一株海杆菌的溶藻活性及基于基因组的溶藻机理分析

为了解新型海杆菌Marinobacter)菌株YWL01溶藻活性及其可能的溶藻机理YWL01与常见的赤潮藻中肋骨条藻Skeletonema costatum)混合培养, 通过肉眼、光电镜观察及藻叶绿素a浓度测定来评估溶藻活性采用Illumina Miseq测序技术测定YWL01基因组将预测基因的蛋白序列分别进行BLASTP比对注释信息分析其可能的溶藻机理结果表明YWL01可直接溶藻藻液颜色由黄褐色逐渐变淡藻细胞裂解藻叶绿素a浓度明显降 低YWL01基因组中许多与溶藻相关的基因     

Inhibitory Effects of Phenylacetic Acid on Proliferation of Human Pancreatic Carcinoma BXPC-3 Cells by the Regulation of Adenosine Deaminases Acting on RNA

The effect and mechanism of phenylacetic acid on the proliferation of pancreatic carcinoma cells were investigated in cultured pancreatic carcinoma BXPC-3 cells by means of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and flow cytometry assay.The results show that the treatment of pancreatic carcinoma cells with phenylacetic acid significantly inhibited the cell proliferation in time-dependent and dose-dependent manners.The proliferation of BXPC-3 cells was inhibited at the stage of S phase,the cells at the end stage of S phase were accumulated abundantly,and thus DNA synthesis could not be accomplished entirely.In addition,the expression of adenosine deaminases acting on RNA(ADARs) mRNA in BXPC-3 cells and pancreatic carcinoma specimen were detected by RT-PCR.Having been treated with phenylacetic acid,ADAR2 mRNA in BXPC-3 cells was significantly decreased,the differences were of statistical significance(P0.01).Taken together,these results suggest that phenylacetic acid may likely regulate the proliferation of pancreatic carcinoma cells through the regulation of ADAR2 mRNA expression.     

In vivo 1H NMR spectroscopy of individual human brain metabolites at moderate field strengths

This article reviews spectral editing techniques for in vivo ¹H NMR spectroscopy of human brain tissue at moderate field strengths of 1.5–3 Tesla. Various aspects of ¹H NMR spectroscopy are discussed with regard to in vivo applications. The parameter set [δ, J, n] (δ being the relative chemical shift, J the scalar coupling constant and n the number of coupled spins) is used to characterize the spin systems under investigation and to classify the editing techniques that are used in in vivo ¹H NMR spectroscopy.     

CRISPR‐Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering

The field of biology has been revolutionized by the recent advancement of an adaptive bacterial immune system as a universal genome engineering tool. Bacteria and archaea use repetitive genomic elements termed clustered regularly interspaced short palindromic repeats (CRISPR) in combination with an RNA‐guided nuclease (CRISPR‐associated nuclease: Cas) to target and destroy invading DNA. By choosing the appropriate sequence of the guide RNA, this two‐component system can be used to efficiently modify, target, and edit genomic loci of interest in plants, insects, fungi, mammalian cells, and whole organisms. This has opened up new frontiers in genome engineering, including the potential to treat or cure human genetic disorders. Now the potential risks as well as the ethical, social, and legal implications of this powerful new technique move into the limelight.     

Analysis of genome sequences for genes of cyanophycin metabolism: identifying putative cyanophycin metabolizing prokaryotes

CGP, a copolymer of aspartate and arginine, serves as a storage compound for nitrogen, carbon and energy in many cyanobacteria. Analysis of available genome sequences from prokaryotes identified ORFs putatively encoding proteins of high similarity to known cyanophycin synthetases and cyanophycinases from cyanobacteria in various strains of bacteria belonging to different phylogenetic taxa and not closely related to cyanobacteria. Genes of CGP metabolism occur in a wide range of bacteria exhibiting diverse metabolic capabilities, including aerobic and anaerobic respiration, fermentation, phototrophy and chemolithoautotrophy. This study identified different groups of cyanophycin synthetases and cyanophycinases, respectively, and proposes a collective terminology for the putative genes and enzymes of cyanophycin metabolism. Among 570 different microbial strains, whose genomes have been partially or completely sequenced and are publicly accessible, we identified 44 prokaryotes which possess a cyanophycin synthetase and are putatively able to synthesize CGP. From these, 31 prokaryotes harbor also a cyanophycinase enabling them to degrade CGP to dipeptides. From the latter, 24 strains possess in addition a dipeptidase necessary to hydrolyze beta-Asp-Arg dipeptides, thereby enabling them to completely utilize CGP. Therefore, CGP seems to have a much wider distribution among prokaryotes than previously recognized. Genes putatively encoding cyanophycin synthetase homologues were not identified in the genomes of Eukarya and Archaea and are therefore obviously only occurring in Eubacteria. In addition, the outcome of this detailed in silico analysis proposes to distinguish 10 different groups of cyanophycin synthetases.     

Prediction of sgRNA Off-Target Activity in CRISPR/Cas9 Gene Editing Using Graph Convolution Network

CRISPR/Cas9 is a powerful genome-editing technology that has been widely applied in targeted gene repair and gene expression regulation. One of the main challenges for the CRISPR/Cas9 system is the occurrence of unexpected cleavage at some sites (off-targets) and predicting them is necessary due to its relevance in gene editing research. Very few deep learning models have been developed so far to predict the off-target propensity of single guide RNA (sgRNA) at specific DNA fragments by using artificial feature extract operations and machine learning techniques; however, this is a convoluted process that is difficult to understand and implement for researchers. In this research work, we introduce a novel graph-based approach to predict off-target efficacy of sgRNA in the CRISPR/Cas9 system that is easy to understand and replicate for researchers. This is achieved by creating a graph with sequences as nodes and by using a link prediction method to predict the presence of links between sgRNA and off-target inducing target DNA sequences. Features for the sequences are extracted from within the sequences. We used HEK293 and K562 t datasets in our experiments. GCN predicted the off-target gene knockouts (using link prediction) by predicting the links between sgRNA and off-target sequences with an auROC value of 0.987.     

Antiparasitic Ovalicin Derivatives from Pseudallescheria boydii,a Mutualistic Fungus of French Guiana Termites

Social insects are in mutualism with microorganisms, contributing to their resistance against infectious diseases. The fungus Pseudallescheria boydii SNB-CN85 isolated from termites produces ovalicin derivatives resulting from the esterification of the less hindered site of the ovalicin epoxide by long-chain fatty acids. Their structures were elucidated using spectroscopic analysis and semisynthesis from ovalicin. For ovalicin, these compounds displayed antiprotozoal activities against Plasmodium falciparum and Trypanosoma brucei, with IC₅₀ values of 19.8 and 1.1 µM, respectively, for the most active compound, i.e., ovalicin linoleate. In parallel, metabolomic profiling of a collection of P. boydii strains associated with termites made it possible to highlight this class of compounds together with tyroscherin derivatives in all strains. Finally, the complete genome of P. boydii strains was obtained by sequencing, and the cluster of potential ovalicin and ovalicin biosynthesis genes was annotated. Through these metabolomic and genomic analyses, a new ovalicin derivative named boyden C, in which the 6-membered ring of ovalicin was opened by oxidative cleavage, was isolated and structurally characterized.     

Transporter Protein-Guided Genome Mining for Head-to-Tail Cyclized Bacteriocins

Head-to-tail cyclized bacteriocins are ribosomally synthesized antimicrobial peptides that are defined by peptide backbone cyclization involving the N- and C- terminal amino acids. Their cyclic nature and overall three-dimensional fold confer superior stability against extreme pH and temperature conditions, and protease degradation. Most of the characterized head-to-tail cyclized bacteriocins were discovered through a traditional approach that involved the screening of bacterial isolates for antimicrobial activity and subsequent isolation and characterization of the active molecule. In this study, we performed genome mining using transporter protein sequences associated with experimentally validated head-to-tail cyclized bacteriocins as driver sequences to search for novel bacteriocins. Biosynthetic gene cluster analysis was then performed to select the high probability functional gene clusters. A total of 387 producer strains that encode putative head-to-tail cyclized bacteriocins were identified. Sequence and phylogenetic analyses revealed that this class of bacteriocins is more diverse than previously thought. Furthermore, our genome mining strategy captured hits that were not identified in precursor-based bioprospecting, showcasing the utility of this approach to expanding the repertoire of head-to-tail cyclized bacteriocins. This work sets the stage for future isolation of novel head-to-tail cyclized bacteriocins to serve as possible alternatives to traditional antibiotics and potentially help address the increasing threat posed by resistant pathogens.     

Improvement of Spectral Editing in Solids: A Sequence for Obtaining CH + CH2-Only C Spectra

An improved spectral editing method for solids is described which allows one to obtain a set of subspectra in roughly two-thirds the amount of time as our original CPPI editing method for the same signal to noise. This improvement is afforded by a new pulse sequence that is used to acquire a ¹³CH + ¹³CH₂ spectrum which has very little ¹³CH₃ or nonprotonated carbon contamination. By using this new sequence the ¹³CH-only subspectrum is obtained much more efficiently. Criteria for optimizing the signal to noise in the edited subspectra are discussed.     

J Coupling between C and H across Hydrogen Bonds in Proteins

Two new two- or three-dimensional NMR methods for measuring ^3hJ_C′N and ^2hJ_C′H coupling constants across hydrogen bonds in proteins are presented. They are tailored to suit the size of the TROSY effect, i.e., the degree of interference between dipolar and chemical shift anisotropy relaxation mechanisms. The methods edit 2D or 3D spectra into two separate subspectra corresponding to the two possible spin states of the ¹H^N spin during evolution of ¹³CO coherences. This allows ^2hJ_C′H to be measured in an E.COSY-type way while ^3hJ_C′N can be measured in the so-called quantitative way provided a reference spectrum is also recorded. A demonstration of the new methods is shown for the ¹⁵N,¹³C-labeled protein chymotrypsin inhibitor 2.