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https://www.readbyqxmd.com/read/30119077/added-value-of-whole-exome-and-transcriptome-sequencing-for-clinical-molecular-screenings-of-advanced-cancer-patients-with-solid-tumors
#1
Florence Koeppel, Alexandre Bobard, Céline Lefebvre, Marion Pedrero, Marc Deloger, Yannick Boursin, Catherine Richon, Romy Chen-Min-Tao, Guillaume Robert, Guillaume Meurice, Etienne Rouleau, Stefan Michiels, Christophe Massard, Jean-Yves Scoazec, Eric Solary, Jean-Charles Soria, Fabrice André, Ludovic Lacroix
Comprehensive genomic profiling using high-throughput sequencing brings a wealth of information, and its place in the clinical setting has been increasingly prominent. This review emphasizes the utility of whole-exome sequencing (WES) and transcriptome sequencing (RNAseq) in patient care and clinical research, based on published reports as well as our experience with the MOSCATO-01 (MOlecular Screening for CAncer Treatment Optimization) molecular triage trial at Gustave Roussy Cancer Center. In this trial, all contributive samples of patients with advanced solid tumors were analyzed prospectively with targeted gene sequencing (TGS) and comparative genomic hybridization...
July 2018: Cancer Journal
https://www.readbyqxmd.com/read/30116983/virus-preparations-from-the-mixed-infected-p70-pinot-noir-accession-exhibit-glrav-1-gva-end-to-end-particles
#2
Antoine Alliaume, Catherine Reinbold, Mathieu Erhardt, Monique Beuve, Jean-Michel Hily, Olivier Lemaire, Etienne Herrbach
P70 is a Pinot Noir grapevine accession that displays strong leafroll disease symptoms. A high-throughput sequencing (HTS)-based analysis established that P70 was mixed-infected by two variants of grapevine leafroll-associated virus 1 (GLRaV-1, genus Ampelovirus) and one of grapevine virus A (GVA, genus Vitivirus) as well as by two viroids (hop stunt viroid [HSVd] and grapevine yellow speckle viroid 1 [GYSVd1]) and four variants of grapevine rupestris stem pitting-associated virus (GRSPaV). Immunogold labelling using gold particles of two different diameters revealed the existence of 'hybrid' particles labelled at one end as GLRaV-1, with the rest labelled as GVA...
August 16, 2018: Archives of Virology
https://www.readbyqxmd.com/read/30116615/characterization-of-the-t-cell-repertoire-after-autologous-hsct-in-patients-with-ankylosing-spondylitis
#3
E A Komech, I V Zvyagin, M V Pogorelyy, I Z Mamedov, D A Fedorenko, Y B Lebedev
Autologous hematopoietic stem cell transplantation (HSCT), a safer type of HSCT than allogeneic HSCT, is a promising therapy for patients with severe autoimmune diseases (ADs). Despite the long history of medical practice, structural changes in the adaptive immune system as a result of autologous HSCT in patients with various types of ADs remain poorly understood. In this study, we used high-throughput sequencing to investigate the structural changes in the peripheral blood T-cell repertoire in adult patients with ankylosing spondylitis (AS) during two years after autologous HSCT...
April 2018: Acta Naturae
https://www.readbyqxmd.com/read/30116227/bacterial-biomarkers-of-marcellus-shale-activity-in-pennsylvania
#4
Jeremy R Chen See, Nikea Ulrich, Hephzibah Nwanosike, Christopher J McLimans, Vasily Tokarev, Justin R Wright, Maria F Campa, Christopher J Grant, Terry C Hazen, Jonathan M Niles, Daniel Ressler, Regina Lamendella
Unconventional oil and gas (UOG) extraction, also known as hydraulic fracturing, is becoming more prevalent with the increasing use and demand for natural gas; however, the full extent of its environmental impacts is still unknown. Here we measured physicochemical properties and bacterial community composition of sediment samples taken from twenty-eight streams within the Marcellus shale formation in northeastern Pennsylvania differentially impacted by hydraulic fracturing activities. Fourteen of the streams were classified as UOG+, and thirteen were classified as UOG- based on the presence of UOG extraction in their respective watersheds...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30113023/-algorithm-for-physiological-interpretation-of-transcriptome-profiling-data-for-non-model-organisms
#5
R F Gubaev, V Y Gorshkov, L M Gapa, N E Gogoleva, E P Vetchinkina, Y V Gogolev
Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the genome sequence and its sufficient annotation for the target organism. However, a list of species with properly annotated genomes is limited. Transcriptome profiling is often performed in the so-called non-model organisms, which are those with unknown or poorly assembled and/or annotated genome sequences...
July 2018: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/30111017/-transcriptome-analysis-reveals-candidate-genes-involved-in-flavonols-biosyhthesis-in-sophora-japonica
#6
Yuan Pan, Da-Xia Chen, Xu-Hong Song, Long-Yun Li
In order to study the pathways of biosynthesis of flavonoids in Sophora japonica, 113 797 unigenes were obtained by Trinity software, with an average length of 803 bp, of which 72 752 unigenes were obtained from the database by high-throughput sequencing, and a total of 38 891 SSR loci were searched. Through the metabolic pathway analysis, we found that there were 135 unigenes involved in the biosynthesis of flavonoids and 959 unigene involved in other secondary metabolic pathways. Further analysis of genes involved in rutin biosynthesis revealed that 24 were associated with CHS, 52 were associated with FLS, and 11 were associated with UFGT...
July 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/30109604/gef-seq-a-simple-procedure-for-base-pair-resolution-chip-seq
#7
Onuma Chumsakul, Kensuke Nakamura, Shu Ishikawa, Taku Oshima
Nucleotide sequences recognized and bound by DNA-binding proteins (DBPs) are critical to control and maintain gene expression, replication, chromosome segregation, cell division, and nucleoid structure in bacterial cells. Therefore, determination of the binding sequences of DBPs is important not only to study DBP recognition mechanisms, but also to understand the fundamentals of cell homeostasis. While ChIP-seq analysis appears to be an effective way to determine DBP-binding sites on the genome, the resolution is sometimes not sufficient to identify the sites precisely...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30109602/determination-of-the-3d-genome-organization-of-bacteria-using-hi-c
#8
Frédéric G Crémazy, Fatema-Zahra M Rashid, James R Haycocks, Lisa E Lamberte, David C Grainger, Remus T Dame
The spatial organization of genomes is based on their hierarchical compartmentalization in topological domains. There is growing evidence that bacterial genomes are organized into insulated domains similar to the Topologically Associating Domains (TADs) detected in eukaryotic cells. Chromosome conformation capture (3C) technologies are used to analyze in vivo DNA proximity based on ligation of distal DNA segments crossed-linked by bridging proteins. By combining 3C and high-throughput sequencing, the Hi-C method reveals genome-wide interactions within topological domains and global genome structure as a whole...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30109145/selection-and-evaluation-of-an-efficient-method-for-the-recovery-of-viral-nucleic-acid-extraction-from-complex-biologicals
#9
Sarmitha Sathiamoorthy, Rebecca J Malott, Lucy Gisonni-Lex, Siemon H S Ng
There is a need for a broad and efficient testing strategy for the detection of both known and novel viral adventitious agents in vaccines and biologicals. High-throughput sequencing (HTS) is an approach for such testing; however, an optimized testing method is one with a sample-processing pipeline that can help detect any viral adventitious agent that may be present. In this study, 11 commercial methods were assessed for efficient extraction of nucleic acids from a panel of viruses. An extraction strategy with two parallel arms, consisting of both the Invitrogen PureLink™ Virus RNA/DNA kit for total nucleic acid extraction and the Wako DNA Extractor® kit with an RNase A digestion for enrichment of double-stranded nucleic acid, was selected as the strategy for the extraction of all viral nucleic acid types (ssRNA, dsRNA, and dsDNA)...
2018: NPJ Vaccines
https://www.readbyqxmd.com/read/30108556/a-hypothetical-bottleneck-in-the-plant-microbiome
#10
George Newcombe, Abby Harding, Mary Ridout, Posy E Busby
The plant microbiome may be bottlenecked at the level of endophytes of individual seeds. Strong defense of developing seeds is predicted by optimal defense theory, and we have experimentally demonstrated exclusionary interactions among endophytic microbes infecting individual seeds of Centaurea stoebe . Having found a single, PDA-culturable microbe per seed or none in an exploratory study with Centaurea stoebe , we completed a more extensive survey of an additional 98 plant species representing 39 families...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30108332/unbiased-shrna-screening-using-a-combination-of-facs-and-high-throughput-sequencing-enables-identification-of-novel-modifiers-of-polycomb-silencing
#11
Kenichi Nishioka, Hitomi Miyazaki, Hidenobu Soejima
Polycomb silencing is an important and rapidly growing field that is relevant to a broad range of aspects of human health, including cancer and stem cell biology. To date, the regulatory mechanisms for the fine-tuning of Polycomb silencing remain unclear, but it is likely that there is a series of unidentified factors that functionally modify or balance the silencing. However, a practical gene screening strategy for identifying such factors has not yet been developed. The failure of screening strategies used thus far is probably due to the effect of the loss-of-function phenotypes of these factors on cell cycle progression...
August 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30107842/qsrna-seq-a-method-for-high-throughput-profiling-and-quantifying-small-rnas
#12
Alla Fishman, Dean Light, Ayelet T Lamm
The ability to profile and quantify small non-coding RNAs (sRNAs), specifically microRNAs (miRNAs), using high-throughput sequencing is challenging because of their small size. We developed QsRNA-seq, a method for preparation of sRNA libraries for high-throughput sequencing that overcomes this difficulty by enabling a gel-free separation of fragments shorter than 100 nt that differ only by 20 nt in length. The method allows the use of unique molecular identifiers for quantification and is more amenable to automation than gel-based methods...
August 14, 2018: Genome Biology
https://www.readbyqxmd.com/read/30107357/characterization-and-variation-of-microbial-community-structure-during-the-anaerobic-treatment-of-n-n-dimethylformamide-containing-wastewater-by-uasb-with-artificially-mixed-consortium
#13
Zhe Kong, Lu Li, Yu-You Li
A lab-scale UASB was operated successfully to anaerobically treat wastewater containing approximately 2000 mg L-1 N, N-dimethylformamide (DMF) by artificially mixing anaerobic granular sludge with DMF-degrading activated sludge. DMF was effectively degraded by the UASB under a low OLR of 1.63-4.22 g COD L-1  d-1 , with over 96% DMF removal efficiency and a high methane production rate. However, the DMF-degrading ability gradually weakened along with increases in the OLR. The analysis of the microbial community structure by high-throughput sequencing revealed a decline in the abundance of the facultatively anaerobic DMF-hydrolyzing bacteria originating from activated sludge with increasing OLR, further deteriorating the methanogenic degradation of DMF...
August 7, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/30107262/comparative-transcriptome-analysis-of-chinese-grass-shrimp-palaemonetes-sinensis-infected-with-isopod-parasite-tachaea-chinensis
#14
Yingdong Li, Weibin Xu, Xin Li, Hongbo Jiang, Qiuxin She, Zhibin Han, Xiaodong Li, Qijun Chen
Parasitic isopods negatively affect reproduction and ingestion in several commercially important crustaceans; however, little is known about such parasite-host interactions. Therefore, we performed high-throughput sequencing of cDNA samples from Chinese grass shrimp Palaemonetes sinensis infected by parasitic isopod Tachaea chinensis and a non-infected control. We randomly assembled 46,858,882 and 41,110,746 clean reads from the parasitized and control groups, respectively. From these, we identified 1323 differentially expressed genes (DEGs) (p < 0...
August 11, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/30107229/transcriptome-characterization-and-gene-expression-analysis-related-to-chemoreception-in-trichogramma-chilonis-an-egg-parasitoid
#15
Jian-Bai Liu, Han Wu, Jie-Qun Yi, Zi-Wei Song, Dun-Song Li, Gu-Ren Zhang
Chemoreception is critical for the survival of insects. Insects have a variety of behavioral responses, such as mating, host searching and ovipositing, in response to different odor signals detected in their living environment. Trichogramma chilonis, an egg parasitoid, acts as an efficient and effective biocontrol reagent for many agricultural and forestry insect pests in many parts of China. However, little is known about the molecular mechanism of the olfaction-evoked behavior in T. chilonis. In the present study, we conducted transcriptome profiling analysis of T...
August 11, 2018: Gene
https://www.readbyqxmd.com/read/30105773/microrna-and-mrna-profiles-in-nucleus-accumbens-underlying-depression-versus-resilience-in-response-to-chronic-stress
#16
Yawei Si, Zhenhua Song, Xiaoyan Sun, Jin-Hui Wang
Major depression in negative mood is presumably induced by chronic stress with lack of reward. However, most individuals who experience chronic stress demonstrate resilience. Molecular mechanisms underlying stress- induced depression versus resilience remain unknown, which are investigated in brain reward circuits. Mice were treated by chronic unpredictable mild stress (CUMS) for 4 weeks. The tests of sucrose preference, Y-maze, and forced swimming were used to identify depression-like emotion behavior or resilience...
August 14, 2018: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/30105520/columbid-circoviruses-detected-in-free-ranging-pigeons-from-southern-brazil-insights-on-picv
#17
M R Loiko, D M Junqueira, A P M Varela, C Tochetto, C M Scheffer, D A Lima, A P Morel, C Cerva, W P Paim, Fabiana Quoos Mayer, P M Roehe
Pigeon circovirus (PiCV) is taxonomically classified as a member of the Circovirus genus, family Circoviridae. The virus contains a single stranded DNA genome of approximately 2 kb, with minor length variations among different isolates. The occurrence of PiCV infections in pigeons (Columba livia) has been documented worldwide over the past 20 years; however, in Brazil there were still no reports on PiCV detection. This study identifies seven PiCV genomes recovered from domestic pigeons of South Brazil through high-throughput sequencing and shows a high frequency of PiCV infection, through quantitative real-time PCR...
August 13, 2018: Archives of Virology
https://www.readbyqxmd.com/read/30105043/sistl2-is-required-for-cell-cycle-leaf-organ-development-chloroplast-biogenesis-and-has-effects-on-c-4-photosynthesis-in-setaria-italica-l-p-beauv
#18
Shuo Zhang, Sha Tang, Chanjuan Tang, Mingzhao Luo, Guanqing Jia, Hui Zhi, Xianmin Diao
Deoxycytidine monophosphate deaminase (DCD) is a key enzyme in the de novo dTTP biosynthesis pathway. Previous studies have indicated that DCD plays key roles in the maintenance of the balance of dNTP pools, cell cycle progression, and plant development. However, few studies have elucidated the functions of the DCD gene in Panicoideae plants. Setaria has been proposed as an ideal model of Panicoideae grasses, especially for C4 photosynthesis research. Here, a Setaria italica stripe leaf mutant ( sistl2 ) was isolated from EMS-induced lines of "Yugu1," the wild-type parent...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/30104536/identification-and-characterization-of-mirnas-in-self-rooted-and-grafted-malus-reveals-critical-networks-associated-with-flowering
#19
Na An, Sheng Fan, Yang Yang, Xilong Chen, Feng Dong, Yibin Wang, Libo Xing, Caiping Zhao, Mingyu Han
Grafting can improve the agricultural traits of crop plants, especially fruit trees. However, the regulatory networks and differentially expressed microRNAs (miRNAs) related to grafting in apple remain unclear. Herein, we conducted high-throughput sequencing and identified differentially expressed miRNAs among self-rooted Fuji, self-rooted M9, and grafted Fuji/M9. We analyzed the flowering rate, leaf morphology, and nutrient and carbohydrate contents in the three materials. The flowering rate, element and carbohydrate contents, and expression levels of flowering genes were higher in Fuji/M9 than in Fuji...
August 13, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/30103661/a-model-free-test-for-detecting-disease-association-signals-with-multiple-genetic-variants-and-covariates
#20
J Y Lee, Chiu-Ying Chen, K F Cheng
Discoveries and analyses of genetic variants at a gene or exome based on high-throughput sequencing technology are increasingly feasible. Although many well-known association tests have already been proposed in literature for testing whether a group of variants in a target region is associated with a disease of interest, however, the analytic challenges still remain profound. The power performance of these tests generally depends on the sample size, numbers of causal and neutral variants, variant frequency, effect size, and direction...
September 2018: Statistical Methods in Medical Research
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