Case–Control Studies of Gene–Environment Interaction: Bayesian Design and Analysis

Summary With increasing frequency, epidemiologic studies are addressing hypotheses regarding gene‐environment interaction. In many well‐studied candidate genes and for standard dietary and behavioral epidemiologic exposures, there is often substantial prior information available that may be used to analyze current data as well as for designing a new study. In this article, first, we propose a proper full Bayesian approach for analyzing studies of gene–environment interaction. The Bayesian approach provides a natural way to incorporate uncertainties around the assumption of gene–environment independence, often used in such an analysis. We then consider Bayesian sample size determination criteria for both estimation and hypothesis testing regarding the multiplicative gene–environment interaction parameter. We illustrate our proposed methods using data from a large ongoing case–control study of colorectal cancer investigating the interaction of N‐acetyl transferase type 2 (NAT2) with smoking and red meat consumption. We use the existing data to elicit a design prior and show how to use this information in allocating cases and controls in planning a future study that investigates the same interaction parameters. The Bayesian design and analysis strategies are compared with their corresponding frequentist counterparts.     

Purification and characterization of a thiol amylase over produced by a non-cereal non-leguminous plant, Tinospora cordifolia

A 43 kDa α-amylase was purified from Tinospora cordifolia by glycogen precipitation, ammonium sulfate precipitation, gel filtration chromatography, and HPGPLC. The enzyme was optimally active in pH 6.0 at 60 °C and had specific activity of 546.2 U/mg of protein. Activity was stable in the pH range of 4-7 and at temperatures up to 60 °C. PCMB, iodoacetic acid, iodoacetamide, DTNB, and heavy metal ions Hg²⁺ > Ag⁺ > Cd²⁺ inhibited enzyme activity while Ca²⁺ improved both activity and thermostability. The enzyme was a thiol amylase (3 SH group/mole) and DTNB inhibition of activity was released by cysteine. N-terminal sequence of the enzyme had poor similarity (12-24%) with those of plant and microbial amylases. The enzyme was equally active on soluble starch and amylopectin and released maltose as the major end product.     

Analysis of the Development of a Morphological Phenotype as a Function of Protein Concentration in Budding Yeast

Gene deletion and protein overexpression are common methods for studying functions of proteins. In this article, we describe a protocol for analysis of phenotype development as a function of protein concentration at population and single-cell levels in Saccharomyces cerevisiae. Although this protocol is based on the overexpression of a protein, it can easily be adapted for morphological phenotypes dependent on suppression of protein expression. Our lab is interested in studying the signaling properties of the endocytic adaptor protein epsin. To that purpose we used a dominant negative approach in which we over-expressed the conserved Epsin N-Terminal Homology (ENTH) domain in order to interfere with the functions of endogenous epsin-2 (Ent2 or YLR206W). We observed that overexpression of the ENTH domain of Ent2 (ENTH2) in wild type cells led to a cell division defect that is dependent on the mislocalization of a family of scaffolding proteins, septins.Download video file.^{(167M, mp4)}     

Enzyme-assisted kinetic resolution of novel 2-naphthol Mannich bases

In an attempt to develop novel Selective Estrogen Receptor Modulators (SERMs) containing a chirality centre, simpler 1-((2-hydroxynaphthalen-1-yl)arylmethyl)piperidin-4-ol prototypes were synthesized as racemic mixtures via the Mannich reaction protocol from 2-naphthol, 4-piperidinol, and 10 different aromatic aldehydes. These 10 chiral Mannich bases were then resolved utilizing an enzyme-assisted chemo-, regio-, and enantioselective acetylation process. The enzyme (Novozyme 435^®; Lipase B from Candida Antarctica) displayed exclusive chemo- and regioselectivity in acetylating the test compounds; the optical enrichment was also achieved as evidenced by measurement of the optical rotation of the mono-acetylated product and unreacted dihydroxy compound.     

Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase 1 from Methicillin-Resistant Staphylococcus aureus MRSA252 Provides Novel Insights into Substrate Binding and Catalytic Mechanism

The dreaded pathogen Staphylococcus aureus is one of the causes of morbidity and mortality worldwide. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the key glycolytic enzymes, is irreversibly oxidized under oxidative stress and is responsible for sustenance of the pathogen inside the host. With an aim to elucidate the catalytic mechanism and identification of intermediates involved, we describe in this study different crystal structures of GAPDH1 from methicillin-resistant S. aureus MRSA252 (SaGAPDH1) in apo and holo forms of wild type, thioacyl intermediate, and ternary complexes of active-site mutants with physiological substrate d-glyceraldehyde-3-phosphate (G3P) and coenzyme NAD⁺. A new phosphate recognition site, “new P_i” site, similar to that observed in GAPDH from Thermotoga maritima, is reported here, which is 3.40 Å away from the “classical P_i” site. Ternary complexes discussed are representatives of noncovalent Michaelis complexes in the ground state. d-G3P is bound to all the four subunits of C151S.NAD and C151G.NAD in more reactive hydrate (gem-di-ol) form. However, in C151S + H178N.NAD, the substrate is bound to two chains in aldehyde form and in gem-di-ol form to the other two. This work reports binding of d-G3P to the C151G mutant in an inverted manner for the very first time. The structure of the thiaocyl complex presented here is formed after the hydride transfer. The C3 phosphate of d-G3P is positioned at the “P_s” site in the ternary complexes but at the “new P_i” site in the thioacyl complex and C1-O1 bond points opposite to His178 disrupting the alignment between itself and NE2 of His178. A new conformation (Conformation I) of the 209-215 loop has also been identified, where the interaction between phosphate ion at the “new P_i” site and conserved Gly212 is lost. Altogether, inferences drawn from the kinetic analyses and crystal structures suggest the “flip-flop” model proposed for the enzyme mechanism.     

Towards commercial production of microbial surfactants

Biosurfactants or microbial surfactants are surface-active biomolecules that are produced by a variety of microorganisms. Biosurfactants have gained importance in the fields of enhanced oil recovery, environmental bioremediation, food processing and pharmaceuticals owing to their unique properties--higher biodegradability, lower toxicity, and effectiveness at extremes of temperature, pH and salinity. However, large-scale production of these molecules has not been realized because of low yields in production processes and high recovery and purification costs. This article describes some practical approaches that have been adopted to make the biosurfactant production process economically attractive: these include the use of cheaper raw materials, optimized and efficient bioprocesses and overproducing mutant and recombinant strains for obtaining maximum productivity. The application of these strategies in biosurfactant production processes, particularly those using hyper-producing recombinant strains in the optimally controlled environment of a bioreactor, might lead towards the successful commercial production of these valuable and versatile biomolecules in near future.     

Process optimization of constitutive human granulocyte–macrophage colony-stimulating factor (hGM-CSF) expression in Pichia pastoris fed-batch culture

Human granulocyte–macrophage colony-stimulating factor (hGM-CSF) is a therapeutically important cytokine that is poorly expressed because of its toxic effects on the host cells. Extracellular expression of hGM-CSF was obtained by cloning its gene in Pichia pastoris under the constitutive glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter with an N-terminal α peptide sequence for its extracellular production. The clones obtained were screened for a hyper producer following which media and cultivation conditions were optimized in shake flasks. Batch and fed-batch studies were performed in a bioreactor where different feed compositions were fed exponentially to obtain high biomass concentrations. Feeding of complex media allowed us to maintain a high specific growth rate of 0.2 h⁻¹ for the longest time period, and a final biomass of 98 g DCW/l was obtained in 34 h. Product formation was found to be growth associated, and the product yield with respect to biomass (Y _P/X) was ∼2.5 mg/g DCW. The above fed-batch strategy allowed us to obtain fairly pure glycosylated hGM-CSF at a final product concentration of 250 mg/l in the culture supernatant with a high volumetric productivity of 7.35 mg l⁻¹ h⁻¹.     

An RNA-binding respiratory component mediates import of type II tRNAs into Leishmania mitochondria

Transport of tRNAs across the inner mitochondrial membrane of the kinetoplastid protozoon Leishmania requires interactions with specific binding proteins (receptors) in a multi-subunit complex. The allosteric model of import regulation proposes cooperative and antagonistic interactions between two or more receptors with binding specificities for distinct tRNA families (types I and II, respectively). To identify the type II receptor, the gene encoding RIC8A, a subunit of the complex, was cloned. The C-terminal region of RIC8A is homologous to subunit 6b of ubiquinol cytochrome c reductase (respiratory complex III), while the N-terminal region has intrinsic affinity for type II, but not for type I, tRNAs. RIC8A is shared by the import complex and complex III, indicating its bi-functionality, but is assembled differently in the two complexes. Knockdown of RIC8A in Leishmania lowered the mitochondrial content of type II tRNAs but raised that of type I tRNAs, with downstream effects on mitochondrial translation and respiration, and cell death. In RIC8A knockdown cells, a subcomplex was formed that interacted with type I tRNA, but the negative regulation by type II tRNA was lost. Mitochondrial extracts from these cells were defective for type II, but not type I, import; import and regulation were restored by purified RIC8A. These results provide evidence for the relevance of allosteric regulation in vivo and indicate that acquisition of new tRNA-binding domains by ancient respiratory components have played a key role in the evolution of mitochondrial tRNA import.