Correction: The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3'-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis.

[This corrects the article DOI: 10.1371/journal.pgen.1004749.].

First record of the genus Paratrichodina (Ciliophora: Trichodinidae) in India from ornamental goldfish (Carassius auratus L.) supplemented with description of a new species Paratrichodina indiana n. sp.

The present investigation deals with the accounts of a novel species of ciliate parasite belonging to the genus Paratrichodina namely, Paratrichodina indiana n. sp. identified from the respiratory organ of goldfish Carassius auratus at Nadia district of West Bengal, India. 276 fish have been collected for parasitological examination from various fish farm of West Bengal, India. The parasitological investigation was conducted using the AgNO3 impregnation technique, which was supplemented by a taxonomic description, morphological variations and data comparison with previously documented closely related species. Paratrichodina indiana n. sp. is a small-sized trichodinid, measures uniquely 19.21 ± 1.6 µm in body diameter, with prominent adhesive disc measure 15.55 ± 1.22 µm. The current investigation supports the first record of the genus from C. auratus and adds one new species to the genus Paratrichodina, as well as report of a new host, region and prevalence rates.

Morroniside interaction with poly (ADP-ribose) polymerase accentuates metabolic mitigation of alloxan-induced genotoxicity and hyperglycaemia: a molecular docking based in vitro and in vivo experimental therapeutic insight.

The present study tends to evaluate the possible potential of bio-active Morroniside (MOR), against alloxan (ALX)-induced genotoxicity and hyperglycaemia. In silico prediction revealed the interaction of MOR with Poly (ADP-ribose) polymerase (PARP) protein which corroborated well with experimental in vitro L6 cell line and in vivo mice models. Data revealed the efficacy of MOR in the selective activation of PARP protein and modulating other stress proteins NF-κB, and TNF-α to initiate protective potential against ALX-induced genotoxicity and hyperglycaemia. Further, the strong interaction of MOR with CT-DNA (calf thymus DNA) analyzed through CD spectroscopy, UV-Vis study and ITC data revealed the concerted action of bio-factors involved in inhibiting chromosomal aberration and micronucleus formation associated with DNA damage. Finally, MOR does not play any role in microbial growth inhibition which often occurs due to hyperglycemic dysbiosis. Thus, from the overall findings, we may conclude that MOR could be a potential drug candidate for the therapeutic management of induced-hyperglycaemia and genotoxicity.Communicated by Ramaswamy H. Sarma.

Synopsis of the species of Monocystis von Stein, 1848 (Apicomplexa: Gregarinomorphea: Arthrogregarida) pathogenic to earthworms described so far.

A synopsis of the species of Monocystis (Apicomplexa: Gregarinomorphea: Arthrogregarida) is presented, including a total of 114 species of worldwide. The most significant morphological and morphometric traits for each species are included together with information on the type-host, type locality, the infection site within the host and the original references. This checklist enumerates total Monocystis spp. in a place described so far in the worldwide pattern.

Non-linear response of colloid monolayers at high-frequency probed by ultrasound-driven microbubble dynamics.

HYPOTHESIS: High-frequency interfacial rheology of complex interfaces remains challenging yet it is central to the performance of multiphase soft matter products. We propose to use ultrasound-driven bubble dynamics to probe the high-frequency rheology of a colloid monolayer used as model system with controlled interactions and simultaneous monitoring of the microstructure. We hypothesize that by comparing the response of colloid-coated bubbles with that of a bare bubble under identical experimental conditions, it is possible to detect the non-linear response of the monolayer and use it to extract interfacial rheological properties at 104s-1. EXPERIMENTS: Using high-speed video-microscopy, the dynamics of colloid-coated bubbles were probed to study the micromechanical response of the monolayer to high-frequency deformation. Protocols analogous to stress-sweep and frequency-sweep were developed to examine the stress-strain relationships. A simple model, motivated by the observed non-linear responses, was developed to estimate the interfacial viscoelastic parameters. FINDINGS: The estimated elastic moduli of colloid monolayers at 104s-1 are about an order of magnitude larger than those measured at 1 s-1. The monolayers exhibit non-linear viscoelasticity for strain amplitudes as small as 1%, and strain-softening behaviour. These findings highlight the applicability of acoustic bubbles as high-frequency interfacial probes.

Buckling versus Crystal Expulsion Controlled by Deformation Rate of Particle-Coated Air Bubbles in Oil.

Oil foams stabilized by crystallizing agents exhibit outstanding stability and show promise for applications in consumer products. The stability and mechanics imparted by the interfacial layer of crystals underpin product shelf life, as well as optimal processing conditions and performance in applications. Shelf life is affected by the stability against bubble dissolution over a long time scale, which leads to slow compression of the interfacial layer. In processing flow conditions, the imposed deformation is characterized by much shorter time scales. In practical situations, the crystal layer is therefore subjected to deformation on extremely different time scales. Despite its importance, our understanding of the behavior of such interfacial layers at different time scales remains limited. To address this gap, here we investigate the dynamics of single, crystal-coated bubbles isolated from an oleofoam, at two extreme time scales: the diffusion-limited time scale characteristic of bubble dissolution, ∼104 s, and a fast time scale characteristic of processing flow conditions, ∼10-3 s. In our experiments, slow deformation is obtained by bubble dissolution, and fast deformation in controlled conditions with real-time imaging is obtained using ultrasound-induced bubble oscillations. The experiments reveal that the fate of the interfacial layer is dramatically affected by the dynamics of deformation: after complete bubble dissolution, a continuous solid layer remains; after fast, oscillatory deformation of the layer, small crystals are expelled from the layer. This observation shows promise toward developing stimuli-responsive systems, with sensitivity to deformation rate, in addition to the already known thermoresponsiveness and photoresponsiveness of oleofoams.

Arsenic contamination, impact and mitigation strategies in rice agro-environment: An inclusive insight.

Arsenic (As) contamination and its adverse consequences on rice agroecosystem are well known. Rice has the credit to feed more than 50% of the world population but concurrently, rice accumulates a substantial amount of As, thereby compromising food security. The gravity of the situation lays in the fact that the population in theAs uncontaminated areas may be accidentally exposed to toxic levels of As from rice consumption. In this review, we are trying to summarize the documents on the impact of As contamination and phytotoxicity in past two decades. The unique feature of this attempt is wide spectrum coverages of topics, and that makes it truly an interdisciplinary review. Aprat from the behaviour of As in rice field soil, we have documented the cellular and molecular response of rice plant upon exposure to As. The potential of various mitigation strategies with particular emphasis on using biochar, seed priming technology, irrigation management, transgenic variety development and other agronomic methods have been critically explored. The review attempts to give a comprehensive and multidiciplinary insight into the behaviour of As in Paddy -Water - Soil - Plate prospective from molecular to post-harvest phase. From the comprehensive literature review, we may conclude that considerable emphasis on rice grain, nutritional and anti-nutritional components, and grain quality traits under arsenic stress condition is yet to be given. Besides these, some emerging mitigation options like seed priming technology, adoption of nanotechnological strategies, applications of biochar should be fortified in large scale without interfering with the proper use of biodiversity.

Selenium Biofortification: Roles, Mechanisms, Responses and Prospects.

The trace element selenium (Se) is a crucial element for many living organisms, including soil microorganisms, plants and animals, including humans. Generally, in Nature Se is taken up in the living cells of microorganisms, plants, animals and humans in several inorganic forms such as selenate, selenite, elemental Se and selenide. These forms are converted to organic forms by biological process, mostly as the two selenoamino acids selenocysteine (SeCys) and selenomethionine (SeMet). The biological systems of plants, animals and humans can fix these amino acids into Se-containing proteins by a modest replacement of methionine with SeMet. While the form SeCys is usually present in the active site of enzymes, which is essential for catalytic activity. Within human cells, organic forms of Se are significant for the accurate functioning of the immune and reproductive systems, the thyroid and the brain, and to enzyme activity within cells. Humans ingest Se through plant and animal foods rich in the element. The concentration of Se in foodstuffs depends on the presence of available forms of Se in soils and its uptake and accumulation by plants and herbivorous animals. Therefore, improving the availability of Se to plants is, therefore, a potential pathway to overcoming human Se deficiencies. Among these prospective pathways, the Se-biofortification of plants has already been established as a pioneering approach for producing Se-enriched agricultural products. To achieve this desirable aim of Se-biofortification, molecular breeding and genetic engineering in combination with novel agronomic and edaphic management approaches should be combined. This current review summarizes the roles, responses, prospects and mechanisms of Se in human nutrition. It also elaborates how biofortification is a plausible approach to resolving Se-deficiency in humans and other animals.

Overexpression of acid ceramidase (ASAH1) protects retinal cells (ARPE19) from oxidative stress.

Over 11 million people in the United States alone have some form of age-related macular degeneration (AMD). Oxidative stress, cell death, and the degeneration of retinal pigment epithelial (RPE) cells contribute to AMD pathology. Recent evidence suggests that ceramide (Cer), a cellular sphingolipid mediator that acts as a second messenger to induce apoptosis, might play a role in RPE cell death. The lysosomal breakdown of Cer by acid ceramidase [N-acylsphingosine amidohydrolase (ASAH)1] into sphingosine (Sph) is the major source for Sph 1-phosphate production, which has an opposing role to Cer and provides cytoprotection. Here, we investigated the role of Cer in human RPE-derived ARPE19 cells under hydrogen peroxide-induced oxidative stress, and show that Cer and hexosyl-Cer levels increase in the oxidatively stressed ARPE19 cells, which can be prevented by overexpression of lysosomal ASAH1. This study demonstrates that oxidative stress generates sphingolipid death mediators in retinal cells and that induction of ASAH1 could rescue retinal cells from oxidative stress by hydrolyzing excess Cers.

The role of the mammalian DNA end-processing enzyme polynucleotide kinase 3'-phosphatase in spinocerebellar ataxia type 3 pathogenesis.

DNA strand-breaks (SBs) with non-ligatable ends are generated by ionizing radiation, oxidative stress, various chemotherapeutic agents, and also as base excision repair (BER) intermediates. Several neurological diseases have already been identified as being due to a deficiency in DNA end-processing activities. Two common dirty ends, 3'-P and 5'-OH, are processed by mammalian polynucleotide kinase 3'-phosphatase (PNKP), a bifunctional enzyme with 3'-phosphatase and 5'-kinase activities. We have made the unexpected observation that PNKP stably associates with Ataxin-3 (ATXN3), a polyglutamine repeat-containing protein mutated in spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph Disease (MJD). This disease is one of the most common dominantly inherited ataxias worldwide; the defect in SCA3 is due to CAG repeat expansion (from the normal 14-41 to 55-82 repeats) in the ATXN3 coding region. However, how the expanded form gains its toxic function is still not clearly understood. Here we report that purified wild-type (WT) ATXN3 stimulates, and by contrast the mutant form specifically inhibits, PNKP's 3' phosphatase activity in vitro. ATXN3-deficient cells also show decreased PNKP activity. Furthermore, transgenic mice conditionally expressing the pathological form of human ATXN3 also showed decreased 3'-phosphatase activity of PNKP, mostly in the deep cerebellar nuclei, one of the most affected regions in MJD patients' brain. Finally, long amplicon quantitative PCR analysis of human MJD patients' brain samples showed a significant accumulation of DNA strand breaks. Our results thus indicate that the accumulation of DNA strand breaks due to functional deficiency of PNKP is etiologically linked to the pathogenesis of SCA3/MJD.

Thirdhand smoke causes DNA damage in human cells.

Exposure to thirdhand smoke (THS) is a newly described health risk. Evidence supports its widespread presence in indoor environments. However, its genotoxic potential, a critical aspect in risk assessment, is virtually untested. An important characteristic of THS is its ability to undergo chemical transformations during aging periods, as demonstrated in a recent study showing that sorbed nicotine reacts with the indoor pollutant nitrous acid (HONO) to form tobacco-specific nitrosamines (TSNAs) such as 4-(methylnitrosamino)-4-(3-pyridyl)butanal (NNA) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). The goal of this study was to assess the genotoxicity of THS in human cell lines using two in vitro assays. THS was generated in laboratory systems that simulated short (acute)- and long (chronic)-term exposures. Analysis by liquid chromatography-tandem mass spectrometry quantified TSNAs and common tobacco alkaloids in extracts of THS that had sorbed onto cellulose substrates. Exposure of human HepG2 cells to either acute or chronic THS for 24h resulted in significant increases in DNA strand breaks in the alkaline Comet assay. Cell cultures exposed to NNA alone showed significantly higher levels of DNA damage in the same assay. NNA is absent in freshly emitted secondhand smoke, but it is the main TSNA formed in THS when nicotine reacts with HONO long after smoking takes place. The long amplicon-quantitative PCR assay quantified significantly higher levels of oxidative DNA damage in hypoxanthine phosphoribosyltransferase 1 (HPRT) and polymerase ß (POLB) genes of cultured human cells exposed to chronic THS for 24h compared with untreated cells, suggesting that THS exposure is related to increased oxidative stress and could be an important contributing factor in THS-mediated toxicity. The findings of this study demonstrate for the first time that exposure to THS is genotoxic in human cell lines.

A soluble diacylglycerol acyltransferase is involved in triacylglycerol biosynthesis in the oleaginous yeast Rhodotorula glutinis.

The biosynthesis of triacylglycerol (TAG) occurs in the microsomal membranes of eukaryotes. Here, we report the identification and functional characterization of diacylglycerol acyltransferase (DGAT), a member of the 10 S cytosolic TAG biosynthetic complex (TBC) in Rhodotorula glutinis. Both a full-length and an N-terminally truncated cDNA clone of a single gene were isolated from R. glutinis. The DGAT activity of the protein encoded by RgDGAT was confirmed in vivo by the heterologous expression of cDNA in a Saccharomyces cerevisiae quadruple mutant (H1246) that is defective in TAG synthesis. RgDGAT overexpression in yeast was found to be capable of acylating diacylglycerol (DAG) in an acyl-CoA-dependent manner. Quadruple mutant yeast cells exhibit growth defects in the presence of oleic acid, but wild-type yeast cells do not. In an in vivo fatty acid supplementation experiment, RgDGAT expression rescued quadruple mutant growth in an oleate-containing medium. We describe a soluble acyl-CoA-dependent DAG acyltransferase from R. glutinis that belongs to the DGAT3 class of enzymes. The study highlights the importance of an alternative TAG biosynthetic pathway in oleaginous yeasts.

Defective in cuticular ridges (DCR) of Arabidopsis thaliana, a gene associated with surface cutin formation, encodes a soluble diacylglycerol acyltransferase.

A key step in the triacylglycerol (TAG) biosynthetic pathway is the final acylation of diacylglycerol (DAG) by DAG acyltransferase. In silico analysis has revealed that the DCR (defective in cuticular ridges) (At5g23940) gene has a typical HX(4)D acyltransferase motif at the N-terminal end and a lipid binding motif VX(2)GF at the middle of the sequence. To understand the biochemical function, the gene was overexpressed in Escherichia coli, and the purified recombinant protein was found to acylate DAG specifically in an acyl-CoA-dependent manner. Overexpression of At5g23940 in a Saccharomyces cerevisiae quadruple mutant deficient in DAG acyltransferases resulted in TAG accumulation. At5g23940 rescued the growth of this quadruple mutant in the oleate-containing medium, whereas empty vector control did not. Lipid particles were localized in the cytosol of At5g23940-transformed quadruple mutant cells, as observed by oil red O staining. There was an incorporation of 16-hydroxyhexadecanoic acid into TAG in At5g23940-transformed cells of quadruple mutant. Here we report a soluble acyl-CoA-dependent DAG acyltransferase from Arabidopsis thaliana. Taken together, these data suggest that a broad specific DAG acyltransferase may be involved in the cutin as well as in the TAG biosynthesis by supplying hydroxy fatty acid.

Cytosolic triacylglycerol biosynthetic pathway in oilseeds. Molecular cloning and expression of peanut cytosolic diacylglycerol acyltransferase.

Triacylglycerols (TAGs) are the most important storage form of energy for eukaryotic cells. TAG biosynthetic activity was identified in the cytosolic fraction of developing peanut (Arachis hypogaea) cotyledons. This activity was NaF insensitive and acyl-coenzyme A (CoA) dependent. Acyl-CoA:diacylglycerol acyltransferase (DGAT) catalyzes the final step in TAG biosynthesis that acylates diacylglycerol to TAG. Soluble DGAT was identified from immature peanuts and purified by conventional column chromatographic procedures. The enzyme has a molecular mass of 41 +/- 1.0 kD. Based on the partial peptide sequence, a degenerate probe was used to obtain the full-length cDNA. The isolated gene shared less than 10% identity with the previously identified DGAT1 and 2 families, but has 13% identity with the bacterial bifunctional wax ester/DGAT. To differentiate the unrelated families, we designate the peanut gene as AhDGAT. Expression of peanut cDNA in Escherichia coli resulted in the formation of labeled TAG and wax ester from [14C]acetate. The recombinant E. coli showed high levels of DGAT activity but no wax ester synthase activity. TAGs were localized in transformed cells with Nile blue A and oil red O staining. The recombinant and native DGAT was specific for 1,2-diacylglycerol and did not utilize hexadecanol, glycerol-3-phosphate, monoacylglycerol, lysophosphatidic acid, and lysophosphatidylcholine. Oleoyl-CoA was the preferred acyl donor as compared to palmitoyl- and stearoyl-CoAs. These data suggest that the cytosol is one of the sites for TAG biosynthesis in oilseeds. The identified pathway may present opportunities of bioengineering oil-yielding plants for increased oil production.

Comparison of the performance of round and rectangular wire in small solenoids for high-field NMR.

This paper considers the effects of conductor geometry on the performance of small solenoidal coils for high-field NMR. First, a simple analytical model is presented for investigating the effects of conductor geometry on the current distribution in such coils. The model was used to derive optimum parameters for coils constructed from wire with either rectangular or circular cross-sections as a function of the length-to-diameter ratio. Second, a commercial software package utilizing full three-dimensional finite-element solutions to Maxwell's equations was used to confirm the basic findings of the simple analytical model, and also to compare simulated S/N estimations with experimental NMR spectra acquired with 2.5 mm and 1.0 mm-diameter solenoid coils: reasonable agreement was found. Third, as a demonstration of the usefulness of such coils for mass-limited samples, multidimensional experiments were performed at 750 MHz on approximately 4.7 nmol (41 microg) of PF1061, a protein from Pyrococcus furiosus.

Design, construction, and validation of a 1-mm triple-resonance high-temperature-superconducting probe for NMR.

We report a 600-MHz 1-mm triple-resonance high-temperature-superconducting (HTS) probe for nuclear magnetic resonance spectroscopy. The probe has a real sample volume of about 7.5 microl, an active volume of 6.3 microl, and appears to have the highest mass sensitivity at any field strength. The probe is constructed with four sets of HTS coils that are tuned to 1H, 2H, 13C, and 15N, and there is a z-axis gradient. The coils are cooled with a conventional Bruker CryoPlatform to about 20 K, and the sample chamber can be regulated above or below room temperature over a moderate range using a Bruker variable temperature unit. The absolute S/N for 0.1% ethylbenzene is approximately 1/3 that of a conventional 5mm probe with just 1/70 of the sample volume. We demonstrate the utility of this probe for small molecules and proteins with 2D spectra of just 1.7 microg of ibuprofen and 400 microM 15N-labeled ubiquitin.

Ion solvation by channel carbonyls characterized by 17O solid-state NMR at 21 T.

Recently available ultrahigh magnetic fields offer new opportunities for studies of quadrupole nuclei in biological solids because of the dramatic enhancement in sensitivity and resolution associated with the reduction of second-order quadrupole interactions. Here, we present a new approach for understanding the function and energetics of ion solvation in channels using solid-state 17O NMR spectroscopy of single-site 17O-labeled gramicidin A. The chemical shift and quadrupole coupling parameters obtained in powder samples of lyophilized material are similar to those shown in the literature for carbonyl oxygens. In lipid bilayers, it is found that the carbonyl 17O anisotropic chemical shift of Leu10, one of the three carbonyl oxygens contributing to the ion binding site in gramicidin A, is altered by 40 ppm when K+ ion binds to the channel, demonstrating a high sensitivity to such interactions. Moreover, considering the large breadth of the carbonyl 17O chemical shift (>500 ppm), the recording of anisotropic 17O chemical shifts in bilayers aligned with respect to magnetic field B0 offers high-quality structural restraints similar to 15N and 13C anisotropic chemical shifts.