SOD2, the principal scavenger of mitochondrial superoxide, is dispensable for embryogenesis and imaginal tissue development but essential for adult survival

Definitive evidence on the impact of MnSOD/SOD2-deficiency and the consequent effects of high flux of mitochondrial reactive oxygen species (ROS) on pre-natal/pre-adult development has yet to be reported for either Drosophila or mice. Here we report that oocytes lacking maternal SOD2 protein develop into adults just like normal SOD2-containing oocytes suggesting that maternal SOD2-mediated protection against mitochondrial ROS is not essential for oocyte viability. However, the capacity of SOD2-null larvae to undergo successful metamorphosis into adults is negatively influenced in the absence of SOD2. We therefore determined the impact of a high superoxide environment on cell size, progression through the cell cycle, cell differentiation, and cell death and found no difference between SOD2-null and SOD2+ larva and pupa. Thus loss of SOD2 activity clearly has no effect on pre-adult imaginal tissues. Instead, we found that the high mitochondrial superoxide environment arising from the absence of SOD2 leads to the induction of autophagy. Such autophagic response may underpin the resistance of pre-adult tissues to unscavenged ROS. Finally, while our data establish that SOD2 activity is less essential for normal development, the mortality of Sod2-/- neonates of both Drosophila and mice suggests that SOD2 activity is indeed essential for the viability of adults. We therefore asked if the early mortality of SOD2-null young adults could be rescued by activation of SOD2 expression. The results support the conclusion that the early mortality of SOD2-null adults is largely attributable to the absence of SOD2 activity in the adult per se. This finding somewhat contradicts the widely held notion that failure to scavenge the high volume of superoxide emanating from the oxidative demands of development would be highly detrimental to developing tissues.     

Human papillomavirus elevated genetic biomarker signature by statistical algorithm

Head and neck squamous cell carcinoma (HNSCC) is the one of the most frequently found cancers in the world. The aim of the study was to find the genes responsible and enriched pathways associated with HNSCC using bioinformatics and survival analysis methods. A total of 646 patients with HNSCC based on clinical information were considered for the study. HNSCC samples were grouped according to the parameters (RFS, DFS, PFS, or OS). The probe ID of these 11 genes was retrieved by Affymetrix using the NetAffx Query algorithm. The protein–protein interaction (PPI) network and Kaplan–Meier curve were used to find associations among the genes' expression data. We found that among these 11 genes, nine genes, CCNA1, MMP3, FLRT3, GJB6, ZFR2, PITX2, SYCP2, MEI1, and UGT8 were significant (p < .05). A survival plot was drawn between the p value and gene expression. This study helped us find the nine significant genes which play vital roles in HNSCC along with their key pathways and their interaction with other genes in the PPI network. Finally, we found the biomarker index for relapse time and risk factors for HNSCC in cancer patients.     

Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites

Thymine DNA glycosylase (TDG) excises T from G·T mispairs and is thought to initiate base excision repair (BER) of deaminated 5-methylcytosine (mC). Recent studies show that TDG, including its glycosylase activity, is essential for active DNA demethylation and embryonic development. These and other findings suggest that active demethylation could involve mC deamination by a deaminase, giving a G·T mispair followed by TDG-initiated BER. An alternative proposal is that demethylation could involve iterative oxidation of mC to 5-hydroxymethylcytosine (hmC) and then to 5-formylcytosine (fC) and 5-carboxylcytosine (caC), mediated by a Tet (ten eleven translocation) enzyme, with conversion of caC to C by a putative decarboxylase. Our previous studies suggest that TDG could excise fC and caC from DNA, which could provide another potential demethylation mechanism. We show here that TDG rapidly removes fC, with higher activity than for G·T mispairs, and has substantial caC excision activity, yet it cannot remove hmC. TDG excision of fC and caC, oxidation products of mC, is consistent with its strong specificity for excising bases from a CpG context. Our findings reveal a remarkable new aspect of specificity for TDG, inform its catalytic mechanism, and suggest that TDG could protect against fC-induced mutagenesis. The results also suggest a new potential mechanism for active DNA demethylation, involving TDG excision of Tet-produced fC (or caC) and subsequent BER. Such a mechanism obviates the need for a decarboxylase and is consistent with findings that TDG glycosylase activity is essential for active demethylation and embryonic development, as are mechanisms involving TDG excision of deaminated mC or hmC.     

Opercular Activity and Temporal Organization of Surfacing Behaviour in Indian Catfishes,Clarias batrachus and Heteropneustes fossilis

Opercular and surfacing activity were observed in the Indian catfish Clarias batrachus and Heteropneustes fossilis. In the series A experiments, the opercular activity was monitored under two experimental conditions, viz., (1) surfacing allowed and (2) surfacing prevented. A statistically significant elevation of the rate of opercular activity was observed when air breathing was prevented in both species. In addition, a significant prevention effect and a time of day dependence of that were noticed in both species. In the series B experiments, temporal patterns of surfacing and air-gulping activities were examined under an artificial LD 12:12 schedule at 2-h intervals over a period of 48 h. The inter air-gulping interval in minutes between two consecutive bouts was also recorded four times each day in both species. A significant 24-h rhythm was found for the rate of surfacing activity and length of the inter air-gulping interval in both species. However, the overall activity appears to be much higher in Heteropneustes fossilis as compared to Clarias batrachus.     

Fluoroquinolone Resistance Mechanisms of Shigella flexneri Isolated in Bangladesh

Objective

To investigate the prevalence and mechanisms of fluoroquinolone resistance in Shigella species isolated in Bangladesh and to compare with similar strains isolated in China.

Methods

A total of 3789 Shigella isolates collected from Clinical Microbiology Laboratory of icddr,b, during 2004–2010 were analyzed for antibiotic susceptibility. Analysis of plasmids, plasmid-mediated quinolone-resistance genes, PFGE, and sequencing of genes of the quinolone-resistance-determining regions (QRDR) were conducted in representative strains isolated in Bangladesh and compared with strains isolated in Zhengding, China. In addition, the role of efflux-pump was studied by using the efflux-pump inhibitor carbonyl cyanide-m-chlorophenylhydrazone (CCCP).

Results

Resistance to ciprofloxacin in Shigella species increased from 0% in 2004 to 44% in 2010 and S. flexneri was the predominant species. Of Shigella spp, ciprofloxacin resistant (Cip^R) strains were mostly found among S. flexneri (8.3%), followed by S. sonnei (1.5%). Within S. flexneri (n = 2181), 14.5% were resistance to ciprofloxacin of which serotype 2a was predominant (96%). MIC of ciprofloxacin, norfloxacin, and ofloxacin were 6–32 mg/L, 8–32 mg/L, and 8–24 mg/L, respectively in S. flexneri 2a isolates. Sequencing of QRDR genes of resistant isolates showed double mutations in gyrA gene (Ser⁸³Leu, Asp⁸⁷Asn/Gly) and single mutation in parC gene (Ser⁸⁰Ile). A difference in amino acid substitution at position 87 was found between strains isolated in Bangladesh (Asp⁸⁷Asn) and China (Asp⁸⁷Gly) except for one. A novel mutation at position 211 (His→Tyr) in gyrA gene was detected only in the Bangladeshi strains. Susceptibility to ciprofloxacin was increased by the presence of CCCP indicating the involvement of energy dependent active efflux pumps. A single PFGE type was found in isolates from Bangladesh and China suggesting their genetic relatedness.

Conclusions

Emergence of fluoroquinolone resistance in Shigella undermines a major challenge in current treatment strategies which needs to be followed up by using empirical therapeutic strategies.     

Theoretical exploration of the mechanism of formylmethanofuran dehydrogenase: the first reductive step in CO<Subscript>2</Subscript> fixation by methanogens

A theoretical exploration of the possible active site models of methanofuran dehydrogenase reveals that the free energy of the reduction of the carbamate group is substantially negative and is driven by the electron withdrawing amide group next to the carbonyl carbon. Comparison of the computed transition state energies with the experimental energy barrier indicates that the active site is likely to have an axial oxo and equatorial hydrosulfide ligand, the substrate is likely to be protonated and a second-sphere hydrogen-bonding interaction with the axial ligand can, substantially, lower the barrier of this reaction which involves reduction of the carbonyl center of the a carbamate to form an N-formyl group via a hydride shift from a Mo(IV) center.     

Interaction of phosphorus and molybdenum and the availability of zinc,copper, manganese,molybdenum and phosphorus in waterlogged rice soil

Summary Laboratory incubation experiments were conducted with low-land rice soil to study the effect of applying three different levels of molybdenum (0, 2.5 and 5.0 ppm) and phosphorus (0, 100 and 200 ppm), in all possible combinations, on the changes in available Mo, P, Mn, Zn and Cu in soil. The results showed that application of Mo at both the levels increased the content of extractable Mo and P but decreased those of Cu and Mo in soil whereas application of Mo at higher level only increased the content of extractable Zn in soil. Application of P at both the levels decreased the content of extractable Mo, Mn and Cu but increased that of P whereas it showed an inconsistent effect on the extractable Zn content in soil. The P × Mo interaction effect was found to be beneficial for the content of P, Mo and Zn only. During the initial period of incubation all elements except Cu recorded an increase but with the progress of incubation period the content of all the elements except Mn gradually declined.