The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation

BACKGROUND: Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, integrated systems usually do not provide mechanisms to generate customized databases to predict particular protein functions. Here, we describe a tool termed PIPA (Pipeline for Protein Annotation) that has these capabilities. RESULTS: PIPA annotates protein functions by combining the results of multiple programs and databases, such as InterPro and the Conserved Domains Database, into common Gene Ontology (GO) terms. The major algorithms implemented in PIPA are: (1) a profile database generation algorithm, which generates customized profile databases to predict particular protein functions, (2) an automated ontology mapping generation algorithm, which maps various classification schemes into GO, and (3) a consensus algorithm to reconcile annotations from the integrated programs and databases. PIPA's profile generation algorithm is employed to construct the enzyme profile database CatFam, which predicts catalytic functions described by Enzyme Commission (EC) numbers. Validation tests show that CatFam yields average recall and precision larger than 95.0%. CatFam is integrated with PIPA. We use an association rule mining algorithm to automatically generate mappings between terms of two ontologies from annotated sample proteins. Incorporating the ontologies' hierarchical topology into the algorithm increases the number of generated mappings. In particular, it generates 40.0% additional mappings from the Clusters of Orthologous Groups (COG) to EC numbers and a six-fold increase in mappings from COG to GO terms. The mappings to EC numbers show a very high precision (99.8%) and recall (96.6%), while the mappings to GO terms show moderate precision (80.0%) and low recall (33.0%). Our consensus algorithm for GO annotation is based on the computation and propagation of likelihood scores associated with GO terms. The test results suggest that, for a given recall, the application of the consensus algorithm yields higher precision than when consensus is not used. CONCLUSION: The algorithms implemented in PIPA provide automated genome-wide protein function annotation based on reconciled predictions from multiple resources

A realist synthesis of educational interventions to improve nutrition care competencies and delivery by doctors and other healthcare professionals

Objective: To determine what, how, for whom, why, and in what circumstances educational interventions improve the delivery of nutrition care by doctors and other healthcare professionals work. Design: Realist synthesis following a published protocol and reported following Realist and Meta-narrative Evidence Synthesis: Evolving Standards (RAMESES) guidelines. A multidisciplinary team searched MEDLINE, CINAHL, ERIC, EMBASE, PsyINFO, Sociological Abstracts, Web of Science, Google Scholar and Science Direct for published and unpublished (grey) literature. The team identified studies with varied designs; appraised their ability to answer the review question; identified relationships between contexts, mechanisms and outcomes (CMOs); and entered them into a spreadsheet configured for the purpose. The final synthesis identified commonalities across CMO configurations. Results: Over half of the 46 studies from which we extracted data originated from the USA. Interventions that improved the delivery of nutrition care improved skills and attitudes rather than just knowledge; provided opportunities for superiors to model nutrition care; removed barriers to nutrition care in health systems; provided participants with local, practically relevant tools and messages; and incorporated non-traditional, innovative teaching strategies. Operating in contexts where student and qualified healthcare professionals provided nutrition care in developed and developing countries, these interventions yielded health outcomes by triggering a range of mechanisms, which included feeling competent, feeling confident and comfortable, having greater self-efficacy, being less inhibited by barriers in healthcare systems and feeling that nutrition care was accepted and recognised. Conclusions: These findings show how important it is to move education for nutrition care beyond the simple acquisition of knowledge. They show how educational interventions embedded within systems of healthcare can improve patients’ health by helping health students and professionals to appreciate the importance of delivering nutrition care and feel competent to deliver it

Xanthohumol improved cognitive flexibility in young mice

The protein palmitoylation cycle has been shown to be important for protein signaling and synaptic plasticity. Data from our lab showed a change in the palmitoylation status of certain proteins with age. A greater percentage of the NMDA receptor subunits GluN2A and GluN2B, along with Fyn and PSD95 proteins, were palmitoylated in the old mice. The higher level of protein palmitoylation was also associated with poorer learning scores. Xanthohumol is a prenylated flavonoid that has been shown to increase beta-oxidation in the livers of rodents, decreasing circulating free fatty acids in the serum. What is not known is whether the application of xanthohumol could influence the palmitoylation status of proteins. In this study, young and old mice were fed a diet supplemented with xanthohumol for 8 weeks. Spatial memory was assessed with the Morris water maze and protein palmitoylation quantified. The young xanthohumol-treated mice showed a significant improvement in cognitive flexibility. However, this appeared to be associated with the young control mice, on a defined, phytoestrogen-deficient diet, performing as poorly as the old mice and xanthohumol reversing this effect. The old mice receiving xanthohumol did not significantly improve their learning scores. Xanthohumol treatment was unable to affect the palmitoylation of NMDA receptor subunits and associated proteins assessed in this study. This evidence suggests that xanthohumol may play a role in improving cognitive flexibility in young animals, but it appears to be ineffective in adjusting the palmitoylation status of neuronal proteins in aged individuals.Keywords: Palmitoylation, Reversal trials, Aging, Memory, PalmitateKeywords: Palmitoylation, Reversal trials, Aging, Memory, Palmitat

Germ Line Origin and Somatic Mutations Determine the Target Tissues in Systemic AL-Amyloidosis

BACKGROUND: Amyloid is insoluble aggregated proteins deposited in the extra cellular space. About 25 different proteins are known to form amyloid in vivo and are associated with severe diseases such as Alzheimer's disease, prion diseases and type-2 diabetes. Light chain (AL) -amyloidosis is unique among amyloid diseases in that the fibril protein, a monoclonal immunoglobulin light chain, varies between individuals and that no two AL-proteins with identical primary structures have been described to date. The variability in tissue distribution of amyloid deposits is considerably larger in systemic AL-amyloidosis than in any other form of amyloidosis. The reason for this variation is believed to be based on the differences in properties of the amyloidogenic immunoglobulin light chain. However, there is presently no known relationship between the structure of an AL-protein and tissue distribution. METHODOLOGY/PRINCIPAL FINDINGS: We compared the pattern of amyloid deposition in four individuals with amyloid protein derived from variable light chain gene O18-O8, the source of a high proportion of amyloidogenic light chains, and in whom all or most of the fibril protein had been determined by amino acid sequencing. In spite of great similarities between the structures of the proteins, there was a pronounced variability in deposition pattern. We also compared the tissue distribution in these four individuals with that of four other patients with AL-amyloid derived from the L2-L16 gene. Although the interindividual variations were pronounced, liver and kidney involvement was much more evident in the latter four. CONCLUSIONS/SIGNIFICANCE: We conclude that although the use of a specific gene influences the tissue distribution of amyloid, each light chain exhibits one or more determinants of organ-specificity, which originate from somatic mutations and post-translational modifications. Eventual identification of such determinants could lead to improved treatment of patients with AL amyloidosis

Genome based cell population heterogeneity promotes tumorigenicity: the evolutionary mechanism of cancer.

Cancer progression represents an evolutionary process where overall genome level changes reflect system instability and serve as a driving force for evolving new systems. To illustrate this principle it must be demonstrated that karyotypic heterogeneity (population diversity) directly contributes to tumorigenicity. Five well characterized in vitro tumor progression models representing various types of cancers were selected for such an analysis. The tumorigenicity of each model has been linked to different molecular pathways, and there is no common molecular mechanism shared among them. According to our hypothesis that genome level heterogeneity is a key to cancer evolution, we expect to reveal that the common link of tumorigenicity between these diverse models is elevated genome diversity. Spectral karyotyping (SKY) was used to compare the degree of karyotypic heterogeneity displayed in various sublines of these five models. The cell population diversity was determined by scoring type and frequencies of clonal and non-clonal chromosome aberrations (CCAs and NCCAs). The tumorigenicity of these models has been separately analyzed. As expected, the highest level of NCCAs was detected coupled with the strongest tumorigenicity among all models analyzed. The karyotypic heterogeneity of both benign hyperplastic lesions and premalignant dysplastic tissues were further analyzed to support this conclusion. This common link between elevated NCCAs and increased tumorigenicity suggests an evolutionary causative relationship between system instability, population diversity, and cancer evolution. This study reconciles the difference between evolutionary and molecular mechanisms of cancer and suggests that NCCAs can serve as a biomarker to monitor the probability of cancer progression

1965: Abilene Christian College Bible Lectures - Full Text

LIFT UP YOUR EYES” Being the Abilene Christian College Annual Bible Lectures 1965 Price: $3.95 Published by ABILENE CHRISTIAN COLLEGE STUDENTS EXCHANGE ACC Station Abilene. Texa

What is memory? The present state of the engram

The mechanism of memory remains one of the great unsolved problems of biology. Grappling with the question more than a hundred years ago, the German zoologist Richard Semon formulated the concept of the engram, lasting connections in the brain that result from simultaneous "excitations", whose precise physical nature and consequences were out of reach of the biology of his day. Neuroscientists now have the knowledge and tools to tackle this question, however, and this Forum brings together leading contemporary views on the mechanisms of memory and what the engram means today

A solar feed for NEID

NEID is a radial velocity (RV) instrument including an ultra-stabilized fiber-fed spectrograph, installed in 2019 at the 3.5m WIYN telescope at Kitt Peak National Observatory. Accompanying it is a solar feed system built to supply the spectrograph with disk-integrated sunlight. Observing the Sun “as a star” is essential for developing and validating mitigation strategies for RV variations due to stellar activity and instrument systematics, thus enabling more-effective detections of lower-mass exoplanets. In this paper, we will detail the design of the NEID solar feed system and showcase early results addressing NEID systematics and solar RV variability