@article {13681, title = {Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity.}, journal = {Proc Natl Acad Sci U S A}, volume = {117}, year = {2020}, month = {2020 03 17}, pages = {6047-6055}, abstract = {


}, keywords = {Animals, CD8-Positive T-Lymphocytes, Cell Differentiation, Cell Line, Tumor, Enzyme Inhibitors, Humans, Immunologic Memory, Immunotherapy, Adoptive, Interleukin-2, Interleukins, L-Lactate Dehydrogenase, Melanoma, Experimental, Mice, Primary Cell Culture, Stem Cells}, issn = {1091-6490}, doi = {10.1073/pnas.1920413117}, author = {Hermans, Dalton and Gautam, Sanjivan and Garc{\'\i}a-Ca{\~n}averas, Juan C and Gromer, Daniel and Mitra, Suman and Spolski, Rosanne and Li, Peng and Christensen, Stephen and Nguyen, Rosa and Lin, Jian-Xin and Oh, Jangsuk and Du, Ning and Veenbergen, Sharon and Fioravanti, Jessica and Ebina-Shibuya, Risa and Bleck, Christopher and Neckers, Leonard M and Rabinowitz, Joshua D and Gattinoni, Luca and Leonard, Warren J} } @article {14786, title = {Lactate: the ugly duckling of energy metabolism.}, journal = {Nat Metab}, volume = {2}, year = {2020}, month = {2020 Jul}, pages = {566-571}, abstract = {

Lactate, perhaps the best-known metabolic waste product, was first isolated from sour milk, in which it is produced by lactobacilli. Whereas microbes also generate other fermentation products, such as ethanol or acetone, lactate dominates in mammals. Lactate production increases when the demand for ATP and oxygen exceeds supply, as occurs during intense exercise and ischaemia. The build-up of lactate in stressed muscle and ischaemic tissues has established lactate\&$\#$39;s reputation as a deleterious waste product. In this Perspective, we summarize emerging evidence that, in mammals, lactate also serves as a major circulating carbohydrate fuel. By providing mammalian cells with both a convenient source and sink for three-carbon compounds, circulating lactate enables the uncoupling of carbohydrate-driven mitochondrial energy generation from glycolysis. Lactate and pyruvate together serve as a circulating redox buffer that equilibrates the NADH/NAD ratio across cells and tissues. This reconceptualization of lactate as a fuel-analogous to how Hans Christian Andersen\&$\#$39;s ugly duckling is actually a beautiful swan-has the potential to reshape the field of energy metabolism.

}, issn = {2522-5812}, doi = {10.1038/s42255-020-0243-4}, author = {Rabinowitz, Joshua D and Enerb{\"a}ck, Sven} } @article {12986, title = {Left-right asymmetric heart jogging increases the robustness of dextral heart looping in zebrafish.}, journal = {Dev Biol}, volume = {459}, year = {2020}, month = {2020 Mar 15}, pages = {79-86}, abstract = {

Building a left-right (L-R) asymmetric organ requires asymmetric information. This comes from various sources, including asymmetries in embryo-scale genetic cascades (including the left-sided Nodal cascade), organ-intrinsic mechanical forces, and cell-level chirality, but the relative influence of these sources and how they collaborate to drive asymmetric morphogenesis is not understood. During zebrafish heart development, the linear heart tube extends to the left of the midline in a process known as jogging. The jogged heart then undergoes dextral (i.e. rightward) looping to correctly position the heart chambers relative to one another. Left lateralized jogging is governed by the left-sided expression of Nodal in mesoderm tissue, while looping laterality is mainly controlled by heart-intrinsic cell-level asymmetries in the actomyosin cytoskeleton. The purpose of lateralized jogging is not known. Moreover, after jogging, the heart tube returns to an almost midline position and so it is not clear whether or how jogging may impact the dextral loop. Here, we characterize a novel loss-of-function mutant in the zebrafish Nodal homolog southpaw (spaw) that appears to be a true null. We then assess the relationship between jogging and looping laterality in embryos lacking asymmetric Spaw signals. We found that the probability of a dextral loop occurring, does not depend on asymmetric Spaw signals per se, but does depend on the laterality of jogging. Thus, we conclude that the role of leftward jogging is to spatially position the heart tube in a manner that promotes robust dextral looping. When jogging laterality is abnormal, the robustness of dextral looping decreases. This establishes a cooperation between embryo-scale Nodal-dependent L-R asymmetries and organ-intrinsic cellular chirality in the control of asymmetric heart morphogenesis and shows that the transient laterality of the early heart tube has consequences for later heart morphogenetic events.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2019.11.012}, author = {Grimes, Daniel T and Patterson, Victoria L and Luna-Arvizu, Gabriel and Schottenfeld-Roames, Jodi and Irons, Zoe H and Burdine, Rebecca D} } @article {14766, title = {Lights up on organelles: Optogenetic tools to control subcellular structure and organization.}, journal = {Wiley Interdiscip Rev Syst Biol Med}, year = {2020}, month = {2020 Jul 26}, pages = {e1500}, abstract = {

Since the neurobiological inception of optogenetics, light-controlled molecular perturbations have been applied in many scientific disciplines to both manipulate and observe cellular function. Proteins exhibiting light-sensitive conformational changes provide researchers with avenues for spatiotemporal control over the cellular environment and serve as valuable alternatives to chemically inducible systems. Optogenetic approaches have been developed to target proteins to specific subcellular compartments, allowing for the manipulation of nuclear translocation and plasma membrane morphology. Additionally, these tools have been harnessed for molecular interrogation of organelle function, location, and dynamics. Optogenetic approaches offer novel ways to answer fundamental biological questions and to improve the efficiency of bioengineered cell factories by controlling the assembly of synthetic organelles. This review first provides a summary of available optogenetic systems with an emphasis on their organelle-specific utility. It then explores the strategies employed for organelle targeting and concludes by discussing our perspective on the future of optogenetics to control subcellular structure and organization. This article is categorized under: Laboratory Methods and Technologies \> Genetic/Genomic Methods Physiology \> Physiology of Model Organisms Biological Mechanisms \> Regulatory Biology Models of Systems Properties and Processes \> Cellular Models.

}, issn = {1939-005X}, doi = {10.1002/wsbm.1500}, author = {Kichuk, Therese C and Carrasco-L{\'o}pez, C{\'e}sar and Avalos, Jos{\'e} L} } @article {13836, title = {A Live-Cell Screen for Altered Erk Dynamics Reveals Principles of Proliferative Control.}, journal = {Cell Syst}, volume = {10}, year = {2020}, month = {2020 Mar 25}, pages = {240-253.e6}, abstract = {

Complex, time-varying responses have been observed widely in cell signaling, but how specific dynamics are generated or regulated is largely unknown. One major obstacle has been that high-throughput screens are typically incompatible with the live-cell assays used to monitor dynamics. Here, we address this challenge by screening a library of 429 kinase inhibitors and monitoring extracellular-regulated kinase (Erk) activity over 5\ h in more than 80,000 single primary mouse keratinocytes. Our screen reveals both known and uncharacterized modulators of Erk dynamics, including inhibitors of non-epidermal growth factor receptor (EGFR) receptor tyrosine kinases (RTKs) that increase Erk pulse frequency and overall activity. Using drug treatment and direct optogenetic control, we demonstrate that drug-induced changes to Erk dynamics alter the conditions under which cells proliferate. Our work opens the door to high-throughput screens using live-cell biosensors and reveals that cell proliferation integrates information from Erk dynamics as well as additional permissive cues.

}, issn = {2405-4720}, doi = {10.1016/j.cels.2020.02.005}, author = {Goglia, Alexander G and Wilson, Maxwell Z and Jena, Siddhartha G and Silbert, Jillian and Basta, Lena P and Devenport, Danelle and Toettcher, Jared E} } @article {14801, title = {Living under Strain: How Epithelia Protect Their Genomes from Repeated Stretching.}, journal = {Biochemistry}, year = {2020}, month = {2020 Jul 23}, issn = {1520-4995}, doi = {10.1021/acs.biochem.0c00545}, author = {Anlas, Alisya A and Nelson, Celeste M} } @article {11926, title = {Light-based control of metabolic flux through assembly of synthetic organelles.}, journal = {Nat Chem Biol}, volume = {15}, year = {2019}, month = {2019 06}, pages = {589-597}, abstract = {

To maximize a desired product, metabolic engineers typically express enzymes to high, constant levels. Yet, permanent pathway activation can have undesirable consequences including competition with essential pathways and accumulation of toxic intermediates. Faced with similar challenges, natural metabolic systems compartmentalize enzymes into organelles or post-translationally induce activity under certain conditions. Here we report that optogenetic control can be used to extend compartmentalization and dynamic control to engineered metabolisms in yeast. We describe a suite of optogenetic tools to trigger assembly and disassembly of metabolically active enzyme clusters. Using the deoxyviolacein biosynthesis pathway as a model system, we find that light-switchable clustering can enhance product formation six-fold and product specificity 18-fold by decreasing the concentration of intermediate metabolites and reducing flux through competing pathways. Inducible compartmentalization of enzymes into synthetic organelles can thus be used to control engineered metabolic pathways, limit intermediates and favor the formation of desired products.

}, keywords = {Indoles, Light, Metabolic Engineering, Metabolic Networks and Pathways, Optogenetics, Organelles, Saccharomyces cerevisiae, Synechocystis, Synthetic Biology}, issn = {1552-4469}, doi = {10.1038/s41589-019-0284-8}, author = {Zhao, Evan M and Suek, Nathan and Wilson, Maxwell Z and Dine, Elliot and Pannucci, Nicole L and Gitai, Zemer and Avalos, Jos{\'e} L and Toettcher, Jared E} } @article {13506, title = {A Likelihood-Free Estimator of Population Structure Bridging Admixture Models and Principal Components Analysis.}, journal = {Genetics}, volume = {212}, year = {2019}, month = {2019 08}, pages = {1009-1029}, abstract = {

We introduce a simple and computationally efficient method for fitting the admixture model of genetic population structure, called ALStructure The strategy of ALStructure is to first estimate the low-dimensional linear subspace of the population admixture components, and then search for a model within this subspace that is consistent with the admixture model{\textquoteright}s natural probabilistic constraints. Central to this strategy is the observation that all models belonging to this constrained space of solutions are risk-minimizing and have equal likelihood, rendering any additional optimization unnecessary. The low-dimensional linear subspace is estimated through a recently introduced principal components analysis method that is appropriate for genotype data, thereby providing a solution that has both principal components and probabilistic admixture interpretations. Our approach differs fundamentally from other existing methods for estimating admixture, which aim to fit the admixture model directly by searching for parameters that maximize the likelihood function or the posterior probability. We observe that ALStructure typically outperforms existing methods both in accuracy and computational speed under a wide array of simulated and real human genotype datasets. Throughout this work, we emphasize that the admixture model is a special case of a much broader class of models for which algorithms similar to ALStructure may be successfully employed.

}, keywords = {Algorithms, Computational Biology, Datasets as Topic, Genetics, Population, Genome, Human, Humans, Likelihood Functions, Models, Genetic, Principal Component Analysis}, issn = {1943-2631}, doi = {10.1534/genetics.119.302159}, author = {Cabreros, Irineo and Storey, John D} } @article {12971, title = {The liquid nucleome - phase transitions in the nucleus at a glance.}, journal = {J Cell Sci}, volume = {132}, year = {2019}, month = {2019 11 21}, abstract = {

Cells organize membrane-less internal compartments through a process called liquid-liquid phase separation (LLPS) to create chemically distinct compartments, referred to as condensates, which emerge from interactions among biological macromolecules. These condensates include various cytoplasmic structures such as P-granules and stress granules. However, an even wider array of condensates subcompartmentalize the cell nucleus, forming liquid-like structures that range from nucleoli and Cajal bodies to nuclear speckles and gems. Phase separation provides a biophysical assembly mechanism underlying this non-covalent form of fluid compartmentalization and functionalization. In this Cell Science at a Glance article and the accompanying poster, we term these phase-separated liquids that organize the nucleus the liquid nucleome; we discuss examples of biological phase transitions in the nucleus, how the cell utilizes biophysical aspects of phase separation to form and regulate condensates, and suggest interpretations for the role of phase separation in nuclear organization and function.

}, keywords = {Cell Nucleus, Liquid-Liquid Extraction}, issn = {1477-9137}, doi = {10.1242/jcs.235093}, author = {Strom, Amy R and Brangwynne, Clifford P} } @article {11331, title = {Localized production of defence chemicals by intracellular symbionts of Haliclona sponges.}, journal = {Nat Microbiol}, volume = {4}, year = {2019}, month = {2019 07}, pages = {1149-1159}, abstract = {

Marine sponges often house small-molecule-producing symbionts extracellularly in their mesohyl, providing the host with a means of chemical defence against predation and microbial infection. Here, we report an intriguing case of chemically mediated symbiosis between the renieramycin-containing sponge Haliclona sp. and its herein discovered renieramycin-producing symbiont Candidatus Endohaliclona renieramycinifaciens. Remarkably, Ca. E. renieramycinifaciens has undergone extreme genome reduction where it has lost almost all necessary elements for free living while maintaining a complex, multi-copy plasmid-encoded biosynthetic gene cluster for renieramycin biosynthesis. In return, the sponge houses Ca. E. renieramycinifaciens in previously uncharacterized cellular reservoirs (chemobacteriocytes), where it can acquire nutrients from the host and avoid bacterial competition. This relationship is highly specific to a single clade of Haliclona sponges. Our study reveals intracellular symbionts as an understudied source for defence chemicals in the oldest-living metazoans and paves the way towards discovering similar systems in other marine sponges.

}, keywords = {Animals, Gammaproteobacteria, Genome Size, Haliclona, Host Specificity, Metagenome, Molecular Structure, Multigene Family, Phylogeny, Plasmids, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Symbiosis, Tetrahydroisoquinolines}, issn = {2058-5276}, doi = {10.1038/s41564-019-0415-8}, author = {Tianero, Ma Diarey and Balaich, Jared N and Donia, Mohamed S} } @article {10481, title = {Location is everything: protein translocations as a viral infection strategy.}, journal = {Curr Opin Chem Biol}, volume = {48}, year = {2019}, month = {2019 02}, pages = {34-43}, abstract = {

Protein movement between different subcellular compartments is an essential aspect of biological processes, including transcriptional and metabolic regulation, and immune and stress responses. As obligate intracellular parasites, viruses are master manipulators of cellular composition and organization. Accumulating evidences have highlighted the importance of infection-induced protein translocations between organelles. Both directional and temporal, these translocation events facilitate localization-dependent protein interactions and changes in protein functions that contribute to either host defense or virus replication. The discovery and characterization of protein movement is technically challenging, given the necessity for sensitive detection and subcellular resolution. Here, we discuss infection-induced translocations of host and viral proteins, and the value of integrating quantitative proteomics with advanced microscopy for understanding the biology of human virus infections.

}, keywords = {Animals, Host-Pathogen Interactions, Humans, Microscopy, Organelles, Protein Interaction Maps, Protein Transport, Proteins, Proteomics, Viral Proteins, Virus Diseases, Virus Replication}, issn = {1879-0402}, doi = {10.1016/j.cbpa.2018.09.021}, author = {Cook, Katelyn C and Cristea, Ileana M} } @article {11071, title = {Long Noncoding RNA GMAN, Up-regulated in Gastric Cancer Tissues, Is Associated With Metastasis in Patients and Promotes Translation of Ephrin A1 by Competitively Binding GMAN-AS.}, journal = {Gastroenterology}, volume = {156}, year = {2019}, month = {2019 02}, pages = {676-691.e11}, abstract = {

BACKGROUND \& AIMS: We aimed to identify long noncoding RNAs (lncRNAs) that are up-regulated in gastric cancer tissues from patients and study their function in gastric tumor metastasis.

METHODS: We collected gastric tumor and nontumor tissues from patients in China and analyzed levels of lncRNAs by microarray analysis, proteins by immunohistochemistry, and RNAs by quantitative reverse-transcription polymerase chain reaction; we compared these with survival times of patients and tumor progression. RNA levels were knocked down or knocked out in BGC-823, SGC-7901, and MKN45 cell lines using small interfering or short hairpin RNAs or clustered regularly interspaced short palindromic repeats (ie, CRISPR)/CRISPR associated protein 9 (ie, Cas9) vectors. Genes were overexpressed from transfected plasmids in HGC-27 cells. Cells were analyzed by Northern blot and immunoblot, polysome profiling assay, and cell invasion assay. Cells were injected into the tail veins or spleens of nude mice or SCID mice; lung and liver tissues were collected, and metastases were counted. lncRNAs were cloned by using rapid amplification of complementary DNA ends. Their interactions with other genes were determined by RNA pulldown and mapping assays.

RESULTS: In microarray analyses, we identified 151 lncRNAs expressed at significantly higher levels in gastric tumor vs nontumor tissues. Levels of an lncRNA that we called gastric cancer metastasis associated long noncoding RNA (GMAN) were increased in gastric tumor tissues, compared with nontumor tissues; its up-regulation was associated with tumor metastasis and shorter survival times of patients. The GMAN gene overlaps with the ephrin A1 gene (EFNA1) and was highly expressed in BGC-823 and MKN45 cells. Knockdown of GMAN in these cells did not affect proliferation, colony formation, or adhesion but did reduce their invasive activity in Transwell assays. Ectopic expression of GMAN increased the invasive activity of HGC-27 cells. BGC-823 and MKN45 cells with knockdown of GMAN formed fewer metastases after injection into tail veins of nude mice. Knockdown or knockout of GMAN also reduced levels of ephrin A1 protein in cells. We found that GMAN promoted translation of ephrin A1 messenger RNA into protein by binding to the antisense GMAN RNA (GMAN-AS)-this antisense sequence is also complementary to that of ephrin A1 mRNA. Levels of ephrin A1 protein were also increased in gastric tumors from patients with metastases than in those without metastases. Knockout of ephrin A1 in BGC-823 cells reduced their invasive activity in Transwell assays and ability to form metastases after injection into SCID mice. Ectopic expression of ephrin A1 in BGC-823 cells with knockdown or knockout of GMAN restored their invasive activities and ability form metastases in nude or SCID mice. A CRISPR/Cas9-based strategy to disrupt the GMAN gene significantly reduced the numbers of metastases formed from SGC-7901 cells in mice.

CONCLUSIONS: We identified an lncRNA, which we call GMAN, that is increased in gastric tumors from patients and associated with survival and formation of metastases. It regulates translation of ephrin A1 mRNA by binding competitively to GMAN-AS. Knockdown or knockout of GMAN or ephrin A1 in gastric cancer cell lines reduces their invasive activity and ability to form metastases after injection into mice. These genes might be targeted to prevent or reduce gastric cancer metastasis.

}, keywords = {Animals, Biomarkers, Tumor, Cell Line, Tumor, Disease Models, Animal, Ephrin-A1, Female, Gene Expression Regulation, Neoplastic, Humans, Mice, Mice, Knockout, Mice, Nude, Mice, SCID, Neoplasm Invasiveness, Neoplasm Metastasis, Random Allocation, Real-Time Polymerase Chain Reaction, RNA Interference, RNA, Long Noncoding, RNA, Messenger, Stomach Neoplasms, Tissue Array Analysis, Tissue Culture Techniques, Transcriptional Activation, Up-Regulation}, issn = {1528-0012}, doi = {10.1053/j.gastro.2018.10.054}, author = {Zhuo, Wei and Liu, Yiman and Li, Shuang and Guo, Dongyang and Sun, Qiang and Jin, Juan and Rao, Xianping and Li, Mengjie and Sun, Meng and Jiang, Mingchun and Xu, Yanjun and Teng, Lisong and Jin, Yongfeng and Si, Jianmin and Liu, Wei and Kang, Yibin and Zhou, Tianhua} } @article {10436, title = {Loss of DksA leads to multi-faceted impairment of nitric oxide detoxification by Escherichia coli.}, journal = {Free Radic Biol Med}, volume = {130}, year = {2019}, month = {2019 01}, pages = {288-296}, abstract = {

Human immune cells use a battery of toxic chemicals to eliminate invading bacteria. One of those compounds is nitric oxide (NO) and pathogens have evolved various strategies to defend themselves against this immune effector. Enzymatic detoxification is a common approach used by many bacteria, and Escherichia coli employs several enzymes to deal with NO, such as Hmp a flavohemoprotein. In addition to nitrosative stress, nutrient deprivation has been found to play an important role in phagosomal antimicrobial activity. Interestingly, recent work in Salmonella has suggested that DksA, a transcription regulator associated with the stringent response, is a molecular node for integration of nutritional and nitrosative stress signals. Here, we found that, in E. coli, loss of DksA profoundly impairs aerobic NO detoxification, approaching the detoxification capacity of Δhmp, which exhibits little-to-no NO detoxification within aerobic conditions. Investigation of this phenotype revealed that under NO stress ΔdksA suffered from low hmp transcript levels, considerably impaired protein output from the hmp promoter, and reduced catalysis by Hmp when present. These data demonstrate that DksA is critical for NO detoxification by E. coli and that loss of this regulator leads to NO defense deficiencies that span multiple levels.

}, keywords = {Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Humans, Immune System, Inactivation, Metabolic, Nitric Oxide}, issn = {1873-4596}, doi = {10.1016/j.freeradbiomed.2018.10.435}, author = {Chou, Wen Kang and Brynildsen, Mark P} } @article {8131, title = {Late-gestation maternal dietary methyl donor and cofactor supplementation in sheep partially reverses protection against allergic sensitization by IUGR.}, journal = {Am J Physiol Regul Integr Comp Physiol}, volume = {314}, year = {2018}, month = {2018 01 01}, pages = {R22-R33}, abstract = {

Perinatal exposures are associated with altered risks of childhood allergy. Human studies and our previous work suggest that restricted growth in utero (IUGR) is protective against allergic disease. The mechanisms are not clearly defined, but reduced fetal abundance and altered metabolism of methyl donors are hypothesized as possible underlying mechanisms. Therefore, we examined whether late-gestation maternal dietary methyl donor and cofactor supplementation of the placentally restricted (PR) sheep pregnancy would reverse allergic protection in progeny. Allergic outcomes were compared between progeny from control pregnancies (CON; n = 49), from PR pregnancies without intervention (PR; n = 28), and from PR pregnancies where the dam was fed a methyl donor plus cofactor supplement from day 120 of pregnancy until delivery (PR + Methyl; n = 25). Both PR and PR + Methyl progeny were smaller than CON; supplementation did not alter birth size. PR was protective against cutaneous hypersensitivity responses to ovalbumin (OVA; P < 0.01 in singletons). Cutaneous hypersensitivity responses to OVA in PR + Methyl progeny were intermediate to and not different from the responses of CON and PR sheep. Cutaneous hypersensitivity responses to house dust mites did not differ between treatments. In singleton progeny, upper dermal mast cell density was greater in PR + Methyl than in PR or CON (each P < 0.05). The differences in the cutaneous allergic response were not explained by treatment effects on circulating immune cells or antibodies. Our results suggest that mechanisms underlying in utero programming of allergic susceptibility by IUGR and methyl donor availability may differ and imply that late-gestation methyl donor supplementation may increase allergy risk.

}, keywords = {Animals, Cobalt, Dermatitis, Dietary Supplements, Disease Models, Animal, DNA Methylation, Female, Fetal Growth Retardation, Folic Acid, Gestational Age, Hypersensitivity, Immunoglobulin E, Mast Cells, Methionine, Ovalbumin, Placenta, Pregnancy, Prenatal Exposure Delayed Effects, Pyroglyphidae, Sheep, Domestic, Skin, Sulfur}, issn = {1522-1490}, doi = {10.1152/ajpregu.00549.2016}, author = {Wooldridge, Amy L and Bischof, Robert J and Liu, Hong and Heinemann, Gary K and Hunter, Damien S and Giles, Lynne C and Simmons, Rebecca A and Lien, Yu-Chin and Lu, Wenyun and Rabinowitz, Joshua D and Kind, Karen L and Owens, Julie A and Clifton, Vicki L and Gatford, Kathryn L} } @article {9791, title = {Latent versus productive infection: the alpha herpesvirus switch.}, journal = {Future Virol}, volume = {13}, year = {2018}, month = {2018 May}, pages = {431-443}, abstract = {


}, issn = {1746-0794}, doi = {10.2217/fvl-2018-0023}, author = {Koyuncu, Orkide O and MacGibeny, Margaret A and Enquist, Lynn W} } @article {9376, title = {The life of a microtubule.}, journal = {Mol Biol Cell}, volume = {29}, year = {2018}, month = {2018 03 15}, pages = {689}, keywords = {Congresses as Topic, Humans, Microtubule-Associated Proteins, Microtubules, Saccharomycetales}, issn = {1939-4586}, doi = {10.1091/mbc.E17-11-0677}, author = {Dixit, Ram and Petry, Sabine} } @article {10732, title = {Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome.}, journal = {Cell}, volume = {175}, year = {2018}, month = {2018 11 29}, pages = {1481-1491.e13}, abstract = {


}, keywords = {Animals, Cell Line, Tumor, Cell Nucleolus, Chromatin, Cytoplasm, Female, Genome, Human, HEK293 Cells, Humans, Intrinsically Disordered Proteins, Male, Mice, NIH 3T3 Cells, Phase Transition}, issn = {1097-4172}, doi = {10.1016/j.cell.2018.10.057}, author = {Shin, Yongdae and Chang, Yi-Che and Lee, Daniel S W and Berry, Joel and Sanders, David W and Ronceray, Pierre and Wingreen, Ned S and Haataja, Mikko and Brangwynne, Clifford P} } @article {8096, title = {Live Imaging of mRNA Synthesis in Drosophila.}, journal = {Methods Mol Biol}, volume = {1649}, year = {2018}, month = {2018}, pages = {349-357}, abstract = {

mRNA synthesis is one of the earliest readouts of the activity of a transcribed gene, which is of particular interest in the context of metazoan cell fate specification. These processes are intrinsically dynamic and stochastic, which makes in vivo single-cell measurements inevitable. Here, we present the application of a technology that has been widely used in single celled organisms to measure transcriptional activity in developing embryos of the fruit fly Drosophila melanogaster. The method allows for quantification of instantaneous polymerase occupancy of active gene loci and thereby enables the development and testing of models of gene regulation in development.

}, keywords = {Animals, Animals, Genetically Modified, Calibration, DNA, Drosophila melanogaster, Embryo, Nonmammalian, Genes, Reporter, Imaging, Three-Dimensional, Microscopy, Fluorescence, Multiphoton, RNA Polymerase II, RNA, Messenger}, issn = {1940-6029}, doi = {10.1007/978-1-4939-7213-5_23}, author = {Garcia, Hernan G and Gregor, Thomas} } @article {8751, title = {Laboratory layered latte.}, journal = {Nat Commun}, volume = {8}, year = {2017}, month = {2017 12 12}, pages = {1960}, abstract = {


}, issn = {2041-1723}, doi = {10.1038/s41467-017-01852-2}, author = {Xue, Nan and Khodaparast, Sepideh and Zhu, Lailai and Nunes, Janine K and Kim, Hyoungsoo and Stone, Howard A} } @article {7721, title = {Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch.}, journal = {J Am Chem Soc}, volume = {139}, year = {2017}, month = {2017 08 02}, pages = {10403-10409}, abstract = {

Mechanically interlocked molecules that change their conformation in response to stimuli have been developed by synthetic chemists as building blocks for molecular machines. Here we describe a natural product, the lasso peptide benenodin-1, which exhibits conformational switching between two distinct threaded conformers upon actuation by heat. We have determined the structures of both conformers and have characterized the kinetics and energetics of the conformational switch. Single amino acid substitutions to benenodin-1 generate peptides that are biased to a single conformer, showing that the switching behavior is potentially an evolvable trait in these peptides. Lasso peptides such as benenodin-1 can be recognized and cleaved by enzymes called lasso peptide isopeptidases. We show that only the native conformer of benenodin-1 is cleaved by its cognate isopeptidase. Thus, thermally induced conformational switching of benenodin-1 may also be relevant to the biological function of these molecules.

}, keywords = {Caulobacteraceae, Kinetics, Peptides, Protein Conformation, Rotaxanes, Temperature}, issn = {1520-5126}, doi = {10.1021/jacs.7b04830}, author = {Zong, Chuhan and Wu, Michelle J and Qin, Jason Z and Link, A James} } @article {7891, title = {An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate.}, journal = {Anal Bioanal Chem}, volume = {409}, year = {2017}, month = {2017 Oct}, pages = {5955-5964}, abstract = {

The cofactor tetrahydrofolate (THF) is used to reduce, oxidize, and transfer one-carbon (1C) units required for the synthesis of nucleotides, glycine, and methionine. Measurement of intracellular THF species is complicated by their chemical instability, signal dilution caused by variable polyglutamation, and the potential for interconversion among these species. Here, we describe a method using negative mode liquid chromatography-mass spectrometry (LC-MS) to measure intracellular folate species from mammalian cells. Application of this method with isotope-labeled substrates revealed abiotic interconversion of THF and methylene-THF, which renders their separate quantitation particularly challenging. Chemical reduction of methylene-THF using deuterated sodium cyanoborohydride traps methylene-THF, which is unstable, as deuterated 5-methyl-THF, which is stable. Together with proper sample handling and LC-MS, this enables effective measurements of five active folate pools (THF, 5-methyl-THF, methylene-THF, methenyl-THF/10-formyl-THF, and 5-formyl-THF) representing the biologically important 1C oxidation states of THF in mammalian cells. Graphical abstract Chemical derivatization with deuterated cyanoborohydride traps unstable methylene-THF as isotope-labeled 5-methyl-THF, enabling accurate quantification by LC-MS.

}, keywords = {Cell Culture Techniques, Chromatography, Liquid, Folic Acid Antagonists, HEK293 Cells, Humans, Leucovorin, Mass Spectrometry, Methotrexate, Tetrahydrofolates}, issn = {1618-2650}, doi = {10.1007/s00216-017-0514-4}, author = {Chen, Li and Ducker, Gregory S and Lu, Wenyun and Teng, Xin and Rabinowitz, Joshua D} } @article {7711, title = {Left-Right Patterning: Breaking Symmetry to Asymmetric Morphogenesis.}, journal = {Trends Genet}, volume = {33}, year = {2017}, month = {2017 09}, pages = {616-628}, abstract = {

Vertebrates exhibit striking left-right (L-R) asymmetries in the structure and position of the internal organs. Symmetry is broken by motile cilia-generated asymmetric fluid flow, resulting in a signaling cascade - the Nodal-Pitx2 pathway - being robustly established within mesodermal tissue on the left side only. This pathway impinges upon various organ primordia to instruct their side-specific development. Recently, progress has been made in understanding both the breaking of embryonic L-R symmetry and how the Nodal-Pitx2 pathway controls lateralized cell differentiation, migration, and other aspects of cell behavior, as well as tissue-level mechanisms, that drive asymmetries in organ formation. Proper execution of asymmetric organogenesis is critical to health, making furthering our understanding of L-R development an important concern.

}, keywords = {Animals, Body Patterning, Morphogenesis}, issn = {0168-9525}, doi = {10.1016/j.tig.2017.06.004}, author = {Grimes, Daniel T and Burdine, Rebecca D} } @article {6781, title = {Lipid Metabolism Fuels Cancer{\textquoteright}s Spread.}, journal = {Cell Metab}, volume = {25}, year = {2017}, month = {2017 02 07}, pages = {228-230}, abstract = {

The ability to prospectively identify metastasis-initiating cells is essential for developing new anti-metastasis therapeutics. In a recent issue of Nature, Pascual et~al. (2017) demonstrate that the fatty acid receptor CD36 marks a subpopulation of cancer cells with unique metastasis-initiating potential, highlighting a key role of lipid metabolism in metastatic colonization.

}, keywords = {Carrier Proteins, Fatty Acids, Humans, Lipid Metabolism, Neoplasms}, issn = {1932-7420}, doi = {10.1016/j.cmet.2017.01.016}, author = {Li, Zhuo and Kang, Yibin} } @article {8021, title = {Liquid phase condensation in cell physiology and disease.}, journal = {Science}, volume = {357}, year = {2017}, month = {2017 09 22}, abstract = {


}, keywords = {Animals, Caenorhabditis elegans, Cell Physiological Phenomena, Intranuclear Inclusion Bodies, Phase Transition, Protein Aggregation, Pathological}, issn = {1095-9203}, doi = {10.1126/science.aaf4382}, author = {Shin, Yongdae and Brangwynne, Clifford P} } @article {6281, title = {Lnc-ing ROR1-HER3 and Hippo signalling in metastasis.}, journal = {Nat Cell Biol}, volume = {19}, year = {2017}, month = {2017 01 31}, pages = {81-83}, abstract = {

Long noncoding RNAs (lncRNAs) are increasingly recognized for their role in cancer progression. The previously uncharacterized lncRNA MAYA is now shown to promote bone metastasis by bridging ROR1-HER3 and Hippo-YAP pathways. Neuregulin-induced HER3 phosphorylation by ROR1 recruits a MAYA-containing protein complex to methylate Hippo/MST1 and activate YAP target genes that are essential for bone metastasis.

}, issn = {1476-4679}, doi = {10.1038/ncb3467}, author = {Zhuo, Wei and Kang, Yibin} } @article {9206, title = {Long-range proton-coupled electron transfer in the class Ia ribonucleotide reductase.}, journal = {Essays Biochem}, volume = {61}, year = {2017}, month = {2017 05 09}, pages = {281-292}, abstract = {

class Ia ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to 2{\textquoteright}-deoxynucleotides using a radical mechanism. Each turnover requires radical transfer from an assembled diferric tyrosyl radical (Y{\textbullet}) cofactor to the enzyme active site over 35 {\r A} away. This unprecedented reaction occurs via an amino acid radical hopping pathway spanning two protein subunits. To study the mechanism of radical transport in RNR, a suite of biochemical approaches have been developed, such as site-directed incorporation of unnatural amino acids with altered electronic properties and photochemical generation of radical intermediates. The resulting variant RNRs have been investigated using a variety of time-resolved physical techniques, including transient absorption and stopped-flow UV-Vis spectroscopy, as well as rapid freeze-quench EPR, ENDOR, and PELDOR spectroscopic methods. The data suggest that radical transport occurs via proton-coupled electron transfer (PCET) and that the protein structure has evolved to manage the proton and electron transfer co-ordinates in order to prevent {\textquoteright}off-pathway{\textquoteright} reactivity and build-up of oxidised intermediates. Thus, precise design and control over the factors that govern PCET is key to enabling reversible and long-range charge transport by amino acid radicals in RNR.

}, keywords = {Electron Transport, Escherichia coli, Escherichia coli Proteins, Metalloproteins, Ribonucleotide Reductases}, issn = {1744-1358}, doi = {10.1042/EBC20160072}, author = {Reece, Steven Y and Seyedsayamdost, Mohammad R} } @article {7731, title = {Long-term hepatitis B infection in a scalable hepatic co-culture system.}, journal = {Nat Commun}, volume = {8}, year = {2017}, month = {2017 07 25}, pages = {125}, abstract = {


}, keywords = {3T3 Cells, Animals, Antiviral Agents, Carcinoma, Hepatocellular, Cells, Cultured, Coculture Techniques, Fibroblasts, HEK293 Cells, Hep G2 Cells, Hepatitis B virus, Hepatitis B, Chronic, Hepatocytes, Humans, Liver Neoplasms, Mice}, issn = {2041-1723}, doi = {10.1038/s41467-017-00200-8}, author = {Winer, Benjamin Y and Huang, Tiffany S and Pludwinski, Eitan and Heller, Brigitte and Wojcik, Felix and Lipkowitz, Gabriel E and Parekh, Amit and Cho, Cheul and Shrirao, Anil and Muir, Tom W and Novik, Eric and Ploss, Alexander} } @article {7416, title = {Low-Cost Zeta Potentiometry Using Solute Gradients.}, journal = {Adv Mater}, volume = {29}, year = {2017}, month = {2017 Aug}, abstract = {

The zeta potential is an electric potential in the Debye screening layer of an electrolyte, which represents a key physicochemical surface property in various fields ranging from electrochemistry to pharmaceuticals. Thus, characterizing the zeta potential is essential for many applications, but available measurement techniques are limited. Electrophoretic light scattering is typically used to measure the zeta potential of particles in suspension, whereas zeta potential measurements of a solid wall in solution rely on either streaming potential or electroosmotic mobility measurement techniques, both of which are expensive and sophisticated. Here, a simple, robust method to simultaneously measure the zeta potential of particles in suspension and solid walls is presented. The method uses solute gradients to induce particle and fluid motions via diffusiophoresis and diffusioosmosis, respectively, which are both sensitive to the zeta potential of the particle and the wall. By visualizing the particle dynamics, both zeta potentials can be determined independently. Finally, a compact microscope is used to demonstrate low-cost zeta potentiometry that allows measurement of both particle and wall zeta potentials, which suggests a cost-effective tool for pharmaceuticals as well as for educational purposes.

}, issn = {1521-4095}, doi = {10.1002/adma.201701516}, author = {Shin, Sangwoo and Ault, Jesse T and Feng, Jie and Warren, Patrick B and Stone, Howard A} } @article {9196, title = {Lysine-Tryptophan-Crosslinked Peptides Produced by Radical SAM Enzymes in Pathogenic Streptococci.}, journal = {ACS Chem Biol}, volume = {12}, year = {2017}, month = {2017 04 21}, pages = {922-927}, abstract = {

Macrocycles represent a common structural framework in many naturally occurring peptides. Several strategies exist for macrocyclization, and the enzymes that incorporate them are of great interest, as they enhance our repertoire for creating complex molecules. We recently discovered a new peptide cyclization reaction involving a crosslink between the side chains of lysine and tryptophan that is installed by a radical SAM enzyme. Herein, we characterize relatives of this metalloenzyme from the pathogens Streptococcus agalactiae and Streptococcus suis. Our results show that the corresponding enzymes, which we call AgaB and SuiB, contain multiple [4Fe-4S] clusters and catalyze Lys-Trp crosslink formation in their respective substrates. Subsequent high-resolution-MS and 2D-NMR analyses located the site of macrocyclization. Moreover, we report that AgaB can accept modified substrates containing natural or unnatural amino acids. Aside from providing insights into the mechanism of this unusual modification, the substrate promiscuity of AgaB may be exploited to create diverse macrocyclic peptides.

}, keywords = {Amino Acid Sequence, Electron Spin Resonance Spectroscopy, Enzymes, Lysine, Peptides, S-Adenosylmethionine, Sequence Homology, Amino Acid, Spectrophotometry, Ultraviolet, Streptococcus agalactiae, Streptococcus suis, Tryptophan}, issn = {1554-8937}, doi = {10.1021/acschembio.6b01069}, author = {Schramma, Kelsey R and Seyedsayamdost, Mohammad R} } @article {6446, title = {Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis.}, journal = {ACS Chem Biol}, volume = {11}, year = {2016}, month = {2016 09 16}, pages = {2420-7}, abstract = {

Metabolomics is a valuable tool for studying tissue- and organism-specific metabolism. In normal mouse testis, we found 70 μM S-2-hydroxyglutarate (2HG), more than 10-fold greater than in other tissues. S-2HG is a competitive inhibitor of α-ketoglutarate-dependent demethylation enzymes and can alter histone or DNA methylation. To identify the source of testis S-2HG, we fractionated testis extracts and identified the fractions that actively produced S-2HG. Through a combination of ion exchange and size exclusion chromatography, we enriched a single active protein, the lactate dehydrogenase isozyme LDHC, which is primarily expressed in testis. At neutral pH, recombinant mouse LDHC rapidly converted both pyruvate into lactate and α-ketoglutarate into S-2HG, whereas recombinant human LDHC only produced lactate. Rapid S-2HG production by LDHC depends on amino acids 100-102 being Met-Val-Ser, a sequence that occurs only in the rodent protein. Other mammalian LDH can also produce some S-2HG, but at acidic pH. Thus, polymorphisms in the Ldhc gene control testis levels of S-2HG, and thereby epigenetics, across mammals.

}, keywords = {Animals, DNA Methylation, Glutarates, Humans, Isoenzymes, L-Lactate Dehydrogenase, Male, Metabolomics, Mice, Mice, Inbred C57BL, Mice, Knockout, Substrate Specificity, Testis}, issn = {1554-8937}, doi = {10.1021/acschembio.6b00290}, author = {Teng, Xin and Emmett, Matthew J and Lazar, Mitchell A and Goldberg, Erwin and Rabinowitz, Joshua D} } @article {6131, title = {Lasso Peptide Biosynthetic Protein LarB1 Binds Both Leader and Core Peptide Regions of the Precursor Protein LarA.}, journal = {ACS Cent Sci}, volume = {2}, year = {2016}, month = {2016 Oct 26}, pages = {702-709}, abstract = {


}, issn = {2374-7943}, doi = {10.1021/acscentsci.6b00184}, author = {Cheung, Wai Ling and Chen, Maria Y and Maksimov, Mikhail O and Link, A James} } @article {6656, title = {Lipopolysaccharide transport and assembly at the outer membrane: the PEZ model.}, journal = {Nat Rev Microbiol}, volume = {14}, year = {2016}, month = {2016 06}, pages = {337-45}, abstract = {

Gram-negative bacteria have a double-membrane cellular envelope that enables them to colonize harsh environments and prevents the entry of many clinically available antibiotics. A main component of most outer membranes is lipopolysaccharide (LPS), a glycolipid containing several fatty acyl chains and up to hundreds of sugars that is synthesized in the cytoplasm. In the past two decades, the proteins that are responsible for transporting LPS across the cellular envelope and assembling it at the cell surface in Escherichia coli have been identified, but it remains unclear how they function. In this Review, we discuss recent advances in this area and present a model that explains how energy from the cytoplasm is used to power LPS transport across the cellular envelope to the cell surface.

}, keywords = {Bacterial Outer Membrane Proteins, Biological Transport, Cell Membrane, Escherichia coli, Escherichia coli Proteins, Lipopolysaccharides, Metabolic Networks and Pathways, Models, Biological}, issn = {1740-1534}, doi = {10.1038/nrmicro.2016.25}, author = {Okuda, Suguru and Sherman, David J and Silhavy, Thomas J and Ruiz, Natividad and Kahne, Daniel} } @article {6636, title = {A lipoprotein/β-barrel complex monitors lipopolysaccharide integrity transducing information across the outer membrane.}, journal = {Elife}, volume = {5}, year = {2016}, month = {2016 06 10}, abstract = {

Lipoprotein RcsF is the OM component of the Rcs envelope stress response. RcsF exists in complexes with β-barrel proteins (OMPs) allowing it to adopt a transmembrane orientation with a lipidated N-terminal domain on the cell surface and a periplasmic C-terminal domain. Here we report that mutations that remove BamE or alter a residue in the RcsF trans-lumen domain specifically prevent assembly of the interlocked complexes without inactivating either RcsF or the OMP. Using these mutations we demonstrate that these RcsF/OMP complexes are required for sensing OM outer leaflet stress. Using mutations that alter the positively charged surface-exposed domain, we show that RcsF monitors lateral interactions between lipopolysaccharide (LPS) molecules. When these interactions are disrupted by cationic antimicrobial peptides, or by the loss of negatively charged phosphate groups on the LPS molecule, this information is transduced to the RcsF C-terminal signaling domain located in the periplasm to activate the stress response.

}, keywords = {Bacterial Outer Membrane Proteins, Cell Membrane, DNA Mutational Analysis, Escherichia coli, Escherichia coli Proteins, Lipopolysaccharides, Mutant Proteins}, issn = {2050-084X}, doi = {10.7554/eLife.15276}, author = {Konovalova, Anna and Mitchell, Angela M and Silhavy, Thomas J} } @article {6691, title = {Liquid Imbibition in Ceramic-Coated Carbon Nanotube Films.}, journal = {Langmuir}, volume = {32}, year = {2016}, month = {2016 12 06}, pages = {12686-12692}, abstract = {

Understanding of the liquid imbibition dynamics in nanoporous materials is important to advances in chemical separations, phase change heat transfer, electrochemical energy storage, and diagnostic assays. We study the liquid imbibition behavior in films of ceramic-coated vertically aligned carbon nanotubes (CNTs). The nanoscale porosity of the films is tuned by conformal ceramic coating via atomic layer deposition (ALD), enabling stable liquid imbibition and precise measurement of the imbibition dynamics without capillary densification of the CNTs. We show that the imbibition rate decreases as the ceramic coating thickness increases, which effectively changes the CNT-CNT spacing and therefore decreases the permeability. We derive a model, based on Darcy{\textquoteright}s law, that incorporates an expression for the permeability of nanoscale post arrays, and we show that the model fits the experimental results with high accuracy. The tailorable porosity, along with controllable surface wettability and mechanical stability of coated CNTs, suggest their suitability for application-guided engineering, and for further investigation of imbibition behavior at finer length scales.

}, issn = {1520-5827}, doi = {10.1021/acs.langmuir.6b03661}, author = {Zhao, Hangbo and Jacob, Christine and Stone, Howard A and Hart, A John} } @article {5786, title = {Local and global consequences of flow on bacterial quorum sensing.}, journal = {Nat Microbiol}, volume = {1}, year = {2016}, month = {2016 Jan 11}, pages = {15005}, abstract = {

Bacteria use a chemical communication process called quorum sensing (QS) to control collective behaviours such as pathogenesis and biofilm formation(1,2). QS relies on the production, release and group-wide detection of signal molecules called autoinducers. To date, studies of bacterial pathogenesis in well-mixed cultures have revealed virulence factors and the regulatory circuits controlling them, including the overarching role of QS(3). Although flow is ubiquitous to nearly all living systems(4), much less explored is how QS influences pathogenic traits in scenarios that mimic host environments, for example, under fluid flow and in complex geometries. Previous studies(5-7) have shown that sufficiently strong flow represses QS. Nonetheless, it is not known how QS functions under constant or intermittent flow, how it varies within biofilms or as a function of position along a confined flow, or how surface topography (grooves, crevices, pores) influence QS-mediated communication. We explore these questions using two common pathogens, Staphylococcus aureus and Vibrio cholerae. We identify conditions where flow represses QS and other conditions where QS is activated despite flow, including characterizing geometric and topographic features that influence the QS response. Our studies highlight that, under flow, genetically identical cells do not exhibit phenotypic uniformity with respect to QS in space and time, leading to complex patterns of pathogenesis and colonization. Understanding the ramifications of spatially and temporally non-uniform QS responses in realistic environments will be crucial for successful deployment of synthetic pro- and anti-QS strategies.

}, keywords = {Biofilms, Gene Expression Regulation, Bacterial, Quorum Sensing, Staphylococcus aureus, Vibrio cholerae, Water Microbiology}, issn = {2058-5276}, doi = {10.1038/nmicrobiol.2015.5}, author = {Kim, Minyoung Kevin and Ingremeau, Francois and Zhao, Aishan and Bassler, Bonnie L and Stone, Howard A} } @article {6766, title = {Long-term dynamics of multisite phosphorylation.}, journal = {Mol Biol Cell}, volume = {27}, year = {2016}, month = {2016 07 15}, pages = {2331-40}, abstract = {

Multisite phosphorylation cycles are ubiquitous in cell regulation systems and are studied at multiple levels of complexity, from molecules to organisms, with the ultimate goal of establishing predictive understanding of the effects of genetic and pharmacological perturbations of protein phosphorylation in vivo. Achieving this goal is essentially impossible without mathematical models, which provide a systematic framework for exploring dynamic interactions of multiple network components. Most of the models studied to date do not discriminate between the distinct partially phosphorylated forms and focus on two limiting reaction regimes, distributive and processive, which differ in the number of enzyme-substrate binding events needed for complete phosphorylation or dephosphorylation. Here we use a minimal model of extracellular signal-related kinase regulation to explore the dynamics of a reaction network that includes all essential phosphorylation forms and arbitrary levels of reaction processivity. In addition to bistability, which has been studied extensively in distributive mechanisms, this network can generate periodic oscillations. Both bistability and oscillations can be realized at high levels of reaction processivity. Our work provides a general framework for systematic analysis of dynamics in multisite phosphorylation systems.

}, keywords = {Models, Biological, Molecular Dynamics Simulation, Phosphorylation, Protein Binding, Proteins}, issn = {1939-4586}, doi = {10.1091/mbc.E16-03-0137}, author = {Rubinstein, Boris Y and Mattingly, Henry H and Berezhkovskii, Alexander M and Shvartsman, Stanislav Y} } @article {6436, title = {Loss of NAD Homeostasis Leads to Progressive and Reversible Degeneration of Skeletal Muscle.}, journal = {Cell Metab}, volume = {24}, year = {2016}, month = {2016 08 09}, pages = {269-82}, abstract = {

NAD is an obligate co-factor for the catabolism of metabolic fuels in all cell types. However, the availability of NAD in several tissues can become limited during genotoxic stress and the course of natural aging. The point at which NAD restriction imposes functional limitations on tissue physiology remains unknown. We examined this question in murine skeletal muscle by specifically depleting Nampt, an essential enzyme in the NAD salvage pathway. Knockout mice exhibited a dramatic 85\% decline in intramuscular NAD content, accompanied by fiber degeneration and progressive loss of both muscle strength and treadmill endurance. Administration of the NAD precursor nicotinamide riboside rapidly ameliorated functional deficits and restored muscle mass despite having only a modest effect on the intramuscular NAD pool. Additionally, lifelong overexpression of Nampt preserved muscle NAD levels and exercise capacity in aged mice, supporting a critical role for tissue-autonomous NAD homeostasis in maintaining muscle mass and function.

}, keywords = {Administration, Oral, Aging, Animals, Biological Availability, Energy Metabolism, Glucose, Homeostasis, Inflammation, Mice, Inbred C57BL, Mice, Knockout, Mitochondria, Muscle Strength, Muscle, Skeletal, NAD, Necrosis, Niacinamide, Nicotinamide Phosphoribosyltransferase, Organ Size, Physical Conditioning, Animal, Transcription, Genetic}, issn = {1932-7420}, doi = {10.1016/j.cmet.2016.07.005}, author = {Frederick, David W and Loro, Emanuele and Liu, Ling and Davila, Antonio and Chellappa, Karthikeyani and Silverman, Ian M and Quinn, William J and Gosai, Sager J and Tichy, Elisia D and Davis, James G and Mourkioti, Foteini and Gregory, Brian D and Dellinger, Ryan W and Redpath, Philip and Migaud, Marie E and Nakamaru-Ogiso, Eiko and Rabinowitz, Joshua D and Khurana, Tejvir S and Baur, Joseph A} } @article {4301, title = {Liquids, Fibers, and Gels: The Many Phases of Neurodegeneration.}, journal = {Dev Cell}, volume = {35}, year = {2015}, month = {2015 Dec 07}, pages = {531-532}, abstract = {

Recent advances suggest that phase transitions of proteins into liquid or hydrogel states could underlie pathological protein aggregation associated with neurodegenerative disease. In a recent issue of Neuron, Murakami et al. (2015) demonstrate that ALS-associated FUS mutations abrogate the reversibility of condensed liquids and/or hydrogels, leading to neurotoxicity in C. elegans.

}, keywords = {Amyotrophic Lateral Sclerosis, Animals, Caenorhabditis elegans Proteins, Frontotemporal Lobar Degeneration, Hydrogels, Motor Activity, Phase Transition, RNA, Messenger, RNA-Binding Protein FUS}, issn = {1878-1551}, doi = {10.1016/j.devcel.2015.11.014}, author = {Elbaum-Garfinkle, Shana and Brangwynne, Clifford P} } @article {4521, title = {Localized Smooth Muscle Differentiation Is Essential for Epithelial Bifurcation during Branching Morphogenesis of the Mammalian Lung.}, journal = {Dev Cell}, volume = {34}, year = {2015}, month = {2015 Sep 28}, pages = {719-26}, abstract = {

The airway epithelium develops into a tree-like structure via branching morphogenesis. Here, we show a critical role for localized differentiation of airway smooth muscle during epithelial bifurcation in the embryonic mouse lung. We found that during terminal bifurcation, changes in the geometry of nascent buds coincided with patterned smooth muscle differentiation. Evaluating spatiotemporal dynamics of α-smooth muscle actin (αSMA) in reporter mice revealed that αSMA-expressing cells appear at the basal surface of the future epithelial cleft prior to bifurcation and then increase in density as they wrap around the bifurcating bud. Disrupting this stereotyped pattern of smooth muscle differentiation prevents terminal bifurcation. Our results reveal stereotyped differentiation of airway smooth muscle adjacent to nascent epithelial buds and suggest that localized smooth muscle wrapping at the cleft site is required for terminal bifurcation during airway branching morphogenesis.

}, keywords = {Actins, Animals, Blotting, Western, Cell Differentiation, Cells, Cultured, Epithelium, Female, Fluorescent Antibody Technique, Lung, Mice, Mice, Transgenic, Morphogenesis, Muscle, Smooth, Organ Culture Techniques, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, RNA, Messenger}, issn = {1878-1551}, doi = {10.1016/j.devcel.2015.08.012}, author = {Kim, Hye Young and Pang, Mei-Fong and Varner, Victor D and Kojima, Lisa and Miller, Erin and Radisky, Derek C and Nelson, Celeste M} } @article {6041, title = {Low-variance RNAs identify Parkinson{\textquoteright}s disease molecular signature in blood.}, journal = {Mov Disord}, volume = {30}, year = {2015}, month = {2015 May}, pages = {813-21}, abstract = {

The diagnosis of Parkinson{\textquoteright}s disease (PD) is usually not established until advanced neurodegeneration leads to clinically detectable symptoms. Previous blood PD transcriptome studies show low concordance, possibly resulting from the use of microarray technology, which has high measurement variation. The Leucine-rich repeat kinase 2 (LRRK2) G2019S mutation predisposes to PD. Using preclinical and clinical studies, we sought to develop a novel statistically motivated transcriptomic-based approach to identify a molecular signature in the blood of Ashkenazi Jewish PD patients, including LRRK2 mutation carriers. Using a digital gene expression platform to quantify 175 messenger RNA (mRNA) markers with low coefficients of variation (CV), we first compared whole-blood transcript levels in mouse models (1) overexpressing wild-type (WT) LRRK2, (2) overexpressing G2019S LRRK2, (3) lacking LRRK2 (knockout), and (4) and in WT controls. We then studied an Ashkenazi Jewish cohort of 34 symptomatic PD patients (both WT LRRK2 and G2019S LRRK2) and 32 asymptomatic controls. The expression profiles distinguished the four mouse groups with different genetic background. In patients, we detected significant differences in blood transcript levels both between individuals differing in LRRK2 genotype and between PD patients and controls. Discriminatory PD markers included genes associated with innate and adaptive immunity and inflammatory disease. Notably, gene expression patterns in levodopa-treated PD patients were significantly closer to those of healthy controls in a dose-dependent manner. We identify whole-blood mRNA signatures correlating with LRRK2 genotype and with PD disease state. This approach may provide insight into pathogenesis and a route to early disease detection.

}, keywords = {Aged, Aged, 80 and over, Animals, Biomarkers, Case-Control Studies, Early Diagnosis, Female, Gene Expression, Genetic Predisposition to Disease, Heterozygote, Humans, Jews, Leucine-Rich Repeat Serine-Threonine Protein Kinase-2, Male, Mice, Mice, Transgenic, Middle Aged, Mutation, Parkinson Disease, Protein-Serine-Threonine Kinases, RNA, Messenger}, issn = {1531-8257}, doi = {10.1002/mds.26205}, author = {Chikina, Maria D and Gerald, Christophe P and Li, Xianting and Ge, Yongchao and Pincas, Hanna and Nair, Venugopalan D and Wong, Aaron K and Krishnan, Arjun and Troyanskaya, Olga G and Raymond, Deborah and Saunders-Pullman, Rachel and Bressman, Susan B and Yue, Zhenyu and Sealfon, Stuart C} } @article {4241, title = {Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans.}, journal = {Mol Biol Evol}, volume = {31}, year = {2014}, month = {2014 Jul}, pages = {1750-66}, abstract = {


}, keywords = {Animals, Drosophila, Evolution, Molecular, Female, Gene Duplication, Genetic Variation, Genome, Genotype, Mutation Rate, Sequence Deletion, Tandem Repeat Sequences}, issn = {1537-1719}, doi = {10.1093/molbev/msu124}, author = {Rogers, Rebekah L and Cridland, Julie M and Shao, Ling and Hu, Tina T and Andolfatto, Peter and Thornton, Kevin R} } @article {4011, title = {Looping back to leap forward: transcription enters a new era.}, journal = {Cell}, volume = {157}, year = {2014}, month = {2014 Mar 27}, pages = {13-25}, abstract = {

Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation. Recent efforts indicate that the human genome likely contains hundreds of thousands of enhancers, with a typical gene embedded in a milieu of tens of enhancers. Proliferation of cis-regulatory DNAs is accompanied by increased complexity and functional diversification of transcriptional machineries recognizing distal enhancers and core promoters and by the high-order spatial organization of genetic elements. We review progress in unraveling one of the outstanding mysteries of modern biology: the dynamic communication of remote enhancers with target promoters in the specification of cellular identity.

}, keywords = {Animals, Cell Differentiation, DNA-Directed RNA Polymerases, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Transcription Factors, Transcription, Genetic}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.02.009}, author = {Levine, Michael and Cattoglio, Claudia and Tjian, Robert} } @article {2101, title = {Ligand and antagonist driven regulation of the Vibrio cholerae quorum-sensing receptor CqsS.}, journal = {Mol Microbiol}, volume = {83}, year = {2012}, month = {2012 Mar}, pages = {1095-108}, abstract = {

Quorum sensing, a bacterial cell-cell communication process, controls biofilm formation and virulence factor production in Vibrio cholerae, a human pathogen that causes the disease cholera. The major V. cholerae autoinducer is (S)-3-hydroxytridecan-4-one (CAI-1). A membrane bound two-component sensor histidine kinase called CqsS detects CAI-1, and the CqsS {\textrightarrow} LuxU {\textrightarrow} LuxO phosphorelay cascade transduces the information encoded in CAI-1 into the cell. Because the CAI-1 ligand is known and because the signalling circuit is simple, consisting of only three proteins, this system is ideal for analysing ligand regulation of a sensor histidine kinase. Here we reconstitute the CqsS {\textrightarrow} LuxU {\textrightarrow} LuxO phosphorylation cascade in vitro. We find that CAI-1 inhibits the initial auto-phosphorylation of CqsS whereas subsequent phosphotransfer steps and CqsS phosphatase activity are not CAI-1-controlled. CAI-1 binding to CqsS causes a conformational change that renders His194 in CqsS inaccessible to the CqsS catalytic domain. CqsS mutants with altered ligand detection specificities are faithfully controlled by their corresponding modified ligands in vitro. Likewise, pairing of agonists and antagonists allows in vitro assessment of their opposing activities. Our data are consistent with a two-state model for ligand control of histidine kinases.

}, keywords = {Bacterial Proteins, Cholera, Gene Expression Regulation, Bacterial, Histidine Kinase, Humans, Ketones, Ligands, Phosphoproteins, Phosphorylation, Protein Binding, Protein Kinases, Protein Structure, Tertiary, Quorum Sensing, Repressor Proteins, Vibrio cholerae}, issn = {1365-2958}, doi = {10.1111/j.1365-2958.2012.07992.x}, author = {Wei, Yunzhou and Ng, Wai-Leung and Cong, Jianping and Bassler, Bonnie L} } @article {2961, title = {Low error discrimination using a correlated population code.}, journal = {J Neurophysiol}, volume = {108}, year = {2012}, month = {2012 Aug}, pages = {1069-88}, abstract = {

We explored the manner in which spatial information is encoded by retinal ganglion cell populations. We flashed a set of 36 shape stimuli onto the tiger salamander retina and used different decoding algorithms to read out information from a population of 162 ganglion cells. We compared the discrimination performance of linear decoders, which ignore correlation induced by common stimulation, with nonlinear decoders, which can accurately model these correlations. Similar to previous studies, decoders that ignored correlation suffered only a modest drop in discrimination performance for groups of up to \~{}30 cells. However, for more realistic groups of 100+ cells, we found order-of-magnitude differences in the error rate. We also compared decoders that used only the presence of a single spike from each cell with more complex decoders that included information from multiple spike counts and multiple time bins. More complex decoders substantially outperformed simpler decoders, showing the importance of spike timing information. Particularly effective was the first spike latency representation, which allowed zero discrimination errors for the majority of shape stimuli. Furthermore, the performance of nonlinear decoders showed even greater enhancement compared with linear decoders for these complex representations. Finally, decoders that approximated the correlation structure in the population by matching all pairwise correlations with a maximum entropy model fit to all 162 neurons were quite successful, especially for the spike latency representation. Together, these results suggest a picture in which linear decoders allow a coarse categorization of shape stimuli, whereas nonlinear decoders, which take advantage of both correlation and spike timing, are needed to achieve high-fidelity discrimination.

}, keywords = {Action Potentials, Ambystoma, Animals, Discrimination, Psychological, Form Perception, Photic Stimulation, Retinal Ganglion Cells}, issn = {1522-1598}, doi = {10.1152/jn.00564.2011}, author = {Schwartz, Greg and Macke, Jakob and Amodei, Dario and Tang, Hanlin and Berry, Michael J} } @article {3661, title = {Light control of plasma membrane recruitment using the Phy-PIF system.}, journal = {Methods Enzymol}, volume = {497}, year = {2011}, month = {2011}, pages = {409-23}, abstract = {

The ability to control the activity of intracellular signaling processes in live cells would be an extraordinarily powerful tool. Ideally, such an intracellular input would be (i) genetically encoded, (ii) able to be turned on and off in defined temporal or spatial patterns, (iii) fast to switch between on and off states, and (iv) orthogonal to other cellular processes. The light-gated interaction between fragments of two plant proteins--termed Phy and PIF--satisfies each of these constraints. In this system, Phy can be switched between two conformations using red and infrared light, while PIF only binds one of these states. This chapter describes known constraints for designing genetic constructs using Phy and PIF and provides protocols for expressing these constructs in mammalian cells, purifying the small molecule chromophore required for the system{\textquoteright}s light responsivity, and measuring light-gated binding by microscopy.

}, keywords = {Animals, Arabidopsis, Arabidopsis Proteins, Cell Line, Cell Membrane, Light, Microscopy, Confocal, Models, Molecular, Peptide Fragments, Phytochrome B, Plant Proteins, Protein Binding, Protein Conformation}, issn = {1557-7988}, doi = {10.1016/B978-0-12-385075-1.00017-2}, author = {Toettcher, Jared E and Gong, Delquin and Lim, Wendell A and Weiner, Orion D} } @article {3651, title = {Light-based feedback for controlling intracellular signaling dynamics.}, journal = {Nat Methods}, volume = {8}, year = {2011}, month = {2011 Sep 11}, pages = {837-9}, abstract = {

The ability to apply precise inputs to signaling species in live cells would be transformative for interrogating and understanding complex cell-signaling systems. Here we report an {\textquoteright}optogenetic{\textquoteright} method for applying custom signaling inputs using feedback control of a light-gated protein-protein interaction. We applied this strategy to perturb protein localization and phosphoinositide 3-kinase activity, generating time-varying signals and clamping signals to buffer against cell-to-cell variability or changes in pathway activity.

}, keywords = {Animals, Cell Membrane, Computational Biology, Feedback, Physiological, Humans, Light, Models, Biological, Phosphatidylinositol 3-Kinases, Phosphoinositide-3 Kinase Inhibitors, Protein Binding, Signal Transduction}, issn = {1548-7105}, doi = {10.1038/nmeth.1700}, author = {Toettcher, Jared E and Gong, Delquin and Lim, Wendell A and Weiner, Orion D} } @article {2251, title = {Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing.}, journal = {Cell}, volume = {126}, year = {2006}, month = {2006 Sep 22}, pages = {1095-108}, abstract = {

Bacteria sense their environment using receptors of the histidine sensor kinase family, but how kinase activity is regulated by ligand binding is not well understood. Autoinducer-2 (AI-2), a secreted signaling molecule originally identified in studies of the marine bacterium Vibrio harveyi, regulates quorum-sensing responses and allows communication between different bacterial species. AI-2 signal transduction in V. harveyi requires the integral membrane receptor LuxPQ, comprised of periplasmic binding protein (LuxP) and histidine sensor kinase (LuxQ) subunits. Combined X-ray crystallographic and functional studies show that AI-2 binding causes a major conformational change within LuxP, which in turn stabilizes a quaternary arrangement in which two LuxPQ monomers are asymmetrically associated. We propose that formation of this asymmetric quaternary structure is responsible for repressing the kinase activity of both LuxQ subunits and triggering the transition of V. harveyi into quorum-sensing mode.

}, keywords = {Bacterial Proteins, Cell Membrane, Crystallography, X-Ray, Homoserine, Lactones, Ligands, Light Signal Transduction, Macromolecular Substances, Models, Molecular, Phosphotransferases, Protein Binding, Protein Conformation, Signal Transduction, Transcription Factors, Vibrio}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.07.032}, author = {Neiditch, Matthew B and Federle, Michael J and Pompeani, Audra J and Kelly, Robert C and Swem, Danielle L and Jeffrey, Philip D and Bassler, Bonnie L and Hughson, Frederick M} } @article {2641, title = {Learning rules and network repair in spike-timing-based computation networks.}, journal = {Proc Natl Acad Sci U S A}, volume = {101}, year = {2004}, month = {2004 Jan 06}, pages = {337-42}, abstract = {

Plasticity in connections between neurons allows learning and adaptation, but it also allows noise to degrade the function of a network. Ongoing network self-repair is thus necessary. We describe a method to derive spike-timing-dependent plasticity rules for self-repair, based on the firing patterns of a functioning network. These plasticity rules for self-repair also provide the basis for unsupervised learning of new tasks. The particular plasticity rule derived for a network depends on the network and task. Here, self-repair is illustrated for a model of the mammalian olfactory system in which the computational task is that of odor recognition. In this olfactory example, the derived rule has qualitative similarity with experimental results seen in spike-timing-dependent plasticity. Unsupervised learning of new tasks by using the derived self-repair rule is demonstrated by learning to recognize new odors.

}, keywords = {Action Potentials, Animals, Learning, Mammals, Models, Neurological, Nerve Net, Neuronal Plasticity, Olfactory Bulb, Smell, Synapses, Time Factors}, issn = {0027-8424}, doi = {10.1073/pnas.2536316100}, author = {Hopfield, J J and Brody, Carlos D} } @article {2346, title = {Lsr-mediated transport and processing of AI-2 in Salmonella typhimurium.}, journal = {Mol Microbiol}, volume = {50}, year = {2003}, month = {2003 Nov}, pages = {1411-27}, abstract = {

The LuxS-dependent autoinducer AI-2 is proposed to function in interspecies cell-cell communication in bacteria. In Salmonella typhimurium, AI-2 is produced and released during exponential growth and is subsequently imported into the bacteria via the Lsr (luxS regulated) ATP binding cassette (ABC) transporter. AI-2 induces transcription of the lsrACDBFGE operon, the first four genes of which encode the Lsr transport apparatus. In this report, we identify and characterize LsrK, a new protein that is required for the regulation of the lsr operon and the AI-2 uptake process. LsrK is a kinase that phosphorylates AI-2 upon entry into the cell. Our data indicate that phosphorylation of AI-2 results in its sequestration in the cytoplasm. We suggest that phospho-AI-2 is the inducer responsible for inactivation of LsrR, the repressor of the lsr operon. We also show that two previously uncharacterized members of the lsr operon, LsrF and LsrG, are necessary for the further processing of phospho-AI-2. Transport and processing of AI-2 could be required for removing the quorum-sensing signal, conveying the signal to an internal detector and/or scavenging boron.

}, keywords = {ATP-Binding Cassette Transporters, Bacterial Proteins, Biological Transport, Epistasis, Genetic, Gene Expression Regulation, Bacterial, Homoserine, Lactones, Operon, Phenotype, Phosphorylation, Protein Kinases, Salmonella typhimurium}, issn = {0950-382X}, doi = {10.1046/j.1365-2958.2003.03781.x}, author = {Taga, Michiko E and Miller, Stephen T and Bassler, Bonnie L} } @article {2341, title = {LuxS quorum sensing: more than just a numbers game.}, journal = {Curr Opin Microbiol}, volume = {6}, year = {2003}, month = {2003 Apr}, pages = {191-7}, abstract = {

Quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. Quorum sensing allows populations of bacteria to collectively control gene expression, and thus synchronize group behavior. Processes controlled by quorum sensing are typically ones that are unproductive unless many bacteria act together. Most autoinducers enable intraspecies communication; however, a recently discovered autoinducer AI-2 has been proposed to serve as a {\textquoteright}universal signal{\textquoteright} for interspecies communication. Studies suggest that AI-2 encodes information in addition to specifics about cell number.

}, keywords = {Bacteria, Bacterial Physiological Phenomena, Bacterial Proteins, Carbon-Sulfur Lyases, Gene Expression Regulation, Bacterial, Homoserine, Lactones, Models, Biological, Models, Molecular, Signal Transduction}, issn = {1369-5274}, doi = {10.1016/s1369-5274(03)00028-6}, author = {Xavier, Karina B and Bassler, Bonnie L} } @article {2401, title = {The languages of bacteria.}, journal = {Genes Dev}, volume = {15}, year = {2001}, month = {2001 Jun 15}, pages = {1468-80}, keywords = {4-Butyrolactone, Bacterial Proteins, Carbon-Sulfur Lyases, Gram-Negative Bacteria, Gram-Positive Bacteria, Oligopeptides}, issn = {0890-9369}, doi = {10.1101/gad.899601}, author = {Schauder, S and Bassler, B L} } @article {2396, title = {The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule.}, journal = {Mol Microbiol}, volume = {41}, year = {2001}, month = {2001 Jul}, pages = {463-76}, abstract = {


}, keywords = {4-Butyrolactone, Bacterial Proteins, Carbon-Sulfur Lyases, Cell Extracts, Cell-Free System, Dialysis, Genomics, Homocysteine, Homoserine, Lactones, Luminescent Measurements, Mass Spectrometry, Multigene Family, S-Adenosylmethionine, Salmonella typhimurium, Signal Transduction, Vibrio}, issn = {0950-382X}, doi = {10.1046/j.1365-2958.2001.02532.x}, author = {Schauder, S and Shokat, K and Surette, M G and Bassler, B L} } @article {2391, title = {The LuxS-dependent autoinducer AI-2 controls the expression of an ABC transporter that functions in AI-2 uptake in Salmonella typhimurium.}, journal = {Mol Microbiol}, volume = {42}, year = {2001}, month = {2001 Nov}, pages = {777-93}, abstract = {

In a process called quorum sensing, bacteria communicate with one another using secreted chemical signalling molecules termed autoinducers. A novel autoinducer called AI-2, originally discovered in the quorum-sensing bacterium Vibrio harveyi, is made by many species of Gram-negative and Gram-positive bacteria. In every case, production of AI-2 is dependent on the LuxS autoinducer synthase. The genes regulated by AI-2 in most of these luxS-containing species of bacteria are not known. Here, we describe the identification and characterization of AI-2-regulated genes in Salmonella typhimurium. We find that LuxS and AI-2 regulate the expression of a previously unidentified operon encoding an ATP binding cassette (ABC)-type transporter. We have named this operon the lsr (luxS regulated) operon. The Lsr transporter has homology to the ribose transporter of Escherichia coli and S. typhimurium. A gene encoding a DNA-binding protein that is located adjacent to the Lsr transporter structural operon is required to link AI-2 detection to operon expression. This gene, which we have named lsrR, encodes a protein that represses lsr operon expression in the absence of AI-2. Mutations in the lsr operon render S. typhimurium unable to eliminate AI-2 from the extracellular environment, suggesting that the role of the Lsr apparatus is to transport AI-2 into the cells. It is intriguing that an operon regulated by AI-2 encodes functions resembling the ribose transporter, given recent findings that AI-2 is derived from the ribosyl moiety of S-ribosylhomocysteine.

}, keywords = {ATP-Binding Cassette Transporters, Bacterial Proteins, Carbon-Sulfur Lyases, Gene Expression Regulation, Bacterial, Operon, Salmonella typhimurium, Signal Transduction, Transcription Factors}, issn = {0950-382X}, doi = {10.1046/j.1365-2958.2001.02669.x}, author = {Taga, M E and Semmelhack, J L and Bassler, B L} }