Transcriptomic Analysis of Thermoanaerobacter tengcongensis Grown at Different Temperatures by RNA Sequencing

<正>Genome sequencing of more than 80 thermophiles has provided powerful databases for the preliminary determination of genes essential to thermal adaptation(Berka et al.,2003;Berezovsky and Shakhnovich,2005;Andrews et al.,2010).A laboratory strain of Thermoanaerobacter tengcongensis MB4 has been shown to grow at temperatures over the range     

矮牵牛(Petunia hybrida)开花过程中的可溶性蛋白质分析

在进行矮牵牛(Petunia hybrida)光周期诱导开花的过程中,对叶子中的可溶性蛋白质进行了分析,其中有4条与开花有关的特异蛋白,分子量分别为49.45 kD(a)、35.45 kD(b)、17.98 kD(c)和11.74 kD(d).在不开放的花苞中不含有蛋白质a和d,只有这4种蛋白质全出现时,才能形成花苞并且开放.花开了以后,蛋白质c和d就消失.即使在开花的植株中,各组织中的蛋白质也是不同的.茎中完全不含有蛋白质c和d,叶子和花中的蛋白质组成也是不同的.     

Genetic analysis of instability in Petunia hybrida

Summary In crossing experiments with Petunia hybrida, new mutations, some unstable, have been found in descendants of plants having an unstable allele of the anthocyanin gene An1. One of the unstable mutations affecting the new anthocyanin gene An11 was genetically analyzed, and it was subsequently established in which step of anthocyanin synthesis that An11 is involved. The discovery of new, unstable mutations at other loci indicates that in Petunia also a relation exists between unstable mutations and the presence of transposable elements in the genome. It was demonstrated that reverted alleles (an1^+/+) originating from unstable An1 alleles are less stable than the original wild-type allele An1, and that reversions do not increase the chances of occurrence of new, stable or unstable mutations at other loci. These results provide additional arguments in favour of the hypothesis posed in an earlier paper that reversions of unstable An1 alleles are not the result of excision of the inserted transposable element, but are due to the repair of secondary mutations induced by the insert in the regulatory region of the locus. Consequently, a reverted allele still contains the inserted element that may again induce mutations leading to inactivation of An1.     

Transcriptomic Profiling Revealed Genes Involved in Response to Drought Stress in Alfalfa

Journal of Plant Growth Regulation - Drought stress is a primary abiotic stress that causes the crop losses worldwide. Under drought conditions, root growth is determined by the action of...     

ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data

High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality.     

Genomic Analysis of Stress Response against Arsenic in Caenorhabditis elegans

Arsenic, a known human carcinogen, is widely distributed around the world and found in particularly high concentrations in certain regions including Southwestern US, Eastern Europe, India, China, Taiwan and Mexico. Chronic arsenic poisoning affects millions of people worldwide and is associated with increased risk of many diseases including arthrosclerosis, diabetes and cancer. In this study, we explored genome level global responses to high and low levels of arsenic exposure in Caenorhabditis elegans using Affymetrix expression microarrays. This experimental design allows us to do microarray analysis of dose-response relationships of global gene expression patterns. High dose (0.03%) exposure caused stronger global gene expression changes in comparison with low dose (0.003%) exposure, suggesting a positive dose-response correlation. Biological processes such as oxidative stress, and iron metabolism, which were previously reported to be involved in arsenic toxicity studies using cultured cells, experimental animals, and humans, were found to be affected in C. elegans. We performed genome-wide gene expression comparisons between our microarray data and publicly available C. elegans microarray datasets of cadmium, and sediment exposure samples of German rivers Rhine and Elbe. Bioinformatics analysis of arsenic-responsive regulatory networks were done using FastMEDUSA program. FastMEDUSA analysis identified cancer-related genes, particularly genes associated with leukemia, such as dnj-11, which encodes a protein orthologous to the mammalian ZRF1/MIDA1/MPP11/DNAJC2 family of ribosome-associated molecular chaperones. We analyzed the protective functions of several of the identified genes using RNAi. Our study indicates that C. elegans could be a substitute model to study the mechanism of metal toxicity using high-throughput expression data and bioinformatics tools such as FastMEDUSA.     

Analysis of pollen-style interactions in Petunia hybrida; the determination of variance in male reproductive success

Summary A factorial cross design was used to evaluate the influence of differences among pollen donors and recipients on variation in stylar attrition of pollen tubes in self-fertile plants of Petunia hybrida. Pollinations to flower buds were used to reduce the inhibitory ability of the style and these crosses were compared with flower pollinations to assess the degree of stylar influence on pollen fertilization ability. There was less pollen tube attrition after bud pollinations than after flower pollinations, indicating that styles of buds were less able to inhibit pollen tubes. The variance component for plants acting as pollen donors tended to be greater after flower pollinations than after bud pollinations. The lower variance in male success after bud pollinations indicates that differences among pollen donors after flower pollinations were due to stylar inhibition of pollen rather than differences in pollen vigor. Since the level of variation in pollen growth after pollination to flowers was greater among clones than among ramets within clones, the differences in pollen fertilization ability are probably genetically based.