Incorporating functional annotation information in prioritizing disease associated SNPs from genome wide association studies

With recent advances in genotyping and sequencing technologies,many disease susceptibility loci have been identified.However,much of the genetic heritability remains unexplained and the replication rate between independent studies is still low.Meanwhile,there have been increasing efforts on functional annotations of the entire human genome,such as the Encyclopedia of DNA Elements(ENCODE)project and other similar projects.It has been shown that incorporating these functional annotations to prioritize genome wide association signals may help identify true association signals.However,to our knowledge,the extent of the improvement when functional annotation data are considered has not been studied in the literature.In this article,we propose a statistical framework to estimate the improvement in replication rate with annotation data,and apply it to Crohn’s disease and DNase I hypersensitive sites.The results show that with cell line specific functional annotations,the expected replication rate is improved,but only at modest level.     

SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways

Amino acid changes due to non-synonymous variation are included as annotations for individual proteins in UniProtKB/Swiss-Prot and RefSeq which present biological data in a protein-or gene-centric fashion. Unfortunately, proteome-wide analysis of non-synonymous singlenucleotide variations (nsSNVs) is not easy to perform because information on nsSNVs and functionally important sites are not well integrated both within and between databases and their search engines. We have developed SNVDis that allows evaluation of proteome-wide nsSNV distribution in functional sites, domains and pathways. More specifically, we have integrated human-specific data from major variation databases (UniProtKB, dbSNP and COSMIC), comprehensive sequence feature annotation from UniProtKB, Pfam, RefSeq, Conserved Domain Database (CDD) and pathway information from Protein ANalysis THrough Evolutionary Relationships (PANTHER) and mapped all of them in a uniform and comprehensive way to the human reference proteome provided by UniProtKB/Swiss-Prot. Integrated information of active sites, pathways, binding sites, domains, which are extracted from a number of different sources, provides a detailed overview of how nsSNVs are distributed over the human proteome and pathways and how they intersect with functional sites of proteins. Additionally, it is possible to find out whether there is an over-or under-representation of nsSNVs in specific domains, pathways or user-defined protein lists. The underlying datasets are updated once every 3 months. SNVDis is freely available at http://hive.biochemistry.gwu.edu/tool/snvdis.     

Multiple 2D approaches to human sexual dimorphism of the distal end of femur

Various studies on the difference of distal femoral condyles between genders have been reported recently in order to provide anatomic information for knee prosthesis design and surgical planning in total knee arthroplasty.They also had the objective to be used as a sex recognition character,as may be needed in forensic medicine.Except for a recent 3D approach on the distal femur,most of the studies used dimensional information or aspect ratio but not shape.Our 2D study aimed to determine the size and shape variation of femoral condyles in Thais,considering age,sex and sides.One hundred and twenty-four cadaveric femurs (male 84 legs and female 40 legs) were dissected.The specimens were photographed by digital camera and images were analyzed using three geometric techniques:(i) the landmark-based method (5 landmarks),(ii) with or without addition of 23 sliding semilandmark and (iii) the outline-based methods.From the resulting geometric coordinates,size and shape were extracted for comparisons between genders and sides.Between sides,directional asymmetry could be detected only for shape variation,and only when introducing curves in the analyses (either through the semilandmarks technique or through the outline-based one).Non-directional asymmetry,probably fluctuating asymmetry,was detected for size,as well as for shape,in both genders.Sex discrimination was performed for each geometric technique using two classification methods:the Mahalanobis distance classification and the Maximum likelihood classification.The latter provided much more satisfactory gender validated reclassification (87％) than shape (72％).     

GPA: A Microbial Genetic Polymorphisms Assignments Tool in Metagenomic Analysis by Bayesian Estimation

Identifying antimicrobial resistant(AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing(NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify genetic polymorphisms or copy number variations(CNVs) for given genes. Here we provide a Bayesian framework for genotype estimation for mixtures of multiple bacteria, named as Genetic Polymorphisms Assignments(GPA). Simulation results showed that GPA has reduced the false discovery rate(FDR) and mean absolute error(MAE) in CNV and single nucleotide variant(SNV) identification. This framework was validated by whole-genome sequencing and Pool-seq data from Klebsiella pneumoniae with multiple bacteria mixture models, and showed the high accuracy in the allele fraction detections of CNVs and SNVs in AMR genes between two populations. The quantitative study on the changes of AMR genes fraction between two samples showed a good consistency with the AMR pattern observed in the individual strains. Also, the framework together with the genome annotation and population comparison tools has been integrated into an application, which could provide a complete solution for AMR gene identification and quantification in unculturable clinical samples. The GPA package is available at https://github.com/IID-DTH/GPA-package.     

A novel receptor-targeted gene delivery system for cancer gene therapy

Some growth factor receptors, such as insulin like growth factor Ⅰ and Ⅱ receptor (IGF Ⅰ R, IGF Ⅱ R) and epidermal growth factor receptor (EGF R), have been proved to be over-expressed in a variety of human cancers derived from different tissue origins. Based on this molecular alteration, a polypeptide conjugate gene delivery system was designed and synthesized. It contains three essential moieties: a ligand oligopeptide (LOP) for receptor recognition, a polycationic polypeptide (PCP) such as protamine (PA) or poly-L-lysine (PL) as a backbone for DNA binding and an endosome-releasing oligopeptide (EROP) such as influenza baenagglutinin oligopeptide (HA20) for endosomolysis. These components are covalently conjugated as LOP-PCP-HA20 or in the form of a mixture of LOP-PCP and HA20-PCP. A 14 amino acid E5 was designed and synthesized as LOP for IGF Ⅰ R and IGF Ⅱ R, and a 16 amino acid GE7 as LOP for EGF R. Both E5 and GE7 systems could form stable complex with the plasmid DNA as E5-PCP/DNA/PCP-HA20 a     

Role of nanotopography in the development of tissue engineered 3D organs and tissues using mesenchymal stem cells

Recent regenerative medicine and tissue engineering strategies(using cells, scaffolds, medical devices and gene therapy) have led to fascinating progress of translation of basic research towards clinical applications. In the past decade, great deal of research has focused on developing various three dimensional(3D) organs, such as bone, skin, liver, kidney and ear,using such strategies in order to replace or regenerate damaged organs for the purpose of maintaining or restoring organs’ functions that may have been lost due to aging, accident or disease. The surface properties of a material or a device are key aspects in determining the success of the implant in biomedicine, as the majority of biological reactions in human body occur on surfaces or interfaces. Furthermore, it has been established in the literature that cell adhesion and proliferation are, to a great extent, influenced by the micro- and nanosurface characteristics of biomaterials and devices. In addition, it has been shown that the functions of stem cells, mesenchymal stem cells in particular, could be regulated through physical interaction with specific nanotopographical cues. Therefore, guided stem cell proliferation, differentiation and function are of great importance in the regeneration of 3D tissues and organs using tissue engineering strategies. This review will provide an update on the impact of nanotopography on mesenchymal stem cells for the purpose of developing laboratory-based 3D organs and tissues, as well as the most recent research and case studies on this topic.     

Absent MicroRNAs in Different Tissues of Patients with Acquired Cardiomyopathy

MicroRNAs (miRNAs) can be found in a wide range of tissues and body fluids, and their specific signatures can be used to determine diseases or predict clinical courses. The miRNA profiles in biological samples (tissue, serum, peripheral blood mononuclear cells or other body fluids) differ significantly even in the same patient and therefore have their own specificity for the presented con-dition. Complex profiles of deregulated miRNAs are of high interest, whereas the importance of non-expressed miRNAs was ignored. Since miRNAs regulate gene expression rather negatively, absent miRNAs could indicate genes with unaltered expression that therefore are normally expressed in specific compartments or under specific disease situations. For the first time, non-detectable miRNAs in different tissues and body fluids from patients with different diseases (cardiomyopathies, Alzheimer’s disease, bladder cancer, and ocular cancer) were analyzed and com-pared in this study. miRNA expression data were generated by microarray or TaqMan PCR-based platforms. Lists of absent miRNAs of primarily cardiac patients (myocardium, blood cells, and serum) were clustered and analyzed for potentially involved pathways using two prediction platforms, i.e., miRNA enrichment analysis and annotation tool (miEAA) and DIANA miRPath. Extensive search in biomedical publication databases for the relevance of non-expressed miRNAs in predicted pathways revealed no evidence for their involvement in heart-related pathways as indicated by software tools, confirming proposed approach.     

Network prediction of surgical complication clusters: a prospective multicenter cohort study

Complicated relationships exist in both occurrence and progression of surgical complications, which are difficult to account for using a separate quantitative method such as prediction or grading. Data of 51,030 surgical inpatients were collected from four academic/teaching hospitals in a prospective cohort study in China. The relationship between preoperative factors, 22 common complications, and death was analyzed. With input from 54 senior clinicians and following a Bayesian network approach,...     

Special Issue on “Gene Regulatory Network”

The journal Genomics Proteomics & Bioinformatics (GPB) is now inviting submissions for a special issue (to be published around Dec 2012) on the topic of "Gene Regulatory Network". The Gene Regulatory Network (GRN) is a collection of DNA sequences which interact with each other and other cellular components, thereby governing the rates at which genes in the network are transcribed to change the genomic activity. GRNs are evolutionally-conserved and play critical roles in various biological processes and attract more and more research interest.     

A Brief Review of Software Tools for Pangenomics

Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline(PGAP) ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.     

A framework to evaluate whether to pool or separate behaviors in a multilayer network

A multilayer network approach combines different network layers,which are connected by interlayer edges,to create a single mathematical object.These networks can contain a variety of information types and represent different aspects of a system.However,the process for selecting which information to include is not always straightforward.Using data on 2 agonistic behaviors in a captive population of monk parakeets(Myiopsitta monachus),we developed a framework for investigating how pooling or splitting behaviors at the scale of dyadic relationships(between 2 individuals)affects individual-and group-level social properties.We designed 2 reference models to test whether randomizing the number of interactions across behavior types results in similar structural patterns as the observed data.Although the behaviors were correlated,the first reference model suggests that the 2 behaviors convey different information about some social properties and should therefore not be pooled.However,once we controlled for data sparsity,we found that the observed measures corresponded with those from the second reference model.Hence,our initial result may have been due to the unequal frequencies of each behavior.Overall,our findings support pooling the 2 behaviors.Awareness of how selected measurements can be affected by data properties is warranted,but nonetheless our framework disentangles these efforts and as a result can be used for myriad types of behaviors and questions.This framework will help researchers make informed and data-driven decisions about which behaviors to pool or separate,prior to using the data in subsequent multilayer network analyses.     

Decreased decidual epithelial sodium channel (ENaC) alpha and gamma subunits in recurrent pregnancy loss (RPL)

正Dear Editor,Recurrent pregnancy loss (RPL) in early pregnancy is a devastating problem for couples who want to become parents and a difficult challenge for their physician. RPL is also referred to as recurrent miscarriage or habitual abortion. It is defined as two or more consecutive clinical miscarriages(CMs) before 20 weeks of gestation (Practice Committee of     

Spatial and temporal regulation of collagenases—3,—4,and stromelysin —3 implicates distinct functions in apoptosis and tissue remodeling during frog metamorphosis

Matrix metalloproteinases (MMPs) are a family of extracellular proteases capable of degrading various proteinaceous components of the extracellular matrix(ECM).They have been implicated to play important roles in a number of developmental and pathological processes,such as tumor metastasis and inflammation.Relatively few studies have been carried out to investigate the function of MMPs during postembryonic organ-development.Using Xenopus laevis development as a model system,we demonstrate here that three MMPs,stromelysin-3(ST3),collagenases-3(Col3),and Col4,have distinct spatial and temporal expression profiles during metamorphosis as the tadpole transforms into a frog.In situ hybridizations reveal a tight,but distinct,association of individual MMPs with tissue remodeling in the tail and intestine during metamorphosis.In particular,ST3 expression is strongly correlated with apoptosis in both organs as demonstrated by analyses of serial sections with in situ hybridization for ST3 mRNA and TUNEL (terminal deoxyribonucleotidyl transferase-mediated dUTP-biotin nick end labeling)for apoptosis,respectively.On the other hand,Col3 and Col4 are present in regions where extensive connective tissue remodeling take place.These results indicate that ST3 is likely to play a role in ECM-remodeling that facilitate apoptotic tissue remodeling or resorption while Col3 and Col4 appear to participate in connective tissue degradation during development.     

Tissue engineered esophagus by copper——small intestinal submucosa graft for esophageal repair in a canine model

Acellular porcine small intestinal submucosa(SIS)has been used for esophagoplasty with success in a canine model.However,it did not lead to complete epithelialization.For better reconstruction,a cellular component is required.Moreover,promotion of angiogenesis with copper has been widely recognized by basic research as well as clinical studies.In this study,we have evaluated the feasibility and effectiveness of combined Cu and SIS(SIS-Cu patch)for the esophageal repair using a canine model.Eighteen male beagle dogs were subjected to surgical resection to produce cervical esophageal defects(5 cm in length,180°in range).SIS with Cu(5 or 25μmol L 1copper)or without Cu was patched on the esophageal defects.Barium esophagram and histology exam were carried out to evaluate the effectiveness of the therapy.As shown,the SIS-Cu graft promoted re-epithelialization,re-vascularization and muscular regeneration.SIS-Cu patch is more effective than SIS alone for esophageal repair,and the SIS+25μmol L 1Cu group demonstrated additional advantages over the SIS+5μmol L 1Cu.     

Species specialization limits movement ability and shapes ecological networks: the case study of 2 forest mammals

To counteract the negative effects of forest fragmentation on wildlife, it is crucial to maintain functional ecological networks. We identified the ecological networks for 2 mammals with very different degrees of forest specialization, the European badger Meles metes and the Roe deer Capreolus capreolus, by differentiati ng 4 agroforestry eleme nts as either no des or conn ectivity elements, and by defining the distanee that provides the functional connectivity between fragments. Species occurrenee data were collected in a wide agroecosystem in northern Italy. To test the role of hedgerows, traditional poplar cultivations, short rotation coppices, and reforestations as ecological network elements for the 2 species we applied the method of simulated species perceptions of the Iandscape (SSPL), comparing the ability of different SSPLs to explain the observed species distribution. All analyses were repeated considering different seenarios of species movement ability through the matrix. Model outputs seem to show that the specialist and highly mobile Roe deer has the same movement ability throughout the matrix (2 km) as the European badger, a smaller, but generalist species. The ecological network identified for the European badger was widespread throughout the area and was composed of woodlands, poplar cultivations and hedgerows as nodes and short rotation coppices as connectivity elements. Conversely, the ecological network of the Roe deer was mostly limited to the main forest areas and was composed of woodlands, poplar cultivations and ref o restat i ons as no des and short rotation coppices and hedgerows as conn ectivity elements. The degree of forest specialization strongly affects both species perception of habitat and movement ability throughout the matrix, regardless of species size. This has important implications for species conservation.     

Mesenchymal stem cells and collagen patches for anterior cruciate ligament repair

AIM: To investigate collagen patches seeded with mesenchymal stem cells(MSCs) and/or tenocytes(TCs) with regards to their suitability for anterior cruciate ligament(ACL) repair. METHODS: Dynamic intraligamentary stabilization utilizes a dynamic screw system to keep ACL remnants in place and promote biological healing, supplemented by collagen patches. How these scaffolds interact with cells and what type of benefit they provide has not yet been investigated in detail. Primary ACL-derived TCs and human bone marrow derived MSCs were seeded onto two different types of 3D collagen scaffolds, Chondro-Gide?(CG) and Novocart?(NC). Cells were seeded onto the scaffolds and cultured for 7 d either as a pure populations or as "premix" containing a 1:1 ratio of TCs to MSCs. Additionally, as controls, cells were seeded in monolayers and in co-cultures on both sides of porous high-density membrane inserts(0.4 μm). We analyzed the patches by real time polymerase chain reaction, glycosaminoglycan(GAG), DNA and hydroxyproline(HYP) content. To determine cell spreading and adherence in the scaffolds microscopic imaging techniques, i.e., confocal laser scanning microscopy(c LSM) and scanning electron microscopy(SEM), were applied.RESULTS: CLSM and SEM imaging analysis confirmed cell adherence onto scaffolds. The metabolic cell activity revealed that patches promote adherence and proliferation of cells. The most dramatic increase in absolute metabolic cell activity was measured for CG samples seeded with tenocytes or a 1:1 cell premix. Analysis of DNA content and c LSM imaging also indicated MSCs were not proliferating as nicely as tenocytes on CG. The HYP to GAG ratio significantly changed for the premix group, resulting from a slightly lower GAG content, demonstrating that the cells are modifying the underlying matrix. Real-time quantitativepolymerase chain reaction data indicated that MSCs showed a trend of differentiation towards a more tenogenic-like phenotype after 7 d.CONCLUSION: CG and NC are both cyto-compatible with primary MSCs and TCs; TCs seemed to perform better on these collagen patches than MSCs.     

Computational Identification of Protein-Protein Interactions in Rice Based on the Predicted Rice Interactome Network

Plant protein-protein interaction networks have not been identified by large-scale experiments. In order to better understand the protein interactions in rice, the Predicted Rice Interactome Network (PRIN; http://bis.zju.edu.cn/ prin/) presented 76,585 predicted interactions involving 5,049 rice proteins. After mapping genomic features of rice (GO annotation, subcellular localization prediction, and gene expression), we found that a well-annotated and biologically significant network is rich enough to capture many significant functional linkages within higher-order biological systems, such as pathways and biological processes. Furthermore, we took MADS-box do- main-containing proteins and circadian rhythm signaling pathways as examples to demonstrate that functional protein complexes and biological pathways could be effectively expanded in our predicted network. The expanded molecular network in PRIN has considerably improved the capability of these analyses to integrate existing knowledge and provide novel insights into the function and coordination of genes and gene networks.     

Multilayer network analyses as a toolkit for measuring social structure

The formalization of multilayer networks allows for new ways to measure sociality in complex social systems,including groups of animals.The same mathematical representation and methods are widely applicable across fields and study systems,and a network can represent drastically different types of data.As such,in order to apply analyses and interpret the results in a meaningful way the researcher must have a deep understanding of what their network is representing and what parts of it are being measured by a given analysis.Multilayer social networks can represent social structure with more detail than is often present in single layer networks,including multiple"types"of individuals,interactions,or relationships,and the extent to which these types are interdependent.Multilayer networks can also encompass a wider range of social scales,which can help overcome complications that are inherent to measuring sociality.In this paper,I dissect multilayer networks into the parts that correspond to different components of social structures.I then discuss common pitfalls to avoid across different stages of multilayer network analyses-some novel and some that always exist in social network analysis but are magnified in multi-layer representations.This paper serves as a primer for building a customized toolkit of multilayer network analyses,to probe components of social structure in animal social systems.