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https://www.readbyqxmd.com/read/27923064/sparse-regression-based-structure-learning-of-stochastic-reaction-networks-from-single-cell-snapshot-time-series
#1
Anna Klimovskaia, Stefan Ganscha, Manfred Claassen
Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27920554/next-generation-sequence-detects-arap3-as-a-novel-oncogene-in-papillary-thyroid-carcinoma
#2
Qing-Xuan Wang, En-Dong Chen, Ye-Feng Cai, Yi-Li Zhou, Zhou-Ci Zheng, Ying-Hao Wang, Yi-Xiang Jin, Wen-Xu Jin, Xiao-Hua Zhang, Ou-Chen Wang
PURPOSE: Thyroid cancer is the most frequent malignancies of the endocrine system, and it has became the fastest growing type of cancer worldwide. Much still remains unknown about the molecular mechanisms of thyroid cancer. Studies have found that some certain relationship between ARAP3 and human cancer. However, the role of ARAP3 in thyroid cancer has not been well explained. This study aimed to investigate the role of ARAP3 gene in papillary thyroid carcinoma. METHODS: Whole exon sequence and whole genome sequence of primary papillary thyroid carcinoma (PTC) samples and matched adjacent normal thyroid tissue samples were performed and then bioinformatics analysis was carried out...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27919066/designed-proteins-induce-the-formation-of-nanocage-containing-extracellular-vesicles
#3
Jörg Votteler, Cassandra Ogohara, Sue Yi, Yang Hsia, Una Nattermann, David M Belnap, Neil P King, Wesley I Sundquist
Complex biological processes are often performed by self-organizing nanostructures comprising multiple classes of macromolecules, such as ribosomes (proteins and RNA) or enveloped viruses (proteins, nucleic acids and lipids). Approaches have been developed for designing self-assembling structures consisting of either nucleic acids or proteins, but strategies for engineering hybrid biological materials are only beginning to emerge. Here we describe the design of self-assembling protein nanocages that direct their own release from human cells inside small vesicles in a manner that resembles some viruses...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27917784/suppression-of-bromodomain-containing-protein-4-by-shrna-a-new-approach-for-cancer-treatment
#4
Turan Kaya, Berke Kahraman, Nurgeldi Bazarov, Alperen S Toker, Ayse Celik, Sadik Cigdem, Esra Gunduz
PURPOSE: MYC is a transcription factor coding gene that is believed to control 15% of the genes in the entire human genome. The central role of c-MYC in cancer pathogenesis makes it a major therapeutic target in field of anticancer agent development. METHODS: We targeted the acetyl-lysine binding modules or bromodomains, which are associated with c-MYC transcriptional activation. RESULTS: Sequence specific inhibition of BET bromodomains with small hairpin RNAs (shRNAs) resulted in cessation of cellular proliferation in different cancer cell lines...
December 1, 2016: Clinical and Investigative Medicine. Médecine Clinique et Experimentale
https://www.readbyqxmd.com/read/27917320/the-complete-chloroplast-genome-sequence-of-helwingia-himalaica-helwingiaceae-aquifoliales-and-a-chloroplast-phylogenomic-analysis-of-the-campanulidae
#5
Xin Yao, Ying-Ying Liu, Yun-Hong Tan, Yu Song, Richard T Corlett
Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels...
2016: PeerJ
https://www.readbyqxmd.com/read/27917182/expression-of-flavone-synthase-ii-and-flavonoid-3-hydroxylase-is-associated-with-color-variation-in-tan-colored-injured-leaves-of-sorghum
#6
Hiroshi Mizuno, Takayuki Yazawa, Shigemitsu Kasuga, Yuji Sawada, Hiroyuki Kanamori, Yuko Ogo, Masami Yokota Hirai, Takashi Matsumoto, Hiroyuki Kawahigashi
Sorghum (Sorghum bicolor L. Moench) exhibits various color changes in injured leaves in response to cutting stress. Here, we aimed to identify key genes for the light brown and dark brown color variations in tan-colored injured leaves of sorghum. For this purpose, sorghum M36001 (light brown injured leaves), Nakei-MS3B (purple), and a progeny, #7 (dark brown), from Nakei-MS3B × M36001, were used. Accumulated pigments were detected by using high-performance liquid chromatography: M36001 accumulated only apigenin in its light brown leaves; #7 accumulated both luteolin and a small amount of apigenin in its dark brown leaves, and Nakei-MS3B accumulated 3-deoxyanthocyanidins (apigeninidin and luteolinidin) in its purple leaves...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27916288/small-non-coding-rna-expression-from-anterior-cingulate-cortex-in-schizophrenia-shows-sex-specific-regulation
#7
Chikako Ragan, Kalpana Patel, Janette Edson, Zong-Hong Zhang, Jacob Gratten, Bryan Mowry
MicroRNAs (miRNAs) are known to regulate the expression of genes that are important for brain development and function, but the roles of other classes of small non-coding RNAs (sncRNAs) are less well understood. Additionally, although miRNA expression studies have been conducted in post-mortem brain samples from schizophrenia (SCZ) patients, other classes of sncRNAs are yet to be investigated in SCZ. We profiled the expression of miRNAs, piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and small nuclear RNAs (snRNAs) in SCZ by applying small RNA sequencing (RNA-Seq) to sncRNA isolated from post-mortem anterior cingulate cortex (ACC) of SCZ-affected individuals (n=22) and matched controls (n=22)...
December 1, 2016: Schizophrenia Research
https://www.readbyqxmd.com/read/27915129/nicotiana-benthamiana-plants-asymptomatically-infected-by-pelargonium-line-pattern-virus-show-unusually-high-accumulation-of-viral-small-rnas-that-is-neither-associated-with-dcl-induction-nor-rdr6-activity
#8
Miryam Pérez-Cañamás, Marta Blanco-Pérez, Javier Forment, Carmen Hernández
Pelargonium line pattern virus (PLPV, Tombusviridae) normally establishes systemic, low-titered and asymptomatic infections in its hosts. This type of interaction may be largely determined by events related to RNA silencing, a major antiviral mechanism in plants. This mechanism is triggered by double or quasi double-stranded (ds) viral RNAs which are cut by DCL ribonucleases into virus small RNAs (vsRNAs). Such vsRNAs are at the core of the silencing process as they guide sequence-specific RNA degradation Host RNA dependent-RNA polymerases (RDRs), and particularly RDR6, strengthen antiviral silencing by promoting biosynthesis of secondary vsRNAs...
December 1, 2016: Virology
https://www.readbyqxmd.com/read/27914101/tuc-338-promotes-invasion-and-metastasis-in-colorectal-cancer
#9
Chenghai Wang, Zheng Wang, Jie Zhou, Shuang Liu, Cong Wu, Caihong Huang, Yongling Ding
Ultraconserved regions (UCRs) are non-protein coding gene sequences that are strictly conserved across among different species. Emerging evidence demonstrates that transcribed ultraconserved regions (TUCRs) encoding noncoding RNAs serve as regulators of gene expression. In recent decades, increasing evidence implicates the involvement of UCRs in carcinogenesis. The role of TUC.338 in cervical cancers was an oncogene in previous studies. Until now, the role of TUC.338 in colorectal cancers remains undefined...
December 3, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27913729/qsea-modelling-of-genome-wide-dna-methylation-from-sequencing-enrichment-experiments
#10
Matthias Lienhard, Sabrina Grasse, Jana Rolff, Steffen Frese, Uwe Schirmer, Michael Becker, Stefan Börno, Bernd Timmermann, Lukas Chavez, Holger Sültmann, Gunda Leschber, Iduna Fichtner, Michal R Schweiger, Ralf Herwig
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913566/th2-responses-are-primed-by-skin-dendritic-cells-with-distinct-transcriptional-profiles
#11
Lisa M Connor, Shiau-Choot Tang, Emmanuelle Cognard, Sotaro Ochiai, Kerry L Hilligan, Samuel I Old, Christophe Pellefigues, Ruby F White, Deepa Patel, Adam Alexander T Smith, David A Eccles, Olivier Lamiable, Melanie J McConnell, Franca Ronchese
The dendritic cell signals required for the in vivo priming of IL-4-producing T cells are unknown. We used RNA sequencing to characterize DCs from skin LN of mice exposed to two different Th2 stimuli: the helminth parasite Nippostrongylus brasiliensis (Nb) and the contact sensitizer dibutyl phthalate (DBP)-FITC. Both Nb and DBP-FITC induced extensive transcriptional changes that involved multiple DC subsets. Surprisingly, these transcriptional changes were highly distinct in the two models, with only a small number of genes being similarly regulated in both conditions...
December 2, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27911848/global-analysis-of-genomic-instability-caused-by-dna-replication-stress-in-saccharomyces-cerevisiae
#12
Dao-Qiong Zheng, Ke Zhang, Xue-Chang Wu, Piotr A Mieczkowski, Thomas D Petes
DNA replication stress (DRS)-induced genomic instability is an important factor driving cancer development. To understand the mechanisms of DRS-associated genomic instability, we measured the rates of genomic alterations throughout the genome in a yeast strain with lowered expression of the replicative DNA polymerase δ. By a genetic test, we showed that most recombinogenic DNA lesions were introduced during S or G2 phase, presumably as a consequence of broken replication forks. We observed a high rate of chromosome loss, likely reflecting a reduced capacity of the low-polymerase strains to repair double-stranded DNA breaks (DSBs)...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911495/synthesis-and-evaluation-of-caged-sirna-with-terminal-single-vitamin-e-modification
#13
Jiali Yang, Lijia Yu, Liangliang Zhang, Xingsu Long, Yuzhuo Ji, Xinjing Tang
RNA-induced gene silencing has been widely applied as a powerful research tool in drug development due to its sequence-specific degradation of target mRNA. Conditional regulation of gene functions with small interfering RNAs (siRNAs) is highly useful, especially when specific gene expression regulation with spatiotemporal resolution and amplitude is desired. Here, the synthesis of a series of new caged siRNAs with vitamin E (vitE) modification and/or a single photolabile linker at the 5' terminal is described...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27909445/identification-and-profiling-of-micrornas-expressed-in-elongating-cotton-fibers-using-small-rna-deep-sequencing
#14
Yanmei Wang, Yan Ding, Jin-Yuan Liu
Plant microRNAs (miRNAs) have been shown to play essential roles in the regulation of gene expression. In this study, small RNA deep sequencing was applied to explore novel miRNAs expressed in elongating cotton fibers. A total of 46 novel and 96 known miRNAs, primarily derived from the corresponding specific loci in genome of Gossypium arboreum, were identified. 64 miRNAs were shown to be differentially expressed during the fiber elongation process; 16 were predicted to be novel miRNAs while the remaining 48 belong to known miRNA families...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27907010/viral-metagenomic-analysis-displays-the-co-infection-situation-in-healthy-and-pmws-affected-pigs
#15
Anne-Lie Blomström, Caroline Fossum, Per Wallgren, Mikael Berg
The development of high-throughput sequencing technologies have allowed the possibility to investigate and characterise the entire microbiome of individuals, providing better insight to the complex interaction between different microorganisms. This will help to understand how the microbiome influence the susceptibility of secondary agents and development of disease. We have applied viral metagenomics to investigate the virome of lymph nodes from Swedish pigs suffering from the multifactorial disease postweaning multisystemic wasting syndrome (PMWS) as well as from healthy pigs...
2016: PloS One
https://www.readbyqxmd.com/read/27906199/microduplication-of-the-arid1a-gene-causes-intellectual-disability-with-recognizable-syndromic-features
#16
Marie Bidart, Michèle El Atifi, Sarra Miladi, John Rendu, Véronique Satre, Pierre F Ray, Caroline Bosson, Françoise Devillard, Daphné Lehalle, Valérie Malan, Jeanne Amiel, Maria Antonietta Mencarelli, Margherita Baldassarri, Alessandra Renieri, Jill Clayton-Smith, Gaëlle Vieville, Julien Thevenon, Florence Amblard, François Berger, Pierre-Simon Jouk, Charles Coutton
PURPOSE: To determine whether duplication of the ARID1A gene is responsible for a new recognizable syndrome. METHODS: We describe four patients with a 1p36.11 microduplication involving ARID1A as identified by array-comparative genomic hybridization . We performed comparative transcriptomic analysis of patient-derived fibroblasts using RNA sequencing and evaluated the impact of ARID1A duplication on the cell cycle using fluorescence-activated cell sorting. Functional relationships between differentially expressed genes were investigated with ingenuity pathway analysis (IPA)...
December 1, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/27902296/allostreptomyces-psammosilenae-gen-nov-sp-nov-an-endophytic-actinobacterium-isolated-from-the-roots-of-psammosilene-tunicoides-and-emended-description-of-the-family-streptomycetaceae-waksman-and-henrici-1943-al-emend-rainey-et-al-1997-emend-kim-et-al-2003-emend
#17
Mei-Juan Huang, Manik Prabhu Narsing Rao, Nimaichand Salam, Min Xiao, Hai-Quan Huang, Wen-Jun Li
A Gram-staining positive actinobacterium, designated strain YIM DR4008T was isolated from the root sample of Psammosilene tunicoides collected from Lijiang, Yunnan, China. Strain YIM DR4008T could grow at temperature ranging from 10 to 50 °C (optimum at 28-30 °C), pH 5.0-11.0 (optimum pH 7.0) and in the presence of up to 4 % (w/v) NaCl. Sequence analysis of the 16S ribosomal RNA gene revealed that strain YIM DR4008T shared highest similarity (95.0 %) with Streptomyces griseoplanus NBRC 12779T and < 95 % similarity with other known members of the genera Streptomyces, Kitasatospora and Streptacidiphilus...
October 27, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902246/allodekkera-sacchari-gen-nov-sp-nov-a-novel-yeast-species-in-the-saccharomycetales-isolated-from-a-sugar-factory-in-thailand
#18
Rumpa Jutakanoke, Rikiya Endoh, Masako Takashima, Moriya Ohkuma, Somboon Tanasupawat, Ancharida Akaracharanya
Three yeast isolates, G5-5(5), G5-9(3) and G5-9(4), were obtained from the sugarcane juice and waste from sugar production plant (Korach Industry Co., Ltd.) in Korach province, Thailand. They were found to be the same species based on DNA sequence identity of the small subunit ribosomal RNA gene (SSU) and the D1/D2 region of the large subunit rRNA gene (LSU D1/D2). A BLASTn search of the GenBank database revealed they had 93% nucleotide sequence identity to D. bruxellensis for the SSU (1742 bp), but their LSU D1/D2 sequence (572 bp) showed less than 90% identity to all available sequences in the database...
October 25, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27901505/first-isolation-of-miamiensis-avidus-ciliophora-scuticociliatida-associated-with-skin-ulcers-from-reared-pharaoh-cuttlefish-sepia-pharaonis
#19
Zhen Tao, Lu Liu, Xiangrui Chen, Suming Zhou, Guoliang Wang
In the winter of 2015, a skin ulcer disease outbreak occurred in a pharaoh cuttlefish Sepia pharaonis population cultured on a land-based fish farm in China. Affected cuttlefish (about 60% of the population) were characterized as having developed ulcers on the dorsal skin, fin fringe, or distal mantle tip. Masses of a ciliated protozoan were isolated from skin ulcers. The ciliate was identified as Miamiensis avidus based on the morphological features of living and protargol-impregnated specimens. This identification was also supported by high sequence similarity of the small subunit ribosomal RNA gene (100%) and another ribosomal DNA region (including the 2 internal transcribed spacers and the 5...
November 22, 2016: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/27901112/depletion-of-trna-halves-enables-effective-small-rna-sequencing-of-low-input-murine-serum-samples
#20
Alan Van Goethem, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, Liselot M Mus, Eveline Barbieri, Frank Speleman, Pieter Mestdagh, Jason Shohet, Tom Van Maerken, Jo Vandesompele
The ongoing ascent of sequencing technologies has enabled researchers to gain unprecedented insights into the RNA content of biological samples. MiRNAs, a class of small non-coding RNAs, play a pivotal role in regulating gene expression. The discovery that miRNAs are stably present in circulation has spiked interest in their potential use as minimally-invasive biomarkers. However, sequencing of blood-derived samples (serum, plasma) is challenging due to the often low RNA concentration, poor RNA quality and the presence of highly abundant RNAs that dominate sequencing libraries...
November 30, 2016: Scientific Reports
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