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Sustainability and Development of Industry 5.0
Published in Pau Loke Show, Kit Wayne Chew, Tau Chuan Ling, The Prospect of Industry 5.0 in Biomanufacturing, 2021
Hui Shi Saw, Abdul Azim bin Azmi, Kit Wayne Chew, Pau Loke Show
At the cellular level, deletion of a gene that hampers overexpression, or generation of a by-product that inhibits the synthesis of a target product can be performed by targeting a known gene. Gene to add or remove can be based on genotype, which is the known sequence, or phenotype, from the traits and characteristics of protein with an unknown sequence. To exemplify, in silico analysis with the establishment of bioinformatics tools and database enables hypothetical protein sequence to be generated, where the potential gene product model can be predicted. Having access to the structure of a protein can help to determine a suitable feature, for example, the hydrophobicity and function of the protein, that needs to be employed via genetic manipulation. The available tools, such as BLAST, ExPASy and Entrez are helpful in increasing the success rate of an experiment, which might reduce the waste of resources as compared to the traditional trial and error approach.
Solid-state fermentation production and characterization of an alkaline lipase from a newly isolated Burkholderia gladioli strain
Published in Preparative Biochemistry & Biotechnology, 2022
Pedro Alves Martins, Thályta Fraga Pacheco, Brenda Rabello de Camargo, Janice Lisboa De Marco, Thaís Fabiana Chan Salum
Experimental proteomic analysis of the optimized crude enzymatic extract returned 698 identifications. Of these, 163 had a predicted signal peptide and the remainder corresponded to intracellular proteins, which may have been released through cell lysis during cultivation or even during the extraction step, due to the use of Triton X-100. Since the purpose of this work was to find and characterize lipases, membrane-bound and periplasmatic proteins were discarded for the final analysis, which consisted of the subset of 64 extracellular proteins. Hypothetical protein sequences were compared to the NCBI database using the Basic Local Alignment Search Tool (BLAST) to infer their biological role. While those with no similarity to known proteins remained as hypothetical proteins, those with BLAST matches were further annotated and categorized accordingly. A representative portion of the secretome (33 proteins; 51.6%) was composed of enzymes, further categorized as peptidases (9 proteins; 14.1%), amidases (1 protein; 1.6%), esterases/lipases (5 proteins; 7.8%), other carboxylesterases (2 proteins; 3.1%), glycosidases (9 proteins; 14.1%), oxidoreductases (3 proteins; 4.7%), isomerases (3 proteins; 4.7%) and lyases (1 protein; 1.6%). Hypothetical proteins were 27 (42.2%), of which 10 had conserved domains of unknown function. Other proteins with no catalytic activity were 4, representing 6.3% of the secretome (Supplementary File 1).
The role of identified and characterized bacteriophage ZCEC13 in controlling pathogenic and multidrug-resistant Escherichia coli in wastewater: in vitro study
Published in Environmental Technology, 2023
Samar Ragab, Shrouk Mohamed Gouda, Mohamed Abdelmoteleb, Ayman El-Shibiny
The genome of ZCEC13 has been sequenced, deposited into the NCBI GenBank (Acc. No. ON086804). Genome assembly metrics were as follows: # contigs 1; % GC 48.87; N50 48021; L50 1 and # N’s per 100 kb 0. Phylogenetic analysis suggested that E. coli Phage vB EcoS-Sa179|w complete genome (Acc. No. NC 054637.1) was closely related to the genome of ZCEC13 (Figure 3). According to the recent taxonomy updated by the International Committee on Taxonomy of Viruses (ICTV), BLASTn results confirmed that ZCEC13 is a member of the Caudoviricetes class [77]. Supplementary Table S2 presents the manually curated annotated genes. RASTtk annotation identified eighty protein-coding genes and, among which 24 proteins have assigned functions, involving cell lysis proteins, structural proteins, DNA packaging/replication/transcription/repair proteins. ZCEC13 didn’t encode any lysogenic genes. Genetic map highlighting functional genes is illustrated in (Figure 4). ZCEC13 has 47 ORFs on the leading strand and 33 ORFs on the complementary strand. Genomic analysis didn’t encode any tRNA genes and uncovered two repeat regions. In addition, genes of temperate lifecycle, antibiotic resistance, and bacterial virulence were not detected using PhageLeads. This suggests the applicability and safety of ZCEC13 for therapeutic purposes. Transmembrane domains (TMDs) were predicted in four putative proteins. The topology of two TMDs was detected in two hypothetical proteins (ORFs: 10 (Figure 5), and 53), while one TMD was detected in hypothetical protein (ORF: 9) and tail fibre protein (ORF: 37).
Simultaneous bioremediation of heavy metals and biodegradation of hydrocarbons by metal resistant Brevibacillus parabrevis OZF5 improves plant growth promotion
Published in Bioremediation Journal, 2023
Parvaze Ahmad Wani, Nusrat Rafi, Uzma Wani, Hashirudeen Bilikis A, Mohd Sajjad Ahmad Khan
Chromium reductase (ChR) gene and amino acid sequence of reductase (chromium) of Brevibacillus parabrevis OZF5 showed 98.53% and 98.51% similarity with chromium reductase protein (ChR) gene of Bacillus sp. strain SFC 500-1ESP (accession number KY656902.1) and chromate reductase protein ChR (Bacillus species), NAD(P)H-dependent Escherichia coli oxidoreductase, putative NADPH-dependent Escherichia coli FMN reductase and hypothetical protein Shigella sp. respectively. Phylogenetic tree of gene is shown in Figure 5A and B, respectively. Sequence was deposited in NCBI under an accession number SAMN13678826.