FASTA barcodes: a simple method for the identification of yeast ORF deletions

A consortium of yeast geneticists have created -6000 individual ORF deletions, representing > 96% of the currently verified or predicted ORFs in S. cerevisiae. Importantly, molecular barcodes (each a unique 20 bp sequence termed either Uptag or Downtag) were used as identifiers for every ORF deletion. Microarray analyses of pooled yeast deletions has been used to identify thousands of genes involved in general fitness, haploinsufficiency, drug resistance and DNA damage repair. However, application of this powerful technology requires considerable expense, expertise and specialized equipment. While standard PCR techniques and specifically designed PCR primers can be used to confirm that a given ORF is in fact deleted, this procedure cannot be used to identify unknown deletions. In theory, every ORF deletion could be determined by barcode sequencing. However, neither a consolidated barcode database nor a reliable search engine is currently available for this purpose. To address this need, we have adapted a FASTA sequence program that utilizes the unique barcode database to allow users to identify individual ORF deletions, based upon simple sequencing reactions of PCR amplifications of either Uptag or Downtag barcodes. In silico and practical testing of this application reveals that it is an inexpensive, reliable and reproducible method for rapidly identifying unknown deletions. This approach allows laboratories to conduct small- or large-scale genetic screens with pooled yeast deletion strains and identify or verify any ORF deletion without the need for microarray technology.     

基于区块链的云数据匿名确定性删除方法

现有确定性删除方案忽略了用户数据与用户身份的关联性,使用户的删除行为暴露给攻击者或云服务提供商。为解决此问题,提出一种基于区块链的云数据匿名确定性删除方法。该方法改进了可链接环签名方案,使用户可以通过控制签名中的链接标记在匿名情况下实现确定性删除;同时,它利用区块链记录删除行为,使其具有不可抵赖性。理论分析和实验表明:该方法不仅能满足用户数据的确定性删除要求,而且具有匿名性可以切断用户数据与其身份的关联,从而有效避免攻击者或云服务提供商对用户行为的追踪分析。     

基于视频修复的运动目标删除篡改行为的检测算法

将运动对象从视频中删除是视频篡改的一种常见 形式,针对删除视频运动对象这一篡改操作, 提出了基于视频修复痕迹的检测方法。运动对象删除后需采用数字视频修复技术填补由于移 除操作产生的 黑洞,使得篡改后的视频遗留有修复痕迹;通过深入分析篡改视频中遗留的修复痕迹,对篡 改后未压缩视 频采用对称帧差法检测运动对象删除区域;对压缩后的篡改视频从运动光流场的角度,由视 频帧光流方向 的不一致性进行检测。实验结果表明,本文方法不依赖于原始视频,计算复杂度低,能够有 效检测运动对象删除操作,并在空时域上对篡改区域进行定位。     

TP53 in Acute Myeloid Leukemia: Molecular Aspects and Patterns of Mutation

Mutation of the tumor suppressor gene, TP53, is associated with abysmal survival outcomes in acute myeloid leukemia (AML). Although it is the most commonly mutated gene in cancer, its occurrence is observed in only 5–10% of de novo AML, and in 30% of therapy related AML (t-AML). TP53 mutation serves as a prognostic marker of poor response to standard-of-care chemotherapy, particularly in t-AML and AML with complex cytogenetics. In light of a poor response to traditional chemotherapy and only a modest improvement in outcome with hypomethylation-based interventions, allogenic stem cell transplant is routinely recommended in these cases, albeit with a response that is often short lived. Despite being frequently mutated across the cancer spectrum, progress and enthusiasm for the development of p53 targeted therapeutic interventions is lacking and to date there is no approved drug that mitigates the effects of TP53 mutation. There is a mounting body of evidence indicating that p53 mutants differ in functionality and form from typical AML cases and subsequently display inconsistent responses to therapy at the cellular level. Understanding this pathobiological activity is imperative to the development of effective therapeutic strategies. This review aims to provide a comprehensive understanding of the effects of TP53 on the hematopoietic system, to describe its varying degree of functionality in tumor suppression, and to illustrate the need for the adoption of personalized therapeutic strategies to target distinct classes of the p53 mutation in AML management.     

Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae

An important recent advance in the functional analysis of Saccharomyces cerevisiae genes is the development of the one-step PCR-mediated technique for deletion and modification of chromosomal genes. This method allows very rapid gene manipulations without requiring plasmid clones of the gene of interest. We describe here a new set of plasmids that serve as templates for the PCR synthesis of fragments that allow a variety of gene modifications. Using as selectable marker the S. cerevisiae TRP1 gene or modules containing the heterologous Schizosaccharomyces pombe his5⁺ or Escherichia coli kan^r gene, these plasmids allow gene deletion, gene overexpression (using the regulatable GAL1 promoter), C- or N-terminal protein tagging [with GFP(S65T), GST, or the 3HA or 13Myc epitope], and partial N- or C-terminal deletions (with or without concomitant protein tagging). Because of the modular nature of the plasmids, they allow efficient and economical use of a small number of PCR primers for a wide variety of gene manipulations. Thus, these plasmids should further facilitate the rapid analysis of gene function in S. cerevisiae. © 1998 John Wiley & Sons, Ltd.     

Disruption of six Saccharomyces cerevisiae genes from chromosome IV and basic phenotypic analysis of deletion mutants

We report here the construction of six deletion mutants and the analysis of their basic phenotype. Deletion cassettes containing the KanMX4 marker module and long flanking regions homologous to the target locus were constructed for each of the six open reading-frames (ORFs YDL088c, YDL087c, YDL086w, YDL085w, YDL084w and YDL082w) located on chromosome IV. Sporulation and tetrad analysis of heterozygous deletant strains revealed that, in the FY1679 genetic background, ORFs YDL088c, YDL087c and YDL084w are essential genes for vegetative growth whereas YDL086w, YDL085w and YDL082w are non-essential. ydl088cΔ and ydl084wΔ haploid strains are viable in the CEN. PK2 genetic background although ydl084wΔ grows at a slower rate than the wild type. Complementation tests by corresponding cognate genes confirmed that gene inactivation was responsible for these growth defects. © 1998 John Wiley & Sons, Ltd.     

The ALD6 gene of Saccharomyces cerevisiae encodes a cytosolic,Mg2+-activated acetaldehyde dehydrogenase

The deduced translation product of an open reading frame on the left arm of chromosome XVI of Saccharomyces cerevisiae, with the systematic name of YPL061w, is 500 amino acids in length and shares significant homology with aldehyde dehydrogenases. Amino acids 2 to 16 of the protein encoded by YPL061w were found to be identical to the N-terminal 15 amino acids of the purified cytosolic, Mg²⁺-activated acetaldehyde dehydrogenase (ACDH) of S. cerevisiae. This enzyme is thought to be involved in the production of acetate from which cytosolic acetyl-CoA is then synthesized. Deletion of YPL061w was detrimental to the growth of haploid strains of yeast; an analysis of one deletion mutant revealed a maximum specific growth rate (in complex medium containing glucose) of one-third of that displayed by the wild-type strain. Mutants deleted in YPL061w were also unable to use ethanol as a carbon source. As expected, the cytosolic, Mg²⁺-activated ACDH activity had been lost from the mutants, although the mitochondrial, K⁺-activated ACDH was readily detected. YPL061w has been registered with the name of ALD6 in the Saccharomyces Genome Database and the nucleotide sequence submitted to GenBank as part of accession number U39205. © 1997 John Wiley & Sons, Ltd.     

Construction of self‐organizing algorithms for vector quantization

Vector quantization is used for both storage and transmission of speech and image data, and an algorithm that minimizes the distortion error is often required. To obtain the minimum distortion error in neural networks for vector quantization, corrective competitive learning has been introduced. In a large number of algorithms, self‐creating neural networks and self‐deleting neural networks have performed well. In this paper, we improve the self‐deleting neural network and propose a generalized algorithm combining the creating and deleting neural networks. First, a few weight (reference) vectors are prepared, the self‐creating algorithm is applied, and vectors are created automatically. Next, the self‐deleting algorithm is applied, and weight vectors are deleted sequentially to reach a predetermined number. Experimental results show the effectiveness of the proposed algorithm. © 1999 Scripta Technica, Electr Eng Jpn, 127(1): 47–55, 1999     

基于竞争性等位基因特异性PCR技术的麦芽品种纯度定性和定量检测

利用测序技术筛选和确认4?个可以区分7?种大麦麦芽的单核苷酸多态性（single nucleotide polymorphisms,SNP）位点,并建立区分图谱。同时,利用竞争性等位基因特异性聚合酶链式反应检测技术对预混样品进行定量测试,其检测的结果与真实性之间相对误差小于3%。该技术的建立对大麦麦芽纯度检测提供方法,对大麦麦芽SNP指纹数据库的完善提供了数据支持。