This collection presents specific laboratory and analytical methods commonly used in HOPE Lab research and student training at the Department of Biochemistry and Molecular Biology, University of Chittagong. The downloadable guides are maintained for convenient access by HOPE Lab members and students, with method summaries covering microbial culture and preservation, antimicrobial susceptibility testing, probiotic aggregation, emulsification, antioxidant screening, hydrolytic enzyme activity and 16S rRNA amplicon analysis.
METHODS USED IN HOPE LAB
Protocols, Methods and Research Workflows
A collection of laboratory and analytical methods employed in HOPE Lab research and used in student training. Protocols may have been adapted to specific organisms, samples, instruments and experimental objectives. Their suitability and reproducibility under different conditions have not necessarily been established. Researchers using these materials outside HOPE Lab should independently assess and validate the methods and assume responsibility for their application and interpretation.
01PDF · METHOD REFERENCE
Microbial Culture Media, Colony Isolation, Purification and Preservation
Objective: Explain the roles of culture-media selection, colony isolation, purity assessment and preservation documentation in supervised microbiology research.
Method overview: Distinguishes streak-plate isolation from spread-plate enumeration, outlines media-performance and sterility checks, and describes the records needed to maintain authenticated cultures. Operational culture conditions are governed by institutionally approved SOPs.
HOPE Lab member copy: retained for convenient student reference to microbial culture media, colony isolation, purification and preservation methods used in relevant research and training.
Objective: Summarize the principles, standardization requirements and reporting considerations for antimicrobial susceptibility testing.
Method overview: Introduces disk-diffusion and dilution-based AST, organism-specific interpretive criteria, reference quality controls and the need to consult the current CLSI standard. It does not reproduce proprietary breakpoint tables or provide an executable AST procedure.
HOPE Lab member copy: retained for convenient student reference to antimicrobial susceptibility testing methods used in relevant research and training.
Objective: Describe in-vitro aggregation characteristics relevant to the phenotypic evaluation of probiotic lactic acid bacteria.
Method overview: Explains optical-density-based assessment, autoaggregation and coaggregation calculations, monoculture comparisons, matrix controls and limitations when inferring adhesion-related properties.
HOPE Lab member copy: retained for convenient student reference to LAB autoaggregation and coaggregation assays used in relevant research and training.
Objective: Estimate the proportion of a liquid mixture represented by a stable emulsion after 24 hours.
Method overview: Uses pre-prepared, cell-free non-viable test material and a selected food-grade oil. The guide describes matched matrix and positive reference controls, the E24 calculation, replicate documentation and interpretation limits.
HOPE Lab member copy: retained for convenient student reference to emulsification index (E24) methods used in relevant research and training.
Objective: Infer amplicon sequence variants and characterize taxonomic composition and microbial community diversity from processed 16S rRNA sequence data.
Method overview: Covers manifest validation, sequence import, quality inspection, DADA2 denoising, taxonomic classification, diversity analysis, control review and provenance retention. It starts from digital FASTQ files and excludes wet-lab sample processing.
HOPE Lab member copy: retained for convenient student reference to 16S rRNA amplicon analysis with QIIME 2 and DADA2 used in relevant research and training.
Hydrolytic Enzyme Screening: Protease, Pectinase, Cellulase and Amylase
Objective: Summarize substrate-specific approaches for evaluating extracellular hydrolytic enzyme-associated activity.
Method overview: Links protease, pectinase, cellulase and amylase activity with appropriate substrate classes and detection principles, and reviews blank/reference controls, growth context and halo reporting.
HOPE Lab member copy: retained for convenient student reference to protease, pectinase, cellulase and amylase screening methods used in relevant research and training.
