Web Tools for Rice Transcriptome Analyses

Gene expression databases provide profiling data for the expression of thousands of genes to researchers worldwide. Oligonucleotide microarray technology is a useful tool that has been employed to produce gene expression profiles in most species. In rice, there are five genome-wide DNA microarray platforms: NSF 45K, BGI/Yale 60K, Affymetrix, Agilent Rice 44K, and NimbleGen 390K. Presently, more than 1,700 hybridizations of microarray gene expression data are available from public microarray depositing databases such as NCBI gene expression omnibus and Arrayexpress at EBI. More processing or reformatting of public gene expression data is required for further applications or analyses. Web-based databases for expression meta-analyses are useful for guiding researchers in designing relevant research schemes. In this review, we summarize various databases for expression meta-analyses of rice genes and web tools for further applications, such as the development of co-expression network or functional gene network.     

A novel small molecule target in human airway smooth muscle for potential treatment of obstructive lung diseases: a staged high-throughput biophysical screening

Background

A newly identified mechanism of smooth muscle relaxation is the interaction between the small heat shock protein 20 (HSP20) and 14-3-3 proteins. Focusing upon this class of interactions, we describe here a novel drug target screening approach for treating airflow obstruction in asthma.

Methods

Using a high-throughput fluorescence polarization (FP) assay, we screened a library of compounds that could act as small molecule modulators of HSP20 signals. We then applied two quantitative, cell-based biophysical methods to assess the functional efficacy of these molecules and rank-ordered their abilities to relax isolated human airway smooth muscle (ASM). Scaling up to the level of an intact tissue, we confirmed in a concentration-responsive manner the potency of the cell-based hit compounds.

Results

Among 58,019 compound tested, 268 compounds caused 20% or more reduction of the polarized emission in the FP assay. A small subset of these primary screen hits, belonging to two scaffolds, caused relaxation of isolated ASM cell in vitro and attenuated active force development of intact tissue ex vivo.

Conclusions

This staged biophysical screening paradigm provides proof-of-principle for high-throughput and cost-effective discovery of new small molecule therapeutic agents for obstructive lung diseases.     

Alien flora of mountains: global comparisons for the development of local preventive measures against plant invasions

Aim We use data from 13 mountain regions and surrounding lowland areas to identify (1) the origins, traits and cultural uses of alien plant species that establish in mountains, (2) the alien species that are most likely to be a threat and (3) how managers might use this information to prevent further invasions. Location Australia, Canada, Chile, India, New Zealand, South Africa, Spain, Switzerland, USA. Methods Lists of alien species were compiled for mountains and their surrounding or nearby lowlands. Principal co‐ordinates analysis was performed on a matrix of similarities created using presence/absence data for alien species. The significance of differences between means for (1) similarity metrics of lowland and mountain groups and (2) species traits of lowland and mountain alien floras was determined using t‐tests. In seven of the 13 mountain regions, lists of alien species undergoing management were compiled. The significance of differences between proportions of traits for species requiring and not requiring management input was determined with chi‐square tests. Results We found that the proximal lowland alien flora is the main determinant of a mountain region’s alien species composition. The highest similarities between mountain floras were in the Americas/Pacific Region. The majority of alien species commonly found in mountains have agricultural origins and are of little concern to land managers. Woody species and those used for ornamental purposes will often pose the greatest threat. Main conclusions Given the documented potential threat of alien species invading mountains, we advise natural resource managers to take preventive measures against the risk of alien plant invasion in mountains. A strategy for prevention should extend to the surrounding lowland areas and in particular regulate the introduction of species that are already of management concern in other mountains as well as climatically pre‐adapted alien mountain plants. These may well become more problematic than the majority of alien plants currently in mountains.     

Molecular cloning of a novel chimeric HMW glutenin subunit gene <Emphasis Type="Italic">1Dx5′</Emphasis> from a common wheat line W958

A novel chimeric high-molecular-weight (HMW) glutenin subunit gene from a new common wheat line W958 (2n = 6x = 42) was isolated and characterized. SDS–PAGE analysis revealed that this glutenin subunit has similar electrophoretic mobility to 1Dx5, so it was designated 1Dx5′. Genomic DNA from W958 was amplified and a 2,505-bp fragment was obtained. The 1Dx5′ subunit showed a chimeric primary structure of 1Dx5 and 1Dx2, with the 1Dx5 sequence in the 5′ and middle repetitive regions and the 1Dx2 sequence in the repetitive domain and 3′ region. MALDI-TOF-MS analysis demonstrated that 1Dx5′ had a molecular weight of 86815.1 Da, close to that of an x-type glutenin subunit. Secondary structure analysis showed that this subunit had six helixes and one strand, including four helixes in the repetitive domain which could enhance the dough properties. Additionally, the promoter of 1Dx5′ was obtained and showed the same sequence as 1Dx5 or 1Dx2 except for a few base conversions. The promoter analysis indicated that the cis-acting regulatory elements of 1Dx5′ were the same as those of 1Dx5 and/or 1Dx2. Previously, we have demonstrated that this novel glutenin subunit is associated with good bread-making quality and comprises a very large proportion of the F2 segregation population. Consequently, we suggest that the amino acid residue composition and the secondary structure of the subunit may contribute to the bread-making quality. In summary, the novel 1Dx5′ gene could have greater potential in wheat quality improvement.     

Enzyme precipitate coatings of lipase on polymer nanofibers

Lipase (LP) was immobilized on electrospun and ethanol-dispersed polystyrene–poly(styrene-co-maleic anhydride) (PS–PSMA) nanofibers (EtOH-NF) in the form of enzyme precipitate coatings (EPCs). LP precipitate coatings (EPCs-LP) were prepared in a three-step process, consisting of covalent attachment, LP precipitation, and crosslinking of precipitated LPs onto the covalently attached LPs via glutaraldehyde treatment. The LP precipitation was performed by adding various concentrations of ammonium sulfate (20–50%, w/v). EPCs-LP improved the LP activity and stability when compared to covalently attached LPs (CA-LP) and the enzyme coatings of LPs (EC-LP) without the LP precipitation. For example, the use of 40% (w/v) ammonium sulfate resulted in EPC40-LP with the highest activity, which was 4.0 and 3.6 times higher than those of CA-LP and EC-LP, respectively. After 165-day incubation under rigorous shaking at 200 rpm, the residual activities of EPC50-LP were 0.5 μM/min mg of EtOH-NF, representing 113 and 75 times higher than those of CA-LP and EC-LP, respectively. When LP was partially purified via a simple ammonium sulfate precipitation and dialysis, both activities and stabilities of EC-LP and EPC-LP could be marginally improved. It is anticipated that the improved LP activity and stability in the form of EPCs would allow for their potential applications in various bioconversion processes such as biodiesel production and ibuprofen resolution.     

Effects of simulated microgravity on embryonic stem cells

There have been many studies on the biological effects of simulated microgravity (SMG) on differentiated cells or adult stem cells. However, there has been no systematic study on the effects of SMG on embryonic stem (ES) cells. In this study, we investigated various effects (including cell proliferation, cell cycle distribution, cell differentiation, cell adhesion, apoptosis, genomic integrity and DNA damage repair) of SMG on mouse embryonic stem (mES) cells. Mouse ES cells cultured under SMG condition had a significantly reduced total cell number compared with cells cultured under 1 g gravity (1G) condition. However, there was no significant difference in cell cycle distribution between SMG and 1G culture conditions, indicating that cell proliferation was not impaired significantly by SMG and was not a major factor contributing to the total cell number reduction. In contrast, a lower adhesion rate cultured under SMG condition contributed to the lower cell number in SMG. Our results also revealed that SMG alone could not induce DNA damage in mES cells while it could affect the repair of radiation-induced DNA lesions of mES cells. Taken together, mES cells were sensitive to SMG and the major alterations in cellular events were cell number expansion, adhesion rate decrease, increased apoptosis and delayed DNA repair progression, which are distinct from the responses of other types of cells to SMG.     

Integrated dataset of screening hits against multiple neglected disease pathogens

New chemical entities are desperately needed that overcome the limitations of existing drugs for neglected diseases. Screening a diverse library of 10,000 drug-like compounds against 7 neglected disease pathogens resulted in an integrated dataset of 744 hits. We discuss the prioritization of these hits for each pathogen and the strong correlation observed between compounds active against more than two pathogens and mammalian cell toxicity. Our work suggests that the efficiency of early drug discovery for neglected diseases can be enhanced through a collaborative, multi-pathogen approach.     

Microsatellite analysis as a tool for discriminating an interfamily hybrid between olive flounder and starry flounder

An interspecific artificial hybrid was produced between two economically important aquaculture flatfish: olive flounder (Paralichthys olivaceus) and starry flounder (P. stellatus). This hybrid displays the rapid growth characteristic of the former and tolerance to low temperatures and low salinity of the latter, but the genetics of inheritance in this hybrid have not been elucidated. Polymorphic microsatellite markers developed for P. olivaceus and P. stellatus were tested to determine if these markers can be used for analysis of parentage and genetic inheritance. Multiplex PCR using two primer sets that were specific to each species produced PCR products of different sizes; these could be used for the identification of interspecific hybrids. Among the 192 primers derived from olive flounder, 25.5% of the primer sets successfully amplified genomic DNA from starry flounder, and 23% of the 56 primer sets originating from starry flounder amplified DNA from olive flounder. Analysis of genetic inheritance in the hybrid using seven of the 62 microsatellite markers common to both species demonstrated classic Mendelian inheritance of these markers in the hybrid progeny, with the exception of one locus identified as a null allele in the hybrid. These results demonstrate that cross-specific microsatellite markers can be used tools for parentage analysis of hybrid flatfish, for mapping quantitative trait loci, for marker-assisted selective breeding, and for studies of the evolution of fish.