Biochemical property analysis of native probiotic isolates from selective poultry

Isolation and identification of probiotic bacteria are the prerequisites for their safer use in the food and feed industry. The objectives of the present study were the isolation of probiotic bacteria from the selective gastrointestinal tract of poultry obtained from Khulna and Barisal Divisions, and their identification based on bacterial morphological characterization and biochemical property analysis. Ten potential native probiotics were isolated from the poultry gastrointestinal tract and assayed for their morphological, physiological and biochemical properties. It was observed that, all the isolates were rod-shaped, gram-positive, endospore-negative, catalase-negative, non-motile and were able to ferment particular sugars which are an indicator for typical probiotic bacteria. The sugar fermentation pattern, ability to survive and growth in inhibitory substances like 1-4% NaCl, 0.3% bile salt as well as their ability to grow in different temperatures and pH levels ensured the presumptive identification of the lactic acid bacteria. All the ten isolates exhibited a clear zone of inhibition when they were grown with five enteric pathogens which are indicative of their antimicrobial activity. Ten isolates were assayed for their susceptibility to eight antibiotics using the disc diffusion method. All the isolates were resistant to tetracycline and nalidixic acid. Further research regarding molecular characterization and identification of specific genes using different technologies may open the door to utilize these isolates in different probiotic-based inventions. Bang. J. Livs. Res. Vol. 27 (1&2), 2020: P. 39-54

CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin

Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level.

Untargeted 1H NMR Metabolomics and Pathway Analysis Reveals Dysregulated Proteostasis in Cyclophilin D (CypD)-deficient Mice Tissues

Cyclophilin D (CypD) is a nuclear-encoded mitochondrial protein. Although best known as a regulator of the mitochondrial permeability transition pore (MPTP), it is also implicated in the regulation of cellular bioenergetics and extramitochondrial activities. In addition, being a peptidyl prolyl cis-trans isomerase (PPIase), deletion of CypD is likely to affect protein stability in the mitochondria; however, there is little direct evidence of this. In this study, untargeted 1H NMR metabolomics, coupled with multivariate analysis, was used to describe simultaneous changes in the metabolic system of CypD-deficient mice liver, heart, and pancreas, with data from the serum to identify systematic changes. Metabolomics Pathway Analyses (MetPA) revealed commonly perturbed metabolites in the different mouse tissues lacking CypD, with significantly enriched pathways that are related to amino acid, glucose and purine metabolisms, and bioenergetics. Serum from CypD-deficient mice confirmed changes in tissue urea cycle, lipid metabolism and ketogenesis. Overall this study reveals the role of CypD in maintaining protein homeostasis, concurring with its biochemical property as a peptidyl-prolyl isomerase and also demonstrates the wider metabolic adaptations induced by the deletion of the ppif gene, resulting in a CypD-deficient mice metabolome that is different from the wild-type system.

HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization

HP1 proteins bind with low affinity but high specificity to histone H3 lysine 9 methylation (H3K9me), forming transcriptionally inactive genomic compartments referred to as heterochromatin. How HP1 proteins traverse a complex and crowded chromatin landscape on the millisecond timescale to bind H3K9me chromatin remains paradoxical. Here, we apply single-molecule imaging to visualize an HP1 homolog, the fission yeast Swi6, in its native chromatin environment. By analyzing Swi6 motions, we identify individual mobility states that map to discrete biochemical intermediates. Using mutants that perturb Swi6 H3K9me recognition, oligomerization, or nucleic acid binding, we mechanistically parse how each biochemical property affects protein dynamics. While nucleic acid binding titrates Swi6 away from heterochromatin, as few as four tandem chromodomains are sufficient to restore H3K9me-dependent localization. Our studies propose a new paradigm where HP1 oligomerization stabilizes higher-order complexes to outcompete inhibitory nucleic acid and non-specific chromatin interactions, enabling high specificity H3K9me recognition in cells.

Yams.

This chapter discusses the extraction of starch from different yam (Dioscorea) species. The physiochemical (biochemical property, amylose and amylopectin content), structural (granular morphology, X-ray diffraction pattern, starch crystallinity, and amylose and amylopectin structure), functional (swelling pattern, solubility, viscosity, rheological properties and retrogradation) and thermal properties of yam starches and their digestibility are described.

Biochemical property and gel-forming ability of mackerel (Auxis thazard) surimi prepared by ultrasonic assisted washing

Ultrasonic assisted washing (UAW) improved gel-forming ability of mackerel surimi. Washing time can be reduced up to 50% compared to the conventional washing.

The Role of Oxidative Stress and Its Counteractive Utility in Colorectal Cancer (CRC)

An altered redox status accompanied by an elevated generation of reactive oxygen/nitrogen species (ROS/RNS) has been implicated in a number of diseases including colorectal cancer (CRC). CRC, being one of the most common cancers worldwide, has been reported to be associated with multiple environmental and lifestyle factors (e.g., dietary habits, obesity, and physical inactivity) and harboring heightened oxidative stress that results in genomic instability. Although under normal condition ROS regulate many signal transduction pathways including cell proliferation and survival, overwhelming of the antioxidant capacity due to metabolic abnormalities and oncogenic signaling leads to a redox adaptation response that imparts drug resistance. Nevertheless, excessive reliance on elevated production of ROS makes the tumor cells increasingly vulnerable to further ROS insults, and the abolition of such drug resistance through redox perturbation could be instrumental to preferentially eliminate them. The goal of this review is to demonstrate the evidence that links redox stress to the development of CRC and assimilate the most up-to-date information that would facilitate future investigation on CRC-associated redox biology. Concomitantly, we argue that the exploitation of this distinct biochemical property of CRC cells might offer a fresh avenue to effectively eradicate these cells.