Metagenomics and proteomics profiling of extracellular polymeric substances from municipal waste sludge and their application for soil and water bioremediation.

This study assessed the components of anaerobically digested sludge, activated sludge, and microbial and extracellular polymeric substance (EPS) enzymes to identify the mechanisms underlying nitrogen removal and soil regeneration. 16S rRNA gene amplicon-based sequencing was used to determine the microbial community composition and the related National Center for Biotechnology Information (NCBI) protein database was used to construct a conventional library from the observed community. EPS components were identified using gel-free proteomic (Liquid Chromatography with tandem mass spectrometry-LC/MS/MS) methods. Alginate-like EPS from aerobically activated sludge have strong potential for soil aggregation and water-holding capacity, whereas total EPS from anaerobic sludge have significant potential for ammonia removal under salt stress. Fourier transform infrared spectroscopy (FTIR) revealed that both EPS may contain proteins, carbohydrates, humic compounds, uronic acid, and DNA and determined the presence of O-H, N-H, C-N, CO, and C-H functional groups. These results demonstrate that the overall enzyme activity may be inactivated at 30 g L-1 of salinity. An annotation found in Kyoto Encyclopedia of Genes and Genomes (KEGG)- KEGG Automatic Annotation Server (KAAS) revealed that the top two metabolic activities in the EPS generated from the anaerobic sludge were methane and nitrogen metabolism. Therefore, we focused on the nitrogen metabolism reference map 00910. EPS from the anaerobically digested sludge exhibited nitrate reductase, nitrite reductase, and dehydrogenase activities. Assimilatory nitrate reduction, denitrification, nitrification, and anammox removed ammonia biochemically. The influence of microbial extracellular metabolites on water-holding capacity and soil aggregation was also investigated. The KAAS-KEGG annotation server was used to identify the main enzymes in the activated sludge-derived alginate-like extracellular EPS (ALE-EPS) samples. These include hydrolases, oxidoreductases, lyases, ligases, and transporters, which contribute to soil fertility and stability. This study improves our understanding of the overall microbial community structure and the associated biochemical processes, which are related to distinct functional genes or enzymes involved in nitrogen removal and soil aggregation. In contrast to conventional methods, microbial association with proteomics can be used to investigate ecological relationships, establishments, key player species, and microbial responses to environmental changes. Linking the metagenome to off-gel proteomics and bioinformatics solves the problem of analyzing metabolic pathways in complex environmental samples in a cost-effective manner.

Green synthesis and characterization of Fe3O4 nanoparticles using Chlorella-K01 extract for potential enhancement of plant growth stimulating and antifungal activity.

The purpose of this research was to determine the efficacy of iron oxide nanoparticles (Fe3O4-NPs) using microalgal products as a plant growth stimulant and antifungal agent. The work was conducted with the phyco-synthesis and characterization of Fe3O4-NPs using 0.1 M ferric/ferrous chloride solution (2:1 ratio; 65 °C) with aqueous extract of the green microalga Chlorella K01. Protein, carbohydrate and polyphenol contents of Chlorella K01 extract were measured. The synthesized microalgal Fe3O4-NPs made a significant contribution to the germination and vigor index of rice, maize, mustard, green grams, and watermelons. Fe3O4-NPs also exhibited antifungal activity against Fusarium oxysporum, Fusarium tricinctum, Fusarium maniliforme, Rhizoctonia solani, and Phythium sp. Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) scanning electron microscopy (SEM), transmission electron microscopy (TEM), particle size analysers (PSA), and zeta potential (ZP) measurements were used to characterize these green fabricated magnetite NPs. FTIR analysis showed that the synergy of microalgal proteins, carbohydrtates and polyphenols is responsible for the biofabrication of iron nanoparticles. A spheroid dispersion of biosynthesized Fe3O4-NPs with an average diameter of 76.5 nm was produced in the synthetic process.

An evaluation into the biosorption and biodegradation of azo dyes by indigenous siderophores-producing bacteria immobilized in chitosan.

The biodegradation and biosorption efficiency of an indigenous siderophores-producing bacterial community on azo dyes with immobilization in chitosan beads was evaluated in this study. 13 bacterial strains were isolated from textile wastewater streams. The bacterial strains were tested for the production of siderophores as well as their ability to decolorize toxic azo dyes in aqueous solution. Both qualitatively and quantitatively, all of the strains displayed high siderophores productivity. Furthermore, they displayed remarkable decolorization efficiency for azo dyes (Acid Black 1 and Reactive Black 5) in both free and immobilized form. The immobilization process was found not only to enhance the decolorization but also the degradation of azo dyes by the bacterial isolates. In a SEM micrograph, bacterial strains were immobilized, and the pores in chitosan bead to be trapped and adsorbed for dyes from synthetic wastewater. The extent of dye compounds degradation were examined using UV-visible and FTIR spectrophotometers on treated water samples and dye absorbed beads. After 72 h of incubation, the UV-visible analysis revealed that the bacterial community could significantly reduce both azo dyes in wastewater by 90% at 300 mgL-1 dyes initial concentration. FTIR study confirmed the bonds of these dyes were broken to form less toxic chemicals via the bacterial community immobilized in chitosan beads. The immobilized bacterial community thus demonstrated effective approach of azo dye biosorption and biodegradation.

Conformational Dynamics of Histone H3 Tails in Chromatin.

Chromatin is a supramolecular DNA-protein complex that compacts eukaryotic genomes and regulates their accessibility and functions. Dynamically disordered histone H3 N-terminal tails are among key chromatin regulatory components. Here, we used high-resolution-magic-angle-spinning NMR measurements of backbone amide 15N spin relaxation rates to investigate, with residue-specific detail, the dynamics and interactions of H3 tails in recombinant 13C,15N-enriched nucleosome arrays containing 15, 30, or 60 bp linker DNA between the nucleosome repeats. These measurements were compared to analogous data available for mononucleosomes devoid of linker DNA or containing two 20 bp DNA overhangs. The H3 tail dynamics in nucleosome arrays were found to be considerably attenuated compared with nucleosomes with or without linker DNA due to transient electrostatic interactions with the linker DNA segments and the structured chromatin environment. Remarkably, however, the H3 tail dynamics were not modulated by the specific linker DNA length within the 15-60 bp range investigated here.

Prevalence and determinants of TB infection in a rural population in northeastern Myanmar.

BACKGROUND: Tuberculosis (TB) is a major human threat, as evidenced by the large numbers of cases and deaths, particularly in developing countries with poor economic and educational statuses. Myanmar has one of the highest TB burdens in the world, but no TB information is available for people living in the rural northeastern regions of Myanmar. The present study estimated the prevalence of TB and identified factors associated with TB infection in people living in rural communities in Shan State. METHODS: A cross-sectional study was performed to gather information from participants. People aged 18-59 years who lived in the three areas with the highest numbers of TB cases in Shan State in northeastern Myanmar were included in the study population. A simple random method was used to select the sample from the villages. A validated questionnaire was used for data collection in face-to-face interviews after obtaining signed informed consent from the selected participants. The Mantoux tuberculin skin test (TST) was administered to detect TB infection, and a result that was 10 mm or greater after 48 h was considered positive. Chi-squared tests and logistic regression were used to identify the associations between the variables at a significance level of α = 0.05. RESULTS: A total of 303 participants were recruited for the study; 64.7% were females, and the mean age was 37 years (SD = 12.5). Most participants were Burmese (25.4%), and 14.95% were Shan. Sixty-three participants (20.8%) had a positive TST. Four variables were associated with TB infection in the multivariate model. Males had a greater chance of TB infection than females (AOR = 2.51; 95% CI = 1.32-4.76). Participants who were ever married had a greater chance of TB infection than participants who were single (AOR = 3.93; 95% CI = 1.18-13.00). Participants who used wood and charcoal as their main sources of energy for cooking had a greater chance of TB infection than participants who used electricity (AOR = 4.23; 95% CI = 1.25-9.64). Participants who had a low level of TB prevention and care knowledge had a greater chance of TB infection than participants with a high level of TB prevention and care knowledge (AOR = 4.49; 95% CI = 1.88-10.72). CONCLUSIONS: Public health programs that focus on improving knowledge of TB prevention and care and avoiding the use of wood and charcoal as the primary sources of energy for cooking, particularly in males and ever-married individuals, are urgently needed.

Sensitivity boosts by the CPMAS CryoProbe for challenging biological assemblies.

Despite breakthroughs in MAS NMR hardware and experimental methodologies, sensitivity remains a major challenge for large and complex biological systems. Here, we report that 3-4 fold higher sensitivities can be obtained in heteronuclear-detected experiments, using a novel HCN CPMAS probe, where the sample coil and the electronics operate at cryogenic temperatures, while the sample is maintained at ambient temperatures (BioSolids CryoProbe™). Such intensity enhancements permit recording 2D and 3D experiments that are otherwise time-prohibitive, such as 2D 15N-15N proton-driven spin diffusion and 15N-13C double cross polarization to natural abundance carbon experiments. The benefits of CPMAS CryoProbe-based experiments are illustrated for assemblies of kinesin Kif5b with microtubules, HIV-1 capsid protein assemblies, and fibrils of human Y145Stop and fungal HET-s prion proteins - demanding systems for conventional MAS solid-state NMR and excellent reference systems in terms of spectral quality. We envision that this probe technology will be beneficial for a wide range of applications, especially for biological systems suffering from low intrinsic sensitivity and at physiological temperatures.

Correlation study between Erythrocyte Acetylcholinesterase activity, Serum Malondialdehyde and Insulin sensitivity in Agricultural workers and non-agricultural workers in Nat-Kan Village, Magway Township / Journal of the ASEAN Federation of Endocrine Societies

Objective@#This study determined the correlation between erythrocyte acetylcholinesterase (AChE) activity, serum malondialdehyde (MDA) and insulin sensitivity in agricultural workers and non-agricultural workers.@*Methodology@#The cross-sectional comparative study was undertaken in 45 agricultural and 45 non-agricultural workers from Nat-Kan Village, Magway Township. Erythrocyte acetylcholinesterase activity and serum malondialdehyde were measured by spectrophotometric method. Insulin sensitivity was calculated by homeostasis model assessment (HOMA-IR).@*Results@#Mean erythrocyte AChE activity was significantly lower in agricultural (3553.99 IU/L) compared with non-agricultural workers (4432.68 IU/L) (p<0.001). A significant high level of mean serum MDA was observed in agricultural workers (0.74 versus 0.28 μmol/L, p<0.001). Median HOMA-IR value was significantly higher in agricultural (2.74) than that of non-agricultural workers (2.28) (p<0.05). The risk of insulin resistance was 2.8 times greater in agricultural workers than non-agricultural workers (OR 2.8, 95% CI, 1.18 to 6.72). Erythrocyte AChE activity had weak negative correlation with serum MDA level (r=-0.357, p<0.001) and HOMA-IR (ρ= -0.305, p<0.05). There was a significant but weak positive correlation between serum MDA level and HOMA-IR (ρ=0.355, p<0.001).@*Conclusion@#Organophosphate pesticide exposure lowered erythrocyte AChE activity and increased oxidative stress. Oxidative stress is partly attributed to the development of insulin resistance

Protein-solvent interfaces in human Y145Stop prion protein amyloid fibrils probed by paramagnetic solid-state NMR spectroscopy.

The C-terminally truncated Y145Stop variant of prion protein (PrP23-144), which is associated with heritable PrP cerebral amyloid angiopathy in humans and also capable of triggering a transmissible prion disease in mice, serves as a useful in vitro model for investigating the molecular and structural basis of amyloid strains and cross-seeding specificities. Here, we determine the protein-solvent interfaces in human PrP23-144 amyloid fibrils generated from recombinant 13C,15N-enriched protein and incubated in aqueous solution containing paramagnetic Cu(II)-EDTA, by measuring residue-specific 15N longitudinal paramagnetic relaxation enhancements using two-dimensional magic-angle spinning solid-state NMR spectroscopy. To further probe the interactions of the amyloid core residues with solvent molecules we perform complementary measurements of amide hydrogen/deuterium exchange detected by solid-state NMR and solution NMR methods. The solvent accessibility data are evaluated in the context of the structural model for human PrP23-144 amyloid.

Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.

Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15 N rotating frame (R1ρ ) relaxation dispersion solid-state nuclear magnetic resonance spectroscopy over a wide range of spin-lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two-state exchange process with a common exchange rate of 1000 s-1 , corresponding to protein backbone motion on the timescale of 1 ms, and an excited-state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited-state populations (∼5-15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100-300 µs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.

Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR.

Multidimensional magic-angle spinning solid-state NMR experiments are described that permit cis and trans peptide bonds in uniformly 13C,15N-labeled peptides and proteins to be unambiguously distinguished in residue-specific manner by determining the relative orientations of the amide 13C' CSA and 1H-15N dipolar coupling tensors. The experiments are demonstrated for model peptides glycylglycine and 2,5-diketopiperazine containing trans and cis peptide bonds, respectively. Subsequently, the measurements are extended to two representative proteins that contain exclusively trans peptide bonds, microcrystalline B3 immunoglobulin domain of protein G and Y145Stop human prion protein amyloid fibrils, to illustrate their applicability to a wide range of protein systems.

Structural Studies of Amyloid Fibrils by Paramagnetic Solid-State Nuclear Magnetic Resonance Spectroscopy.

Application of paramagnetic solid-state NMR to amyloids is demonstrated, using Y145Stop human prion protein modified with nitroxide spin-label or EDTA-Cu2+ tags as a model. By using sample preparation protocols based on seeding with preformed fibrils, we show that paramagnetic protein analogs can be induced into adopting the wild-type amyloid structure. Measurements of residue-specific intramolecular and intermolecular paramagnetic relaxation enhancements enable determination of protein fold within the fibril core and protofilament assembly. These methods are expected to be widely applicable to other amyloids and protein assemblies.

Species-dependent structural polymorphism of Y145Stop prion protein amyloid revealed by solid-state NMR spectroscopy.

One of the most puzzling aspects of the prion diseases is the intricate relationship between prion strains and interspecies transmissibility barriers. Previously we have shown that certain fundamental aspects of mammalian prion propagation, including the strain phenomenon and species barriers, can be reproduced in vitro in seeded fibrillization of the Y145Stop prion protein variant. Here, we use solid-state nuclear magnetic resonance spectroscopy to gain atomic level insight into the structural differences between Y145Stop prion protein amyloids from three species: human, mouse, and Syrian hamster. Remarkably, we find that these structural differences are largely controlled by only two amino acids at positions 112 and 139, and that the same residues appear to be key to the emergence of structurally distinct amyloid strains within the same protein sequence. The role of these residues as conformational switches can be rationalized based on a model for human Y145Stop prion protein amyloid, providing a foundation for understanding cross-seeding specificity.Prion diseases can be transmitted across species. Here the authors use solid-state NMR to study prion protein (PrP) amyloids from human, mouse and Syrian hamster and show that their structural differences are mainly governed by two residues, which helps to understand interspecies PrP propagation on a molecular level.

13C and 15N chemical shift assignments of mammalian Y145Stop prion protein amyloid fibrils.

The Y145Stop prion protein (PrP23-144), which has been linked to the development of a heritable prionopathy in humans, is a valuable in vitro model for elucidating the structural and molecular basis of amyloid seeding specificities. Here we report the sequential backbone and side-chain 13C and 15N assignments of mouse and Syrian hamster PrP23-144 amyloid fibrils determined by using 2D and 3D magic-angle spinning solid-state NMR. The assigned chemical shifts were used to predict the secondary structures for the core regions of the mouse and Syrian hamster PrP23-144 amyloids, and the results compared to those for human PrP23-144 amyloid, which has previously been analyzed by solid-state NMR techniques.

Monitoring the microbial community shift throughout the shock changes of hydraulic retention time in an anaerobic moving bed membrane bioreactor.

An anaerobic moving bed membrane bioreactor (AnMBMBR) fed with synthetic domestic wastewater was investigated under hydraulic retention time (HRT) shocks to assess the effects on the microbial (bacteria and archaea) community and reactor performance. 16S rDNA targeted polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach was optimized to relate the metabolic and community composition with biogas generation, methane content and COD removal efficiency. From the drastic decrease of HRT (from 8 h to 4 h), the methane production was significantly reduced due to the HRT shock, while the COD removal efficiency was not affected. The enhanced growth of homoacetogenic bacteria, Thermoanaerobacteraceae competes with methanogens under shock period. When the HRT was recovered to 8 h, the methane generation rate was higher than the initial operation before the shock HRT changes, which would be ascribed to the activity of new emerging hydrogenotrophic archaea, Methanocella sp. and Methanofollis sp.