Broadening of neutralization activity to directly block a dominant antibody-driven SARS-coronavirus evolution pathway

Phylogenetic analyses have provided strong evidence that amino acid changes in spike (S) protein of animal and human SARS coronaviruses (SARS-CoVs) during and between two zoonotic transfers (2002/03 and 2003/04) are the result of positive selection. While several studies support that some amino acid changes between animal and human viruses are the result of inter-species adaptation, the role of neutralizing antibodies (nAbs) in driving SARS-CoV evolution, particularly during intra-species transmission, is unknown. A detailed examination of SARS-CoV infected animal and human convalescent sera could provide evidence of nAb pressure which, if found, may lead to strategies to effectively block virus evolution pathways by broadening the activity of nAbs. Here we show, by focusing on a dominant neutralization epitope, that contemporaneous- and cross-strain nAb responses against SARS-CoV spike protein exist during natural infection. In vitro immune pressure on this epitope using 2002/03 strain-specific nAb 80R recapitulated a dominant escape mutation that was present in all 2003/04 animal and human viruses. Strategies to block this nAb escape/naturally occurring evolution pathway by generating broad nAbs (BnAbs) with activity against 80R escape mutants and both 2002/03 and 2003/04 strains were explored. Structure-based amino acid changes in an activation-induced cytidine deaminase (AID) "hot spot" in a light chain CDR (complementarity determining region) alone, introduced through shuffling of naturally occurring non-immune human VL chain repertoire or by targeted mutagenesis, were successful in generating these BnAbs. These results demonstrate that nAb-mediated immune pressure is likely a driving force for positive selection during intra-species transmission of SARS-CoV. Somatic hypermutation (SHM) of a single VL CDR can markedly broaden the activity of a strain-specific nAb. The strategies investigated in this study, in particular the use of structural information in combination of chain-shuffling as well as hot-spot CDR mutagenesis, can be exploited to broaden neutralization activity, to improve anti-viral nAb therapies, and directly manipulate virus evolution.     

Transgenic tobacco and peanut plants expressing a mustard defensin show resistance to fungal pathogens

Defensins are small positively charged, antimicrobial peptides (~5 kDa in size) and some of them exhibit potent antifungal activity. We have cloned the complete cDNA containing an ORF of 243 bp of a defensin of mustard. The deduced amino acid sequence of the peptide showed more than 90% identity to the amino acid sequence of the well-characterized defensins, RsAFP-1 and RsAFP-2 of Raphanus sativus. We have generated and characterized transgenic tobacco and peanut plants constitutively expressing the mustard defensin. Transgenic tobacco plants were resistant to the fungal pathogens, Fusarium moniliforme and Phytophthora parasitica pv. nicotianae. Transgenic peanut plants showed enhanced resistance against the pathogens, Pheaoisariopsis personata and Cercospora arachidicola, which jointly cause serious late leaf spot disease. These observations indicate that the mustard defensin gene can be deployed for deriving fungal disease resistance in transgenic crops.     

Differential bioleaching of copper by mesophilic and moderately thermophilic acidophilic consortium enriched from same copper mine water sample

Three acidophilic enrichment consortium were developed from mine water sample of copper mine site at Khetri, India were compared for their copper leaching efficiency. Out of these one was mesophilic (35 degrees C) and two were moderately thermophilic (50 degrees C). Consortia were named as mesophilic acidophilic chemolithotrophic consortia (MACC), thermophilic acidophilic chemolithotrophic consortia (TACC), and Sulfobacillus acidophilic consortia (SAC). Copper extraction ability of both the thermophilic consortia (77-78% extraction) was almost double to that of mesophilic consortia (40% extraction) at 10% pulp density after 55 days. Both the thermophilic consortia were equally effective in leaching of other metals like Ni, Co, Zn, Mn. After 55 days, the percentage of extractions of copper by TACC was 76, 74, 67, 48 and 45 at 5%, 10%, 15%, 20% and 30% pulp density, respectively. Total number of bacteria was maximum at 5% pulp density which decreases with increase in pulp density. Sulfobacillus-like bacteria were seen in the Sulfobacillus enrichment cultures. Moderately thermophilic consortia proved to be better in leaching performance than the mesophilic counterpart.     

Multiple antiapoptotic targets of the PI3K/Akt survival pathway are activated by epoxyeicosatrienoic acids to protect cardiomyocytes from hypoxia/anoxia

Epoxyeicosatrienoic acids (EETs) reduce infarction of the myocardium after ischemia-reperfusion injury to rodent and dog hearts mainly by opening sarcolemmal and mitochondrial potassium channels. Other mediators for the action of EET have been proposed, although no definitive pathway or mechanism has yet been reported. Using cultured cells from two rodent species, immortalized myocytes from a mouse atrial lineage (HL-1) and primary myocytes derived from neonatal rat hearts, we observed that pretreatment with EETs (1 microM of 14,15-, 11,12-, or 8,9-EET) attenuated apoptosis after exposure to hypoxia and reoxygenation (H/R). EETs also preserved the functional beating of neonatal myocytes in culture after exposure to H/R. We demonstrated that EETs increased the activity of the prosurvival enzyme phosphatidylinositol 3-kinase (PI3K). In fact, cardiomyocytes pretreated with EET and exposed to H/R exhibited antiapoptotic changes in at least five downstream effectors of PI3K, protein kinase B (Akt), Bcl-x(L)/Bcl-2-associated death promoter, caspases-9 and -3 activities, and the expression of the X-linked inhibitor of apoptosis, compared with vehicle-treated controls. The PI3K/Akt pathway is one of the strongest intracellular prosurvival signaling systems. Our studies show that EETs regulate multiple molecular effectors of this pathway. Understanding the targets of action of EET-mediated protection will promote the development of these fatty acids as therapeutic agents against cardiac ischemia-reperfusion.     

Cloning and Overexpression of Alkaline Phosphatase PhoK from Sphingomonas sp. Strain BSAR-1 for Bioprecipitation of Uranium from Alkaline Solutions

Cells of Sphingomonas sp. strain BSAR-1 constitutively expressed an alkaline phosphatase, which was also secreted in the extracellular medium. A null mutant lacking this alkaline phosphatase activity was isolated by Tn5 random mutagenesis. The corresponding gene, designated phoK, was cloned and overexpressed in Escherichia coli strain BL21(DE3). The resultant E. coli strain EK4 overexpressed cellular activity 55 times higher and secreted extracellular PhoK activity 13 times higher than did BSAR-1. The recombinant strain very rapidly precipitated >90% of input uranium in less than 2 h from alkaline solutions (pH, 9 ± 0.2) containing 0.5 to 5 mM of uranyl carbonate, compared to BSAR-1, which precipitated uranium in >7 h. In both strains BSAR-1 and EK4, precipitated uranium remained cell bound. The EK4 cells exhibited a much higher loading capacity of 3.8 g U/g dry weight in <2 h compared to only 1.5 g U/g dry weight in >7 h in BSAR-1. The data demonstrate the potential utility of genetically engineering PhoK for the bioprecipitation of uranium from alkaline solutions.     

A novel paradigm of fatty acid beta-oxidation exemplified by the thioesterase-dependent partial degradation of conjugated linoleic acid that fully supports growth of Escherichia coli

An alternative pathway of beta-oxidation for unsaturated fatty acids was studied in Escherichia coli. 9- cis,11- trans-Octadecadienoic acid (conjugated linoleic acid), a potential substrate of this pathway, was shown to support growth of E. coli in the absence of any other carbon source. The identification of 3,5-dodecadienoic acid in the growth medium revealed the partial beta-oxidation of conjugated linoleic acid to 3,5-dodecadienoyl-CoA, which was hydrolyzed to 3,5-dodecadienoic acid and released from cells. The involvement of acyl-CoA thioesterases in this process was evaluated by determining the substrate specificity of thioesterase II and comparing it with that of a novel thioesterase (thioesterase III) and by assessing mutant strains devoid of one or both of these thioesterases for growth on conjugated linoleic acid. Both thioesterases were highly active with 3,5-dodecadienoyl-CoA as substrate. A deficiency of either thioesterase decreased the growth rate of cells on conjugated linoleic acid but not on palmitic acid. The absence of both thioesterases reduced the cellular growth in a cumulative manner but did not abolish it. It is concluded that thioesterases II and III and at least one other thioesterase function in the partial degradation of conjugated linoleic acid via the thioesterase-dependent pathway of beta-oxidation, which provides all energy and carbon precursors required for the growth of E. coli.     

Protein phosphatase 2A negatively regulates integrin alpha(IIb)beta(3) signaling

Integrin alpha(IIb)beta(3) activation is critical for platelet physiology and is controlled by signal transduction through kinases and phosphatases. Compared with kinases, a role for phosphatases in platelet integrin alpha(IIb)beta(3) signaling is less understood. We report that the catalytic subunit of protein phosphatase 2A (PP2Ac) associates constitutively with the integrin alpha(IIb)beta(3) in resting platelets and in human embryonal kidney 293 cells expressing alpha(IIb)beta(3). The membrane proximal KVGFFKR sequence within the cytoplasmic domain of integrin alpha(IIb) is sufficient to support a direct interaction with PP2Ac. Fibrinogen binding to alpha(IIb)beta(3) during platelet adhesion decreased integrin-associated PP2A activity and increased the phosphorylation of a PP2A substrate, vasodilator associated phosphoprotein. Overexpression of PP2Ac(alpha) in 293 cells decreased alpha(IIb)beta(3)-mediated adhesion to immobilized fibrinogen. Conversely, small interference RNA mediated knockdown of endogenous PP2Ac(alpha) expression in 293 cells, enhanced extracellular signal-regulated kinase (ERK1/2) and p38 activation, and accelerated alpha(IIb)beta(3) adhesion to fibrinogen and von Willebrand factor. Inhibition of ERK1/2, but not p38 activation, abolished the increased adhesiveness of PP2Ac (alpha)-depleted 293 cells to fibrinogen. Furthermore, knockdown of PP2A(calpha) expression in bone marrow-derived murine megakaryocytes increased soluble fibrinogen binding induced by protease-activated receptor 4-activating peptide. These studies demonstrate that PP2Ac (alpha) can negatively regulate integrin alpha(IIb)beta(3) signaling by suppressing the ERK1/2 signaling pathway.     

Phaeohyphomycosis Caused by <Emphasis Type="Italic">Rhytidhysteron rufulum</Emphasis> and Review of Literature

Phaeohyphomycosis is caused by a heterogeneous group of mycelial dematiaceous (phaeoid) fungi, which produce melanin pigment. This condition is often confused with chromoblastomycosis. Rhytidhysteron is a dematiaceous fungus, which has been recently found to be causing human infections. Till date only three cases of infection with Rhytidhysteron rufulum have been reported in the literature. All three cases have been from North India. Hereby, we present another two cases where Rhytidhysteron was isolated. Both the patients belonged to Chandigarh (India) and presented with subcutaneous lesions. The isolates were confirmed by ITS sequencing. Both the patients were immunocompetent and gave no history of trauma or any other predisposing factor. Phaeohyphomycosis are often missed due to lack of knowledge regarding the fungi causing the infections and there is need for clinical, pathological and microbiological correlation for effective diagnosis and treatment in these cases.     

Auxin biosynthetic intermediate genes and their role in developmental growth and plasticity in higher plants

Auxins are a group of phytohormones that regulate several aspects of plant growth and development. Indole-3-acetic acid (IAA) is the predominant form of auxin in plants and several IAA biosynthetic pathways have been previously proposed but remain genetically uncharacterized. One of the proposed pathways is the indole-3-pyruvic acid (IPyA) pathway, which is inferred to regulate key developmental processes such as apical hook formation and shade avoidance. Recent molecular evidence suggests the existence of the pathway in higher plants but remains unverified due to the elusive nature of IPyA in vitro. Extending on these recent advances, this research was aimed at investigating aspects of IPyA-dependent auxin biology in Pisum sativum (pea) using reverse genetics, expression profiling, and analytical techniques. As a result the genes PsTAR2, PsTAR 5g Mt 80, and PsTAR 5g Mt 90, which are inferred to encode key enzymes in the IPyA pathway, were cloned. On expression analysis PsTAR2 was found to be slightly heightened in response to IPyA-inducing conditions (shade) while IAA levels remained unaltered contrary to previous reports. Moreover, the inferred homologs PsTAR 5g Mt 80 and PsTAR 5g Mt 90 appeared down-regulated in the same conditions suggesting functional divergence in the gene family. Thus, PsTAR2 was thought to be solely responsible for regulating IPyA-dependent auxin synthesis. Consequently, using a reverse genetic approach, called TILLING, the PsTAR2 gene was mutated in order to study the down-stream effects of IPyA deficiency. The procedure is currently underway and in the process of isolating two novel pstar2 (IPyA) mutant lines consisting of a missense mutation (pstar2 4280) and a highly desired knockout mutation (pstar2 918). On completion the novel mutants are anticipated to be indispensable to future IPyA-auxin investigations in higher plants. In light of the unstable nature of IPyA, a protocol has been formulated using UPLC for fractioning followed by MS/MS analysis. This technique appears to be very promising as a robust IPyA detection protocol in plant extracts.