HIV相关癌症的动力学模型研究(英文)

本文通过建立两个动力学模型,研究了HIV感染者中癌症的高发现象。我们分别研究了其平衡态的存在性及稳定性。对正平衡态还发现了Hopf分支的存在,并发现随着分支参数的变化,系统出现了周期解与混沌交替出现的现象。     

Modelling co-translational dimerization for programmable nonlinearity in synthetic biology

Nonlinearity plays a fundamental role in the performance of both natural and synthetic biological networks. Key functional motifs in living microbial systems, such as the emergence of bistability or oscillations, rely on nonlinear molecular dynamics. Despite its core importance, the rational design of nonlinearity remains an unmet challenge. This is largely due to a lack of mathematical modelling that accounts for the mechanistic basis of nonlinearity. We introduce a model for gene regulatory circuits that explicitly simulates protein dimerization—a well-known source of nonlinear dynamics. Specifically, our approach focuses on modelling co-translational dimerization: the formation of protein dimers during—and not after—translation. This is in contrast to the prevailing assumption that dimer generation is only viable between freely diffusing monomers (i.e. post-translational dimerization). We provide a method for fine-tuning nonlinearity on demand by balancing the impact of co- versus post-translational dimerization. Furthermore, we suggest design rules, such as protein length or physical separation between genes, that may be used to adjust dimerization dynamics in vivo. The design, build and test of genetic circuits with on-demand nonlinear dynamics will greatly improve the programmability of synthetic biological systems.     

Modelling the dynamics of viral suppressors of RNA silencing

Virus infection in plants is limited by RNA silencing. In turn, viruses can counter RNA silencing with silencing suppressors. Viral suppressors of RNA silencing have been shown to play a role in symptom development in plants. We here study four different strategies employed by silencing suppressors: small interfering RNA (siRNA) binding, double-strand RNA (dsRNA) binding and degrading or inactivating Argonaute. We study the effect of the suppressors on viral accumulation within the cell as well as its spread on a tissue with mathematical and computational models. We find that suppressors which target Argonaute are very effective in a single cell, but that targeting dsRNA or siRNA is much more effective at the tissue level. Although targeting Argonaute can be beneficial for viral spread, it can also cause hindrance in some cases owing to raised levels of siRNAs that can spread to other cells.     

Timing HIV infection with a simple and accurate population viral dynamics model

Clinical trials for HIV prevention can require knowledge of infection times to subsequently determine protective drug levels. Yet, infection timing is difficult when study visits are sparse. Using population nonlinear mixed-effects (pNLME) statistical inference and viral loads from 46 RV217 study participants, we developed a relatively simple HIV primary infection model that achieved an excellent fit to all data. We also discovered that Aptima assay values from the study strongly correlated with viral loads, enabling imputation of very early viral loads for 28/46 participants. Estimated times between infecting exposures and first positives were generally longer than prior estimates (average of two weeks) and were robust to missing viral upslope data. On simulated data, we found that tighter sampling before diagnosis improved estimation more than tighter sampling after diagnosis. Sampling weekly before and monthly after diagnosis was a pragmatic design for good timing accuracy. Our pNLME timing approach is widely applicable to other infections with existing mathematical models. The present model could be used to simulate future HIV trials and may help estimate protective thresholds from the recently completed antibody-mediated prevention trials.     

HIV-2 env基因在重组痘苗病毒中的表达

以痘苗病毒复制非必需区血凝素（ＨＡ）基因为侧翼，将人Ⅱ型免疫缺陷病毒ｇｐ１２０和ｇｐ３６基因分别置于不同类型的自然型痘苗病毒复合启动子下游，构建了４种表达质粒，经同源重组和血凝素阴性空斑筛选，获得了４株重组痘苗病毒，经免疫荧光试验和Ｗｅｓｔｅｒｎ ｂｌｏｔ检测证明，４株重组病毒均能表达目的蛋白。在重组病毒感染早期、晚期、不同株表达量略有不同，表达产物分子量分别约为５７ｋＤａ和４２ｋＤａ，具有良好的     

Effect of different modes of viral spread on the dynamics of multiply infected cells in human immunodeficiency virus infection

Infection of individual cells with more than one HIV particle is an important feature of HIV replication, which may contribute to HIV pathogenesis via the occurrence of recombination, viral complementation and other outcomes that influence HIV replication and evolutionary dynamics. A previous mathematical model of co-infection has shown that the number of cells infected with i viruses correlates with the ith power of the singly infected cell population, and this has partly been observed in experiments. This model, however, assumed that virus spread from cell to cell occurs only via free virus particles, and that viruses and cells mix perfectly. Here, we introduce a cellular automaton model that takes into account different modes of virus spread among cells, including cell to cell transmission via the virological synapse, and spatially constrained virus spread. In these scenarios, it is found that the number of multiply infected cells correlates linearly with the number of singly infected cells, meaning that co-infection plays a greater role at lower virus loads. The model further indicates that current experimental systems that are used to study co-infection dynamics fail to reflect the true dynamics of multiply infected cells under these specific assumptions, and that new experimental techniques need to be designed to distinguish between the different assumptions.     

A century of transitions in New York City's measles dynamics

Infectious diseases spreading in a human population occasionally exhibit sudden transitions in their qualitative dynamics. Previous work has successfully predicted such transitions in New York City''s historical measles incidence using the seasonally forced susceptible–infectious–recovered (SIR) model. This work relied on a dataset spanning 45 years (1928–1973), which we have extended to 93 years (1891–1984). We identify additional dynamical transitions in the longer dataset and successfully explain them by analysing attractors and transients of the same mechanistic epidemiological model.     

Modelling the functional roles of synaptic and extra-synaptic γ-aminobutyric acid receptor dynamics in circadian timekeeping

In the suprachiasmatic nucleus (SCN), γ-aminobutyric acid (GABA) is a primary neurotransmitter. GABA can signal through two types of GABA_A receptor subunits, often referred to as synaptic GABA_A (gamma subunit) and extra-synaptic GABA_A (delta subunit). To test the functional roles of these distinct GABA_A in regulating circadian rhythms, we developed a multicellular SCN model where we could separately compare the effects of manipulating GABA neurotransmitter or receptor dynamics. Our model predicted that blocking GABA signalling modestly increased synchrony among circadian cells, consistent with published SCN pharmacology. Conversely, the model predicted that lowering GABA_A receptor density reduced firing rate, circadian cell fraction, amplitude and synchrony among individual neurons. When we tested these predictions, we found that the knockdown of delta GABA_A reduced the amplitude and synchrony of clock gene expression among cells in SCN explants. The model further predicted that increasing gamma GABA_A densities could enhance synchrony, as opposed to increasing delta GABA_A densities. Overall, our model reveals how blocking GABA_A receptors can modestly increase synchrony, while increasing the relative density of gamma over delta subunits can dramatically increase synchrony. We hypothesize that increased gamma GABA_A density in the winter could underlie the tighter phase relationships among SCN cells.     

基于危险网络上的吸毒人群中HIV的传播(英文)

通过建立吸毒人群中交往关系(包括针具共用和性关系)的"危险关系网络",我们研究了一个关于HIV在此人群中传播的随机模型,得到了基本再生数和最终感染者比例。使用四川省西昌市的调查数据,我们研究了针具共用以及性关系的网络规模对模型最终结果的影响。模拟发现,每个注射吸毒者每增加一个"三人小圈子"网络,将最终导致增加10%的感染者。结果提示:减少危险关系网络的规模,尤其是针具共用的网络规模,对控制HIV的传播有重要的作用。     

HIV-1核心蛋白的表达与纯化

将编码人I型免疫缺陷病毒(HIV1)核心蛋白p24gag的基因序列克隆到原核表达载体pET28(b)中,高效表达了N,C端融合His·Tagp24蛋白,所表达的重组p24蛋白占菌体总蛋白的46%。在变性条件下,使用NiNTA亲和层析法纯化了p24蛋白,纯度为94%。菌体中及纯化、复性后的目的蛋白均能与抗HIV1p24单克隆抗体发生特异性反应。用纯化的p24蛋白免疫小鼠,4周时小鼠血清抗p24抗体效价达1∶400。实验结果表明:大肠杆菌表达的HIV1p24蛋白纯化后可用作HIV1检测试剂的原料。     

HIV-1中国流行株gp120基因在痘苗病毒中的表达及其与核酸疫苗的实验免疫研究

将HIV－1中国流行株gp120基因在痘苗病毒中进行表达,以期获得重组痘苗病毒,与核酸疫苗混合免疫,评价免疫效果,为艾滋病疫苗开发研制打下基础。将HIV－1中国流行株gp120基因片段插入到pJ38载体启动子下游,经同源重组和血凝素阴性空斑筛选重组痘苗病毒,SDS－PAGE、Western blot检测目的蛋白。以重组病毒和核酸疫苗免疫BALB／c小鼠,进行淋巴细胞转化实验、CTL、CD4＋CD8＋T细胞数目以及血清抗体等细胞免疫和体液免疫指标检测。结果获得的重组痘苗病毒vJ38pg120能够表达Gp120蛋白并诱导机体产生细胞免疫和体液免疫,具有良好的免疫原性,其免疫效果以2rVV-DNA混合方式为最好。重组痘苗病毒vJ38gp120。     

抗HIV-1 gp120单链抗体导向SEAD227A融合蛋白原核温控型表达载体构建及表达

人工合成了能广泛识别HIV—1 gp120的单链抗体(SeFv120)基因和金黄色葡萄菌外毒素A(SEA)基因,将SEA基因第227位编码Asp(D)的密码子GAT转换成编码Ala(A)的密码子GCT,并对两基因进行密码子优化。构建原核温控型表达质粒pBV—120和pBV—SL120,经条件优化,pBV—120和pBV—SL120分别在E．coli BL21(DE3)plys中44℃诱导6h、42℃诱导7h获得最佳表达,表达量分别占菌体总蛋白的27．673％和32．519％。目的蛋白经包涵体洗脱、分子筛层析折叠复性后可与HIV—1抗原条发生良好的结合反应。     

Modelling and inference reveal nonlinear length-dependent suppression of somatic instability for small disease associated alleles in myotonic dystrophy type 1 and Huntington disease

More than 20 human genetic diseases are associated with inheriting an unstable expanded DNA simple sequence tandem repeat, for example, CTG (cytosine–thymine–guanine) repeats in myotonic dystrophy type 1 (DM1) and CAG (cytosine–adenine–guanine) repeats in Huntington disease (HD). These sequences mutate by changing the number of repeats not just between generations, but also during the lifetime of affected individuals. Levels of somatic instability contribute to disease onset and progression but as changes are tissue-specific, age- and repeat length-dependent, interpretation of the level of somatic instability in an individual is confounded by these considerations. Mathematical models, fitted to CTG repeat length distributions derived from blood DNA, from a large cohort of DM1-affected or at risk individuals, have recently been used to quantify inherited repeat lengths and mutation rates. Taking into account age, the estimated mutation rates are lower than predicted among individuals with small alleles (inherited repeat lengths less than 100 CTGs), suggesting that these rates may be suppressed at the lower end of the disease-causing range. In this study, we propose that a length-specific effect operates within this range and tested this hypothesis using a model comparison approach. To calibrate the extended model, we used data derived from blood DNA from DM1 individuals and, for the first time, buccal DNA from HD individuals. In a novel application of this extended model, we identified individuals whose effective repeat length, with regards to somatic instability, is less than their actual repeat length. A plausible explanation for this distinction is that the expanded repeat tract is compromised by interruptions or other unusual features. We quantified effective length for a large cohort of DM1 individuals and showed that effective length better predicts age of onset than inherited repeat length, thus improving the genotype–phenotype correlation. Under the extended model, we removed some of the bias in mutation rates making them less length-dependent. Consequently, rates adjusted in this way will be better suited as quantitative traits to investigate cis- or trans-acting modifiers of somatic mosaicism, disease onset and progression.     

Impact of the implementation of rest days in live bird markets on the dynamics of H5N1 highly pathogenic avian influenza

Live bird markets (LBMs) act as a network ‘hub’ and potential reservoir of infection for domestic poultry. They may therefore be responsible for sustaining H5N1 highly pathogenic avian influenza (HPAI) virus circulation within the poultry sector, and thus a suitable target for implementing control strategies. We developed a stochastic transmission model to understand how market functioning impacts on the transmission dynamics. We then investigated the potential for rest days—periods during which markets are emptied and disinfected—to modulate the dynamics of H5N1 HPAI within the poultry sector using a stochastic meta-population model. Our results suggest that under plausible parameter scenarios, HPAI H5N1 could be sustained silently within LBMs with the time spent by poultry in markets and the frequency of introduction of new susceptible birds'' dominant factors determining sustained silent spread. Compared with interventions applied in farms (i.e. stamping out, vaccination), our model shows that frequent rest days are an effective means to reduce HPAI transmission. Furthermore, our model predicts that full market closure would be only slightly more effective than rest days to reduce transmission. Strategies applied within markets could thus help to control transmission of the disease.     

A dose and time response Markov model for the in-host dynamics of infection with intracellular bacteria following inhalation: with application to Francisella tularensis

In a novel approach, the standard birth–death process is extended to incorporate a fundamental mechanism undergone by intracellular bacteria, phagocytosis. The model accounts for stochastic interaction between bacteria and cells of the immune system and heterogeneity in susceptibility to infection of individual hosts within a population. Model output is the dose–response relation and the dose-dependent distribution of time until response, where response is the onset of symptoms. The model is thereafter parametrized with respect to the highly virulent Schu S4 strain of Francisella tularensis, in the first such study to consider a biologically plausible mathematical model for early human infection with this bacterium. Results indicate a median infectious dose of about 23 organisms, which is higher than previously thought, and an average incubation period of between 3 and 7 days depending on dose. The distribution of incubation periods is right-skewed up to about 100 organisms and symmetric for larger doses. Moreover, there are some interesting parallels to the hypotheses of some of the classical dose–response models, such as independent action (single-hit model) and individual effective dose (probit model). The findings of this study support experimental evidence and postulations from other investigations that response is, in fact, influenced by both in-host and between-host variability.     

Integrating toxin gene expression,growth and fumonisin B1 and B2 production by a strain of Fusarium verticillioides under different environmental factors

The objective of this study was to integrate data on the effect of water activity (a_w; 0.995–0.93) and temperature (20–35°C) on activation of the biosynthetic FUM genes, growth and the mycotoxins fumonisin (FB₁, FB₂) by Fusarium verticillioides in vitro. The relative expression of nine biosynthetic cluster genes (FUM1, FUM7, FUM10, FUM11, FUM12, FUM13, FUM14, FUM16 and FUM19) in relation to the environmental factors was determined using a microarray analysis. The expression was related to growth and phenotypic FB₁ and FB₂ production. These data were used to develop a mixed-growth-associated product formation model and link this to a linear combination of the expression data for the nine genes. The model was then validated by examining datasets outside the model fitting conditions used (35°C). The relationship between the key gene (FUM1) and other genes in the cluster (FUM11, FUM13, FUM9, FUM14) were examined in relation to a_w, temperature, FB₁ and FB₂ production by developing ternary diagrams of relative expression. This model is important in developing an integrated systems approach to develop prevention strategies to control fumonisin biosynthesis in staple food commodities and could also be used to predict the potential impact that climate change factors may have on toxin production.