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https://www.readbyqxmd.com/read/28732084/increased-parb-level-affects-expression-of-stress-response-adaptation-and-virulence-operons-and-potentiates-repression-of-promoters-adjacent-to-the-high-affinity-binding-sites-pars3-and-pars4-in-pseudomonas-aeruginosa
#1
Adam Kawalek, Krzysztof Glabski, Aneta Agnieszka Bartosik, Anna Fogtman, Grazyna Jagura-Burdzy
Similarly to its homologs in other bacteria, Pseudomonas aeruginosa partitioning protein ParB facilitates segregation of newly replicated chromosomes. Lack of ParB is not lethal but results in increased frequency of anucleate cells production, longer division time, cell elongation, altered colony morphology and defective swarming and swimming motility. Unlike in other bacteria, inactivation of parB leads to major changes of the transcriptome, suggesting that, directly or indirectly, ParB plays a role in regulation of gene expression in this organism...
2017: PloS One
https://www.readbyqxmd.com/read/28732065/direct-targets-of-pstat5-signalling-in-erythropoiesis
#2
Kevin R Gillinder, Hugh Tuckey, Charles C Bell, Graham W Magor, Stephen Huang, Melissa D Ilsley, Andrew C Perkins
Erythropoietin (EPO) acts through the dimeric erythropoietin receptor to stimulate proliferation, survival, differentiation and enucleation of erythroid progenitor cells. We undertook two complimentary approaches to find EPO-dependent pSTAT5 target genes in murine erythroid cells: RNA-seq of newly transcribed (4sU-labelled) RNA, and ChIP-seq for pSTAT5 30 minutes after EPO stimulation. We found 302 pSTAT5-occupied sites: ~15% of these reside in promoters while the rest reside within intronic enhancers or intergenic regions, some >100kb from the nearest TSS...
2017: PloS One
https://www.readbyqxmd.com/read/28732030/identification-of-odorant-binding-proteins-and-chemosensory-proteins-in-microplitis-mediator-as-well-as-functional-characterization-of-chemosensory-protein-3
#3
Yong Peng, Shan-Ning Wang, Ke-Ming Li, Jing-Tao Liu, Yao Zheng, Shuang Shan, Ye-Qing Yang, Rui-Jun Li, Yong-Jun Zhang, Yu-Yuan Guo
Odorant binding proteins (OBPs) and chemosensory proteins (CSPs) play important roles in transporting semiochemicals through the sensillar lymph to olfactory receptors in insect antennae. In the present study, twenty OBPs and three CSPs were identified from the antennal transcriptome of Microplitis mediator. Ten OBPs (MmedOBP11-20) and two CSPs (MmedCSP2-3) were newly identified. The expression patterns of these new genes in olfactory and non-olfactory tissues were investigated by real-time quantitative PCR (qPCR) measurement...
2017: PloS One
https://www.readbyqxmd.com/read/28731788/identification-of-osr2-transcriptional-target-genes-in-palate-development
#4
X Fu, J Xu, P Chaturvedi, H Liu, R Jiang, Y Lan
Previous studies have identified the odd-skipped related 2 (Osr2) transcription factor as a key intrinsic regulator of palatal shelf growth and morphogenesis. However, little is known about the molecular program acting downstream of Osr2 in the regulation of palatogenesis. In this study, we isolated palatal mesenchyme cells from embryonic day 12.5 (E12.5) and E13.5 Osr2(RFP/+) and Osr2(RFP/-) mutant mouse embryos and performed whole transcriptome RNA sequencing analyses. Differential expression analysis of the RNA sequencing datasets revealed that expression of 70 genes was upregulated and expression of 61 genes was downregulated by >1...
July 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28731643/transcriptome-based-identification-of-the-optimal-reference-cho-genes-for-normalisation-of-qpcr-data
#5
Adam J Brown, Suzanne Gibson, Diane Hatton, David C James
Real-time quantitative PCR (qPCR) is the standard method for determination of relative changes in mRNA transcript abundance. Analytical accuracy, precision, and reliability are critically dependent on the selection of internal control reference genes. In this study we have identified optimal reference genes that can be utilized universally for qPCR analysis of CHO cell mRNAs. Initially, transcriptomic datasets were analysed to identify eight endogenous genes that exhibited high expression stability across four distinct CHO cell lines sampled in different culture phases...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731630/improved-pks-gene-expression-with-strong-endogenous-promoter-resulted-in-geldanamycin-yield-increase
#6
Xinran Wang, Xinjuan Ning, Qinqin Zhao, Qianjin Kang, Linquan Bai
The type I polyketide geldanamycin is a potent anti-tumor reagent. Its biosynthesis includes three steps: the biosynthesis of precursors, such as 3-amino-5-hydroxybenzoic acid (AHBA), the PKS chain extension, and the post-PKS modifications. According to the genomic and transcriptomic analysis, the PKS chain extension was deduced to be the rate-limiting step for geldanamycin production in Streptomyces hygroscopicus XM201. in order to improve the expression of PKS genes, a strong endogenous promoter 5063p was obtained based on the transcriptomic analysis and XylE enzymatic assay...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731474/bacterial-transcriptome-remodeling-during-sequential-co-culture-with-a-marine-dinoflagellate-and-diatom
#7
Marine Landa, Andrew S Burns, Selena J Roth, Mary Ann Moran
In their role as primary producers, marine phytoplankton modulate heterotrophic bacterial activities through differences in the types and amounts of organic matter they release. This study investigates the transcriptional response of bacterium Ruegeria pomeroyi, a member of the Roseobacter clade known to affiliate with diverse phytoplankton groups in the ocean, during a shift in phytoplankton taxonomy. The bacterium was initially introduced into a culture of the dinoflagellate Alexandrium tamarense, and then experienced a change in phytoplankton community composition as the diatom Thalassiosira pseudonana gradually outcompeted the dinoflagellate...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731472/high-abundance-and-expression-of-transposases-in-bacteria-from-the-baltic-sea
#8
Theoden Vigil-Stenman, Karolina Ininbergs, Birgitta Bergman, Martin Ekman
Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731347/integrated-venomics-and-venom-gland-transcriptome-analysis-of-juvenile-and-adult-mexican-rattlesnakes-crotalus-simus-c-tzabcan-and-c-culminatus-revealed-mirna-modulated-ontogenetic-shifts
#9
Jordi Durban, Libia Sanz, Dilza Trevisan-Silva, Edgar Neri-Castro, Alejandro Alagón, Juan Jose Calvete
Adult rattlesnakes within genus Crotalus express one of two distinct venom phenotypes, type I (haemorrhagic) and type II (neurotoxic). In Costa Rican Central American rattlesnake, ontogenetic changes in the concentration of miRNAs modulate venom type II to type I transition. Venomics and venom gland transcriptome analyses showed that adult C. simus and C. tzabcan expressed intermediate patterns between type II and type I venoms, whereas C. culminatus had a canonical type I venom. Neonate/juvenile and adult Mexican rattlesnakes showed notable inter- and intraspecific variability in the number, type, abundance and ontogenetic shifts of the transcriptional and translational venom gland activities...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28731049/composite-hemangioendothelioma-with-neuroendocrine-marker-expression-an-aggressive-variant
#10
Kyle D Perry, Alyaa Al-Lbraheemi, Brian P Rubin, Jin Jen, Hongzheng Ren, Jin Sung Jang, Asha Nair, Jaime Davila, Stefan Pambuccian, Andrew Horvai, William Sukov, Henry D Tazelaar, Andrew L Folpe
Aberrant expression of neuroendocrine markers is extremely rare in endothelial neoplasms, with only a single report describing three cases. Although originally classified as conventional angiosarcoma, further assessment of these tumors revealed a strikingly composite morphology composed of retiform and epithelioid elements reminiscent of composite hemangioendothelioma, a rare subtype of hemangioendothelioma. To further investigate these findings, available materials from 11 morphologically distinctive endothelial tumors showing neuroendocrine marker expression were retrieved from our archives...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28731043/gastroblastoma-harbors-a-recurrent-somatic-malat1-gli1-fusion-gene
#11
Rondell P Graham, Asha A Nair, Jaime I Davila, Long Jin, Jin Jen, William R Sukov, Tsung-Teh Wu, Henry D Appelman, Jorge Torres-Mora, Kyle D Perry, Lizhi Zhang, Sara M Kloft-Nelson, Ryan A Knudson, Patricia T Greipp, Andrew L Folpe
Gastroblastoma is a rare distinctive biphasic tumor of the stomach. The molecular biology of gastroblastoma has not been studied, and no affirmative diagnostic markers have been developed. We retrieved two gastroblastomas from the consultation practices of the authors and performed transcriptome sequencing on formalin-fixed paraffin-embedded tissue. Recurrent predicted fusion genes were validated at genomic and RNA levels. The presence of the fusion gene was confirmed on two additional paraffin-embedded cases of gastroblastoma...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28730636/the-reduction-in-maize-leaf-growth-under-mild-drought-affects-the-transition-between-cell-division-and-cell-expansion-and-cannot-be-restored-by-elevated-gibberellic-acid-levels
#12
Hilde Nelissen, Xiao-Huan Sun, Bart Rymen, Yusuke Jikumaru, Mikko Kojima, Yumiko Takebayashi, Rafael Abbeloos, Kirin Demuynck, Veronique Storme, Marnik Vuylsteke, Jolien De Block, Dorota Herman, Frederik Coppens, Steven Maere, Yuji Kamiya, Hitoshi Sakakibara, Gerrit T S Beemster, Dirk Inzé
Growth is characterized by the interplay between cell division and cell expansion, two processes that occur separated along the growth zone at the maize leaf. To gain further insight into the transition between cell division and cell expansion, conditions were investigated in which the position of this transition zone was positively or negatively affected. High levels of gibberellic acid (GA) in plants overexpressing the GA biosynthesis gene GA20-OXIDASE (GA20OX-1(OE) ) shifted the transition zone more distally, whereas mild drought, which is associated with lowered GA biosynthesis, resulted in a more basal positioning...
July 21, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28730342/transcriptome-analysis-of-three-cotton-pests-reveals-features-of-gene-expressions-in-the-mesophyll-feeder-apolygus-lucorum
#13
Dianyang Chen, Fangyan Chen, Chunyu Chen, Xiaoya Chen, Yingbo Mao
The green mirid bug Apolygus lucorum is an agricultural pest that is known to cause damage to more than 150 plant species. Here, we report the transcriptomes of A. lucorum at three different developmental stages (the second and fifth instar nymphs and adults). A total of 98,236 unigenes with an average length of 1,335 nt was obtained, of which 50,640 were annotated, including those encoding digestive enzymes and cytochrome P450s. Comparisons with cotton bollworm and cotton aphid transcriptomes revealed distinct features of A...
July 18, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28730152/zebrafish-get-connected-investigating-neurotransmission-targets-and-alterations-in-chemical-toxicity
#14
Katharine A Horzmann, Jennifer L Freeman
Neurotransmission is the basis of neuronal communication and is critical for normal brain development, behavior, learning, and memory. Exposure to drugs and chemicals can alter neurotransmission, often through unknown pathways and mechanisms. The zebrafish (Danio rerio) model system is increasingly being used to study the brain and chemical neurotoxicity. In this review, the major neurotransmitter systems, including glutamate, GABA, dopamine, norepinephrine, serotonin, acetylcholine, histamine, and glutamate are surveyed and pathways of synthesis, transport, metabolism, and action are examined...
September 2016: Toxics
https://www.readbyqxmd.com/read/28729959/shot-gun-proteome-and-transcriptome-mapping-of-the-jujube-floral-organ-and-identification-of-a-pollen-specific-s-locus-f-box-gene
#15
Ruihong Chen, Guoliang Chen, Jian Huang
The flower is a plant reproductive organ that forms part of the fruit produced as the flowering season ends. While the number and identity of proteins expressed in a jujube (Ziziphus jujuba Mill.) flower is currently unknown, integrative proteomic and transcriptomic analyses provide a systematic strategy of characterizing the floral biology of plants. We conducted a shotgun proteomic analysis on jujube flowers by using a filter-aided sample preparation tryptic digestion, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
2017: PeerJ
https://www.readbyqxmd.com/read/28729859/transcriptomic-insight-in-the-control-of-legume-root-secondary-infection-by-the-sinorhizobium-meliloti-transcriptional-regulator-clr
#16
Lan Zou, Amandine Gastebois, Céline Mathieu-Demazière, Fernando Sorroche, Catherine Masson-Boivin, Jacques Batut, Anne-Marie Garnerone
The cAMP-dependent transcriptional regulator Clr of Sinorhizobium meliloti regulates the overall number of infection events on Medicago roots by a so-far unknown mechanism requiring smc02178, a Clr-target gene of unknown function. In order to shed light on the mode of action of Clr on infection and potentially reveal additional biological functions for Clr, we inventoried genomic Clr target genes by transcriptome profiling. We have found that Clr positively controls the synthesis of cAMP-dependent succinoglycan as well as the expression of genes involved in the synthesis of a so-far unknown polysaccharide compound...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729858/toxin-antitoxin-systems-in-estuarine-synechococcus-strain-cb0101-and-their-transcriptomic-responses-to-environmental-stressors
#17
David Marsan, Allen Place, Daniel Fucich, Feng Chen
Bacterial toxin-antitoxin (TA) systems are genetic elements composed of a toxin gene and its cognate antitoxin, with the ability to regulate growth. TA systems have not previously been reported in marine Synechococcus or Prochlorococcus. Here we report the finding of seven TA system pairs (Type II) in the estuarine Synechococcus CB0101, and their responses of these TA genes to under different stress conditions, which include; nitrogen and phosphate starvation, phage infection, zinc toxicity, and photo-oxidation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729759/transcriptome-wide-identification-and-characterization-of-starch-branching-enzyme-in-finger-millet
#18
Rajhans Tyagi, Apoorv Tiwari, Vijay Kumar Garg, Sanjay Gupta
Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and play an important role in determining the structure and physical properties of starch granules. Multiple SBEs are involved in starch biosynthesis in plants. Finger millet is calcium rich important serial crop belongs to grass family and the transcriptome data of developing spikes is available on NCBI. In this study it was try to find out the gene sequence of starch branching enzyme and annotate the sequence and submit the sequence for further use...
2017: Bioinformation
https://www.readbyqxmd.com/read/28729720/comparative-gene-expression-profiling-of-the-large-cell-variant-of-gastrointestinal-marginal-zone-b-cell-lymphoma
#19
Thomas F E Barth, Johann M Kraus, Ludwig Lausser, Lucia Flossbach, Lukas Schulte, Karlheinz Holzmann, Hans A Kestler, Peter Möller
Gastrointestinal (g.i.) large cell lymphoma is currently regarded as diffuse large B-cell lymphoma (DLBCL) despite a more favorable clinical outcome compared to other DLBCL. Cluster analyses on a transcriptome signature of NF-κB target genes of 30 g.i. marginal zone B-cell lymphomas (MZBL; 8 g.i. MZBL, 22 large cell MZBL - among them 9 with coexisting small cell component) and 6 DLBCL (3 activated B-cell like (ABC), 3 germinal center-like (GCB)) reveals a distinct pattern. The distinctiveness of large cell MZBL samples is further confirmed by a cohort of 270 available B-cell lymphoma and B-cell in silico profiles...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729698/dynamic-transcriptomic-analysis-of-the-early-response-of-female-flowers-of-populus-alba%C3%A2-%C3%A3-%C3%A2-p-glandulosa-to-pollination
#20
Pian Rao, Zhong Chen, Xiaoyu Yang, Kai Gao, Xiong Yang, Tianyun Zhao, Siyan Li, Bo Wu, Xinmin An
Pollination is an important event in plant sexual reproduction, and post-pollination response is an essential process for reproduction. Populus alba × P. glandulosa is used widely in scientific research, especially in cross breeding as parents. Adult female P. alba × P. glandulosa flowers are highly compatible with pollen from male P. tomentosa, but the early post-pollination response of flowers at the molecular levels is unclear. In this study, RNA-seq was employed to comprehensively understand the response of female P...
July 20, 2017: Scientific Reports
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