Shahid Ali
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Shahid Ali has a total of 9 co-authors. Here are the top co-authors by number of shared publications:
- Baolong Bao
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
2 shared publications - Haichuan Li
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
1 shared publication - Heng Xu
Yueqing Municipal Agricultural and Rural Development Center, Yueqing, Wenzhou 325600, China
1 shared publication - Hufeng Chen
Yueqing Municipal Agricultural and Rural Development Center, Yueqing, Wenzhou 325600, China
1 shared publication - Jinyuan Che
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
1 shared publication - Libing Zhang
Yueqing Municipal Agricultural and Rural Development Center, Yueqing, Wenzhou 325600, China
1 shared publication
Latest Publications
- Open Access
Seasonal Dynamics of the Gut Microbiota of Ayu (Plecoglossus altivelis) Revealed by a Cross-Sectional Seasonal Survey in the Dajing Stream, Zhejiang Province, China
Ayu (Plecoglossus altivelis) is an East Asian amphidromous river fish, yet seasonal microbiota dynamics remain unclear. We investigated ayu in the Dajing Stream (Zhejiang Province, China) by synchronously sampling water microbiota (H), gut content microbiota (N), and gut tissue-associated microbiota (C) across four seasons. Each season, four fish were collected, and an overlapping pooling strategy (abc/abd/bcd) generated three composite replicates for C and N (n = 3 composites/season); water was collected as three field replicates (n = 3/season), yielding 36 samples (12 per niche). Using 16S rRNA amplicon sequencing and COI barcoding of stomach contents, we observed the clearest seasonal differentiation in H and seasonal variation in N consistent with diet shifts, whereas C was comparatively stable. COI signals indicated a diet dominated by aquatic insects in spring/summer, which shifted toward smaller prey (e.g., rotifers) in winter. Together, these results highlight strong niche partitioning and season-linked shifts in water and gut content communities relative to the more stable tissue-associated microbiota. These findings should be interpreted as exploratory and require validation in larger individual-level studies.
Open AccessSeasonal Dynamics of the Gut Microbiota of Ayu (Plecoglossus altivelis) Revealed by a Cross-Sectional Seasonal Survey in the Dajing Stream, Zhejiang Province, China
Ayu (Plecoglossus altivelis) is an East Asian amphidromous river fish, yet seasonal microbiota dynamics remain unclear. We investigated ayu in the Dajing Stream (Zhejiang Province, China) by synchronously sampling water microbiota (H), gut content microbiota (N), and gut tissue-associated microbiota (C) across four seasons. Each season, four fish were collected, and an overlapping pooling strategy (abc/abd/bcd) generated three composite replicates for C and N (n = 3 composites/season); water was collected as three field replicates (n = 3/season), yielding 36 samples (12 per niche). Using 16S rRNA amplicon sequencing and COI barcoding of stomach contents, we observed the clearest seasonal differentiation in H and seasonal variation in N consistent with diet shifts, whereas C was comparatively stable. COI signals indicated a diet dominated by aquatic insects in spring/summer, which shifted toward smaller prey (e.g., rotifers) in winter. Together, these results highlight strong niche partitioning and season-linked shifts in water and gut content communities relative to the more stable tissue-associated microbiota. These findings should be interpreted as exploratory and require validation in larger individual-level studies.
- Open Access
Precision, Reproducibility, and Validation in Zebrafish Genome Editing: A Critical Review of CRISPR, Base, and Prime Editing Technologies
The rapid evolution of CRISPR/Cas technology has transformed genome editing across biological systems in which zebrafish have emerged as a powerful vertebrate model for functional genomics and disease research. Due to its transparency, genetic similarity to humans, and suitability for large-scale screening, zebrafish is an appropriate system for translating molecular discoveries into biomedical and environmental applications. Thereby, this review highlights the recent progress in zebrafish gene editing, targeting innovations in ribonucleoprotein delivery, PAM-flexible Cas variants, and precision editors. These approaches have greatly improved editing accuracy, reduced mosaicism, and enabled efficient F0 phenotyping. In the near future, automated microinjections, optimized guide RNA design, and multi-omics validation pipelines are expected to enhance reproducibility and scalability. Although recent innovations such as ribonucleoprotein delivery, PAM-flexible Cas variants, and precision editors have expanded the zebrafish genome-editing toolkit, their benefits are often incremental and context-dependent. Mosaicism, allele complexity, and variable germline transmission remain common, particularly in F0 embryos. Precision editors enable defined nucleotide changes but typically exhibit modest efficiencies and locus-specific constraints in zebrafish. Consequently, rigorous validation, standardized workflows, and careful interpretation of F0 phenotypes remain essential. This review critically examines both the capabilities and limitations of current zebrafish gene-editing technologies, emphasizing experimental trade-offs, reproducibility challenges, and realistic use cases.
Open AccessPrecision, Reproducibility, and Validation in Zebrafish Genome Editing: A Critical Review of CRISPR, Base, and Prime Editing Technologies
The rapid evolution of CRISPR/Cas technology has transformed genome editing across biological systems in which zebrafish have emerged as a powerful vertebrate model for functional genomics and disease research. Due to its transparency, genetic similarity to humans, and suitability for large-scale screening, zebrafish is an appropriate system for translating molecular discoveries into biomedical and environmental applications. Thereby, this review highlights the recent progress in zebrafish gene editing, targeting innovations in ribonucleoprotein delivery, PAM-flexible Cas variants, and precision editors. These approaches have greatly improved editing accuracy, reduced mosaicism, and enabled efficient F0 phenotyping. In the near future, automated microinjections, optimized guide RNA design, and multi-omics validation pipelines are expected to enhance reproducibility and scalability. Although recent innovations such as ribonucleoprotein delivery, PAM-flexible Cas variants, and precision editors have expanded the zebrafish genome-editing toolkit, their benefits are often incremental and context-dependent. Mosaicism, allele complexity, and variable germline transmission remain common, particularly in F0 embryos. Precision editors enable defined nucleotide changes but typically exhibit modest efficiencies and locus-specific constraints in zebrafish. Consequently, rigorous validation, standardized workflows, and careful interpretation of F0 phenotypes remain essential. This review critically examines both the capabilities and limitations of current zebrafish gene-editing technologies, emphasizing experimental trade-offs, reproducibility challenges, and realistic use cases.
- Open Access
- 25 July 2023
- Published by TSF Nexus in Nature's Symphony
- Vol. 1 (2) , 01-07
Exploring Evolution: A Brief Journey through Mechanisms and Milestones
This mini-review deals with the journey of evolution and the related mechanisms which play a pivotal role in diversification of living beings. Various factors are involved in the process like mutations and environment. Charles Darwin was the first one to propose the idea of natural selection which ensures the development of beneficial traits in species of a particular region, thus resulting in mass propagation. The review highlights the development of species ranging from unicellular organisms to multicellular complex species including the appearance of Homo sapiens. Various eras like Cambrian and Mesozoic periods have also been explained showing the changes in environmental conditions which resulted in the natural selection of different species. This review provides an understanding of mechanisms and milestones of evolution, helping in a better perception of life.
- 25 July 2023
- Published by TSF Nexus in Nature's Symphony
- Vol. 1 (2) , 01-07
Open AccessExploring Evolution: A Brief Journey through Mechanisms and Milestones
This mini-review deals with the journey of evolution and the related mechanisms which play a pivotal role in diversification of living beings. Various factors are involved in the process like mutations and environment. Charles Darwin was the first one to propose the idea of natural selection which ensures the development of beneficial traits in species of a particular region, thus resulting in mass propagation. The review highlights the development of species ranging from unicellular organisms to multicellular complex species including the appearance of Homo sapiens. Various eras like Cambrian and Mesozoic periods have also been explained showing the changes in environmental conditions which resulted in the natural selection of different species. This review provides an understanding of mechanisms and milestones of evolution, helping in a better perception of life.