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Translational genomics

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https://www.readbyqxmd.com/read/28108585/histone-h3k4-and-h3k36-methylation-independently-recruit-the-nua3-histone-acetyltransferase-in-saccharomyces-cerevisiae
#1
Benjamin J E Martin, Kristina L McBurney, Vicki E Maltby, Kristoffer N Jensen, Julie Brind'Amour, LeAnn Howe
Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. In S. cerevisiae, the NuA3 histone acetyltransferase complex contains three domains, the PHD finger in Yng1, the PWWP domain in Pdp3, and the YEATS domain in Taf14, which in vitro bind to H3K4 methylation, H3K36 methylation, and acetylated and crotonylated H3K9 respectively...
January 20, 2017: Genetics
https://www.readbyqxmd.com/read/28106782/from-clinical-standards-to-translating-next-generation-sequencing-research-into-patient-care-improvement-for-hepatobiliary-and-pancreatic-cancers
#2
REVIEW
Ioannis D Kyrochristos, Georgios K Glantzounis, Demosthenes E Ziogas, Ioannis Gizas, Dimitrios Schizas, Efstathios G Lykoudis, Evangelos Felekouras, Anastasios Machairas, Christos Katsios, Theodoros Liakakos, William C Cho, Dimitrios H Roukos
Hepatobiliary and pancreatic (HBP) cancers are associated with high cancer-related death rates. Surgery aiming for complete tumor resection (R0) remains the cornerstone of the treatment for HBP cancers. The current progress in the adjuvant treatment is quite slow, with gemcitabine chemotherapy available only for pancreatic ductal adenocarcinoma (PDA). In the advanced and metastatic setting, only two targeted drugs have been approved by the Food & Drug Administration (FDA), which are sorafenib for hepatocellular carcinoma and erlotinib for PDA...
January 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106333/translating-precision
#3
EDITORIAL
Michael A Pacanowski
Precision medicine is based on a simple precept that deep information about an individual patient can be used to guide his or her health care. In the not-too-distant future, clinicians may have point-of-care access to an individual's entire genome, dense data captured from wearable devices, and informatics tools that aggregate data from clinical experience to allow for real-time decision support. The innovative technologies being developed in pursuit of precision medicine afford researchers and clinicians the opportunity to generate and consume information at an unprecedented scale...
January 20, 2017: Clinical and Translational Science
https://www.readbyqxmd.com/read/28105933/haploid-yeast-cells-undergo-a-reversible-phenotypic-switch-associated-with-chromosome-ii-copy-number
#4
Polina Drozdova, Ludmila Mironova, Galina Zhouravleva
BACKGROUND: SUP35 and SUP45 are essential genes encoding polypeptide chain release factors. However, mutants for these genes may be viable but display pleiotropic phenotypes which include, but are not limited to, nonsense suppressor phenotype due to translation termination defect. [PSI (+)] prion formation is another Sup35p-associated mechanism leading to nonsense suppression through decreased availability of functional Sup35p. [PSI (+)] differs from genuine sup35 mutations by the possibility of its elimination and subsequent re-induction...
December 22, 2016: BMC Genetics
https://www.readbyqxmd.com/read/28105698/characterization-and-in-vivo-regulon-determination-of-an-ecf-sigma-factor-and-its-cognate-anti-sigma-factor-in-nostoc-punctiforme
#5
Nicole Bell, Jamie J Lee, Michael L Summers
Based on primary sequence comparisons and genomic context, Npun_F4153 (SigG)/Npun_F4154 (SapG) of the cyanobacterium Nostoc punctiforme were hypothesized to encode an ECF sigma factor/anti-sigma factor pair. Transcription of sigG increased in heterocysts and akinetes, and after EDTA treatment. Interaction between SigG and the predicted cytoplasmic domain of SapG was observed in vitro. A SigG-GFP translational fusion protein localized to the periphery of vegetative cells in vivo, but lost this association following heat stress...
January 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28101536/host-range-restriction-of-insect-specific-flaviviruses-occurs-at-several-levels-of-the-viral-life-cycle
#6
Sandra Junglen, Marvin Korries, Wolfgang Grasse, Janett Wieseler, Anne Kopp, Kyra Hermanns, Moises León-Juárez, Christian Drosten, Beate Mareike Kümmerer
The genus Flavivirus contains emerging arthropod-borne viruses (arboviruses) infecting vertebrates, as well as insect-specific viruses (ISVs) (i.e., viruses whose host range is restricted to insects). ISVs are evolutionary precursors to arboviruses. Knowledge of the nature of the ISV infection block in vertebrates could identify functions necessary for the expansion of the host range toward vertebrates. Mapping of host restrictions by complementation of ISV and arbovirus genome functions could generate knowledge critical to predicting arbovirus emergence...
January 2017: MSphere
https://www.readbyqxmd.com/read/28100786/inositol-depletion-induced-by-acute-treatment-of-the-bipolar-disorder-drug-valproate-increases-levels-of-phytosphingosine
#7
Shyamalagauri Jadhav, Sarah Russo, L Ashley Cowart, Miriam L Greenberg
Bipolar disorder (BD) is a severe psychiatric illness affecting ~2% of the world population. Valproate (VPA) and lithium, though widely used for the treatment of BD, are not universally effective. These drugs have been shown to cause inositol depletion, but translating this observation to a specific therapeutic mechanism has been difficult, hampering the development of more effective therapies. We have shown previously in yeast that chronic VPA treatment induces the unfolded protein response due to increasing ceramide levels...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100663/leveraging-genome-wide-datasets-to-quantify-the-functional-role-of-the-anti-shine-dalgarno-sequence-in-regulating-translation-efficiency
#8
Adam J Hockenberry, Adam R Pah, Michael C Jewett, Luís A N Amaral
Studies dating back to the 1970s established that sequence complementarity between the anti-Shine-Dalgarno (aSD) sequence on prokaryotic ribosomes and the 5' untranslated region of mRNAs helps to facilitate translation initiation. The optimal location of aSD sequence binding relative to the start codon, the full extents of the aSD sequence and the functional form of the relationship between aSD sequence complementarity and translation efficiency have not been fully resolved. Here, we investigate these relationships by leveraging the sequence diversity of endogenous genes and recently available genome-wide estimates of translation efficiency...
January 2017: Open Biology
https://www.readbyqxmd.com/read/28100080/the-commercialization-of-genome-editing-technologies
#9
Katelyn Brinegar, Ali K Yetisen, Sun Choi, Emily Vallillo, Guillermo U Ruiz-Esparza, Anand M Prabhakar, Ali Khademhosseini, Seok-Hyun Yun
The emergence of new gene-editing technologies is profoundly transforming human therapeutics, agriculture, and industrial biotechnology. Advances in clustered regularly interspaced short palindromic repeats (CRISPR) have created a fertile environment for mass-scale manufacturing of cost-effective products ranging from basic research to translational medicine. In our analyses, we evaluated the patent landscape of gene-editing technologies and found that in comparison to earlier gene-editing techniques, CRISPR has gained significant traction and this has established dominance...
January 18, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28097059/the-complete-chloroplast-genome-sequence-of-an-endemic-monotypic-genus-hagenia-rosaceae-structural-comparative-analysis-gene-content-and-microsatellite-detection
#10
Andrew W Gichira, Zhizhong Li, Josphat K Saina, Zhicheng Long, Guangwan Hu, Robert W Gituru, Qingfeng Wang, Jinming Chen
Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H...
2017: PeerJ
https://www.readbyqxmd.com/read/28096882/design-and-methods-of-the-mood-disorder-cohort-research-consortium-mdcrc-study
#11
Chul-Hyun Cho, Yong-Min Ahn, Se Joo Kim, Tae Hyun Ha, Hong Jin Jeon, Boseok Cha, Eunsoo Moon, Dong Yeon Park, Ji Hyun Baek, Hee-Ju Kang, Vin Ryu, Hyonggin An, Heon-Jeong Lee
The Mood Disorder Cohort Research Consortium (MDCRC) study is designed as a naturalistic observational prospective cohort study for early-onset mood disorders (major depressive disorders, bipolar disorders type 1 and 2) in South Korea. The study subjects consist of two populations: 1) patients with mood disorders under 25 years old and 2) patients with mood disorders within 2 years of treatment under 35 years old. After successful screening, the subjects are evaluated using baseline assessments and serial follow-up assessments at 3-month intervals...
January 2017: Psychiatry Investigation
https://www.readbyqxmd.com/read/28096492/identification-of-glutaminyl-cyclase-genes-involved-in-pyroglutamate-modification-of-fungal-lignocellulolytic-enzymes
#12
Vincent W Wu, Craig M Dana, Anthony T Iavarone, Douglas S Clark, N Louise Glass
: The breakdown of plant biomass to simple sugars is essential for the production of second-generation biofuels and high-value bioproducts. Currently, enzymes produced from filamentous fungi are used for deconstructing plant cell wall polysaccharides into fermentable sugars for biorefinery applications. A post-translational N-terminal pyroglutamate modification observed in some of these enzymes occurs when N-terminal glutamine or glutamate is cyclized to form a five-membered ring. This modification has been shown to confer resistance to thermal denaturation for CBH-1 and EG-1 cellulases...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096131/nutrition-micrornas-and-human-health
#13
REVIEW
Juan Cui, Beiyan Zhou, Sharon A Ross, Janos Zempleni
MicroRNAs (miRs) hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA. Over 60% of human protein-coding genes are regulated by miRs, and 1881 high-confidence miRs are encoded in the human genome. Evidence suggests that miRs not only are synthesized endogenously, but also might be obtained from dietary sources, and that food compounds alter the expression of endogenous miR genes. The main food matrices for studies of biological activity of dietary miRs include plant foods and cow milk...
January 2017: Advances in Nutrition
https://www.readbyqxmd.com/read/28095828/improved-genome-sequencing-using-an-engineered-transposase
#14
Amirali Kia, Christian Gloeckner, Trina Osothprarop, Niall Gormley, Erin Bomati, Michelle Stephenson, Igor Goryshin, Molly Min He
BACKGROUND: Next-generation sequencing (NGS) has transformed genomic research by reducing turnaround time and cost. However, no major breakthrough has been made in the upstream library preparation methods until the transposase-based Nextera method was invented. Nextera combines DNA fragmentation and barcoding in a single tube reaction and therefore enables a very fast workflow to sequencing-ready DNA libraries within a couple of hours. When compared to the traditional ligation-based methods, transposed-based Nextera has a slight insertion bias...
January 17, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28095775/ara-peps-a-repository-of-putative-sorf-encoded-peptides-in-arabidopsis-thaliana
#15
Rashmi R Hazarika, Barbara De Coninck, Lidia R Yamamoto, Laura R Martin, Bruno P A Cammue, Vera van Noort
BACKGROUND: Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana. RESULTS: To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www...
January 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28095645/what-we-can-learn-from-a-tadpole-about-ciliopathies-and-airway-diseases-using-systems-biology-in-xenopus-to-study-cilia-and-mucociliary-epithelia
#16
REVIEW
Peter Walentek, Ian K Quigley
Over the past years, the Xenopus embryo has emerged as an incredibly useful model organism for studying the formation and function of cilia and ciliated epithelia in vivo. This has led to a variety of findings elucidating the molecular mechanisms of ciliated cell specification, basal body biogenesis, cilia assembly and ciliary motility. These findings also revealed the deep functional conservation of signaling, transcriptional, post-transcriptional and protein networks employed in the formation and function of vertebrate ciliated cells...
January 17, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28095450/non-lytic-egression-of-infectious-bursal-disease-virus-ibdv-particles-from-infected-cells
#17
Fernando Méndez, Nicolás Romero, Liliana L Cubas, Laura R Delgui, Dolores Rodríguez, José F Rodríguez
Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is responsible for a devastating immunosuppressive disease affecting juvenile domestic chickens. IBDV particles are naked icosahedrons enclosing a bipartite double-stranded RNA genome harboring three open reading frames (ORF). One of these ORFs codes for VP5, a non-structural polypeptide dispensable for virus replication in tissue culture but essential for IBDV pathogenesis. Using two previously described recombinant viruses, whose genomes differ in a single nucleotide, expressing or not the VP5 polypeptide, we have analyzed the role of this polypeptide during the IBDV replication process...
2017: PloS One
https://www.readbyqxmd.com/read/28093680/the-international-diffuse-intrinsic-pontine-glioma-registry-an-infrastructure-to-accelerate-collaborative-research-for-an-orphan-disease
#18
Joshua Baugh, Ute Bartels, James Leach, Blaise Jones, Brooklyn Chaney, Katherine E Warren, Jenavieve Kirkendall, Renee Doughman, Cynthia Hawkins, Lili Miles, Christine Fuller, Tim Hassall, Eric Bouffet, Adam Lane, Darren Hargrave, Jacques Grill, Lindsey M Hoffman, Chris Jones, Alex Towbin, Sharon A Savage, Michelle Monje, Xiao-Nan Li, David S Ziegler, Sophie Veldhuijzen van Zanten, Christof M Kramm, Dannis G van Vuurden, Maryam Fouladi
Diffuse intrinsic pontine glioma (DIPG), a rare, often fatal childhood brain tumor, remains a major therapeutic challenge. In 2012, investigators, funded by the DIPG Collaborative (a philanthropic partnership among 29 private foundations), launched the International DIPG Registry (IDIPGR) to advance understanding of DIPG. Comprised of comprehensive deidentified but linked clinical, imaging, histopathological, and genomic repositories, the IDIPGR uses standardized case report forms for uniform data collection; serial imaging and histopathology are centrally reviewed by IDIPGR neuro-radiologists and neuro-pathologists, respectively...
January 16, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28093273/identification-of-fhit-as-a-post-transcriptional-effector-of-thymidine-kinase-1-expression
#19
Daniel L Kiss, Catherine E Waters, Iman M Ouda, Joshua C Saldivar, Jenna R Karras, Zaynab A Amin, Seham Mahrous, Teresa Druck, Ralf A Bundschuh, Daniel R Schoenberg, Kay Huebner
FHIT is a genome caretaker gene that is silenced in >50% of cancers. Loss of Fhit protein expression promotes accumulation of DNA damage, affects apoptosis and epithelial-mesenchymal transition, though molecular mechanisms underlying these alterations have not been fully elucidated. Initiation of genome instability directly follows Fhit loss and the associated reduced Thymidine Kinase 1 (TK1) protein expression. The effects on TK1 of Fhit knockdown and Fhit induction in the current study confirmed the role of Fhit in regulating TK1 expression...
January 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28092471/genomics-pipelines-and-data-integration-challenges-and-opportunities-in-the-research-setting
#20
Jeremy Davis-Turak, Sean M Courtney, E Starr Hazard, W Bailey Glen, Willian da Silveira, Timothy Wesselman, Larry P Harbin, Bethany J Wolf, Dongjun Chung, Gary Hardiman
The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine...
January 16, 2017: Expert Review of Molecular Diagnostics
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