keyword
MENU ▼
Read by QxMD icon Read
search

Structural bioinformatics

keyword
https://www.readbyqxmd.com/read/29792177/investigation-of-the-thermophilic-mechanism-in-the-genus-porphyrobacter-by-comparative-genomic-analysis
#1
Lin Xu, Yue-Hong Wu, Peng Zhou, Hong Cheng, Qian Liu, Xue-Wei Xu
BACKGROUND: Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079T and P. tepidarius DSM 10594T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29790921/mascot-parameter-and-state-inference-under-the-marginal-structured-coalescent-approximation
#2
Nicola F Müller, David Rasmussen, Tanja Stadler
Motivation: The structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many sub-populations, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790909/ebic-an-evolutionary-based-parallel-biclustering-algorithm-for-pattern-discovery
#3
Patryk Orzechowski, Moshe Sipper, Xiuzhen Huang, Jason H Moore
Motivation: Biclustering algorithms are commonly used for gene expression data analysis. However, accurate identification of meaningful structures is very challenging and state-of-the-art methods are incapable of discovering with high accuracy different patterns of high biological relevance. Results: In this paper a novel biclustering algorithm based on evolutionary computation, a subfield of artificial intelligence (AI), is introduced. The method called EBIC aims to detect order-preserving patterns in complex data...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790906/bcseq-an-r-package-for-fast-sequence-mapping-in-high-throughput-shrna-and-crispr-screens
#4
Jiaxing Lin, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S Damrauer, Scott Floyd, Joshua Granek, Andrew Allen, Cliburn Chan, Jichun Xie, Kouros Owzar
Summary: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29787242/membrane-topology-of-trafficking-regulator-of-glut4-1-trarg1
#5
Xiaowen Duan, James Krycer, Kristen Cooke, Guang Yang, David E James, Daniel Fazakerley
Trafficking regulator of GLUT4 1 (TRARG1) was recently identified to localise to glucose transporter type 4 (GLUT4) storage vesicles (GSVs) and to positively regulate GLUT4 trafficking. Our knowledge of TRARG1 structure and membrane topology is limited to predictive models, hampering efforts to further our mechanistic understanding of how it carries out its functions. Here, we use a combination of bioinformatics prediction tools and biochemical assays to define the membrane topology of the 173-amino acid mouse TRARG1...
May 22, 2018: Biochemistry
https://www.readbyqxmd.com/read/29786967/developmental-chromatin-restriction-of-pro-growth-gene-networks-acts-as-an-epigenetic-barrier-to-axon-regeneration-in-cortical-neurons
#6
Ishwariya Venkatesh, Vatsal Mehra, Zimei Wang, Ben Califf, Murray G Blackmore
Axon regeneration in the central nervous system is prevented in part by a developmental decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth ability likely reflects widespread changes in gene expression, but the mechanisms that drive this shift remain unclear. Chromatin accessibility has emerged as a key regulatory mechanism in other cellular contexts, raising the possibility that chromatin structure may contribute to the age-dependent loss of regenerative potential. Here we establish an integrated bioinformatic pipeline that combines analysis of developmentally dynamic gene networks with transcription factor regulation and genome-wide maps of chromatin accessibility...
May 22, 2018: Developmental Neurobiology
https://www.readbyqxmd.com/read/29784931/reconstruction-of-the-diapsid-ancestral-genome-permits-chromosome-evolution-tracing-in-avian-and-non-avian-dinosaurs
#7
Rebecca E O'Connor, Michael N Romanov, Lucas G Kiazim, Paul M Barrett, Marta Farré, Joana Damas, Malcolm Ferguson-Smith, Nicole Valenzuela, Denis M Larkin, Darren K Griffin
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical 'avian-like' karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya...
May 21, 2018: Nature Communications
https://www.readbyqxmd.com/read/29784056/biomarker-micrornas-for-prostate-cancer-metastasis-screened-with-a-network-vulnerability-analysis-model
#8
Yuxin Lin, Feifei Chen, Li Shen, Xiaoyu Tang, Cui Du, Zhandong Sun, Huijie Ding, Jiajia Chen, Bairong Shen
BACKGROUND: Prostate cancer (PCa) is a fatal malignant tumor among males in the world and the metastasis is a leading cause for PCa death. Biomarkers are therefore urgently needed to detect PCa metastatic signature at the early time. MicroRNAs are small non-coding RNAs with the potential to be biomarkers for disease prediction. In addition, computer-aided biomarker discovery is now becoming an attractive paradigm for precision diagnosis and prognosis of complex diseases. METHODS: In this study, we identified key microRNAs as biomarkers for predicting PCa metastasis based on network vulnerability analysis...
May 21, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29783665/identification-of-novel-somatic-tp53-mutations-in-patients-with-high-grade-serous-ovarian-cancer-hgsoc-using-next-generation-sequencing-ngs
#9
Marica Garziera, Erika Cecchin, Vincenzo Canzonieri, Roberto Sorio, Giorgio Giorda, Simona Scalone, Elena De Mattia, Rossana Roncato, Sara Gagno, Elena Poletto, Loredana Romanato, Franca Sartor, Jerry Polesel, Giuseppe Toffoli
Somatic mutations in TP53 are a hallmark of high-grade serous ovarian cancer (HGSOC), although their prognostic and predictive value as markers is not well defined. Next-generation sequencing (NGS) can identify novel mutations with high sensitivity, that may be repurposed as potential druggable anti-cancer targets and aid in therapeutic decisions. Here, a commercial NGS cancer panel comprising 26 genes, including TP53 , was used to identify new genetic markers of platinum resistance and patient prognosis in a retrospective set of patients diagnosed with epithelial ovarian cancer...
May 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29780242/immune-informatic-analysis-and-design-of-peptide-vaccine-from-multi-epitopes-against-corynebacterium-pseudotuberculosis
#10
Daniela Droppa-Almeida, Elton Franceschi, Francine Ferreira Padilha
Caseous lymphadenitis (CLA) is a disease caused by Corynebacterium pseudotuberculosis bacteria that affects sheep and goats. The absence of a serologic diagnose is a factor that contributes for the disease dissemination, and due to the formation of granuloma, the treatment is very expensive. Therefore, prophylaxis is the approach with best cost-benefit relation; however, it still lacks an effective vaccine. In this sense, this work seeks to apply bioinformatic tools to design an effective vaccine against CLA, using CP40 protein as standard for the design of immunodominant epitopes, from which a total of 6 sequences were obtained, varying from 10 to 16 amino acid residues...
2018: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/29779657/collection-culturing-and-genome-analyses-of-tropical-marine-filamentous-benthic-cyanobacteria
#11
Nathan A Moss, Tiago Leao, Evgenia Glukhov, Lena Gerwick, William H Gerwick
Decreasing sequencing costs has sparked widespread investigation of the use of microbial genomics to accelerate the discovery and development of natural products for therapeutic uses. Tropical marine filamentous cyanobacteria have historically produced many structurally novel natural products, and therefore present an excellent opportunity for the systematic discovery of new metabolites via the information derived from genomics and molecular genetics. Adequate knowledge transfer and institutional know-how are important to maintain the capability for studying filamentous cyanobacteria due to their unusual microbial morphology and characteristics...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29778844/identification-of-micrornas-with-heat-stress-responsive-and-immune-properties-in-marsupenaeus-japonicus-based-on-next-generation-sequencing-and-bioinformatics-analysis-essential-regulators-in-the-heat-stress-host-interactions
#12
Jinbin Zheng, Jiawen Cao, Yong Mao, Yongquan Su, Jun Wang
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29777624/characterisation-of-a-putative-glutamate-5-kinase-from-leishmania-donovani
#13
Natasha Sienkiewicz, Han B Ong, Alan H Fairlamb
Previous metabolic studies have demonstrated that leishmania parasites are able to synthesise proline from glutamic acid and threonine from aspartic acid. The first committed step in both biosynthetic pathways involves an amino acid kinase, either a glutamate 5-kinase (EC 2.7.2.11) or an aspartokinase (EC 2.7.2.4). Bioinformatic analysis of multiple leishmania genomes identifies a single amino-acid-kinase gene (LdBPK 262740.1) variously annotated as either a putative glutamate or aspartate kinase. To establish the catalytic function of this Leishmania donovani gene product, we have determined the physical and kinetic properties of the recombinant enzyme purified from Escherichia coli...
May 19, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29775751/expression-pattern-and-functional-analysis-of-the-two-ring-box-protein-rbx-in-spermatogenesis-of-chinese-mitten-crab-eriocheir-sinensis
#14
Jia-Shun Zhang, Xue-Jie Li, Lei Yang, Wei-Wei Li, Qun Wang
Studies in E. sinensis have shown that ubiquitination mediated by Cullin-RING E3 ligases (CRLs) plays important roles in spermatogenesis. In other species, CRLs are also essential in cell cycle progression, DNA replication, signal transduction, gene transcription, and development. The catalytic RING component, the RING box protein, is an important part of CRLs. However, there have been few studies on CRLs in crustaceans. In this study, we cloned two RING box protein genes from the Chinese mitten crab, Eriocheir sinensis, termed Es-RBX1 and Es-RBX2 The full length Es-RBX1 cDNA comprises 741 nucleotides, and encodes a protein of 124 amino acid residues, whereas the Es-RBX2 cDNA comprises 1325 nucleotides, and encodes a protein of 110 amino acid residues...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29775563/anolis-carolinensis-as-a-model-to-understand-molecular-and-cellular-basis-of-foveal-development
#15
Naif S Sannan, Xianghong Shan, Kevin Gregory-Evans, Kenro Kusumi, Cheryl Y Gregory-Evans
The fovea is an anatomical specialization of the central retina containing closely packed cone-photoreceptors providing an area of high acuity vision in humans and primates. Despite its key role in the clarity of vision, little is known about the molecular and cellular basis of foveal development, due to the absence of a foveal structure in commonly used laboratory animal models. Of the amniotes the retina in birds of prey and some reptiles do exhibit a typical foveal structure, but they have not been studied in the context of foveal development due to lack of availability of embryonic tissue, lack of captive breeding programs, and limited genomic information...
May 15, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29775430/gene-expression-profile-analysis-of-aortic-vascular-smooth-muscle-cells-reveals-upregulation-of-cadherin-genes-in-myocardial-infarction-patients
#16
Anselm A Derda, Chin Cheng Woo, Thidathip Wongsurawat, Mark Richards, Chuen Neng Lee, Theo Kofidis, Vladimir A Kuznetsov, Vitaly A Sorokin
Myocardial infarction (MI) induced by acute coronary arterial occlusion is usually secondary to atherosclerotic plaque rupture. Dysregulated response of vascular smooth muscle cells (VSMCs) in atherosclerotic plaques may promote plaque rupture. Cadherins (CDHs) form adherens junctions and are known stabilizers of atherosclerotic plaques. To date, the expression patterns of cadherin have not been well investigated in MI aortic VSMCs. We aimed to investigate the expression of cadherin genes in the aortic wall of patients with and without MI...
May 18, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29775224/circular-rnas-are-differentially-expressed-in-liver-ischemia-reperfusion-injury-model
#17
Zhiqiang Ye, Qinglei Kong, Jianhua Han, Jingyi Deng, Miaolue Wu, Hong Deng
Liver ischemia/reperfusion (I/R) injury has high mortality due to the intense inflammatory process occurs in the liver. However, the pathological mechanism underlying I/R injury is still not clear. Recent works showed that circular RNAs play critical roles in many human diseases. In this study, the occurrence of liver I/R injury was validated by an analysis of the blood samples and hematoxylin-eosin (HE) staining of liver tissues. Total RNA was purified and followed by RNA-seq in the purpose of screening the circRNAs in significant differentially expression, which were validated by quantitative PCR...
May 18, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29774118/proteomic-profiling-of-skeletal-and-cardiac-muscle-in-cancer-cachexia-alterations-in-sarcomeric-and-mitochondrial-protein-expression
#18
Angie M Y Shum, Anne Poljak, Nicholas L Bentley, Nigel Turner, Timothy C Tan, Patsie Polly
Background: Cancer cachexia is observed in more than 50% of advanced cancer patients, and impairs quality of life and prognosis. A variety of pathways are likely to be dysregulated. Hence, a broad-spectrum understanding of the disease process is best achieved by a discovery based approach such as proteomics. Results: More than 300 proteins were identified with > 95% confidence in correct sequence identification, of which 5-10% were significantly differentially expressed in cachectic tissues ( p -value of 0...
April 24, 2018: Oncotarget
https://www.readbyqxmd.com/read/29772753/dietary-polysaccharide-from-enteromorpha-clathrata-modulates-gut-microbiota-and-promotes-the-growth-of-akkermansia-muciniphila-bifidobacterium-spp-and-lactobacillus-spp
#19
Qingsen Shang, Ya Wang, Lin Pan, Qingfeng Niu, Chao Li, Hao Jiang, Chao Cai, Jiejie Hao, Guoyun Li, Guangli Yu
Recently, accumulating evidence has suggested that Enteromorpha clathrata polysaccharide (ECP) could contribute to the treatment of diseases. However, as a promising candidate for marine drug development, although ECP has been extensively studied, less consideration has been given to exploring its effect on gut microbiota. In this light, given the critical role of gut microbiota in health and disease, we investigated here the effect of ECP on gut microbiota using 16S rRNA high-throughput sequencing. As revealed by bioinformatic analyses, ECP considerably changed the structure of the gut microbiota and significantly promoted the growth of probiotic bacteria in C57BL/6J mice...
May 17, 2018: Marine Drugs
https://www.readbyqxmd.com/read/29772751/what-we-do-not-know-about-fungal-cell-adhesion-molecules
#20
REVIEW
Peter N Lipke
There has been extensive research on structure and function of fungal cell adhesion molecules, but the most of the work has been about adhesins in Candida albicans and Saccharomyces cerevisiae. These yeasts are members of a single ascomycete order, and adhesion molecules from the six other fungal phyla are only sparsely described in the literature. In these other phyla, most of the research is at the cellular level, rather than at the molecular level, so there has been little characterization of the adhesion molecules themselves...
May 17, 2018: Journal of Fungi (Basel, Switzerland)
keyword
keyword
13141
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"