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Daniel L Rolnik, Fabricio da Silva Costa, Daljit Sahota, Jon Hyett, Andrew McLennan
AIM: To assess the quality of mean uterine artery pulsatility index (UtAPI) measurement in a first trimester pre-eclampsia screening program. METHODS: Consecutive patients attending first trimester screening for fetal chromosomal abnormalities also had combined screening for pre-eclampsia based on the Fetal Medicine Foundation (FMF) algorithm, in a large practice in Sydney, Australia, from May 2014 to February 2017. Distributions of mean UtAPI multiples of the median (MoM) on the logarithmic scale were plotted in relation to the normal median with 95% confidence interval (CI) for each operator and for each month...
June 19, 2018: Ultrasound in Obstetrics & Gynecology
Susanne Horn, Sonia Leonardelli, Antje Sucker, Dirk Schadendorf, Klaus G Griewank, Annette Paschen
Poor clinical responses to checkpoint blockade with anti-CTLA-4 and anti-PD-1 antibodies in melanoma have recently been associated with acquired IFNγ resistance that protects tumor cells from the antiproliferative and pro-apoptotic cytokine activity. IFNγ-resistant melanoma cells very often lack functional expression of the IFNγ signaling pathway gene JAK2 due to gene deletions or inactivating gene mutations. Analyzing melanoma cell lines (n = 46, applying next-generation targeted sequencing and single nucleotide polymorphism arrays) as well as available genomic data sets from The Cancer Genome Atlas (TCGA) tumor tissue samples (cutaneous melanoma n = 367, lung squamous cell carcinoma n = 501, bladder urothelial carcinoma n = 408, breast invasive carcinoma n = 768, colorectal adenocarcinoma n = 257), we demonstrate that the frequent chromosomal losses of the tumor suppressor CDKN2A in melanoma and other tumor entities enhance the susceptibility to IFNγ resistance by concomitant deletion of the JAK2 gene (odds ratio = 223...
June 1, 2018: Journal of the National Cancer Institute
Denisse Carvajal-Maldonado, Andrea K Byrum, Jessica Jackson, Sarah Wessel, Delphine Lemaçon, Laure Guitton-Sert, Annabel Quinet, Stephanie Tirman, Simona Graziano, Jean-Yves Masson, David Cortez, Susana Gonzalo, Nima Mosammaparast, Alessandro Vindigni
Pds5 is required for sister chromatid cohesion, and somewhat paradoxically, to remove cohesin from chromosomes. We found that Pds5 plays a critical role during DNA replication that is distinct from its previously known functions. Loss of Pds5 hinders replication fork progression in unperturbed human and mouse cells. Inhibition of MRE11 nuclease activity restores fork progression, suggesting that Pds5 protects forks from MRE11-activity. Loss of Pds5 also leads to double-strand breaks, which are again reduced by MRE11 inhibition...
June 18, 2018: Nucleic Acids Research
Yao Bian, Chunwu Yang, Xiufang Ou, Zhibin Zhang, Bin Wang, Weiwei Ma, Lei Gong, Huakun Zhang, Bao Liu
Polyploidy is a prominent route to speciation in plants; however, this entails resolving the challenges of meiotic instability facing abrupt doubling of chromosome complement. This issue remains poorly understood. We subjected progenies of a synthetic hexaploid wheat, analogous to natural common wheat, but exhibiting extensive meiotic chromosome instability, to heat or salt stress. We selected stress-tolerant cohorts and generated their progenies under normal condition. We conducted fluorescent in situ hybridization/genomic in situ hybridization-based meiotic/mitotic analysis, RNA-Seq and virus-induced gene silencing (VIGS)-mediated assay of meiosis candidate genes...
June 19, 2018: New Phytologist
Shasha Zhang, Alejandro Sánchez Alvarado
High-quality large molecular weight genomic DNA is important for genomic studies. Most commercial available genomic DNA purification kits have failed to generate high molecular weight DNA of sufficient quality from planarians. Here, we describe a simple and efficient genomic DNA isolation method, which has worked for several different planarian species, including Schmidtea mediterranea. This phenol-chloroform based method can be used to obtain genomic DNA of up to 150 kb and can be used for bacterial artificial chromosome (BAC) library construction, next-generation sequencing and PCR cloning...
2018: Methods in Molecular Biology
Zhi Miao, Qian Li, Jian Zhao, Peng Wang, Lei Wang, Hong-Peng He, Nan Wang, Hao Zhou, Tong-Cun Zhang, Xue-Gang Luo
OBJECTIVES: To establish stable infliximab-expressing Chinese hamster ovary (CHO) cells with high tolerance to serum-free culture. RESULTS: Bcl-2 antagonist/killer 1 (BAK1), which is a key mediator of the apoptosis pathway, was disrupted, and infliximab, which is a broadly used monoclonal antibody for the treatment of rheumatoid arthritis and other autoimmune diseases, was incorporated into the BAK1 locus of the CHO chromosome using the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas genome-editing technique...
June 18, 2018: Biotechnology Letters
Zexun Huai, Lishun Peng, Sheliang Wang, Hua Zhao, Lei Shi, Fangsen Xu
Boron (B) is an essential micronutrient of plants. In the present study, we characterized an Arabidopsis mutant lbt with significant l ow -b oron t olerance that was identified based on our previous mapping of QTL for B efficiency in Arabidopsis . Multiple nutrient-deficiency analyses point out that lbt mutant is insensitive to only B-limitation stress. Compared with wild-type Col-0, the fresh weight, leaf area, root length and root elongation rate of lbt mutant were significantly improved under B deficiency during vegetative growth...
2018: Frontiers in Plant Science
James M Dunce, Orla M Dunne, Matthew Ratcliff, Claudia Millán, Suzanne Madgwick, Isabel Usón, Owen R Davies
Meiotic chromosomes adopt unique structures in which linear arrays of chromatin loops are bound together in homologous chromosome pairs by a supramolecular protein assembly, the synaptonemal complex. This three-dimensional scaffold provides the essential structural framework for genetic exchange by crossing over and subsequent homolog segregation. The core architecture of the synaptonemal complex is provided by SYCP1. Here we report the structure and self-assembly mechanism of human SYCP1 through X-ray crystallographic and biophysical studies...
June 18, 2018: Nature Structural & Molecular Biology
Darrel Waggoner, Karen E Wain, Adrian M Dubuc, Laura Conlin, Scott E Hickey, Allen N Lamb, Christa Lese Martin, Cynthia C Morton, Kristen Rasmussen, Jane L Schuette, Stuart Schwartz, David T Miller
PURPOSE: Chromosomal microarray (CMA) is recommended as the first-tier test in evaluation of individuals with neurodevelopmental disability and congenital anomalies. CMA may not detect balanced cytogenomic abnormalities or uniparental disomy (UPD), and deletion/duplications and regions of homozygosity may require additional testing to clarify the mechanism and inform accurate counseling. We conducted an evidence review to synthesize data regarding the benefit of additional testing after CMA to inform a genetic diagnosis...
June 18, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
A Bouam, N Armstrong, A Levasseur, M Drancourt
Three slowly growing mycobacteria named strain AB308, strain AB215 and strain AB57 were isolated from the tomato plant roots. The 16S rRNA and rpoB gene sequence analyses suggested that each strain was representative of one hitherto unidentified slowly-growing Mycobacterium species of the Mycobacterium simiae complex. Genome sequencing indicated that each strain contained one chromosome of 6.015-6.029 Mbp. A total of 1,197, 1,239 and 1,175 proteins were found to be associated with virulence and 107, 76 and 82 proteins were associated with toxin/antitoxin systems for strains AB308, AB215 and AB57, respectively...
June 18, 2018: Scientific Reports
Carlos Sacristan, Misbha Ud Din Ahmad, Jenny Keller, Job Fermie, Vincent Groenewold, Eelco Tromer, Alexander Fish, Roberto Melero, José María Carazo, Judith Klumperman, Andrea Musacchio, Anastassis Perrakis, Geert Jpl Kops
Faithful chromosome segregation depends on the ability of sister kinetochores to attach to spindle microtubules. The outer layer of kinetochores transiently expands in early mitosis to form a fibrous corona, and compacts following microtubule capture. Here we show that the dynein adaptor Spindly and the RZZ (ROD-Zwilch-ZW10) complex drive kinetochore expansion in a dynein-independent manner. C-terminal farnesylation and MPS1 kinase activity cause conformational changes of Spindly that promote oligomerization of RZZ-Spindly complexes into a filamentous meshwork in cells and in vitro...
June 18, 2018: Nature Cell Biology
Zigui Zou, Tianshi Ma, Xuezhi He, Jinxing Zhou, Hongwei Ma, Min Xie, Yanhua Liu, Die Lu, Shihao Di, Zhihong Zhang
Substantial evidence shows that long non-coding RNAs (lncRNAs) participate in many biological mechanisms, and their dysregulation are also involved in the development and progression of cancers, including gastric cancer (GC). Long intergenic non-coding RNA 00324 (LINC00324), a 2115 bp ncRNA, is located on chromosome 17p13.1. The biological function and molecular mechanisms of LINC00324 in GC remains undiscovered. In this paper, we found that the expression level of LINC00324 was significantly upregulated in GC tissues compared with the corresponding normal tissues...
June 18, 2018: Cell Death & Disease
Boram Park, So-My Koo, Jaehoon An, MoonGyu Lee, Hae Yeon Kang, Dandi Qiao, Michael H Cho, Joohon Sung, Edwin K Silverman, Hyeon-Jong Yang, Sungho Won
Cigarette smoke exposure is a major risk factor in chronic obstructive pulmonary disease (COPD) and its interactions with genetic variants could affect lung function. However, few gene-smoking interactions have been reported. In this report, we evaluated the effects of gene-smoking interactions on lung function using Korea Associated Resource (KARE) data with the spirometric variables-forced expiratory volume in 1 s (FEV1 ). We found that variations in FEV1 were different among smoking status. Thus, we considered a linear mixed model for association analysis under heteroscedasticity according to smoking status...
June 18, 2018: Scientific Reports
Pandiyan Muthuramalingam, Subramanian Radhesh Krishnan, Subramani Pandian, Narayanan Mareeswaran, Wilson Aruni, Shunmugiah Karutha Pandian, Manikandan Ramesh
The diversity in plant metabolites with improved phytonutrients is essential to achieve global food security and sustainable crop yield. Our study using computational metabolomics genome wide association study (cmGWAS) reports on a comprehensive profiling of threonine (Thr) metabolite in rice. Sixteen abiotic stress responsive (AbSR) - Thr metabolite producing genes (ThrMPG), modulate metabolite levels and play a significant role determining both physiological and nutritional importance of rice. These AbSR-ThrMPG were computationally analysed for their protein properties using OryzaCyc through plant metabolic network analyser...
June 18, 2018: Scientific Reports
Penghao Li, Zhe Song, Yaxin Yao, Tianhua Huang, Rurong Mao, Jun Huang, Yongyi Ma, Xin Dong, Wenlong Huang, Jihua Huang, Tianjian Chen, Ting Qu, Lingxiao Li, Ying Zhong, Jiang Gu
Preimplantation genetic screening (PGS) detects chromosomal aneuploidy from DNA extracted from trophectodermal biopsy of the embryos before implantation. Although a controlled study showed no difference in pregnancy rates between this invasive cell biopsy technique and a non-biopsied control group, the potential long-term damage by the current PGS method has not be completely ruled out. We therefore tested a less-invasive protocol which utilizes spent culture medium combining with blastocoel fluid (ECB) to assess chromosomal aneuploidy...
June 18, 2018: Scientific Reports
Claire Bedez, Christophe Lotz, Claire Batisse, Arnaud Vanden Broeck, Roland H Stote, Eduardo Howard, Karine Pradeau-Aubreton, Marc Ruff, Valérie Lamour
Type 2 DNA topoisomerases (Top2) are critical components of key protein complexes involved in DNA replication, chromosome condensation and segregation, as well as gene transcription. The Top2 were found to be the main targets of anticancer agents, leading to intensive efforts to understand their functional and physiological role as well as their molecular structure. Post-translational modifications have been reported to influence Top2 enzyme activities in particular those of the mammalian Top2α isoform. In this study, we identified phosphorylation, and for the first time, acetylation sites in the human Top2α isoform produced in eukaryotic expression systems...
June 18, 2018: Scientific Reports
Mengyu Shen, Yuhui Yang, Wei Shen, Lujia Cen, Jeffrey S McLean, Wenyuan Shi, Shuai Le, Xuesong He
The human oral cavity is home to a large number of bacteria and bacteriophages (phages). However, the biology of oral phages as members of the human microbiome is not well understood. Recently, we isolated an Actinomyces odontolyticus subsp. Actinosynbacte r strain XH001 from human oral cavity, and genomic analysis revealed the presence of an intact prophage, named xhp1. Here we demonstrated that xhp1 is a linear plasmid-like prophage, which is a newly identified phage of A. odontolyticus Prophage xhp1 genome is 35 kb linear double-stranded DNA with 10 bp single-stranded cohesive ends at 3' of both ends...
June 18, 2018: Applied and Environmental Microbiology
Melissa Tumen-Velasquez, Christopher W Johnson, Alaa Ahmed, Graham Dominick, Emily M Fulk, Payal Khanna, Sarah A Lee, Alicia L Schmidt, Jeffrey G Linger, Mark A Eiteman, Gregg T Beckham, Ellen L Neidle
Experimental evolution is a critical tool in many disciplines, including metabolic engineering and synthetic biology. However, current methods rely on the chance occurrence of a key step that can dramatically accelerate evolution in natural systems, namely increased gene dosage. Our studies sought to induce the targeted amplification of chromosomal segments to facilitate rapid evolution. Since increased gene dosage confers novel phenotypes and genetic redundancy, we developed a method, Evolution by Amplification and Synthetic Biology (EASy), to create tandem arrays of chromosomal regions...
June 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
Raj K Gopal, Sarah E Calvo, Angela R Shih, Frances L Chaves, Declan McGuone, Eran Mick, Kerry A Pierce, Yang Li, Andrea Garofalo, Eliezer M Van Allen, Clary B Clish, Esther Oliva, Vamsi K Mootha
Renal oncocytomas are benign tumors characterized by a marked accumulation of mitochondria. We report a combined exome, transcriptome, and metabolome analysis of these tumors. Joint analysis of the nuclear and mitochondrial (mtDNA) genomes reveals loss-of-function mtDNA mutations occurring at high variant allele fractions, consistent with positive selection, in genes encoding complex I as the most frequent genetic events. A subset of these tumors also exhibits chromosome 1 loss and/or cyclin D1 overexpression, suggesting they follow complex I loss...
June 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
Nathan H Lazar, Kimberly A Nevonen, Brendan O'Connell, Christine McCann, Rachel J O'Neill, Richard E Green, Thomas J Meyer, Mariam Okhovat, Lucia Carbone
The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here, we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons...
June 18, 2018: Genome Research
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