[Mutation signatures in head and neck squamous cell carcinoma : Pathogenesis and therapeutic potential]. / Mutationssignaturen beim Kopf- und Hals-Tumor : Pathogenese und Potenzial für die Therapie.

BACKGROUND: The pathogenesis of head and neck squamous cell carcinoma (HNSCC) is a complex and multistage process which results from the interaction of exogenous and endogenous cellular processes. Each of these processes leaves a characteristic pattern of mutations on the tumor genome, a so-called mutational signature. STATE OF THE ART: The subject of current studies is to decipher specific signatures of mutational processes operating during HNSCC pathogenesis and to address their prognostic value. Computational analysis of genomic sequencing data by The Cancer Genome Atlas (TCGA) revealed mutational signatures 1, 2, 4, 5, 7, and 13 as the main players in HNSCC pathogenesis. Signature 16 was first discovered in human papillomavirus (HPV)-negative oral and oropharyngeal tumors. In many studies, an association of signature 16 with alcohol and tobacco consumption as well as with an unfavorable prognosis was described.

Quality of life after nasal cancer resection - surgical versus prosthetic rehabilitation.

BACKGROUND: Nose reconstruction following resection of nasal carcinomas is controversial. The objective of this study is to investigate the effect of surgical reconstruction versus prosthetic rehabilitation on patient quality of life (QOL). DESIGN: This was a monocentric prospective study of patients diagnosed with nasal carcinoma from 2003 to 2013. QOL was evaluated using two organ-specific questionnaires (Rhinoplasty Outcome Evaluation [ROE] and the Functional Rhinoplasty Outcome Inventory-17 [FROI-17]) and a generic questionnaire, the Short-Form 36 Health Survey (SF-36). MATERIAL AND METHODS: Sixty-four patients were included. Patients completed the ROE, FROI-17, and SF-36 questionnaires after nasal reconstruction. Questionnaires were completed by 62.8% of the 51 alive patients. RESULTS: Recurrence-free survival (RFS) was 89.9%, disease-specific survival was 94.5%, and overall survival was 75.5% after five years according to the Kaplan-Meier method. Considering initial tumor stage, early stage patients had a significantly higher self-confidence score in FROI-17 subgroup analysis. In contrast, advanced stage patients showed a significantly higher score for social functioning in SF-36. Prosthetically fitted patients scored highly on the ROE questionnaire showing a high degree of aesthetic satisfaction. Surgically reconstructed patients showed a high degree of self-confidence on the FROI-17 questionnaire. However, the organ-specific ROE and FROI-17 scores were not significantly different between patients who received surgical reconstruction and prosthetic rehabilitation after oncological resection. When comparing the rehabilitation method as a function of tumor stage, there was significantly better score for physical functioning in early stage surgically reconstructed patients in the SF-36, but no significant differences in organ-specific QOL. CONCLUSION: Surgical reconstruction and prosthetic rehabilitation after nasal cancer resection have the same effect on organ- and non-organ-specific QOL.

Whole Mitogenomes Reveal the History of Swamp Buffalo: Initially Shaped by Glacial Periods and Eventually Modelled by Domestication.

The newly sequenced mitochondrial genomes of 107 Asian swamp buffalo (Bubalus bubalis carabensis) allowed the reconstruction of the matrilineal divergence since ~900 Kya. Phylogenetic trees and Bayesian skyline plots suggest a role of the glacial periods in the demographic history of swamp buffalo. The ancestral swamp-buffalo mitogenome is dated ~232 ± 35 Kya. Two major macro-lineages diverged during the 2nd Pleistocene Glacial Period (~200-130 Kya), but most (~99%) of the current matrilines derive from only two ancestors (SA1'2 and SB) that lived around the Last Glacial Maximum (~26-19 Kya). During the late Holocene optimum (11-6 Kya) lineages differentiated further, and at least eight matrilines (SA1, SA2, SB1a, SB1b, SB2a, SB2b, SB3 and SB4) were domesticated around 7-3 Kya. Haplotype distributions support an initial domestication process in Southeast Asia, while subsequent captures of wild females probably introduced some additional rare lineages (SA3, SC, SD and SE). Dispersal of domestic buffaloes created local population bottlenecks and founder events that further differentiated haplogroup distributions. A lack of maternal gene flow between neighboring populations apparently maintained the strong phylogeography of the swamp buffalo matrilines, which is the more remarkable because of an almost complete absence of phenotypic differentiation.

Global transcriptional profiling of longissimus thoracis muscle tissue in fetal and juvenile domestic goat using RNA sequencing.

Domestic goats are important meat production animals; however, data from transcriptional profiling of skeletal muscle tissue in goat have thus far been scarce. We used comparative transcriptional profiling based on RNA sequencing of longissimus thoracis muscle tissue obtained from fetal goat muscle tissue (27 512 850 clean cDNA reads) and 6-month-old goat muscle tissue (27 582 908 reads) to identify genes that are differentially expressed, novel transcript units and alternative splicing events. Gene annotation revealed that 15 960 and 14 981 genes were expressed in the fetal and juvenile libraries respectively. We detected 6432 differentially expressed genes and, when considering GO terms, found 34, 27 and 55 terms to be significantly enriched in molecular function, cellular component and biological process categories respectively. Pathway analysis revealed that larger numbers of differentially expressed genes were enriched in fetal myogenesis or cell proliferation and differentiation-related pathways (such as Wnt), genes involved in the cell cycle and the Notch signaling pathway, and most of the differentially expressed genes involved in these pathways were downregulated in the juvenile goat library. These genes may be involved in various regulation mechanisms during muscle tissue differentiation between the two development stages examined herein. The identified novel transcript units, including both non-coding and coding RNA, as well as alternative splicing events increase the level of complexity of regulation mechanisms during muscle tissue formation and differentiation. Our study provides a comparative transcriptome analysis on goat muscle tissue, which will provide a valuable genomic resource for future studies investigating the molecular basis of skeletal muscle development.

Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations.

The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).

Texture and nano-scale internal microstructure of otoliths in the Atlantic molly, Poecilia mexicana: a high-resolution EBSD study.

Otoliths of modern bony fishes are massive polycrystalline structures consisting mainly of calcium carbonate (primarily aragonite), and 1-10% organic residuals. Unlike other biomineralisates like shells, teeth and bones, they are not optimized for mechanical loads but serve the senses of hearing and balance in the inner ear. We examined internal structural variation of otoliths through microstructural and texture analyses. Our study applied the electron backscattered diffraction technique (EBSD) to whole sections of saccular otoliths on cave- and surface-dwelling fish. Application of high spatial resolution EBSD on otoliths of the livebearing fish Poecilia mexicana allowed for an investigation of crystal orientation despite the small size (<150 nm) of aragonite crystallites. Crystallites at the rims of otoliths had a higher structural organization than those situated near the center, where no dominant orientation pattern was discernible. Moreover, the medial (sulcal) face of otoliths, which makes contact with the sensory epithelium, was more structured than the lateral (antisulcal) face.

Dietary niche overlap in sympatric asexual and sexual livebearing fishes Poecilia spp.

The present study investigated the spatiotemporal patterns in trophic resource use in a system of a gynogenetic poeciliid fish, the Amazon molly Poecilia formosa, and its sexual congeners the sailfin molly Poecilia latipinna and the Atlantic molly Poecilia mexicana using gut contents analysis. No statistically significant differences in trophic resource use were found between sexual and gynogenetic species, but gut contents varied significantly across sites and over time. In addition, variation in trophic morphology (i.e. gut length) was significant across sites but not species, and laboratory experiments indicated that gut length is phenotypically plastic. Overall, trophic differentiation between coexisting asexual and sexual Poecilia appears to be minimal, and it is unlikely that niche differentiation contributes to a stable coexistence of the two reproductive forms.

Toxic hydrogen sulphide and dark caves: pronounced male life-history divergence among locally adapted Poecilia mexicana (Poeciliidae).

Chronic environmental stress is known to induce evolutionary change. Here, we assessed male life-history trait divergence in the neotropical fish Poecilia mexicana from a system that has been described to undergo incipient ecological speciation in adjacent, but reproductively isolated toxic/nontoxic and surface/cave habitats. Examining both field-caught and common garden-reared specimens, we investigated the extent of differentiation and plasticity of life-history strategies employed by male P. mexicana. We found strong site-specific life-history divergence in traits such as fat content, standard length and gonadosomatic index. The majority of site-specific life-history differences were also expressed under common garden-rearing conditions. We propose that apparent conservatism of male life histories is the result of other (genetically based) changes in physiology and behaviour between populations. Together with the results from previous studies, this is strong evidence for local adaptation as a result of ecologically based divergent selection.

An indigenous religious ritual selects for resistance to a toxicant in a livebearing fish.

Human-induced environmental change can affect the evolutionary trajectory of populations. In Mexico, indigenous Zoque people annually introduce barbasco, a fish toxicant, into the Cueva del Azufre to harvest fish during a religious ceremony. Here, we investigated tolerance to barbasco in fish from sites exposed and unexposed to the ritual. We found that barbasco tolerance increases with body size and differs between the sexes. Furthermore, fish from sites exposed to the ceremony had a significantly higher tolerance. Consequently, the annual ceremony may not only affect population structure and gene flow among habitat types, but the increased tolerance in exposed fish may indicate adaptation to human cultural practices in a natural population on a very small spatial scale.

Using video playback to study the effect of an audience on male mating behavior in the Sailfin molly (Poecilia latipinna).

Sexual conflict in poeciliid fishes is well-documented, particularly male sexual harassment and its effects on females. For instance, male attempts to force copulations influence female feeding, energy allocation, and preference for shoaling partners. However, there has been little research conducted to determine how the social environment shapes the occurrence and intensity of sexual harassment. In this study we ask whether an audience male influences the sexual behaviors of a focal male, the correlated feeding time reduction of female Poecilia latipinna, and if the size of the audience male (larger or smaller than the focal male) influences these behaviors. We presented a video of a male, either smaller or larger than the focal male, or an empty tank (control) to a female interacting with a male or female partner and measured feeding times and sexual behaviors. We found that male sexual behaviors increased in the presence of an audience male, especially if the audience male was larger than the focal male. Females fed more in the presence of a partner female than in the presence of a male, which was independent of the audience (i.e., video treatment). Focal female aggression towards the partner female increased with the size of the audience male. The present study shows that an audience male has multiple interacting influences on both male and female behavior.

Natural and sexual selection against immigrants maintains differentiation among micro-allopatric populations.

Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence lead to speciation. But what mechanisms contribute to reproductive isolation among diverging populations? We tested for natural and sexual selection against immigrants in a fish species inhabiting (and adapting to) nonsulphidic surface habitats, sulphidic surface habitats and a sulphidic cave. Gene flow is strong among sample sites situated within the same habitat type, but low among divergent habitat types. Our results indicate that females of both sulphidic populations discriminate against immigrant males during mate choice. Furthermore, using reciprocal translocation experiments, we document natural selection against migrants between nonsulphidic and sulphidic habitats, whereas migrants between sulphidic cave and surface habitats did not exhibit increased mortality within the same time period. Consequently, both natural and sexual selection may contribute to isolation among parapatric populations, and selection against immigrants may be a powerful mechanism facilitating speciation among locally adapted populations even over very small spatial distances.

Local adaptation and pronounced genetic differentiation in an extremophile fish, Poecilia mexicana, inhabiting a Mexican cave with toxic hydrogen sulphide.

We investigated genetic differentiation and migration patterns in a small livebearing fish, Poecilia mexicana, inhabiting a sulfidic Mexican limestone cave (Cueva del Azufre). We examined fish from three different cave chambers, the sulfidic surface creek draining the cave (El Azufre) and a nearby surface creek without the toxic hydrogen sulphide (Arroyo Cristal). Using microsatellite analysis of 10 unlinked loci, we found pronounced genetic differentiation among the three major habitats: Arroyo Cristal, El Azufre and the cave. Genetic differentiation was also found within the cave between different pools. An estimation of first-generation migrants suggests that (i) migration is unidirectional, out of the cave, and (ii) migration among different cave chambers occurs to some extent. We investigated if the pattern of genetic differentiation is also reflected in a morphological trait, eye size. Relatively large eyes were found in surface habitats, small eyes in the anterior cave chambers, and the smallest eyes were detected in the innermost cave chamber (XIII). This pattern shows some congruence with a previously proposed morphocline in eye size. However, our data do not support the proposed mechanism for this morphocline, namely that it would be maintained by migration from both directions into the middle cave chambers. This would have led to an increased variance in eye size in the middle cave chambers, which we did not find. Restricted gene flow between the cave and the surface can be explained by local adaptations to extreme environmental conditions, namely H2S and absence of light. Within the cave system, habitat properties are patchy, and genetic differentiation between cave chambers despite migration could indicate local adaptation at an even smaller scale.

Activity patterns of bushbuck (Tragelaphus scriptus) in Queen Elizabeth National Park.

Activity patterns and time budgets of bushbuck (Tragelaphus scriptus) were studied in a free-ranging population in Queen Elizabeth National Park, Uganda from August 2000 to January 2002. We investigated differences in activity patterns in relation to daytime, season, sun radiation, moonlight, age and sex. Bushbuck were found to show peak activities around sunrise and at dawn. No difference in the mean activity rates was found between the dry and wet season. Daytime activity was not predicted by differences in sun radiation, nor was nighttime activity predicted by the presence or absence of moonlight. We found the activity of adult territorial males to be strongly positively correlated with that of females, whereas the activity of young-adult non-territorial males was not significantly correlated with the activity of females. This suggests that young-adult males shift their peak activity to phases when adult territorial males are less active.

Patterns of gastrointestinal parasitic infections in the bushbuck Tragelaphus scriptus from the Queen Elizabeth National Park, Uganda.

Seasonal, host sex and age-related variations in helminth egg and coccidian oocyst counts were investigated in a naturally infected wild bushbuck (Tragelaphus scriptus) population in Queen Elizabeth National Park, western Uganda from April 2000 to February 2002. The prevalence and mean intensity quantified as the number of eggs and oocysts per gram of faeces were taken as a measure of parasite burdens. Host sex and age-related differences in prevalence values were not found but the overall prevalence of Eimeria sp. was significantly higher during the rainy season, and peak counts were recorded either during or soon after a peak rainfall. A similar trend was observed for Moniezia spp., although the results were marginally not significant. There were also no significant differences in mean intensity values, relative to host sex, age or season.

Male mate choice and sperm allocation in a sexual/asexual mating complex of Poecilia (Poeciliidae, Teleostei).

Male mate choice is critical for understanding the evolution and maintenance of sexual/asexual mating complexes involving sperm-dependent, gynogenetic species. Amazon mollies (Poecilia formosa) require sperm to trigger embryogenesis, but the males (e.g. Poecilia mexicana) do not contribute genes. Males benefit from mating with Amazon mollies, because such matings make males more attractive to conspecific females, but they might control the cost of such matings by providing less sperm to Amazon mollies. We examined this at the behavioural and sperm levels. P. mexicana males preferred to mate with, and transferred more sperm to conspecific females. However, if males mated with P. formosa, sperm was readily transferred. This underscores the importance of male choice in this system.

Benzyl-functionalized cycloSal-d4T monophosphates.

Synthetic routes to benzyl-functionalized cycloSal-d4T monophosphates (7CH2X-cycloSal-d4TMP) have been developed. Their hydrolytic behavior in basic aqueous solution (pH = 7.3) was studied and their hydrolysis half-lives were determined. It turned out that two different degradation pathways are leading to different products: beside the formation of the expected d4TMP and a styrene type derivative, a phenyl-d4T-phosphodiester was obtained as well. The product distribution was specified.

Retinoic acid reduces apoptosis and oxidative stress by preservation of SOD protein level.

Retinoic acid (RA) has already been shown to exert antiapoptotic and antioxidative activity in various cells. In this study, we determined the effect of RA on the mRNA and protein levels of the Cu-,Zn-superoxide dismutase (SOD-1) and Mn-superoxide dismutase (SOD-2) during staurosporine-induced apoptosis in primary cultures from neonatal rat hippocampus. Exposure to staurosporine (300 nM, 24 h) increased the percentage of apoptotic neurons to 62% compared with 18% in controls. We determined an increase in the reactive oxygen species (ROS) content from 4 up to 48 h after the induction of the injury. Treatment with staurosporine did not significantly change the mRNA levels of SOD-1 and SOD-2. However, the SOD-1 and SOD-2 protein levels markedly decreased 24 and 48 h after the addition of staurosporine. Compared with staurosporine-exposed controls, RA (10 nM)-treated cultures showed a significant increase in neuronal survival, a reduced neuronal ROS content, and enhanced protein levels of SOD-1 and SOD-2 24 and 48 h after the start of the exposure to staurosporine. The results suggest that RA reduced staurosporine-induced oxidative stress and apoptosis by preventing the decrease in the protein levels of SOD-1 and SOD-2, and thus supported the antioxidant defense system.