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https://www.readbyqxmd.com/read/29771282/ac-diamond-v1-accelerating-large-scale-dna-protein-alignment
#1
Huijun Mai, Yifan Zhang, Dinghua Li, Henry Chi-Ming Leung, Ruibang Luo, Chi-Kwong Wong, Hing-Fung Ting, Tak-Wah Lam
Summary: AC-DIAMOND (v1) is a DNA-protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed up the matching between query and reference sequences; second, adopting a compact form of dynamic programming to fully utilize the parallelism of the SIMD capability...
May 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29770145/-%C3%AE-carboline-silver-compound-binding-studies-with-human-serum-albumin-a-comprehensive-multispectroscopic-analysis-and-molecular-modeling-study
#2
Ali Alsalme, Rais Ahmad Khan, Arwa M Alkathiri, Mohd Sajid Ali, Sartaj Tabassum, Mohammed Jaafar, Hamad A Al-Lohedan
β -Carbolines ( β Cs) belong to the naturally occurring alkaloid family, derived from 9H-pyrido[3,4-b]indole, also known as norharmane (Hnor). Knowing the importance of the β Cs alkaloid family in biological processes, a comprehensive binding study is reported of four Ag(I) compounds containing the ligand Hnor and having different counteranions, namely, NO3 - , ClO4 - , BF4 - , and PF6 - , with human serum albumin (HSA) as a model protein. Different approaches like UV-visible, fluorescence spectroscopy, circular dichroism (CD), and molecular docking studies have been used for this purpose...
2018: Bioinorganic Chemistry and Applications
https://www.readbyqxmd.com/read/29769145/phylogenetic-relationships-stage-specific-expression-and-localisation-of-a-unique-family-of-inactive-cysteine-proteases-in-sarcoptes-scabiei
#3
Deepani D Fernando, Simone L Reynolds, Martha Zakrzewski, Ehtesham Mofiz, Anthony T Papenfuss, Deborah Holt, Katja Fischer
BACKGROUND: Scabies is worldwide one of the most common, yet neglected, parasitic skin infections, affecting a wide range of mammals including humans. Limited treatment options and evidence of emerging mite resistance against the currently used drugs drive our research to explore new therapeutic candidates. Previously, we discovered a multicopy family of genes encoding cysteine proteases with their catalytic sites inactivated by mutation (SMIPP-Cs). This protein family is unique in parasitic scabies mites and is absent in related non-burrowing mites...
May 16, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29765317/sodium-tanshinone-iia-sulfonate-decreases-cigarette-smoke-induced-inflammation-and-oxidative-stress-via-blocking-the-activation-of-mapk-hif-1%C3%AE-signaling-pathway
#4
Ruijuan Guan, Jian Wang, Ziying Li, Mingjing Ding, Defu Li, Guihua Xu, Tao Wang, Yuqin Chen, Qian Yang, Zhen Long, Zhou Cai, Chenting Zhang, Xue Liang, Lian Dong, Li Zhao, Haiyun Zhang, Dejun Sun, Wenju Lu
Aberrant activation of hypoxia-inducible factor (HIF)-1α is frequently encountered and promotes oxidative stress and inflammation in chronic obstructive pulmonary disease (COPD). The present study investigated whether sodium tanshinone IIA sulfonate (STS), a water-soluble derivative of tanshinone IIA, can mediate its effect through inhibiting HIF-1α-induced oxidative stress and inflammation in cigarette smoke (CS)-induced COPD in mice. Here, we found that STS improved pulmonary function, ameliorated emphysema and decreased the infiltration of inflammatory cells in the lungs of CS-exposed mice...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29765284/influence-of-serum-leptin-levels-and-q223r-leptin-receptor-polymorphism-on-clinical-characteristic-of-patients-with-rheumatoid-arthritis-from-western-mexico
#5
Luis I Angel-Chávez, Elizabeth Ruelas-Cinco, Jorge Hernández-Bello, Elena Castro, Mirna Vázquez-Villamar, Isela Parra-Rojas, L Michele Brennan-Bourdon, Salvador Muñoz-Barrios, Celia Guerrero-Velázquez, José Francisco Muñoz-Valle
Objective: The aim of the present study was to evaluate the possible association between the Q223R Leptin receptor (LEPR) polymorphism (A>G; rs1137101) and leptin levels in patients with rheumatoid arthritis (RA) from Western Mexico. Methods: A cross-sectional study was performed with 70 RA patients and 74 controls subject (CS). Disease activity was evaluated using DAS28 score, the Q223R LEPR polymorphism was determined by the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and serum leptin levels, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) and rheumatoid factor (RF) were quantified...
April 2018: EJIFCC
https://www.readbyqxmd.com/read/29765063/long-non-coding-rna-expression-patterns-in-lung-tissues-of-chronic-cigarette-smoke-induced-copd-mouse-model
#6
Haiyun Zhang, Dejun Sun, Defu Li, Zeguang Zheng, Jingyi Xu, Xue Liang, Chenting Zhang, Sheng Wang, Jian Wang, Wenju Lu
Long non-coding RNAs (lncRNAs) have critical regulatory roles in protein-coding gene expression. Aberrant expression profiles of lncRNAs have been observed in various human diseases. In this study, we investigated transcriptome profiles in lung tissues of chronic cigarette smoke (CS)-induced COPD mouse model. We found that 109 lncRNAs and 260 mRNAs were significantly differential expressed in lungs of chronic CS-induced COPD mouse model compared with control animals. GO and KEGG analyses indicated that differentially expressed lncRNAs associated protein-coding genes were mainly involved in protein processing of endoplasmic reticulum pathway, and taurine and hypotaurine metabolism pathway...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29763375/chromosomal-architecture-and-placental-expression-of-the-human-growth-hormone-gene-family-are-targeted-by-pre-pregnancy-maternal-obesity
#7
Yan Jin, Hana Vakili, SongYan Liu, Savas Menticoglou, Margaret E Bock, Peter A Cattini
The human (h) placental lactogenic hormone chorionic somatomammotropin (CS) is highly produced during pregnancy and acts as a metabolic adaptor in response to maternal insulin resistance. Maternal obesity can exacerbate this "resistance" and a >75% decrease in CS RNA levels was observed in term placentas from obese versus lean women. The genes coding for hCS (hCS-A and hCS-B) and placental growth hormone (hGH-V) as well as the hCS-L pseudogene and pituitary growth hormone (GH) gene (hGH-N) are located at a single locus on chromosome 17...
May 15, 2018: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29758377/global-insights-of-protein-responses-to-cold-stress-in-plants-signaling-defence-and-degradation
#8
Seyyedeh-Sanam Kazemi-Shahandashti, Reza Maali-Amiri
Cold stress (CS) as one of the unfavorable abiotic tensions proceeds different aspects of plant responses. These responses are generated through CS effects on crucial processes such as photosynthesis, energy metabolism, ROS homeostasis, membrane fluidity and cell wall architecture. As a tolerance response, plants apply proteins in various strategies such as transferring the message of cold entrance named as signaling, producing defensive and protective molecules against the stress and degrading some unfavorable or unnecessary proteins to produce other required ones...
May 4, 2018: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29758019/ginkgo-biloba-l-extract-reduces-h2o2-induced-bone-marrow-mesenchymal-stem-cells-cytotoxicity-by-regulating-mitogen-activated-protein-kinase-mapk-signaling-pathways-and-oxidative-stress
#9
Ao Wang, Qiwei Yang, Qiuju Li, Xiaonan Wang, Shuhong Hao, Jincheng Wang, Ming Ren
BACKGROUND The oxidative stress environment of pathological tissue has an adverse effect on the survival of bone marrow mesenchymal stem cells (BMSCs) transplantation. Ginkgo biloba L. extract (EGB) has a potent antioxidant effect. In this research, we assessed the protective effects of EGB and EGB-Containing Serum (EGB CS) on BMSCs against injury induced by hydrogen peroxide (H2O2). MATERIAL AND METHODS BMSCs were pretreated with EGB or EGB CS and treated with H2O2. The cell counting kit-8 (CCK-8) method was utilized to detect cell viability...
May 14, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29756266/the-analysis-of-false-prolongation-of-the-activated-partial-thromboplastin-time-activator-silica-interference-of-c-reactive-protein
#10
Jie Liu, Fanfan Li, Kuangyi Shu, Tao Chen, Xiaoou Wang, Yaoqi Xie, Shanshan Li, Zhaohua Zhang, Susu Jin, Minghua Jiang
BACKGROUND: To investigate the effect of C-reactive protein on the activated partial thromboplastin time (APTT) (different activators) in different detecting systems. METHODS: The C-reactive protein and coagulation test of 112 patients with the infectious disease were determined by automation protein analyzer IMMAG 800 and automation coagulation analyzer STA-R Evolution, respectively. The pooled plasma APTT with different concentrations of C-reactive protein was measured by different detecting system: STA-R Evolution (activator: silica, kaolin), Sysmex CS-2000i (activator: ellagic acid), and ACL TOP 700 (activator: colloidal silica)...
May 13, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29754632/genetics-of-cushing-s-syndrome
#11
REVIEW
Laura C Hernández-Ramírez, Constantine A Stratakis
The knowledge on the molecular and genetic causes of Cushing's syndrome (CS) has greatly increased in the recent years. Somatic mutations leading to overactive 3',5'-cyclic adenosine monophosphate/protein kinase A and wingless-type MMTV integration site family/beta-catenin pathways are the main molecular mechanisms underlying adrenocortical tumorigenesis. Corticotropinomas are characterized by resistance to glucocorticoid negative feedback, impaired cell cycle control and overexpression of pathways sustaining ACTH secretion...
June 2018: Endocrinology and Metabolism Clinics of North America
https://www.readbyqxmd.com/read/29753202/effects-of-supplementing-corn-silage-with-different-nitrogen-sources-on-ruminal-fermentation-and-microbial-populations-in-vitro
#12
Maren Witzig, Melanie B Lengowski, Karin H R Zuber, Jens Möhring, Markus Rodehutscord
Compared to grass silage (GS)-, corn silage (CS)-based diets appear to increase the efficiency of microbial protein synthesis (EMPS) in the rumen. Opposite results for the EMPS obtained in vitro have raised the question of whether an inadequate supply of amino N for microbes might explain the low EMPS. We examined the effects of supplementation with different N sources in CS on the EMPS and microbial populations in vitro. GS and CS were used as substrates for in vitro incubation. CS was non-supplemented or supplemented with urea, mixed amino acids (AA), peptone, or protein to adjust the N content to that of GS...
May 1, 2018: Anaerobe
https://www.readbyqxmd.com/read/29753087/effects-of-salazosulfapyridine-on-the-profile-of-cell-surface-proteins-revealed-by-biotinylation-of-cell-surface-proteins-and-2-dimentional-electrophoresis
#13
Kazuki Omoteyama, Toshiyuki Sato, Mitsumi Arito, Masaaki Sato, Naoya Suematsu, Manae S Kurokawa, Tomohiro Kato
OBJECTIVE: We investigated effects of salazosulfapyridine (SASP) on the protein profile of cell surface (CS)-proteins of SW982, a human synovial sarcoma cell line, using biotinylation of CS-proteins and 2-dimensional fluorescence difference gel electrophoresis (2D-DIGE). METHODS: SW982 cells were treated with SASP and its metabolites, sulfapyridine (SP) and 5-aminosalicylic acid (5ASA). Then the cells were treated with a membrane-impermeable biotinylating reagent...
May 9, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29752110/evaluation-of-nano-hydrogel-composite-based-on-gelatin-ha-cs-suffused-with-asiatic-acid-zno-and-cuo-nanoparticles-for-second-degree-burns
#14
Thanusha A V, Amit Kumar Dinda, Veena Koul
In the present work, a hydrogel platform composed of biopolymer gelatin, and glycosaminoglycan's (Hyaluronic acid and Chondroitin sulfate) incorporated with Asiatic acid (a triterpenoid) and nanoparticles (Zinc oxide and Copper oxide) has been designed and developed to find out the efficacy of healing in second degree burn wounds in Wistar rats. The developed hydrogel composite has been characterized by physico-chemical methods such as; SEM, swelling, mechanical strength, degradation and drug release kinetics...
August 1, 2018: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/29750912/ras-signalling-in-energy-metabolism-and-rare-human-diseases
#15
REVIEW
L Dard, N Bellance, D Lacombe, R Rossignol
The RAS pathway is a highly conserved cascade of protein-protein interactions and phosphorylation that is at the heart of signalling networks that govern proliferation, differentiation and cell survival. Recent findings indicate that the RAS pathway plays a role in the regulation of energy metabolism via the control of mitochondrial form and function but little is known on the participation of this effect in RAS-related rare human genetic diseases. Germline mutations that hyperactivate the RAS pathway have been discovered and linked to human developmental disorders that are known as RASopathies...
May 8, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29748802/binding-of-cu-co-and-cs-to-fluorescent-components-of-natural-organic-matter-nom-from-three-contrasting-sites
#16
Scott Hume, François Caron, Stefan Siemann
Aqueous natural organic matter (NOM) contains different types of functional groups (carboxylic, phenolic, sulfidic, etc.), and hence could change the speciation of metals in environmental systems. This work is a proof-of-concept study on the interaction of three metals (Cu, Co, and Cs) with NOM using fluorescence spectroscopy. The specific aim was to determine the conditional stability constants for these three metals with NOM optical components, obtained from the quenching of fluorescence signals. Three contrasting water types were sampled in Northern Ontario: a pristine source (Cross Rd...
May 10, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29745830/megadock-web-an-integrated-database-of-high-throughput-structure-based-protein-protein-interaction-predictions
#17
Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
BACKGROUND: Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required...
May 8, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29742419/loss-of-proteostasis-is-a-pathomechanism-in-cockayne-syndrome
#18
Marius Costel Alupei, Pallab Maity, Philipp Ralf Esser, Ioanna Krikki, Francesca Tuorto, Rosanna Parlato, Marianna Penzo, Adrian Schelling, Vincent Laugel, Lorenzo Montanaro, Karin Scharffetter-Kochanek, Sebastian Iben
Retarded growth and neurodegeneration are hallmarks of the premature aging disease Cockayne syndrome (CS). Cockayne syndrome proteins take part in the key step of ribosomal biogenesis, transcription of RNA polymerase I. Here, we identify a mechanism originating from a disturbed RNA polymerase I transcription that impacts translational fidelity of the ribosomes and consequently produces misfolded proteins. In cells from CS patients, the misfolded proteins are oxidized by the elevated reactive oxygen species (ROS) and provoke an unfolded protein response that represses RNA polymerase I transcription...
May 8, 2018: Cell Reports
https://www.readbyqxmd.com/read/29736870/can-we-predict-thrombotic-tendency-in-rheumatoid-arthritis-a-thromboelastographic-analysis-with-rotem
#19
Sümeyye Merve Türk, Döndü Üsküdar Cansu, Hava Üsküdar Teke, Timuçin Kaşifoğlu, O Meltem Akay, Muzaffer Bilgin, Cengiz Korkmaz
The higher incidence of arterial and venous events is well established in patients with rheumatoid arthritis (RA). Our aim here was to investigate whether there is a prothrombotic state in RA patients by using rotational thromboelastometry (ROTEM) method and to demonstrate whether the disease variables play a role in this process. A total of 85 patients who met the 2010 RA classification criteria were consecutively included in the study. The patients with RA who have been using antiaggregant, anticoagulant, or nonsteroidal anti-inflammatory drugs (NSAIDs) and had a history of arterial or venous thromboembolism were excluded from the study...
May 7, 2018: Clinical Rheumatology
https://www.readbyqxmd.com/read/29733382/an-integrative-model-for-alternative-polyadenylation-intmap-delineates-mtor-modulated-endoplasmic-reticulum-stress-response
#20
Jae-Woong Chang, Wei Zhang, Hsin-Sung Yeh, Meeyeon Park, Chengguo Yao, Yongsheng Shi, Rui Kuang, Jeongsik Yong
3'-untranslated regions (UTRs) can vary through the use of alternative polyadenylation sites during pre-mRNA processing. Multiple publically available pipelines combining high profiling technologies and bioinformatics tools have been developed to catalog changes in 3'-UTR lengths. In our recent RNA-seq experiments using cells with hyper-activated mammalian target of rapamycin (mTOR), we found that cellular mTOR activation leads to transcriptome-wide alternative polyadenylation (APA), resulting in the activation of multiple cellular pathways...
May 4, 2018: Nucleic Acids Research
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