Th1/Th2 differentiation and cross-regulation

The T helper (Th) phenotypes, Th1/Th2, are acquired upon interaction of a naive T helper cell and an antigen presenting cell (APC). Naive T helper cells may differentiate into either phenotype, and the actual outcome is determined by the density and avidity of the antigenic determinants presented by the APC, and the APCs inherent costimulatory properties. Until recently it was thought that differentiation is further affected by cytokines. However, Murphy et al. (1996, J. Exp. Med. 183, 901) have demonstrated that the experimental results, formerly interpreted as Th1/Th2 differentiation, in effect comprise an observation of two consecutive processes. (i) An interaction between naive T cells and APC creates a mixture of mature cells irreversibly committed to Th1 or Th2 phenotype. (ii) Subsequent addition of regulatory cytokines, promotes expansion of one phenotype while suppressing the other. The consequent shift in the per culture production of marker cytokines mimics the appearance of a cellular phenotype switch. We present and analyse a mathematical model that extrapolates these experimental facts into systemic behavior during an immune response. Despite the fact that differentiation produces cells of Th1 and Th2 phenotypes with the same receptor specificity, our results indicate that competition for antigenic stimulation, mediated by the APCs, combines with cytokine mediated cross-suppression between phenotypes to yield a response that is eventually dominated by T helper cells that are uniform in both receptor specificity (clonotype) and in cytokine secretion phenotype.     

Signatures of competition and strain structure within the major blood‐stage antigen of Plasmodium falciparum in a local community in Ghana

The concept of niche partitioning has received considerable theoretical attention at the interface of ecology and evolution of infectious diseases. Strain theory postulates that pathogen populations can be structured into distinct nonoverlapping strains by frequency‐dependent selection in response to intraspecific competition for host immune space. The malaria parasite Plasmodium falciparum presents an opportunity to investigate this phenomenon in nature, under conditions of high recombination rate and extensive antigenic diversity. The parasite's major blood‐stage antigen, PfEMP1, is encoded by the hyperdiverse var genes. With a dataset that includes thousands of var DBLα sequence types sampled from asymptomatic cases within an area of high endemicity in Ghana, we address how var diversity is distributed within isolates and compare this to the distribution of microsatellite allelic diversity within isolates to test whether antigenic and neutral regions of the genome are structured differently. With respect to var DBLα sequence types, we find that on average isolates exhibit significantly lower overlap than expected randomly, but that there also exists frequent pairs of isolates that are highly related. Furthermore, the linkage network of var DBLα sequence types reveals a pattern of nonrandom modularity unique to these antigenic genes, and we find that modules of highly linked DBLα types are not explainable by neutral forces related to var recombination constraints, microsatellite diversity, sampling location, host age, or multiplicity of infection. These findings of reduced overlap and modularity among the var antigenic genes are consistent with a role for immune selection as proposed by strain theory. Identifying the evolutionary and ecological dynamics that are responsible for the nonrandom structure in P. falciparum antigenic diversity is important for designing effective intervention in endemic areas.     

基于响应面分析的高抗原活性鸭疫里默氏杆菌疫苗培养基的研制及其效果评价

【背景】鸭疫里默氏杆菌广泛存在于养殖场,引起雏鸭发生传染性浆膜炎,严重危害养鸭业的发展。【目的】提高鸭疫里默氏杆菌发酵培养水平和抗原活性,为鸭疫里默氏杆菌灭活疫苗的研制提供技术指引。【方法】利用单因素及响应面的试验设计方法,针对鸭疫里默氏杆菌进行疫苗培养基的研制,并探究不同发酵时间点该菌的抗原活性,选择抗原活性最高点时制备灭活疫苗,通过动物免疫保护试验评价疫苗免疫效果。【结果】使用研制的疫苗培养基发酵培养鸭疫里默氏杆菌,其活菌数能够达到4.68×1010 CFU/mL,较市面上该菌专用的培养基提高2.29倍。该菌发酵12 h后抗原活性达到最高,在此时制备的灭活疫苗诱导小鼠产生的抗体水平显著高于商品化灭活疫苗,攻毒保护率达到了100%。【结论】本研究研制的培养基具有优异的增菌效果,可作为生产鸭疫里默氏杆菌灭活疫苗抗原的发酵培养基,疫苗生产过程中可选择菌株抗原活性达到最高时收集菌体。     

Ribonucleic acid in the immune response

Summary In the studies of experimental salmonellosis, immunization of mice with a live vaccine SER of S. enteritidis was found to be effective against further infection with virulent S. enteritidis 116-54. Macrophages obtained from the peritoneal cavity, subcutaneous tissue or liver of immunized mice inhibited intracellular growth of bacteria and resisted cell degeneration caused by engulfment of virulent 116-54 bacteria. This immunity was called cellular immunity.We discovered by chance in 1961 a transfer agent of immunity (TA) from the culture fluid of immunized macrophages. This agent is RNA in nature and can be extracted from the spleen, peritoneal exudate cells or the lymph node of immunized animals and is called immune (i) RNA. We could demonstrate antibody activity in macrophages treated in vitro or in vivo with iRNA by the immune adherence hemagglutination technique.Cellular immunity against tumor cells could be transferred in vitro or in vivo to lymphocytes through iRNA prepared from the spleen cells of syngeneic, allogeneic and xenogeneic animals immunized with the tumor cells.We prepared iRNA against antigens capable of inducing humoral antibody production in animals, i.e., RBCs, bacterial toxin, bacterial flagella and hapten-protein conjugates. Serum antibody was not demonstrated in recipient animals of iRNAs by single or repeated injections of these agents. However, in these animals an increase in the number of specific antibody-carrying cells was found as rosette-formers. It was found further that prior injection of iRNA could induce immunologic memory and produced a high titer of humoral antibody after a boosting stimulation with a small dose of the corresponding antigen. The required interval between the first iRNA and the second antigenic stimulation, and the minimal effective doses of iRNA and antigen are described.We studied the interaction of iRNA with either T- or B-cells and with both cells using adoptive transfer system, athymic nude mice and neonatally thymectomized (NT) mice. Immune RNAs against T-dependent and T-independent antigens could not induce the proliferation of antibody-carrying cells in cyclophosphamide-treated (B-cell depleted) mice. But these agents could induce the proliferation of rosette-formers, implying that iRNAs can replace some role of T-cells even against T-dependent antigens. B-cells can be directly activated by treatment with iRNA against both T-dependent and T-independent antigens, and they differentiated into rosette-formers.Passive transfers of iRNA were successful in establishing immunity against infection with S. enteritidis, or immunity to Salmonella flagella, RBCs and hapten-protein conjugates. The ability of iRNA to confer a secondary response of antibody formation is serially and passively transmissible in recipient animals. These facts suggest the presence of some mechanism that is responsible for the amplification of antigenic stimulation in the immune response. The RNA-dependent RNA polymerase and RNA-dependent DNA polymerase are presented and their role in the immune response is discussed.     

Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches

Abstract

Elizabethkingia anophelis is an emerging human pathogen causing neonatal meningitis, catheter-associated infections and nosocomial outbreaks with high mortality rates. Besides, they are resistant to most antibiotics used in empirical therapy. In this study, therefore, we used immunoinformatic approaches to design a prophylactic peptide vaccine against E. anophelis as an alternative preventive measure. Initially, cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B-lymphocyte (LBL) epitopes were predicted from the highest antigenic protein. The CTL and HTL epitopes together had a population coverage of 99.97% around the world. Eventually, six CTL, seven HTL, and two LBL epitopes were selected and used to construct a multi-epitope vaccine. The vaccine protein was found to be highly immunogenic, non-allergenic, and non-toxic. Codon adaptation and in silico cloning were performed to ensure better expression within E. coli K12 host system. The stability of the vaccine structure was also improved by disulphide bridging. In addition, molecular docking and dynamics simulation revealed strong and stable binding affinity between the vaccine and toll-like receptor 4 (TLR4) molecule. The immune simulation showed higher levels of T-cell and B-cell activities which was in coherence with actual immune response. Repeated exposure simulation resulted in higher clonal selection and faster antigen clearance. Nevertheless, experimental validation is required to ensure the immunogenic potency and safety of this vaccine to control E. anophelis infection in the future.

Communicated by Ramaswamy H. Sarma     

Modeling immunotherapy of the tumor – immune interaction

 A number of lines of evidence suggest that immunotherapy with the cytokine interleukin-2 (IL-2) may boost the immune system to fight tumors. CD4⁺ T cells, the cells that orchestrate the immune response, use these cytokines as signaling mechanisms for immune-response stimulation as well as lymphocyte stimulation, growth, and differentiation. Because tumor cells begin as ‘self’, the immune system may not respond in an effective way to eradicate them. Adoptive cellular immunotherapy can potentially restore or enhance these effects. We illustrate through mathematical modeling the dynamics between tumor cells, immune-effector cells, and IL-2. These efforts are able to explain both short tumor oscillations in tumor sizes as well as long-term tumor relapse. We then explore the effects of adoptive cellular immunotherapy on the model and describe under what circumstances the tumor can be eliminated. Received: 22 October 1997 / Revised version: 27 November 1997     

Periodicity,persistence, and collapse in host–parasitoid systems with egg limitation

There is an emerging consensus that parasitoids are limited by the number of eggs which they can lay as well as the amount of time they can search for their hosts. Since egg limitation tends to destabilize host–parasitoid dynamics, successful control of insect pests by parasitoids requires additional stabilizing mechanisms such as heterogeneity in the distribution of parasitoid attacks and host density-dependence. To better understand how egg limitation, search limitation, heterogeneity in parasitoid attacks, and host density-dependence influence host–parasitoid dynamics, discrete time models accounting for these factors are analyzed. When parasitoids are purely egg-limited, a complete anaylsis of the host–parasitoid dynamics are possible. The analysis implies that the parasitoid can invade the host system only if the parasitoid’s intrinsic fitness exceeds the host’s intrinsic fitness. When the parasitoid can invade, there is a critical threshold, CV ^*>1, of the coefficient of variation (CV) of the distribution of parasitoid attacks that determines that outcome of the invasion. If parasitoid attacks sufficiently aggregated (i.e., CV>CV ^*), then the host and parasitoid coexist. Typically (in a topological sense), this coexistence is shown to occur about a periodic attractor or a stable equilibrium. If the parasitoid attacks are sufficiently random (i.e. CV<CV ^*), then the parasitoid drives the host to extinction. When parasitoids are weakly search-limited as well as egg-limited, coexistence about a global attractor occurs even if CV<CV ^*. However, numerical simulations suggest that the nature of this attractor depends critically on whether CV<1 or CV>1. When CV<1, the parasitoid exhibits highly oscillatory dynamics. Alternatively, when parasitoid attacks are sufficiently aggregated but not overly aggregated (i.e. CV>1 but close to 1), the host and parasitoid coexist about a stable equilibrium with low host densities. The implications of these results for classical biological control are discussed.     

基于响应面法的高抗原活性禽多杀性巴氏杆菌疫苗培养基的研制与效果评价

【背景】禽多杀性巴氏杆菌(Pasteurella multocida)引发的禽霍乱疫情造成了巨大的危害,而现有培养基存在培养菌密度较低的问题。【目的】研制高抗原活性的禽多杀性巴氏杆菌疫苗培养基。【方法】通过单因素试验、Plackett-Burman试验和响应面分析方法对禽多杀性巴氏杆菌培养基的成分进行调整,并对不同发酵阶段的菌体进行免疫原性测定。最后使用该培养基培养细菌后制备疫苗并通过动物攻毒试验评价其保护效果。【结果】使用研制的培养基培养禽多杀性巴氏杆菌,活菌密度能够在6 h达到约1.84×1010 CFU/mL,增菌效果是对照培养基的2.6倍;免疫原性测定结果显示在生长平台期菌体的抗原活性最高;攻毒试验表明制备的疫苗能够很好地抵抗禽多杀性巴氏杆菌的侵袭。【结论】研制出了高抗原活性的禽多杀性巴氏杆菌疫苗培养基,为疫苗的生产奠定了基础。     

Optimal deep brain stimulation of the subthalamic nucleus—a computational study

Deep brain stimulation (DBS) of the subthalamic nucleus, typically with periodic, high frequency pulse trains, has proven to be an effective treatment for the motor symptoms of Parkinson’s disease (PD). Here, we use a biophysically-based model of spiking cells in the basal ganglia (Terman et al., Journal of Neuroscience, 22, 2963–2976, 2002; Rubin and Terman, Journal of Computational Neuroscience, 16, 211–235, 2004) to provide computational evidence that alternative temporal patterns of DBS inputs might be equally effective as the standard high-frequency waveforms, but require lower amplitudes. Within this model, DBS performance is assessed in two ways. First, we determine the extent to which DBS causes Gpi (globus pallidus pars interna) synaptic outputs, which are burstlike and synchronized in the unstimulated Parkinsonian state, to cease their pathological modulation of simulated thalamocortical cells. Second, we evaluate how DBS affects the GPi cells’ auto- and cross-correlograms. In both cases, a nonlinear closed-loop learning algorithm identifies effective DBS inputs that are optimized to have minimal strength. The network dynamics that result differ from the regular, entrained firing which some previous studies have associated with conventional high-frequency DBS. This type of optimized solution is also found with heterogeneity in both the intrinsic network dynamics and the strength of DBS inputs received at various cells. Such alternative DBS inputs could potentially be identified, guided by the model-free learning algorithm, in experimental or eventual clinical settings. Action Editor: Steven J. Schiff Xiao-Jiang Feng and Eric Shea-Brown contributed equally to this work.     

Evolutionary tradeoff and equilibrium in an aquatic predator-prey system

Due to the conventional distinction between ecological (rapid) and evolutionary (slow) timescales, ecological and population models have typically ignored the effects of evolution. Yet the potential for rapid evolutionary change has been recently established and may be critical to understanding how populations persist in changing environments. In this paper we examine the relationship between ecological and evolutionary dynamics, focusing on a well-studied experimental aquatic predator-prey system (Fussmann et al., 2000, Science, 290, 1358–1360; Shertzer et al., 2002, J. Anim. Ecol., 71, 802–815; Yoshida et al., 2003, Nature, 424, 303–306). Major properties of predator-prey cycles in this system are determined by ongoing evolutionary dynamics in the prey population. Under some conditions, however, the populations tend to apparently stable steady-state densities. These are the subject of the present paper. We examine a previously developed model for the system, to determine how evolution shapes properties of the equilibria, in particular the number and identity of coexisting prey genotypes. We then apply these results to explore how evolutionary dynamics can shape the responses of the system to ‘management’: externally imposed alterations in conditions. Specifically, we compare the behavior of the system including evolutionary dynamics, with predictions that would be made if the potential for rapid evolutionary change is neglected. Finally, we posit some simple experiments to verify our prediction that evolution can have significant qualitative effects on observed population-level responses to changing conditions.     

Evolutionary Stable Strategies and Trade-Offs in Generalized Beverton and Holt Growth Models

A generalized Beverton–Holt model is considered in which a parameterγcharacterizes the onset of density dependence. An evolutionary stable strategy analysis of this parameter, reported in Getz (1996), is developed further here, using invasion exponents and the strategy dynamics of Vincentet al.(1993). The parameterγis also allowed to be density dependent, and it is shown that the most successful strategies of this type are those for whichγis large for low densities and close to its minimum for high densities. A biological interpretation is given in the context of mobile females depositing their relatively sessile young on patches of resource, namely, females should overdisperse their young on resources when adult densities are high and underdisperse them when these densities are low. Finally the per capita growth rate parameter is also allowed to depend onγ. It is shown that this dependence provides a mechanism by which periodic or chaotic attractor dynamics could evolve towards equilibrium attractor dynamics.     

Peptide epitope mapping in vaccine development: Introduction

Protection from infectious disease by the host immune response requires specific molecular recognition of unique antigenic determinants of a given pathogen. An epitope is an antigenic determinant which: 1) specifically stimulates the immune response (either B or T cell mediated); and 2) is acted upon by the products of these protective mechanisms. In B cell immunity, antibodies produced from stimulation by specific epitopes recognize and bind to these same antigenic structures. Identification of protective epitopes is extremely valuable to successful vaccine development. In order to be protective these antibodies must, in addition to recognition and binding, interfere with some vital step in pathogenesis such as adherence or toxin action. Protein B cell epitopes are frequently composed of the side chains (R-groups) of the amino acids found at solvent-exposed surfaces. These epitopes are classified as continuous (also linear or sequential) if composed of a single antibody-recognizing element located at a single locus of the primary structure. They are discontinuous (or assembled) if more than one physically separated entity is involved. T cell epitopes are peptides on the surface of antigen-presenting cells (macrophages, dendritic cells, and B cells) that are bound to major histocompatibility proteins; the T cell recognizes this peptide-MHC complex. Received 12 August 1996/ Accepted in revised form 03 November 1996     

A model of cell firing patterns during epileptic seizures

A simplified model is presented of the dynamics of excitatory and inhibitory neurons in the cerebral cortex. A key feature of the model is that neurons may cease to fire when strongly depolarized (spike inactivation). Computer simulations for different parameters reveal five classes of solutons: a) steady states in which neither excitatory nor inhibitory cells are active, b) steady states in which one or both types of cells fire repetitively, c) states in which one type of cell fluctuates rapidly between bursts of action potentials and inactivity due to strong depolarization, d) rhythmic activity in which both types of cells fire in unison followed by a period of spike inactivation and e) states similar to d but in which the inhibitory cells never produce action potentials. Solutions b, c, d, and e qualitatively resemble the different firing patterns observed during experimental seizures. It is shown that changes in those parameters that are functions of potassium concentration can induce changes in the type of solution. It is therefore proposed that the increase in extracellular potassium concentration during seizures may be responsible for the progressive changes observed in firing patterns and particularly for the transition from tonic to clonic patterns. A method is also outlined for testing the predictions of the model.     

多囊卵巢综合征患者肠道菌群和生化免疫分子特征

【目的】比较多囊卵巢综合征(polycysticovariansyndrome,PCOS)患者与健康对照间肠道菌群谱结构特征差异,并探讨多囊卵巢综合征患者差异菌群与生化免疫指标之间的联系。【方法】选取初诊多囊卵巢综合征患者23例和健康女性对照23例,每例患者于初诊时留取粪便标本和血液标本,粪便标本提取DNA进行宏基因组测序,血清用于检测性激素和炎症因子。通过生物信息分析比较多囊卵巢综合征患者与健康对照间肠道菌群谱结构特征差异,以及与相关指标的联系。【结果】发现多囊卵巢综合征患者与健康对照的肠道菌群在门、属、种水平均有明显差异。两组间差异菌种为4个,普通拟杆菌(Bacteroides vulgatus)和弗格森埃希菌(Escherichia fergusonii)在PCOS组中的相对丰度高于对照组,并且这两种菌与PCOS的发病机制密切相关。凸腹真杆菌(Eubacteriumventriosum)和Subdoligranulum unclassified菌的相对丰度低于健康对照组。其中普通拟杆菌、凸腹真杆菌和Subdoligranulum unclassified菌3个菌种彼此间存在相关性...     

RT1-Linked Ir and Is genes control the immune response to bovine insulin in the rat

The immune response to bovine or pork insulin (BI or PI, respectively) was studied in the rat using the in vitro insulin-induced lymphocyte-proliferation assay. Results indicated that 11 inbred rat strains were divided into categories of high and low responders. Two high responders, SDJ (RT1 ^u) and BN(RT1 ⁿ) inbred rat strains, appeared to recognize different antigenic determinant(s) on the insulin molecule. The results of linkage and segregation analyses in F₁, F₂, backcross, and partially congenic rats showed that the Ir gene (Ir-BI), which encodes the high responsiveness in the SDJ rats, is inherited associated with RT1 ^u, whereas the immune suppression gene (Is-BI), which encodes the low responsiveness in the WKA(_RT1 ^k) rats, is inherited together with RT1 ^k. The Is-BI is the first major histocompatibility complex (MHC)-linked Is gene reported in the rat. The LEJ(RTI-A ^u B ^b) inbred rat strain showed a low response to BI, indicating that Ir-BI is closer to RTI-B/RTI-D region than to RTI-A.Abbreviations used in this paper BI bovine insulin - HEPES N-2-hydroxyethylpiperazine-N-2-ethanesulfonic acid - It immune response - Is immune suppression - MHC major histocompatibility complex - mol. wt. molecular weight - PI pork insulin - sc subcutaneously - SD standard deviation - SI stimulation index     

On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques

Abstract

The molecular simulation technique of stochastic dynamics (SD) is tested by application to the immunosuppressive drug cyclosporin A (CPA). Two stochastic dynamics simulations are performed, one (SD_CCl4 ) with atomic friction coefficients proportional to the viscosity of the nonpolar solvent CCl₄, and one (SD_H2O) with atomic friction coefficients corresponding to an aqueous solution. The atomic friction coefficients are also taken proportional to an approximate expression for the atomic accessible surface area. The properties of both stochastic dynamics simulations are compared to those of two full molecular dynamics (MD) simulations of cyclosporin A, one in a box with 591 CCl₄ molecules, and one in a box with 632 H₂O molecules.

The properties of cyclosporin A as found in the molecular dynamics simulation in CCl₄ are well reproduced by the SD_CCl4 simulation. This indicates that the neglect of a mean force reresenting the average solvent effects on the solute is justified in the case of nonpolar solvents. For polar solvents, like water, this mean force may not be neglected. The SD_H2O simulation of cyclosporin A clearly fails to reproduce the amount of hydrogen bonding found in the molecular dynamics stimulation of cyclosporin A in water.

A comparison with a molecular dynamics simulation of cyclosporin A in vacuo shows that both the SD_CCl4 and the SD_H2O simulation come closer to the properties of the molecular dynamics simulations in CCl₄ and in H₂O than a molecular dynamics simulation in vacuo.     

Life Stages: Interactions and Spatial Patterns

In many stage-structured species, different life stages often occupy separate spatial niches in a heterogeneous environment. Life stages of the giant flour beetle Tribolium brevicornis (Leconte), in particular adults and pupae, occupy different locations in a homogeneous habitat. This unique spatial pattern does not occur in the well-studied stored grain pests T. castaneum (Herbst) and T. confusum (Duval). We propose density dependent dispersal as a causal mechanism for this spatial pattern. We model and explore the spatial dynamics of T. brevicornis with a set of four density dependent integrodifference and difference equations. The spatial model exhibits multiple attractors: a spatially uniform attractor and a patchy attractor with pupae and adults spatially separated. The model attractors are consistent with experimental observations.     

猪链球菌4型疫苗用菌株的筛选

【背景】猪链球菌4型（Streptococcus suis serotype 4,SS4）分离率日益升高,对养殖业和公共卫生安全造成严重危害,目前尚无有效的SS4疫苗。【目的】筛选致病力强、抗原性好、遗传性状稳定的SS4疫苗菌种。【方法】以7株SS4分离株（代号为A1—A7）为受试菌株,通过累积法测定菌株半数致死量（LD₅₀）,ELISA测定免疫小鼠血清中IgG效价,攻毒保护试验测定免疫保护率,并采集小鼠脏器观察病理组织学变化。再连续传代培养受试菌株,分别对第10、20、30代菌株进行致病性和抗原性试验。【结果】A1—A7菌株对小鼠的LD₅₀分别为2.19×10⁸、1.76×10⁸、1.83×10⁸、1.01×10⁸、4.05×10⁸、1.19×10⁸和9.03×10⁷ CFU。二免7 d后,A1、A2、A3、A4、A6、A7免疫组IgG效价分别为1：1 600、1：1 600、1：3 200、1：6 400、1：3 200和1：6 400,免疫保护率分别为30%、30%、50%、70%、60%和80%,而且A4、A7免疫组小鼠组织病变较其余4组轻微。体外传至30代后,A4菌株的LD₅₀上升至3.81×10⁸ CFU,IgG效价下降至1：1 600,免疫保护率下降至40%,而A7菌株的LD₅₀上升至2.49×10⁸ CFU,IgG效价和免疫保护率稳定保持为1：6 400和80%,而且A7免疫组小鼠的组织病变较A4免疫组轻微。【结论】A7菌株（原始编号为HBgu18-4）具有强致病力和良好的抗原性,而且遗传性状均一、稳定,可作为SS4制苗候选菌株。     

Residue Specific Ribose and Nucleobase Dynamics of the cUUCGg RNA Tetraloop Motif by MNMR 13C Relaxation

The dynamics of the nucleobase and the ribose moieties in a 14-nt RNA cUUCGg hairpin-loop uniformly labeled with ¹³C and ¹⁵N were studied by ¹³C spin relaxation experiments. R₁, R_1ρ and the ¹³C-{¹H} steady-state NOE of C₆ and C_1′ in pyrimidine and C₈ and C_1′ in purine residues were obtained at 298 K. The relaxation data were analyzed by the model-free formalism to yield dynamic information on timescales of pico-, nano- and milli-seconds. An axially symmetric diffusion tensor with an overall rotational correlation time τ_c of 2.31±0.13 ns and an axial ratio of 1.35±0.02 were determined. Both findings are in agreement with hydrodynamic calculations. For the nucleobase carbons, the validity of different reported ¹³C chemical shift anisotropy values (Stueber, D. and Grant, D. M., 2002 J. Am. Chem. Soc. 124, 10539–10551; Fiala et al., 2000 J. Biomol. NMR 16, 291–302; Sitkoff, D. and Case, D. A., 1998 Prog. NMR Spectroscopy 32, 165–190) is discussed. The resulting dynamics are in agreement with the structural features of the cUUCGg motif in that all residues are mostly rigid (0.82 < S² < 0.96) in both the nucleobase and the ribose moiety except for the nucleobase of U7, which is protruding into solution (S² = 0.76). In general, ribose mobility follows nucleobase dynamics, but is less pronounced. Nucleobase dynamics resulting from the analysis of ¹³C relaxation rates were found to be in agreement with ¹⁵N relaxation data derived dynamic information (Akke et al., 1997 RNA 3, 702–709). Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Automata network theories in immunology: Their utility and their underdetermination

Small networks of threshold automata are used to model complex interactions between populations of regulatory cells (helpers and suppressors, antigen specific and anti-idiotypic) which participate in the immune response. The models, being discrete and semiquantitative, are well adapted to the situation of incomplete information often encounteredin vivo. However, the dynamics of many different network structures usually end up in the same attractor set. Thus, many different theories are equivalent in their explicative power for the same facts. This property, known as underdetermination of the theories by the facts, is given a quantitative estimate. It appears that such an underdetermination, as a kind of irreductible complexity, can be expected in manyin vivo biological processes, even when the number of interacting and functionally coupled elements is relatively small.