A Laplace mixture model for identification of differential expression in microarray experiments

Microarrays have become an important tool for studying the molecular basis of complex disease traits and fundamental biological processes. A common purpose of microarray experiments is the detection of genes that are differentially expressed under two conditions, such as treatment versus control or wild type versus knockout. We introduce a Laplace mixture model as a long-tailed alternative to the normal distribution when identifying differentially expressed genes in microarray experiments, and provide an extension to asymmetric over- or underexpression. This model permits greater flexibility than models in current use as it has the potential, at least with sufficient data, to accommodate both whole genome and restricted coverage arrays. We also propose likelihood approaches to hyperparameter estimation which are equally applicable in the Normal mixture case. The Laplace model appears to give some improvement in fit to data, though simulation studies show that our method performs similarly to several other statistical approaches to the problem of identification of differential expression.     

Moisture sorption characteristics and thermophysical properties of trehalose-PBS mixtures

The goal of the study was to quantify the thermophysical properties and the moisture sorption characteristics of the trehalose-PBS (phosphate-buffered saline) from the desiccation preservation perspective. A moisture sorption study was undertaken to determine the desorption isotherms of the trehalose-PBS mixtures. The Brunauer, Emmett, and Teller (BET)-equation and the Guggenheim, Anderson, and de Boer equation were used to quantify the desorption data. The glass transition temperature of the mixtures of trehalose-PBS, equilibrated at different relative humidities was studied using a differential scanning calorimeter. Fourier transform infrared spectroscopy was used to study the molecular interaction between the trehalose and PBS mixtures. The results showed that the addition of PBS to the trehalose mixture causes a shift from the type II isotherm to a type III isotherm (characterized by BET equation) which may have detrimental effect on cell desiccation. The results showed that an increase in PBS mass fraction in the trehalose-PBS mixture causes a decrease in the glass transition temperature (Tg) of the mixture and also a decrease in the hydrogen bonding capacity of the trehalose glasses. The addition of PBS to trehalose posed some challenges and should be subject to further optimization to use it in desiccation preservation of biologics.     

Forced and natural convective drying of trehalose/water thin films: implication in the desiccation preservation of Mammalian cells

Trehalose is believed to offer desiccation protection to mammalian cells by forming stable glassy matrices. The goal of the current study was to explore the desiccation kinetics of thin films of trehalose-water solution under forced and natural convective conditions and to investigate the thermophysical state of mammalian cells at the bottom of the thin film. We developed a finite difference model based on the mass and energy conservation equations coupled to the water transport model from the cells. The boundary conditions were obtained from correlations or experimental measurements and the Gordon-Taylor equation was used to predict the glass transition temperature at every location. Results indicated that there are three distinct regimes for drying for both forced and natural convection, characterized by the slope of the moisture content plot as a function of time. Our results also indicate that the surface of the solution reached the glassy state in less than 10 min for the Reynolds (forced) numbers explored and approximately 30 min for some Rayleigh (natural convective) numbers; however, significant water was trapped at this instant. Larger drying force hastened quicker glass formation but trapped more water. The numerical model was capable of predicting the drying kinetics for the dilute region accurately, but deviated while predicting the other regimes. Based on these experimental validations of the model, the osmotic response of different cells located at the bottom of the solution with orders of magnitude difference in their membrane permeability (Lp) was predicted. The results suggested that extracellular glass formed around cells at the bottom of a trehalose-water solution by the propagation of glass into the solution; however it takes more than an order of magnitude time (approximately 7 min to >100 min for forced convective drying) to remove sufficient water to form glass around cells from the time when the first surface glass is formed. This is attributed to low diffusivity of water through the glass. In addition, the water transport from the glassy matrix could be either diffusion or Lp limited. For diffusion-limited transport, lowering the film thickness at the beginning of drying by half almost lowers the drying time by an order of magnitude. In summary, the optimal design of convective desiccation protocols requires accounting for the size of the cell, their membrane permeability (Lp) and the starting thickness of the solution.     

Gene targeting to the stroma of the prostate and bone

Abstract Stromal–epithelial interactions mediated by paracrine signaling mechanisms dictate prostate development and progression of prostate cancer. The regulatory role of androgens in both the prostate stromal and epithelial compartments set the prostate apart from many other organs and tissues with regard to gene targeting. The identification of androgen-dependent prostate epithelial promoters has allowed successful gene targeting to the prostate epithelial compartment. Currently, there are no transgenic mouse models available to specifically alter gene expression within the prostate stromal compartment. As a primary metastatic site for prostate cancer is bone, the functional dissection of the bone stromal compartment is important for understanding stromal–epithelial interactions associated with metastatic tumor growth. Use of currently available methodologies for the expression or deletion of gene expression in recent research studies has advanced our understanding of the stroma. However, the complexity of stromal heterogeneity within the prostate remains a challenge to obtaining compartment or cell-lineage-specific in vivo models necessary for furthering our understanding of prostatic developmental, benign, tumorigenic, and metastatic growth.     

Molecular typing of Vibrio parahaemolyticus isolated from seafood harvested along the south-west coast of India

Aims: Evaluation of protein profiling for typing Vibrio parahaemolyticus using 71 strains isolated from different seafood and comparison with other molecular typing techniques such as random amplified polymorphic DNA analysis (RAPD) and enterobacterial repetitive intergenic consensus sequence (ERIC)‐PCR. Methods and Results: Three molecular typing methods were used for the typing of 71 V. parahaemolyticus isolates from seafood. RAPD had a discriminatory index (DI) of 0·95, while ERIC‐PCR showed a DI of 0·94. Though protein profiling had less discriminatory power, use of this method can be helpful in identifying new proteins which might have a role in establishment in the host or virulence of the organism. Conclusions: The use of protein profiling in combination with other established typing methods such as RAPD and ERIC‐PCR generates useful information in the case of V. parahaemolyticus associated with seafood. Significance and Impact of the Study: The study demonstrates the usefulness of nucleic acid and protein‐based studies in understanding the relationship between various isolates from seafood.     

MICROBIAL SYNTHESIS OF RHAMNOLIPIDS BY Pseudomonas aeruginosa (ATCC 10145) ON WASTE FRYING OIL AS LOW COST CARBON SOURCE

Vegetable edible oils and fats are mainly used for frying purposes in households and the food industry. The oil undergoes degradation during frying and hence has to be replaced from time to time. Rhamnolipids are produced by microbial cultivation using refined vegetable oils as a carbon source and Pseudomonas aeruginosa (ATCC 10145). The raw material cost accounts for 10–30% of the overall cost of biosurfactant production and can be reduced by using low-cost substrates. In this research, attention was focused on the preparation of rhamnolipids, which are biosurfactants, using potential frying edible oils as a carbon source via a microbial fermentation technique. The use of low-cost substrates as a carbon source was emphasized to tilt the cost of production for rhamnolipids. The yield was 2.8 g/L and 7.5 g/L from waste frying oil before and after activated earth treatment, respectively. The crude product contained mainly dirhamnolipids, confirmed by thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC), liquid chromatography–mass spectroscopy (LC-MS), and ¹H-nuclear magnetic resonance (NMR). Hence, the treatment can be used to convert waste frying oil as a low-cost substrate into a cost-effective carbon source.     

The Role of Collagen Charge Clusters in the Modulation of Matrix Metalloproteinase Activity

Members of the matrix metalloproteinase (MMP) family selectively cleave collagens in vivo. Several substrate structural features that direct MMP collagenolysis have been identified. The present study evaluated the role of charged residue clusters in the regulation of MMP collagenolysis. A series of 10 triple-helical peptide (THP) substrates were constructed in which either Lys-Gly-Asp or Gly-Asp-Lys motifs replaced Gly-Pro-Hyp (where Hyp is 4-hydroxy-l-proline) repeats. The stabilities of THPs containing the two different motifs were analyzed, and kinetic parameters for substrate hydrolysis by six MMPs were determined. A general trend for virtually all enzymes was that, as Gly-Asp-Lys motifs were moved from the extreme N and C termini to the interior next to the cleavage site sequence, k_cat/K_m values increased. Additionally, all Gly-Asp-Lys THPs were as good or better substrates than the parent THP in which Gly-Asp-Lys was not present. In turn, the Lys-Gly-Asp THPs were also always better substrates than the parent THP, but the magnitude of the difference was considerably less compared with the Gly-Asp-Lys series. Of the MMPs tested, MMP-2 and MMP-9 most greatly favored the presence of charged residues with preference for the Gly-Asp-Lys series. Lys-Gly-(Asp/Glu) motifs are more commonly found near potential MMP cleavage sites than Gly-(Asp/Glu)-Lys motifs. As Lys-Gly-Asp is not as favored by MMPs as Gly-Asp-Lys, the Lys-Gly-Asp motif appears advantageous over the Gly-Asp-Lys motif by preventing unwanted MMP hydrolysis. More specifically, the lack of Gly-Asp-Lys clusters may diminish potential MMP-2 and MMP-9 collagenolytic activity. The present study indicates that MMPs have interactions spanning the P₂₃–P₂₃′ subsites of collagenous substrates.     

Conservation of floral,fruit and chromosomal diversity: a review on diploid and polyploid Capsicum annuum complex in India

Capsicum as a spice crop, has wild and cultivated forms admired globally, including Indian subcontinent with vast climatic ranges. Systematic representation of the Indian Capsicum is required to address species relationships and sustainable agriculture, in face of unpredictable climatic conditions. We have updated the catalogue of Indian ‘C. annuum complex’ with 28 landraces and populations from different agro-climatic regions. The agro-climatic influence on the origin of stable chili landraces in India is remarkable, especially in the North East. The floral and fruit morphotype standards and chromosomal attributes have been considered for four distinct ‘C. annuum complex’ members under three species. The highlights of study are: (1) comparative profiling of Indian Capsicum species revealing less infraspecific variation within C. frutescens and C. chinense than C. annuum, at par with cultivation status, (2) karyotype analysis of some unique diploid landraces of C. annuum, (3) karyotypic confirmation of the polyploid Dalle Khursani landraces exclusive to India. To obtain more information, we attempted to correlate diversity of fruit and floral morphotype with chromosomal diversity. Existence of elite and rare germplasm found in the regional pockets offer great scope for enriching the agricultural tradition. The present dataset may serve as a template to be continuously upgraded by taxonomists, genomicists and breeders.

     

Tumor-stroma interactions

The importance of stromal cells and the factors that they express during cancer initiation and progression has been highlighted by recent literature. The cellular components of the stroma of epithelial tissues are well-recognized as having a supportive role in carcinogenesis, where the initiating mutations of a tumor originate in the epithelial cells. The use of mouse models and xenografts suggests that mutations in the stromal fibroblasts can also initiate epithelial tumors. Many of these tumors result from the alteration of paracrine growth factor pathways that act on the epithelia. However, the tissue specificity of the responses to the growth factors is a mystery not yet solved.