Context-Dependent Competition in a Model Gut Bacterial Community

Understanding the ecological processes that generate complex community structures may provide insight into the establishment and maintenance of a normal microbial community in the human gastrointestinal tract, yet very little is known about how biotic interactions influence community dynamics in this system. Here, we use natural strains of Escherichia coli and a simplified model microbiota to demonstrate that the colonization process on the strain level can be context dependent, in the sense that the outcome of intra-specific competition may be determined by the composition of the background community. These results are consistent with previous models for competition between organisms where one competitor has adapted to low resource environments whereas the other is optimized for rapid reproduction when resources are abundant. The genomic profiles of E. coli strains representing these differing ecological strategies provide clues for deciphering the genetic underpinnings of niche adaptation within a single species. Our findings extend the role of ecological theory in understanding microbial systems and the conceptual toolbox for describing microbial community dynamics. There are few, if any, concrete examples of context-dependent competition on a single trophic level. However, this phenomenon can have potentially dramatic effects on which bacteria will successfully establish and persist in the gastrointestinal system, and the principle should be equally applicable to other microbial ecosystems.     

基于反馈控制离散Lotka-Volterra竞争模型的持续生存和稳定性

针对一类具有偏离自变量的离散Lotka-Volterra竞争模型,考虑到不可避免的外界扰动,通过引入反馈控制,基于一定的分析技巧得到该系统持久性与全局稳定性的充分条件.生态意义上表明:在外界扰动下,具有偏离自变量的离散Lotka-Volterra竞争模型仍能持续生存并保持全局稳定发展.     

广义隐Markov模型在基因识别中的应用

广义隐Markov模型(GHMM)是基因识别的一种重要模型,但是其计算量比传统的隐Markov模型大得多,以至于不能直 接在基因识别中使用。根据原核生物基因的结构特点,提出了一种高效的简化算法,其计算量是序列长度的线性函数。在此 基础上,构建了针对原核生物基因的识别程序GeneMiner,对实际数据的测试表明,此算法是有效的。     

The Global Hidden Hunger Indices and Maps: An Advocacy Tool for Action

The unified global efforts to mitigate the high burden of vitamin and mineral deficiency, known as hidden hunger, in populations around the world are crucial to the achievement of most of the Millennium Development Goals (MDGs). We developed indices and maps of global hidden hunger to help prioritize program assistance, and to serve as an evidence-based global advocacy tool. Two types of hidden hunger indices and maps were created based on i) national prevalence data on stunting, anemia due to iron deficiency, and low serum retinol levels among preschool-aged children in 149 countries; and ii) estimates of Disability Adjusted Life Years (DALYs) attributed to micronutrient deficiencies in 136 countries. A number of countries in sub-Saharan Africa, as well as India and Afghanistan, had an alarmingly high level of hidden hunger, with stunting, iron deficiency anemia, and vitamin A deficiency all being highly prevalent. The total DALY rates per 100,000 population, attributed to micronutrient deficiencies, were generally the highest in sub-Saharan African countries. In 36 countries, home to 90% of the world’s stunted children, deficiencies of micronutrients were responsible for 1.5-12% of the total DALYs. The pattern and magnitude of iodine deficiency did not conform to that of other micronutrients. The greatest proportions of children with iodine deficiency were in the Eastern Mediterranean (46.6%), European (44.2%), and African (40.4%) regions. The current indices and maps provide crucial data to optimize the prioritization of program assistance addressing global multiple micronutrient deficiencies. Moreover, the indices and maps serve as a useful advocacy tool in the call for increased commitments to scale up effective nutrition interventions.     

具有抑制剂和营养循环的恒化器竞争模型

在具有抑制剂的恒化器竞争模型中考虑营养循环的作用,得到系统有界和持久的充分条件。     

NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

Background  

Nuclear localization signals (NLSs) are stretches of residues within a protein that are important for the regulated nuclear import of the protein. Of the many import pathways that exist in yeast, the best characterized is termed the 'classical' NLS pathway. The classical NLS contains specific patterns of basic residues and computational methods have been designed to predict the location of these motifs on proteins. The consensus sequences, or patterns, for the other import pathways are less well-understood.     

具有抑制剂的恒化器竞争模型的分析（英文）

考虑了具有抑制剂的两种群竞争一种微生物的恒化器模型,其中吸收函数和功能反应函数都是营养的一般单调递增函数,并且一种微生物能够分泌一种对另一种微生物起致命影响的抑制剂.利用常微分方程定性理论,首先得到了平衡点的存在条件和局部渐进稳定性;然后讨论了全局渐进稳定性,以及极限环和Hopf分支的存在性.     

Exploring the Competition between Proliferative and Invasive Cancer Phenotypes in a Continuous Spatial Model

Tumor is characterized by extensive heterogeneity with respect to its microenvironment and its genetic composition. We extend a previously developed monoclonal continuous spatial model of tumor growth to account for polyclonal cell populations and investigate the interplay between a more proliferative and a more invasive phenotype under different conditions. The model simulations demonstrate a transition from the dominance of the proliferative to the dominance of the invasive phenotype resembling malignant tumor progression and show a time period where both subpopulations are abundant. As the dominant phenotype switches from proliferative to invasive, the geometry of tumor changes from a compact and almost spherical shape to a more diffusive and fingered morphology with the proliferative phenotype to be restricted in the tumor bulk and the invasive to dominate at tumor edges. Different micro-environmental conditions and different phenotypic properties can promote or inhibit invasion demonstrating their mutual importance. The model provides a computational framework to investigate tumor heterogeneity and the constant interplay between the environment and the specific characteristics of phenotypes that should be taken into account for the prediction of tumor evolution, morphology and effective treatment.     

Action Potential Initiation in the Hodgkin-Huxley Model

A recent paper of B. Naundorf et al. described an intriguing negative correlation between variability of the onset potential at which an action potential occurs (the onset span) and the rapidity of action potential initiation (the onset rapidity). This correlation was demonstrated in numerical simulations of the Hodgkin-Huxley model. Due to this antagonism, it is argued that Hodgkin-Huxley-type models are unable to explain action potential initiation observed in cortical neurons in vivo or in vitro. Here we apply a method from theoretical physics to derive an analytical characterization of this problem. We analytically compute the probability distribution of onset potentials and analytically derive the inverse relationship between onset span and onset rapidity. We find that the relationship between onset span and onset rapidity depends on the level of synaptic background activity. Hence we are able to elucidate the regions of parameter space for which the Hodgkin-Huxley model is able to accurately describe the behavior of this system.     

Variational Bayes Analysis of a Photon-Based Hidden Markov Model for Single-Molecule FRET Trajectories

Single-molecule fluorescence resonance energy transfer (smFRET) measurement is a powerful technique for investigating dynamics of biomolecules, for which various efforts have been made to overcome significant stochastic noise. Time stamp (TS) measurement has been employed experimentally to enrich information within the signals, while data analyses such as the hidden Markov model (HMM) have been successfully applied to recover the trajectories of molecular state transitions from time-binned photon counting signals or images. In this article, we introduce the HMM for TS-FRET signals, employing the variational Bayes (VB) inference to solve the model, and demonstrate the application of VB-HMM-TS-FRET to simulated TS-FRET data. The same analysis using VB-HMM is conducted for other models and the previously reported change point detection scheme. The performance is compared to other analysis methods or data types and we show that our VB-HMM-TS-FRET analysis can achieve the best performance and results in the highest time resolution. Finally, an smFRET experiment was conducted to observe spontaneous branch migration of Holliday-junction DNA. VB-HMM-TS-FRET was successfully applied to reconstruct the state transition trajectory with the number of states consistent with the nucleotide sequence. The results suggest that a single migration process frequently involves rearrangement of multiple basepairs.     

Hidden altruism in a real-world setting

Concerns for reputation can promote cooperative behaviour. Individuals that behave cooperatively stand to benefit if they gain in influence, status or are more likely to be chosen as interaction partners by others. Most theoretical and empirical models of cooperation predict that image score will increase with cooperative contributions. Individuals are therefore expected to make higher contributions when observed by others and should opt to make contributions publicly rather than privately, particularly when contributions are higher than average. Here, however, I find the opposite effect. Using data from an online fundraising website, I show that donors are more likely to opt for anonymity when making extremely low and extremely high donations. Mid-range donations, on the other hand, are typically publicized. Recent work has shown that extremely generous individuals may be ostracized or punished by group members. The data presented here suggest that individuals may hide high donations to avoid these repercussions.     

Density-Dependent Selection Incorporating Intraspecific Competition. II. a Diploid Model

A diploid model is introduced and analyzed in which intraspecific competition is incorporated within the context of density-regulated selection. It is assumed that each genotype has a unique carrying capacity corresponding to the equilibrium population size when only that type is present. Each genotypic fitness at a single diallelic autosomal locus is a decreasing function of a distinctive effective population size perceived as a result of intraspecific competition. The resulting fitnesses are both density and frequency dependent with selective advantage determined by a balance between genotypic carrying capacity and sensitivity to intraspecific competition. A major finding is that intergenotypic interactions may allow genetic variation to be more easily maintained than in the corresponding model of purely density-dependent selection. In addition, numerical study confirms the possible existence of multiple interior equilibria and that neither overdominance in fitness nor carrying capacity is necessary for stability. The magnitude of the equilibrium population size and optimization principles are also discussed.     

一类微生物连续培养竞争模型的定性分析

研究一类微生物连续培养竞争模型的解的结构,分析了平衡点的稳定性及平衡点附近极限环存在唯一性,证明系统存在正向不变集。     

MicroRNA target prediction based on second-order Hidden Markov Model

MicroRNAs are one class of small single-stranded RNA of about 22 nt serving as important negative gene regulators. In animals, miRNAs mainly repress protein translation by binding itself to the 3′ UTR regions of mRNAs with imperfect complementary pairing. Although bioinformatics investigations have resulted in a number of target prediction tools, all of these have a common shortcoming—a high false positive rate. Therefore, it is important to further filter the predicted targets. In this paper, based on miRNA:target duplex, we construct a second-order Hidden Markov Model, implement Baum-Welch training algorithm and apply this model to further process predicted targets. The model trains the classifier by 244 positive and 49 negative miRNA:target interaction pairs and achieves a sensitivity of 72.54%, specificity of 55.10% and accuracy of 69.62% by 10-fold cross-validation experiments. In order to further verify the applicability of the algorithm, previously collected datasets, including 195 positive and 38 negative, are chosen to test it, with consistent results. We believe that our method will provide some guidance for experimental biologists, especially in choosing miRNA targets for validation.     

Model for the Action of Calcium in Muscle

CALCIUM ions play an important part in contraction^1–3, but little is known of the way that changes in internal calcium actually control the events that lead to the development of tension. Most experiments involving calcium have been performed under steady state conditions at different stabilized calcium concentrations^4–9 and can only give limited information as to the action of calcium. Recently, tension transient experiments have been described at either constant calcium concentration^6,7 or when the calcium concentration was varying in a known manner^10,11. From these and related experiments, a model for the kinetics of calcium has been deduced which predicts not only the time course of tension development from just a knowledge of the free calcium concentration, but which is also able to correlate the ATPase, tension and calcium binding responses in the steady state. The model considers that two calciums act as separate effectors with a de-repressant action in the same functional unit.     

Competition in a pHauxostat

Summary Competition between a rapidly growing bacterium and a slower growing yeast was studied in a bioreactor with feed rate controlled by the rate of consumption of substrate. The dilution rate increase indicates the take over by the faster organism. Simple models track well with the actual data.     

杂草与作物竞争模型研究进展

杂草的历史与人类农业史并存。最早科学报道竞争现象是在１４世纪,而开始杂草与作物竞争关系的定量研究则是在本世纪初叶［１］。杂草科学研究较农业病虫害研究起步晚,与许多发达国家相比,我国杂草科学在基础理论方面比较落后,但应用方面发展较快。从系统生态学的高度研究杂草与作物竞争关系是杂草科学研究的一个重要领域,前人为此作了许多有益的工作,并建立了有关的模型,这些模型为解决草害问题起了应有的作用。下面就杂草与作物竞争经验模型的建立、杂草与作物竞争的动态模拟研究、杂草与作物竞争研究在杂草科学管理中的应用等三个…