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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Isolation and characterization of 13 microsatellite loci for the Neotropical otter, Lontra longicaudis, by next generation sequencing

The Neotropical otter, Lontra longicaudis, is an ecologically important species for freshwater ecosystems that is threatened due to habitat destruction and hunting. However, there is limited information regarding the population sizes, genetic diversity, genetic structure and gene flow of the species, which is crucial for the elaboration of conservation plans. The aim of this study was to isolate and characterize microsatellites for L. longicaudis, using Illumina paired-end-sequencing. Initial amplification tests were performed in 48 loci, out of which, 13 yielded high-quality PCR products and thus were further evaluated. Genetic diversity and discrimination power of the 13 microsatellite loci was assessed using 19 non-invasive samples collected in the Jamapa basin in Veracruz, Mexico and blood samples from six captive individuals. All loci were polymorphic, the number of alleles per locus ranged from 4 to 10, the observed heterozygosity from 0.21 to 0.69, and the expected heterozygosity from 0.55 to 0.82. The combined set of 13 microsatellites showed a high power for discriminating among individuals (probability of identity P ID = 1.551 × 10 -16 ) and among siblings (probability of identity of siblings P IDSIB = 3.349 × 10 -06 ). A combination of nine loci are sufficient to discriminate among siblings with high confidence (P IDSIB < 0.0001). The new set of microsatellites for the Neotropical otter reported here will provide a useful genetic tool to assess population genetic patterns and ecological parameters of the species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Microsatellite Markers for Aronia melanocarpa (Black Chokeberry) and Their Transferability to Other Aronia Species

This study reports the development, characterization, and cross-species transferability of 20 genomic microsatellite markers for Aronia melanocarpa, an important nutraceutical fruit crop. The markers were developed with Illumina paired-end genomic sequencing technology using DNA from Professor Ed cultivar that was originally collected from the wild in New Hampshire. The markers were highly polymorphic and transferable to Aronia arbutifolia and Aronia prunifolia genomes. The average number of alleles per locus was 9.1, 4.5, and 5.6 for A. melanocarpa, A. arbutifolia, and A. prunifolia, respectively. The polymorphism information content (PIC) of loci ranged from 0.38 to 0.95 for all taxa, with an average of 0.80, 0.68, and 0.87 for A. melanocarpa, A. arbutifolia, and A. prunifolia, respectively. This is the first study to develop microsatellite markers in the Aronia genus. Furthermore, these markers will be very useful in studying the genetic diversity and population structure of wild Aronia and expediting the breeding efforts of this emerging fruit crop through marker-assisted selection.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Gene amplification and microsatellite instability induced in tumorigenic human bronchial epithelial cells by alpha particles and heavy ions

Gene amplification and microsatellite alteration are useful markers of genomic instability in tumor and transformed cell lines. It has been suggested that genomic instability contributes to the progression of tumorigenesis by accumulating genetic changes. In this study, amplification of the carbamyl-P-synthetase, aspartate transcarbamylase, dihydro-orotase (CAD) gene in transformed and tumorigenic human bronchial epithelial (BEP2D) cells induced by either alpha particles or (56)Fe ions was assessed by measuring resistance to N-(phosphonacetyl)-l-aspartate (PALA). In addition, alterations of microsatellite loci located on chromosomes 3p and 18q were analyzed in a series of primary and secondary tumor cell lines generated in nude mice. The frequency of PALA-resistant colonies was 1-3 x 10(-3) in tumor cell lines, 5-8 x 10(-5) in transformed cells prior to inoculation into nude mice, and less than 10(-7) in control BEP2D cells. Microsatellite alterations were detected in all 11 tumor cell lines examined at the following loci: D18S34, D18S363, D18S877, D3S1038 and D3S1607. No significant difference in either PALA resistance or microsatellite instability was found in tumor cell lines that were induced by alpha particles compared to those induced by (56)Fe ions.

Non-NASA Center↗
DOE OSTI2017

Distinction of saffron cod ( Eleginus gracilis ) from several other gadid species by using microsatellite markers

Nine microsatellite loci isolated in saffron cod ( Eleginus gracilis ) have potential applications for population genetics. Polymerase chain reaction products of samples of E. gracilis from northwestern Alaska amplified reliably, produced only one or two microsatellite bands, and had no apparent homozygote excess. A collection of E. gracilis sampled in the Gulf of Alaska (GOA) near Kodiak Island did not amplify reliably at one locus, and allele frequency profiles clustered distinctly (with principal component analysis [PCA]) from the northwestern Alaska collection. Northwestern Alaska and GOA E. gracilis collections were genetically different (on the basis of a standardized genetic differentiation measure [ G ' ST ]=0.313, chord distance [ D chord ]=0.078, P<0.0001) and differed in expected aver-age heterozygosities at shared loci (0.859 and 0.689, respectively). We tested the microsatellite primers on other gadid species endemic to the northern Pacific Ocean, Bering Sea, and Arctic Ocean for cross-species amplification. Not all loci amplified reliably in navaga ( E. nawaga ), Pacific tomcod ( Microgadus proximus ), Arctic cod ( Boreogadus saida ), Pacific cod ( Gadus macrocephalus ), or walleye pollock ( G. chalcogrammus ). Reliable loci varied in microsatellite size profiles and produced distinct PCA clusters and accurate genotype assignments that allowed accurate species identification. Furthermore the identifications support previous morphological and genetically determined systematic classifications and distinguished the geographically separated collections of E. gracilis .

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Microsatellites in the Eukaryotic DNA Mismatch Repair Genes as Modulators of Evolutionary Mutation Rate

All "minor" components of the human DNA mismatch repair (MMR) system-MSH3, MSH6, PMS2, and the recently discovered MLH3-contain mononucleotide microsatellites in their coding sequences. This intriguing finding contrasts with the situation found in the major components of the DNA MMR system-MSH2 and MLH1-and, in fact, most human genes. Although eukaryotic genomes are rich in microsatellites, non-triplet microsatellites are rare in coding regions. The recurring presence of exonal mononucleotide repeat sequences within a single family of human genes would therefore be considered exceptional.

Chang, Dong Kyung↗
DOE OSTI2016

Identification of robust microsatellite markers for wild pig fecal DNA

ABSTRACT Collection of fecal samples for use in a genetic capture‐mark‐recapture framework has become popular as a noninvasive method of monitoring wildlife populations. A major caveat to this process, however, is that fecal samples often yield low quality DNA that is prone to genotyping errors, potentially leading to biases in population parameter estimation. Therefore, considerable care is required to identify robust genetic markers, especially in hot or humid conditions that may accelerate DNA degradation. We identified microsatellite loci in wild pig ( Sus scrofa ) fecal samples that were robust and informative within warm, humid ecosystems. To examine how degradation affected genotyping success, we sampled pig feces across 5 days and calculated how the number of quantitative polymerase chain reaction (qPCR) cycles required to reach the fluorescent threshold ( C t ) changed over time. We identified 17 microsatellite loci that had high polymorphism and amplification success and low genotyping error rates (0–0.050 per locus). In the degradation experiment, C t increased over the 5 days, but in the absence of rain, the majority of samples produced accurate genotypes after 5 days (2,211/2,550 genotypes). Based on the high amplification success and low error rates, even after 5 days of exposure to warm, humid conditions, these loci are useful for estimating population parameters in pig fecal samples. © 2016 The Wildlife Society.

Kierepka, Elizabeth M.↗
DOE OSTI2019

Radiomics-based prediction of microsatellite instability in colorectal cancer at initial computed tomography evaluation

Purpose: To predict microsatellite instability (MSI) status of colon cancer on preoperative CT imaging using radiomic analysis. Methods: This retrospective study involved radiomic analysis of preoperative CT imaging of patients who underwent resection of stage II–III colon cancer from 2004 to 2012. A radiologist blinded to MSI status manually segmented the tumor region on CT images. 254 Intensity-based radiomic features were extracted from the tumor region. Three prediction models were developed with (1) only clinical features, (2) only radiomic features, and (3) “combined” clinical and radiomic features. Patients were randomly separated into training (n = 139) and test (n = 59) sets. The model was constructed from training data only; the test set was reserved for validation only. Model performance was evaluated using AUC, sensitivity, specificity, PPV, and NPV. Results: Of the total 198 patients, 134 (68%) patients had microsatellite stable tumors and 64 (32%) patients had MSI tumors. The combined model performed slightly better than the other models, predicting MSI with an AUC of 0.80 for the training set and 0.79 for the test set (specificity = 96.8% and 92.5%, respectively), whereas the model with only clinical features achieved an AUC of 0.74 and the model with only radiomic features achieved an AUC of 0.76. The model with clinical features alone had the lowest specificity (70%) compared with the model with radiomic features alone (95%) and the combined model (92.5%). Conclusions: Preoperative prediction of MSI status via radiomic analysis of preoperative CT adds specificity to clinical assessment and could contribute to personalized treatment selection.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes

Background: Guayule ( Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. Results: The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50 = 22 kb), maps > 95% of the shotgun reads and is essentially complete. Approximately 40,000 transcribed, protein encoding genes were annotated on the assembly. Further characterization of this genome revealed 15 families of small, microsatellite-associated, transposable elements (TEs) with unexpected chromosomal distribution profiles. These SaTar (Satellite Targeted) elements, which are non-autonomous Mu-like elements (MULEs), were frequently observed in multimeric linear arrays of unrelated individual elements within which no individual element is interrupted by another. This uniformly non-nested TE multimer architecture has not been previously described in either eukaryotic or prokaryotic genomes. Five families of similarly distributed non-autonomous MULEs (microsatellite associated, modularly assembled) were characterized in the rice genome. Families of TEs with similar structures and distribution profiles were identified in sorghum and citrus. Conclusion: The sequencing and assembly of the guayule genome provides a foundation for application of current crop improvement technologies to this plant. In addition, characterization of this genome revealed SaTar elements with distribution profiles unique among TEs. Satar targeting appears based on an alternative MULE recombination mechanism with the potential to impact gene evolution.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

A Constellation of Microsatellites Promises to Help in a Range of Geoscience Research

An octet of microsatellites to be launched in 2003 promises to deliver a large amount of useful data for meteorological, climatic, ionospheric, and geodetic research as well as for operational weather forecasting and space weather monitoring. Known as the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC), the joint Taiwan-U.S. scientific satellite project makes use of Global Positioning System (GPS) occultation and tracking signals. COSMIC's final operational configuration is depicted in Figure 1. Each of the eight microsatellites in low-Earth-orbit (LEO, shown relative to the high-altitude GPS satellite orbits) will carry in particular an advanced limb-sounding GPS receiver, a Tiny Ionospheric Photometer, and a triband beacon transmitter.

Kuo, Y. H.↗
NASA NTRS2001

Development of the Variable Emittance Thermal Suite for the Space Technology 5 Microsatellite

The advent of very small satellites, such as nano and microsatellites, logically leads to a requirement for smaller thermal control subsystems. In addition, the thermal control needs of the smaller spacecraft/instrument may well be different from more traditional situations. For example, power for traditional heaters may be very limited or unavailable, mass allocations may be severely limited, and fleets of nano/microsatellites will require a generic thermal design as the cost of unique designs will be prohibitive. Some applications may require significantly increased power levels while others may require extremely low heat loss for extended periods. Small spacecraft will have low thermal capacitance thus subjecting them to large temperature swings when either the heat generation rate changes or the thermal sink temperature changes. This situation, combined with the need for tighter temperature control, will present a challenging situation during transient operation. The use of "off-the-shelf" commercial spacecraft buses for science instruments will also present challenges. Older thermal technology, such as heaters, thermostats, and heat pipes, will almost certainly not be sufficient to meet the requirements of these new spacecraft/instruments. They are generally too heavy, not scalable to very small sizes, and may consume inordinate amounts of power. Hence there is a strong driver to develop new technology to meet these emerging needs. Variable emittance coatings offer an exciting alternative to traditional control methodologies and are one of the technologies that will be flown on Space Technology 5, a mission of three microsatellites designed to validate "enabling" technologies. Several studies have identified variable emittance coatings as applicable to a wide range of spacecraft, and to potentially offer substantial savings in mass and/or power over traditional approaches. This paper discusses the development of the variable emittance thermal suite for ST-5. More specifically, it provides a description of and the infusion and validation plans for the variable emittance coatings.

Douglas, Donya M.↗
DOE OSTI2023

Genome-Wide Informative Microsatellite Markers and Population Structure of Fusarium virguliforme from Argentina and the USA

Soybean sudden death syndrome (SDS) is a destructive disease that causes substantial yield losses in South and North America. Whereas four Fusarium species were identified as the causal agents, F. virguliforme is the primary SDS-causing pathogen in North America and it also contributes substantially to SDS in Argentina. In this study, we comparatively analyzed genome assemblies of four F. virguliforme strains and identified 29 informative microsatellite markers. Sixteen of the 29 markers were used to investigate the genetic diversity and population structure of this pathogen in a collection of 90 strains from Argentina and the USA. A total of 37 multilocus genotypes (MLGs) were identified, including 10 MLGs in Argentina and 26 in the USA. Only MLG2, the most dominant MLG, was found in both countries. Analyses with three different approaches showed that these MLGs could be grouped into three clusters. Cluster IA consisting of four MLGs exclusively from the USA has much higher genetic diversity than the other two clusters, suggesting that it may be the ancestral cluster although additional data are necessary to support this hypothesis. Clusters IB and II consisted of 13 and 21 MLGs, respectively. MLGs belonging to these two clusters were present in all four sampled states in Argentina and all five sampled states in the USA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Identifying Whitemouth Croaker (Micropogonias furnieri) Populations along the Rio de Janeiro Coast, Brazil, through Microsatellite and Otolith Analyses

The inshore area of the Southwestern Atlantic between 22 °S and 29 °S (South Brazilian Bight) is a transitional climatic zone, where the tropical and warm temperate provinces mix. In its northern part, i.e., in the coastal waters of Rio de Janeiro, Brazil, local oceanographic conditions, such as upwelling in the north, and great bays with different degrees of anthropogenic influences in the center and south can determine the population structure of several fish stocks. The Whitemouth croaker (Micropogonias furnieri) is one the most heavily exploited fishing resources in this area, but there are still some doubts about its population structure. In this study, through combined analyses using nuclear genetic markers and morphological and geochemical signatures of otoliths, a divergence of individuals between two populations was identified using microsatellites, while a finer spatial structure with three populations (north, center and south, respectively) was found based on otolith shapes and elemental signatures. This regional population structure may have direct implications for rational fisheries management and conservation of the species.

Franco, Taynara Pontes (ORCID:0000000167381096)↗
DOE OSTI2016

Development of Microsatellite Markers for Buffalograss ( Buchloë dactyloides ; Poaceae), a Drought-Tolerant Turfgrass Alternative

Buchloë dactyloides (Nutt.) Engelm. (buffalograss; Poaceae) is a low-growing, perennial C4 grass that is a dominant component of shortgrass prairies of the North American Great Plains (Shearman et al., 2004). Beyond this significant ecosystem role, buffalograss has been widely adopted as a drought-tolerant turfgrass alternative, particularly notable as a native-species option in North America. Like many dominant Great Plains grasses, B. dactyloides comprises an autopolypoid series, including diploids (2n = 20), tetraploids, pentaploids, and hexaploids (Johnson et al., 2001). Preserving the full range of buffalograss phenotypic and genotypic diversity and utilizing this diversity for crop improvement will require an understanding of the distribution of genetic variation among cytotypes and across its large geographic range. Beyond numerous methodological advantages (Guichoux et al., 2011), microsatellites, or simple sequence repeat (SSR) markers,are an attractive genetic tool for studies of wide-ranging polyploid series given their codominant nature and applicability to museum-derived DNAs. Because SSR data are routinely obtainable from DNA extracted from museum tissue (Wandeler et al., 2007), these samples can be used to quickly and economically obtain comparative genotypic data from all portions of a large geographic range. Currently no buffalograss-specific SSR loci are available, as previous studies have relied on a mixture of dominant and codominant loci that were designed for other taxa (Budak et al., 2004). In this study, a set of SSR loci are designed from B. dactyloides genomic sequence data. The variability of these loci are then evaluated in six populations from numerous portions of the buffalograss range.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Development, Characterization, and Utility of 13 Polymorphic Microsatellite Loci in Praticolella (Gastropoda: Polygyridae) Species from South Texas, U.S.A.

We developed and characterized 13 polymorphic microsatellite loci in South Texas species of Praticolella. To make this new genomic tool more broadly useful, instead of characterizing loci in many individuals of a single species, we tested them across five populations of four different species. Twelve loci amplified in all four species tested, and eleven loci showed deviations from Hardy-Weinberg equilibrium. Observed heterozygosity calculated across species at each locus ranged from 0.050 to 0.727. These loci will be valuable in assessing species identity and population genetic connectivity among South Texas Praticolella.

59 BASIC BIOLOGICAL SCIENCES↗