Development of a fructose based medium for biosynthesis of cyclosporin-A byBeauveria nivea

Summary A new fructose based medium was developed to growBeauveria nivea ATCC 34921 for the production of Cyclosporin A (CyA). Two different sugars and three different nitrogen sources were used for CyA production. Different pH levels in the broth revealed that the best pH for CyA production was 5.5. Maximum concentration of 170 mg CyA/L of broth was obtained with the new medium in 8 days corresponding to yields of 14.8 mg CyA/g dry weight biomass and 5.67 mg CyA/g fructose supplied.     

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.     

Nuclear envelope dispersion triggered by deregulated Cdk5 precedes neuronal death

Nuclear fragmentation is a common feature in many neurodegenerative diseases, including Alzheimer's disease (AD). In this study, we show that nuclear lamina dispersion is an early and irreversible trigger for cell death initiated by deregulated Cdk5, rather than a consequence of apoptosis. Cyclin-dependent kinase 5 (Cdk5) activity is significantly increased in AD and contributes to all three hallmarks: neurotoxic amyloid-β (Aβ), neurofibrillary tangles (NFT), and extensive cell death. Using Aβ and glutamate as the neurotoxic stimuli, we show that deregulated Cdk5 induces nuclear lamina dispersion by direct phosphorylation of lamin A and lamin B1 in neuronal cells and primary cortical neurons. Phosphorylation-resistant mutants of lamins confer resistance to nuclear dispersion and cell death on neurotoxic stimulation, highlighting this as a major mechanism for neuronal death. Rapid alteration of lamin localization pattern and nuclear membrane change are further supported by in vivo data using an AD mouse model. After p25 induction, the pattern of lamin localization was significantly altered, preceding neuronal death, suggesting that it is an early pathological event in p25-inducible transgenic mice. Importantly, lamin dispersion is coupled with Cdk5 nuclear localization, which is highly neurotoxic. Inhibition of nuclear dispersion rescues neuronal cells from cell death, underscoring the significance of this event to Cdk5-mediated neurotoxicity.     

Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis

ABSTRACT: BACKGROUND: An approach to molecular classification based on the comparative expression of protein pairs is presented.The method overcomes some of the present limitations in using peptide intensity data for class prediction forproblems such as the detection of a disease, disease prognosis, or for predicting treatment response. Dataanalysis is particularly challenging in these situations due to sample size (typically tens) being much smallerthan the large number of peptides (typically thousands). Methods based upon high dimensional statisticalmodels, machine learning or other complex classifiers generate decisions which may be very accurate butcan be complex and difficult to interpret in simple or biologically meaningful terms. A classificationscheme, called ProtPair, is presented that generates simple decision rules leading to accurate classificationwhich is based on measurement of very few proteins and requires only relative expression values, providingspecific targeted hypotheses suitable for straightforward validation. RESULTS: ProtPair has been tested against clinical data from 21 patients following a bone marrow transplant, 13 ofwhich progress to idiopathic pneumonia syndrome (IPS). The approach combines multiple peptide pairsoriginating from the same set of proteins, with each unique peptide pair providing an independent measureof discriminatory power. The prediction rate of the ProtPair for IPS study as measured by leave-one-out CVis 69.1%, which can be very beneficial for clinical diagnosis as it may flag patients in need of closer monitoring. The "top ranked" proteins provided by ProtPair are known to be associated with the biologicalprocesses and pathways intimately associated with known IPS biology based on mouse models. CONCLUSIONS: An approach to biomarker discovery, called ProtPair, is presented. ProtPair is based on the differentialexpression of pairs of peptides and the associated proteins. Using mass spectrometry data from "bottom up"proteomics methods, functionally related proteins/peptide pairs exhibiting co-ordinated changes expressionprofile are discovered, which represent a signature for patients progressing to various disease conditions.The method has been tested against clinical data from patients progressing to idiopthatic pneumoniasyndrome (IPS) following a bone marrow transplant. The data indicates that patients with improperregulation in the concentration of specific acute phase response proteins at the time of bone marrowtransplant are highly likely to develop IPS within few weeks. The results lead to a specific set of proteinpairs that can be efficiently verified by investigating the pairwise abundance change in independent cohortsusing ELISA or targeted mass spectrometry techniques. This generalized classifier can be extended to otherclinical problems in a variety of contexts.     

Regeneration of fertile green plants from oat isolated microspore culture

Regeneration of fertile green plants from isolated oat microspores is reported for the first time. Factors critical for microspore growth and regeneration include cold pre-treatment, pH of culture medium and the use of conditioned culture medium. It was found that cold pre-treatment at 4°C in the dark for a minimum of 6 weeks was necessary to consistently achieve microspore growth into multicellular structures (MCS). Longer pre-treatments of up to 9 weeks were tested and found to be positively correlated with the number of MCS produced. Microspore culture medium with pH 8.0 produced significantly more MCS larger than eight cells in size than media with pH 5.8. The use of medium conditioned by actively growing barley microspores significantly increased the numbers of MCS larger than eight cells in size compared to non-conditioned media. Plants were regenerated only from cultures using conditioned medium. A total of 2 green plants and 15 albinos were regenerated. Of the green plants, one had the haploid chromosome complement (n = 3x = 21) and the other had the parental hexaploid chromosome complement (2n = 6x = 42) which may be due to spontaneous chromosome doubling. The hexaploid plant set seed naturally and the haploid plant set seed after its chromosome complement was doubled with colchicine.