scholarly journals Genetic Introgression Between Different Groups Reveals the Differential Process of Asian cultivated Rice

2021 ◽  
Author(s):  
Hao Gong ◽  
Bin Han
Keyword(s):  
Genetic Introgression ◽  
Biological Functions ◽  
Rice Gene ◽  
Cultivated Rice ◽  
Genome Wide ◽  
Variation Data ◽  
Domestication Process ◽  
Genome Level ◽  
Differential Process

Abstract Genetic introgression plays an important role in the domestication of crops. The Asian cultivate rice consists of two major subspecies, they are indica and japonica. There are already many reports about existence of genetic introgression between the two subspecies. However, those studies often use few limited markers to characterize the genetic introgression that exists in some specific small populations. In this study we use the genome wide variation data of Asia cultivated rice to investigate their genetic introgression on the whole genome level. We detect a total of 13 significantly high introgression loci between the tropical japonica and indica population. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions they generally get consistent results. Some previous known introgression genes are detected in the identified introgression loci, such as heat resistance gene TT1 and GLW7. The biological functions for these genetic introgression regions are annotated by the published QTL mapping results. We find that genetic introgression plays an important role in both the determination of the phenotype and the domestication process of different groups. Our study also provides useful information and resources for the study of rice gene function and domestication process.

Methods for the Determination of the Purity of Exosomes

2020 ◽  
Vol 25 (42) ◽  
pp. 4464-4485 ◽  
Author(s):  
Katarzyna Kluszczyńska ◽  
Liliana Czernek ◽  
Wojciech Cypryk ◽  
Łukasz Pęczek ◽  
Markus Düchler
Keyword(s):  
Drug Transport ◽  
Biological Fluids ◽  
Drug Carriers ◽  
Biological Functions ◽  
Isolation And Purification ◽  
Pubmed Database ◽  
High Concentrations ◽  
Targeted Release

Background: Exosomes open exciting new opportunities for advanced drug transport and targeted release. Furthermore, exosomes may be used for vaccination, immunosuppression or wound healing. To fully utilize their potential as drug carriers or immune-modulatory agents, the optimal purity of exosome preparations is of crucial importance. Methods: Articles describing the isolation and purification of exosomes were retrieved from the PubMed database. Results: Exosomes are often separated from biological fluids containing high concentrations of proteins, lipids and other molecules that keep vesicle purification challenging. A great number of purification protocols have been published, however, their outcome is difficult to compare because the assessment of purity has not been standardized. In this review, we first give an overview of the generation and composition of exosomes, as well as their multifaceted biological functions that stimulated various medical applications. Finally, we describe various methods that have been used to purify small vesicles and to assess the purity of exosome preparations and critically compare the quality of these evaluation protocols. Conclusion: Combinations of various techniques have to be applied to reach the required purity and quality control of exosome preparations.

Genome-wide investigation on transcriptional responses to drought stress in wild and cultivated rice

2021 ◽  
pp. 104555
Author(s):  
Mu-Fan Geng ◽  
Xiu-Hua Wang ◽  
Mei-Xia Wang ◽  
Zhe Cai ◽  
Qing-Lin Meng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Cultivated Rice ◽  
Transcriptional Responses ◽  
Genome Wide

scholarly journals Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

2021 ◽  
Author(s):  
Zhen Tian ◽  
Xiaodong Qin ◽  
Hui Wang ◽  
Ji Li ◽  
Jinfeng Chen
Keyword(s):  
Floral Induction ◽  
Structural Characteristics ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Biological Functions ◽  
Promoter Regions ◽  
Cucumis Sativus L ◽  
Cis Acting ◽  
Genome Wide ◽  
Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

scholarly journals Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0171088 ◽  
Author(s):  
George Msalya ◽  
Eui-Soo Kim ◽  
Emmanuel L. K. Laisser ◽  
Maulilio J. Kipanyula ◽  
Esron D. Karimuribo ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genome Wide ◽  
Signatures Of Selection ◽  
Friesian Cattle

scholarly journals Regulation of Recombination betweengtfB/gtfCGenes inStreptococcus mutansby Recombinase A

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Satoko Inagaki ◽  
Kazuyo Fujita ◽  
Yukiko Takashima ◽  
Kayoko Nagayama ◽  
Arifah C. Ardin ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Streptococcus Mutans ◽  
Reca Protein ◽  
Cellular Adhesion ◽  
Colony Morphology ◽  
Biological Functions ◽  
Clinical Strains ◽  
Cooperative Action

Streptococcus mutansproduces 3 types of glucosyltransferases (GTFs), whose cooperative action is essential for cellular adhesion. The recombinase A (RecA) protein is required for homologous recombination. In our previous study, we isolated several strains with a smooth colony morphology and low GTF activity, characteristics speculated to be derived from the GTF fusions. The purpose of the present study was to investigate the mechanism of those fusions.S. mutansstrain MT8148 was grown in the presence of recombinant RecA (rRecA) protein, after which smooth colonies were isolated. The biological functions and sequences of thegtfBandgtfCgenes of this as well as other clinical strains were determined. The sucrose-dependent adherence rates of those strains were reduced as compared to that of MT8148. Determination of the sequences of thegtfBandgtfCgenes showed that an approximately 3500 bp region was deleted from the area between them. Furthermore, expression of therecAgene was elevated in those strains as compared to MT8148. These results suggest that RecA has an important role in fusions ofgtfBandgtfCgenes, leading to alteration of colony morphology and reduction in sucrose-dependent adhesion.

scholarly journals Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12617
Author(s):  
Yarui Wei ◽  
Shuliang Zhao ◽  
Na Liu ◽  
Yuxing Zhang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Systemic Acquired Resistance ◽  
Acquired Resistance ◽  
Signal Transduction Pathway ◽  
Promoter Regions ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Genome Level

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

scholarly journals Protocol for examining and eliminating base editor-induced genome-wide and transcriptome-wide off-target mutations

2021 ◽  
Author(s):  
Lijie Wang ◽  
Wei Xue ◽  
Hongxia Zhang ◽  
Runze Gao ◽  
Houyuan Qiu ◽  
...  
Keyword(s):  
Clinical Applications ◽  
Cytidine Deaminases ◽  
Base Editing ◽  
Plasmid Construction ◽  
Background Levels ◽  
Genome Wide ◽  
Deoxycytidine Deaminase

Abstract Fusion of CRISPR-Cas9 with cytidine deaminases leads to base editors (BEs) for programmable C-to-T editing, which holds potentials in clinical applications but suffers from off-target (OT) mutations. Here, we applied a cleavable deoxycytidine deaminase inhibitor (dCDI) domain to construct a transformer BE (tBE) system that induces efficient editing with only background levels of genome-wide and transcriptome-wide OT mutations. This step-by-step protocol describes the plasmid construction of tBE system, determination of genome/transcriptome-wide OT mutations and tBE-mediated base editing in vivo.

scholarly journals Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

2019 ◽  
Author(s):  
Yongbin Wang ◽  
Zhenfeng Jiang ◽  
Zhenxiang Li ◽  
Yuanling Zhao ◽  
Weiwei Tan ◽  
...  
Keyword(s):  
Glycine Max ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Biological Functions ◽  
Conserved Domain ◽  
Genome Wide ◽  
Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

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