Folding domain B of protein A on a dynamically partitioned free energy landscape

The B domain of staphylococcal protein A (BdpA) is a small helical protein that has been studied intensively in kinetics experiments and detailed computer simulations that include explicit water. The simulations indicate that BdpA needs to reorganize in crossing the transition barrier to facilitate folding its C-terminal helix (H3) onto the nucleus formed from helices H1 and H2. This process suggests frustration between two partially ordered forms of the protein, but recent φ value measurements indicate that the transition structure is relatively constant over a broad range of temperatures. Here we develop a simplistic model to investigate the folding transition in which properties of the free energy landscape can be quantitatively compared with experimental data. The model is a continuation of the Muñoz–Eaton model to include the intermittency of contacts between structured parts of the protein, and the results compare variations in the landscape with denaturant and temperature to φ value measurements and chevron plots of the kinetic rates. The topography of the model landscape (in particular, the feature of frustration) is consistent with detailed simulations even though variations in the φ values are close to measured values. The transition barrier is smaller than indicated by the chevron data, but it agrees in order of magnitude with a similar α-carbon type of model. Discrepancies with the chevron plots are investigated from the point of view of solvent effects, and an approach is suggested to account for solvent participation in the model.     

An experimentally determined protein folding energy landscape

Energy landscapes have been used to conceptually describe and model protein folding but have been difficult to measure experimentally, in large part because of the myriad of partly folded protein conformations that cannot be isolated and thermodynamically characterized. Here we experimentally determine a detailed energy landscape for protein folding. We generated a series of overlapping constructs containing subsets of the seven ankyrin repeats of the Drosophila Notch receptor, a protein domain whose linear arrangement of modular structural units can be fragmented without disrupting structure. To a good approximation, stabilities of each construct can be described as a sum of energy terms associated with each repeat. The magnitude of each energy term indicates that each repeat is intrinsically unstable but is strongly stabilized by interactions with its nearest neighbors. These linear energy terms define an equilibrium free energy landscape, which shows an early free energy barrier and suggests preferred low-energy routes for folding.     

Kinetics are probe-dependent during downhill folding of an engineered lambda6-85 protein

The Y22W/Q33Y/G46,48A mutant of the protein lambda6-85 folds in a few microseconds at room temperature. We find that its folding kinetics are probe-dependent under a strong bias toward the native state, a new signature for downhill folding. The IR- and fluorescence-detected relaxation time scales converge when the native bias is removed by raising the temperature, recovering activated two-state folding. Langevin dynamics simulations on one- and 2D free energy surfaces tunable from two-state to downhill folding reproduce the difference between the IR and fluorescence experiments, as well as the temperature and viscosity trends. In addition, the 2D surface reproduces the stretched exponential dynamics that we fit to the glucose solution experimental data at short times. Nonexponential dynamics at <10 micros is a signature either for local free energy minima along the reaction coordinate ("longitudinal roughness"), or for folding on a higher-dimensional free energy surface ("transverse roughness").     

CovDif,a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants

The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification and diagnosis, therapeutics development and epidemiological surveillance to detect the emergence of new viral variants. An intense surveillance of virus variants has led to the identification of Variants of Interest and Variants of Concern. Although these classifications dynamically change as the pandemic evolves, they have been useful to guide public health efforts on containment and mitigation. In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes. CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups. CovDif is able to identify loss in conservation due to point mutations, deletions, inversions and chromosomal rearrangements. In this work, we applied CovDif to SARS-CoV-2 clades (G, GH, GR, GV, L, O, S and G) and variants. We identified all regions for any defining SNPs. We also applied CovDif to a group of population genomes and evaluated the conservation of primer regions for current SARS-CoV-2 detection and diagnostic protocols. We found that some of these protocols should be applied with caution as few of the primer-template regions are no longer conserved in some SARS-CoV-2 variants. We conclude that CovDif is a tool that could be widely applied to study the conservation of any group of viral genomes as long as whole genomes exist.     

The prognostic effect of PNN in digestive tract cancers and its correlation with the tumor immune landscape in colon adenocarcinoma

BackgroundThe present study investigated the expression, mutation, and methylation profile of PNN and its prognostic value in digestive tract cancers. The disparities in signaling pathways and the immune landscape in colon adenocarcinoma (COAD) based on PNN expression were specifically explored.MethodsThe expression, mutation, methylation levels of PNN, and survival data in esophageal cancer, gastric adenocarcinoma, COAD, and rectal adenocarcinoma were evaluated using several bioinformatic databases. Gene Ontology (GO) enrichment analysis and gene set enrichment analysis (GSEA) were performed to investigate the enriched biological functions and pathways in COAD. Several acknowledged bioinformatic algorithms were employed to assess the correlation between PNN expression and the tumor immune landscape in COAD.ResultsPNN was upregulated and remarkably related to tumor stage in digestive tract cancers. High expression of PNN was positively associated with poor progression‐free survival and overall survival time, specifically in COAD. PNN expression was identified as an independent prognostic factor in COAD. GO and GSEA analyses revealed that PNN participates in multiple biological processes underlying carcinogenicity in COAD. Further investigation showed that PNN expression was significantly associated with tumor‐infiltrating immune cells, immune cell functions, and several immune checkpoints in COAD. The PNN low expression group had a lower tumor immune dysfunction and exclusion (TIDE) score and a higher immunophenoscore (IPS), indicating a better response to immunotherapy.ConclusionPNN was highly expressed in digestive tract cancers and could act as an independent prognostic factor and a response predictor for immunotherapy in COAD.     

Uterine artery embolization should not be recommended without careful consideration in the treatment of symptomatic uterine fibroids

AIM: To evaluate convalescence and the incidence of adverse symptoms associated with uterine artery embolization (UAE) in the treatment of uterine fibroids, several parameters after UAE were compared with those after laparoscopic surgery. METHODS: For the treatment of uterine fibroids, 78 patients underwent UAE and 58 received laparoscopic surgery (31 were laparoscopic myomectomy [LM] and 27 were laparoscopy-assisted myomectomy [LAM]) during the period July 2001 to July 2004. The length of hospitalization, and the periods until the beginning of a normal daily life, work and exercise, long-term follow up data in the UAE and laparoscopy groups were compared, and the incidence of adverse symptoms after each procedure was compared. RESULTS: The length of hospitalization for the UAE group 2.1 +/- 0.1 (mean +/- S.E) was significantly shorter than those for the LM and LAM groups (2.6 +/- 0.1 and 3.8 +/- 0.2 days, respectively; P < 0.0001 and P < 0.0001). The period until beginning of normal daily life and work were similar between the UAE and LM groups. The degree of improved symptoms after each procedure were similar among the three groups, but the incidence of adverse symptoms after UAE was significantly higher than after laparoscopic surgery. CONCLUSIONS: The UAE group showed a significantly shorter period of hospitalization, but the convalescence of the UAE group was similar to the LA group, with a higher incidence of adverse symptoms than laparoscopic surgeries. Therefore, UAE should not be recommended without careful consideration, in the treatment of symptomatic uterine fibroids.     

创园林环卫品牌建长效管理机制

青岛市城阳区园林环卫处通过创立园林环卫品牌,摸索和建立了一套园林环卫长效管理机制.介绍了该管理机制和实施措施.     

医院建筑户外疗愈景观设计策略研究

针对医院建筑户外景观的发展现状,阐述了疗愈概念在医院户外景观设计中的必要性以及医院疗愈景观的设计原则,并总结了当前我国医院户外景观环境中存在的一些问题,提出针对性的疗愈景观优化设计策略,为未来的医院景观环境建设提供一定的参考.     

Convalescence after colonic surgery with fast-track vs conventional care

OBJECTIVE: To compare convalescence after colonic surgery with a fast-track rehabilitation programme vs conventional care. BACKGROUND: Introduction of a multimodal rehabilitation programme (fast-track) with focus on epidural anaesthesia, minimal invasive surgical techniques, optimal pain control, and early nutrition and mobilization together with detailed patient information have led to a shorter hospital stay after colonic surgery. There are not much data on convalescence after discharge. METHODS: A prospective, controlled, non-randomized interview-based assessment in 160 patients undergoing an elective, uncomplicated, open colonic resection or the Hartmann reversal procedure with a fast-track or a conventional care programme in two university hospitals. A structured interview-based assessment was performed preoperatively, and day 14 and 30 postoperatively. RESULTS: Patients undergoing colonic surgery with a fast-track programme regained functional capabilities earlier with less fatigue and need for sleep compared with patients having conventional care. Despite early discharge of the fast-track patients (mean 3.4 days vs 7.5 days), no differences were found according to the need for home care, social care and visit to general practitioners, although the fast-track group had an increased number of visits at the outpatient clinic for wound care. More patients in the fast-track group were re-admitted, but the overall mean total hospital stay was 4.2 days vs 8.3 days in the conventional group. CONCLUSION: A fast-track rehabillitation programme led to a shorter hospital stay, less fatigue and earlier resumption of normal activities, without the increased need for support after discharge compared with conventionally treated patients after uncomplicated colonic resection.     

脑梗死老年患者康复治疗前后的脑血流动力学

目的　观察脑梗死老年患者康复治疗期的脑血流动力学变化。　方法　应用经颅多普勒超声仪检测30例脑梗死康复期老年患者治疗前后以及 2 0例老年健康对照组的双侧大脑中动脉 (MCA)血流参数 :收缩期血流速度 (Vs)、舒张期血流速度 (Vd)、平均流速 (Vm)、阻力指数 (RI)、搏动指数 (PI)。　结果　 (1)与对照组比较 ,脑梗死组 MCA流速 Vs、Vd、Vm显著降低 ,RI、PI显著增高 (P<0 .0 1) ;(2 )体疗组经海水浴体疗运动 4疗程后 MCA流速 Vs、Vd、Vm明显增高 (P<0 .0 1) ,RI、PI显著降低 (P<0 .0 1) ,而休养组患者则改变不明显 (P>0 .0 5 )。　结论　脑梗死老年患者恢复期脑循环及血管贮备功能尚差 ,海水浴体疗运动一定疗程后可改善患者心脑血氧供应和脑血流动力学状况。