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https://www.readbyqxmd.com/read/28091580/population-expansions-dominate-demographic-histories-of-endemic-and-widespread-pacific-reef-fishes
#1
Erwan Delrieu-Trottin, Stefano Mona, Jeffrey Maynard, Valentina Neglia, Michel Veuille, Serge Planes
Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28073050/genome-wide-identification-of-atp-binding-cassette-abc-transporters-and-their-roles-in-response-to-polycyclic-aromatic-hydrocarbons-pahs-in-the-copepod-paracyclopina-nana
#2
Chang-Bum Jeong, Duck-Hyun Kim, Hye-Min Kang, Young Hwan Lee, Hui-Su Kim, Il-Chan Kim, Jae-Seong Lee
The ATP-binding cassette (ABC) protein superfamily is one of the largest gene families and is highly conserved in all domains. The ABC proteins play roles in several biological processes, including multi-xenobiotic resistance (MXR), by functioning as transporters in the cellular membrane. They also mediate the cellular efflux of a wide range of substrates against concentration gradients. In this study, 37 ABC genes belonging to eight distinct subfamilies were identified in the marine copepod Paracyclopina nana and annotated based on a phylogenetic analysis...
December 30, 2016: Aquatic Toxicology
https://www.readbyqxmd.com/read/28062095/the-liver-transcriptome-of-suckermouth-armoured-catfish-pterygoplichthys-anisitsi-loricariidae-identification-of-expansions-in-defensome-gene-families
#3
Thiago E Parente, Daniel A Moreira, Maithê G P Magalhães, Paula C C de Andrade, Carolina Furtado, Brian J Haas, John J Stegeman, Mark E Hahn
Pterygoplichthys is a genus of related suckermouth armoured catfishes native to South America, which have invaded tropical and subtropical regions worldwide. Physiological features, including an augmented resistance to organic xenobiotics, may have aided their settlement in foreign habitats. The liver transcriptome of Pterygoplichthys anisitsi was sequenced and used to characterize the diversity of mRNAs potentially involved in the responses to natural and anthropogenic chemicals. In total, 66,642 transcripts were assembled...
January 3, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28035596/biosynthesis-and-uptake-of-glycine-betaine-as-cold-stress-response-to-low-temperature-in-fish-pathogen-vibrio-anguillarum
#4
Yue Ma, Qiyao Wang, Xiating Gao, Yuanxing Zhang
Fish pathogen Vibrio anguillarum, a mesophile bacterium, is usually found in estuarine and marine coastal ecosystems worldwide that pose a constant stress to local organism by its fluctuation in salinity as well as notable temperature change. Though V. anguillarum is able to proliferate while maintain its pathogenicity under low temperature (5-18°C), so far, coldadaption molecular mechanism of the bacteria is unknown. In this study, V. anguillarum was found possessing a putative glycine betaine synthesis system, which is encoded by betABI and synthesizes glycine betaine from its precursor choline...
January 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28029654/abcg2-confers-promotion-in-gastric-cancer-through-modulating-downstream-crkl-in-vitro-combining-with-biostatistics-mining
#5
Junqing Wang, Zhou Yunyun, Lu Wang, Xuehua Chen, Zhenggang Zhu
ABCG2, member of ATP-binding cassette (ABC) transporter family, is known as crucial regulator related to multi-drug resistance in human tumors and has recently been putatively studied as human carcinoma cell biomarker. While, effects of ABCG2 on human gastric cancer (GC) has not been illustrated thoroughly. In this study, by applying biostatistics mining methods, we observed that ABCG2 is frequently aberrantly expressed in GC patients through exploring dataset of GSE19826 in NCBI GEO database. Contemporary, extreme up-regulation of ABCG2 was discovered in both GC specimens and cell lines of our center, from which we observed high level of ABCG2 associated with GC clinicopathologic features and poor outcomes...
December 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/28025333/modulation-of-bilirubin-neurotoxicity-by-the-abcb1-transporter-in-the-ugt1-lethal-mouse-model-of-neonatal-hyperbilirubinemia
#6
Luka Bočkor, Giulia Bortolussi, Simone Vodret, Alessandra Iaconcig, Jana Jašprová, Jaroslav Zelenka, Libor Vitek, Claudio Tiribelli, Andrés F Muro
Moderate neonatal jaundice is the most common clinical condition during newborn life. However, a combination of factors may result in acute hyperbilirubinemia, placing infants at risk of developing bilirubin encephalopathy and death by kernicterus. While most risk factors are known, the mechanisms acting to reduce susceptibility to bilirubin neurotoxicity remain unclear. The presence of modifier genes modulating the risk of developing bilirubin-induced brain damage is increasingly being recognised. The Abcb1 and Abcc1 members of the ABC family of transporters have been suggested to have an active role in exporting unconjugated bilirubin from the central nervous system into plasma...
December 25, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28019039/integration-of-gene-expression-and-methylation-to-unravel-biological-networks-in-glioblastoma-patients
#7
Francesco Gadaleta, Kyrylo Bessonov, Kristel Van Steen
The vast amount of heterogeneous omics data, encompassing a broad range of biomolecular information, requires novel methods of analysis, including those that integrate the available levels of information. In this work, we describe Regression2Net, a computational approach that is able to integrate gene expression and genomic or methylation data in two steps. First, penalized regressions are used to build Expression-Expression (EEnet) and Expression-Genomic or Expression-Methylation (EMnet) networks. Second, network theory is used to highlight important communities of genes...
December 26, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/28018382/identification-and-analysis-of-nahco3-stress-responsive-genes-in-wild-soybean-glycine-soja-roots-by-rna-seq
#8
Jinlong Zhang, Jiaxue Wang, Wei Jiang, Juge Liu, Songnan Yang, Junyi Gai, Yan Li
Soil alkalinity is a major abiotic constraint to crop productivity and quality. Wild soybean (Glycine soja) is considered to be more stress-tolerant than cultivated soybean (G. max), and has considerable genetic variation for increasing alkalinity tolerance of soybean. In this study, we analyzed the transcriptome profile in the roots of an alkalinity tolerant wild soybean variety N24852 at 12 and 24 h after 90 mM NaHCO3 stress by RNA-sequencing. Compared with the controls, a total of 449 differentially expressed genes (DEGs) were identified, including 95 and 140 up-regulated genes, and 108 and 135 down-regulated genes at 12 and 24 h after NaHCO3 treatment, respectively...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28012258/functional-defect-of-variants-in-the-adenosine-triphosphate-binding-sites-of-abcb4-and-their-rescue-by-the-cystic-fibrosis-transmembrane-conductance-regulator-potentiator-ivacaftor-vx-770
#9
Jean-Louis Delaunay, Alix Bruneau, Brice Hoffmann, Anne-Marie Durand-Schneider, Véronique Barbu, Emmanuel Jacquemin, Michèle Maurice, Chantal Housset, Isabelle Callebaut, Tounsia Aït-Slimane
: ABCB4 (MDR3) is an adenosine triphosphate (ATP)-binding cassette (ABC) transporter expressed at the canalicular membrane of hepatocytes, where it mediates phosphatidylcholine (PC) secretion. Variations in the ABCB4 gene are responsible for several biliary diseases, including progressive familial intrahepatic cholestasis type 3 (PFIC3), a rare disease that can be lethal in the absence of liver transplantation. In this study, we investigated the effect and potential rescue of ABCB4 missense variations that reside in the highly conserved motifs of ABC transporters, involved in ATP binding...
November 5, 2016: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/27997355/role-of-abc-transporters-in-the-pathology-of-alzheimer-s-disease
#10
Yan Zhao, Deren Hou, Xialu Feng, Fangbo Lin, Jing Luo
The ATP-binding cassette (ABC) transporter superfamily is a large family of proteins that transport specific molecules across membranes. These proteins are associated with both cholesterol metabolism and Alzheimer's disease (AD). Cholesterol homeostasis has a key role in AD, and ABC transporters are important mediators of lipid transportation. Emerging evidence suggests that decreased expression and hypofunction of ABC transporters are crucial to the occurrence and development of AD. In the present article, we review the current knowledge regarding ABC transporters and speculate on their role in the pathogenesis of AD...
December 20, 2016: Reviews in the Neurosciences
https://www.readbyqxmd.com/read/27994018/a-conserved-abc-transport-system-regulated-by-the-general-stress-response-pathways-of-alpha-and-gammaproteobacteria
#11
Julien Herrou, Jonathan W Willett, Daniel M Czyż, Gyorgy Babnigg, Youngchang Kim, Sean Crosson
: Brucella abortus σ(E1) is an EcfG-family sigma factor that regulates transcription of dozens of genes in response to diverse stress conditions, and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon, bab1_0223-bab1_0226, is among the most highly activated gene sets in the σ(E1) regulon. The proteins encoded by this operon resemble quaternary ammonium compatible solute importers, but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized...
December 19, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27981238/new-insights-into-autoinducer-2-signaling-as-a-virulence-regulator-in-a-mouse-model-of-pneumonic-plague
#12
Eric C Fitts, Jourdan A Andersson, Michelle L Kirtley, Jian Sha, Tatiana E Erova, Sadhana Chauhan, Vladimir L Motin, Ashok K Chopra
The Enterobacteriaceae family members, including the infamous Yersinia pestis, the causative agent of plague, have a highly conserved interbacterial signaling system that is mediated by the autoinducer-2 (AI-2) quorum-sensing molecule. The AI-2 system is implicated in regulating various bacterial virulence genes in diverse environmental niches. Deletion of the gene encoding the synthetic enzyme for the AI-2 substrate, luxS, leads to either no significant change or, paradoxically, an increase in in vivo bacterial virulence...
November 2016: MSphere
https://www.readbyqxmd.com/read/27977217/identification-and-characterization-of-trimethylamine-n-oxide-uptake-and-efflux-transporters
#13
Wendy A Teft, Bridget L Morse, Brenda F Leake, Aze Wilson, Sara E Mansell, Robert A Hegele, Richard H Ho, Richard B Kim
Trimethylamine-N-oxide (TMAO) is a recently identified predictor of cardiovascular and chronic kidney disease. TMAO is primarily generated through gut-microbiome mediated conversion of dietary choline and carnitine to TMA, which is converted to TMAO by hepatic flavin monooxygenase 3 (FMO3) and subsequently undergoes renal elimination. We investigated the role of uptake and efflux drug transporters in TMAO disposition in vitro and in vivo. After screening a large array of uptake transporters, we show organic cation transporter 2 (OCT2) is the key transporter for TMAO cellular uptake...
January 3, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/27912062/atomic-structure-of-the-cystic-fibrosis-transmembrane-conductance-regulator
#14
Zhe Zhang, Jue Chen
The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27907212/diffuse-large-b-cell-lymphoma-cell-line-u-2946-model-for-mcl1-inhibitor-testing
#15
Hilmar Quentmeier, Hans G Drexler, Vivien Hauer, Roderick A F MacLeod, Claudia Pommerenke, Cord C Uphoff, Margarete Zaborski, Mattias Berglund, Gunilla Enblad, Rose-Marie Amini
Diffuse large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma worldwide. We describe the establishment and molecular characteristics of the DLBCL cell line U-2946. This cell line was derived from a 52-year-old male with DLBCL. U-2946 cells carried the chromosomal translocation t(8;14) and strongly expressed MYC, but not the mature B-cell lymphoma associated oncogenes BCL2 and BCL6. Instead, U-2946 cells expressed the antiapoptotic BCL2 family member MCL1 which was highly amplified genomically (14n)...
2016: PloS One
https://www.readbyqxmd.com/read/27906699/reversal-effects-of-local-anesthetics-on-p-glycoprotein-mediated-cancer-multidrug-resistance
#16
Yong Hu, Xiaobing Qin, Haixia Cao, Shaorong Yu, Jifeng Feng
The existence of multidrug resistance (MDR) is the main reason for failure in cancer chemotherapy. The main mechanism of MDR is the overexpression of P-glycoprotein (P-gp). P-gp, a 170 kDa transmembrane phosphorylated glycoprotein encoded by ABCB1 belonging to a member of the ATP-binding cassette (ABC) super-family of the membrane transporters, is also known as the MDR protein. Local anesthetics (LAs) are a major contributor to medical practice. As a cornerstone of analgesia, LAs provides myriad benefits...
November 30, 2016: Anti-cancer Drugs
https://www.readbyqxmd.com/read/27902408/sequencing-rare-marine-actinomycete-genomes-reveals-high-density-of-unique-natural-product-biosynthetic-gene-clusters
#17
Michelle A Schorn, Mohammad M Alanjary, Kristen Aguinaldo, Anton Korobeynikov, Sheila Podell, Nastassia Patin, Tommie Lincecum, Paul R Jensen, Nadine Ziemert, Bradley S Moore
Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases...
December 2016: Microbiology
https://www.readbyqxmd.com/read/27901114/genome-wide-diversity-and-association-mapping-for-capsaicinoids-and-fruit-weight-in-capsicum-annuum-l
#18
Padma Nimmakayala, Venkata L Abburi, Thangasamy Saminathan, Suresh B Alaparthi, Aldo Almeida, Brittany Davenport, Marjan Nadimi, Joshua Davidson, Krittika Tonapi, Lav Yadav, Sridhar Malkaram, Gopinath Vajja, Gerald Hankins, Robert Harris, Minkyu Park, Doil Choi, John Stommel, Umesh K Reddy
Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27886333/association-between-the-polymorphisms-in-the-atp-binding-cassette-genes-abcb1-and-abcc2-and-the-risk-of-drug-resistant-epilepsy-in-a-chinese-han-population
#19
T Xue, Z N Lu
Epilepsy is a common disease of the nervous system; approximately 20-30% of all patients with epilepsy are reported resistant to antiepileptic drugs. ABCB1 and ABCC2 are members of ATP-binding cassette transporter (ABC) family that is involved in the excretion of antiepileptic drugs. In this case-control study, we have investigated the role of ABCB1 rs1045642 and rs2032582 and ABCC2 rs2273697 and rs717620 single nucleotide polymorphisms in antiepileptic drug-resistance in patients with epilepsy. A total of 254 patients with epilepsy (104 drug-resistant and 150 drug-responsive) were recruited from the People's Hospital of Wuhan University between March 2013 and April 2014...
November 25, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27859397/global-transcriptomic-response-of-anoxybacillus-sp-sk-3-4-to-aluminum-exposure
#20
Jia Chun Lim, Suganthi Thevarajoo, Chitra Selvaratnam, Kian Mau Goh, Mohd Shahir Shamsir, Zaharah Ibrahim, Chun Shiong Chong
Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L(-1) of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture...
November 17, 2016: Journal of Basic Microbiology
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