Control of isoperoxidases involved in chlorophyll degradation of stored broccoli (Brassica oleracea) florets by heat treatment

Changes in isoperoxidases involved in chlorophyll (Chl) degradation of stored broccoli (Brassica oleracea L.) florets and their control by heat treatment (HT) were determined. Chl a and b contents in non-heat-treated broccoli florets decreased greatly after 2 days at 15 degrees C, whereas the contents in heat-treated florets (50 degrees C for 2 h) showed almost no change. Three isoperoxidases involved in Chl degradation were detected by means of molecular exclusion chromatography and the molecular weights of those isoperoxidases were about 95 (Type I), 67 (Type II) and 56 (Type III) kDa, respectively. Only Type I was detected in broccoli florets immediately after harvest, and its activity in non-heat-treated broccoli increased greatly during storage. Both Type II and Type III were present in non-heat-treated broccoli with floret senescence. HT suppressed the enhancement of all of the isoperoxidase activities. Cycloheximide treatment also effectively retarded the increase in Types I, II and III isoperoxidase activities concomitant with the suppression of floret yellowing. The K(m) values corresponding to Chl a of Type II and Type III were lower than Type I, and the V(max)/K(m) values corresponding to Chl a of Type II and Type III were higher than Type I. This suggests that both Types II and III could be closely associated with Chl degradation in broccoli florets and that HT might inhibit floret senescence by suppression of isoperoxidase activities.     

A graphene-based platform for single nucleotide polymorphism (SNP) genotyping

A facile, rapid, stable and sensitive approach for fluorescent detection of single nucleotide polymorphism (SNP) is designed based on DNA ligase reaction and π-stacking between the graphene and the nucleotide bases. In the presence of perfectly matched DNA, DNA ligase can catalyze the linkage of fluorescein amidite-labeled single-stranded DNA (ssDNA) and a phosphorylated ssDNA, and thus the formation of a stable duplex in high yield. However, the catalytic reaction cannot effectively carry out with one-base mismatched DNA target. In this case, we add graphene to the system in order to produce different quenching signals due to its different adsorption affinity for ssDNA and double-stranded DNA. Taking advantage of the unique surface property of graphene and the high discriminability of DNA ligase, the proposed protocol exhibits good performance in SNP genotyping. The results indicate that it is possible to accurately determine SNP with frequency as low as 2.6% within 40 min. Furthermore, the presented flexible strategy facilitates the development of other biosensing applications in the future.     

A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array

Background  

DNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybridization (array-CGH), the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required.     

Recent patents on high-throughput single nucleotide polymorphism (SNP) genotyping methods

Single nucleotide polymorphisms (SNPs) are single-base inheritable variations in a given and defined genetic location that occur in at least 1% of the population. SNPs are useful markers for genetic association studies in disease susceptibility or adverse drug reactions, in evolutionary studies and forensic science. Given the potential impact of SNPs, the biotechnology industry has focused on the development of high-throughput methods for SNP genotyping. Many highthroughput SNP genotyping technologies are currently available and many others are being patented recently. Each offers a unique combination of scale, accuracy, throughput and cost. In this review, we described some of the most important recent SNP genotyping methods and also recent patents associated with it.     

Taxonomy and evolution of broccoli (Brassica oleracea var. italica)

The origin and application of the name broccoli are discussed and a distinction between cauliflower and broccoli is proposed, based on their relative ontogeny at marketable maturity. The history and evolution of broccoli is considered in relation to cauliflower and its diversification into annual and biennial types is discussed. White-sprouting broccoli is considered to be closely related to English winter-hardy cauliflower. Calabrese, though representing only a small part of the italica gene pool, has been the most intensively developed, being currently represented by many cultivars, including F₁ hybrids. The potential for breeding new Cape and sprouting broccolis is discussed, and the need to conserve existing genetic variability of existing cultivars within Cape and sprouting broccoli is stressed.     

Nanoparticle-based detection and quantification of DNA with single nucleotide polymorphism (SNP) discrimination selectivity

Sequence-specific DNA detection is important in various biomedical applications such as gene expression profiling, disease diagnosis and treatment, drug discovery and forensic analysis. Here we report a gold nanoparticle-based method that allows DNA detection and quantification and is capable of single nucleotide polymorphism (SNP) discrimination. The precise quantification of single-stranded DNA is due to the formation of defined nanoparticle-DNA conjugate groupings in the presence of target/linker DNA. Conjugate groupings were characterized and quantified by gel electrophoresis. A linear correlation between the amount of target DNA and conjugate groupings was found. For SNP detection, single base mismatch discrimination was achieved for both the end- and center-base mismatch. The method described here may be useful for the development of a simple and quantitative DNA detection assay.     

Single nucleotide polymorphism (SNP) discovery and linkage mapping of bovine cytokine genes

Polymorphic markers at bovine gene loci facilitate the integration of cattle genetic maps with those of humans and mice. To this end, 31 single nucleotide polymorphism (SNP) markers were developed for seven bovine chemokine genes. Loci were amplified from bovine genomic DNA by the polymerase chain reaction, and candidate amplicons were sequenced to determine their identity. Amplified loci from 24 founding parents and select progeny from a beef cattle reference population were sequenced and analyzed for SNPs. SNP haplotype alleles were determined by examining segregation patterns and used to establish the locus position on the bovine linkage map. Loci for growth-related proteins (GRO3, GRO1, and GROX) were clustered with the related CXC chemokine genes, interleukin (IL) 8, and epithelial cell inflammatory protein 1, at 84 cM from the centromeric end of the bovine chromosome (BTA) 6 linkage group. Bovine loci for a cluster of IL8 receptors, a stromal cell-derived factor 1, interferon-γ, and tumor necrosis factor-α were mapped at 90, 55, 59, and 34 cM, respectively, from the centromeric ends of the BTA 2, 28, 5, and 23 linkage groups. The positions of these bovine loci were compared with those of orthologous loci on the human map to refine the boundaries of conserved synteny. These seven loci provide examples of SNP development in which the efficiency was largely dependent on the availability of bovine genomic or cDNA sequence. The polymorphic nature of these SNP haplotype markers suggests that they will be useful for mapping complex traits in cattle, such as resistance to infectious disease. Received: 30 April 1999 / Accepted: 12 July 1999     

High-density single nucleotide polymorphism array analysis in patients with germline deletions of 22q11.2 and malignant rhabdoid tumor

Malignant rhabdoid tumors are highly aggressive neoplasms found primarily in infants and young children. The majority of rhabdoid tumors arise as a result of homozygous inactivating deletions or mutations of the INI1 gene located in chromosome band 22q11.2. Germline mutations of INI1 predispose to the development of rhabdoid tumors of the brain, kidney and extra-renal tissues, consistent with its function as a tumor suppressor gene. We now describe five patients with germline deletions in chromosome band 22q11.2 that included the INI1 gene locus, leading to the development of rhabdoid tumors. Two patients had phenotypic findings that were suggestive but not diagnostic for DiGeorge/Velocardiofacial syndrome (DGS/VCFS). The other three infants had highly aggressive disease with multiple tumors at the time of presentation. The extent of the deletions was determined by fluorescence in situ hybridization and high-density oligonucleotide based single nucleotide polymorphism arrays. The deletions in the two patients with features of DGS/VCFS were distal to the region typically deleted in patients with this genetic disorder. The three infants with multiple primary tumors had smaller but overlapping deletions, primarily involving INI1. The data suggest that the mechanisms underlying the deletions in these patients may be similar to those that lead to DGS/VCFS, as they also appear to be mediated by related, low copy repeats (LCRs) in 22q11.2. These are the first reported cases in which an association has been established between recurrent, interstitial deletions mediated by LCRs in 22q11.2 and a predisposition to cancer. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Isolation and characterization of gene-derived single nucleotide polymorphism (SNP) markers in Scylla paramamosain

Single nucleotide polymorphisms (SNPs) are thought to be well suitable for genetic and evolutionary studies. In this study, we reported the first set of SNP markers in a commercially important crab species, Scylla paramamosain. A total of 12,500 base pairs high quality DNA sequences were obtained from 15 genes, and thirty-seven SNPs were identified, representing one SNP every 338 base pairs. Twenty-four SNPs were successfully genotyped in a single population. All loci had two alleles and the minor allele frequency ranged from 0.02 to 0.44. The observed and expected heterozygosity ranged from 0.04 to 0.59 and from 0.04 to 0.50, respectively. No significant departures from Hardy–Weinberg equilibrium at each locus was found. The linkage disequilibrium was detected in six loci pairs, but absent after sequential Bonferroni correction. These SNP markers will provide a useful addition to the genetic tools for genetic and evolutionary studies for S. paramamosain.     

Multiplex single nucleotide polymorphism (SNP)-based genotyping in allohexaploid wheat using padlock probes

Single nucleotide polymorphisms are the most common polymorphism in plant and animal genomes and, as such, are the logical choice for marker-assisted selection. However, many plants are also polyploid, and marker-assisted selection can be complicated by the presence of highly similar, but non-allelic, homoeologous sequences. Despite this, there is practical and academic demand for high-throughput genotyping in several polyploid crop species, such as allohexaploid wheat. In this paper, we present such a system, which utilizes public single nucleotide polymorphisms previously identified in both agronomically important genes and in randomly selected, mapped, expressed sequence tags developed by the wheat community. To achieve relatively high levels of multiplexing, we used non-amplified genomic DNA and padlock probe pairs, together with high annealing temperatures, to differentiate between similar sequences in the wheat genome. Our results suggest that padlock probes are capable of discriminating between homoeologous sequences and hence can be used to efficiently genotype wheat varieties.     

Heat shock response during anther culture of broccoli (Brassica oleracea var italica)

Embryo formation from microspores of Brassica oleracea var Italica (Broccoli) and other Brassica species is greatly enhanced by an initial incubation at elevated temperatures (eg 35°C) followed by continued incubation of 25°C. In the present study we observed that a three hour high temperature treatment induced the formation of heat shock proteins in cultured anthers. These were identified in two dimensional gels by silver staining, and labelled heat shock proteins were synthesised in vitro from isolated anther RNA. The appearance of heat shock proteins in anthers followed a similar pattern and displayed similar characteristics to that from leaves. Comparison of the heat shock proteins induced in isolated cultured anthers of known highly embryogenic and less embryogenic plans did not reveal obvious qualitative differences.     

Effects of temperature and irradiance on vegetative growth of cauliflower (Brassica oleracea L. botrytis) and broccoli (Brassica oleracea L. italica)

Cauliflower (Brassica oleracea L. botrytis) and broccoli (Brassicaoleracea L. italica) plants were grown in large pots in growthchambers for a range of temperatures (mean air temperaturesfrom 7.0-25.3 C) and irradi-ances (from 9.3-50.8 mol m^–2d^–1 or 4.7-25.4 MJ m^–2 d^–1). The extinctioncoefficient for PAR decreased with plant size reaching a valueof 0.55 in cauliflower and 0.45 in broccoli at plant leaf areasof 0.235 m² and 0.227 m², respectively. The leaf area expansionrate was unaffected by irradiance when compared at identicalleaf surface temperatures. The response of expansion rate tosurface temperature was fitted to a broken stick model witha base temperature of –0.7C and an optimum temperatureof 21.0C. The radiation conversion coefficient increased withair temperature below 13.8C and remained constant above this.The estimated radiation conversion coefficient above 13.8Cand for a PPFD of 20 mol m^–2 d^–1 was 0.77 g mol^–1in cauliflower and 0.87 g mol^–1 in broccoli. The radiationconversion coefficient declined with increasing irradiance levelfrom a maximum of 1.89 g mol^–1 at near nil irradiancein cauliflower. Key words: Leaf area, dry matter, radiation use efficiency, extinction coefficient     

中华蜜蜂的单核苷酸多态性和插入缺失突变位点鉴定

【目的】本研究拟利用已获得的中华蜜蜂Apis cerana cerana幼虫肠道的转录组数据对单核苷酸多态性（Single nucleotide polymorphism,SNP）和插入缺失（Insertion-Deletion,InDel）突变位点进行挖掘和分析,旨在丰富中华蜜蜂的SNP和InDel信息,并为新型分子标记的开发提供基础。【方法】根据有效读段与东方蜜蜂Apis cerana参考基因组的比对情况,采用GATK软件识别单碱基错配和碱基的插入缺失情况,再利用ANNOVAR软件对SNP位点和InDel位点进行分析。通过相关生物信息学软件将SNP和InDel位点所在基因分别比对GO和KEGG数据库,以获得相应的功能和通路注释。【结果】共鉴定到中华蜜蜂的58 919个SNP位点,包括24 548个纯合位点和34 371个杂合位点;发生转换和颠换的SNP位点分别有49102和9817个;数量最多和最少的突变类型分别是C/T和T/G;分布在外显子区的SNP位点数量最多,达到22 649个;此外,发生同义突变的SNP位点数量最多,其次是非同义突变;SNP位点所在基因可注释到46个GO条目和121条KEGG通路。共鉴定到6 551个InDel位点,包括3 270个插入突变和3 281个缺失突变;分布在内含子区InDel位点最多,共计2 793个;发生移码插入的InDel位点最多;进一步分析结果显示InDel位点所在基因可注释到27个GO条目和28条KEGG通路。【结论】本研究鉴定到中华蜜蜂的大量SNP位点和InDel位点,解析了SNP和InDel位点的突变类型、基因组功能元件分布和密码子突变类型,并揭示SNP和InDel位点对中华蜜蜂的重要生物学过程具有潜在影响。