Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

Aberrant DNA methylation often occurs in colorectal cancer (CRC). In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions (DMRs) in 24 tumors and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potential biomarkers for CRC diagnosis. Hypermethylation in the tumor samples was enriched at CpG islands and gene promoters, while hypomethylation was distributed throughout the genome. Using epigenetic data from human embryonic stem cells, we show that frequently hypermethylated regions coincide with bivalent loci in human embryonic stem cells. DNA methylation is commonly thought to lead to gene silencing; however, integration of publically available gene expression data indicates that 75% of the frequently hypermethylated genes were most likely already lowly or not expressed in normal tissue. Collectively, our study provides genome-wide DNA methylation maps of CRC, comprehensive lists of DMRs, and gives insights into the role of aberrant DNA methylation in CRC formation.     

SNPstream UHT: ultra-high throughput SNP genotyping for pharmacogenomics and drug discovery

Single nucleotide polymorphism (SNP) genotyping is playing an increasing role in genome mapping, pharmacogenetic studies, and drug discovery. To date, genome-wide scans and studies involving thousands of SNPs and samples have been hampered by the lack of a system that can perform genotyping with cost-effective throughput, accuracy, and reliability. To address this need, Orrhid has developed an automated, ultra-high throughput system, SNPstream UHT, which uses multiplexed PCR in conjunction with our next generation SNP-IT tag array single base extension genotyping technology The system employs oligonucleotide microarrays manufactured in a 384-well format on a novel glass-bottomed plate. Multiplexed PCR and genotyping are performed in homogeneous reactions, and assay results are read by direct two-color fluorescence on the SNPstream UHTArray Imager. The systems flexibility enables large projects involving thousands of SNPs and thousands of samples as well as small projects that have hundreds of SNPs and hundreds of samples to be done cost effectively. We have successfully demonstrated this system in greater than 1,000,000 genotyping assays with >96% of samples giving genotypes with >99% accuracy     

A network-based analysis of polyanion-binding proteins utilizing human protein arrays

The existence of interactions between many cellular proteins and various polyanionic surfaces within a cell is now well established. The functional role of such interactions, however, remains to be clearly defined. The existence of protein arrays, with a large selection of different kinds of proteins, provides a way to better address a number of aspects of this question. We have therefore investigated the interaction between five cellular polyanions (actin, tubulin, heparin, heparan sulfate, and DNA) and approximately 5,000 human proteins using protein microarrays in an attempt to better understand the functional nature of such interaction(s). We demonstrate that a large number of polyanion-binding proteins exist that contain multiple positively charged regions, are often disordered, are involved in phosphorylation processes, and appear to play a role in protein-protein interaction networks. Considering the crowded nature of cellular interiors, we propose that polyanion-binding proteins interact with a wide variety of polyanionic surfaces in cells in a functionally significant manner.     

非齐次的食饵——捕食模型

为了建立被捕食与捕食模型,我们在ｚ＾ｄ上考虑两种群的相互作用,还考虑了在被捕食者数目很大时,捕食者变化地趋于一个常数的情况,最后,给出了关于两种群共存的与非共存问题的研究。     

In vitro shoot proliferation and production of sets from garlic and shallot

A procedure is described to regenerate shoots and bulbs in vitro with high frequency from shoot tips of garlic and shallot plants using benzyladenine or thidiazuron. Regenerated shoots were induced to form bulbs in Murashige and Skoog medium (1962) containing 5 g l^-1 activated charcoal and 120 g l^-1 sucrose under a long-day photoperiod. Bulbs formed in vitro were transferred to soil without acclimatization and produced viable plants. This method could be useful to produce low-cost bulbs, which are easy to handle and store until needed.Abbreviations AC activated charcoal - BA benzyladenine - IBA indolebutyric acid - MS Murashige & Skoog's (1962) medium - NAA naphthaleneacetic acid - TDZ thidiazuron     

In vitro bulb production fromAllium spp.

Summary A procedure for bulb formation from onion, garlic, and shallot explants is described. Explants from cut stem bases were cultured in shoot induction medium composed of Murashige and Skoog (MS) medium with or without N⁶-benzyladenine. Shoots produced were then transferred to bulb induction medium composed of MS medium containing 5 g/liter activated charcoal and 120 g/liter sucrose under a long-day photoperiod and 28° C. Bulbs were also produced from onion and garlic directly, without passing through shoot formation, when explants were cultured in the bulb induction medium described above. Bulbs were transferred to soil without acclimatization and produced viable plants.     

A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays

The high affinity of certain cellular polyanions for many proteins (polyanion-binding proteins (PABPs)) has been demonstrated previously. It has been hypothesized that such polyanions may be involved in protein structure stabilization, stimulation of folding through chaperone-like activity, and intra- and extracellular protein transport as well as intracellular organization. The purpose of the proteomics studies reported here was to seek evidence for the idea that the nonspecific but high affinity interactions of PABPs with polyanions have a functional role in intracellular processes. Utilizing yeast protein arrays and five biotinylated cellular polyanion probes (actin, tubulin, heparin, heparan sulfate, and DNA), we identified proteins that interact with these probes and analyzed their structural and amino acid sequence requirements as well as their predicted functions in the yeast proteome. We also provide evidence for the existence of a network-like system for PABPs and their potential roles as critical hubs in intracellular behavior. This investigation takes a first step toward achieving a better understanding of the nature of polyanion-protein interactions within cells and introduces an alternative way of thinking about intracellular organization.     

In vitro shoot proliferation and plant regeneration from kurrat (Allium ampeloprasum var. kurrat) seedlings

Shoots were produced from kurrat seedling and mature plant explants cultured in Murashige and Skoog medium (MS) alone or supplemented with 4.4 M benzyladenine (BA). Shoots were also produced from explants through a two-step procedure. Regenerated shoots were induced to form roots on MS medium with 5 g I^-1 activated charcoal. Plants were successfully established in soil.Abbreviations AC activated charcoal - BA benzyladenine - MS Murashige & Skoog's (1962) medium - 2,4-d 2,4-dichlorophenoxyacetic acid     

The role of seed coats in seed viability

The seed coat is the seed’s primary defense against adverse environmental conditions. A hard seed coat protects the seed not only from mechanical stress but also from microorganism invasion and from temperature and humidity fluctuations during storage. Phenolic compounds in the seed coat contribute to seed hardness and inhibition of microorganism growth. During germination, the seed coat protects the seed from hydration stress and electrolyte leakage.