Biotechnology - Sci-Tech Bulletin

JPred4: Advanced Protein Secondary Structure Prediction for Modern Bioinformatics

JPred4 is an upgraded protein secondary structure prediction server designed to help researchers analyze protein sequences when experimental structures are unavailable. Its JNet 2.3.1 algorithm combines neural-network prediction, PSI-BLAST-derived evolutionary information, multiple sequence alignments, and improved HMM processing. Blind testing of the server efficiency on 150 previously unseen sequences achieved 82.0% three-state secondary structure accuracy, while solvent accessibility prediction reached up to 90.0%. The platform also offers batch processing, faster analysis, improved visualizations, and comprehensive alignment reports for protein structure modeling, fold recognition, functional-domain identification, mutation planning, and large-scale bioinformatics research.

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Early Antibiotic use increases Antibiotic Resistance in Preterm Infants

Study found that early antibiotic exposure affects antibiotic resistance in preterm infants. Analysis of meconium and stool samples from 30 preterm neonates, using metagenomic sequencing identified 175 antibiotic resistance genes (ARGs) across 15 drug classes. Beta-lactam, tetracycline, and aminoglycoside resistance are the most prevalent antibiotic resistance discovered. As found, ARG diversity increases as infants grow, while treated infants show greater beta-lactam and tetracycline resistance. Antibiotic exposure also alter bacterial metabolic pathways linked to survival, adaptation, and stress tolerance, highlighting the importance of responsible antibiotic use and stewardship in neonatal care.

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PEtracer Technology: Revolutionizing Cell Lineage Mapping in Cancer Research

PEtracer is a novel prime editing-based lineage tracing technology that enables simultaneous mapping of cell lineage, gene expression, and spatial organization within intact tissues. By integrating prime editing with single-cell RNA sequencing and MERFISH spatial transcriptomics, cellular phylogenies are accurately reconstructed and tracked tumor evolution in a mouse model of metastatic breast cancer. PEtracer achieves high accuracy in lineage reconstruction while preserving spatial context, making it a powerful tool for studying development, tissue regeneration, cancer progression, and other complex biological processes.

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Portable Oxford Nanopore MinION for Forensic SNP Genotyping and DNA identification

Scientists have developed a portable MinION sequencer by Oxford Nanopore Technologies’ that has a strong potential for forensic single nucleotide polymorphism (SNP) genotyping. The device can accurately genotype 51 of the 52 SNP markers tested, underscoring its promise for forensic DNA identification. This portable nanopore sequencing could become a valuable tool for forensic DNA profiling, provided SNP panels are optimized and additional validation studies establish its reliability for routine forensic use.

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Epigenetic changes explain why we regain weight after weight loss

Fat cells retain persistent obesity-related gene expression and epigenetic changes even after body weight returns to normal. Single-nucleus RNA sequencing revealed that adipose tissue continues to exhibit obesity-induced transcriptional changes despite significant weight loss. These lasting epigenetic alterations impair adipocyte function and prime the body for accelerated weight regain when re-exposed to a high-fat diet. The findings suggest that obesity leaves a durable cellular imprint, offering a biological explanation for the common “yo-yo” effect and identifying epigenetic memory as a promising target for improving long-term weight management and metabolic health.

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Vaccinium-Rich Berries May Support Diabetes and Kidney Health

Vaccinium berries, including blueberries, bilberries, cranberries, and lingonberries have been studied to be effective in managing diabetes, preventing diabetic kidney disease and diabetic retinopathy. Evidences from animal and human studies suggests that these berries, rich in anthocyanins and other polyphenols, may improve blood glucose control, reduce oxidative stress and inflammation, and protect kidney and retinal tissues. Vaccinium berries may thus serve as valuable dietary complements to conventional diabetes management strategies.

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Seven microbial solutions revolutionizing environmental biotechnology

Seven microbial solutions for sustainable environment

Microbial bioprocesses offer promising solutions to global environmental challenges through innovative strategies such as enhanced carbon dioxide (CO₂) capture, improved soil water retention, plastic biodegradation, removal of pharmaceuticals and endocrine-disrupting chemicals, biological nitrogen fixation, phosphorus recovery and recycling, and efficient conversion of lignocellulosic biomass. These advances demonstrate the practical potential of engineered microorganisms for sustainable development. Technological advancements in microbial biotechnology can support climate action, resource conservation, pollution control, sustainable agriculture, and the transition to a resilient, circular bioeconomy with tangible environmental and societal benefits.

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Artificial Intelligence Enhances Breast Cancer Diagnosis Through Deep Learning

Deep learning and convolutional neural networks (CNNs) are transforming breast cancer diagnosis by automating the analysis of histopathological images. Researchers developed a workflow that integrates image preprocessing, hematoxylin–eosin stain separation, K-means clustering, and CNN-based classification to enhance diagnostic accuracy. By filtering poor-quality images and focusing on tumor-rich regions, the model achieved strong classification performance, with 79.0% Top-1 accuracy and 94.5% Top-5 accuracy. Thus, potential use of AI is able to reduce diagnostic variability, support pathologists in clinical decision-making, streamline pathology workflows, and improve access to reliable breast cancer diagnosis, particularly in resource-limited healthcare settings.

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Plant-Made Proteins: The Future of Sustainable Biopharmaceutical Production

Plant-made proteins are emerging as a transformative platform for producing vaccines, antibodies, enzymes, and other biopharmaceuticals, offering a sustainable, cost-effective, and scalable alternative to conventional protein production systems. Advances in plant-based expression systems, genetic engineering, process optimization, and downstream manufacturing have significantly improved protein yield, quality, and scalability. Commercial successes such as Elelyso® and the Ebola therapy ZMapp demonstrate the growing maturity of molecular farming. Plant-made proteins have promising applications in rapid pandemic response, oral drug delivery through bioencapsulation, veterinary medicine, and affordable pharmaceutical production for developing countries.

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IMOP-Cancer Predicts Tumor Behaviour Through Mutation Order

IMOP-Cancer, a computational framework identifies how the order of genetic mutations influences cancer progression, prognosis, immune response, and treatment outcomes. Using genomic and transcriptomic data from over 9,000 tumours across 33 cancer types; 106,034 mutation order pairs have been identified that significantly affects cancer phenotypes. The framework integrates mutation timing, cancer cell fraction, phylogenetic analysis, and gene expression profiling to reveal biologically meaningful mutation sequences that influences tumour proliferation, immune activity, drug sensitivity, and patient survival, highlighting its potential in advance precision oncology, prognostic prediction, and personalized cancer therapy.

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