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https://www.readbyqxmd.com/read/29031244/development-of-new-recombinant-dgk-antigen-for-diagnosis-of-dirofilaria-immitis-infections-in-dogs-using-elisa-technique-and-its-comparison-to-molecular-methods
#1
Rahmat Solgi, Seyed Mahmoud Sadjjadi, Mehdi Mohebali, Zabihollah Zarei, Majid Golkar, Abbasali Raz
Background: Dirofilaria immitis is a cosmopolitan zoonotic, vector-borne parasite of carnivorous animals causing dirofilariasis in human beings. Common commercial serodiagnostic tests for canine dirofilariasis usually lead to different results in their sensitivity and specificity. The present study reports development of recombinant DgK (rDgK) antigen of D. immitis for accurate immunodiagnosis of D. Immitis-infected dogs using indirect ELISA test. Methods: The rDgK coding sequence was successfully sequenced, codon optimized and cloned in pET-24a(+) expression vector and then expressed in Escherichia coli...
October 15, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/29031201/long-non-coding-rna-or3a4-promotes-proliferation-and-migration-in-breast-cancer
#2
Genxiang Liu, Xingchi Hu, Guangjun Zhou
More and more researches have shown the vital functions of long non-coding RNAs (LncRNAs) in modulating the biological progresses in tumorigenesis. OR3A4 is such a type of lncRNA. The long non-coding RNA (lncRNA) OR3A4 has recently been exposed to be exceptionally expressed and referred to the development of several cancers. Nevertheless, the biological function and clinical significance of OR3A4 in the carcinogenesis of breast cancer (BC) are still blurry. Therefore, we carried out the following study to make sure the underlying functions of OR3A4 in breast cancer...
October 11, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29031161/understanding-the-role-of-dna-polymerase-%C3%AE-gene-in-different-growth-and-developmental-stages-of-oryza-sativa-l-indica-rice-cultivars
#3
Sayantani Sihi, Soumitra Maiti, Sankar Bakshi, Arup Nayak, Shubho Chaudhuri, Dibyendu Narayan Sengupta
DNA polymerase λ (Pol λ) is the only member of DNA polymerase family X present in plants. The enzyme is ddNTP sensitive as it contains the conserved C-terminal Pol β domain. The 1.1 kb partial coding sequence isolated spanned the whole 3' regions of the gene containing functionally important domains of the Pol λ gene. Comparative in silico studies from both indica and japonica cultivars involving homology modelling showed that the model for the partial Pol λ gene was stable and acceptable. The alignment of both the protein models showed a RMS value of 0...
October 4, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29031127/patients-perceptions-and-experiences-of-living-with-a-surgical-wound-healing-by-secondary-intention-a-qualitative-study
#4
Dorothy McCaughan, Laura Sheard, Nicky Cullum, Jo Dumville, Ian Chetter
BACKGROUND: Most surgical wounds heal by primary intention, that is to say, the edges of the wound are brought together with sutures, staples, adhesive glue or clips. However, some wounds may be left open to heal (if there is a risk of infection, or if there has been significant tissue loss), and are known as 'surgical wounds healing by secondary intention'. They are estimated to comprise approximately 28% of all surgical wounds and are frequently complex to manage. However, they are under researched and little is known of their impact on patients' lives...
September 28, 2017: International Journal of Nursing Studies
https://www.readbyqxmd.com/read/29031026/genome-wide-characterization-of-differential-transcript-usage-in-arabidopsis-thaliana
#5
Dries Vaneechoutte, April R Estrada, Ying-Chen Lin, Ann E Loraine, Klaas Vandepoele
Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of Differential Transcript Usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes and have been linked to development and stress response...
October 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29029368/who-accesses-surgery-at-district-level-in-sub-saharan-africa-evidence-from-malawi-and-zambia
#6
Jakub Gajewski, Rachel Dharamshi, Michael Strader, John Kachimba, Eric Borgstein, Gerald Mwapasa, Mweene Cheelo, Tracey McCauley, Leon Bijlmakers, Ruairi Brugha
OBJECTIVES: To examine age and gender distribution for the most common types of surgery in Malawi and Zambia. METHODS: Data were collected from major operating theatres in 8 district hospitals in Malawi and 9 in Zambia. Raw data on surgical procedures were coded by specialist surgeons for frequency analyses. RESULTS: In Malawi, female surgical patients had a mean age of 25 years, with 91% aged 16-40 years. Females accounted for 85%, and obstetric cases for 75%, of all surgical patients...
October 13, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/29029327/the-exonization-and-functionalization-of-an-alu-j-element-in-the-protein-coding-region-of-glycoprotein-hormone-alpha-gene-represent-a-novel-mechanism-to-the-evolution-of-hemochorial-placentation-in-primates
#7
Haidi Chen, Li Chen, Yune Wu, Hao Shen, Guang Yang, Cheng Deng
Alu elements contribute considerably to gene regulation and genome evolution in primates. The generation of new exons from Alu elements has been found in various human genes, and the regulatory function of the Alu exon has been investigated in many studies. However, the functionalization of Alu elements in protein coding regions remains unknown. Here, we reported that an Alu-J element exonized in the glycoprotein hormone alpha (GPHA) gene and encoded an additional N-terminal peptide (Alu-J encoding peptide) of the mature GPHA peptide, leading to a splicing variant of Alu-GPHA in anthropoid primates approximately 35 million years ago...
September 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029289/post-traumatic-hydrocephalus-in-children-a-retrospective-study-in-42-pediatric-hospitals-using-the-pediatric-health-information-system
#8
Robert H Bonow, Assaf P Oron, Brian W Hanak, Samuel R Browd, Randall M Chesnut, Richard G Ellenbogen, Monica S Vavilala, Frederick P Rivara
BACKGROUND: Post-traumatic hydrocephalus (PTH) is a potentially treatable cause of poor recovery from traumatic brain injury (TBI) that remains poorly understood, particularly among children. OBJECTIVE: To better understand the risk factors for pediatric PTH using a large, multi-institutional database. METHODS: We conducted a retrospective cohort study using administrative data from 42 pediatric hospitals participating in the Pediatric Health Information System...
October 6, 2017: Neurosurgery
https://www.readbyqxmd.com/read/29029264/a-general-model-for-estimating-macroevolutionary-landscapes
#9
Florian C Boucher, Vincent Démery, Elena Conti, Luke J Harmon, Josef Uyeda
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks...
September 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029014/1-25-dihydroxyvitamin-d-regulation-of-glutamine-synthetase-and-glutamine-metabolism-in-human-mammary-epithelial-cells
#10
Sarah Beaudin, JoEllen Welsh
Genomic profiling has identified a subset of metabolic genes that are altered by 1,25-dihydroxyvitamin D (1,25D) in breast cells including GLUL, the gene that encodes glutamine synthetase (GS). Here, we explored the relevance of vitamin D modulation of GLUL and other metabolic genes in the context of glutamine utilization and dependence. We show that exposure of breast epithelial cells to glutamine deprivation or a GS inhibitor reduced growth and these effects were exacerbated by co-treatment with 1,25D. 1,25D down-regulation of GLUL was sufficient to reduce abundance and activity of GS...
September 28, 2017: Endocrinology
https://www.readbyqxmd.com/read/29028988/quasar-mpra-accurate-allele-specific-analysis-for-massively-parallel-reporter-assays
#11
Cynthia A Kalita, Gregory A Moyerbrailean, Christopher Brown, Xiaoquan Wen, Francesca Luca, Roger Pique-Regi
Motivation: The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRA), have been used to functionally validate non-coding variants...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028987/in-silico-structural-modelling-of-multiple-epigenetic-marks-on-dna
#12
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M Deane, Peter Minary
Summary: There are four known epigenetic cytosine modifications in mammals: 5mC, 5hmC, 5fC and 5caC. The biological effects of 5mC are well understood but the roles of the remaining modifications remain elusive. Experimental and computational studies suggest that a single epigenetic mark has little structural effect but six of them can radically change the structure of DNA to a new form, F-DNA. Investigating the collective effect of multiple epigenetic marks requires the ability to interrogate all possible combinations of epigenetic states (e...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028986/a-new-haplotype-block-detection-method-for-dense-genome-sequencing-data-based-on-interval-graph-modeling-of-clusters-of-highly-correlated-snps
#13
Sun Ah Kim, Chang-Sung Cho, Suh-Ryung Kim, Shelley B Bull, Yun Joo Yoo
Motivation: Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation...
September 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028931/deepgo-predicting-protein-functions-from-sequence-and-interactions-using-a-deep-ontology-aware-classifier
#14
Maxat Kulmanov, Mohammed Asif Khan, Robert Hoehndorf
Motivation: A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often only done rigorously for few selected model organisms. Computational function prediction approaches have been suggested to fill this gap. The functions of proteins are classified using the Gene Ontology (GO), which contains over 40,000 classes...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028927/tumor-origin-detection-with-tissue-specific-mirna-and-dna-methylation-markers
#15
Wei Tang, Shixiang Wan, Zhen Yang, Andrew E Teschendorff, Quan Zou
Motivation: A clear identification of the primary site of tumor is of great importance to the next targeted site-specific treatments and could efficiently improve patient's overall survival. Even though many classifiers based on gene expression had been proposed to predict the tumor primary, only a few studies focus on using DNA methylation profiles to develop classifiers, and none of them compares the performance of classifiers based on different profiles. Results: We introduced novel selection strategies to identify highly tissue-specific CpG sites and then used the random forest approach to construct the classifiers to predict the origin of tumors...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028905/quality-of-biological-images-reconstructed-using-localization-microscopy-data
#16
Blazej Ruszczycki, Tytus Bernas
Motivation: Fluorescence localization microscopy is extensively used to study the details of spatial architecture of subcellular compartments. This modality relies on determination of spatial positions of fluorophores, labeling an extended biological structure, with precision exceeding the diffraction limit. Several established models describe influence of pixel size, signal-to-noise ratio and optical resolution on the localization precision. The labeling density has been also recognized as important factor affecting reconstruction fidelity of the imaged biological structure...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028902/graphkernels-r-and-python-packages-for-graph-comparison
#17
Mahito Sugiyama, M Elisabetta Ghisu, Felipe Llinares-López, Karsten Borgwardt
Summary: Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based kernels, and the state-of-the-art Weisfeiler-Lehman graph kernel...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028901/a-collaborative-filtering-based-approach-to-biomedical-knowledge-discovery
#18
Jake Lever, Sitanshu Gakkhar, Michael Gottlieb, Tahereh Rashnavadi, Santina Lin, Celia Siu, Maia Smith, Martin Jones, Martin Krzywinski, Steven J Jones
Motivation: The increase in publication rates makes it challenging for an individual researcher to stay abreast of all relevant research in order to find novel research hypotheses. Literature-based discovery methods make use of knowledge graphs built using text mining and can infer future associations between biomedical concepts that will likely occur in new publications. These predictions are a valuable resource for researchers to explore a research topic. Current methods for prediction are based on the local structure of the knowledge graph...
September 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028899/phandango-an-interactive-viewer-for-bacterial-population-genomics
#19
James Hadfield, Nicholas J Croucher, Richard J Goater, Khalil Abudahab, David M Aanensen, Simon R Harris
Summary: Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesising and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028894/aqua-an-adaptive-framework-for-compression-of-sequencing-quality-scores-with-random-access-functionality
#20
Tom Paridaens, Glenn Van Wallendael, Wesley De Neve, Peter Lambert
Motivation: The past decade has seen the introduction of new technologies that significantly lowered the cost of genome sequencing. As a result, the amount of genomic data that must be stored and transmitted is increasing exponentially. To mitigate storage and transmission issues, we introduce a framework for lossless compression of quality scores. Results: This paper proposes AQUa, an adaptive framework for lossless compression of quality scores. To compress these quality scores, AQUa makes use of a configurable set of coding tools, extended with a Context-Adaptive Binary Arithmetic Coding scheme (CABAC)...
September 25, 2017: Bioinformatics
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