Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

<p>Abstract</p> <p>Background</p> <p>Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. However, determining protein-coding genes for most new genomes is almost completely performed by inference using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no information on biologically important post-translational processing events critical for protein function.</p> <p>Results</p> <p>We experimentally annotated the bacterial pathogen <it>Salmonella </it>Typhimurium 14028, using "shotgun" proteomics to accurately uncover the translational landscape and post-translational features. The data provide protein-level experimental validation for approximately half of the predicted protein-coding genes in <it>Salmonella </it>and suggest revisions to several genes that appear to have incorrectly assigned translational start sites, including a potential novel alternate start codon. Additionally, we uncovered 12 non-annotated genes missed by gene prediction programs, as well as evidence suggesting a role for one of these novel ORFs in <it>Salmonella </it>pathogenesis. We also characterized post-translational features in the <it>Salmonella </it>genome, including chemical modifications and proteolytic cleavages. We find that bacteria have a much larger and more complex repertoire of chemical modifications than previously thought including several novel modifications. Our <it>in vivo </it>proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function.</p> <p>Conclusion</p> <p>This work highlights several ways in which application of proteomics data can improve the quality of genome annotations to facilitate novel biological insights and provides a comprehensive proteome map of <it>Salmonella </it>as a resource for systems analysis.</p

Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP)

This report contains the charge to the panel, the panel's discussions and panel recommendations

Intellectual and developmental disability nursing: current challenges in the USA

Kathy Auberry Indiana University School of Nursing, Indiana University-Purdue University Columbus, Columbus, IN, USA Background: Nursing in the field of intellectual and developmental disability (IDD) has evolved over the last decade. With this evolution new challenges related to this field of nursing practice have surfaced. The field of IDD nursing is complex and considered out of the realm of common nursing practice. Given the complexity and uniqueness of this area of nursing practice, nurses face challenges when supporting this population. The purpose of this commentary is to highlight current challenges faced by nurses working in the field of IDD in the USA in order to generate conversation and solutions. Methods: A review of literature and clinical practice experience was conducted. Articles were analyzed for content related to nursing practice in the field of IDD. Textbook references were incorporated to substantiate key points. Additionally, the author&rsquo;s 24 years of clinical practice and nursing administrative experience were included. Results: Nurses face varied challenges in the field of IDD: lack of education regarding this population, healthcare complexity of this population, role ambiguity, varied practice settings, nursing model of care controversy, and caseload distribution and acuity. Conclusion: Nurses working with the IDD population face challenges that may be distinctive to this field of nursing. Educational preparation for nurses, physicians, and health care professionals is minimal. The multifaceted needs of persons with IDD and diverse practice settings nurses encounter create a fragmented system that is difficult to navigate. Evidence-based interventions to guide IDD nursing practice are lacking. Standardization of care principles and role clarification for the IDD nurse across settings are varied. The IDD field requires a synthesized approach to healthcare management that currently does not appear to exist across settings. An increase in nursing research for this population and area of practice should occur. Nursing and medical programs must seek ways to include or expand content specific to the health intricacies of this population. Keywords: intellectual, disability, learning disability, nursing, challenges, role

Nurses' perspectives on technical skill requirements in primary and tertiary healthcare services

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