<i>Aspergillus tubingensis</i> Causes Leaf Spot of Cotton (<i>Gossypium hirsutum</i> L.) in Pakistan

Cotton (Gossypium hirsutum L.) is a key fiber crop of great commercial importance. Numerous phytopathogens decimate crop production by causing various diseases. During July-August 2018, leaf spot symptoms were recurrently observed on cotton leaves in Rahim Yar Khan, Pakistan and adjacent areas. Infected leaf samples were collected and plated on potato dextrose agar (PDA) media. Causal agent of cotton leaf spot was isolated, characterized and identified as Aspergillus tubingensis based on morphological and microscopic observations. Conclusive identification of pathogen was done on the comparative molecular analysis of CaM and β-tubulin gene sequences. BLAST analysis of both sequenced genes showed 99% similarity with A. tubingensis. Koch’s postulates were followed to confirm the pathogenicity of the isolated fungus. Healthy plants were inoculated with fungus and similar disease symptoms were observed. Fungus was re-isolated and identified to be identical to the inoculated fungus. To our knowledge, this is the first report describing the involvement of A. tubingensis in causing leaf spot disease of cotton in Pakistan and around the world.     

Nutritional composition of black soldier fly larvae feeding on agro-industrial by-products

Black soldier fly (BSF) larvae, Hermetia illucens L. (Diptera: Stratiomyidae), bio-convert organic side streams into high-quality biomass, the composition of which largely depends on the side stream used. In the present study, BSF larvae were reared on feed substrates composed of dried brewers’ spent grains, each supplemented with either water, waste brewer’s yeast, or a mixture of waste brewer’s yeast and cane molasses to obtain 12 different substrates: barley/water, barley/yeast, barley/yeast/molasses, malted barley/water, malted barley/yeast, malted barley/yeast/molasses, malted corn/water, malted corn/yeast, malted corn/yeast/molasses, sorghum-barley/water, sorghum-barley/yeast, and sorghum-barley/yeast/molasses. The crude protein, fat, ash, and mineral contents of the BSF larvae fed each feed substrate were quantified by chemical analyses. The effect of substrate, supplementation, and their interaction on crude protein, fat, and ash contents of BSF larval body composition was significant. Calcium, phosphorus, and potassium were the most abundant macrominerals in the larvae and their concentrations differed significantly among substrates. These findings provide important information to support the use of BSF larval meal as potential new source of nutrient-rich and sustainable animal feed ingredients to substitute expensive and scarce protein sources such as fishmeal and soya bean meal.     

Behavioural crypsis in a South African galaxiid fish induced by predatory and non-predatory heterospecifics

This study investigated recognition of, and behavioural responses to, predatory and non-predatory heterospecifics by a small cryptically coloured fish species, Galaxias ‘nebula’. Nebula recognised and differentiated between predatory and non-predatory heterospecifics and altered its behaviour facultatively. With both predatory and non-predatory fishes, the proportion of time spent motionless increased, whereas refugia use was affected only by predators and neither heterospecific affected the time spent active. Although nebula appeared to face no conflict, in that their responses to predatory and non-predatory heterospecifics varied in the same direction and differed only in intensity, the presence of both heterospecifics together induced responses midway between those for each heterospecific separately. Non-predatory heterospecifics thus modified nebula's responses towards predators, potentially making time available for other essential activities such as foraging. This modified predator response may aid its survival in an increasingly threatened habitat.     

Scaling of species diversity and body mass in mammals: Cope’s rule and the evolutionary cost of large size

Abstract

Equations are constructed describing the inverse correlation of species diversity and body mass in extant and Cenozoic mammals. Cope’s rule, the tendency for many mammal clades to increase in body size through time, through phyletic change in single lineages or turnover within species groups, is interpreted as a probability function reducing diversity potential as a tradeoff for ecological/evolutionary gains. The inverse rule predicts that large species in clades will be less diverse than smaller species and, unless origination rates remain high among smaller clade members, clades conforming to Cope’s rule will decline in diversity, moving towards extinction. This proposition is evaluated in the Cenozoic histories of five North American mammal clades; cotton rats, felids, canids, hyaenodontids, and equids. Diversity potential of different size classes within the 3.75 million year phyletic history of the muskrat, Ondatra zibethicus, is also examined. A corollary prediction of the inverse rule, that large species should have longer durations (species lifespans) than small species, is unresolved. Successful clades maintain small size or a significant number of smaller species relative to clade average size. The potential loss of unique extant large mammal species justifies the conservation effort to protect them. The similarity of scaling exponents of species diversity to mass around a slope of -1.0 suggests that species diversity is correlated with home range size, the latter related to the probability of population fragmentation.     

Rutin as promising drug for the treatment of Parkinson’s disease: an assessment of MAO-B inhibitory potential by docking,molecular dynamics and DFT studies

ABSTRACT

Inhibitors of monoamine oxidase (MAO)-B have been used for many years in the therapy of Parkinson’s disease (PD). Owing to the safety concerns of the currently used agents, the discovery of novel scaffolds is of considerable interest. MAO-B inhibitory potential of rutin, a flavonoid derived from natural sources, has been established in experimental findings. Hence, the current study seeks to examine the interactions between rutin and crystal structure of human MAO-B enzyme. Molecular docking calculations, as well as molecular dynamics simulations, were employed to investigate the binding mode and the stability of the rutin/MAO-B complex. Energies of highest occupied/lowest unoccupied molecular orbitals were computed through DFT studies and used to calculate electron affinity, hardness, chemical potential, electronegativity, and electrophilicity index in order to investigate the capability of these parameters to influence the ligand–receptor interactions. It was found that rutin traverses both the entrance cavity and the substrate cavity, forcing the Ile-199 ‘gate’ to rotate into its open conformation. It results in the fusion of the two cavities of the MAO-B binding site and directly leads to better binding interactions. Results of the current study can be used for lead modification and development of novel drugs for the treatment of PD.     

Study of PE and iPP orientations on the surface of carbon nanotubes by using molecular dynamic simulations

In this study, the early stage of interfacial crystallisation behaviour of low molecular weight polyethylene (PE) and isotactic polypropylene (iPP) oligomer on the surface of carbon nanotubes (CNTs) with different diameters, chiralities and topography structures was studied using MD simulations. We started to simulate the effect of CNTs chirality and diameter on PE molecular chain orientation, and then the effect of CNTs topography structure on PE and iPP molecular chain orientation was investigated. Finally, some experiments were carried out to prove the simulated results. Our study shows that for CNTs with a diameter comparable with the radius of gyration (R_g) of a polymer chain, an easy orientation of PE chains along CNTs axis is observed for all the systems of the CNTs with different chiralities due to a geometric confinement effect. For CNTs with a much larger diameter, multiple orientation of PE chains is induced on its surface due to the lattice matching between graphite lattice and PE molecular chains. In this case, the chirality of CNTs dominates the orientation of graphite lattice, which determines the orientation of PE chains arrangement on CNTs surface. More importantly, it was found that the groove structure formed by CNT bundles is very useful for the stabilisation of polymer chain, and thus facilitates the orientation of molecular chain along the long axis of CNTs. As a result, a novel nanohybrid shish–kebab (NHSK) structure with CNTs acting as central shish while polymer lamellae as kebab can be successfully obtained for both PE with zigzag conformation and iPP with helical conformation. This simulation result was well supported by the experimental observation. Our study could provide not only a deep understanding of the origin of the polymer chain orientation on CNTs surface but also the guidance for the preparation of polymer/CNTs nanocomposites with novel NHSK structure.     

Studies On The Cross Strand Hydrogen Bonds In DNA Double Helices

Abstract

A systematic analysis has been carried out to examine all the stereochemically possible bifurcated hydrogen bonds including those of cross strand type between propeller twisted base pairs in DNA double helices by stereochemical considerations involving base pairs alone and by molecular mechanics studies on dimer and trimer duplexes. The results show that there are limited number of combinations of adjacent base pairs that would facilitate bifurcated cross- strand hydrogen bond (CSH). B-type helices concomitant with negative propeller twist seem to be more favored for the occurrence of CSH than canonical A-type helices because of slide in the latter. The results also demonstrate that helices with appropriate sequences may possess continuous run of these propeller twist driven cross strand hydrogen bonds indicating that they may infact be considered as yet another general structural feature of DNA helices.     

Compensatory nature of Chargaff’s second parity rule

The second parity rule of Chargaff (A≈T and G≈C within one strand) holds all over the living world with minor exceptions. It is maintained with higher accuracy for long sequences. The question addressed in the article is how different sequence types, with different biases from the parity, contribute to the general effect. It appears that the sequence segments with biases of opposite sign are intermingled, so that with sufficient sequence lengths the parity is established. The parity rule seems to be a cumulative result of a number of independent processes in the genome evolution, with the parity as their intrinsic property. Symmetrical appearance of simple repeats and of Alu sequences in the human DNA strands, and other contributions to the Chargaff parity II rule are discussed.     

Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.