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Oxygen sensitive sequence

Ying-Chun Shih, Chao-Ling Chen, Yan Zhang, Rebecca L Mellor, Evelyn M Kanter, Yun Fang, Hua-Chi Wang, Chen-Ting Hung, Jing-Yi Nong, Hui-Ju Chen, Tzu-Han Lee, Yi-Shuan Tseng, Chiung-Nien Chen, Chau-Chung Wu, Shuei-Liong Lin, Kathryn A Yamada, Jeanne M Nerbonne, Kai-Chien Yang
<u>Rationale:</u> Cardiac fibrosis plays a critical role in the pathogenesis of heart failure (HF). Excessive accumulation of extracellular matrix (ECM) resulting from cardiac fibrosis impairs cardiac contractile function and increases arrhythmogenicity. Current treatment options for cardiac fibrosis, however, are limited and there is a clear need to identify novel mediators of cardiac fibrosis to facilitate the development of better therapeutics. Exploiting co-expression gene network analysis on RNA sequencing data from failing human heart, we identified thioredoxin domain containing 5 (TXNDC5), a cardiac fibroblast (CF)-enriched endoplasmic reticulum (ER) protein, as a potential novel mediator of cardiac fibrosis and we completed experiments to test this hypothesis directly...
March 13, 2018: Circulation Research
Lu-Ping Li, Jon Thacker, Wei Li, Huan Tan, Chi Wang, Orly Kohn, Stuart Sprague, Pottumarthi Prasad
BACKGROUND: Identification of patients with progressive chronic kidney disease (CKD) and those likely to respond to candidate therapeutics is urgently needed. Functional MRI measurements have shown promise. However, knowledge about the consistency of the measurements is essential to conduct longitudinal studies. PURPOSE/HYPOTHESIS: To investigate the consistency of repeated functional MRI measurements in healthy subjects. STUDY TYPE: Prospective, longitudinal study...
March 8, 2018: Journal of Magnetic Resonance Imaging: JMRI
Daniela Strobbe, Leonardo Caporali, Luisa Iommarini, Alessandra Maresca, Monica Montopoli, Andrea Martinuzzi, Alessandro Achilli, Anna Olivieri, Antonio Torroni, Valerio Carelli, Anna Ghelli
There is growing evidence that the sequence variation of mitochondrial DNA (mtDNA), which clusters in population- and/or geographic-specific haplogroups, may result in functional effects that, in turn, become relevant in disease predisposition or protection, interaction with environmental factors and ultimately in modulating longevity. To unravel functional differences between mtDNA haplogroups we here employed transmitochondrial cytoplasmic hybrid cells (cybrids) grown in galactose medium, culture condition that force oxidative phosphorylation, and in the presence of rotenone, the classic inhibitor of respiratory Complex I...
February 24, 2018: Neurobiology of Disease
Xi Ning, Yao Sun, Changchun Wang, Weilin Zhang, Meihao Sun, Haitao Hu, Jianzhong Liu, Ling Yang
Glutaredoxins (GRXs) belong to the antioxidants involved in the cellular stress responses. In spite of the identification 48 GRX genes in rice genomes, the biological functions of most of them remain unknown. Especially, the biological roles of members of GRX family in disease resistance are still lacking. Our proteomic analysis found that OsGRX20 increased by 2.7-fold after infection by bacterial blight. In this study, we isolated and characterized the full-length nucleotide sequences of the rice OsGRX20 gene, which encodes a GRX family protein with CPFC active site of CPYC-type class...
2018: Frontiers in Plant Science
Timothy S Pardee, Rebecca G Anderson, Kristin M Pladna, Scott Isom, Lais P Ghiraldeli, Lance D Miller, Jeff A Chou, Guangxu Jin, Wei Zhang, Leslie R Ellis, Dmitriy Berenzon, Dianna S Howard, David Hurd, Megan Manuel, Sarah Dralle, Susan Lyerly, Bayard L Powell
PURPOSE: CPI-613, a lipoate analog that inhibits pyruvate dehydrogenase (PDH) and α-ketogluterate dehydrogenase (KGDH) has activity in patients with myeloid malignancies. This study explored the role of mitochondrial metabolism in chemotherapy response, determined the maximally tolerated dose, efficacy and safety of CPI-613 combined with high dose cytarabine and mitoxantrone in patients with relapsed or refractory acute myeloid leukemia. METHODS: The role of mitochondrial response to chemotherapy was assessed in cell lines and animal models...
February 6, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Katherine R Miller, Jai N Patel, Qing Zhang, Eric J Norris, James Symanowski, Chad Michener, Jalid Sehouli, Ioana Braicu, Darla D Destephanis, Ashley P Sutker, Wendell Jones, Chad A Livasy, Charles Biscotti, Ram N Ganapathi, David L Tait, Mahrukh K Ganapathi
OBJECTIVES: Aberrant homeobox (HOX) gene expression is reported in high-grade serous ovarian carcinoma (HGSOC), however, its prognostic significance remains unclear. METHODS: HOX genes associated with progression-free survival (PFS) in a discovery cohort of primary HGSOC samples with RNA sequencing data, and those previously reported to be associated with clinical outcomes, were selected for qPCR testing in an independent training cohort of primary HGSOC samples (n=71)...
February 2, 2018: Gynecologic Oncology
Alexander D Cohen, Andrew S Nencka, Yang Wang
Typical simultaneous blood oxygenation-level dependent (BOLD) and arterial spin labeling (ASL) sequences acquire two echoes, one perfusion-sensitive and one BOLD-sensitive. However, for ASL, spatial resolution and brain coverage are limited due to the T1 decay of the labeled blood. This study applies a sequence combining a multiband acquisition with four echoes for simultaneous BOLD and pseudo-continuous ASL (pCASL) echo planar imaging (MBME ASL/BOLD) for block-design task-fMRI. A multiband acceleration of four was employed to increase brain coverage and reduce slice-timing effects on the ASL signal...
2018: PloS One
Lauren E Friedman, Thomas D Gilmore, John R Finnerty
Nematostella vectensis is a member of the phylum Cnidaria, a lineage that includes anemones, corals, hydras, and jellyfishes. This estuarine anemone is an excellent model system for investigating the evolution of stress tolerance because it is easy to collect in its natural habitat and to culture in the laboratory, and it has a sequenced genome. Additionally, there is evidence of local adaptation to environmental stress in different N. vectensis populations, and abundant protein-coding polymorphisms have been identified, including polymorphisms in proteins that are implicated in stress responses...
2018: PloS One
Dengrong Jiang, Peiying Liu, Yang Li, Deng Mao, Cuimei Xu, Hanzhang Lu
PURPOSE: Cerebral venous oxygenation (Yv ) is an important physiological parameter and has potential clinical application in many brain diseases. T2 -relaxation-under-spin-tagging (TRUST) is a commonly used MRI method to measure Yv . Harmonization of this technique across MRI vendors is important for dissemination and multicenter studies of brain oxygenation and metabolism as a disease biomarker. METHODS: TRUST pulse sequence components and imaging parameters were carefully matched between two major MRI vendors, Philips and Siemens...
January 25, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Manushka V Vaidya, Mariana Lazar, Cem M Deniz, Gillian G Haemer, Gang Chen, Mary Bruno, Daniel K Sodickson, Riccardo Lattanzi, Christopher M Collins
BACKGROUND: There is growing interest in detecting cerebro-cerebellar circuits, which requires adequate blood oxygenation level dependent contrast and signal-to-noise ratio (SNR) throughout the brain. Although 7T scanners offer increased SNR, coverage of commercial head coils is currently limited to the cerebrum. PURPOSE: To improve cerebellar functional MRI (fMRI) at 7T with high permittivity material (HPM) pads extending the sensitivity of a commercial coil. STUDY TYPE: Simulations were used to determine HPM pad configuration and assess radiofrequency (RF) safety...
January 21, 2018: Journal of Magnetic Resonance Imaging: JMRI
Anton V Savchenkov, Anna V Vologzhanina, Artem O Dmitrienko, Yan V Zubavichus, Denis V Pushkin, Larisa B Serezhkina, Viktor N Serezhkin
Single crystals of Na[(UO2)(i-C3H7COO)3]·0.7H2O (I), Cs[(UO2)(i-C3H7COO)3] (II) and (NH4)[(UO2)(i-C4H9COO)3] (III) were obtained via isothermal evaporation and their structures were solved using X-ray diffraction techniques. Even though the ligands are branched, bulky and spatial, many carbon and hydrogen atoms are still disordered in these crystal structures at low temperature. A new type of Na coordination is observed for the first time for this family of compounds, proposing high sensitivity of compound I to humidity...
January 16, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Takayuki Ishige, Sakae Itoga, Kazuyuki Matsushita
The molecular diagnosis of the cancer mutational status is essential for modern clinical laboratory medicine. Mutations in EGFR, KRAS, BRAF, and PIK3CA genes are widely analyzed in solid tumors such as lung cancer, colorectal cancer, breast cancer, and melanoma. The allele-specific polymerase chain reaction, high-resolution melting, and Sanger sequencing are used for detecting and identifying gene mutations in many clinical laboratories. The locked nucleic acid (LNA) is a class of nucleic acid analogs that contain a methylene bridge connecting the 2' oxygen and 4' carbon in the ribose moiety...
2018: Advances in Clinical Chemistry
Nicholas R Pannunzio, Michael R Lieber
DNA double-strand breaks (DSBs) occurring within fragile zones of less than 200 base pairs account for the formation of the most common human chromosomal translocations in lymphoid malignancies, yet the mechanism of how breaks occur remains unknown. Here, we have transferred human fragile zones into S. cerevisiae in the context of a genetic assay to understand the mechanism leading to DSBs at these sites. Our findings indicate that a combination of factors is required to sensitize these regions. Foremost, DNA strand separation by transcription or increased torsional stress can expose these DNA regions to damage from either the expression of human AID or increased oxidative stress...
December 7, 2017: Molecular Cell
Xiaoqing Rong-Mullins, Michael C Ayers, Mahmoud Summers, Jennifer E G Gallagher
Cellular metabolism can change the potency of a chemical's tumorigenicity. 4-nitroquinoline-1-oxide (4NQO) is a tumorigenic drug widely used on animal models for cancer research. Polymorphisms of the transcription factor Yrr1 confer different levels of resistance to 4NQO in Saccharomyces cerevisiae To study how different Yrr1 alleles regulate gene expression leading to resistance, transcriptomes of three isogenic S cerevisiae strains carrying different Yrr1 alleles were profiled via RNA sequencing (RNA-Seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-Seq) in the presence and absence of 4NQO...
February 2, 2018: G3: Genes—Genomes—Genetics
Martin Frederik Laursen, Rikke Pilmann Laursen, Anni Larnkjær, Christian Mølgaard, Kim F Michaelsen, Hanne Frøkiær, Martin Iain Bahl, Tine Rask Licht
Faecalibacterium prausnitzii is a highly abundant human gut microbe in healthy individuals, but it is present at reduced levels in individuals with gastrointestinal inflammatory diseases. It has therefore been suggested to constitute a marker of a healthy gut and is associated with anti-inflammatory properties. However, factors affecting the colonization of F. prausnitzii in the human gut during early life are very poorly understood. By analysis of 16S rRNA amplicon sequencing data from three separate infant study populations, we determined the colonization dynamics of Faecalibacterium and factors affecting its establishment in the gut...
November 2017: MSphere
Zemao Yang, Zhigang Dai, Ruike Lu, Bibo Wu, Qing Tang, Ying Xu, Chaohua Cheng, Jianguang Su
Drought stress results in significant crop yield losses. Comparative transcriptome analysis between tolerant and sensitive species can provide insights into drought tolerance mechanisms in jute. We present a comprehensive study on drought tolerance in two jute species-a drought tolerant species (Corchorus olitorius L., GF) and a drought sensitive species (Corchorus capsularis L., YY). In total, 45,831 non-redundant unigenes with average sequence length of 1421 bp were identified. Higher numbers of differentially expressed genes (DEGs) were discovered in YY (794) than in GF (39), implying that YY was relatively more vulnerable or hyper-responsive to drought stress at the molecular level; the two main pathways, phenylpropanoid biosynthesis and peroxisome pathway, significantly involved in scavenging of reactive oxygen species (ROS) and 14 unigenes in the two pathways presented a significant differential expression in response to increase of superoxide...
November 29, 2017: Scientific Reports
V R Samygina, A V Sokolov, G Bourenkov, T R Schneider, V A Anashkin, S O Kozlov, N N Kolmakov, V B Vasilyev
Ceruloplasmin (Cp) is a copper-containing multifunctional oxidase of plasma, an antioxidant, an acute-phase protein and a free radical scavenger. The structural organization of Cp causes its sensitivity to proteolysis and ROS (reactive oxygen species), which can alter some of the important Cp functions. Elucidation of the orthorhombic crystal structure of rat Cp at 2.3 Å resolution revealed the basis for stronger resistance of rat Cp to proteolysis and a new labile copper binding site. The presence of this site appears as a very rare and distinctive feature of rat Cp as was shown by sequence alignment of ceruloplasmin, hephaestin and zyklopen in the Deuterostomia taxonomic group...
December 1, 2017: Metallomics: Integrated Biometal Science
Vitaliy Khlebnikov, Jeroen C W Siero, Alex A Bhogal, Peter R Luijten, Dennis W J Klomp, Hans Hoogduin
PURPOSE: To detect neuronal activity-evoked pH changes by amide proton transfer-chemical exchange saturation transfer (APT-CEST) MRI at 7 T. METHODS: Three healthy subjects participated in the study. A low-power 3-dimensional APT-CEST sequence was optimized through the Bloch-McConnell equations. pH sensitivity of the sequence was estimated both in phantoms and in vivo. The feasibility of pH-functional MRI was tested in Bloch-McConnell-simulated data using the optimized sequence...
November 20, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Zhe Lyu, Yahai Lu
Methanogens have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders...
November 14, 2017: ISME Journal
Marion Darnaud, Alexandre Dos Santos, Patrick Gonzalez, Sandrine Augui, Claire Lacoste, Christophe Desterke, Gert De Hertogh, Emma Valentino, Emilie Braun, Jinzi Zheng, Raphael Boisgard, Christel Neut, Laurent Dubuquoy, Franck Chiappini, Didier Samuel, Patricia Lepage, Francesca Guerrieri, Joel Doré, Christian Bréchot, Nicolas Moniaux, Jamila Faivre
BACKGROUND & AIMS: Paneth cell dysfunction causes deficiencies in intestinal C-type lectins and antimicrobial peptides, which leads to dysbiosis of the intestinal microbiota, alters the mucosal barrier, and promotes development of inflammatory bowel diseases. We investigated whether transgenic expression of the human regenerating family member 3 alpha gene (REG3A) alters the fecal microbiota and affects development of colitis in mice. METHODS: We performed studies with C57BL/6 mice that express human regenerating family member 3 alpha (hREG3A) in hepatocytes, via the albumin gene promoter...
November 10, 2017: Gastroenterology
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