Experimental evidence of the reciprocal oxidation of Bovine Serum Albumin and Linoleate in aqueous solution,initiated by HO free radicals

An investigation of radiation-induced oxidation of aqueous bovine serum albumin (BSA) in the presence of linoleate (LH) at pH 10.5 has been carried out in order to better understand the respective oxidative processes involved in both lipid and protein phases. Solutions containing BSA (15 μmol L⁻¹) and linoleate (15–600 μmol L⁻¹) below the critical micellar concentration (cmc = 2000 μmol L⁻¹), have been irradiated by γ-rays (¹³⁷Cs) at radiation doses ranging from 10 to 400 Gy (dose rate 9.5 Gy min⁻¹). It can be noticed that, in the absence of BSA, the main hydroperoxides formed from HO^•-induced linoleate oxidation below the cmc, do not exhibit a conjugated dienic structure. This was also verified in the presence of BSA. Selected chemical markers of oxidation have been monitored: non-conjugated dienic hydroperoxides and conjugated dienes (without hydroperoxide function) for linoleate oxidation, and carbonyl groups for BSA oxidation. We have shown that for the lowest linoleate concentration (15 μmol L⁻¹) in the presence of BSA (15 μmol L⁻¹), the formation of conjugated dienes was not observed, meaning that LH was not exposed to HO^• radicals attack. However, non-conjugated dienic lipid hydroperoxides were simultaneously detected, indicating that LH was secondarily oxidised by BSA oxidised species. Moreover, the oxidation of linoleate was found to be enhanced by the presence of BSA. For the highest linoleate concentration (600 μmol L⁻¹), the expected protection of BSA by LH was not observed, even if LH monomers were responsible for the total scavenging of HO^• radicals. In this latter case, the formation of non-conjugated dienic lipid hydroperoxides was lower than expected. Those results showed that BSA was not oxidised by the direct action of HO^• radicals but was undergoing a secondary oxidation by non-dienic lipid hydroperoxides and/or lipid radical intermediates, coming from the HO^•-induced linoleate oxidation.     

Inheritance of lambda-cyhalothrin resistance in the predator lady beetle Eriopis connexa (Germar) (Coleoptera: Coccinellidae)

Lambda-cyhalothrin is a pyrethroid insecticide widely used to control pests in various crop ecosystems, in which the lady beetle occurs naturally. Therefore, lady beetle populations are exposed to lambda-cyhalothrin sprays that may foster tolerance to this insecticide. This study was conducted to confirm the occurrence of resistance in the lady beetle Eriopis connexa (Germar) (Coleoptera: Coccinellidae) to lambda-cyhalothrin and to characterize the inheritance of resistance after eight progressive selection with insecticide dosages based on the LD₅₀ determined for the F1 generation. Dose–mortality curves were determined for parental populations, F1 hybrids and backcross progenies. Parameters regarding the heritability of resistance to lambda-cyhalothrin in E. connexa allow estimating 10-fold increase in the initial LD₅₀ after 54.5 generations of successive selections. The resistance of E. connexa to lambda-cyhalothrin was characterized as autosomally inherited and incompletely dominant, and influenced by a major gene with possible influence of secondary genes. Additionally, the resistance in E. connexa varies from functionally dominant to functionally recessive depending on the dose used. These findings indicate that insecticide resistance in E. connexa can be selected in the field as determined for field-collected individuals, and subsequently enhanced under laboratory conditions. Its characterization presented here is an important step toward linking biological and chemical control within pest management regarding the lady beetle and lambda-cyhalothrin targeting different pest groups.     

Diclofenac Mediated Demodulation of Alkaline Phosphatase and Renal Cortical Damage in Experimental Albino Mice

Diclofenac sodium is known to interfere with renal physiology by inhibiting prostaglandins. Previous studies indicate that various nephrotoxins damage proximal renal tubules by altering alkaline phosphatase (APase) activity. APase has been reported to be a function related marker in renal proximal tubular epithelia where it is highly expressed. Present investigation deals with toxicity caused in mice kidney at histological and biochemical levels after diclofenac administration. Diclofenac toxicity was assessed by localizing APase in kidney histochemically and biochemically. Intramuscular diclofenac administration (10 mg/kg/body wt) for 30 days exhibited substantial degeneration in kidney. A marked change in APase activity was observed in histochemical and biochemical studies. A change was noticed in specific activity of APase at different periods of diclofenac treatment. Decrease in specific activity of APase after 10 days (18.41 %) and 30 days (55.3 %) of diclofenac exposure was observed. However, an insignificant hike in APase was observed after 20 days of drug therapy. Similar trends in APase activity were evidenced by the electrophoretic analysis. Histological and ultrastructural observations also corroborated above mentioned findings. Present investigation gives an insight into probable mechanism of renal pathology caused by diclofenac administration in mice.     

Hrr25 kinase promotes selective autophagy by phosphorylating the cargo receptor Atg19

Autophagy is the major pathway for the delivery of cytoplasmic material to the vacuole or lysosome. Selective autophagy is mediated by cargo receptors, which link the cargo to the scaffold protein Atg11 and to Atg8 family proteins on the forming autophagosomal membrane. We show that the essential kinase Hrr25 activates the cargo receptor Atg19 by phosphorylation, which is required to link cargo to the Atg11 scaffold, allowing selective autophagy to proceed. We also find that the Atg34 cargo receptor is regulated in a similar manner, suggesting a conserved mechanism.     

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database

Background

The NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different organisms. The NCBI Entrez online web-search interface is convenient for simple manual search for a small number of genes but impractical for the kinds of outputs seen in typical genomics projects.

Results

We have developed an efficient open source tool implemented in Python called Annokey, which annotates gene lists with the results of a keyword search of the NCBI Entrez Gene database and linked Pubmed article information. The user steers the search by specifying a ranked list of keywords (including multi-word phrases and regular expressions) that are correlated with their topic of interest. Rank information of matched terms allows the user to guide further investigation.We applied Annokey to the entire human Entrez Gene database using the key-term “DNA repair” and assessed its performance in identifying the 176 members of a published “gold standard” list of genes established to be involved in this pathway. For this test case we observed a sensitivity and specificity of 97% and 96%, respectively.

Conclusions

Annokey facilitates the identification of genes related to an area of interest, a task which can be onerous if performed manually on a large number of genes. Annokey provides a way to capitalize on the high quality information provided by the Entrez Gene database allowing both scalability and compatibility with automated analysis pipelines, thus offering the potential to significantly enhance research productivity.

     

Pollux: platform independent error correction of single and mixed genomes

Background

Second-generation sequencers generate millions of relatively short, but error-prone, reads. These errors make sequence assembly and other downstream projects more challenging. Correcting these errors improves the quality of assemblies and projects which benefit from error-free reads.

Results

We have developed a general-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.

Conclusions

Pollux is highly effective at correcting errors across platforms, and is consistently able to perform as well or better than currently available error correction software. Pollux provides general-purpose error correction and may be used in applications with or without assembly.     

Effects of Atrazine,Metolachlor, Carbaryl and Chlorothalonil on Benthic Microbes and Their Nutrient Dynamics

Atrazine, metolachlor, carbaryl, and chlorothalonil are detected in streams throughout the U.S. at concentrations that may have adverse effects on benthic microbes. Sediment samples were exposed to these pesticides to quantify responses of ammonium, nitrate, and phosphate uptake by the benthic microbial community. Control uptake rates of sediments had net remineralization of nitrate (−1.58 NO₃ µg gdm⁻¹ h⁻¹), and net assimilation of phosphate (1.34 PO₄ µg gdm⁻¹ h⁻¹) and ammonium (0.03 NH₄ µg gdm⁻¹ h⁻¹). Metolachlor decreased ammonium and phosphate uptake. Chlorothalonil decreased nitrate remineralization and phosphate uptake. Nitrate, ammonium, and phosphate uptake rates are more pronounced in the presence of these pesticides due to microbial adaptations to toxicants. Our interpretation of pesticide availability based on their water/solid affinities supports no effects for atrazine and carbaryl, decreasing nitrate remineralization, and phosphate assimilation in response to chlorothalonil. Further, decreased ammonium and phosphate uptake in response to metolachlor is likely due to affinity. Because atrazine target autotrophs, and carbaryl synaptic activity, effects on benthic microbes were not hypothesized, consistent with results. Metolachlor and chlorothalonil (non-specific modes of action) had significant effects on sediment microbial nutrient dynamics. Thus, pesticides with a higher affinity to sediments and/or broad modes of action are likely to affect sediment microbes'' nutrient dynamics than pesticides dissolved in water or specific modes of action. Predicted nutrient uptake rates were calculated at mean and peak concentrations of metolachlor and chlorothalonil in freshwaters using polynomial equations generated in this experiment. We concluded that in natural ecosystems, peak chlorothalonil and metolachlor concentrations could affect phosphate and ammonium by decreasing net assimilation, and nitrate uptake rates by decreasing remineralization, relative to mean concentrations of metolachlor and chlorothalonil. Our regression equations can complement models of nitrogen and phosphorus availability in streams to predict potential changes in nutrient dynamics in response to pesticides in freshwaters.