Approximations, idealizations and 'experiments' at the physics-biology interface

This paper, which is based on recent empirical research at the University of Leeds, the University of Edinburgh, and the University of Bristol, presents two difficulties which arise when condensed matter physicists interact with molecular biologists: (1) the former use models which appear to be too coarse-grained, approximate and/or idealized to serve a useful scientific purpose to the latter; and (2) the latter have a rather narrower view of what counts as an experiment, particularly when it comes to computer simulations, than the former. It argues that these findings are related; that computer simulations are considered to be undeserving of experimental status, by molecular biologists, precisely because of the idealizations and approximations that they involve. The complexity of biological systems is a key factor. The paper concludes by critically examining whether the new research programme of 'systems biology' offers a genuine alternative to the modelling strategies used by physicists. It argues that it does not.     

Simple models of stimulation of neurones in the brain by electric fields

The excitation of pyramidal cells in the motor cortex, produced by electric fields generated by distant electrodes or by electromagnetic induction, has been modelled. Linear, steady-state models of myelinated axons capture most of the geometrical aspects of neurone activation in electric fields. Some non-linear features can be approximated. Models with a proximal sealed-end and distal infinite axon, or of finite length, are both serviceable. Surface anodal stimulation produces hyperpolarisation of the proximal axon (closest to the anode) and depolarisation in the distal axon. The point of maximum depolarisation can be influenced by the location of the cathode (greater separation of anode and cathode causes more distal depolarisation). Axon bends can produce very localised depolarisation. Cathodal stimulation may be less effective than anodal as a result of anodal block of conduction of action potentials in the distal axon. The latencies of responses to anodal stimulation, recorded in the distal axon, will decrease as the stimulus strength is increased and the point of action potential initiation moves distally node by node. Larger jumps in latency will be produced when the point of action potential initiation moves from one axon bend to another.     

结扎大鼠左冠状动脉不同时间制备心肌梗死模型的比较

目的探索大鼠左冠状动脉前降支不同结扎处理后,对心肌形态学及心功能的影响,以建立适合移植干细胞再生修复心肌梗死研究的稳定、可靠和更合乎发病机制的动物模型。方法雄性SD大鼠70只,随机分为五组。即:结扎(15、30、456、0 min)再灌、结扎非再灌。于处理后1 d、1周2、周或4周动态观察心肌梗死变化,并于处理一月后测量动脉收缩压(ASP)、动脉舒张压(ADP),左室收缩压(LVSP),左室舒张末压(LVEDP)及左室压力上升及下降最大速度(±dp/dtmax)。结果引起明显的心肌梗死至少需要结扎30 min。结扎(456、0 min)再灌、结扎非再灌的心肌梗死明显,并观察到梗死区域心肌已绝大部分纤维化,且梗死面积变化较恒定。同时测定不同结扎时间心功能的变化发现,结扎(456、0 min)再灌或结扎非再灌各组ASP、DAP、LVSP、±dp/dtmax显著下降,LVEDP明显升高。并见不同结扎时间处理后,大鼠心功能的变化与心肌梗死后的梗死面积变化密切相关。结论建立了实验大鼠左冠状动脉前降支中上1/3处结扎45 min以上的大鼠心肌梗死模型。不仅合乎临床心肌梗死的发病机制,而且梗死部位、梗死区域面积稳定,适合于移植细胞再生修复心肌梗死的研究。     

AdTGF-β1223/225气管内注射制备大鼠肺间质纤维化动物模型

目的观察TGF-β1基因过表达诱发大鼠肺间质纤维化动物模型的组织病理学变化.方法成年健康SD大鼠30只,随机分为空白对照组10只,模型组10只和空载体对照组10只,其中对模型组大鼠气管内一次性注射携带TGF-β1基因腺病毒载体(AdTGF-β1 223/225,1×109 pfu,0.4 mL),空白对照组大鼠气管内注射等量的生理盐水,空载体对照组大鼠气管内注射等量的腺病毒空载体.结果一次性肺气管内注射 AdTGF-β1 223/225可造成肺急性炎症和肺间质纤维化,而对照(腺病毒空载体)并不引起相应的变化.结论肺组织局部分泌的细胞因子TGF-β1可以单独诱发肺间质纤维化.     

建立胃癌实验动物模型方法的研究

目的通过对人低分化胃癌细胞系SGC-7901状态和接种细胞数目的研究,建立良好的皮下接种胃癌的动物模型。方法采用腹腔注射SGC-7901细胞,使裸鼠形成腹水;光镜及电镜观察细胞状态;将购买的SGC-7901细胞以及形成腹水后的肿瘤细胞分别以1×108、1×107和1×106个进行裸鼠皮下接种,每组接种5只。观察其肿瘤形成时间、大小、状态及病理学变化。结果SGC-7901细胞接种裸鼠形成腹水后进行培养的肿瘤细胞增殖状态发生改变;购买的SGC-7901细胞以1×108及1×107接种裸鼠,在第21天肿瘤组织中央均出现出血和坏死;1×106的裸鼠第21天未见肉眼可见的肿瘤形成。腹水培养的肿瘤细胞,接种1×108的裸鼠在第21天肿瘤组织中央可见大面积的出血和坏死;接种1×107及1×106的裸鼠在第21天均未见出血和坏死,接种1×107的肿瘤组织体积较大。结论SGC-7901细胞接种裸鼠形成腹水后的细胞,更容易建立SGC-7901细胞皮下接种的胃癌动物模型,其中以接种细胞数为1×107的肿瘤生长较好,更适用于胃癌的实验研究。     

帕金森病小鼠模型行为学检测方法的比较研究

目的比较目前常用的5种帕金森病(PD)小鼠模型行为学检测方法在PD研究中的作用。方法用MPTP建立C57BL小鼠PD模型,通过行为学检测(自主活动计数、滚轴实验、游泳实验、爬杆实验、悬挂实验)、免疫组织化学和荧光分光光度法,对比5种行为学检测方法的平均数与变异系数,观察MPTP对PD小鼠模型的行为学、黑质多巴胺(DA)神经元和纹状体酪氨酸羟化酶免疫反应阳性(TH-ir)神经纤维以及纹状体DA水平的影响。结果给与MPTP后,小鼠行为学计数降低,爬杆实验未能得到检测结果,悬挂实验变异系数很高,结果有明显的偶然性,滚轴实验结果变异系数中等,平均数呈现一定的上升趋势,自主活动计数中移动与站立和游泳实验的平均数则呈现明显的下降趋势,变异系数很低,而黑质DA神经元数目减少约58%,纹状体TH-ir神经纤维密度减低,纹状体DA水平明显降低约88%,两组相比差异有显著性(P<0.01)。结论MPTP所致的C57BL小鼠的神经病理、生化改变与PD患者近似,自主活动计数和游泳实验优于其他行为学检测方法。     

链脲佐菌素诱导长爪沙鼠Ⅰ型糖尿病模型的实验研究

目的探讨链脲佐菌素(STZ)诱导长爪沙鼠Ⅰ型糖尿病模型的可能性,并观察模型动物早期肾脏损害情况。方法雄性长爪沙鼠96只,随机分为正常对照组(NC组)、模型组1(DM1组)、模型组2(DM2组),DM1及DM2组沙鼠分别一次性腹腔注射100 mg/kg、200 mg/kg STZ,NC组注射等量柠檬酸盐缓冲溶液。注射STZ后1、2、4、6周末,分别监测沙鼠一般情况,血糖、胰岛素等血清学指标和尿液指标,并处死沙鼠进行胰腺和肾脏组织的病理学检查。结果注射STZ 24 h后,DM2组及DM1组部分沙鼠逐渐出现典型的"三多一少"症状,随着病程的发展,DM2组沙鼠持续高血糖,DM1组沙鼠血糖值与NC组差异有显著性(P0.05),但有下降趋势;DM2组沙鼠胰岛素显著性降低(P0.05),其他血清学指标及尿液指标均显著性升高(P0.05),DM1组沙鼠各指标差异无显著性。DM2组沙鼠及DM1组少数沙鼠胰腺组织中可见胰岛β细胞减少、空泡样变性等变化,DM2组沙鼠肾脏组织中出现肾小球基质增多,毛细血管襻扩张等病变,DM1组沙鼠肾脏组织未见明显变化。结论 STZ 200 mg/kg可成功诱导长爪沙鼠Ⅰ型糖尿病模型,在病程早期沙鼠肾脏结构和功能已经发生改变。     

Steric Hindrance Mutagenesis in the Conserved Extracellular Vestibule Impedes Allosteric Binding of Antidepressants to the Serotonin Transporter

The serotonin transporter (SERT) controls synaptic serotonin levels and is the primary target for antidepressants, including selective serotonin reuptake inhibitors (e.g. (S)-citalopram) and tricyclic antidepressants (e.g. clomipramine). In addition to a high affinity binding site, SERT possesses a low affinity allosteric site for antidepressants. Binding to the allosteric site impedes dissociation of antidepressants from the high affinity site, which may enhance antidepressant efficacy. Here we employ an induced fit docking/molecular dynamics protocol to identify the residues that may be involved in the allosteric binding in the extracellular vestibule located above the central substrate binding (S1) site. Indeed, mutagenesis of selected residues in the vestibule reduces the allosteric potency of (S)-citalopram and clomipramine. The identified site is further supported by the inhibitory effects of Zn²⁺ binding in an engineered site and the covalent attachment of benzocaine-methanethiosulfonate to a cysteine introduced in the extracellular vestibule. The data provide a mechanistic explanation for the allosteric action of antidepressants at SERT and suggest that the role of the vestibule is evolutionarily conserved among neurotransmitter:sodium symporter proteins as a binding pocket for small molecule ligands.