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https://www.readbyqxmd.com/read/28231515/computational-tools-for-enzyme-improvement-why-everyone-can-and-should-use-them
#1
REVIEW
Maximilian Ccjc Ebert, Joelle N Pelletier
This review presents computational methods that experimentalists can readily use to create smart libraries for enzyme engineering and to obtain insights into protein-substrate complexes. Computational tools have the reputation of being hard to use and inaccurate compared to experimental methods in enzyme engineering, yet they are essential to probe datasets of ever-increasing size and complexity. In recent years, bioinformatics groups have made a huge leap forward in providing user-friendly interfaces and accurate algorithms for experimentalists...
February 20, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28231327/functionally-focused-algorithmic-analysis-of-high-resolution-microarray-cgh-genomic-landscapes-demonstrates-comparable-genomic-copy-number-aberrations-in-msi-and-mss-sporadic-colorectal-cancer
#2
Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers...
2017: PloS One
https://www.readbyqxmd.com/read/28231302/bioinformatic-prediction-of-g-protein-coupled-receptor-encoding-sequences-from-the-transcriptome-of-the-foreleg-including-the-haller-s-organ-of-the-cattle-tick-rhipicephalus-australis
#3
Sergio Munoz, Felix D Guerrero, Anastasia Kellogg, Andrew M Heekin, Ming-Ying Leung
The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28230851/using-hiclip-to-identify-rna-duplexes-that-interact-with-a-specific-rna-binding-protein
#4
Yoichiro Sugimoto, Anob M Chakrabarti, Nicholas M Luscombe, Jernej Ule
The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28230813/characterization-of-carbonic-anhydrase-9-in-the-alimentary-canal-of-aedes-aegypti-and-its-relationship-to-homologous-mosquito-carbonic-anhydrases
#5
Daniel P Dixon, Leslie Van Ekeris, Paul J Linser
In the mosquito midgut, luminal pH regulation and cellular ion transport processes are important for the digestion of food and maintenance of cellular homeostasis. pH regulation in the mosquito gut is affected by the vectorial movement of the principal ions including bicarbonate/carbonate and protons. As in all metazoans, mosquitoes employ the product of aerobic metabolism carbon dioxide in its bicarbonate/carbonate form as one of the major buffers of cellular and extracellular pH. The conversion of metabolic carbon dioxide to bicarbonate/carbonate is accomplished by a family of enzymes encoded by the carbonic anhydrase gene family...
February 21, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28230768/bioinformatic-analysis-reveals-archaeal-trna-tyr-and-trna-trp-identities-in-bacteria
#6
Takahito Mukai, Noah M Reynolds, Ana Crnković, Dieter Söll
The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA(Tyr) and tRNA(Trp) genes reveal bacterial or archaeal origins...
February 21, 2017: Life
https://www.readbyqxmd.com/read/28230760/bioinformatics-approaches-for-fetal-dna-fraction-estimation-in-noninvasive-prenatal-testing
#7
REVIEW
Xianlu Laura Peng, Peiyong Jiang
The discovery of cell-free fetal DNA molecules in plasma of pregnant women has created a paradigm shift in noninvasive prenatal testing (NIPT). Circulating cell-free DNA in maternal plasma has been increasingly recognized as an important proxy to detect fetal abnormalities in a noninvasive manner. A variety of approaches for NIPT using next-generation sequencing have been developed, which have been rapidly transforming clinical practices nowadays. In such approaches, the fetal DNA fraction is a pivotal parameter governing the overall performance and guaranteeing the proper clinical interpretation of testing results...
February 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28230250/metformin-attenuates-angiotensin-ii-induced-tgf%C3%AE-1-expression-by-targeting-hepatocyte-nuclear-factor-4%C3%AE
#8
Ruifei Chen, Yenan Feng, Jimin Wu, Yao Song, Hao Li, Qiang Shen, Dan Li, Jianshu Zhang, Zhizhen Lu, Han Xiao, Youyi Zhang
BACKGROUND AND PURPOSE: Metformin, a small molecule antihyperglycaemic agent, is well-known as an AMP-activated protein kinase (AMPK) activator and protects against cardiac fibrosis. However, the underlying mechanisms remain elusive. Transforming growth factor-β1 (TGFβ1) is a key cytokine mediating cardiac fibrosis. Here, we investigated the effects of metformin on TGFβ1 production induced by angiotensin II (AngII) and the underlying mechanisms. EXPERIMENTAL APPROACH: Wild-type and AMPKα2(-/-) C57BL/6 mice were subcutaneously injected with metformin or saline and infused with AngII (3 mg kg(-1) day(-1) ) for 7 days...
February 23, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28230206/mirna-21-mediates-the-antiangiogenic-activity-of-metformin-through-targeting-pten-and-smad7-expression-and-pi3k-akt-pathway
#9
Mao Luo, Xiaoyong Tan, Lin Mu, Yulin Luo, Rong Li, Xin Deng, Ni Chen, Meiping Ren, Yongjie Li, Liqun Wang, Jianbo Wu, Qin Wan
Metformin, an anti-diabetic drug commonly used for type 2 diabetes therapy, is associated with anti-angiogenic effects in conditions beyond diabetes. miR-21 has been reported to be involved in the process of angiogenesis. However, the precise regulatory mechanisms by which the metformin-induced endothelial suppression and its effects on miR-21-dependent pathways are still unclear. Bioinformatic analysis and identification of miR-21 and its targets and their effects on metformin-induced antiangiogenic activity were assessed using luciferase assays, quantitative real-time PCR, western blots, scratch assays, CCK-8 assays and tubule formation assays...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230161/robust-high-dimensional-bioinformatics-data-streams-mining-by-odr-iovfdt
#10
Dantong Wang, Simon Fong, Raymond K Wong, Sabah Mohammed, Jinan Fiaidhi, Kelvin K L Wong
Outlier detection in bioinformatics data streaming mining has received significant attention by research communities in recent years. The problems of how to distinguish noise from an exception and deciding whether to discard it or to devise an extra decision path for accommodating it are causing dilemma. In this paper, we propose a novel algorithm called ODR with incrementally Optimized Very Fast Decision Tree (ODR-ioVFDT) for taking care of outliers in the progress of continuous data learning. By using an adaptive interquartile-range based identification method, a tolerance threshold is set...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28229969/microrna-144-inhibits-hepatocellular-carcinoma-cell-proliferation-invasion-and-migration-by-targeting-zfx
#11
Hongbin Bao, Xinguo Li, Hengli Li, Hongli Xing, Binghui Xu, Xianfeng Zhang, Zhaoming Liu
MicroRNA 144 (miR-144), a small non-coding RNA, is frequently dysregulated in human several tumour progression, but its role and the underlying mechanisms in hepatocellular carcinoma (HCC) is poorly investigated. In the present study, the expression of miR-144 was firstly analysed in datasets derived from GSE21362 and TCGA, and then detected in HCC tissues and cell lines by quantitative RT-PCR (qRT-PCR) analysis. MiR-144 was shown to be significantly down-regulated in HCC tissues and cell lines. Subsequently, overexpression of miR-144 was transfected into HCC cell lines so as to investigate its biological function, including MTT, colony formation, and transwell assays...
March 2017: Journal of Biosciences
https://www.readbyqxmd.com/read/28229366/mining-cancer-transcriptomes-bioinformatic-tools-and-the-remaining-challenges
#12
Thomas Milan, Brian T Wilhelm
The development of next-generation sequencing technologies has had a profound impact on the field of cancer genomics. With the enormous quantities of data being generated from tumor samples, researchers have had to rapidly adapt tools or develop new ones to analyse the raw data to maximize its value. While much of this effort has been focused on improving specific algorithms to get faster and more precise results, the accessibility of the final data for the research community remains a significant problem. Large amounts of data exist but are not easily available to researchers who lack the resources and experience to download and reanalyze them...
February 22, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28228978/population-and-clinical-genetics-of-human-transposable-elements-in-the-post-genomic-era
#13
REVIEW
Lavanya Rishishwar, Lu Wang, Evan A Clayton, Leonardo Mariño-Ramírez, John F McDonald, I King Jordan
Recent technological developments-in genomics, bioinformatics and high-throughput experimental techniques-are providing opportunities to study ongoing human transposable element (TE) activity at an unprecedented level of detail. It is now possible to characterize genome-wide collections of TE insertion sites for multiple human individuals, within and between populations, and for a variety of tissue types. Comparison of TE insertion site profiles between individuals captures the germline activity of TEs and reveals insertion site variants that segregate as polymorphisms among human populations, whereas comparison among tissue types ascertains somatic TE activity that generates cellular heterogeneity...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28228760/perturbed-microrna-expression-by-mycobacterium-tuberculosis-promotes-macrophage-polarization-leading-to-pro-survival-foam-cell
#14
Pankaj Kumar Ahluwalia, Rajan Kumar Pandey, Prabodh Kumar Sehajpal, Vijay Kumar Prajapati
Tuberculosis (TB) is one of the prevalent causes of death worldwide, with 95% of these deaths occurring in developing countries, like India. The causative agent, Mycobacterium tuberculosis (MTb) has the tenacious ability to circumvent the host's immune system for its own advantage. Macrophages are one of the phagocytic cells that are central to immunity against MTb. These are highly plastic cells dependent on the milieu and can showcase M1/M2 polarization. M1 macrophages are bactericidal in action, but M2 macrophages are anti-inflammatory in their immune response...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28228536/a-viral-satellite-dna-vector-tylccnv-for-functional-analysis-of-mirnas-and-sirnas-in-plants
#15
Zheng Ju, Dongyan Cao, Chao Gao, Jinhua Zuo, Baiqiang Zhai, Shan Li, Hongliang Zhu, Daqi Fu, Yunbo Luo, Benzhong Zhu
With experimental and bioinformatical methods, numerous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), have been found in plants, and they play vital roles in various biological regulation processes. However, most of these small RNAs remain to be functionally characterized. Until now, only several viral vectors were developed to overexpress miRNAs with limited application in plants. In this study, we reported a new small RNAs overexpression system via viral satellite DNA associated with Tomato yellow leaf curl China virus (TYLCCNV) vector, which could highly overexpress not only artificial and endogenous miRNAs but also endogenous siRNAs in Nicotiana benthamiana...
February 22, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28228490/short-read-whole-genome-sequencing-for-laboratory-based-surveillance-of-bordetella-pertussis
#16
Alex Marchand-Austin, Raymond S W Tsang, Jennifer L Guthrie, Jennifer H Ma, Gillian Lim, Natasha S Crowcroft, Shelley L Deeks, David J Farrell, Frances B Jamieson
Bordetella pertussis (BP) is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of BP acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labour intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole genome sequencing data generated from 40 clinical BP isolates and analyzed using the SRST2 bioinformatic package...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28228481/a-helical-bundle-in-the-n-terminal-domain-of-the-blm-helicase-mediates-dimer-and-potentially-hexamer-formation
#17
Jing Shi, Wei-Fei Chen, Bo Zhang, San-Hong Fan, Xia Ai, Na-Nv Liu, Stephane Rety, Xu-Guang Xi
Helicases play a critical role in processes such as replication or recombination by unwinding double-stranded DNA; mutations of these genes can therefore have devastating biological consequences. In human, mutations in genes of three members of the RecQ family helicases (blm, wrn and recq4) give rise to three strikingly distinctive clinical phenotypes: Bloom syndrome, Werner syndrome and Rothmund-Thomson syndrome, respectively. However, the molecular basis for these varying phenotypic outcomes is unclear, in part because a full mechanistic description of helicase activity is lacking...
February 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28228108/expression-profiling-and-bioinformatic-analyses-suggest-new-target-genes-and-pathways-for-human-hair-follicle-related-micrornas
#18
Lara M Hochfeld, Thomas Anhalt, Céline S Reinbold, Marisol Herrera-Rivero, Nadine Fricker, Markus M Nöthen, Stefanie Heilmann-Heimbach
BACKGROUND: Human hair follicle (HF) cycling is characterised by the tight orchestration and regulation of signalling cascades. Research shows that micro(mi)RNAs are potent regulators of these pathways. However, knowledge of the expression of miRNAs and their target genes and pathways in the human HF is limited. The objective of this study was to improve understanding of the role of miRNAs and their regulatory interactions in the human HF. METHODS: Expression levels of ten candidate miRNAs with reported functions in hair biology were assessed in HFs from 25 healthy male donors...
February 22, 2017: BMC Dermatology
https://www.readbyqxmd.com/read/28227256/binding-affinity-prediction-of-s-cerevisiae-14-3-3-and-gyf-peptide-recognition-domains-using-support-vector-regression
#19
Volkan Uslan, Huseyin Seker, Volkan Uslan, Huseyin Seker, Huseyin Seker, Volkan Uslan
Proteins interact with other proteins and bio-molecules to carry out biological processes in a cell. Computational models help understanding complex biochemical processes that happens throughout the life of a cell. Domain-mediated protein interaction to peptides one such complex problem in bioinformatics that requires computational predictive models to identify meaningful bindings. In this study, domain-peptide binding affinity prediction models are proposed based on support vector regression. Proposed models are applied to yeast bmh 14-3-3 and syh GYF peptide-recognition domains...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227172/path-based-connectivity-for-clustering-genome-sequences
#20
Oznur Sengel, Olcay Kursun, Oznur Sengel, Olcay Kursun, Olcay Kursun, Oznur Sengel
Clustering is an unsupervised data mining tool and in bioinformatics, clustering genome sequences is used to group related biological sequences when there is no additional supervision. Sequence clusters are often related with gene/protein families, which can shed some light onto determining tertiary structures. To extract such hidden and valuable structures in a data set of genome sequences can benefit from better clustering methods such as the recently popular Spectral Clustering. In this study, we apply spectral clustering and its improved variations to sequence clustering task in our efforts to develop a novel approach for improving it...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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