A Quantitative Cell Migration Assay for Murine Enteric Neural Progenitors

Neural crest cells (NCC) are a transient and multipotent cell population that originates from the dorsal neural tube and migrates extensively throughout the developing vertebrate embryo. In addition to providing peripheral glia and neurons, NCC generate melanocytes as well as most of the cranio-facial skeleton. NCC migration and differentiation is controlled by a combination of their axial origin along the neural tube and their exposure to regionally distinct extracellular cues. Such contribution of extracellular ligands is especially evident during the formation of the enteric nervous system (ENS), a complex interconnected network of neural ganglia that locally controls (among other things) gut muscle movement and intestinal motility. Most of the ENS is derived from a small initial pool of NCC that undertake a long journey in order to colonize - in a rostral to caudal fashion - the entire length of the prospective gut. Among several signaling pathways known to influence enteric NCC colonization, GDNF/RET signaling is recognized as the most important. Indeed, spatiotemporally controlled secretion of the RET ligand GDNF by the gut mesenchyme is chiefly responsible for the attraction and guidance of RET-expressing enteric NCC to and within the embryonic gut. Here, we describe an ex vivo cell migration assay, making use of a transgenic mouse line possessing fluorescently labeled NCC, which allows precise quantification of enteric NCC migration potential in the presence of various growth factors, including GDNF.     

A Quantitative Theory of Affinity-driven T Cell Repertoire Selection

Binding of the T cell antigen receptor (TCR) to peptides presented on molecules encoded by major histocompatibility complex (MHC) genes is the key event driving T cell development and activation. Selection of the T cell repertoire in the thymus involves two steps. First, positive selection promotes the survival of cells binding thymic self-MHC-peptide complexes with sufficient affinity. The resulting repertoire is self-MHC restricted: it recognizes foreign peptides presented on self, but not foreign MHC. Second, negative selection deletes cells which may be potentially harmful because their receptors interact with self-MHC-peptide complexes with too high an affinity. The mature repertoire is also highly alloreactive: a large fraction of T cells respond to tissues harboring foreign MHC. We derive mathematical expressions giving the frequency of alloreactivity, the level of self-MHC restriction, and the fraction of the repertoire activated by a foreign peptide, as a function of the parameters driving the generation and selection of the repertoire: self-MHC and self-peptide diversity, the stringencies of positive and negative selection, and the number of peptide and MHC polymorphic residues that contribute to T cell receptor binding. Although the model is based on a simplified digit string representation of receptors, all the parameters but one relate directly to experimentally determined quantities. The only parameter without a biological counterpart has no effect on the model's behavior besides a trivial and easily preventable discretization effect. We further analyse the role of the MHC and peptide contribution to TCR binding, and find that their relative, rather than absolute value, is important in shaping the mature repertoire. This result makes it possible to adopt different physical interpretations for the digit string formalism. We also find that the alloreactivity level can be inferred directly from data on the stringency of selection, and that, in agreement with recent experiments, it is not affected by thymic selection.     

Neural Mechanisms of Cortical Motion Computation Based on a Neuromorphic Sensory System

The visual cortex analyzes motion information along hierarchically arranged visual areas that interact through bidirectional interconnections. This work suggests a bio-inspired visual model focusing on the interactions of the cortical areas in which a new mechanism of feedforward and feedback processing are introduced. The model uses a neuromorphic vision sensor (silicon retina) that simulates the spike-generation functionality of the biological retina. Our model takes into account two main model visual areas, namely V1 and MT, with different feature selectivities. The initial motion is estimated in model area V1 using spatiotemporal filters to locally detect the direction of motion. Here, we adapt the filtering scheme originally suggested by Adelson and Bergen to make it consistent with the spike representation of the DVS. The responses of area V1 are weighted and pooled by area MT cells which are selective to different velocities, i.e. direction and speed. Such feature selectivity is here derived from compositions of activities in the spatio-temporal domain and integrating over larger space-time regions (receptive fields). In order to account for the bidirectional coupling of cortical areas we match properties of the feature selectivity in both areas for feedback processing. For such linkage we integrate the responses over different speeds along a particular preferred direction. Normalization of activities is carried out over the spatial as well as the feature domains to balance the activities of individual neurons in model areas V1 and MT. Our model was tested using different stimuli that moved in different directions. The results reveal that the error margin between the estimated motion and synthetic ground truth is decreased in area MT comparing with the initial estimation of area V1. In addition, the modulated V1 cell activations shows an enhancement of the initial motion estimation that is steered by feedback signals from MT cells.     

Quantitative Aspects of a Theory of Translocation

An analysis is made of two aspects of the behaviour of a proposedmechanism of translocation based on the mixing effect withina sieve-tube of streaming transcellular strands of protoplasmpassing through the sieve-pores and through a vacuole-like reservoirof sucrose solution in each sieve-element. First, the behaviour of the model is considered when it is transportinga solute (sucrose, for example) in the steady-state conditionof constant consumption and supply. It is found that the concentrationsof solute in the regions of the model are readily determinedat all points of the sieve-tube, and that the gradients of concentrationare all equal, the concentrations differing by constant amountsat all points. Transport is analogous to diffusive transferin that the steepness of the concentration gradient is proportionalto the rate of transfer and simple expressions are derived forthe net transport of solute and for the apparent diffusion coefficientin terms of the properties of the model. Transfer is found tobe rapid over a short path and slower over a longer path; thereis a maximum distance beyond which a given rate of transfercannot take place. Second, an analysis is made of the unsteady behaviour of themodel when changing concentrations of solute are introducedinto the system. The concept of strand diffusion time is introduced.This is the time taken for the concentration in the strand surroundedby an infinite reservoir to fall to I/e of its initial value.The results of this analysis are used to determine how radioactivesolute will become distributed when it is introduced into thesteady-state model. If the time over which the translocationof radioactive solute has proceeded is small compared with thestrand diffusion time, a wave-like profile of radioactivitywith distance is produced, and if large, the profile is of adiffusive kind; intermediate conditions give a profile displayingboth characteristics which is termed the transition type. Thesethree types of profile of radioactivity are exemplified by experimentsin different plants (Salix, Tropaeolum, and Helianthus), andthe experimental profiles are used to estimate (1) the apparentdiffusion coefficient of translocated sucrose in the sense ofMason and Maskell, and (2) the permeability constant of thestrand-reservoir boundary. The close correspondence betweenthese two sets of figures derived from the radioactive profileswith the experimental values obtained directly is regarded asstrong confirmation of the theory.     

Computation of the Full Likelihood Function for Estimating Variance at a Quantitative Trait Locus

The proportion of alleles identical by descent (IBD) determines the genetic covariance between relatives, and thus is crucial in estimating genetic variances of quantitative trait loci (QTL). However, IBD proportions at QTL are unobservable and must be inferred from marker information. The conventional method of QTL variance analysis maximizes the likelihood function by replacing the missing IBDs by their conditional expectations (the expectation method), while in fact the full likelihood function should take into account the conditional distribution of IBDs (the distribution method). The distribution method for families of more than two sibs has not been obvious because there are n(n - 1)/2 IBD variables in a family of size n, forming an n X n symmetrical matrix. In this paper, I use four binary variables, where each indicates the event that an allele from one of the four grandparents has passed to the individual. The IBD proportion between any two sibs is then expressed as a function of the indicators. Subsequently, the joint distribution of the IBD matrix is derived from the distribution of the indicator variables. Given the joint distribution of the unknown IBDs, a method to compute the full likelihood function is developed for families of arbitrary sizes.     

Psychosis-Proneness and Neural Correlates of Self-Inhibition in Theory of Mind

Impaired Theory of Mind (ToM) has been repeatedly reported as a feature of psychotic disorders. ToM is crucial in social interactions and for the development of social behavior. It has been suggested that reasoning about the belief of others, requires inhibition of the self-perspective. We investigated the neural correlates of self-inhibition in nineteen low psychosis prone (PP) and eighteen high PP subjects presenting with subclinical features. High PP subjects have a more than tenfold increased risk of developing a schizophrenia-spectrum disorder. Brain activation was measured with functional Magnetic Resonance Imaging during a ToM task differentiating between self-perspective inhibition and belief reasoning. Furthermore, to test underlying inhibitory mechanisms, we included a stop-signal task. We predicted worse behavioral performance for high compared to low PP subjects on both tasks. Moreover, based on previous neuroimaging results, different activation patterns were expected in the inferior frontal gyrus (IFG) in high versus low PP subjects in self-perspective inhibition and simple response inhibition. Results showed increased activation in left IFG during self-perspective inhibition, but not during simple response inhibition, for high PP subjects as compared to low PP subjects. High and low PP subjects showed equal behavioral performance. The results suggest that at a neural level, high PP subjects need more resources for inhibiting the self-perspective, but not for simple motor response inhibition, to equal the performance of low PP subjects. This may reflect a compensatory mechanism, which may no longer be available for patients with schizophrenia-spectrum disorders resulting in ToM impairments.     

BP人工神经网络在光谱定量预测中的应用

人工神经网络是模仿大脑神经元网络结构和功能而建立的一种信息处理系统,广泛的应用于各种波谱数据处理。误差反向传播多层前馈式网络(back-propagation network,简称BP网络)应用最广,发展最为迅速。将BP神经网络用于紫外-可见吸收光谱和拉曼光谱数据的定量分析和预测,与原文的一元线性回归模型数据处理方法相比,获得了比较满意的预测结果,预测精度有显著提高。这为相关的光谱分析和数据处理提供了一种更有效、更精确的方法。     

形成于细胞骨架微管中的量子计算

微管是细胞骨架中的重要组成部分和功能组件,其中充满了液体水。本文基于腔量子电动力学描述了微管中水的电偶极子与电磁辐射场的相互作用,并论述了基于量子力学原理的量子计算,进而探讨了微管实现量子计算的一种可能机理。     

混沌理论及其在建立神经网络模型中的应用

随着许多学科的相互紧密交叉以及混沌理论的日益深入的研究,人们从生物现象中提出了许多与混沌有关的神经网络模型,本文对混沌理论的基本原理做了简要概述,并着重介绍了四种有代表性的混沌神经网络模型及其应用．同时指出这一研究方向无论在理论还是在应用方面都具有十分诱人的前景．     

Quantitative Design of Regulatory Elements Based on High-Precision Strength Prediction Using Artificial Neural Network

Accurate and controllable regulatory elements such as promoters and ribosome binding sites (RBSs) are indispensable tools to quantitatively regulate gene expression for rational pathway engineering. Therefore, de novo designing regulatory elements is brought back to the forefront of synthetic biology research. Here we developed a quantitative design method for regulatory elements based on strength prediction using artificial neural network (ANN). One hundred mutated Trc promoter & RBS sequences, which were finely characterized with a strength distribution from 0 to 3.559 (relative to the strength of the original sequence which was defined as 1), were used for model training and test. A precise strength prediction model, NET90_19_576, was finally constructed with high regression correlation coefficients of 0.98 for both model training and test. Sixteen artificial elements were in silico designed using this model. All of them were proved to have good consistency between the measured strength and our desired strength. The functional reliability of the designed elements was validated in two different genetic contexts. The designed parts were successfully utilized to improve the expression of BmK1 peptide toxin and fine-tune deoxy-xylulose phosphate pathway in Escherichia coli. Our results demonstrate that the methodology based on ANN model can de novo and quantitatively design regulatory elements with desired strengths, which are of great importance for synthetic biology applications.     

Towards a Quantitative Theory of Epidermal Calcium Profile Formation in Unwounded Skin

We propose and mathematically examine a theory of calcium profile formation in unwounded mammalian epidermis based on: changes in keratinocyte proliferation, fluid and calcium exchange with the extracellular fluid during these cells’ passage through the epidermal sublayers, and the barrier functions of both the stratum corneum and tight junctions localised in the stratum granulosum. Using this theory, we develop a mathematical model that predicts epidermal sublayer transit times, partitioning of the epidermal calcium gradient between intracellular and extracellular domains, and the permeability of the tight junction barrier to calcium ions. Comparison of our model’s predictions of epidermal transit times with experimental data indicates that keratinocytes lose at least 87% of their volume during their disintegration to become corneocytes. Intracellular calcium is suggested as the main contributor to the epidermal calcium gradient, with its distribution actively regulated by a phenotypic switch in calcium exchange between keratinocytes and extracellular fluid present at the boundary between the stratum spinosum and the stratum granulosum. Formation of the extracellular calcium distribution, which rises in concentration through the stratum granulosum towards the skin surface, is attributed to a tight junction barrier in this sublayer possessing permeability to calcium ions that is less than 15 nm s⁻¹ in human epidermis and less than 37 nm s⁻¹ in murine epidermis. Future experimental work may refine the presented theory and reduce the mathematical uncertainty present in the model predictions.     

Advancing Genetic Theory and Application by Metabolic Quantitative Trait Loci Analysis

This review describes recent advances in the analysis of metabolism using quantitative genetics. It focuses on how recent metabolic quantitative trait loci (QTL) studies enhance our understanding of the genetic architecture underlying naturally variable phenotypes and the impact of this fundamental research on agriculture, specifically crop breeding. In particular, the role of whole-genome duplications in generating quantitative genetic variation within a species is highlighted and the potential uses of this phenomenon presented. Additionally, the review describes how new observations from metabolic QTL mapping analyses are helping to shape and expand the concepts of genetic epistasis.     

Quantitative Reconstruction of Weaning Ages in Archaeological Human Populations Using Bone Collagen Nitrogen Isotope Ratios and Approximate Bayesian Computation

BackgroundNitrogen isotope analysis of bone collagen has been used to reconstruct the breastfeeding practices of archaeological human populations. However, weaning ages have been estimated subjectively because of a lack of both information on subadult bone collagen turnover rates and appropriate analytical models.MethodologyTemporal changes in human subadult bone collagen turnover rates were estimated from data on tissue-level bone metabolism reported in previous studies. A model for reconstructing precise weaning ages was then developed using a framework of approximate Bayesian computation and incorporating the estimated turnover rates. The model is presented as a new open source R package, WARN (Weaning Age Reconstruction with Nitrogen isotope analysis), which computes the age at the start and end of weaning, ¹⁵N-enrichment through maternal to infant tissue, and value of collagen synthesized entirely from weaning foods with their posterior probabilities. The model was applied to 39 previously reported Holocene skeletal populations from around the world, and the results were compared with weaning ages observed in ethnographic studies.ConclusionsThere were no significant differences in the age at the end of weaning between the archaeological (2.80±1.32 years) and ethnographic populations. By comparing archaeological populations, it appears that weaning ages did not differ with the type of subsistence practiced (i.e., hunting–gathering or not). Most of -enrichment (2.44±0.90‰) was consistent with biologically valid values. The nitrogen isotope ratios of subadults after the weaning process were lower than those of adults in most of the archaeological populations (−0.48±0.61‰), and this depletion was greater in non-hunter–gatherer populations. Our results suggest that the breastfeeding period in humans had already been shortened by the early Holocene compared with those in extant great apes.     

Computation of biopolymers: A general approach to different problems

A comparative analysis of some effective algorithms widely used in analysis, computation and comparison of chain molecules is presented. A notion of a stream in an oriented hypergraph is introduced, which generalizes a notion of a path in a graph. All considered algorithms looking over exponential sets of structures in polynomial time can be described as variants of a general algorithm of analysis of paths in graphs and of streams in oriented hypergraphs.     

Condor-G: A Computation Management Agent for Multi-Institutional Grids

In recent years, there has been a dramatic increase in the number of available computing and storage resources. Yet few tools exist that allow these resources to be exploited effectively in an aggregated form. We present the Condor-G system, which leverages software from Globus and Condor to enable users to harness multi-domain resources as if they all belong to one personal domain. We describe the structure of Condor-G and how it handles job management, resource selection, security, and fault tolerance. We also present results from application experiments with the Condor-G system. We assert that Condor-G can serve as a general-purpose interface to Grid resources, for use by both end users and higher-level program development tools.     

A Quantitative Study of Cellular Rheotropism

Sparsely sowed, hence independent Botrytis spores, which are fixed to the wall of a laminar flow chamber, tend to germinate downstream. For a velocity, v_∞, one cell radius from the wall, of 0.1 to 1000 μ/second, this tendency, expressed as a percentage of perfect orientation, approximates 9 · log (10 v_∞). Indirect proof is given that this rheotropic response is mediated by the convection across each cell of a diffusible stimulator emitted by it. Analysis of the response indicates that this stimulator has a diffusion constant of the order of 10^-7 cm²/second and thus is macromolecular, and a half-life of the order of 10 seconds and thus a radius of action in a stagnant medium of about one cell diameter. The rate of germination falls so slowly with increasing flow rate as to indicate a much lower sensitivity of the rate than of the localization of growth to this stimulator's concentration.     

A Quantitative Measure of Field Illumination

In this paper, we describe a statistically based algorithm to quantify the uniformity of illumination in an optical light microscopy imaging system that outputs a single quality factor (QF) score. The importance of homogeneous field illumination in quantitative light microscopy is well understood and often checked. However, there is currently no standard automatic quantitative measure of the uniformity of the field illumination. Images from 89 different laser-scanning confocal microscopes (LSCMs), which were collected as part of an international study on microscope quality assessment, were used as a “training” set to build the algorithm. To validate the algorithm and verify its robustness, images from 33 additional microscopes, including LSCM and wide-field (WF) microscopes, were used. The statistical paradigm used for developing the quality scoring scale was a regression approach to supervised learning. Three intensity profiles across each image—2 corner-to-corner diagonals and a center horizontal—were used to generate pixel-intensity data. All of the lines passed through the center of the image. The intensity profile data then were converted into a single-field illumination QF score in the range of 0–100, with 0 having extreme variation, and therefore, essentially unusable, and 100 having no deviation, i.e., straight lines with a constant uniform intensity. Empirically, a QF ≥ 83 was determined to be the minimum acceptable value based on manufacturer acceptance tests and reasonably achievable values. This new QF is an invaluable metric to ascertain objectively and easily the uniformity of illumination quality, provide a traceable reference for monitoring field uniformity over time, and make a direct comparison among different microscopes. The QF can also be used as an indicator of system failure and the need for alignment or service of the instrument.