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Human genome

Eric Seiti Yamanaka, Luis A Tortajada-Genaro, Nuria Pastor, Ángel Maquieira
The genotyping of a single-nucleotide polymorphism (SNP) is addressed through methods based on loop-mediated isothermal amplification (LAMP) combined with user-friendly optical read-outs to cover the current demand for point-of-care DNA biomarker detection. The modification of primer design and reaction composition improved the assay selectivity yielding allele-specific results and reducing false-positive frequency. Furthermore, the reduced cost, ease of use and effectiveness of colorimetric detection (solution and hybridisation chip formats) were availed for the image capture by a smartphone, reching high sensitivity...
March 8, 2018: Biosensors & Bioelectronics
Amber Hilliard, Dara Leong, Amy O'Callaghan, Eamonn P Culligan, Ciara A Morgan, Niall DeLappe, Colin Hill, Kieran Jordan, Martin Cormican, Cormac G M Gahan
Listeria monocytogenes is a major human foodborne pathogen that is prevalent in the natural environment and has a high case fatality rate. Whole genome sequencing (WGS) analysis has emerged as a valuable methodology for the classification of L. monocytogenes isolates and the identification of virulence islands that may influence infectivity. In this study, WGS was used to provide an insight into 25 L. monocytogenes isolates from cases of clinical infection in Ireland between 2013 and 2015. Clinical strains were either lineage I (14 isolates) or lineage II (11 isolates), with 12 clonal complexes (CC) represented, of which CC1 (6) and CC101 (4) were the most common...
March 20, 2018: Genes
Theo N Kirkland
This special issue, "Genomic Data in Pathogenic Fungi," focuses on the genomics of human and plant pathogens. Efforts like this are important because so little information about these organisms is available.[...].
March 20, 2018: Journal of Fungi (Basel, Switzerland)
Xiaoyan Liu, Wen Yuan, Lei Yang, Jing Li, Jun Cai
The role and miRNA expression profile of exosomes in hypertension remain largely unknown. Therefore, next-generation sequencing was used to define the miRNA expression profile of plasma exosomes in spontaneously hypertensive rats (SHRs), the most widely used animal model of human essential hypertension, and their controls, normotensive Wistar-Kyoto rats (WKYs). Results revealed that percentages of miRNA in the total small RNA isolated from SHRs and WKYs were not significantly different. Twenty-seven miRNAs were significantly differentially expressed (DE) between SHR and WKY exosomes, including 23 up-regulated and four down-regulated in SHR exosomes as compared to WKY exosomes...
March 20, 2018: Journal of Cardiovascular Translational Research
Qian Zhou, Hui Zeng, Peng Ye, Yu Shi, Juan Guo, Xinghua Long
Increasing evidence has shown that the dysregulation of microRNAs (miRNAs) is associated with drug resistance. Fulvestrant and tamoxifen represent the major endocrine drugs for the treatment of breast cancer patients, and yet little is known about the biological mechanisms of acquiring resistance to fulvestrant and tamoxifen, let alone the differences between cell lines resistant to these two drugs. Exploration of the differential miRNA profiles between these two cell lines is a useful way to further clarify these resistance mechanisms...
March 19, 2018: Anti-cancer Drugs
Karin Kosulin, Elena Lam, Albert Heim, Thomas Dobner, Estefanía Rodríguez
BACKGROUND: Human adenoviral (HAdV) infections are usually mild and self-limited, however, some infections from species A, B, C, D and E, can cause severe illnesses, which have raised public health concerns over the past few years. Current available antiviral therapies have limited efficacy and severe toxicity; therefore, finding new targets for specific anti-adenoviral drug design is urgently needed. Our previous work showed that the small molecule compound, HBX, inhibits HAdV type 5 (species C, HAdV-C5) replication and oncogenic transformation through inhibition of the cellular pro-viral factor ubiquitin-specific protease 7 (USP7)...
March 20, 2018: Antiviral Therapy
Marijke Linschoten, Arco J Teske, Maarten J Cramer, Elsken van der Wall, Folkert W Asselbergs
Chemotherapy-related cardiac dysfunction is a significant side effect of anticancer treatment. Risk stratification is based on clinical- and treatment-related risk factors that do not adequately explain individual susceptibility. The addition of genetic variants may improve risk assessment. We conducted a systematic literature search in PubMed and Embase, to identify studies investigating genetic risk factors for chemotherapy-related cardiac dysfunction. Included were articles describing genetic variants in humans altering susceptibility to chemotherapy-related cardiac dysfunction...
January 2018: Circ Genom Precis Med
Xiaoping Su, Kuiqing Cui, Shanshan Du, Hongli Li, Fenghua Lu, Deshun Shi, Qingyou Liu
Myostatin (MSTN), a protein encoded by growth differentiation factor 8 (GDF8), is primarily expressed in skeletal muscle and negatively regulates the development and regeneration of muscle. Accordingly, myostatin-deficient animals exhibit a double-muscling phenotype. The CRISPR/Cas9 system has proven to be an efficient genome-editing tool and has been applied to gene modification in cells from many model organisms such as Drosophila melanogaster, zebrafish, mouse, rat, sheep, and human. Here, we edited the GDF8 gene in fibroblasts and embryos of Debao pig and swamp buffalo using the CRISPR/Cas9 system...
March 19, 2018: In Vitro Cellular & Developmental Biology. Animal
Vikas C Ghattargi, Yogesh S Nimonkar, Shaunak A Burse, Dimple Davray, Shreyas V Kumbhare, Sudarshan A Shetty, Meghana A Gaikwad, Mangesh V Suryavanshi, Swapnil P Doijad, Bhimashankar Utage, Om Prakash Sharma, Yogesh S Shouche, Bharati S Meti, Shrikant P Pawar
The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity...
March 19, 2018: Functional & Integrative Genomics
Xueliang Cao, Xinbo Liu, Shiying Zheng, Lihua Xu, Haibo Wu, Jie Liu
Previous studies have shown that dogs are susceptible to influenza A viruses, and the close contact between dogs and humans poses a threat to public health. In 2015, a novel H3N8 influenza virus was isolated from a dog in eastern China. This strain was characterized by whole-genome sequencing with subsequent phylogenetic analysis and genetic comparison and found to be most closely related to avian influenza viruses co-circulating in China. It was able to replicate in mice without prior adaptation. The continued circulation of this novel H3N8 influenza virus in dogs could endanger other mammalian species...
March 20, 2018: Archives of Virology
David L Duewer, Margaret C Kline, Erica L Romsos, Blaza Toman
The highly multiplexed polymerase chain reaction (PCR) assays used for forensic human identification perform best when used with an accurately determined quantity of input DNA. To help ensure the reliable performance of these assays, we are developing a certified reference material (CRM) for calibrating human genomic DNA working standards. To enable sharing information over time and place, CRMs must provide accurate and stable values that are metrologically traceable to a common reference. We have shown that droplet digital PCR (ddPCR) limiting dilution end-point measurements of the concentration of DNA copies per volume of sample can be traceably linked to the International System of Units (SI)...
March 19, 2018: Analytical and Bioanalytical Chemistry
Hessa S Alsaif, Arif O Khan, Nisha Patel, Hisham Alkuraya, Mais Hashem, Firdous Abdulwahab, Niema Ibrahim, Mohammed A Aldahmesh, Fowzan S Alkuraya
Primary congenital glaucoma is a trabecular meshwork dysgenesis with resultant increased intraocular pressure and ocular damage. CYP1B1 mutations remain the most common identifiable genetic cause. However, important questions about the penetrance of CYP1B1-related congenital glaucoma remain unanswered. Furthermore, mutations in other genes have been described although their exact contribution and potential genetic interaction, if any, with CYP1B1 mutations are not fully explored. In this study, we employed modern genomic approaches to re-examine CYP1B1-related congenital glaucoma...
March 19, 2018: Human Genetics
B Yun, T Zhang, M A K Azad, J Wang, C J Nowell, P Kalitsis, T Velkov, D F Hudson, J Li
Increasing incidence of multidrug-resistant bacteria presents an imminent risk to global health. Polymyxins are 'last-resort' antibiotics against Gram-negative 'superbugs'; however, nephrotoxicity remains a key impediment in their clinical use. Molecular mechanisms underlying this nephrotoxicity remain poorly defined. Here, we examined the pathways which led to polymyxin B induced cell death in vitro and in vivo. Human proximal tubular cells were treated with polymyxin B (12.5-100 μM) for up to 24 h and showed a significant increase in micronuclei frequency, as well as abnormal mitotic events (over 40% in treated cells, p < 0...
March 20, 2018: Archives of Toxicology
Qingxia Yao, Karl P Fischer, D Lorne Tyrrell, Klaus S Gutfreund
Programmed death-1 (PD-1), upon engagement by its ligands, programmed death ligand-1 (PD-L1) and programmed death ligand-2 (PD-L2), provides signals that attenuate adaptive immune responses. Here we describe the identification of the Pekin duck PD-L2 (duPD-L2) and its gene structure. The duPD-L2 cDNA encodes a 321 amino acid protein that has an amino acid identity of 76% and 35% with chicken and human PD-L2, respectively. Mapping of the duPD-L2 cDNA with duck genomic sequences revealed an exonic structure similar to that of the human P dcd1lg2 gene...
March 2018: Biochemistry and Biophysics Reports
Peter J Turnbaugh
Although the importance of human genetic polymorphisms in therapeutic outcomes is well established, the role of specific genotypic or copy number variants in our "second genome" (the microbiome) has been largely overlooked. In this Perspective, I will discuss three major barriers to integrating metagenomics into pharmacology, highlighting ongoing research by us and others that has begun to shed light on the mechanisms that link the human microbiome to the efficacy and toxicity of small-molecule and biological therapies...
March 2018: MSystems
Levi Waldron
The Waldron lab for computational biostatistics bridges the areas of cancer genomics and microbiome studies for public health, developing methods to exploit publicly available data resources and to integrate -omics studies.
March 2018: MSystems
Nicola Segata
Metagenomics has transformed microbiology, but its potential has not been fully expressed yet. From computational methods for digging deeper into metagenomes to study designs for addressing specific hypotheses, the Segata Lab is pursuing an integrative metagenomic approach to describe and model human-associated microbial communities as collections of strains. Linking strain variants to host phenotypes and performing cultivation-free population genomics require large cohorts and meta-analysis strategies to synthesize available cohorts but can revolutionize our understanding of the personalized host-microbiome interface which is at the base of human health...
March 2018: MSystems
Anthony J Mannion, Heather R Martin, Zeli Shen, Ellen M Buckley, JoAnn L Dzink-Fox, Alexis Garcia, Robert P Marini, Mary M Patterson, James G Fox
Non-human primates (NHPs) for biomedical research are commonly infected with Shigella spp. that can cause acute dysentery or chronic episodic diarrhea. These animals are often prophylactically and clinically treated with quinolone antibiotics to eradicate these possible infections. However, chromosomally- and plasmid-mediated antibiotic resistance has become an emerging concern for species in the family Enterobacteriaceae . In this study, five individual isolates of multi-drug resistant Shigella flexneri were isolated from the feces of three macaques...
2018: Frontiers in Microbiology
Melanie Tramontano, Sergej Andrejev, Mihaela Pruteanu, Martina Klünemann, Michael Kuhn, Marco Galardini, Paula Jouhten, Aleksej Zelezniak, Georg Zeller, Peer Bork, Athanasios Typas, Kiran Raosaheb Patil
Bacterial metabolism plays a fundamental role in gut microbiota ecology and host-microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences...
March 19, 2018: Nature Microbiology
Joaquín Letelier, Elisa de la Calle-Mustienes, Joyce Pieretti, Silvia Naranjo, Ignacio Maeso, Tetsuya Nakamura, Juan Pascual-Anaya, Neil H Shubin, Igor Schneider, Juan Ramón Martinez-Morales, José Luis Gómez-Skarmeta
Despite their evolutionary, developmental and functional importance, the origin of vertebrate paired appendages remains uncertain. In mice, a single enhancer termed ZRS is solely responsible for Shh expression in limbs. Here, zebrafish and mouse transgenic assays trace the functional equivalence of ZRS across the gnathostome phylogeny. CRISPR/Cas9-mediated deletion of the medaka (Oryzias latipes) ZRS and enhancer assays identify the existence of ZRS shadow enhancers in both teleost and human genomes. Deletion of both ZRS and shadow ZRS abolishes shh expression and completely truncates pectoral fin formation...
March 19, 2018: Nature Genetics
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