Synergistic effect of TRM2/RNC1 and EXO1 in DNA double-strand break repair in Saccharomyces cerevisiae

In our recently published study, we provided in vitro as well as in vivo data demonstrating the involvement of TRM2/RNC1 in homologous recombination based repair (HRR) of DNA double strand breaks (DSBs), in support of such claims reported earlier. To further validate its role in DNA DSB processing, our present study revealed that the trm2 single mutant displays higher sensitivity to persistent induction of specific DSBs at the MAT locus by HO-endonuclease with higher sterility rate among the survivors compared to wild type (wt) or exo1 single mutants. Intriguingly, both sensitivity and sterility rate increased dramatically in trm2exo1 double mutants lacking both endo-exonucleases with a progressively increased sterility rate in trm2exo1 double mutants with short-induction periods, reaching a very high level of sterility with persistent DSB inductions. Mutation analysis of the mating type (MAT) locus among the sterile survivors with persistent HO-induction in trm2 and exo1 single mutants as well as in trm2exo1 double mutants revealed a similar small insertions and deletions events, characteristic of non-homologous end joining (NHEJ) that might have occurred due to the lack of proper processing function in these mutants. In addition, trm2ku80 and trm2rad52 double mutants also displayed significantly higher sterility with persistent DSB induction compared to ku80 and rad52 single mutants, respectively, exhibiting a mutation spectra that shifted from base substitution (in ku80 and rad52 single mutants) to small insertions and deletions in the double mutants (in trm2ku80 and trm2rad52 mutants). These data indicate a defective processing in absence of TRM2, with a synergistic effect of TRM2, and EXO1 in such processing.     

Unravelling the mechanism of the interactions of oxazolidine A and E with collagens in ovine skin

Cross-linking agents play an important part in the physical properties of collagen based biomaterials. Oxazolidines are novel aldehydic tanning agents that are widely used to stabilise collagens in the leather industry. The exact mechanism through which they cross-link collagens is, however, not well understood. When they are combined with vegetable tannins, it is thought that oxazolidines form carbocationic intermediates through ring opening, which are then able to interact with the amino acid side chains of collagens and flavonoid ring systems of vegetable tannins. In this study, the interactions of oxazolidines, with collagens, have been investigated using a number of analytical techniques. High pressure liquid chromatography (HPLC) analysis of oxazolidine tanned collagen samples showed that there is an irreversible reaction with tyrosine side chains. Mass spectrometry (MS) revealed the formation of a Schiff's base adduct with lysine residues, which was reversible in nature. MS analysis of reaction of oxazolidines with a model peptide Suc-Ala-Phe-Lys-AMC in presence of NaCNBH(3), indicated the formation of a product with an increase in molecular weight of 28 kD characteristic of the addition of two methyl groups to lysine. Differential scanning calorimetry showed a synergistic effect for combination tannage, with best results being obtained when vegetable tan was added prior to the aldehydic tanning agents. Circular dichroism (CD) studies of collagen in presence of the more reactive oxazolidine A showed that there was a loss in ellipticity simply because of aggregation of collagen molecules rather than a change in the secondary structure. Based on the results obtained, a scheme has been proposed to explain the possible mechanism of action of oxazolidines with the collagen amino acid side chains.     

Availability of Essential Elements in Nutrient Supplements Used as Antidiabetic Herbal Formulations

Five brands of antidiabetic herbal formulations as tablets, Diabetex, Divya Madhu Nashini, Jambrushila, Diabeticin, and Madhumeh Nashini, from different pharmacies were analyzed for six minor (Na, K, Ca, Cl, Mg, and P) and 20 trace (As, Ba, Br, Ce, Co, Cr, Cs, Cu, Fe, Hg, La, Mn, Rb, Sb, Sc, Se, Sm, Th, V, and Zn) elements by thermal neutron irradiation followed by high-resolution gamma ray spectrometry. Further Ni, Cd, and Pb were determined by atomic absorption spectrophotometry. Most elements vary in a narrow range by a factor of 2–4 while a few others vary in a wide range, e.g., Na (0.05–0.67 mg/g), Mn (26.7–250 μg/g), and V (0.26–2.50 μg/g). All the five brands contain K, Cl, Mg, P, and Ca as minor constituents along with mean trace amounts of Cr (2.11 ± 0.67 μg/g), Cu (15.7 ± 7.11 μg/g), Fe (459 ± 171 μg/g), Mn (143 ± 23 μg/g), Se (238 ± 112 ng/g), and V (0.99 ± 0.93 μg/g). Jambrushila is enriched in Na, Ca, Mg, Cl, Fe, Cu, Se, and Zn, essential nutrients responsible for curing diabetes. Dietary intake of Mn, Fe, and Cu are greater than 10% of the recommended dietary allowance, whereas that for Zn and Se is less than 2%. Mean contents of toxic elements (As, Cd, Hg, and Pb) were found below permissible limits except in Jambrushila. Cr and Zn were inversely correlated with r = −0.81, whereas Rb and Cs exhibit linear correlation (r = 0.93) in five brands. C, H, N analysis showed C ∼ 55%, H ∼ 12%, and N ∼ 2% with a total of ∼70% organic matter. However, thermal decomposition studies at 700°C suggest less than 5% nonvolatile metal oxides. Herbal formulations contain minor and trace elements in bioavailable forms that favorably influence glucose tolerance and possibly increase the body’s ability to ameliorate development of diabetes.     

Composition and distribution of benthic isopod (Crustacea,Malacostraca) families off the Victoria-Land Coast (Ross Sea,Antarctica)

The benthic fauna off the Victoria-Land-Coast, Ross Sea (Antarctica) was investigated during the 19th Italica expedition in February 2004. Samples were taken along a latitudinal transect from Cape Adare down to Terra Nova Bay at water depths ranging from 84 to 515 m. A Rauschert dredge was used at 18 stations to collect epi- and infaunal macrobenthos. 9,494 specimens of Isopoda were collected, representing 19 families. Desmosomatidae were the most abundant family (35,297 ind/1,000 m²), followed by Paramunnidae (23,973 ind/1,000 m²). Paramunnidae was the most frequent taxon and was collected at all stations, in contrast to the Desmosomatidae, which did not occur at any station off Cape Adare.     

Chloride channel accessory 1 integrates chloride channel activity and mTORC1 in aging‐related kidney injury

The mechanism of kidney injury in aging are not well understood. In order to identify hitherto unknown pathways of aging‐related kidney injury, we performed RNA‐Seq on kidney extracts of young and aged mice. Expression of chloride (Cl) channel accessory 1 (CLCA1) mRNA and protein was increased in the kidneys of aged mice. Immunostaining showed a marked increase in CLCLA1 expression in the proximal tubules of the kidney from aged mice. Increased kidney CLCA1 gene expression also correlated with aging in marmosets and in a human cohort. In aging mice, increased renal cortical CLCA1 content was associated with hydrogen sulfide (H₂S) deficiency, which was ameliorated by administering sodium hydrosulfide (NaHS), a source of H₂S. In order to study whether increased CLCA1 expression leads to injury phenotype and the mechanisms involved, stable transfection of proximal tubule epithelial cells overexpressing human CLCA1 (hCLCA1) was performed. Overexpression of hCLCA1 augmented Cl⁻ current via the Ca⁺⁺‐dependent Cl⁻ channel TMEM16A (anoctamin‐1) by patch‐clamp studies. hCLCA1 overexpression also increased the expression of fibronectin, a matrix protein, and induced the senescence‐associated secretory phenotype (SASP). Mechanistic studies underlying these changes showed that hCLCA1 overexpression leads to inhibition of AMPK activity and stimulation of mTORC1 as cellular signaling determinants of injury. Both TMEM16A inhibitor and NaHS reversed these signaling events and prevented changes in fibronectin and SASP. We conclude that CLCA1‐TMEM16A‐Cl⁻ current pathway is a novel mediator of kidney injury in aging that is regulated by endogenous H₂S.     

Molecular chaperone function of stress inducible Hsp70 is critical for intracellular multiplication of Toxoplasma gondii

Intracellular pathogens like Toxoplasma gondii often target proteins and pathways critical for host cell survival and stress response. Molecular chaperones encoded by the evolutionary conserved Heat shock proteins (Hsps) maintain proteostasis and are vital to cell survival following exposure to any form of stress. A key protein of this family is Hsp70, an ATP-driven molecular chaperone, which is stress inducible and often indiscernible in normal cells. Role of this protein with respect to intracellular survival and multiplication of protozoan parasite like T. gondii remains to be examined. We find that T. gondii infection upregulates expression of host Hsp70. Hsp70 selective inhibitor 2-phenylethynesulfonamide (PES) attenuates intracellular T. gondii multiplication. Biotinylated PES confirms selective interaction of this small molecule inhibitor with Hsp70. We show that PES acts by disrupting Hsp70 chaperone function which leads to dysregulation of host autophagy. Silencing of host Hsp70 underscores its importance for intracellular multiplication of T. gondii, however, attenuation achieved using PES is not completely attributable to host Hsp70 indicating the presence of other intracellular targets of PES in infected host cells. We find that PES is also able to target T. gondii Hsp70 homologue which was shown using PES binding assay. Detailed molecular docking analysis substantiates PES targeting of TgHsp70 in addition to host Hsp70. While establishing the importance of protein quality control in infection, this study brings to the fore a unique opportunity of dual targeting of host and parasite Hsp70 demonstrating how structural conservation of these proteins may be exploited for therapeutic design.     

Synthesis, characterization and crystal structure of manganese (IV) complex derived from salicylic acid

The binuclear manganese (IV) [Mn₂(Hsal)₄(OH)₄] (H₂sal = salicylic acid) complex has been obtained from a complex reaction mixture in methanol consisting of Mn(II)(OAc)₂ · 4H₂O, GS ( a reagent obtained by refluxing glycine and salicylaldehyde in 1:1 molar ratio in methanol), monosodium salicylate and pyridine. The compound contains a distorted octahedral MnO₆ coordination unit of potential importance to high oxidation state manganese bimolecules.     

Visualising fouling of a chromatographic matrix using confocal scanning laser microscopy

Confocal scanning laser microscopy (CSLM) was used to visualise the spatial location of foulants during the fouling of Q Sepharose FF matrix in finite batch experiments and for examining the subsequent effectiveness of clean-in-place (CIP) treatments in cleaning the heavily fouled beads. Beads were severely fouled with partially clarified E. coli homogenate by contacting the beads with the foulant for contact times of 5 min, 1 or 12 h. The use of two different fluorescent dyes, PicoGreen and Cy5.5, for labelling genomic PicoGreen-labelled dsDNA and protein respectively, allowed the direct observation of the chromatographic beads. The extent of fouling was assessed by measuring the subsequent adsorption of Cy5.5-labelled BSA to the beads. Control studies established that the labelling of BSA did not affect significantly the protein properties. In the control case of contacting the unfouled matrix with Cy5.5-labelled BSA, protein was able to penetrate the entire matrix volume. After fouling, Cy5.5-labelled BSA was unable to penetrate the bead but only to bind near the bead surface where it slowly displaced PicoGreen-conjugated dsDNA, which bound only at the exterior of the beads. Labelled host cell proteins bound throughout the bead interior but considerably less at the core; suggesting that other species might have occupied that space. The gross levels of fouling achieved drastically reduced the binding capacity and maximum Cy5.5-labelled BSA uptake rate. The capacity of the resin was reduced by 2.5-fold when incubated with foulant for up to 1 h. However, when the resin was fouled for a prolonged time of 12 h a further sixfold decrease in capacity was seen. The uptake rate of Cy5.5-labelled BSA decreased with increased fouling time of the resin. Incubating the fouled beads in 1 M NaCl dissociated PicoGreen-labelled dsDNA from the bead exterior within 15 min of incubation but proved ineffective in removing all the foulant protein. Cy5.5-labelled BSA was still unable to bind beyond the outer region of the beads. A harsher CIP treatment of 1 M NaCl dissolved in 1 M NaOH was also ineffective in removing all the foulant protein but did remove PicoGreen-conjugated dsDNA within 15 min of incubation. Cy5.5-labelled BSA was able to bind throughout the bead interior after this more aggressive CIP treatment but at a lower capacity than in the case of fresh beads. The competitive adsorption of BacLight Red-labelled whole cells or cell debris and PicoGreen-conjugated dsDNA was also visualised using CSLM.     

O-Acetylation of the terminal N-acetylglucosamine of the lipooligosaccharide inner core in Neisseria meningitidis. Influence on inner core structure and assembly

O-Acetylation is a common decoration on endotoxins derived from many Gram-negative bacterial species, and it has been shown to be instrumental (e.g. in Salmonella typhimurium) in determining the final tertiary structure of the endotoxin and the immunogenicity of the molecule. Structural heterogeneity of endotoxins produced by mucosal pathogens such as Neisseria meningitidis is determined by decorations on the heptose inner core, including O-acetylation of the terminal N-acetylglucosamine (GlcNAc) attached to HepII. In this report, we show that O-acetylation of the meningococcal lipooligosaccharide (LOS) inner core has an important role in determining inner core assembly and immunotype expression. The gene encoding the LOS O-acetyltransferase, lot3, was identified by homology to NodX from Rhizobium leguminosarum. Inactivation of lot3 in strain NMB resulted in the loss of the O-acetyl group located at the C-3 position of the terminal GlcNAc of the LOS inner core. Inactivation of either lot3 or lgtG, which encodes the HepII glucosyltransferase, did not result in the appearance of the O-3-linked phosphoethanolamine (PEA) groups on the LOS inner core. Construction of a double mutant in which both lot3 and lgtG were inactivated resulted in the appearance of O-3-linked PEA groups on the LOS inner core. In conclusion, O-acetylation status of the terminal GlcNAc of the gamma-chain of the meningococcal LOS inner core is an important determinant for the appearance or exclusion of the O-3-linked PEA group on the LOS inner core and contributes to LOS structural diversity. O-Acetylation also likely influences resistance to complement-mediated lysis and may be important in LOS conjugate vaccine design.