sox gene
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Author(s):  
Linyi Zhang ◽  
Chen Song ◽  
Yaoyao Xu ◽  
Yajun Shi ◽  
Xiaoling Liu

Abstract A single strain capable of efficient S2−-oxidizing was isolated from a black-odor river in Beijing. The single strain was identified as Stenotrophomonas through the physiology and biochemical characteristics as well as the 16S rRNA sequencing experiment. This strain was named as Stenotrophomonas sp.sp3 (strain sp3). The experimental results showed that for the strain sp3 growth and S2− oxidization, the optimal conditions were as follows: 25 °C of temperature, initial pH 7, 2.5 g/L of initial glucose concentration and 1.00 g/L of initial cell concentration. It was found that there were 31 kinds of sulfur oxidation related genes in the strain sp3 through the whole genomic analysis. The results of the transcriptome analysis suggested that the main metabolic pathway of S2− to SO42− was the paracoccus sulfur oxidation process. The bioconversion processes of S2− to S0, S2− to SO32−, S2O32− to S0 and SO32−, and SO32− to SO42− were controlled by hdrA, cysIJ, tst and sox gene, respectively.


2021 ◽  
Vol 22 (21) ◽  
pp. 11321
Author(s):  
Ali Dehshahri ◽  
Alessio Biagioni ◽  
Hadi Bayat ◽  
E Hui Clarissa Lee ◽  
Mohammad Hashemabadi ◽  
...  

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its associated proteins (Cas) is an adaptive immune system in archaea and most bacteria. By repurposing these systems for use in eukaryote cells, a substantial revolution has arisen in the genome engineering field. In recent years, CRISPR-Cas technology was rapidly developed and different types of DNA or RNA sequence editors, gene activator or repressor, and epigenome modulators established. The versatility and feasibility of CRISPR-Cas technology has introduced this system as the most suitable tool for discovering and studying the mechanism of specific genes and also for generating appropriate cell and animal models. SOX genes play crucial roles in development processes and stemness. To elucidate the exact roles of SOX factors and their partners in tissue hemostasis and cell regeneration, generating appropriate in vitro and in vivo models is crucial. In line with these premises, CRISPR-Cas technology is a promising tool for studying different family members of SOX transcription factors. In this review, we aim to highlight the importance of CRISPR-Cas and summarize the applications of this novel, promising technology in studying and decoding the function of different members of the SOX gene family.


2021 ◽  
Author(s):  
Leslie S Babonis ◽  
Camille Enjolras ◽  
Abigail J Reft ◽  
Brent M Foster ◽  
Fredrik Hugosson ◽  
...  

Cnidocytes are the explosive stinging cells found only in cnidarians (corals, jellyfish, etc). Specialized for prey capture and defense, cnidocytes are morphologically complex and vary widely in form and function across taxa; how such diversity evolved is unknown. Using CRISPR/Cas9-mediated genome editing in the burrowing sea anemone Nematostella vectensis, we show that a single transcription factor (NvSox2) acts as a binary switch between two alternative cnidocyte fates. Knockout of NvSox2 caused a complete transformation of nematocytes (piercing cells) into spirocytes (ensnaring cells). The type of spirocyte induced by NvSox2 knockout (robust spirocyte) is not normally found in N. vectensis but is common in sea anemones from other habitats. Homeotic control of cell fate provides a mechanistic explanation for the discontinuous distribution of cnidocyte types across cnidarians and demonstrates how simple counts of cell types can underestimate biodiversity.


2021 ◽  
Vol 11 (8) ◽  
pp. 823
Author(s):  
Jaekwon Seok ◽  
Minchan Gil ◽  
Ahmed Abdal Dayem ◽  
Subbroto Kumar Saha ◽  
Ssang-Goo Cho

The Sry-related HMG BOX (SOX) gene family encodes transcription factors containing highly conserved high-mobility group domains that bind to the minor groove in DNA. Although some SOX genes are known to be associated with tumorigenesis and cancer progression, their expression and prognostic value have not been systematically studied. We performed multi-omic analysis to investigate the expression of SOX genes in human cancers. Expression and phylogenetic tree analyses of the SOX gene family revealed that the expression of three closely related SOX members, SOX4, SOX11, and SOX12, was increased in multiple cancers. Expression, mutation, and alteration of the three SOX members were evaluated using the Oncomine and cBioPortal databases, and the correlation between these genes and clinical outcomes in various cancers was examined using the Kaplan–Meier, PrognoScan, and R2 database analyses. The genes commonly correlated with the three SOX members were categorized in key pathways related to the cell cycle, mitosis, immune system, and cancer progression in liver cancer and sarcoma. Additionally, functional protein partners with three SOX proteins and their probable signaling pathways were explored using the STRING database. This study suggests the prognostic value of the expression of three SOX genes and their associated pathways in various human cancers.


2021 ◽  
pp. e00607
Author(s):  
Imran Zafar ◽  
Rida Iftikhar ◽  
Syed Umair Ahmad ◽  
Jitendra Kumar Sundaray ◽  
Mohd Ashraf Rather

2020 ◽  
Vol 11 ◽  
Author(s):  
Xu Huang ◽  
Chang Wu ◽  
Kaijun Gong ◽  
Qian Chen ◽  
Qianhong Gu ◽  
...  

2020 ◽  
Vol 36 ◽  
pp. 119112
Author(s):  
Jianbo Zheng ◽  
Yongyi Jia ◽  
Shili Liu ◽  
Meili Chi ◽  
Shun Cheng ◽  
...  

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