Structural insights into the calcium-dependent interaction between calbindin-D28K and caspase-3

AbstractThe regulation of apoptosis involves a complicated cascade requiring numerous protein interactions including the pro-apoptotic executioner protein caspase-3 and the anti-apoptotic calcium-binding protein calbindin-D28K. Using isothermal titration calorimetry, we show that calbindin-D28K binds caspase-3 in a Ca2+-dependent fashion. Molecular docking and conformational sampling studies of the Ca2+-loaded capase-3/calbindin-D28K interaction were performed in order to isolate potentially crucial intermolecular contacts. Residues in the active site loops of caspase-3 and EF-hands 1 and 2 of calbindin-D28K were shown to be critical to the interaction. Based on these studies, a model is proposed to help understand how calbindin-D28K may deactivate caspase-3 upon binding.Structured summary of protein interactionsCalbindin-D28K and Caspase-3 bind by isothermal titration calorimetry (View interaction

Using the Consolidated Framework for Implementation Research to Evaluate Clinical Trials: An Example from Multisite Nursing Research

Background The Consolidated Framework for Implementation Research (CFIR) is a comprehensive guide for determining the factors that affect successful implementation of complex interventions embedded in real-time clinical practice. Purpose The study aim was to understand implementation constructs in a multi-site translational research study on readiness for hospital discharge that distinguished study sites with low versus high implementation fidelity. Methods In this descriptive study, site Principal Investigator interviews (from 8 highest and 8 lowest fidelity sites) were framed with questions from 20 relevant CFIR constructs. Analysis used CFIR rules and rating scale (+2 to −2 per site) and memos created in NVivo 11. Findings From a bimodal distribution of differences (1.5 and 5), 7 constructs distinguished high and low fidelity sites with ≥5-point difference. Discussion CFIR provided a determinant framework for identifying elements of a study site\u27s context that impact implementation fidelity and clinical research outcomes

Clinical Nurses\u27 Perspectives on Discharge Practice Changes from Participating in a Translational Research Study

Aim To describe clinical nurses\u27 experiences with practice change associated with participation in a multi‐site nursing translational research study implementing new protocols for hospital discharge readiness assessment. Background Nurses\u27 participation in translational research studies provides an opportunity to evaluate how implementation of new nursing interventions affects care processes within a local context. These insights can provide information that leads to successful adoption and sustainability of the intervention. Methods Semi‐structured focus groups from 30 of 33 participating study hospitals lead by team nurse researchers. Results Nurses reported improved and earlier awareness of patients\u27 discharge needs, changes in discharge practices, greater patient/family involvement in discharge, synergy and enhanced discharge processes, and implementation challenges. Participating nurses related the benefits of participation in nursing research. Conclusion Participation in a unit‐level translational research project was a successful strategy for engaging nurses in practice change to improve hospital discharge. Implications for Nursing Management Leading unit‐based implementation of a structured discharge readiness assessment including nurse assessment and patient self‐assessment encourages earlier awareness of patients\u27 discharge needs, improved patient assessment and greater patient/family involvement in discharge preparation. Integrating discharge readiness assessments into existing discharge care promotes communication between health team members that facilitates a timely, coordinated discharge

Effectiveness of Home Health Care in Reducing Return to Hospital: Evidence from a Multi-hospital Study in the US

Background Home health care, a commonly used bridge strategy for transitioning from hospital to home-based care, is expected to contribute to readmission avoidance efforts. However, in studies using disease-specific samples, evidence about the effectiveness of home health care in reducing readmissions is mixed. Objective To examine the effectiveness of home health care in reducing return to hospital across a diverse sample of patients discharged home following acute care hospitalization. Research design Secondary analysis of a multi-site dataset from a study of discharge readiness assessment and post-discharge return to hospital, comparing matched samples of patients referred and not referred for home health care at the time of hospital discharge. Setting Acute care, Magnet-designated hospitals in the United States Participants The available sample (n = 18,555) included hospitalized patients discharged from medical-surgical units who were referred (n = 3,579) and not referred (n = 14,976) to home health care. The matched sample included 2767 pairs of home health care and non- home health care patients matched on patient and hospitalization characteristics using exact and Mahalanobis distance matching. Methods Unadjusted t-tests and adjusted multinomial logit regression analyses to compare the occurrence of readmissions and Emergency Department/Observation visits within 30 and 60-days post-discharge. Results No statistically significant differences in readmissions or Emergency Department /Observation visits between home health care and non-home health care patients were observed. Conclusions Home health care referral was not associated with lower rates of return to hospital within 30 and 60 days in this US sample matched on patient and clinical condition characteristics. This result raises the question of why home health care services did not produce evidence of lower post-discharge return to hospital rates. Focused attention by home health care programs on strategies to reduce readmissions is needed

Effect of Implementing Discharge Readiness Assessment in Adult Medical-Surgical Units on 30-Day Return to Hospital The READI Randomized Clinical Trial

Importance: The downward trend in readmissions has recently slowed. New enhancements to hospital readmission reduction efforts are needed. Structured assessment of patient readiness for discharge has been recommended as an addition to discharge preparation standards of care to assist with tailoring of risk-mitigating actions. Objective: To determine the effect of unit-based implementation of readiness evaluation and discharge intervention protocols on readmissions and emergency department or observation visits. Design, Setting, and Participants: The Readiness Evaluation and Discharge Interventions (READI) cluster randomized clinical trial conducted in medical-surgical units of 33 Magnet hospitals between September 15, 2014, and March 31, 2017, included all adult (aged ≥18 years) patients discharged to home. Baseline and risk-adjusted intent-to-treat analyses used difference-in-differences multilevel logistic regression models with controls for patient characteristics. Interventions: Of 2 adult medical-surgical nursing units from each hospital, 1 was randomized to the intervention and 1 to usual care conditions. Using the 8-item Readiness for Hospital Discharge Scale, the 33 intervention units implemented a sequence of protocols with increasing numbers of components: READI1, in which nurses assessed patients to inform discharge preparation; READI2, which added patient self-assessment; and READI3, which added an instruction to act on a specified Readiness for Hospital Discharge Scale cutoff score indicative of low readiness. Main Outcomes and Measures: Thirty-day return to hospital (readmission or emergency department and observation visits). Intervention units above median baseline readmission rate (\u3e11.3%) were categorized as high-readmission units. Among the 33 intervention units, 17 were low-readmission units and 16 were high-readmission units. Results: The sample included 144 868 patient discharges (mean [SD] age, 59.6 [17.5] years; 51% female; 74 605 in the intervention group and 70 263 in the control group); 17 667 (12.2%) were readmitted and 12 732 (8.8%) had an emergency department visit or observation stay. None of the READI protocols reduced the primary outcome of return to hospital in intent-to-treat analysis of the full sample. In exploratory subgroup analysis, when patient self-assessments were combined with readiness assessment by nurses (READI2), readmissions were reduced by 1.79 percentage points (95% CI, −3.20 to −0.40 percentage points; P = .009) on high-readmission units. With nurse assessment alone and on low-readmission units, results were mixed. Conclusions and Relevance: Implemented in a broad range of hospitals and patients, the READI interventions were not effective in reducing return to hospital. However, adding a structured discharge readiness assessment that incorporates the patient’s own perspective to usual discharge care practices holds promise for mitigating high rates of return to the hospital following discharge

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion.

Interference competition among bacteria requires a highly specialized, narrow-spectrum weaponry when targeting closely-related competitors while sparing individuals from the same clonal population. Here we investigated mechanisms by which environmentally important Pseudomonas bacteria with plant-beneficial activity perform kin interference competition. We show that killing between phylogenetically closely-related strains involves contractile phage tail-like devices called R-tailocins that puncture target cell membranes. Using live-cell imaging, we evidence that R-tailocins are produced at the cell center, transported to the cell poles and ejected by explosive cell lysis. This enables their dispersal over several tens of micrometers to reach targeted cells. We visualize R-tailocin-mediated competition dynamics between closely-related Pseudomonas strains at the single-cell level, both in non-induced condition and upon artificial induction. We document the fatal impact of cellular self-sacrifice coupled to deployment of phage tail-like weaponry in the microenvironment of kin bacterial competitors, emphasizing the necessity for microscale assessment of microbial competitions

Transcript analysis of the extended hyp-operon in the cyanobacteria Nostoc sp. strain PCC 7120 and Nostoc punctiforme ATCC 29133

<p>Abstract</p> <p>Background</p> <p>Cyanobacteria harbor two [NiFe]-type hydrogenases consisting of a large and a small subunit, the Hup- and Hox-hydrogenase, respectively. Insertion of ligands and correct folding of nickel-iron hydrogenases require assistance of accessory maturation proteins (encoded by the <it>hyp</it>-genes). The intergenic region between the structural genes encoding the uptake hydrogenase (<it>hupSL</it>) and the accessory maturation proteins (<it>hyp </it>genes) in the cyanobacteria <it>Nostoc </it>PCC 7120 and <it>N. punctiforme </it>were analysed using molecular methods.</p> <p>Findings</p> <p>The five ORFs, located in between the uptake hydrogenase structural genes and the <it>hyp</it>-genes, can form a transcript with the <it>hyp</it>-genes. An identical genomic localization of these ORFs are found in other filamentous, N₂-fixing cyanobacterial strains. In <it>N. punctiforme </it>and <it>Nostoc </it>PCC 7120 the ORFs upstream of the <it>hyp</it>-genes showed similar transcript level profiles as <it>hupS </it>(hydrogenase structural gene), <it>nifD </it>(nitrogenase structural gene), <it>hypC </it>and <it>hypF </it>(accessory hydrogenase maturation genes) after nitrogen depletion. <it>In silico </it>analyzes showed that these ORFs in <it>N. punctiform</it>e harbor the same conserved regions as their homologues in <it>Nostoc </it>PCC 7120 and that they, like their homologues in <it>Nostoc </it>PCC 7120, can be transcribed together with the <it>hyp</it>-genes forming a larger extended <it>hyp-</it>operon. DNA binding studies showed interactions of the transcriptional regulators CalA and CalB to the promoter regions of the extended <it>hyp</it>-operon in <it>N. punctiforme </it>and <it>Nostoc </it>PCC 7120.</p> <p>Conclusions</p> <p>The five ORFs upstream of the <it>hyp</it>-genes in several filamentous N₂-fixing cyanobacteria have an identical genomic localization, in between the genes encoding the uptake hydrogenase and the maturation protein genes. In <it>N. punctiforme </it>and <it>Nostoc </it>PCC 7120 they are transcribed as one operon and may form transcripts together with the <it>hyp</it>-genes. The expression pattern of the five ORFs within the extended <it>hyp</it>-operon in both <it>Nostoc punctiforme </it>and <it>Nostoc </it>PCC 7120 is similar to the expression patterns of <it>hupS</it>, <it>nifD</it>, <it>hypF </it>and <it>hypC</it>. CalA, a known transcription factor, interacts with the promoter region between <it>hupSL </it>and the five ORFs in the extended <it>hyp</it>-operon in both <it>Nostoc </it>strains.</p

Genomic analysis of Acinetobacter baumannii prophages reveals remarkable diversity and suggests significant impact on bacterial virulence and fitness

[Abstract] Bacterial genomics has revealed substantial amounts of prophage DNA in bacterial genomes. This integrated viral DNA has been shown to play important roles in the evolution of bacterial pathogenicity. Acinetobacter baumannii has shown a fast progression as a nosocomial multi-resistant pathogen in recent years, and is now considered one of the most dangerous microorganisms in hospital environments. The role of prophages in the evolution of A. baumannii pathogenicity has not yet been explored. In this context, we aimed at evaluating the impact of prophages on A. baumannii genomic diversity and pathogenicity. [...]info:eu-repo/semantics/publishedVersio