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Toward Understanding the Intelligent Properties of Biological Macromolecules
Published in George K. Knopf, Amarjeet S. Bassi, Smart Biosensor Technology, 2018
Important discoveries have already been made using approaches where machine learning and informatics applied to large data sets have played a prominent role. One example is a biosensor called TIGER from Isis Pharmaceuticals, Inc., which is reaching commercialization. The development of this biosensor first involved discovering bacterial RNA sequence motifs that are conserved to varying extents and that can reveal the presence of different bacteria and different strains within a given species. In patient fluid samples, the sequences to be detected are first amplified using the PCR reaction. Then, in a high-throughput mode, the amplified samples are examined using high-resolution mass spectrometry. Subsequent informatics treatment of the data reveals characteristic sequence motifs for different bacterial species and strains. Using this biosensor, these investigators were able to detect three different species of pathogenic bacteria within the respiratory fluid samples from a disease outbreak at a U.S. military base (197). They identified a particularly virulent strain of Streptococcus pyrogenes as the primary cause of the outbreak in all the disease samples analyzed. The TIGER biosensor has unique capabilities. Without using bacterial culturing techniques, it is able to rapidly detect different bacterial species and strains within species, as well as provide rapid identification of the source of infections, even in cases where the bacteria has not yet been characterized.
A review of DNA sequence data analysis technologies and their combination with data mining methods
Published in Lin Liu, Automotive, Mechanical and Electrical Engineering, 2017
Tiange Yu, Yang Chen, Bowen Zhang
Though sequencing data could be obtained more and more easily with the development of next-generation sequencing technology, we are still facing the challenges of understanding the functions and evolution of these sequences. DNA sequence motifs are the short patterns that appear frequently in the genome which carries out biological functions, including transcriptional factor binding sites, mRNA splicing signaling, transcriptional termination signal, etc (P. D’Haeseleer, 2006). By extracting them and comprehending the functions, it would be much easier to uncover the regulatory mechanisms of genes, which could facilitate understanding the functions of new sequences without conducting laborious and costly functional assays on candidate genes individually.
by Genetically Engineered Filamentous Fungs
Published in Yoshikatsu Murooka, Tadayuki Imanaka, Recombinant Microbes for Industrial and Agricultural Applications, 2020
T. Vichitsoonthonkul, Y. W. Chu, H. S. Sodhi, G. Saunders
Most eukaryotic promoter sequences have certain characteristic sequence motifs, thought to be involved in transcription initiation. The CCAAT sequence is one such motif and has indeed been found within the upstream regions of several genes cloned from filamentous fungi [76], although there are several examples in which they are absent [77]. It seems clear from studies carried out with yeast and mammalian cells that the CCAAT sequence is a target for the binding of transcription factors. However, there seems to be no single protein specific to all CCAAT regions found in promoters.
Optimization of ultraviolet/ozone (UVO3) process conditions for the preparation of gelatin coated polystyrene (PS) microcarriers
Published in Preparative Biochemistry & Biotechnology, 2022
Mohd Azmir Arifin, Maizirwan Mel, Sia Yiik Swan, Nurhusna Samsudin, Yumi Zuhanis Has-Yun Hashim, Hamzah Mohd Salleh
Gelatin is a natural biopolymer derived from acid or alkaline hydrolysis of collagen, which is the most abundant structural protein found in skins, bones and connective tissues of animals.[19,20] Gelatin is widely employed in pharmaceutical and medical applications due to its many advantages.[21,22] The biopolymer has excellent biocompatibility, biodegradability, processing flexibility, low antigenicity and is commercially available at low cost.[23,24] Moreover, arginine-glycine-aspartic (RGD) sequence motif that mediate cell attachment and spreading, is abundantly present in gelatin chains with better accessibility when compared to those in collagen.[25,26] In cell and tissue engineering, this feature was commonly benefited by incorporation of gelatin on polymer surfaces and in polymer scaffolds or hydrogels that were made from polymer that lack cell binding sites.[18,20,22,27] The presence of gelatin improves cytocompatibility of their surfaces and many studies have reported that increasing gelatin content have increased adhesion and proliferation rates of various cell lines which most probably contributed by higher availability of the RGD motifs.[28–31]
COVID-19;-The origin, genetics,and management of the infection of mothers and babies
Published in Egyptian Journal of Basic and Applied Sciences, 2020
Hassan Ih El-Sayyad, Yousef Ka Abdalhafid
Aside from RaTG13, Pangolin-CoV is the most closely related CoV to SARS-CoV-2. The S1 protein of Pangolin-CoV is much more closely related to SARS-CoV-2 than to RaTG13. Five key amino acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and SARS-CoV-2, but four amino acid mutations are present in RaTG13. Both Pangolin-CoV and RaTG13 lost the putative furin recognition sequence motif at the S1/S2 cleavage site which can be observed in the SARS-CoV-2. Conclusively, this study suggests that pangolin species are a natural reservoir of SARS-CoV-2-like CoVs [28].