keyword
MENU ▼
Read by QxMD icon Read
search

Human genome

keyword
https://www.readbyqxmd.com/read/28324984/prediction-method-for-intronic-alternative-polyadenylation-sites
#1
Shanxin Zhang
Alternative Polyadenylation (APA) of mRNAs has been proven as a considerable mechanism for post-transcriptional gene regulation. The interplay between Intronic APA and splicing may affect the isoforms of mRNAs. In this paper, we have found four prevalent motifs, i.e. AATAAA, TTTTTTTT, CCAGSCTGG and RGYRYRGTGG surrounding the polyadenylation sites; then we proposed a new computational method to identify the Intronic APA sites in the human genome, which is based on a Support Vector Machine (SVM) with weighted degree string kernel...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28324503/visualization-of-human-telomerase-localization-by-fluorescence-microscopy-techniques
#2
Eladio Abreu, Rebecca M Terns, Michael P Terns
Human telomerase is a ribonucleoprotein (RNP) that synthesizes DNA repeats at the ends of chromosomes and maintains telomere length and genome stability. The enzyme is comprised of telomerase RNA (hTR) (which provides the template for telomere addition) and several protein subunits including telomerase reverse transcriptase (hTERT) (the catalytic component). Intracellular trafficking of the enzyme has emerged as an important factor in the regulation of telomerase activity. Telomerase trafficking between nuclear Cajal bodies (proposed sites of telomerase biogenesis and regulation) and telomeres (sites of action) is regulated by the cell cycle in concordance with telomere synthesis during S phase...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324498/telomere-g-overhang-length-measurement-method-2-g-tail-telomere-hpa
#3
Hidetoshi Tahara
Both telomere length and telomere G-tail length are altered in human diseases such as cancer and age-related diseases. While most methods for measurement of G-tail and telomere length require electrophoresis, centrifugation, radioisotope labeling and autoradiography, G-tail telomere HPA provides a convenient and useful tool for the examination of G-tail length with a high-throughput platform using genomic DNA or cell lysate. G-tail telomere HPA may be applicable for clinical diagnostics as well as drug target screening...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324494/analysis-of-average-telomere-length-in-human-telomeric-protein-knockout-cells-generated-by-crispr-cas9
#4
Jun Xu, Zhou Songyang, Dan Liu, Hyeung Kim
Telomeres play an important role in ensuring the integrity of the genome. Telomere shortening can lead to loss of genetic information and trigger DNA damage responses. Cultured mammalian cells have served as critical model systems for studying the function of telomere binding proteins and telomerase. Tremendous heterogeneity can be observed both between species and within a single cell population. Recent advances in genome editing (such as the development of the CRISPR/Cas9 platform) have further enabled researchers to carry out loss-of-function analysis of how disrupting key players in telomere maintenance affects telomere length regulation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324015/paternally-inherited-dlk1-deletion-associated-with-familial-central-precocious-puberty
#5
Andrew Dauber, Marina Cunha-Silva, Delanie B Macedo, Vinicius N Brito, Ana Paula Abreu, Stephanie A Roberts, Luciana R Montenegro, Melissa Andrew, Andrew Kirby, Matthew T Weirauch, Guillaume Labilloy, Danielle S Bessa, Rona S Carroll, Dakota C Jacobs, Patrick E Chappell, Berenice B Mendonca, David Haig, Ursula B Kaiser, Ana Claudia Latronico
Context: Central precocious puberty (CPP) results from premature activation of the hypothalamic-pituitary-gonadal axis. Few genetic causes of CPP have been identified with the most common being mutations in the paternally expressed imprinted gene MKRN3. Objective: To identify the genetic etiology of CPP in a large multigenerational family. Design: Linkage analysis followed by whole genome sequencing was performed in a family with 5 female members with nonsyndromic CPP...
January 27, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28324014/variation-in-the-insulin-like-growth-factor-1-gene-in-primates
#6
Peter Rotwein
Insulin-like growth factor 1 (IGF1) is a multifunctional peptide that is involved in a wide range of physiological and patho-physiological processes in many animal species, ranging from somatic growth in children to metabolism, and tissue regeneration and repair in adults. The IGF1 gene is under multifactorial regulation in the few species in which it has been studied, with major control being exerted by growth hormone (GH) through a gene expression pathway involving inducible binding of the STAT5b transcription factor to dispersed enhancer elements...
January 18, 2017: Endocrinology
https://www.readbyqxmd.com/read/28323406/affinity-selection-mass-spectrometry-identifies-a-novel-antibacterial-rna-polymerase-inhibitor
#7
Scott S Walker, David Degen, Elliott Nickbarg, Donna Carr, Aileen Soriano, Mihir Baran Mandal, Ronald E Painter, Payal R Sheth, Li Xiao, Xinwei Sher, Nicholas Murgolo, Jing Su, David B Olsen, Richard H Ebright, Katherine Young
The growing prevalence of drug-resistant Gram-negative bacteria is a significant global threat to human health. Rifampicin, an RNA polymerase-targeting agent, is an important part of the antibacterial armamentarium; however the emergence of resistance requires that it be used against only certain infections and usually in combination with another antibiotic. While rifampicin has significant clinical limitations, it does show that bacterial RNA polymerase can be an effective target for antibacterial intervention...
March 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28319896/a-dynamic-sandwich-assay-on-magnetic-beads-for-selective-detection-of-single-nucleotide-mutations-at-room-temperature
#8
Junxiu Wang, Guoliang Xiong, Liang Ma, Shihui Wang, Xu Zhou, Lei Wang, Lehui Xiao, Xin Su, Changyuan Yu
Single-nucleotide mutation (SNM) has proven to be associated with a variety of human diseases. Development of reliable methods for the detection of SNM is crucial for molecular diagnosis and personalized medicine. The sandwich assays are widely used tools for detecting nucleic acid biomarkers due to their low cost and rapid signaling. However, the poor hybridization specificity of signal probe at room temperature hampers the discrimination of mutant and wild type. Here, we demonstrate a dynamic sandwich assay on magnetic beads for SNM detection based on the transient binding between signal probe and target...
March 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28319150/high-throughput-transformation-of-saccharomyces-cerevisiae-using-liquid-handling-robots
#9
Guangbo Liu, Clayton Lanham, J Ross Buchan, Matthew E Kaplan
Saccharomyces cerevisiae (budding yeast) is a powerful eukaryotic model organism ideally suited to high-throughput genetic analyses, which time and again has yielded insights that further our understanding of cell biology processes conserved in humans. Lithium Acetate (LiAc) transformation of yeast with DNA for the purposes of exogenous protein expression (e.g., plasmids) or genome mutation (e.g., gene mutation, deletion, epitope tagging) is a useful and long established method. However, a reliable and optimized high throughput transformation protocol that runs almost no risk of human error has not been described in the literature...
2017: PloS One
https://www.readbyqxmd.com/read/28319063/compromised-brca1-palb2-interaction-is-associated-with-breast-cancer-risk
#10
T K Foo, M Tischkowitz, S Simhadri, T Boshari, N Zayed, K A Burke, S H Berman, P Blecua, N Riaz, Y Huo, Y C Ding, S L Neuhausen, B Weigelt, J S Reis-Filho, W D Foulkes, B Xia
The major breast cancer suppressor proteins BRCA1 and BRCA2 play essential roles in homologous recombination (HR)-mediated DNA repair, which is thought to be critical for tumor suppression. The two BRCA proteins are linked by a third tumor suppressor, PALB2, in the HR pathway. While truncating mutations in these genes are generally pathogenic, interpretation of missense variants remains a challenge. To date, patient-derived missense variants that disrupt PALB2 binding have been identified in BRCA1 and BRCA2; however, there has not been sufficient evidence to prove their pathogenicity in humans, and no variants in PALB2 that disrupt either its BRCA1 or BRCA2 binding have been reported...
March 20, 2017: Oncogene
https://www.readbyqxmd.com/read/28319047/isocitrate-dehydrogenase-mutations-suppress-stat1-and-cd8-t-cell-accumulation-in-gliomas
#11
Gary Kohanbash, Diego A Carrera, Shruti Shrivastav, Brian J Ahn, Naznin Jahan, Tali Mazor, Zinal S Chheda, Kira M Downey, Payal B Watchmaker, Casey Beppler, Rolf Warta, Nduka A Amankulor, Christel Herold-Mende, Joseph F Costello, Hideho Okada
Mutations in the isocitrate dehydrogenase genes IDH1 and IDH2 are among the first genetic alterations observed during the development of lower-grade glioma (LGG). LGG-associated IDH mutations confer gain-of-function activity by converting α-ketoglutarate to the oncometabolite R-2-hydroxyglutarate (2HG). Clinical samples and gene expression data from The Cancer Genome Atlas (TCGA) demonstrate reduced expression of cytotoxic T lymphocyte-associated genes and IFN-γ-inducible chemokines, including CXCL10, in IDH-mutated (IDH-MUT) tumors compared with IDH-WT tumors...
March 20, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28319011/resequencing-helminth-genomes-for-population-and-genetic-studies
#12
REVIEW
Janneke Wit, John S Gilleard
Next-generation sequencing has become increasingly accessible and economical, making genome-wide studies routine for many species, including humans, model organisms, and domestic livestock. However, in the case of helminth parasites, there are still major practical challenges to the application of these approaches for genetic and population studies. Dozens to hundreds of individual parasites from multiple populations may need to be re-sequenced which, together with the relatively large size of helminth genomes, can still make whole-genome resequencing of individual parasites unfeasible for many studies...
March 16, 2017: Trends in Parasitology
https://www.readbyqxmd.com/read/28318978/the-mitochondrial-dna-polymerase-promotes-elimination-of-paternal-mitochondrial-genomes
#13
Zhongsheng Yu, Patrick H O'Farrell, Nikita Yakubovich, Steven Z DeLuca
Mitochondrial DNA (mtDNA) is typically inherited from only one parent [1-3]. In animals, this is usually the mother. Maternal inheritance is often presented as the passive outcome of the difference in cytoplasmic content of egg and sperm; however, active programs enforce uniparental inheritance at two levels, eliminating paternal mitochondrial genomes or destroying mitochondria delivered to the zygote by the sperm [4-13]. Both levels operate in Drosophila [8, 12, 13]. As sperm formation begins, hundreds of doomed mitochondrial genomes are visualized within the two huge mitochondria of each spermatid...
March 11, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28318822/genome-wide-analysis-of-rna-polymerase-ii-termination-at-protein-coding-genes
#14
Carlo Baejen, Jessica Andreani, Phillipp Torkler, Sofia Battaglia, Bjoern Schwalb, Michael Lidschreiber, Kerstin C Maier, Andrea Boltendahl, Petra Rus, Stephanie Esslinger, Johannes Söding, Patrick Cramer
At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3'-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide analysis of the 3'-transition in budding yeast. We find that the 3'-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the "torpedo" exonuclease Rat1 (XRN2 in human)...
March 6, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28318500/mutations-in-tmem260-cause-a-pediatric-neurodevelopmental-cardiac-and-renal-syndrome
#15
Asaf Ta-Shma, Tahir N Khan, Asaf Vivante, Jason R Willer, Pavle Matak, Chaim Jalas, Ben Pode-Shakked, Yishay Salem, Yair Anikster, Friedhelm Hildebrandt, Nicholas Katsanis, Orly Elpeleg, Erica E Davis
Despite the accelerated discovery of genes associated with syndromic traits, the majority of families affected by such conditions remain undiagnosed. Here, we employed whole-exome sequencing in two unrelated consanguineous kindreds with central nervous system (CNS), cardiac, renal, and digit abnormalities. We identified homozygous truncating mutations in TMEM260, a locus predicted to encode numerous splice isoforms. Systematic expression analyses across tissues and developmental stages validated two such isoforms, which differ in the utilization of an internal exon...
March 11, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28317894/swim-a-computational-tool-to-unveiling-crucial-nodes-in-complex-biological-networks
#16
Paola Paci, Teresa Colombo, Giulia Fiscon, Aymone Gurtner, Giulio Pavesi, Lorenzo Farina
SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called "fight-club hubs", characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called "switch genes", appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317605/use-of-foodomics-for-control-of-food-processing-and-assessing-of-food-safety
#17
D Josić, Ž Peršurić, D Rešetar, T Martinović, L Saftić, S Kraljević Pavelić
Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required...
2017: Advances in Food and Nutrition Research
https://www.readbyqxmd.com/read/28317453/ebola-virus-epidemiology-diagnosis-and-control-threat-to-humans-lessons-learnt-and-preparedness-plans-an-update-on-its-40-year-s-journey
#18
Raj Kumar Singh, Kuldeep Dhama, Yashpal Singh Malik, Muthannan Andavar Ramakrishnan, Kumaragurubaran Karthik, Rekha Khandia, Ruchi Tiwari, Ashok Munjal, Mani Saminathan, Swati Sachan, Perumal Arumugam Desingu, Jobin Jose Kattoor, Hafiz M N Iqbal, Sunil Kumar Joshi
Ebola virus (EBOV) is an extremely contagious pathogen and causes lethal hemorrhagic fever disease in man and animals with high fatality rates. The recently occurred Ebola virus disease (EVD) outbreaks in the West African countries have categorized it as an international health concern. For the virus maintenance and transmission, the non-human primates and reservoir hosts like fruit bats have played a vital role. Furthermore, the virus may also get transferred through contaminated biological fluids like breast milk, tears, urine, semen, blood, etc...
March 20, 2017: Veterinary Quarterly
https://www.readbyqxmd.com/read/28316881/occurrence-of-concurrent-infections-with-multiple-serotypes-of-dengue-viruses-during-2013-2015-in-northern-kerala-india
#19
Manchala Nageswar Reddy, Ranjeet Dungdung, Lathika Valliyott, Rajendra Pilankatta
BACKGROUND: Dengue is a global human public health threat, causing severe morbidity and mortality. The occurrence of sequential infection by more than one serotype of dengue virus (DENV) is a major contributing factor for the induction of Dengue Hemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS), two major medical conditions caused by DENV infection. However, there is no specific drug or vaccine available against dengue infection. There are reports indicating the increased incidence of concurrent infection of dengue in several tropical and subtropical regions...
2017: PeerJ
https://www.readbyqxmd.com/read/28316365/extracting-databases-from-dark-data-with-deepdive
#20
Ce Zhang, Jaeho Shin, Christopher Ré, Michael Cafarella, Feng Niu
DeepDive is a system for extracting relational databases from dark data: the mass of text, tables, and images that are widely collected and stored but which cannot be exploited by standard relational tools. If the information in dark data - scientific papers, Web classified ads, customer service notes, and so on - were instead in a relational database, it would give analysts a massive and valuable new set of "big data." DeepDive is distinctive when compared to previous information extraction systems in its ability to obtain very high precision and recall at reasonable engineering cost; in a number of applications, we have used DeepDive to create databases with accuracy that meets that of human annotators...
June 2016: Proceedings
keyword
keyword
76425
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"