The recent availability of plant genome sequences, combined with a robust evolutionary scenario of the modern monocot and eudicot karyotypes from their diploid ancestors, offers an opportunity to gain insights into microRNA (miRNA) gene paleohistory in plants. Characterization and comparison of miRNAs and associated protein-coding targets in plants allowed us ...

As the most efficient natural enemy of mealybugs, the ladybird Cryptolaemus montrouzieri Mulasnt 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 26 million ...

The WRKY transcription factors have been implicated in multiple biological processes in plants, especially in regulating defense against biotic and abiotic stresses. However, little information is available about the WRKYs in tomato (Solanum lycopersicum). The recent release of the whole-genome sequence of tomato allowed us to perform a genome-wide investigation ...

Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. Nucleotide diversity varied among species and was highest for ...

Pseudomonas extremaustralis 14-3b presents genes involved in the synthesis of different polyhydroxyalkanoates, in tolerance and degradation of pollutants, and in microaerobic metabolism. Several genomic islands were detected. Genetic machinery could contribute to the adaptability to stressful conditions. This is the first genome sequence reported from a Pseudomonas isolated from cold ...

The MHC class I-A and -B genes of cynomolgus macaques are highly polymorphic. These genes encode proteins presenting peptides to CD8+ T cells to initiate adaptive immune response. Recombination events are one way the diversity of these alleles can be increased. Such events have been well characterized in humans, but ...

Predicting organismal phenotypes from genotype data is important for plant and animal breeding, medicine, and evolutionary biology. Genomic-based phenotype prediction has been applied for single-nucleotide polymorphism (SNP) genotyping platforms, but not using complete genome sequences. Here, we report genomic prediction for starvation stress resistance and startle response in Drosophila melanogaster, ...

Bacterial small regulatory RNAs (sRNAs) function in post-transcriptional control of gene expression and control a variety of processes including metabolic reactions, stress responses and pathogenesis in response to environmental signals. A variety of approaches have been used previously to identify 44 sRNAs in the opportunistic human pathogen Pseudomonas aeruginosa. In ...

The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep ...

ABSTRACT: BACKGROUND: MicroRNAs (miRNAs) play key roles in diverse developmental processes, nutrient homeostasis and responses to biotic and abiotic stresses. The biogenesis and regulatory functions of miRNAs have been intensively studied in model angiosperms, such as Arabidopsis thaliana, Oryza sativa and Populus trichocarpa. However, global identification of Pinus densata miRNAs ...

Heat shock proteins (HSPs) production in cell is inducible by many physical and chemical stressors, providing adaptive significance for organisms when faced with environmental changes. In this study, we characterized a novel small HSP gene from disk abalone, designated as HdHSP20, and investigated its temporal expression by different environmental stimuli. ...

Aims: sRNA regulation is supposedly involved in the stress response of a pathogen during infection. Yersinia pestis, the etiologic agent of plague, must encounter temperature and microenvironment changes, given its lifestyle. Here, we used the cDNA cloning approach to discover full-length sRNA candidates that are highly expressed in Y. pestis ...

ABSTRACT: BACKGROUND: MicroRNA (miRNA) is a class of functional non-coding small RNA with 19-25 nucleotides in length while Amur grape (Vitis amurensis Rupr.) is an important wild fruit crop with the strongest cold resistance among the Vitis species, is used as an excellent breeding parent for grapevine, and has elicited ...

ABSTRACT: BACKGROUND: Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNAi machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, and yeasts. However, many questions remain regarding the features ...

Dehydrins are one of the major stress-induced gene families, and the expression of dehydrin 6 (Dhn6) is strictly related to drought in barley. In order to investigate how the evolution of the Dhn6 gene is associated with adaptation to environmental changes, we examined 48 genotypes of wild barley, Hordeum spontaneum, ...

MicroRNAs (miRNAs) are short RNAs with essential roles in gene regulation in various organisms including higher plants. In contrast to the vast information on miRNAs from many economically important plants, almost nothing has been reported on the identification or analysis of miRNAs from rubber tree (Hevea brasiliensis L.), the most ...

Heat shock protein 90 (HSP90) is an abundant and highly conserved molecular chaperone, playing important roles in multiple cellular stress responses. The full-length cDNA of planarian Dugesia japonica Hsp90 (designated DjHsp90) was firstly cloned using rapid amplification of cDNA ends (RACE) techniques. It is 2,354 bp, including an open reading frame ...

The genome of the parasitic platyhelminth Schistosoma mansoni is composed of approximately 40% of repetitive sequences of which roughly 20% correspond to transposable elements. When the genome sequence became available, conventional repeat prediction programs were used to find these repeats, but only a fraction could be identified. To exhaustively characterize ...

In this study, four methionine sulfoxide reductase A (MSRA) genes, SlMSRA2-5, were identified in Micro-Tom (Solanum lycopersicum cv.'Micro-Tom') based on the tomato database. Exon/intron distribution assays indicated that the gene sequence of SlMSRA2, SlMSRA3, and SlMSRA4 contained two exons and one intron in the tomato genome, while the coding sequence ...

About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters ...

ABSTRACT: BACKGROUND: Plants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs. Of these, microRNAs (miRNAs) play a crucial role. They negatively regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs (mRNAs). In Hevea brasiliensis, environmental and harvesting stresses ...

Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. ...

• Premise of the study: High-throughput sequencing of cDNA libraries prepared from diverse samples (RNA-seq) can reveal genome-wide changes in alternative splicing. Using RNA-seq data to assess splicing at the level of individual genes requires the ability to visualize read alignments alongside genomic annotations. To meet this need, we added ...

Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small ...

Oxylipins generated by the lipoxygenase (LOX) pathway play an important role in plant defense against biotic and abiotic stress. In chitosan-treated Adelostemma gracillimum seedlings, obvious accumulation of 9-LOX-derived oxylipins, namely 9,10,11-trihydroxy-12-octadecenoic acid, was detected. Using degenerate primers, a LOX-specific fragment putatively encoding LOX was obtained by RT-PCR, and a 2.9-kb ...

Within an evolutionary framework of Gastrotricha Marinellina flagellata and Redudasys fornerise bear special interest, as they are the only Macrodasyida that inhabit freshwater ecosystems. Notwithstanding, these rare animals are poorly known; found only once (Austria and Brazil), they are currently systematised as incertae sedis. Here we report on the rediscovery ...

Phytophthora megakarya, the causative agent of cacao black pod disease in West African countries causes an extensive loss of yield. In this study we have analyzed 4 libraries of ESTs derived from Phytophthora megakarya infected cocoa leaf and pod tissues. Totally 6379 redundant sequences were retrieved from ESTtik database and ...

Knowledge of rice genome brings new dimensions to the management of abiotic stresses; however, gene sequences in the rice genome are yet to be assigned structure and function. Hydrogen peroxide, salicylates and jasmonates act as signal molecules in plants employing common machinery to manage abiotic stress. The present work is ...

Chickpea (Cicer arietinum L.) is an important food legume crop, particularly for the arid regions including Indian subcontinent. Considering the detrimental effect of drought, temperature and salt stress on crop yield, efforts have been initiated in the direction of developing improved varieties and designing alternate strategies to sustain chickpea production ...

Glycine-rich proteins (GRPs) are a group of proteins characterized by their high content of glycine residues often occurring in repetitive blocs. The diverse expression pattern and sub cellular localization of various GRPs suggest their implication in different physiological processes. Several GRPs has been isolated and characterized from different monocots and ...

A brief history of taxonomy, for the most part plant oriented, is provided, which demonstrates the use of morphology early on, through the stages when different technologies became available at different times until the present use of genomic tools. Genomic authentication facilitates with greater precision than ever before the identification ...

ABSTRACT To help define the biological functions of nonessential genes of Francisella novicida, we measured the growth of arrayed members of a comprehensive transposon mutant library under a variety of nutrition and stress conditions. Mutant phenotypes were identified for 37% of the genes, corresponding to ten carbon source utilization pathways, ...

MicroRNAs (miRNAs) are endogenous small RNAs playing an important regulatory function in plant development and stress responses. Among them, some are evolutionally conserved in plant and others are only expressed in certain species, tissue or developmental stages. Cucumber is among the most important greenhouse species in the world, but only ...

MicroRNAs (miRNAs) are small RNAs (21-24 bp) providing an RNA-based system of gene regulation highly conserved in plants and animals. In plants, miRNAs control mRNA degradation or restrain translation, affecting development and responses to stresses. Plant miRNAs show imperfect but extensive complementarity to mRNA targets, making their computational prediction possible, ...

The analysis of similar earthquakes, such as events in a seismic sequence, is an effective tool with which to monitor and study source processes and to understand the mechanical and dynamic states of active fault systems. We are observing seismicity that is primarily concentrated in very limited regions along the ...

Chitinase is an enzyme that catalyzes the degradation of chitin, commonly induced upon the attack of pathogens and other stresses. A cDNA (MsChi1) was isolated from Metroxylon sagu and expressed predominantly in the inflorescence tissue of M. sagu, suggesting its role in developmental processes. The chitinase cDNA was detected and ...

In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3'-adjacent to the UGA. However, analysis of variability at ...

Enterovirus environmental surveillance on sewage from the city of Jinan, Shandong Province, China, was initiated in 2008. Thirty echovirus 6 (E6) strains-1 in 2008 and 29 in 2010-were isolated and identified. Most E6 isolates (n = 21) came from the sewage collected on August 2010, revealing high local E6 activity ...

BACKGROUND: Human enteroviruses (HEVs) are a rare cause of encephalitis, presenting in endemic or epidemic form. OBJECTIVES: The aim of the study is to identify and characterise the causative agent of the encephalitis epidemic, which occurred in Uttar Pradesh, India during the summer of 2008. STUDY DESIGN: A total of ...

The 288-nucleotide (nt) 3' untranslated region (UTR) in the genome of the bovine coronavirus (BCoV) and 339-nt 3' UTR in the severe acute respiratory syndrome (SARS) coronavirus (SCoV) can each replace the 301-nt 3' UTR in the mouse hepatitis coronavirus (MHV) for virus replication, thus demonstrating common 3' cis-replication signals. ...

Among the 21 O-polysaccharide (OPS) O-antigen based serotypes described for Yersinia pseudotuberculosis, those of O:6 and O:7 are unusual in that both contain colitose (4-keto-3,6 dideoxy-D-mannose or 4-keto-3,6-dideoxy-L-xylo-hexose), which has not otherwise been reported for this species, and the O:6 OPS also contains yersiniose A (4-C[(R)-1-hydroxyethyl]-3,6,dideoxy-D-xylo-hexose), another unusual dideoxyhexose sugar. ...

Lactobacillus animalis is one of the most prevalent lactic acid bacteria present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of Lactobacillus animalis type strain KCTC 3501 (1,882,795 bp, with a G+C content of 41.1%), which consists of 7 scaffolds.

Crimean-Congo haemorrhagic fever (CCHF) is a viral zoonotic disease with a high mortality rate in humans. The CCHF virus is transmitted to humans through the bite of Ixodid ticks or contact with blood or tissues of CCHF patients or infected livestock. In December 2008, a re-emerging outbreak of CCHF occurred ...

Post-transcriptional gene regulation frequently occurs through elements in mRNA 3' untranslated regions (UTRs). Although crucial roles for 3'UTR-mediated gene regulation have been found in Caenorhabditis elegans, most C. elegans genes have lacked annotated 3'UTRs. Here we describe a high-throughput method for reliable identification of polyadenylated RNA termini, and we apply ...

Leuconostoc fallax is known to be present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of the type strain Leuconostoc fallax KCTC 3537 (1,638,971 bp, with a G+C content of 37.5%), which consists of 30 large contigs (>100 bp in ...

Outbreaks of African swine fever (ASF) have been reported in the past from several countries in sub-Saharan Africa. The aim of this study was to genotype ASF viruses (ASFVs) from the 2008 outbreak in Morogoro and Dar es Salaam regions of Tanzania. Tissue samples from domestic pigs that died as ...

The prophage is one of the most important components of variable regions in bacterial genomes. Some prophages carry additional genes that may enhance the toxicity and survival ability of their host bacteria. This phenomenon is predominant in Staphylococcus aureus, a very common human pathogen. Bioinformatics analysis of several staphylococcal prophages ...

Sequence analysis of the upstream region of the cry1Ac gene in the HD-73 strain of B. thuringiensis showed a putative sigma(H)-like promoter. The potential regulating role of this sequence was tested by transforming an acrystaliferous mutant of the HD-73 strain with three different constructs: (1) a construct consisting of the ...

Sequenced bacterial genomes provide a wealth of information but little understanding of transcriptional regulatory circuits largely because accurate prediction of promoters is difficult. We examined two important issues for accurate promoter prediction: (1) the ability to predict promoter strength and (2) the sequence properties that distinguish between active and weak/inactive ...

Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(N)) associated RNA polymerase are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site. Using DNA microarrays representing the entire Escherichia coli ...