@article { ISI:000357034800003, title = {Cell line development for biomanufacturing processes: recent advances and an outlook}, journal = {Biotechnology Letters}, volume = {37}, number = {8}, year = {2015}, month = {AUG}, pages = {1553-1564}, publisher = {SPRINGER}, address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, abstract = {

At the core of a biomanufacturing process for recombinant proteins is the production cell line. It influences the productivity and product quality. Its characteristics also dictate process development, as the process is optimized to complement the producing cell to achieve the target productivity and quality. Advances in the past decade, from vector design to cell line screening, have greatly expanded our capability to attain producing cell lines with certain desired traits. Increasing availability of genomic and transcriptomic resources for industrially important cell lines coupled with advances in genome editing technology have opened new avenues for cell line development. These developments are poised to help biosimilar manufacturing, which requires targeting pre-defined product quality attributes, e.g., glycoform, to match the innovator{\textquoteright}s range. This review summarizes recent advances and discusses future possibilities in this area.

}, keywords = {Biomanufacturing, Biosimilars, Cell line development, CHO cells genomics, Genome editing, Transcriptomics}, issn = {0141-5492}, doi = {10.1007/s10529-015-1843-z}, author = {Le, Huong and Vishwanathan, Nandita and Jacob, Nitya M. and Gadgil, Mugdha and Hu, Wei-Shou} } @article {46331, title = {Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {OCT}, pages = {20959-20968}, type = {Article}, abstract = {

Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off-targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target single-guide RNA (sgRNA) are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher homology-directed repair rates, and very low nonspecific genome editing compared to SpCas9. We demonstrate FnCas9-mediated correction of the sickle cell mutation in patient-derived induced pluripotent stem cells and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.

}, keywords = {CRISPR Cas9, gene therapy, Genome editing, iPSCs, sickle cell anemia}, issn = {0027-8424}, doi = {10.1073/pnas.1818461116}, author = {Acharya, Sundaram and Mishra, Arpit and Paul, Deepanjan and Ansari, Asgar Hussain and Azhar, Mohd and Kumar, Manoj and Rauthan, Riya and Sharma, Namrata and Aich, Meghali and Sinha, Dipanjali and Sharma, Saumya and Jain, Shivani and Ray, Arjun and Jain, Suman and Ramalingam, Sivaprakash and Maiti, Souvik and Chakraborty, Debojyoti} } @article {47425, title = {Advanced genome editing strategies for manipulation of plant specialized metabolites pertaining to biofortification}, journal = {Phytochemistry Reviews}, volume = {21}, year = {2022}, month = {FEB}, pages = {81-99}, type = {Article}, abstract = {

Emerging trends in molecular biology have progressed the knowledge of plant specialized metabolites with respect to diversity in structure, function and biosynthetic pathways. Being powerful genome-editing tools, Zinc Finger Nuclease, Transcription Activator-Like Effector Nuclease, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems have found potential application in genome and epigenome engineering. CRISPR/Cas9 is being used for studying the functions of multiple genes and gene families in plants. Our analysis suggests that although a rapid progress has occurred for utilization of CRISPR/Cas9 tool in crop improvement, limited studies are available for its application in manipulation of gene clusters of useful specialized metabolites in plants. In this review, after describing briefly about the recent advancements in genome editing techniques, we have further discussed their applicability in the modulation of metabolite production and biofortification of food crops. We have also emphasized the importance of CRISPR/Cas9-based targeted deletion of larger chromosomal fragments or gene clusters towards value addition of crop plants. The current policies for CRISPR/Cas9-edited crop plants in different countries and their acceptability in market place is also discussed. We propose that advanced genome editing techniques, including a multiplex CRISPR/Cas9 system could serve as a versatile tool for rewiring of metabolite gene clusters and improving the levels of useful metabolites in plants.

}, keywords = {Cas9, Chromosomal fragment, CRISPR, Gene cluster, Genome editing, Plant specialized metabolites}, issn = {1568-7767}, doi = {10.1007/s11101-021-09749-1}, author = {Bhambhani, Sweta and Kondhare, Kirtikumar R. and Giri, Ashok P.} } @article {48452, title = {Speed breeding opportunities and challenges for crop improvement}, journal = {Journal of Plant Growth Regulation}, volume = {42}, year = {2023}, month = {JAN}, pages = {46-59}, type = {Article}, abstract = {

Crop improvement in light of the rapidly changing climate and the increasing human population continues to be one of the primary concerns for researchers across the globe. The rate at which current crop improvement programs are progressing is essentially inadequate to meet the food demand. There is an urgent need for redesigning the crops for climate resilience and sustainable yield and nutrition. The rate of crop improvement is largely impeded owing to the long generation time taken by crop plants during the breeding process. As a solution in this direction, speed breeding is now being practiced at a large scale to reduce generation time to accommodate multiple generations of crops per year. To enhance the efficiency of breeding, researchers are now adopting an integrated approach where speed breeding is used along with modern plant breeding and genetic engineering technologies. In the present review, we have summarized the technological aspects, opportunities, and limitations associated with speed breeding. The application of speed breeding such as mapping population development, haplotype-based breeding, transgenic breeding, and genome-edited line advancement has also been discussed. Speed breeding is a promising technology that expedites the goals of food and industrial crop improvement by reducing the breeding cycles for establishing nutritional security and sustainable agriculture.

}, keywords = {Genome editing, Genomic selection, Haplotype breeding, Speed breeding, Transgenic breeding}, issn = {0721-7595}, doi = {10.1007/s00344-021-10551-8}, author = {Sharma, Shivani and Kumar, Amit and Dhakte, Priyanka and Raturi, Gaurav and Vishwakarma, Gautam and Barbadikar, Kalyani M. and Das, B. K. and Shivaraj, S. M. and Sonah, Humira and Deshmukh, Rupesh} }