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Comparative genomics

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https://www.readbyqxmd.com/read/28103252/comparative-and-evolutionary-analysis-of-grass-pollen-allergens-using-brachypodium-distachyon-as-a-model-system
#1
Akanksha Sharma, Niharika Sharma, Prem Bhalla, Mohan Singh
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses...
2017: PloS One
https://www.readbyqxmd.com/read/28103008/quantitative-tracking-of-combinatorially-engineered-populations-with-multiplexed-binary-assemblies
#2
Ramsey Zeitoun, Gur Pines, William C Grau, Ryan T Gill
Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory timescales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28102516/production-of-lovastatin-and-itaconic-acid-by-aspergillus-terreus-a-comparative-perspective
#3
REVIEW
Tomasz Boruta, Marcin Bizukojc
Aspergillus terreus is a textbook example of an industrially relevant filamentous fungus. It is used for the biotechnological production of two valuable metabolites, namely itaconic acid and lovastatin. Itaconic acid serves as a precursor in polymer industry, whereas lovastatin found its place in the pharmaceutical market as a cholesterol-lowering statin drug and a precursor for semisynthetic statins. Interestingly, their biosynthetic gene clusters were shown to reside in the common genetic neighborhood. Despite the genomic proximity of the underlying biosynthetic genes, the production of lovastatin and itaconic acid was shown to be favored by different factors, especially with respect to pH values of the broth...
February 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28102150/ultra-rare-genetic-variation-in-common-epilepsies-a-case-control-sequencing-study
#4
(no author information available yet)
BACKGROUND: Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies. METHODS: We did a case-control sequencing study with exome sequence data from unrelated individuals clinically evaluated for one of the two most common epilepsy syndromes: familial genetic generalised epilepsy, or familial or sporadic non-acquired focal epilepsy...
February 2017: Lancet Neurology
https://www.readbyqxmd.com/read/28102032/nonpromoter-methylation-of-the-cdkn2a-gene-with-active-transcription-is-associated-with-improved-locoregional-control-in-laryngeal-squamous-cell-carcinoma
#5
Miriam M Ben-Dayan, Thomas J Ow, Thomas J Belbin, Joshua Wetzler, Richard V Smith, Geoffrey Childs, Brenda Diergaarde, D Neil Hayes, Jennifer R Grandis, Michael B Prystowsky, Nicolas F Schlecht
We previously reported a novel association between CDKN2A nonpromoter methylation and transcription (ARF/INK4a) in human papillomavirus associated oropharyngeal tumors. In this study we assessed whether nonpromoter CDKN2A methylation in laryngeal squamous cell carcinomas (LXSCC) conferred a similar association with transcription that predicted patient outcome. We compared DNA methylation and ARF/INK4a RNA expression levels for the CDKN2A locus using the Illumina HumanMethylation27 beadchip and RT-PCR in 43 LXSCC tumor samples collected from a prospective study of head and neck cancer patients treated at Montefiore Medical Center (MMC)...
January 19, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28101801/identification-of-changes-in-the-human-papilloma-virus-16-hpv16-genome-during-early-dissemination-of-cervical-cancer-cells-may-complement-histological-diagnosis-of-lymph-node-metastasis
#6
Anirban Roychowdhury, Sudip Samadder, Md Saimul Islam, Kalyansree Chaudhury, Anup Roy, Dipanwita Banerjee, Ranajit Mandal, Partha S Basu, Susanta Roychoudhury, Chinmay Kumar Panda
Cancer of the uterine cervix (CACX) is one of the most common carcinoma affecting women worldwide. During treatment, histologically lymph node (LN) metastasis and presence of HPV DNA in blood plasma act as a major prognostic factor. Despite the lack of apparent LN involvement, some early-invasive CACX patients have shown recurrences and poor survival. This is suggestive of undetected early dissemination of cancer cells characterized by presence of HPV DNA in histologically non-metastatic LNs which finally progresses into histologically visible metastasis...
January 19, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28101273/who-scared-the-cat-a-molecular-crime-scene-investigation-laboratory-exercise
#7
Laura E Ott, Susan D Carson
This introductory laboratory exercise gives first-year life science majors or nonmajors an opportunity to gain knowledge and experience in basic bioinformatics and molecular biology laboratory techniques and analysis in the context of a mock crime scene investigation. In this laboratory, students determine if a human (Lady) or dog (Kona) committed the fictional crime of scaring a cat. Students begin by performing in silico PCR using provided dog- and human-specific PCR primers to determine the sequences to be amplified and predict PCR amplicon sizes...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101224/impact-of-chromosome-17q-deletion-in-the-primary-lesion-of-colorectal-cancer-on-liver-metastasis
#8
Masaya Kawai, Hiromitsu Komiyama, Masaki Hosoya, Haruna Okubo, Tomoaki Fujii, Norihiko Yokoyama, Chiyo Sato, Takae Ueyama, Atsushi Okuzawa, Michitoshi Goto, Yutaka Kojima, Makoto Takahashi, Kiichi Sugimoto, Shun Ishiyama, Shinya Munakata, Dai Ogura, Shin-Ichiro Niwa, Yuichi Tomiki, Takumi Ochiai, Kazuhiro Sakamoto
Colorectal cancer is a prevalent malignancy worldwide, and investigations are required to elucidate the underlying carcinogenic mechanisms. Amongst these mechanisms, de novo carcinogenesis and the adenoma to carcinoma sequence, are the most understood. Metastasis of colorectal cancer to the liver often results in fatality, therefore, it is important for any associated risk factors to be identified. Regarding the treatment of the disease, it is important to manage not only the primary colorectal tumor, but also the liver metastases...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28101207/structure-function-analysis-of-dna-helicase-helq-a-new-diagnostic-marker-in-ovarian-cancer
#9
Ya-Ping Li, Jun-Juan Yang, Hui Xu, En-Yu Guo, Yan Yu
It has been previously reported that a deficiency of the helicase, POLQ-like (HELQ) gene increases the risk of ovarian cancer. The present study aimed to explore the structure-function association of HELQ and discuss the effect of molecular structure on the occurrence of tumors. ExPASy tools were employed to analyze the physicochemical properties and secondary structure of the genes. PHYRE2 Protein Fold Recognition Server was used to construct the three-dimensional model and find the ligand-binding sites of HELQ...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28101186/comparative-analysis-of-signaling-pathways-in-peripheral-blood-from-patients-with-kashin-beck-disease-and-osteoarthritis
#10
Yujie Ning, Xi Wang, Sen Wang, Xiong Guo
The aim of the present study was to investigate the early diagnostic biomarkers of Kashin-Beck disease (KBD), and to compare the common signaling pathways of peripheral mononuclear cells between patients with KBD and those with osteoarthritis (OA). A total of 20 and 12 peripheral blood samples were separately collected from KBD patients and normal control subjects, respectively, in an endemic area according to the diagnosis criteria. Total RNAs were extracted and gene expression levels were determined using an Agilent whole genome expression microarrays...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28101157/functional-analysis-of-keratinocyte-and-fibroblast-gene-expression-in-skin-and-keloid-scar-tissue-based-on-deviation-analysis-of-dynamic-capabilities
#11
Mingming Li, Lei Wu
The aim of the present study was to select key genes that are associated with fibroblasts and keratinocytes during keloid scar progression and development. The gene expression profile of GSE44270, which includes 32 samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in case samples compared with control samples were screened using the Limma R package followed by hierarchical clustering analysis. Protein-protein interaction (PPI) networks of the total selected DEGs were constructed using Cytoscape...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28100790/genome-wide-analysis-in-brazilians-reveals-highly-differentiated-native-american-genome-regions
#12
Josyf C Mychaleckyj, Alexandre Havt, Uma Nayak, Relana Pinkerton, Emily Farber, Patrick Concannon, Aldo A Lima, Richard L Guerrant
Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared to the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh)...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100699/proteogenomics-produces-comprehensive-and-highly-accurate-protein-coding-gene-annotation-in-a-complete-genome-assembly-of-malassezia-sympodialis
#13
Yafeng Zhu, Pär G Engström, Christian Tellgren-Roth, Charles D Baudo, John C Kennell, Sheng Sun, R Blake Billmyre, Markus S Schröder, Anna Andersson, Tina Holm, Benjamin Sigurgeirsson, Guangxi Wu, Sundar Ram Sankaranarayanan, Rahul Siddharthan, Kaustuv Sanyal, Joakim Lundeberg, Björn Nystedt, Teun Boekhout, Thomas L Dawson, Joseph Heitman, Annika Scheynius, Janne Lehtiö
Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28100623/temperature-sensitive-lesion-in-the-n-terminal-domain-of-the-rotavirus-polymerase-affects-its-intracellular-localization-and-enzymatic-activity
#14
Allison O McKell, Leslie E W LaConte, Sarah M McDonald
: Temperature-sensitive (ts) mutants of simian rotavirus (RV) strain SA11 have been previously created to investigate the functions of viral proteins during replication. One mutant, SA11-tsC, maps to the gene encoding the VP1 polymerase and shows diminished growth and RNA synthesis at 39°C as compared to 31°C. In the current study, we sequenced all 11 genes of SA11-tsC, confirming the presence of an L138P mutation in the VP1 N-terminal domain and identifying 52 additional mutations in four other viral proteins (VP7, VP4, NSP2, and NSP1)...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28100619/functional-analysis-of-hcv-envelope-protein-e1-using-a-trans-complementation-system-reveals-a-dual-role-of-a-putative-fusion-peptide-of-e1-in-both-hcv-entry-and-morphogenesis
#15
Yimin Tong, Xiaojing Chi, Wei Yang, Jin Zhong
: Hepatitis C virus (HCV) is an enveloped RNA virus belonging to the Flaviviridae family. It mainly infects human hepatocytes and causes chronic liver diseases including cirrhosis and cancer. HCV encodes two envelope proteins E1 and E2 that form a heterodimer and mediate virus entry. While E2 has been extensively studied, less has been done so for E1, and its role in HCV life cycle still needs to be elucidated. Here we developed a new cell culture model for HCV infection based on trans-complementation of E1...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28100596/genomic-epidemiology-of-penicillin-non-susceptible-pneumococci-with-non-vaccine-serotypes-causing-invasive-disease-in-the-usa
#16
Cheryl P Andam, Patrick K Mitchell, Alanna Callendrello, Qiuzhi Chang, Jukka Corander, Chrispin Chaguza, Lesley McGee, Bernard W Beall, William P Hanage
Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic resistant strains throughout the 2000s; however, disease caused by resistant non-vaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) that had changed their capsule by recombination. The introduction of vaccine targeting 13 serotypes (PCV13) in 2010 has led to concern that this scenario will repeat itself. We generated high quality draft genomes from 265 isolates of NVT pneumococci not susceptible to penicillin (PNSP) in 2009 and compared them with 581 isolates from 2012-2013, collected by the Active Bacterial Core surveillance (ABCs) of the Centers for Disease Control and Prevention (CDC)...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100593/clinical-implications-of-dnmt3a-mutations-in-a-southeast-asian-cohort-of-acute-myeloid-leukaemia-patients
#17
Marcus Tan, Isaac K S Ng, Zhaojin Chen, Kenneth Ban, Christopher Ng, Lily Chiu, Elaine Seah, Mingxuan Lin, Bee Choo Tai, Benedict Yan, Chin Hin Ng, Wee-Joo Chng
AIMS: In recent years, genomic technologies have enabled the identification of mutations in acute myeloid leukaemia (AML). DNMT3A is a recurrently mutated epigenetic modifier gene in AML. To date, the prognostic significance of DNMT3A mutations has not been studied in a Southeast Asian AML population. We sought to investigate the clinical implications of DNMT3A mutations in a Southeast Asian cohort of AML patients. METHODS: DNMT3A mutations were identified using a targeted next-generation sequencing panel in 157 AML patients...
January 18, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28100394/replication-study-melanoma-genome-sequencing-reveals-frequent-prex2-mutations
#18
Stephen K Horrigan, Pascal Courville, Darryl Sampey, Faren Zhou, Steve Cai
In 2015, as part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Chroscinski et al., 2014) that described how we intended to replicate selected experiments from the paper "Melanoma genome sequencing reveals frequent PREX2 mutations" (Berger et al., 2012). Here we report the results of those experiments. We regenerated cells stably expressing ectopic wild-type and mutant phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2 (PREX2) using the same immortalized human NRAS(G12D) melanocytes as the original study...
January 19, 2017: ELife
https://www.readbyqxmd.com/read/28100302/fecal-virome-of-healthy-chickens-reveals-a-large-diversity-of-the-eukaryote-viral-community-including-novel-circular-single-stranded-dna-viruses
#19
Diane Lima, Samuel Paulo Cibulski, Fabrine Finkler, Thais Teixeira, Ana Paula Varela, Cristine Cerva, Márcia Loiko, Camila Scheffer, Helton Dos Santos, Fabiana Mayer, Paulo Roehe
This study is focused on the identification of the fecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7,743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with BLASTx revealed that 279 contigs (4%) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes...
January 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28100285/characterization-of-the-complete-mitochondrial-genome-of-setaria-digitata-nematoda-setariidae-from-china
#20
G-H Liu, J-Y Li, X-Q Zhu
Setaria digitata is a filarial parasite that causes fatal cerebrospinal nematodiasis in goats, horses and sheep, resulting in substantial economic losses to livestock farmers. In the present study, the complete mitochondrial (mt) genome of S. digitata from China was determined, characterized and compared with that of S. digitata from Sri Lanka. The identity of the mt genomes was 98.3% between S. digitata from China and Sri Lanka, and the complete mt genome sequence of S. digitata from China was slightly shorter (25 bp) than that from Sri Lanka...
January 19, 2017: Journal of Helminthology
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