DnaJs,the critical drivers of Hsp70s: genome-wide screening,characterization and expression of DnaJ family genes in Sorghum bicolor

Molecular Biology Reports - The DnaJ/Hsp40s, are important components in the chaperone machine, and play pivotal roles in plant growth, development and stress tolerance. Sorghum, the semi-arid...     

Species‐habitat relationships and ecological correlates of butterfly abundance in a transformed tropical landscape

Tropical butterfly conservation strategies often focus on total and/or common species richness to assess the conservation value of a patch or habitat. However, such a strategy overlooks the unique dynamics of rare species. We evaluated the species‐habitat relationships of 209 common, intermediate, and rare butterfly species (including morphospecies) across four habitat types (mature, degraded, or fragmented forest, and urban parks) and two patch sizes (<400 ha, ≥400 ha) in Singapore. Common species richness was consistent across habitat types. Intermediate species richness declined by more than 50 percent in urban parks (relative to all forest habitats), and rare species richness was reduced by 50 percent in degraded and fragmented forest and by 90 percent in urban parks (relative to mature forest). Large patches had comparable overall richness to small patches, but they supported more rare species and three times as many habitat‐restricted species over a similar area. Importantly, a number of rare species were confined to single small patches. Mixed‐effects regression models were constructed to identify habitat and ecological/life history variables associated with butterfly abundance. These models revealed that species with greater habitat specialization, rare larval host plants, few larval host plant genera, and narrow global geographic ranges were more likely to be rare species. Overall, these results demonstrate that the richness of habitat‐restricted and rare species do not follow the same spatial distribution patterns as common species. Therefore, while conserving mature forests is key, effective butterfly conservation in a transformed landscape should take into account rare and habitat‐restricted species.     

Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries

Background

Transgenesis by random integration of a transgene into the genome of a zygote has become a reliable and powerful method for the creation of new mouse strains that express exogenous genes, including human disease genes, tissue specific reporter genes or genes that allow for tissue specific recombination. Nearly 6,500 transgenic alleles have been created by random integration in embryos over the last 30 years, but for the vast majority of these strains, the transgene insertion sites remain uncharacterized.

Results

To obtain a complete understanding of how insertion sites might contribute to phenotypic outcomes, to more cost effectively manage transgenic strains, and to fully understand mechanisms of instability in transgene expression, we’ve developed methodology and a scoring scheme for transgene insertion site discovery using high throughput sequencing data.

Conclusions

Similar to other molecular approaches to transgene insertion site discovery, high-throughput sequencing of standard paired-end libraries is hindered by low signal to noise ratios. This problem is exacerbated when the transgene consists of sequences that are also present in the host genome. We’ve found that high throughput sequencing data from mate-pair libraries are more informative when compared to data from standard paired end libraries. We also show examples of the genomic regions that harbor transgenes, which have in common a preponderance of repetitive sequences.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-367) contains supplementary material, which is available to authorized users.     

Potential role of nicotinamide analogues against SARS-COV-2 target proteins

Background and objectiveCoronavirus 2019 (COVID-19) is caused by ‘severe acute respiratory syndrome coronavirus 2′ (SARS-CoV-2), first reported in Wuhan, China in December 2019, which eventually became a global disaster. Various key mediators have been reported in the pathogenesis of COVID-19. However, no effective pharmacological intervention has been available to combat COVID-19 complications. The present study screens nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN) as potential inhibitors of this present generation coronavirus infection using an in-silico approach.Materials and methodsThe SARS-CoV-2 proteins (nucleocapsid, proteases, post-fusion core, phosphatase, endoriboruclease) and ACE-2 protein were selected. The 2D structure of nicotinamide ribonucleoside and nicotinamide ribonucleotide was drawn using ChemDraw 14.0 and saved in .cdx format. The results were analyzed using two parameters: full fitness energy and binding free energy (ΔG).ResultsThe full fitness energy and estimated ΔG values from docking of NM, and NMN with selected SARS-CoV-2 target proteins, ADMET prediction and Target prediction indicate the interaction of NR and NMN in the treatment of COVID-19.ConclusionsBased on full fitness energy and estimated ΔG values from docking studies of NM and NAM with selected SARS-CoV-2 target proteins, ADME prediction, target prediction and toxicity prediction, we expect a possible therapeutic efficacy of NR in the treatment of COVID-19.Keyword: COVID-19, SARS-CoV-2, Molecular docking, Poly (ADP-ribose) polymerase enzyme, Nicotinamide     

Marginal bone loss around axial and straight implants supported with prefabricated SFI-Bar with mandibular overdentures

To assess the role of prefabricated SFI-Bar in peri-implant bone loss around immediately axially loaded and straight implants. This study comprised of 40 complete denture wearer patients who received two axially parallel implants connected by SFI-Bars in group I and two 15° mesially tilted implants connected by SFI-Bars in group II. Peri- implant bone loss (PiBL) was measured at 1 year, 2 years and 3 years. The mean PiBL at 1 year in group I was 0.21 mm and I group II was 0.22, at 2 years in group I was 0.26 mm and in group II was 0.23 mm and at 3 years, in group I was 0.29 mm and in group II was 0.34 mm. The difference was significant at 3 years (P< 0.05). The mean mesial PIBL at 1 year in group I was 0.18 mm, in group II was 0.20 mm, at 2 years in group I was 0.19 mm and in group II was 0.07 mm and at 3 years, in group I was 0.25 mm and in group II was 0.29 mm. The difference found to be significant in each time duration in both groups (P< 0.05).The mean distal PIBL at 1 year in group I was 0.23 mm, in group II was 0.22 mm, at 2 years in group I was 0.33 mm and in group II was 0.39 mm and at 3 years, in group I was 0.34 mm and in group II was 0.39 mm. The difference found to be significant at 2 and 3 years in both groups (P< 0.05). Authors found that mandibular overdentures retained with Prefabricated SFI-Bar with axial and straight inserted implants may be useful in patients with reduced bone height.     

A novel metabolic pathway of melatonin: oxidation by cytochrome C

The indoleamine melatonin is ubiquitously distributed, and because of its small size and amphiphilic nature, it is able to reach easily all cellular compartments. The highest intracellular melatonin concentrations are found in the mitochondria, suggestive of local metabolism and/or direct participation in organelle function. In mitochondria cytochrome c (cyt c) could represent a melatonin target since it has the capability to oxidize organic molecules in the presence of H2O2, and mitochondria are the main site of H2O2 production in nonphagocytic cells. Therefore, we investigated oxidation of melatonin by cyt c/H2O2 couple as a potential pathway for its metabolism in the mitochondria. We found melatonin conversion into N(1)-acetyl-N(2)-formyl-5-methoxykynuramine via sequential steps that generate the intermediates 2-hydroxymelatonin and 2,3-dihydroxymelatonin. We experimentally excluded mediation by a Fenton/Haber-Weiss-type reaction and documented the dependence on oxoferryl heme for melatonin oxidation. Given the high mitochondrial concentrations of both melatonin and cyt c as well as the continuous generation of H2O2 during respiration, it is entirely possible that mitochondrial cyt c-mediated oxidation of melatonin may be a plausible pathway of its biotransformation in vivo.