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Bioinformatics and Biology Insights

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https://www.readbyqxmd.com/read/29051702/finding-the-sources-of-missing-heritability-within-rare-variants-through-simulation
#1
Baishali Bandyopadhyay, Veda Chanda, Yupeng Wang
Thousands of genome-wide association studies (GWAS) have been conducted to identify the genetic variants associated with complex disorders. However, only a small proportion of phenotypic variances can be explained by the reported variants. Moreover, many GWAS failed to identify genetic variants associated with disorders displaying hereditary features. The "missing heritability" problem can be partly explained by rare variants. We simulated a causality scenario that gestational ages, a quantitative trait that can distinguish preterm (<37 weeks) and term births, were significantly correlated with the rare variant aggregations at 1000 single-nucleotide polymorphism loci...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28989277/a-metagenomic-analysis-of-bacterial-microbiota-in-the-digestive-tract-of-triatomines
#2
Nicolas Carels, Marcial Gumiel, Fabio Faria da Mota, Carlos José de Carvalho Moreira, Patricia Azambuja
The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. The enzymatic reactions encoded by coding sequences of both rare and common bacterial species were then compared and revealed key functions explaining why some genera outcompete others in the DTT...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28932107/bioinformatics-study-of-m-9053g-a-mutation-at-the-atp6-gene-in-relation-to-type-2-diabetes-mellitus-and-cataract-diseases
#3
Iman Permana Maksum, Sandy Risfi Saputra, Nenden Indrayati, Muhammad Yusuf, Toto Subroto
The mitochondrial disease often associated with various illnesses in relation to the activity of cells metabolites and the synthesis of adenosine triphosphate (ATP), including alteration in the mitochondrial DNA. The mutation of m.9053G>A at the ATP6 gene was found in patients with type 2 diabetes mellitus (DM type 2) and cataract. Therefore, this mutation is predicted to be clinical features of the 2 diseases. ATP6 gene encodes protein subunit of ATPase6, a part of ATP synthase, which is important in the electron transfer and proton translocation in intracellular respiration system...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28757797/reverse-nearest-neighbor-search-on-a-protein-protein-interaction-network-to-infer-protein-disease-associations
#4
Apichat Suratanee, Kitiporn Plaimas
The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. In this study, an analysis framework to infer associations between proteins and diseases was developed based on a large data set of a human protein-protein interaction network integrating an effective network search, namely, the reverse k-nearest neighbor (RkNN) search. The RkNN search was used to identify an impact of a protein on other proteins...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28659714/celltrans-an-r-package-to-quantify-stochastic-cell-state-transitions
#5
Thomas Buder, Andreas Deutsch, Michael Seifert, Anja Voss-Böhme
Many normal and cancerous cell lines exhibit a stable composition of cells in distinct states which can, e.g., be defined on the basis of cell surface markers. There is evidence that such an equilibrium is associated with stochastic transitions between distinct states. Quantifying these transitions has the potential to better understand cell lineage compositions. We introduce CellTrans, an R package to quantify stochastic cell state transitions from cell state proportion data from fluorescence-activated cell sorting and flow cytometry experiments...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28638238/a-computational-methodology-to-overcome-the-challenges-associated-with-the-search-for-specific-enzyme-targets-to-develop-drugs-against-leishmania-major
#6
Larissa Catharina, Carlyle Ribeiro Lima, Alexander Franca, Ana Carolina Ramos Guimarães, Marcelo Alves-Ferreira, Pierre Tuffery, Philippe Derreumaux, Nicolas Carels
We present an approach for detecting enzymes that are specific of Leishmania major compared with Homo sapiens and provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific for L major compared with H sapiens, only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific of L major and 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with H sapiens...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28579762/prepartal-energy-intake-alters-blood-polymorphonuclear-leukocyte-transcriptome-during-the-peripartal-period-in-holstein-cows
#7
A Agrawal, M J Khan, D E Graugnard, M Vailati-Riboni, S L Rodriguez-Zas, J S Osorio, J J Loor
In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Holstein cows were fed a high-straw, control-energy diet (CON; NEL = 1...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28469420/in-silico-approach-for-characterization-and-comparison-of-repeats-in-the-genomes-of-oil-and-date-palms
#8
Jaire Alves Ferreira Filho, Lucas Soares de Brito, André Pereira Leão, Alexandre Alonso Alves, Eduardo Fernandes Formighieri, Manoel Teixeira Souza Júnior
Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28469419/an-insight-into-structure-function-and-expression-analysis-of-3-hydroxy-3-methylglutaryl-coa-reductase-of-cymbopogon-winterianus
#9
Kamalakshi Devi, Lochana Patar, Mahendra K Modi, Priyabrata Sen
Citronella (Cymbopogon winterianus) is one of the richest sources of high-value isoprenoid aromatic compounds used as flavour, fragrance, and therapeutic elements. These isoprenoid compounds are synthesized by 2 independent pathways: mevalonate pathway and 2-C-methyl-d-erythritol-4-phosphate pathway. Evidence suggests that 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a rate-controlling enzyme for the synthesis of variety of isoprenoids. This study reports the isolation, characterization, and tissue-specific expression analysis of HMGR from citronella...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28469418/pisma-a-visual-representation-of-motif-distribution-in-dna-sequences
#10
Rogelio Alcántara-Silva, Moisés Alvarado-Hermida, Gibrán Díaz-Contreras, Martha Sánchez-Barrios, Samantha Carrera, Silvia Carolina Galván
BACKGROUND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. RESULTS: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28469417/plasma-microrna-levels-following-resection-of-metastatic-melanoma
#11
Nicholas Latchana, Zachary B Abrams, J Harrison Howard, Kelly Regan, Naduparambil Jacob, Paolo Fadda, Alicia Terando, Joseph Markowitz, Doreen Agnese, Philip Payne, William E Carson
Melanoma remains the leading cause of skin cancer-related deaths. Surgical resection and adjuvant therapies can result in disease-free intervals for stage III and stage IV disease; however, recurrence is common. Understanding microRNA (miR) dynamics following surgical resection of melanomas is critical to accurately interpret miR changes suggestive of melanoma recurrence. Plasma of 6 patients with stage III (n = 2) and stage IV (n = 4) melanoma was evaluated using the NanoString platform to determine pre- and postsurgical miR expression profiles, enabling analysis of more than 800 miRs simultaneously in 12 samples...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28469416/transcriptologs-a-transcriptome-based-approach-to-predict-orthology-relationships
#12
Luca Ambrosino, Maria Luisa Chiusano
The detection of orthologs is a key approach in genomics, useful to understand gene evolution and phylogenetic relationships and essential for gene function prediction. However, a reliable annotation of the encoded protein regions is still a limiting aspect in genomics, mainly due to the lack of confirmatory experimental evidence at proteome level. Nevertheless, the current ortholog collections are generally based on protein sequence comparisons, in addition to the availability of large transcriptome sequence collections...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28469415/current-developments-in-machine-learning-techniques-in-biological-data-mining
#13
EDITORIAL
Gerard G Dumancas, Indra Adrianto, Ghalib Bello, Mikhail Dozmorov
This supplement is intended to focus on the use of machine learning techniques to generate meaningful information on biological data. This supplement under Bioinformatics and Biology Insights aims to provide scientists and researchers working in this rapid and evolving field with online, open-access articles authored by leading international experts in this field. Advances in the field of biology have generated massive opportunities to allow the implementation of modern computational and statistical techniques...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28050127/molecular-modeling-and-phylogeny-of-the-kr%C3%A3-ppel-like-factor-4-cklf4-protein-from-the-arabian-camel-camelus-dromedarius
#14
Abdullah O Alawad, Sultan N Alharbi, Othman A Alhazzaa, Faisal S Alagrafi, Mohammad N Alkhrayef, Ziyad A Alhamdan, Abdullah D Alenazi, Mohamed Hammad, Sami A Alyahya, Hasan A AlJohi, Ibrahim O Alanazi
Krüppel-like factor 4 (KLF4) is a pluripotency transcription factor that helps in generating induced pluripotent stem cells (iPSCs). We sequenced for the first time the full coding sequence of Camelus dromedarius KLF4 (cKLF4), which is also known as the Arabian camel. Bioinformatics analysis revealed the molecular weight and the isoelectric point of cKLF4 protein to be 53.043 kDa and 8.74, respectively. The predicted cKLF4 protein sequence shows high identity with some other species as follows: 98% with Bactrian camel and 89% with alpaca KLF4 proteins...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27980397/integrating-epigenomics-into-the-understanding-of-biomedical-insight
#15
REVIEW
Yixing Han, Ximiao He
Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27932868/analysis-of-parallel-algorithms-on-smp-node-and-cluster-of-workstations-using-parallel-programming-models-with-new-tile-based-method-for-large-biological-datasets
#16
D D Shrimankar, S R Sathe
Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed with particular emphasis on time, speedup, and efficiency optimizations. Parallel programming presents a number of critical challenges to application developers...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27932867/clustering-algorithms-their-application-to-gene-expression-data
#17
REVIEW
Jelili Oyelade, Itunuoluwa Isewon, Funke Oladipupo, Olufemi Aromolaran, Efosa Uwoghiren, Faridah Ameh, Moses Achas, Ezekiel Adebiyi
Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27812283/structural-prediction-and-in-silico-physicochemical-characterization-for-mouse-caltrin-i-and-bovine-caltrin-proteins
#18
Ernesto J Grasso, Adolfo E Sottile, Carlos E Coronel
It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca(2+) uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Surface electrostatic potentials and electric fields were calculated using the Poisson-Boltzmann equation...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27812282/iterative-fragmentation-improves-the-detection-of-chip-seq-peaks-for-inactive-histone-marks
#19
Miklós Laczik, Jan Hendrickx, Anne-Clémence Veillard, Mustafa Tammoh, Sarah Marzi, Dominique Poncelet
As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication - sending the fragmented DNA after ChIP through additional round(s) of shearing - to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27695302/survey-of-genes-involved-in-biosynthesis-transport-and-signaling-of-phytohormones-with-focus-on-solanum-lycopersicum
#20
Stefan Simm, Klaus-Dieter Scharf, Sridharan Jegadeesan, Maria Luisa Chiusano, Nurit Firon, Enrico Schleiff
Phytohormones control the development and growth of plants, as well as their response to biotic and abiotic stress. The seven most well-studied phytohormone classes defined today are as follows: auxins, ethylene, cytokinin, abscisic acid, jasmonic acid, gibberellins, and brassinosteroids. The basic principle of hormone regulation is conserved in all plants, but recent results suggest adaptations of synthesis, transport, or signaling pathways to the architecture and growth environment of different plant species...
2016: Bioinformatics and Biology Insights
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