journal
MENU ▼
Read by QxMD icon Read
search

Bioinformatics and Biology Insights

journal
https://www.readbyqxmd.com/read/28579762/prepartal-energy-intake-alters-blood-polymorphonuclear-leukocyte-transcriptome-during-the-peripartal-period-in-holstein-cows
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/27688709/evolution-of-synonymous-codon-usage-in-the-mitogenomes-of-certain-species-of-bilaterian-lineage-with-special-reference-to-chaetognatha
#15
Sudeesh Karumathil, Vijaya R Dirisala, Uthpala Srinadh, Valaboju Nikhil, N Satya Sampath Kumar, Rahul R Nair
Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27594785/interaction-analysis-of-t7-rna-polymerase-with-heparin-and-its-low-molecular-weight-derivatives-an-in-silico-approach
#16
Subhomoi Borkotoky, Chetan Kumar Meena, Ayaluru Murali
The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27559295/in-silico-structure-prediction-of-human-fatty-acid-synthase-dehydratase-a-plausible-model-for-understanding-active-site-interactions
#17
Arun John, Vetrivel Umashankar, A Samdani, Manoharan Sangeetha, Subramanian Krishnakumar, Perinkulam Ravi Deepa
Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as β-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, β-ketoacyl reductase, and thioesterase, (TE) are already reported...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27499617/osg-gem-gene-expression-matrix-construction-using-the-open-science-grid
#18
William L Poehlman, Mats Rynge, Chris Branton, D Balamurugan, Frank A Feltus
High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG)...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27493475/computational-identification-of-novel-genes-current-and-future-perspectives
#19
REVIEW
Steffen Klasberg, Tristan Bitard-Feildel, Ludovic Mallet
While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Besides the theoretical breakthrough, increasing evidence accumulated that novel genes play important roles in evolutionary processes, including adaptation and speciation events...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27486314/phylogenetic-and-structural-analysis-of-the-pluripotency-factor-sex-determining-region-y-box2-gene-of-camelus-dromedarius-csox2
#20
Abdullah Alawad, Sultan Alharbi, Othman Alhazzaa, Faisal Alagrafi, Mohammed Alkhrayef, Ziyad Alhamdan, Abdullah Alenazi, Hasan Al-Johi, Ibrahim O Alanazi, Mohamed Hammad
Although the sequencing information of Sox2 cDNA for many mammalian is available, the Sox2 cDNA of Camelus dromedaries has not yet been characterized. The objective of this study was to sequence and characterize Sox2 cDNA from the brain of C. dromedarius (also known as Arabian camel). A full coding sequence of the Sox2 gene from the brain of C. dromedarius was amplified by reverse transcription PCRjmc and then sequenced using the 3730XL series platform Sequencer (Applied Biosystem) for the first time. The cDNA sequence displayed an open reading frame of 822 nucleotides, encoding a protein of 273 amino acids...
2016: Bioinformatics and Biology Insights
journal
journal
41891
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"