WildSilkbase: An EST database of wild silkmoths

<p>Abstract</p> <p>Background</p> <p>Functional genomics has particular promise in silkworm biology for identifying genes involved in a variety of biological functions that include: synthesis and secretion of silk, sex determination pathways, insect-pathogen interactions, chorionogenesis, molecular clocks. Wild silkmoths have hardly been the subject of detailed scientific investigations, owing largely to non-availability of molecular and genetic data on these species. As a first step, in the present study we generated large scale expressed sequence tags (EST) in three economically important species of wild silkmoths. In order to make these resources available for the use of global scientific community, an EST database called 'WildSilkbase' was developed.</p> <p>Description</p> <p>WildSilkbase is a catalogue of ESTs generated from several tissues at different developmental stages of 3 economically important saturniid silkmoths, an Indian golden silkmoth, <it>Antheraea assama</it>, an Indian tropical tasar silkmoth, <it>A. mylitta </it>and eri silkmoth, <it>Samia cynthia ricini</it>. Currently the database is provided with 57,113 ESTs which are clustered and assembled into 4,019 contigs and 10,019 singletons. Data can be browsed and downloaded using a standard web browser. Users can search the database either by BLAST query, keywords or Gene Ontology query. There are options to carry out searches for species, tissue and developmental stage specific ESTs in BLAST page. Other features of the WildSilkbase include cSNP discovery, GO viewer, homologue finder, SSR finder and links to all other related databases. The WildSilkbase is freely available from <url>http://www.cdfd.org.in/wildsilkbase/</url>.</p> <p>Conclusion</p> <p>A total of 14,038 putative unigenes was identified in 3 species of wild silkmoths. These genes provide important resources to gain insight into the functional and evolutionary study of wild silkmoths. We believe that WildSilkbase will be extremely useful for all those researchers working in the areas of comparative genomics, functional genomics and molecular evolution in general, and gene discovery, gene organization, transposable elements and genome variability of insect species in particular.</p

Conformal solids and holography

We argue that a $SO(d)$ magnetic monopole in an asymptotically AdS space-time is dual to a $d$-dimensional strongly coupled system in a solid state. In light of this, it would be remiss of us not to dub such a field configuration $solidon$. In the presence of mixed boundary conditions, a solidon spontaneously breaks translations (among many other symmetries) and gives rise to Goldstone excitations on the boundary$-$the phonons of the solid. We derive the quadratic action for the boundary phonons in the probe limit and show that, when the mixed boundary conditions preserve conformal symmetry, the longitudinal and transverse sound speeds are related to each other as expected from effective field theory arguments. We then include backreaction and calculate the free energy of the solidon for a particular choice of mixed boundary conditions, corresponding to a relevant multi-trace deformation of the boundary theory. We find such free energy to be lower than that of thermal AdS. This suggests that our solidon undergoes a solid-to-liquid first order phase transition by melting into a Schwarzschild-AdS black hole as the temperature is raised.Comment: 31 pages; v2: incorrect calculation in sec. 4 has been deleted; main results unchange

Multicomponent synthesis of 4H-pyran derivatives using KOH loaded calcium oxide as catalyst in solvent free condition

A Convenient and green synthesis of 4H-pyran derivatives via one-pot multicomponent reaction of aromatic aldehydes, malononitrile and ethyl acetoacetate using KOH loaded CaO as a catalyst under solvent free condition is reported. The morphology of the catalyst has been characterized by XRD and TEM. This protocol have numerous advantages like lesser reaction time, environment friendly, low cost, easy to separate, and provide higher yield. The synthesized compounds have been characterized and confirmed by different spectroscopic techniques like 1H NMR, 13C NMR, FT- IR, and LC- MS

Optimization of the use of cellulolytic enzyme preparation for the extraction of health promoting anthocyanins from black carrot using response surface methodology

Anthocyanin-rich extracts from black carrots are being considered as a candidate replacer for the red colour in processed foods. The present investigation optimizes the extraction of anthocyanins with high phenolic content and low degradation parameters from black carrots using a cellulolytic multi-enzyme preparation known as Viscozyme. The optimized conditions for Viscozyme using a Box-Behnken design (BBD) of response surface methodology (RSM) were as follow: temperature (50.2 ◦C), extraction time (58.4 min) and enzyme concentration (0.20%). The predicted value of anthocyanins content was 1380 mg/L, which was near to the optimized experimental value of 1375 mg/L. The extracted anthocyanins based on above mentioned conditions exhibited the lowest degradation parameters such as degradation index (DI) of (0.86), browning index of (BI) (1.31) and were characterized with cyanidin 3-sinapoylxylosylglucosylgalactoside as being the most abundant. The findings clearly reveal that Viscozyme-assisted extraction (VAE) is the best approach for extracting superior quality extracts from black carrots with high anthocyanin and other phenolic component concentrations

Disruption of paternal circadian rhythm affects metabolic health in male offspring via nongerm cell factors

Circadian rhythm synchronizes each body function with the environment and regulates physiology. Disruption of normal circadian rhythm alters organismal physiology and increases disease risk. Recent epidemiological data and studies in model organisms have shown that maternal circadian disruption is important for offspring health and adult phenotypes. Less is known about the role of paternal circadian rhythm for offspring health. Here, we disrupted circadian rhythm in male mice by night-restricted feeding and showed that paternal circadian disruption at conception is important for offspring feeding behavior, metabolic health, and oscillatory transcription. Mechanistically, our data suggest that the effect of paternal circadian disruption is not transferred to the offspring via the germ cells but initiated by corticosterone-based parental communication at conception and programmed during in utero development through a state of fetal growth restriction. These findings indicate paternal circadian health at conception as a newly identified determinant of offspring phenotypes

Role of sequence encoded κB DNA geometry in gene regulation by Dorsal

Many proteins of the Rel family can act as both transcriptional activators and repressors. However, mechanism that discerns the ‘activator/repressor’ functions of Rel-proteins such as Dorsal (Drosophila homologue of mammalian NFκB) is not understood. Using genomic, biophysical and biochemical approaches, we demonstrate that the underlying principle of this functional specificity lies in the ‘sequence-encoded structure’ of the κB-DNA. We show that Dorsal-binding motifs exist in distinct activator and repressor conformations. Molecular dynamics of DNA-Dorsal complexes revealed that repressor κB-motifs typically have A-tract and flexible conformation that facilitates interaction with co-repressors. Deformable structure of repressor motifs, is due to changes in the hydrogen bonding in A:T pair in the ‘A-tract’ core. The sixth nucleotide in the nonameric κB-motif, ‘A’ (A6) in the repressor motifs and ‘T’ (T6) in the activator motifs, is critical to confer this functional specificity as A6 → T6 mutation transformed flexible repressor conformation into a rigid activator conformation. These results highlight that ‘sequence encoded κB DNA-geometry’ regulates gene expression by exerting allosteric effect on binding of Rel proteins which in turn regulates interaction with co-regulators. Further, we identified and characterized putative repressor motifs in Dl-target genes, which can potentially aid in functional annotation of Dorsal gene regulatory network

De Novo assembly and transcriptome analysis of the mediterranean fruit fly ceratitis capitata early embryos

The agricultural pest Ceratitis capitata, also known as the Mediterranean fruit fly or Medfly, belongs to the Tephritidae family, which includes a large number of other damaging pest species. The Medfly has been the first non-drosophilid fly species which has been genetically transformed paving the way for designing geneticbased pest control strategies. Furthermore, it is an experimentally tractable model, in which transient and transgene-mediated RNAi have been successfully used. We applied Illumina sequencing to total RNA preparations of 8-10 hours old embryos of C. capitata, This developmental window corresponds to the blastoderm cellularization stage. In summary, we assembled 42,614 transcripts which cluster in 26,319 unique transcripts of which 11,045 correspond to protein coding genes; we identified several hundreds of long ncRNAs; we found an enrichment of transcripts encoding RNA binding proteins among the highly expressed transcripts, such as CcTRA-2, known to be necessary to establish and, most likely, to maintain female sex of C. capitata. Our study is the first de novo assembly performed for Ceratitis capitata based on Illumina NGS technology during embryogenesis and it adds novel data to the previously published C. capitata EST databases. We expect that it will be useful for a variety of applications such as gene cloning and phylogenetic analyses, as well as to advance genetic research and biotechnological applications in the Medfly and other related Tephritidae

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Not AvailableThe genetic divergence of 61 extant varieties of rice (Oryza sativa L.) was assessed by using principal component analysis (PCA). The variables considered in the multivariate analyses were morphological, phenological and grain traits. The correlation analysis revealed that a number of traits were directly associated with other traits regardless of plant type or architectural configuration of the whole plant. The first four components in the PC analysis with Eigen values >1 contributed 74.25% of the variability among genotypes evaluated. Across various PCs, each of the accessions contributed both vegetatively and reproductively and in some cases only one-sidedly, either reproductively or vegetatively. The study grouped the genotypes into seven clusters. Cluster I had maximum number of genotypes (17). The cluster VII had second highest number of genotypes (12), while cluster II, III, IV, V, VI contained nine, four, six, five and eight genotypes, respectively. The overall composition of the clustering pattern showed that genotypes collected from the same geographic origin were distributed in different clusters. A critical appraisal of the observations suggested that none of the clusters contained genotypes with all the desirable traits, which could be directly selected and utilized. Hence, depending on the per se performance of the best genotypes within the clusters, they may be directly used for adaptation or maybe used as parents in future breeding programs.Not Availabl