Molecular characterization of Osh6p, an oxysterol binding protein homolog in the yeast Saccharomyces cerevisiae

Oxysterol binding protein (OSBP) and its homologs have been shown to regulate lipid metabolism and vesicular transport. However, the exact molecular function of individual OSBP homologs remains uncharacterized. Here we demonstrate that the yeast OSBP homolog, Osh6p, bound phosphatidic acid and phosphoinositides via its N-terminal half containing the conserved OSBP-related domain (ORD). Using a green fluorescent protein fusion chimera, Osh6p was found to localize to the cytosol and patch-like or punctate structures in the vicinity of the plasma membrane. Further examination by domain mapping demonstrated that the N-terminal half was associated with FM4-64 positive membrane compartments; however, the C-terminal half containing a putative coiled-coil was localized to the nucleoplasm. Functional analysis showed that the deletion of OSH6 led to a significant increase in total cellular ergosterols, whereas OSH6 overexpression caused both a significant decrease in ergosterol levels and resistance to nystatin. Oleate incorporation into sterol esters was affected in OSH6 overexpressing cells. However, Lucifer yellow internalization, and FM4-64 uptake and transport were unaffected in both OSH6 deletion and overexpressing cells. Furthermore, osh6Δ exhibited no defect in carboxypeptidase Y transport and maturation. Lastly, we demonstrated that both the conserved ORD and the putative coiled-coil motif were indispensable for the in vivo function of Osh6p. These data suggest that Osh6p plays a role primarily in regulating cellular sterol metabolism, possibly stero transport.

Molecular characterization and analysis of a truncated serotonin receptor gene expressed in neural and reproductive tissues of abalone

In molluscs, the neurotransmitter serotonin (5-HT) has been linked to a variety of biological roles including gamete maturation and spawning. The possible involvement of 5-HT in abalone gamete release was demonstrated by a dose-dependent increase in Haliotis rubra gonad contractile bioactivity following 5-HT stimulation. Physiological functions associated with 5-HT, are mediated through binding to 5-HT receptors. A cDNA encoding a putative 5-HT receptor consisting of 359 amino acids was isolated from the tropical abalone H. asinina, termed 5-HT_{1 ha}. The 5-HT_{1 ha} shares G-protein-coupled receptor motifs with metazoan 5-HT receptors, including predicted transmembrane domains, active sites for protein kinase action, and N-linked glycosylation sites. However, the third intracellular loop of 5-HT_{1 ha} is relatively short, and only six transmembrane domains are predicted, implying a truncated receptor. Phylogenetic analysis with known 5-HT receptor genes suggests that 5-HT_{1 ha} belongs to the type 1 5-HT receptor family. Expression analysis by RT-PCR showed that 5-HT_{1 ha}  mRNA was present in all tissues examined, including the neural ganglia and gonad tissues. Immunocytochemistry revealed the presence of 5-HT_{1 ha} specifically within the soma of neuronal cells located in the outer cortex of both cerebral and pleuropedal ganglia. In ovarian and testicular tissues, 5-HT_{1 ha} immunoreactivity was observed in epithelial cells of the outer capsule and connective tissue of the trabeculae to which the gamete follicles adhere. Whether this receptor transcript is translated to a functional protein needs to be verified, but if so, it could play a role in reproduction.

Molecular characterization and enzymatic hydrolysis of flavanoid extracted from citrus waste

The citrus fruit processing industry generates substantial quantities of waste rich in phenolic substances, which is a valuable natural source of polyphenols (flavonoids) such as naringin and its disposal is becoming a major problem. In the US alone, the juice processing of oranges and grapefruit generates over 5 Mt of citrus waste every year. In the case of India, about 2.15 Mt of citrus peel out of 6.28 Mt of citrus fruits are produced yearly from citrus juice processing. In case of Australia, about 15-40% of citrus peel waste is generated by processing of citrus fruit (0.85 Mt). Thus Isolation of functional compounds (mostly flavanoids) and their further processing can be of interest to the food and pharmaceutical industry. This peel is rich in naringin and may be used for rhamnose production by utilizing α-L-rhamnosidase (EC 3.2.1.40), an enzyme that catalyzes the cleavage of terminal rhamnosyl groups from naringin to yield prunin and rhamnose. We recently purified recombinant α-L-rhamnosidase from E. coli cells using immobilized metal-chelate affinity chromatography (IMAC) and used it for naringin hydrolysis. The purified enzyme established hydrolysis of naringin extracted from citrus peel and thus endorses its industrial applicability for producing rhamnose. Infrared (IR) spectroscopy confirmed molecular characteristics of naringin extracted from citrus peel waste.

Morphometric and molecular characterization of the species of Uncinaria Frölich, 1789 (Nematoda) parasitic in the Australian fur seal Arctocephalus pusillus doriferus (Schreber), with notes on hookworms in three other pinniped hosts

This study presents morphological and molecular data on hookworms from the Australian fur seal Arctocephalus pusillus doriferus (Schreber) currently identified in Australian waters as Uncinaria hamiltoni Baylis, 1933. Additional specimens from the Australian sea lion Neophoca cinerea (Péron) and the New Zealand fur seal Arctocephalus forsteri (Lesson) from Australia, and the Southern elephant seal Mirounga leonina (Linnaeus) from Antarctica, were included. Using the internal transcribed spacer (ITS), hookworms from A. p. doriferus, N. cinerea and A. forsteri were found to be genetically similar but distinct from Uncinaria spp. found in M. leonina from Antarctica, as well as from Zalophus californianus (Lesson) and Callorhinus ursinus (Linnaeus) from California. Few morphological differences were detected between these taxa.

Synchrotron-FTIR microspectroscopy enables the distinction of lipid accumulation in thraustochytrid strains through analysis of individual live cells

The superior characteristics of high photon flux and diffraction-limited spatial resolution achieved by synchrotron-FTIR microspectroscopy allowed molecular characterization of individual live thraustochytrids. Principal component analysis revealed distinct separation of the single live cell spectra into their corresponding strains, comprised of new Australasian thraustochytrids (AMCQS5-5 and S7) and standard cultures (AH-2 and S31). Unsupervised hierarchical cluster analysis (UHCA) indicated close similarities between S7 and AH-7 strains, with AMCQS5-5 being distinctly different. UHCA correlation conformed well to the fatty acid profiles, indicating the type of fatty acids as a critical factor in chemotaxonomic discrimination of these thraustochytrids and also revealing the distinctively high polyunsaturated fatty acid content as key identity of AMCQS5-5. Partial least squares discriminant analysis using cross-validation approach between two replicate datasets was demonstrated to be a powerful classification method leading to models of high robustness and 100% predictive accuracy for strain identification. The results emphasized the exceptional S-FTIR capability to perform real-time in vivo measurement of single live cells directly within their original medium, providing unique information on cell variability among the population of each isolate and evidence of spontaneous lipid peroxidation that could lead to deeper understanding of lipid production and oxidation in thraustochytrids for single-cell oil development.

Identification, characterisation and expression analysis of natural killer receptor genes in chlamydia pecorum infected koalas (phascolarctos cinereus)

BACKGROUND: Koalas (Phascolarctos cinereus), an iconic Australian marsupial, are being heavily impacted by the spread of Chlamydia pecorum, an obligate intracellular bacterial pathogen. Koalas vary in their response to this pathogen, with some showing no symptoms, while others suffer severe symptoms leading to infertility, blindness or death. Little is known about the pathology of this disease and the immune response against it in this host. Studies have demonstrated that natural killer (NK) cells, key components of the innate immune system, are involved in the immune response to chlamydial infections in humans. These cells can directly lyse cells infected by intracellular pathogens and their ability to recognise these infected cells is mediated through NK receptors on their surface. These are encoded in two regions of the genome, the leukocyte receptor complex (LRC) and the natural killer complex (NKC). These two families evolve rapidly and different repertoires of genes, which have evolved by gene duplication, are seen in different species. METHODS: In this study we aimed to characterise genes belonging to the NK receptor clusters in the koala by searching available koala transcriptomes using a combination of search methods. We developed a qPCR assay to quantify relative expression of four genes, two encoded within the NK receptor cluster (CLEC1B, CLEC4E) and two known to play a role in NK response to Chalmydia in humans (NCR3, PRF1). RESULTS: We found that the NK receptor repertoire of the koala closely resembles that of the Tasmanian devil, with minimal genes in the NKC, but with lineage specific expansions in the LRC. Additional genes important for NK cell activity, NCR3 and PRF1, were also identified and characterised. In a preliminary study to investigate whether these genes are involved in the koala immune response to infection by its chlamydial pathogen, C. pecorum, we investigated the expression of four genes in koalas with active chlamydia infection, those with past infection and those without infection using qPCR. This analysis revealed that one of these four, CLEC4E, may be upregulated in response to chlamydia infection. CONCLUSION: We have characterised genes of the NKC and LRC in koalas and have discovered evidence that one of these genes may be upregulated in koalas with chlamydia, suggesting that these receptors may play a role in the immune response of koalas to chlamydia infection.

Purification and characterization of a low molecular mass alkaliphilic lipase of Bacillus cereus MTCC 8372

A low molecular mass alkaliphilic extra-cellular lipase of Bacillus cereus MTCC 8372 was purified 35-fold by hydrophobic interaction (Octyl-Sepharose) chromatography. The purified enzyme was found to be electrophoretically pure by denaturing gel electrophoresis and possessed a molecular mass of approximately 8 kDa. It is a homopentamer of 40 kDa as revealed by native-PAGE. The lipase was optimally active at 55 °C and retained approximately half of its original activity after 40 min incubation at 55 °C. The enzyme was maximally active at pH 8.5. Mg ²⁺ , Cu ²⁺ , Ca ²⁺ , Hg ²⁺ , Al ³⁺ and Fe ³⁺ at 1 mM enhanced hydrolytic activity of the lipase. Interestingly, Hg ²⁺ ions synergized and Zn ²⁺ and Co ²⁺ ions antagonized the lipase activity. Among surfactants, Tween 80 promoted the lipase activity. Phenyl methyl sulfonyl fluoride (PMSF, 15 mM) decreased 98% of original activity of lipase. The lipase was highly specific towards p -nitrophenyl palmitate and showed a V _max and K _m of 0.70 mmol.mg ⁻¹ .min ⁻¹ and 32 mM for hydrolysis of p NPP.

Characterization of structure and energy of TixCy cluster at early formation stage in iron matrix by molecular dynamics

The structure, energy and bonding property of TixCy clusters formed in iron matrix were studied through molecular dynamics (MD) simulation method. The initial clusters with 1D-linear, 2D-ring, and 3D-tetrahedral structures were determined and their stability was calculated. The effect of temperature on the stability of the clusters was also discussed. In addition, the dissociation path of TiC clusters in iron matrix and the corresponding energy variation were analyzed. © 2014 Elsevier B.V. All rights reserved.

Molecular dynamics approach to the structural characterization and transport properties of poly(acrylonitrile)/N,N-dimethylformamide solutions

Poly(acrylonitrile) (PAN) in N,N-dimethylformamide (DMF) is a popular solution for producing large variety of polymer products. To precisely describe the behaviours of PAN and DMF in the synthesis processes, it is significant to call for more details about the structure, some thermodynamic and dynamical properties of PAN-DMF solutions. A PAN-DMF solution was simulated via molecular dynamics with an all-atom OPLS type potential in both the NPT and NVT ensembles. The simulation results were evaluated with quantum mechanical calculations (MP2/6-311 ++G(d,p) and counterpoise procedure) and were compared with available experimental results. The liquid structure was illustrated with pair correlation functions and transport and dynamics properties were calculated with the mean-square displacements MSD and the velocity autocorrelation functions. The strong H-bonds of C≡N « H-C=O, CH » O=C-H and CH2 O=C-H, with distances of 2.55 Å, 2.55 Å and 2.65 Å, respectively, were found. The largest interaction energy of - 7.157 kcal/mol between DMF molecules and PAN molecules was found at 4.9 Å center-of-mass distance. A potential profile of intermolecular interaction of DMF with PAN along the interaction distance was presented, clearly showing an increase of DMF vaporisation heat when it getting close to PAN molecules. This provided very useful information to analyse the vaporisation behaviours of DMF at the microscopic level, which is essential to comprehensively understand molecular rearrangements towards the design of synthetic processes. The impact of the presence of the PAN on the DMF solution properties were also benchmarked with pure DMF solution.

Molecular identification and characterization of Pseudomonas sp. NCCP-407 for phenol degradation isolated from industrial waste

Phenol is a toxic pollutant found in effluent of numerous industries and its elimination is a foremost challenge. The utilization of bacteria plays a crucial role in phenol bioremediation. For isolation of phenol degrading bacteria, sample was collected from industrial waste and enriched in mineral salt medium (MSM) contained 300 mg/L phenol. The strain was identified based on 16S rRNA gene analysis as Pseudomonas species and the phylogenetic analysis affiliated the strain with Pseudomonas monteilii (AF064458) as the most closely related species. Phenol tolerance of the strain in MSM supplemented with various concentrations of phenol indicates that the strain NCCP-407 can grow best at 750 mg L-1 phenol. The strain showed complete degradation of 750 mg L-1 phenol in 56 hours when supplement as a sole source of carbon and energy with the average degradation rate of 28 mg L-1h-1. The doubling time was recorded approximately as 12.49 h-1. The present study suggests that this strain is efficient in phenol degradation and can be used in treatment of wastewater containing phenol.