Metagenomics analysis of the fecal microbiota in Ring-necked pheasants (Phasianus colchicus) and Green pheasants (Phasianus versicolor) using next generation sequencing

Pheasant reintroduction and conservation efforts have been in place in Pakistan since the 1980 s, yet there is still a scarcity of data on pheasant microbiome and zoonosis. Instead of growing vast numbers of bacteria in the laboratory, to investigate the fecal microbiome, pheasants (green and ring neck pheasant) were analyzed using 16S rRNA metagenomics and using IonS5TMXL sequencing from two flocks more than 10 birds. Operational taxonomic unit (OTU) cluster analysis and phylogenetic tree analysis was performed using Mothur software against the SSUrRNA database of SILVA and the MUSCLE (Version 3.8.31) software. Results of the analysis showed that firmicutes were the most abundant phylum among the top ten phyla, in both pheasant species, followed by other phyla such as actinobacteria and proteobacteria in ring necked pheasant and bacteroidetes in green necked pheasant. Bacillus was the most relatively abundant genus in both pheasants followed by Oceanobacillus and Teribacillus for ring necked pheasant and Lactobacillus for green necked pheasant. Because of their well-known beneficial characteristics, these genus warrants special attention. Bird droppings comprise germs from the urinary system, gut, and reproductive sites, making it difficult to research each anatomical site at the same time. We conclude that metagenomic analysis and classification provides baseline information of the pheasant fecal microbiome that plays a role in disease and health.     

Target size analysis of neurotensin receptors

The neurotensin receptors from rat brain synaptosomal membranes differed in subunit structure from those in rat gastric fundus smooth muscle plasma membranes when studied following photoaffinity labelling or after exposure to cross-linking reagents. However, these two receptors were similar in their recognition properties. In this study we compared the target size of the two receptors by radiation inactivation and observed that the receptors in both tissues had similar target sizes (mean values 103,000 and 108,000 daltons). This suggests that the differences in size observed in biochemical studies may reflect changes occurring during the isolation procedures, or, on the other hand, there might be inherent difference in the subunit structure of these receptors.     

Use of response surface methodology to study the effect of media composition on aflatoxin production by Aspergillus flavus

Aflatoxins are one of the most important secondary metabolites. These extrolites are produced by a number of Aspergillus fungi. In this study, we demonstrate the effect of media components and enhanced aflatoxin yield shown by A. flavus using response surface methodology in response to different nutrients. Different components of a chemically defined media that influence the aflatoxin production were monitored using Plackett–Burman experimental design and further optimized by Box–Behnken factorial design of response surface methodology in liquid culture. Interactions were studied with five variables, namely sorbitol, fructose, ammonium sulfate, KH₂PO₄, and MgSO₄.7H₂O. Maximum aflatoxin production was envisaged in medium containing 4.94 g/l sorbitol, 5.56 g/l fructose, 0.62 g/l ammonium sulfate, 1.33 g/l KH₂PO₄, and 0.65 g/l MgSO₄·7H₂O using response surface plots and the point prediction tool of the DESIGN EXPERT 8.1.0 (Stat-Ease, USA) software. However, a production of 5.25 μg/ml aflatoxin production was obtained, which was in agreement with the prediction observed in verification experiment. The other component (MgSO₄.7H₂O) was found to be an insignificant variable.     

Susceptibility of three lepidopteran pests to five entomopathogenic nematodes and in vivo mass production of these nematodes

Abstract

An investigation was conducted in pots to access the susceptibility of three lepidopteran pests, namely, gram pod borer, Helicoverpa armigera, greater wax moth, Galleria mellonella, and rice moth, Corcyra cephalonica, to two recently described species, Steinernema masoodi, S. seemae, and three indigenous S. carpocapsae, S. glaseri and S. thermophilum entomopathogenic nematodes (EPN). The suitability of these lepidopterans for the in vivo mass production of the nematodes was also estimated. Among the five species of EPN, S. masoodi, S. seemae and S. carpocapsae were found most pathogenic to C. cephalonica, bringing about mortality within 24 h, followed by H. armigera (36, 38 and 48 h, respectively) and G. mellonella (30, 36 and 48 h, respectively). The other species of EPN, viz., S. glaseri and S. thermophilum was the least pathogenic, which killed the larvae of C. cephalonica in 29 and 36 h, respectively, G. mellonella in 48 h, and H. armigera in 38 and 56 h, respectively. Galleria mellonella was found the most suitable host for the mass production of infective juveniles (IJs) of S. seemae, which yielded higher IJs than S. carpocapsae. Helicoverpa armigera was the next best suitable alternate host, which produced maximum IJs in case of S. seemae followed by S. masoodi, S. carpocapsae, S. glaseri and S. thermophilum. Rice moth, Corcyra cephalonica was the least suitable host. The susceptibility of H. armigera to five tested EPN species and susceptibility of G. mellonella and C. cephalonica to S. masoodi and S. seemae are new records.     

Flow cytometric quantification of rat spermatogenic cells after hypophysectomy and gonadotropin treatment

DNA flow cytometry was evaluated as a tool to analyze stage-specific changes that occur in absolute cell numbers in the testes. Hypophysectomy was selected as a model system for perturbing testicular cell types, since the cytological sequelae of this treatment post-hypophysectomy in the rat are well documented in the literature. Rat spermatogenic cells in stages II-V, VII, and IX-XIII of the seminiferous epithelial cycle (as defined by Leblond and Clermont, 1952) were quantified in numbers per standard length of seminiferous tubule by DNA flow cytometry after hypophysectomy and subsequent gonadotropin treatment. In agreement with previous histological studies, we found that acrosome- and maturation-phase spermatids disappeared from the seminiferous epithelium after 17 days post-hypophysectomy, whereas meiosis and early spermiogenesis continued at least 164 days. The number of meiotic cells and round spermatids gradually decreased after hypophysectomy. Changes were observed as early as Day 6 post-hypophysectomy. Treatment with human chorionic gonadotropin (hCG) alone maintained most cell numbers within normal limits, and follicle-stimulating hormone (FSH) was needed in addition to hCG to maintain the normal number of cells with the amount of DNA contained in primary spermatocytes and spermatogonia in G2/M-phase (4C) in stages IX-XIII and elongated spermatids (1C') in stages II-V of the epithelial cycle. The absolute numbers of spermatogenic cells at different phases of maturation provide a useful reference for quantitative studies of spermatogenesis. Pathological changes in the seminiferous epithelium can be detected and quantified by DNA flow cytometry.     

Adsorption and spin state properties of Cr,Ni, Mo,and Pt deposited on Li+ and Na+ monovalent cation impurities of MgO (001) surface: DFT calculations

We have analyzed, by means of density functional theory calculations and the embedded cluster model, the adsorption and spin-state properties of Cr, Ni, Mo, and Pt deposited on a MgO crystal. We considered deposition at the Mg²⁺ site of a defect-free surface and at Li⁺ and Na⁺ sites of impurity-containing surfaces. To avoid artificial polarization effects, clusters of moderate sizes with no border anions were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. The interaction between a transition metal atom and a surface results from a competition between Hund's rule for the adsorbed atom and the formation of a chemical bond at the interface. We found that the adsorption energies of the metal atoms are significantly enhanced by the cation impurities, and the adsorption energies of the low-spin states of spin-quenched complexes are always more favorable than those of the high-spin states. Spin polarization effects tend to preserve the spin states of the adsorbed atoms relative to those of the isolated atoms. The metal–support interactions stabilize the low-spin states of the adsorbed metals with respect to the isolated metals, but the effect is not always enough to quench the spin. Spin quenching occurs for Cr and Mo complexes at the Mg²⁺ site of the pure surface and at Li⁺ and Na⁺ sites of the impurity-containing surfaces. Variations of the spin-state properties of free metals and of the adsorption and spin-state properties of metal complexes are correlated with the energies of the frontier orbitals. The electrostatic potential energy curves provide further understanding of the nature of the examined properties.     

Managing and mining protein crystallization data

The crystallization of macromolecules remains a major bottleneck in structural biology. The routine screening of more than one thousand crystallization conditions and subsequent optimization by fine screening presents a challenge to conventional laboratory notebook keeping. In addition, the development of high-throughput robotic crystallization and imaging systems presents a pressing need for low-cost laboratory information management system (LIMS). Here we describe CLIMS2, a crystallization LIMS that features a simple, user-friendly graphical interface, allowing the storage, management, retrieval and mining of crystallization data. The CLIMS2 executable and documentation is freely available at http://clims.med.monash.edu.au.