Crystal structure of the nucleotide‐binding domain of mortalin,the mitochondrial Hsp70 chaperone

Mortalin, a member of the Hsp70‐family of molecular chaperones, functions in a variety of processes including mitochondrial protein import and quality control, Fe‐S cluster protein biogenesis, mitochondrial homeostasis, and regulation of p53. Mortalin is implicated in regulation of apoptosis, cell stress response, neurodegeneration, and cancer and is a target of the antitumor compound MKT‐077. Like other Hsp70‐family members, Mortalin consists of a nucleotide‐binding domain (NBD) and a substrate‐binding domain. We determined the crystal structure of the NBD of human Mortalin at 2.8 Å resolution. Although the Mortalin nucleotide‐binding pocket is highly conserved relative to other Hsp70 family members, we find that its nucleotide affinity is weaker than that of Hsc70. A Parkinson's disease‐associated mutation is located on the Mortalin‐NBD surface and may contribute to Mortalin aggregation. We present structure‐based models for how the Mortalin‐NBD may interact with the nucleotide exchange factor GrpEL1, with p53, and with MKT‐077. Our structure may contribute to the understanding of disease‐associated Mortalin mutations and to improved Mortalin‐targeting antitumor compounds.     

Roundup: a multi-genome repository of orthologs and evolutionary distances

SUMMARY: We have created a tool for ortholog and phylogenetic profile retrieval called Roundup. Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the reciprocal smallest distance algorithm, an approach that has been shown to improve upon alternative approaches of ortholog detection, such as reciprocal blast. Presently, the Roundup repository contains all possible pair-wise comparisons for over 250 genomes, including 32 Eukaryotes, more than doubling the coverage of any similar resource. The orthologs are accessible through an intuitive web interface that allows searches by genome or gene identifier, presenting results as phylogenetic profiles together with gene and molecular function annotations. Results may be downloaded as phylogenetic matrices for subsequent analysis, including the construction of whole-genome phylogenies based on gene-content data. AVAILABILITY: http://rodeo.med.harvard.edu/tools/roundup.     

Isolation of a factor stimulatory to Bradyrhizobium japonicum in broth culture

Previous experiments indicated that water extracts of lambsquarters (Chenopodium album) and green foxtail (Setaria viridis), among others, stimulated growth of Bradyrhizobium japonicum in broth culture. Water extracts of lambsquarters shoots collected before or after anthesis were equally stimulatory. The stimulatory effect of extracts of lambsquarters when heated to 100°C for 30 min or autoclaved for 15 min was reduced by about 20% compared to untreated extracts. Extracts of green foxtail were less affected by higher temperature under similar conditions. Extracts of both green foxtail and lambsquarters completely lost their stimulatory effect following exposure to aerial microflora for 120 h. Water extract of lambsquarters shoots was more stimulatory than methanol extract, and neither ether nor butanol extracts resulted in stimulation. Both shoots and roots of lambsquarters and green foxtail were sequentially extracted first by water followed by methanol and vice-versa. The bioassay of these extracts indicated that there could be two components of the growth factor-one, larger component is soluble in water, the other, smaller component is soluble in methanol. After fractionation of the crude aqueous extract of lambsquarters shoots by four organic solvents, the residual aqueous extract retained the growth factor. Dialysis of the residual aqueous extract of lambsquarters shoots through a membrane (MWCO 1000) indicated that the molecular weight of the growth factor was less than 1000. The fraction having molecular weight <1000 was separated by paper chromatography using 6% acetic acid as developer. The fraction with Rf 0.91 showed the highest stimulation of the bacterium.     

Effects of Ledum groenlandicum amendments on soil characteristics and black spruce seedling growth

The effects of leaves and litter of the boreal forest understory shrub, Ledum groenlandicum, on soil characteristics and black spruce (Picea mariana) seedling growth were investigated. Organic and mineral soils, not previously associated with L. groenlandicum, were amended with leaves and litter of this species. The objectives of the present study were: (i) to determine the changes in soil characteristics after amending with L. groenlandicum, (ii) to determine the quantitative variation in the concentration of water-soluble phenolic allelochemicals in mineral and organic soil layers modified by L. groenlandicum and (iii) to study the growth response of black spruce in soils treated with different L. groenlandicum amendments. The amended organic and mineral soils were analyzed for pH, organic matter, PO₄, N, Ba, Cu, Zn, Fe, Mn, Ca, Na, K, Mg, Al and total phenolics equivalence. Results indicate that organic soils amended with L. groenlandicum leaves and litter were significantly different from unamended control soil for most of the chemical characteristics, while amended mineral soil was different from that of unmodified mineral soil for PO₄, organic matter, K and total phenolics equivalence. Water-soluble phenolics from L. groenlandicum and changes in nutrient availability are plausible causes of L. groenlandicum interference with black spruce seedling growth.     

Belowground interactions between Kalmia angustifolia and Picea mariana: roles of competition,root exudates and ectomycorrhizal association

Plant and Soil - Belowground competition and allelopathic interference of neighbouring plants play important roles in shaping plant performance. We assessed the effect of belowground interactions...     

CO-WOA: Novel Optimization Approach for Deep Learning Classification of Fish Image

The most significant groupings of cold-blooded creatures are the fish family. It is crucial to recognize and categorize the most significant species of fish since various species of seafood diseases and decay exhibit different symptoms. Systems based on enhanced deep learning can replace the area's currently cumbersome and sluggish traditional approaches. Although it seems straightforward, classifying fish images is a complex procedure. In addition, the scientific study of population distribution and geographic patterns is important for advancing the field's present advancements. The goal of the proposed work is to identify the best performing strategy using cutting-edge computer vision, the Chaotic Oppositional Based Whale Optimization Algorithm (CO-WOA), and data mining techniques. Performance comparisons with leading models, such as Convolutional Neural Networks (CNN) and VGG-19, are made to confirm the applicability of the suggested method. The suggested feature extraction approach with Proposed Deep Learning Model was used in the research, yielding accuracy rates of 100 %. The performance was also compared to cutting-edge image processing models with an accuracy of 98.48 %, 98.58 %, 99.04 %, 98.44 %, 99.18 % and 99.63 % such as Convolutional Neural Networks, ResNet150V2, DenseNet, Visual Geometry Group-19, Inception V3, Xception. Using an empirical method leveraging artificial neural networks, the Proposed Deep Learning model was shown to be the best model.     

Morphological alterations in erythrocytes treated with silver nanoparticles biomineralized by marine sediment-derived Bacillus sp. VITSSN01

Biomineralization-inspired preparation of nanoparticles by marine microorganisms is in the limelight of modern nanotechnology. In recent years, the use of marine microorganisms for the synthesis of nanoparticles has been gaining importance due to the simplicity and eco-friendliness of the approach. Here we describe the synthesis of silver nanoparticles using halotolerant Bacillus sp. isolated from the southern coastal waters of India. Our selective and enriched isolation technique resulted in the isolation of a silver nitrate-resistant novel marine Bacillus sp. isolated from sediments collected at Ennore Port, Chennai, India. The strain was characterized by the polyphasic taxonomic approach, and phenotypic and phylogenetic analysis identified the strain as Bacillus sp. VITSSN01. The resistant strain was further assayed for the synthesis of silver nanoparticles and its biological activity evaluated. Nanoparticles were synthesized under optimized nutritional and cultural conditions with shaking and the production continuously monitored. The nanoparticles thus produced were then characterized by atomic force microscopy, X-ray diffraction, Fourier transform-infrared spectrophotometer and transmission electron microscopy. The mean particle size was 46 nm. Hemotological toxicity of nanoparticles is very severe form and less studied. We therefore checked the synthesized silver nanoparticles for toxicity against erythrocytes and found that the silver nanoparticles exhibited moderate hemolytic activity against human erythrocytes, with a half maximal effective concentration (EC₅₀) value of 60 μg/ml. Microscopic studies of the treated erythrocytes showed slight structural perturbations. The results of our study strongly suggest that marine microorganisms could be a potential source for the rapid and eco-friendly synthesis of nanoparticles.