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Repertoire Sequencing

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https://www.readbyqxmd.com/read/28723557/crystal-structure-of-the-human-ribosome-in-complex-with-denr-mct-1
#1
Ivan B Lomakin, Elena A Stolboushkina, Anand T Vaidya, Chenguang Zhao, Maria B Garber, Sergey E Dmitriev, Thomas A Steitz
The repertoire of the density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein was recently expanded to include translational control of a specific set of cancer-related mRNAs. DENR and MCT-1 form the heterodimer, which binds to the ribosome and operates at both translation initiation and reinitiation steps, though by a mechanism that is yet unclear. Here, we determined the crystal structure of the human small ribosomal subunit in complex with DENR-MCT-1. The structure reveals the location of the DENR-MCT-1 dimer bound to the small ribosomal subunit...
July 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28720902/comparative-genomic-analysis-of-paenibacillus-sp-ssg-1-and-its-closely-related-strains-reveals-the-effect-of-glycometabolism-on-environmental-adaptation
#2
Hui Xu, Shishang Qin, Yanhong Lan, Mengjia Liu, Xiyue Cao, Dairong Qiao, Yu Cao, Yi Cao
The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720874/knowledge-transfer-learning-for-prediction-of-matrix-metalloprotease-substrate-cleavage-sites
#3
Yanan Wang, Jiangning Song, Tatiana T Marquez-Lago, André Leier, Chen Li, Trevor Lithgow, Geoffrey I Webb, Hong-Bin Shen
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies have identified type-specific target substrates; however, the complete repertoire of MMP substrates remains uncharacterized. Indeed, computational prediction of substrate-cleavage sites associated with MMPs is a challenging problem. This holds especially true when considering MMPs with few experimentally verified cleavage sites, such as for MMP-2, -3, -7, and -8...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720323/rapid-divergence-of-histones-in-hydrozoa-cnidaria-and-evolution-of-a-novel-histone-involved-in-dna-damage-response-in-hydra
#4
Puli Chandramouli Reddy, Suyog Ubhe, Neha Sirwani, Rasika Lohokare, Sanjeev Galande
Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra...
June 15, 2017: Zoology: Analysis of Complex Systems, ZACS
https://www.readbyqxmd.com/read/28720171/pacbio-assembly-of-a-plasmodium-knowlesi-genome-sequence-with-hi-c-correction-and-manual-annotation-of-the-sicavar-gene-family
#5
S A Lapp, J A Geraldo, J-T Chien, F Ay, S B Pakala, G Batugedara, J Humphrey, J D DeBARRY, K G Le Roch, M R Galinski, J C Kissinger
Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia. The P. knowlesi genome sequence generated in 2008 highlighted and confirmed many similarities and differences in Plasmodium species, including a global view of several multigene families, such as the large SICAvar multigene family encoding the variant antigens known as the schizont-infected cell agglutination proteins. However, repetitive DNA sequences are the bane of any genome project, and this and other Plasmodium genome projects have not been immune to the gaps, rearrangements and other pitfalls created by these genomic features...
July 19, 2017: Parasitology
https://www.readbyqxmd.com/read/28718916/the-genetic-landscape-of-endometrial-clear-cell-carcinomas
#6
Deborah F DeLair, Kathleen A Burke, Pier Selenica, Raymond S Lim, Sasinya N Scott, Sumit Middha, Abhinita S Mohanty, Donavan T Cheng, Michael F Berger, Robert A Soslow, Britta Weigelt
Clear cell carcinoma of the endometrium is a rare type of endometrial cancer generally associated with an aggressive clinical behavior. Here we sought to define the repertoire of somatic genetic alterations in endometrial clear cell carcinomas (ECCs) and whether ECCs could be classified into the molecular subtypes described for endometrial endometrioid and serous carcinomas. We performed a rigorous histopathological review, immunohistochemical analysis and massively parallel sequencing targeting 300 cancer-related genes of 32 pure ECCs...
July 18, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28717023/the-evolution-of-diatoms-and-their-biogeochemical-functions
#7
REVIEW
Anne-Sophie Benoiston, Federico M Ibarbalz, Lucie Bittner, Lionel Guidi, Oliver Jahn, Stephanie Dutkiewicz, Chris Bowler
In contemporary oceans diatoms are an important group of eukaryotic phytoplankton that typically dominate in upwelling regions and at high latitudes. They also make significant contributions to sporadic blooms that often occur in springtime. Recent surveys have revealed global information about their abundance and diversity, as well as their contributions to biogeochemical cycles, both as primary producers of organic material and as conduits facilitating the export of carbon and silicon to the ocean interior...
September 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28716078/cognate-comparative-gene-annotation-characterizer
#8
Jeanne Wilbrandt, Bernhard Misof, Oliver Niehuis
BACKGROUND: The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics...
July 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28715506/analysis-of-aquaporins-from-the-euryhaline-barnacle-balanus-improvisus-reveals-differential-expression-in-response-to-changes-in-salinity
#9
Ulrika Lind, Michael Järvå, Magnus Alm Rosenblad, Piero Pingitore, Emil Karlsson, Anna-Lisa Wrange, Emelie Kamdal, Kristina Sundell, Carl André, Per R Jonsson, Jon Havenhand, Leif A Eriksson, Kristina Hedfalk, Anders Blomberg
Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms...
2017: PloS One
https://www.readbyqxmd.com/read/28710945/ancient-signal-for-nitrogen-status-sensing-in-the-green-lineage-functional-evidence-of-cdpk-repertoire-in-ostreococcus-tauri
#10
Gonzalo Caló, Dana Scheidegger, Giselle M A Martínez-Noël, Graciela L Salerno
Calcium-dependent protein kinases (CDPKs) regulate plant development and many stress signalling pathways through the complex cytosolic [Ca(2+)] signalling. The genome of Ostreococcus tauri (Ot), a model prasinophyte organism that is on the base of the green lineage, harbours three sequences homologous to those encoding plant CDPKs with the three characteristic conserved domains (protein kinase, autoregulatory/autoinhibitory, and regulatory domain). Phylogenetic and structural analyses revealed that putative OtCDPK proteins are closely related to CDPKs from other Chlorophytes...
July 8, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28709111/genome-wide-identification-of-52-cytochrome-p450-cyp-genes-in-the-copepod-tigriopus-japonicus-and-their-b-%C3%AE-p-induced-expression-patterns
#11
Jeonghoon Han, Duck-Hyun Kim, Hui-Su Kim, David R Nelson, Jae-Seong Lee
Cytochrome P450s (CYPs) are enzymes with a heme-binding domain that are found in all living organisms. CYP enzymes have important roles associated with detoxification of xenobiotics and endogenous compounds (e.g. steroids, fatty acids, and hormones). Although CYP enzymes have been reported in several invertebrates, including insects, little is known about copepod CYPs. Here, we identified the entire repertoire of CYP genes (n=52) from whole genome and transcriptome sequences of the benthic copepod Tigriopus japonicus, including a tandem duplication (CYP3026A3, CYP3026A4, CYP3026A5), and examined patterns of gene expression over various developmental stages and in response to benzo[α]pyrene (B[α]P) exposure...
July 6, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28706301/a-haystack-heuristic-for-autoimmune-disease-biomarker-discovery-using-next-gen-immune-repertoire-sequencing-data
#12
Leonard Apeltsin, Shengzhi Wang, H-Christian von Büdingen, Marina Sirota
Large-scale DNA sequencing of immunological repertoires offers an opportunity for the discovery of novel biomarkers for autoimmune disease. Available bioinformatics techniques however, are not adequately suited for elucidating possible biomarker candidates from within large immunosequencing datasets due to unsatisfactory scalability and sensitivity. Here, we present the Haystack Heuristic, an algorithm customized to computationally extract disease-associated motifs from next-generation-sequenced repertoires by contrasting disease and healthy subjects...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28706143/integrated-analysis-of-somatic-mutations-and-immune-microenvironment-of-multiple-regions-in-breast-cancers
#13
Taigo Kato, Jae-Hyun Park, Kazuma Kiyotani, Yuji Ikeda, Yasuo Miyoshi, Yusuke Nakamura
Next-generation sequencing technology enables us to analyze the complexity of intra- and inter-tumoral heterogeneity, which may influence to prognosis of cancer patients. In this study, we collected surgically-resected tumor tissues from five breast cancer patients and characterized three different portions of individual tumors through somatic mutation analysis by whole exome sequencing, T cell receptor beta (TCRB) repertoire analysis of tumor-infiltrating lymphocytes (TILs), and the expression analysis of immune-related genes at 15 different sites...
June 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28705718/antimicrobial-peptide-repertoire-of-thitarodes-armoricanus-a-host-species-of-ophiocordyceps-sinensis-predicted-based-on-de-novo-transcriptome-sequencing-and-analysis
#14
Min Wang, Xianda Hu
Ophiocordyceps sinensis is an entomopathogenic fungus that parasitizes the larvae of ghost moths. The fungus-caterpillar complex resulting from fungal parasitism is a medicinally and economically important traditional Chinese medicine famous for its tonic, aphrodisiac and immunomodulatory activity. Antimicrobial peptides (AMPs), which play predominant roles in responding to infection of pathogenic microorganisms in the immune system of ghost moths, may remain behind the fungus-caterpillar complex. Thitarodes armoricanus, as a widely distributed ghost moth on the Tibetan Plateau, is the first reported and one of the most common host insects of O...
July 11, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28698278/on-the-origin-of-reverse-transcriptase-using-crispr-cas-systems-and-their-hyperdiverse-enigmatic-spacer-repertoires
#15
Sukrit Silas, Kira S Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R Krishnamurthy, Becky Xu Hua Fu, Loren L Hansen, David Wang, Matthew B Sullivan, Andrew Millard, Martha R Clokie, Devaki Bhaya, Alan M Lambowitz, Nikos C Kyrpides, Eugene V Koonin, Andrew Z Fire
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28697819/functional-characterization-of-single-domain-cystatin-like-cysteine-proteinase-inhibitors-expressed-by-the-trematode-fasciola-hepatica
#16
Martín Cancela, Ileana Corvo, Edileuza DA Silva, Aline Teichmann, Leda Roche, Alvaro Díaz, José Fransisco Tort, Henrique B Ferreira, Arnaldo Zaha
Cystatins are small, phylogenetically conserved proteins that are tight-binding inhibitors of cysteine proteinases. The liver fluke Fasciola hepatica uses a diverse set of cysteine proteinases of the papain superfamily for host invasion, immune evasion and nutrition, but little is known about the regulation of these enzymes. The aim of this work is to characterize the cystatin repertoire of F. hepatica. For this purpose, we first surveyed the available sequence databases, identifying three different F. hepatica single-domain cystatins...
July 12, 2017: Parasitology
https://www.readbyqxmd.com/read/28697735/v-j-combinations-of-t-cell-receptor-predict-responses-to-erythropoietin-in-end-stage-renal-disease-patients
#17
Henry Sung-Ching Wong, Che-Mai Chang, Chih-Chin Kao, Yu-Wen Hsu, Xiao Liu, Wen-Chang Chang, Mai-Szu Wu, Wei-Chiao Chang
BACKGROUND: Anemia is common among end-stage renal disease (ESRD) patients who undergone hemodialysis. The total reduction of red blood cell (RBC) count is associated with poor prognosis in these patients. Although erythropoietin (EPO) has been used as an effective treatment for ESRD patients with anemia, a large number of patients still present poor responses to EPO treatment. METHODS: We measured T-cell receptor sequencing profiles, including length of complementarity-deteremining region 3 (CDR3), intra- and inter-group (EPO resistant vs...
July 11, 2017: Journal of Biomedical Science
https://www.readbyqxmd.com/read/28696422/metagenomic-binning-of-a-marine-sponge-microbiome-reveals-unity-in-defense-but-metabolic-specialization
#18
Beate M Slaby, Thomas Hackl, Hannes Horn, Kristina Bayer, Ute Hentschel
Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts...
July 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28693586/impaired-b-cell-immunity-in-acute-myeloid-leukemia-patients-after-chemotherapy
#19
Meghali Goswami, Gabrielle Prince, Angelique Biancotto, Susan Moir, Lela Kardava, Brian H Santich, Foo Cheung, Yuri Kotliarov, Jinguo Chen, Rongye Shi, Huizhi Zhou, Hana Golding, Jody Manischewitz, Lisa King, Lauren M Kunz, Kimberly Noonan, Ivan M Borrello, B Douglas Smith, Christopher S Hourigan
BACKGROUND: Changes in adaptive immune cells after chemotherapy in adult acute myeloid leukemia (AML) may have implications for the success of immunotherapy. This study was designed to determine the functional capacity of the immune system in adult patients with AML who have completed chemotherapy and are potential candidates for immunotherapy. METHODS: We used the response to seasonal influenza vaccination as a surrogate for the robustness of the immune system in 10 AML patients in a complete remission post-chemotherapy and performed genetic, phenotypic, and functional characterization of adaptive immune cell subsets...
July 10, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28693542/overview-of-methodologies-for-t-cell-receptor-repertoire-analysis
#20
Elisa Rosati, C Marie Dowds, Evaggelia Liaskou, Eva Kristine Klemsdal Henriksen, Tom H Karlsen, Andre Franke
BACKGROUND: The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth...
July 10, 2017: BMC Biotechnology
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