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At least 199 records · Page 11

Genome shuffling enables quantitative trait locus mapping in Bacillus subtilis

Genetic mapping is a powerful tool for eukaryotic genetics that has only been applied to bacteria in limited circumstances. Quantitative trait locus (QTL) mapping generally relies on sexual recombination to break linkages between genes, yet bacteria rarely undergo sufficient homologous recombination to generate suitable mapping populations. In this work, we used iterative biparental genome shuffling by protoplast fusion in Bacillus subtilis to generate a population of bacteria with substantial random recombination throughout their genomes. Individual shuffled progeny were arrayed in well plates, resequenced, and characterized for a range of complex phenotypes including spore germination and swarming motility. Genetic mapping of the resulting phenotypes identified high-confidence QTLs of moderate size (~10 kb), and these associations were validated through targeted genetic swaps. This B. subtilis QTL population can easily be used to map additional phenotypes, and the general approach for QTL mapping is applicable in a wide range of bacteria.

Vasileva, Delyana [ORNL] (ORCID:0000000279197883)↗

Development of a strip-shaped X-ray mapping system for 9-cell superconducting cavities

Electrons emitted via field emission during superconducting (SC) radio-frequency (RF) cavity tests at vertical test stands often collide with the iris region inside the cavity, generating X-rays at these locations. In 1.3 GHz 9-cell SC RF cavities designed for the International Linear Collider (ILC), stiffener rings located outside the iris region between cells can interfere with X-ray detection, complicating the precise identification of field emission sites. Hence, in this study, we developed a high-density strip X-ray mapping systems (sX-map) that can be inserted into the iris region of ILC-type 9-cell SC RF cavities. This sX-map facilitates efficient and accurate detection of X-rays generated near the irises, unaffected by the presence of stiffener rings. The sX-map consisted of 32 sensors per strip, with sensors spaced approximately 10 mm apart. It was deployed in every iris of the 9-cell cavity, using a total of 320 sensors. A multiplexer was employed to facilitate the readout of a large number of detectors using a minimal number of signal lines, connecting the strips inside within the vertical test cryostat. In a vertical test conducted at Jefferson Lab (JLab), we demonstrated the capability of sX-map to detect X-rays despite the presence of a stiffener ring. This paper presents the detailed design of the sX-map and the results from the vertical test at JLab.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.

59 BASIC BIOLOGICAL SCIENCES↗

Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora

Abstract Background Over their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond to rapid change. Genome structure and genetic diversity contained within may highlight their adaptive potential. Results We present chromosome-scale genome assemblies and linkage maps of the critically endangered Atlantic acroporids,Acropora palmataandA. cervicornis. Both assemblies and linkage maps were resolved into 14 chromosomes with their gene content and colinearity. Repeats and chromosome arrangements were largely preserved between the species. The family Acroporidae and the genusAcroporaexhibited many phylogenetically significant gene family expansions. Macrosynteny decreased with phylogenetic distance. Nevertheless, scleractinians shared six of the 21 cnidarian ancestral linkage groups as well as numerous fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were constructed from oneA. palmatafamily and 16A. cervicornisfamilies using a genotyping array. The consensus maps span 1,013.42 cM and 927.36 cM forA. palmataandA. cervicornis, respectively. Both species exhibited high genome-wide recombination rates (3.04 to 3.53 cM/Mb) and pronounced sex-based differences, known as heterochiasmy, with 2 to 2.5X higher recombination rates estimated in the female maps. Conclusions Together, the chromosome-scale assemblies and genetic maps we present here are the first detailed look at the genomic landscapes of the critically endangered Atlantic acroporids. These data sets revealed that adaptive capacity of Atlantic acroporids is not limited by their recombination rates. The sister species maintain macrosynteny with few genes with high sequence divergence that may act as reproductive barriers between them. In the AtlanticAcropora, hybridization between the two sister species yields an F1 hybrid with limited fertility despite the high levels of macrosynteny and gene colinearity of their genomes. Together, these resources now enable genome-wide association studies and discovery of quantitative trait loci, two tools that can aid in the conservation of these species.

Biotechnology & Applied Microbiology↗

Transformation rate maps of dissolved organic carbon in the contiguous US

Riverine dissolved organic carbon (DOC) plays a vital role in regional and global carbon cycles. However, the processes of DOC conversion from soil organic carbon (SOC) and leaching into rivers are insufficiently understood, inconsistently represented, and poorly parameterized, particularly in land surface and Earth system models. As a first attempt to fill this gap, we propose a generic formula that directly connects SOC concentration with DOC concentration in headwater streams, where a single parameter, the transformation rate from SOC in the soil to DOC leaching flux (P r ), accounts for the overall processes governing SOC conversion to DOC and leaching from soils (along with runoff) into headwater streams. We then derive high-resolution P r maps over the contiguous US (CONUS) using SOC data from two different sources: the Harmonized World Soil Database v1.2 (HWSD) and SoilGrids 2.0. Both maps are developed following the same five major steps: (1) selecting independent catchments where observed riverine DOC data are available with reasonable quality; (2) estimating catchment-average SOC for the independent catchments; (3) estimating the P r values for these catchments based on the generic formula and catchment-average SOC; (4) developing a predictive model of P r with machine learning (ML) techniques and catchment-scale climate, hydrology, geology, and other attributes; and (5) deriving a national map of P r based on the ML model. For evaluation, we compare the DOC concentration derived using the P r map and the observed DOC concentration values at evaluation catchments. The resulting mean absolute scaled error and coefficient of determination are 0.73 and 0.47 for the HWSD-based model and 0.58 and 0.72 for the SoilGrids-based model, respectively, suggesting the effectiveness of the overall methodology. Efforts to constrain uncertainty and evaluate sensitivity of P r to different factors are discussed. To illustrate the use of such maps, we derive a riverine DOC concentration reanalysis dataset over CONUS. The two P r maps, robustly derived and empirically validated, lay a critical cornerstone for better simulating the terrestrial carbon cycle in land surface and Earth system models. Our findings not only set a foundation for improving our predictive understanding of the terrestrial carbon cycle at the regional and global scales, but also hold promises for informing policy decisions related to decarbonization and climate change mitigation. The data presented in this study are publicly available at https://doi.org/10.5281/zenodo.14563816 (Li et al., 2024).

54 ENVIRONMENTAL SCIENCES↗

Automated geologic mapping using rock reflectances.

Investigation of the feasibility of preparing geologic maps automatically through computer processing of calibrated narrow-band visible and near IR reflectivity data collected with a 12-channel scanner. Five procedures were followed in the computer analysis of the radiances recorded as voltages on analog magnetic tape. Three recognition maps have been generated iteratively using a progressively more complex classification scheme. The overall accuracy of the first recognition map was 80%, but the discrimination of the limestone and dolomite was only 50-60%. All three maps are very accurate outcrop maps. The results demonstrate the feasibility of automated geologic mapping in this relatively simple setting.

Watson, R. D.↗

Application of Remote Sensing to Planimetric, Thematic, and Topographic Mapping

Results of studies indicate some of the potential applications of space photography to mapping. The imagery used was not optimum for mapping purposes, and there is considerable room for improvement. The ERTS A and B satellites are expected to provide imagery that will be useful for small scale mapping, both planimetric and thematic. The repetitive coverage capability will certainly be useful for monitoring changing phenomena. However, to solve the world mapping problems, other imaging systems will have to be flown. Film-return satellites and geosynchronous satellites may have to be used together with aircraft to provide imagery for rapid and efficient mapping operations. Until such systems are in use on a worldwide basis, there is little likelihood that the planimetric and topographic map needs, particularly of the developing countries, will be met.

Mclaurin, J. D.↗

A new vegetation map of the western Seward Peninsula, Alaska, based on ERTS-1 imagery

The author has identified the following significant results. A reconstituted, simulated color-infrared ERTS-1 image covering the western Seward Peninsula was prepared and it is used for identifying and mapping vegetation types by direct visual examination. The image, NASA ERTS E-1009-22095, was obtained approximately at 1110 hours, 165 degrees WMT on August 1, 1972. Seven major colors are identified. Four of these are matched with units on existing vegetation maps: bright red - shrub thicket; light gray-red - upland tundra; medium gray-red - coastal coastal wet tundra; gray - alpine barrens. The three colors having no map equivalents are tentatively interpreted as follows: pink - grassland tundra; dark gray-red - burn scars; light orange-red - senescent vegetation. A vegetation map, drawn by tracing on an acetate overlay of the image is presented. Significantly more information is depicted than on existing maps with regards to vegetation types and their areal distribution. Furthermore the preparation of the new map from ERTS-1 imagery required little time relative to conventional methods and extent of areal coverage.

Anderson, J. H.↗

Evaluation of ERTS-1 imagery for mapping Quaternary deposits and landforms in the Great Plains and Midwest

The author has identified the following significant results. The main landform associations and larger landforms are readily identifiable on the better images and commonly the gross associations of surficial Quaternary deposits also can be determined primarily by information on landforms and soils (obtained by analysis of stream dissection and drainage and stream-divide patterns, land use patterns, etc.). Maps showing the Quaternary geologic-terrain units that can be distinguished on the ERTS-1 images are being prepared for study areas in Illinois, Iowa, Missouri, Kansas, Nebraska, and South Dakota. Preliminary maps of 1:1,000,000 scale are included for three of the study areas: the Grand Island and Fremont, Nebraska, and the Davenport, Iowa-Illinois, 1 deg x 2 deg quadrangles. These maps exemplify the first phase of investigations, which consists of identifying and mapping landform and land use characteristics and geologic-surficial materials directly from the ERTS-1 images alone, with no additional information. These maps show that commonly the boundaries of geologic-terrain units can be delineated more accurately on ERTS-1 images than on topographic maps at 1:250,000 scale.

Morrison, R. B.↗

Automated land-use mapping from spacecraft data

The author has identified the following significant results. In response to the need for a faster, more economical means of producing land use maps, this study evaluated the suitability of using ERTS-1 computer compatible tape (CCT) data as a basis for automatic mapping. Significant findings are: (1) automatic classification accuracy greater than 90% is achieved on categories of deep and shallow water, tended grass, rangeland, extractive (bare earth), urban, forest land, and nonforested wet lands; (2) computer-generated printouts by target class provide a quantitative measure of land use; and (3) the generation of map overlays showing land use from ERTS-1 CCTs offers a significant breakthrough in the rate at which land use maps are generated. Rather than uncorrected classified imagery or computer line printer outputs, the processing results in geometrically-corrected computer-driven pen drawing of land categories, drawn on a transparent material at a scale specified by the operator. These map overlays are economically produced and provide an efficient means of rapidly updating maps showing land use.

Chase, P. E.↗

Sediment concentration mapping in tidal estuaries

An analytical procedure has been developed that considers the ERTS-1 multispectral scanner as a reflectance spectrophotometer. ADP techniques requiring only very limited computer capability are utilized to search the data defining the spectral reflectance characteristics of a scene on a pixel-by-pixel basis, identify each pixel whose spectral reflectance matches a reference spectrum, and generate maps that identify pixel locations where spectrum matches occur and identify the spectrum that was matched. If the reference spectra are known to represent a specific condition on the ground, a map of the distribution of that condition can be output as a dimensionally accurate overlay to maps of any selected scale. Two applications are described: (1) mapping the distribution of water masses exhibiting specific suspended sediment concentrations; and (2) determining the location and delineation of surface water bodies in the southeastern U. S. The techniques described are being successfully used to map the land area inundated by the 1973 spring flood in the Lower Mississippi River Valley, map sediment distributions in Lake Pontchartrain (in Louisiana) as a result of opening the Bonnet Carre Floodway during the spring flood, and inventory lakes and reservoirs.

Williamson, A. N.↗

Applications of Skylab EREP photographs to mapping of landforms and environmental geology in the Great Plains and Midwest

The author has identified the following significant results. The utility of Skylab 2 and 3 S-190A multispectral photos for environmental-geologic/geomorphic applications is being tested by using them to prepare 1:250,000-scale maps of geomorphic features, surficial geology, geologic linear features, and soil associations of large, representative parts of the Great Plains and Midwest. Parts of Nebraska, Iowa, Missouri, and South Dakota were mapped. The maps were prepared primarily by interpretation of the S-190A photos, supplemented by information from topographic, geologic, and soil maps and reports. The color band provides the greatest information on geology, soils, and geomorphology; its resolution also is the best of all the multispectral bands and permits maximum detail of mapping. The color-IR band shows well the differences in soil drainage and moisture, and vegetative types, but has only moderate resolution. The B/W-red band is superior for topographic detail and stream alinements. The B/W-infrared bands best show differences in soil moisture and drainage but have poor resolution, especially those from SL 2. The B/W-green band generally is so low contrast and degraded by haze as to be nearly useless. Where stereoscopic coverage is provided, interpretation and mapping are done most efficiently using a Kern PG-2 stereoplotter.

Morrison, R. B.↗

Evaluation of EREP techniques for geological mapping

The author has identified the following significant results. Skylab photographs may be successfully utilized for preparing a reconnaissance geological map in the areas where no maps or semi-detailed maps exist. Large coverage of area and regional perspective from Skylab photographs can help better coordination in regional mapping. It is possible to delineate major structural trends and other features like mega-lineaments, geofractures, and faults, which have evaded their detection by conventional methods. The photointerpretability is better in areas dominated by sedimentary rocks. Rock units of smaller extent and having poor geomorphic expressions are difficult to map. Demarcation of quaternary river alluvium can be made with better precision and ease with the Skylab photographs. Stereoscopic viewing greatly helps in interpretation of area structures. Skylab photographs are not good for preparing geological maps larger than 1:270,000 scale.

Vandermeermohr, H. E. C.↗

Small scale thematic mapping - A case for radar imagery

Small scale thematic maps (1:250,000 and smaller) of physical and cultural phenomena manifested on the landscape are a major concern to scientists and investigators in diverse disciplines. A strip of K-band radar imagery consisting of a traverse from eastern Minnesota to northern Utah was employed to evaluate the potential of radar imagery for small scale land use mapping. In the course of this investigation, it was discovered that certain borders derived from radar imagery were compatible with borders found on the nonland use thematic maps used for comparison. Specifically, numerous borders and regions of small scale maps of landforms, soils, vegetation, and geology are found to be similar to the radar land use regions. Although far from conclusive it appears that radar imagery can be employed in the small scale mapping of landforms and possibly for mapping physiognomic or economic vegetation.

Henderson, F. M.↗

An interactive method for digitizing zone maps

A method is presented for digitizing maps that consist of zones, such as contour or climatic zone maps. A color-coded map is prepared by any convenient process. The map is then read into memory of an Image 100 computer by means of its table scanner, using colored filters. Zones are separated and stored in themes, using standard classification procedures. Thematic data are written on magnetic tape and these data, appropriately coded, are combined to make a digitized image on tape. Step-by-step procedures are given for digitization of crop moisture index maps with this procedure. In addition, a complete example of the digitization of a climatic zone map is given.

Giddings, L. E.↗

A new image enhancement algorithm with applications to forestry stand mapping

The theory and applications are presented of a new image enhancement algorithm which refines computer classification maps of multispectral data. The refinement eliminates connected sets smaller than a prespecified size and merges them to the surrounding area. Conventional practices in forestry timber stand mapping requires small geographic areas to be absorbed by surrounding large areas to form homogeneous stands. This homogeneity is often incompatible with the statistical formulation of homogeneity. Elements within a timber stand which should be labeled as one feature often correspond to more than one class mapped by existing computer classification techniques. The new algorithm is designed to postprocess classification maps to result in more usable timber stand maps. The new image enhancement technique is compared with an accepted neighbor-checking postprocessing technique, demonstrating the superiority of the new technique for forestry stand mapping.

Kan, E. P.↗

The prediction and mapping of geoidal undulations from GEOS-3 altimetry

From the adjusted altimeter data an approximation to the geoid height in ocean areas is obtained. Methods are developed to produce geoid maps in these areas. Geoid heights are obtained for grid points in the region to be mapped, and two of the parameters critical to the production of an accurate map are investigated. These are the spacing of the grid, which must be related to the half-wavelength of the altimeter signal whose amplitude is the desired accuracy of the contour; and the method adopted to predict the grid values. Least squares collocation was used to find geoid undulations on a 1 deg grid in the mapping area. Twenty maps, with their associated precisions, were produced and are included. These maps cover the Indian Ocean, Southwestern and Northeastern portions of the Pacific Ocean, and Southwest Atlantic and the U.S. Calibration Area.

Kearsley, W.↗

Mars synthetic topographic mapping

Topographic contour maps of Mars are compiled by synthesizing data acquired from various scientific experiments of the Mariner 9 mission, including S-band radio occultation, the UV spectrometer, the IR radiometer, the IR interferometer spectrometer, and television imagery, as well as earth-based radar information. The entire planet is mapped at scales of 1:25,000,000 and 1:5,000,000 using Mercator, Lambert, and polar stereographic map projections. For the computation of map projections, a biaxial spheroid figure is adopted. The semimajor and semiminor axes are 3393.4 and 3375.7 km, respectively, with a polar flattening of 0.0052. For the computation of elevations, a topographic datum is defined by a gravity field described in terms of spherical harmonics of fourth order and fourth degree combined with a 6.1-mbar occultation pressure surface. This areoid can be approximated by a triaxial ellipsoid with semimajor axes of A = 3394.6 km and B = 3393.3 km and a semiminor axis of C = 3376.3 km. The semimajor axis A intersects the Martian surface at longitude 105 deg W. The dynamic flattening of Mars is 0.00525. The contour interval of the maps is 1 km. For some prominent features where overlapping pictures from Mariner 9 are available, local contour maps at relatively larger scales were also compiled by photogrammetric methods on stereo plotters.

Wu, S. S. C.↗