FAN1 removes triplet repeat extrusions via a PCNA- and RFC-dependent mechanism.

Human genome-wide association studies have identified FAN1 and several DNA mismatch repair (MMR) genes as modifiers of Huntington's disease age of onset. In animal models, FAN1 prevents somatic expansion of CAG triplet repeats, whereas MMR proteins promote this process. To understand the molecular basis of these opposing effects, we evaluated FAN1 nuclease function on DNA extrahelical extrusions that represent key intermediates in triplet repeat expansion. Here, we describe a strand-directed, extrusion-provoked nuclease function of FAN1 that is activated by RFC, PCNA, and ATP at physiological ionic strength. Activation of FAN1 in this manner results in DNA cleavage in the vicinity of triplet repeat extrahelical extrusions thereby leading to their removal in human cell extracts. The role of PCNA and RFC is to confer strand directionality to the FAN1 nuclease, and this reaction requires a physical interaction between PCNA and FAN1. Using cell extracts, we show that FAN1-dependent CAG extrusion removal relies on a very short patch excision-repair mechanism that competes with MutSß-dependent MMR which is characterized by longer excision tracts. These results provide a mechanistic basis for the role of FAN1 in preventing repeat expansion and could explain the antagonistic effects of MMR and FAN1 in disease onset/progression.

Portable X-ray Fluorescence as a Rapid Determination Tool to Detect Parts per Million Levels of Ni, Zn, As, Se, and Pb in Human Toenails: A South India Case Study.

Chronic exposure to inorganic pollutants adversely affects human health. Inductively coupled plasma mass spectrometry (ICP-MS) is the most common method used for trace metal(loid) analysis of human biomarkers. However, it leads to sample destruction, generation of secondary waste, and significant recurring costs. Portable X-ray fluorescence (XRF) instruments can rapidly and nondestructively determine low concentrations of metal(loid)s. In this work, we evaluated the applicability of portable XRF as a rapid method for analyzing trace metal(loid)s in toenail samples from three populations (n = 97) near the city of Chennai, India. A Passing-Bablok regression analysis of results from both methods revealed that there was no proportional bias among the two methods for nickel (measurement range ∼25 to 420 mg/kg), zinc (10 to 890 mg/kg), and lead (0.29 to 4.47 mg/kg). There was a small absolute bias between the two methods. There was a strong proportional bias (slope = 0.253, 95% CI: 0.027, 0.614) between the two methods for arsenic (below detection to 3.8 mg/kg) and for selenium when the concentrations were lower than 2 mg/kg. Limits of agreement between the two methods using Bland-Altman analysis were derived for nickel, zinc, and lead. Overall, a suitably calibrated and evaluated portable XRF shows promise in making high-throughput assessments at population scales.

In silico modelling and molecular dynamics simulation studies on L-Asparaginase isolated from bacterial endophyte of Ocimum tenuiflorum.

Bioactive compounds from endophytes have been used to treat various diseases. In the present study, L-Asparaginase producing endophytes were isolated from Ocimum tenuiflorum (Tulasi) from NIT Warangal, Telangana, India to treat Acute Lymphoblastic Leukemia (ALL) in which L-Asparagine (L-Asn) deamination plays a vital role in ALL treatment. 20 (bacteria and fungi) out of 35 endophytes have been screened for L-Asparaginase production using rapid plate assay technique, in which four strains produced high amounts of L-Asparaginase. 16 s Ribosomal RNA sequencing studies were performed, Bacillus stratosphericus organism was identified, and purified L-Asparaginase sequence has been tailored using MALDI/TOF (Applied Biosystems). The homology model was developed by using MODELLER 9.15v as the endophyte lacks crystal structure of L-Asparaginase enzyme and validated by dint of quality index tools. Docking studies were performed using iGemdock 2.1v. In comparison, free energy binding efficiency of receptor towards L-Asparagine (L-Asn) is good with lesser energy -71.6 kcal/mol in comparison to L-Glutamine (L-Gln) having -67.7 kcal/mol. In order to find the stability of the docked complexes in dynamics environment, molecular dynamics and simulation studies were performed using GROMACS V4.6.5. The trajectory analysis for 10 ns shows the better RMSD, RMSF, Rg and average number of hydrogen bonds for complex 1 (L-Asparaginase + L-Asn docked complex). Hence, complex 1 was found to be more stable than Complex 2 (L-Asparaginase + L-Gln docked complex).

Synthesis and implication of novel poly(acrylic acid)/nanosorbent embedded hydrogel composite for lead ion removal.

Lead stands second among the deadly heavy metal pollutants owing to the incompetent mechanism possessed by the human body for its removal. A polymeric hydrogel in the form of composite was prepared using acrylic acid (monomer) and novel nanofiller that possess super adsorbent properties with restricted gel seepage into flowing ionic liquid. The filler used is an adsorbent which is biocompatible, biodegradable, economical, abundant, non-hazardous and easy to synthesize. The invariably porous nanofiller, the Nanobentonite(clay), was synthesized using ion exchange reaction by creating acidic environment for accelerated dispersion with exfoliation by CTAB to enhance cation exchange capacity. NanobentoFnite was capable of removing >97% lead ion in batch adsorption study and followed pseudo-second order kinetic model. Freundlich isotherm suggested a removal capacity of ~20 mg/g. Thus, the successfully experimented adsorbent was implicated as filler to form polyacrylic acid nanoclay hydrogel polymerized in ultrasonic bath. The amount of filler was varied from 0.25 to 2 wt% to get 94% removal, analyzed using ICP-OES. The prepared adsorbents were characterized before and after adsorption using TEM, FESEM, XRD, FTIR and DSC to understand the structural changes and metal-sorbent interaction. Thus, the novel nanosorbent/composite are promiscuous and competent in terms of availability, reusability and longevity to remove heavy metal ions.

Molecular dynamic simulations of Escherichia coli L-asparaginase to illuminate its role in deamination of asparagine and glutamine residues.

Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-Glutamine (L-Gln) deamination play a crucial role in ALL treatment. Role of Elspar® (L-asparaginase from Escherichia coli) in regulation of L-Asn and L-Gln has been confirmed by the other researchers through experimental studies. Therapeutic research against ALL remained elusive with the lack of information on molecular interactions of Elspar® with amino acid substrates. In the present study, using different docking tools binding cavities, key residues in binding and ligand binding mechanisms were identified. For the apo state enzyme and ligand bound state complexes, MD simulations were performed. Trajectory analysis for 30 ns run confirmed the kinship of L-Asn with L-asparaginase enzyme in the dynamic system with less stability in comparison to L-Gln docked complex. Overall findings strongly supported the bi-functional nature of the enzyme drug. A good number of conformational changes were observed with 1NNS structure due to ligand binding. Results of present study give much more information on structural and functional aspects of E. coli L-asparaginase upon the interaction with its ligands which may be useful in designing effective therapeutics for ALL.

Isolation and characterization of a novel chlorpyrifos degrading flavobacterium species EMBS0145 by 16S rRNA gene sequencing.

Indiscriminate application of pesticides like chlorpyrifos, diazinon, or malathion contaminate the soil in addition has being unsafe often it has raised severe health concerns. Conversely, microorganisms like Trichoderma, Aspergillus and Bacteria like Rhizobium Bacillus, Azotobacter, Flavobacterium etc have evolved that are endowed with degradation of pesticides aforementioned to non-toxic products. The current study pitches into identification of a novel species of Flavobacterium bacteria capable to degrade the Organophosphorous pesticides. The bacterium was isolated from agricultural soil collected from Guntur District, Andhra Pradesh, India. The samples were serially diluted and the aliquots were incubated for a suitable time following which the suspected colony was subjected to 16S rDNA sequencing. The sequence thus obtained was aligned pairwise against Flavobacterium species, which resulted in identification of novel specie of Flavobacterium later named as EMBS0145, the sequence of which was deposited in in GenBank with accession number JN794045.

Implications of a novel Pseudomonas species on low density polyethylene biodegradation: an in vitro to in silico approach.

Degradation of Petroleum-plastics like Low Density Polyethylene (LDPE) is a budding challenge due to increasing white pollution. The present investigation has focused the aspect through microbial assisted biodegradation. Various indigenous microorganisms were isolated from collected municipal landfill soil. Growth medium enriched with 0.2 g of LDPE powder was used to screen the soil bacteria with biodegradation potential. The screened bacteria were subjected to biodegradation assay in presence of LDPE sheets in growth medium. Four strains gave 5%, 17.8%, 0.9% and 0.6% degradation rate based on weight loss in the conducted in vitro assay for four days. The maximum degraded sheet was analyzed through Scanning Electron Microscopy, Fourier transform infrared spectroscopy and Thermogravimetry, taking undegraded LDPE sheet as control. Results illustrated one-step weight loss with control and three-step weight loss with test. Thus, it proved the efficacy of isolated strain. The strain identification was carried out by genomic DNA isolation followed by PCR and 16S rRNA sequencing. Genotypic identification revealed the bacterium as Pseudomonas citronellolis. BLAST gave a similarity with the database of 96%, thus phylogenetic assessment clarified the bacterium as a novel strain. The isolate was named as Pseudomonas citronellolis EMBS027 and sequence was deposited as LDPE degrading species, in GenBank with accession number KF361478.