Efficiency of Functional Regression Estimators for Combining Multiple Laser Scans of cDNA Microarrays

The first stage in the analysis of cDNA microarray data is estimation of the level of expression of each gene, from laser scans of hybridised microarrays. Typically, data are used from a single scan, although, if multiple scans are available, there is the opportunity to reduce sampling error by using all of them. Combining multiple laser scans can be formulated as multivariate functional regression through the origin. Maximum likelihood estimation fails, but many alternative estimators exist, one of which is to maximise the likelihood of a Gaussian structural regression model. We show by simulation that, surprisingly, this estimator is efficient for our problem, even though the distribution of gene expression values is far from Gaussian. Further, it performs well if errors have a heavier tailed distribution or the model includes intercept terms, but not necessarily in other regions of parameter space. Finally, we show that by combining multiple laser scans we increase the power to detect differential expression of genes. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Progress and Prospects of Developing Climate Resilient Wheat in South Asia Using Modern Pre-Breeding Methods

Developing climate-resilient wheat is a priority for South Asia since the effect of climate change will be pronounced on the major crops that are staple to the region. South Asia must produce >400 million metric tons (MMT) of wheat by 2050 to meet the demand. However, the current average yield <3 t/ha is not sufficient to meet the requirement. In this review, we are addressing how pre-breeding methods in wheat can address the gap in grain yield as well as reduce the bottleneck of genetic diversity. Physiological pre-breeding which incorporates screening of diverse germplasm from gene banks for physiological and agronomic traits, the strategic crossing of complementary traits, high throughput phenotyping, molecular markers-based generation advancement, genomic prediction, and validation of high-value heat and drought tolerant lines to South Asia can help to alleviate the drastic effect of climate change on wheat production. There are several gene banks, if utilized well, can play a major role in breeding for climate-resilient wheat. CIMMYT’s wheat physiological pre-breeding has delivered several hundred lines via the Stress Adapted Trait Yield Nursery (SATYN) to the NARS in many South Asian countries; India, Pakistan, Nepal, Bangladesh, Afghanistan, and Iran. Some of these improved germplasms have resulted in varieties for farmer''s field. We conclude the review by pointing out the importance of collaborative interdisciplinary translational research to alleviate the effects of climate change on wheat production in South Asia.     

Flacourtia indica fruit extract modulated antioxidant gene expression,prevented oxidative stress and ameliorated kidney dysfunction in isoprenaline administered rats

This study evaluated the effect of Flacourtia indica fruit extract against isoprenaline (ISO) induced renal damage in rats. This investigation showed that ISO administration in rats increased the level oxidative stress biomarkers such as malondialdehyde (MDA), nitric oxide (NO), advanced protein oxidation product (APOP) in kidneys followed by a decrease in antioxidant enzymes functions. Flacourtia indica fruit extract, which is rich in strong antioxidants, also reduced the MDA, NO and APOP level in kidney of ISO administered rats. Inflammation and necrosis was also visible in kidney section of ISO administered rats which was significantly prevented by atenolol and Flacourtia indica fruit extract. Moreover, atenolol and Flacourtia indica fruit extract also modulated the genes expressions related to inflammation and oxidative stress in kidneys. The beneficial effects could be attributed to the presence of a number of phenolic antioxidants. This study suggests that Flacourtia indica fruit extract may prevent kidney dysfunction in ISO administered rats, probably by preventing oxidative stress and inflammation.     

Scintigraphically detected "hot" thyroid nodules in the specimens from patients of the Thyroid Disease Clinic in Gda'nsk--clinico- histopathological analysis

A group of 153 patients with scintigraphically detected autonomic "hot" nodules of the thyroid has been subjected to clinical and histopathological analysis. Substantial part of these patients (30.1%) had hyperthyroidism, partly (in 19.9% of cases) in the form of the thyrocardiac syndrome. A most frequent histopathological lesion found within "hot" nodules was follicular adenoma. The occurrence of malignancy in the form of highly differentiated thyroid carcinoma was observed in 2.6% of cases. The incidence of thyroid carcinoma within "hot" nodules was in our material only two and half times smaller than in a previously analyzed group of patients with "cold" nodules of the thyroid.     

Variability in biofilm formation correlates with hydrophobicity and quorum sensing among Vibrio parahaemolyticus isolates from food contact surfaces and the distribution of the genes involved in biofilm formation

Vibrio parahaemolyticus is one of the leading foodborne pathogens causing seafood contamination. Here, 22 V. parahaemolyticus strains were analyzed for biofilm formation to determine whether there is a correlation between biofilm formation and quorum sensing (QS), swimming motility, or hydrophobicity. The results indicate that the biofilm formation ability of V. parahaemolyticus is positively correlated with cell surface hydrophobicity, autoinducer (AI-2) production, and protease activity. Field emission scanning electron microscopy (FESEM) showed that strong-biofilm-forming strains established thick 3-D structures, whereas poor-biofilm-forming strains produced thin inconsistent biofilms. In addition, the distribution of the genes encoding pandemic clone factors, type VI secretion systems (T6SS), biofilm functions, and the type I pilus in the V. parahaemolyticus seafood isolates were examined. Biofilm-associated genes were present in almost all the strains, irrespective of other phenotypes. These results indicate that biofilm formation on/in seafood may constitute a major factor in the dissemination of V. parahaemolyticus and the ensuing diseases.     

In vitro salt and thermal tolerance of fungal endophytes of Nicotiana spp. growing in arid regions of north-western Australia

Abstract

Endophytic fungal strains isolated from indigenous Nicotiana plants naturally growing in dry and hot regions of north-western Australia were characterised based on their tolerance to salinity and temperature. Sixty-eight fungal isolates were tested on eight levels (0.5 M, 1.0 M, 1.5 M, 2.0 M, 2.5 M, 3.0 M, 3.5 M and 4.0 M) of five different of salts solutions NaCl, KCl, MgCl₂, CaCl₂ and MgSO₄ and at various temperatures (25–50?°C). The salt adaptation test indicated that the fungal strains namely Aspergillus niger (E-202), A. ochraceous-A (E-134), Aurantiporus sp. (E-135), Cladosporium halotolerance (E-128), Pleurostomophora richardsiae (E-13) and Trichoderma sp. (E-185.1) were tolerant to higher concentrations of various salts. The most growth-limiting salt turned out to be MgCl₂ followed by the chaotrope CaCl₂. Responses to temperature tolerance revealed that most fungi tested could grow at 30?°C. About 50% all the fungi did not show any growth when the temperature was raised above 30?°C. When the temperature was raised up to 50?°C all the fungi failed to grow but the fungus Rasamsonia piperina (E-172). Endophyte strains identified could be promising candidates for future research in investigating the fungus–plant interactions and their roles in plant adaptation to inhospitable environments.     

Cloning and characterization of sialidases with 2-6' and 2-3' sialyl lactose specificity from Pasteurella multocida

Pasteurella multocida is a mucosal pathogen that colonizes the respiratory system of susceptible hosts. Most isolates of P. multocida produce sialidase activity, which may contribute to colonization of the respiratory tract or the production of lesions in an active infection. We have cloned and sequenced a sialidase gene, nanH, from a fowl cholera isolate of P. multocida. Sequence analysis of NanH revealed that it exhibited significant amino acid sequence homology with many microbial sialidases. Insertional inactivation of nanH resulted in a mutant strain that was not deficient in sialidase production. However, this mutant exhibited reduced enzyme activity and growth rate on 2-3' sialyl lactose compared to the wild type. Subsequently, we demonstrated the presence of two sialidases by cloning another sialidase gene that differed from nanH in DNA sequence and substrate specificity. NanB demonstrated activity on both 2-3' and 2-6' sialyl lactose, while NanH demonstrated activity only on 2-3' sialyl lactose. Neither enzyme liberated sialic acid from colominic acid (2-8' sialyl lactose). Recombinant E. coli containing the sialidase genes were able to utilize several sialoconjugants when they were provided as sole carbon sources in minimal medium. These data suggest that sialidases have a nutritional function and may contribute to the ability of P. multocida to colonize and persist on vertebrate mucosal surfaces.