Formation of Linear Amplicons with Inverted Duplications in Leishmania Requires the MRE11 Nuclease

Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance. The extrachromosomal amplified DNA is either circular or linear, and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome. The RAD51 recombinase plays an important role in circular amplicons formation, but the mechanism by which linear amplicons are formed is unknown. We hypothesized that the Leishmania infantum DNA repair protein MRE11 is required for linear amplicons following rearrangements at the level of inverted repeats. The purified LiMRE11 protein showed both DNA binding and exonuclease activities. Inactivation of the LiMRE11 gene led to parasites with enhanced sensitivity to DNA damaging agents. The MRE11^−/− parasites had a reduced capacity to form linear amplicons after drug selection, and the reintroduction of an MRE11 allele led to parasites regaining their capacity to generate linear amplicons, but only when MRE11 had an active nuclease activity. These results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment.     

Molecular characterization of Mycobacterium tuberculosis cystathionine gamma synthase—Apo- and holoforms

Multiple probes like absorbance, circular dichroism, fluorescence and biochemical changes have been exploited to understand the role of PLP (pyridoxal 5′ phosphate) in guanidine hydrochloride (GdnHCl) mediated unfolding and refolding processes of cystathionine gamma synthase from Mycobacterium tuberculosis (MtCGS). Unfolding by GdnHCl inactivates the enzyme due to loss of ketoenamine tautomer. Though PLP induces difference in secondary structure content, it is unable to provide stabilizing effect during the overall secondary structure unfolding process. But it induces tertiary structure stability of the protein thereby counteracting the deleterious effect of denaturant. In silico modelling and cofactor docking provide insights into molecular structure of the enzyme.     

Proteome Analysis of Plasmodium falciparum Extracellular Secretory Antigens at Asexual Blood Stages Reveals a Cohort of Proteins with Possible Roles in Immune Modulation and Signaling

The highly co-evolved relationship of parasites and their hosts appears to include modulation of host immune signals, although the molecular mechanisms involved in the host-parasite interplay remain poorly understood. Characterization of these key genes and their cognate proteins related to the host-parasite interplay should lead to a better understanding of this intriguing biological phenomenon. The malaria agent Plasmodium falciparum is predicted to export a cohort of several hundred proteins to remodel the host erythrocyte. However, proteins actively exported by the asexual intracellular parasite beyond the host red blood cell membrane (before merozoite egress) have been poorly investigated so far. Here we used two complementary methodologies, two-dimensional gel electrophoresis/MS and LC-MS/MS, to examine the extracellular secreted antigens at asexual blood stages of P. falciparum. We identified 27 novel antigens exported by P. falciparum in the culture medium of which some showed clustering with highly polymorphic genes on chromosomes, suggesting that they may encode putative antigenic determinants of the parasite. Immunolocalization of four novel secreted proteins confirmed their export beyond the infected red blood cell membrane. Of these, preliminary functional characterization of two novel (Sel1 repeat-containing) parasite proteins, PfSEL1 and PfSEL2 revealed that they down-regulate expression of cell surface Notch signaling molecules in host cells. Also a novel protein kinase (PfEK) and a novel protein phosphatase (PfEP) were found to, respectively, phosphorylate/dephosphorylate parasite-specific proteins in the extracellular culture supernatant. Our study thus sheds new light on malaria parasite extracellular secreted antigens of which some may be essential for parasite development and could constitute promising new drug targets.Plasmodium falciparum is a wide spread protozoan parasite responsible for over a million deaths annually mainly among children in sub-Saharan Africa (1). Like other apicomplexan parasites such as Leishmania, Trypanosoma, and Toxoplasma, Plasmodia depend on a series of intricate and highly evolved adaptations that enable them to evade destruction by the host immune responses. These protozoan parasites have provided some of the best leads in elucidating the mechanisms to circumvent innate immunity and adaptive humoral and cellular immunity (2). Ingenious strategies to escape innate defenses include subversion of attack by humoral effector mechanisms such as complement lysis and lysis by other serum components (3), remodeling of phagosomal compartments in which they reside (4), modulation of host cell signaling pathways (5), and modification of the antigen-presenting and immunoregulatory functions of dendritic cells, which provide a crucial link with the adaptive immune response (6). Malaria parasites also predominantly use antigenic diversity and clonal antigenic variation to evade adaptive immunity of the host (7). Surface-associated and secreted parasite proteins are major players in host-parasite cross-talk and are advantageously used by the parasite to counter the host immune system. Proteins secreted by a wide range of parasitic pathogens into the host microenvironment result in symptomatic infections. For example, the excretory-secretory (ES)¹ products of the parasitic fluke Fasciola hepatica are key players in host-parasite interactions (8). Among the apicomplexans, proteomics analyses of rhoptry organelles of Toxoplasma gondii have revealed many novel constituents of host-parasite interactions (9).The identification and trafficking of Plasmodium proteins exported into the host erythrocyte have been subjects of recent detailed investigations. A number of studies have identified Plasmodium proteins that contain signature sequence motifs, the host cell targeting signal or the Plasmodium export element (PEXEL), that target these proteins into the infected erythrocytes (10, 11). Recent proteomics analyses have identified novel proteins in the raftlike membranes of the parasite and on the surface of infected erythrocytes (12, 13). P. falciparum translationally controlled tumor protein (PfTCTP), a homolog of the mammalian histamine-releasing factor, has been shown to be released into the culture supernatant from intact as well as ruptured infected RBCs and causes histamine release from human basophils and IL-8 secretion from eosinophils (14). However, the total spectrum of proteins actively exported by the asexual intracellular parasite beyond the host RBC membrane (before merozoite egress) has been poorly investigated so far.In the present study, we used two complementary methodologies, two-dimensional gel electrophoresis (2DE)/MS and LC-MS/MS to examine the cohort of extracellular secreted antigens (ESAs) at asexual blood stages of P. falciparum. Our findings reveal that malaria parasites secrete a number of effector molecules such as immunomodulators and signaling proteins that are potentially involved in host-parasite interactions. Prominent among these are proteins with Sel1 domain, a protein of the LCCL family, a novel protein kinase, and a novel protein phosphatase. Secreted-extracellular/iRBC surface localization of some of these proteins was validated by immunolocalization studies. We also characterized the functions of some of these proteins in the culture supernatant, thus providing an insight into the nature of some of the malaria parasite extracellular antigens.     

Protection of half sulfur mustard gas–induced lung injury in guinea pigs by antioxidant liposomes

The purpose of this study was to develop antioxidant liposomes as an antidote for mustard gas–induced lung injury in a guinea pig model. Five liposomes (LIP‐1, LIP‐2, LIP‐3, LIP‐4, and LIP‐5) were tested with differing levels of phospholipid, cholesterol, phosphatidic acid, tocopherol (α, γ, δ), N‐acetylcysteine (NAC), and glutathione (GSH). A single dose (200 µL) of liposome was administered intratracheally 5 min or 1 h after exposure to 2‐chloroethyl ethyl sulfide (CEES). The animals were sacrificed either 2 h after exposure (for lung injury study) or 30 days after exposure (for histology study). The liposomes offered 9%–76% protection against lung injury. The maximum protection was with LIP‐2 (71.5% protection) and LIP‐4 (75.4%) when administered 5 min after CEES exposure. Delaying the liposome administration 1 h after CEES exposure decreased the efficacy. Both liposomes contained 11 mM α‐tocopherol, 11 mM γ‐tocopherol, and 75 mM NAC. However, LIP‐2 contained additionally 5 mM δ‐tocopherol. Overall, LIP‐2 and LIP‐4 offered significant protection by controlling the recruitment of neutrophils, eosinophils, and the accumulation of septal and perivascular fibrin and collagen. However, LIP‐2 showed better protection than LIP‐4 against the accumulation of red blood cells in the bronchi, alveolar space, arterioles and veins, and fibrin and collagen deposition in the alveolar space. The antifibrotic effect of the liposomes, particularly LIP‐2, was further evident by a decreased level of lipid peroxidation and hydroxyproline in the lung. Thus, antioxidant liposomes containing both NAC and vitamin E are an effective antidote against CEES‐induced lung injury. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:143–153, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20279     

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.     

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.     

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.     

Regulation of guanylyl cyclase by intracellular Ca2+ in relation to the infectivity of the protozoan parasite, Leishmania donovani

A neuronal type Ca2+ stimulated nitric oxide synthase was earlier reported by us to be present in the protozoan parasite Leishmania donovani. As part of nitric oxide-cyclic GMP transduction signaling operative in higher eukaryotes and involved in the long-term potentiation, a soluble guanylyl cyclase has also been detected in this lower eukaryote. However, detailed biochemical characterization revealed the enzyme to be Ca2+ modulated and unstimulated by nitric oxide donors as opposed to higher eukaryotes. The possible role of intracellular Ca2+ level in the regulation of guanylyl cyclase activity as well as L. donovani infectivity was explored by measuring the intracellular survival of the parasites in mammalian macrophages after treatments, which decrease or elevate the intracellular Ca2+. Parasites loaded with intracellular Ca2+ chelators displayed significantly decreased infectivity and cyclic GMP level. In contrast, pretreatment with Ca2+ ionophores, which elevated Ca2+ levels in L. donovani, significantly enhanced the cyclic GMP level as well as the infectivity of the parasites. Moreover, treatment with selective inhibitors of soluble guanylyl cyclase also reduced infectivity, even in cases of calcium ionophore-treated parasites. The gene encoding the soluble guanylyl cyclase was cloned, sequenced and over expressed in bacterial system. The recombinant protein showed enzyme characteristics similar to that obtained in L. donovani promastigote cytosol. Together these results suggest a possible link between guanylyl cyclase, intracellular Ca2+ content and parasite infectivity.