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Yongbing Zhao, Jinyue Wang, Fang Liang, Yanxia Liu, Qi Wang, Hao Zhang, Meiye Jiang, Zhewen Zhang, Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan W Asmann, Rujiao Li, Jingfa Xiao
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, NucMap includes 798 experimental data from 477 samples across 15 species...
October 18, 2018: Nucleic Acids Research
Mehdi Moustaqil, Frank Fontaine, Jeroen Overman, Alex McCann, Timothy L Bailey, Paulina Rudolffi Soto, Akshay Bhumkar, Nichole Giles, Dominic J B Hunter, Yann Gambin, Mathias Francois, Emma Sierecki
During embryogenesis, vascular development relies on a handful of transcription factors that instruct cell fate in a distinct sub-population of the endothelium (1). The SOXF proteins that comprise SOX7, 17 and 18, are molecular switches modulating arterio-venous and lymphatic endothelial differentiation (2,3). Here, we show that, in the SOX-F family, only SOX18 has the ability to switch between a monomeric and a dimeric form. We characterized the SOX18 dimer in binding assays in vitro, and using a split-GFP reporter assay in a zebrafish model system in vivo...
October 18, 2018: Nucleic Acids Research
Hongwei Wang, Ludong Yang, Yan Wang, Leshi Chen, Huihui Li, Zhi Xie
RPFdb ( or is a public database for hosting, analyzing and visualizing ribosome profiling (ribo-seq) data. Since its initial release in 2015, the amount of new ribo-seq data has been considerably enlarged with the increasing popularity of ribo-seq technique. Here, we describe an updated version, RPFdb v2.0, which brings significant data expansion, feature improvements, and functionality optimization: (i) RPFdb v2.0 currently hosts 2884 ribo-seq datasets from 293 studies, covering 29 different species, in comparison with 777 datasets from 82 studies and 8 species in the previous version; (ii) A refined analysis pipeline with multi-step quality controls has been applied to improve the pre-processing and alignment of ribo-seq data; (iii) New functional modules have been added to provide actively translated open reading frames (ORFs) information for each ribo-seq data; (iv) More features have been made available to increase database usability...
October 18, 2018: Nucleic Acids Research
Yanle Ye, Feng Zhang, Qingxia Chen, Zhiyang Huang, Meijun Li
This investigation was purposed to extrapolate whether and how lncRNA MALAT1, miR-194-5p and ACVR2B altered development of clear cell kidney carcinoma (KIRC). We totally gathered 318 pairs of KIRC tissues and adjacent normal tissues, and also purchased human KIRC cell lines and normal human proximal tubular epithelial cell line. Besides, si-MALAT1, pcDNA-MALAT1, miR-194-5p mimic, miR-194-5p inhibitor and negative control (NC) were, respectively, transfected into KIRC cells. The viability, proliferation and apoptosis of the cells were determined with CCK-8 assay, colony formation assay and flow cytometry...
October 18, 2018: Molecular Carcinogenesis
Giada Graziana Genchi, Andrea Degl'Innocenti, Alice Rita Salgarella, Ilaria Pezzini, Attilio Marino, Arianna Menciassi, Sara Piccirillo, Michele Balsamo, Gianni Ciofani
AIM: Oxidative stress (OS) is strictly associated with senescence/pathogenesis of biological systems. As putative countermeasure to environmental OS, cerium oxide nanoparticles (nanoceria [NC]) were administered to muscle cells on ground and aboard the International Space Station. MATERIALS & METHODS: Transcriptional analyses were conducted through microarray technology and hierarchical clustering. Venn diagram and gene ontology analyses were also performed on selected gene lists...
October 18, 2018: Nanomedicine
Yingxiang Hou, Xin Li, Qianhua Li, Juntao Xu, Huijie Yang, Min Xue, Gang Niu, Shu Zhuo, Kun Mu, Gaosong Wu, Xiumin Li, Hui Wang, Jian Zhu, Ting Zhuang
Oestrogen receptor α (ERα) is overexpressed in two-thirds of all breast cancer cases and is involved in breast cancer development and progression. Although ERα -positive breast cancer can be effectively treated by endocrine therapy, endocrine resistance is an urgent clinical problem. Thus, further understanding of the underlying mechanisms involved in ERα signalling is critical in dealing with endocrine resistance in patients with breast cancer. In the present study, unbiased RNA sequence analysis was conducted between the MCF-7 and MCF-7 tamoxifen-resistant (LCC2) cell lines in order to identify differentially expressed genes...
October 17, 2018: Journal of Cellular and Molecular Medicine
Cristina Agliardi, Franca Rosa Guerini, Milena Zanzottera, Giulio Riboldazzi, Roberta Zangaglia, Andrea Sturchio, Carlo Casali, Cherubino Di Lorenzo, Brigida Minafra, Raffaello Nemni, Mario Clerici
Parkinson's disease (PD) is a α-synucleinopathy in which intracellular aggregates of α-synuclein (α-syn) result in neurodegeneration and in the impairment of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex-mediated release of neurotransmitters. SNAP25 is a SNARE complex component: its concentration is increased in the cerebrospinal fluid of PD patients and this is related to the severity of cognitive and motor symptoms. Five SNAP25 single-nucleotide polymorphisms (SNPs) that modulate gene expression and were described to play a role in neurologic conditions (rs363050, rs363039, rs363043, rs3746544, and rs1051312) were analyzed in a cohort of 412 sporadic Italian PD patients and 1103 healthy controls (HC) in order to identify possible correlation with the disease...
October 17, 2018: Molecular Neurobiology
Fuxi Rong, Feifan Chen, Li Huang, Jiayu Zhang, Chaowen Zhang, Dong Hou, Zhihui Cheng, Yiqun Weng, Peng Chen, Yuhong Li
We identified two curly-leaf (cul) mutants in cucumber. Map-based cloning revealed that both mutants are due to allelic mutations in the CsPHB gene, a homolog of the Arabidopsis PHABULOSA which encodes a class III homeodomain-leucine zipper (HD-ZIP III) transcription factor. Leaf rolling is an important agronomic trait in crop breeding. Moderate leaf rolling minimizes shadowing between leaves, leading to improved photosynthetic efficiency. Although a number of genes controlling rolled leaf have been identified from rice and other plant species, none have been mapped or cloned in cucurbit crops...
October 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Haihong Fang, Lei Liu, Yiquan Zhang, Huiying Yang, Yanfeng Yan, Xiaojuan Ding, Yanping Han, Dongsheng Zhou, Ruifu Yang
Biofilm formation is critical for blocking flea foregut and hence for transmission of Y. pestis by flea biting. In this study, we identified the regulatory role of the AraC-family transcriptional regulator BfvR (YPO1737 in strain CO92) in biofilm formation and virulence of Yersinia pestis biovar Microtus. Crystal violet staining, Caenorhabditis elegans biofilm assay, colony morphology assay, intracellular c-di-GMP concentration determination, and BALB/c mice challenge were employed to reveal that BfvR enhanced Y...
2018: Frontiers in Cellular and Infection Microbiology
Sneeha Veerakumar, Ramesh Pathy Manian
Agarases (agarose 4-glycanohydrolase; EC are class of enzymes that belong to glycoside hydrolase (GH) family capable of hydrolyzing agar. Their classification depends on hydrolysis pattern and product formation. Among all the agarases, β-agarases and the oligosaccharides formed by its action have fascinated quite a lot of industries. Ample of β-agarase genes have been endowed from marine sources such as algae, sea water, and marine sediments, and the expression of these genes into suitable host gives rise to recombinant β-agarases...
October 2018: 3 Biotech
B Tartarotti, A Alfreider, M Egg, N Saul, T Schneider, R Sommaruga, A Tischler, J Vetter
Zooplankton from clear alpine lakes is exposed to stressful levels of solar UV radiation (UVR). As these pelagic organisms experience high UVR and large changes in solar radiation conditions between ice-free and ice-cover periods, they have evolved various strategies to minimize UVR exposure and damage. Here, we studied the relation between photoprotection levels (mycosporine-like amino acids, carotenoids), antioxidant capacities, and gene expression of heat shock proteins ( hsps ) as indicator of stress in the copepod Cyclops abyssorum tatricus during the course of a year...
July 2018: Limnology and Oceanography
Mingyao Meng, Lin Li, Ruhong Li, Wenju Wang, Yang Chen, Yanhua Xie, Rui Han, Kai Zhu, Wenwen Huang, Lili Yang, Shuo Li, Jianlin Shi, Weiwei Tan, Hui Gao, Yiyi Zhao, Li Yang, Jing Tan, Zongliu Hou
Several clinical immunotherapy trials with cytokine-induced killer (CIK) cells have been reported. However, molecular evidence of cell expansion, acquisition of tumor cytotoxicity, and safety of CIK cells is required before putting them to clinical use. Here, we performed dynamic transcriptomic analyses of CIKs generated from primary peripheral blood mononuclear cells exposed to interferon-γ, OKT3, and interleukin-2. CIK mRNAs were extracted and sequenced at days 0, 1, 7, and 14 and subjected to bioinformatics analyses...
October 17, 2018: Journal of Biological Chemistry
Lisa M Sharkey, Nathaniel Safren, Amit S Pithadia, Julia E Gerson, Mark Dulchavsky, Svetlana Fischer, Ronak Patel, Gabrielle Lantis, Naila Ashraf, John H Kim, Alia Meliki, Eiko N Minakawa, Sami J Barmada, Magdalena I Ivanova, Henry L Paulson
UBQLN2 is one of a family of proteins implicated in ubiquitin-dependent protein quality control and integrally tied to human neurodegenerative disease. Whereas wild-type UBQLN2 accumulates in intraneuronal deposits in several common age-related neurodegenerative diseases, mutations in the gene encoding this protein result in X-linked amyotrophic lateral sclerosis/frontotemporal dementia associated with TDP43 accumulation. Using in vitro protein analysis, longitudinal fluorescence imaging and cellular, neuronal, and transgenic mouse models, we establish that UBQLN2 is intrinsically prone to self-assemble into higher-order complexes, including liquid-like droplets and amyloid aggregates...
October 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
Tamotsu Kato, Kyoko Yamazaki, Mayuka Nakajima, Yasuhiro Date, Jun Kikuchi, Koji Hase, Hiroshi Ohno, Kazuhisa Yamazaki
Periodontal disease induced by periodontopathic bacteria like Porphyromonas gingivalis is demonstrated to increase the risk of metabolic, inflammatory, and autoimmune disorders. Although precise mechanisms for this connection have not been elucidated, we have proposed mechanisms by which orally administered periodontopathic bacteria might induce changes in gut microbiota composition, barrier function, and immune system, resulting in an increased risk of diseases characterized by low-grade systemic inflammation...
October 17, 2018: MSphere
Lucas Busta, Won Yim, Evan William LaBrant, Peng Wang, Lindsey Grimes, Kiah Malyszka, John C Cushman, Patricia Santos, Dylan K Kosma, Edgar B Cahoon
Polyacetylenic lipids accumulate in various Apiaceae species after pathogen attack, suggesting that these compounds are naturally occurring pesticides and potentially valuable resources for crop improvement. These compounds also promote human health and slow tumor growth. Even though polyacetylenic lipids were discovered decades ago, the biosynthetic pathway underlying their production is unknown. To begin filling this gap, and ultimately enable polyacetylene engineering, we studied polyacetylenes and their biosynthesis in the major Apiaceae crop carrot (Daucus carota subsp...
October 17, 2018: Plant Physiology
Zi-Qing Miao, Ping-Xia Zhao, Jieli Mao, Linhui Yu, Yang Yuan, Hui Tang, Zhen-Bang Liu, Chengbin Xiang
The gaseous hormone ethylene participates in many physiological processes in plants. Ethylene-inhibited root elongation involves PIN-FORMED2 (PIN2)-mediated basipetal auxin transport, but the molecular mechanisms underlying the regulation of PIN2 function by ethylene (and therefore auxin distribution) are poorly understood. Here, we report that the plant-specific and ethylene-responsive HD-Zip gene HB52 is involved in ethylene-mediated inhibition of primary root elongation in Arabidopsis thaliana. Biochemical and genetic analyses demonstrated that HB52 is ethylene responsive and acts downstream of ETHYLENE-INSENSITIVE3 (EIN3)...
October 17, 2018: Plant Cell
Vijayapalani Paramasivan, Tarek Hewezi, Frederic Pontvianne, Thomas J Baum
Cyst nematodes are plant-pathogenic animals that secrete effector proteins into plant root cells to alter host gene expression and reprogram these cells to form specialized feeding sites, known as syncytia. The molecular mechanisms of these effectors are mostly unknown. We determined that the sugar beet cyst nematode (Heterodera schachtii) 32E03 effector protein strongly inhibits the activities of Arabidopsis thaliana histone deacetylases including the HDT1 enzyme, which has a known function in the regulation of rRNA gene expression through chromatin modifications...
October 17, 2018: Plant Cell
Christoph Niemietz, Lutz Fleischhauer, Vanessa Sandfort, Sarah Guttmann, Andree Zibert, Hartmut H-J Schmidt
Transthyretin (TTR)-related familial amyloid polyneuropathy (ATTR) results from aggregation and extracellular disposition of misfolded TTR variants. Growing evidence suggests the importance of hepatic chaperones for modulation of pathogenesis. We took advantage of iPSC-derived hepatocyte-like cells (HLCs) derived from ATTR patients (ATTR-HLCs) to compare chaperone gene expression to healthy individuals (H-HLCs). From the set of genes analyzed, chaperones that are predominantly located extracellularly were differently expressed...
October 17, 2018: Journal of Cell Science
Jhee Hong Koh, Lei Wang, Caroline Beaudoin-Chabot, Guillaume Thibault
Metabolic disorders such as nonalcoholic fatty liver disease (NAFLD) are emerging epidemics that affect the global population. One facet of these disorders is attributed to the disturbance of membrane lipid composition. Perturbation of endoplasmic reticulum (ER) homeostasis through alteration in membrane phospholipids activates the unfolded protein response (UPR) and causes dramatic transcriptional and translational changes in the cell. To restore cellular homeostasis, the three highly conserved UPR transducers ATF6, IRE1, and PERK mediate adaptive responses upon ER stress...
October 17, 2018: Journal of Cell Science
He-Nan Liu, Nan-Jue Cao, Xun Li, Wei Qian, Xiao-Long Chen
Diabetic retinopathy (DR) is a progressive microvascular complication associated with diabetes, and remains the leading cause of preventable blindness worldwide. Recent studies have revealed that microRNAs (miRNAs) were involving in the physiological and pathophysiological processes of diabetes and its microvascular and macrovascular complications. The purpose of the current investigation is to identify the candidate miR-211 as a novel biomarker for occurrence and progression of DR in clinical study and experimental research...
October 14, 2018: Biochemical and Biophysical Research Communications
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