Fish Assemblages in Three Tidal Saltmarsh and Mangrove Flats in Temperate NSW, Australia: A Comparison Based on Species Diversity and Abundance

Fish assemblages in three geographically distinct saltmarsh meadows and mangrove forests in the Sydney region were examined using fyke nets over three common sampling periods. The saltmarshes at Towra Point and Allens Creek, though of contrasting geomorphic setting, showed similar fish assemblages during spring tides, with relatively high diversity and abundance. The saltmarsh at Bicentennial Park, reclaimed from dredge spoil in the early 1960’s, showed significantly lower diversity and abundance. Fish assemblages in the three mangrove settings were each distinct, though with no significant differences in diversity and abundance between sites. The result raises questions about the efficacy of created saltmarsh as a compensatory habitat for fish.     

Isolation and Characterization of Antidermatophytic Bioactive Molecules from Piper longum L. Leaves

Piper longum L. (Piperaceae) commonly known as “long pepper” is a well known medicinal plant in ayurveda. Different parts of this plant, such as root, seed, fruit, whole plant etc. are used traditionally in various ailments. Here we have investigated the antidermatophytic activity of sequentially extracted petroleum ether, chloroform, methanol and water extracts from P. longum leaf against Trichophytonmentagrophytes, T. rubrum, T. tonsurans, Microsporum fulvum and M. gypseum. Better activity of chloroform and methanol extracts was observed. The chloroform extract was selected for further study and the MIC value was recorded as 5.0 mg ml⁻¹ against the test organisms. In the chloroform extract, tannins and phenolic compounds were detected. Further activity-guided fractionation of chloroform extract by silica gel column chromatography yielded nine major fractions. Among these, fraction-1, 4, 5 and 7 showed higher antidermatophytic activity. Fraction-4 on further purification by repeated column chromatography yielded a potential antidermatophytic fraction showing MIC value of 0.625 mg ml⁻¹ against T. mentagrophytes and T. rubrum as determined by broth microdilution method. The major compounds were identified as 1,2-benzenedicarboxylic acid, bis(2-ethylhexyl) ester (C₂₄H₃₈O₄] (41.45 %), 2,2-dimethoxybutane (C₆H₁₄O₂] (13.6 %) and β-myrcene (C₁₀H₁₆) (6.75 %) based on GC–MS data.     

Dark proteins: effect of inclusion body formation on quantification of protein expression

Plasmid-borne gene expression systems have found wide application in the emerging fields of systems biology and synthetic biology, where plasmids are used to implement simple network architectures, either to test systems biology hypotheses about issues such as gene expression noise or as a means of exerting artificial control over a cell's dynamics. In both these cases, fluorescent proteins are commonly applied as a means of monitoring the expression of genes in the living cell, and efforts have been made to quantify protein expression levels through fluorescence intensity calibration and by monitoring the partitioning of proteins among the two daughter cells after division; such quantification is important in formulating the predictive models desired in systems and synthetic biology research. A potential pitfall of using plasmid-based gene expression systems is that the high protein levels associated with expression from plasmids can lead to the formation of inclusion bodies, insoluble aggregates of misfolded, nonfunctional proteins that will not generate fluorescence output; proteins caught in these inclusion bodies are thus "dark" to fluorescence-based detection methods. If significant numbers of proteins are incorporated into inclusion bodies rather than becoming biologically active, quantitative results obtained by fluorescent measurements will be skewed; we investigate this phenomenon here. We have created two plasmid constructs with differing average copy numbers, both incorporating an unregulated promoter (P(LtetO-1) in the absence of TetR) expressing the GFP derivative enhanced green fluorescent protein (EGFP), and inserted them into Escherichia coli bacterial cells (a common model organism for work on the dynamics of prokaryotic gene expression). We extracted the inclusion bodies, denatured them, and refolded them to render them active, obtaining a measurement of the average number of EGFP per cell locked into these aggregates; at the same time, we used calibrated fluorescent intensity measurements to determine the average number of active EGFP present per cell. Both measurements were carried out as a function of cellular doubling time, over a range of 45-75 min. We found that the ratio of inclusion body EGFP to active EGFP varied strongly as a function of the cellular growth rate, and that the number of "dark" proteins in the aggregates could in fact be substantial, reaching ratios as high as approximately five proteins locked into inclusion bodies for every active protein (at the fastest growth rate), and dropping to ratios well below 1 (for the slowest growth rate). Our results suggest that efforts to compare computational models to protein numbers derived from fluorescence measurements should take inclusion body loss into account, especially when working with rapidly growing cells.     

The effect of C-terminal domain deletion on the catalytic activity of Leishmania donovani surface proteinase GP63: Role of Ser446 in proteolysis

The kinetoplastid protozoan Leishmania encodes major surface glycoprotein GP63, a zinc metallo-peptidase (EC.3.4.24.36) expressed both in promastigote and amastigote life stages. In the present study, we explored for the first time the role of C-terminal domain (CTD) in proteinase activity by serial truncation of Leishmania donovani GP63 (LdGP63) from carboxyl terminal end (CTend). Deletion of 180–211 amino acids from CTend (Δ420 and Δ389) resulted in almost 50% loss of catalytic activity against azocasein, casein and gelatin. Moreover, all the truncated constructs showed reduced activity towards immunoglobulin (IgG). Upon homology modeling, we identified two residues, S446, and F448 in CTD, conserved in different Leishmania species, which were positioned 6.8–11 Å apart from the active site. To ascertain the role of S446 and F448 in catalysis, we replaced S446 with Ala and Thr, and F448 with Val and Tyr by site-directed mutagenesis. The variant enzymes (S446T, F448V, and F448Y) maintained near wild-type activity, whereas S446A demonstrated 50% loss of catalytic activity towards the cleavage of various biological substrates. Kinetic analysis of S446A resulted in a 2.6-fold decrease in the affinity, 10-fold decrease in turn-over rates, and large increase in transition-state binding energy (1.4 kcal/mol) for the quenched peptide substrates. These results emphasize the relevance of CTD in the proteolytic activity of LdGP63. Fluorescence spectroscopy, and CD analysis however, indicated that the reduced activities showed by Δ389 and S446A were not due to global changes in the enzyme structures. Indeed, identification of S446 and its possible role in the stabilization of transition-state binding between enzyme and substrate can be exploited towards understanding of structure–function relationship of GP63.     

Characterization of a galactose binding serum lectin from the Indian catfish, Clarias batrachus: possible involvement of fish lectins in differential recognition of pathogens

A lectin with molecular mass around 200 kDa was isolated from the serum of the Indian catfish Clarias batrachus. The bioactivity of this serum lectin was Ca2+ and pH dependent. The lectin appeared to be specific for alpha-methyl galactose and sialoglycoproteins like porcine and bovine submaxillary mucin and could agglutinate human, rabbit, mice, rat and chicken erythrocytes. This fish lectin was able to specifically agglutinate different gram negative bacteria. When it was checked against different strains of the fish pathogen Aeromonas sp., it significantly altered the viability and pathogenicity of the bacteria. Binding of the lectin to Aeromonas sp., resulted in a dose dependent increase in the bactericidal activity of fish macrophages. However, when the lectin was checked against different gram positive bacteria it could not agglutinate or affect the viability of those strains and also failed to bring about any significant change in the bactericidal potential of fish macrophages. The lectin was able to induce the proliferation of head kidney lymphocytes of Clarias and helped in the release of 'IL-1' like cytokines from head kidney macrophages.     

Changes in membrane lipids and amino acid transport in a nystatin-resistant Aspergillus niger

A nystatin-resistant mutant of Aspergillus niger is described that has quantitative changes in phospholipid composition compared with the wild type. The proportion of linoleic acid in total phospholipids was elevated in the mutant from 38 to 56% and the proportion of oleic acid was lowered from 28 to 12%. Amino acid transport is also altered, the Vmax values for the uptake of leucine, lysine, and glutamic acid being generally higher in the mutant; for glutamic acid the increase was from 15 to 35 nmol.mg-1.min-1.     

Synthesis and SAR of alkanediamide-linked bisbenzamidines with anti-trypanosomal and anti-pneumocystis activity

A series of alkanediamide-linked bisbenzamidines was synthesized and tested in vitro against a drug-sensitive strain of Trypanosoma brucei brucei, a drug-resistant strain of Trypanosoma brucei rhodesiense and Pneumocystis carinii. Bisbenzamidines linked with longer alkanediamide chains were potent inhibitors of both strains of T. brucei. However, bisbenzamidines linked with shorter alkanediamide chains were the most potent compounds against P. carinii. N,N′-Bis[4-(aminoiminomethyl)phenyl] hexanediamide, 4 displayed potent inhibition (IC₅₀ = 2–3 nM) against T. brucei and P. carinii, and was non-cytotoxic in the A549 human lung carcinoma cell line. The inhibitory bioactivity was significantly reduced when the amidine groups in 4 were moved from the para to the meta positions or replaced with amides.     

A novel approach for predicting the evolutionary time of acquisition of foreign genes by bacteria: Application of codon usage analyses

Lysogenic bacteriophages are considered as a major player for the introduction of foreign genes into bacterial strains. At the time of introduction foreign genes do not fit well into the translation system of the recipient host bacterium as they tend to retain the characteristics of the donor bacterium from which they have been transferred. Consequently foreign genes are poorly transcribed at the early phase of their evolution within the host bacterium. This is largely due to the difference in the codon usage pattern between the horizontally transferred genes and the host bacterium. In this study we present detailed analyses of various parameters of the codon usages such as codon adaptation index (CAI), mean difference (MD) of the relative adaptiveness, synonymous substitution rate (SSR) of six different phage encoded toxin genes (cholera toxin, shiga toxin, diphtheria toxin, neurotoxin C1, enterotoxin type A and cytotoxin), and proposed conceptual relationship between the evolutionary time of acquisition of the foreign genes and the selected set of parameters of the codon usage. On the basis of the observed data we hypothesize that CAI, MD and SSR of the phage encoded toxin genes are correlated with the evolutionary time of their acquisition, and have developed a novel approach based on the analyses of these parameters, which can be used to predict the evolutionary time of their acquisition by the corresponding host bacterium.     

Population structure,seasonal genotypic differentiation,and clonal diversity of weedy dandelions in three Boston area populations (Taraxacum sp.)

Weedy dandelions have a worldwide distribution and thrive in urban environments despite a lack of sexual reproduction throughout most of its range. North American dandelions, introduced from Eurasia, are believed to be primarily, if not exclusively, apomictic triploids. In some European populations, apomicts co‐occur with diploid sexual individuals and hybridizations can create genetically unique apomicts, which may subsequently disperse and establish new populations globally. Using six nuclear microsatellite markers and a cpDNA intergenic spacer, we investigate the impact of this unusual natural history on population structure and diversity in three urban Boston area dandelion populations. Our results show high levels of genetic diversity within populations, spatial population structure, and seasonal genotypic differentiation in flowering times. We find evidence that sexual reproduction and recombination, presumably in Europe, and extensive gene flow drive these patterns of diversity and create the appearance of panmixia despite the lack of evidence for local sexual reproduction.     

Effect of Sulfur-Containing Compounds on Growth of Methanosarcina barkeri in Defined Medium

Methanosarcina barkeri Fusaro (DSM 804) could grow on methanol in a mineral medium containing cysteine or thiosulfate as the sole sulfur source. Optimum growth occurred at cysteine concentrations of 1 to 2.8 mM and at thiosulfate concentrations of 2.5 to 5 mM. No inhibition of growth was observed even when these concentrations were doubled in the culture medium. Under the optimum cysteine and thiosulfate concentrations, the generation times of the organism were about 8 to 10 and 10 to 12 h, respectively, giving a cell yield of about 0.14 to 0.17 and 0.08 to 0.11 g (dry weight)/g of methanol consumed. The organism metabolized cysteine and thiosulfate during growth, giving rise to sulfide in the culture medium. H₂S evolution from cysteine and thiosulfate was catalyzed by two enzymes, namely cysteine desulfhydrase and thiosulfate reductase, respectively, as revealed by enzyme assay in the crude cell-free extract of the organism.