Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?

<p>Abstract</p> <p>Background</p> <p>A wealth of unannotated and functionally unknown protein sequences has accumulated in recent years with rapid progresses in sequence genomics, giving rise to ever increasing demands for developing methods to efficiently assess functional sites. Sequence and structure conservations have traditionally been the major criteria adopted in various algorithms to identify functional sites. Here, we focus on the distributions of the 20³different types of <it>3</it>-grams (or triplets of sequentially contiguous amino acid) in the entire space of sequences accumulated to date in the UniProt database, and focus in particular on the rare <it>3</it>-grams distinguished by their high entropy-based information content.</p> <p>Results</p> <p>Comparison of the UniProt distributions with those observed near/at the active sites on a non-redundant dataset of 59 enzyme/ligand complexes shows that the active sites preferentially recruit <it>3</it>-grams distinguished by their low frequency in the UniProt. Three cases, Src kinase, hemoglobin, and tyrosyl-tRNA synthetase, are discussed in details to illustrate the biological significance of the results.</p> <p>Conclusion</p> <p>The results suggest that recruitment of rare <it>3</it>-grams may be an efficient mechanism for increasing specificity at functional sites. Rareness/scarcity emerges as a feature that may assist in identifying key sites for proteins function, providing information complementary to that derived from sequence alignments. In addition it provides us (for the first time) with a means of identifying potentially functional sites from sequence information alone, when sequence conservation properties are not available.</p

Dietary Lactoferrin Alleviates Age-Related Lacrimal Gland Dysfunction in Mice

BACKGROUND: Decrease in lacrimal gland secretory function is related to age-induced dry eye disease. Lactoferrin, the main glycoprotein component of tears, has multiple functions, including anti-inflammatory effects and the promotion of cell growth. We investigated how oral administration of lactoferrin affects age-related lacrimal dysfunction. METHODS AND FINDINGS: Twelve-month-old male C57BL/6Cr Slc mice were randomly divided into a control fed group and an oral lactoferrin treatment group. Tear function was measured at a 6-month time-point. After euthanasia, the lacrimal glands were subjected to histological examination with 8-hydroxy-2'-deoxyguanosine (8-OHdG) antibodies, and serum concentrations of 8-OHdG and hexanoyl-lysine adduct (HEL) were evaluated. Additionally, monocyte chemotactic protein-1(MCP-1) and tumor necrosis factor-α (TNF-α) gene expression levels were determined by real-time PCR. The volume of tear secretion was significantly larger in the treated group than in the control. Lactoferrin administration reduced inflammatory cell infiltration and the MCP-1 and TNF-α expression levels. Serum concentrations of 8-OHdG and HEL in the lactoferrin group were lower than those in the control group and were associated with attenuated 8-OHdG immunostaining of the lacrimal glands. CONCLUSION: Oral lactoferrin administration preserves lacrimal gland function in aged mice by attenuating oxidative damage and suppressing subsequent gland inflammation

Public Claims about Automatic External Defibrillators: An Online Consumer Opinions Study

Patients are no longer passive recipients of health care, and increasingly engage in health communications outside of the traditional patient and health care professional relationship. As a result, patient opinions and health related judgements are now being informed by a wide range of social, media, and online information sources. Government initiatives recognise self-delivery of health care as a valuable means of responding to the anticipated increased global demand for health resources. Automated External Defibrillators (AEDs), designed for the treatment of Sudden Cardiac Arrest (SCA), have recently become available for 'over the counter' purchase with no need for a prescription. This paper explores the claims and argumentation of lay persons and health care practitioners and professionals relating to these, and how these may impact on the acceptance, adoption and use of these devices within the home context. METHODS: We carry out a thematic content analysis of a novel form of Internet-based data: online consumer opinions of AED devices posted on Amazon.com, the world's largest online retailer. A total of 83 online consumer reviews of home AEDs are analysed. The analysis is both inductive, identifying themes that emerged from the data, exploring the parameters of public debate relating to these devices, and also driven by theory, centring around the parameters that may impact upon the acceptance, adoption and use of these devices within the home as indicated by the Technology Acceptance Model (TAM). RESULTS: Five high-level themes around which arguments for and against the adoption of home AEDs are identified and considered in the context of TAM. These include opinions relating to device usability, usefulness, cost, emotional implications of device ownership, and individual patient risk status. Emotional implications associated with AED acceptance, adoption and use emerged as a notable factor that is not currently reflected within the existing TAM. CONCLUSIONS: The value and credibility of the findings of this study are considered within the context of existing AED research, and related to technology acceptance theory, and current methods and practice. From a methodological perspective, this study demonstrates the potential value of online consumer reviews as a novel data source for exploring the parameters of public debate relating to emerging health care technologies

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Effect of Synthetic Emulsifier and Natural Biosurfactant on Feed Process and Quality of Pelletized Feed in Broiler Diet

A feed production trial was conducted to study the effect of synthetic emulsifier and natural biosurfactant the process and quality of pelletized broiler feed. A corn-soy based broiler diet was formulated with fixed ratio 2:1 of oil-to-water with two types of emulsifiers, namely glyceryl polyethylene glycol ricinoleate synthetic emulsifier and lysophosphatidylcholine natural biosurfactant. T1: Basal diet with no water and no emulsifier; T2: Basal diet with water and no emulsifier; T3: Basal diet with water and synthetic emulsifier glyceryl polyethylene glycol ricinoleate; T4: Basal diet with water and a natural biosurfactant lysophosphatidylcholine as comparative treatment. The treatment diets were manufactured by a commercial feed mill. The electricity cost and meal temperature were measured during the process of milling. Composite samples were collected from different processed points, tested for physical properties, chemical stability and biostability of pelletized feed. Pellet quality of emulsifier supplemented diets was significantly (p<0.05) improved in crumble and pellet intact form. Correlation between emulsifier and pelletize processed cost was not observed in this present study. No deteriorate effect was observed in hydrolytic rancidity (AV), oxidation rancidity (PV), mold count, moisture content and water activity. However, percentage of starch gelatinization on pelletized feed was significantly (p< 0.0001) improved in both types of emulsifier treated diets. These results demonstrated that the addition of emulsifier to broiler diet improved pellet quality to some extent although significant difference between synthetic emulsifier and natural biosurfactant was not observed