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Laboratory

Techniques at the bench

The hands-on half of the research programme, starting with the data itself: a gel, a chromatogram, and a quality profile from the MMP variant study. Techniques and computational tooling follow.

Primary data

Generated at the bench

Three figures from the M.Sc. thesis cohort. The electropherogram and quality profile are rendered straight from the raw .ab1 records, so every point shown is measured data.

Figure 1

PCR amplification of the MMP3 target region

Agarose gel electrophoresis showing a 100 bp ladder followed by fifteen lanes - three controls (C1–C3) and twelve patients (P1–P12) - each with a single clean band at 986 bp, between the 500 bp and 1000 bp ladder markers.

Amplicon

986 bp

Lanes

3 controls + 12 patients

Specificity

Single band, all lanes

A single, clean 986 bp product in every lane, with no primer dimer and no secondary bands. Controls (C1–C3) and patients (P1–P12) amplify at equal intensity, confirming the reaction was specific and consistent across the plate before any sample went forward to sequencing.

Method. Genomic DNA extracted from whole blood; MMP3 target amplified by PCR and resolved on agarose gel against a 100 bp ladder.

Figure 2

Sanger electropherogram with a heterozygous call

Sanger chromatogram across 35 bases of an MMP3 forward read. Single sharp peaks flank a highlighted position where the cytosine and thymine traces reach almost equal height, giving an IUPAC Y heterozygous call.

Call

Heterozygous C/T

Peak ratio

45% C / 44% T

Flanking quality

Q58 and Q46

Thirty-five bases from the MMP3 forward read of sample P36. The highlighted position carries two overlapping peaks of near-equal height - 45% C against 44% T - which the base caller reports as IUPAC Y. Flanking bases call at Q58 and Q46, so the ambiguity is genuine heterozygosity rather than poor signal. The same position resolves as a heterozygote in all five high-quality reads on the plate.

Method. Rendered directly from the raw .ab1 trace: four dye channels, peak locations, and per-base quality read from the ABIF record.

Figure 3

Per-base quality across 18 Sanger reads

Quality control plot of mean Phred score against base position for eighteen MMP3 reads, with a shaded percentile band. Quality climbs steeply over the first thirty bases, holds above Q30 through the middle of the read, and falls away after roughly base 700.

Reads

18 · mean 965 bp

Q30 plateau

Base 32 – 708

Bases ≥ Q20

56.4% of read

Mean Phred quality by base position across all 18 MMP3 reads, with the 12th–88th percentile band showing spread between samples. The profile is the expected Sanger shape: an unusable leader, a high-confidence plateau above Q30 from base 32 to base 708, then decay. Variant calls were taken only from the plateau, and every candidate was confirmed on the reverse read.

Method. Phred scores read from the PCON record of each .ab1 file; no smoothing applied.

Primary data from the M.Sc. thesis cohort, generated at the Functional Genomics & Proteomics Laboratory, University of Chittagong. Patient and control samples carry study codes only.

Wet-lab techniques

Hands-on

Performed at the Functional Genomics & Proteomics Laboratory, University of Chittagong, and during research placements at the National Institute of Biotechnology and the Alternative Medicine & Natural Product Research Lab.

Hands-on

Molecular Biology - Bench

Daily bench work at the Functional Genomics & Proteomics Laboratory, University of Chittagong.

  • Genomic DNA extraction, quantification, and quality assessment
  • PCR, qPCR, and RT-PCR - primer design through optimisation
  • Agarose gel electrophoresis and PAGE
  • Protein isolation, SDS-PAGE, and ELISA
  • Centrifugation, sample fractionation, and karyotyping
  • Plant extract preparation and organic compound fractionation
Hands-on

Sequencing - Bench to Chromatogram

Certified in Sanger sequencing at FGPL; NGS workflow training at the National Institute of Biotechnology.

  • Sanger sequencing: sample prep, purification, cartridge loading, chromatogram calling
  • Targeted panel sequencing library preparation
  • Whole-exome sequencing sample handling and QC
  • Troubleshooting failed reads and ambiguous base calls
  • Sanger confirmation of NGS-called variants
Hands-on

Biochemical & Cellular Assays

Alternative Medicine & Natural Product Research Lab, and thesis assay work.

  • Phytochemical screening
  • Anti-inflammatory assays - protein denaturation, membrane stabilisation
  • Antioxidant and antimicrobial assays
  • Determination of blood components
  • Animal-model toxicity and bioactivity testing

Where these were applied

Studies in which I generated the underlying data at the bench, with sample counts where a cohort was involved.

BenchOngoing

MMP1, MMP3 & MMP9 Variant Profiling in Periodontitis and Diabetes

M.Sc. thesis cohort

Identify disease-associated matrix metalloproteinase variants in patients with apical periodontitis influenced by diabetes.

BenchIn preparation

Common and Rare Coding Variants in Polycystic Ovary Syndrome

300 patients · 300 matched controls

Test whether common polymorphisms and rare coding variants implicate the same reproductive and metabolic pathways in Bangladeshi women with PCOS.

BenchIn preparation

Targeted Panel Sequencing of Cystic Kidney Disease Genes in ADPKD

37 patients · 9 controls · 9-gene panel

Describe the first ADPKD variant spectrum reported from a Bangladeshi cohort across a nine-gene cystic kidney disease panel.

BenchIn preparation

Clone- and Plasmid-Structured Resistance in ESBL-Producing E. coli

38 isolates · 3 regions

Determine whether antimicrobial resistance in Bangladeshi ESBL E. coli is structured by geography or by clone and plasmid.

BenchCompleted

P53 Nanophytocompound Screening & MD Validation

Investigate natural compounds targeting P53, with computational predictions tested experimentally.

BenchCompleted

Sanger Sequencing & NGS Training - NIB

Gain hands-on command of Sanger workflows and next-generation sequencing instrumentation.

BenchCompleted

Nanophytocompound Extraction & Animal Testing

Experimentally validate two lead compounds with high binding affinity to P53.

Sequencing analysis & computation

What happens to the data after it leaves the bench.

Sequencing & analysis

Variant Analysis & Genomics

Applied across the ADPKD panel, PCOS exome, and ESBL surveillance datasets.

  • GATK Best Practices and HaplotypeCaller
  • Alignment with BWA and Hisat2; SAMtools and VCFtools
  • FastQC and Trimmomatic quality control
  • Annotation against ClinVar, gnomAD v4, VEP, and SnpEff
  • Rare-variant prioritisation and protein stability prediction
  • Call-set QC: Ti/Tv ratio, mapping quality, reference-allele verification
Sequencing & analysis

Microbial & Population Genomics

Whole-genome surveillance of 38 ESBL-producing E. coli isolates.

  • SPAdes assembly with QUAST assessment
  • Prokka annotation, Panaroo pan-genome, IQ-TREE phylogenomics
  • In silico MLST and Mash genome-distance comparison
  • ABRicate with ResFinder and CARD; PlasmidFinder; MOB-suite mobility typing
  • Snippy SNP calling and IntegronFinder mobile-element profiling
Computational

Computational Structure & Simulation

The method stack behind two Q1 first-author publications.

  • AutoDock, PyRx, Schrödinger Suite, CB-Dock2
  • GROMACS, NAMD, VMD molecular dynamics
  • SWISS-MODEL, AlphaFold, Discovery Studio, LigandScout
  • SwissADME, ADMETlab, Gaussian and DFT-based analysis
  • IEDB, NetMHCpan, VaxiJen for epitope and antigenicity work
  • Cytoscape, STRING, KEGG, MEGA
Computational

Programming & Analysis

Used for analysis, figures, and pipeline automation.

  • R - ggplot2, Bioconductor
  • Python - Biopython, Pandas, NumPy
  • Linux / Ubuntu command line and bash scripting
  • SPSS, GraphPad Prism, OriginPro
  • LaTeX, Git

Training & certification

Sanger Sequencing Training

FGPL, University of Chittagong

  • Sample preparation and purification
  • Cartridge filling and sequence loading
  • Chromatogram interpretation and troubleshooting

Research Methodology

BRAC University (Red & White)

  • Research proposal writing
  • Scientific project design
  • Basic bioinformatics tools

Diabetes Course

University of Copenhagen (Coursera)

  • Diabetes pathophysiology
  • Clinical management and treatment strategies
  • Epigenetic factors and diet-exercise interactions

Advanced Bioinformatics & Data Analysis

NextGenHelper, India

  • Network construction with Cytoscape, microbiome data analysis
  • Python and Biopython pipelines, R and RStudio statistics
  • Linux workflows and NGS techniques (assembly, annotation, RNA-seq, GWAS, variant analysis)

Linux Training

Bioscience Factory Research Center, Bangladesh

  • Linux essentials and bash scripting for biologists
  • File and data handling
  • Pipeline automation

From the laboratory

Reading a real-time PCR amplification plot at the QuantStudio, Functional Genomics & Proteomics Laboratory, University of Chittagong.
Reading a real-time PCR amplification plot at the QuantStudio, Functional Genomics & Proteomics Laboratory, University of Chittagong.
Starting a run on the thermal cycler during a variant-screening batch.
Starting a run on the thermal cycler during a variant-screening batch.
Loading a PCR plate into the thermal cycler at the Functional Genomics & Proteomics Laboratory.
Loading a PCR plate into the thermal cycler at the Functional Genomics & Proteomics Laboratory.
Preparing samples at the benchtop centrifuge with a colleague.
Preparing samples at the benchtop centrifuge with a colleague.
Setting up a PCR reaction at the bench alongside the laboratory supervisor.
Setting up a PCR reaction at the bench alongside the laboratory supervisor.
A working afternoon in the molecular biology laboratory.
A working afternoon in the molecular biology laboratory.
The Functional Genomics & Proteomics Laboratory group, University of Chittagong.
The Functional Genomics & Proteomics Laboratory group, University of Chittagong.
In the Sanger Sequencing Laboratory with the research team.
In the Sanger Sequencing Laboratory with the research team.
Gowned for the molecular biology suite during the National Institute of Biotechnology internship.
Gowned for the molecular biology suite during the National Institute of Biotechnology internship.
In full PPE at the RT-PCR laboratory, Department of Microbiology, Shaheed Syed Nazrul Islam Medical College - COVID-19 testing service.
In full PPE at the RT-PCR laboratory, Department of Microbiology, Shaheed Syed Nazrul Islam Medical College - COVID-19 testing service.