FasParser:a package for manipulating sequence data

A computer software package called ＇FasParser＇ was developed for manipulating sequence data. It can be used on personal computers to perform series of analyses, including counting and viewing differences between two sequences at both DNA and codon levels, identifying overlapping regions between two alignments, sorting of sequences according to their IDs or lengths, concatenating sequences of multiple loci for a particular set of samples, translating nucleotide sequences to amino acids, and constructing alignments in several different formats, as well as some extracting and filtrating of data for a particular FASTA file. Majority of these functions can be run in a batch mode, which is very useful for analyzing large data sets. This package can be used by a broad audience, and is designed for researchers that do not have programming experience in sequence analyses. The GUI version of FasParser can be downloaded from https：//github.com/Sun-Yanbo/FasParser, free of charge

AutoSeqMan:batch assembly of contigs for Sanger sequences

With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan （in the LaserGene package） is an excellent program with an easy-to-use graphical user interface （GUI） employed to assemble Sanger sequences into contigs. However, with increasing data size, larger sample sets and more sequenced loci make contig assemble complicated due to the considerable number of manual operations required to run SeqMan. Here, we present the ＇autoSeqMan＇ software program, which can automatedly assemble contigs using SeqMan scripting language. There are two main modules available, namely, ＇Classification＇ and ＇Assembly＇. Classification first undertakes preprocessing work, whereas Assembly generates a SeqMan script to consecutively assemble contigs for the classified files. Through comparison with manual operation, we showed that autoSeqMan saved substantial time in the preprocessing and assembly of Sanger sequences. We hope this tool will be useful for those with large sample sets to analyze, but with little programming experience. It is freely available at https：//github.com/ Sun-Yanbo/autoSeqMan.

Expression ofα2-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.Theα2-Na/K-ATPase is an important isoform of Na/K-ATPase.The expression ofα2-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 theα2-Na/K-ATPase expression pattern was confirmed in the inner ear.It was foundα2-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 ofα2-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 ofα2-Na/K-ATPase might play an important role in the pathogenesis of age-related hearing loss.

Capture Probe: a java tool for designing probes for capture Hi-C applications

DEAR EDITOR,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.

Expression Patterns and Implications of LaminBl in Rat Cochleae

LaminB1,a major component of the nuclear lamina,is a potent regulator of cellular proliferation and senescence and also known to be essential for neuronal migration and brain development.However,the expression patterns of LaminB1 in the rat cochleae are still not fully revealed.Utilizing immunofluorescence.Western blotting,and quantitative real-time PCR,we identified the distribution and expression of LaminB1 in the rat cochleae.Immunofluorescence staining indicated that LaminBl was mainly localized in the auditory hair cells(HCs),spiral ganglion cells(SGC),stria vascularis(STV,including spiral ligament),Reissner's membrane(RM),and limbus laminae spiralis(LLS).Western blotting analysis illustrated that the distribution of LaminBl in rat cochleae was characterized by tissue specificity.The LaminB1 protein was expressed more in SGC and basilar membrane(BM)than in STV.Meanwhile,the mRNA expression of LaminB1 displayed difference in cochlear tissues.These observations preliminarily revealed the expression patterns of LaminB1,providing a theoretical basis for further study on the role of LaminB1 in auditory function.

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.

Integrative analyses of RNA editing,alternative splicing,and expression of young genes in human brain transcriptome by deep RNA sequencing

Next-generation RNA sequencing has been successfully used for identification of transcript assembly,evaluation of gene expression levels,and detection of post-transcriptional modifications.Despite these large-scale studies,additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome.Here,we provide a total of 6.5 billion RNA-seq reads fromdifferent subregions of the human brain.A significant correlation was observed between the levels of alternative splicing and RNA editing,which might be explained by a competition between the molecularmachineries responsible for the splicing and editing of RNA.Younghuman protein-coding genesdemonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans.Wealso found that a significantly greater number of young human protein-coding genes are expressed in the putamen,a tissue that was also observed to have the highest level of RNA-editing activity.The putamen,which previously received little attention,plays an important role in cognitive ability,and our data suggest a potential contribution of the putamen to human evolution.

Nocturnal to Diurnal Transition in the Common Ancestor of Haplorrhines:Evidence from Genomic-Scan for Positively Selected Genes

Transition from a nocturnal to a diurnal lifestyle represents a major shift in primate evolution, plays a central role in the adaptation of these species to new habitats, and is involved in modifications to their physiological and social behaviors （Heesy and Ross, 2001; Shultz et al., 2011）. However, two core problems concerning the circadian rhythm transition re- mains unresolved. First, there is controversy concerning the activity pattern of the ancestral primate （Heesy and Ross, 2001; Tan et al., 2005）. Second, the transition process for circadian rhythm in primate evolutionary history is unre- solved. Although most research suggests that primates trans- formed from a nocturnal to a diurnal circadian rhythm in the lineage leading to the common ancestor of the anthropoids or the haplorrhines （anthropoids and tarsier） （Ross, 2000; Heesy and Ross, 2001）, evidence has been insufficient to determine whether this occurred in the lineage leading to the common ancestor of the haplorrhines or the anthroooids.