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Target sequencing

Ding-Hui Dai, Izhar Hyder Qazi, Ming-Xia Ran, Kai Liang, Yan Zhang, Ming Zhang, Guang-Bin Zhou, Christiana Angel, Chang-Jun Zeng
Due to lower farrowing rate and reduced litter size with frozen-thawed semen, over 90% of artificial insemination (AI) is conducted using liquid stored boar semen. Although substantial progress has been made towards optimizing the cryopreservation protocols for boar sperm, the influencing factors and underlying mechanisms related to cryoinjury and freeze tolerance of boar sperm remain largely unknown. In this study, we report the differential expression of mRNAs and miRNAs between fresh and frozen-thawed boar sperm using high-throughput RNA sequencing...
February 13, 2019: International Journal of Molecular Sciences
Rebecca Heß, Michael Storcksdieck Genannt Bonsmann, Dennis Lapuente, Andre Maaske, Carsten Kirschning, Jürgen Ruland, Bernd Lepenies, Drew Hannaman, Matthias Tenbusch, Klaus Überla
The envelope protein (Env) is the only surface protein of the human immunodeficiency virus (HIV) and as such the exclusive target for protective antibody responses. Experimental evidences from mouse models suggest a modulating property of Env to steer antibody class switching towards the less effective antibody subclass IgG1 accompanied with strong TH2 helper responses. By simple physical linkage we were able to imprint this bias, exemplified by a low IgG2a/IgG1 ratio of antigen-specific antibodies, onto an unrelated antigen, namely the HIV capsid protein p24...
February 13, 2019: Viruses
Karen Huen, Daneida Lizarraga, Katherine Kogut, Brenda Eskenazi, Nina Holland
Epigenetic mechanisms have emerged as an important pathway through which environmental exposures can affect health through the regulation of gene expression without changes in DNA sequence: microRNAs (miRNAs) are short non-coding RNAs that target protein-coding mRNAs, leading to post-transcriptional repression. They are involved in important physiologic processes, but little is known about how miRNA expression may change with age in children. We used an nCounter miRNA assay to assess the expression of 43 miRNAs in buffy coat samples collected from newborns ( n = 121) and 7-year-old ( n = 142) children...
February 13, 2019: International Journal of Environmental Research and Public Health
Corinna Keup, Markus Storbeck, Siegfried Hauch, Peter Hahn, Markus Sprenger-Haussels, Mitra Tewes, Pawel Mach, Oliver Hoffmann, Rainer Kimmig, Sabine Kasimir-Bauer
Liquid biopsy analytes such as cell-free DNA (cfDNA) and circulating tumor cells (CTCs) exhibit great potential for personalized treatment. Since cfDNA and CTCs are considered to give additive information and blood specimens are limited, isolation of cfDNA and CTC in an "all from one tube" format is desired. We investigated whether cfDNA variant sequencing from CTC-depleted blood (CTC-depl. B; obtained after positive immunomagnetic isolation of CTCs (AdnaTest EMT-2/Stem Cell Select, QIAGEN)) impacts the results compared to cfDNA variant sequencing from matched whole blood (WB)...
February 18, 2019: Cancers
Danton H O'Day
The nucleoli of Dictyostelium discoideum have a comparatively unique, non-canonical, localization adjacent to the inner nuclear membrane. The verified nucleolar proteins of this eukaryotic microbe are detailed while other potential proteins are introduced. Heat shock protein 32 (Hsp32), eukaryotic translation initiation factor 6 (eIF6), and tumour necrosis factor receptor-associated protein 1 (TRAP1) are essential for cell survival. NumA1, a breast cancer type 1 susceptibility protein-C Terminus domain-containing protein linked to cell cycle, functions in the regulation of nuclear number...
February 17, 2019: Cells
Moe Yokoshi, Takashi Fukaya
Transcriptional enhancers are regulatory DNAs that instruct when and where genes should be transcribed in response to a variety of intrinsic and external signals. They contain a cluster of binding sites for sequence-specific transcription factors and co-activators to determine the spatiotemporal specificity of gene activities during development. Enhancers are often positioned in distal locations from their target promoters. In some cases, they work over a million base pairs or more. In the traditional view, enhancers have been thought to stably interact with promoters in a targeted manner...
February 19, 2019: Development, Growth & Differentiation
Peder Rustøen Braadland, Alfonso Urbanucci
Tumor evolution is based on the ability to constantly mutate and activate different pathways under the selective pressure of targeted therapies. Epigenetic alterations including those of the chromatin structure are associated with tumor initiation, progression, and drug resistance. Many cancers, including prostate cancer, present enlarged nuclei and chromatin appears altered and irregular. These phenotypic changes are likely to result from epigenetic dysregulation. High-throughput sequencing applied to bulk samples and now to single cells has made it possible to study these processes in unprecedented detail...
February 1, 2019: Endocrine-related Cancer
Thi Dao Dinh, Jacob Njaramba Ngatia, Liang Yu Cui, Yue Ma, Thomas D Dhamer, Yan Chun Xu
Species identification is fundamental to wildlife forensic practice. The desirability of molecular genetic methods is increasing rapidly. The sequence of a marker, rather than its particular diagnostic nucleotides, provides greater safety through comparisons between intra- and inter-specific pairwise genetic distances. However, it has not been well described how reliability of species assignment is influenced by distance computing methods and reference sample sizes. In this study, the influences were tested using 12 species from 4 genera of passerine birds and the sequences of partial Cytochrome b (Cyt b) and Cytochrome Oxidase subunit I (COI) genes...
February 13, 2019: Forensic Science International. Genetics
Elżbieta Łopieńska-Biernat, Łukasz Paukszto, Jan Paweł Jastrzębski, Karol Makowczenko, Robert Stryiński
Trehalase plays an important role in catabolism of trehalose, disaccharide which is one of the most widespread carbohydrates in nematode tissues. This enzyme might be a major adaptation of the nematode to parasitic lifestyle. The current study revealed five trehalase isotypes of A. simplex not yet detected in any parasitic nematode. Anisakiasis is a relatively new and rapidly spreading zoonosis that possesses a serious threat for humans and animals. The lack of methods for combating this parasite causes continuous search for new targets important in their metabolism...
February 16, 2019: International Journal of Biological Macromolecules
Katherine L Williams, Megan Stumpf, Nicole Elise Naiman, Shilei Ding, Meghan Garrett, Theodore Gobillot, Dani Vézina, Katharine Dusenbury, Nitya S Ramadoss, Ryan Basom, Peter S Kim, Andrés Finzi, Julie Overbaugh
Antibodies that mediate killing of HIV-infected cells through antibody-dependent cellular cytotoxicity (ADCC) have been implicated in protection from HIV infection and disease progression. Despite these observations, these types of HIV antibodies are understudied compared to neutralizing antibodies. Here we describe four monoclonal antibodies (mAbs) obtained from one individual that target the HIV transmembrane protein, gp41, and mediate ADCC activity. These four mAbs arose from independent B cell lineages suggesting that in this individual, multiple B cell responses were induced by the gp41 antigen...
February 19, 2019: PLoS Pathogens
Stephen M Chiweshe, Pieter C Steketee, Siddharth Jayaraman, Edith Paxton, Kyriaki Neophytou, Heidi Erasmus, Michel Labuschagne, Anneli Cooper, Annette MacLeod, Finn E Grey, Liam J Morrison
Human and animal African trypanosomiasis (HAT & AAT, respectively) remain a significant health and economic issue across much of sub-Saharan Africa. Effective control of AAT and potential eradication of HAT requires affordable, sensitive and specific diagnostic tests that can be used in the field. Small RNAs in the blood or serum are attractive disease biomarkers due to their stability, accessibility and available technologies for detection. Using RNAseq, we have identified a trypanosome specific small RNA to be present at high levels in the serum of infected cattle...
February 19, 2019: PLoS Neglected Tropical Diseases
Chloé Oudinet, Fatima-Zohra Braikia, Audrey Dauba, Joana M Santos, Ahmed Amine Khamlichi
DNA cytosine methylation is involved in the regulation of gene expression during development and its deregulation is often associated with disease. Mammalian genomes are predominantly methylated at CpG dinucleotides. Unmethylated CpGs are often associated with active regulatory sequences while methylated CpGs are often linked to transcriptional silencing. Previous studies on CpG methylation led to the notion that transcription initiation is more sensitive to CpG methylation than transcriptional elongation. The immunoglobulin heavy chain (IgH) constant locus comprises multiple inducible constant genes and is expressed exclusively in B lymphocytes...
February 2019: PLoS Genetics
Lee Seligman, Ilhami Kovanlikaya, David J Pisapia, David M Naeger, Rajiv Magge, Howard A Fine, Gloria C Chiang
OBJECTIVE: Both 18 F-FDG PET and perfusion MRI are commonly used techniques for posttreatment glioma surveillance. Using integrated PET-MRI, we assessed the rate of discordance between simultaneously acquired FDG PET images and dynamic contrast-enhanced (DCE) perfusion MR images and determined whether tumor genetics predicts discordance. MATERIALS AND METHODS: Forty-one consecutive patients with high-grade gliomas (20 with grade IV gliomas and 21 with grade III gliomas) underwent a standardized tumor protocol performed using an integrated 3-T PET-MRI scanner...
February 19, 2019: AJR. American Journal of Roentgenology
M A Soltan, R M A Dohreig, H Abbas, M Ellawa, I Yousif, A E Aly, M Wasfy, M M El-Sayed
Foot and mouth disease (FMD) is a highly contagious and sometimes fatal viral disease of cloven footed animals. The disease exhibits overwhelming economic impacts and has been caused by seven antigenically distinct foot and mouth disease virus (FMDV) serotypes; O, A, C, Asia1, SAT1, SAT2 and SAT3, all belonging to genus Aphthovirus, Family picornaviradae. Further genetic analysis of viral protein 1 (VP1 gene) classifies the strains within each serotype into topotypes, lineages and/ or genotypes; this classification is important for studying virus molecular epidemiology and tracing the source of newly emerging strains...
February 18, 2019: Transboundary and Emerging Diseases
Zhihua Guo, Zhanhong Xie, Huifang Shi, Wei Du, Lijun Peng, Wei Han, Feidie Duan, Xin Zhang, Mingyan Chen, Junli Duan, Jing Lin, Xuewei Chen, Analyn Ang Lizaso, Han Han-Zhang, Jianxing He, Weiqiang Yin
BACKGROUND: The clinical utility of malignant pleural effusion (MPE) to detect mutation has been well documented; however, routine practice of the use of MPE involves collection of the cell pellet to detect mutation, and limited studies have interrogated the MPE supernatant as an alternative source of tumor-derived DNA for mutation profiling. In this study, we investigated the potential of MPE supernatant as a liquid biopsy specimen by comparing its mutation profile with that of matched MPE cell pellets, tissue, and plasma samples...
February 18, 2019: Thoracic Cancer
Dili Mao, Simon Michelmore, Jeff Paull, Christopher Preston, Tim Sutton, Klaus Oldach, Shi Y Yang, Larn McMurray
BACKGROUND: Faba bean (Vicia faba L.) is an important crop in Australian farming systems, however, weed control is a major constraint due to a lack of in-crop broadleaf herbicide options. To address this, we developed acetohydroxyacid synthase (AHAS) inhibitor herbicide tolerance in faba bean using mutagenesis techniques. Dose response experiments, agronomic field evaluation and DNA sequencing of the AHAS gene were used to quantify and validate tolerance traits. RESULTS: Four M2 faba bean single plant biotypes (IMI-1, IMI-2, IMI-3 and IMI-4) at a frequency of 3...
February 18, 2019: Pest Management Science
Jiao Jiao Zhang, Wei Rong Yang, Yi Wang, Liang Chen, Dong Kee Jeong, Xian Zhong Wang
Adenosine monophosphate-activated protein kinase (AMPK) plays a key role in cellular energy homeostasis and cell proliferation. MicroRNAs (miRNAs) function as posttranscriptional regulators of gene expression in biological processes. It is unclear to whether miRNAs are involved in AMPK-regulated Sertoli cell (SC) proliferation. To further understand the regulation of miRNAs in the immature boar SC proliferation, 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) was added to activate AMPK. By an Illumina small RNA deep sequencing, we obtained sequences and relative expression levels of 272 known mature miRNAs, among which 9 miRNAs were significantly upregulated whereas 16 miRNAs were downregulated following the AICAR treatment...
February 18, 2019: Molecular Reproduction and Development
Dominique Penther, Pierre-Julien Viailly, Sylvain Latour, Pascaline Etancelin, Elodie Bohers, Hélène Vellemans, Vincent Camus, Anne Lise Menard, Sophie Coutant, Hélène Lanic, Emilie Lemasle, Fanny Drieux, Liana Veresezan, Philippe Ruminy, Anna Raimbault, Jean Soulier, Thierry Frebourg, Hervé Tilly, Fabrice Jardin
Burkitt lymphoma (BL) is characterized by a translocation of the MYC oncogene that leads to the upregulation of MYC expression, cell growth and proliferation. It is well-established that MYC translocation is not a sufficient genetic event to cause BL. Next-generation sequencing has recently provided a comprehensive analysis of the landscape of additional genetic events that contribute to BL lymphomagenesis. Refractory BL or relapsing BL are almost always incurable as a result of the selection of a highly chemoresistant clonally related cell population...
February 18, 2019: Genes, Chromosomes & Cancer
Marc Hoferer, Valerij Akimkin, Julia Skrypski, Heike Schütze, Reinhard Sting
Infectious haematopoietic necrosis (IHN) and viral haemorrhagic septicaemia (VHS) are OIE-listed and notifiable viral fish diseases which are controlled by eradication and surveillance programmes globally. The present study provides improved RT-qPCR procedures based on recently described OIE protocols. Improvements comprise the design of a new TaqMan® probe, replacing a TaqMan® MGB probe that turned out to show impaired binding. Reason for this is SNPs detected in the nucleoprotein N gene sequences of IHNV strains targeted by the RT-qPCR...
February 19, 2019: Journal of Fish Diseases
Li-Ping Wang, Xiao-Yu Peng, Xiao-Qin Lv, Lin Liu, Xue-Li Li, Xiao He, Fang Lv, Yu Pan, Li Wang, Kai-Feng Liu, Xiao-Mei Zhang
Polycystic ovary syndrome (PCOS) is one of the most prevalent reproductive disorders in women worldwide. Despite rigorous research, the exact molecular mechanism that governs PCOS pathogenesis remains unclear. To investigate the potential roles of circular RNAs (circRNAs), this study sequenced ribosomal RNA-depleted total RNA from exosomes of follicle fluids obtained from PCOS patients using non-PCOS samples as controls. Bioinformatic analysis identified 167 upregulated and 245 downregulated circRNAs from a total of 16,771 detected candidates...
February 18, 2019: Journal of Cellular Physiology
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