Configuration-dependent properties of randomly coiling polynucleotide chains. II. The role of the phosphodiester linkage

The dependence of the unperturbed dimensions of randomly coiling polynucleotides on the rotations about the phosphodiester linkages of the chain has been examined in order to understand the conformational discrepancies, set forth in paper I, regarding these angles (ω′ and ω). Large values of the characteristic ratio 〈r²〉₀/nl² , which agree with the experimental behavior of the chain, are obtained only if a sizeable proportion of the polymer residues have trans ω′ values. The asymmetric torsional potential that is believed to arise from gauche effects associated with the P-O bonds has been approximated using a hard core model. The calculated characteristic ratio exhibits a strong dependence upon the magnitude of this torsional barrier (separating trans and gauche conformations) and shows agreement with experimental values for polyribonucleotides only if this energy difference is 1 kcal/mol or less.     

Estimating cell lineage from distributions of randomly introduced markers

Cell lineage of a multicellular organism has been analysed by introducing a genetic or chemical marker that is inherited from a cell to its daughter cells and is detectable even after several cell divisions. To construct a complete cell lineage, all the cells at different developmental stages need to be identified, and then the intracellular marker must be introduced to each cell. In this paper, I study a new method of estimating cell lineage based on distributions of intercellular markers observed at a single stage, which are introduced randomly at earlier stages. Assumptions are: (1) cell lineage is invariant between embryos; (2) a small number of cells are marked in each experiment; and (3) the total number of replicate experiments is sufficiently large. Then we identify the most likely cell lineage pattern (or tree topology) as the one that requires the least marker insertions to be compatible with the observed distributions of cell markers. This method is essentially the same as the principle of persimony widely used for ancestral phylogeny reconstruction in evolutionary biology. When the total number of cells is small, we can generate all the possible cell lineages and calculate the minimum number of marker insertions for each candidate, and then choose the cell lineage that requires the least marker insertions. If the number of cells is large, we can use clustering method in which a pair of cells with the highest correlation in marker labelling are merged sequentially. The efficiency of the clustering method in estimating the correct cell lineage is confirmed by computer simulations. Finally, the clustering method is applied to reconstruct the cell lineage of ascidian from experimental data.     

Nonhomogeneous spatial distributions of populations

Summary Spatial inhomogeneities such as nonconstant population densities usually will be attributed to random effects or to an inhomogeneous substrate. Such an explanation may be incorrect since from certain chemical reactions it is known that the interaction of species together with diffusion may generate nonhomogeneous spatial structures. However, the effect of boundary conditions has been so far neglected. In this paper nonlinear and linear interaction-diffusion models are investigated under various side-conditions by analytic methods and by computer simulations. A remarkable fact, as compared with earlier results in the field, is the example of an interaction-diffusion process which in the whole space has only the constant as a stable limit distribution, whereas the introduction of a side condition, e.g. a population reservoir or a barrier, leads to standing spatial population waves.     

The measurement of spatial precursor distributions in cell culture

Summary The distribution of incorporated radioactive precursors, for both DNA and protein synthesis, has been measured with a resolution of about 1 mm in cell cultures, using a scanning technique. Either γ radiation and X-rays or β radiation (electrons) were detected by scintillation detectors. Spectrophotometer measurements with a resolution of 1 mm gave good estimates of cell density changes. Glioma cell colonies were used to compared this technique with autoradiography. Variables such as the density of labelled cells and percentage of labelled cells could be estimated rather accurately. For example, an increased cell density was correlated to a local decrease in DNA synthesis. The work has been supported financially by the Swedish Cancer Society and the Swedish Natural Science Research Council.     

Configuration-dependent properties of randomly coiling polynucleotide chains. I. A comparison of theoretical energy estimates

Various theoretical estimates of the conformational energy associated with polynucleotides in solution have been compared with each other and also with the experimentally observed conformations found in X-ray crystallographic investigations of low-molecular-weight nucleic acid analogs. In view of the disparities between these data, certain configuration-dependent properties (i.e., the mean-square unperturbed end-to-end distance 〈r²〉₀ and the average vicinal nmr coupling constant 〈J〉) appropriate to randomly coiling polynucleotides described by either the energy estimates or by the crystallographically preferred conformations have also been calculated and compared with the known solution behavior of polynucleotide chains. Both the theoretical energy surfaces and the X-ray data show good agreement with the nmr coupling constant indications of the preferred rotations about the O-C and C-C bonds of the chain backbone. The principal discrepancies between the theoretical methods and X-ray data arise in their ability to predict successfully the preferred rotations about the two phosphodiester bonds of the chain backbone and the unperturbed dimensions of randomly coiling polynucleotide chains.     

中国潜在植被空间分布格局

潜在植被作为一种与所处立地达到平衡的演替终态,反映的是无人类干扰情况下,立地所能发育形成的最稳定成熟的一种顶极植被类型,是一个地区现状植被的发展趋势。潜在植被的研究能够真实反映气候条件对植被形态变化的影响,是植被-环境分类与关系研究的起点,也是全球变化与陆地生态系统研究的关键。以综合顺序分类法为基本理论基础,在GIS研究方法支持下,利用我国2348个气象台站1961～1990年30a的气候资料,对我国潜在植被类型进行了划分,得出以下结论：（1）分布在我国的潜在植被类型有41类,表现出了我国潜在植被的多样性特征;从面积相对比例来看,我国潜在植被在分布面积上很不均匀,面积最大的寒冷潮湿多雨冻原、高山草甸类分布面积达到1526188km^2,面积最小的炎热微干稀树草原类分布面积仅为13km^2。（2）海拔0～6800m之间,是我国潜在植被主要分布的海拔界限,并且此海拔段植被多样性随海拔变化呈现出一定的规律性,即随海拔增加植被多样性显著下降。（3）我国潜在植被的空间分布很好的体现了三向地带性规律,而决定这种分布的主要原因是太阳辐射的纬度性变化、距离海洋的远近引起水分条件变化以及由海拔高度引起的从基带向上热量和干湿变化。（4）我国潜在植被空间格局在重心分布上,主要表现为空间聚集（P1、P2、P3、P4、P5、P6）和空间线型邻接（L1、L2、L3）两个主要特征。     

Measurement of non-randomness in spatial distributions

The measurement of departure from randomness in spatial distributions has widespread application in ecological work. Several “indices of non-randomness” are compared with regard to their dependence on sample number, sample size and density. Criteria for the best choice of index for specific situations are discussed. A new coefficient C_x is proposed for use with positively contagious distributions and tests of significance are given. When C_x and another index (S²/m−1) are used for positive and negative contagion respectively, values ranging from −1 through 0 (random) to +1 are obtained, regardless of sample number, sample size or density.     

The effects of various spatial distributions of weak noise on rhythmic spiking

We consider the response of the classical Hodgkin–Huxley (HH) spatial system in the weak to intermediate noise regime near the bifurcation to repetitive spiking. The deterministic component of the input (signal) is restricted to a small segment near the origin whereas noise, with parameter σ, occurs either only in the signal region or throughout the whole neuron. In both cases small noise inhibits the spiking and there is a minimum in the spike counts at σ ≈ 0.15. At the same value of σ, the variance of the spike counts undergoes a pronounced maximum. For spatially restricted noise, the spike count continues to increase beyond the minimum until σ = 0.5, but in the case of spatially extended noise the spike count begins to decline around σ = 0.35 to give a local maximum. For both spatial distributions of noise, the variance of the spike count is found to also have a local minimum at about σ = 0.4. Examples are given of the probability distributions of the spike counts and the spatial distributions of spikes with varying noise level. The differences in behaviours of the spike counts as noise increases beyond 0.3 are attributable to noise-induced spiking outside the signal region, which has a larger probability of occurrence when the noise is over an extended region. This aspect is investigated by ascertaining the probability of noise-induced spiking as a function of noise level and examination of the corresponding latency distributions. These findings prompt a definition of weak noise in the standard HH model as that for which the probability of secondary phenomena is negligible, which occurs when σ is less than about 0.3. Finally, if signal and weak (σ < 0.3) noise are applied on disjoint intervals, then the noise has no effect on the instigation or propagation of spikes, no matter how large its region of application. These results are expected to apply to type 2 neurons in general, including the majority of cortical pyramidal cells.     

Colonization rules and spatial distributions in ecology

Because they are intuitive and mathematically straight-forward, colonization rules are often used to model spatial patterns in ecology. Colonization rules assign individuals to categories according to the locations of previous colonists. In this note, a compact introduction to colonization rules in ecology is presented with implications for autocorrelation and spatial distributions. I use the colonization rule approach to unify a diverse set of spatial and species diversity analyses, exploring future extensions to incorporate greater realism.     

Larval trematode infections and spatial distributions of snails

Abstract. The hypothesis that infecting trematodes influence the spatial distribution of the estuarine snail Ilyanassa obsoleta was tested. This work was conducted in the Savages Ditch habitat, Rehoboth Bay, DE, USA, which has an essentially flat, sandy-mud bottom bordered by saltmarsh shorelines and many infected snails. In 1996, two groups of snails were individually marked and released from one location after being screened for trematode infections. One group, transplanted from sites where snails tended not to be infected, consisted of snails that tested as uninfected. The other group consisted of snails native to Savages Ditch. Species of trematode carried by each snail was recorded. Marked snails were found and their positions were recorded until 2001. Snails were in five infection categories: (1) not infected, and infected with (2) Himasthla quissetensis , or (3) Lepocreadium setiferoides or (4) Zoogonus rubellus , or (5) with both H. quissetensis and Z. rubellus . The results show that the spatial distributions of snails depended on whether or not they were infected and, if infected, on which trematode species they carried. To complete life cycles, these parasites must accomplish transmission from the first (the snail) to the second intermediate hosts by short-lived, swimming cercariae. These data do not allow resolution of why snails distributed as they did, but sighting distributions of infected snails can be related to distributions of second hosts and it is proposed that parasites engender host snail distributions that improve chances of transmission.     

The nature of stacking equilibria in polynucleotides

Temperature melting profiles of adenylyladenosine and cytidylylcytidine were examined by ultraviolet absorption, circular dichroism, and optical rotatory dispersion. They showed the following characteristics: profiles for different absorption wavelengths are identical as defined by least-squares computed optical and thermodynamic parameters; melting curves obtained by the three spectroscopic methods are likewise in all cases identical by a series of criteria; in terms of the operational equilibrium constant for base-stacking all van't Hoff plots are linear; absorption spectra and circular dichroism curves at a series of temperatures for both dinucleoside phosphates give excellent isosbestic points; a matrix-rank analysis of the family of complete spectra at different temperatures gives a value of two for the numbers of components in both cases. Four criteria are thus fulfilled of a two-state system for the stacking equilibrium. The results are not compatible with a multi-state scheme in which the substates are optically distinguishable. There is no measurable effect of ionic strength up to 1.0. In a presence of high concentrations of lithium chloride the criteria for two-state behavior are no longer fulfilled, and examination of infrared spectra gives evidence of complex formation by this salt, though not by sodium chloride. A destacking profile, similar to that observed on heating, is obtained by progressive addition of ethylene glycol to the solution. It is suggested that in dimers, though not in higher oligomers or polymers, the stacking equilibrium can be operationally regarded as a two-state system, and that the meaningful thermodynamic parameters can be extracted by analytical treatment, of the type here developed, of the melting profiles.     

Landscape configuration drives persistent spatial patterns of occupant distributions

Variation in the density of organisms among habitat patches is often attributed to variation in inherent patch properties. For example, higher quality patches might have higher densities because they attract more colonists or confer better post-colonization survival. However, variation in occupant density can also be driven by landscape configuration if neighboring patches draw potential colonists away from the focal habitat (a phenomenon we call propagule redirection). Here, we develop and analyze a stochastic model to quantify the role of landscape configuration and propagule redirection on occupant density patterns. We model a system with a dispersive larval stage and a sedentary adult stage. The model includes sensing and decision-making in the colonization stage and density-dependent mortality (a proxy for patch quality) in the post-colonization stage. We demonstrate that spatial variation in colonization is retained when the supply of colonists is not too high, post-colonization density-dependent survival is not too strong, and colonization events are not too frequent. Using a reef fish system, we show that the spatial variation produced by propagule redirection is comparable to spatial variation expected when patch quality varies. Thus, variation in density arising from the spatial patterning of otherwise identical habitat can play an important role in shaping long-term spatial patterns of organisms occupying patchy habitats. Propagule redirection is a potentially powerful mechanism by which landscape configuration can drive variation in occupant densities, and may therefore offer new insights into how populations may shift as landscapes change in response to natural and anthropogenic forces.     

Modeling of spatial metabolite distributions in the cardiac sarcomere

Although a high ATP diffusion rate implies homogeneous distribution of the principal energetic currency in the cytosol, local diffusion barriers represented by macromolecular structures can render ATP concentrations to be inhomogeneous. A method is presented here that provides apparent diffusion coefficient values in local intracellular regions and allows the estimation of spatial metabolite distribution. The apparent local diffusion coefficient for ATP in cardiac myofibrils was determined from the analysis of diffusion-dependent rightward shift of the substrate dependence for actomyosin ATPase activity using the reaction-diffusion model, which accounted for the properties of phosphotransfer reactions. This functional analysis, which took into account the local diffusional ATP delivery to the active sites, provided an apparent value that was three orders of magnitude lower than that defined by direct methods for the cytosol. The low value of the diffusion coefficient was shown to define unusual properties of the intracellular space in working heart, where small reductions in ATP levels in the surrounding cytosol result in a large drop in [ATP] inside myofibrils. This drop is critical for vital cellular functions, and the analysis presented here defines its physical basis. The diffusion barriers thus defined explain the coexistence of pathological energy deficit with almost normal average ATP levels.     

Improved spatial estimates of climate predict patchier species distributions

Aim

Correlative species distribution models (SDMs) combined with spatial layers of climate and species' localities represent a frequently utilized and rapid method for generating spatial estimates of species distributions. However, an SDM is only as accurate as the inputs upon which it is based. Current best‐practice climate layers commonly utilized in SDM (e.g. ANUCLIM) are frequently inaccurate and biased spatially. Here, we statistically downscale 30 years of existing spatial weather estimates against empirical weather data and spatial layers of topography and vegetation to produce highly accurate spatial layers of weather. We proceed to demonstrate the effect of inaccurately quantified spatial data on SDM outcomes.

Location

The Australian Wet Tropics.

Methods

We use Boosted Regression Trees (BRTs) to generate 30 years of spatial estimates of daily maximum and minimum temperature for the study region and aggregate the resultant weather layers into ‘accuCLIM’ climate summaries, comparable with those generated by current best‐practice climate layers. We proceed to generate for seven species of rainforest skink comparable SDMs within species; one model based on ANUCLIM climate estimates and another based on accuCLIM climate estimates.

Results

Boosted Regression Trees weather layers are more accurate with respect to empirically measured temperature, particularly for maximum temperature, when compared to current best‐practice weather layers. ANUCLIM climate layers are least accurate in heavily forested upland regions, frequently over‐predicting empirical mean maximum temperature by as much as 7°. Distributions of the focal species as predicted by accuCLIM were more fragmented and contained less core distributional area.

Conclusion

Combined these results reveal a source of bias in climate‐based SDMs and indicate a solution in the form of statistical downscaling. This technique will allow researchers to produce fine‐grained, ground‐truthed spatial estimates of weather based on existing estimates, which can be aggregated in novel ways, and applied to correlative or process‐based modelling techniques.