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Collaborative practice: an essential component of the service to vulnerable children and their families
Published in Taylor Julie, Thoburn June, Barr Hugh, Marion Helme, Collaborative Practice with Vulnerable Children and their Families, 2017
Taylor Julie, Thoburn June, Barr Hugh, Marion Helme
Co-located teams are sometimes confused with interagency teams. Co-located teams will usually be teams of workers accountable for a particular service but based in the same or an adjacent building, with easy access to other services facilitating interpro- fessional communication. They often share some facilities; for example, canteens or meeting rooms, or reception facilities. A wide range of services may be co-located, and they appear to work best when there is easy (and non-stigmatised) access for members of the community; for example, neighbourhood housing offices or com- munity health centres.
Exon globin mutation of β-thalassemia in Indonesian ethnic groups: A bioinformatics approach
Published in Robert Hofstra, Noriyuki Koibuchi, Suthat Fucharoen, Advances in Biomolecular Medicine, 2017
N.I. Sumantri, D. Setiawan, A. Sazali
The wild-type residue was positively charged, and the mutant residue is neutral (Fig 5). The difference in hydrophobicity will affect hydrogen bond formation. The wild-type residue forms a salt bridge with glutamic acid at position 27. The difference in charge will disturb the ionic interaction made by the original, wild-type residue. The mutation introduces a smaller residue at this position. The new residue might be too small to make multimeric contacts. A more hydrophobic residue is introduced here. Any hydrogen bond that could be made by the wild-type residue to other monomers will be lost now and affect the multimeric contacts. The mutated residue is not in direct contact with a ligand; however, the mutation could affect the local stability which in turn could affect the ligand con102tacts made by one of the neighboring residues. The wild-type residue forms a hydrogen bond with glutamic acid at position 27. This residue is part of an Interpro domain named hemoglobin β-type. This is a strong indication that the residue is indeed in contact with other proteins. The mutated residue is located in a domain that is important for binding of other molecules and in contact with residues in a domain that is also important for binding. The mutation might disturb the interaction between these two domains and as such affect the function of the protein. This domain is annotated with the following Gene-Ontology (GO) terms to indicate its function: heme, oxygen, and iron ion binding.
Detection of Food Allergen Residues by Immunoassays and Mass Spectrometry
Published in Andreas L. Lopata, Food Allergy, 2017
Sridevi Muralidharan, Yiqing Zhao, Steve L. Taylor, Nanju A. Lee
The shotgun proteomics workflow is suited for discovery studies and typically adopts the bottom-up approach, where proteins are pre-fractionated, subjected to proteolytic digestion, followed by nanoflow-liquid chromatography- tandem mass spectrometry (nLC-MS/MS). This workflow is becoming ideal for identifying proteins and characterizing post translational modifications. Alternatively, top-down approach is more suited for characterizing intact proteins typically analysed by high resolution mass analysers, followed by MS/MS based on collision induced dissociation of ions. Gene ontology annotations and analysis have been possible from using databases such as UniProt, Interpro, KEGG, and new tools such as WEGO (Ye et al. 2006), MaxQuant (Cox and Mann 2008), STRAP (Bhatia et al. 2009), DAVID or MAPMAN. This approach is predominantly used for biomarker discovery across different areas of research but has recently been successfully demonstrated for discovery of potential allergens in uncharacterised novel allergenic foods (in house unpublished). As an alternative, data acquired using data-independent acquisition mode based on simultaneous fragmentation activation of all ions (all co-eluting peptides) could exponentially enhance the depth of data available for analysis, and has the potential for multiple retrospective analyses from a single experiment. This approach has been exploited in certain other areas of research, however it requires the generation of high quality spectral libraries for peptide identification and quantification and its application in food allergen research is still at infancy.
Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design
Published in Pathogens and Global Health, 2023
Chin Peng Lim, Boon Hui Kok, Hui Ting Lim, Candy Chuah, Badarulhisam Abdul Rahman, Abu Bakar Abdul Majeed, Michelle Wykes, Chiuan Herng Leow, Chiuan Yee Leow
GenBank serves as a public database of genetic sequences, focusing on the expansion and dissemination of information. The repository relies on the submissions of sequence data from authors and whole-genome shotgun (WGS) as well as high-throughput data from sequencing centres and issued patents from The U.S. Patent and Trademark Office. GenBank is a partner of the International Nucleotide Sequence Database Collaboration (INSDC) along with European Nucleotide Archive (ENA) and Data Bank of Japan (DDBJ) in which data exchange is done on a daily basis so that a systematic collection of sequence information is accessible worldwide. GenBank also collects and stores amino acid sequences from databases like SWISS-PROT, Protein Research Foundation (PRF) and Protein Data Bank (PDB) [94]. GISAID has gained its reputation as a trustworthy means for international sharing of all influenza virus data including genetic sequence and metadata [95]. In response to the COVID-19 pandemic, related data have also been shared via this public domain recently. InterPro is a unified resource resulting from the integration of protein signature databases including PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The major application is annotation and functional classification of uncharacterized sequences. Based on sequence positions and protein coverage, protein signatures that fall into the same family or functional domain are grouped into single entry with respective annotation and cross-references [96–98].
TMT-Based proteomics analysis of LPS-induced acute lung injury
Published in Experimental Lung Research, 2021
Shengsong Chen, Yi Zhang, Qingyuan Zhan
Proteins are composed of structural domains that control function and provide insight into protein evolution. The study of protein domains is of great importance for understanding the biological functions and evolution of proteins. InterPro is a database that combines information on protein families, domains, and functional sites. We used this database to analyze the annotation and enrichment of the functional domains of the DEPs and list the top 10 items that were significantly enriched with the smallest P value. The results (Figure 4C) showed enrichment of the DEPs in the following sites, proteins, families, and functions: minichromosome maintenance proteins, minichromosome maintenance, conserved sites, the MCM N-terminal domain, the MCM OB domain, the MCM domain, peptidase S1A, the chymotrypsin family, serine proteases, the trypsin domain, the DAPIN domain, peptidase S1, the PA clan, and the serpin domain.