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https://www.readbyqxmd.com/read/29134727/a-srna-in-a-reduced-mutualistic-symbiont-genome-regulates-its-own-gene-expression
#1
Margaret W Thairu, Siyuan Cheng, Allison K Hansen
Similar to other nutritional endosymbionts that are obligate for host survival, the mutualistic aphid endosymbiont, Buchnera, has a highly reduced genome with few regulatory elements. Until recently, it was thought that aphid hosts were primarily responsible for regulating their symbiotic relationship. However, we recently revealed that Buchnera displays differential protein regulation, but not mRNA expression. We also identified a number of conserved small RNAs (sRNAs) that are expressed among Buchnera taxa...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29133557/a-novel-mechanism-of-inactivating-antibacterial-nitro-compounds-in-the-human-pathogen-staphylococcus-aureus-by-overexpression-of-a-nadh-dependent-flavin-nitroreductase
#2
Ebaa M El-Hossary, Konrad U Förstner, Patrice François, Damien Baud, Karin Streker, Jacques Schrenzel, Knut Ohlsen, Ulrike Holzgrabe
Recently, the nitro substituted bisquaternary bisnaphthalimides were reported to have substantial anti-infective activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Here, we selected resistant S. aureus clones by cultivation in increasing concentrations of the most active compound MT02. Interestingly, MT02 resistant variants induced a diffusible red color of the broth. Chromatographic and spectroscopic investigations revealed a stepwise reduction of the bisquaternary bisnaphthalimides̀ nitro groups to amino groups...
November 13, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29130173/global-expression-analysis-of-quorum-sensing-controlled-genes-by-rnaseq
#3
Charlotte D Majerczyk
RNA sequencing (RNAseq) enables transcriptional profiling of many organisms. This chapter describes the use of RNAseq in prokaryotes to identify quorum sensing (QS)-controlled transcripts by comparing samples from QS-induced and -uninduced conditions. Briefly, each RNA sample is converted to ds-cDNA in a method that limits amplification of ribosomal RNA species. The ds-cDNA contains adapters that enable sequencing and quantification by next-generation sequencing (NGS).
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29129226/measuring-bovine-%C3%AE-%C3%AE-t-cell-function-at-the-site-of-mycobacterium-bovis-infection
#4
Rachel A Rusk, Mitchell V Palmer, W Ray Waters, Jodi L McGill
Bovine γδ T cells are amongst the first cells to accumulate at the site of Mycobacterium bovis infection; however, their role in the developing lesion remains unclear. We utilized transcriptomics analysis, in situ hybridization, and a macrophage/γδ T cell co-culture system to elucidate the role of γδ T cells in local immunity to M. bovis infection. Transcriptomics analysis revealed that γδ T cells upregulated expression of several novel, immune-associated genes in response to stimulation with M. bovis antigen...
December 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/29128880/the-immunophilin-repertoire-of-plasmodiophora-brassicae-and-functional-analysis-of-pbcyp3-cyclophilin
#5
Khushwant Singh, Georgios Tzelepis, Miloslav Zouhar, Pavel Ryšánek, Christina Dixelius
Plasmodiophora brassicae is a soil-borne pathogen that belongs to Rhizaria, an almost unexplored eukaryotic organism group. This pathogen requires a living host for growth and multiplication, which makes molecular analysis further complicated. To broaden our understanding of a plasmodiophorid such as P. brassicae, we here chose to study immunophilins, a group of proteins known to have various cellular functions, including involvement in plant defense and pathogen virulence. Searches in the P. brassicae genome resulted in 20 putative immunophilins comprising of 11 cyclophilins (CYPs), 7 FK506-binding proteins (FKBPs) and 2 parvulin-like proteins...
November 11, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29126391/microrna-195-acts-as-an-anti-proliferative-mirna-in-human-melanoma-cells-by-targeting-prohibitin-1
#6
Priscila Daniele Ramos Cirilo, Luciana Nogueira de Sousa Andrade, Bruna Renata Silva Corrêa, Mei Qiao, Tatiane Katsue Furuya, Roger Chammas, Luiz Otavio Ferraz Penalva
BACKGROUND: Melanoma is the most lethal type of skin cancer. Since chemoresistance is a significant barrier, identification of regulators affecting chemosensitivity is necessary in order to create new forms of intervention. Prohibitin 1 (PHB1) can act as anti-apoptotic or tumor suppressor molecule, depending on its subcellular localization. Our recent data shown that accumulation of PHB1 protects melanoma cells from chemotherapy-induced cell death. Lacking of post-transcriptional regulation of PHB1 could explain this accumulation...
November 10, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29122986/identification-of-dehydrogenases-involved-in-the-biosynthesis-of-the-monoterpene-moiety-of-pyrethrin
#7
Haiyang Xu, Gaurav D Moghe, Krystle Wiegert-Rininger, Anthony L Schilmiller, Cornelius S Barry, Robert L Last, Eran Pichersky
Flowers of Tanacetum cinerariifolium produce a set of compounds known collectively as pyrethrins, which are commercially important pesticides that are strongly toxic to flying insects but not to most vertebrates. A pyrethrin molecule is an ester consisting of either trans-chrysanthemic acid or its modified form, pyrethric acid, and one of three alcohols - jasmolone, pyrethrolone, and cinerolone - that appear to be derived from jasmonic acid. Chrysanthemyl diphosphate synthase (CDS), the first enzyme involved in the synthesis of trans-chrysanthemic acid, was previously characterized and its gene isolated...
November 9, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29122848/reducing-insulin-via-conditional-partial-gene-ablation-in-adults-reverses-diet-induced-weight-gain
#8
Melissa M Page, Søs Skovsø, Haoning Cen, Amy P Chiu, Derek A Dionne, Daria F Hutchinson, Gareth E Lim, Marta Szabat, Stephane Flibotte, Sunita Sinha, Corey Nislow, Brian Rodrigues, James D Johnson
Excess circulating insulin is associated with obesity in humans and in animal models. However, the physiologic causality of hyperinsulinemia in adult obesity has rightfully been questioned because of the absence of clear evidence that weight loss can be induced by acutely reversing diet-induced hyperinsulinemia. Herein, we describe the consequences of inducible, partial insulin gene deletion in a mouse model in which animals have already been made obese by consuming a high-fat diet. A modest reduction in insulin production/secretion was sufficient to cause significant weight loss within 5 wk, with a specific effect on visceral adipose tissue...
November 9, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29116131/context-dependent-compensation-among-phosphatidylserine-recognition-receptors
#9
Kristen K Penberthy, Claudia Rival, Laura S Shankman, Michael H Raymond, Jianye Zhang, Justin S A Perry, Chang Sup Lee, Claudia Z Han, Suna Onengut-Gumuscu, Krzysztof Palczewski, Jeffrey J Lysiak, Kodi S Ravichandran
Phagocytes express multiple phosphatidylserine (PtdSer) receptors that recognize apoptotic cells. It is unknown whether these receptors are interchangeable or if they play unique roles during cell clearance. Loss of the PtdSer receptor Mertk is associated with apoptotic corpse accumulation in the testes and degeneration of photoreceptors in the eye. Both phenotypes are linked to impaired phagocytosis by specialized phagocytes: Sertoli cells and the retinal pigmented epithelium (RPE). Here, we overexpressed the PtdSer receptor BAI1 in mice lacking MerTK (Mertk (-/-) Bai1 (Tg) ) to evaluate PtdSer receptor compensation in vivo...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29115926/co-expression-network-analysis-of-the-transcriptomes-of-rice-roots-exposed-to-various-cadmium-stresses-reveals-universal-cadmium-responsive-genes
#10
Mingpu Tan, Dan Cheng, Yuening Yang, Guoqiang Zhang, Mengjie Qin, Jun Chen, Yahua Chen, Mingyi Jiang
BACKGROUND: The migration of cadmium (Cd) from contaminated soil to rice is a cause for concern. However, the molecular mechanism underlying the response of rice roots to various Cd stresses remains to be clarified from the viewpoint of the co-expression network at a system-wide scale. RESULTS: We employed a comparative RNAseq-based approach to identify early Cd-responsive differentially expressed genes (DEGs) in rice 'Nipponbare' seedling roots after 1 h of high-Cd treatment...
November 7, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29107231/influence-of-the-rdl-a301s-mutation-in-the-brown-planthopper-nilaparvata-lugens-on-the-activity-of-phenylpyrazole-insecticides
#11
William T Garrood, Christoph T Zimmer, Oliver Gutbrod, Bettina Lüke, Martin S Williamson, Chris Bass, Ralf Nauen, T G Emyr Davies
We discovered the A301S mutation in the RDL GABA-gated chloride channel of fiprole resistant rice brown planthopper, Nilaparvata lugens populations by DNA sequencing and SNP calling via RNASeq. Ethiprole selection of two field N. lugens populations resulted in strong resistance to both ethiprole and fipronil and resulted in fixation of the A301S mutation, as well as the emergence of another mutation, Q359E in one of the selected strains. To analyse the roles of these mutations in resistance to phenylpyrazoles, three Rdl constructs: wild type, A301S and A301S+Q359E were expressed in Xenopus laevis oocytes and assessed for their sensitivity to ethiprole and fipronil using two-electrode voltage-clamp electrophysiology...
October 2017: Pesticide Biochemistry and Physiology
https://www.readbyqxmd.com/read/29106373/the-formation-of-the-light-sensing-compartment-of-cone-photoreceptors-coincides-with-a-transcriptional-switch
#12
Janine M Daum, Özkan Keles, Sjoerd Jb Holwerda, Hubertus Kohler, Filippo M Rijli, Michael Stadler, Botond Roska
High-resolution daylight vision is mediated by cone photoreceptors. The molecular program responsible for the formation of their light sensor, the outer segment, is not well understood. We correlated daily changes in ultrastructure and gene expression in postmitotic mouse cones, between birth and eye opening, using serial block-face electron microscopy (EM) and RNA sequencing. Outer segments appeared rapidly at postnatal day six and their appearance coincided with a switch in gene expression. The switch affected over 14% of all expressed genes...
November 6, 2017: ELife
https://www.readbyqxmd.com/read/29105020/identification-of-tomato-mirnas-responsive-to-root-colonization-by-endophytic-pochonia-chlamydosporia
#13
Isabella Pentimone, Ricardo Lebrón, Michael Hackenberg, Laura C Rosso, Mariantonietta Colagiero, Franco Nigro, Aurelio Ciancio
The molecular mechanisms active during the endophytic phase of the fungus Pochonia chlamydosporia are still poorly understood. In particular, few data are available on the links between the endophyte and the root response, as modulated by noncoding small RNAs. In this study, we describe the microRNAs (miRNAs) that are differentially expressed (DE) in the roots of tomato, colonized by P. chlamydosporia. A genome-wide NGS expression profiling of small RNAs in roots, either colonized or not by the fungus, showed 26 miRNAs upregulated in inoculated roots...
November 5, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29101321/contribution-of-epigenetic-landscapes-and-transcription-factors-to-x-chromosome-reactivation-in-the-inner-cell-mass
#14
Maud Borensztein, Ikuhiro Okamoto, Laurène Syx, Guillaume Guilbaud, Christel Picard, Katia Ancelin, Rafael Galupa, Patricia Diabangouaya, Nicolas Servant, Emmanuel Barillot, Azim Surani, Mitinori Saitou, Chong-Jian Chen, Konstantinos Anastassiadis, Edith Heard
X-chromosome inactivation is established during early development. In mice, transcriptional repression of the paternal X-chromosome (Xp) and enrichment in epigenetic marks such as H3K27me3 is achieved by the early blastocyst stage. X-chromosome inactivation is then reversed in the inner cell mass. The mechanisms underlying Xp reactivation remain enigmatic. Using in vivo single-cell approaches (allele-specific RNAseq, nascent RNA-fluorescent in situ hybridization and immunofluorescence), we show here that different genes are reactivated at different stages, with more slowly reactivated genes tending to be enriched in H3meK27...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29097150/prenatal-bisphenol-a-bpa-exposure-alters-the-transcriptome-of-the-neonate-rat-amygdala-in-a-sex-specific-manner-a-clarity-bpa-consortium-study
#15
Sheryl E Arambula, Dereje Jima, Heather B Patisaul
Bisphenol A (BPA) is a widely recognized endocrine disruptor prevalent in many household items. Because experimental and epidemiological data suggest links between prenatal BPA exposure and altered affective behaviors in children, even at levels below the current US FDA No Observed Adverse Effect Level (NOAEL) of 5mg/kg body weight (bw)/day, there is concern that early life exposure may alter neurodevelopment. The current study was conducted as part of the CLARITY-BPA (Consortium Linking Academic and Regulatory Insights on BPA Toxicity) program and examined the full amygdalar transcriptome on postnatal day (PND) 1, with the hypothesis that prenatal BPA exposure would alter the expression of genes and pathways fundamental to sex-specific affective behaviors...
October 28, 2017: Neurotoxicology
https://www.readbyqxmd.com/read/29093017/a-population-of-heterogeneous-breast-cancer-patient-derived-xenografts-demonstrate-broad-activity-of-parp-inhibitor-in-brca1-2-wild-type-tumors
#16
Kurt W Evans, Erkan Yuca, Argun Akcakanat, Stephen M Scott, Natalia Paez Arango, Xiaofeng Zheng, Ken Chen, Coya Tapia, Emily Tarco, Agda K Eterovic, Dalliah M Black, Jennifer K Litton, Timothy A Yap, Debu Tripathy, Gordon B Mills, Funda Meric-Bernstam
Background: Breast cancer patients who do not respond to neoadjuvant therapy have a poor prognosis. There is a pressing need for novel targets and models for preclinical testing. Here we report characterization of breast cancer patient-derived xenografts (PDX) largely generated from residual tumors following neoadjuvant chemotherapy.Experimental Design: PDXs were derived from surgical samples of primary or locally recurrent tumors. Normal and tumor DNA sequencing, RNASeq, and reverse phase protein arrays (RPPA) were performed...
November 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29092041/a-3-way-hybrid-approach-to-generate-a-new-high-quality-chimpanzee-reference-genome-pan_tro_3-0
#17
Lukas F K Kuderna, Chad Tomlinson, LaDeana W Hillier, Annabel Tran, Ian T Fiddes, Joel Armstrong, Hafid Laayouni, David Gordon, John Huddleston, Raquel Garcia Perez, Inna Povolotskaya, Aitor Serres Armero, Jèssica Gómez Garrido, Daniel Ho, Paolo Ribeca, Tyler Alioto, Richard E Green, Benedict Paten, Arcadi Navarro, Jaume Betranpetit, Javier Herrero, Evan E Eichler, Andrew J Sharp, Lars Feuk, Wesley C Warren, Tomas Marques-Bonet
The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current iteration of the chimpanzee reference genome assembly is highly fragmented. In the current iteration of the chimpanzee reference genome assembly (Pan_tro_2.1.4), the sequence is scattered across more then 183 000 contigs, incorporating more than 159 000 gaps, with a genome-wide contig N50 of 51 Kbp...
November 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29090474/sclerostin-antibody-augments-the-anabolic-bone-formation-response-in-a-mouse-model-of-mechanical-tibial-loading
#18
A Morse, A Schindeler, M M McDonald, M Kneissel, I Kramer, D G Little
Decreased activity or expression of sclerostin, an endogenous inhibitor of Wnt/β-catenin signaling, results in increased bone formation and mass. Antibodies targeting and neutralizing sclerostin (Scl-Ab) have been shown to increase bone mass and reduce fracture risk. Sclerostin is also important in modulating the response of bone to changes in its biomechanical environment. However, the effects of Scl-Ab on mechanotransduction are unclear, and it was speculated that the loading response may be altered for individuals receiving Scl-Ab therapy...
November 1, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/29080867/-multiomics-study-of-hepg2-cell-line-proteome
#19
E V Poverennaya, O I Kiseleva, E A Ponomarenko, S N Naryzhny, V G Zgoda, A V Lisitsa
Current proteomic studies are generally focused on the most abundant proteoforms encoded by canonical nucleic sequences. Transcriptomic and proteomic data, accumulated in a variety of postgenome sources and coupled with state-of-art analytical technologies, allow to start the identification of aberrant (non-canonical) proteoforms. The main sources of aberrant proteoforms are alternative splicing, single nucleotide polymorphism, and post-translational modifications. The aim of this work was to estimate the heterogeneity of HepG2 proteome...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29073243/rna-seq-transcriptome-analysis-of-formalin-fixed-paraffin-embedded-canine-meningioma
#20
Jennifer K Grenier, Polly A Foureman, Erica A Sloma, Andrew D Miller
Meningiomas are the most commonly reported primary intracranial tumor in dogs and humans and between the two species there are similarities in histology and biologic behavior. Due to these similarities, dogs have been proposed as models for meningioma pathobiology. However, little is known about specific pathways and individual genes that are involved in the development and progression of canine meningioma. In addition, studies are lacking that utilize RNAseq to characterize gene expression in clinical cases of canine meningioma...
2017: PloS One
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