Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure

Summary A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived from complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect (NOE) spectral peak intensities. As in the case of restrained molecular dynamics (rMD) refinement of structures, the experimental distance restraints and bounds are incorporated as a pseudo-energy term (or penalty function) into the mathematical expression for the molecular energy. However, the use of generalized helical parameters, rather than Cartesian coordinates, to define DNA conformation increases efficiency by decreasing by an order of magnitude the number of parameters needed to describe a conformation and by simplifying the potential energy profile. The Metropolis Monte Carlo method is employed to simulate an annealing process. The rMC method was applied to experimental 2D NOE data from the octamer duplex d(GTA-TAATG)·d(CATTATAC). Using starting structures from different locations in conformational space (e.g. A-DNA and B-DNA), the rMC calculations readily converged, with a root-mean-square deviation (RMSD) of <0.3 Å between structures generated using different protocols and starting structures. Theoretical 2D NOE peak intensities were calculated for the rMC-generated structures using the complete relaxation matrix program CORMA, enabling a comparison with experimental intensities via residual indices. Simulation of the vicinal proton coupling constants was carried out for the structures generated, enabling a comparison with the experimental deoxyribose ring coupling constants, which were not utilized in the structure determination in the case of the rMC simulations. Agreement with experimental 2D NOE and scalar coupling data was good in all cases. The rMC structures are quite similar to that refined by a traditional restrained MD approach (RMSD<0.5 Å) despite the different force fields used and despite the fact that MD refinement was conducted with additional restraints imposed on the endocyclic torsion angles of deoxyriboses. The computational time required for the rMC and rMD calculations is about the same. A comparison of structural parameters is made and some limitations of both methods are discussed with regard to the average nature of the experimental restraints used in the refinement.Abbreviations MC Monte Carlo - rMC restrained Monte Carlo - MD molecular dynamics - rMD restrained molecular dynamics - DG distance geometry - EM energy minimization - 2D NOE two-dimensional nuclear Overhauser effect - DQF-COSY double-quantum-filtered correlation spectroscopy - RMSD root-mean-square deviation To whom correspondence should be addressed.     

Regulated spatial expression of fusion gene constructs with the 5′ upstream region of Halocynthia roretzi muscle actin gene in Ciona savignyi embryos

pHrMA4a-Z is a recombinant plasmid in which about 1.4 kb of the 5 flanking region of a gene for muscle actin HrMA4a from the ascidian Halocynthia roretzi is fused with the coding sequence of a bacterial gene for -galactosidase (lac-Z). In this study, we examined the expression of the fusion gene construct when it was introduced into eggs of another ascidian, namely Ciona savignyi. When a moderate amount of linearized pHrMA4a-Z was introduced into fertilized Ciona eggs, the expression of the reporter gene was evident in muscle cells of the larvae, suggesting that both species share a common machinery for the expression of muscle actin genes. The 5 upstream region of HrMA4a contains several consensus sequences, including a TATA box at -30, a CArG box at -116 and four E-boxes within a region of 200 bp. A deletion construct, in which only the 216-bp 5 flanking region of HrMA4a was fused with lac-Z, was expressed primarily in larval muscle cells. However, another deletion construct consisting of only the 61-bp upstream region of HrMA4a fused with lac-Z was not expressed at all. When pHrMA4a-Z or pHrMA4a-Z (–216) was injected into each of the muscle-precursor blastomeres of the 8-cell embryo, expression of the reporter gene was observed in larval muscle cells in a lineage-specific fashion. However, expression of the reporter gene was not observed when the plasmid was injected into non-muscle lineage. Therefore, the expression of the reporter gene may depend on some difference in cytoplasmic constituents between blastomeres of muscle and non-muscle lineage in the 8-cell embyo.     

In Vitro and Molecular Docking Evaluation of Larvicidal Effects of Essential Oils of Five Aromatic Plants on the Fall Armyworm Spodoptera frugiperda JE. Smith (Lepidoptera: Noctuidae) from Ivory Coast

Faced with the serious consequences resulting from the abusive and repeated use of synthetic chemicals, today rethinking crop protection is more than necessary. It is in this context that the essential oils of the Lamiaceae Ocimum gratissimum and Ocimum canum, the Poaceae Cymbopogon citratus and nardus and a Rutaceae Citrus sp. of known chemical compositions were experimented. The evaluation of the larvicidal potential of the essential oils was done by the method of topical application of the test solutions, on the L1−L2 stage larvae from the first generation of S. frugiperda obtained after rearing in an air-conditioned room. Lethal concentrations (LC₁₀, LC₅₀ and LC₉₀) were determined after 48 h. After assessing the larvicidal potential of essential oils, molecular docking was carried out to study protein-ligand interactions and their propensity to bind to insect enzyme sites (AChE). The essential oil of O. gratissimum was the most effective with the lowest lethal concentrations (LC₁₀=0.91 %, LC₅₀=1.91 % and LC₉₀=3.92 %). The least toxic oil to larvae was Citrus sp. (LC₁₀=5.44 %, LC₅₀=20.50 % and LC₉₀=77.41 %). Molecular docking revealed that p-cymene and thymol from O. gratissimum essential oil are structurally similar and bind to the AChE active site via predominantly hydrophobic interactions and a H-bond with Tyr374 in the case of thymol. The essential oil of O. gratissimum constitutes a potential candidate for the development of biological insecticides for the fight against insect pests and for the protection of the environment.     

高频重复经颅磁刺激联合Brunnstrom分期训练对脑卒中恢复期患者康复效果的影响

摘要 目的：探讨高频重复经颅磁刺激（rTMS）联合Brunnstrom分期训练对脑卒中恢复期患者康复效果的影响。方法：根据随机数字表法将新疆医科大学第一附属医院2020年1月~2022年2月期间收治的脑卒中恢复期患者80例分为对照组（40例,Brunnstrom分期训练）和研究组（40例,高频rTMS联合Brunnstrom分期训练）。对比两组疗效、美国国立卫生研究院卒中量表（NIHSS）评分、功能独立性量表（FIM）评分、生活质量评分、血清神经因子指标[髓鞘碱性蛋白（MBP）、神经元特异性烯醇化酶（NSE）、神经生长因子-1（NGF-1）]。结果：研究组的临床总有效率（92.50%）明显高于对照组（70.00%）（P<0.05）。治疗4周后,研究组MBP、NSE低于对照组,NGF-1高于对照组（P<0.05）。与对照组比较,治疗4周后,研究组NIHSS评分降低,FIM评分升高（P<0.05）。治疗4周后,研究组心理/躯体/物质/社会功能评分较对照组高（P<0.05）。结论：高频rTMS联合Brunnstrom分期训练有助于提高脑卒中恢复期患者的康复效果,同时还可调节血清神经指标,提高生活质量。     

重组牛碱性成纤维细胞生长因子眼用凝胶作为角膜保护剂在翼状胬肉手术中的临床应用研究

摘要 目的：探讨重组牛碱性成纤维细胞生长因子（r-bFGF）眼用凝胶在翼状胬肉手术中的临床应用价值。方法：按照随机数字表法,将我院2019年1月~2020年12月期间收治的100例翼状胬肉手术患者分为对照组（n=50）和研究组（n=50）。手术方式均采用翼状胬肉切除联合结膜瓣转移术,对照组术中接受常规处理,研究组在对照组的基础上结合r-bFGF眼用凝胶。对比两组手术效果、眼表相关指标、视力、眼压、不良反应和并发症发生率。结果：两组术后3个月视觉疼痛模拟评分（VAS）、眼表疾病指数（OSDI）下降,泪膜破裂时间（BUT）、基础泪液分泌试验（SIT）升高（P<0.05）,研究组术后3个月VAS、OSDI低于对照组,BUT、SIT高于对照组（P<0.05）。两组术后3个月视力升高,眼压下降（P<0.05）,研究组术后3个月视力高于对照组,眼压低于对照组（P<0.05）。两组不良反应发生率比较无差异（P>0.05）。研究组的临床治愈率较对照组高（P<0.05）。研究组的并发症发生率低于对照组（P<0.05）。结论：r-bFGF眼用凝胶用于翼状胬肉手术中,可减少翼状胬肉患者的术后痛苦,改善眼角、视力和眼压症状,获得更好的临床治愈率。     

丙泊酚联合七氟醚麻醉在先天性心脏病介入手术患儿中的心肌保护作用及对苏醒质量和应激反应的影响

摘要 目的：研究丙泊酚联合七氟醚麻醉在先天性心脏病介入手术患儿中的心肌保护作用及对苏醒质量和应激反应的影响。方法：选择2020年1月~2022年4月期间在苏州大学附属儿童医院接受先天性心脏病介入手术患儿96例,按照双色球法将患儿分为对照组（n=48,接受瑞芬太尼、丙泊酚麻醉）和观察组（n=48,接受丙泊酚、七氟醚麻醉）。对比两组患儿心率、呼吸频率、平均动脉压、苏醒质量、心肌损伤指标、应激反应指标和不良反应发生率。结果：两组置喉罩时（T1）~拔除喉罩（T4）时间点心率、呼吸频率、平均动脉压下降后升高,观察组高于对照组同时间点（P<0.05）。观察组的苏醒时间、拔管时间均短于对照组（P<0.05）。两组术毕、术后24 h肌酸磷酸激酶同工酶（CK-MB）、心肌肌钙蛋白（cTnI）升高后下降,观察组低于对照组同时间点（P<0.05）。两组术毕、术后24 h血糖、皮质醇升高后下降,观察组低于对照组同时间点（P<0.05）。两组不良反应发生率组间对比,差异不显著（P>0.05）。结论：丙泊酚联合七氟醚麻醉应用于先天性心脏病介入手术中,可减轻患儿的应激反应,稳定机体血流动力学波动,同时还可发挥心肌保护作用,提高苏醒质量。     

不同剂量右美托咪定联合超声引导下多点髂筋膜间隙阻滞在老年全髋关节置换术中的应用效果分析

摘要 目的：探讨超声引导下多点髂筋膜间隙阻滞联合不同剂量右美托咪定在老年全髋关节置换术（THA）中的应用效果。方法：选取2019年11月-2022年12月北京积水潭医院贵州医院择期行THA的老年患者120例,按照随机数字表法分为A组（n=40）、B组（n=40）、C组（n=40）,三组均接受超声引导下多点髂筋膜间隙阻滞治疗,在此基础上,A组、B组、C组分别给予0.5 μg/kg、1.0 μg/kg、1.5 μg/kg右美托咪定注射液。对比三组临床指标、血流动力学指标、应激反应指标、脑神经损伤情况,观察三组围术期间不良反应发生情况。结果：B组、C组的阻滞消退时间、拔管时间长于A组,首次下床时间短于A组（P<0.05）。B组、C组的阻滞消退时间、拔管时间、首次下床时间对比无差异（P>0.05）。三组麻醉诱导后即刻（T1）~手术结束时（T3）时间点心率（HR）、平均动脉压（MAP）升高后降低（P<0.05）。B组、C组的T1~T3时间点HR、MAP均低于A组,且B组低于C组（P<0.05）。三组T3时间点皮质醇（Cor）、白介素-6（IL-6）、肿瘤坏死因子-α（TNF-α）升高（P<0.05）。B组、C组的T3时间点Cor、IL-6、TNF-α均低于A组,且B组低于C组（P<0.05）。B组、C组的T3时间点中枢神经特异性蛋白（S100β）均低于A组,且B组低于C组（P<0.05）。B组、C组的T3时间点脑源性神经生长因子（BDNF）均高于A组,且B组高于C组（P<0.05）。三组不良反应发生率组间对比无差异（P>0.05）。结论：超声引导下多点髂筋膜间隙阻滞联合1.0 μg/kg右美托咪定在THA中具有更好的麻醉效果,可缩短首次下床时间,减轻机体应激反应、血流动力学波动以及脑部神经损伤。     

腹式呼吸训练联合短刺法针刺对气滞血瘀型腰椎间盘突出症患者康复效果的影响

摘要 目的：探讨腹式呼吸训练联合短刺法针刺对气滞血瘀型腰椎间盘突出症（LDH）患者康复效果的影响。方法：将2020年1月至2022年6月湖南中医药大学第一附属医院收治的478例气滞血瘀型LDH患者,随机数字表法分为两组,对照组239例患者实施短刺法针刺治疗,观察组239例患者行腹式呼吸训练联合短刺法针刺治疗。比较两组治疗效果、治疗前后中医症候评分、肌电值（坐位、直立位、前屈位、后伸位）、疼痛因子水平[前列腺素E₂（PGE₂）、β-内啡肽（β-EP）、5-羟色胺（5-HT）、P物质（SP）]水平、视觉模拟量表（VAS）评分、Oswestry功能障碍指数（ODI）、日本骨科协会评估治疗分数（JOA）评分、腰椎关节活动度（左屈、左旋、右屈、右旋）及安全性。结果：治疗后,两组治疗效果分级经秩和检验差异具有统计学意义（P＜0.05）,且观察组治疗总有效率显著高于对照组（P＜0.05）。治疗后观察组各中医症候评分低于对照组（P＜0.05）。治疗后观察组坐位、直立位、前屈位、后伸位肌电值高于对照组（P＜0.05）。治疗后观察组疼痛因子PGE₂、5-HT、SP水平低于对照组,β-EP水平高于对照组（P＜0.05）。治疗后观察组VAS评分、ODI低于对照组,JOA评分高于对照组（P＜0.05）。治疗后观察组左屈、左旋、右屈、右旋活动度优于对照组（P＜0.05）。两组不良事件发生率比较无显著差异（P＞0.05）。结论：腹式呼吸训练联合短刺法针刺可提高气滞血瘀型LDH患者临床疗效,增强患者肌力,改善腰椎功能,恢复关节活动度,同时通过调控疼痛介质水平,减轻患者疼痛症状,且具有较好安全性,值得临床借鉴应用。     

胶原生物膜在耳内镜下中耳胆脂瘤乳突根治术中的应用效果分析

摘要 目的：探讨胶原生物膜在耳内镜下乳突根治术中的应用效果。方法：选取徐州医科大学附属医院2021年4月至2022年 2月收治的51例中耳胆脂瘤患者进行回顾性分析,其中研究组27例患者予以胶原生物膜修复皮肤缺损,对照组予以颞肌筋膜修复术腔皮肤缺损,观察两组患者术后临床症状,手术时长,术腔完全上皮化时间、干耳时间及术前术后听力改变。结果：研究组术后患者因外耳道进水,存在感染及肉芽生长者1例,予以清理后未再次生长;对照组术后发生1例外耳道口狭窄的情况,予以橡胶扩张管进行扩张并后并定期清理术腔肉芽、脱落痂皮,患者外耳道恢复良好。两组术前耳闷、耳痛、耳鸣及术后耳痛VAS评分无明显差异（P>0.05）;研究组术后耳闷及耳鸣VAS评分较对照组降低（P<0.05）。研究组平均手术时长、术后术腔完全上皮化时间及平均干耳时间短于对照组（P<0.05）。两组术前术后气骨导差（ABG）、平均气导听阈（AC）比较差异均无统计学意义（P＞0.05）。结论：作为术区移植物,胶原生物膜应用于耳内镜下中耳胆脂瘤乳突根治术可加快创面术腔的修复,减少局部创伤与操作步骤,改善临床症状,缩短手术时间、术后术腔完全上皮化时间及获得干耳时间,可作为临床上有效的修复材料。     

PHOTOADAPTATION AND THE “PACKAGE” EFFECT IN DUNALIELLA TERTIOLECTA (CHLOROPHYCEAE)1

In the marine unicellular chlorophyte, Dunaliella tertiolecta Butcher, the spectrally averaged m vivo absorption cross section, normalized to chlorophyll a (so-called a* values), vary two-fold in response to changes in growth irradiance. We used a kinetic approach to examine the specific factors which account for these changes in optical properties as cells photoadapt. Using Triton X-100 to solubilize membranes, we were able to differentiate between “package” effects and pigmentation effects. Our analyses suggest that 43–49% of the variability in a* is due to changes in pigmentation, whereas 51–57% is due to the “package” effect. Further analyses revealed that changes in cell sue did not significantly affect packaging, while thylakoid stacking and the transparency of thylakoid membranes were important factors. Our results suggest that thylakoid membrane protein/lipid ratios change during photoadaptation, and these changes influence the effective rate of light harvesting per unit chlorophyll a.