Classical Mapping Research Articles

Structure of the Variscan metamorphic complexes in the central transect of the Posada-Asinara Line (SW Gallura region, Northern Sardinia, Italy)

This study represents the first detailed tectono-metamorphic map of the metamorphic complexes cropping out in the inner portion of the Variscan belt in north-central Sardinia Island (Italy). The Main Map is at a 1:30.000 scale and covers an area of c. 148 km2. It is based on 1: 10.000 scale classic field mapping and represents an overview of the lithological and structural complexities documented in the metasedimentary and migmatite domes cropping out along the central transect of the Posada-Asinara Line (PAL). The PAL is a crustal scale discontinuity that divides migmatites from the metasedimentary sequences affected by greenschist- to amphibolite-facies metamorphism. The map shows the orientations of the superimposed foliations, fold axes and mineral lineations on the basis of geometric crosscutting relationships and, for the first time, the location of ductile-brittle and brittle shear zones developed during the long-lived activity of the Posada-Asinara Line.

Efficient linkage mapping using exome capture and extreme QTL in schistosome parasites.

BackgroundIdentification of parasite genes that underlie traits such as drug resistance and host specificity is challenging using classical linkage mapping approaches. Extreme QTL (X-QTL) methods, originally developed by rodent malaria and yeast researchers, promise to increase the power and simplify logistics of linkage mapping in experimental crosses of schistosomes (or other helminth parasites), because many 1000s of progeny can be analysed, phenotyping is not required, and progeny pools rather than individuals are genotyped. We explored the utility of this method for mapping a drug resistance gene in the human parasitic fluke Schistosoma mansoni.ResultsWe staged a genetic cross between oxamniquine sensitive and resistant parasites, then between two F1 progeny, to generate multiple F2 progeny. One group of F2s infecting hamsters was treated with oxamniquine, while a second group was left untreated. We used exome capture to reduce the size of the genome (from 363 Mb to 15 Mb) and exomes from pooled F2 progeny (treated males, untreated males, treated females, untreated females) and the two parent parasites were sequenced to high read depth (mean = 95-366×) and allele frequencies at 14,489 variants compared. We observed dramatic enrichment of alleles from the resistant parent in a small region of chromosome 6 in drug-treated male and female pools (combined analysis: = 11.07, p = 8.74 × 10-29). This region contains Smp_089320 a gene encoding a sulfotransferase recently implicated in oxamniquine resistance using classical linkage mapping methods.ConclusionsThese results (a) demonstrate the utility of exome capture for generating reduced representation libraries in Schistosoma mansoni, and (b) provide proof-of-principle that X-QTL methods can be successfully applied to an important human helminth. The combination of these methods will simplify linkage analysis of biomedically or biologically important traits in this parasite.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-617) contains supplementary material, which is available to authorized users.

A novel viable allele of Arabidopsis CULLIN1 identified in a screen for superroot2 suppressors by next generation sequencing-assisted mapping.

Map-based cloning (MBC) is the conventional approach for linking phenotypes to genotypes, and has been successfully used to identify causal mutations in diverse organisms. Next-generation sequencing (NGS) technologies offer unprecedented possibilities to sequence the entire genomes of organisms, thereby in principle enabling direct identification of causal mutations without mapping. However, although mapping-by-sequencing has proven to be a cost effective alternative to classical MBC in particular situations, methods based solely on NGS still have limitations and need to be refined. Aiming to identify the causal mutations in suppressors of Arabidopsis thaliana superroot2 phenotype, generated by ethyl methane sulfonate (EMS) treatment, we combined NGS and classical mapping, to rapidly identify the point mutations and restrict the number of testable candidates by defining the chromosomal intervals containing the causal mutations, respectively. The NGS-assisted mapping approach we describe here facilitates unbiased identification of virtually any causal EMS-generated mutation by overlapping the identification (deep sequencing) and validation (mapping) steps. To exemplify the useful marriage of the two approaches we discuss the strategy used to identify a new viable recessive allele of the Arabidopsis CULLIN1 gene in the non-reference Wassilewskija (Ws-4) accession.

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.

Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.

P166: Continuous dynamic mapping of the corticospinal tract during surgery of motor eloquent brain tumors

Introduction The objective was to establish a mapping technique to overcome the temporal and spatial limitations of classical subcortical mapping of the corticospinal tract (CST). The feasibility and safety of continuous subcortical mapping synchronized with tissue resection was evaluated. Methods This prospective study included 69 patients who underwent tumour surgery adjacent to the CST ( 1 cm using diffusion tension imaging and fiber tracking) with simultaneous subcortical monopolar mapping (short train of 5 cathodal stimuli, inter-stimulus interval 4.0 ms, pulse duration 0.5 ms) and an acoustic motor evoked potential alarm. Continuous (temporal coverage) and dynamic (spatial coverage) mapping was technically realized by integrating the mapping probe at the tip of a suction device with the concept that this device will be in contact with the tissue where the resection is performed. Motor function was assessed one day after surgery, at discharge, and at 3 months. Results All procedures were technically successful. There was a 1:1 correlation of motor thresholds (MTs) for stimulation sites simultaneously mapped with the new suction mapping device and the classic fingerstick probe (24 patients, 74 stimulation points, r = 0.996, p 0.001). Lowest individual MTs were as follows (MT, number of patients): > 20 mA, n = 7; 11–20 mA, n = 13; 6–10 mA, n = 8; 4–5 mA, n = 17; 1–3 mA, n = 24. At 3 months, two patients (3%) had a persisting postoperative motor deficit, both of which were caused by a vascular injury. No patient had a permanent motor deficit caused by a mechanical injury of the CST. Conclusion Continuous dynamic mapping was found to be a feasible and ergonomic technique for localizing the CST. The acoustic feedback and the ability to continuously stimulate the tissue exactly at the site of tissue removal might improve the accuracy of mapping, especially at low stimulation intensities. This technique may increase the safety of motor eloquent tumour surgery.

Classical mapping for Hubbard operators: application to the double-Anderson model.

A classical Cartesian mapping for Hubbard operators is developed to describe the nonequilibrium transport of an open quantum system with many electrons. The mapping of the Hubbard operators representing the many-body Hamiltonian is derived by using analogies from classical mappings of boson creation and annihilation operators vis-à-vis a coherent state representation. The approach provides qualitative results for a double quantum dot array (double Anderson impurity model) coupled to fermionic leads for a range of bias voltages, Coulomb couplings, and hopping terms. While the width and height of the conduction peaks show deviations from the master equation approach considered to be accurate in the limit of weak system-leads couplings and high temperatures, the Hubbard mapping captures all transport channels involving transition between many electron states, some of which are not captured by approximate nonequilibrium Green function closures.

QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber.

Next-generation sequencing enabled a fast discovery of a major QTL controlling early flowering in cucumber, corresponding to the FT gene conditioning flowering time in Arabidopsis. Next-generation sequencing technologies are making it faster and more efficient to establish the association of agronomic traits with molecular markers or candidate genes, which is the requirement for marker-assisted selection in molecular breeding. Early flowering is an important agronomic trait in cucumber (Cucumis sativus L.), but the underlying genetic mechanism is unknown. In this study, we identified a candidate gene for early flowering QTL, Ef1.1 through QTL-seq. Segregation analysis in F2 and BC1 populations derived from a cross between two inbred lines "Muromskij" (early flowering) and "9930" (late flowering) suggested quantitative nature of flowering time in cucumber. Genome-wide comparison of SNP profiles between the early and late-flowering bulks constructed from F2 plants identified a major QTL, designated Ef1.1 on cucumber chromosome 1 for early flowering in Muromskij, which was confirmed by microsatellite marker-based classical QTL mapping in the F2 population. Joint QTL-seq and traditional QTL analysis delimited Ef1.1 to an 890 kb genomic region. A cucumber gene, Csa1G651710, was identified in this region, which is a homolog of the FLOWERING LOCUS T (FT), the main flowering switch gene in Arabidopsis. Quantitative RT-PCR study of the expression level of Csa1G651710 revealed significantly higher expression in early flowering genotypes. Data presented here provide support for Csa1G651710 as a possible candidate gene for early flowering in the cucumber line Muromskij.

Genome wide association mapping to identify aluminium tolerance loci in bread wheat

Aluminium (Al) toxicity in acid soils continues to be a major concern for crop production, especially for wheat which is a moderately tolerant cereal crop species. So far, Al tolerance was known to be controlled by few genetic loci detected clearly by classical mapping studies. Here, we report the outcome of a genome wide association mapping approach in bread wheat (Triticum aestivum L.) using 525 Diversity Array Technology markers genotyped in a core collection of 96 winter wheat accessions. Marker-trait associations (MTAs) were detected using both general linear model (GLM) and mixed linear model (MLM). Five significant MTAs were identified as shared by models on chromosomes 1A, 1D, 3B and 6A. Highly significant MTAs were identified by MLM on chromosomes 1D and 3B which could be new candidate loci for future studies. Some of our results are in line with prior reports, but some appear to be novel. Potential candidate genes have been searched in respective chromosomal bins for highly significant MTAs detected by MLM. The loci identified in our study have the potential to improve Al tolerance in wheat and hence need to be verified and utilized for breeding tolerant cultivars worldwide.

25. Continuous dynamic mapping of the corticospinal tract during surgery of motor eloquent brain tumours

The objective was to establish a mapping technique to overcome the temporal and spatial limitations of classical subcortical mapping of the corticospinal tract (CST). The feasibility and safety of continuous subcortical mapping synchronized with tissue resection was evaluated. This prospective study included 69 patients who underwent tumour surgery adjacent to the CST (<1 cm using diffusion tension imaging and fiber tracking) with simultaneous subcortical monopolar mapping (short train of 5 cathodal stimuli, inter-stimulus interval 4.0 ms, pulse duration 0.5 ms) and an acoustic motor evoked potential alarm. Continuous (temporal coverage) and dynamic (spatial coverage) mapping was technically realized by integrating the mapping probe at the tip of a suction device with the concept that this device will be in contact with the tissue where the resection is performed. Motor function was assessed one day after surgery, at discharge, and at 3 months. All procedures were technically successful. There was a 1:1 correlation of motor thresholds (MTs) for stimulation sites simultaneously mapped with the new suction mapping device and the classic fingerstick probe (24 patients, 74 stimulation points, r = 0.996, p < 0.001). Lowest individual MTs were as follows (MT, number of patients): >20 mA, n = 7; 11–20 mA, n = 13; 6–10 mA, n = 8; 4–5 mA, n = 17; 1–3 mA, n = 24. At 3 months, two patients (3%) had a persisting postoperative motor deficit, both of which were caused by a vascular injury. No patient had a permanent motor deficit caused by a mechanical injury of the CST. Continuous dynamic mapping was found to be a feasible and ergonomic technique for localizing the CST. The acoustic feedback and the ability to continuously stimulate the tissue exactly at the site of tissue removal might improve the accuracy of mapping, especially at low stimulation intensities. This technique may increase the safety of motor eloquent tumour surgery.

The shape of things to come in the study of the origin of species?

Perhaps Darwin would agree that speciation is no longer the mystery of mysteries that it used to be. It is now generally accepted that evolution by natural selection can contribute to ecological adaptation, resulting in the evolution of reproductive barriers and, hence, to the evolution of new species (Schluter & Conte 2009; Meyer 2011; Nosil 2012). From genes that encode silencing proteins that cause infertility in hybrid mice (Mihola et al. 2009), to segregation distorters linked to speciation in fruit flies (Phadnis & Orr 2009), or pollinator-mediated selection on flower colour alleles driving reinforcement in Texan wildflowers (Hopkins & Rausher 2012), characterization of the genes that drive speciation is providing clues to the origin of species (Nosil & Schluter 2011). It is becoming apparent that, while recent work continues to overturn historical ideas about sympatric speciation (e.g. Barluenga et al. 2006), ecological circumstances strongly influence patterns of genomic divergence, and ultimately the establishment of reproductive isolation when gene flow is present (Elmer & Meyer 2011). Less clear, however, are the genetic mechanisms that cause speciation, particularly when ongoing gene flow is occurring. Now, in this issue, Franchini et al. (2014) employ a classic genetic mapping approach augmented with new genomic tools to elucidate the genomic architecture of ecologically divergent body shapes in a pair of sympatric crater lake cichlid fishes. From over 450 segregating SNPs in an F2 cross, 72 SNPs were linked to 11 QTL associated with external morphology measured by means of traditional and geometric morphometrics. Annotation of two highly supported QTL further pointed to genes that might contribute to ecological divergence in body shape in Midas cichlids, overall supporting the hypothesis that genomic regions of large phenotypic effect may be contributing to early-stage divergence in Midas cichlids.

Continuous dynamic mapping of the corticospinal tract during surgery of motor eloquent brain tumors: evaluation of a new method

The authors developed a new mapping technique to overcome the temporal and spatial limitations of classic subcortical mapping of the corticospinal tract (CST). The feasibility and safety of continuous (0.4-2 Hz) and dynamic (at the site of and synchronized with tissue resection) subcortical motor mapping was evaluated. The authors prospectively studied 69 patients who underwent tumor surgery adjacent to the CST (< 1 cm using diffusion tensor imaging and fiber tracking) with simultaneous subcortical monopolar motor mapping (short train, interstimulus interval 4 msec, pulse duration 500 μsec) and a new acoustic motor evoked potential alarm. Continuous (temporal coverage) and dynamic (spatial coverage) mapping was technically realized by integrating the mapping probe at the tip of a new suction device, with the concept that this device will be in contact with the tissue where the resection is performed. Motor function was assessed 1 day after surgery, at discharge, and at 3 months. All procedures were technically successful. There was a 1:1 correlation of motor thresholds for stimulation sites simultaneously mapped with the new suction mapping device and the classic fingerstick probe (24 patients, 74 stimulation points; r(2) = 0.98, p < 0.001). The lowest individual motor thresholds were as follows: > 20 mA, 7 patients; 11-20 mA, 13 patients; 6-10 mA, 8 patients; 4-5 mA, 17 patients; and 1-3 mA, 24 patients. At 3 months, 2 patients (3%) had a persistent postoperative motor deficit, both of which were caused by a vascular injury. No patient had a permanent motor deficit caused by a mechanical injury of the CST. Continuous dynamic mapping was found to be a feasible and ergonomic technique for localizing the exact site of the CST and distance to the motor fibers. The acoustic feedback and the ability to stimulate the tissue continuously and exactly at the site of tissue removal improves the accuracy of mapping, especially at low (< 5 mA) stimulation intensities. This new technique may increase the safety of motor eloquent tumor surgery.

A quasi-classical mapping approach to vibrationally coupled electron transport in molecular junctions

We develop a classical mapping approach suitable to describe vibrationally coupled charge transport in molecular junctions based on the Cartesian mapping for many-electron systems [B. Li and W. H. Miller, J. Chem. Phys. 137, 154107 (2012)]. To properly describe vibrational quantum effects in the transport characteristics, we introduce a simple transformation rewriting the Hamiltonian in terms of occupation numbers and use a binning function to facilitate quantization. The approach provides accurate results for the nonequilibrium Holstein model for a range of bias voltages, vibrational frequencies, and temperatures. It also captures the hallmarks of vibrational quantum effects apparent in step-like structure in the current-voltage characteristics at low temperatures as well as the phenomenon of Franck-Condon blockade.

Improving the accuracy of discontinuous Galerkin schemes at boundary layers

SUMMARYThe resolution of boundary layers typically requires fine grids in the wall normal direction, which leads to anisotropic elements being refined towards the wall. Best practice guidelines for the mesh generation of stretched boundary layer grids exist for the finite volume or finite difference discretizations. A similar resolution of boundary layers with DG schemes can be achieved with a coarser grid because of the subgrid resolution of the DG scheme. High order schemes incorporate the possibility of high order element mappings, resulting in different resolution properties inside the element. In this paper, we show that the use of an internal element mapping in combination with a stretched grid can be used to reduce the error of the boundary layer approximation by an order of magnitude in comparison with the classical linear internal element mapping. The boundary layer is modeled by a one‐dimensional singular perturbation problem. In addition, we discuss the construction of the element mappings by interpolation and investigate the limits of the stretching function such that the resulting element Jacobian remains positive. A parameter study shows the influence of the element mapping for different polynomial degrees on the solution. Copyright © 2014 John Wiley &amp; Sons, Ltd.

How to discover a metabolic pathway? An update on gene identification in aliphatic glucosinolate biosynthesis, regulation and transport

Identification of enzymes, regulators and transporters involved in different metabolic processes is the foundation to understand how organisms function. There are, however, many difficulties in identifying candidate genes as well as in proving their in vivo roles. In this review, we describe different approaches utilized in Arabidopsis thaliana to identify gene candidates and experiments required to prove the function of a given candidate. For example, we use the production of methionine-derived aliphatic glucosinolates that represent major defence compounds in A. thaliana. Nearly all biosynthetic genes, as well as the first sets of regulators and transporters, have been identified. An array of approaches, i.e. classical mapping, quantitative trait loci (QTL) mapping, eQTL mapping, co-expression, genome wide association studies (GWAS), mutant screens and phylogenetic analyses, has been exploited to increase the number of identified genes. Here we summarize the lessons learned from the different approaches used over the years with the aim to help designing and combining new approaches in the future.

A bridge-functional-based classical mapping method for predicting the correlation functions of uniform electron gases at finite temperature

Efficient and accurate prediction of the correlation functions of uniform electron gases is of great importance for both practical and theoretical applications. This paper presents a bridge-functional-based classical mapping method for calculating the correlation functions of uniform spin-unpolarized electron gases at finite temperature. The bridge functional is formulated by following Rosenfeld's universality ansatz in combination with the modified fundamental measure theory. The theoretical predictions are in good agreement with recent quantum Monte Carlo results but with negligible computational cost, and the accuracy is better than a previous attempt based on the hypernetted-chain approximation. We find that the classical mapping method is most accurate if the effective mass of electrons increases as the density falls.

Combined geophysical techniques for detailed groundwater flow investigation in tectonically deformed fractured rocks

&lt;p&gt;In this paper we present a combination of several near surface geophysical investigation techniques with high resolution remote sensing image interpretations, in order to define the groundwater flow paths and whether they can be affected by future seismic events. A seasonal spring (Amvrakia) located at the foot of Meteora pillars near the village of Kastraki (Greece) was chosen as a test site. The Meteora conglomeratic formations crop out throughout the study area and are characterized by large discontinuities caused by post Miocene till present tectonic deformation [Ferriere et al. 2011, Royden and Papanikolaou 2011]. A network of groundwater pathways has been developed above the impermeable marls underlying the conglomeratic strata. Our research aims to define these water pathways in order to investigate and understand the exact mechanism of the spring by mapping the exposed discontinuity network with classic field mapping and remote sensing image interpretation and define their underground continuity with the contribution of near surface geophysical techniques. Five Very Low Frequency (VLF) profiles were conducted with different directions around the spring aiming to detect possible conductive zones in the conglomeratic formations that the study area consists of. Moreover, two Electrical Resistivity Tomography (ERT) sections of a total length of 140m were carried out parallel to the VLF profiles for cross-checking and verifying the geophysical information. Both techniques revealed important conductive zones (&amp;lt;200 Ohm m) within the conglomerate strata, which we interpret as discontinuities filled with water supplying the spring, which are quite vulnerable to displacements as the hydraulic connections between them might be easily disturbed after a future seismic event.&lt;/p&gt;

Humanoid Robot Navigation: Getting Localization Information from Vision

AbstractIn this article, we present our work to provide a navigation and localization system on a constrained humanoid platform, the NAO robot, without modifying the robot sensors. First, we tried to implement a simple and light version of classic monocular Simultaneous Localization and Mapping (SLAM) algorithms, while adapting to the CPU and camera quality, which turned out to be insufficient on the platform for the moment. From our work on keypoints tracking, we identified that some keypoints can be still accurately tracked at little cost, and used them to build a visual compass. This compass was then used to correct the robot walk because it makes it possible to control the robot orientation accurately.

Growing random 3-connected maps or Comment s'enfuir de l'Hexagone

We use a growth procedure for binary trees due to Luczak and Winkler, a bijection between binary trees and irreducible quadrangulations of the hexagon due to Fusy, Poulalhon and Schaeffer, and the classical angular mapping between quadrangulations and maps, to define a growth procedure for maps. The growth procedure is local, in that every map is obtained from its predecessor by an operation that only modifies vertices lying on a common face with some fixed vertex. As n tends to infinity, the probability that the n'th map in the sequence is 3-connected tends to 2^8/3^6. The sequence of maps has an almost sure limit G, and we show that G is the distributional local limit of large, uniformly random 3-connected graphs.

Chapter Eight - Genetics of Gene Expression in CNS

Transcriptome studies have revealed a surprisingly high level of variation among individuals in expression of key genes in the CNS under both normal and experimental conditions. Ten-fold variation is common, yet the specific causes and consequences of this variation are largely unknown. By combining classic gene mapping methods-family linkage studies and genomewide association-with high-throughput genomics, it is now possible to define quantitative trait loci (QTLs), single-gene variants, and even single SNPs and indels that control gene expression in different brain regions and cells. This review considers some of the major technical and conceptual challenges in analyzing variation in expression in the CNS with a focus on mRNAs, rather than noncoding RNAs or proteins. At one level of analysis, this work has been highly successful, and we finally have techniques that can be used to track down small numbers of loci that control expression in the CNS. But at a higher level of analysis, we still do not understand the genetic architecture of gene expression in brain, the consequences of expression QTLs on protein levels or on cell function, or the combined impact of expression differences on behavior and disease risk. These important gaps are likely to be bridged over the next several decades using (1) much larger sample sizes, (2) more powerful RNA sequencing and proteomic methods, and (3) novel statistical and computational models to predict genome-to-phenome relations.

A new exchange–correlation functional free of delocalization and static correlation errors

Predicting the correct binding curves of H2(+) and H2 systems presents a great challenge in current applications of electronic density functional theory. Here we report a new functional for the exchange-correlation energy based on the weighted density approximation and the classical mapping method. With the exact sum rule for the exchange-correlation hole and accurate correlation functions of uniform electrons as the input, the new functional is free of delocalization and static correlation errors. It yields the exact results for any one-electron systems and the correct asymptotic limit of the binding energy between hydrogen atoms.