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Homology modelling

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https://www.readbyqxmd.com/read/29792968/applicability-of-endochitinase-of-flavobacterium-johnsoniae-with-transglycosylation-activity-in-generating-long-chain-chitooligosaccharides
#1
Papa Rao Vaikuntapu, Mohan Krishna Mallakuntla, Subha Narayan Das, Bhoopal Bhuvanachandra, Bellamkonda Ramakrishna, Sandhya Rani Nadendla, Appa Rao Podile
Chitin and its derivatives are used for a variety of applications. Flavobacterium johnsoniae UW1 is an aerobic Gram-negative bacterium and genome analysis revealed the presence of 10 glycoside hydrolases (GHs) that may degrade or modify chitin. The gene encoding chitinase B (FjchiB), which encodes a single catalytic GH18 domain has been cloned and heterologously expressed in Escherichia coli. FjChiB was optimally active in 50 mM sodium citrate buffer (pH 6.0) at 40 °C. FjChiB was salt-tolerant and catalytically versatile, with substrate specificity towards 75% DDA (degree of de-acetylation) chitosan, followed by colloidal chitin...
May 21, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29792930/functional-genomics-for-the-oleaginous-yeast-yarrowia-lipolytica
#2
Kurt Patterson, James Yu, Jenny Landberg, Ivan Chang, Farbod Shavarebi, Virginia Bilanchone, Suzanne Sandmeyer
Oleaginous yeasts are valuable systems for biosustainable production of hydrocarbon-based chemicals. Yarrowia lipolytica is one of the best characterized of these yeast with respect to genome annotation and flux analysis of metabolic processes. Nonetheless, progress is hampered by a dearth of genome-wide tools enabling functional genomics. In order to remedy this deficiency, we developed a library of Y. lipolytica insertion mutants via transposon mutagenesis. The Hermes DNA transposon was expressed to achieve saturation mutagenesis of the genome...
May 21, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29792847/the-polymorphisms-of-atoh-7-et-1-and-ace-in-non-arteritic-anterior-ischemic-optic-neuropathy
#3
Ting Chen, Jin Ma, Guangliang Shan, Yong Zhong
Non-arteritic anterior ischemic optic neuropathy (NAION) is a common cause of acute optic neuropathy in the elderly. The role of the genetic polymorphisms of Atonal Homolog 7 (ATOH7), Endothelin-1 (ET-1) and Angiotensin Converting Enzyme (ACE) in NAION and the combined effects of the gene-gene and gene-medical comorbidities on NAION were not clear. We conducted a perspective, case-control study. 71 NAION patients and 142 age and sex-matched healthy controls were enrolled. Single nucleotide polymorphisms of ATOH7 (rs1900004), ET-1 (rs5370) and ACE (rs1799752) were identified by polymerase chain reaction (PCR) method and all PCR products were screened with Sanger sequencing...
May 21, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29792386/disparate-effects-of-shb-gene-deficiency-on-disease-characteristics-in-murine-models-of-myeloid-b-cell-and-t-cell-leukemia
#4
Maria Jamalpour, Xiujuan Li, Karin Gustafsson, Jeffrey W Tyner, Michael Welsh
The Src homology-2 domain protein B is an adaptor protein operating downstream of tyrosine kinases. The Shb gene knockout has been found to accelerate p210 Breakpoint cluster region-cAbl oncogene 1 tyrosine kinase-induced leukemia. In human myeloid leukemia were tumors with high Src homology-2 domain protein B mRNA content, tumors were, however, associated with decreased latency and myeloid leukemia exhibiting immune cell characteristics. Thus, the aim of this study was to investigate the effects of Shb knockout on the development of leukemia in three additional models, that is, colony stimulating factor 3 receptor-T618I-induced neutrophilic leukemia, p190 Breakpoint cluster region-cAbl oncogene 1 tyrosine kinase-induced B-cell leukemia, and G12D-Kras-induced T-cell leukemia/thymic lymphoma...
April 2018: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29789360/bat-caliciviruses-and-human-noroviruses-are-antigenically-similar-and-have-overlapping-histo-blood-group-antigen-binding-profiles
#5
Jacob F Kocher, Lisa C Lindesmith, Kari Debbink, Anne Beall, Michael L Mallory, Boyd L Yount, Rachel L Graham, Jeremy Huynh, J Edward Gates, Eric F Donaldson, Ralph S Baric
Emerging zoonotic viral diseases remain a challenge to global public health. Recent surveillance studies have implicated bats as potential reservoirs for a number of viral pathogens, including coronaviruses and Ebola viruses. Caliciviridae represent a major viral family contributing to emerging diseases in both human and animal populations and have been recently identified in bats. In this study, we blended metagenomics, phylogenetics, homology modeling, and in vitro assays to characterize two novel bat calicivirus (BtCalV) capsid sequences, corresponding to strain BtCalV/A10/USA/2009, identified in Perimyotis subflavus near Little Orleans, MD, and bat norovirus...
May 22, 2018: MBio
https://www.readbyqxmd.com/read/29788456/kinact-a-computational-approach-for-predicting-activating-missense-mutations-in-protein-kinases
#6
Carlos H M Rodrigues, David B Ascher, Douglas E V Pires
Protein phosphorylation is tightly regulated due to its vital role in many cellular processes. While gain of function mutations leading to constitutive activation of protein kinases are known to be driver events of many cancers, the identification of these mutations has proven challenging. Here we present Kinact, a novel machine learning approach for predicting kinase activating missense mutations using information from sequence and structure. By adapting our graph-based signatures, Kinact represents both structural and sequence information, which are used as evidence to train predictive models...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788355/swiss-model-homology-modelling-of-protein-structures-and-complexes
#7
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli, Rosalba Lepore, Torsten Schwede
Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788177/gpcrm-a-homology-modeling-web-service-with-triple-membrane-fitted-quality-assessment-of-gpcr-models
#8
Przemyslaw Miszta, Pawel Pasznik, Jakub Jakowiecki, Agnieszka Sztyler, Dorota Latek, Slawomir Filipek
Due to the involvement of G protein-coupled receptors (GPCRs) in most of the physiological and pathological processes in humans they have been attracting a lot of attention from pharmaceutical industry as well as from scientific community. Therefore, the need for new, high quality structures of GPCRs is enormous. The updated homology modeling service GPCRM (http://gpcrm.biomodellab.eu/) meets those expectations by greatly reducing the execution time of submissions (from days to hours/minutes) with nearly the same average quality of obtained models...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788132/freiburg-rna-tools-a-central-online-resource-for-rna-focused-research-and-teaching
#9
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen
The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788004/juvenile-traumatic-brain-injury-results-in-cognitive-deficits-associated-with-impaired-endoplasmic-reticulum-stress-and-early-tauopathy
#10
Michael J Hylin, Ryan C Holden, Aidan C Smith, Aric F Logsdon, Rabia Qaiser, Brandon P Lucke-Wold
The leading cause of death in the juvenile population is trauma, and in particular neurotrauma. The juvenile brain response to neurotrauma is not completely understood. Endoplasmic reticulum (ER) stress has been shown to contribute to injury expansion and behavioral deficits in adult rodents and furthermore has been seen in adult postmortem human brains diagnosed with chronic traumatic encephalopathy. Whether endoplasmic reticulum stress is increased in juveniles with traumatic brain injury (TBI) is poorly delineated...
May 22, 2018: Developmental Neuroscience
https://www.readbyqxmd.com/read/29787771/inhibition-of-pten-protects-pc12-cells-against-oxygen-glucose-deprivation-induced-cell-death-through-mitoprotection
#11
Fereshteh Farajdokht, Gisou Mohaddes, Elham Karimi-Sales, Taiebeh Kafshdooz, Javad Mahmoudi, Seyed Mohsen Aberoumandi, Pouran Karimi
Mitochondria involve in the determination of ischemic neuronal cell fate through regulation of apoptotic and necrotic cell death. Phosphatase and tensin homolog (PTEN) protein negatively regulates Akt/PKB signaling which is the major cell survival pathway. The current study aimed to examine the impact of SF1670, a potent PTEN inhibitor, on mitochondria-mediated cell survival pathways in an in vitro stroke-like model. PC12 cells were exposed to one hour oxygen and glucose deprivation (OGD) followed by different time points of reperfusion (0, 30, 60, 120 and 180 min) and SF1670 treatments...
May 19, 2018: Brain Research
https://www.readbyqxmd.com/read/29787760/in-vivo-gene-correction-with-targeted-sequence-substitution-through-microhomology-mediated-end-joining
#12
Jeong Hong Shin, Soobin Jung, Suresh Ramakrishna, Hyongbum Henry Kim, Junwon Lee
Genome editing technology using programmable nucleases has rapidly evolved in recent years. The primary mechanism to achieve precise integration of a transgene is mainly based on homology-directed repair (HDR). However, an HDR-based genome-editing approach is less efficient than non-homologous end-joining (NHEJ). Recently, a microhomology-mediated end-joining (MMEJ)-based transgene integration approach was developed, showing feasibility both in vitro and in vivo. We expanded this method to achieve targeted sequence substitution (TSS) of mutated sequences with normal sequences using double-guide RNAs (gRNAs), and a donor template flanking the microhomologies and target sequence of the gRNAs in vitro and in vivo...
May 19, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29786750/microrna%C3%A2-20b%C3%A2-5p-promotes-ventricular-remodeling-by-targeting-the-tgf%C3%A2-%C3%AE-smad-signaling-pathway-in-a-rat-model-of-ischemia%C3%A2-reperfusion-injury
#13
Zhao-Guang Liang, Hong Yao, Rong-Sheng Xie, Chun-Lin Gong, Ye Tian
Myocardial ischemic injury results from severe impairment of the coronary blood supply and may lead to metabolic and ultrastructural changes, thereby causing irreversible damage. MicroRNA (miR)‑20b‑5p has been demonstrated to be involved in malignancies of the breast, colorectum, stomach, blood and oropharynx. The present study aimed to investigate the effects of miR‑20b‑5p on ventricular remodeling following myocardial ischemia‑reperfusion (IR) injury in rats by targeting small mothers against decapentaplegic homolog 7 (Smad7) via the transforming growth factor‑β (TGF‑β)/Smad signaling pathway...
May 18, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29786744/mir%C3%A2-133b-regulates-proliferation-and-apoptosis-in-high%C3%A2-glucose%C3%A2-induced-human-retinal-endothelial-cells-by-targeting-ras-homolog-family-member-a
#14
Jun Yao, Jihong Wang, Yong Yao, Kelei Wang, Qianqian Zhou, Ying Tang
The aim of the present study was to investigate the role of microRNA (miR)‑133b in high‑glucose‑induced human retinal endothelial cells (hRECs), particularly regarding its potential targeting of ras homolog family member A (RhoA). To establish the high‑glucose‑induced diabetic retinopathy (DR) model, hRECs were cultured in high‑glucose medium for 1, 2 and 3 days. An Annexin allophycocyanin (APC)/7‑aminoactinomycin D (7‑AAD) staining assay was performed to measure the apoptosis of hRECs. Next, the cells were transfected with miR‑133b inhibitors or mimics, and the cell proliferation and apoptosis were measured by MTT and Annexin‑APC/7‑AAD staining assays, respectively...
May 18, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29786422/mechanisms-regulating-the-association-of-protein-phosphatase-1-with-spinophilin-and-neurabin
#15
Michael C Edler, Asma B Salek, Darryl S Watkins, Harjot Kaur, Cameron W Morris, Bryan K Yamamoto, Anthony J Baucum
Protein phosphorylation is a key mediator of signal transduction, allowing for dynamic regulation of substrate activity. Whereas protein kinases obtain substrate specificity by targeting specific amino acid sequences, serine/threonine phosphatase catalytic subunits are much more promiscuous in their ability to dephosphorylate substrates. To obtain substrate specificity, serine/threonine phosphatases utilize targeting proteins to regulate phosphatase subcellular localization and catalytic activity. Spinophilin and its homolog neurabin are two of the most abundant dendritic spine-localized protein phosphatase 1 (PP1) targeting proteins...
May 22, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29785067/-in-silico-physicochemical-characterization-and-topology-analysis-of-respiratory-burst-oxidase-homolog-rboh-proteins-from-arabidopsis-and-rice
#16
Gurpreet Kaur, Pratap Kumar Pati
NADPH oxidase (NOX) is a key enzyme involved in the production of apoplastic superoxide (O2-), a type of reactive oxygen species (ROS). Plant Noxes are the homologs of mammalian NADPH oxidase's catalytic subunit and are documented as respiratory burst oxidase homologs (Rbohs). A number of studies have reported their diverse functions in combating various stresses and in plant growth and development. In the present study, a total of 19 Rboh proteins (10 from Arabidopsis thaliana and 9 from Oryza sativa Japonica) were analyzed...
2018: Bioinformation
https://www.readbyqxmd.com/read/29785042/inducible-high-efficiency-crispr-cas9-targeted-gene-editing-and-precision-base-editing-in-african-trypanosomes
#17
Eva Rico, Laura Jeacock, Julie Kovářová, David Horn
The Cas9 endonuclease can be programmed by guide RNA to introduce sequence-specific breaks in genomic DNA. Thus, Cas9-based approaches present a range of novel options for genome manipulation and precision editing. African trypanosomes are parasites that cause lethal human and animal diseases. They also serve as models for studies on eukaryotic biology, including 'divergent' biology. Genome modification, exploiting the native homologous recombination machinery, has been important for studies on trypanosomes but often requires multiple rounds of transfection using selectable markers that integrate at low efficiency...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784884/the-effector-gene-xopae-of-xanthomonas-euvesicatoria-85-10-is-part-of-an-operon-and-encodes-an-e3-ubiquitin-ligase
#18
Georgy Popov, Bharat Bhusan Majhi, Guido Sessa
The type III effector XopAE from the Xanthomonas euvesicatoria strain 85-10 ( Xe 85-10) was previously shown to inhibit plant immunity and enhance pathogen-induced disease symptoms. Evolutionary analysis of 60 xopAE alleles ( AEal ) revealed that the xopAE locus is conserved in multiple Xanthomonas species. The majority of xopAE alleles (55 out of 60) encodes a single ORF ( xopAE ), while in 5 alleles, including AEal 37 of the Xe 85-10 strain, a frame-shift splits the locus into two ORFs ( hpaF and a truncated xopAE )...
May 21, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29784881/structural-basis-for-adp-dependent-glucokinase-inhibition-by-8-bromo-substituted-adenosine-nucleotide
#19
Przemyslaw Grudnik, Marcin M Kaminski, Krzysztof P Rembacz, Katarzyna Kuska, Mariusz Madej, Jan Potempa, Maciej Dawidowski, Grzegorz Dubin
In higher eukaryotes, several ATP-utilizing enzymes known as hexokinases activate glucose in the glycolysis pathway by phosphorylation to glucose-6-phosphate. In contrast to canonical hexokinases which use ATP, ADP-dependent glucokinase (ADPGK) catalyzes non-canonical phosphorylation of glucose to glucose-6-phosphate using ADP as a phosphate donor. Initially discovered in Archaea, the human homolog of ADPGK was described only recently. ADPGK's involvement in modified bioenergetics of activated T cells has been postulated and elevated ADPGK expression has been reported in various cancer tissues...
May 21, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29784876/chca-1-is-a-copper-regulated-ctr1-homolog-required-for-normal-development-copper-accumulation-and-copper-sensing-behavior-in-caenorhabditis-elegans
#20
Sai Yuan, Anuj Kumar Sharma, Alexandria Richart, Jaekwon Lee, Byung-Eun Kim
Copper (Cu) plays key roles in catalytic and regulatory biochemical reactions essential for normal growth, development, and health. Dietary Cu deficiencies or mutations in Cu homeostasis genes can lead to abnormal musculoskeletal development, cognitive disorders, and poor growth. In yeast and mammals, Cu is acquired through the activities of the Ctr1 family of high-affinity Cu transporters. However, the mechanisms of systemic responses to dietary or tissue-specific Cu deficiency remain unclear. Here, taking advantage of the animal model Caenorhabditis elegans for studying whole-body Cu homeostasis, we investigated the role of a C...
May 21, 2018: Journal of Biological Chemistry
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