The mutation causing the black-and-tan pigmentation phenotype of Mangalitza pigs maps to the porcine ASIP locus but does not affect its coding sequence

The gene for agouti signaling protein (ASIP) is centrally involved in the expression of coat color traits in animals. The Mangalitza pig breed is characterized by a black-and-tan phenotype with black dorsal pigmentation and yellow or white ventral pigmentation. We investigated a Mangalitza x Piétrain cross and observed a coat color segregation pattern in the F2 generation that can be explained by virtue of two alleles at the MC1R locus and two alleles at the ASIP locus. Complete linkage of the black-and-tan phenotype to microsatellite alleles at the ASIP locus on SSC 17q21 was observed. Corroborated by the knowledge of similar mouse coat color mutants, it seems therefore conceivable that the black-and-tan pigmentation of Mangalitza pigs is caused by an ASIP allele a(t), which is recessive to the wild-type allele A. Toward positional cloning of the a(t) mutation, a 200-kb genomic BAC/PAC contig of this chromosomal region has been constructed and subsequently sequenced. Full-length ASIP cDNAs obtained by RACE differed in their 5' untranslated regions, whereas they shared a common open reading frame. Comparative sequencing of all ASIP exons and ASIP cDNAs between Mangalitza and Piétrain pigs did not reveal any differences associated with the coat color phenotype. Relative qRT-PCR analyses showed different dorsoventral skin expression intensities of the five ASIP transcripts in black-and-tan Mangalitza. The a(t) mutation is therefore probably a regulatory ASIP mutation that alters its dorsoventral expression pattern.

The locus for bovine dilated cardiomyopathy maps to chromosome 18

Bovine dilated cardiomyopathy (BDCMP) is a severe and terminal disease of the heart muscle observed in Holstein-Friesian cattle over the last 30 years. There is strong evidence for an autosomal recessive mode of inheritance for BDCMP. The objective of this study was to genetically map BDCMP, with the ultimate goal of identifying the causative mutation. A whole-genome scan using 199 microsatellite markers and one SNP revealed an assignment of BDCMP to BTA18. Fine-mapping on BTA18 refined the candidate region to the MSBDCMP06-BMS2785 interval. The interval containing the BDCMP locus was confirmed by multipoint linkage analysis using the software loki. The interval is about 6.7 Mb on the bovine genome sequence (Btau 3.1). The corresponding region of HSA19 is very gene-rich and contains roughly 200 genes. Although telomeric of the marker interval, TNNI3 is a possible positional and a functional candidate for BDCMP given its involvement in a human form of dilated cardiomyopathy. Sequence analysis of TNNI3 in cattle revealed no mutation in the coding sequence, but there was a G-to-A transition in intron 6 (AJ842179:c.378+315G>A). The analysis of this SNP using the study's BDCMP pedigree did not conclusively exclude TNNI3 as a candidate gene for BDCMP. Considering the high density of genes on the homologous region of HSA19, further refinement of the interval on BTA18 containing the BDCMP locus is needed.

Genetic maps of the proximal half of chromosome arm 2L of Drosophila melanogaster

Drosophila mutants have played an important role in elucidating the physiologic function of genes. Large-scale projects have succeeded in producing mutations in a large proportion of Drosophila genes. Many mutant fly lines have also been produced through the efforts of individual laboratories over the past century. In an effort to make some of these mutants more useful to the research community, we systematically mapped a large number of mutations affecting genes in the proximal half of chromosome arm 2L to more precisely defined regions, defined by deficiency intervals, and, when possible, by individual complementation groups. To further analyze regions 36 and 39-40, we produced 11 new deficiencies with gamma irradiation, and we constructed 6 new deficiencies in region 30-33, using the DrosDel system. trans-heterozygous combinations of deficiencies revealed 5 additional functions, essential for viability or fertility.

Arachnomelia in Brown Swiss cattle maps to chromosome 5

Arachnomelia in Brown Swiss cattle is a monogenic autosomal recessive inherited congenital disorder of the skeletal system giving affected calves a spidery look (OMIA ID 000059). Over a period of 20 years 15 cases were sampled in the Swiss and Italian Brown cattle population. Pedigree data revealed that all affected individuals trace back to a single acknowledged carrier founder sire. A genome scan using 240 microsatellites spanning the 29 bovine autosomes showed homozygosity at three adjacent microsatellite markers on bovine Chr 5 in all cases. Linkage analysis confirmed the localization of the arachnomelia mutation in the region of the marker ETH10. Fine-mapping and haplotype analysis using a total of 34 markers in this region refined the critical region of the arachnomelia locus to a 7.19-Mb interval on bovine Chr 5. The disease-associated IBD haplotype was shared by 36 proven carrier animals and allows marker-assisted selection. As the corresponding human and mouse chromosome segments do not contain any clear functional candidate genes for this disorder, the mutation causing arachnomelia in the Brown Swiss cattle might help to identify an unknown gene in bone development.

Two historical maps from nineteenth-century Palestine, with links to digitized maps in shapefile format

Reconstructing past landscapes from historical maps requires quantifying the accuracy and completeness of these sources. The accuracy and completeness of two historical maps of the same period covering the same area in Israel were examined: the 1:63,360 British Palestine Exploration Fund map (1871-1877) and the 1:100,000 French Levés en Galilée (LG) map (1870). These maps cover the mountainous area of the Galilee (northern Israel), a region with significant natural and topographical diversity, and a long history of human presence. Land-cover features from both maps, as well as the contours drawn on the LG map, were digitized. The overall correspondence between land-cover features shown on both maps was 59% and we found that the geo-referencing method employed (transformation type and source of control points) did not significantly affect these correspondence measures. Both maps show that in the 1870s, 35% of the Galilee was covered by Mediterranean maquis, with less than 8% of the area used for permanent agricultural cropland (e.g., plantations). This article presents how the reliability of the maps was assessed by using two spatial historical sources, and how land-cover classes that were mapped with lower certainty and completeness are identified. Some of the causes that led to observed differences between the maps, including mapping scale, time of year, and the interests of the surveyors, are also identified.

Maps and acoustic profiles of free gas distribution, Western Baltic Sea and Kattgat-Skagerrak area

A shallow gas depth-contour map covering the Skagerrak-western Baltic Sea region has been constructed using a relatively dense grid of existing shallow seismic lines. The digital map is stored as an ESRI shape file in order to facilitate comparison with other data from the region. Free gas usually occurs in mud and sandy mud but is observed only when sediment thickness exceeds a certain threshold value, depending on the water depth of the area in question. Gassy sediments exist at all water depths from approx. 20 m in the coastal waters of the Kattegat to 360 m in the Skagerrak. In spite of the large difference in water depths, the depth of free gas below seabed varies only little within the region, indicating a relatively fast movement of methane in the gas phase towards the seabed compared to the rate of diffusion of dissolved methane. Seeps of old microbial methane occur in the northern Kattegat where a relatively thin cover of sandy sediments exists over shallow, glacially deformed Pleistocene marine sediments. Previous estimates of total methane escape from the area may be correct but the extrapolation of local methane seepage rate data to much larger areas on the continental shelf is probably not justified. Preliminary data on porewater chemistry were compared with the free gas depth contours in the Aarhus Bay area, which occasionally suffers from oxygen deficiency, in order to examine if acoustic gas mapping may be used for monitoring the condition of the bay.

Magnetic anomaly map of the Weddell Sea Region, Antarctic (Scale 1:2 500 000)

This paper describes a 1 : 2 500 000 scale aeromagnetic anomaly map produced by the joint efforts of VNIIOkeangeologia, Polar Marine Geological Research Expedition (PMGRE) and the Alfred Wegener Institute for Polar and Marine Research (AWl) for the Weddell Sea region covering 1 850 000 km' of West Antarctica. Extensive regional magnetic survey flights with line-spacing of about 20 km and 5 km were carried out by the PMGRE between 1977 and 1989. In course of these investigations the PMGRE flew 9 surveys with flight-line spacing of 20 km and 6 surveys with flight-line spacing of 5 km mainly over the mountain areas of southern Palmer Land, western Dronning Maud Land, Coats Land and Pensacola Mountains, over the Ronne lee Shelf and the Filchner Ice Shelf and the central part of the Weddell Sea. More than 215 000 line-kilometers of total field aeromagnetic data have been acquired by using an Ilyushin Il-14 ski-equipped aircraft. Survey operations were centered on the field base stations Druzhnaya-1, -2, and -3, from which the majority of the Weddell Sea region network was completed. The composite map of the Weddell Sea region is prepared in colour, showing magnetic anomaly contours at intervals of 50-100 nT with supplemental contours at an interval of 25 nT in low gradient areas, on a polar stereographic projection. The compiled colour magnetic anomaly map of the Weddell Sea region demonstrates that features of large areal extent, such as geologic provinces, fold-belts, ancient eratonic fragments and other regional structural features can be readily delineated. The map allows a comparison of regional magnetic features with similar-scale geological structures on geological and geophysical maps. It also provides a database for the future production of the ''Digital Magnetic Anomaly Map of Antarctica'' in the framework of the Scientific Committee on Antarctic Research/International Association of Geomagnetism and Aeronomy (SCAR/IAGA) compilation.

Gravity mapping in the southern Weddell Sea region, Antarctica (Scale 1:2 000 000)

New maps of free-air and the Bouguer gravity anomalies on the Weddell Sea sector (70-81° S, 6-75° W) of Antarctica are presented. These maps are based on the first computer compilation of available gravity data collected by ''Sevmorgeologia'' in 1976-89 in the southern Weddell Sea and adjacent coasts of western Dronning Maud Land (WDML) and Coats Land. The accomplished gravity studies comprise airborne observations with a line spacing of about 20 km and conventional measurements at over-the-ice points, which were spaced at 10-30 km and supplemented by seismic soundings. Hence, anomalies on the maps represent mainly large-scale and deep crustal features. The dominant feature in free-air gravity map is a large dipolar gravity anomaly stretching along the continental margin. Following the major grain of seabed morphology this shelf-edge/slope anomaly (SESA) is clearly divided into three segments characterized by diverse anomaly amplitudes, wavelengths and trends. They are associated with continental margins of different geotectonic provinces of Antarctica surrounding the Weddell Sea. Apparent distinctions in the SESA signatures are interpreted as the gravity expression of tectonic, deep crustal structure segmentation of the continental margin. The prominent gravity highs (100-140 mGal) of the shelf edge anomaly mapped along WDML are assumed to represent high-density mantle injections intruded into the middle/lower crust during initial rifting of continental breakup. Enlarged wavelengths and diminished amplitudes of the gravity anomaly westwards, along the Weddell Sea embayment (WSE) margin, reflect a widening of the continental slope and a significant increase in thickness of underlying sediment strata. Low amplitude, negative free-air anomalies in the Filchner-Ronne Ice Shelves (FRIS) contrast sharply with the dominating positive anomalies offshore. This indicates a greater sedimentary thickness of the basin in this area. Crustal response to the enlarged sediment load is impressed in mostly positive features of the Bouguer gravity field observed here. Two pronounced positive Bouguer anomalies of 50-70 mGal and an average widths of 200 km dominate the Weddell Sea embayment margins towards the Antarctic Peninsula and the East Antarctic craton. They correlate well with very deep seabed troughs (> 1000 m below sea level). The gravity highs are most likely caused by a shallow upper mantle underneath graben-rift structures evolved at the margins of the WSE basin. A regional zone (> 100 km in width) of the prominent Bouguer and free-air negative anomalies (-40 to -60 mGal) adjacent Coats Land to the north of the ice shelf edge may indicate the presence of the thick old cratonic crust far offshore beneath the Weddell Sea Embayment.

Daily pan-Arctic sea-ice lead maps for 2003-2015, with links to maps in netCDF format

The presence of sea-ice leads represents a key feature of the Arctic sea ice cover. Leads promote the flux of sensible and latent heat from the ocean to the cold winter atmosphere and are thereby crucial for air-sea-ice-ocean interactions. We here apply a binary segmentation procedure to identify leads from MODIS thermal infrared imagery on a daily time scale. The method separates identified leads into two uncertainty categories, with the high uncertainty being attributed to artifacts that arise from warm signatures of unrecognized clouds. Based on the obtained lead detections, we compute quasi-daily pan-Arctic lead maps for the months of January to April, 2003-2015. Our results highlight the marginal ice zone in the Fram Strait and Barents Sea as the primary region for lead activity. The spatial distribution of the average pan-Arctic lead frequencies reveals, moreover, distinct patterns of predominant fracture zones in the Beaufort Sea and along the shelf-breaks, mainly in the Siberian sector of the Arctic Ocean as well as the well-known polynya and fast-ice locations. Additionally, a substantial inter-annual variability of lead occurrences in the Arctic is indicated.

Geospatial analysis of groundwater depth for manual well drilling suitability in the Zinder Region, Niger

Manual and low-tech well drilling techniques have potential to assist in reaching the United Nations' millennium development goal for water in sub-Saharan Africa. This study used publicly available geospatial data in a regression tree analysis to predict groundwater depth in the Zinder region of Niger to identify suitable areas for manual well drilling. Regression trees were developed and tested on a database for 3681 wells in the Zinder region. A tree with 17 terminal leaves provided a range of ground water depth estimates that were appropriate for manual drilling, though much of the tree's complexity was associated with depths that were beyond manual methods. A natural log transformation of groundwater depth was tested to see if rescaling dataset variance would result in finer distinctions for regions of shallow groundwater. The RMSE for a log-transformed tree with only 10 terminal leaves was almost half that of the untransformed 17 leaf tree for groundwater depths less than 10 m. This analysis indicated important groundwater relationships for commonly available maps of geology, soils, elevation, and enhanced vegetation index from the MODIS satellite imaging system.

Probability sampling protocol of classification maps from spaceborne/airborne image

To deliver sample estimates provided with the necessary probability foundation to permit generalization from the sample data subset to the whole target population being sampled, probability sampling strategies are required to satisfy three necessary not sufficient conditions: (i) All inclusion probabilities be greater than zero in the target population to be sampled. If some sampling units have an inclusion probability of zero, then a map accuracy assessment does not represent the entire target region depicted in the map to be assessed. (ii) The inclusion probabilities must be: (a) knowable for nonsampled units and (b) known for those units selected in the sample: since the inclusion probability determines the weight attached to each sampling unit in the accuracy estimation formulas, if the inclusion probabilities are unknown, so are the estimation weights. This original work presents a novel (to the best of these authors' knowledge, the first) probability sampling protocol for quality assessment and comparison of thematic maps generated from spaceborne/airborne Very High Resolution (VHR) images, where: (I) an original Categorical Variable Pair Similarity Index (CVPSI, proposed in two different formulations) is estimated as a fuzzy degree of match between a reference and a test semantic vocabulary, which may not coincide, and (II) both symbolic pixel-based thematic quality indicators (TQIs) and sub-symbolic object-based spatial quality indicators (SQIs) are estimated with a degree of uncertainty in measurement in compliance with the well-known Quality Assurance Framework for Earth Observation (QA4EO) guidelines. Like a decision-tree, any protocol (guidelines for best practice) comprises a set of rules, equivalent to structural knowledge, and an order of presentation of the rule set, known as procedural knowledge. The combination of these two levels of knowledge makes an original protocol worth more than the sum of its parts. The several degrees of novelty of the proposed probability sampling protocol are highlighted in this paper, at the levels of understanding of both structural and procedural knowledge, in comparison with related multi-disciplinary works selected from the existing literature. In the experimental session the proposed protocol is tested for accuracy validation of preliminary classification maps automatically generated by the Satellite Image Automatic MapperT (SIAMT) software product from two WorldView-2 images and one QuickBird-2 image provided by DigitalGlobe for testing purposes. In these experiments, collected TQIs and SQIs are statistically valid, statistically significant, consistent across maps and in agreement with theoretical expectations, visual (qualitative) evidence and quantitative quality indexes of operativeness (OQIs) claimed for SIAMT by related papers. As a subsidiary conclusion, the statistically consistent and statistically significant accuracy validation of the SIAMT pre-classification maps proposed in this contribution, together with OQIs claimed for SIAMT by related works, make the operational (automatic, accurate, near real-time, robust, scalable) SIAMT software product eligible for opening up new inter-disciplinary research and market opportunities in accordance with the visionary goal of the Global Earth Observation System of Systems (GEOSS) initiative and the QA4EO international guidelines.

Characterization of the Abydos region through OSIRIS high-resolution images in support of CIVA measurements

Context. On 12 November 2014, the European mission Rosetta delivered the Philae lander on the nucleus of comet 67P /Churyumov-Gerasimenko (67P). After the first touchdown, the lander bounced three times before finally landing at a site named Abydos. Aims. We provide a morphologically detailed analysis of the Abydos landing site to support Philae's measurements and to give context for the interpretation of the images coming from the Comet Infrared and Visible Analyser (CIVA) camera system onboard the lander. Methods. We used images acquired by the OSIRIS Narrow Angle Camera (NAC) on 6 December 2014 to perform the analysis of the Abydos landing site, which provided the geomorphological map, the gravitational slope map, the size-frequency distribution of the boulders. We also computed the albedo and spectral reddening maps. Results. The morphological analysis of the region could suggest that Philae is located on a primordial terrain. The Abydos site is surrounded by two layered and fractured outcrops and presents a 0.02 km(2) talus deposit rich in boulders. The boulder size frequency distribution gives a cumulative power-law index of 4.0 + 0.3/0.4, which is correlated with gravitational events triggered by sublimation and /or thermal fracturing causing regressive erosion. The average value of the albedo is 5.8% at lambda(1) = 480.7 nm and 7.4% at lambda(2) = 649.2 nm, which is similar to the global albedos derived by OSIRIS and CIVA, respectively.

Effects of different soil management practices on soil mechanic resistance and seed depth placement in a maize crop in Alentejo, Portugal Mediterranean region.

No tillage, minimum tillage and conventional tillage practices are commonly used in maize crops in Alentejo, affecting soil physic conditions and determining seeders performance. Seeders distribution can be evaluated in the longitudinal and vertical planes. Vertical plane is specified by seeding depth (Karayel et al., 2008). If, in one hand seeding depth uniformity is a goal for all crop establishment , in the other hand, seeders furrow openers depth control is never constant depending on soil conditions. Seed depth uniformity affects crop emergence, Liu et al. (2004) showed an higher correlation between crop productivity and emergence uniformity than with longitudinal plants distribution. Neto et al. (2007) evaluating seed depth placement by measuring maize mesocotyl length under no tillage conditions in 38 farms concluded that 20% of coefficient of variation suggests the need of improvement seeders depth control mechanisms. The objective of this study was to evaluate casual relationships and create spatial variability maps between soil mechanic resistance and vertical distribution under three different soil practices to improve seed depth uniformity.