Integrated mRNA, MicroRNA Transcriptome and Degradome Analyses Provide Insights into Stamen Development in Moso Bamboo

2019 ◽  
Vol 61 (1) ◽  
pp. 76-87 ◽  
Author(s):  
Zhanchao Cheng ◽  
Dan Hou ◽  
Wei Ge ◽  
Xiangyu Li ◽  
Lihua Xie ◽  
...  
Keyword(s):  
Small Rna ◽  
Moso Bamboo ◽  
Molecular Networks ◽  
Anther Dehiscence ◽  
Floral Organs ◽  
Stamen Development ◽  
Secondary Thickening ◽  
Expression Of Genes ◽  
Section Result

Abstract A flower is an essential organ for sexual reproduction in flowering plants, which has been extensively studied in model plants. In this study, we used transcriptomic, small RNA and degradome analyses to characterize key microRNAs (miRNAs) and their targets in floral organs of moso bamboo. In total, we identified 13,051 differentially expressed genes and 109 known miRNAs from 26 miRNA families. We aligned the miRNAs to known miRNA databases and revealed some conserved as well as novel miRNAs. Sixteen conserved miRNAs were specifically and highly expressed in stamens, including miRNA159 and miRNA166. In situ hybridization shows that miRNA159 plays a key role in the regulation of stamen development, and the expression levels of its targets PheMYB98 and PheMYB42 were low. Furthermore, Phe-MIRNA159 partially recovers phenotypes of mir159ab double mutant. Overexpression of Phe-MIR159 could cause failure in anther dehisce, and the mature pollens could not be dispersed and further reduce fertility in Arabidopsis. Semi-thin section result shows that anther endothelial layer of Phe-MIRNA159 overexpressing lines is lack of secondary thickening, resulting in limited force for anther opening. Phe-miR159 may regulate the expression of genes related to secondary thickening through negative regulation of AtMYB33, affecting the anther dehiscence. Taken together, this study provides insights regarding molecular networks underlying floral organs development of moso bamboo.

Herpesvirus-Associated Proliferative Skin Disease in Frogs and Toads: Proposed Pathogenesis

2021 ◽  
pp. 030098582110063
Author(s):  
Francesco C. Origgi ◽  
Patricia Otten ◽  
Petra Lohmann ◽  
Ursula Sattler ◽  
Thomas Wahli ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Rana Temporaria ◽  
Skin Lesions ◽  
Bufo Bufo ◽  
Careful Examination ◽  
Altered Expression ◽  
Expression Of Genes ◽  
Cell Remodeling ◽  
Tissue Changes

A comparative study was carried out on common and agile frogs ( Rana temporaria and R. dalmatina) naturally infected with ranid herpesvirus 3 (RaHV3) and common toads ( Bufo bufo) naturally infected with bufonid herpesvirus 1 (BfHV1) to investigate common pathogenetic pathways and molecular mechanisms based on macroscopic, microscopic, and ultrastructural pathology as well as evaluation of gene expression. Careful examination of the tissue changes, supported by in situ hybridization, at different stages of development in 6 frogs and 14 toads revealed that the skin lesions are likely transient, and part of a tissue cycle necessary for viral replication in the infected hosts. Transcriptomic analysis, carried out on 2 naturally infected and 2 naïve common frogs ( Rana temporaria) and 2 naturally infected and 2 naïve common toads ( Bufo bufo), revealed altered expression of genes involved in signaling and cell remodeling in diseased animals. Finally, virus transcriptomics revealed that both RaHV3 and BfHV1 had relatively high expression of a putative immunomodulating gene predicted to encode a decoy receptor for tumor necrosis factor in the skin of the infected hosts. Thus, the comparable lesions in infected frogs and toads appear to reflect a concerted epidermal and viral cycle, with presumptive involvement of signaling and gene remodeling host and immunomodulatory viral genes.

scholarly journals BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2748 ◽  
Author(s):  
Andrea Komljenovic ◽  
Julien Roux ◽  
Marc Robinson-Rechavi ◽  
Frederic B. Bastian
Keyword(s):  
Gene Expression ◽  
Gene List ◽  
R Package ◽  
Rna Seq ◽  
Anatomical Structures ◽  
Enrichment Test ◽  
Expression Of Genes ◽  
Affymetrix Microarrays ◽  
New Gene

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover, BgeeDB includes a new gene set enrichment test for preferred localization of expression of genes in anatomical structures (“TopAnat”). Along with the classical Gene Ontology enrichment test, this test provides a complementary way to interpret gene lists. Availability: http://www.bioconductor.org/packages/BgeeDB/

scholarly journals Arrdc2 and Arrdc3 elicit divergent changes in gene expression in skeletal muscle following anabolic and catabolic stimuli

2019 ◽  
Vol 51 (6) ◽  
pp. 208-217 ◽  
Author(s):  
Bradley S. Gordon ◽  
Michael L. Rossetti ◽  
Alexey M. Eroshkin
Keyword(s):  
Skeletal Muscle ◽  
Muscle Mass ◽  
Tibialis Anterior ◽  
Gene Networks ◽  
Tibialis Anterior Muscle ◽  
The Body ◽  
Molecular Networks ◽  
Expression Of Genes ◽  
Consistent Change ◽  
Mechanical Overload

Skeletal muscle is a highly plastic organ regulating various processes in the body. As such, loss of skeletal muscle underlies the increased morbidity and mortality risk that is associated with numerous conditions. However, no therapies are available to combat the loss of muscle mass during atrophic conditions, which is due in part to the incomplete understanding of the molecular networks altered by anabolic and catabolic stimuli. Thus, the current objective was to identify novel gene networks modulated by such stimuli. For this, total RNA from the tibialis anterior muscle of mice that were fasted overnight or fasted overnight and refed the next morning was subjected to microarray analysis. The refeeding stimulus altered the expression of genes associated with signal transduction. Specifically, expression of alpha arrestin domain containing 2 (Arrdc2) and alpha arrestin domain containing 3 (Arrdc3) was significantly lowered 70–85% by refeeding. Subsequent analysis showed that expression of these genes was also lowered 50–75% by mechanical overload, with the combination of nutrients and mechanical overload acting synergistically to lower Arrdc2 and Arrdc3 expression. On the converse, stimuli that suppress growth such as testosterone depletion or acute aerobic exercise increased Arrdc2 and Arrdc3 expression in skeletal muscle. While Arrdc2 and Arrdc3 exhibited divergent changes in expression following anabolic or catabolic stimuli, no other member of the Arrdc family of genes exhibited the consistent change in expression across the analyzed conditions. Thus, Arrdc2 and Arrdc3 are a novel set of genes that may be implicated in the regulation of skeletal muscle mass.

scholarly journals Small RNA Profile in Moso Bamboo Root and Leaf Obtained by High Definition Adapters

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e103590 ◽  
Author(s):  
Ping Xu ◽  
Irina Mohorianu ◽  
Li Yang ◽  
Hansheng Zhao ◽  
Zhimin Gao ◽  
...  
Keyword(s):  
Small Rna ◽  
Moso Bamboo ◽  
High Definition

scholarly journals Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Lulu Wang ◽  
Yi Li ◽  
Xingyue Jin ◽  
Liping Liu ◽  
Xiaozhuan Dai ◽  
...  
Keyword(s):  
Fruit Development ◽  
Gene Networks ◽  
Floral Organ ◽  
Reproductive Organ ◽  
Molecular Networks ◽  
Organ Growth ◽  
Petal Development ◽  
Genomic Resource

AbstractProper flower development is essential for sexual reproductive success and the setting of fruits and seeds. The availability of a high quality genome sequence for pineapple makes it an excellent model for studying fruit and floral organ development. In this study, we sequenced 27 different pineapple floral samples and integrated nine published RNA-seq datasets to generate tissue- and stage-specific transcriptomic profiles. Pairwise comparisons and weighted gene co-expression network analysis successfully identified ovule-, stamen-, petal- and fruit-specific modules as well as hub genes involved in ovule, fruit and petal development. In situ hybridization confirmed the enriched expression of six genes in developing ovules and stamens. Mutant characterization and complementation analysis revealed the important role of the subtilase gene AcSBT1.8 in petal development. This work provides an important genomic resource for functional analysis of pineapple floral organ growth and fruit development and sheds light on molecular networks underlying pineapple reproductive organ growth.

scholarly journals In Situ Detection of Mycobacterium tuberculosis Transcripts in Human Lung Granulomas Reveals Differential Gene Expression in Necrotic Lesions

2002 ◽  
Vol 70 (11) ◽  
pp. 6330-6338 ◽  
Author(s):  
Gael Fenhalls ◽  
Liesel Stevens ◽  
Lorraine Moses ◽  
Juanita Bezuidenhout ◽  
Joanna C. Betts ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mycobacterium Tuberculosis ◽  
Transition Zone ◽  
Expression Of Genes ◽  
Metabolic States ◽  
Necrotic Region ◽  
Rna In Situ Hybridization ◽  
In Situ Detection

ABSTRACT We have used RNA-RNA in situ hybridization to detect the expression of several Mycobacterium tuberculosis genes in tuberculous granulomas in lung tissue sections from tuberculosis patients. The M. tuberculosis genes chosen fall into two classes. Four genes (icl, narX, and Rv2557 and Rv2558) have been implicated in the persistence of the bacterium in the host, and two genes (iniB and kasA) are upregulated in response to isoniazid exposure. Both necrotic and nonnecrotic granulomas were identified in all of the patients. Necrotic granulomas were divided into three zones: an outer lymphocyte cuff containing lymphocytes and macrophages, a transition zone consisting of necrotic material interspersed with macrophages, and a central acellular necrotic region. Transcripts of all of the genes studied were found in nonnecrotic granulomas and in the lymphocyte cuff of necrotic granulomas. Mycobacterial gene expression was associated with CD68-positive myeloid cells. Rv2557 and/or its homologue Rv2558, kasA, and iniB were expressed within the transition zone of necrotic granulomas, whereas icl and narX transcripts were absent from this area. There was no evidence of transcription of any of the genes examined in the central necrotic region, although mycobacterial DNA was present. The differential expression of genes within granulomas demonstrates that M. tuberculosis exists in a variety of metabolic states and may be indicative of the response to different microenvironments. These observations confirm that genes identified in models of persistence or in response to drug treatment in vitro are expressed in the human host.

scholarly journals Comparing the Expression of Genes Related to Serotonin (5-HT) in C57BL/6J Mice and Humans Based on Data Available at the Allen Mouse Brain Atlas and Allen Human Brain Atlas

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
C. A. Acevedo-Triana ◽  
L. A. León ◽  
F. P. Cardenas
Keyword(s):  
Human Brain ◽  
Mouse Brain ◽  
Expression Patterns ◽  
Brain Atlas ◽  
Expression Data ◽  
Expression Of Genes ◽  
High Degree ◽  
The Relationship ◽  
Allen Mouse Brain Atlas

Brain atlases are tools based on comprehensive studies used to locate biological characteristics (structures, connections, proteins, and gene expression) in different regions of the brain. These atlases have been disseminated to the point where tools have been created to store, manage, and share the information they contain. This study used the data published by the Allen Mouse Brain Atlas (2004) for mice (C57BL/6J) and Allen Human Brain Atlas (2010) for humans (6 donors) to compare the expression of serotonin-related genes. Genes of interest were searched for manually in each case (in situ hybridization for mice and microarrays for humans), normalized expression data (z-scores) were extracted, and the results were graphed. Despite the differences in methodology, quantification, and subjects used in the process, a high degree of similarity was found between expression data. Here we compare expression in a way that allows the use of translational research methods to infer and validate knowledge. This type of study allows part of the relationship between structures and functions to be identified, by examining expression patterns and comparing levels of expression in different states, anatomical correlations, and phenotypes between different species. The study concludes by discussing the importance of knowing, managing, and disseminating comprehensive, open-access studies in neuroscience.

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