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https://www.readbyqxmd.com/read/28732077/mutations-in-the-caenorhabditis-elegans-orthologs-of-human-genes-required-for-mitochondrial-trna-modification-cause-similar-electron-transport-chain-defects-but-different-nuclear-responses
#1
Carmen Navarro-González, Ismaïl Moukadiri, Magda Villarroya, Ernesto López-Pascual, Simon Tuck, M-Eugenia Armengod
Several oxidative phosphorylation (OXPHOS) diseases are caused by defects in the post-transcriptional modification of mitochondrial tRNAs (mt-tRNAs). Mutations in MTO1 or GTPBP3 impair the modification of the wobble uridine at position 5 of the pyrimidine ring and cause heart failure. Mutations in TRMU affect modification at position 2 and cause liver disease. Presently, the molecular basis of the diseases and why mutations in the different genes lead to such different clinical symptoms is poorly understood...
July 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28731643/transcriptome-based-identification-of-the-optimal-reference-cho-genes-for-normalisation-of-qpcr-data
#2
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/28731474/bacterial-transcriptome-remodeling-during-sequential-co-culture-with-a-marine-dinoflagellate-and-diatom
#3
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/28731464/trophoblast-survival-signaling-during-human-placentation-requires-hsp70-activation-of-mmp2-mediated-hbegf-shedding
#4
Chandni V Jain, Philip Jessmon, Charbel T Barrak, Alan D Bolnick, Brian A Kilburn, Michael Hertz, D Randall Armant
Survival of trophoblast cells in the low oxygen environment of human placentation requires metalloproteinase-mediated shedding of HBEGF and downstream signaling. A matrix metalloproteinase (MMP) antibody array and quantitative RT-PCR revealed upregulation of MMP2 post-transcriptionally in human first trimester HTR-8/SVneo trophoblast cells and placental villous explants exposed to 2% O2. Specific MMP inhibitors established the requirement for MMP2 in HBEGF shedding and upregulation. Because α-amanitin inhibited the upregulation of HBEGF, differentially expressed genes were identified by next-generation sequencing of RNA from trophoblast cells cultured at 2% O2 for 0, 1, 2 and 4 h...
July 21, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28730077/proteomic-profiling-of-early-degenerative-retina-of-rcs-rats
#5
Zhi-Hong Zhu, Yan Fu, Chuan-Huang Weng, Cong-Jian Zhao, Zheng-Qin Yin
AIM: To identify the underlying cellular and molecular changes in retinitis pigmentosa (RP). METHODS: Label-free quantification-based proteomics analysis, with its advantages of being more economic and consisting of simpler procedures, has been used with increasing frequency in modern biological research. Dystrophic RCS rats, the first laboratory animal model for the study of RP, possess a similar pathological course as human beings with the diseases. Thus, we employed a comparative proteomics analysis approach for in-depth proteome profiling of retinas from dystrophic RCS rats and non-dystrophic congenic controls through Linear Trap Quadrupole - orbitrap MS/MS, to identify the significant differentially expressed proteins (DEPs)...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28729440/the-transcription-factor-foxg1-promotes-optic-fissure-closure-in-the-mouse-by-suppressing-wnt8b-in-the-nasal-optic-stalk
#6
Rowena Smith, Yu-Ting Huang, Tian Tian, Dominika Vojtasova, Oscar Mesalles-Naranjo, Steven M Pollard, Thomas Pratt, David J Price, Vassiliki Fotaki
During vertebrate eye morphogenesis a transient fissure forms at its inferior part, known as the optic fissure. This will gradually close giving rise to a healthy, spherical optic cup. Failure of the optic fissure to close gives rise to an ocular disorder known as coloboma. During this developmental process Foxg1 is expressed in the optic neuroepithelium, with highest levels of expression in the nasal optic stalk. Foxg1-/- mutant mice have microphthalmic eyes with a large ventral coloboma. We found Wnt8b expression upregulated in the Foxg1-/- optic stalk and hypothesized that, similar to what is observed in telencephalic development, Foxg1 directs development of the optic neuroepithelium through transcriptional suppression of Wnt8b To test this, we generated Foxg1-/-;Wnt8b-/- double mutants of either sex and found that the morphology of the optic cup and stalk and the closure of the optic fissure were substantially rescued in these embryos...
July 20, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28729418/myc-regulated-mevalonate-metabolism-maintains-brain-tumor-initiating-cells
#7
Xiuxing Wang, Zhi Huang, Qiulian Wu, Briana C Prager, Stephen C Mack, Kailin Yang, Leo J Y Kim, Ryan C Gimple, Yu Shi, Sisi Lai, Qi Xie, Tyler E Miller, Christopher G Hubert, Anne Song, Zhen Dong, Wenchao Zhou, Xiaoguang Fang, Zhe Zhu, Vaidehi Mahadev, Shideng Bao, Jeremy N Rich
Metabolic dysregulation drives tumor initiation in a subset of glioblastomas harboring isocitrate dehydrogenase (IDH) mutations, but metabolic alterations in glioblastomas with wildtype IDH are poorly understood. MYC promotes metabolic reprogramming in cancer, but targeting MYC has proven notoriously challenging. Here, we link metabolic dysregulation in patient-derived brain tumor initiating cells (BTICs) to a nexus between MYC and mevalonate signaling, which can be inhibited by statin or 6-fluoromevalonate treatment...
July 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28729249/deletion-of-transcription-factor-binding-motifs-using-the-crispr-spcas9-system-in-the-%C3%AE-globin-lcr
#8
Yea Woon Kim, AeRi Kim
Transcription factors play roles in gene transcription through direct binding to their motifs in genome, and inhibiting this binding provides an effective strategy for studying their roles. Here we applied the CRISPR/spCas9 system to mutate the binding motifs of transcription factors. Binding motifs for erythroid specific transcription factors were mutated in the locus control region hypersensitive sites of the human β-globin locus. Guide RNAs targeting binding motifs were cloned into lentiviral CRISPR vector containing the spCas9 gene, and transduced into MEL/ch11 cells carrying a human chromosome 11...
July 20, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28728844/long-non-coding-rna-pcat7-regulates-elf2-signaling-through-inhibition-of-mir-134-5p-in-nasopharyngeal-carcinoma
#9
Yejun Liu, Zezhang Tao, Jining Qu, Xuhong Zhou, Chenghong Zhang
While some long noncoding RNAs (lncRNAs) might promote nasopharyngeal carcinoma (NPC) initiation and progression, the involved molecular mechanisms remain largely unclear. Here, we discovered the novel LncRNA, prostate cancer associated transcript 7 (PCAT7), which was overexpressed and associated with worse prognosis in NPC. Decreased PCAT7 expression was found to significantly suppress tumor cell proliferation in vitro, and inhibited tumor growth and reduced the expression of proliferation antigen Ki-67 in vivo...
July 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28728565/identification-of-differential-co-expressed-gene-networks-in-early-rheumatoid-arthritis-achieving-sustained-drug-free-remission-after-treatment-with-a-tocilizumab-based-or-methotrexate-based-strategy
#10
Xavier M Teitsma, Johannes W G Jacobs, Michal Mokry, Michelle E A Borm, Attila Pethö-Schramm, Jacob M van Laar, Johannes W J Bijlsma, Floris P J Lafeber
BACKGROUND: Methotrexate is endorsed to be used as first-line treatment in rheumatoid arthritis (RA). However, a large proportion of patients need additional treatment with a biological disease-modifying anti-rheumatic drug (DMARD) to adequately suppress their disease activity. A better understanding of genotypes could help to distinguish between patients with different pathogenic mechanisms. The aim of this study was therefore to identify networks of genes within DMARD-naive early RA patients associated with achieving sustained drug-free remission (sDFR) after initiating tocilizumab plus methotrexate, tocilizumab, or methotrexate therapy...
July 20, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28728562/low-oxygen-tension-increases-mitochondrial-membrane-potential-and-enhances-expression-of-antioxidant-genes-and-implantation-protein-of-mouse-blastocyst-cultured-in-vitro
#11
Yun-Yi Ma, Huei-Wen Chen, Chii-Ruey Tzeng
BACKGROUND: In human IVF, embryos cultured with a lower O2 tension (5%) can give rise to higher success rates when compared with normoxic conditions (20%). However, the mechanisms behind the beneficial effects of reduced oxygen tension in embryogenesis remain unclear. The aim of this study was to evaluate the expression of oxygen related and antioxidant genes and mitochondrial function in mouse embryo cultured under hypoxic and normoxic conditions, to investigate the beneficial effect of low oxygen tension in preimplantation embryogenesis...
July 20, 2017: Journal of Ovarian Research
https://www.readbyqxmd.com/read/28728163/nuclear-expression-of-gli-1-is-predictive-of-pathologic-complete-response-to-chemoradiation-in-trimodality-treated-oesophageal-cancer-patients
#12
Roopma Wadhwa, Xuemei Wang, Veerabhadran Baladandayuthapani, Bin Liu, Hironori Shiozaki, Yusuke Shimodaira, Quan Lin, Elena Elimova, Wayne L Hofstetter, Stephen G Swisher, David C Rice, Dipen M Maru, Neda Kalhor, Manoop S Bhutani, Brian Weston, Jeffrey H Lee, Heath D Skinner, Ailing W Scott, Dilsa Mizrak Kaya, Kazuto Harada, Donald Berry, Shumei Song, Jaffer A Ajani
BACKGROUND: Predictive biomarkers or signature(s) for oesophageal cancer (OC) patients undergoing preoperative therapy could help administration of effective therapy, avoidance of ineffective ones, and establishment new strategies. Since the hedgehog pathway is often upregulated in OC, we examined its transcriptional factor, Gli-1, which confers therapy resistance, we wanted to assess Gli-1 as a predictive biomarker for chemoradiation response and validate it. METHODS: Untreated OC tissues from patients who underwent chemoradiation and surgery were assessed for nuclear Gli-1 by immunohistochemistry and labelling indices (LIs) were correlated with pathologic complete response (pathCR) or <pathCR (resistance) and validated in a unique cohort...
July 20, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28727848/the-nuclear-proteome-of-trypanosoma-brucei
#13
Carina Goos, Mario Dejung, Christian J Janzen, Falk Butter, Susanne Kramer
Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host...
2017: PloS One
https://www.readbyqxmd.com/read/28726780/foxq1-regulates-senescence-associated-inflammation-via-activation-of-sirt1-expression
#14
Pan Wang, Cuicui Lv, Tao Zhang, Junling Liu, Jin Yang, Fangxia Guan, Tianpei Hong
Cellular senescence is an initial barrier to tumor development that prevents the proliferation of premalignant cells. However, some of the features of senescent cells seem to promote tumor progression via senescence-associated secretory phenotype (SASP). Here, we demonstrated that the protein level of forkhead box Q1 (FOXQ1), which highly overexpresses in several kinds of tumors, was significantly downregulated during both replicative and oncogene-induced senescence. Moreover, overexpression of FOXQ1 delayed senescence, whereas FOXQ1 silence led to premature senescence in human fibroblasts...
July 20, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28726637/microrna-101-attenuates-pulmonary-fibrosis-by-inhibiting-fibroblast-proliferation-and-activation
#15
Chaoqun Huang, Xiao Xiao, Ye Yang, Amarjit Mishra, Yurong Liang, Xiangming Zeng, Xiaoyun Yang, Dao Xu, Michael R Blackburn, Craig A Henke, Lin Liu
Aberrant proliferation and activation of lung fibroblasts contribute to the initiation and progression of idiopathic pulmonary fibrosis (IPF). However, the mechanisms responsible for the proliferation and activation of fibroblasts are not fully understood. The objective of the current study was to investigate the role of miR-101 in the proliferation and activation of lung fibroblasts. miR-101 expression was determined in lung tissues from patients with IPF and mice with bleomycin-induced pulmonary fibrosis...
July 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28726096/identification-and-characterization-of-the-flower-meristem-identity-gene-mhylfy-in-mycoheterotrophic-plant-monotropa-hypopitys
#16
A V Shchennikova, O A Shulga, A V Beletsky, M A Filyushin, E Z Kochieva, N V Ravin, K G Skryabin
The gene encoding the transcription factor LEAFY was identified in the genome of the mycoheterotrophic plant, pinesap Monotropa hypopitys. In the transcriptomes of roots, bracts, and flowers of flowering pinesaps, the MhyLFY gene expression was absent. These data suggest the conservativeness of the LFY-dependent mechanism of flower meristem identity and flower formation in heterotrophic species with some differences associated to the specificity of development and the structure of such plants. The pinesap flowering under the control of the transcription factor MhyLFY may be initiated either in an embryonic inflorescence during spring dormancy release of adventitious root buds or in an inflorescence of a growing reproductive stem after photoperiodic induction...
May 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28725954/proteasome-stress-triggers-death-of-sh-sy5y-and-t98g-cells-via-different-cellular-mechanisms
#17
Ivana Pilchova, Katarina Klacanova, Katarina Dibdiakova, Simona Saksonova, Andrea Stefanikova, Eva Vidomanova, Lucia Lichardusova, Jozef Hatok, Peter Racay
Overload or dysfunction of ubiquitin-proteasome system (UPS) is implicated in mechanisms of neurodegeneration associated with neurodegenerative diseases, e.g. Parkinson and Alzheimer disease, and ischemia-reperfusion injury. The aim of this study was to investigate the possible association between viability of neuroblastoma SH-SY5Y and glioblastoma T98G cells treated with bortezomib, inhibitor of 26S proteasome, and accumulation of ubiquitin-conjugated proteins with respect to direct cytotoxicity of aggregates of ubiquitin-conjugated proteins...
July 19, 2017: Neurochemical Research
https://www.readbyqxmd.com/read/28725263/modeling-and-simulation-of-the-redox-regulation-of-the-metabolism-in-escherichia-coli-at-different-oxygen-concentrations
#18
Yu Matsuoka, Hiroyuki Kurata
BACKGROUND: Microbial production of biofuels and biochemicals from renewable feedstocks has received considerable recent attention from environmental protection and energy production perspectives. Many biofuels and biochemicals are produced by fermentation under oxygen-limited conditions following initiation of aerobic cultivation to enhance the cell growth rate. Thus, it is of significant interest to investigate the effect of dissolved oxygen concentration on redox regulation in Escherichia coli, a particularly popular cellular factory due to its high growth rate and well-characterized physiology...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28724960/sgrna-expression-of-cripsr-cas9-system-based-on-mirna-polycistrons-as-a-versatile-tool-to-manipulate-multiple-and-tissue-specific-genome-editing
#19
Chen Xie, Yan-Lian Chen, Dong-Fang Wang, Yi-Lin Wang, Tian-Peng Zhang, Hui Li, Fu Liang, Yong Zhao, Guang-Ya Zhang
CRISPR/Cas9-mediated genome editing is a next-generation strategy for genetic modifications. Typically, sgRNA is constitutively expressed relying on RNA polymerase III promoters. Polymerase II promoters initiate transcription in a flexible manner, but sgRNAs generated by RNA polymerase II promoter lost their nuclease activity. To express sgRNAs in a tissue-specific fashion and endow CRISPR with more versatile function, a novel system was established in a polycistron, where miRNAs (or shRNAs) and sgRNAs alternately emerged and co-expressed under the control of a single polymerase II promoter...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724647/physiological-responses-to-fluctuating-temperatures-are-characterized-by-distinct-transcriptional-profiles-in-a-solitary-bee
#20
Alex S Torson, George D Yocum, Joseph P Rinehart, Sean A Nash, Kally M Kvidera, Julia H Bowsher
Exposure to stressful low temperatures during development can result in the accumulation of deleterious physiological effects called chill injury. Metabolic imbalances, disruptions in ion homeostasis, and oxidative stress contribute to the increased mortality of chill-injured insects. Interestingly, survival can be significantly increased when chill susceptible insects are exposed to a daily warm-temperature pulse during chilling. We hypothesize that warm pulses allow for the repair of damage associated with chill-injury...
July 19, 2017: Journal of Experimental Biology
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