Biodegradation of chrysene by the bacterial strains isolated from oily sludge

The biodegradation studies were conducted to test the ability of the bacterial strains (Chry2 and Chry3) isolated from the oily sludge obtained from Gujarat refinery, India, for utilization of chrysene in the liquid medium. Biodegradation of the compound was confirmed using gas chromatography and the percent degradation was calculated to be 15.0 and 17% by Chry2 and Chry3, respectively. The biodegradation results were supported by increase in viable cell count and dry biomass, in the presence of chrysene as the sole carbon source. Both the cultures produced biosurfactant which was indicated by the reduction in surface tension of the growth medium. Presence of catechol 2, 3-dioxygenase gene in Chry3 indicated its potential for degradation of PAHs through meta cleavage degradation pathway. Both the strains were found to possess catechol 1,2-dioxygenase and catechol 2,3-dioxygenase enzyme activities. Based on morphological and biochemical tests, the cultures were tentatively identified as Bacillus sp. (Chry2) and Pseudomonas sp. (Chry3).     

Probing the Periplasmic-Open State of Lactose Permease in Response to Sugar Binding and Proton Translocation

Based on the crystal structure of lactose permease (LacY) open to the cytoplasm, a hybrid molecular simulation approach with self-guided Langevin dynamics is used to describe conformational changes that lead to a periplasmic-open state. This hybrid approach consists of implicit (IM) and explicit (EX) membrane simulations and requires self-guided Langevin dynamics to enhance protein motions during the IM simulations. The pore radius of the lumen increases by 3.5 Å on the periplasmic side and decreases by 2.5 Å on the cytoplasmic side (relative to the crystal structure), suggesting a lumen that is fully open to the periplasm to allow for extracellular sugar transport and closed to the cytoplasm. Based on our simulations, the mechanism that triggers this conformational change to the periplasmic-open state is the protonation of Glu269 and binding of the disaccharide. Then, helix packing is destabilized by breaking of several side chains involved in hydrogen bonding (Asn245, Ser41, Glu374, Lys42, and Gln242). For the periplasmic-open conformations obtained from our simulations, helix-helix distances agree well with experimental measurements using double electron-electron resonance, fluorescence resonance energy transfer, and varying sized cross-linkers. The periplasmic-open conformations are also in compliance with various substrate accessibility/reactivity measurements that indicate an opening of the protein lumen on the periplasmic side on sugar binding. The comparison with these measurements suggests a possible incomplete closure of the cytoplasmic half in our simulations. However, the closure is sufficient to prevent the disaccharide from transporting to the cytoplasm, which is in accordance with the well-established alternating access model. Ser53, Gln60, and Phe354 are determined to be important in sugar transport during the periplasmic-open stage of the sugar transport cycle and the sugar is found to undergo an orientational change in order to escape the protein lumen.     

ISOLATION OF THREE NOVEL LONG‐CHAIN POLYUNSATURATED FATTY ACID Δ9‐ELONGASES AND THE TRANSGENIC ASSEMBLY OF THE ENTIRE PAVLOVA SALINA DOCOSAHEXAENOIC ACID PATHWAY IN NICOTIANA BENTHAMIANA1

The transgenic aerobic synthesis of long‐chain polyunsaturated fatty acids (LC‐PUFA) will in most land plants commence with either a Δ6‐desaturation or a Δ9‐elongation. Numerous Δ6‐desaturases have been characterized, but only one Δ9‐elongase has been reported in peer‐reviewed literature. In the present study, we describe the isolation of three additional Δ9‐elongases from the class Haptophyceae and demonstrate that the Δ9‐elongase group contains highly conserved regions, which differentiate them from other ELO‐type elongases. One such important difference is the presence of an LQxFHH motif instead of the usual LHxYHH motif, a feature that should simplify further gene discovery efforts in this group of enzymes. Moreover, the identification of the Pavlova salina (N. Carter) J. C. Green Δ9‐elongase completes the isolation of the entire P. salina docosahexaenoic acid (DHA) pathway, and we describe the assembly of this pathway in Nicotiana benthamiana. Finally, we comment on possible explanations for the widespread presence of the Δ6‐desaturated fatty acid stearidonic acid (SDA, 18:4^Δ6,9,12,15) in the plastidial lipids of organisms using the Δ9‐elongase pathway.     

PfPKB, a protein kinase B-like enzyme from Plasmodium falciparum: II. Identification of calcium/calmodulin as its upstream activator and dissection of a novel signaling pathway

Intracellular cell signaling cascades of protozoan parasite Plasmodium falciparum are not clearly understood. We have reported previously (Kumar, A., Vaid, A., Syin, C., and Sharma, P. (2004) J. Biol. Chem. 279, 24255-24264) the identification and characterization of a protein kinase B-like enzyme in P. falciparum (PfPKB). PfPKB lacks the phosphoinositide-interacting pleckstrin homology domain present in mammalian protein kinase B. Therefore, the mechanism of PfPKB regulation was expected to be different from that of the host and had remained unknown. We have identified calmodulin (CaM) as the regulator of PfPKB activity. A CaM binding domain was mapped in the N-terminal region of PfPKB. CaM, in a calcium-dependent manner, interacts with this domain and activates PfPKB. CaM associates with PfPKB in the parasite and regulates its activity. Furthermore phospholipase C acts as an upstream regulator of this cascade as it facilitates the release of calcium from intracellular stores. This is one of the first multicomponent signaling pathways to be dissected in the malaria parasite.     

High-resolution structure of the photosynthetic Mn4Ca catalyst from X-ray spectroscopy

The application of high-resolution X-ray spectroscopy methods to study the photosynthetic water oxidizing complex, which contains a unique hetero-nuclear catalytic Mn4Ca cluster, is described. Issues of X-ray damage, especially at the metal sites in the Mn4Ca cluster, are discussed. The structure of the Mn4Ca catalyst at high resolution, which has so far eluded attempts of determination by X-ray diffraction, X-ray absorption fine structure (EXAFS) and other spectroscopic techniques, has been addressed using polarized EXAFS techniques applied to oriented photosystem II (PSII) membrane preparations and PSII single crystals. A review of how the resolution of traditional EXAFS techniques can be improved, using methods such as range-extended EXAFS, is presented, and the changes that occur in the structure of the cluster as it advances through the catalytic cycle are described. X-ray absorption and emission techniques (XANES and Kbeta emission) have been used earlier to determine the oxidation states of the Mn4Ca cluster, and in this report we review the use of X-ray resonant Raman spectroscopy to understand the electronic structure of the Mn4Ca cluster as it cycles through the intermediate S-states.     

Breast cancer metastasis suppressor-1 differentially modulates growth factor signaling

That metastatic tumor cells grow in selective non-native environments suggests an ability to differentially respond to local microenvironments. BRMS1, like other metastasis suppressors, halts ectopic growth (metastasis) without blocking orthotopic tumor formation. BRMS1-expressing tumor cells reach secondary sites but do not colonize distant tissues, compelling the hypothesis that BRMS1 selectively restricts the ability of tumor cells to respond to exogenous regulators in different tissues. Here we report that BRMS1 expression in metastatic human breast cancer cells leads to a selective reduction in epidermal growth factor receptor expression and downstream (AKT) signaling. Signaling through another receptor tyrosine kinase, hepatocyte growth factor receptor (c-Met), remains unaltered despite reduced levels of the signaling intermediate phosphatidylinositol (4,5)-bisphosphate. Interestingly, reduced downstream calcium signaling is observed following treatment with platelet-derived growth factor, consistent with decreased phosphatidylinositol (4,5)-bisphosphate. However, platelet-derived growth factor receptor expression is unaltered. Thus, BRMS1 differentially attenuates cellular responses to mitogenic signals, not only dependent upon the specific signal received, but at varying steps within the same signaling cascade. Specific modulation of signaling responses received from the microenvironment may ultimately dictate which environments are permissive/restrictive for tumor cell growth and provide insights into the biology underlying metastasis.     

On the mechanism of cryoprotection by polyethylene oxide.

Bone marrow cells and peripheral blood leukocytes have been exposed to a 15% solution of polyethylene oxide of molecular weight 400 (PEO-400) and the effect on DNA synthesis, oxygen uptake, and the activity of oxidative-reductive enzymes has been studied. All the metabolic activities studied were reduced during exposure to PEO-400, but in each case the effect was completely reversed when the cryoprotective agent was removed. It is suggested that the cryoprotective action of PEO-400 may be linked with its ability not only to dehydrate cells but also to depress oxidative metabolism.     

Healthcare Worker Contact Networks and the Prevention of Hospital-Acquired Infections

We present a comprehensive approach to using electronic medical records (EMR) for constructing contact networks of healthcare workers in a hospital. This approach is applied at the University of Iowa Hospitals and Clinics (UIHC) – a 3.2 million square foot facility with 700 beds and about 8,000 healthcare workers – by obtaining 19.8 million EMR data points, spread over more than 21 months. We use these data to construct 9,000 different healthcare worker contact networks, which serve as proxies for patterns of actual healthcare worker contacts. Unlike earlier approaches, our methods are based on large-scale data and do not make any a priori assumptions about edges (contacts) between healthcare workers, degree distributions of healthcare workers, their assignment to wards, etc. Preliminary validation using data gathered from a 10-day long deployment of a wireless sensor network in the Medical Intensive Care Unit suggests that EMR logins can serve as realistic proxies for hospital-wide healthcare worker movement and contact patterns. Despite spatial and job-related constraints on healthcare worker movement and interactions, analysis reveals a strong structural similarity between the healthcare worker contact networks we generate and social networks that arise in other (e.g., online) settings. Furthermore, our analysis shows that disease can spread much more rapidly within the constructed contact networks as compared to random networks of similar size and density. Using the generated contact networks, we evaluate several alternate vaccination policies and conclude that a simple policy that vaccinates the most mobile healthcare workers first, is robust and quite effective relative to a random vaccination policy.     

Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus

We report the first whole-genome sequences for five strains, two carried and three pathogenic, of the emerging pathogen Haemophilus haemolyticus. Preliminary analyses indicate that these genome sequences encode markers that distinguish H. haemolyticus from its closest Haemophilus relatives and provide clues to the identity of its virulence factors.