Can Molecular Motors Drive Distance Measurements in Injured Neurons?

Injury to nerve axons induces diverse responses in neuronal cell bodies, some of which are influenced by the distance from the site of injury. This suggests that neurons have the capacity to estimate the distance of the injury site from their cell body. Recent work has shown that the molecular motor dynein transports importin-mediated retrograde signaling complexes from axonal lesion sites to cell bodies, raising the question whether dynein-based mechanisms enable axonal distance estimations in injured neurons? We used computer simulations to examine mechanisms that may provide nerve cells with dynein-dependent distance assessment capabilities. A multiple-signals model was postulated based on the time delay between the arrival of two or more signals produced at the site of injury–a rapid signal carried by action potentials or similar mechanisms and slower signals carried by dynein. The time delay between the arrivals of these two types of signals should reflect the distance traversed, and simulations of this model show that it can indeed provide a basis for distance measurements in the context of nerve injuries. The analyses indicate that the suggested mechanism can allow nerve cells to discriminate between distances differing by 10% or more of their total axon length, and suggest that dynein-based retrograde signaling in neurons can be utilized for this purpose over different scales of nerves and organisms. Moreover, such a mechanism might also function in synapse to nucleus signaling in uninjured neurons. This could potentially allow a neuron to dynamically sense the relative lengths of its processes on an ongoing basis, enabling appropriate metabolic output from cell body to processes.     

χ Recombination Activity in Phage λ Decays as a Function of Genetic Distance

In Escherichia coli, χ is a recombination hotspot that stimulates RecBCD-dependent exchange at and to one side of itself. χ activity is highest at χ and decreases with distance from χ. The decrease in χ activity may be a simple property of the physical distance over which χ can stimulate recombination. Alternatively, the decay in χ activity with distance may reflect the high likelihood that χ-stimulated recombination occurs in a single χ-proximal act, to the exclusion of additional χ-stimulated exchanges more distal to χ. To test the models, we determined if χ activity decreases as a function of physical distance (i.e., DNA base pairs) or genetic distance (homologous DNA base pairs). Our results indicate that χ activity decays as a function of genetic distance. In addition, we found that the sbcB gene product (exonuclease I, a 3' -> 5' ssDNA exonuclease) modulates the distance over which χ can act. In contrast, the recJ gene product (a 5' -> 3' ssDNA exonuclease) does not alter the decay of χ activity.     

Are Lateral Roots of Tomato Spaced by Multiples of a Fundamental Distance?

Roots of tomato (Lycopersicon esculentum Miller) were culturedin vitro for 8-16 d at the end of which period the number ofdaughter roots (first order laterals), and their distributionon the mother root axis, were recorded. It was observed thatthe daughter roots are distributed along the mother root intwo series, and that their longitudinal distribution, in bothseries and in the total series, was non-random, in the senseof being systematically spaced out rather than systematicallyclustered. There was an approximately two-thirds probabilitythat a daughter root would be on the opposite side of the rootfrom its closest sister in the proximal direction, but thisfinding seemed explicable by the observed 'spaced-out' distributionin each series, without invoking any interaction between thetwo side series. Earlier, it had been suggested that distancesbetween successive sister roots in a series are multiples ofa quantum distance, probably because the daughter roots observedare a subset of a set of evenly spaced candidate root primordia,the rest of which are developmentally arrested. The sister-sisterdistances were analysed statistically for the presence of sucha quantum. However, although some daughter root series showeda statistically significant quantal tendency, this did not seemto be a general feature of the mother roots.Copyright 1993,1999 Academic Press Angiosperms, Lycopersicon esculentum, tomato, lateral root, root primordia, roots in vitro, cosine quantogram     

Does Locomotor Ability Influence Flight Initiation Distance in Yellow‐Bellied Marmots?

Flight initiation distance (FID) is the distance between a potential threat and the point at which a potential prey flees. Animals may modify their FID to compensate for increased risk generated by external/extrinsic factors such as habitat type, visibility, group size, time of year, predator‐approach velocity, and distance to burrow, as well as internal/intrinsic factors such as physical condition, body temperature, crypsis, and morphological antipredator defenses. The intrinsic speed at which an animal can escape a predator is a factor that should influence FID. We studied the relationship between an individual's intrinsic escape speed and FID in yellow‐bellied marmots (Marmota flaviventris) to determine whether marmots compensated for slower escape speeds by fleeing at greater distances. We found no evidence of risk compensation. Rather, we found that slower marmots tolerated closer approaches. This behavioral syndrome may be explained by a coevolution of FID and escape speed in determining an individual's antipredator behavior, an idea upon which we expand.     

Priming of Social Distance? Failure to Replicate Effects on Social and Food Judgments

Williams and Bargh (2008) reported an experiment in which participants were simply asked to plot a single pair of points on a piece of graph paper, with the coordinates provided by the experimenter specifying a pair of points that lay at one of three different distances (close, intermediate, or far, relative to the range available on the graph paper). The participants who had graphed a more distant pair reported themselves as being significantly less close to members of their own family than did those who had plotted a more closely-situated pair. In another experiment, people's estimates of the caloric content of different foods were reportedly altered by the same type of spatial distance priming. Direct replications of both results were attempted, with precautions to ensure that the experimenter did not know what condition the participant was assigned to. The results showed no hint of the priming effects reported by Williams and Bargh (2008).     

婚姻地域距离及其变化的研究 A Study of Distance and Variation of Marriage

对居住在新疆伊犁的1494对汉族夫妇进行了婚姻地域距离调查,并按不同年代、居住地、职业及文化程度分组进行了比较分析和统计学处理。结果表明,不同年代间、不同地域间、不同职业及不同文化程度间平均婚姻距离有显著性差异。 Abstract:A study of distance between birth places of husband and wife was carried out in Yili district,Xinjiang.In this study 1 494 couples of Han nationality were investigated.All couples were divided into different groups according to year of marriage,place,occupation and education.The averages of different groups were compared with each other and tested statistically.Significant difference of distance between birth places,of husband and wife was observed between different groups.     

An Empirical Exploration of the (δμ)2 Genetic Distance for 213 Human Microsatellite Markers

Microsatellites are now used ubiquitously as genetic markers. One important application is to the assessment of population subdivision and phylogenetic relatedness. Such applications require a method of estimation of genetic distance. Here we examine the most widely used measure of microsatellite genetic distance, Goldstein et al.'s delta-mu squared ([delta mu]2), with respect to a large data set of 213 markers typed across samples from four diverse human populations. We find that (delta mu)2 yields plausible interpopulation distances. For the first time, we report significant interpopulation differences in mean microsatellite length, although the effect of these differences on (delta mu)2 is negligible. However, we also show that the method is extremely sensitive to one or two loci that contribute extreme values, even when a sample size of >200 loci is used. Some of these extreme loci can be removed on the grounds that some alleles carry large indels, but for others there is no clear justification for exclusion a priori. Our data suggest a rather recent African/non-African split, with an upper limit of some 70,000-80,000 years ago.     

A Geometric Buildup Algorithm for the Solution of the Distance Geometry Problem Using Least-Squares Approximation

We propose a new geometric buildup algorithm for the solution of the distance geometry problem in protein modeling, which can prevent the accumulation of the rounding errors in the buildup calculations successfully and also tolerate small errors in given distances. In this algorithm, we use all instead of a subset of available distances for the determination of each unknown atom and obtain the position of the atom by using a least-squares approximation instead of an exact solution to the system of distance equations. We show that the least-squares approximation can be obtained by using a special singular value decomposition method, which not only tolerates and minimizes small distance errors, but also prevents the rounding errors from propagation effectively, especially when the distance data is sparse. We describe the least-squares formulations and their solution methods, and present the test results from applying the new algorithm for the determination of a set of protein structures with varying degrees of availability and accuracy of the distances. We show that the new development of the algorithm increases the modeling ability, and improves stability and robustness of the geometric buildup approach significantly from both theoretical and practical points of view.     

Distance,dams and drift: what structures populations of an endangered,benthic stream fish?

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IAEA/NUS Distance Learning Diploma Training Course for Tissue Bank Operators – Past, Present and Future

National University Hospital (NUH) Tissue Bank as the Regional Training Centre for Asia Pacific Region provided National University of Singapore (NUS) Diploma Course in Tissue Banking - a long distance diploma course since 1997. To date, five batches have participated - 94 tissue bank operators. Sixty-three tissue bank operators have convocated with NUS Diploma in Tissue Banking.From Regional Co-operative Agreement (RCA) Project, RAS 7/008 technology transfer was effected to Latin America and to Africa.A Memorandum of Understanding has been signed between International Atomic Energy Agency (IAEA) and NUS in July 2002 making Singapore the International Training Centre. An Internet NUS Diploma Course in Tissue Banking has been developed by IAEA and NUS. The first on-line diploma course will be launched in 2003.     

Distance Measurements and Conformational Analysis of sn-2-Arachidonoylglycerol-Membrane Sample by 2H–31P REDOR NMR

The purpose of these studies is to determine the intermolecular distances that define the location, orientation, and conformation of 2-AG in palmitoyl-oleoyl-phosphatidylcholine (POPC) lipid bilayers using rotational-echo double-resonance (REDOR) NMR. All five protons on the glycerol backbone of 2-AG were replaced with ²H and the distance between the deuterons and naturally occurring ³¹P on the POPC lipid headgroup determined with REDOR. To determine the distance from each deuteron to the phosphorus, the POPC headgroup was arranged in a hexagonal array. The 2-AG intercalates between the lipid molecules and the ²H labels, resulting in an average distance of z directly above or below the center of the parallelogram of the four phosphorus atoms P₁, P₂, P₃, and P₄. For different z values, the ²H–³¹P inter-nuclear distances were 7.6–9.1 Å (²H–³¹P₁ and ²H–³¹P₃₁) and 4.4–6.7 Å (²H–³¹P₂ and ²H–³¹P₄). Each result involved the calculations and summation of 893,101 terms. Based on the curve-fitting parameters, the calculations with z = 0 fits the data the best, which means these methylene ²H atoms are at the same level as the phosphate group of the POPC lipid bilayer. Molecular dynamic simulation data suggested that the ²H atoms at the glycerol backbone of 2-AG are involved in an extended H-bonding network with the phosphorus atoms after 10-ns simulation.     

Distance decay of similarity in freshwater communities: do macro‐ and microorganisms follow the same rules?

Aim An intensively debated issue in macroecology is whether unicellular organisms show biogeographic patterns different from those of macroorganisms. One aspect of this debate addresses beta diversity, that is, do microbial organisms exhibit distance‐decay patterns similar to those of macroorganisms? And if so, is the decay of community similarity caused by spatially limited dispersal or by niche‐related factors? We studied the community similarity of stream diatoms, macroinvertebrates and bryophytes across the same set of sites in relation to environmental and geographic distance. Location A geographical gradient of c. 1100 km in Finland. Methods We first identified the subset of environmental variables that produced the highest correlation with community similarities for each taxonomic group. Based on these variables, we used partial Mantel tests to separate the independent influences of environmental and geographical distance for distance decay of community similarity, separately for diatoms, bryophytes and macroinvertebrates. Finally, macroinvertebrates were divided into three groups based on their different dispersal categories and a partial Mantel test was used to assess whether each of these groups were differently affected by environmental versus geographic distance, i.e. is dispersal a key factor in tests of niche versus neutral models. Results The level of environmental control was by far the strongest for diatoms; however, all groups were controlled more by environmental factors than by limited dispersal. Macroinvertebrate species with low dispersal ability were significantly related to geographic distance, while more effective dispersers showed no relationship to geography but were instead strongly related to environmental distance. Main conclusions Our results suggest that patterns between macro‐ and microorganisms are not fundamentally different, but the level of environmental control varies according to dispersal ability. The relative importance of niche versus dispersal processes is not simply a function of organism size but other traits (e.g. life‐history type, dispersal capacity) may obscure this relationship.     

How Close Do We Live to Water? A Global Analysis of Population Distance to Freshwater Bodies

Traditionally, people have inhabited places with ready access to fresh water. Today, over 50% of the global population lives in urban areas, and water can be directed via tens of kilometres of pipelines. Still, however, a large part of the world''s population is directly dependent on access to natural freshwater sources. So how are inhabited places related to the location of freshwater bodies today? We present a high-resolution global analysis of how close present-day populations live to surface freshwater. We aim to increase the understanding of the relationship between inhabited places, distance to surface freshwater bodies, and climatic characteristics in different climate zones and administrative regions. Our results show that over 50% of the world''s population lives closer than 3 km to a surface freshwater body, and only 10% of the population lives further than 10 km away. There are, however, remarkable differences between administrative regions and climatic zones. Populations in Australia, Asia, and Europe live closest to water. Although populations in arid zones live furthest away from freshwater bodies in absolute terms, relatively speaking they live closest to water considering the limited number of freshwater bodies in those areas. Population distributions in arid zones show statistically significant relationships with a combination of climatic factors and distance to water, whilst in other zones there is no statistically significant relationship with distance to water. Global studies on development and climate adaptation can benefit from an improved understanding of these relationships between human populations and the distance to fresh water.     

β-Diversity and Species Accumulation in Antarctic Coastal Benthos: Influence of Habitat,Distance and Productivity on Ecological Connectivity

High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in β-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100''s of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and β–diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on β-diversity at scales <290 km, while the effects of productivity were low and significant only at scales >40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance.     

Earth Mover’s Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations

Changes in the frequencies of cell subsets that (co)express characteristic biomarkers, or levels of the biomarkers on the subsets, are widely used as indices of drug response, disease prognosis, stem cell reconstitution, etc. However, although the currently available computational “gating” tools accurately reveal subset frequencies and marker expression levels, they fail to enable statistically reliable judgements as to whether these frequencies and expression levels differ significantly between/among subject groups. Here we introduce flow cytometry data analysis pipeline which includes the Earth Mover’s Distance (EMD) metric as solution to this problem. Well known as an informative quantitative measure of differences between distributions, we present three exemplary studies showing that EMD 1) reveals clinically-relevant shifts in two markers on blood basophils responding to an offending allergen; 2) shows that ablative tumor radiation induces significant changes in the murine colon cancer tumor microenvironment; and, 3) ranks immunological differences in mouse peritoneal cavity cells harvested from three genetically distinct mouse strains.     

On the Use of Distance in the Taxonomic Study of Critical Plant Groups—Case Studies of Western European Orchidaceae

Four distance coefficients are compared on four data sets composed of samples coming from western European populations of the genera Dactylorhiza, Orchis and Epipactis (Orchidaceae). The performance of the distance coefficients is evaluated through: (a) the quality of clusters obtained by five classical methods (as compared to a priori classification), (b) the Mantel statistic with respect to an a priori distance matrix resulting from previous knowledge, (c) the result obtained with the k-means method, and (d) principal coordinate diagrams. It appears that: (a) the Mahalanobis distance based on the pooled dispersion matrix performs best on the whole; (b) a distance based on the recently developed Common Principal Component model, used with a log transformation, also provides useful information and performs best on the largest data set; (c) the Gölz and Reinhard taxonomic distance, widely used among orchidologists, is attractive for its simplicity, yet good performance and the valuable information it provides, despite its theoretical shortcomings. A brief taxonomic discussion is made on the results obtained for the Dactylorhiza samples, especially about samples whose identification was in doubt.     

Monophyly,Distance and Character–Based Multigene Barcoding Reveal Extraordinary Cryptic Diversity in Nassarius: A Complex and Dangerous Community

Background

Correct identification and cryptic biodiversity revelation for marine organisms are pressing since the marine life is important in maintaining the balance of ecological system and is facing the problem of biodiversity crisis or food safety. DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Nassarius, the common mudsnail, plays an important role in marine environment and has problem in food safety, but the classification of it is quite confused because of the complex morphological diversity.

Methodology/Principal Findings

Here we report a comprehensive barcoding analysis of 22 Nassarius species. We integrated the mitochondrial and nuclear sequences and the morphological characters to determine 13 Nassarius species studied and reveal four cryptic species and one pair synonyms. Distance, monophyly, and character–based barcoding methods were employed.

Conclusions/Significance

Such successful identification and unexpected cryptic discovery is significant for Nassarius in food safety and species conversation and remind us to pay more attention to the hidden cryptic biodiversity ignored in marine life. Distance, monophyly, and character–based barcoding methods are all very helpful in identification but the character-based method shows some advantages.     

Does Competition Really Bring Out the Worst? Testosterone,Social Distance and Inter-Male Competition Shape Parochial Altruism in Human Males

Parochial altruism, defined as increased ingroup favoritism and heightened outgroup hostility, is a widespread feature of human societies that affects altruistic cooperation and punishment behavior, particularly in intergroup conflicts. Humans tend to protect fellow group members and fight against outsiders, even at substantial costs for themselves. Testosterone modulates responses to competition and social threat, but its exact role in the context of parochial altruism remains controversial. Here, we investigated how testosterone influences altruistic punishment tendencies in the presence of an intergroup competition. Fifty male soccer fans played an ultimatum game (UG), in which they faced anonymous proposers that could either be a fan of the same soccer team (ingroup) or were fans of other teams (outgroups) that differed in the degree of social distance and enmity to the ingroup. The UG was played in two contexts with varying degrees of intergroup rivalry. Our data show that unfair offers were rejected more frequently than fair proposals and the frequency of altruistic punishment increased with increasing social distance to the outgroups. Adding an intergroup competition led to a further escalation of outgroup hostility and reduced punishment of unfair ingroup members. High testosterone levels were associated with a relatively increased ingroup favoritism and also a change towards enhanced outgroup hostility in the intergroup competition. High testosterone concentrations further predicted increased proposer generosity in interactions with the ingroup. Altogether, a significant relation between testosterone and parochial altruism could be demonstrated, but only in the presence of an intergroup competition. In human males, testosterone may promote group coherence in the face of external threat, even against the urge to selfishly maximize personal reward. In that way, our observation refutes the view that testosterone generally promotes antisocial behaviors and aggressive responses, but underlines its rather specific role in the fine-tuning of male social cognition.