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bioinformatics lab

Leonie A Cluse, Iva Nikolic, Deborah Knight, Piyush B Madhamshettiwar, Jennii Luu, Karla J Cowley, Timothy Semple, Gisela Mir Arnau, Jake Shortt, Ricky W Johnstone, Kaylene J Simpson
This chapter details a compendium of protocols that collectively enable the reader to perform a pooled shRNA and/or CRISPR screen-with methods to identify and validate positive controls and subsequent hits; establish a viral titer in the cell line of choice; create and screen libraries, sequence strategies, and bioinformatics resources to analyze outcomes. Collectively, this provides an overarching resource from the start to finish of a screening project, making this technology possible in all laboratories.
2018: Methods in Molecular Biology
Aaron M Fleming, Judy Zhu, Yun Ding, Joshua A Visser, Julia Zhu, Cynthia J Burrows
The cellular response to oxidative stress includes transcriptional changes, particularly for genes involved in DNA repair. Recently, our laboratory demonstrated that oxidation of 2`-deoxyguanosine (G) to 8-oxo-7,8-dihydro-2`-deoxyguanosine (OG) in G-rich potential G-quadruplex sequences (PQSs) in gene promoters impacts the level of gene expression up or down depending on the position of the PQS in the promoter. In the present report, bioinformatic analysis found that the 390 human DNA repair genes in the genome ontology initiative harbor 2,936 PQSs in their promoters and 5`-untranslated regions (5`-UTRs)...
January 10, 2018: Biochemistry
Xiaohua Douglas Zhang, Zhaozhi Zhang, Dandan Wang
Summary: The R package CGManalyzer contains functions for analyzing data from a continuous glucose monitoring (CGM) study. It covers a wide and comprehensive range of data analysis methods including reading a series of datasets, obtaining summary statistics of glucose levels, plotting data, transforming the time stamp format, fixing missing values, evaluating the mean of daily difference (MODD) and continuous overlapping net glycemic action (CONGA), calculating multiscale sample entropy (MSE), conducting pairwise comparison, displaying results using various plots including a new type of plot called an antenna plot, etc...
January 5, 2018: Bioinformatics
Jiaojiao Miao, Na Han, Yujun Qiang, Tingting Zhang, Xiuwen Li, Wen Zhang
BACKGROUND: Pathogen detection in clinical samples based on 16S metagenomic sequencing technology in microbiology laboratories is an important strategy for clinical diagnosis, public health surveillance, and investigations of outbreaks. However, the implementation of the technology is limited by its accuracy and the time required for bioinformatics analysis. Therefore, a simple, standardized, and rapid analysis pipeline from the receipt of clinical samples to the generation of a test report is needed to increase the use of metagenomic analyses in clinical settings...
December 28, 2017: BMC Bioinformatics
Arun V Everest-Dass, Edward S X Moh, Christopher Ashwood, Abdulrahman M M Shathili, Nicolle H Packer
Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics)...
December 29, 2017: Expert Review of Proteomics
James L Bodnar, Sergio Fitch, Allison Rosati, Jianmin Zhong
Although nonpathogenic bacterial endosymbionts have been shown to contribute to their arthropod host's fitness by supplying them with essential vitamins and amino acids, little is known about the nutritional basis for the symbiotic relationship of endosymbionts in ticks. Our lab has previously reported that Rickettsia species phylotype G021 in Ixodes pacificus carries all five genes for de novo folate synthesis, and that these genes are monophyletic with homologs from other Rickettsia species. In this study, the rickettsial folate synthesis folA gene, coding for dihydrofolate reductase, was PCR amplified, cloned into an expression vector, and overexpressed in E...
December 24, 2017: Ticks and Tick-borne Diseases
Martin Oti, Attilio Pane, Michael Sammeth
Since the pioneering studies of Thomas Hunt Morgan and coworkers at the dawn of the twentieth century, Drosophila melanogaster and its sister species have tremendously contributed to unveil the rules underlying animal genetics, development, behavior, evolution, and human disease. Recent advances in DNA sequencing technologies launched Drosophila into the post-genomic era and paved the way for unprecedented comparative genomics investigations. The complete sequencing and systematic comparison of the genomes from 12 Drosophila species represents a milestone achievement in modern biology, which allowed a plethora of different studies ranging from the annotation of known and novel genomic features to the evolution of chromosomes and, ultimately, of entire genomes...
2018: Methods in Molecular Biology
Keng Po Lai, Jing Woei Li, Simon Yuan Wang, Miles Teng Wan, Ting Fung Chan, Wing Yee Lui, Doris Wai-Ting Au, Rudolf Shiu-Sun Wu, Richard Yuen-Chong Kong
There are over 400 hypoxic zones in the ocean worldwide. Both laboratory and field studies have shown that hypoxia causes endocrine disruption and reproductive impairments in vertebrates. More importantly, our recent study discovered that parental (F0) hypoxia exposure resulted in the transgenerational impairment of sperm quality in the F2 generation through the epigenetic regulation of germ cells. In the present study, we aim to test the hypothesis that the brain, as the major regulator of the brain-pituitary-gonad (BPG) axis, is also involved in the observed transgenerational effect...
December 16, 2017: Aquatic Toxicology
Yao-Yuan Liu, SallyAnn Harbison
Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data...
December 12, 2017: Forensic Science International. Genetics
Kenneth D Doig, Jason Ellul, Andrew Fellowes, Ella R Thompson, Georgina Ryland, Piers Blombery, Anthony T Papenfuss, Stephen B Fox
BACKGROUND: High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants...
December 15, 2017: BMC Bioinformatics
Clémentine Henri, Pimlapas Leekitcharoenphon, Heather A Carleton, Nicolas Radomski, Rolf S Kaas, Jean-François Mariet, Arnaud Felten, Frank M Aarestrup, Peter Gerner Smidt, Sophie Roussel, Laurent Guillier, Michel-Yves Mistou, René S Hendriksen
Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST)...
2017: Frontiers in Microbiology
Gregory C A Amos, Takayoshi Awakawa, Robert N Tuttle, Anne-Catrin Letzel, Min Cheol Kim, Yuta Kudo, William Fenical, Bradley S Moore, Paul R Jensen
Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of genome mining techniques based on the premise that many are transcriptionally silent during normal laboratory cultivation. Here, we employ comparative transcriptomics to assess BGC expression among four closely related strains of marine bacteria belonging to the genus Salinispora The results reveal that slightly more than half of the BGCs are expressed at levels that should facilitate product detection...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
Paul A Christensen, Yunyun Ni, Feifei Bao, Heather L Hendrickson, Michael Greenwood, Jessica S Thomas, S Wesley Long, Randall J Olsen
Introduction: Next-generation-sequencing (NGS) is increasingly used in clinical and research protocols for patients with cancer. NGS assays are routinely used in clinical laboratories to detect mutations bearing on cancer diagnosis, prognosis and personalized therapy. A typical assay may interrogate 50 or more gene targets that encompass many thousands of possible gene variants. Analysis of NGS data in cancer is a labor-intensive process that can become overwhelming to the molecular pathologist or research scientist...
2017: Journal of Pathology Informatics
Gillian Ellison, Miika Ahdesmäki, Sally Luke, Paul M Waring, Andrew Wallace, Ronnie Wright, Benno Röthlisberger, Katja Ludin, Sabine Merkelbach-Bruse, Carina Heydt, Marjolijn J L Ligtenberg, Arjen R Mensenkamp, David Gonzalez Castro, Thomas Jones, Ana Vivancos, Olga Kondrashova, Patrick Pauwels, Christine Weyn, Eric Hahnen, Jan Hauke, Richie Soong, Zhongwu Lai, Brian Dougherty, T Hedley Carr, Justin Johnson, John Mills, J Carl Barrett
Ovarian cancer patients with germline or somatic pathogenic variants benefit from treatment with PARP inhibitors. Tumour BRCA1/2 testing is more challenging than germline testing as the majority of samples are formalin fixed paraffin embedded (FFPE), the tumour genome is complex and the allelic fraction of somatic variants can be low. We collaborated with 10 laboratories testing BRCA1/2 in tumours to compare different approaches to identify clinically important variants within FFPE tumour DNA samples. This was not a proficiency study but an inter-laboratory comparison to identify common issues...
December 7, 2017: Human Mutation
Zilong He, Chengwei Zhang, Wanfei Liu, Qiang Lin, Ting Wei, Hasan A Aljohi, Wei-Hua Chen, Songnian Hu
Background: Date palm (Phoenix dactylifera L.) is a cultivated woody plant with agricultural and economic importance in many countries around the world. With the advantages of next generation sequencing technologies, genome sequences for many date palm cultivars have been released recently. Short sequence repeat (SSR) and single nucleotide polymorphism (SNP) can be identified from these genomic data, and have been proven to be very useful biomarkers in plant genome analysis and breeding. Results: Here, we first improved the date palm genome assembly using 130X of HiSeq data generated in our lab...
2017: Frontiers in Plant Science
Lama Alfaraidi, Abrar Alfaifi, Rawan Alquaiz, Faten Almijmaj, Horia Mawlawi
Isolated hypoaldosteronism is a rare autosomal recessive disease presenting with severe salt wasting and failure to thrive in infancy. A 6-month-old Saudi girl born to consanguineous parents was referred from primary health care for failure to thrive and developmental delay. Laboratory tests revealed hyponatremia, hyperkalemia, and metabolic acidosis with high renin and low aldosterone. Blood samples were collected for endocrine and genetic studies. Sequence analysis of the CYP11B2 revealed a T to A transition at position 1398 + 2 in exon 8 of the gene in a homozygous state (c...
2017: Case Reports in Endocrinology
Stephan Fuchs, Henry Mehlan, Jörg Bernhardt, André Hennig, Stephan Michalik, Kristin Surmann, Jan Pané-Farré, Anne Giese, Stefan Weiss, Linus Backert, Alexander Herbig, Kay Nieselt, Michael Hecker, Uwe Völker, Ulrike Mäder
In light of continuously accumulating data and knowledge on major human pathogens, comprehensive and up-to-date sources of easily accessible information are urgently required. The AureoWiki database ( provides detailed information on the genes and proteins of clinically and experimentally relevant S. aureus strains, currently covering NCTC 8325, COL, Newman, USA300_FPR3757, and N315. By implementing a pan-genome approach, AureoWiki facilitates the transfer of knowledge gained in studies with different S...
November 24, 2017: International Journal of Medical Microbiology: IJMM
Hua Yin, Jianjun Dong, Junhong Yu, Yanmei Li, Yang Deng
As one of the most popular beverage, beer has strong resistance to bacteria except for lactic acid bacteria (LAB), as its strong viability in beer. Contaminating LAB results in beer spoilage. HorA gene carried by beer spoilage lactobacillus confers hop resistance and is associated with the growth of Lactobacillus in beer, thus can be used as a perfectly valid genetic marker for the detection of beer spoilage Lactobacillus strains. This study applied genome and bioinformatics analyses, together with genetic alignment and comparison techniques to build a rolling circle amplification (RCA) detection method targeted on horA for beer spoilage Lactobacillus...
November 29, 2017: Microbial Pathogenesis
Dominic Guanzon, Juvita Delancy Iljas, Gregory E Rice, Carlos Salomon
Next-generation sequencing is a powerful method to interrogate the nucleotide composition for millions of DNA strands simultaneously. This technology can be utilized to profile microRNAs from multiple origins, such as tissues, cells, and body fluids. Next-generation sequencing is increasingly becoming a common and readily available technique for all laboratories. However, the bottleneck for next-generation sequencing is not within the laboratory but with the bioinformatics and data analysis of next-generation sequencing data...
2018: Methods in Molecular Biology
Yuxin Lin, Fuliang Qian, Li Shen, Feifei Chen, Jiajia Chen, Bairong Shen
Biomarkers are a class of measurable and evaluable indicators with the potential to predict disease initiation and progression. In contrast to disease-associated factors, biomarkers hold the promise to capture the changeable signatures of biological states. With methodological advances, computer-aided biomarker discovery has now become a burgeoning paradigm in the field of biomedical science. In recent years, the 'big data' term has accumulated for the systematical investigation of complex biological phenomena and promoted the flourishing of computational methods for systems-level biomarker screening...
November 29, 2017: Briefings in Bioinformatics
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