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https://www.readbyqxmd.com/read/29156779/selecting-lncrnas-in-gastric-cancer-cells-for-directed-therapy-with-bioactive-peptides-and-chemotherapy-drugs
#1
Wenyan Han, Rui Xiao, Chuanling Zhang, Qimuge Suyila, Xian Li, Xiulan Su
Selecting lncRNAs for directed therapy with bioactive peptides and chemotherapy drugs may be an effective approach to treating gastric cancer (GC). We show genome-scale identification and characterization of differentially expressed lncRNAs in GC cells treated with a novel anti-cancer bioactive peptide (ACBP) and the chemotherapy drug oxaliplatin (ASLB). A total of 17,897 lncRNAs were identified through pairwise comparison, including 2,074 novel lncRNAs. Of those, 1,386 lncRNAs were differentially expressed (over 1...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156585/pan-cellulosomics-of-mesophilic-clostridia-variations-on-a-theme
#2
Bareket Dassa, Ilya Borovok, Vincent Lombard, Bernard Henrissat, Raphael Lamed, Edward A Bayer, Sarah Moraïs
The bacterial cellulosome is an extracellular, multi-enzyme machinery, which efficiently depolymerizes plant biomass by degrading plant cell wall polysaccharides. Several cellulolytic bacteria have evolved various elaborate modular architectures of active cellulosomes. We present here a genome-wide analysis of a dozen mesophilic clostridia species, including both well-studied and yet-undescribed cellulosome-producing bacteria. We first report here, the presence of cellulosomal elements, thus expanding our knowledge regarding the prevalence of the cellulosomal paradigm in nature...
November 18, 2017: Microorganisms
https://www.readbyqxmd.com/read/29156309/recent-development-of-computational-resources-for-new-antibiotics-discovery
#3
REVIEW
Hyun Uk Kim, Kai Blin, Sang Yup Lee, Tilmann Weber
Understanding a complex working mechanism of biosynthetic gene clusters (BGCs) encoding secondary metabolites is a key to discovery of new antibiotics. Computational resources continue to be developed in order to better process increasing volumes of genome and chemistry data, and thereby better understand BGCs. In this context, this review highlights recent advances in computational resources for secondary metabolites with emphasis on genome mining, compound identification and dereplication as well as databases...
November 16, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29155979/epigenetic-editing-of-the-dlg4-psd95-gene-improves-cognition-in-aged-and-alzheimer-s-disease-mice
#4
Fernando J Bustos, Estibaliz Ampuero, Nur Jury, Rodrigo Aguilar, Fahimeh Falahi, Jorge Toledo, Juan Ahumada, Jaclyn Lata, Paula Cubillos, Berta Henríquez, Miguel V Guerra, Jimmy Stehberg, Rachael L Neve, Nibaldo C Inestrosa, Ursula Wyneken, Marco Fuenzalida, Steffen Härtel, Miguel Sena-Esteves, Lorena Varela-Nallar, Marianne G Rots, Martin Montecino, Brigitte van Zundert
The Dlg4 gene encodes for post-synaptic density protein 95 (PSD95), a major synaptic protein that clusters glutamate receptors and is critical for plasticity. PSD95 levels are diminished in ageing and neurodegenerative disorders, including Alzheimer's disease and Huntington's disease. The epigenetic mechanisms that (dys)regulate transcription of Dlg4/PSD95, or other plasticity genes, are largely unknown, limiting the development of targeted epigenome therapy. We analysed the Dlg4/PSD95 epigenetic landscape in hippocampal tissue and designed a Dlg4/PSD95 gene-targeting strategy: a Dlg4/PSD95 zinc finger DNA-binding domain was engineered and fused to effector domains to either repress (G9a, Suvdel76, SKD) or activate (VP64) transcription, generating artificial transcription factors or epigenetic editors (methylating H3K9)...
November 16, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29155478/alternative-polyadenylation-is-involved-in-auxin-based-plant-growth-and-development
#5
Liwei Hong, Congting Ye, Juncheng Lin, Haihui Fu, Xiaohui Wu, Qingshun Q Li
Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, impact of auxin on pre-mRNA posttranscriptional regulation is mostly unknown. By using a poly(A) tag (PAT) sequencing approach, mRNA alternative polyadenylation (APA) profiles after auxin treatment were revealed. We showed that hundreds of poly(A) site clusters (PACs) are affected by auxin at the transcriptome level, where auxin reduces PAC distribution in 5'UTR, but increases in 3'UTR...
November 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29155332/unusual-features-of-the-large-linear-plasmid-psa3239-from-streptomyces-aureofaciens-ccm-3239
#6
Erik Mingyar, Renata Novakova, Renata Knirschova, Lubomira Feckova, Carmen Bekeova, Jan Kormanec
We previously identified the aur1 gene cluster, responsible for the production of the angucycline antibiotic auricin in Streptomyces aureofaciens CCM 3239. Pulse-field gel electrophoresis showed a single, 241kb linear plasmid, pSA3239, in this strain, and several approaches confirmed the presence of the aur1 cluster in this plasmid. We report here the nucleotide sequence of this 241,076-bp plasmid. pSA3239 contains an unprecedentedly small (13bp) telomeric sequence CCCGCGGAGCGGG, which is identical to the conserved Palindrome I sequence involved in the priming of end-patching replication...
November 16, 2017: Gene
https://www.readbyqxmd.com/read/29155089/genotyping-and-macrolide-resistance-of-mycoplasma-pneumoniae-identified-in-children-with-community-acquired-pneumonia-cap-in-medellin-colombia
#7
Angela Rocio Copete, Yudy Alexandra Aguilar, Zulma Vanessa Rueda, Lázaro Agustín Vélez
OBJECTIVES: Our aim was to describe the genotypes and the main characteristics of the CAP cases caused by M. pneumoniae in hospitalized children in Medellin and in neighboring municipalities in 2011-2012. METHODOLOGY: The M. pneumoniae genotype was determined by PCR and sequencing of the p1 and 23S rRNA genes from induced sputum samples and nasopharyngeal swabs (NPS) from children with CAP who were hospitalized in 13 healthcare centers. In addition, a spatio-temporal analysis was performed to identify the potential risk areas and clustering of the cases over time...
November 15, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/29155030/transcriptome-analysis-and-discovery-of-genes-involved-in-immune-pathways-from-coelomocytes-of-onchidium-struma-after-bacterial-challenge
#8
Mingming Zhang, Guo Qiao, Qiang Li, De-Hai Xu, Zhitao Qi, Aiming Wang, Mengyao Xu, Jintian Huang
Onchidium struma widely distributes in subtidal and low-tidal zones, which is considered to be an economical species with rich nutrition, a valuable biomonitor for heavy metal pollution and a representative species for evolution from ocean to land. However, there is limited genetic information available for O. struma development. This study compared transcriptomic profiles of coelomocytes from normal and bacteria infected O. struma by Illumina-based paired-end sequencing to explore the molecular immune mechanism of O...
November 15, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29154789/biosynthesis-of-microcystin-hepatotoxins-in-the-cyanobacterial-genus-fischerella
#9
Karina Heck, Danillo O Alvarenga, Tania K Shishido, Alessandro M Varani, Felipe A Dörr, Ernani Pinto, Leo Rouhiainen, Jouni Jokela, Kaarina Sivonen, Marli F Fiore
Microcystins (MCs) are serine/threonine phosphatase inhibitors synthesized by several members of the phylum Cyanobacteria. Mining the draft genome sequence of the nostocalean MC-producing Fischerella sp. strain CENA161 led to the identification of three contigs containing mcy genes. Subsequent PCR and Sanger sequencing allowed the assembling of its complete biosynthetic mcy gene cluster with 55,016 bases in length. The cluster encoding ten genes (mcyA-J) with a central bidirectional promoter was organized in a similar manner as found in other genera of nostocalean cyanobacteria...
November 14, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/29154167/genetic-clustering-of-depressed-patients-and-normal-controls-based-on-single-nucleotide-variant-proportion
#10
Chenglong Yu, Bernhard T Baune, Ke-Ang Fu, Ma-Li Wong, Julio Licinio
BACKGROUND: Genetic components play important roles in the susceptibility to major depressive disorder (MDD). The rapid development of sequencing technologies is allowing scientists to contribute new ideas for personalized medicine; thus, it is essential to design non-invasive genetic tests on sequencing data, which can help physicians diagnose and differentiate depressed patients and healthy individuals. METHODS: We have recently proposed a genetic concept involving single-nucleotide variant proportion (SNVP) in genes to study MDD...
November 10, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29154013/the-potential-of-the-newly-isolated-thermotolerant-yeast-pichia-kudriavzevii-rz8-1-for-high-temperature-ethanol-production
#11
Nuttaporn Chamnipa, Sudarat Thanonkeo, Preekamol Klanrit, Pornthap Thanonkeo
High potential, thermotolerant, ethanol-producing yeasts were successfully isolated in this study. Based on molecular identification and phylogenetic analysis, the isolated thermotolerant yeasts were clustered in the genera of Pichia kudriavzevii, Candida tropicalis, Candida orthopsilosis, Candida glabrata and Kodamea ohmeri. A comparative study of ethanol production using 160g/L glucose as a substrate revealed several yeast strains that could produce high ethanol concentrations at high temperatures. When sugarcane bagasse (SCB) hydrolysate containing 85g/L glucose was used as a substrate, the yeast strain designated P...
November 4, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29153988/isolation-and-comparative-transcriptome-analysis-of-human-fetal-and-ipsc-derived-cone-photoreceptor-cells
#12
Emily Welby, Jorn Lakowski, Valentina Di Foggia, Dimitri Budinger, Anai Gonzalez-Cordero, Aaron T L Lun, Michael Epstein, Aara Patel, Elisa Cuevas, Kamil Kruczek, Arifa Naeem, Federico Minneci, Mike Hubank, David T Jones, John C Marioni, Robin R Ali, Jane C Sowden
Loss of cone photoreceptors, crucial for daylight vision, has the greatest impact on sight in retinal degeneration. Transplantation of stem cell-derived L/M-opsin cones, which form 90% of the human cone population, could provide a feasible therapy to restore vision. However, transcriptomic similarities between fetal and stem cell-derived cones remain to be defined, in addition to development of cone cell purification strategies. Here, we report an analysis of the human L/M-opsin cone photoreceptor transcriptome using an AAV2/9...
November 14, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/29153522/short-communication-growth-of-dairy-isolates-of-geobacillus-thermoglucosidans-in-skim-milk-depends-on-lactose-degradation-products-supplied-by-anoxybacillus-flavithermus-as-secondary-species
#13
Y Zhao, M Kumar, M P M Caspers, M N Nierop Groot, J M B M van der Vossen, T Abee
Thermophilic bacilli such as Anoxybacillus and Geobacillus are important contaminants in dairy powder products. Remarkably, one of the common contaminants, Geobacillus thermoglucosidans, showed poor growth in skim milk, whereas significant growth of G. thermoglucosidans was observed in the presence of an Anoxybacillus flavithermus dairy isolate. In the present study, we investigated the underlying reason for this growth dependence of G. thermoglucosidans. Whole-genome sequences of 4 A. flavithermus strains and 4 G...
November 15, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29153518/subacute-ruminal-acidosis-affects-fermentation-and-endotoxin-concentration-in-the-rumen-and-relative-expression-of-the-cd14-tlr4-md2-genes-involved-in-lipopolysaccharide-systemic-immune-response-in-dairy-cows
#14
B Stefanska, W Człapa, E Pruszynska-Oszmałek, D Szczepankiewicz, V Fievez, J Komisarek, K Stajek, W Nowak
The first objective of this study was to investigate the effects of subacute ruminal acidosis (SARA) on fermentation, ruminal free lipopolysaccharides (LPS), and expression of the cluster of differentiation 14 (CD14), toll-like receptor 4 (TLR4), and myeloid differentiation protein 2 (MD2) complex in white blood cells involved in the systemic immune response in dairy cows. The second objective was a study of whether increased expression of the LPS receptor complex led to increases in the concentrations of plasma high-density lipoprotein (HDL) and serum Ca...
November 15, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29153399/fungal-gene-cluster-diversity-and-evolution
#15
Jason C Slot
Metabolic gene clusters (MGCs) have provided some of the earliest glimpses at the biochemical machinery of yeast and filamentous fungi. MGCs encode diverse genetic mechanisms for nutrient acquisition and the synthesis/degradation of essential and adaptive metabolites. Beyond encoding the enzymes performing these discrete anabolic or catabolic processes, MGCs may encode a range of mechanisms that enable their persistence as genetic consortia; these include enzymatic mechanisms to protect their host fungi from their inherent toxicities, and integrated regulatory machinery...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29152844/faecal-microbiota-in-dogs-with-multicentric-lymphoma
#16
A Gavazza, G Rossi, G Lubas, M Cerquetella, Y Minamoto, J S Suchodolski
Malignant lymphoma B-cell type is the most common canine haematopoietic malignancy. Changes in intestinal microbiota have been implicated in few types of cancer in humans. The aim of this prospective and case-control study was to determine differences in faecal microbiota between healthy control dogs and dogs with multicentric lymphoma. Twelve dogs affected by multicentric, B-cell, stage III-IV lymphoma, and 21 healthy dogs were enrolled in the study. For each dog, faecal samples were analysed by Illumina sequencing of 16S rRNA genes and quantitative PCR (qPCR) for selected bacterial groups...
November 20, 2017: Veterinary and Comparative Oncology
https://www.readbyqxmd.com/read/29152836/modulation-of-fatty-acid-metabolism-and-immune-suppression-are-features-of-in-vitro-tumour-sphere-formation-in-ontogenetically-distinct-dog-cancers
#17
J-H Kim, A M Frantz, A L Sarver, B H Gorden Klukas, M Lewellen, T D O'Brien, E B Dickerson, J F Modiano
Non-adherent, 3-dimensional sphere formation is used as an in vitro surrogate to evaluate cellular potential for tumour initiation and self-renewal. To determine if a shared molecular program underlies the capacity for sphere formation by cells originating from diverse tumour types, we characterized molecular and functional properties of 10 independent cell lines derived from 3 ontogenetically distinct dog cancers: hemangiosarcoma, osteosarcoma and glial brain tumours. Genome-wide gene expression profiling identified tumour-of-origin-dependent patterns of adjustment to sphere formation in a uniform culture condition...
November 20, 2017: Veterinary and Comparative Oncology
https://www.readbyqxmd.com/read/29152584/large-scale-bioinformatics-analysis-of-bacillus-genomes-uncovers-conserved-roles-of-natural-products-in-bacterial-physiology
#18
Kirk J Grubbs, Rachel M Bleich, Kevin C Santa Maria, Scott E Allen, Sherif Farag, Elizabeth A Shank, Albert A Bowers
Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs...
November 2017: MSystems
https://www.readbyqxmd.com/read/29152580/chromosomal-targeting-by-the-type-iii-a-crispr-cas-system-can-reshape-genomes-in-staphylococcus-aureus
#19
Jing Guan, Wanying Wang, Baolin Sun
CRISPR-Cas (clustered regularly interspaced short palindromic repeat [CRISPR]-CRISPR-associated protein [Cas]) systems can provide protection against invading genetic elements by using CRISPR RNAs (crRNAs) as a guide to locate and degrade the target DNA. CRISPR-Cas systems have been classified into two classes and five types according to the content of cas genes. Previous studies have indicated that CRISPR-Cas systems can avoid viral infection and block plasmid transfer. Here we show that chromosomal targeting by the Staphylococcus aureus type III-A CRISPR-Cas system can drive large-scale genome deletion and alteration within integrated staphylococcal cassette chromosome mec (SCCmec)...
November 2017: MSphere
https://www.readbyqxmd.com/read/29152205/genetic-structure-and-demographic-history-of-lymantria-dispar-linnaeus-1758-lepidoptera-erebidae-in-its-area-of-origin-and-adjacent-areas
#20
Tae Hwa Kang, Sang Hoon Han, Heung Sik Lee
We analyzed the population genetic structure and demographic history of 20 Lymantria dispar populations from Far East Asia using microsatellite loci and mitochondrial genes. In the microsatellite analysis, the genetic distances based on pairwise FST values ranged from 0.0087 to 0.1171. A NeighborNet network based on pairwise FST genetic distances showed that the 20 regional populations were divided into five groups. Bayesian clustering analysis (K = 3) demonstrated the same groupings. The populations in the Korean Peninsula and adjacent regions, in particular, showed a mixed genetic pattern...
November 2017: Ecology and Evolution
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