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https://www.readbyqxmd.com/read/27933214/integrating-next-generation-sequencing-into-clinical-oncology-strategies-promises-and-pitfalls
#1
REVIEW
Peter Horak, Stefan Fröhling, Hanno Glimm
We live in an era of genomic medicine. The past five years brought about many significant achievements in the field of cancer genetics, driven by rapidly evolving technologies and plummeting costs of next-generation sequencing (NGS). The official completion of the Cancer Genome Project in 2014 led many to envision the clinical implementation of cancer genomic data as the next logical step in cancer therapy. Stemming from this vision, the term 'precision oncology' was coined to illustrate the novelty of this individualised approach...
2016: ESMO Open
https://www.readbyqxmd.com/read/27932412/universal-haplotype-based-noninvasive-prenatal-testing-for-single-gene-diseases
#2
Winnie W I Hui, Peiyong Jiang, Yu K Tong, Wing-Shan Lee, Yvonne K Y Cheng, Maria I New, Rezan A Kadir, K C Allen Chan, Tak Y Leung, Y M Dennis Lo, Rossa W K Chiu
BACKGROUND: Researchers have developed approaches for the noninvasive prenatal testing of single gene diseases. One approach that allows for the noninvasive assessment of both maternally and paternally inherited mutations involves the analysis of single nucleotide polymorphisms (SNPs) in maternal plasma DNA with reference to parental haplotype information. In the past, parental haplotypes were resolved by complex experimental methods or inferential approaches, such as through the analysis of DNA from other affected family members...
December 8, 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27932294/large-scale-structure-based-prediction-and-identification-of-novel-protease-substrates-using-computational-protein-design
#3
Manasi A Pethe, Aliza B Rubenstein, Sagar D Khare
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data...
December 5, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27931678/diagnosing-tuberculosis-in-the-21st-century-dawn-of-a-genomics-revolution
#4
REVIEW
Christopher Jeanes, Justin O'Grady
Tuberculosis (TB) ranks alongside HIV as the leading cause of death worldwide, killing 1.5million people in 2014. Traditional laboratory techniques do not provide sufficiently rapid results to inform clinicians on appropriate treatment, especially in the face of increasingly prevalent drug-resistant TB. Rapid molecular methods such as PCR and LAMP are vital tools in the fight against TB, however, rapid advances in next generation sequencing (NGS) technology are allowing increasingly rapid and accurate sequencing of entire bacterial genomes at ever decreasing cost, providing unprecedented depth of information...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27931186/transcriptome-profiling-reveals-differential-gene-expression-of-detoxification-enzymes-in-a-hemimetabolous-tobacco-pest-after-feeding-on-jasmonate-silenced-nicotiana-attenuata-plants
#5
Cristina M Crava, Christoph Brütting, Ian T Baldwin
BACKGROUND: The evolutionary arms race between plants and insects has driven the co-evolution of sophisticated defense mechanisms used by plants to deter herbivores and equally sophisticated strategies that enable phytophagous insects to rapidly detoxify the plant's defense metabolites. In this study, we identify the genetic determinants that enable the mirid, Tupiocoris notatus, to feed on its well-defended host plant, Nicotiana attenuata, an outstanding model for plant-insect interaction studies...
December 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27931183/evolution-of-mitosome-metabolism-and-invasion-related-proteins-in-cryptosporidium
#6
Shiyou Liu, Dawn M Roellig, Yaqiong Guo, Na Li, Michael A Frace, Kevin Tang, Longxian Zhang, Yaoyu Feng, Lihua Xiao
BACKGROUND: The switch from photosynthetic or predatory to parasitic life strategies by apicomplexans is accompanied with a reductive evolution of genomes and losses of metabolic capabilities. Cryptosporidium is an extreme example of reductive evolution among apicomplexans, with losses of both the mitosome genome and many metabolic pathways. Previous observations on reductive evolution were largely based on comparative studies of various groups of apicomplexans. In this study, we sequenced two divergent Cryptosporidium species and conducted a comparative genomic analysis to infer the reductive evolution of metabolic pathways and differential evolution of invasion-related proteins within the Cryptosporidium lineage...
December 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27930689/determination-of-a-screening-metric-for-high-diversity-dna-libraries
#7
Nicholas J Guido, Steven Handerson, Elaine M Joseph, Devin Leake, Li A Kung
The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants...
2016: PloS One
https://www.readbyqxmd.com/read/27930677/de-novo-sequencing-and-comparative-analysis-of-schima-superba-seedlings-to-explore-the-response-to-drought-stress
#8
Bao-Cai Han, Wei Wei, Xiang-Cheng Mi, Ke-Ping Ma
Schima superba is an important dominant species in subtropical evergreen broadleaved forests of China, and plays a vital role in community structure and dynamics. However, the survival rate of its seedlings in the field is low, and water shortage could be a factor that limits its regeneration. In order to better understand the response of its seedlings to drought stress on a functional genomics scale, RNA-seq technology was utilized in this study to perform a large-scale transcriptome sequencing of the S. superba seedlings under drought stress...
2016: PloS One
https://www.readbyqxmd.com/read/27930648/isothermal-diagnostic-assays-for-monitoring-single-nucleotide-polymorphisms-in-necator-americanus-associated-with-benzimidazole-drug-resistance
#9
Nour Rashwan, Catherine Bourguinat, Kathy Keller, Nipul Kithsiri Gunawardena, Nilanthi de Silva, Roger Prichard
BACKGROUND: Soil-transmitted helminths (STHs) are the most prevalent intestinal helminths of humans, and a major cause of morbidity in tropical and subtropical countries. The benzimidazole (BZ) drugs albendazole (ABZ) and mebendazole (MBZ) are used for treatment of human STH infections and this use is increasing dramatically with massive drug donations. Frequent and prolonged use of these drugs could lead to the emergence of anthelmintic resistance as has occurred in nematodes of livestock...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27930536/the-effect-of-sequential-therapy-for-postmenopausal-women-with-osteoporosis-a-prisma-compliant-meta-analysis-of-randomized-controlled-trials
#10
Shenghan Lou, Houchen Lv, Guoqi Wang, Zhirui Li, Ming Li, Licheng Zhang, Peifu Tang
BACKGROUND: Osteoporosis, more likely to occur in postmenopausal women, is a chronic condition that usually requires a long-term treatment strategy, but the use of either antiresorptive or anabolic drugs should be limited to 18 to 24 months. Discontinuing antiosteoporosis drugs may result in rapidly declining bone mineral density (BMD). Therefore, many patients are treated with the sequential use of 2 or more drugs. However, whether switching treatment from anabolic to antiresorptive drugs or the reverse could maintain or further increase BMD; and whether the sequential therapy could outperform the monotherapy under the same treatment duration still remains unclear...
December 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27930389/therapy-related-myeloid-neoplasms
#11
Arnold Ganser, Michael Heuser
PURPOSE OF REVIEW: Advances in the genetic characterization of patients with therapy-related myeloid neoplasms (t-MNs) have changed our understanding of the pathogenesis of these diseases. In addition, extensive sequencing studies have identified recurrent mutations with diagnostic and prognostic impact. Thus, the revised version of the WHO classification combines therapy-related myelodysplastic syndromes (t-MDS) and therapy-related acute myeloid leukemia (t-AML) in the one entity of t-MNs because of their similar pathogenesis, rapid progression from t-MDS to t-AML, and their equally poor prognosis...
December 7, 2016: Current Opinion in Hematology
https://www.readbyqxmd.com/read/27929461/isolation-of-high-density-lipoproteins-for-non-coding-small-rna-quantification
#12
Danielle L Michell, Ryan M Allen, Stuart R Landstreet, Shilin Zhao, Cynthia L Toth, Quanhu Sheng, Kasey C Vickers
The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most interestingly, sRNAs are also found outside of cells and are stably present in all biological fluids. As such, extracellular sRNAs represent a novel class of disease biomarkers and are likely involved in cell signaling and intercellular communication networks. To assess their potential as biomarkers, sRNAs can be quantified in plasma, urine, and other fluids...
November 28, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27929456/high-throughput-detection-of-respiratory-pathogens-in-animal-specimens-by-nanoscale-pcr
#13
Laura B Goodman, Renee R Anderson, Marcia Slater, Elen Ortenberg, Randall W Renshaw, Brittany D Chilson, Melissa A Laverack, John S Beeby, Edward J Dubovi, Amy L Glaser
Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions...
November 28, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27929351/expression-of-the-cardiac-maintenance-and-survival-factor-fgf-16-gene-is-regulated-by-csx-nkx2-5-and-is-an-early-target-of-doxorubicin-cardiotoxicity
#14
Jie Wang, Yan Jin, Peter A Cattini
The fibroblast growth factor (FGF) 16 gene (Fgf-16) is preferentially expressed by neonatal cardiomyocytes after birth, with levels increasing into adulthood. Null mice and isolated heart studies suggest a role for FGF-16 in cardiac maintenance and survival, including increased resistance to doxorubicin (DOX)-induced injury. However, the effect of DOX on endogenous FGF-16 synthesis and specifically regulation of cardiac Fgf-16 expression has not been reported. To assess the effect of DOX on FGF-16 RNA levels and stability, as well as promoter activity and use sequence analysis, knockdown, and overexpression to investigate the role of cardiac transcription factor(s) implicated in the response...
December 8, 2016: DNA and Cell Biology
https://www.readbyqxmd.com/read/27927919/clinical-evaluation-and-cost-analysis-of-the-great-basin-shiga-toxin-direct-molecular-assay-for-the-detection-of-shiga-toxin-producing-escherichia-coli-stec-in-diarrheal-stool-specimens
#15
Matthew L Faron, Nathan A Ledeboer, Jessica Connolly, Paul A Granato, Brenda R Alkins, Jennifer Dien Bard, Judy A Daly, Stephen Young, Blake W Buchan
The Shiga Toxin Direct molecular assay (ST Direct) relies on nucleic acid amplification and solid array-based amplicon detection to identify Shiga toxin-encoding E. coli (STEC) in preserved stool specimens. Genes encoding Shiga toxin (stx1, stx2), as well as the E. coli serotype O:157-specific marker rfbE, are simultaneously detected within 2 hours. ST Direct was evaluated using 1,084 prospectively collected preserved stool specimens across five clinical centers. An additional 55 retrospectively collected, frozen specimens were included to increase the number of positive specimens evaluated...
December 7, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27927177/initiator-trna-genes-template-the-3-cca-end-at-high-frequencies-in-bacteria
#16
David H Ardell, Ya-Ming Hou
BACKGROUND: While the CCA sequence at the mature 3' end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically. RESULTS: In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0...
December 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27926873/foxa1-directs-h3k4-monomethylation-at-enhancers-via-recruitment-of-the-methyltransferase-mll3
#17
Kamila M Jozwik, Igor Chernukhin, Aurelien A Serandour, Sankari Nagarajan, Jason S Carroll
FOXA1 is a pioneer factor that binds to enhancer regions that are enriched in H3K4 mono- and dimethylation (H3K4me1 and H3K4me2). We performed a FOXA1 rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) screen in ERα-positive MCF-7 breast cancer cells and found histone-lysine N-methyltransferase (MLL3) as the top FOXA1-interacting protein. MLL3 is typically thought to induce H3K4me3 at promoter regions, but recent findings suggest it may contribute to H3K4me1 deposition. We performed MLL3 chromatin immunoprecipitation sequencing (ChIP-seq) in breast cancer cells, and MLL3 was shown to occupy regions marked by FOXA1 occupancy and H3K4me1 and H3K4me2...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27925593/a-review-of-machine-learning-and-statistical-approaches-for-detecting-snp-interactions-in-high-dimensional-genomic-data
#18
Suneetha Uppu, Aneesh Krishna, Raj Gopalan
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature...
December 2, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27925288/genomic-sequence-and-virulence-evaluation-of-mn184a-like-porcine-reproductive-and-respiratory-syndrome-virus-in-japan
#19
Hiroshi Iseki, Takeya Morozumi, Michihiro Takagi, Kenji Kawashima, Tomoyuki Shibahara, Hirohide Uenishi, Hiroshi Tsunemitsu
This study characterized a porcine reproductive and respiratory syndrome virus (PRRSV) that was isolated in Japan from a 9-week-old diseased pig on a farm with an increased mortality rate during 2007-2008. This unique isolate, designated as Jpn5-37, did not have a high nucleotide identity in open reading frame 5 against any Japanese isolates. Among all available type 2 PRRSV complete genome sequences, Jpn5-37 shared the highest nucleotide identity (93.6%) with virulent strain MN184A. The genomic characteristics of Jpn5-37 were highly conserved with respect to the virulent MN184A, including a continuous 8-amino acid deletion in the nonstructural protein 2 region...
December 7, 2016: Microbiology and Immunology
https://www.readbyqxmd.com/read/27925264/three-intronic-lncrnas-with-monoallelic-expression-derived-from-the-meg8-gene-in-cattle
#20
W Yang, D Li, G Wang, C Zhang, M Zhang, W Zhang, S Li
The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Antisense lncRNAs, intergenetic lncRNAs and enhancer lncRNAs can regulate genomic imprinting, which leads to parent-origin-specific monoalletic expression of genes. However, the function of intronic ncRNAs in genomic imprinting remains unclear. Previously, we obtained the cDNA sequence of cattle MEG8 gene, which is located in the DLK1-DIO3 imprinted clusters of cattle chromosome 21. In this study, we undertook a systematic search for transcripts mapping to the MEG8 intronic region and identified three novel lncRNAs, named MEG8 intronic RNA 1 (MEG8-IT1), MEG8 intronic RNA 2 (MEG8-IT2) and MEG8 intronic RNA 3 (MEG8-IT3) according to the GENCODE annotated bibliography...
December 7, 2016: Animal Genetics
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