Field-scale bioremediation of arsenic-contaminated groundwater using sulfate-reducing bacteria and biogenic pyrite

This research demonstrates that biogenic pyrite formed by stimulation of indigenous sulfate-reducing bacteria (SRB) in a natural aquifer can remove dissolved arsenic from contaminated groundwater under strongly reducing conditions. SRB metabolism led to the precipitation of biogenic pyrite nanoparticles capable of sorbing and co-precipitating arsenic. The field site is an industrial site where shallow groundwater in an unconfined sandy aquifer is contaminated by arsenic. Therefore, biodegradable organic carbon, ferrous iron, sulfate, and fertilizer were injected into groundwater and SRB metabolism began about 1 week later. Microscopic, X-ray diffraction, X-ray fluorescence, and electron microprobe analyses confirm the bio-mineralization of pyrite and over time, pyrite nanoparticles grew to form well-formed crystals (1–10?µm in diameter) or spherical aggregates that contain 0.05–0.4?wt. % arsenic, indicative of their capacity to sequester arsenic. Consequently, dissolved arsenic decreased from its initial concentration of 0.3–0.5?mg/L to below the regulatory clean-up standard for the site of 0.05?mg/L in three downgradient wells in a matter of weeks after injection. The main sequestration stage, with total arsenic removal rates greater than 90%, lasted for at least 6 months until the arrival and mixing of untreated groundwater from upgradient. Treated groundwater with most active bacterial sulfate reduction became enriched in heavy ³⁴S (range from 2.02 to 4.00 ‰) compared to unaffected well water (0.40–0.61 ‰). One to three orders of magnitude increases in SRB cells were observed in treated wells for at least 2?months after injection. For a full-scale remediation, the injection of solution should start at positions hydrologically upgradient from the major plume and proceed downgradient. If needed, aquifers may be repeatedly amended with biodegradable organic carbon to reestablish the reducing conditions that favor arsenic sequestration.     

Crocodylian Tracks from Lower Oligocene Flysch deposits of the Barail Group,Manipur, India

A marine tidal delta siltstone from Gelmon locality in Northeast India preserved three crocodylian footprints and an elongate depression that appears to be a tail drag mark. Similar drag marks occur in nearby bedding surfaces. The discovery of crocodylian tracks from the basal part of Laisong Formation, Barail Group (Late Eocene–Early Oligocene age) of Manipur, India is noteworthy because of the age and the geographic location. Crocodylian tracks are rare in Cenozoic formations and they have not previously been reported from Asia. The footprints are herein named as a new ichnogenus and ichnospecies, Indosuchipes manipurensis.     

The Burden and Determinants of Non Communicable Diseases Risk Factors in Nepal: Findings from a Nationwide STEPS Survey

Background

World Health Organization (WHO) estimates for deaths attributed to Non Communicable Diseases (NCDs) in Nepal have risen from 51% in 2010 to 60% in 2014. This study assessed the distribution and determinants of NCD risk factors among the Nepalese adult population.

Methods and Findings

A nationally representative cross-sectional survey was conducted from Jan to June 2013 on the prevalence of NCD risk factors using the WHO NCD STEPS instrument. A multistage cluster sampling method was used to randomly select the 4,200 respondents. The adjusted prevalence ratio (APR) was used to assess the determinants of NCD risk factors using a Poisson regression model. The prevalence of current smoking (last 30 days) was 19% (95%CI:16.6-20.6), and harmful alcohol consumption (≥60 g of pure alcohol for men and ≥40 g of pure alcohol for women on an average day) was 2% (95%CI:1.4-2.9). Almost all (99%, 95%CI:98.3-99.3) of the respondents consumed less than five servings of fruits and vegetables combined on an average day and 3% (95%CI:2.7-4.3) had low physical activity. Around 21% (95%CI:19.3-23.7) were overweight or obese (BMI≥25). The prevalence of raised blood pressure (SBP≥140 mm of Hg or DBP≥90 mm of Hg) and raised blood glucose (fasting blood glucose ≥126 mg/dl), including those on medication were 26% (95%CI:23.6-28.0) and 4% (95%CI:2.9-4.5) respectively. Almost one quarter of respondents, 23% (95%CI:20.5-24.9), had raised total cholesterol (total cholesterol ≥190 mg/dl or under current medication for raised cholesterol). he study revealed a lower prevalence of smoking among women than men (APR:0.30; 95%CI:0.25-0.36), and in those who had higher education levels compared to those with no formal education (APR:0.39; 95%CI:0.26-0.58). Harmful alcohol use was also lower in women than men (APR:0.26; 95%CI:0.14-0.48), and in Terai residents compared to hill residents (APR:0.16; 95%CI:0.07-0.36). Physical inactivity was lower among women than men (APR:0.55; 95%CI:0.38-0.80), however women were significantly more overweight and obese (APR:1.19; 95%CI:1.02-1.39). Being overweight or obese was significantly less prevalent in mountain residents than in hill residents (APR:0.41; 95%CI:0.21-0.80), and in rural compared to urban residents (APR:1.39; 95%CI:1.15-1.67). Lower prevalence of raised blood pressure was observed among women than men (APR:0.69; 95%CI: 0.60-0.80). Higher prevalence of raised blood glucose was observed among urban residents compared to rural residents (APR:2.05; 95%CI:1.29-3.25). A higher prevalence of raised total cholesterol was observed among the respondents having higher education levels compared to those respondents having no formal education (APR:1.76; 95%CI:1.35-2.28).

Conclusion

The prevalence of low fruit and vegetable consumption, overweight and obesity, raised blood pressure and raised total cholesterol is markedly high among the Nepalese population, with variation by demographic and ecological factors and urbanization. Prevention, treatment and control of NCDs and their risk factors in Nepal is an emerging public health problem in the country, and targeted interventions with a multi-sectoral approach need to be urgently implemented.     

ATP independent type IB topoisomerase of Leishmania donovani is stimulated by ATP: an insight into the functional mechanism

Most type IB topoisomerases do not require ATP and Mg(2+) for activity. However, as shown previously for vaccinia topoisomerase I, we demonstrate that ATP stimulates the relaxation activity of the unusual heterodimeric type IB topoisomerase from Leishmania donovani (LdTOP1L/S) in the absence of Mg(2+). The stimulation is independent of ATP hydrolysis but requires salt as a co-activator. ATP binds to LdTOP1L/S and increases its rate of strand rotation. Docking studies indicate that the amino acid residues His93, Tyr95, Arg188 and Arg190 of the large subunit may be involved in ATP binding. Site directed mutagenesis of these four residues individually to alanine and subsequent relaxation assays reveal that the R190A mutant topoisomerase is unable to exhibit ATP-mediated stimulation in the absence of Mg(2+). However, the ATP-independent relaxation activities of all the four mutant enzymes remain unaffected. Additionally, we provide evidence that ATP binds LdTOP1L/S and modulates the activity of the otherwise ATP-independent enzyme. This study establishes ATP as an activator of LdTOP1L/S in the absence of Mg(2+).     

Phylogenetic diversity and symbiotic functioning in mungbean (Vigna radiata L. Wilczek) bradyrhizobia from contrast agro-ecological regions of Nepal

Nepal consists wide range of climatic and topographical variations. Here, we explored the phylogeny of native mungbean bradyrhizobia isolated from different agro-ecological regions of Nepal and accessed their nodulation and nitrogen fixation characteristics. Soil samples were collected from three agro-ecological regions with contrasting climate and topography. A local mungbean cultivar, Kalyan, was used as a trap plant. We characterized isolates based on the full nucleotide sequence of the 16S rRNA, ITS region, and nodA genes; and partial sequences of nodD1 and nifD genes. We found 50% of isolates phylogenetically related to B. yuanmingense, 13% to B. japonicum, 8% to B. elkanii, and 29% to novel phylogenetic origin. Results of the inoculation test suggested that expression of different symbiotic genes in isolates resulted in different degrees of symbiotic functioning. Our results indicate B. yuanmingense and novel strains are more efficient symbiotic partners than B. elkanii for the local mungbean cv. Kalyan. We also found most mungbean rhizobial genotypes were conserved across agro-ecological regions. All the strains from tropical Terai region belonged to B. yuanmingense or a novel lineage of B. yuanmingense, and dominance of B. japonicum related strains was observed in the Hill region. Higher genetic diversity of Bradyrhizobium strains was observed in temperate and sub-tropical region than in the tropical region.     

G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA

G-quadruplex has demonstrated its biological functions in vivo. Although G-quadruplex in single-stranded DNA (ssDNA) has been well characterized, investigation of this species in double-stranded DNA (dsDNA) lags behind. Here we use chemical footprinting and laser-tweezers-based single-molecule approaches to demonstrate that a dsDNA fragment found in the insulin-linked polymorphic region (ILPR), 5'-(ACA GGGG TGT GGGG)2 TGT, can fold into a G-quadruplex at pH 7.4 with 100 mM K+, and an i-motif at pH 5.5 with 100 mM Li+. Surprisingly, under a condition that favors the formation of both G-quadruplex and i-motif (pH 5.5, 100 mM K+), a unique determination of change in the free energy of unfolding (ΔGunfold) by laser-tweezers experiments provides compelling evidence that only one species is present in each dsDNA. Under this condition, molecules containing G-quadruplex are more stable than those with i-motif. These two species have mechanical stabilities (rupture force≥17 pN) comparable to the stall force of RNA polymerases, which, from a mechanical perspective alone, could justify a regulatory mechanism for tetraplex structures in the expression of human insulin.     

Functional dissection of the C-terminal domain of type II DNA topoisomerase from the kinetoplastid hemoflagellate Leishmania donovani

The amino acid sequences of the C-terminal domain (CTD) of the type II DNA topoisomerases are divergent and species specific as compared with the highly conserved N-terminal and central domains. A set of C-terminal deletion mutants of Leishmania donovani topoisomerase II was constructed. Removal of more than 178 amino acids out of 1236 amino acid residues from the C-terminus inactivates the enzyme, whereas removal of 118 amino acids or less has no apparent effect on the ability of the parasite enzyme to complement a temperature-sensitive mutation of the Saccharomyces cerevisiae topoisomerase II gene. Deletion analysis revealed a potent nuclear localization signal (NLS) within the amino acid residues 998–1058. Immunomicroscopy results suggest that the removal of an NLS in the CTD is likely to contribute to the physiological dysfunction of these proteins. Modeling of the LdTOP2 based on the crystal structure of the yeast type II DNA topoisomerase showed that the parasite protein assumes a structure similar to its yeast counterpart harboring all the conserved residues in a structurally similar position. However, a marked difference in electrostatic potential was found in a span of 60 amino acid residues (998–1058), which also do not have any homology with topoisomerase II sequences. Such significant differences can be exploited by the structure-based design of selective inhibitors using the structure of the Leishmania enzyme as a template.     

Resumption of postpartum ovarian cyclicity in high-producing Holstein cows

The objective of this study was to investigate the resumption of ovarian cyclicity postpartum in high-producing dairy cows in commercial dairy farms under subtropical conditions. The cows were kept in a free-stall or tie-stall barn. Milk samples were collected from cows twice weekly, and progesterone in the skim milk was assayed by double-antibody ELISA. Cows were examined rectally and vaginoscopically at 2-week intervals after calving. Body condition score (BCS) and body weights were taken before and after calving. A cow was considered to have resumed ovarian cyclicity on the day of ovulation if followed by regular ovarian cycles. Thirty seven percent (n=20/54) of the cows had normal resumption of ovarian cyclicity (resumption within 45 days after calving), and 63% (n=34/54) had delayed resumption (resumption did not occur until >45 days after calving). Delayed resumption Type I (one or more ovarian cycles with luteal phase >20 days, i.e. prolonged luteal phase; 31.5%) and delayed resumption Type II (first ovulation did not occur until > or =45 days after calving, i.e. delayed first ovulation; 24.1%) were the most common types of delayed resumptions. Almost half (46.3%) of the cows did not resume their ovarian cyclicity until >65 days postpartum. Cows with delayed resumption Type I had a higher incidence of abnormal cervico-vaginal discharge (64.7%) and incomplete uterine involution (94.1%) compared to cows with normal resumption (P<0.01). The BCS of cows with delayed resumption Type II were lower than those of normal resumption cows at 5 weeks and later in the postpartum period (P<0.05). Approximately two-thirds of high-producing cows had delayed resumption of ovarian cyclicity postpartum. Prolonged luteal phase and delayed first ovulation were two important ovarian dysfunctions that delayed postpartum resumption of cyclicity in high-producing dairy cows.     

Biophysical characterization and molecular modeling of the coordinative-intercalative DNA monoadduct of a platinum-acridinylthiourea agent in a site-specifically modified dodecamer

The guanine-N7 monoadduct of [Pt(en)Cl(ACRAMTU)](NO₃)₂ (PT-ACRAMTU; en=ethane-1,2-diamine, ACRAMTU=1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea), a dual metalating/intercalating cytotoxic agent, was generated in a double-stranded dodecamer, d(CCTCTCG*TCTCC/GGAGACGAGAGG) (III*), and isolated by preparative reverse-phase high-performance liquid chromatography (HPLC). The adduct was characterized using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), circular-dichroism spectropolarimetry (CD), UV-melting curves, and NMR spectroscopy. In addition, a molecular mechanics/restrained molecular dynamics (MM/rMD) study was performed for this adduct using the AMBER force field. Monoadduction of the sequence leads to a pronounced increase in melting temperature, T_m=T_m(III*)–T_m(III)=9.7 °C. Because there is complete enthalpy–entropy compensation, binding occurs without noticeable thermodynamic destabilization. This feature and the CD (induced-ligand circular dichroism) and NMR (upfield shifts of aromatic acridine proton signals) data are indicative of a unique, nondenaturing dual-binding mode that involves partial intercalation of the acridine chromophore. An energy-minimized AMBER model of III* demonstrates that platination of G7-N7 of guanine in the major groove and partial insertion of the acridine moiety into the C6G19/G7C18 base step on the 5 face of the modified purine base is feasible and supportive of the experimental results. Differences in the biophysical properties between III* and duplexes containing adducts of the clinical-drug cisplatin are outlined, and possible biological consequences are discussed.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0534-3Abbreviations ACRAMTU 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea - dGuo 2-deoxyguanosine - dGuo* [Pt(en)(ACRAMTU-S)(dGuo-N7)]³⁺ - en ethane-1,2-diamine - ICD Induced circular dichroism - MALDI-TOF MS Matrix-assisted laser desorption ionization time-of-flight mass spectrometry - MM Molecular mechanics - PIPES 1,4-piperazinediethanesulfonic acid - PT-ACRAMTU [Pt(en)Cl(ACRAMTU)](NO₃)₂ - rMD Restrained molecular dynamics