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https://www.readbyqxmd.com/read/29454184/exploration-and-exploitation-of-the-environment-for-novel-specialized-metabolites
#1
REVIEW
Catarina Loureiro, Marnix H Medema, John van der Oost, Detmer Sipkema
Microorganisms are Nature's little engineers of a remarkable array of bioactive small molecules that represent most of our new drugs. The wealth of genomic and metagenomic sequence data generated in the last decade has shown that the majority of novel biosynthetic gene clusters (BGCs) is identified from cultivation-independent studies, which has led to a strong expansion of the number of microbial taxa known to harbour BGCs. The large size and repeat sequences of BGCs remain a bioinformatic challenge, but newly developed software tools have been created to overcome these issues and are paramount to identify and select the most promising BGCs for further research and exploitation...
February 14, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29454093/silencing-circular-rna-hsa_circ_0000977-suppresses-pancreatic-ductal-adenocarcinoma-progression-by-stimulating-mir-874-3p-and-inhibiting-plk1-expression
#2
Wen-Jie Huang, Yun-Chao Wang, Song-Song Liu, Jia-Li Yang, Shi-Xiang Guo, Li-Jiang Wang, Huai-Zhi Wang, Ying-Fang Fan
Circular RNAs (CircRNAs) are a novel type of endogenous noncoding RNAs that regulate target gene expression by interacting with microRNA (miRNA). Emerging evidence shows that dysregulation of circRNAs plays important roles in biological and pathological processes, including cancer development and progression. The functional role of circRNA in PDAC (pancreatic ductal adenocarcinoma) remains to be investigated. In this study, high throughput microarray assay revealed that hsa_circ_0000977 was aberrantly up-regulated in pancreatic cancer tissues; this was also validated by qRT-PCR...
February 14, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29454089/genome-wide-gene-expression-analysis-of-45-days-pregnant-fetal-cotyledons-vis-a-vis-non-pregnant-caruncles-in-buffalo-bubalus-bubalis
#3
Masoud Lotfan, Syed Azmal Ali, Munnalal Yadav, Suman Chuadhary, Manoj Kumar Jena, Sudarshan Kumar, Ashok Kumar Mohanty
The crosstalk between fetus and mother starts with the onset of placental attachment to the uterus. The cotyledons and caruncles are the two anatomically distinct structures that play a crucial role in this physiological communication. Using Agilent Gene Chip Genome microarray, we measured the expression profile of pregnancy cotyledons in comparison to caruncular reminiscence of the uteri in non-pregnant buffalo (Bubalus bubalis) for the detection of the early post-pregnancy rapid changes in cellular expression of mRNA transcripts...
February 14, 2018: Gene
https://www.readbyqxmd.com/read/29453993/the-tegumental-allergen-like-proteins-of-schistosoma-mansoni-a-biochemical-study-of-smtal4-tal13
#4
Jack Carson, Charlotte M Thomas, Aaron McGinty, Gustavo Takata, David J Timson
Schistosoma mansoni, like other trematodes, expresses a number of unusual calcium binding proteins which consist of an EF-hand domain joined to a dynein light chain-like (DLC-like) domain by a flexible linker. These proteins have been implicated in host immune responses and drug binding. Three members of this protein family from S. mansoni (SmTAL1, SmTAL2 and SmTAL3) have been well characterised biochemically. Here we characterise the remaining family members from this species (SmTAL4-13). All of these proteins form homodimers and all except SmTAL5 bind to calcium and manganese ions...
February 14, 2018: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29453991/identification-of-branched-chain-amino-acid-aminotransferases-active-towards-r-1-phenylethylamine-among-plp-fold-type-iv-transaminases
#5
Ekaterina Yu Bezsudnova, Daria V Dibrova, Alena Yu Nikolaeva, Tatiana V Rakitina, Vladimir O Popov
New class IV transaminases with activity towards L-Leu, which is typical of branched-chain amino acid aminotransferases (BCAT), and with activity towards (R)-(+)-1-phenylethylamine ((R)-PEA), which is typical of (R)-selective (R)-amine:pyruvate transaminases, were identified by bioinformatics analysis, obtained in recombinant form, and analyzed. The values of catalytic activities in the reaction with L-Leu and (R)-PEA are comparable to those measured for characteristic transaminases with the corresponding specificity...
February 14, 2018: Journal of Biotechnology
https://www.readbyqxmd.com/read/29453987/the-role-of-foxq1-in-proliferation-of-human-dental-pulp-stem-cell
#6
Shaoqin Tu, Junming Zheng, Xin Gao, Chenyu Guan, Bin Cai, Lusai Xiang
This study aimed to investigate the role for Foxq1 in proliferation activity regulation of dental pulp stem cells (DPSCs). Proliferation of DPSC was induced by calcium hydroxide, then expression alteration of Foxq1 was evaluated. Lentivirus was employed to manipulate Foxq1 level in DPSC, and proliferation activities were evaluated. To look into mechanism regulating Foxq1 level after calcium hydroxide stimulation, expressions of various microRNAs were evaluated, then bioinformatics study and dual-luciferase study were carried out to confirm targeting relationship between microRNA and Foxq1...
February 14, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29453956/frequent-mutations-of-retnet-genes-in-eohm-further-confirmation-in-325-probands-and-comparison-with-late-onset-high-myopia-based-on-exome-sequencing
#7
Lin Zhou, Xueshan Xiao, Shiqiang Li, Xiaoyun Jia, Qingjiong Zhang
In our previous study, potential pathological mutations of RetNet genes were detected in 23.8% (71/298) of probands with early-onset high myopia (eoHM), based on whole exome sequencing (WES). The current study aimed to confirm this finding in an additional 325 probands with eoHM and to clarify its specificity by comparison of 195 probands with late-onset high myopia (loHM). Variants in the 234 RetNet genes were selected from whole-exome sequencing data and were filtered using multistep bioinformatics analyses...
February 14, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29453813/association-between-two-common-transitions-of-h2bfwt-gene-and-male-infertility-a-case-control-meta-and-structural-analysis
#8
M Teimouri, H Najaran, A Hosseinzadeh, T Mazoochi
H2BFWT is one of the testis-specific histones that plays a fundamental role in spermatogenesis, and single nucleotide polymorphisms (SNPs) in this gene may result in male infertility. This study aimed to investigate the association between -9C>T and 368A>G transitions of H2BFWT gene and male infertility through a case-control, meta-analysis, and a bioinformatics approach. In this case-control study, 490 subjects including 240 idiopathic infertile men and 250 healthy controls were included. The -9C>T and 368A>G SNPs genotyping were performed by a PCR-RFLP method...
February 17, 2018: Andrology
https://www.readbyqxmd.com/read/29453572/proteome-profiling-of-sertoli-cells-using-a-gelc-ms-ms-strategy
#9
Rita Ferreira, Fábio Trindade, Rui Vitorino
Proteomics is a technology that allows to decipher the molecular networks involved in the regulation of biological processes such as spermatogenesis. Sertoli cells (SCs) are key players in the paracrine control of this process. Envisioning to increase the knowledge on the molecular networks harbored in SCs, we propose a methodology based on GeLC-MS/MS for the characterization of these cells' proteome. Proteins are separated by SDS-PAGE hyphenated to HPLC and identified by mass spectrometry. The integration of data with bioinformatics tools such as ClueGO + CluePedia from Cytoscape allows the identification of the biological pathways more prevalent in SCs, and that might be modulated by pathophysiological conditions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29453400/a-survey-of-metastasis-suppressors-in-metazoa
#10
REVIEW
Helena Ćetković, Matija Harcet, Maša Roller, Maja Herak Bosnar
Metastasis suppressors are genes/proteins involved in regulation of one or more steps of the metastatic cascade while having little or no effect on tumor growth. The list of putative metastasis suppressors is constantly increasing although thorough understanding of their biochemical mechanism(s) and evolutionary history is still lacking. Little is known about tumor-related genes in invertebrates, especially non-bilaterians and unicellular relatives of animals. However, in the last few years we have been witnessing a growing interest in this subject since it has been shown that many disease-related genes are already present in simple non-bilateral animals and even in their unicellular relatives...
February 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29453251/a-novel-adipokine-fam19a5-inhibits-postinjury-neointima-formation-through-sphingosine-1-phosphate-receptor-2
#11
Yingbao Wang, Dixin Chen, Yan Zhang, Pingzhang Wang, Can Zheng, Songyang Zhang, Bing Yu, Lu Zhang, Guizhen Zhao, Baihui Ma, Zeyu Cai, Nan Xie, Shiyang Huang, Ziyi Liu, Xiaoning Mo, Youfei Guan, Xian Wang, Yi Fu, Dalong Ma, Ying Wang, Wei Kong
Background -Obesity plays crucial roles in the development of cardiovascular diseases (CVDs). However, the mechanisms that link obesity and CVDs remain elusive. Compelling evidence indicates that adipokines play an important role in obesity-related CVDs. Here, we found a new adipokine named family with sequence similarity 19, member A5 (FAM19A5), a protein with unknown function that was predicted to be distantly related to the CC-chemokine family. We aimed to test whether adipose-derived FAM19A5 regulates vascular pathology upon injury...
February 16, 2018: Circulation
https://www.readbyqxmd.com/read/29452580/measuring-integrated-hiv-dna-ex-vivo-and-in-vitro-provides-insights-about-how-reservoirs-are-formed-and-maintained
#12
REVIEW
Marilia Rita Pinzone, Una O'Doherty
The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained...
February 17, 2018: Retrovirology
https://www.readbyqxmd.com/read/29452392/pbrit-gene-prioritization-by-correlating-functional-and-phenotypic-annotations-through-integrative-data-fusion
#13
Ajay Anand Kumar, Lut Van Laer, Maaike Alaerts, Amin Ardeshirdavani, Yves Moreau, Kris Laukens, Bart Loeys, Geert Vandeweyer, Inanc Birol
Motivation: Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrating Pubmed abstracts, Gene Ontology, Sequence similarities, Mammalian and Human Phenotype Ontology, Pathway, Interactions, Disease Ontology, Gene Association database and Human Genome Epidemiology database, into the prediction model.We explore and address effects of sparsity and inter-feature dependencies within annotation sources, and the impact of bias towards specific annotations...
February 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29452363/structuremapper-a-high-throughput-algorithm-for-analyzing-protein-sequence-locations-in-structural-data
#14
Anssi Nurminen, Vesa P Hytönen, Alfonso Valencia
Motivation: StructureMapper is a high-throughput algorithm for automated mapping of protein primary amino sequence locations to existing three-dimensional protein structures. The algorithm is intended for facilitating easy and efficient utilization of structural information in protein characterization and proteomics. StructureMapper provides an analysis of the identified structural locations that includes surface accessibility, flexibility, protein-protein interfacing, intrinsic disorder prediction, secondary structure assignment, biological assembly information, and sequence identity percentages, among other metrics...
February 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29452334/seed-2-a-user-friendly-platform-for-amplicon-high-throughput-sequencing-data-analyses
#15
Tomáš Vetrovský, Petr Baldrian, Daniel Morais, Bonnie Berger
Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use...
February 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29452232/long-noncoding-rna-pvt1-promotes-emt-via-mediating-microrna-186-targeting-of-twist1-in-prostate-cancer
#16
Zhongwen Chang, Jun Cui, Yongsheng Song
The pathogenesis and the underlying mechanism of endothelial-mesenchymal transition in prostate cancer remain unclear. Plasmacytoma variant translocation 1 (PVT1), a novel long non-coding RNA maps to 8q24.21, and in many tumor studies the up-regulation of PVT1 has already been reported. PVT1 is closely related to tumor cell proliferation, invasion, and metastasis. In this study, we employed a combination of techniques to study the role of PVT1 in prostate cancer, which included bioinformatic analysis, Western blotting and cell migration assays of prostate cancer cell lines...
February 13, 2018: Gene
https://www.readbyqxmd.com/read/29451920/an-upstream-sequence-modulates-phenazine-production-at-the-level-of-transcription-and-translation-in-the-biological-control-strain-pseudomonas-chlororaphis-30-84
#17
Jun Myoung Yu, Dongping Wang, Tessa R Ries, Leland S Pierson, Elizabeth A Pierson
Phenazines are bacterial secondary metabolites and play important roles in the antagonistic activity of the biological control strain P. chlororaphis 30-84 against take-all disease of wheat. The expression of the P. chlororaphis 30-84 phenazine biosynthetic operon (phzXYFABCD) is dependent on the PhzR/PhzI quorum sensing system located immediately upstream of the biosynthetic operon as well as other regulatory systems including Gac/Rsm. Bioinformatic analysis of the sequence between the divergently oriented phzR and phzX promoters identified features within the 5'-untranslated region (5'-UTR) of phzX that are conserved only among 2OHPCA producing Pseudomonas...
2018: PloS One
https://www.readbyqxmd.com/read/29451897/selective-identification-of-somatic-mutations-in-pancreatic-cancer-cells-through-a-combination-of-next-generation-sequencing-of-plasma-dna-using-molecular-barcodes-and-a-bioinformatic-variant-filter
#18
Yoji Kukita, Kazuyoshi Ohkawa, Ryoji Takada, Hiroyuki Uehara, Kazuhiro Katayama, Kikuya Kato
The accuracy of next-generation sequencing (NGS) for detecting tumor-specific mutations in plasma DNA is hindered by errors introduced during PCR/sequencing, base substitutions caused by DNA damage, and pre-existing mutations in normal cells that are present at a low frequency. Here, we performed NGS of genes related to pancreatic cancer (comprising 2.8 kb of genomic DNA) in plasma DNA (average 4.5 ng) using molecular barcodes. The average number of sequenced molecules was 900, and the sequencing depth per molecule was 100 or more...
2018: PloS One
https://www.readbyqxmd.com/read/29451327/microrna-365-modulates-astrocyte-conversion-into-neuron-in-adult-rat-brain-after-stroke-by-targeting-pax6
#19
Jia-Lin Mo, Qi Liu, Zeng-Wei Kou, Kun-Wei Wu, Ping Yang, Xian-Hua Chen, Feng-Yan Sun
Reactive astrocytes induced by ischemia can transdifferentiate into mature neurons. This neurogenic potential of astrocytes may have therapeutic value for brain injury. Epigenetic modifications are widely known to involve in developmental and adult neurogenesis. PAX6, a neurogenic fate determinant, contributes to the astrocyte-to-neuron conversion. However, it is unclear whether microRNAs (miRs) modulate PAX6-mediated astrocyte-to-neuron conversion. In the present study we used bioinformatic approaches to predict miRs potentially targeting Pax6, and transient middle cerebral artery occlusion (MCAO) to model cerebral ischemic injury in adult rats...
February 16, 2018: Glia
https://www.readbyqxmd.com/read/29451210/intravenous-morphine-self-administration-alters-accumbal-microrna-profiles-in-the-mouse-brain
#20
Juhwan Kim, Heh-In Im, Changjong Moon
A significant amount of evidence indicates that microRNAs (miRNAs) play an important role in drug addiction. The nucleus accumbens (NAc) is a critical part of the brain's reward circuit and is involved in a variety of psychiatric disorders, including depression, anxiety, and drug addiction. However, few studies have examined the expression of miRNAs and their functional roles in the NAc under conditions of morphine addiction. In this study, mice were intravenously infused with morphine (0.01, 0.03, 0.3, 1 and 3 mg/kg/infusion) and showed inverted U-shaped response...
January 2018: Neural Regeneration Research
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