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https://www.readbyqxmd.com/read/29050437/development-and-validation-of-a-novel-snp-panel-for-the-genetic-characterization-of-italian-chicken-breeds-by-next-generation-sequencing-discovery-and-array-genotyping
#1
E Viale, E Zanetti, D Özdemir, C Broccanello, A Dalmasso, M De Marchi, M Cassandro
The aim of this study was to compare the intra and inter genetic variability and population structure of 7 indigenous chicken breeds of the Veneto region, through a novel panel of 64 SNP, each located in an exonic region and mostly on different chromosomes. A total of 753 blood samples from 7 local chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo, Polverara, Pepòi, Robusta Lionata, Robusta Maculata, and Padovana) was collected and analyzed. Two strains of Polverara (Nera and Bianca) and Padovana (Dorata and Camosciata) were included in the study...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29050359/next-generation-sequencing-in-chronic-lymphocytic-leukemia-recent-findings-and-new-horizons
#2
REVIEW
Ana E Rodríguez-Vicente, Vasilis Bikos, María Hernández-Sánchez, Jitka Malcikova, Jesús-María Hernández-Rivas, Sarka Pospisilova
The rapid progress in next-generation sequencing technologies has significantly contributed to our knowledge of the genetic events associated with the development, progression and treatment resistance of chronic lymphocytic leukemia patients. Together with the discovery of new driver mutations, next-generation sequencing has revealed an immense degree of both intra- and inter-tumor heterogeneity and enabled us to describe marked clonal evolution. Advances in immunogenetics may be implemented to detect minimal residual disease more sensitively and to track clonal B cell populations, their dynamics and molecular characteristics...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049091/tumor-microenvironment-and-models-of-ovarian-cancer-the-11th-biennial-rivkin-center-ovarian-cancer-research-symposium
#3
Karen McLean, Geeta Mehta
OBJECTIVE: The aim of this study was to review the latest research advances on the topics of the ovarian cancer tumor microenvironment and models of ovarian cancer. METHODS: In September 2016, a symposium of the leaders in the field of ovarian cancer research was convened to present and discuss current advances and future directions in ovarian cancer research. RESULTS: One session was dedicated to Tumor Microenvironment and Models of Ovarian Cancer, and included a keynote presentation from Anil Sood, MD, and an invited oral presentation from David Huntsman, MD...
October 18, 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/29048876/microchemical-plant-in-a-liquid-droplet-plasmonic-liquid-marble-for-sequential-reactions-and-attomole-detection-of-toxin-at-microliter-scale
#4
Xuemei Han, Charlynn Sher Lin Koh, Hiang Kwee Lee, Wee Shern Chew, Xing Yi Ling
Miniaturizing the continuous multi-step operations of a factory into a microchemical plant offers a safe and cost-effective approach to promote high-throughput screening in drug development and enforcement of industrial/environment safety. While particle-assembled microdroplets in the form of liquid marble are ideal as microchemical plant, these platforms are mainly restricted to single-step reactions and limited to ex-situ reaction monitoring. Herein, we utilize plasmonic liquid marble (PLM), formed by encapsulating liquid droplet with Ag nanocubes, to address these issues and demonstrate it as an ideal microchemical plant to conduct reaction-and-detection sequences on-demand in a non-disruptive manner...
October 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29048727/mutations-of-kif5c-cause-a-neurodevelopmental-disorder-of-infantile-onset-epilepsy-absent-language-and-distinctive-malformations-of-cortical-development
#5
Savannah Michels, Kimberly Foss, Kaylee Park, Katie Golden-Grant, Russell Saneto, Jonathan Lopez, Ghayda M Mirzaa
The clinical diagnosis of malformations of cortical development (MCDs) is often challenging due to the complexity of the brain malformation by neuroimaging, the rarity of individual malformation syndromes, and the rapidly evolving genetic landscape of these disorders facilitated with the use of Next Generation Sequencing (NGS) methods. While the clinical and molecular diagnosis of severe cortical malformations, such as classic lissencephaly, is often straightforward, the diagnosis of more subtle and complex types of cortical malformations, such as pachygyria and polymicrogyria (PMG), can be more challenging due to limited knowledge regarding their genetic etiologies...
October 19, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29048620/dna-methylation-and-histone-modifications-as-epigenetic-regulation-in-prostate-cancer-review
#6
Maria Nowacka-Zawisza, Ewelina Wiśnik
Prostate cancer is the second most commonly diagnosed cancer in men in Poland after lung cancer and the third leading cause of cancer-related mortality after lung and colon cancer. The etiology of most cases of prostate cancer are not fully known, and therefore it is essential to search for the molecular basis of prostate cancer and markers for the early diagnosis of this type of cancer. Epigenetics deals with changes in gene expression that are not determined by changes in the DNA sequence. Epigenetic changes refer to changes in the structure of DNA, which are the result of DNA modification after replication and/or post-translational modification of proteins associated with DNA...
September 20, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29048594/neptune-a-bioinformatics-tool-for-rapid-discovery-of-genomic-variation-in-bacterial-populations
#7
Eric Marinier, Rahat Zaheer, Chrystal Berry, Kelly A Weedmark, Michael Domaratzki, Philip Mabon, Natalie C Knox, Aleisha R Reimer, Morag R Graham, Linda Chui, Laura Patterson-Fortin, Jian Zhang, Franco Pagotto, Jeff Farber, Jim Mahony, Karine Seyer, Sadjia Bekal, Cécile Tremblay, Judy Isaac-Renton, Natalie Prystajecky, Jessica Chen, Peter Slade, Gary Van Domselaar
The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29048539/indexcov-fast-coverage-quality-control-for-whole-genome-sequencing
#8
Brent S Pedersen, Ryan L Collins, Michael E Talkowski, Aaron R Quinlan
The BAM1 and CRAM2 formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample...
September 18, 2017: GigaScience
https://www.readbyqxmd.com/read/29048531/origin-and-spread-of-spliceosomal-introns-insights-from-the-fungal-clade-zymoseptoria
#9
Baojun Wu, Allison I Macielog, Weilong Hao
Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29048530/population-genomic-analysis-of-a-pitviper-reveals-microevolutionary-forces-underlying-venom-chemistry
#10
Steven D Aird, Jigyasa Arora, Agneesh Barua, Lijun Qiu, Kouki Terada, Alexander S Mikheyev
Venoms are among the most biologically active secretions known, and are commonly believed to evolve under extreme positive selection. Many venom gene families, however, have undergone duplication, and are often deployed in doses vastly exceeding the LD50 for most prey species, which should reduce the strength of positive selection. Here, we contrast these selective regimes using snake venoms, which consist of rapidly evolving protein formulations. Though decades of extensive studies have found that snake venom proteins are subject to strong positive selection, the greater action of drift has been hypothesized, but never tested...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29048527/the-evolution-of-dark-matter-in-the-mitogenome-of-seed-beetles
#11
Ahmed Sayadi, Elina Immonen, Christian Tellgren-Roth, Göran Arnqvist
Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114-10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29048112/how-we-diagnose-and-treat-systemic-mastocytosis-in-adults
#12
REVIEW
Robyn M Scherber, Uma Borate
Rapid advances in the understanding of the molecular biology, data from translational and clinical trials, and retrospective analyses has influenced the diagnosis and treatment of systemic mastocytosis (SM). Many options have existed for the symptomatic management of SM patients, but recent evolution in regards to the molecular underpinnings of this disease and our ability to distinguish clonal mastocytosis from mast cell activation syndrome has changed our treatment paradigm and opened new opportunities for understanding genetic risk, transformation to mast cell leukaemia, and treatment choices...
October 19, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/29047387/isothermal-diagnostic-assays-for-the-detection-of-soil-transmitted-helminths-based-on-the-smartamp2-method
#13
Nour Rashwan, Aïssatou Diawara, Marilyn E Scott, Roger K Prichard
BACKGROUND: Diagnosis of soil-transmitted helminths (STHs) has traditionally relied on stool microscopy, which has a number of critical deficiencies. Molecular diagnostics are powerful tools to identify closely related species, but the requirement for costly equipment makes their implementation difficult in low-resource or field settings. Rapid, sensitive and cost-effective diagnostic tools are crucial for accurate estimation of STH infection intensity in MDA programmes in which the goal is to reduce morbidity following repeated rounds of chemotherapy...
October 18, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29047334/a-support-vector-machine-based-method-to-distinguish-long-non-coding-rnas-from-protein-coding-transcripts
#14
Hugo W Schneider, Taina Raiol, Marcelo M Brigido, Maria Emilia M T Walter, Peter F Stadler
BACKGROUND: In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) based method to distinguish lncRNAs from PCTs, using features based on frequencies of nucleotide patterns and ORF lengths, in transcripts...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29046975/the-genetics-of-physical-activity
#15
REVIEW
Xiaochen Lin, Charles B Eaton, JoAnn E Manson, Simin Liu
PURPOSE OF REVIEW: Physical activity (PA) is a well-established modifiable lifestyle determinant for multiple cardio-metabolic outcomes. While many psychosocial and environmental correlates of PA have been identified, current understanding of the genetic architecture that contributes to PA is still very limited, especially when compared to other phenotypes such as obesity and diabetes. RECENT FINDINGS: This review systematically and comprehensively assesses available evidence from animal experiments, family studies, population-based candidate gene analyses, and genome-wide association studies (GWAS) studying the genetics of physical activity patterns...
October 18, 2017: Current Cardiology Reports
https://www.readbyqxmd.com/read/29046769/factors-that-affect-the-onset-of-action-of-non-depolarizing-neuromuscular-blocking-agents
#16
REVIEW
Yong Byum Kim, Tae-Yun Sung, Hong Seuk Yang
Neuromuscular blockade plays an important role in the safe management of patient airways, surgical field improvement, and respiratory care. Rapid-sequence induction of anesthesia is indispensable to emergency surgery and obstetric anesthesia, and its purpose is to obtain a stable airway, adequate depth of anesthesia, and appropriate respiration within a short period of time without causing irritation or damage to the patient. There has been a continued search for new neuromuscular blocking drugs (NMBDs) with a rapid onset of action...
October 2017: Korean Journal of Anesthesiology
https://www.readbyqxmd.com/read/29046666/molecular-serotype-specific-identification-of-non-type-b-haemophilus-influenzae-by-loop-mediated-isothermal-amplification
#17
Chika Takano, Mitsuko Seki, Dong Wook Kim, Paul E Kilgore, Kazumasa Fuwa, Koji Takahashi, Toshiaki Inazaki, Satoshi Hayakawa
Over the past four decades, the incidence of meningitis caused by Haemophilus influenzae in children has decreased due to widespread vaccination against H. influenzae type b (Hib). The incidence of invasive diseases due to H. influenzae types not included in the vaccines, however, has increased. At present, there are a limited number of diagnostics available to detect non-type b H. influenzae. To address this issue, we developed a rapid, simple, and cost-effective method for detecting serotypes of H. influenzae...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29046518/pretreatment-with-oxycodone-simultaneously-reduces-etomidate-induced-myoclonus-and-rocuronium-induced-withdrawal-movements-during-rapid-sequence-induction
#18
Xiaoxia An, Caixia Li, Zayd Sahebally, Xiaohong Wen, Bing Zhao, Xiangming Fang
BACKGROUND Etomidate and rocuronium are often paired in rapid-sequence anesthesia induction. However, the effect of pretreatment with oxycodone on myoclonic and withdrawal movements has not been previously investigated. The aim of this study was to evaluate the effects of oxycodone on the incidence and severity of etomidate-induced myoclonus and rocuronium-induced nociceptive withdrawal movements during rapid-sequence anesthesia induction. MATERIAL AND METHODS We randomly divided 120 patients into the saline group (group S) and the oxycodone group (group O) (n=60 in each group)...
October 19, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29045724/effects-of-demographic-history-on-the-detection-of-recombination-hotspots-from-linkage-disequilibrium
#19
Amy L Dapper, Bret A Payseur
In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach...
October 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29045665/dna-barcode-reference-library-for-the-african-citrus-triozid-trioza-erytreae-hemiptera-triozidae-vector-of-african-citrus-greening
#20
F M Khamis, I Rwomushana, L O Ombura, G Cook, S A Mohamed, C M Tanga, P W Nderitu, C Borgemeister, M Sétamou, T G Grout, S Ekesi, Stephen Garczynski
Citrus (Citrus spp.) production continues to decline in East Africa, particularly in Kenya and Tanzania, the two major producers in the region. This decline is attributed to pests and diseases including infestation by the African citrus triozid, Trioza erytreae (Del Guercio) (Hemiptera: Triozidae). Besides direct feeding damage by adults and immature stages, T. erytreae is the main vector of 'Candidatus Liberibacter africanus', the causative agent of Greening disease in Africa, closely related to Huanglongbing...
October 16, 2017: Journal of Economic Entomology
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