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https://www.readbyqxmd.com/read/28944589/evolution-of-gene-expression-after-whole-genome-duplication-new-insights-from-the-spotted-gar-genome
#1
Jeremy Pasquier, Ingo Braasch, Peter Batzel, Cedric Cabau, Jérome Montfort, Thaovi Nguyen, Elodie Jouanno, Camille Berthelot, Christophe Klopp, Laurent Journot, John H Postlethwait, Yann Guiguen, Julien Bobe
Whole-genome duplications (WGDs) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however, remains incomplete. Teleost fish experienced a common WGD (teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of all vertebrate species. The analysis of gene expression patterns following TGD at the genome level has been limited by the lack of suitable genomic resources. The recent concomitant release of the genome sequence of spotted gar (a representative of holosteans, the closest-related lineage of teleosts that lacks the TGD) and the tissue-specific gene expression repertoires of over 20 holostean and teleostean fish species, including spotted gar, zebrafish, and medaka (the PhyloFish project), offers a unique opportunity to study the evolution of gene expression following TGD in teleosts...
September 25, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28943840/corrigendum-divergent-neuroinflammatory-regulation-of-microglial-trem-expression-and-involvement-of-nf-%C3%AE%C2%BAb
#2
Rosie Owens, Kathleen Grabert, Claire L Davies, Alessio Alfieri, Jack P Antel, Luke M Healy, Barry W McColl
[This corrects the article on p. 56 in vol. 11, PMID: 28303091.].
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28942298/immunohistochemical-expression-profiles-of-cell-adhesion-molecules-matrix-metalloproteinases-and-their-tissue-inhibitors-in-central-and-peripheral-neoplastic-foci-of-feline-mammary-carcinoma
#3
S Pisamai, A Rungsipipat, N Kunnasut, G Suriyaphol
Feline mammary carcinoma (FMC) is a common cancer with high metastatic potential and high mortality rate. Loss of cell-cell interactions and degradation of the extracellular matrix by proteinases enhances tumour invasion and metastasis. Peripheral neoplastic foci (PNF) are defined as the presence of discrete tumour cell clusters, splitting off from central neoplastic foci (CNF) and lodging around these CNF. PNF therefore locate at the tumour-host interface at the site of invasion. The aim of this study was to evaluate immunohistochemically the expression of cell adhesion molecules (e-cadherin [CDH-1], syndecan 1 [SDC-1] and nectin-2), matrix metalloproteinases (matrix metalloproteinase [MMP]-2, MMP-7 and MMP-9) and their tissue inhibitors (tissue inhibitor of matrix metalloproteinase [TIMP]-1 and TIMP-2) together with the cellular proliferation marker, Ki67, in CNF and PNF of FMCs of different clinical stages and histological grades...
August 2017: Journal of Comparative Pathology
https://www.readbyqxmd.com/read/28942194/the-2-oxoglutarate-carrier-promotes-liver-cancer-by-sustaining-mitochondrial-gsh-despite-cholesterol-loading
#4
Anna Baulies, Joan Montero, Nuria Matías, Naroa Insausti, Oihana Terrones, Gorka Basañez, Carmen Vallejo, Laura Conde de La Rosa, Laura Martinez, David Robles, Albert Morales, Joaquin Abian, Montserrat Carrascal, Keigo Machida, Dinesh B U Kumar, Hidekazu Tsukamoto, Neil Kaplowitz, Carmen Garcia-Ruiz, José C Fernández-Checa
Cancer cells exhibit mitochondrial cholesterol (mt-cholesterol) accumulation, which contributes to cell death resistance by antagonizing mitochondrial outer membrane (MOM) permeabilization. Hepatocellular mt-cholesterol loading, however, promotes steatohepatitis, an advanced stage of chronic liver disease that precedes hepatocellular carcinoma (HCC), by depleting mitochondrial GSH (mGSH) due to a cholesterol-mediated impairment in mGSH transport. Whether and how HCC cells overcome the restriction of mGSH transport imposed by mt-cholesterol loading to support mGSH uptake remains unknown...
September 14, 2017: Redox Biology
https://www.readbyqxmd.com/read/28940959/biochemical-and-structural-characterization-of-cyp109a2-a-vitamin-d3-25-hydroxylase-from-bacillus-megaterium
#5
Ammar Abdulmughni, Ilona K Jóźwik, Elisa Brill, Frank Hannemann, Andy-Mark W H Thunnissen, Rita Bernhardt
Cytochrome P450 enzymes are increasingly investigated due to their potential application as biocatalysts with high regio- and/or stereo-selectivity and under mild conditions. Vitamin D3 metabolites are of pharmaceutical importance and are applied for the treatment of vitamin D3 deficiency and other disorders. However, the chemical synthesis of vitamin D3 derivatives shows low specificity and low yields. In this study, cytochrome P450 CYP109A2 from Bacillus megaterium DSM319 was expressed, purified and shown to oxidize vitamin D3 with high regio-selectivity...
September 22, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28940688/clinical-values-of-circular-rna-0000181-in-the-screening-of-gastric-cancer
#6
Qianfu Zhao, Shijun Chen, Tianwen Li, Bingxiu Xiao, Xinjun Zhang
BACKGROUND: Circular RNAs (circRNAs) are recently found involved in cancer occurrence and development. However, their values in the diagnosis of gastric cancers are largely unknown. In this study, we analyzed the values of hsa_circ_0000181 in the diagnosis of gastric cancer. METHODS: Using divergent primers, hsa_circ_0000181 expression levels in fresh gastric cancer tissues and paired adjacent non-tumorous tissues, and plasmas from patient with gastric cancer and health people were detected by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR)...
September 22, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28938869/chemosensory-gene-expression-in-olfactory-organs-of-the-anthropophilic-anopheles-coluzzii-and-zoophilic-anopheles-quadriannulatus
#7
G Athrey, L V Cosme, Z Popkin-Hall, S Pathikonda, W Takken, M A Slotman
BACKGROUND: Anopheles (An.) coluzzii, one of Africa's primary malaria vectors, is highly anthropophilic. This human host preference contributes greatly to its ability to transmit malaria. In contrast, the closely related An. quadriannulatus prefers to feed on bovids and is not thought to contribute to malaria transmission. The diverged preference for host odor profiles between these sibling species is likely reflected in chemosensory gene expression levels in the olfactory organs. Therefore, we compared the transcriptomes of the antennae and maxillary palps between An...
September 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28938404/the-transcriptome-of-estrogen-independent-mammary-growth-in-female-mice-reveals-that-not-all-mammary-glands-are-created-equally
#8
Grace E Berryhill, Danielle G Lemay, Josephine F Trott, Lucila Aimo, Adam L Lock, Russell C Hovey
Allometric growth of ducts in the mammary glands (MG) is widely-held to be estrogen (E)-dependent. We previously discovered that the dietary fatty acid trans-10, cis-12 conjugated linoleic acid (CLA) stimulates E-independent allometric growth and TEB formation in ovariectomized mice. Given the similar phenotype induced by E and CLA, we investigated the shared and/or divergent mechanisms underlying these changes. We confirmed MG growth induced by CLA is temporally distinct from that elicited by E, then used RNA-Sequencing to compare the transcriptome of the MG during similar proliferative and morphological states...
July 27, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938001/cell-cycle-stage-specific-transcriptional-activation-of-cyclins-mediated-by-hat2-dependant-h4k10-acetylation-of-promoters-in-leishmania-donovani
#9
Udita Chandra, Aarti Yadav, Devanand Kumar, Swati Saha
Chromatin modifications affect several processes. In investigating the Leishmania donovani histone acetyltransferase HAT2, using in vitro biochemical assays and HAT2-heterozygous genomic knockout we found the constitutively nuclear HAT2 acetylated histone H4K10 in vitro and in vivo. HAT2 was essential. HAT2-depleted cells displayed growth and cell cycle defects, and poor survival in host cells. Real time PCR and DNA microarray analyses, as well as rescue experiments, revealed that downregulation of cyclins CYC4 and CYC9 were responsible for S phase and G2/M defects of HAT2-depleted cells respectively...
September 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28935753/mechanisms-of-transmission-ratio-distortion-at-hybrid-sterility-loci-within-and-between-mimulus-species
#10
Rachel E Kerwin, Andrea L Sweigart
Hybrid incompatibilities are a common correlate of genomic divergence and a potentially important contributor to reproductive isolation. However, we do not yet have a detailed understanding of how hybrid incompatibility loci function and evolve within their native species, or why they are dysfunctional in hybrids. Here, we explore these issues for a well-studied, two-locus hybrid incompatibility between hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2) in the closely related yellow monkeyflower species Mimulus guttatus and M...
September 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28935583/role-of-elasmobranchs-and-holocephalans-in-understanding-peptide-evolution-in-the-vertebrates-lessons-learned-from-gonadotropin-releasing-hormone-gnrh-and-corticotropin-releasing-factor-crf-phylogenies
#11
REVIEW
David A Lovejoy, Ola M Michalec, David W Hogg, David I Wosnick
The cartilaginous fishes (Class Chondrichthyes) comprise two morphologically distinct subclasses; Elasmobranchii and Holocephali. Evidence indicates early divergence of these subclasses, suggesting monophyly of their lineage. However, such a phylogenetic understanding is not yet developed within two highly conserved peptide lineages, GnRH and CRF. Various GnRH forms exist across the Chondrichthyes. Although 4-7 immunoreactive forms have been described in Elasmobranchii, only one has been elucidated in Holocephali...
September 18, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28934927/evolution-and-expression-analysis-reveal-the-potential-role-of-the-hd-zip-gene-family-in-regulation-of-embryo-abortion-in-grapes-vitis-vinifera-l
#12
Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang, Yan Xu
BACKGROUND: The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs. RESULTS: A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#13
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28930519/divergent-impact-of-gender-in-advancement-of-liver-injuries-diseases-and-carcinogenesis
#14
Subhrajit Biswas, Sampa Ghose
Several investigations have revealed that liver diseases exhibit gender biases, but identifying the root causes of such biases has been challenging. Evidence of gender differences in liver function is present from the early stage of embryonic development. The differences in access to care and treatment as well as diagnostic deliberation may affect gender-specific differences in liver disease progression. Apart from the pathogenesis, xenobiotic metabolism, immune responses, gene expressions, mitochondrial function, lipid composition, and enzyme activities also differ in this sexually dimorphic organ...
January 1, 2018: Frontiers in Bioscience (Scholar Edition)
https://www.readbyqxmd.com/read/28929377/opposing-roles-of-the-aldo-keto-reductases-akr1b1-and-akr1b10-in-colorectal-cancer
#15
Betul Taskoparan, Esin Gulce Seza, Secil Demirkol, Sinem Tuncer, Milan Stefek, Ali Osmay Gure, Sreeparna Banerjee
PURPOSE: Aldo-keto reductases (including AKR1B1 and AKR1B10) constitute a family of oxidoreductases that have been implicated in the pathophysiology of diabetes and cancer, including colorectal cancer (CRC). Available data indicate that, despite their similarities in structure and enzymatic functions, their roles in CRC may be divergent. Here, we aimed to determine the expression and functional implications of AKR1B1 and AKR1B10 in CRC. METHODS: AKR1B1 and AKR1B10 gene expression levels were analyzed using publicly available microarray data and ex vivo CRC-derived cDNA samples...
September 19, 2017: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/28929376/divergent-coronary-flow-responses-to-uridine-adenosine-tetraphosphate-in-atherosclerotic-apoe-knockout-mice
#16
Bunyen Teng, Hicham Labazi, Changyan Sun, Yan Yang, Xiaorong Zeng, S Jamal Mustafa, Zhichao Zhou
Uridine adenosine tetraphosphate (Up4A) exerts potent relaxation in porcine coronary arteries that is reduced following myocardial infarction, suggesting a crucial role for Up4A in the regulation of coronary flow (CF) in cardiovascular disorders. We evaluated the vasoactive effects of Up4A on CF in atherosclerosis using ApoE knockout (KO) mice ex vivo and in vivo. Functional studies were conducted in isolated mouse hearts using the Langendorff technique. Immunofluorescence was performed to assess purinergic P2X1 receptor (P2X1R) expression in isolated mouse coronary arteries...
September 20, 2017: Purinergic Signalling
https://www.readbyqxmd.com/read/28928222/single-subunit-oligosaccharyltransferases-of-trypanosoma-brucei-display-different-and-predictable-peptide-acceptor-specificities
#17
Anders A J Jinnelov, Liaqat Ali, Michele Tinti, Michael A J Ferguson
Trypanosoma brucei causes African trypanosomiasis and contains three full-length oligosaccharyltransferase (OST) genes; two of which, TbSTT3A and TbSTT3B, are expressed in the bloodstream form of the parasite. These OSTs have different peptide acceptor and lipid-linked oligosaccharide donor specificities and trypanosomes do not follow many of the canonical rules developed for other eukaryotic N-glycosylation pathways, raising questions as to the basic architecture and detailed function of trypanosome OSTs. Here, we show by blue-native gel electrophoresis and stable isotope labelling in cell culture proteomics that the TbSTT3A and TbSTT3B proteins associate with each other in large complexes that contain no other detectable protein subunits...
September 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28928065/molecular-cloning-and-biophysical-characterization-of-cxcl3-chemokine
#18
Khushboo Gulati, Krishnakant Gangele, Nipanshu Agarwal, Minal Jamsandekar, Dinesh Kumar, Krishna Mohan Poluri
CXCL3 is a neutrophil activating chemokine that belongs to GRO subfamily of CXC chemokines. GRO chemokine family comprises of three chemokines GRO α (CXCL1), GROβ (CXCL2), and GRO γ (CXCL3), which arose as a result of gene duplication events during the course of chemokine evolution. Although primary sequences of GRO chemokines are highly similar, they performs several protein specific functions in addition to their common property of neutrophil trafficking. However, the molecular basis for their differential functions has not well understood...
September 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28926624/molecular-characterization-expression-analysis-and-heterologous-expression-of-two-translationally-controlled-tumor-protein-genes-from-cucumis-sativus
#19
Xiang Nan Meng, Qiu Min Chen, Hai Yan Fan, Tie Feng Song, Na Cui, Ju Yong Zhao, Shu Min Jia, Ke Xin Meng
The translationally controlled tumor protein (TCTP) is a family of abundant and ubiquitous proteins involved in several important primary functions. Cucumbers harbor two TCTP genes, CsTCTP1 and CsTCTP2; however, their functional roles remain unclear. In this study, we isolated CsTCTP1 and CsTCTP2 (XP-004134215 and XP-004135602, respectively) promoters, full-length cDNA and genomic sequences from Cucumis sativus. Bioinformatics analysis, containing cis-acting elements, structural domains, phylogenetic tree and conserved motifs, suggested the conservation and divergence of CsTCTP1 and CsTCTP2, thus providing knowledge regarding their functions...
2017: PloS One
https://www.readbyqxmd.com/read/28926506/family-perspectives-on-visiting-the-pediatric-emergency-department-for-migraine-a-qualitative-study
#20
Serena Laura Orr, Liam OʼSullivan, Roger Zemek, Natalie M Ward, Hugh J McMillan
OBJECTIVE: The aim of this study was to explore the perspectives of families regarding their expectations and experience of visiting the emergency department (ED) for migraine. METHODS: This was a qualitative study involving the families of 25 patients aged 10 to 18 years receiving ED care for acute migraine. Following their visit, independent semistructured telephone interviews were conducted with both the patient and parent or guardian. Questions were designed to explore factors pertaining to the family's perspective regarding their visit to the ED and expectations for the ED visit...
September 18, 2017: Pediatric Emergency Care
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