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As the most efficient natural enemy of mealybugs, the ladybird Cryptolaemus montrouzieri Mulsant plays an important role in integrated pest management. We report here a profiling analysis of C. montrouzieri under insecticide stress to gain a deeper view of insecticide resistance in ladybirds. For transcriptome sequencing, more than 26million sequencing reads were produced. These reads were assembled...
A wealth of genomic information is available in public and private databases. However, this information is underutilized for uncovering population specific and functionally relevant markers underlying complex human traits. Given the huge amount of SNP data available from the annotation of human genetic variation, data mining is a faster and cost effective approach for investigating the number of SNPs...
Fiber length is a key determinant of cotton yield and quality. Using a monogenic dominant cotton mutant Ligon lintless-1 with extremely short fibers, we employed microarray technology and quantitative real time PCR to compare transcriptomes of Li 1 and the normal wild-type TM-1, the results showed that only a few genes differentially expressed in 0days postanthesis (DPA) ovules and 3 DPA fibers,...
The 28S rRNA genes of several metazoans are interrupted by site-specific targeting non-LTR retrotransposons, such as R2. R2 elements have been deeply analyzed but aspects of their retrotransposition mechanism and the origin of the wide diversity observed are still debated. We characterized six new R2 lineages in four tadpole shrimp species (Notostraca), samples deriving from a parthenogenetic population...
We investigated the behavior of renal cells cultivated in microfluidic biochips when exposed to 50μM of ifosfamide, an antineoplastic drug treatment. The microarray analysis revealed that ifosfamide had any effect in Petri conditions. The microfluidic biochips induced an early inflammatory response in the MDCK in the untreated cells. This was attributed to cells adapting to the dynamics and micro...
With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative...
There are major gaps in our knowledge regarding the exact mechanisms and genetic basis of psoriasis. To investigate the pathogenesis of psoriasis, gene expression in 10 skin (5 lesional, 5 nonlesional) and 11 blood (6 psoriatic, 5 nonpsoriatic) samples were examined using Affymetrix HG-U95A microarrays. We detected 535 (425 upregulated, 110 downregulated) DEGs in lesional skin at 1% false discovery...
A conjoined gene is defined as one formed at the time of transcription by combining at least part of one exon from each of two or more distinct genes that lie on the same chromosome, in the same or opposite orientation, which translate independently into different proteins. We comparatively studied the extent of conjoined genes in thirteen genomes by analyzing the public databases of expressed sequence...
Microarrays and more recently RNA sequencing has led to an increase in available gene expression data. How to manage and store this data is becoming a key issue. In response we have developed EXP-PAC, a web based software package for storage, management and analysis of gene expression and sequence data. Unique to this package is SQL based querying of gene expression data sets, distributed normalization...
The aim of this paper is to provide an introduction to the rapidly developing field of genetic programming (GP). Particular emphasis is placed on the application of GP to genomics. First, the basic methodology of GP is introduced. This is followed by a review of applications in the areas of gene network inference, gene expression data analysis, SNP analysis, epistasis analysis and gene annotation...
Induction of a pluripotent cell mass termed callus is the first step in an in vitro plant regeneration system, which is required for subsequent regeneration of new organs or whole plants. However, the early molecular mechanism underlying callus initiation is largely elusive. Here, we analyzed the dynamic transcriptome profiling of callus initiation in Arabidopsis aerial and root explants and identified...
We have developed a graphical image database CancerProView (URL: http://cancerproview.dmb.med.keio.ac.jp/php/cpv.html) to assist the search for alterations of the motifs/domains in the cancer-related proteins that are caused by mutations in the corresponding genes. For the CancerProView, we have collected various kinds of data on 180 cancer-related proteins in terms of the motifs/domains, genomic...
The “5′ end mRNA artifact” issue refers to the incorrect assignment of the first AUG codon in an mRNA, due to the incomplete determination of its 5′ end sequence. We performed a systematic identification of coding regions at the 5′ end of all human known mRNAs, using an automated expressed sequence tag (EST)-based approach. Following parsing of more than 7million BLAT alignments, we found 477 human...
Genetic alterations like point mutations, insertions, deletions, inversions and translocations are frequently found in cancers. Chromosomal translocations are one of the most common genomic aberrations associated with nearly all types of cancers especially leukemia and lymphoma. Recent studies have shown the role of non-B DNA structures in generation of translocations. In the present study, using...
National/ethnic mutation databases aim to document the genetic heterogeneity in various populations and ethnic groups worldwide. We have previously reported the development and upgrade of FINDbase (www.findbase.org), a database recording causative mutations and pharmacogenomic marker allele frequencies in various populations around the globe. Although this database has recently been upgraded, we continuously...
Recent breakthrough on identification and characterization of PYR/PYLs as ABA receptors enables us to better understand the perception, signaling and transportation of ABA in plant. Based on publicly available microarray data, transcriptional levels of ABA signaling pathway core components were compared after stress and phytohormone treatments, including these involved in ABA metabolism, signal transduction,...
This study focused on identifying the conserved epitopes in a single subtype A (H3N2)—as candidates for vaccine targets. We identified a total of 32 conserved epitopes in four viral proteins [22 HA, 4PB1, 3 NA, 3 NP]. Evaluation of conserved epitopes in coverage during 1968–2010 revealed that (1) 12 HA conserved epitopes were highly present in the circulating viruses; (2) the remaining 10 HA conserved...
Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs’ genomic locations and their biological properties is essential for understanding their roles in the pathophysiology...
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