Relationships among 3 Kochia species based on PCR-generated molecular sequences and molecular cytogenetics

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1104-1115 ◽  
Author(s):  
B S Lee ◽  
M Y Kim ◽  
R R.-C Wang ◽  
B L Waldron
Keyword(s):  
United States ◽  
In Situ Hybridization ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
5S Rdna ◽  
The United States ◽  
Cross Hybridization ◽  
Forage Kochia

Forage kochia (Kochia prostrata ssp. virescens 'Immigrant' is native to the arid and semiarid regions of central Eurasia. It was introduced into the United States in 1966 as PI 314929 and released as a perennial forage shrub in 1984. Kochia americana is a perennial native to the United States, whereas Kochia scorparia is an introduced annual species that became a weed. To assess both the breeding potential and the possibility of genetic contamination, relationships among the 3 Kochia species were analyzed using random amplified polymorphic DNA (RAPD) markers, sequence tagged site (STS) marker sequences of the chloroplast NADH dehydrogenase gene (ndhF), genomic in situ hybridization (GISH), and multicolor fluorescence in situ hybridization (MC-FISH). Seventy decamer random primers yielded 458 polymorphic bands from 9 plants of K. americana, 20 plants of K. prostrata, and 7 plants of K. scoparia. Fifty-four and 55 species-specific RAPD markers were identified for K. americana and K. prostrata, whereas 80 RAPD markers were specific to K. scoparia. Based on the presence or absence of informative RAPD markers, the 3 species always grouped into 3 distinct clusters in a NTSYSpc2.01b-generated dendrogram. The same relationships were found among the 3 Kochia species based on ndhF DNA sequence divergence. Using a set of 7 STS markers that can identify each Kochia species, we did not find a single interspecific hybrid from artificial hybridizations among the 3 Kochia species. In GISH studies, chromosomes of 1 species fluoresced in green only when they were probed by genomic DNA of the same species. Cross-hybridization by genomic DNA of another species was not observed. In FISH studies using pTa71 (for 18S–5.8S–26S rDNAs) and pScT7 (for 5S rDNA) as probes, there were 1, 1 and 3 pTa71 sites and 2, 1, and 1 pScT7 sites in each haplome of K. prostrata, K. americana, and K. scoparia, respectively. It is concluded that these 3 Kochia species are so genomically distinct that gene introgression among them would be extremely rare.Key words: RAPD, STS, ndhF, GISH, FISH, mixoploidy, forage kochia.

Molecular contribution to selection of intergeneric hybrids between sugarcane and the wild species Erianthus arundinaceus

Genome ◽  
2000 ◽  
Vol 43 (6) ◽  
pp. 1033-1037 ◽  
Author(s):  
George Piperidis ◽  
Mandy J Christopher ◽  
Bernie J Carroll ◽  
Nils Berding ◽  
Angélique D'Hont
Keyword(s):  
In Situ Hybridization ◽  
5S Rdna ◽  
Saccharum Officinarum ◽  
Genomic In Situ Hybridization ◽  
Early Screening ◽  
Selfed Progeny ◽  
Cross Hybridization ◽  
Rdna Cluster ◽  
Erianthus Arundinaceus

Erianthus arundinaceus has great potential as a germplasm source for better ratoonability, vigour, tolerance to environmental stresses, and disease resistance in sugarcane. Many unsuccessful attempts have been made to introduce these characters into modern sugarcane cultivars. We report on significant progress made since molecular tools were implemented. Sequence-tagged PCR, revealing size variation in the 5S rDNA cluster, was performed on intact leaf tissue to identify genuine hybrids six weeks after germination. This early screening of seedlings avoids the loss of genuine hybrids due to competition with selfed progeny. Of 96 crosses made involving female Saccharum officinarum or sugarcane cultivars (Saccharum spp.) and male E. arundinaceus, 26 were fertile producing 1328 seedlings. Thirty-seven genuine hybrids were unequivocally identified but only 19 have survived. Genuine hybrids were produced from only three crosses, all involving S. officinarum as the female parent. Chromosome elimination was observed in all seven hybrids analyzed using genomic in situ hybridization (GISH). Very little cross-hybridization was observed between the genomes of the two species after GISH, confirming recent molecular studies which showed that E. arundinaceus is quite distant from the genus Saccharum. The major limitation in the introgression of E. arundinaceus resides now in the apparent sterility of the hybrids.Key words: sugarcane, Erianthus, intergeneric hybrid, genomic in situ hybridization, 5S rDNA, sequence-tagged PCR.

scholarly journals ALK Testing Trends and Patterns Among Community Practices in the United States

2018 ◽  
pp. 1-11 ◽  
Author(s):  
Peter B. Illei ◽  
William Wong ◽  
Ning Wu ◽  
Laura Chu ◽  
Ravindra Gupta ◽  
...  
Keyword(s):  
United States ◽  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
The United States ◽  
Stage Iiib ◽  
Molecular Testing ◽  
Western Us ◽  
Test Result ◽  
Over Time

Purpose Targeted therapy of ALK in patients with metastatic nonsquamous non–small-cell lung cancer (NSCLC) and ALK rearrangements improves outcomes compared with chemotherapy. This study assessed real-world ALK testing patterns among community practices in the United States in patients with advanced (stage IIIB or IV) NSCLC. Methods Patients age ≥ 18 years with two or more visits within the Flatiron Health electronic health record–derived database after January 2011 and diagnosed with stage IIIB or IV NSCLC through May 2017 were included in this analysis. Logistic regression was used to examine the association between demographic and clinical characteristics and testing for ALK rearrangements. Results Of 31,483 patients analyzed from the database, 16,726 patients (53.1%) were tested for ALK rearrangements. ALK testing rates were 66.9% and 18.5% in patients with nonsquamous and squamous histology, respectively. Average ALK testing rates increased over time from 32.4% in 2011 to 62.1% in 2016. Fluorescent in situ hybridization was the most common ALK testing method. Agreement between fluorescent in situ hybridization and other assays ranged from 94.1% to 97.9%. Median (interquartile range) time from laboratory receipt of sample to first ALK test result was 7 (7) days; median time from advanced diagnosis to first ALK test result was 25 (29) days. Patients who were older, male, had a history of smoking, lived in non-Western US regions, and who had recurrent disease or squamous histology were less likely to be tested for ALK. Patients with Medicaid and Medicare insurance were less likely to be tested than patients with commercial insurance. Overall, 21.5% of patients initiated therapy (20.4% chemotherapy) before receiving test results. Conclusion ALK testing rates have increased over time. However, certain subgroups of patients are less likely to be tested, suggesting that additional education on molecular testing is warranted.

scholarly journals Temporal Variation in Setosphaeria turcica Between 1974 and 1994 and Origin of Races 1, 23, and 23N in the United States

2007 ◽  
Vol 97 (11) ◽  
pp. 1501-1511 ◽  
Author(s):  
L. M. Ferguson ◽  
M. L. Carson
Keyword(s):  
United States ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Eastern United States ◽  
Setosphaeria Turcica ◽  
Distinct Subgroup ◽  
World Survey ◽  
Race 1 ◽  
And Cluster Analysis

Setosphaeria turcica causes northern leaf blight, an economically important disease of maize throughout the world. Survey collections of S. turcica isolates from 1974 to 1994 provided a unique opportunity to examine temporal diversity in the eastern United States. Two hundred forty-two isolates of S. turcica from maize were studied with random amplified polymorphic DNA (RAPD) markers, mating type, and virulence on maize differential inbred lines with known Ht resistance genes to examine changes over time. One hundred forty-nine RAPD haplotypes were identified. Nearly 20% of haplotypes recurred in more than one year. Race 0 isolates declined in frequency from 83% in 1974 to near 50% in the 1990s, most likely in response to the widespread deployment of Ht1 in commercial maize hybrids. Races 23 and 23N were present in the collection at low levels throughout the study period and were also found among isolates from Virginia in 1957. The frequency of MAT1-2 isolates increased sharply after 1979 and was associated with the emergence of race 1 during the same period. RAPD markers were used to investigate the genetic diversity among a subset of isolates collected in the United States from 1976 to 1982, the period in which this dramatic shift in race frequency occurred. Multilocus haplotypes were not exclusively associated with known races of S. turcica. Based on shared haplotypes and cluster analysis, race 1 isolates share greater similarity with race 0 than with 23 or 23N isolates, indicating race 1 probably evolved from multiple lineages of race 0. Sorghum spp.-infecting isolates share greater similarity with one another than with maize-infecting isolates and represent a distinct subgroup.

C-banding and fluorescence in situ hybridization studies of the wheat–alien hybrid 'Agrotana'

Genome ◽  
1994 ◽  
Vol 37 (3) ◽  
pp. 477-481 ◽  
Author(s):  
Jie Xu ◽  
R. L. Conner ◽  
A. Laroche
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Chromosome Engineering ◽  
C Banding ◽  
Chinese Spring Wheat ◽  
Mother Cells ◽  
Alien Chromatin ◽  
Chromosome Segments

'Agrotana', a wheat-alien hybrid (2n = 56), is a potential source of resistance to common root rot, stem rust, wheat streak mosaic virus, and the wheat curl mite. However, the origin of 'Agrotana', reported to be durum wheat × Agropyron trichophorum (pubescent wheatgrass), is uncertain. The objective of this investigation was to determine the chromosome constitution of 'Agrotana' using C-banding and fluorescence in situ hybridization techniques. The F1 hybrid of 'Agrotana' × 'Chinese Spring' wheat showed 7 I + 21 II in 14.9% of the pollen mother cells, evidence of the presence of the A, B, and D genomes in 'Agrotana'. The hybrid had 16 heavily C-banded chromosomes, namely 4A, and 1-7B of wheat, and a translocation that probably involved wheat chromosomes 2A and 2D. In situ hybridization using biotinylated genomic DNA of Ag. trichophorum cv. Greenleaf blocked with CS DNA failed to identify the alien chromosomes in 'Agrotana', indicating that the alien chromosomes were not likely derived from pubescent wheatgrass. In situ hybridization using labelled wheat genomic DNA blocked with 'Agrotana' DNA revealed that 'Agrotana' had 40 wheat, 14 alien, and 2 (a pair) wheat–alien translocated chromosomes. There was no homology between wheat and the alien chromosomes or chromosome segments involved in the wheat–alien recombinant. Two of the seven pairs of alien chromosomes were homoeologous to each other. The ability to identify alien chromatin in wheat using labelled wheat DNA instead of labelled alien DNA will be particularly useful in chromosome engineering of wheat germplasms having alien chromatin of unknown origin.Key words: wheat–alien hybrid, C-banding, fluorescence in situ hybridization, labelled wheat DNA as probe.

scholarly journals International Arctic Systems for Observing the Atmosphere: An International Polar Year Legacy Consortium

2016 ◽  
Vol 97 (6) ◽  
pp. 1033-1056 ◽  
Author(s):  
Taneil Uttal ◽  
Sandra Starkweather ◽  
James R. Drummond ◽  
Timo Vihma ◽  
Alexander P. Makshtas ◽  
...  
Keyword(s):  
United States ◽  
The United States ◽  
Satellite Observations ◽  
The Arctic ◽  
International Polar Year ◽  
Network Measurements ◽  
International Polar ◽  
In Situ Observations ◽  
Arctic Atmosphere

Abstract International Arctic Systems for Observing the Atmosphere (IASOA) activities and partnerships were initiated as a part of the 2007–09 International Polar Year (IPY) and are expected to continue for many decades as a legacy program. The IASOA focus is on coordinating intensive measurements of the Arctic atmosphere collected in the United States, Canada, Russia, Norway, Finland, and Greenland to create synthesis science that leads to an understanding of why and not just how the Arctic atmosphere is evolving. The IASOA premise is that there are limitations with Arctic modeling and satellite observations that can only be addressed with boots-on-the-ground, in situ observations and that the potential of combining individual station and network measurements into an integrated observing system is tremendous. The IASOA vision is that by further integrating with other network observing programs focusing on hydrology, glaciology, oceanography, terrestrial, and biological systems it will be possible to understand the mechanisms of the entire Arctic system, perhaps well enough for humans to mitigate undesirable variations and adapt to inevitable change.

scholarly journals Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott C. Thomas ◽  
Devon Payne ◽  
Kevin O. Tamadonfar ◽  
Cale O. Seymour ◽  
Jian-Yu Jiao ◽  
...  
Keyword(s):  
United States ◽  
Amino Acids ◽  
Draft Genome ◽  
The United States ◽  
Pentose Phosphate ◽  
High Abundance ◽  
Comparative Genomic ◽  
Labeled Compounds ◽  
Geothermal Systems

Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S–5.8S–26S rDNA and a C genome specific DNA sequence in the genus Avena

Genome ◽  
1996 ◽  
Vol 39 (3) ◽  
pp. 535-542 ◽  
Author(s):  
Concha Linares ◽  
Juan González ◽  
Esther Ferrer ◽  
Araceli Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Diploid Species ◽  
5S Rdna ◽  
Rdna Genes ◽  
26S Rdna ◽  
A Genome ◽  
Rdna Loci ◽  
C Genome

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S–5.8S–26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A–C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C–A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S–5.8S–26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

A rapid procedure for the isolation of C0t-1 DNA from plants

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 138-142 ◽  
Author(s):  
Michael S. Zwick ◽  
Robert E. Hanson ◽  
M. Nurul Islam-Faridi ◽  
David M. Stelly ◽  
Rod A. Wing ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Copy Number ◽  
Genomic Dna ◽  
Mammalian Species ◽  
Repetitive Dnas ◽  
Rapid Procedure ◽  
Dna Elements ◽  
Repetitive Dna Elements

In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.

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