The Rv1651c-encoded PE-PGRS30 protein expressed in Mycobacterium smegmatis exhibits polar localization and modulates its growth profile

Sequencing analysis of the complete genome of Mycobacterium tuberculosis (Mtb) H37Rv resulted in the identification of a novel multigene, the PE family of genes. The genes of the largest PE_PGRS subfamily of the PE family are mainly restricted to pathogenic mycobacteria, and their exact role in the biology of Mtb is not clearly understood. Based on their sequence homology, PE_PGRS proteins were initially thought to serve common functions. However, studies on individual proteins reveal that the individual proteins of this subfamily could be performing several unrelated tasks. In the present study, we investigated the function of PE_PGRS30 by expressing it in Mycobacterium smegmatis. PE_PGRS30 expression in M. smegmatis resulted in phenotypic changes with altered colony morphology and growth profile. The recombinant PE_PGRS30 showed polar localization and was found to be associated with the cell wall of M. smegmatis. Thus, the present study suggests that the prolonged lag phase of growth caused by the PE_PGRS30 may, in part, contribute to the latency of Mtb.     

Dissolved phosphorus concentrations and sediment interactions in effluent–dominated Ozark streams

Phosphorus (P) loads from point sources have a significant influence on dissolved P concentrations in streams and sediment-water column dynamics. The goal of this study was to quantify dissolved P concentrations and sediment-P interactions in Ozark (USA) headwater streams with high point source P loads. Specifically, the objectives were to: (1) compare soluble reactive P (SRP) upstream and downstream from wastewater treatment plant (WWTP) effluent discharges; (2) examine longitudinal gradients in SRP downstream from WWTPs; (3) evaluate the effect of WTTP P inputs on sediment-water column P equilibrium and sediment exchangeable P. Water and sediment samples were collected, extracted and analyzed from July 2002 through June 2003 at these Ozark streams. Mean SRP concentrations in the select Ozark streams were significantly greater downstream from effluent discharges (0.08–2.10 mg L⁻¹) compared to upstream (0.02–0.12 mg L⁻¹). Effluent discharge from the WWTPs increased equilibrium concentrations between stream sediments and the water column; mean sediment equilibrium P concentration (EPC₀) was between 0.01–0.07 mg L⁻¹ upstream from WWTP and the increase downstream was proportional to that observed in water column SRP. Sediment exchangeable P (EXP) was greater downstream from the effluent discharges (0.3–6.8 mg kg⁻¹) compared to upstream (0.03–1.4 mg kg⁻¹), representing a substantial transient storage of P inputs from WWTPs. Furthermore, P was generally not retained in these stream reaches when dilution was considered using a hydrologic tracer and was released in one stream reach where effluent P concentrations decreased over the study period. Thus, the effect of the WWTPs was profound in these streams increasing water column and sediment-bound P, and also reducing the ability of these stream reaches to retain P. In P-enriched streams, effluent P discharges likely regulate sediment and aqueous phase P equilibrium and sediment bioavailable P, not the sediments.     

Comparison of three methods to estimate genetic ancestry and control for stratification in genetic association studies among admixed populations

Population stratification may confound the results of genetic association studies among unrelated individuals from admixed populations. Several methods have been proposed to estimate the ancestral information in admixed populations and used to adjust the population stratification in genetic association tests. We evaluate the performances of three different methods: maximum likelihood estimation, ADMIXMAP and Structure through various simulated data sets and real data from Latino subjects participating in a genetic study of asthma. All three methods provide similar information on the accuracy of ancestral estimates and control type I error rate at an approximately similar rate. The most important factor in determining accuracy of the ancestry estimate and in minimizing type I error rate is the number of markers used to estimate ancestry. We demonstrate that approximately 100 ancestry informative markers (AIMs) are required to obtain estimates of ancestry that correlate with correlation coefficients more than 0.9 with the true individual ancestral proportions. In addition, after accounting for the ancestry information in association tests, the excess of type I error rate is controlled at the 5% level when 100 markers are used to estimate ancestry. However, since the effect of admixture on the type I error rate worsens with sample size, the accuracy of ancestry estimates also needs to increase to make the appropriate correction. Using data from the Latino subjects, we also apply these methods to an association study between body mass index and 44 AIMs. These simulations are meant to provide some practical guidelines for investigators conducting association studies in admixed populations.     

Exploring biological network structure with clustered random networks

Background  

Complex biological systems are often modeled as networks of interacting units. Networks of biochemical interactions among proteins, epidemiological contacts among hosts, and trophic interactions in ecosystems, to name a few, have provided useful insights into the dynamical processes that shape and traverse these systems. The degrees of nodes (numbers of interactions) and the extent of clustering (the tendency for a set of three nodes to be interconnected) are two of many well-studied network properties that can fundamentally shape a system. Disentangling the interdependent effects of the various network properties, however, can be difficult. Simple network models can help us quantify the structure of empirical networked systems and understand the impact of various topological properties on dynamics.     

Modeling Water Quality Impacts of Cellulosic Biofuel Production from Corn Silage

The growing interest in the use of alternative biomass products for fuel production requires a thorough understanding of the environmental impacts associated with the production of these bioenergy crops. Corn silage is a potential bioenergy feedstock; however, water quality implications for its utilization as a biofeedstock are not understood. The objective of this work was to evaluate water quality impacts associated with corn silage production. The GLEAMS-NAPRA model was used to quantify runoff, percolation, erosion, nitrate-nitrogen, total phosphorus, and pesticide losses attributed to the production of corn silage with and without winter cover crops for two tillage options (conventional tillage and no till) on three Indiana soils. Results revealed that corn silage would generate greater annual surface runoff (1 to 6 mm) and percolation (1 to 20 mm) compared with corn grain and grain plus stover cropping systems. Silage/winter cereal rye cover crop reduced annual surface runoff and percolation and was strongly influenced by increases in evapotranspiration, when compared with continuous silage production. Silage managed with winter cereal rye cover crop influenced water quality by reducing annual nitrate losses with runoff from a low of 14 % to a high of 27 %, with relatively no effect because of tillage management. No-till practice on silage system produced significantly greater phosphorus losses (7.46 to 18.07 kg/ha) in comparison to silage/cereal rye, corn grain, and grain plus stover harvest (p?<?0.05). For every 1,000 l of ethanol produced from corn silage, erosion losses ranged from 0.07 to 0.95 t/ha for conventional tillage practices and from 0.06 to 0.83 t/ha for no-till practices. The feasibility of cropping systems such as corn silage/cereal rye could contribute to large-scale biomass production but should be further investigated.     

History shaped the geographic distribution of genomic admixture on the island of Puerto Rico

Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations.     

Synthesis of chromenochalcones and evaluation of their in vitro antileishmanial activity

A large number of novel chromenochalcones were synthesized by pyridine-catalysed chromenylation of mono-chelated meta-dihydric acetophenones with the monoterpene, citral dimethyl acetal and subsequent Claisen-Schmidt condensation of the resultant acylchromenes with appropriate aromatic aldehydes. These chromenochalcones 1-19 were screened against in vitro extracellular promastigotes and intracellular amastigotes of Leishmania donovani. The most potent compound in this series was compound 9 with a pyridine ring-A, which showed 99% inhibition of promastigotes at 10 microg/ml, 82% at 0.25 microg/ml and 96% at 10 microg/ml concentration against amastigotes.     

Synthesis, physico-chemical studies of manganese(II), cobalt(II), nickel(II), copper(II) and zinc(II) complexes with some p-substituted acetophenone benzoylhydrazones and their antimicrobial activity

Complexes of the type [M(pabh)(H2O)Cl], [M(pcbh)(H2O)Cl] and [M(Hpabh)(H2O)2 (SO4)] where, M = Mn(II), Co(II), Ni(II), Cu(II) and Zn(II); Hpabh = p-amino acetophenone benzoyl hydrazone and Hpcbh = p-chloro acetophenone benzoyl hydrazone have been synthesized and characterized with the help of elemental analyses, electrical conductance, magnetic susceptibility measurements, electronic, ESR and IR spectra, thermal (TGA & DTA) and X-ray diffraction studies. Co(II), Ni(II) and Cu(II) chloride complexes are square planar, whereas their sulfate complexes have spin-free octahedral geometry. ESR spectra of Cu(II) complexes with Hpabh are axial and suggest d(x(2)-y(2) as the ground state. The ligand is bidentate bonding through > C = N--and deprotonated enolate group in all the chloro complexes, whereas, >C = N and >C = O groups in all the sulfato complexes. Thermal studies (TGA & DTA) on [Cu(Hpabh)(H2O)2(SO4)] indicate a multistep decomposition pattern, which are both exothermic and endothermic in nature. X-ray powder diffraction parameters for [Co(pabh)(H2O)Cl] and [Ni(Hpabh)(H2O)2(SO4)] correspond to tetragonal and orthorhombic crystal lattices, respectively. The ligands as well as their complexes show a significant antifungal and antibacterial activity. The metal complexes are more active than the ligand.