Biomedical subjects

Muhammad Shafiq

Publications and source records attributed to Muhammad Shafiq.

4 recordsLinked to original sources

PubMed2026

From commensal to pathobiont: The emergence of virulence-enhanced Escherichia coli in China's food-animal systems - insights with future implications.

A fundamental shift in Escherichia coli epidemiology is being driven by convergence of virulence determinants and antimicrobial resistance within linked human-animal-environment systems. In China, the rapid growth of food-animal production, extensive antimicrobial use, and complex food networks are accelerating the emergence and dissemination of virulence-enhanced E. coli pathobionts. This review synthesizes recent epidemiological, genomics, and outbreak data to characterize China's evolving landscape of food-animal-associated E. coli. We highlight a significant shift from classical pathotypes to hybrid lineages that simultaneously carry virulence factors and last-resort antibiotic resistance determinants, including mcr-1, tet(X4), and blaNDM. These traits disseminate rapidly via plasmid-mediated horizontal gene transfer, facilitating rapid adaptation and enabling cross-sectoral One Health transmission. National surveillance, foodborne outbreak investigations, and whole-genome sequencing data show that food-animal reservoirs are active evolutionary niches that drive pathogen diversity and fitness, rather than serving merely as contamination sources. Whole-genome sequencing also pinpoints high-risk clones (e.g., ST394) and plasmid-mediated co-selection of virulence and AMR. The emergence of hybrid pathotypes (e.g., STEC/ETEC) and AMR-virulence co-selection challenges traditional classification and limits the effectiveness of conventional surveillance approaches. The 2017 colistin ban reduced mcr-1, yet ongoing resistance and emerging tet(X4) demand integrated surveillance. Collectively, these findings call for reconceptualizing E. coli as a dynamic genomic entity embedded within a unified ecological network. Addressing this threat requires an integrated One Health strategy including genomic surveillance, agricultural antimicrobial stewardship, and coordinated food-environment-clinical monitoring to prevent high-risk clone emergence and global spread.

Animals↗

PubMed2026

Genome-wide identification and characterization of 1-amino-cyclopropane-1- carboxylate synthase (ACS) gene family in Carica papaya and expression insights in response to hormone stress.

ACC-synthase (1-aminocyclopropane-1-carboxylate synthase), also known as the ACS gene, plays a pivotal role in ethylene production, which is of great importance in the fruit ripening process for producing saleable yield (marketable fruit). The ACS gene family presumably controls stress responses, plant growth and development, and particularly fruit ripening. Computational biology was used as an essential tool to identify seven ACS genes in Carica papaya (red hermaphrodite) using an RNA-seq database (NCBI GEO). Further, the phylogenetic relationships of ACS genes determined gene family resemblance in the genomes of Hordeum vulgare, Musa acuminata, C. papaya, and Arabidopsis thaliana; therefore, the identified gene families were further classified into four distinct clades (Type-I, Type-II, Type-III, and Type-IV) in alignment with the well-established Arabidopsis classification. Moreover, encompassing gene structure, domain motifs, cis-element phylogenetic profiling, synteny, and transcriptomic profiling unveiled latent structural and functional attributes within CpACS genes. Through segmental duplication of CpACS, insights into evolutionary duplication events were predicted. The paralogous behavior of ACS genes in C. papaya and a comprehensive transcriptomic analysis demonstrated both up- and down-regulation patterns in response to ethylene treatment at different time points during the fruit ripening process, using the papaya manual handbook V2 (2021). Gene expression showed upregulation of two essential CpACS genes, CpACS5 and CpACS6. RT-qPCR validates the expression of these important genes during fruit ripening. However, one gene, CpACS7, is expressed in the later stages of fruit development. Our results demonstrated novel avenues for understanding the expression pathways of the ACS gene family in red hermaphrodite papaya, and most of these genes were linked to regulating various abiotic stresses, plant growth, and fruit development.

Carica↗

PubMed2025

Comprehensive transcriptomic analysis of myostatin-knockout pigs: insights into muscle growth and lipid metabolism.

Pigs are a vital source of protein worldwide, contributing approximately 43% of global meat production. Recent genetic advancements in the myostatin (MSTN) gene have facilitated the development of double-muscling traits in livestock. In this study, we investigate the transcriptomic profiles of second-generation MSTN-knockout (MSTN-/-) pigs, generated through CRISPR/Cas9 gene editing and somatic cell nuclear transfer (SCNT). Using RNA sequencing, we compared the transcriptomic landscapes of muscle tissues from MSTN-/- pigs and wild-type (WT) counterparts. The sequencing yielded an average unique read mapping rate of 86.7% to the Sus scrofa reference genome. Our analysis revealed 15,142 differentially expressed genes (DEGs), including 121 novel genes, with 2554 genes upregulated and 1629 downregulated in the MSTN-/- group relative to the wild-type group. Notable transcriptomic changes were identified in genes associated with muscle development, lipid metabolism, and other physiological processes. These findings provide valuable insights into the molecular consequences of MSTN inactivation, with potential applications in the optimization of livestock breeding and advancements in biomedical research.

Animals↗

PubMed2024

Over expression of modified Isomaltulose Synthase Gene II (ImSyGII) under single and double promoters drive unprecedented sugar contents in sugarcane.

Sugarcane has been grown all around the world to meet sugar demands for industrial sector. The current sugar recovery percentage in sugarcane cultivars is dismally low which demands scientific efforts for improvements. Multiple approaches were adopted to enhance sugar contents in commercial sugarcane plants in contrast to conventional plant breeding methods. The exploitation of biotechnological methods and exploration of isomaltulose synthetic genes presented a promising solution to increase the existing low level of sugar recovery percentage in Saccharum officinarum L. Isomaltulose synthase gene II was employed and integrated into plant expression vector driven under the leaf and stem specific promoters terminated by nopaline synthase gene in a cloning strategy shown in the present study. Three gene constructs were developed in various combinations driven under promoters Zea mays ubiquitin and Cestrum Yellow Leaf Curl virus in the single and double combined stacked system. The transformation was executed in multiple formats with single transformed events, double promoter transformation events and triple construct stacked promoters in sugarcane induced calli via the particle gene gun. The transformation of ImSyGII in sugarcane genotype HSF-240 was confirmed by molecular gene analysis while expression quantification was determined through Real Time PCR. Furthermore, HPLC was also done to harvest the increased amounts of Isomaltulose in transgenic sugarcane juice. The present work upheld the enhanced ImSyGII expression in leaves owing to the exploitation of ubiquitin, while the Cestrum Yellow Leaf Curl virus promoter enhanced gene expression in sugarcane stems. The employment of three gene constructs collectively produced elite sugar lines producing more than 78% enhancements in whole sugar recovery percentage. The mature internode proved highly efficient and receptive regarding the production of isomaltulose. Quantifications and sugar contents evaluations upheld an increased Brix ratio of transgenic sugarcane lines than control lines.

Saccharum↗