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Homology modelling

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https://www.readbyqxmd.com/read/28934497/systematic-analysis-of-dna-crosslink-repair-pathways-during-development-and-aging-in-caenorhabditis-elegans
#1
David M Wilson, Matthias Rieckher, Ashley B Williams, Björn Schumacher
DNA interstrand crosslinks (ICLs) are generated by endogenous sources and chemotherapeutics, and pose a threat to genome stability and cell survival. Using Caenorhabditis elegans mutants, we identify DNA repair factors that protect against the genotoxicity of ICLs generated by trioxsalen/ultraviolet A (TMP/UVA) during development and aging. Mutations in nucleotide excision repair (NER) components (e.g. XPA-1 and XPF-1) imparted extreme sensitivity to TMP/UVA relative to wild-type animals, manifested as developmental arrest, defects in adult tissue morphology and functionality, and shortened lifespan...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934487/supernalign-a-new-tool-for-flexible-superposition-of-homologous-rna-structures-and-inference-of-accurate-structure-based-sequence-alignments
#2
Pawel Piatkowski, Jagoda Jablonska, Adriana Zyla, Dorota Niedzialek, Dorota Matelska, Elzbieta Jankowska, Tomasz Walen, Wayne K Dawson, Janusz M Bujnicki
RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in the characterization of functional motifs and in structure prediction by comparative modeling. However, compared to the numerous methods for protein structure superposition, there are few tools dedicated to the superimposing of RNA 3D structures...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934389/the-16p11-2-homologs-fam57ba-and-doc2a-generate-certain-brain-and-body-phenotypes
#3
Jasmine M McCammon, Alicia Blaker-Lee, Xiao Chen, Hazel Sive
Deletion of the 16p11.2 CNV affects 25 core genes and is associated with multiple symptoms affecting brain and body, including seizures, hyperactivity, macrocephaly, and obesity. Available data suggest that most symptoms are controlled by haploinsufficiency of two or more 16p11.2 genes. To identify interacting 16p11.2 genes, we used a pairwise partial loss of function antisense screen for embryonic brain morphology, using the accessible zebrafish model. fam57ba, encoding a ceramide synthase, was identified as interacting with the doc2a gene, encoding a calcium-sensitive exocytosis regulator, a genetic interaction not previously described...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28934241/hla-dr7-and-hla-dq2-transgenic-mouse-strains-tested-as-a-model-system-for-ximelagatran-hepatotoxicity
#4
Hanna Lundgren, Klara Martinsson, Karin Cederbrant, Johan Jirholt, Daniel Mucs, Katja Madeyski-Bengtson, Said Havarinasab, Per Hultman
The oral thrombin inhibitor ximelagatran was withdrawn in the late clinical trial phase because it adversely affected the liver. In approximately 8% of treated patients, drug-induced liver injury (DILI) was expressed as transient alanine transaminase (ALT) elevations. No evidence of DILI had been revealed in the pre-clinical in vivo studies. A whole genome scan study performed on the clinical study material identified a strong genetic association between the major histocompatibility complex alleles for human leucocyte antigens (HLA) (HLA-DR7 and HLA-DQ2) and elevated ALT levels in treated patients...
2017: PloS One
https://www.readbyqxmd.com/read/28933688/v2-from-a-curtovirus-is-a-suppressor-of-post-transcriptional-gene-silencing
#5
Ana P Luna, Edgar A Rodríguez-Negrete, Gabriel Morilla, Liping Wang, Rosa Lozano-Durán, Araceli G Castillo, Eduardo R Bejarano
The suppression of gene silencing is a key mechanism for the success of viral infection in plants. DNA viruses from the Geminiviridae family encode several proteins that suppress transcriptional and post-transcriptional gene silencing (TGS/PTGS). In Begomovirus, the most abundant genus of this family, three out of six genome-encoded proteins, namely C2, C4 and V2, have been shown to suppress PTGS, with V2 being the strongest PTGS suppressor in transient assays. Beet curly top virus (BCTV), the model species for the Curtovirus genus, is able to infect the widest range of plants among geminiviruses...
September 21, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28933646/visualizing-trna-dependent-mistranslation-in-human-cells
#6
Jeremy T Lant, Matthew D Berg, Daniel Hw Sze, Kyle S Hoffman, Ibukunoluwa C Akinpelu, Matthew Turk, Ilka U Heinemann, Martin L Duennwald, Christopher J Brandl, Patrick O'Donoghue
High-fidelity translation and a strictly accurate proteome were originally assumed as essential to life and cellular viability. Yet recent studies in bacteria and eukaryotic model organisms suggest that proteome-wide mistranslation can provide selective advantages and is tolerated in the cell at higher levels than previously thought (one error in 6.9 × 10(-4) in yeast) with a limited impact on phenotype. Previously, we selected a tRNA(Pro) containing a single mutation that induces mistranslation with alanine at proline codons in yeast...
September 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28933591/suppression-of-chrn-endocytosis-by-carbonic-anhydrase-car3-in-the-pathogenesis-of-myasthenia-gravis
#7
Ailian Du, Shiqian Huang, Xiaonan Zhao, Kuan Feng, Shuangyan Zhang, Jiefang Huang, Xiang Miao, Fulvio Baggi, Rennolds S Ostrom, Yanyun Zhang, Xiangjun Chen, Congfeng Xu
Myasthenia gravis is an autoimmune disorder of the neuromuscular junction manifested as fatigable muscle weakness, which is typically caused by pathogenic autoantibodies against postsynaptic CHRN/AChR (cholinergic receptor nicotinic) in the endplate of skeletal muscle. Our previous studies have identified CA3 (carbonic anhydrase 3) as a specific protein insufficient in skeletal muscle from myasthenia gravis patients. In this study, we investigated the underlying mechanism of how CA3 insufficiency might contribute to myasthenia gravis...
September 21, 2017: Autophagy
https://www.readbyqxmd.com/read/28932945/necrostatin-1-mitigates-endoplasmic-reticulum-stress-after-spinal-cord-injury
#8
Shuang Wang, Jin Wu, Yu-Zhe Zeng, Song-Song Wu, Guo-Rong Deng, Zhi-Da Chen, Bin Lin
Necrostatin-1 (Nec-1) has been shown to inhibit necroptosis and convey a significant protective effect after spinal cord injury (SCI). This small molecule inhibitor may reduce tissue damage and restore neurological function by lessening mitochondrial injury after SCI and preserving energy homeostasis. However, the effects of Nec-1 on endoplasmic reticulum stress (ERS)-an important pathological consequence of SCI-are still not clear. The present study investigates the relationship between necroptosis and ERS in a rat model of SCI...
September 20, 2017: Neurochemical Research
https://www.readbyqxmd.com/read/28932931/usefulness-of-zebrafish-larvae-to-evaluate-drug-induced-functional-and-morphological-renal-tubular-alterations
#9
Rita Gorgulho, Raquel Jacinto, Susana S Lopes, Sofia A Pereira, Erin M Tranfield, Gabriel G Martins, Emilio J Gualda, Rico J E Derks, Ana C Correia, Evelyne Steenvoorden, Petra Pintado, Oleg A Mayboroda, Emilia C Monteiro, Judit Morello
Prediction and management of drug-induced renal injury (DIRI) rely on the knowledge of the mechanisms of drug insult and on the availability of appropriate animal models to explore it. Zebrafish (Danio rerio) offers unique advantages for assessing DIRI because the larval pronephric kidney has a high homology with its human counterpart and it is fully mature at 3.5 days post-fertilization. Herein, we aimed to evaluate the usefulness of zebrafish larvae as a model of renal tubular toxicity through a comprehensive analysis of the renal alterations induced by the lethal concentrations for 10% of the larvae for gentamicin, paracetamol and tenofovir...
September 20, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28932816/a-quorum-sensing-system-that-regulates-streptococcus-pneumoniae-biofilm-formation-and-surface-polysaccharide-production
#10
Roger Junges, Gabriela Salvadori, Sudhanshu Shekhar, Heidi A Åmdal, Jimstan N Periselneris, Tsute Chen, Jeremy S Brown, Fernanda C Petersen
Despite vaccines, Streptococcus pneumoniae kills more than a million people yearly. Thus, understanding how pneumococci transition from commensals to pathogens is particularly relevant. Quorum sensing regulates collective behaviors and thus represents a potential driver of commensal-to-pathogen transitions. Rgg/small hydrophobic peptide (SHP) quorum-sensing systems are widespread in streptococci, yet they remain largely uncharacterized in S. pneumoniae. Using directional transcriptome sequencing, we show that the S...
September 2017: MSphere
https://www.readbyqxmd.com/read/28932739/agonist-binding-to-chemosensory-receptors-a-systematic-bioinformatics-analysis
#11
Fabrizio Fierro, Eda Suku, Mercedes Alfonso-Prieto, Alejandro Giorgetti, Sven Cichon, Paolo Carloni
Human G-protein coupled receptors (hGPCRs) constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28932107/bioinformatics-study-of-m-9053g-a-mutation-at-the-atp6-gene-in-relation-to-type-2-diabetes-mellitus-and-cataract-diseases
#12
Iman Permana Maksum, Sandy Risfi Saputra, Nenden Indrayati, Muhammad Yusuf, Toto Subroto
The mitochondrial disease often associated with various illnesses in relation to the activity of cells metabolites and the synthesis of adenosine triphosphate (ATP), including alteration in the mitochondrial DNA. The mutation of m.9053G>A at the ATP6 gene was found in patients with type 2 diabetes mellitus (DM type 2) and cataract. Therefore, this mutation is predicted to be clinical features of the 2 diseases. ATP6 gene encodes protein subunit of ATPase6, a part of ATP synthase, which is important in the electron transfer and proton translocation in intracellular respiration system...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28931965/polymorphisms-in-lncrna-ptenp1-and-the-risk-of-gastric-cancer-in-a-chinese-population
#13
Yugang Ge, Yu He, Mingkun Jiang, Dakui Luo, Xiangkun Huan, Weizhi Wang, Diancai Zhang, Li Yang, Jundong Zhou
Long noncoding RNA (lncRNA) phosphatase and tensin homolog pseudogene 1 (PTENP1) is significantly downregulated in gastric cancer (GC), playing critical roles in GC progression. However, the association between PTENP1 genetic variants and GC risk has not yet been reported. Using TaqMan technology, three lncRNA PTENP1 tag single nucleotide polymorphisms (tagSNPs) (rs7853346 C>G, rs865005 C>T, and rs10971638 G>A) were genotyped in 768 GC patients and 768 cancer-free controls in a Chinese population. We found that subjects with rs7853346 G allele had a remarkably decreased risk of GC, compared with those carrying C allele (P = 0...
2017: Disease Markers
https://www.readbyqxmd.com/read/28931689/vaccination-with-recombinant-parainfluenza-virus-5-expressing-neuraminidase-protects-against-homologous-and-heterologous-influenza-virus-challenge
#14
Alaina J Mooney, Jon D Gabbard, Zhuo Li, Daniel A Dlugolenski, Scott K Johnson, Ralph A Tripp, Biao He, S Mark Tompkins
Seasonal human influenza virus continues to cause morbidity and mortality annually, and highly pathogenic avian influenza (HPAI) along with other emerging influenzas continue to pose pandemic threats. Vaccination is considered the most effective measure for controlling influenza; however, current strategies rely on a precise vaccine match with currently circulating virus strains for efficacy, requiring constant surveillance and regular development of matched vaccines. Current vaccines focus on eliciting specific antibody responses against the hemagglutinin (HA) surface glycoprotein; however, the diversity of HAs across species and antigenic drift of circulating strains enables evasion of virus-inhibiting antibody responses, resulting in vaccine failure...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28931053/identification-and-molecular-characterization-of-a-metagenome-derived-l-lysine-decarboxylase-gene-from-subtropical-soil-microorganisms
#15
Jie Deng, Hua Gao, Zhen Gao, Huaxian Zhao, Ying Yang, Qiaofen Wu, Bo Wu, Chengjian Jiang
L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs...
2017: PloS One
https://www.readbyqxmd.com/read/28930579/using-comparative-genomics-to-decode-the-genetics-of-acaricide-resistance
#16
Janice P Van Zee, Catherine A Hill
The availability of genome assemblies and other genomic resources is facilitating investigations of complex genetic traits for several species of ticks. Understanding the genetics of acaricide resistance is a priority for tick and tick-borne disease control. The synaptic enzyme acetylcholinesterase (ACE) is recognized as the target of organophosphates (OPs) and carbamates, and mutations in ACE have been tied to resistance. Multiple studies support three ACE (ace) loci in R. microplus but the molecular basis of OP-resistance in this tick remains elusive...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28929682/-virtual-screening-for-components-in-chicory-combined-with-cnt2-target-based-on-molecular-docking
#17
Yue Zhou, Bing Zhang, Zhi-Jian Lin, Xiao-Meng Zhang, Fan Li, Hai-Ge Wang, Xue-Jie Wang
To virtual screen the compound of Chicory combined with the concentrative nucleoside transporter 2 (CNT2) in molecular docking technology.The homology model of hCNT2 was produced, and then the Vina software was employed to virtual screen the Chicory compound combined with CNT2. Compared with 7,8,3'-trihydroxyflavone, a CNT2 inhibitors, 23 score higher chicory compounds were hit.Meanwhile, the ten top compounds have been revealed that play important role in decrease the uric level. The bioactivity to CNT2 needs to be investigatedin experiment...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28928895/mir-340-inhibits-triple-negative-breast-cancer-progression-by-reversing-ezh2-mediated-mirnas-dysregulated-expressions
#18
Zhendong Shi, Yang Li, Xiaomin Qian, Yunhui Hu, Jingjing Liu, Sheng Zhang, Jin Zhang
The anti-tumor efficacy of miR-340 has been recently characterized in cancers. However, the underlying mechanisms of miR-340 inhibited cell growth and invasion in triple-negative breast cancer (TNBC) have not been well elucidated. In this study, we found that miR-340 expression was negatively correlated with EZH2 (Enhancer of zeste homolog 2) expression in TNBC tissues and cell lines. Subsequent luciferase reporter assay confirmed that EZH2 was a novel molecule target of miR-340. Upregulated miR-340 levels by mimics transfection significantly inhibited the MDA-MB-231 and MDA-MB-468 breast cancer cells proliferation, invasion and migration, and induced more cell apoptosis...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28928719/the-green-berry-consortia-of-the-sippewissett-salt-marsh-millimeter-sized-aggregates-of-diazotrophic-unicellular-cyanobacteria
#19
Elizabeth G Wilbanks, Verena Salman-Carvalho, Ulrike Jaekel, Parris T Humphrey, Jonathan A Eisen, Daniel H Buckley, Stephen H Zinder
Microbial interactions driving key biogeochemical fluxes often occur within multispecies consortia that form spatially heterogeneous microenvironments. Here, we describe the "green berry" consortia of the Sippewissett salt marsh (Falmouth, MA, United States): millimeter-sized aggregates dominated by an uncultured, diazotrophic unicellular cyanobacterium of the order Chroococcales (termed GB-CYN1). We show that GB-CYN1 is closely related to Crocosphaera watsonii (UCYN-B) and "Candidatus Atelocyanobacterium thalassa" (UCYN-A), two groups of unicellular diazotrophic cyanobacteria that play an important role in marine primary production...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28927382/a-rapid-seamless-method-for-gene-knockout-in-pseudomonas-aeruginosa
#20
Weiliang Huang, Angela Wilks
BACKGROUND: Pseudomonas aeruginosa is a model organism for the study of quorum sensing, biofilm formation, and also leading cause of nosocomial infections in immune compromised patients. As such P. aeruginosa is one of the most well studied organisms in terms of its genetics. However, the construction of gene deletions and replacements in Pseudomonas aeruginosa is relatively time-consuming, requiring multiple steps including suicide vector construction, conjugation, inactivation with insertion of antibiotic resistance cassettes and allelic exchange...
September 19, 2017: BMC Microbiology
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