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.     

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.     

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.     

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.     

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     

Real-time closed tube single nucleotide polymorphism (SNP) quantification in pooled samples by quencher extension (QEXT)

Quencher extension (QEXT) is a novel single step closed tube real-time method to quantify SNPs using reporters and quenchers in combination with primer extension. A probe with a 5′-reporter dye is single base extended with a dideoxy nucleotide containing a quencher dye if the target SNP allele is present. The extension is recorded from the quenching (reduced fluorescence) of the reporter dye. This avoids the influence of the unincorporated dye-labeled nucleotides, resulting in high accuracy and a high signal-to-noise ratio. The relative amount of a specific SNP allele is determined from the nucleotide incorporation rate in a thermo-cycling reaction. We tested the QEXT assay using five SNPs in the Listeria monocytogenes inlA gene as a model system. The presence of the target SNP alleles was determined with high statistical confidence (P < 0.0005). The quantitative detection limits were between 0 and 5% for the targeted SNP alleles on a background of other SNP alleles (P < 0.05). The QEXT method is directly adaptable to current real-time PCR equipment and is thus suited for high throughput and a wide application range.     

Genotype-specific response of cultured broccoli (Brassica oleracea var. italica) anthers to cytokinins

Anther culture medium was prepared with different types and concentrations of cytokinins to gain greater insight into the control of embryo formation during Brassica oleracea L. var. italica (broccoli) anther culture. The independent addition of the four cytokinins tested had widely divergent effects dependent upon cytokinin concentration and the genetic background of the test plants. All cytokinins were generally inhibitory at high concentrations, however, individual plants showed significant stimulation of embyro formation at typical physiological levels. The influence of cytokinins was highly cultivar-specific, some lines were stimulated, others inhibited and still other test lines were largely unaffected. Although the addition of cytokinins was needed for embryo formation for some plants, in no instance were cytokinins able to replace the inductive effect of high-temperature treatments.     

CD36 single nucleotide polymorphism is associated with variation in low-density lipoprotein-cholesterol in young Japanese men

Macrophages uptake oxidized low-density lipoprotein (LDL) via a scavenger receptor such as CD36 from plasma, and then become foam cells. We examined the association of CD36 gene single nucleotide polymorphisms (SNPs) with certain metabolic characteristics in a young male Japanese population (n?=?494). The G allele in a SNP located at +30215 on the 3’-untranslated region (UTR) was significantly correlated with the plasma LDL-cholesterol concentrations (r?=?0.13, p?<0.01). The difference in LDL-cholesterol concentrations was 10?mg dl^?1 between GG- and AA-genotype carriers (p?<0.05). The CD36 gene SNP is a novel maker of the variation in the LDL-cholesterol levels in young Japanese men.     

Single nucleotide polymorphism (SNP) discovery in porcine expressed genes

High-throughput genotyping of swine populations is a potentially efficient method for establishing animal lineage and identification of loci important to animal health and efficient pork production. Markers were developed based upon single nucleotide polymorphisms (SNPs), which are abundant and amenable to automated genotyping platforms. The focus of this research was SNP discovery in expressed porcine genes providing markers to develop the porcine/human comparative map. Locus specific amplification (LSA) and comparative sequencing were used to generate PCR products and allelic information from parents of a swine reference family. Discovery of 1650 SNPs in 403 amplicons and strategies for optimizing LSA-based SNP discovery using alternative methods of PCR primer design, data analysis, and germplasm selection that are applicable to other populations and species are described. These data were the first large-scale assessment of frequency and distribution of porcine SNPs.     

A single nucleotide polymorphism (SNP) in the leptin receptor is associated with BMI, fat mass and leptin levels in postmenopausal Caucasian women

The human leptin (obese) receptor gene contains a number of single nucleotide polymorphisms, including GLN223ARG, which changes an amino acid on the extracellular region common to all isoforms of the receptor. Here, we demonstrate that, in postmenopausal Caucasian women, genotypes at that locus are associated with differences in body mass index (BMI), fat mass and serum leptin levels. Measurement of serum leptin-binding activity indicates that this may reflect changed receptor function associated with genotype. These observations indicate that functional variations in the leptin receptor gene are important factors in the regulation of adiposity and BMI.