Biodegradation of diesel oil by an Arabian Sea sediment culture isolated from the vicinity of an oil field

Laboratory scale batch studies were performed to test the diesel oil biodegradation ability of ES1 cultures isolated from Arabian Sea sediments obtained from the vicinity of an oil field. This culture could utilize diesel as the sole source of carbon and energy. Under aerobic conditions, 39% loss of diesel oil was observed over 8 days where 80% of the loss was due to aliphatic constituents. Under anoxic nitrate reducing conditions the rate and extent of degradation was significantly lower, i.e., 18% over 50 days. Salt acclimatized cultures could tolerate salinities up to 3.5% and demonstrated optimal performance at a salinity of 0.5%. The optimum N/P ratio for these cultures was found to be in the range of 2:1-5:1. Addition of two trace elemental substance formulations exhibited a significant inhibitory effect on culture growth. This culture has good potential for decontamination of oil-contaminated marine and subsurface environments.     

Identification, sequence characterization, and analysis of expression profiles of three novel CC chemokines from domestic duck (Anas platyrhynchos)

Chemokines are low-molecular weight-chemotactic cytokines, which are involved in lymphocyte trafficking and migration of leucocytes to sites of injury, in immune surveillance and in healing process. They also play a role in pathogenesis of inflammatory diseases. Three novel CC chemokines were identified from domestic duck (Anas platyrhynchos) by screening of an enriched cDNA library constructed from mitogen-stimulated splenic mononuclear cells. Two of the clones (AB163 and AB330) had a very high nucleotide (both about 81%) and predicted amino acid level (71 and 76%, respectively) identity to the reported chicken macrophage inflammatory protein 1- (MIP-1; SCYA4) and regulated upon activation of normal T-cell expressed and secreted (RANTES; SCYA5) sequences. In phylogenetic analysis, these molecules clustered together with corresponding chemokines reported from other vertebrates. The third clone (AB187) had highest homology to chicken MIP-1 (36% amino acid identity) and showed closer relation to a number of chemokines belonging to monocyte chemoattractant proteins and MIP-1 chemokines. Expression of these molecules was upregulated upon mitogen stimulation of splenocytes as detected by semiquantitative RT-PCR. AB187 showed several fold increases (about 8.5 times) in the mRNA expression. Basal level expression of some of these chemokines was detected in both lymphoid and nonlymphoid tissues, including spleen, liver, lung, and bone marrow. Considering the importance of this animal species as a model for diseases such as chronic human hepatitis B, further studies will offer valuable insights into the role of these molecules in immunopathology of such diseases.The nucleotide sequences that are reported in this paper have been submitted to the NCBI Genbank database. Accession nos. AB163 (AY641435), AB187 (AY641436), and AB330 (AY641437).     

NMR structure of a 2',5' RNA favors A type duplex with compact C2'endo nucleotide repeat

In order to provide a structural basis for the unusual properties of 2',5' nucleic acids, especially their unsuitability as information molecules, we report here a high resolution NMR structure of a 2',5' RNA fragment r(GCCGCGGC). It forms an A type duplex with C2'endo compact nucleotide repeat, instead of the familiar C3'endo compact nucleotide (seen in RNA) supporting the deductions made earlier from stereochemical considerations. This data together with the observation that 2',5' nucleic acids require mandatory slide and displacement for duplex and triplex structure formation suggest their reluctance to form the biologically relevant B type duplex. It is argued that this lack of flexibility for helical polymorphism and other inadequacies as a consequence of this may be a contributing factor for the rejection of 2',5' links by nature. The structure exhibits interesting features such as the syn glycosyl conformation for the terminal guanine and a hydrogen bond between O3' hydroxyl and anionic oxygen of the phosphate.     

Bioactivity,mechanism of action,and cytotoxicity of copper-based nanoparticles: A review

Nanotechnology is an emerging branch of science, which has potential to solve many problems in different fields. The union of nanotechnology with other fields of sciences including physics, chemistry, and biology has brought the concept of synthesis of nanoparticles from their respective metals. Till date, many types of nanoparticles have been synthesized and being used in different fields for various applications. Moreover, copper nanoparticles attract biologists because of their significant and broad-spectrum bioactivity. Due to the large surface area to volume ratio, copper nanoparticles have been used as potential antimicrobial agent in many biomedical applications. But the excess use of any metal nanoparticles increase the chance of toxicity to humans, other living beings, and environment. In this article, we have critically reviewed the bioactivities and cytotoxicity of copper nanoparticles. We have also focused on possible mechanism involved in its interaction with microbes.     

Modulation of granulocyte colony stimulating factor conformation and receptor binding by methionine oxidation

Biosimilars offer an avenue for potential cost savings and enhanced patient access to various emerging therapies in a budget neutral way. Biosimilars of the granulocyte colony stimulating factor (GCSF) are an excellent example in this regard with as many as 18 versions of the drug being currently approved across globe for treatment of neutropenia. Here, we identified oxidation of the various methionine residues in GCSF as a key heterogeneity that adversely impact its efficacy. In agreement with earlier studies, it was found that oxidation of Met 122 and Met 127 significantly contributes toward reduction of GCSF efficacy, measured using binding affinity to the GCSF receptor. The combination of molecular dynamics simulation along with structural characterization studies established that oxidation of Met 127 and Met 122 brings about a small local conformational change around the B‐C loop in GCSF structure due to slight displacement of Asp113 and Thr117 residues. The simulation studies were validated using fluorescence quenching experiments using acrylamide as quencher and site‐directed mutagenesis by replacing Met 122 and Met 127 residues with alanine. The results of this study lead to an enhanced mechanistic understanding of the oxidation in GCSF and should be useful in protein engineering efforts to design stable, safe, and efficacious GCSF product. In addition, the structure‐function information can provide targets for protein engineering during early drug development and setting specifications of allowable limits of product variants in biosimilar products.     

Clathrin senses membrane curvature

The ability of proteins to assemble at sites of high membrane curvature is essential to diverse membrane remodeling processes, including clathrin-mediated endocytosis. Multiple adaptor proteins within the clathrin pathway have been shown to sense regions of high membrane curvature, leading to local recruitment of the clathrin coat. Because clathrin triskelia do not bind to the membrane directly, it has remained unclear whether the clathrin coat plays an active role in sensing membrane curvature or is passively recruited by adaptor proteins. Using a synthetic tag to assemble clathrin directly on membrane surfaces, here we show that clathrin is a strong sensor of membrane curvature, comparable with previously studied adaptor proteins. Interestingly, this sensitivity arises from clathrin assembly rather than from the properties of unassembled triskelia, suggesting that triskelia have preferred angles of interaction, as predicted by earlier structural data. Furthermore, when clathrin is recruited by adaptors, its curvature sensitivity is amplified by 2- to 10-fold, such that the resulting protein complex is up to 100 times more likely to assemble on a highly curved surface compared with a flatter one. This exquisite sensitivity points to a synergistic relationship between the coat and its adaptor proteins, which enables clathrin to pinpoint sites of high membrane curvature, an essential step in ensuring robust membrane traffic. More broadly, these findings suggest that protein networks, rather than individual protein domains, are likely the most potent drivers of membrane curvature sensing.     

Cathelicidin is involved in the intracellular killing of mycobacteria in macrophages

Macrophages have been shown to kill Mycobacterium tuberculosis through the action of the antimicrobial peptide cathelicidin (CAMP), whose expression was shown to be induced by 1,25-dihydroxyvitamin D3 (1,25D3). Here, we investigated in detail the antimycobacterial effect of murine and human cathelicidin against Mycobacterium smegmatis and M. bovis BCG infections. We have synthesized novel LL-37 peptide variants that exhibited potent in vitro bactericidal activity against M. smegmatis, M. bovis BCG and M. tuberculosis H37Rv, as compared with parental peptide. We show that the exogenous addition of LL-37 or endogenous overexpression of cathelicidin in macrophages significantly reduced the intracellular survival of mycobacteria relative to control cells. An upregulation of cathelicidin mRNA expression was observed that correlated with known M. smegmatis killing phases in J774 macrophages. Moreover, RNAi-based Camp knock-down macrophages and Camp(-/-) bone marrow derived mouse macrophages were significantly impaired in their ability to kill mycobacteria. M. smegmatis killing in Camp(-/-) macrophages was less extensive than in Camp(+/+) cells following activation with FSL-1, an inducer of cathelicidin expression. Finally we show that LL-37 and 1,25D3 treatment results in increase in colocalization of BCG-containing phagosomes with lysosomes. Altogether, these data demonstrate that cathelicidin plays an important role in controlling intracellular survival of mycobacteria.     

Fast parallel tandem mass spectral library searching using GPU hardware acceleration

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.