The coordinated mapping of visual space and response features in visual cortex

Whether general principles can explain the layouts of cortical maps remains unresolved. In primary visual cortex of ferret, the relationships between the maps of visual space and response features are predicted by a "dimension-reduction" model. The representation of visual space is anisotropic, with the elevation and azimuth axes having different magnification. This anisotropy is reflected in the orientation, ocular dominance, and spatial frequency domains, which are elongated such that their directions of rapid change, or high-gradient axes, are orthogonal to the high-gradient axis of the visual map. The feature maps are also strongly interdependent-their high-gradient regions avoid one another and intersect orthogonally where essential, so that overlap is minimized. Our results demonstrate a clear influence of the visual map on each feature map. In turn, the local representation of visual space is smooth, as predicted when many features are mapped within a cortical area.     

ODS2: a multiplatform software application for creating integrated physical and genetic maps

A contig map is a physical map that shows the native order of a library of overlapping genomic clones. One common method for creating such maps involves using hybridization to detect clone overlaps. False- positive and false-negative hybridization errors, the presence of chimeric clones, and gaps in library coverage lead to ambiguity and error in the clone order. Genomes with good genetic maps, such as Neurospora crassa, provide a means for reducing ambiguities and errors when constructing contig maps if clones can be anchored with genetic markers to the genetic map. A software application called ODS2 for creating contig maps based on clone-clone hybridization data is presented. This application is also designed to exploit partial ordering information provided by anchorage of clones to a genetic map. This information, along with clone-clone hybridization data, is used by a clone ordering algorithm and is represented graphically, allowing users to interactively align physical and genetic maps. ODS2 has a graphical user interface and is implemented entirely in Java, so it runs on multiple platforms. Other features include the flexibility of storing data in a local file or relational database and the ability to create full or minimum tiling contig maps.     

Nhs: network-based hierarchical segmentation for cryo-electron microscopy density maps

Cryo-electron microscopy (cryo-EM) experiments yield low-resolution (3-30 ?) 3D-density maps of macromolecules. These density maps are segmented to identify structurally distinct proteins, protein domains, and subunits. Such partitioning aids the inference of protein motions and guides fitting of high-resolution atomistic structures. Cryo-EM density map segmentation has traditionally required tedious and subjective manual partitioning or semisupervised computational methods, whereas validation of resulting segmentations has remained an open problem in this field. We introduce a network-based hierarchical segmentation (Nhs) method, that provides a multi-scale partitioning, reflecting local and global clustering, while requiring no user input. This approach models each map as a graph, where map voxels constitute nodes and weighted edges connect neighboring voxels. Nhs initiates Markov diffusion (or random walk) on the weighted graph. As Markov probabilities homogenize through diffusion, an intrinsic segmentation emerges. We validate the segmentations with ground-truth maps based on atomistic models. When implemented on density maps in the 2010 Cryo-EM Modeling Challenge, Nhs efficiently and objectively partitions macromolecules into structurally and functionally relevant subregions at multiple scales.     

SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps

In this paper the theoretical framework used to build a superfamily probability in electron microscopy (SPI-EM) is presented. SPI-EM is a new tool for determining the homologous superfamily to which a protein domain belongs looking at its three-dimensional electron microscopy map. The homologous superfamily is assigned according to the domain-architecture database CATH. Our method follows a probabilistic approach applied to the results of fitting protein domains into maps of proteins and the computation of local cross-correlation coefficient measures. The method has been tested and its usefulness proven with isolated domains at a resolution of 8 A and 12 A. Results obtained with simulated and experimental data at 10 A suggest that it is also feasible to detect the correct superfamily of the domains when dealing with electron microscopy maps containing multi-domain proteins. The inherent difficulties and limitations that multi-domain proteins impose are discussed. Our procedure is complementary to other techniques existing in the field to detect structural elements in electron microscopy maps like alpha-helices and beta-sheets. Based on the proposed methodology, a database of relevant distributions is being built to serve the community.     

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage

MOTIVATION: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning. RESULTS: This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage. AVAILABILITY: http://sbg.cib.csic.es/Software/ADP_EM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

An integrated computational workflow for efficient and quantitative modeling of renin inhibitors

A new integrated computational workflow that couples the strength of the molecular overlay methods to achieve rapid and automated alignments along with 3D-QSAR techniques like CoMFA and CoMSIA for quantitative binding affinity prediction is presented. The results obtained from such techniques are compared with rule-based Topomer CoMFA method, where possible. The developed 3D-QSAR models were prospectively used to predict the affinities of new compounds designed through R-group deconvolution starting from the core chemical scaffold and subsequent virtual combinatorial library enumeration. The general applicability of the seamless in silico modeling workflow is demonstrated using several datasets reported for small molecule inhibitors of renin.     

Relationships between plant communities and late snow melting on Mount Prado (Northern Apennines,Italy)

Relationships between the spatial and temporal distribution of long-lasting snow-cover and the spatial distribution of plant communities above timberline were studied on Mount Prado (2054 m), a representative sample area of the summit vegetation of the Northern Apennines (Italy). The spatial analysis was carried out by creating a geographic information system. Vegetation map and two snow-cover maps were both georeferenced to a scale 1 : 2000. The vegetation map is formed by 28 plant communities (including 7 combinations of communities, or vegetation mosaics) distributed into 277 map polygons. The maps were compared by an overlay procedure. The results show that the six plant communities (including three mosaics) which have a June snow-cover higher than 60% are diversified by a snow-melting gradient from early June to mid-July. The slowest snow melt corresponds to a snow-bed community (Salicetum herbaceae) and to a mesophytic grassland (Trifolium thalii-Festuca puccinellii community, Luzula alpino-pilosa variant).     

Cover-Encodings of Fitness Landscapes

The traditional way of tackling discrete optimization problems is by using local search on suitably defined cost or fitness landscapes. Such approaches are however limited by the slowing down that occurs when the local minima that are a feature of the typically rugged landscapes encountered arrest the progress of the search process. Another way of tackling optimization problems is by the use of heuristic approximations to estimate a global cost minimum. Here, we present a combination of these two approaches by using cover-encoding maps which map processes from a larger search space to subsets of the original search space. The key idea is to construct cover-encoding maps with the help of suitable heuristics that single out near-optimal solutions and result in landscapes on the larger search space that no longer exhibit trapping local minima. We present cover-encoding maps for the problems of the traveling salesman, number partitioning, maximum matching and maximum clique; the practical feasibility of our method is demonstrated by simulations of adaptive walks on the corresponding encoded landscapes which find the global minima for these problems.     

Discrete structure of van der Waals domains in globular proteins

Most globular proteins are divisible by domains, distinct substructures of the globule. The notion of hierarchy of the domains was introduced earlier via van der Waals energy profiles that allow one to subdivide the proteins into domains (subdomains). The question remains open as to what is the possible structural connection of the energy profiles. The recent discovery of the loop-n-lock elements in the globular proteins suggests such a structural connection. A direct comparison of the segmentation by van der Waals energy criteria with the maps of the locked loops of nearly standard size reveals a striking correlation: domains in general appear to consist of one to several such loops. In addition, it was demonstrated that a variety of subdivisions of the same protein into domains is just a regrouping of the loop-n-lock elements.     

Reliability of map accuracy assessments: A comment on Hunter et al. (2016)

Map validation data that are ambiguously allocated to map units and collected via poorly designed sampling methods are not statistically reliable and will misrepresent map quality. A recent paper published in Ecological Management and Restoration (Ecological Management & Restoration, 17, 2016 and 40) reported that a map in south‐eastern Australia provided little or no predictive accuracy based on new field data, but the validation suffered from the aforementioned pitfalls. In this comment, we outline the basic guidelines for a robust, reliable and transparent accuracy assessment of thematic maps, pointing out where (Ecological Management & Restoration, 17, 2016 and 40) fails to meets these guidelines.     

An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence.

The genome of the model plant species Arabidopsis thaliana has recently been sequenced. To accelerate its current genome research, we developed a whole-genome, BAC/BIBAC-based, integrated physical, genetic, and sequence map of the A. thaliana ecotype Columbia. This new map was constructed from the clones of a new plant-transformation-competent BIBAC library and is integrated with the existing sequence map. The clones were restriction fingerprinted by DNA sequencing gel-based electrophoresis, assembled into contigs, and anchored to an existing genetic map. The map consists of 194 BAC/BIBAC contigs, spanning 126 Mb of the 130-Mb Arabidopsis genome. A total of 120 contigs, spanning 114 Mb, were anchored to the chromosomes of Arabidopsis. Accuracy of the integrated map was verified using the existing physical and sequence maps and numerous DNA markers. Integration of the new map with the sequence map has enabled gap closure of the sequence map and will facilitate functional analysis of the genome sequence. The method used here has been demonstrated to be sufficient for whole-genome physical mapping from large-insert random bacterial clones and thus is applicable to rapid development of whole-genome physical maps for other species.     

Mapping functional traits: comparing abundance and presence-absence estimates at large spatial scales

Efforts to quantify the composition of biological communities increasingly focus on functional traits. The composition of communities in terms of traits can be summarized in several ways. Ecologists are beginning to map the geographic distribution of trait-based metrics from various sources of data, but the maps have not been tested against independent data. Using data for birds of the Western Hemisphere, we test for the first time the most commonly used method for mapping community trait composition - overlaying range maps, which assumes that the local abundance of a given species is unrelated to the traits in question - and three new methods that as well as the range maps include varying degrees of information about interspecific and geographic variation in abundance. For each method, and for four traits (body mass, generation length, migratory behaviour, diet) we calculated community-weighted mean of trait values, functional richness and functional divergence. The maps based on species ranges and limited abundance data were compared with independent data on community species composition from the American Christmas Bird Count (CBC) scheme coupled with data on traits. The correspondence with observed community composition at the CBC sites was mostly positive (62/73 correlations) but varied widely depending on the metric of community composition and method used (R(2): 5.6×10(-7) to 0.82, with a median of 0.12). Importantly, the commonly-used range-overlap method resulted in the best fit (21/22 correlations positive; R(2): 0.004 to 0.8, with a median of 0.33). Given the paucity of data on the local abundance of species, overlaying range maps appears to be the best available method for estimating patterns of community composition, but the poor fit for some metrics suggests that local abundance data are urgently needed to allow more accurate estimates of the composition of communities.     

CPROP: a rule-based program for constructing genetic maps.

Gene mapping assigns chromosomal coordinates to genetic loci based on analysis of fragmentary ordering and metric data. In assembling genetic maps, geneticists use rules of inference to derive new facts about order and distance between loci from experimentally derived conclusions about order and distance. They construct comprehensive maps by merging related sets of data and resolving conflicts between them. In this article we describe software that formalizes and automates some of these rules of inference to yield a useful map construction utility called CPROP.     

Derivation of a physical map of chloroplast DNA from Nicotiana tabacum by two-dimensional gel and computer-aided restriction analysis

A combined approach was used to derive a detailed physical map of Nicotiana tabacum chloroplast DNA for the restriction enzymes SalI, SmaI, KpnI, and BamHI. Complete maps for the restriction enzymes SalI, SmaI, and KpnI were derived by using two-dimensional agarose gel analysis of fragments obtained by reciprocal double digestion of chloroplast DNA. We have characterized a complete cloned library of N. tabacum chloroplast DNA which contains overlapping restriction fragments resulting from partial digestion by BamHI. With these clones and existing data, we used a novel computer-aided analysis to derive a detailed map for the enzyme BamHI. A comparison and compilation of all published N. tabacum chloroplast DNA restriction maps is presented. Differences between ours and a previously published SmaI and BamHI restriction map are discussed.     

Mapping genes for common diseases: the case for genetic (LD) maps

We examine the current effort to develop a haplotype map of the human genome and suggest an alternative approach which represents linkage disequilibrium patterns in the form of a metric LD map. LD maps have some of the useful properties of genetic linkage maps but have a much higher resolution which is optimal for SNP-based association mapping of common diseases. The studies that have been undertaken to date suggest that LD and recombination maps show some close similarities because of abundant, narrow, recombination hot spots. These hot spots are co-localised in all populations but, unlike linkage maps, LD maps differ in scale for different populations because of differences in population history. The prospects for developing optimized panels of SNPs and the use of linkage disequilibrium maps in disease gene localisation are assessed in the light of recent evidence.     

Misuse of bird digital distribution maps creates reversed spatial diversity patterns in the Amazon

It is well known that bird richness in the Amazon is greater in upland forests and that seasonally flooded forest is particularly species poor. However, the misleading pattern of greater bird richness in seasonally flooded forest has emerged seemingly unnoticed numerous times in richness maps in the literature. We hypothesize that commission errors in digital distribution maps (DDMs) are the cause behind the misleading richness pattern. In the Amazon, commission errors are a consequence of the different methodological treatment given to large‐ranged versus small‐ranged habitat specialists when mapping distributions. DDMs of 1007 Amazonian birds were examined, and maps that had commission errors were corrected. We generated two richness maps, one from the overlay of original DDMs and another from the overlay of the corrected ones. We identified 291 species whose distribution maps had errors. In the original data, seasonally flooded forests showed higher species richness than upland forest, but this pattern was reverted in the corrected richness map. Commission errors were 35 times more likely in the seasonally flooded forest. We conclude that DDMs accurately portray the distribution of single species in the Amazon. Commission errors in individual maps, however, accumulate when they are overlaid, explaining the misleading pattern for birds in the Amazon. DDMs can continue to be used mapping richness, as long as, at a regional scale: (1) basic map refinements are carried, or (2) only small‐range species are used for mapping species richness.     

Cognitive and Geographic Maps: Study of Individual Variation Among Tojolabal Mayans

Disease and geography are related domains for Tojolabal-Maya. Using multidimensional methods, we compare two domains: (1) individual cognitive "maps" from disease terms and (2) hand-drawn maps, both with one another and with an official topographic map. Multivariate study of individual informant data demonstrates correspondence of the axes of maps. Least squares fitting of dimensional representations using a method specifically modified for ethnosemantic data allows meaningful comparisons both among and within informants, and with an aggregate from a related survey of 33 informants as well. These multivariate operations help integrate individual data, sampled simultaneously for several domains, tasks, and occasions, with aggregate data. For semantic domains, we achieved rapprochement between psychological and anthropological approaches. [disease, folk theories, ethnosemantics, cognition, multivariate, Tojolabal-Maya]     

First International Workshop on Porcine Chromosome 6

Recent advances in the use of microsatellite markers and the development of comparative gene mapping techniques have made the construction of high resolution genetic maps of livestock species possible. Framework and comprehensive genetic linkage maps of porcine chromosome 6 have resulted from the first international effort to integrate genetic maps from multiple laboratories. Eleven highly polymorphic genetic markers were exchanged and mapped by four independent laboratories on a total of 583 animals derived from four reference populations. The chromosome 6 framework map consists of 10 markers ordered with high local support. The average marker interval of the framework map is 15.1 cM (sex averaged). The framework map is 135, 175 and 109 cM in length (for sex averaged, female and male maps, respectively). The comprehensive map includes a total of 48 type I and type II markers with a sex averaged interval of 3.5 cM and is 166, 196 and 126 cM (for sex averaged, female and male maps, respectively). Additional markers within framework map marker intervals can thus be selected from the comprehensive map for further analysis of quantitive trait loci (QTL) located on chromosome 6. The resulting maps of swine chromosome 6 provide a valuable tool for analysing and locating QTL.     

A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12

A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F₂ mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman''s rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R₁₂, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.