The highest-elevation frog provides insights into mechanisms and evolution of defenses against high UV radiation.

Defense against ultraviolet (UV) radiation exposure is essential for survival, especially in high-elevation species. Although some specific genes involved in UV response have been reported, the full view of UV defense mechanisms remains largely unexplored. Herein, we used integrated approaches to analyze UV responses in the highest-elevation frog, Nanorana parkeri. We show less damage and more efficient antioxidant activity in skin of this frog than those of its lower-elevation relatives after UV exposure. We also reveal genes related to UV defense and a corresponding temporal expression pattern in N. parkeri. Genomic and metabolomic analysis along with large-scale transcriptomic profiling revealed a time-dependent coordinated defense mechanism in N. parkeri. We also identified several microRNAs that play important regulatory roles, especially in decreasing the expression levels of cell cycle genes. Moreover, multiple defense genes (i.e., TYR for melanogenesis) exhibit positive selection with function-enhancing substitutions. Thus, both expression shifts and gene mutations contribute to UV adaptation in N. parkeri. Our work demonstrates a genetic framework for evolution of UV defense in a natural environment.

Comparative genomics reveals insights into anuran genome size evolution.

BACKGROUND: Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole genome datasets in the past, the genomic elements and evolutionary causes of anuran genome size variation are poorly understood. To address this, we analyzed whole-genome sequences of 14 anuran species ranging in size from 1.1 to 6.8 Gb. By annotating multiple genomic elements, we investigated the genomic correlates of anuran genome size variation and further examined whether the genome size relates to habitat types. RESULTS: Our results showed that intron expansions or contraction and Transposable Elements (TEs) diversity do not contribute significantly to genome size variation. However, the recent accumulation of transposable elements (TEs) and the lack of deletion of ancient TEs primarily accounted for the evolution of anuran genome sizes. Our study showed that the abundance and density of simple repeat sequences positively correlate with genome size. Ancestral state reconstruction revealed that genome size exhibits a taxon-specific pattern of evolution, with families Bufonidae and Pipidae experiencing extreme genome expansion and contraction events, respectively. Our result showed no relationship between genome size and habitat types, although large genome-sized species are predominantly found in humid habitats. CONCLUSIONS: Overall, our study identified the genomic element and their evolutionary dynamics accounting for anuran genome size variation, thus paving a path to a greater understanding of the size evolution of the genome in amphibians.

Genomic and transcriptomic investigations of the evolutionary transition from oviparity to viviparity.

Viviparous (live-bearing) vertebrates have evolved repeatedly within otherwise oviparous (egg-laying) clades. Over two-thirds of these changes in vertebrate reproductive parity mode happened in squamate reptiles, where the transition has happened between 98 and 129 times. The transition from oviparity to viviparity requires numerous physiological, morphological, and immunological changes to the female reproductive tract, including eggshell reduction, delayed oviposition, placental development for supply of water and nutrition to the embryo by the mother, enhanced gas exchange, and suppression of maternal immune rejection of the embryo. We performed genomic and transcriptomic analyses of a closely related oviparous-viviparous pair of lizards (Phrynocephalus przewalskii and Phrynocephalus vlangalii) to examine these transitions. Expression patterns of maternal oviduct through reproductive development of the egg and embryo differ markedly between the two species. We found changes in expression patterns of appropriate genes that account for each of the major aspects of the oviparity to viviparity transition. In addition, we compared the gene sequences in transcriptomes of four oviparous-viviparous pairs of lizards in different genera (Phrynocephalus, Eremias, Scincella, and Sphenomorphus) to look for possible gene convergence at the sequence level. We discovered low levels of convergence in both amino acid replacement and evolutionary rate shift. This suggests that most of the changes that produce the oviparity-viviparity transition are changes in gene expression, so occasional reversals to oviparity from viviparity may not be as difficult to achieve as has been previously suggested.

A randomised controlled study on the effects of hernial sac stump fenestration on ultrasound seroma prevention in laparoscopic Type III inguinal hernia repair.

BACKGROUND: The incidence of ultrasound seromas has significantly increased after large hernial sac surgery. Several methods are available for preventing ultrasound seromas, but the clinical results are poor. It has also been demonstrated that hernial sac stump fenestration during laparoscopic incisional hernia repair surgery can significantly decrease the incidence of ultrasound seromas. MATERIALS AND METHODS: Ninety patients aged 18-75 years who were treated in our hospital for primary Type III indirect inguinal hernia from March 2017 to March 2018 were randomised to a preventive fenestration group and a control group. All patients underwent transabdominal preperitoneal repair. The number of ultrasound seromas in the inguinal regions and ultrasound seroma volume on day 6 and months 1 and 3 after surgery in the two groups were compared. The secondary outcomes included length of surgery, urinary retention, acute pain, chronic pain, length of hospitalisation, recurrence rate and other complications. RESULTS: There were no significant differences in demographic characteristics. Ultrasound seroma incidence and ultrasound seroma volume on day 6 and months 1 and 3 after surgery were significantly lower in the preventive fenestration group than that in the control group. There were no significant differences in the length of hospitalisation or incidence of acute pain or urinary retention between the two groups. CONCLUSIONS: Hernial sac stump fenestration after hernial sac transection in inguinal hernia repair surgery is a simple method that can effectively reduce post-operative ultrasound seromas.

Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations.

Although many cases of genetic adaptations to high elevations have been reported, the processes driving these modifications and the pace of their evolution remain unclear. Many high-elevation adaptations (HEAs) are thought to have arisen in situ as populations rose with growing mountains. In contrast, most high-elevation lineages of the Qinghai-Tibetan Plateau appear to have colonized from low-elevation areas. These lineages provide an opportunity for studying recent HEAs and comparing them with ancestral low-elevation alternatives. Herein, we compare four frogs (three species of Nanorana and a close lowland relative) and four lizards (Phrynocephalus) that inhabit a range of elevations on or along the slopes of the Qinghai-Tibetan Plateau. The sequential cladogenesis of these species across an elevational gradient allows us to examine the gradual accumulation of HEA at increasing elevations. Many adaptations to high elevations appear to arise gradually and evolve continuously with increasing elevational distributions. Numerous related functions, especially DNA repair and energy metabolism pathways, exhibit rapid change and continuous positive selection with increasing elevations. Although the two studied genera are distantly related, they exhibit numerous convergent evolutionary changes, especially at the functional level. This functional convergence appears to be more extensive than convergence at the individual gene level, although we found 32 homologous genes undergoing positive selection for change in both high-elevation groups. We argue that species groups distributed along a broad elevational gradient provide a more powerful system for testing adaptations to high-elevation environments compared with studies that compare only pairs of high-elevation versus low-elevation species.

Isolation and Genome Sequencing of a Novel Pseudomonas aeruginosa Phage PA-YS35.

Phage PA-YS35 is a novel lytic Pseudomonas aeruginosa phage belonging to the Myoviridae family and was isolated from the sewage of the First Hospital of Jilin University. The biological properties testing indicated that phage PA-YS35 is stable between - 20 and 60 °C and pH 4-9. The one-step growth curve shows that the latent period of PA-YS35 was 9 min, and the burst period was about 21 min by the size of approximately 380 progeny phages per host cell. The genome of phage PA-YS35 is linear double-stranded DNA with a size of 93,296 bp and a GC content of 49.35%. The results from RAST gene annotation analysis showed that the PA-YS35 genome contains 172 open reading frames (ORFs); the function of 41 ORFs can be predicted, whereas the product of remaining 131 ORFs are hypothetical proteins. According to phylogenetic tree of RNA ligase encoding sequence, phage PA-YS35 has a close evolutionary relationship with Pseudomonas phage PAK P1 because both of them are located on the same branch. The study of phage PA-YS35 genome will provide useful information for further research on the interaction between phages and their hosts.

FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data.

Summary: FasParser is a graphical platform for manipulating sequences and alignments in a batch mode. It is particularly useful for biologists handling large datasets of sequences, even without an experience in programming. Here, I present an updated version 'FasParser2', featuring numerous improvements with sets of novel functions that can facilitate sequence manipulation. Its main additional features include (i) re-designed graphical interface which greatly improves its capability for batch processing, (ii) a trimming function to strip poorly-aligned regions in multiple sequence alignments, (iii) a series of functions that can identify as well as remove 'bad' sequence (either too short or too divergent sequences), (iv) an Editor tool for viewing and editing of biological sequences and (v) interfaces (with other programs) for detection of positive selection as well as primer design. Availability and implementation: The compiled Windows binary is freely available at https://github.com/Sun-Yanbo/FasParser/releases.

Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

Comparison of multi-modal early oral nutrition for the tolerance of oral nutrition with conventional care after major abdominal surgery: a prospective, randomized, single-blind trial.

BACKGROUND & AIMS: Early oral nutrition (EON) has been shown to improve recovery of gastrointestinal function, length of stay and mortality after abdominal surgery; however, early oral nutrition often fails during the first week after surgery. Here, a multi-modal early oral nutrition program is introduced to promote recovery of gastrointestinal function and tolerance of oral nutrition. METHODS: Consecutive patients scheduled for abdominal surgery were randomized to the multimodal EON group or a group receiving conventional care. The primary endpoint was the time of first defecation. The secondary endpoints were outcomes and the cost-effectiveness ratio in treating infectious complications. The rate of infectious-free patients was regarded as the index of effectiveness. RESULTS: One hundred seven patients were randomly assigned to groups. Baseline characteristics were similar for both groups. In intention-to-treat analysis, the success rate of oral nutrition during the first week after surgery in the multimodal EON group was 44 (83.0%) versus 31 (57.4%) in the conventional care group (P = 0.004). Time to first defecation, time to flatus, recovery time of bowel sounds, and prolonged postoperative ileus were all less in the multimodal EON group (P < 0.05). The median postoperative length of stay in the multimodal EON group was 8 days (6, 12) versus 10 days (7, 18) in the conventional care group (P < 0.001). The total cost of treatment and nutritional support were also less in the multi-modal early oral nutrition group (P < 0.001). The effectiveness was 84.9 and 79.9% in the multimodal EON and conventional care group, respectively (P = 0.475). However, the cost-effectiveness ratio was USD 537.6 (506.1, 589.3) and USD 637.8 (593.9, 710.3), respectively (P < 0.001). CONCLUSION: The multi-modal early oral nutrition program was an effective way to improve tolerance of oral nutrition during the first week after surgery, decrease the length of stay and improve cost-effectiveness after abdominal surgery. TRIAL REGISTRATION: Registration number: ChiCTR-TRC-14004395 . Registered 15 March 2014.

Impact of nutritional support that does and does not meet guideline standards on clinical outcome in surgical patients at nutritional risk: a prospective cohort study.

OBJECTIVE: To investigate the impact of nutritional support on clinical outcomes in patients at nutritional risk who receive nutritional support that meets guideline standards and those who do not. METHODS: This prospective cohort study enrolled hospitalized patients from the Second Affiliated Hospital of Kunming Medical University from February 2010 to June 2012. The research protocols were approved by the university's ethics committee, and the patients signed informed consent forms. The clinical data were collected based on nutritional risk screening, administration of enteral and parenteral nutrition, surgical information, complications, and length of hospital stay. RESULTS: During the study period, 525 patients at nutritional risk were enrolled in the cohorts. Among patients who received nutritional support that met the guideline standards (Cohort 1), the incidence of infectious complications was lower than that in patients who did not meet guideline standards (Cohort 2) (17.1 % vs. 26.9 %, P = 0.01). Subgroup analysis showed that individuals who received a combination of parenteral nutrition (PN) and enteral nutrition (EN) for 7 or more days had a significantly lower incidence of infectious complications (P = 0.001) than those who received only PN for 7 or more days or those who received nutritional support for less than 7 days or at less than 10 kcal/kg/d. Binary logistic regression analysis showed that, after adjusting for confounding factors, nutritional support that met guideline standards for patients with nutritional risk was a protective factor for complications (OR: 0.870, P < 0.002). CONCLUSIONS: In patients at nutritional risk after abdominal surgery, nutritional support that meets recommended nutrient guidelines (especially regimens involving PN + EN ≥ 7 days) might decrease the incidence of infectious complications and is worth recommending; however, well-designed trials are needed to confirm our findings. Nutritional support that does not meet the guideline standards is considered clinically undesirable.

Self-assembly of block copolymers on lithographically patterned template with ordered posts.

Dissipative particle dynamics simulations are employed to study the self-assembly of block copolymers on a template modified with ordered posts. Templates with hexagonally arranged and rectangularly arranged posts are both studied. For the systems with hexagonally arranged posts, morphologies with bending alignments are seen most often. We find that the different kinds of patterns, which can be directly observed in experiments, are substantially induced by the pattern of the bottom layer. In the simulations with a template modified with rectangularly arranged posts, by finely adjusting the distances between neighboring posts in both x and y directions, mesh-shaped structures with different angles between the bottom and the sub-bottom layers can be obtained. These results shed light on the better design of lithographically patterned materials on the scale of 10 nm via the directed self-assembly of BCPs by templating.

Deciphering the signature of selective constraints on cancerous mitochondrial genome.

In accordance with the hypothesis that cancer formation is a process of somatic evolution driven by natural selection, signature of positive selection has been detected on a number of cancer-related nuclear genes. It remains, however, controversial whether a similar selective pressure has also acted on mitochondrial DNA (mtDNA), a small molecule in mitochondrion that may play an important role in tumorigenesis by altering oxidative phosphorylation. To better understand the mutational pattern on cancerous mtDNA and decipher the genetic signature left by natural selection, a total of 186 entire mitochondrial genomes of cancerous and adjacent normal tissues from 93 esophageal cancer patients were obtained and extensively studied. Our results revealed that the observed mutational pattern on the cancerous mtDNAs might be best explained as relaxation of negative selection. Taking into account an additional 1,235 cancerous (nearly) complete mtDNA sequences retrieved from the literature, our results suggested that the relaxed selective pressure was the most likely explanation for the accumulation of mtDNA variation in different types of cancer. This notion is in good agreement with the observation that aerobic glycolysis, instead of mitochondrial respiration, plays the key role in generating energy in cancer cells. Furthermore, our study provided solid evidence demonstrating that problems in some of the published cancerous mtDNA data adequately explained the previously contradictory conclusions about the selective pressure on cancer mtDNA, thus serving as a paradigm emphasizing the importance of data quality in affecting our understanding on the role of mtDNA in tumorigenesis.

Evaluating the roles of energetic functional constraints on teleost mitochondrial-encoded protein evolution.

Mitochondria are the power plant of cells, which play critical roles not only in energy metabolism but also in thermoregulation. These two roles have been individually suggested to influence mitochondrial DNA (mtDNA) evolution, however their relative importance is still rarely considered. Here, we conduct a comparative genomic analysis of 401 teleost complete mitochondrial genomes and test the roles of these dual functional constraints on mitochondria to provide a more complete view of mtDNA evolution. We found that mitochondrial protein-coding genes of migratory fishes have significantly smaller Ka/Ks than nonmigratory fishes. The same data set showed that the genes of fishes living in cold climates have significantly smaller Ka/Ks than tropical fishes. In contrast, these trends were not observed for two nuclear genes that are not involved in energy metabolism. The differences in selection patterns observed between mitochondrial and nuclear genes suggest that the functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mitochondrial-encoded proteins in teleosts.

Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability.

The evolution of flight is the most important feature of birds, and this ability has helped them become one of the most successful groups of vertebrates. However, some species have independently lost their ability to fly. The degeneration of flight ability is a long process, and some species remain transitional locomotive models. Most of the energy required for locomotion is supplied by mitochondria via oxidative phosphorylation. Thus, rapidly flying birds should require a more energy efficient metabolism than weakly flying or flightless species. Therefore, we speculated that evolutionary constraints acted on the mtDNA of birds with different locomotive abilities. To test this hypothesis, we compared 76 complete avian mitochondrial genomes. Weakly flying and flightless birds, compared to rapidly flying birds, accumulated more nonsynonymous nucleotide substitutions relative to synonymous substitutions. Even after controlling for mutation rate, this trend remained significant. This finding was further tested for its generality by examining 214 complete mammalian mitochondrial genomes. The same as birds, a negative correlation was also found for the K(a)/K(s) ratio and locomotive speed. Our results demonstrated that, in addition to the previously described role for effective population size, functional constraints due to locomotion play an important role in the evolution of mtDNA.

Expression Plasticity of Transposable Elements Is Highly Associated with Organismal Re-adaptation to Ancestral Environments.

Understanding the roles of phenotypic plasticity in adaptive evolution has gained recognition for decades. Studies involving multiple taxa have shown that gene expression plasticity serves as "long-term memory" to facilitate re-adaptations to ancestral environments. Nevertheless, the general pattern and the underlying genetic basis of expression plasticity remain unclear. The transposable elements (TEs) play crucial roles in gene expression regulation and are widely distributed within the genome. Given this, we re-analyzed the transcriptomic data of chicken (Gallus gallus) generated from a reciprocal transplant experiment to examine whether expression shifts of TEs are involved in the re-adaptation process. Similar to the protein-coding genes, the plastic changes of TEs overwhelmingly exceed the genetic changes in the re-adaptation process. Further, the associated TEs co-expressed with diverse genes to perform a regulatory activity. Thus, our study supports the general function of phenotypic plasticity in adaptive evolution, and suggests a regulatory functions of TEs in this process.

Expression of α2-Na/K-ATPase in C57BL/6J Mice Inner Ear and Its Relationship with Age-related Hearing Loss.

K+ cycling in the cochlea is critical to maintain hearing. Many sodium-potassium pumps are proved to participate in K+ cycling, such as Na/K-ATPase. The α2-Na/K-ATPase is an important isoform of Na/K-ATPase. The expression of α2-Na/K-ATPase in the cochlea is not clear. In this study, we used C57BL/6 mice as a model of presbycusis and implemented immunohistochemistry staining and quantitative real time-PCR, and the α2-Na/K-ATPase expression pattern was confirmed in the inner ear. It was found α2-Na/K-ATPase was expressed widely in cochlea and its mRNA and protein expression was gradually reduced with aging (4-, 14-, 26- and 48-weeks old mice). We suspected that, the down-regulation of α2-Na/K-ATPase expression might be associated with the remodeling of K+ cycling, degeneration of morphological structure and decrease of hearing function in aging C57 mice. In conclusion, we speculated that the reduction of α2-Na/K-ATPase might play an important role in the pathogenesis of age-related hearing loss.

A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae.

BACKGROUND: The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. RESULTS: We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). CONCLUSIONS: The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.

Theoretical mechanistic study on the ion-molecule reaction of CHCl- with CS2.

A detailed theoretical study for the poorly understood ion-molecule reaction of CHCl(-) with CS(2) is explored at the B3LYP/6-311++G(d,p) and CCSD(T)/6-311++G(3df,2p) (single-point) levels. Various possible reaction pathways are considered. On the doublet potential energy surface, five dissociation products are both thermodynamically and kinetically possible. Among these products, P(7) (SCHCl(-) + CS) may be the most favorable product with predominant abundances, whereas P(1) (Cl(-) + SCHCS) and P(2) (Cl(-) + HCCSS) may be the second and third feasible products followed by the almost negligible P(3) (Cl(-) + HSCCS), P(4) (CClS(-) + HCS), and P(6) (S-cCCS(-) + HCl). Because the isomers and transition states involved in the most feasible pathways all lie below the reactant, the title reaction is expected to be fast, which is consistent with the measured large rate constant in recent experiment. The present paper may provide a useful guide for understanding other analogous ion-molecule reactions such as CHF(-) and CHBr(-) with CS(2), COS, and CO(2).

Perspectives on studying molecular adaptations of amphibians in the genomic era.

Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.

CaptureProbe: a java tool for designing probes for capture Hi-C applications.

Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding, making it difficult for scientists to reveal the genetic regulatory mechanisms. Capture Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic regions. It can identify interactions among target loci and all other loci in a genome with low cost and high resolution. Here, we developed CaptureProbe, a user-friendly, graphical Java tool for the design of capture probes across a range of target sites or regions. Numerous parameters helped to achieve and optimize the designed probes. Design testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe specificity. Hence, this program will help scientists conduct genome spatial interaction research. CaptureProbe and source code are available at https://sourceforge.net/projects/captureprobe/.