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Gene construction

Si Li, Ruijie Zhang, Jingrun Hu, Wanzi Shi, Yuzhu Kuang, Xiaoyu Guo, Weiling Sun
Simultaneous elimination of antibiotics and antibiotic resistance genes (ARGs) is rarely investigated in full-scale riverine wetlands. Here, we compared the occurrence, abundance, and removal of 60 antibiotics and 27 ARGs in natural (Yeya Lake (YL)) and constructed (Bai River (BR)) riverine wetlands in Beijing, China. The concentrations of antibiotics in YL wetland were ND-51.9 ng/L in water and ND-37.9 ng/g in sediments. Significantly higher concentrations were found in BR wetland (ND-546 ng/L in water and ND-118 ng/g in sediments), which locates at the downstream of a reclaimed water treatment plant...
February 5, 2019: Science of the Total Environment
Bailong Tao, Yiman Deng, Liying Song, Wenwen Ma, Ying Qian, Chuanchuan Lin, Zhang Yuan, Lu Lu, Maowen Chen, Xin Yang, Kaiyong Cai
Bacterial infection and surface biointertness are two main causes for titanium (Ti)-based orthopedic implants failure. To improve the antibacterial ability and enhance poor osteogenic property of Ti substrates, in this work, we employed titania nanotubes (TNTs) as Bone Morphogenetic Protein 2 (BMP2) carrier, and a pH-responsive multilayer film composed of alginate dialdehyde-gentamicin (ADA-Gen) and chitosan (Chi) was constructed onto BMP2-loaded TNTs substrates through layer-by-layer (LBL) assembly technique, resulting in TNT-BMP2-LBLg samples...
February 7, 2019: Colloids and Surfaces. B, Biointerfaces
Saúl Jijón-Moreno, Beatriz Eugenia Baca, Diana Carolina Castro-Fernández, Alberto Ramírez-Mata
Azospirillum brasilense is one of the most studied species of diverse agronomic plants worldwide. The benefits conferred to plants inoculated with Azospirillum have been primarily attributed to its capacity to fix atmospheric nitrogen and synthesize phytohormones, especially indole-3-acetic acid (IAA). The principal pathway for IAA synthesis involves the intermediate metabolite indole pyruvic acid. Successful colonization of plants by Azospirillum species is fundamental to the ability of these bacteria to promote the beneficial effects observed in plants...
2019: PloS One
Mengyu Gao, Bingqi Zhang, Yuting He, Qing Yang, Lihong Deng, Yuqi Zhu, Enjiang Lai, Menghua Wang, Laduona Wang, Guang Yang, Guangneng Liao, Ji Bao, Hong Bu
The shortage of human hepatocytes continues to be a significant limitation for the widespread application of hepatocyte transplantation and bioartificial liver (BAL) support therapy. Recombinant activation gene 2 (Rag2) and fumarylacetoacetate hydrolase (Fah)-deficient mice could be highly repopulated with human hepatocytes. However, Fah/Rag2-deficient mice can only produce up to 1 × 108 human hepatocytes per mouse. We hypothesized that 2-10 × 1010 human hepatocytes can be produced per Fah/Rag2-deficient pig, which is an adequate supply for hepatocyte transplantation and BAL therapy...
February 14, 2019: DNA and Cell Biology
Yucheng Guo, Chen Bao, Dacheng Ma, Yubing Cao, Yanda Li, Zhen Xie, Shao Li
Tumorigenesis is a complex process that is driven by a combination of the networks of genes and environmental factors; however, efficient approaches for identifying functional networks that are perturbed by the process of tumorigenesis is poorly understood. Then, the identification of functional synergistic modules and pathways is often limited by computational method and experiment measures. Here, we propose an integrated network-based approach for the systematic discovery of functional synergistic modules that are causal determinants of inflammation-induced tumorigenesis, by prioritizing candidate genes of integrating clinical-based and network-based genome-wide gene prediction methods and identify functional synergistic modules based on combinatorial CRISPR-Cas9 screens...
February 14, 2019: ACS Synthetic Biology
Guillermo Anda-Jáuregui, Brett A McGregor, Kai Guo, Junguk Hur
Drug-induced peripheral neuropathy (DIPN) is a side effect of a variety of therapeutic agents, which can affect therapeutic adherence and lead to regimen modifications, impacting patient quality of life. The molecular mechanisms involved in the development of this condition have yet to be completely described in the literature. We used a computational network pharmacology approach to explore the Connectivity Map, a large collection of transcriptional profiles from drug perturbation experiments to identify common genes affected by peripheral neuropathy-inducing drugs (NID)...
February 14, 2019: CPT: Pharmacometrics & Systems Pharmacology
I-Chen Kimberly Chen, Brandon M Satinsky, Gregory J Velicer, Yuen-Tsu Nicco Yu
Small non-coding RNAs (sRNAs) control bacterial gene expression involved in a wide range of important cellular processes. In the highly social bacterium Myxococcus xanthus, the sRNA Pxr prevents multicellular fruiting-body development when nutrients are abundant. Pxr was discovered from the evolution of a developmentally defective strain (OC) into a developmentally proficient strain (PX). In OC, Pxr is constitutively expressed and blocks development even during starvation. In PX, one mutation deactivates Pxr allowing development to proceed...
February 14, 2019: Evolution & Development
Zhixin Wu, Zhongqiu Chen, Xinyue Gao, Jing Li, Guangdong Shang
Pseudomonas putida KT2440 is a Gram-negative, biosafety strain that plays important roles in environmental and biotechnological applications. Highly efficient genome editing strategy is essential to the elucidation of gene function and construction of metabolic engineered strains. Building on our previously established recombineering-mediated markerless and scarless P. putida KT2440 chromosomal gene deletion methods, herein we combined single-stranded DNA (ssDNA) recombineering and CRISPR-Cas9 technologies for P...
February 14, 2019: Applied Microbiology and Biotechnology
Yohei Nakayama, Ryoki Kobayashi, Yasunobu Iwai, Keisuke Noda, Mizuho Yamazaki, Tomoko Kurita-Ochiai, Atsutoshi Yoshimura, Bernhard Ganss, Yorimasa Ogata
Junctional epithelium (JE) develops from reduced enamel epithelium during tooth formation and is critical for the maintenance of healthy periodontal tissue through ensuring appropriate immune responses and the rapid turnover of gingival epithelial cells. We have previously shown a relationship between inflammatory cytokines and expression of JE-specific genes, such as amelotin (AMTN), in gingival epithelial cells. Here, we elucidated the effects of Porphyromonas gingivalis -derived lipopolysaccharide ( Pg LPS) on Amtn gene transcription and the interaction of transcription factors...
February 2019: FEBS Open Bio
Huifang Yu, Jiansheng Wang, Zhenqing Zhao, Xiaoguang Sheng, Yusen Shen, Ferdinando Branca, Honghui Gu
A high-quality genetic map is important for mapping of compound traits. In this study, a genetic map was constructed based on the reference genome TO1000 after specific locus amplified fragment (SLAF) sequencing in a double-haploid segregation population of broccoli, and loci controlling hollow stem trait were identified in the genetic map. The genetic map contains 4,787 SLAF markers, with a mean marker distance of 0.22 cM and the mean sequencing depths of 91.14-fold in the maternal line, 88.97-fold in the paternal line and 17...
2019: Frontiers in Plant Science
Kalyana Babu B, Mary Rani K L, Sarika Sahu, R K Mathur, Naveen Kumar P, Ravichandran G, Anitha P, Bhagya H P
The availability of large expressed sequence tag (EST) and whole genome databases of oil palm enabled the development of a data base of microsatellite markers. For this purpose, an EST database consisting of 40,979 EST sequences spanning 27 Mb and a chromosome-wise whole genome databases were downloaded. A total of 3,950 primer pairs were identified and developed from EST sequences. The tri and tetra nucleotide repeat motifs were most prevalent (each 24.75%) followed by di-nucleotide repeat motifs. Whole genome-wide analysis found a total of 245,654 SSR repeats across the 16 chromosomes of oil palm, of which 38,717 were compound microsatellite repeats...
February 13, 2019: Scientific Reports
Lauren Wensing, Jehoshua Sharma, Deeva Uthayakumar, Yannic Proteau, Alejandro Chavez, Rebecca S Shapiro
Fungal pathogens are emerging as an important cause of human disease, and Candida albicans is among the most common causative agents of fungal infections. Studying this fungal pathogen is of the utmost importance and necessitates the development of molecular technologies to perform comprehensive genetic and functional genomic analysis. Here, we designed and developed a novel clustered regularly interspaced short palindromic repeat interference (CRISPRi) system for targeted genetic repression in C. albicans We engineered a nuclease-dead Cas9 (dCas9) construct that, paired with a guide RNA targeted to the promoter of an endogenous gene, is capable of targeting that gene for transcriptional repression...
February 13, 2019: MSphere
Elvira Román, Ioana Coman, Daniel Prieto, Rebeca Alonso-Monge, Jesús Pla
Clustered regularly interspaced short palindromic repeat (CRISPR) methodology is not only an efficient tool in gene editing but also an attractive platform to facilitate DNA, RNA, and protein interactions. We describe here the implementation of a CRISPR-based system to regulate expression in the clinically important yeast Candida albicans By fusing an allele of Streptococcus pyogenes Cas9 devoid of nuclease activity to a transcriptional repressor (Nrg1) or activator (Gal4), we were able to show specific repression or activation of the tester gene CAT1 , encoding the cytosolic catalase...
February 13, 2019: MSphere
Anna Detman, Damian Mielecki, Aleksandra Chojnacka, Agnieszka Salamon, Mieczysław K Błaszczyk, Anna Sikora
BACKGROUND: Interactions between microorganisms during specific steps of anaerobic digestion determine metabolic pathways in bioreactors and consequently the efficiency of fermentation processes. This study focuses on conversion of lactate and acetate to butyrate by bacteria of dark fermentation. The recently recognized flavin-based electron bifurcation as a mode of energy coupling by anaerobes increases our knowledge of anaerobic lactate oxidation and butyrate formation. RESULTS: Microbial communities from dark fermentation bioreactors or pure culture of Clostridium butyricum are able to convert lactate and acetate to butyrate in batch experiments...
February 13, 2019: Microbial Cell Factories
Yongzhi Yang, Ying Li, Qiao Chen, Yongshuai Sun, Zhiqiang Lu
BACKGROUND: With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for detecting footprints of WGDs has been restricted to a well-assembled genome. However, the massive poor quality genomes and the more accessible transcriptomes have been largely ignored, and in theoretically they are also likely to contribute to detect WGD using dS based method...
February 13, 2019: BMC Bioinformatics
Hanhae Kim, Anna Joe, Muyoung Lee, Sunmo Yang, Xiaozhi Ma, Pamela C Ronald, Insuk Lee
Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonasvirulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryzepv. oryzae (Xoo) genes, XooNet (www...
February 1, 2019: Molecules and Cells
Juan Carlos Crespo-Rivas, Pilar Navarro-Gómez, Cynthia Alias-Villegas, Jie Shi, Tao Zhen, Yanbo Niu, Virginia Cuéllar, Javier Moreno, Teresa Cubo, José María Vinardell, José Enrique Ruiz-Sainz, Sebastián Acosta-Jurado, María José Soto
Members of Rhizobiaceae contain a homologue of the iron-responsive regulatory protein RirA. In different bacteria, RirA acts as a repressor of iron uptake systems under iron-replete conditions and contributes to ameliorate cell damage during oxidative stress. In Rhizobium leguminosarum and Sinorhizobium meliloti , mutations in rirA do not impair symbiotic nitrogen fixation. In this study, a rirA mutant of broad host range S. fredii HH103 has been constructed (SVQ780) and its free-living and symbiotic phenotypes evaluated...
February 12, 2019: International Journal of Molecular Sciences
Meng Wu, Min Si, Xieyu Li, Linyan Song, Jianlong Liu, Rui Zhai, Liu Cong, Rongrong Yue, Chengquan Yang, Fengwang Ma, Lingfei Xu, Zhigang Wang
The synthesis of anthocyanin in pear ( Pyrus bretschneideri ) fruit is regulated by light. However, little is known about the molecular mechanisms of pear fruit coloring mediated by upstream light-signaling regulators. Here, the photoresponse factors CONSTITUTIVE PHOTOMORPHOGENIC (COP) 1.1 and 1.2 were cloned from 'Red Zaosu' peel to study their functions in pear fruit coloring. The overexpression vectors pBI121-PbCOP1.1 and pBI121-PbCOP1.2 were constructed to analyze their effects on anthocyanin synthesis in pear fruit...
February 12, 2019: Plants (Basel, Switzerland)
Gaole An, Jiaqi Sun, Chao Ren, Zhangyi Ouyang, Lingyun Zhu, Xiaochen Bo, Shaoliang Peng, Wenjie Shu
Advances in studies of long noncoding RNAs (lncRNAs) have provided data regarding the regulatory roles of lncRNAs, which perform functional roles through interactions with other functional elements. To track the underlying relationships among lncRNAs, various databases have been developed as repositories for lncRNA data. However, the ability to comprehensively explore the diverse interactions between lncRNAs and other functional elements is limited. To this end, we developed LIVE (LncRNA Interaction Validated Encyclopaedia), an interactive resource to integrate the diverse interactions of functional elements with lncRNAs...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Jan M Klenk, Max-Philipp Fischer, Paulina Dubiel, Mahima Sharma, Benjamin Rowlinson, Gideon Grogan, Bernhard Hauer
Cytochrome P450 monooxygenases (P450s) play crucial roles in the cell metabolism and provide an unsurpassed diversity of catalyzed reactions. Here, we report the identification and biochemical characterization of two P450s from Arthrobacter sp., a gram-positive organism known to degrade the opium alkaloid papaverine. Combining phylogenetic and genomic analysis suggested physiological roles for P450s in metabolism, and revealed potential gene clusters with redox partners facilitating the reconstitution of the P450 activities in vitro...
February 13, 2019: Journal of Biochemistry
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