discontinued treatment because of clinical remission (p = 0.045).

CONCLUSION: An analysis of the ETA efficacy in different age groups comparable in terms of the diagnosis and disease severity demonstrated a higher efficacy of earlier ETA therapy in children of the same age at disease onset. In children at the early stage of arthritis (≤ 2.5 years long), ETA was more efficient in those with an earlier disease onset.

RevDate: 2019-03-05
CmpDate: 2019-02-26

Slon V, Mafessoni F, Vernot B, et al (2018)


Nature, 561(7721):113-116.

Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago1,2. Here we present the genome of 'Denisova 11', a bone fragment from Denisova Cave (Russia)3 and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave4-6. The mother came from a population more closely related to Neanderthals who lived later in Europe2,7 than to an earlier Neanderthal found in Denisova Cave8, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal-Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.

RevDate: 2019-02-15
CmpDate: 2019-02-13

Warren M (2018)

Mum's a Neanderthal, Dad's a Denisovan: First discovery of an ancient-human hybrid.

Nature, 560(7719):417-418.

RevDate: 2018-11-19
CmpDate: 2018-11-19

Zotova TY, Blagonravov ML, Lapaev NN, et al (2018)

Hemodynamic Allostasis of Pregnant Women against the Background of Preeclampsia.

Bulletin of experimental biology and medicine, 165(4):440-444.

We analyzed diurnal hemodynamic parameters (HR, systolic BP, and diastolic BP) recorded from two groups of edematous and preeclamptic pregnant women. The unidirectional character of changes in the control over the functional state of cardiovascular system was revealed except for the indices, which mark a pathological process: elevated diurnal BP in preeclampsia and diminished percentage of oscillation power in edematous patients. Uniformity of the regulatory changes in patients with and without arterial hypertension can be viewed as manifestation of allostasis developed by the cardiovascular system during pregnancy. In preeclampsia, the greater allostatic load was reflected by the changes in diurnal, daytime, and nighttime BP and in the circadian index calculated for HR, systolic BP, and diastolic BP. In edematous patients, elevation of allostatic load was indicated by the percentage of ultradian rhythms.

RevDate: 2019-01-15
CmpDate: 2019-01-15

Helsen CW, Hammill JA, Lau VWC, et al (2018)


Nature communications, 9(1):3049.

Engineering T cells with chimeric antigen receptors (CARs) is an effective method for directing T cells to attack tumors, but may cause adverse side effects such as the potentially lethal cytokine release syndrome. Here the authors show that the T cell antigen coupler (TAC), a chimeric receptor that co-opts the endogenous TCR, induces more efficient anti-tumor responses and reduced toxicity when compared with past-generation CARs. TAC-engineered T cells induce robust and antigen-specific cytokine production and cytotoxicity in vitro, and strong anti-tumor activity in a variety of xenograft models including solid and liquid tumors. In a solid tumor model, TAC-T cells outperform CD28-based CAR-T cells with increased anti-tumor efficacy, reduced toxicity, and faster tumor infiltration. Intratumoral TAC-T cells are enriched for Ki-67+ CD8+ T cells, demonstrating local expansion. These results indicate that TAC-T cells may have a superior therapeutic index relative to CAR-T cells.

RevDate: 2018-08-01

Morgunov LY, Denisova IA, Rozhkova TI, et al (2018)

Hypogonadism and its treatment following ischaemic stroke in men with type 2 diabetes mellitus.

The aging male : the official journal of the International Society for the Study of the Aging Male [Epub ahead of print].

Premature mortality in Russia is a major socio-economic problem, especially from acute cerebrovascular diseases which constitute 21.4% of the total mortality and is a considerable contributor to chronic disability. Risk of vascular catastrophe is higher in males than females, thought, in part, due to anti-atherosclerotic effects of oestrogens in females whilst an associated age-related deficiency of testosterone is observed in men. Clinical symptoms such as high blood pressure, changes in lipid profile, insulin resistance, obesity, and blood coagulation factors often accompany declining testosterone in males and reduced total testosterone is considered a cardiovascular risk factor. In the present study, the prevalence of hypogonadism in men who had suffered ischaemic stroke was evaluated along with the efficacy of testosterone undecanoate injections (TU) in patients with testosterone deficiency and type-2 diabetes (T2DM) in the acute phase of hemispheric ischaemic stroke. Hypogonadism was present in 66.3% of patients with ischaemic stroke, 50% with T2DM, and 26.3% without T2DM, respectively. TU treatment, at both the 2 and 5-year observation points, demonstrated significant improvements in biochemical, physical, and mental parameters. This supports that testosterone deficiency is a contributing factor in ischaemic events and that long-term testosterone therapy could play an important role in patient recovery.

RevDate: 2018-11-14

Dolgova O, O Lao (2018)

Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes.

Genes, 9(7):.

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

RevDate: 2019-03-07
CmpDate: 2019-03-07

Denisova K (2019)

Neurobiology, not artifacts: Challenges and guidelines for imaging the high risk infant.

NeuroImage, 185:624-640.

The search for the brain-basis of atypical development in human infants is challenging because the process of imaging and the generation of the MR signal itself relies on assumptions that reflect biophysical properties of the brain tissue. These assumptions are not inviolate, have been questioned by recent empirical evidence from high risk infant-sibling studies, and to date remain largely underexamined at the between-group level. In particular, I consider recent work showing that infants at High vs. Low familial risk (HR vs. LR, respectively) for developing Autism Spectrum Disorders (ASD) have atypical patterns of head movements during an MR scan that are functionally important-they are linked to future learning trajectories in toddlerhood. Addressing head movement issues in neuroimaging analyses in infant research as well as understanding the causes of these movements from a developmental perspective requires acknowledging the complexity of this endeavor. For example, head movement signatures in infants can interact with experimental task conditions (such as listening to language compared to sleeping), autism risk, and age. How can new knowledge about newborns' individual, subject-specific behavioral differences which may impact MR signal acquisition and statistical inference ignite critical thinking for the field of infant brain imaging across the spectrum of typical and atypical development? Early behavioral differences between HR and LR infant cohorts that are often examples of "artifactual" confounds in MR work provide insight into nascent neurobiological differences, including biophysical tissue properties and hemodynamic response variability, in these and related populations at risk for atypical development. Are these neurobiological drivers of atypical development? This work identifies important knowledge gaps and suggests guidelines at the leading edge of baby imaging science to transform our understanding of atypical brain development in humans. The precise study of the neurobiological underpinnings of atypical development in humans calls for approaches including quantitative MRI (qMRI) pulse sequences, multi-modal imaging (including DTI, MRS, as well as MEG), and infant-specific HRF shapes when modeling BOLD signal.

RevDate: 2018-07-13

Raevis JJ, Denisova K, Mechel E, et al (2018)


Retinal cases & brief reports [Epub ahead of print].

BACKGROUND/PURPOSE: Report a case of markedly asymmetric retinal tessellations and propose mosaicism as a mechanism.

METHODS AND RESULTS: A 59-year-old pseudophakic woman presented with uncorrected 20/20 vision and was found to have markedly different retinal tessellation appearances in both eyes. The axial lengths were 25.66 mm and 25.88 mm in the right and left eyes, respectively, and no significant asymmetrical choroidal thinning was seen on optical coherence tomography or optical coherence tomography angiography. Fluorescein angiogram showed significant hyperfluorescence, representing the underlying choroid, which correlated with the tessellation patterns in the left eye. She had no other ocular or systemic findings such as stripes or whorled skin.

CONCLUSION: This is the first reported case of markedly asymmetric retinal tessellation patterns that are not due to asymmetric axial myopia or choroidal thinning. We propose that mosaicism is a possible mechanism causing this finding.

RevDate: 2018-12-27
CmpDate: 2018-12-27

Zhao G, Walsh K, Long J, et al (2018)

Reduced structural complexity of the right cerebellar cortex in male children with autism spectrum disorder.

PloS one, 13(7):e0196964.


RevDate: 2018-11-14
CmpDate: 2018-10-22

Malyarchuk B, Derenko M, Denisova G, et al (2018)

Whole mitochondrial genome diversity in two Hungarian populations.

Molecular genetics and genomics : MGG, 293(5):1255-1263.


RevDate: 2018-09-05

Rzaev DA, Denisova NP, Moisak GI, et al (2018)

[Experience of the use of gasserian ganglion balloon compression in patients with trigeminal neuralgia associated with multiple sclerosis].

Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova, 118(5):30-35.

AIM: To evaluate the efficacy of gasserian ganglion balloon compression in patients with trigeminal neuralgia associated with multiple sclerosis (MS).

MATERIAL AND METHODS: Eight patients (3 men, 5 women), aged from 46 to 66 years (mean age 55 years), with trigeminal neuralgia associated with MS underwent surgery. An average duration of the pain syndrome was 8,4 years. Six patients had previous surgeries due to facial pain. Percutaneous balloon compression of gasserian ganglion was performed to all patients. Follow up period was from 2 to 24 months.

RESULTS: Six patients (75%) reported 100% of pain relief right after the surgery, 2 patients (25%) reported a significant decrease of pain (2-3 points on VAS). Pain recurrence occurred in 3 patients: in 4 months, in 12 months and in 6 months. All of them were operated repeatedly. After the surgery, hypoesthesia on the side of surgery was observed in all patients with a trend towards regression. There was no keratopathy or any complications.

CONCLUSION: Percutaneous balloon compression of gasserian ganglion is an effective and minimally invasive method which can be performed repeatedly in patients with trigeminal neuralgia associated with MS.

RevDate: 2019-01-16
CmpDate: 2019-01-16

Cserhati MF, Mooter ME, Peterson L, et al (2018)

Motifome comparison between modern human, Neanderthal and Denisovan.

BMC genomics, 19(1):472.

BACKGROUND: The availability of the genomes of two archaic humans, Neanderthal and Denisovan, and that of modern humans provides researchers an opportunity to investigate genetic differences between these three subspecies on a genome-wide scale. Here we describe an algorithm that predicts statistically significant motifs based on the difference between a given motif's actual and expected distributions. The algorithm was previously applied to plants but was modified for this work.

RESULTS: The result of applying the algorithm to the human, Neanderthal, and Denisovan genomes is a catalog of potential regulatory motifs in these three human subspecies. We examined the distributions of these motifs in genetic elements including human retroviruses, human accelerated regions, and human accelerated conserved noncoding sequences regions. Differences in these distributions could be the origin of differences in phenotype between the three subspecies. Twenty significant motifs common to all three genomes were found; thirty-three were found in endogenous retroviruses in Neanderthal and Denisovan. Ten of these motifs mapped to the 22 bp core of MiR-1304. The core of this genetic element regulates the ENAM and AMTN genes, which take part in odontogenesis and whose 3' UTRs contained significant motifs. The introns of 20 genes were found to contain a large number of significant motifs, which were also overrepresented in 49 human accelerated regions. These genes include NAV2, SorCS2, TRAPPC9, GRID1, PRDM16, CAMTA1, and ASIC which are all involved in neuroregulation. Further analysis of these genes using the GO database indicates that many are associated with neurodevelopment. Also, varying numbers of significant motifs were found to occur in regions of the Neanderthal and Denisovan genomes that are missing from the human genome, suggesting further functional differences between modern and archaic humans.

CONCLUSION: Although Neanderthal and Denisovan are now extinct, detailed examination of elements from their genomes can shed light on possible phenotypic and cognitive differences between these two archaic human subspecies and modern humans. Genetic similarities and differences between these three subspecies and other fossil hominids would also be of interest.

RevDate: 2018-11-14
CmpDate: 2018-10-15

Banerjee N, Polushina T, Bettella F, et al (2018)

Recently evolved human-specific methylated regions are enriched in schizophrenia signals.

BMC evolutionary biology, 18(1):63.

BACKGROUND: One explanation for the persistence of schizophrenia despite the reduced fertility of patients is that it is a by-product of recent human evolution. This hypothesis is supported by evidence suggesting that recently-evolved genomic regions in humans are involved in the genetic risk for schizophrenia. Using summary statistics from genome-wide association studies (GWAS) of schizophrenia and 11 other phenotypes, we tested for enrichment of association with GWAS traits in regions that have undergone methylation changes in the human lineage compared to Neanderthals and Denisovans, i.e. human-specific differentially methylated regions (DMRs). We used analytical tools that evaluate polygenic enrichment of a subset of genomic variants against all variants.

RESULTS: Schizophrenia was the only trait in which DMR SNPs showed clear enrichment of association that passed the genome-wide significance threshold. The enrichment was not observed for Neanderthal or Denisovan DMRs. The enrichment seen in human DMRs is comparable to that for genomic regions tagged by Neanderthal Selective Sweep markers, and stronger than that for Human Accelerated Regions. The enrichment survives multiple testing performed through permutation (n = 10,000) and bootstrapping (n = 5000) in INRICH (p < 0.01). Some enrichment of association with height was observed at the gene level.

CONCLUSIONS: Regions where DNA methylation modifications have changed during recent human evolution show enrichment of association with schizophrenia and possibly with height. Our study further supports the hypothesis that genetic variants conferring risk of schizophrenia co-occur in genomic regions that have changed as the human species evolved. Since methylation is an epigenetic mark, potentially mediated by environmental changes, our results also suggest that interaction with the environment might have contributed to that association.

RevDate: 2019-04-08

Akkuratov EE, Gelfand MS, EE Khrameeva (2018)

Neanderthal and Denisovan ancestry in Papuans: A functional study.

Journal of bioinformatics and computational biology, 16(2):1840011.

Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan alleles. Here, we have shown that the Papuan genomes contain different gene functional groups inherited from each of the ancient people. The Papuan genomes demonstrate a relative prevalence of Neanderthal alleles in genes responsible for the regulation of transcription and neurogenesis. The enrichment of specific functional groups with Denisovan alleles is less pronounced; these groups are responsible for bone and tissue remodeling. This analysis shows that introgression of alleles from Neanderthals and Denisovans to Papuans occurred independently and retention of these alleles may carry specific adaptive advantages.

RevDate: 2018-06-05
CmpDate: 2018-06-05

Shkliaev AE, Denisova NI, IV Kulikov (2018)

[Splenic artery aneurysm masked by postcholecystectomy syndrome].

Angiologiia i sosudistaia khirurgiia = Angiology and vascular surgery, 24(1):175-178.

Visceral artery aneurysms appear to belong to uncommon and potentially lethal vascular diseases. They are usually revealed accidentally during an ultrasonographic examination, magnetic resonance imaging, or computed tomography. Described in the article is a clinical case report concerning a sacciform aneurysm of the splenic artery, detected in a 53-year-old woman presenting with postcholecystectomy syndrome and followed up for abdominalgia by therapeutists and gastroenterologists. Timely performed radiodiagnosis (including multispiral computed tomography and angiography of the abdominal vessels) made it possible not only to detect the aneurysm, having thus verified the volumetric formation previously found on ultrasonographic examination, but to take adequate measures aimed at preventing rupture of the aneurysm and consisting in endovascular occlusion of the aneurysmatic cavity with metal spirals. Lack of complete clarity in the understanding of the mechanisms of the origin of and no distinctly defined therapeutic-and-diagnostic algorithm for visceral artery aneurysms dictate the necessity to continue collecting and generalizing clinical case reports regarding this rarely encountered vascular pathology.

RevDate: 2018-09-11
CmpDate: 2018-09-11

Bogomolov DV, Fetisov VA, Denisova OP, et al (2018)

[The principal and auxiliary immunohistochemical markers of intravital mechanical strangulation asphyxia].

Sudebno-meditsinskaia ekspertiza, 61(2):11-13.

The objective of the present study was the evaluation of the auxiliary methods for the diagnostics of the intravital formation of the constriction marks; the secondary objective was to determine the pace at which the death and asphyxia occur.

MATERIAL AND METHODS: The materials on which the study was based included 17 cases of mechanical strangulation asphyxia involving 13 men and 4 women at the age from 8 to 28 years. All cases of hanging were associated with different blood alcohol levels. Their characteristic feature was the formation of the obliquely ascending constriction marks. The group of comparison was comprised of three cases of death by drowning and one case of manual strangulation. The control group consisted of 10 patients who died from the acute form of coronary heart disease and 5 cases of death from traumatic shock. All the corpses were examined with the use of the traditional methods within the first 24 hours after death. The special laboratory studies were performed by means of the standard histological and immunohistochemical methods with the use of the polyclonal antibodies against total cytokeratin, fibrinogen, immunoglobulin-lambda, fibronectin, and CD-117 antigen. The histological preparations were stained by the method of Spielmeyer and with toluidine blue.

RESULTS: The results of the study give evidence of the possibility of diagnostics of mechanical strangulation asphyxia making use of the reaction with anti-fibrinogen antibodies in the stromal tissue of the constriction mark even in the absence of other intravital signs of death. Such diagnostics is also possible with the use of the CD-117 antigen in the pulmonary tissue. The expression of this antigen is characteristic of the cases of alveolar hypoxia. The possibility of application of other markers for the differential diagnostics of mechanical strangulation asphyxia from other causes of death is discussed.

RevDate: 2018-11-14

Khabarova EA, Denisova NP, Dmitriev AB, et al (2018)

Deep Brain Stimulation of the Subthalamic Nucleus in Patients with Parkinson Disease with Prior Pallidotomy or Thalamotomy.

Brain sciences, 8(4):.

Objective. To evaluate the efficacy of deep brain stimulation of the subthalamic nucleus (STN DBS) in patients with Parkinson disease (PD) who previously underwent lesioning of the basal ganglia. Material and methods. The study included 22 patients who underwent STN DBS. Eleven patients had undergone prior unilateral pallidotomy (n = 6) or VL/VIM thalamotomy (n = 5) while the other 11 patients had not. The primary outcome was the change from baseline in the motor subscore of the Unified Parkinson Disease Rating Scale (UPDRS-III) 12 months after STN DBS. Secondary outcomes included change in motor response complications (UPDRS-IV) and change in levodopa equivalent daily dose (LEDD). Results. In the group with prior lesioning UPDRS-III improved by 45%, from 51.5 &plusmn; 9.0% (range, 35&ndash;65) to 26.5 &plusmn; 8.4 (range, 21&ndash;50) (p < 0.01) and UPDRS-IV by 75%, from 8.0 &plusmn; 2.01 (range, 5&ndash;11) to 2.1 &plusmn; 0.74 (range, 1&ndash;3) (p < 0.01). In the group without prior lesioning UPDRS-III improved by 61%, from 74.2% &plusmn; 7.32 (range, 63&ndash;82) to 29.3 &plusmn; 5.99 (range, 20&ndash;42) (p < 0.01) and UPDRS-IV by 77%, from 9.1 &plusmn; 2.46 (range, 5&ndash;12) to 2.0 &plusmn; 1.1 (range, 1&ndash;4) (p < 0.01). Comparing the two groups (with and without lesioning) no significant differences were found either in UPDRS-III (p > 0.05) or UPDRS-IV scores (p > 0.05) at 12 months post-DBS. The LEDD was reduced by 51.4%, from 1008.2 &plusmn; 346.4 to 490.0 &plusmn; 194.3 in those with prior surgery (p < 0.01) and by 55.0%, from 963.4 &plusmn; 96.2 to 433.3 &plusmn; 160.2 in those without (p < 0.01).UPDRS-III improved by 51.8%, from 53.7 &plusmn; 4.6 (range, 50&ndash;62) to 25.0 &plusmn; 3.8 (range, 21&ndash;31) in those with prior pallidotomy (p < 0.01), and by 37.5%, from 48.8 &plusmn; 12.6 (range, 35&ndash;65) to 29.8 &plusmn; 13.6 (range, 22&ndash;50) in those with prior thalamotomy (p < 0.01). This numerical difference in improvement was not statistically significant (p > 0.05). Conclusion. Our comparative study indicates that bilateral STN DBS is effective and can be used in patients with Parkinson disease with prior unilateral stereotactic destructive operations on subcortical structures. The results in our patient cohort are generally consistent with previously published reports of smaller series from multiple centers worldwide.

RevDate: 2018-11-14

Viscardi LH, Paixão-Côrtes VR, Comas D, et al (2018)

Searching for ancient balanced polymorphisms shared between Neanderthals and Modern Humans.

Genetics and molecular biology, 41(1):67-81.

Hominin evolution is characterized by adaptive solutions often rooted in behavioral and cognitive changes. If balancing selection had an important and long-lasting impact on the evolution of these traits, it can be hypothesized that genes associated with them should carry an excess of shared polymorphisms (trans- SNPs) across recent Homo species. In this study, we investigate the role of balancing selection in human evolution using available exomes from modern (Homo sapiens) and archaic humans (H. neanderthalensis and Denisovan) for an excess of trans-SNP in two gene sets: one associated with the immune system (IMMS) and another one with behavioral system (BEHS). We identified a significant excess of trans-SNPs in IMMS (N=547), of which six of these located within genes previously associated with schizophrenia. No excess of trans-SNPs was found in BEHS, but five genes in this system harbor potential signals for balancing selection and are associated with psychiatric or neurodevelopmental disorders. Our approach evidenced recent Homo trans-SNPs that have been previously implicated in psychiatric diseases such as schizophrenia, suggesting that a genetic repertoire common to the immune and behavioral systems could have been maintained by balancing selection starting before the split between archaic and modern humans.

RevDate: 2018-11-14
CmpDate: 2018-10-02

Zehra R, AA Abbasi (2018)

Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population.

Genome biology and evolution, 10(3):956-966.

Empirical assessments of human accelerated noncoding DNA frgaments have delineated presence of many cis-regulatory elements. Enhancers make up an important category of such accelerated cis-regulatory elements that efficiently control the spatiotemporal expression of many developmental genes. Establishing plausible reasons for accelerated enhancer sequence divergence in Homo sapiens has been termed significant in various previously published studies. This acceleration by including closely related primates and archaic human data has the potential to open up evolutionary avenues for deducing present-day brain structure. This study relied on empirically confirmed brain exclusive enhancers to avoid any misjudgments about their regulatory status and categorized among them a subset of enhancers with an exceptionally accelerated rate of lineage specific divergence in humans. In this assorted set, 13 distinct transcription factor binding sites were located that possessed unique existence in humans. Three of 13 such sites belonging to transcription factors SOX2, RUNX1/3, and FOS/JUND possessed single nucleotide variants that made them unique to H. sapiens upon comparisons with Neandertal and Denisovan orthologous sequences. These variants modifying the binding sites in modern human lineage were further substantiated as single nucleotide polymorphisms via exploiting 1000 Genomes Project Phase3 data. Long range haplotype based tests laid out evidence of positive selection to be governing in African population on two of the modern human motif modifying alleles with strongest results for SOX2 binding site. In sum, our study acknowledges acceleration in noncoding regulatory landscape of the genome and highlights functional parts within it to have undergone accelerated divergence in present-day human population.

RevDate: 2019-01-21
CmpDate: 2019-01-21

Vernot B, S Pääbo (2018)

The Predecessors Within . . .

Cell, 173(1):6-7.

By examining the genomes of present-day people from Asia, researchers show that modern humans met and interbred with Denisovans, distant relatives to Neanderthals, on at least two occasions. As a result, people today carry DNA from two different Denisovan populations.

RevDate: 2019-03-29
CmpDate: 2019-01-31

Browning SR, Browning BL, Zhou Y, et al (2018)

Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.

Cell, 173(1):53-61.e9.


RevDate: 2018-02-25

Warren KA, Ritzman TB, Humphreys RA, et al (2018)

Craniomandibular form and body size variation of first generation mouse hybrids: A model for hominin hybridization.

Journal of human evolution, 116:57-74.

Hybridization occurs in a number of mammalian lineages, including among primate taxa. Analyses of ancient genomes have shown that hybridization between our lineage and other archaic hominins in Eurasia occurred numerous times in the past. However, we still have limited empirical data on what a hybrid skeleton looks like, or how to spot patterns of hybridization among fossils for which there are no genetic data. Here we use experimental mouse models to supplement previous studies of primates. We characterize size and shape variation in the cranium and mandible of three wild-derived inbred mouse strains and their first generation (F1) hybrids. The three parent taxa in our analysis represent lineages that diverged over approximately the same period as the human/Neanderthal/Denisovan lineages and their hybrids are variably successful in the wild. Comparisons of body size, as quantified by long bone measurements, are also presented to determine whether the identified phenotypic effects of hybridization are localized to the cranium or represent overall body size changes. The results indicate that hybrid cranial and mandibular sizes, as well as limb length, exceed that of the parent taxa in all cases. All three F1 hybrid crosses display similar patterns of size and form variation. These results are generally consistent with earlier studies on primates and other mammals, suggesting that the effects of hybridization may be similar across very different scenarios of hybridization, including different levels of hybrid fitness. This paper serves to supplement previous studies aimed at identifying F1 hybrids in the fossil record and to introduce further research that will explore hybrid morphologies using mice as a proxy for better understanding hybridization in the hominin fossil record.

RevDate: 2018-11-13

Leacock S, Syed P, James VM, et al (2018)

Structure/Function Studies of the α4 Subunit Reveal Evolutionary Loss of a GlyR Subtype Involved in Startle and Escape Responses.

Frontiers in molecular neuroscience, 11:23.

Inhibitory glycine receptors (GlyRs) are pentameric ligand-gated anion channels with major roles in startle disease/hyperekplexia (GlyR α1), cortical neuronal migration/autism spectrum disorder (GlyR α2), and inflammatory pain sensitization/rhythmic breathing (GlyR α3). However, the role of the GlyR α4 subunit has remained enigmatic, because the corresponding human gene (GLRA4) is thought to be a pseudogene due to an in-frame stop codon at position 390 within the fourth membrane-spanning domain (M4). Despite this, a recent genetic study has implicated GLRA4 in intellectual disability, behavioral problems and craniofacial anomalies. Analyzing data from sequenced genomes, we found that GlyR α4 subunit genes are predicted to be intact and functional in the majority of vertebrate species-with the exception of humans. Cloning of human GlyR α4 cDNAs excluded alternative splicing and RNA editing as mechanisms for restoring a full-length GlyR α4 subunit. Moreover, artificial restoration of the missing conserved arginine (R390) in the human cDNA was not sufficient to restore GlyR α4 function. Further bioinformatic and mutagenesis analysis revealed an additional damaging substitution at K59 that ablates human GlyR α4 function, which is not present in other vertebrate GlyR α4 sequences. The substitutions K59 and X390 were also present in the genome of an ancient Denisovan individual, indicating that GLRA4 has been a pseudogene for at least 30,000-50,000 years. In artificial synapses, we found that both mouse and gorilla α4β GlyRs mediate synaptic currents with unusually slow decay kinetics. Lastly, to gain insights into the biological role of GlyR α4 function, we studied the duplicated genes glra4a and glra4b in zebrafish. While glra4b expression is restricted to the retina, using a novel tol2-GAL4FF gene trap line (SAIGFF16B), we found that the zebrafish GlyR α4a subunit gene (glra4a) is strongly expressed in spinal cord and hindbrain commissural neurones. Using gene knockdown and a dominant-negative GlyR α4aR278Q mutant, we found that GlyR α4a contributes to touch-evoked escape behaviors in zebrafish. Thus, although GlyR α4 is unlikely to be involved in human startle responses or disease states, this subtype may contribute to escape behaviors in other organisms.

RevDate: 2018-12-02
CmpDate: 2018-10-31

Jiang L, Peng J, Huang M, et al (2018)

Differentiation analysis for estimating individual ancestry from the Tibetan Plateau by an archaic altitude adaptation EPAS1 haplotype among East Asian populations.

International journal of legal medicine, 132(6):1527-1535.

Tibetans have adapted to the extreme environment of high altitude for hundreds of generations. A highly differentiated 5-SNP (Single Nucleotide Polymorphism) haplotype motif (AGGAA) on a hypoxic pathway gene, EPAS1, is observed in Tibetans and lowlanders. To evaluate the potential usage of the 5-SNP haplotype in ancestry inference for Tibetan or Tibetan-related populations, we analyzed this haplotype in 1053 individuals of 12 Chinese populations residing on the Tibetan Plateau, peripheral regions of Tibet, and plain regions. These data were integrated with the genotypes from the 1000 Genome populations and populations in a previously reported paper for population structure analyses. We found that populations representing highland and lowland groups have different dominant ancestry components. The core Denisovan haplotype (AGGAA) was observed at a frequency of 72.32% in the Tibetan Plateau, with a frequency range from 9.48 to 21.05% in the peripheral regions and < 2.5% in the plains area. From the individual perspective, 87.57% of the individuals from the Tibetan Plateau carried the archaic haplotype, while < 5% of the Chinese Han people carried the haplotype. Our findings indicate that the 5-SNP haplotype has a special distribution pattern in populations of Tibet and peripheral regions and could be integrated into AISNP (Ancestry Informative Single Nucleotide Polymorphism) panels to enhance ancestry resolution.

RevDate: 2019-02-08
CmpDate: 2018-03-13

Rodríguez-Paredes M, Bormann F, Raddatz G, et al (2018)

Methylation profiling identifies two subclasses of squamous cell carcinoma related to distinct cells of origin.

Nature communications, 9(1):577.

Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer and usually progresses from a UV-induced precancerous lesion termed actinic keratosis (AK). Despite various efforts to characterize these lesions molecularly, the etiology of AK and its progression to cSCC remain partially understood. Here, we use Infinium MethylationEPIC BeadChips to interrogate the DNA methylation status in healthy, AK and cSCC epidermis samples. Importantly, we show that AK methylation patterns already display classical features of cancer methylomes and are highly similar to cSCC profiles. Further analysis identifies typical features of stem cell methylomes, such as reduced DNA methylation age, non-CpG methylation, and stem cell-related keratin and enhancer methylation patterns. Interestingly, this signature is detected only in half of the samples, while the other half shows patterns more closely related to healthy epidermis. These findings suggest the existence of two subclasses of AK and cSCC emerging from distinct keratinocyte differentiation stages.

RevDate: 2019-03-26
CmpDate: 2019-03-26

Yew CW, Lu D, Deng L, et al (2018)


Human genetics, 137(2):161-173.

Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28-37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays. The analysis of time of divergence suggested that ancestors of Negrito were the earliest settlers in the Malay Peninsula, whom first separated from the Papuans ~ 50-33 thousand years ago (kya), followed by East Asian (~ 40-15 kya), while the divergence time frame between North Borneo and East Asia populations predates the Austronesian expansion period implies a possible pre-Neolithic colonization. Substantial Neanderthal ancestry was confirmed in our genomes, as was observed in other East Asians. However, no significant difference was observed, in terms of the proportion of Denisovan gene flow into these native inhabitants from Malaysia. Judging from the similar amount of introgression in the Southeast Asians and East Asians, our findings suggest that the Denisovan gene flow may have occurred before the divergence of these populations and that the shared similarities are likely an ancestral component.

RevDate: 2018-06-27
CmpDate: 2018-06-27

Shipilovskikh SA, Vaganov VY, Denisova EI, et al (2018)

Dehydration of Amides to Nitriles under Conditions of a Catalytic Appel Reaction.

Organic letters, 20(3):728-731.

A highly expedient protocol for a catalytic Appel-type dehydration of amides to nitriles has been developed that employs oxalyl chloride and triethylamine along with triphenylphosphine oxide as a catalyst. The reactions are usually complete in less than 10 min with only a 1 mol % catalyst loading. The reaction scope includes aromatic, heteroaromatic, and aliphatic amides, including derivatives of α-hydroxy and α-amino acids.

RevDate: 2019-04-08
CmpDate: 2018-12-11

Belousov AB, Nishimune H, Denisova JV, et al (2018)

A potential role for neuronal connexin 36 in the pathogenesis of amyotrophic lateral sclerosis.

Neuroscience letters, 666:1-4.

Neuronal gap junctional protein connexin 36 (Cx36) contributes to neuronal death following a range of acute brain insults such as ischemia, traumatic brain injury and epilepsy. Whether Cx36 contributes to neuronal death and pathological outcomes in chronic neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), is not known. We show here that the expression of Cx36 is significantly decreased in lumbar segments of the spinal cord of both human ALS subjects and SOD1G93A mice as compared to healthy human and wild-type mouse controls, respectively. In purified neuronal cultures prepared from the spinal cord of wild-type mice, knockdown of Cx36 reduces neuronal death caused by overexpression of the mutant human SOD1-G93A protein. Taken together, these data suggest a possible contribution of Cx36 to ALS pathogenesis. A perspective for the use of blockers of Cx36 gap junction channels for ALS therapy is discussed.

RevDate: 2018-11-13
CmpDate: 2018-07-26

Derenko M, Denisova G, Malyarchuk B, et al (2018)

Mitogenomic diversity and differentiation of the Buryats.

Journal of human genetics, 63(1):71-81.

In this paper we present a results of first comprehensive study of the complete mitogenomes in the Buryats with regard to their belonging to the main regional (eastern and western Buryats); tribal (Khori, Ekhirid, Bulagad, and Khongodor), and ethno-territorial (Aginsk, Alar, Balagansk, Barguzin, Ida, Khorinsk, Kuda, Selenga, Verkholensk, Olkhon, Tunka, and Shenehen Buryats) groups. The analysis of molecular variation performed using regional, tribal, and ethno-territorial divisions of the Buryats showed lack of genetic differentiation at all levels. Nonetheless, the complete mitogenome analysis revealed a very high level of genetic diversity in the Buryats which is the highest among Siberian populations and comparable to that in populations of eastern and western Asia. The AMOVA and MDS analyses results imply to a strong genetic similarity between the Buryats and eastern Asian populations of Chinese and Japanese, suggesting their origin on the basis of common maternal ancestry components. Several new Buryat-specific branches of haplogroup G (G2a2a, G2a1i, G2a5a) display signals of dispersals dating to 2.6-6.6 kya with a possible origin in eastern Asia, thus testifying Bronze Age and Neolithic arrival of ancestral eastern Asian component to the South Siberia region.

RevDate: 2019-01-16
CmpDate: 2018-07-23

Walter Costa MB, Höner Zu Siederdissen C, Tulpan D, et al (2018)

Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1.

Journal of theoretical biology, 438:143-150.

The Human Accelerated Region 1 (HAR1) is the most rapidly evolving region in the human genome. It is part of two overlapping long non-coding RNAs, has a length of only 118 nucleotides and features 18 human specific changes compared to an ancestral sequence that is extremely well conserved across non-human primates. The human HAR1 forms a stable secondary structure that is strikingly different from the one in chimpanzee as well as other closely related species, again emphasizing its human-specific evolutionary history. This suggests that positive selection has acted to stabilize human-specific features in the ensemble of HAR1 secondary structures. To investigate the evolutionary history of the human HAR1 structure, we developed a computational model that evaluates the relative likelihood of evolutionary trajectories as a probabilistic version of a Hamiltonian path problem. The model predicts that the most likely last step in turning the ancestral primate HAR1 into the human HAR1 was exactly the substitution that distinguishes the modern human HAR1 sequence from that of Denisovan, an archaic human, providing independent support for our model. The MutationOrder software is available for download and can be applied to other instances of RNA structure evolution.

RevDate: 2018-03-27
CmpDate: 2018-03-27

Kovalkova NA, Ragino YI, Travnikova NY, et al (2017)

[Associations between metabolic syndrome and reduced lung function in young people].

Terapevticheskii arkhiv, 89(10):54-61.

AIM: To reveal possible associations between metabolic syndrome (MS) and reduced lung function.

SUBJECTS AND METHODS: In 2013-016, a cross-sectional survey was conducted in 908 Novosibirsk dwellers, which included spirometry to evaluate external respiratory function (ERF). For the detection of MS, the investigators used the 2009 All-Russian Research Society of Cardiologists criteria: waist circumference (WC) > 80 cm for women and >94 cm for men in combination with two of the following criteria: blood pressure (BP) ≥130/85 mm Hg, triglycerides (TG) ≥1.7 mmol/l, high-density lipoproteins (HDL) cholesterol <1.0 mmol/l for men and <1.2 mmol/l for women, low-density lipoprotein (LDL) cholesterol >3.0 mmol/l, and glucose ≥6.1 mmol/l.

RESULTS: The mean values of WC were significantly greater with a forced expiratory volume in one second (FEV1) <80% than those with a FEV1 of ≥80% in both men (p=0.002) and women (p=0.050); in women, the mean values of WS were higher than those with a FEV1/forced vital capacity (FVC) <70% than those with a FEV1/FVC of ≥70% (p=0.047); the mean systolic and diastolic BP levels were significantly more with reductions in FEV1 and FVC, and the level of HDL cholesterol was significantly lower than that with a FEV1 of < 80% in men only. Significant correlations were found between FEV1 and all components of MS in men, between the majority of components of MS and FVC in men, between WC, BP, and FEV1/FVC in men and women, between plasma glucose levels and FEV1/FVC in women. Linear regression analysis revealed significant inverse correlations of FEV1 with TG, glucose, BP; those of FVC with TG, glucose; at the same time a positive association with HDL cholesterol in men, and only a negative correlation of FEV1/FVC with WC.

CONCLUSION: The revealed associations between MS and reduced lung function can most likely be explained by the greater prevalence of both MS and its components (hypertension, hypertriglyceridemia, hyperglycemia, LDL hypercholesterolemia) among Novosibirsk men. This is consistent with the assertion that the decline in ERF, particularly FEV1, may be a marker of future cardiovascular disease morbidity and mortality.

RevDate: 2018-03-15
CmpDate: 2018-03-15

Soldatsky YL, Denisova OA, SA Bulynko (2017)

[The specific features of the past medical history and etiology of pharyngeal abscess in the children].

Vestnik otorinolaringologii, 82(5):12-14.

The present study was undertaken for the purpose of elucidating the specific features of the past medical history and the etiological factors responsible for the development of tonsillogenic pharyngeal abscesses in the children. We performed the retrospective analysis of the medical histories of 291 children presenting with this condition who had been admitted for the treatment to the ENT Department of the Morozovskzya City Children's Clinical Hospital during the period from January till December 2015. The study has demonstrated the following most common shortcomings of the outpatient treatment of the patients suffering from chronic tonsillitis at the stage preceding formation of paratonsillar abscess: inadequate antibacterial therapy of acute chronic tonsillitis or its exacerbation and limited indications for tonsillectomy at the level of the outpatient treatment. The leading role in the etiology of tonsillogenic pharyngeal abscesses in the children is played by beta-hemolytic Streptococcus of group A. It is concluded that the medical history suggesting past paratonsillar abscess is the absolute indication for the subsequent tonsillectomy in the children of any age.

RevDate: 2018-04-18
CmpDate: 2018-04-18

Yazdanyar A, Rizzuti AE, Mechel E, et al (2018)

Gout Keratitis: A Case of Peripheral Ulcerative Keratitis Secondary to Gout With a Review of the Literature.

Cornea, 37(3):379-381.

PURPOSE: To report a case of peripheral ulcerative keratitis secondary to gout.

METHODS: A 41-year-old man with a history of severe gout disease presented with pain and redness of the right eye. Physical examination revealed 2 areas of peripheral corneal thinning with overlying epithelial defects. Adjacent to these areas, reflective crystals were identified in the corneal stroma. Anterior segment optical coherence tomography demonstrated stromal corneal deposits.

RESULTS: Systemic workup was negative aside from an elevated serum uric acid level. The patient was administered oral prednisone, allopurinol, and colchicine. At his 2-month follow-up visit, the patient was asymptomatic and his corneal thinning had significantly improved.

CONCLUSIONS: Gout is the most common type of inflammatory arthritis in adults with rising incidence and prevalence. Ocular findings in gout are common, but patients are usually asymptomatic. Monosodium urate crystal deposition has been reported to occur in various parts of the eye, with and without ocular inflammation. Crystal deposition in the cornea is extremely rare and may be a cause of peripheral ulcerative keratitis.

RevDate: 2019-01-22

Vashee S, Stockwell TB, Alperovich N, et al (2017)


mSphere, 2(5):.


RevDate: 2018-04-17
CmpDate: 2018-04-17

Saakyan SV, Katargina LA, Krichevskaya GI, et al (2017)

[Specific immunoglobulins G and M in blood serum in retinoblastoma and 'pseudoretinoblastoma'].

Vestnik oftalmologii, 133(4):12-16.

Perinatal inflammatory retinal diseases and intrauterine retinal maldevelopments are mistaken for retinoblastoma as often as in 8-16% of cases.

AIM: To analyze the infectious status in children with retinoblastoma and pseudoretinoblastoma at different ages.

MATERIAL AND METHODS: A total of 47 retinoblastoma suspects aged 4-69 months were enrolled. Pseudoretinoblastoma (inflammatory retinal diseases and intrauterine maldevelopments of the retina) was detected in 14 children (group 1), retinoblastoma - in 33 children (group 2). In each group, two subgroups were identified: 'a' - children under 12 months of age (1a - 5 patients, 2a - 10 patients) and 'b'- children over 12 months of age (1b - 9 patients, 2b - 23 patients). Their blood sera were examined for antibodies to herpes simplex virus types 1 and 2, cytomegalovirus, Epstein-Barr virus, toxoplasma, toxocara, chlamydia, and mycoplasma (enzyme-linked immunosorbent assay).

RESULTS: According to serological screening, all patients from group 1a (children under 12 months of age with pseudoretinoblastoma), in contrast to other groups, were infected perinatally with cytomegalovirus infection. All 47 patients were seronegative to toxoplasma. Toxocara infection was identified in children over 12 months of age: in 3 out of 9 patients with pseudoretinoblastoma and in 2 out of 23 patients with retinoblastoma (p>0.05). Markers of Epstein-Barr viral activity were detected only in 3 retinoblastoma children over 12 months of age.

CONCLUSION: The results suggest that cytomegalovirus infection plays the leading role in the development of perinatal eye pathology, which, in infants, is clinically similar to retinoblastoma. In children over 12 months of age we found no serological signs that could be regarded as specific of either retinoblastoma, or pseudoretinoblastoma. The only thing worth paying attention to is the activation of Epstein-Barr virus infection in children over 12 months of age with retinoblastoma.

RevDate: 2019-01-16
CmpDate: 2018-01-08

Xu D, Jaber Y, Pavlidis P, et al (2017)


BMC bioinformatics, 18(1):426.

BACKGROUND: Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies.

RESULTS: Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format.

CONCLUSION: VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

RevDate: 2018-11-13
CmpDate: 2017-10-31

Zanolli C, Hourset M, Esclassan R, et al (2017)

Neanderthal and Denisova tooth protein variants in present-day humans.

PloS one, 12(9):e0183802.

Environment parameters, diet and genetic factors interact to shape tooth morphostructure. In the human lineage, archaic and modern hominins show differences in dental traits, including enamel thickness, but variability also exists among living populations. Several polymorphisms, in particular in the non-collagenous extracellular matrix proteins of the tooth hard tissues, like enamelin, are involved in dental structure variation and defects and may be associated with dental disorders or susceptibility to caries. To gain insights into the relationships between tooth protein polymorphisms and dental structural morphology and defects, we searched for non-synonymous polymorphisms in tooth proteins from Neanderthal and Denisova hominins. The objective was to identify archaic-specific missense variants that may explain the dental morphostructural variability between extinct and modern humans, and to explore their putative impact on present-day dental phenotypes. Thirteen non-collagenous extracellular matrix proteins specific to hard dental tissues have been selected, searched in the publicly available sequence databases of Neanderthal and Denisova individuals and compared with modern human genome data. A total of 16 non-synonymous polymorphisms were identified in 6 proteins (ameloblastin, amelotin, cementum protein 1, dentin matrix acidic phosphoprotein 1, enamelin and matrix Gla protein). Most of them are encoded by dentin and enamel genes located on chromosome 4, previously reported to show signs of archaic introgression within Africa. Among the variants shared with modern humans, two are ancestral (common with apes) and one is the derived enamelin major variant, T648I (rs7671281), associated with a thinner enamel and specific to the Homo lineage. All the others are specific to Neanderthals and Denisova, and are found at a very low frequency in modern Africans or East and South Asians, suggesting that they may be related to particular dental traits or disease susceptibility in these populations. This modern regional distribution of archaic dental polymorphisms may reflect persistence of archaic variants in some populations and may contribute in part to the geographic dental variations described in modern humans.

RevDate: 2019-04-11

Denisova K, G Zhao (2017)

Inflexible neurobiological signatures precede atypical development in infants at high risk for autism.

Scientific reports, 7(1):11285.

Variability in neurobiological signatures is ubiquitous in early life but the link to adverse developmental milestones in humans is unknown. We examined how levels of signal and noise in movement signatures during the 1st year of life constrain early development in 71 healthy typically developing infants, either at High or Low familial Risk (HR or LR, respectively) for developing Autism Spectrum Disorders (ASD). Delays in early learning developmental trajectories in HR infants (validated in an analysis of 1,445 infants from representative inf﻿ant-sibling studies) were predicted by worse stochastic patterns in their spontaneous head movements as early as 1-2 months after birth, relative to HR infants who showed more rapid developmental progress, as well as relative to all LR infants. While LR 1-2 mo-old infants' movements were significantly different during a language listening task compared to during sleep, HR infants' movements were more similar during both conditions, a striking lack of diversity that reveals context-inflexible experience of ambient information. Contrary to expectation, it is not the level of variability per se that is particularly detrimental in early life. Rather, inflexible sensorimotor systems and/or atypical transition between behavioral states may interfere with the establishment of capacity to extract structure and important cues from sensory input at birth, preceding and contributing to an atypical brain developmental trajectory in toddlerhood.

RevDate: 2018-11-13
CmpDate: 2018-06-12

Gardner EJ, Lam VK, Harris DN, et al (2017)

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology.

Genome research, 27(11):1916-1929.

Mobile element insertions (MEIs) represent ∼25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases, and clinical genomics. Here, we describe the Mobile Element Locator Tool (MELT), which was developed as part of the 1000 Genomes Project to perform MEI discovery on a population scale. Using both Illumina WGS data and simulations, we demonstrate that MELT outperforms existing MEI discovery tools in terms of speed, scalability, specificity, and sensitivity, while also detecting a broader spectrum of MEI-associated features. Several run modes were developed to perform MEI discovery on local and cloud systems. In addition to using MELT to discover MEIs in modern humans as part of the 1000 Genomes Project, we also used it to discover MEIs in chimpanzees and ancient (Neanderthal and Denisovan) hominids. We detected diverse patterns of MEI stratification across these populations that likely were caused by (1) diverse rates of MEI production from source elements, (2) diverse patterns of MEI inheritance, and (3) the introgression of ancient MEIs into modern human genomes. Overall, our study provides the most comprehensive map of MEIs to date spanning chimpanzees, ancient hominids, and modern humans and reveals new aspects of MEI biology in these lineages. We also demonstrate that MELT is a robust platform for MEI discovery and analysis in a variety of experimental settings.

RevDate: 2018-11-13
CmpDate: 2018-05-15

Jinam TA, Phipps ME, Aghakhanian F, et al (2017)

Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture.

Genome biology and evolution, 9(8):2013-2022.


RevDate: 2019-01-15
CmpDate: 2018-04-27

Sharbrough J, Havird JC, Noe GR, et al (2017)

The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes.

Genome biology and evolution, 9(6):1567-1581.

Some human populations interbred with Neanderthals and Denisovans, resulting in substantial contributions to modern-human genomes. Therefore, it is now possible to use genomic data to investigate mechanisms that shaped historical gene flow between humans and our closest hominin relatives. More generally, in eukaryotes, mitonuclear interactions have been argued to play a disproportionate role in generating reproductive isolation. There is no evidence of mtDNA introgression into modern human populations, which means that all introgressed nuclear alleles from archaic hominins must function on a modern-human mitochondrial background. Therefore, mitonuclear interactions are also potentially relevant to hominin evolution. We performed a detailed accounting of mtDNA divergence among hominin lineages and used population-genomic data to test the hypothesis that mitonuclear incompatibilities have preferentially restricted the introgression of nuclear genes with mitochondrial functions. We found a small but significant underrepresentation of introgressed Neanderthal alleles at such nuclear loci. Structural analyses of mitochondrial enzyme complexes revealed that these effects are unlikely to be mediated by physically interacting sites in mitochondrial and nuclear gene products. We did not detect any underrepresentation of introgressed Denisovan alleles at mitochondrial-targeted loci, but this may reflect reduced power because locus-specific estimates of Denisovan introgression are more conservative. Overall, we conclude that genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes.

RevDate: 2018-11-13
CmpDate: 2018-05-31

Rogers AR, Bohlender RJ, CD Huff (2017)

Early history of Neanderthals and Denisovans.

Proceedings of the National Academy of Sciences of the United States of America, 114(37):9859-9863.


RevDate: 2018-11-13

Slon V, Viola B, Renaud G, et al (2017)

A fourth Denisovan individual.

Science advances, 3(7):e1700186.

The presence of Neandertals in Europe and Western Eurasia before the arrival of anatomically modern humans is well supported by archaeological and paleontological data. In contrast, fossil evidence for Denisovans, a sister group of Neandertals recently identified on the basis of DNA sequences, is limited to three specimens, all of which originate from Denisova Cave in the Altai Mountains (Siberia, Russia). We report the retrieval of DNA from a deciduous lower second molar (Denisova 2), discovered in a deep stratigraphic layer in Denisova Cave, and show that this tooth comes from a female Denisovan individual. On the basis of the number of "missing substitutions" in the mitochondrial DNA determined from the specimen, we find that Denisova 2 is substantially older than two of the other Denisovans, reinforcing the view that Denisovans were likely to have been present in the vicinity of Denisova Cave over an extended time period. We show that the level of nuclear DNA sequence diversity found among Denisovans is within the lower range of that of present-day human populations.

RevDate: 2018-07-31
CmpDate: 2018-07-31

Margaryan A, Derenko M, Hovhannisyan H, et al (2017)

Eight Millennia of Matrilineal Genetic Continuity in the South Caucasus.

Current biology : CB, 27(13):2023-2028.e7.


RevDate: 2018-12-02
CmpDate: 2017-09-25

Easton JD, Aunes M, Albers GW, et al (2017)


Circulation, 136(10):907-916.


METHODS: An independent adjudication committee blinded to study treatment classified bleeds according to the PLATO, TIMI (Thrombolysis in Myocardial Infarction), and GUSTO (Global Use of Strategies to Open Occluded Coronary Arteries) definitions. The definitions of ICrH and major bleeding excluded cerebral microbleeds and asymptomatic hemorrhagic transformations of cerebral infarctions so that the definitions better discriminated important events in the acute stroke population.

RESULTS: A total of 13 130 of 13 199 randomized patients received at least 1 dose of study drug and were included in the safety analysis set. PLATO major bleeds occurred in 31 patients (0.5%) on ticagrelor and 38 patients (0.6%) on aspirin (hazard ratio, 0.83; 95% confidence interval, 0.52-1.34). The most common locations of major bleeds were intracranial and gastrointestinal. ICrH was reported in 12 patients (0.2%) on ticagrelor and 18 patients (0.3%) on aspirin. Thirteen of all 30 ICrHs (4 on ticagrelor and 9 on aspirin) were hemorrhagic strokes, and 4 (2 in each group) were symptomatic hemorrhagic transformations of brain infarctions. The ICrHs were spontaneous in 6 and 13, traumatic in 3 and 3, and procedural in 3 and 2 patients on ticagrelor and aspirin, respectively. In total, 9 fatal bleeds occurred on ticagrelor and 4 on aspirin. The composite of ICrH or fatal bleeding included 15 patients on ticagrelor and 18 on aspirin. Independently of bleeding classification, PLATO, TIMI, or GUSTO, the relative difference between treatments for major/severe bleeds was similar. Nonmajor bleeds were more common on ticagrelor.

CONCLUSIONS: Antiplatelet therapy with ticagrelor in patients with acute ischemic stroke or transient ischemic attack showed a bleeding profile similar to that of aspirin for major bleeds. There were few ICrHs.

CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov. Unique identifier: NCT01994720.

RevDate: 2018-11-13
CmpDate: 2018-04-25

Alexeeva EI, Namazova-Baranova LS, Bzarova TM, et al (2017)

Predictors of the response to etanercept in patients with juvenile idiopathic arthritis without systemic manifestations within 12 months: results of an open-label, prospective study conducted at the National Scientific and Practical Center of Children's Health, Russia.

Pediatric rheumatology online journal, 15(1):51.

BACKGROUND: The aim of this study was to investigate the efficacy of etanercept treatment and to identify predictors of response to therapy within 12 months in patients with juvenile idiopathic arthritis (JIA) without systemic manifestations.

METHODS: A total of 197 juvenile patients were enrolled in this study. Response to therapy was assessed using the ACRPedi 30/50/70/90 criteria, the Wallace criteria, and the Juvenile Arthritis Disease Activity Score 71 (JADAS-71). Univariate and multivariate logistic regression analyses were performed to identify potential baseline factors associated with treatment response in different JIA categories.

RESULTS: One year after treatment initiation, 179 (90.9%) patients achieved ACRPedi30; 177 (89.8%) patients achieved ACRPedi50; 168 (85.3%) patients achieved ACRPedi70; and 135 (68.5%) patients achieved ACRPedi90 response. A total of 132 (67.0%) and 92 (46.7%) patients achieved inactive disease according to the Wallace criteria and the JADAS-71 cut-off point, respectively. Excellent response (achieving ACRPedi90 and clinically inactive disease according both to the Wallace criteria and the JADAS71 cut-off point) was associated with persistent oligoarticular JIA category, shorter disease duration before the start of etanercept, a lower number of DMARDs used before the introduction of etanercept, a lower number of joints with limited motion, and lower C-reactive protein at baseline. Poor response (failure to achieve ACR 70 or active disease according to both the Wallace criteria and JADAS71 even when ACR 70 was achieved) was associated with the polyarticular or enthesitis-related JIA categories, higher disease duration before the start of etanercept, and older age at disease onset.

CONCLUSION: Almost half (45.7%) of the patients who initiated etanercept treatment achieved an excellent response (inactive disease and ACRPedi90) after 1 year. What may be novel is our finding that the response to etanercept therapy was strongly associated with the JIA category. The response to etanercept therapy was also associated with the disease duration before the start of etanercept treatment.

RevDate: 2018-11-13

Guo S, Lai C, Wu C, et al (2017)

Conversion Discriminative Analysis on Mild Cognitive Impairment Using Multiple Cortical Features from MR Images.

Frontiers in aging neuroscience, 9:146.

Neuroimaging measurements derived from magnetic resonance imaging provide important information required for detecting changes related to the progression of mild cognitive impairment (MCI). Cortical features and changes play a crucial role in revealing unique anatomical patterns of brain regions, and further differentiate MCI patients from normal states. Four cortical features, namely, gray matter volume, cortical thickness, surface area, and mean curvature, were explored for discriminative analysis among three groups including the stable MCI (sMCI), the converted MCI (cMCI), and the normal control (NC) groups. In this study, 158 subjects (72 NC, 46 sMCI, and 40 cMCI) were selected from the Alzheimer's Disease Neuroimaging Initiative. A sparse-constrained regression model based on the l2-1-norm was introduced to reduce the feature dimensionality and retrieve essential features for the discrimination of the three groups by using a support vector machine (SVM). An optimized strategy of feature addition based on the weight of each feature was adopted for the SVM classifier in order to achieve the best classification performance. The baseline cortical features combined with the longitudinal measurements for 2 years of follow-up data yielded prominent classification results. In particular, the cortical thickness produced a classification with 98.84% accuracy, 97.5% sensitivity, and 100% specificity for the sMCI-cMCI comparison; 92.37% accuracy, 84.78% sensitivity, and 97.22% specificity for the cMCI-NC comparison; and 93.75% accuracy, 92.5% sensitivity, and 94.44% specificity for the sMCI-NC comparison. The best performances obtained by the SVM classifier using the essential features were 5-40% more than those using all of the retained features. The feasibility of the cortical features for the recognition of anatomical patterns was certified; thus, the proposed method has the potential to improve the clinical diagnosis of sub-types of MCI and predict the risk of its conversion to Alzheimer's disease.

RevDate: 2019-04-08
CmpDate: 2019-04-08

Denisova OA, Livzan MA, AP Denisov (2017)

[Comparative characteristics of patients with gastroesophageal reflux disease in the age aspect].

Terapevticheskii arkhiv, 89(4):53-56.

AIM: To compare the characteristics of patients with gastroesophageal reflux disease (GERD) by age groups, a wide range of clinical signs, including life-of-quality (QOL) indicators, and instrumental findings.

SUBJECTS AND METHODS: A total of 110 patients aged 18 to 86 years with GERD were examined in accordance with the standard protocol. Two groups with equal numbers of patents were formed. A study group included elderly and senile patients and a control group consisted of young and adult ones.

RESULTS: The elderly patients with GERD were observed to have a number of age-related clinical features and age-unrelated symptoms. The scores in the scales characterizing the physical health component and those in the general health and vital activity scales were markedly decreased in patients older than 60 years of age. No age-related statistically significant differences were found in the esophageal, gastric, and duodenal mucosae. Daily pH-metry in the elderly showed indirect evidence for esophageal hypomotor dyskinesia in the predominance of alkaline refluxes.

CONCLUSION: The cohort of elderly patients with GERD was ascertained to have statistically significant clinical characteristics, and QOL and pH-metry indicators, which will be able to improve methods for diagnosis and early prevention in this age group.

RevDate: 2018-02-14
CmpDate: 2017-08-21

Reales G, Rovaris DL, Jacovas VC, et al (2017)

A tale of agriculturalists and hunter-gatherers: Exploring the thrifty genotype hypothesis in native South Americans.

American journal of physical anthropology, 163(3):591-601.

OBJECTIVES: To determine genetic differences between agriculturalist and hunter-gatherer southern Native American populations for selected metabolism-related markers and to test whether Neel's thrifty genotype hypothesis (TGH) could explain the genetic patterns observed in these populations.

MATERIALS AND METHODS: 375 Native South American individuals from 17 populations were genotyped using six markers (APOE rs429358 and rs7412; APOA2 rs5082; CD36 rs3211883; TCF7L2 rs11196205; and IGF2BP2 rs11705701). Additionally, APOE genotypes from 39 individuals were obtained from the literature. AMOVA, main effects, and gene-gene interaction tests were performed.

RESULTS: We observed differences in allele distribution patterns between agriculturalists and hunter-gatherers for some markers. For instance, between-groups component of genetic variance (FCT) for APOE rs429358 showed strong differences in allelic distributions between hunter-gatherers and agriculturalists (p = 0.00196). Gene-gene interaction analysis indicated that the APOE E4/CD36 TT and APOE E4/IGF2BP2 A carrier combinations occur at a higher frequency in hunter-gatherers, but this combination is not replicated in archaic (Neanderthal and Denisovan) and ancient (Anzick, Saqqaq, Ust-Ishim, Mal'ta) hunter-gatherer individuals.

DISCUSSION: A complex scenario explains the observed frequencies of the tested markers in hunter-gatherers. Different factors, such as pleotropic alleles, rainforest selective pressures, and population dynamics, may be collectively shaping the observed genetic patterns. We conclude that although TGH seems a plausible hypothesis to explain part of the data, other factors may be important in our tested populations.

RevDate: 2018-08-08
CmpDate: 2018-01-25

Slon V, Hopfe C, Weiß CL, et al (2017)

Neandertal and Denisovan DNA from Pleistocene sediments.

Science (New York, N.Y.), 356(6338):605-608.

Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave, we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains are found.

RevDate: 2019-02-02
CmpDate: 2017-05-30

Hu H, Petousi N, Glusman G, et al (2017)

Evolutionary history of Tibetans inferred from whole-genome sequencing.

PLoS genetics, 13(4):e1006675.

The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.

RevDate: 2018-11-13
CmpDate: 2018-02-01

Jégou B, Sankararaman S, Rolland AD, et al (2017)

Meiotic Genes Are Enriched in Regions of Reduced Archaic Ancestry.

Molecular biology and evolution, 34(8):1974-1980.

About 1-6% of the genetic ancestry of modern humans today originates from admixture with archaic humans. It has recently been shown that autosomal genomic regions with a reduced proportion of Neanderthal and Denisovan ancestries (NA and DA) are significantly enriched in genes that are more expressed in testis than in other tissues. To determine whether a cellular segregation pattern would exist, we combined maps of archaic introgression with a cross-analysis of three transcriptomic datasets deciphering the transcriptional landscape of human gonadal cell types. We reveal that the regions deficient in both NA and DA contain a significant enrichment of genes transcribed in meiotic germ cells. The interbreeding of anatomically modern humans with archaic humans may have introduced archaic-derived alleles that contributed to genetic incompatibilities affecting meiosis that were subsequently purged by natural selection.

RevDate: 2018-12-02
CmpDate: 2018-04-04

Ao H, Liu CR, Roberts AP, et al (2017)

An updated age for the Xujiayao hominin from the Nihewan Basin, North China: Implications for Middle Pleistocene human evolution in East Asia.

Journal of human evolution, 106:54-65.

The Xujiayao site in the Nihewan Basin (North China) is one of the most important Paleolithic sites in East Asia. Twenty Homo fossils, which were previously assigned to an archaic Homo sapiens group, have been excavated along with more than 30,000 lithic artifacts and ∼5000 mammalian fossil specimens. Dating of the Xujiayao hominin has been pursued since its excavation in the 1970s, but its age has remained controversial because of limitations of the dating techniques that have been applied to available materials. Here, we report new ages for the Xujiayao hominin based on combined electron spin resonance (ESR) dating of quartz in the sediments and high-resolution magnetostratigraphy of the fluvio-lacustrine sequence. The magnetostratigraphy suggests that the upper Matuyama and Brunhes polarity chrons are recorded at Xujiayao. The ESR dating results indicate a pooled average age of 260-370 ka for the Homo-bearing layer, which is consistent with its position within the middle Brunhes normal polarity chron indicated by magnetostratigraphy. This age estimate makes the Xujiayao hominin among the oldest mid-Pleistocene hominins with derived Neanderthal traits in East Asia. This age is consistent with the time when early Denisovans, a sister group of Neanderthals, appeared and colonized eastern Eurasia. Our updated age and the Neanderthal-like traits of the Xujiayao Homo fossils, particularly the Denisovan-like molar teeth, make it possible that the Xujiayao hominin could represent an early Denisovan.

RevDate: 2018-11-13
CmpDate: 2018-03-26

Heidenreich B, Denisova E, Rachakonda S, et al (2017)

Genetic alterations in seborrheic keratoses.

Oncotarget, 8(22):36639-36649.

Seborrheic keratoses are common benign epidermal lesions that are associated with increased age and sun-exposure. Those lesions despite harboring multiple somatic alterations in contrast to malignant tumors appear to be genetically stable. In order to investigate and characterize the presence of recurrent mutations, we performed exome sequencing on DNA from one seborrheic keratosis lesion and corresponding blood cells from the same patients with follow up investigation of alterations identified by exome sequencing in 24 additional lesions from as many patients. In addition we investigated alterations in all lesions at specific genes loci that included FGFR3, PIK3CA, HRAS, BRAF, CDKN2A and TERT and DHPH3 promoters. The exome sequencing data indicated three mutations per Mb of the targeted sequence. The mutational pattern depicted typical UV signature with majority of alterations being C>T and CC>TT base changes at dipyrimidinic sites. The FGFR3 mutations were the most frequent, detected in 12 of 25 (48%) lesions, followed by the PIK3CA (32%), TERT promoter (24%) and DPH3 promoter mutations (24%). TERT promoter mutations associated with increased age and were present mainly in the lesions excised from head and neck. Three lesions also carried alterations in CDKN2A. FGFR3, TERT and DPH3 expression did not correlate with mutations in the respective genes and promoters; however, increased FGFR3 transcript levels were associated with increased FOXN1 levels, a suggested positive feedback loop that stalls malignant progression. Thus, in this study we report overall mutation rate through exome sequencing and show the most frequent mutations seborrheic keratosis.

RevDate: 2018-12-02
CmpDate: 2017-08-21

Kharitonova MI, Denisova AO, Andronova VL, et al (2017)

New modified 2-aminobenzimidazole nucleosides: Synthesis and evaluation of their activity against herpes simplex virus type 1.

Bioorganic & medicinal chemistry letters, 27(11):2484-2487.

Using the enzymatic transglycosylation reaction β-d-ribo- and 2'-deoxyribofuranosides of 2-amino-5,6-difluorobenzimidazole nucleosides have been synthesized. 2-Amino-5,6-difluoro-benzimidazole riboside proved to exhibit a selective antiviral activity (selectivity index >32) against a wild strain of the herpes simplex virus type 1, as well as towards virus strains that are resistant to acyclovir, cidofovir, and foscarnet. We believe that this compound might be used for treatment of herpes infections in those cases, when acyclovir is not efficient.

RevDate: 2018-12-02
CmpDate: 2017-08-14

Hu Y, Malyutina S, Pikhart H, et al (2017)

The Relationship between Body Mass Index and 10-Year Trajectories of Physical Functioning in Middle-Aged and Older Russians: Prospective Results of the Russian HAPIEE Study.

The journal of nutrition, health & aging, 21(4):381-388.


DESIGN: Prospective cohort study.






RevDate: 2018-01-18
CmpDate: 2018-01-18

Baklanova YV, Lipina OA, Maksimova LG, et al (2017)

Nd3+, Ho3+-codoped garnet-related Li7La3Hf2O12 phosphor with NIR luminescence.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy, 180:105-109.

Simultaneous emission lines around 1.05μm, 1.3μm, 1.8μm, 2.1μm and 2.7μm have been observed in Li7La3-xNdxHf2O12:Ho3+ (x=0.00-0.15) under 808nm laser diode excitation. Near-infrared luminescence due to holmium ions with residual concentration in the Li7La3Hf2O12 host has been studied. The intensity of 2.1 and 2.7μm lines associated with 5I7→5I8 and 5I6→5I7 transitions in Ho3+ depends on the neodymium codopant concentration. This result indicates that Nd3+ ions can be potentially used as sensitizers for Ho3+ ions to stimulate the intense near-infrared emission in this system. Possible energy transfer mechanisms between lanthanide ions have been briefly discussed.

RevDate: 2018-12-07
CmpDate: 2017-05-09

Denisova AV, Tibbelin J, Emanuelsson R, et al (2017)

A Computational Investigation of the Substituent Effects on Geometric, Electronic, and Optical Properties of Siloles and 1,4-Disilacyclohexa-2,5-dienes.

Molecules (Basel, Switzerland), 22(3):.

Thirty two differently substituted siloles 1a-1p and 1,4-disilacyclohexa-2,5-dienes 2a-2p were investigated by quantum chemical calculations using the PBE0 hybrid density functional theory (DFT) method. The substituents included σ-electron donating and withdrawing, as well as π-electron donating and withdrawing groups, and their effects when placed at the Si atom(s) or at the C atoms were examined. Focus was placed on geometries, frontier orbital energies and the energies of the first allowed electronic excitations. We analyzed the variation in energies between the orbitals which correspond to HOMO and LUMO for the two parent species, here represented as ΔεHL, motivated by the fact that the first allowed transitions involve excitation between these orbitals. Even though ΔεHL and the excitation energies are lower for siloles than for 1,4-disilacyclohexa-2,5-dienes the latter display significantly larger variations with substitution. The ΔεHL of the siloles vary within 4.57-5.35 eV (ΔΔεHL = 0.78 eV) while for the 1,4-disilacyclohexa-2,5-dienes the range is 5.49-7.15 eV (ΔΔεHL = 1.66 eV). The excitation energy of the first allowed transitions display a moderate variation for siloles (3.60-4.41 eV) whereas the variation for 1,4-disilacyclohexa-2,5-dienes is nearly doubled (4.69-6.21 eV). Cyclobutadisiloles combine the characteristics of siloles and 1,4-disilacyclohexa-2,5-diene by having even lower excitation energies than siloles yet also extensive variation in excitation energies to substitution of 1,4-disilacyclohexa-2,5-dienes (3.47-4.77 eV, variation of 1.30 eV).

RevDate: 2018-10-23
CmpDate: 2017-07-06

Bogomolov DV, Putintsev VA, Zbrueva YV, et al (2017)

[Certain immunohistochemical markers of the intravitality of strangulation mechanical asphyxia].

Sudebno-meditsinskaia ekspertiza, 60(1):8-10.

Thus article was designed to report the results of the investigations into specific histological features of the skin and soft tissue samples taken from the strangulation areas on the neck and from the lungs of the persons who had committed suicide by hanging. The studies revealed the well apparent expression of fibrinogen in the derma and the subdermal cellolocutaneous layer of the skin subjected to intravital strangulation. Similar changes were absent in lung alveoli.

RevDate: 2017-03-15
CmpDate: 2017-03-15

Bugaeva LI, Denisova TD, Sergeeva SA, et al (2017)

Effects of Afobazole on Postnatal Development of Rat Offspring.

Bulletin of experimental biology and medicine, 162(4):441-444.

Physical development, development of sensory and motor reflexes, behavioral and mnestic patterns were studied infantile and juvenile rat pups born by female rats receiving Afobazole during pregnancy. Physical development and development of sensory and motor reflexes in rats were completed without pathologies by the age of 2 months. During the infantile period, the rat pups demonstrated reduced body weight gain, delayed eye opening and pupillary response formation, decreased muscle force, and suppressed motor behavior. During the juvenile period, body weight gain and development of motor behavior were intensified. Females demonstrated later vagina opening and poorer mnestic responses. In males, the terms of sexual maturation were unchanged and processes of learning and memory retrieval were not impaired.

RevDate: 2019-01-14
CmpDate: 2017-10-30

Denisova K, Zhao G, Wang Z, et al (2017)

Cortical interactions during the resolution of information processing demands in autism spectrum disorders.

Brain and behavior, 7(2):e00596.

INTRODUCTION: Our flexible and adaptive interactions with the environment are guided by our individual representation of the physical world, estimated through sensation and evaluation of available information against prior knowledge. When linking sensory evidence with higher-level expectations for action, the central nervous system (CNS) in typically developing (TD) individuals relies in part on distributed and interacting cortical regions to communicate neuronal signals flexibly across the brain. Increasing evidence suggests that the balance between levels of signal and noise during information processing may be disrupted in individuals with Autism Spectrum Disorders (ASD).

METHODS: Participants with and without ASD performed a visuospatial interference task while undergoing functional Magnetic Resonance Imaging (fMRI). We empirically estimated parameters characterizing participants' latencies and their subtle fluctuations (noise accumulation) over the 16-min scan. We modeled hemodynamic activation and used seed-based analyses of neural coupling to study dysfunction in interference-specific connectivity in a subset of ASD participants who were nonparametrically matched to TD participants on age, male-to-female ratio, and magnitude of movement during the scan.

RESULTS: Stochastic patterns of response fluctuations reveal significantly higher noise-to-signal levels and a more random and noisy structure in ASD versus TD participants, and in particular ASD adults who have the greatest clinical autistic deficits. While individuals with ASD show an overall weaker modulation of interference-specific functional connectivity relative to TD individuals, in particular between the seeds of Anterior Cingulate Cortex (ACC) and Inferior Parietal Sulcus (IPS) and the rest of the brain, we found that in ASD, higher uncertainty during the task is linked to increased interference-specific coupling between bilateral anterior insula and prefrontal cortex.

CONCLUSIONS: Subtle and informative differences in the structure of experiencing information exist between ASD and TD individuals. Our findings reveal in ASD an atypical capacity to apply previously perceived information in a manner optimal for adaptive functioning, plausibly revealing suboptimal message-passing across the CNS.

RevDate: 2019-02-07
CmpDate: 2018-03-08

Tashi T, Scott Reading N, Wuren T, et al (2017)

Gain-of-function EGLN1 prolyl hydroxylase (PHD2 D4E:C127S) in combination with EPAS1 (HIF-2α) polymorphism lowers hemoglobin concentration in Tibetan highlanders.

Journal of molecular medicine (Berlin, Germany), 95(6):665-670.

Tibetans have lived at high altitude for generations and are thought to be genetically adapted to hypoxic environments. Most are protected from hypoxia-induced polycythemia, and a haplotype of EPAS1, encoding hypoxia-inducible factor (HIF-2α), has been associated with lower hemoglobin levels. We earlier reported a Tibetan-specific EGLN1 haplotype encoding PHD2 which abrogates HIF augmentation in hypoxia. We genotyped 347 Tibetan individuals from varying altitudes for both the Tibetan-specific EGLN1 haplotype and 10 candidate SNPs in the EPAS1 haplotype and correlated their association with hemoglobin levels. The effect of the EGLN1 haplotype on hemoglobin exhibited age dependency at low altitude, while at higher altitudes, it showed a trend to lower hemoglobin levels in the presence of the Tibetan-selected EPAS1 rs142764723 C/C allele. The observed gene-environment and gene-gene interactions and the moderate effect of the EGLN1 and EPAS1 haplotypes on hemoglobin indicate that other modifiers exist. It remains to be determined whether a blunting of erythropoiesis or other physiological consequences of HIF downregulation are the primary drivers of these genetic adaptations among Tibetans.

KEY MESSAGE: Most Tibetans are protected from polycythemia while living in high altitude. An EGLN1 co-adapted haplotype, EGLN1 c.12C>G, c.380G>C is uniquely Tibetan. The Tibetan EPAS1 haplotype has introgressed from the Denisovan genome. While EGLN1 and EPAS1 genotypes lower Hb, this study indicates additional Hb modifiers.

RevDate: 2018-11-13
CmpDate: 2018-01-26

Povysil G, S Hochreiter (2016)

IBD Sharing between Africans, Neandertals, and Denisovans.

Genome biology and evolution, 8(12):3406-3416.

Interbreeding between ancestors of humans and other hominins outside of Africa has been studied intensively, while their common history within Africa still lacks proper attention. However, shedding light on human evolution in this time period about which little is known, is essential for understanding subsequent events outside of Africa. We investigate the genetic relationships of humans, Neandertals, and Denisovans by identifying very short DNA segments in the 1000 Genomes Phase 3 data that these hominins share identical by descent (IBD). By focusing on low frequency and rare variants, we identify very short IBD segments with high confidence. These segments reveal events from a very distant past because shorter IBD segments are presumably older than longer ones. We extracted two types of very old IBD segments that are not only shared among humans, but also with Neandertals and/or Denisovans. The first type contains longer segments that are found primarily in Asians and Europeans where more segments are found in South Asians than in East Asians for both Neandertal and Denisovan. These longer segments indicate complex admixture events outside of Africa. The second type consists of shorter segments that are shared mainly by Africans and therefore may indicate events involving ancestors of humans and other ancient hominins within Africa. Our results from the autosomes are further supported by an analysis of chromosome X, on which segments that are shared by Africans and match the Neandertal and/or Denisovan genome were even more prominent. Our results indicate that interbreeding with other hominins was a common feature of human evolution starting already long before ancestors of modern humans left Africa.

RevDate: 2018-11-13
CmpDate: 2017-07-11

Carus-Cadavieco M, Gorbati M, Ye L, et al (2017)

Gamma oscillations organize top-down signalling to hypothalamus and enable food seeking.

Nature, 542(7640):232-236.


RevDate: 2018-10-23
CmpDate: 2017-06-29

Khabarova EA, Denisova NP, Rogov DY, et al (2016)

[The preliminary results of subthalamic nucleus stimulation after destructive surgery in Parkinson's disease].

Zhurnal voprosy neirokhirurgii imeni N. N. Burdenko, 80(6):36-41.

OBJECTIVE: To evaluate the efficacy of bilateral electrical stimulation (ES) of the subthalamic nucleus (STN) in patients with Parkinson's disease (PD) after preceding pallidotomy or ventrolateral (VL) thalamotomy.

MATERIAL AND METHODS: The study included 9 patients with bilateral STN ES who had undergone previous unilateral destructive surgery on the subcortical structures: pallidotomy (5 patients) and VL thalamotomy (4). A control group consisted of 9 patients with STN ES, without prior destructive surgery. A clinical and neurological examination included quantitative assessment of motor disturbances using the Hoehn-Yahr scale and Unified Parkinson's disease rating scale (UPDRS). UPDRS was used to evaluate the motor activity (IIIrd part of the scale) and severity of drug-induced dyskinesia and motor fluctuations (IVth part of the scale).

RESULTS: In the group of STN ES with preceding destruction of the subcortical structures, an improvement in motor functions in the early period (6 months) was 45%, and severity of drug-induced complications was decreased by 75%. In a group of STN DBS without destruction, motor disturbances were improved by 61%, and drug-induced complications were decreased by 77%. Improvement in motor functions amounted to 51.9% in patients with preceding pallidotomy (GPi destruction) and 37.5% in a group with preceding VL thalamotomy. The equivalent dose of levodopa was reduced by 51.39%, from 1,008±346 to 490±194, in the study group and by 55.04%, from 963±96 to 433±160, in the control group.

CONCLUSION: Bilateral STN neurostimulation is effective after unilateral stereotaxic destruction of the subcortical structures in PD patients.

RevDate: 2019-02-15
CmpDate: 2019-02-04

Kulyutsina ER, Tatarchenko IP, Levashova OA, et al (2017)

[The interrelationship of indices of hemocysteine and genetic polymorphisms conditioning disorders of folates metabolism in healthy population].

Klinicheskaia laboratornaia diagnostika, 62(2):82-87.

The study was carried out to investigate relationship of the level of homocysteine and genetic polymorphisms conditioning disorders of metabolism of folates in healthy population and of various age and gender groups. The study covered 168 donors: 98 males and 70 females. Two gender groups were singled out and in each of them age groups: 18-31, 32-45 and 46-60 years old. The analysis of concentration of homocysteine was implemented using immune chemiluminescence analysis. The polymerase chain reaction was applied for analyzing genetic polymorphisms associated with disorders of folate cycle by genes MTHFR (met hylentetrahydrofolatereductase) (polymorphisms MTHFR: 677 C>T and MTHFR: 1298 A>C), MTR (B12-dependent methionine-synthetase) (polymorphism MTR: 2756 A>G) and MTRR (methionine-synthetase-reductase) (polymorphism MTRR: 66 A>G). The level of homocysteine in blood of donors was reliably higher in male groups of 18-31 and 32-45 years old as against female groups comparable by age. The study established higher rate of occurrence of heterozygous genotypes bringing unfavorable types of polymorphisms of MTHFR and MTRR genes both in male and female groups. The study established higher rate of occurrence of unfavorable genotypes in examined patients in comparison with publications' data. The established statistically significant inverse correlation of concentration of homocysteine and genetic polymorphisms associated with disorders of folate cycle in individuals of young and middle age mainly males, permits to draw a conclusion about absence of their direct relationship. Therefore, implementation of genetic liability to increasing of homocysteine can occur under effect of external unfavorable factors.

RevDate: 2018-06-26
CmpDate: 2018-06-26

Bugaeva LI, Denisova TD, Mazanova YA, et al (2017)


Eksperimental'naia i klinicheskaia farmakologiia, 80(1):28-31.

It is experimentally established that afobazole produces no damaging action on the organogenesis and fetogenic processes registered in the postnatal period of rat offspring development. It was noted that, in rat babies in lactation age, the dynamics of body weight gain was lower on average by 7.4% (p < 0.05) in males and 17.0% (p < 0.001) in females; the rate of muscular force maturing was lower by 2.7% (p < 0.05); and the locomotive activity was lower (by 19.4% for ver- tical standings and by 50% for looking into floor holes, p < 0.05) compared to control values. For the same offspring passed to definitive food, the body weight gain and behavioral activity did not differ from control indicators, while the terms of sexual development were delayed in females and did not change in males. By two-month age, the physical development of rat offspring was completely created and met physiological standards.

RevDate: 2018-11-13
CmpDate: 2017-07-24

Racimo F, Gokhman D, Fumagalli M, et al (2017)

Archaic Adaptive Introgression in TBX15/WARS2.

Molecular biology and evolution, 34(3):509-524.

A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.


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One of the most intriguing, and philosophically suggestive, recent scientific findings has been the discovery that the human lineage included several branches at the species level in which each species had developed culture (tool making, mastery of fire, burial of the dead). Before the Chicxulub impact that ended the realm of the dinosaurs, sentience and culture had not occurred in any lineage, despite several hundred million years of evolution. However, in the mammalian radiation that occurred afterwards, several primate lineages occurred. In just the last few million years, one of those lineages diverged into several sentient, culture-developing species. This book explores how only one of those species (ours) survived, while the others went extinct. Recommended. R. Robbins

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