Chitosan is a versatile polysaccharide with applications across various industries due to its characteristics and antimicrobial properties. The physicochemical features and biological properties of chitosan are closely associated with its degree of deacetylation (DDA), which can be influenced by the selection of raw materials and the extraction process. This study aimed to evaluate the characteristics and antimicrobial potential of chitosan obtained from squid pen cartilage originating from different waste sources, namely restaurant waste (S) and market waste (SS), using chemical extraction methods, with and without demineralization step. Analyses using Ultraviolet-visible and Fourier-transform infrared spectroscopy spectrophotometers showed the presence of chitosan in all samples and identified the functional groups within the chitosan molecules. Chitosan yields ranged from 55-82.4%, while the DDA values were between 73.67- 76.64%. All chitosan samples demonstrated antimicrobial activity against the tested Grampositive and Gram-negative bacteria, with inhibition zones ranging from 9.5 ± 0.7 mm to 13.5 ± 2.1 mm using the agar well diffusion method. The MIC values for all chitosan samples varied from 25 to 100 μg/mL, while MBC values were in the range of 50 to 100 μg/mL, and MFC values against A. niger ranged from 25 to 100 μg/mL. The results indicate that chitosan derived from squid pen waste sources exhibits potential as a natural antimicrobial agent, and its DDA remains unaffected by the omission of the demineralization step.

Global sharing of SARS-CoV-2 sequences enabled comprehensive analyses of COVID-19 genomic diversity and demographics. Yet, regional genomic surveillance is often neglected, leading to the possible oversight of novel mutations by public health authorities. Our study used the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyse infection patterns in the state of Negeri Sembilan, and compare infection patterns to the state of Selangor, in Malaysia. We discuss the impact of rapid vaccination on resulting single nucleotide variants (SNVs) and identified novel sporadic mutations may affect viral fitness and pathogenicity. Four hundred and seventeen SARS-CoV-2 sequences extracted from Negeri Sembilan from July 2021 until June 2022. Infection patterns based on pangolin lineages from Negeri Sembilan was compared to infections of the same period from Selangor. SNVs from the spike protein were sorted by frequency, with the lowest frequency variant submitted for functional prediction using PredictSNP. Negeri Sembilan exhibited a comparable infection pattern to Selangor, but with fewer Omicron sequences which was postulated to occur due to the rapid vaccination strategies by Negeri Sembilan. Omicron outbreaks were associated with eased lockdowns and policy changes in December 2021. From our extracted data, seventy novel SNVs in the spike protein of SARS-CoV-2 were extracted from this study. In silico predictions indicated five of the SNVs (S221L, L226S, V826L, C1240F and C1243F) to may cause functional defects to the spike protein. Rapid sequencing and analysis will aid policymaking for public health controls by detecting potential outbreaks within transient variants.

Shrimp aquaculture contributes significantly to global economic growth, and the whiteleg shrimp, Penaeus vannamei, is a leading species in this industry. However, Vibrio parahaemolyticus infection poses a major challenge in ensuring the success of P. vannamei aquaculture. Despite its significance in this industry, the biological knowledge of its pathogenesis remains unclear. Hence, this study was conducted to identify the interaction sites and binding affinity between several immune-related proteins of P. vannamei with V. parahaemolyticus proteins associated with virulence factors. Potential interaction sites and the binding affinity between host and pathogen proteins were identified using molecular docking and dynamics (MD) simulation. The P. vannamei-V. parahaemolyticus protein-protein interaction of Complex 1 (Ferritin-HrpE/YscL family type III secretion apparatus protein), Complex 2 (Protein kinase domain-containing protein-Chemotaxis CheY protein), and Complex 3 (GPCR-Chemotaxis CheY protein) was found to interact with -4319.76, -5271.39, and -4725.57 of the docked score and the formation of intermolecular bonds at several interacting residues. The docked scores of Complex 1, Complex 2, and Complex 3 were validated using MD simulation analysis, which revealed these complexes greatly contribute to the interactions between P. vannamei and V. parahaemolyticus proteins, with binding free energies of -22.50 kJ/mol, -30.20 kJ/mol, and -26.27 kJ/mol, respectively. This finding illustrates the capability of computational approaches to search for molecular binding sites between host and pathogen, which could increase the knowledge of Vibrio spp. infection on shrimps, which then can be used to assist in the development of effective treatment.

Antimicrobial resistance has emerged as a global public health concern. Gram-negative bacteria such as Escherichia coli (E. coli) pose a significant threat to human health due to their increasing antibiotic resistance. For instance, Shiga toxin-producing E. coli (STEC) is a strain that produces toxins that cause damage to the lining of the intestines and kidneys. Antibiotic exposures to STEC would induce the hemolytic uraemic syndrome and bloody diarrhea, a potentially fatal-condition to the patient. The outer membrane architecture in Gram-negatives, specifically the OmpC–Mla complex, maintains the outer membrane lipid asymmetry. The MlaC protein transfers phospholipids from outer membranes to inner membranes and ensures the integrity of the membrane. Inactivation of MlaC protein increases the penetrability of OM and increases the antibiotic’s sensitivity. Therefore, screening for inhibitor compounds that can bind and inhibit the function of MlaC is a viable strategy for antibiotic development.This study aims to understand the interactions of four types of inhibitors in MlaC protein from E. coli via docking and molecular dynamic (MD) simulation. The four types of inhibitors namely albacarcin V, clorobiocin, 1-N,4-N-bis(3- phenylphenyl)piperazine-1,4-dicarboxamide (piperazine dicarboxamide) and -2-[2-[(6- oxobenzo[c]chromen-2-yl)carbamoyl]phenyl]benzoic acid (salicylanilide benzoate). The docking showed that the inhibitors fit into the lipid pocket of MlaC. MD for each system run at 100 ns showed that the system has stable Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and reasonable Radius of Gyration (Rg) value. The RMSD, RMSF and Rg were comparable to the native phospholipid binding in the crystal structure, which suggests the potential use of these four types of inhibitors. Salicylanilide benzoate was revealed to be the most stable in complex with MlaC, with the least deviation, least fluctuation, and most compact throughout the simulation

Macrobrachium rosenbergii nodavirus is a major viral pathogen responsible for white tail disease in giant freshwater prawn aquaculture, leading to significant economic losses. In this study, a truncated DNA aptamer, TrAptm-1 was investigated for its binding properties against both monomeric and trimeric forms of the MrNV capsid proteins. Molecular dynamics simulations coupled with MM/PBSA binding free energy calculations revealed that TrAptm-1 exhibited a higher binding affinity to the trimeric capsid protein (-153.95 ± 6.74 kcal/mol) compared to the monomeric form (-120.77 ± 2.46 kcal/mol). TrAptm-1 binding induced significant conformational changes and structural rearrangements in the capsid protein, highlighted the antiviral potential of TrAptm-1 to interfere with the capsid protein self-assembly process. The observed structural changes demonstrated the importance of the oligomeric state in aptamer-capsid protein interactions, emphasizing that extended simulations up-to microseconds are required to capture the slow conformational rearrangements characteristic of large oligomeric protein complexes. These findings provide a molecular basis for the development of aptamer-based antiviral strategies, and the design of biosensor for early detection of MrNV in aquaculture settings.

The increasing prevalence of pathogenic Escherichia coli (E. coli) in water and food sources poses a significant threat to public health, necessitating the development of rapid and accurate biosensor detection methods such as aptamerbased biosensors due to their high specificity and sensitivity. Aptamers are nucleic acids that can bind with high affinity and specificity to a range of target molecules. In this study, 1,000 shuffled variants of a known aptamer (PDB ID: 2AU4) were generated and evaluated for stability using RNAfold and RNALfoldz based on minimum free energy (MFE). The five most stable sequences were selected and analyzed for their secondary and tertiary structures using RNAComposer. The target protein, Shiga toxin (Stx, PDB ID: 1C48), was modeled with AlphaFold 3 and validated through Ramachandran plot analysis. Molecular docking using the HDOCK server revealed aptamer-protein binding interactions, offering insights into the structural features that influence binding specificity and stability. In conclusion, this research bridges theory for future applications, thereby establishing a theoretical framework to support the future development of aptamer-based biosensors targeting E. coli O157:H7.