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      Cuticular protein genes involve heat acclimation of insect larvae under global warming

      1 , 1 , 1
      Insect Molecular Biology
      Wiley

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          Abstract

          Cuticular proteins (CPs) play important roles in insect growth and development. However, it is unknown whether CPs are related to heat tolerance. Cnaphalocrocis medinalis, a serious pest of rice, occurs in summer and exhibits strong adaptability to high temperature, but the underlying mechanism is unclear. Here, the role of CP genes in heat acclimation was studied. Heat tolerance of the heat‐acclimated larvae was significantly stronger than the unacclimated larvae. The cuticular protein content in the heat‐acclimated larvae was higher than that of the unacclimated larvae. 191 presumed CP genes of C. medinalis (CmCPs) were identified. Expression patterns of 14 CmCPs were different between the heat acclimated (S39) and unacclimated (S27) larvae under heat stress. CmCPs were specifically expressed in epidermis and the head except CmCPR20 mainly expressed in Malpighian tubules. CmCPR20 was upregulated in S39 while downregulated in S27, but CmTweedle1 and CmCPG1 were upregulated in S27 and downregulated in S39. RNAi CmTweedle1 or CmCPG1 remarkably decreased heat tolerance and cuticular protein content of the heat‐acclimated larvae but not the unacclimated larvae. RNAi CmCPR20 decreased heat tolerance and cuticular protein content of the unacclimated larvae but not the heat‐acclimated larvae. CmTweedle1 and CmCPG1 genes involve heat acclimation of C. medinalis.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            Is Open Access

            Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

            In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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              Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

              S Altschul (1997)
              The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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                Author and article information

                Journal
                Insect Molecular Biology
                Insect Molecular Biology
                Wiley
                0962-1075
                1365-2583
                August 2022
                April 25 2022
                August 2022
                : 31
                : 4
                : 519-532
                Affiliations
                [1 ] Department of Entomology, College of Plant Protection Nanjing Agricultural University Nanjing China
                Article
                10.1111/imb.12777
                936e9055-1813-4697-9518-06a46f036008
                © 2022

                http://onlinelibrary.wiley.com/termsAndConditions#vor

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