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https://www.readbyqxmd.com/read/30316186/transcriptome-analysis-of-differentially-expressed-genes-involved-in-innate-immunity-following-bacillus-thuringiensis-challenge-in-bombyx-mori-larvae
#1
Gongqing Wu, Yunhong Yi
In this study, we describe RNA-seq expression profiling of larval Bombyx mori response to hemocoel injection of Bacillus thuringiensis (Bt). Two transcriptomes were generated from the hemocytes of the PBS- and Bt-injected B. mori larvae. More than 49 million 100-bp paired-end reads, encompassing over 7.3 Gb of sequence data, were generated for each library. After filtering the raw reads and removing the rRNA mapped reads, more than 89% of the reads in each library could be mapped to the silkworm genome reference sequence...
October 10, 2018: Molecular Immunology
https://www.readbyqxmd.com/read/30316012/neoantigenic-potential-of-complex-chromosomal-rearrangements-in-mesothelioma
#2
Aaron S Mansfield, Tobias Peikert, James B Smadbeck, Julia B M Udell, Enrique Garcia-Rivera, Laura Elsbernd, Courtney L Erskine, Virginia P Van Keulen, Farhad Kosari, Stephen J Murphy, Hongzheng Ren, Vishnu V Serla, Janet L Schaefer Klein, Giannoula Karagouga, Faye R Harris, Carlos Sosa, Sarah H Johnson, Wendy Nevala, Svetomir N Markovic, Aaron O Bungum, Eric S Edell, Haidong Dong, John C Cheville, Marie Christine Aubry, Jin Jen, George Vasmatzis
INTRODUCTION: Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Whereas other carcinogen-related tumors are associated with a high tumor mutation burden, mesothelioma is not. We sought to resolve this discrepancy. MATERIAL AND METHODS: We used mate-pair (n=22), RNA (n=28) and T cell receptor sequencing along with in silico predictions and immunologic assays to understand how structural variants of chromosomes affect the transcriptome...
October 10, 2018: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/30315931/post-translational-histone-modifications-and-their-interaction-with-sex-influence-normal-brain-development-and-elaboration-of-neuropsychiatric-disorders
#3
REVIEW
G Singh, V Singh, J S Schneider
Sex differences in the risk for and expression of various brain disorders have been known for some time. Yet, the molecular underpinnings of these sex differences as well as how sex modifies normal brain development are still poorly understood. It has recently become known that epigenetic mechanisms play an essential role in establishing and maintaining sex differences in neurodevelopment and disease susceptibility. Epigenetic mechanisms such as post-translational modifications of histones (histone PTMs) integrate various hormonal and external environmental influences to affect genomic output, and this appears to occur in a sex-dependent manner...
October 10, 2018: Biochimica et biophysica acta. Molecular basis of disease
https://www.readbyqxmd.com/read/30315893/identification-of-sparganosis-based-on-next-generation-sequencing
#4
Bailu Du, Yue Tao, Jing Ma, Xing Weng, Yanping Gong, Yang Lin, Nan Shen, Xi Mo, Qing Cao
The incidence of sparganosis, a parasitic disease caused by plerocercoid larvae of the genus Spirometra, has gradually risen worldwide (especially in remote areas) in recent years. Pulmonary and pleural sparganosis, as well as other sites of infestation, including the subcutaneous tissues, the abdominal viscera, brain and eyes, has been reported. In clinical practice, due to the atypical signs and symptoms and limited laboratory approaches for the specific detection of sparganum, sparganosis is often misdiagnosed...
October 10, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30315882/mitochondrial-dna-and-their-nuclear-copies-in-parasitic-wasp-pteromalus-puparum-a-comparative-analysis-in-chalcidoidea
#5
Zhichao Yan, Qi Fang, Yu Tian, Fang Wang, Xuexin Chen, John H Werren, Gongyin Ye
Chalcidoidea (chalcidoid wasps) are an abundant and megadiverse insect group with both ecological and economical importance. Here we report a complete mitochondrial genome in Chalcidoidea from Pteromalus puparum (Pteromalidae). Eight tandem repeats followed by 6 reversed repeats were detected in its 3308 bp control region. This long and complex control region may explain failures of amplifying and sequencing of complete mitochondrial genomes in some chalcidoids. In addition to 37 typical mitochondrial genes, an extra identical isoleucine tRNA (trnI) was detected...
October 10, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/30315880/characterization-and-comparison-of-the-mitochondrial-genomes-from-two-lyophyllum-fungal-species-and-insights-into-phylogeny-of-agaricomycetes
#6
Qiang Li, Qiangfeng Wang, Xin Jin, Zuqin Chen, Chuan Xiong, Ping Li, Jian Zhao, Wenli Huang
Lyophyllum decastes and Lyophyllum shimeji are the two primary species within the L. decastes complex, and they differ considerably in their nutritional lifestyles and preferred growth environments. However, differences in their mitogenomes have not yet been investigated. In this study, the mitogenomes of the two species were sequenced by next-generation sequencing technology, successfully assembled, and compared. The two mitogenomes of L. decastes and L. shimeji comprised circular DNA molecules of sizes 50,643 bp and 73,678 bp, respectively...
October 10, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/30315876/substituted-3-benzylcoumarins-13-and-14-suppress-enterovirus-a71-replication-by-impairing-viral-2a-pro-dependent-ires-driven-translation
#7
Hao Zhang, Xin Wang, Yuya Wang, Xinyi Pei, Chao Wang, Yan Niu, Ping Xu, Yihong Peng
Activation of the ERK signaling cascade in host cells has been demonstrated to be essential for Enterovirus A71 (EV-A71) replication. Our previous study showed that MEK kinase, which specially activated downstream ERK kinase, is an important and potential target against EV-A71. Furthermore, we reported that a series of substituted 3-benzylcoumarins designed and synthesized as well as verified for inhibiting the MEK-ERK cascade were found to be effective on anti-EV-A71. In this study, we further demonstrated that two substituted 3-benzylcoumarins designated as 13 and 14 were more effective anti-MEK/ERK activity, less cytotoxicity and stronger antiviral effect represented by inhibition of viral-induced CPE, the expression of viral proteins and the replication of the viral genome, as well as the production of progeny virions, compared to those of U0126, an available MEK inhibitor, and sorafenib, a multiple-targeted kinase inhibitor in clinical use...
October 10, 2018: Antiviral Research
https://www.readbyqxmd.com/read/30315875/clinical-management-and-viral-genomic-diversity-analysis-of-a-child-s-influenza-a-h1n1-pdm09-infection-in-the-context-of-a-severe-combined-immunodeficiency
#8
Maxime Pichon, Caroline Picard, Bruno Simon, Alexandre Gaymard, Cécile Renard, Bruno Massenavette, Christophe Malcus, Guillaume Monneret, Florence Morfin-Sherpa, Martine Valette, Etienne Javouhey, Gilles Millat, Bruno Lina, Laurence Josset, Vanessa Escuret
INTRODUCTION: A child with severe combined immunodeficiency (SCID) had an influenza A(H1N1)pdm09 infection with viral excretion longer than 6 months, during 2013-2014 influenza season, despite cord blood transplantation and antiviral treatments. METHODS: Conventional real-time RT-PCR methods were used to estimate viral load and to detect the presence of the common N1 neuraminidase (NA) H275Y substitution responsible for oseltamivir resistance. Next-generation sequencing (NGS) of influenza viruses was performed retrospectively to characterize viral quasispecies in specimens...
October 10, 2018: Antiviral Research
https://www.readbyqxmd.com/read/30315870/synthetic-biology-tools-for-engineering-yarrowia-lipolytica
#9
REVIEW
M Larroude, T Rossignol, J-M Nicaud, R Ledesma-Amaro
The non-conventional oleaginous yeast Yarrowia lipolytica shows great industrial promise. It naturally produces certain compounds of interest but can also artificially generate non-native metabolites, thanks to an engineering process made possible by the significant expansion of a dedicated genetic toolbox. In this review, we present recently developed synthetic biology tools that facilitate the manipulation of Y. lipolytica, including 1) DNA assembly techniques, 2) DNA parts for constructing expression cassettes, 3) genome-editing techniques, and 4) computational tools...
October 10, 2018: Biotechnology Advances
https://www.readbyqxmd.com/read/30315815/the-role-of-telomere-shortening-in-carcinogenesis-a-hybrid-stochastic-deterministic-approach
#10
Ignacio A Rodriguez-Brenes, Natalia L Komarova, Dominik Wodarz
Genome instability is a characteristic of most cancers, contributing to the acquisition of genetic alterations that drive tumor progression. One important source of genome instability is linked to telomere dysfunction in cells with critically short telomeres that lack p53-mediated surveillance of genomic integrity. Here we research the probability that cancer emerges through an evolutionary pathway that includes a telomere-induced phase of genome instability. To implement our models we use a hybrid stochastic-deterministic approach, which allows us to perform large numbers of simulations using biologically realistic population sizes and mutation rates, circumventing the traditional limitations of fully stochastic algorithms...
October 10, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30315781/enhancer-connectome-nominates-target-genes-of-inherited-risk-variants-from-inflammatory-skin-disorders
#11
Mark Y Jeng, Maxwell R Mumbach, Jeffrey M Granja, Ansuman T Satpathy, Howard Y Chang, Anne Lynn S Chang
The vast majority of polymorphisms for human dermatologic diseases fall in non-coding DNA regions, leading to difficulty interpreting their functional significance. Recent work utilizing chromosome conformation capture (3C) technology in combination with chromatin immunoprecipitation (ChIP) has provided a systematic means of linking non-coding variants within active enhancer loci to putative gene targets. Here, we apply H3K27ac HiChIP high-resolution contact maps, generated from primary human T-cell subsets (CD4+ Naïve, TH 17, and Treg ), to 21 dermatologic conditions associated with single nucleotide polymorphisms (SNPs) from 106 genome-wide association studies (GWAS)...
October 10, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/30315724/ddca-antagonizes-a-bacterial-dna-damage-checkpoint
#12
Peter E Burby, Zackary W Simmons, Lyle A Simmons
Bacteria coordinate DNA replication and cell division, ensuring a complete set of genetic material is passed onto the next generation. When bacteria encounter DNA damage, a cell cycle checkpoint is activated by expressing a cell division inhibitor. The prevailing model is that activation of the DNA damage response and protease mediated degradation of the inhibitor is sufficient to regulate the checkpoint process. Our recent genome-wide screens identified the gene ddcA as critical for surviving exposure to DNA damage...
October 13, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/30315721/expression-analysis-of-cellulose-synthases-that-comprise-the-type-ii-complex-in-hybrid-aspen
#13
Yuki Osako, Naoki Takata, Nuoendagula, Shinnosuke Ishikawa, Taishi Umezawa, Toru Taniguchi, Shinya Kajita
Gene duplication in plants occurs via several different mechanisms, including whole-genome duplication, and the copied genes acquire various forms and types. The cellulose synthase (CesA) family functions in cellulose synthesis complex (CSC) formation, which is involved in the synthesis of primary and secondary cell walls in plants. In the genome of Populus, 17 CesAs have been annotated, and some of them have appeared by whole-genome duplication. The nucleotide sequence of the duplicated genes has changed during subsequent evolution, and functional differentiation of the genes might have occurred...
October 13, 2018: Plant Biology
https://www.readbyqxmd.com/read/30315682/human-genomics-of-acute-liver-failure-due-to-hepatitis-b-virus-infection-an-exome-sequencing-study-in-liver-transplant-recipients
#14
Samira Asgari, Nimisha Chaturvedi, Petar Scepanovic, Christian Hammer, Nasser Semmo, Emiliano Giostra, Beat Müllhaupt, Peter Angus, Alexander J Thompson, Darius Moradpour, Jacques Fellay
Acute liver failure (ALF) or fulminant hepatitis is a rare, yet severe outcome of infection with hepatitis B virus (HBV) that carries a high mortality rate. The occurrence of a life-threatening condition upon infection with a prevalent virus in individuals without known risk factors is suggestive of pathogen-specific immune dysregulation. In the absence of established differences in HBV virulence, we hypothesized that ALF upon primary infection with HBV could be due to rare deleterious variants in the human genome...
October 13, 2018: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/30315669/patterns-of-mutation-within-an-emerging-endemic-lineage-of-hev-3a
#15
Yuan O Zhu, Pauline Aw, Myo Myint Aung, Hong Kai Lee, Martin Hibberd, Guan Huei Lee
The hepatitis E virus can cause chronic infections in immuno-suppressed patients, and cases have been on the rise globally. Viral mutations during such infections are difficult to characterize. We deep sequenced viral populations from 15 immuno-compromised patients with chronic HEV to identify the viral lineage and describe viral mutational hotspots within and across patients. 21 viral RNA samples were collected between 2012-2017 from a single hospital in Singapore. Sequences covering a total of 3894bp of the HEV genome were obtained...
October 13, 2018: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/30315621/insight-into-the-evolution-and-functional-characteristics-of-the-pan-genome-assembly-from-sesame-landraces-and-modern-cultivars
#16
Jingyin Yu, Agnieszka A Golicz, Kun Lu, Komivi Dossa, Yanxin Zhang, Jinfeng Chen, Linhai Wang, Jun You, Dingding Fan, David Edwards, Xiurong Zhang
Sesame (Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces (S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars (S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference-assisted assembly approach to improve the draft assemblies of four of the sesame varieties...
October 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/30315615/acceleration-of-cancer-science-with-genome-editing-and-related-technologies
#17
REVIEW
Tetsushi Sakuma, Takashi Yamamoto
Genome editing includes various edits of the genome, such as short insertions and deletions, substitutions, and chromosomal rearrangements including inversions, duplications, and translocations. These varieties are based on single or multiple DNA double strand break (DSB)-triggered in cellulo repair machineries. In addition to these "conventional" genome editing strategies, tools enabling customized, site-specific recognition of particular nucleic acid sequences have been coming into wider use, e...
October 13, 2018: Cancer Science
https://www.readbyqxmd.com/read/30315582/reticulate-evolution-within-a-spruce-picea-species-complex-revealed-by-population-genomic-analysis
#18
Yongshuai Sun, Richard J Abbott, Zhiqiang Lu, Kangshan Mao, Lei Zhang, Xiaojuan Wang, Dafu Ru, Jianquan Liu
The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Evidence of genetic exchange between diverging taxa is reported frequently, although most studies fail to show how hybridization and introgression contribute to the adaptation and differentiation of introgressed taxa. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex, which comprises four taxa occurring in the biodiversity hotspot of the Hengduan-Himalayan mountains...
October 12, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/30315522/profiling-of-glucose-induced-transcription-in-sulfolobus-acidocaldarius-dsm-639
#19
Jungwook Park, Areum Lee, Hyun-Hee Lee, Inmyoung Park, Young-Su Seo, Jaeho Cha
Sulfolobus species can grow on a variety of organic compounds as carbon and energy sources. These species degrade glucose to pyruvate by the modified branched Entner-Doudoroff pathway. We attempted to determine the differentially expressed genes (DEGs) under sugar-limited and sugar-rich conditions. RNA sequencing (RNA-seq) was used to quantify the expression of the genes and identify those DEGs between the S. acidocaldarius cells grown under sugar-rich (YT with glucose) and sugar-limited (YT only) conditions...
November 2018: Genes & Genomics
https://www.readbyqxmd.com/read/30315521/transcriptome-profiling-of-rubber-tree-hevea-brasiliensis-discovers-candidate-regulators-of-the-cold-stress-response
#20
Xiao-Xiao Gong, Bing-Yu Yan, Jin Hu, Cui-Ping Yang, Yi-Jian Li, Jin-Ping Liu, Wen-Bin Liao
Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at 4 °C for 2 h) and LT24 (cold treatment at 4 °C for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling...
November 2018: Genes & Genomics
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