Wastewater utilization for poly-β-hydroxybutyrate production by the cyanobacterium Aulosira fertilissima in a recirculatory aquaculture system

Intensive aquaculture releases large quantities of nutrients into aquatic bodies, which can lead to eutrophication. The objective of this study was the development of a biological recirculatory wastewater treatment system with a diazotrophic cyanobacterium, Aulosira fertilissima, and simultaneous production of valuable product in the form of poly-β-hydroxybutyrate (PHB). To investigate this possible synergy, batch scale tests were conducted under a recirculatory aquaculture system in fiber-reinforced plastic tanks enhanced by several manageable parameters (e.g., sedimentation, inoculum size, depth, turbulence, and light intensity), an adequate combination of which showed better productivity. The dissolved-oxygen level increased in the range of 3.2 to 6.9 mg liter⁻¹ during the culture period. Nutrients such as ammonia, nitrite, and phosphate decreased to as low as zero within 15 days of incubation, indicating the system''s bioremediation capability while yielding valuable cyanobacterial biomass for PHB production. Maximum PHB accumulation in A. fertilissima was found in sedimented fish pond discharge at 20-cm culture depth with stirring and an initial inoculum size of 80 mg dry cell weight (dcw) liter⁻¹. Under optimized conditions, the PHB yield was boosted to 92, 89, and 80 g m⁻², respectively for the summer, rainy, and winter seasons. Extrapolation of the result showed that a hectare of A. fertilissima cultivation in fish pond discharge would give an annual harvest of ∼17 tons dry biomass, consisting of 14 tons of PHB with material properties comparable to those of the bacterial polymer, with simultaneous treatment of 32,640 m³ water discharge.     

IL-10- and TGF-beta-mediated susceptibility in kala-azar and post-kala-azar dermal leishmaniasis: the significance of amphotericin B in the control of Leishmania donovani infection in India

Visceral leishmaniasis (VL) or kala-azar is known to be associated with a mixed Th1-Th2 response, and effective host defense requires the induction of IFN-gamma and IL-12. We address the role of the differential decline of IL-10 and TGF-beta in response to sodium antimony gluconate (SAG) and amphotericin B (AmB), the therapeutic success of SAG and AmB in Indian VL, and the significance of IL-10 and TGF-beta in the development and progression of post-kazla-azar dermal leishmaniasis (PKDL). In the active disease, PBMC from VL patients showed suppressed Ag-specific lymphoproliferation, IFN-gamma and IL-12 production, and elevation of IL-10 and TGF-beta. Cure corresponded with an elevation in IFN-gamma and IL-12 production and down-regulation of IL-10 and TGF-beta. Both CD4(+) and CD8(+) T cells were involved in IFN-gamma and IL-10 production. Interestingly, the retention and maintenance of residual IL-10 and TGF-beta in some SAG-treated individuals and the elevation of IL-10 and TGF-beta in PKDL, a sequel to kala-azar, probably reflects the role of these cytokines in reactivation of the disease in the form of PKDL. Contrastingly, AmB treatment of VL resulted in negligible TGF-beta levels and absolute elimination of IL-10, reflecting the better therapeutic activity of AmB and its probable role in the recent decline in PKDL occurrences in India. Moreover, elucidation of immune responses in Indian PKDL patients revealed a spectral pattern of disease progression where disease severity could be correlated inversely with lymphoproliferation and directly with TGF-beta, IL-10, and Ab production. In addition, the enhancement of CD4(+)CD25(+) T cells in active VL, their decline at cure, and reactivation in PKDL suggest their probable immunosuppressive role in these disease forms.     

Cytodiagnosis of filarial infections from an endemic area

OBJECTIVE: To throw light on cytologic findings as a possible mode of diagnosis of lymphatic filariasis. STUDY DESIGN: Filariasis has worldwide distribution, but lymphatic filariasis predominantly affects tropical and subtropical regions. Demonstration of microfilaremia, the specific test for diagnosis of lymphatic filariasis, often shows false negative results in endemic areas. The present study, done in an endemic area, showed the presence of microfilariae or adult worms of Wuchereria bancrofti in fine needle aspirates collected from amicrofilariaemic cases. In a few cases the discovery was incidental. A total 4,534 cases undergoing cytologic evaluation were carefully screened for the presence of adult worms or larvae, irrespective of clinical diagnosis. Microfilariae were demonstrated in both clinically suspected cases of filariasis and asymptomatic cases. RESULTS: A total of 1 positive cases were found; in 4 cases the clinical diagnosis was lymphatic filariasis, and 7 cases were asymptomatic. All 11 cases were amicrofilariaemic. CONCLUSION: Various sophisticated investigations are used for diagnosis of lymphatic filariasis without microfilaremia. Fine needle aspiration cytology, being a cheap, simple and easy procedure, may have some role in this field, but further detailed studies are needed before any final claim.     

Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion‐corrected density functional theory study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence‐directed features, such as small roll values for the purine–pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near‐zero slide to be most favorable for the purine–pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar–phosphate backbone with C3′‐endo sugars and this demands C1′–C1′ distance of about 5.4 Å along the chains. Consideration of an energy penalty term for deviation of C1′–C1′ distance from the mean value, to the recent DFT‐D functionals, specifically ωB97X‐D appears to predict reliable energy contour for AU/AU step. Such distance‐based penalty improves energy contours for the other purine–pyrimidine sequences also. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 107–120, 2014.     

In silico study of binding motifs in squalene synthase enzyme of secondary metabolic pathway solanaceae family

Solanaceae is an important family with several plants of medicinal importance. These medicinal plants have distinctive pathways for secondary metabolite biosynthesis. In most of the plants, two important compounds, dimethylallyl diphosphate and isopentenyl diphosphate, synthesize isoprenoid or terpenoids. Squalene synthase (SQS) is a key enzyme of the biosynthesis of isoprenoid (farnesyl pyrophosphate (FPP) → squalene). Withania somnifera (ashwagandha), an important medicinal plant of family solanaceae produces withanolides. Withanolides are secondary metabolites synthesized through isoprenoid pathway. In this study, 13 SQS protein sequences from the plants of solanacae family and Arabidopsis thaliana were analyzed. The conserved domains in corresponding sequences were searched. The multiple sequence alignment of conserved domains revealed the important motifs and identified the residue substitution in each motif. Our result further indicated that residue substitution in motifs might not lead to functional variation, although it may affect the binding affinity of Mg⁺⁺, FPP and NAD(P)H. In addition, the homology modelling of SQS enzyme of W. somnifera was done for the prediction of three-dimensional structure. Molecular docking study of considered substrates with WsSQS was performed and the docked structure were analyzed further. The docked structures showed binding affinity for motif 2 of WsSQS. Our analysis revealed that 29 residues of motif 2 might be important for catalytic/functional activity of SQS enzyme of W. somnifera. This study may provide an understanding of metabolic pathways responsible for the production of secondary metabolites. The motifs may play a key role in regulating the pathway towards enhanced production of metabolites.     

Direct regulation of topoisomerase activity by a nucleoid-associated protein

The topological homeostasis of bacterial chromosomes is maintained by the balance between compaction and the topological organization of genomes. Two classes of proteins play major roles in chromosome organization: the nucleoid-associated proteins (NAPs) and topoisomerases. The NAPs bind DNA to compact the chromosome, whereas topoisomerases catalytically remove or introduce supercoils into the genome. We demonstrate that HU, a major NAP of Mycobacterium tuberculosis specifically stimulates the DNA relaxation ability of mycobacterial topoisomerase I (TopoI) at lower concentrations but interferes at higher concentrations. A direct physical interaction between M. tuberculosis HU (MtHU) and TopoI is necessary for enhancing enzyme activity both in vitro and in vivo. The interaction is between the amino terminal domain of MtHU and the carboxyl terminal domain of TopoI. Binding of MtHU did not affect the two catalytic trans-esterification steps but enhanced the DNA strand passage, requisite for the completion of DNA relaxation, a new mechanism for the regulation of topoisomerase activity. An interaction-deficient mutant of MtHU was compromised in enhancing the strand passage activity. The species-specific physical and functional cooperation between MtHU and TopoI may be the key to achieve the DNA relaxation levels needed to maintain the optimal superhelical density of mycobacterial genomes.     

Syphilis and Its Correlates among Heterosexual Males Attending Sexually Transmitted Infection Clinics – Observation from a Multicity Cohort in Jiangsu Province,China

Objectives

To estimate the prevalence of HIV and syphilis, incidence of syphilis and to identify the correlates of syphilis infection among heterosexual male attendees of sexually transmitted infection (STI) clinics (MSC).

Methods

A cohort study of one-year duration was conducted in Yangzhou and Changzhou cities in Jiangsu province of China. The baseline survey commenced in June 2009, recruited 1225 consenting adult MSCs (609 in Yangzhou and 617 in Changzhou) through STI-clinic based convenience sampling.

Results

Baseline HIV and syphilis prevalence were 0.49% and 17.29% respectively. Syphilis incidence rate was 7.22 per 100 person-years (6.53 in Yangzhou and 7.76 in Changzhou) during the 6-month follow-up with retention fractions of 27.38% and 35.15% for Yangzhou and Changzhou respectively. Majority of the participants were middle-aged, high school educated, married, living with partners and non-migrants. Very few subjects reported recent and consistent condom-use with regular partners. Although considerable number of MSCs reported recent sexual exposure with female sex workers (FSW) and non-FSW casual partners, the proportion of reported condom use was very low during those exposures. In multivariate analyses higher age, having recent sex with FSWs and being HIV-positive were associated with higher syphilis sero-positivity while higher education was protective. In bivariate analyses, being married, divorced/widowed, official residency of the study cities and non-use of condom with regular partners predicted higher risk.

Conclusions

Considering the potential bridging role of MSCs between high and low-risk populations, effective intervention strategies among them targeting the correlates of syphilis infection are urgently called for in Jiangsu province of China.     

Bayesian hierarchical spatially correlated functional data analysis with application to colon carcinogenesis

Summary .   In this article, we present new methods to analyze data from an experiment using rodent models to investigate the role of p27, an important cell-cycle mediator, in early colon carcinogenesis. The responses modeled here are essentially functions nested within a two-stage hierarchy. Standard functional data analysis literature focuses on a single stage of hierarchy and conditionally independent functions with near white noise. However, in our experiment, there is substantial biological motivation for the existence of spatial correlation among the functions, which arise from the locations of biological structures called colonic crypts: this possible functional correlation is a phenomenon we term crypt signaling . Thus, as a point of general methodology, we require an analysis that allows for functions to be correlated at the deepest level of the hierarchy. Our approach is fully Bayesian and uses Markov chain Monte Carlo methods for inference and estimation. Analysis of this data set gives new insights into the structure of p27 expression in early colon carcinogenesis and suggests the existence of significant crypt signaling. Our methodology uses regression splines, and because of the hierarchical nature of the data, dimension reduction of the covariance matrix of the spline coefficients is important: we suggest simple methods for overcoming this problem.