scholarly journals A Cluster of Genes at the Terminal Region of Chromosome 1 Contributes to Silk Yield in Bombyx Mori.

2021 ◽  
Author(s):  
Yue Luan ◽  
Chunlin Li ◽  
Yanyu Liu ◽  
Bili Zhang ◽  
Rui Gao ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Forward Genetics ◽  
Chromosome 1 ◽  
High Yield ◽  
Shell Weight ◽  
Association Analyses ◽  
Study Selection ◽  
Silk Glands

Abstract Background: The silk yield is the most economically important trait in sericulture. In the domestication of the silkworm, traits related to silk yield are the main selective targets. In previous studies, linkage and association analyses were performed, which narrowed the region of the locus controlling the cocoon shell weight (CSW), an important index of silk yield, to the interval of 0–134 kb on the 1st chromosome. Results In this study, selection pressure analysis showed that most of the loci in this interval were co-selected during silkworm domestication. Association analysis conducted with 95 strains found that there is a 110 kb region that was significantly associated with CSW. An expression profile correlation analysis of eight genes in the region showed that their expression patterns were very similar. Sequence variation analysis detected mutations in the exon regions of BMgn002066 and BMgn002073, leading to premature termination of translation. The sequence variation was significantly correlated with CSW. In addition, another two genes, BMgn002067 and BMgn002071, had significantly different expression levels in the posterior silk glands of 11 high-yield strains and 11 low-yield strains. Therefore, we speculate that the abovementioned four genes and the gene BmAbl1 detected in previous studies may co-regulate CSW. Conclusions This study is the first to identify the gene clusters that affect CSW by forward genetics, thereby providing new evidence for gene clusters that regulate quantitative traits.

22 Characterization of tRNA Expression Profiles in Large Offspring Syndrome

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 13-14
Author(s):  
Anna K Goldkamp ◽  
Yahan Li ◽  
Rocio M Rivera ◽  
Darren Hagen
Keyword(s):  
Skeletal Muscle ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tumor Development ◽  
Gene Clusters ◽  
Tissue Type ◽  
Trna Genes ◽  
Translational Machinery ◽  
Trna Species

Abstract Differentially methylated regions (DMRs) have been associated with Large Offspring Syndrome (LOS) in cattle. Some DMRs overlap transfer RNA (tRNA) gene clusters, potentially altering tRNA expression patterns uniquely by treatment group or tissue type. tRNAs are classified as adapter molecules, serving a key role in the translational machinery implementing genetic code. Variation in tRNA expression has been identified in several disease pathways suggesting an important role in the regulation of biological processes. tRNAs also serve as a source of small non-coding RNAs. To better understand the role of tRNA expression in LOS, total RNA was extracted from skeletal muscle and liver of 105-day fetuses and the tRNAs sequenced. Although there are nearly three times the number of tRNA genes in cattle as compared to human (1,659 vs 597), there is a shared occurrence of transcriptionally silent tRNA genes in both species. This study detected expression of 474 and 487 bovine tRNA genes in skeletal muscle and liver, respectively, with the remainder being very lowly expressed or transcriptionally silent. Eleven tRNA isodecoders are transcriptionally silent in both skeletal muscle and liver and another isodecoder is silent in the liver (SerGGA). Further, the highest expressed isodecoders differ by treatment or tissue type with roughly half correlated to codon frequency. While the absence of certain isodecoders may be relieved by wobble base pairing, missing tRNA species could likely increase the likelihood of mistranslation or mRNA degradation. Differential expression of tissue- and treatment-specific tRNA genes may modulate translation during protein homeostasis or cellular stress, altering regulatory products targeting genes associated with overgrowth in skeletal muscle and/or tumor development in the liver of LOS individuals.

scholarly journals Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost

2021 ◽  
Author(s):  
Gilda Varliero ◽  
Muhammad Rafiq ◽  
Swati Singh ◽  
Annabel Summerfield ◽  
Fotis Sgouridis ◽  
...  
Keyword(s):  
Active Layer ◽  
Sequence Variation ◽  
Gene Clusters ◽  
Taxonomic Composition ◽  
Sequence Information ◽  
Biosynthetic Gene Clusters ◽  
Medical Settings ◽  
Cold Adapted ◽  
Database Construction ◽  
Medium Quality

Abstract Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.

scholarly journals Efficient prediction of a spatial transcriptomics profile better characterizes breast cancer tissue sections without costly experimentation

2021 ◽  
Author(s):  
Taku Monjo ◽  
Masaru Koido ◽  
Satoi Nagasawa ◽  
Yutaka Suzuki ◽  
Yoichiro Kamatani
Keyword(s):  
Breast Cancer ◽  
Small Sample Size ◽  
Expression Patterns ◽  
Imputation Accuracy ◽  
Gene Clusters ◽  
Small Sample ◽  
Breast Cancer Tissue ◽  
Cancer Tissue ◽  
Gene Expressions ◽  
Tissue Sections

Spatial transcriptomics is an emerging technology requiring costly reagents and considerable skills, limiting the identification of transcriptional markers related to histology. Here, we show that predicted spatial gene-expressions in unmeasured regions and tissues can enhance biologists' histological interpretations. We developed the Deep learning model for Spatial gene Clusters and Expression, DeepSpaCE and confirmed its performance using the spatial-transcriptome profiles and immunohistochemistry images of consecutive human breast cancer tissue sections. For example, the predicted expression patterns of SPARC, an invasion marker, highlighted a small tumor-invasion region that is difficult to identify using raw data of spatial transcriptome alone because of a lack of measurements. We further developed semi-supervised DeepSpaCE using unlabeled histology images and increased the imputation accuracy of consecutive sections, enhancing applicability for a small sample size. Our method enables users to derive hidden histological characters via spatial transcriptome and gene annotations, leading to accelerated biological discoveries without additional experiments.

scholarly journals An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA

2019 ◽  
Vol 7 (1) ◽  
pp. 9 ◽  
Author(s):  
Dae-Eun Cheong ◽  
So-Youn Park ◽  
Ho-Dong Lim ◽  
Geun-Joong Kim
Keyword(s):  
Gene Expression ◽  
Regulatory Element ◽  
Expression System ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Single Element ◽  
Reading Frame ◽  
Cis Acting ◽  
Dna Libraries ◽  
Expression Module

Many integrated gene clusters beyond a single genetic element are commonly trapped as the result of promoter traps in (meta)genomic DNA libraries. Generally, a single element, which is mainly the promoter, is deduced from the resulting gene clusters and employed to construct a new expression vector. However, expression patterns of target proteins under the incorporated promoter are often inconsistent with those shown in clones harboring plasmids with gene clusters. These results suggest that the integrated set of gene clusters with diverse cis- and trans-acting elements is evolutionarily tuned as a complete set for gene expression, and is an expression module with all the components for the expression of a nested open reading frame (ORF). This possibility is further supported by truncation and/or serial deletion analysis of this module in which the expression of the nested ORF is highly fluctuated or reduced frequently, despite being supported by plentiful cis-acting elements in the spanning regions around the ORF such as the promoter, ribosome binding site (RBS), terminator, and 3′-/5′-UTRs for gene expression. Here, we examined whether an innate module with a naturally overexpressed gene could be considered as a scaffold for an expression system. For a proof-of-principle study, we mined a complete expression module with an innately overexpressed ORF in E. coli from a metagenomics DNA library, and incorporated it into a vector that had no regulatory element for expressing the insert. We obtained successful expression of several inserts such as MBP, GFPuv, β-glucosidase, and esterase using this simple construct without tuning and codon optimization of the target insert.

scholarly journals Genome-Wide Identification and Characterization of the OPR Gene Family in Wheat (Triticum aestivum L.)

2019 ◽  
Vol 20 (8) ◽  
pp. 1914 ◽  
Author(s):  
Yifei Mou ◽  
Yuanyuan Liu ◽  
Shujun Tian ◽  
Qiping Guo ◽  
Chengshe Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Defense Responses ◽  
High Yield ◽  
Flavin Mononucleotide ◽  
Duplicated Genes ◽  
Old Yellow Enzyme ◽  
Specific Expression ◽  
Protein Motifs

The 12-oxo-phytodienoic acid reductases (OPRs), which belong to the old yellow enzyme (OYE) family, are flavin mononucleotide (FMN)-dependent oxidoreductases with critical functions in plants. Despite the clear characteristics of growth and development, as well as the defense responses in Arabidopsis, tomato, rice, and maize, the potential roles of OPRs in wheat are not fully understood. Here, forty-eight putative OPR genes were found and classified into five subfamilies, with 6 in sub. I, 4 in sub. II, 33 in sub. III, 3 in sub. IV, and 2 in sub. V. Similar gene structures and conserved protein motifs of TaOPRs in wheat were identified in the same subfamilies. An analysis of cis-acting elements in promoters revealed that the functions of OPRs in wheat were mostly related to growth, development, hormones, biotic, and abiotic stresses. A total of 14 wheat OPR genes were identified as tandem duplicated genes, while 37 OPR genes were segmentally duplicated genes. The expression patterns of TaOPRs were tissue- and stress-specific, and the expression of TaOPRs could be regulated or induced by phytohormones and various stresses. Therefore, there were multiple wheat OPR genes, classified into five subfamilies, with functional diversification and specific expression patterns, and to our knowledge, this was the first study to systematically investigate the wheat OPR gene family. The findings not only provide a scientific foundation for the comprehensive understanding of the wheat OPR gene family, but could also be helpful for screening more candidate genes and breeding new varieties of wheat, with a high yield and stress resistance.

Subcellular localization, expression patterns, SNPs and association analyses of the porcine HUMMLC2B gene

2006 ◽  
Vol 276 (3) ◽  
pp. 264-272 ◽  
Author(s):  
Huan L. Wang ◽  
Heng Wang ◽  
Zheng M. Zhu ◽  
Chen F. Wang ◽  
Meng J. Zhu ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Expression Patterns ◽  
Association Analyses

scholarly journals Integrative Analysis of miRNA-mRNA and miRNA-miRNA Interactions

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Li Guo ◽  
Yang Zhao ◽  
Sheng Yang ◽  
Hui Zhang ◽  
Feng Chen
Keyword(s):  
Expression Patterns ◽  
Gene Families ◽  
Gene Clusters ◽  
Integrative Analysis ◽  
Biological Processes ◽  
Change Analysis ◽  
Functional Relationships ◽  
Collaborative Interactions ◽  
Or Gene ◽  
Fold Change Analysis

MicroRNAs (miRNAs) are small, noncoding regulatory molecules. They are involved in many essential biological processes and act by suppressing gene expression. The present work reports an integrative analysis of miRNA-mRNA and miRNA-miRNA interactions and their regulatory patterns using high-throughput miRNA and mRNA datasets. Aberrantly expressed miRNA and mRNA profiles were obtained based on fold change analysis, and qRT-PCR was used for further validation of deregulated miRNAs. miRNAs and target mRNAs were found to show various expression patterns. miRNA-miRNA interactions and clustered/homologous miRNAs were also found to contribute to the flexible and selective regulatory network. Interacting miRNAs (e.g., miRNA-103a and miR-103b) showed more pronounced differences in expression, which suggests the potential “restricted interaction” in the miRNA world. miRNAs from the same gene clusters (e.g., miR-23b gene cluster) or gene families (e.g., miR-10 gene family) always showed the same types of deregulation patterns, although they sometimes differed in expression levels. These clustered and homologous miRNAs may have close functional relationships, which may indicate collaborative interactions between miRNAs. The integrative analysis of miRNA-mRNA based on biological characteristics of miRNA will further enrich miRNA study.

scholarly journals Multi-organ transcriptomic landscape of Ambystoma velasci metamorphosis

2020 ◽  
Author(s):  
Palacios-Martínez Janet ◽  
Caballero-Pérez Juan ◽  
Espinal-Centeno Annie ◽  
Marquez-Chavoya Gilberto ◽  
Lomelí Hilda ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Developmental Process ◽  
Global Analysis ◽  
Expression Patterns ◽  
Coronary Vessels ◽  
Aquatic Organisms ◽  
Gene Clusters ◽  
Differentially Expressed ◽  
Transcriptional Responses ◽  
Terrestrial Environment

Metamorphosis is a postembryonic developmental process that involves morphophysiological and behavioral changes, allowing organisms to adapt into a novel environment. In some amphibians, aquatic organisms undergo metamorphosis to adapt in a terrestrial environment. These organisms experience major changes in their circulatory, respiratory, digestive, excretory and reproductive systems. We performed a transcriptional global analysis of heart, lung and gills during diverse stages of Ambystoma velasci metamorphosis. In our analyses, we identified eight gene clusters for each organ, according to the expression patterns of differentially expressed genes. We found 4,064 differentially expressed genes in the heart, 4,107 in the lung and 8,265 in the gills. Among the differentially expressed genes in the heart, we observed genes involved in the differentiation of cardiomyocytes in the interatrial zone, vasculogenesis and in the maturation of coronary vessels. In the lung, we found genes differentially expressed related to angiogenesis, alveolarization and synthesis of the surfactant protein. In the case of the gills, the most prominent biological processes identified are degradation of extracellular matrix, apoptosis and keratin production. Our study sheds light on the transcriptional responses and the pathways involved in the transformation of the facultative metamorphic salamander A. velasci in an organ-specific manner.

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