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222 papers found.
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Three isoforms of the Atg16L1 protein contribute different autophagic properties

The mammalian Atg16L1 protein consists of a coiled-coil domain and a tryptophan-aspartic acid (WD) repeat domain and is involved in the process of autophagy. However, the mechanisms underlying the effect of the Atg16L1 isoforms on autophagy remain to be elucidated in humans. In the present study, we successfully cloned three isoforms: Atg16L1-1, which contains the complete...

An Efficient Algorithm for Haplotype Inference on Pedigrees with a Small Number of Recombinants

Combinatorial (or rule-based) methods for inferring haplotypes from genotypes on a pedigree have been studied extensively in the recent literature. These methods generally try to reconstruct the haplotypes of each individual so that the total number of recombinants is minimized in the pedigree. The problem is NP-hard, although it is known that the number of recombinants in a...

Is laparoscopic colorectal cancer surgery associated with an increased risk in obese patients? A retrospective study from China

Xiang Xia 0 Chen Huang 0 Tao Jiang Gang Cen Jun Cao Kejian Huang Zhengjun Qiu 0 Equal contributors Department of General Surgery, Shanghai Jiaotong University Affiliated First People's Hospital

Time-course changes in left ventricular myocardial deformation in STZ-induced rabbits on velocity vector imaging

Objectives To clarify the time-course changes in left ventricular myocardial deformation using velocity vector imaging and to provide insights into our understanding of the cardiac pathophysiology in diabetes mellitus. Methods Thirty New Zealand white rabbits were randomly divided into either the control group (n = 10) or the diabetes mellitus (DM) group (induced with STZ, n = 20...

Isocitrate dehydrogenase 1 Gene Mutation Is Associated with Prognosis in Clinical Low-Grade Gliomas

Isocitrate dehydrogenase 1 gene mutations are found in most World Health Organization grade II and III gliomas and secondary glioblastomas. Isocitrate dehydrogenase 1 mutations are known to have prognostic value in high-grade gliomas. However, their prognostic significance in low-grade gliomas remains controversial. We determined the predictive and prognostic value of isocitrate...

Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter

CLC secondary active transporters exchange Cl- for H+. Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Gluex) upon its protonation. Using 19F NMR, we show that as [H+] is increased to protonate Gluex and enrich the outward-facing state, a residue ~20...

Detecting genome-wide epistases based on the clustering of relatively frequent items

Motivation: In genome-wide association studies (GWAS), up to millions of single nucleotide polymorphisms (SNPs) are genotyped for thousands of individuals. However, conventional single locus-based approaches are usually unable to detect gene–gene interactions underlying complex diseases. Due to the huge search space for complicated high order interactions, many existing multi...

Novel core promoter elements in the oomycete pathogen Phytophthora infestans and their influence on expression detected by genome-wide analysis

Background The core promoter is the region flanking the transcription start site (TSS) that directs formation of the pre-initiation complex. Core promoters have been studied intensively in mammals and yeast, but not in more diverse eukaryotes. Here we investigate core promoters in oomycetes, a group within the Stramenopile kingdom that includes important plant and animal...

Influence of bulking agents on CH4, N2O, and NH3 emissions during rapid composting of pig manure from the Chinese Ganqinfen system

small influence on the loss of total organic carbon, whereas it significantly influenced the loss of total nitrogen. Compliance with ethics guidelines Xiang-ping SUN, Peng LU, Tao JIANG, Frank

Prognostic Significance of Complications after Laparoscopic Colectomy for Colon Cancer

, decision to publish, or preparation of the manuscript. Competing Interests: The co-author Tao Jiang is a PLOS ONE Editorial Board member. The authors confirm that this does not alter their adherence to PLOS

Indian-Ink Perfusion Based Method for Reconstructing Continuous Vascular Networks in Whole Mouse Brain

The topology of the cerebral vasculature, which is the energy transport corridor of the brain, can be used to study cerebral circulatory pathways. Limited by the restrictions of the vascular markers and imaging methods, studies on cerebral vascular structure now mainly focus on either observation of the macro vessels in a whole brain or imaging of the micro vessels in a small...

Structural insights into the assembly of human translesion polymerase complexes

In addition to DNA repair pathways, cells utilize translesion DNA synthesis (TLS) to bypass DNA lesions during replication. During TLS, Y-family DNA polymerase (Polη, Polκ, Polı and Rev1) inserts specific nucleotide opposite preferred DNA lesions, and then Polζ consisting of two subunits, Rev3 and Rev7, carries out primer extension. Here, we report the complex structures of Rev3...

Visual Working Memory Load-Related Changes in Neural Activity and Functional Connectivity

Background Visual working memory (VWM) helps us store visual information to prepare for subsequent behavior. The neuronal mechanisms for sustaining coherent visual information and the mechanisms for limited VWM capacity have remained uncharacterized. Although numerous studies have utilized behavioral accuracy, neural activity, and connectivity to explore the mechanism of VWM...

Uncover disease genes by maximizing information flow in the phenome–interactome network

Motivation: Pinpointing genes that underlie human inherited diseases among candidate genes in susceptibility genetic regions is the primary step towards the understanding of pathogenesis of diseases. Although several probabilistic models have been proposed to prioritize candidate genes using phenotype similarities and protein–protein interactions, no combinatorial approaches have...

Association of TLR2 and TLR4 Polymorphisms with Risk of Cancer: A Meta-Analysis

Backgrounds The activation of Toll-like receptors (TLRs) may be an important event in the immune evasion of tumor cell. Recently, numerous studies have investigated the associations between TLR2 −196 to −174 del and two SNPs of TLR4 (rs4986790 and rs4986791) and the susceptibility to different types of cancer; however, the results remain conflicting. The aim of this study was to...

MultiMSOAR 2.0: An Accurate Tool to Identify Ortholog Groups among Multiple Genomes

The identification of orthologous genes shared by multiple genomes plays an important role in evolutionary studies and gene functional analyses. Based on a recently developed accurate tool, called MSOAR 2.0, for ortholog assignment between a pair of closely related genomes based on genome rearrangement, we present a new system MultiMSOAR 2.0, to identify ortholog groups among...

Oncogene addiction in gliomas: Implications for molecular targeted therapy

Oncogene addiction is a phenomenon that the survival of cancer cells depends on an activated oncogene or inactivation of tumor suppressor gene, and is regarded as the 'Achilles heel' of the successful molecular targeted therapies in cancer. However, the role of oncogene addiction in gliomas has not been elucidated systematically. In this review, we summarize the current...

Characterization of a Novel Dengue Serotype 4 Virus-Specific Neutralizing Epitope on the Envelope Protein Domain III

The dengue virus (DENV) envelope protein domain III (ED3) has been suggested to contain receptor recognition sites and the critical neutralizing epitopes. Up to date, relatively little work has been done on fine mapping of neutralizing epitopes on ED3 for DENV4. In this study, a novel mouse type-specific neutralizing antibody 1G6 against DENV4 was obtained with both prophylactic...

Genetically shaping morphology of the filamentous fungus Aspergillus glaucus for production of antitumor polyketide aspergiolide A

Zhenzhong Yu Weiqiang Zhou Tao Jiang Xiangshan Zhou Yuanxing Zhang 0 Equal contributors State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai 200237

Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons

Background Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with different variable 16S rRNA gene targets and by different sequencing methods has become an intriguing prospect that remains to be evaluated experimentally. Results We...