of the parasite. the glycan component is particularly variable and different lipophosphoglycan variants can be used as a molecular marker for different lifecycle stages. lectins, a group of proteins which bind different glycans, are often used to detect these lipophosphoglycan variants. for example, peanut agglutinin binds a particular lipophosphoglycan found on the surface of the infective form of l. major. lipophosphoglycan is used by the parasite to promote its survival in the host and the mechanisms by which the parasite does this center around modulating the immune response of the host. this is vital, as the leishmania parasites live within macrophages and need to prevent the macrophages from killing them. lipophosphoglycan has a role in resisting the complement system, inhibiting the oxidative burst response, inducing an inflammation response and preventing natural killer t cells recognising that the macrophage is infected with the leishmania parasite. type pathogen location cutaneous leishmaniasis (localised and diffuse) infections appear as obvious skin reactions. the most common is the oriental sore (caused by old world species l. major, l. tropica, and l. aethiopica). in the new world, the most common culprits is l. mexicana. cutaneous infections are most common in afghanistan, brazil, iran, peru, saudi arabia and syria. mucocutaneous leishmaniasis infections start off as a reaction at the bite, and can go by metastasis into the mucous membrane and become fatal. l. braziliensis mucocutaneous infections are most common in bolivia, brazil and peru. mucocutaneous infections are also found in karamay, china xinjiang uygur autonomous region. visceral leishmaniasis infections are often recognised by fever, swelling of the liver and spleen, and anemia. they are known by many local names, of which the most common is probably kala azar, caused exclusively by species of the l. donovani complex (l. donovani, l. infantum syn. l. chagasi). found in tropical and subtropical areas of all continents except australia, visceral infections are most common in bangladesh, brazil, india, nepal, and sudan. visceral leishmaniasis also found in part of china, such as sichuan province, gansu province, and xinjiang uygur autonomous region. intracellular mechanism of infection in order to avoid destruction by the immune system and thrive, the leishmania 'hides' inside its host's cells. this location enables it to avoid the action of the humoral immune response (because the pathogen is safely inside a cell and outside the open bloodstream), and furthermore it may prevent the immune system from destroying its host through nondanger surface signals which discourage apoptosis. the primary cell types leishmania infiltrates are phagocytotic cells such as neutrophils and macrophages. usually, a phagocytotic immune cell like a macrophage will ingest a pathogen within an enclosed endosome and then fill this endosome with enzymes which digest the pathogen. however, in the case of leishmania, these enzymes have no effect, allowing the parasite to multiply rapidly. this uninhibited growth of parasites eventually overwhelms the host macrophage or other immune cell, causing it to die. transmitted by the sandfly, the protozoan parasites of l. major may switch the strategy of the first immune defense from eating/inflammation/killing to eating/no inflammation/no killing of their host phagocyte and corrupt it for their own benefit. they use the willingly phagocytosing polymorphonuclear neutrophil granulocytes (pmns) rigorously as a tricky hideout, where they proliferate unrecognized from the immune system and enter the long-lived macrophages to establish a "hidden" infection. uptake and survival lifecycle of leishmania upon microbial infection, pmns move out from the bloodstream through the vessels' endothelial layer, to the site of the infected tissue (dermal tissue after fly bite). they immediately initiate the first immune response and phagocytize the invader by recognition of foreign and activating surfaces on the parasite. activated pmn secrete chemokines, il-8 particularly, to attract further granulocytes and stimulate phagocytosis. further, l. major increases the secretion of il-8 by pmns. this mechanism is observed during infection with other obligate intracellular parasites, as well. for microbes like these, multiple intracellular survival mechanisms exist. surprisingly, the coinjection of apoptotic and viable pathogens causes by far a more fulminate course of disease than injection of only viable parasites. when the anti-inflammatory signal phosphatidylserine usually found on apoptotic cells, is exposed on the surface of dead parasites, l. major switches off the oxidative burst, thereby preventing killing and degradation of the viable pathogen. in the case of leishmania, progeny are not generated in pmns, but in this way they can survive and persist untangled in the primary site of infection. the promastigote forms also release leishmania chemotactic factor (lcf) to actively recruit neutrophils, but not other leukocytes, for instance monocytes or nk cells. in addition to that, the production of interferon gamma (ifnγ)-inducible protein 10 (ip10) by pmns is blocked in attendance of leishmania, what involves the shut down of inflammatory and protective immune response by nk and th1 cell recruitment. the pathogens stay viable during phagocytosis since their primary hosts, the pmns, expose apoptotic cell-associated molecular pattern (acamp) signaling "no pathogen". persistency and attraction the lifespan of neutrophil granulocytes is quite short. they circulate in bloodstream for about 6 to 10 hours after leaving bone marrow, whereupon they undergo spontaneous apoptosis. microbial pathogens have been reported to influence cellular apoptosis by different strategies. obviously because of the inhibition of caspase3-activation, l. major can induce the delay of neutrophils apoptosis and extend their lifespan for at least 2–3 days. the fact of extended lifespan is very beneficial for the development of infection because the final host cells for these parasites are macrophages, which normally migrate to the sites of infection within two or three days. the pathogens are not dronish; instead they take over the command at the primary site of infection. they induce the production by pmns of the chemokines mip-1α and mip-1β (macrophage inflammatory protein) to recruit macrophages. an important factor in prolonging infection is the inhibition of the adaptive immune system. this occurs especially during the intercellular phases, when amastigotes search for new macrophages to infect and are more susceptible to immune responses. nearly all types of phagocytes are targeted. for example, mincle has been shown to be targeted by l. major. interaction between mincle and a protein released by the parasite results in a weakened immune response in dendritic cells. silent phagocytosis theory to save the integrity of the surrounding tissue from the toxic cell components and proteolytic enzymes contained in neutrophils, the apoptotic pmns are silently cleared by macrophages. dying pmns expose the "eat me"-signal phosphatidylserine which is transferred to the outer leaflet of the plasma membrane during apoptosis. by reason of delayed apoptosis, the parasites that persist in pmns are taken up into macrophages, employing an absolutely physiological and nonphlogistic process. the strategy of this "silent phagocytosis" has the following advantages for the parasite: taking up apoptotic cells silences macrophage killing activity leading to a survival of the pathogens. pathogens inside of pmns have no direct contact to the macrophage surface receptors, because they can not see the parasite inside the apoptotic cell. so, the activation of the phagocyte for immune activation does not occur. however, studies have shown this is unlikely, as the pathogens are seen to leave apoptopic cells and no evidence is known of macrophage uptake by this method. molecular biology an important aspect of the leishmania protozoan is its glycoconjugate layer of lipophosphoglycan (lpg). this is held together with a phosphoinositide membrane anchor, and has a tripartite structure consisting of a lipid domain, a neutral hexasaccharide, and a phosphorylated galactose-mannose, with a termination in a neutral cap. not only do these parasites develop postphlebotomus digestion, but it is also thought to be essential to oxidative bursts, thus allowing passage for infection. characteristics of intracellular digestion include an endosome fusing with a lysosome, releasing acid hydrolases which degrade dna, rna, proteins and carbohydrates. genomics leishmania tropica the genomes of four leishmania species (l. major, l. infantum, l. donovani and l. braziliensis) have been sequenced, revealing more than 8300 protein-coding and 900 rna genes. almost 40% of protein-coding genes fall into 662 families containing between two and 500 members. most of the smaller gene families are tandem arrays of one to three genes, while the larger gene families are often dispersed in tandem arrays at different loci throughout the genome. each of the 35 or 36 chromosomes is organized into a small number of gene clusters of tens-to-hundreds of genes on the same dna strand. these clusters can be organized in head-to-head (divergent) or tail-to-tail (convergent) fashion, with the latter often separated by trna, rrna and/or snrna genes. transcription of protein-coding genes initiates bidirectionally in the divergent strand-switch regions between gene clusters and extends polycistronically through each gene cluster before terminating in the strand-switch region separating convergent clusters. leishmania telomeres are usually relatively small, consisting of a few different types of repeat sequence. evidence can be found for recombination between several different groups of telomeres. the l. major and l. infantum genomes contain only about 50 copies of inactive degenerated ingi/l1tc-related elements (dires), while l. braziliensis also contains several telomere-associated transposable elements and spliced leader-associated retroelements. the leishmania genomes share a conserved core proteome of about 6200 genes with the related trypanosomatids trypanosoma brucei and trypanosoma cruzi, but around 1000 leishmania-specific genes are known, which are mostly randomly distributed throughout the genome. relatively few (about 200) species-specific differences in gene content exist between the three sequenced leishmania genomes, but about 8% of the genes appear to be evolving at different rates between the three species, indicative of different selective pressures that could be related to disease pathology. about 65% of protein-coding genes currently lack functional assignment. leishmania species produce several different heat shock proteins. these include hsp83, a homolog of hsp90. a regulatory element in the 3' utr of hsp83 controls translation of hsp83 in a temperature-sensitive manner. this region forms a stable rna structure which melts at higher temperatures. genomic instability leishmania lacks of promoter-dependent regulation, so its genomic regulation is at post-transcriptional level through copy number variations (cnv) of transcripts, a mechanism capable of controlling the abundance of these transcripts according to the situation in which the organism finds itself. these processes cause a great susceptibility to genomic instability in the parasite. this involves epistatic interactions between genes, which drive these changes in gene expression, leading to compensatory mechanisms in the leishmania genome that result in the adaptive evolution of the parasite. during the research carried out by giovanni bussotti and collaborators at the pasteur institute, belonging to the university of paris, a genome-wide association study (gwas) of leishmania donovani identified cnvs in 14% of the coding regions and in 4% of the non-coding regions. in addition, an experimental evolution study (ee approach) was performed on l. donovani amastigotes obtained from clinical cases of hamsters. by extracting these amastigotes from infected organisms and culturing them in vitro for 36 weeks (3800 generations), it was demonstrated how genomic instability in this parasite is capable of adapting to complicated situations, such as in vitro culture. an 11kb deletion was detected in the gene coding for ld1s_360735700, a nima-related kinase with key functions in the correct progression of mitosis. with the advancement of in vitro culture generations the loss of the kinase becomes more notorious, decreasing growth rate of the parasite, but the genomic instability of leishmania manages, through compensatory mechanisms, to attenuate this reduction in growth so that the in vitro culture is maintained. first, as an adaptation of the culture to the loss of this kinase, it was detected an increase in the expression of another orthologous kinase (ld1s_360735800) whose coding region is adjacent to that of the lost kinase. secondly, a reduction in the expression of 23 transcripts related to flagellar biogenesis was observed. so adaptation in leishmania leads the parasite to eliminate flagellar movement from its needs, since it is not necessary in in vitro culture, preserving the energy invested in this movement to increase the growth rate and compensating the loss of the kinase. finally, coamplification of ribosomal protein clusters, ribosomal rna (rrna), transfer rna (trna) and nucleolar small rna (snorna) was observed. increased expression of these clusters leads to increased ribosomal biogenesis and protein biosynthesis. this is most evident in the case of small nucleolar rnas (snorna), for which amplification of a large cluster of 15 snornas was observed on chromosome 33. the function of these nucleic acids is methylation and inclusion of