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https://www.readbyqxmd.com/read/28819222/identification-and-functional-characterization-of-tomato-circrnas-derived-from-genes-involved-in-fruit-pigment-accumulation
#1
Jinjuan Tan, Zhongjing Zhou, Yujie Niu, Xiaoyong Sun, Zhiping Deng
CircRNAs, a class of widespread circular RNAs produced from precursor mRNA back-splicing, have been implicated in regulation of gene expression in eukaryotes, but their biological functions in plants have not yet been elucidated. By deep sequencing of rRNA-removed and RNase R-digested RNA samples we have identified several thousands of putative back-splicing sites in tomato fruit (Solanum lycopersicum) and show that the abundance of some of these circRNAs derived from fruit pigment biosynthesis genes are regulated by fruit ripening...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818908/deep-sequencing-reveals-a-divergent-ugandan-cassava-brown-streak-virus-isolate-from-malawi
#2
Willard Mbewe, Stephan Winter, Settumba Mukasa, Fred Tairo, Peter Sseruwagi, Joseph Ndunguru, Siobain Duffy
Illumina sequencing of RNA from a cassava cutting from northern Malawi produced a genome of Ugandan cassava brown streak virus (UCBSV-MW-NB7_2013). Sequence comparisons revealed stronger similarity to an isolate from nearby Tanzania (93.4% pairwise nucleotide identity) than to those previously reported from Malawi (86.9 to 87.0%).
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818615/deep-transcriptome-profiling-sheds-light-on-key-players-in-nucleus-implantation-induced-immune-response-in-the-pearl-oyster-pinctada-martensii
#3
Wei Wang, Yuyuan Wu, Qiannan Lei, Haiying Liang, Yuewen Deng
Immunological rejection of the pearl oysters following nucleus implantation is a major issue limiting the successful rate of cultured pearls. To date, the molecular mechanism of immune tolerance during pearl formation in the pearl oysters is still largely unknown. Through the RNA sequencing platform and comparative transcriptomic analysis, we investigated the chronic gene expression changes at seven time points (0, 5, 10, 15, 20, 30, 60 days post implantation or dpi) over a period of 60 days following nucleus implantation in the pearl oyster Pinctada martensii...
August 14, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28818587/phenanthrene-responsive-micrornas-and-their-targets-in-wheat-roots
#4
Jinfeng Li, Le Yue, Yu Shen, Yu Sheng, Xinhua Zhan, Guohua Xu, Baoshan Xing
MicroRNAs (miRNAs) play key roles in plant growth, development and responses to abiotic stress. Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants. However, it is yet unknown how miRNAs work during PAH uptake by plant roots. Thus, in this study we ascertain phenanthrene (a model PAH)-responsive miRNAs using small RNA high-throughput deep sequencing and their target genes in wheat roots. We identified 108 conserved and non-conserved miRNA members belonging to 82 miRNA families and found 11 differentially expressed miRNAs, among which four miRNAs (miR156, miR164, miR171a and miR9678-3p) were up-regulated and the other seven miRNAs (miR398, miR531, miR1121, miR5048-5p, miR9653b, miR9773 and miR9778) were down-regulated...
August 8, 2017: Chemosphere
https://www.readbyqxmd.com/read/28817234/osmium-mediated-4su-to-c-transformation-as-key-to-study-rna-dynamics-by-sequencing-tuc-seq
#5
Christian Riml, Thomas Amort, Dietmar Rieder, Catherina Gasser, Alexandra Lusser, Ronald Micura
To understand the functional roles of RNA in the cell, it is essential to elucidate the dynamics of their production, processing and decay. A recent method for assessing mRNA dynamics is metabolic labeling with 4-thiouridine (4sU), followed by thio-selective attachment of affinity tags. Detection of labeled transcripts by affinity purification and hybridization to microarrays or by deep sequencing then reveals RNA expression levels. Here, we present a novel sequencing method that eliminates affinity purification and allows for direct assessment of 4sU labeled RNA...
August 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28816587/dna-methylation-independent-growth-restriction-and-altered-developmental-programming-in-a-mouse-model-of-preconception-male-alcohol-exposure
#6
Richard C Chang, William M Skiles, S Chronister Sarah, Haiqing Wang, Gabrielle I Sutton, Yudhishtar S Bedi, Matthew Snyder, Charles R Long, Michael C Golding
The preconception environment is a significant modifier of dysgenesis and the development of environmentally-induced disease. To date, Fetal Alcohol Spectrum Disorders (FASDs) have been exclusively associated with maternal exposures, yet emerging evidence suggests male-inherited alterations in the developmental program of sperm may be relevant to the growth-restriction phenotypes of this condition. Using a mouse model of voluntary consumption, we find chronic preconception male ethanol exposure associates with fetal growth restriction, decreased placental efficiency, abnormalities in cholesterol trafficking, sex-specific alterations in the genetic pathways regulating hepatic fibrosis, and disruptions in the regulation of imprinted genes...
August 17, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28815944/neonatal-fractures-as-a-presenting-feature-of-lmod3-associated-congenital-myopathy
#7
Megan Abbott, Mahim Jain, Rachel Pferdehirt, Yuqing Chen, Alyssa Tran, Mehmet B Duz, Mehmet Seven, Richard A Gibbs, Donna Muzny, Brendan Lee, Ronit Marom, Lindsay C Burrage
Nemaline myopathy is a rare inherited disorder characterized by weakness, hypotonia, and depressed deep tendon reflexes. It is clinically and genetically heterogeneous, with the most severe phenotype presenting as perinatal akinesia, severe muscle weakness, feeding difficulties and respiratory failure, leading to early mortality. Pathogenic variants in 12 genes, encoding components of the sarcomere or factors related to myogenesis, have been reported in patients affected with the disorder. Here, we describe an early, lethal presentation of decreased fetal movements, hypotonia, muscle weakness, and neonatal respiratory failure requiring ventilator support in three siblings from a consanguineous family...
August 16, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28815891/cystic-kidneys-in-fetal-walker-warburg-syndrome-with-pomt2-mutation-intrafamilial-phenotypic-variability-in-four-siblings-and-review-of-literature
#8
Marwa M Nabhan, Nour ElKhateeb, Daniela A Braun, Sungho Eun, Sahar N Saleem, Heon YungGee, Friedhelm Hildebrandt, Neveen A Soliman
Walker-Warburg syndrome (WWS) is a severe form of congenital muscular dystrophy secondary to α-dystroglycanopathy with muscle, brain, and eye abnormalities often leading to death in the first weeks of life. It is transmitted in an autosomal recessive pattern, and has been linked to at least 15 different genes; including protein O-mannosyltransferase 1 (POMT1), protein O-mannosyltransferase 2 (POMT2), protein O-mannose beta-1,2-N acetylglucosaminyltransferase (POMGNT1), fukutin (FKTN), isoprenoid synthase domain-containing protein (ISPD), and other genes...
August 17, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28813580/genetic-association-of-the-parl-abcc5-htr3d-htr3c-locus-with-primary-angle-closure-glaucoma-in-chinese
#9
Fang Yao Tang, Li Ma, Pancy O S Tam, Chi Pui Pang, Clement C Y Tham, Li Jia Chen
Purpose: This study evaluates the associations of haplotype-tagging single nucleotide polymorphisms (SNPs) in the PARL-ABCC5-HTR3D-HTR3C region with primary angle closure glaucoma (PACG), with a view to identify the responsible SNP in this region. Methods: Thirty SNPs from the PARL-ABCC5-HTR3D-HTR3C region were genotyped in a Hong Kong Chinese cohort of 422 PACG patients and 400 control subjects, using TaqMan SNP genotyping assays. Single marker and haplotype-based association analyses were performed...
August 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28813460/mechanisms-for-pattern-specificity-of-deep-brain-stimulation-in-parkinson-s-disease
#10
Osvaldo Matías Velarde, Germán Mato, Damián Dellavale
Deep brain stimulation (DBS) has become a widely used technique for treating advanced stages of neurological and psychiatric illness. In the case of motor disorders related to basal ganglia (BG) dysfunction, several mechanisms of action for the DBS therapy have been identified which might be involved simultaneously or in sequence. However, the identification of a common key mechanism underlying the clinical relevant DBS configurations has remained elusive due to the inherent complexity related to the interaction between the electrical stimulation and the neural tissue, and the intricate circuital structure of the BG-thalamocortical network...
2017: PloS One
https://www.readbyqxmd.com/read/28811565/iss-pc-identifying-splicing-sites-via-physical-chemical-properties-using-deep-sparse-auto-encoder
#11
Zhao-Chun Xu, Peng Wang, Wang-Ren Qiu, Xuan Xiao
Gene splicing is one of the most significant biological processes in eukaryotic gene expression, such as RNA splicing, which can cause a pre-mRNA to produce one or more mature messenger RNAs containing the coded information with multiple biological functions. Thus, identifying splicing sites in DNA/RNA sequences is significant for both the bio-medical research and the discovery of new drugs. However, it is expensive and time consuming based only on experimental technique, so new computational methods are needed...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811498/genome-re-sequencing-reveals-the-history-of-apple-and-supports-a-two-stage-model-for-fruit-enlargement
#12
Naibin Duan, Yang Bai, Honghe Sun, Nan Wang, Yumin Ma, Mingjun Li, Xin Wang, Chen Jiao, Noah Legall, Linyong Mao, Sibao Wan, Kun Wang, Tianming He, Shouqian Feng, Zongying Zhang, Zhiquan Mao, Xiang Shen, Xiaoliu Chen, Yuanmao Jiang, Shujing Wu, Chengmiao Yin, Shunfeng Ge, Long Yang, Shenghui Jiang, Haifeng Xu, Jingxuan Liu, Deyun Wang, Changzhi Qu, Yicheng Wang, Weifang Zuo, Li Xiang, Chang Liu, Daoyuan Zhang, Yuan Gao, Yimin Xu, Kenong Xu, Thomas Chao, Gennaro Fazio, Huairui Shu, Gan-Yuan Zhong, Lailiang Cheng, Zhangjun Fei, Xuesen Chen
Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an "ancient" isolated ecotype not directly contributing to apple domestication...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28810905/omni-polya-a-method-and-tool-for-accurate-recognition-of-poly-a-signals-in-human-genomic-dna
#13
Arturo Magana-Mora, Manal Kalkatawi, Vladimir B Bajic
BACKGROUND: Polyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3'-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810144/integrated-genomic-characterization-of-pancreatic-ductal-adenocarcinoma
#14
(no author information available yet)
We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic drivers, including GNAS, BRAF, CTNNB1, and additional RAS pathway genes. A subset of tumors harbored multiple KRAS mutations, with some showing evidence of biallelic mutations...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28809941/analysis-of-agoshrna-maturation-and-loading-into-ago2
#15
Alex Harwig, Zita Kruize, Zhenhuang Yang, Tobias Restle, Ben Berkhout
The RNA interference (RNAi) pathway was recently expanded by the discovery of multiple alternative pathways for processing of natural microRNA (miRNA) and man-made short hairpin RNA (shRNA) molecules. One non-canonical pathway bypasses Dicer cleavage and requires instead processing by Argonaute2 (Ago2), which also executes the subsequent silencing step. We named these molecules AgoshRNA, which generate only a single active RNA strand and thus avoid off-target effects that can be induced by the passenger strand of a regular shRNA...
2017: PloS One
https://www.readbyqxmd.com/read/28809698/deep-6-dof-tracking
#16
Mathieu Garon, Jean-Francois Lalonde
We present a temporal 6-DOF tracking method which leverages deep learning to achieve state-of-the-art performance on challenging datasets of real world capture. Our method is both more accurate and more robust to occlusions than the existing best performing approaches while maintaining real-time performance. To assess its efficacy, we evaluate our approach on several challenging RGBD sequences of real objects in a variety of conditions. Notably, we systematically evaluate robustness to occlusions through a series of sequences where the object to be tracked is increasingly occluded...
August 10, 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/28808767/identification-and-expression-analysis-of-micrornas-during-ovule-development-in-rice-oryza-sativa-by-deep-sequencing
#17
Ya Wu, Liyu Yang, Meiling Yu, Jianbo Wang
MicroRNA (miRNA) expression profiles during rice ovule development revealed the possible miRNA-mediated regulation between ovule sporophytic tissue and female gametophyte and the involvement of miRNAs in programmed cell death. MiRNAs are 20-24-nucleotide small RNAs that play key roles in the regulation of many growth and developmental processes in plants. Rice ovule development comprises a series of biological events, which are regulated by complex molecular mechanisms. To gain insight into miRNA-mediated regulation of rice ovule development, Illumina sequencing was used to examine the expression of miRNAs from the megaspore mother cell meiosis stage to the fertilized ovule stage...
August 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28808284/molecular-rationale-behind-the-differential-substrate-specificity-of-bacterial-rnd-multi-drug-transporters
#18
Venkata Krishnan Ramaswamy, Attilio V Vargiu, Giuliano Malloci, Jürg Dreier, Paolo Ruggerone
Resistance-Nodulation-cell Division (RND) transporters AcrB and AcrD of Escherichia coli expel a wide range of substrates out of the cell in conjunction with AcrA and TolC, contributing to the onset of bacterial multidrug resistance. Despite sharing an overall sequence identity of ~66% (similarity ~80%), these RND transporters feature distinct substrate specificity patterns whose underlying basis remains elusive. We performed exhaustive comparative analyses of the putative substrate binding pockets considering crystal structures, homology models and conformations extracted from multi-copy μs-long molecular dynamics simulations of both AcrB and AcrD...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808201/thalamic-paramagnetic-iron-by-t2-relaxometry-correlates-with-severity-of-multiple-sclerosis
#19
Eva Baranovicova, Ema Kantorova, Dagmar Kalenska, Lucia Lichardusova, Michal Bittsan-Sky, Dusan Dobrota
Iron can contribute to the pathogenesis and progression of multiple sclerosis (MS) due to its accumulation in the human brain. We focus on the thalamus as an information transmitter between various subcortical and cortical areas. Thalamic iron seems to follow different rules than iron in other deep gray matter structures and its relation to the clinical outcomes of MS is still indistinct. In our study, we investigated a connection between thalamic iron and patients' disability and course of the disease. The presence of paramagnetic substances in the tissues was tracked by T2* quantification...
July 13, 2017: Journal of Biomedical Research
https://www.readbyqxmd.com/read/28806732/loss-of-the-chromatin-modifier-kdm2aa-causes-brafv600e-independent-spontaneous-melanoma-in-zebrafish
#20
Catherine M Scahill, Zsofia Digby, Ian M Sealy, Sonia Wojciechowska, Richard J White, John E Collins, Derek L Stemple, Till Bartke, Marie E Mathers, E Elizabeth Patton, Elisabeth M Busch-Nentwich
KDM2A is a histone demethylase associated with transcriptional silencing, however very little is known about its in vivo role in development and disease. Here we demonstrate that loss of the orthologue kdm2aa in zebrafish causes widespread transcriptional disruption and leads to spontaneous melanomas at a high frequency. Fish homozygous for two independent premature stop codon alleles show reduced growth and survival, a strong male sex bias, and homozygous females exhibit a progressive oogenesis defect. kdm2aa mutant fish also develop melanomas from early adulthood onwards which are independent from mutations in braf and other common oncogenes and tumour suppressors as revealed by deep whole exome sequencing...
August 14, 2017: PLoS Genetics
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