How good are comparative models in the understanding of protein dynamics?

The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three-dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long-range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active-site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state-specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.     

Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages

Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations.     

Effects of nicotinamide on NAD and poly (ADP-ribose) metabolism in DNA-damaged human lymphocytes

The effect of nicotinamide on unscheduled DNA synthesis was studied in resting human lymphocytes. In cells treated with UV irradiation or with MNNG, nicotinamide caused a two-fold stimulation of unscheduled DNA synthesis and retarded the rate of NAD⁺ lowering caused by these treatments. Nicotinamide also reduced the burst of poly(ADP-ribose) synthesis caused by MNNG treat-ment. Thus under conditions that it enhances unscheduled DNA synthesis, nicotinamide causes marked effects on the metabolism of NAD⁺ and poly(ADP-ribose). The effect of nicotinamide on unscheduled DNA synthesis was shown to be independent of protein or polyamine synthesis.     

Comparison between paper and electronic sleep diary

This study aimed to test the concurrent validity of an electronic version (to run on tablet) of a sleep diary derived from the core Consensus Sleep Diary compared with the traditional paper and pencil version. To this end, 15 healthy volunteers (6 males; mean age 37.20 ± 17.55 years) every morning, for at least 7 consecutive days, filled both paper and electronic sleep diary. Furthermore, sleep was objectively assessed through actigraphy. With reference to all sleep parameters examined, no significant differences were observed between paper and electronic sleep diary. As expected, paper and electronic sleep diary showed the same poor agreement with actigraphic estimates of sleep quantity and sleep quality. On the basis of the present data, we can conclude that electronic sleep diary performs like paper sleep diary. Bearing in mind that electronic sleep diary presents several benefits in comparison to the paper sleep diary (e.g. avoiding of the “parking lot syndrome”, in which patient retrospectively completes more days at the same time; reducing the time for data entry and scoring), we suggest that, if the present findings will be confirmed also in clinical populations, electronic sleep diary should replace paper sleep diary in both research and clinical settings.     

Basing the Analysis of Comparative Bioavailability Trials on an Individualized Statistical Definition of Equivalence

The conventional definition of bioequivalence in terms of population means only, is criticized for lacking relevance to the individual subject. Both approaches to bioequivalence assessment proposed here for avoiding this shortcoming, focus on the probability of an event induced by the response of a randomly selected subject to two formulations of a given active agent. The first approach leads to converting the basic idea underlying the well-known 75-rule into an exact statistical procedure. The second approach is of a parametric nature. It reduces bioequivalence assessment to testing against the alternative hypothesis that the standardized expected value of a Gaussian distribution is contained in a short interval around zero. For this problem, an exact optimal solution is provided as well.     

Utility of liquid-based cytology in endometrial pathology: diagnosis of endometrial carcinoma

Objective: The purpose of this study was to examine the utility of SurePath‐liquid‐based cytology (LBC) compared to conventional cytological preparations (CCP) in the identification of endometrial carcinoma. Methods: During a 13‐month period, direct endometrial samples were collected from 120 patients using the Uterobrush. The material comprised 30 cases each of endometrial carcinoma, proliferative endometrium, secretory endometrium and atrophic endometrium. The following points were investigated:(i) the frequency of cell clumps in endometrial carcinoma; (ii) the area of cell nuclei; (iii) overlapping nuclei. Results: (i) Comparison of the frequency of cell clumps with irregular protrusion pattern and papillo‐tubular pattern showed no statistically significant difference in either type of cell clump between CCP and LBC. (ii) Comparison of the nuclear area of cells showed a sequential decrease from endometrial carcinoma to secretory endometrium, to proliferative endometrium and to atrophic endometrium, which was significant in CCP and LBC. (iii) Nuclear area was significantly lower with LBC compared with CCP in endometrial carcinoma, secretory endometrium and proliferative endometrium but not atrophic endometrium. (iv) Comparison of the degree of overlapping nuclei showed a sequential decrease from endometrial carcinoma to proliferative endometrium, to secretory endometrium and to atrophic endometrium, which was significant in both CCP and LBC. (v) Comparison of the degree of overlapping nuclei between CCP and LBC showed no significant difference for normal types of endometrium, but LBC had significantly higher values (P < 0.0001) in endometrial carcinoma than in CCP. Conclusions: The results of this study revealed that applying diagnostic criteria used in CCP to LBC was easy to achieve, because LBC had excellent cytoarchitectural preservation and cells were well presented. Although we have not examined all cytological features of malignancy and have not considered atypical hyperplasia, we believe that this method may be a useful tool in the diagnosis of endometrial cytology.     

In-depth Profiling and Quantification of the Lysine Acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide with limited therapeutic options. Comprehensive investigation of protein posttranslational modifications in HCC is still limited. Lysine acetylation is one of the most common types of posttranslational modification involved in many cellular processes and plays crucial roles in the regulation of cancer. In this study, we analyzed the proteome and K-acetylome in eight pairs of HCC tumors and normal adjacent tissues using a timsTOF Pro instrument. As a result, we identified 9219 K-acetylation sites in 2625 proteins, of which 1003 sites exhibited differential acetylation levels between tumors and normal adjacent tissues. Interestingly, many novel tumor-specific K-acetylation sites were characterized, for example, filamin A (K865), filamin B (K697), and cofilin (K19), suggesting altered activities of these cytoskeleton-modulating molecules, which may contribute to tumor metastasis. In addition, we observed an overall suppression of protein K-acetylation in HCC tumors, especially for enzymes from various metabolic pathways, for example, glycolysis, tricarboxylic acid cycle, and fatty acid metabolism. Moreover, the expression of deacetylase sirtuin 2 (SIRT2) was upregulated in HCC tumors, and its role of deacetylation in HCC cells was further explored by examining the impact of SIRT2 overexpression on the proteome and K-acetylome in Huh7 HCC cells. SIRT2 overexpression reduced K-acetylation of proteins involved in a wide range of cellular processes, including energy metabolism. Furthermore, cellular assays showed that overexpression of SIRT2 in HCC cells inhibited both glycolysis and oxidative phosphorylation. Taken together, our findings provide valuable information to better understand the roles of K-acetylation in HCC and to treat this disease by correcting the aberrant acetylation patterns.     

重庆市生态风险预警等级划分及演化趋势模拟

生态风险预警等级评估和演化趋势模拟，可为生态风险管理提供可靠的辅助决策。以重庆市为研究对象，基于驱动力-压力-状态-影响-响应模型，构建重庆市生态风险预警指标体系，采用正态云模型和集对分析法，定量分析重庆市生态风险时空分异特征和演化趋势。研究结果表明：（1）2013-2019年，重庆市生态风险值呈"上升-下降"的波动趋势，综合生态风险隶属于重警等级，生态风险综合值从0.295下降到0.278，生态环境逐年好转；（2）重庆市生态风险有下降、不变、先上升后降低、先降低后上升以及一直升高5种演化趋势，分别占比39%、16%、5%、21%、24%；（3）重庆市生态风险转移分为两个方向，2013-2016年生态风险空间分异性增大，中警、轻警和无警风险等级不断向东北、东南和西部四周分散转移；2016-2019年生态风险分布格局变化较小，重警风险区在东部聚集；（4）演化趋势模拟结果表明，未来重庆市生态风险降低的区县有13个，占比34%，生态环境有向好发展的趋势；生态风险上升的区县有25个，占比66%，生态环境会有所恶化，但是恶化程度较低。将生态风险等级划分与预警演化趋势相结合，能为城市生态风险管理提供科学依据。