Strong matching preclusion

The matching preclusion problem, introduced by Brigham et al. [R.C. Brigham, F. Harary, E.C. Violin, and J. Yellen, Perfect-matching preclusion, Congressus Numerantium 174 (2005) 185-192], studies how to effectively make a graph have neither perfect matchings nor almost perfect matchings by deleting as small a number of edges as possible. Extending this concept, we consider a more general matching preclusion problem, called the strong matching preclusion, in which deletion of vertices is additionally permitted. We establish the strong matching preclusion number and all possible minimum strong matching preclusion sets for various classes of graphs.     

On codes defined by bio-operations

We consider the classes of ⊕$\oplus$-codes and ⊗$\otimes$-codes, which are superclasses of outfix and hyper-codes, respectively. These restrictions are based on the synchronized insertion operation, which serves as a model for the gene rearrangement function in certain unicellular organisms. We investigate the classes of ⊕$\oplus$-codes and ⊗$\otimes$-codes from a theoretical perspective, examine their relationships with traditional code classes and consider related decidability problems.     

Deletion, replacement and mean-shift for diagnostics in linear mixed models

Deletion, replacement and mean-shift model are three approaches frequently used to detect influential observations and outliers. For general linear model with known covariance matrix, it is known that these three approaches lead to the same update formulae for the estimates of the regression coefficients. However if the covariance matrix is indexed by some unknown parameters which also need to be estimated, the situation is unclear. In this paper, we show under a common subclass of linear mixed models that the three approaches are no longer equivalent. For maximum likelihood estimation, replacement is equivalent to mean-shift model but both are not equivalent to case deletion. For restricted maximum likelihood estimation, mean-shift model is equivalent to case deletion but both are not equivalent to replacement. We also demonstrate with real data that misuse of replacement and mean-shift model in place of case deletion can lead to incorrect results.     

A White Plaque,Associated with Genomic Deletion,Derived from M13KE-Based Peptide Library Is Enriched in a Target-Unrelated Manner during Phage Display Biopanning Due to Propagation Advantage

The nonspecific enrichment of target-unrelated peptides during biopanning remains a major drawback for phage display technology. The commercial Ph.D.^TM-7 phage display library is used extensively for peptide discovery. This library is based on the M13KE vector, which carries the lacZα sequence, leading to the formation of blue plaques on IPTG-X-gal agar plates. In the current study, we report the isolation of a fast-propagating white clone (displaying WSLGYTG peptide) identified through screening against a recombinant protein. Sanger sequencing demonstrated that white plaques are not contamination from environmental M13-like phages, but derive from the library itself. Whole genome sequencing revealed that the white color of the plaques results from a large 827-nucleotide genomic deletion. The phenotypic characterization of propagation capacity through plaque count- and NGS-based competitive propagation assay supported the higher propagation rate of Ph-WSLGYTG clone compared with the library. According to our data, white plaques are likely to arise endogenously in Ph.D. libraries due to mutations in the M13KE genome and should not always be viewed as exogenous contamination. Our findings also led to the conclusion that the deletion observed here might be an ancestral mutation already present in the naïve library, which causes target-unrelated nonspecific enrichment of white clone during biopanning due to propagation advantage.     

区域性赤峪断层落差及延展方向分析

为深入研究赤峪断层在紫晟煤业的落差及延展方向,减少构造损失煤量。通过地表踏勘查看断层出露情况,井下钻探探测断层延展位置,补充施工地质勘探钻孔对比岩层缺失层位,判明了区域性赤峪断层在紫晟煤业东南部呈现为4条密集分布的断层组,断层组在2-107工作面外围约115m,断层破碎带宽约220m,总落差190~325m,由西南至东北部总落差逐步减小。     

Identification and Allele Combination Analysis of Rice Grain Shape-Related Genes by Genome-Wide Association Study

Grain shape is an important agronomic character of rice, which affects the appearance, processing, and the edible quality. Screening and identifying more new genes associated with grain shape is beneficial to further understanding the genetic basis of grain shape and provides more gene resources for genetic breeding. This study has a natural population containing 623 indica rice cultivars. Genome-wide association studies/GWAS of several traits related to grain shape (grain length/GL, grain width/GW, grain length to width ratio/GLWR, grain circumferences/GC, and grain size/grain area/GS) were conducted by combining phenotypic data from four environments and the second-generation resequencing data, which have identified 39 important Quantitative trait locus/QTLs. We analyzed the 39 QTLs using three methods: gene-based association analysis, haplotype analysis, and functional annotation and identified three cloned genes (GS3, GW5, OsDER1) and seven new candidate genes in the candidate interval. At the same time, to effectively utilize the genes in the grain shape-related gene bank, we have also analyzed the allelic combinations of the three cloned genes. Finally, the extreme allele combination corresponding to each trait was found through statistical analysis. This study’s novel candidate genes and allele combinations will provide a valuable reference for future breeding work.     

猪繁殖与呼吸综合征弱毒疫苗的安全性及新型疫苗的研究进展

猪繁殖与呼吸综合征(Porcine reproductive and respiratory syndrome,PRRS)是影响养猪业的重大传染病,应用PRRS弱毒疫苗免疫是主要的预防措施。尽管各种PRRS弱毒疫苗已在我国使用,但PRRS仍持续流行,每年均有不同程度的暴发,且造成巨大的经济损失。最新研究提示,基因缺失疫苗能有效提升猪对PRRS的特异性免疫力。本文就PRRS弱毒疫苗在使用过程中可能存在的安全隐患及新型疫苗的研究进展作一综述。     

A two-step cloning-free PCR-based method for the deletion of genes in the opportunistic pathogenic yeast Candida lusitaniae

We describe a new cloning-free strategy to delete genes in the opportunistic pathogenic yeast Candida lusitaniae. We first constructed two ura3 Δ strains in C. lusitaniae for their use in transformation experiments. One was deleted for the entire URA3 coding sequence; the other possessed a partial deletion within the coding region, which was used to determine the minimum amount of homology required for efficient homologous recombination by double crossing-over of a linear DNA fragment restoring URA3 expression. This amount was estimated to 200 bp on each side of the DNA fragment. These data constituted the basis of the development of a strategy to construct DNA cassettes for gene deletion by a cloning-free overlapping PCR method. Two cassettes were necessary in two successive transformation steps for the complete removal of a gene of interest. As an example, we report here the deletion of the LEU2 gene. The first cassette was constituted by the URA3 gene flanked by two large fragments (500 bp) homologous to the 5' and 3' non-coding regions of LEU2. After transformation of an ura3 Δ recipient strain and integration of the cassette at the LEU2 locus, the URA3 gene was removed by a second transformation round with a DNA cassette made by the fusion between the 5' and 3' non-coding regions of the LEU2 gene. The overall procedure takes less than 2 weeks and allows the creation of a clean null mutant that retains no foreign DNA sequence integrated in its genome.     

Modulation of the antioxidant/pro-oxidant balance,cytotoxicity and antiviral actions of grape seed extracts

Grape seed extracts (GSEs) were investigated in yeast cells harbouring defects in their antioxidant system (regarding the cellular growth and growth recovery from H₂O₂ insult). GSEs antioxidant activity was detected in wild-type and mutant strains Δcta1, Δgsh1 and Δoye2glr1, while pro-oxidant activity in Δsod1 cells was seen. Assessment of proliferation of prostate cancer PC3 and HBV-replicating HepG2 2.2.15 cells treated with GSEs has shown higher cytotoxicity of red grape seed extract (RW) than white grape seed extract (WW) subjective to dose and period of administration. No antiviral effect was detected by measuring the secreted virion particles in HepG2 2.2.15 cells treated with GSEs. The GSEs play a dual antioxidant/pro-oxidant role in vivo according with the cellular antioxidant system deficiencies and exhibit cytotoxic properties in PC3 and HepG2 2.2.15 cell lines, but no antiviral action against HBV.     

Efficient PCR-based gene disruption in Saccharomyces strains using intergenic primers

Gene disruptions are a vital tool for understanding Saccharomyces cerevisiae gene function. An arrayed library of gene disruption strains has been produced by a consortium of yeast laboratories; however their use is limited to a single genetic background. Since the yeast research community works with several different strain backgrounds, disruption libraries in other common laboratory strains are desirable. We have developed simple PCR-based methods that allow transfer of gene disruptions from the S288C-derived strain library into any Saccharomyces strain. One method transfers the unique sequence tags that flank each of the disrupted genes and replaces the kanamycin resistance marker with a recyclable URA3 gene from Kluyveromyces lactis. All gene-specific PCR amplifications for this method are performed using a pre-existing set of primers that are commercially available. We have also extended this PCR technique to develop a second general gene disruption method suitable for any transformable strain of Saccharomyces.