Genetic classification of Aegilops columnaris Zhuk. (2n=4x=28, UcUcXcXc) chromosomes based on FISH analysis and substitution patterns in common wheat × Ae. columnaris introgressive lines

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 131-143 ◽  
Author(s):  
E.D. Badaeva ◽  
A.S. Ruban ◽  
A.A. Shishkina ◽  
S.N. Sibikeev ◽  
A.E. Druzhin ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Wheat Breeding ◽  
Grass Species ◽  
Fish Analysis ◽  
Genetic Classification ◽  
Genetic Groups ◽  
Lack Of Information ◽  
Introgressive Lines

Aegilops columnaris is a tetraploid species originated from Ae. umbellulata (2n=2x=14, UU) and a yet unknown diploid grass species. Although Ae. columnaris possesses some agronomically valuable traits, such as heat and drought tolerance and resistance to pests, it has never been used in wheat breeding because of difficulties in producing hybrids and a lack of information on the relationships between Ae. columnaris and common wheat chromosomes. In this paper, we report the development of 57 wheat – Ae. columnaris introgressive lines covering 8 of the14 chromosomes of Aegilops. Based on substitution spectra of hybrids and the results of FISH analysis of the parental Ae. columnaris line with seven DNA probes, we have developed the genetic nomenclature of the Uc and Xc chromosomes. Genetic groups and genome affinities were established for 11 of 14 chromosomes; the classification of the remaining three chromosomes remains unsolved. Each Ae. columnaris chromosome was characterized on the basis of C-banding pattern and the distribution of seven DNA sequences. Introgression processes were shown to depend on the parental wheat genotype and the level of divergence of homoeologous chromosomes. We found that lines carrying chromosome 5Xc are resistant to leaf rust; therefore, this chromosome could possess novel resistance genes that have never been utilized in wheat breeding.

scholarly journals Congruity of the Polymorphisms in the Expressed and Noncoding Parts of the Gli-B1 Locus in Common Wheat

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1510
Author(s):  
Yulia Popovych ◽  
Sabina Chebotar ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
Laura Pascual ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Evolutionary Significance ◽  
Sequence Length ◽  
Noncoding Dna ◽  
Important Region ◽  
Novel Variants ◽  
Specific Sequences

The previously defined pairs of primers GliB1.1 and GliB1.2 were found to produce three and four principal variants, respectively, of PCR sequence length for the γ-gliadin pseudogene in 46 Triticum aestivum L. cultivars from 15 countries carrying 19 known alleles at the Gli-B1 locus. A congruity was established between this polymorphism, allelic sets of the Gli-B1-produced gliadins (especially of the electrophoretic mobility in acid gels of the encoded γ-gliadin) and the presence in the wheat genotype of the Gli-B5b + Rg-1 allelic combination. Six different alleles at the Gli-B1 locus encoding an identical γ-gliadin produced a PCR sequence of about 400 bp (GliB1.1). Nine Gli-B1d-carrying genotypes from four countries produced an identical sequence of about 409 bp (GliB1.2), while three cultivars with Gli-B1h and four with Gli-B1b produced three and two specific sequences, respectively, of slightly different length. Allele Gli-B1j might be the result of recombination between coding and noncoding DNA sequences within the Gli-B1 locus. These observations imply that genetic diversity of the agriculturally important region of chromosome 1B marked by variants of the Gli-B1 locus is rather limited among common wheat cultivars of the 20th century, specifically to eight principal versions. These might have been incorporated into common wheat from diverged genotypes of diploid donor(s), and, due to the scarcity of recombination, subsequently maintained relatively intact. As well as its evolutionary significance, this information is of potential use in wheat breeding and we consider it likely that novel variants of the Gli-B1 locus will be found in hitherto unstudied germplasm.

scholarly journals Location pattern and genetic classification of granite pegmatites of the Ukrainian Shield

2019 ◽  
Vol 28 (4) ◽  
pp. 673-691
Author(s):  
Leonid V. Isakov ◽  
Maria L. Isakova
Keyword(s):  
Classification Scheme ◽  
Granite Gneiss ◽  
Mineralogical Composition ◽  
Rare Metal ◽  
Ukrainian Shield ◽  
Genetic Classification ◽  
Genetic Groups ◽  
Crystalline Core ◽  
Tectonic Zones

The pegmatites of the Ukrainian Shield, their formation and occurrence are con- sidered. It is shown that the Ukrainian Shield is a pegmatite province encompassing seven regions: Middle Prydniprovia, Western Pryazovia, Eastern Pryazovia, Ingulski, Rosynsko- Tikytski, Dnistersko-Buzki and Volyn, respectively encompassing megastructures of the same names and including pegmatite fields of different mineralogical composition and geochemical specialization. The Volynski, Ingulski, Middle Prydniprovia, Western Pryazovia regions have rare-earth and rare-metal specialization presented by pegmatites of different origin and petrological and mineral composition and occurring in different structural and tectonic conditions, having different formation age, which allows a full classification scheme of the pegmatites of Ukrainian Shield to be given. These structures can be considered as having formed as a result of abyssal magmatic plumes. The geological-structural position of these megastructures with obvious signs of influence of certain abyssal processes on their formation supports this assumption. We present the main geological structural and genetic factors of formation of pegmatite-bearing megastructures of the Ukrainian crystalline core-area, these factors forming the basis of a classification scheme of pegmatites of Pre-Cambrian shields. We have systematized the pegmatites of the Ukrai- nian Shield , and designed their classification scheme . We have distinguished the following groups of pegmatites by the development of pegmatite-generating zones: - three genetic groups of pegmatites: ultrametamorphogenic, magmatogenic and metamorphogenic-meta- somatic; - six genetic subgroups of pegmatites: migmatic; autochthonous granite massifs; metamorphogenic and metasomatic displaced and formed pegmatites; multiphase intrusive granite massifs; multiphase intrusive alkaline massifs; multiphase granite batholiths. By the nature of pegmatite-bearing structures, the following structural groups have been singled out: granite-gneiss regional structures and domes; dome- synclinore and dome-trough plume-structures (subgroups: interdome synclinore and trough structures, in particular greenstone structures; intrusive domes and batholiths); specific tectonic zones of stress tensions.

Cytogenetic Classification of T Lineage Acute Lymphoblastic Leukaemia: Multiple Partners of BCL11B and Other Novel Rearrangements.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2062-2062
Author(s):  
Christine J. Harrison ◽  
Kerry Barber ◽  
Zoë Broadfield ◽  
Adam Stewart ◽  
Sarah Wright ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukaemia ◽  
Lymphoblastic Leukaemia ◽  
Target Genes ◽  
Rare Variants ◽  
Simultaneous Occurrence ◽  
Fish Analysis ◽  
Genetic Classification ◽  
Genetic Changes ◽  
Multiple Partners

Abstract Increasing numbers of genetic changes are being described in T lineage acute lymphoblastic leukaemia (T ALL), which may be used to classify patients into subgroups, defining multi-step oncogenic pathways. We have integrated the significant abnormalities into a comprehensive genetic classification of T ALL, using appropriate probes for fluorescence in situ hybridization (FISH). Break-apart probes were designed, which detected rearrangements of the TCR loci. Metaphase FISH, confirmed by informative break-apart probes for the significant oncogenes, were used to identify partner genes, as shown in the table. This approach revealed new recurrent translocation partners, as well as determining the incidence and simultaneous occurrence of the different abnormalities. The series included 295 patients, children 0–14 years (n=206) and adults ≥ 15 years (n=89), with a diagnosis of T ALL, entered to one of the UK MRC/NCRI ALL treatment trials. The incidences of the common cryptic abnormalities, SIL-TAL1 fusion and TLX3 were more prevalent in children (20% and 17%, respectively) compared to adults (9% each). There was no difference in event free survival between the childhood patients with SIL-TAL1 fusion and TLX3 rearrangements. CALM-AF10 fusion and MLL rearrangements accounted for 4% each. A single patient was found with a BCR-ABL fusion, but the same probe identified nine (3%) with NUP214-ABL1 amplification. Deletions involving CDKN2A were present in 49% of patients, in association with all abnormalities. Among the patients with NUP214-ABL1 amplification, associated abnormalities were: CDKN2A deletions (n=9), TRA@-TLX1 (n=2), BCL11B-TLX3 (n=2), TRB@-TLX3 (n=1). Concurrent rearrangements were found between the TCR genes, as well as associations between MYC, IGH and the other oncogenes. For example, (1) complex abnormalities between (a) TRA@, TRG@, BCL11B (n=2) and (b) HOXA@ (n=1); (2) deletions of 3′TRB@ in association with (a) complex ring chromosomes (n=2) and (b) cytogenetically visible deletions (n=2). FISH detected several novel, recurrent rearrangements, in particular a t(6;14) involving BCL11B and the 6q26 region (n=5) and a t(9;14)(p24;q31.1) involving JAK2 (n=2), the partners of which are currently being defined. BCL11B was also involved with (a) LMO2 and (b) the 2q23 region; LMO2 was rearranged with an unidentified partner in a complex translocation with chromosomes 16 and 18; TLX1 was involved in a translocation with 3q; new partners of TRB@ were found at (a) 1q11, (b) on 12p (n=2), (c) on 21q. These findings demonstrate the valuable role of FISH analysis, with a panel of carefully selected probes, to classify T ALL patients into genetic subgroups, including rare variants, and provide information on the relationship between them. A metaphase FISH approach has facilitated the identification of potential new target genes. In particular, multiple partners of TRB@ and BCL11B, other than the known TLX3 and HOXA@ genes, have emerged, highlighting the importance of these genes in the pathogenesis of T ALL. Promotor and Oncogenes in T ALL Promotor Genes Oncogenes BCL11B TRA@ TRB@ TRG@ CDK6 Novel***/Unknown *includes 3 telomeric deletions, **includes 3 centromeric deletions, ***listed in text TLX3 38* 3 1 2 TLX1 12 3 1 HOXA@ 1 5 1 LMO1 1 LMO2 1 14 3 1 4** LYL1 2 TAL2 6 NOTCH1 1 MYC 2 3 1 MYB 1 IGH@ 4

scholarly journals Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

2021 ◽  
Vol 22 (4) ◽  
pp. 1832
Author(s):  
Eugene Metakovsky ◽  
Laura Pascual ◽  
Patrizia Vaccino ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Group Iv ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Olivia M Gearner ◽  
Marcin J Kamiński ◽  
Kojun Kanda ◽  
Kali Swichtenberg ◽  
Aaron D Smith
Keyword(s):  
Dna Sequences ◽  
Species Group ◽  
Phylogenetic Placement ◽  
Darkling Beetles ◽  
Species Groups ◽  
Taxonomic Groups ◽  
Inference Methods ◽  
A New Species ◽  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

scholarly journals NIMG-53. GLUTAMATE/GABA RATIO ON MRS IS ELEVATED IN PATIENTS WITH LOWER GRADE GLIOMAS AND SEIZURES

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii159-ii160
Author(s):  
Roberta Rudà ◽  
Riccardo Pascuzzo ◽  
Francesca Mo ◽  
Alessia Pellerino ◽  
Peter B Barker ◽  
...  
Keyword(s):  
Tumor Location ◽  
Resonance Spectroscopy ◽  
Lower Grade ◽  
Lack Of Information ◽  
Baseline Evaluation ◽  
Grade Ii ◽  
Grade Iii

Abstract BACKGROUND There is lack of information on the role of excitatory and inhibitory neurotransmitters in the development of seizures in patients with lower grade gliomas. Increase of glutamate and downregulation of GABA have been suggested in preclinical models and human surgical samples to be associated with brain tumor-related epilepsy. MATERIAL AND METHODS We prospectively investigated with the use of magnetic resonance spectroscopy (MRS) the differences in the ratio of metabolites (glutamate/GABA, glutamate/creatine and GABA/creatine) in the peritumoral areas between patients with or without seizures in a series of lower grade gliomas. Tumors were classified according to WHO Classification of 2016 as follows:11 grade II IDH mutated and 1p/19q codeleted; 3 grade III IDH mutated and 1p/19q codeleted; 6 grade II IDH mutated and 1p/19q intact; 1 grade III IDH mutated and 1p/19q intact; 1 grade II IDH wild-type. Patients received surgery alone or followed by temozolomide chemotherapy according to the presence of risk factors. RESULTS At baseline evaluation, maximum glutamate/GABA values were significantly higher (p=0.023) in the peritumoral area of patients with seizures (1.008 ± 0.368) with respect to those without seizures (0.691 ± 0.170). No other metabolites ratio showed significant differences between the two groups. Similar results were obtained when analyzing the metabolites ratio in the examinations during the follow-up. In the cohort of patients with seizures (n.14) variations of metabolite ratios were not associated with tumor location, 1p/19q codeletion, use of AEDs, concomitant chemotherapy or seizure characteristics (type, duration, frequency). CONCLUSIONS The study is ongoing with the aim of analyzing further the correlations between ratio of metabolites and status of the tumor (stable vs progressive).

Abstract 2276: Genetic classification of colorectal cancer

2021 ◽  
Author(s):  
Yoshikage Inoue ◽  
Nobuyuki Kakiuchi ◽  
Kenichi Yoshida ◽  
Yasuhito Nanya ◽  
Yusuke Shiozawa ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Genetic Classification

PENYUSUNAN BUKU PANDUAN PRAKTIK WISATA YANG BERTANGGUNG JAWAB DALAM PENDAKIAN GUNUNG

2017 ◽  
Vol 11 (03) ◽  
pp. 53-64
Author(s):  
Jussac Maulana Masjhoer ◽  
Dwi Wibowo ◽  
Bijak Qoulan Sadida ◽  
Inosensius Tito Ogista
Keyword(s):  
Best Practices ◽  
Survey Research ◽  
Research Method ◽  
Mountain Climbing ◽  
Tourist Behavior ◽  
The Public ◽  
Lack Of Information ◽  
Strongly Agree ◽  
Responsible Tourism

The lack of information related to the best practices in responsible tourism is one of the causes to tourist behavior problems. This study aims to determine the behavior of tourists in hiking, the adoption of responsible tourism practices, and to compile a responsible tourism practices guidebook. The research method used is survey research by spreading the questionnaire. Based on Likert analysis, at the pre-ascending stage, the classification of attitudes indicated by the respondents for cost and transportation is quite agreeable, while for equipment, guide, and simaksi is agreed. The ascent stage, the indicator when going up the mountain is quite agree, camping is not agree, the cook is agree, and when down the mountain is strongly agree. The post-ascent stage shows quite agreeable attitude. The public test of the guidebook, for the aspect of size and language of submission shows an agreeable attitude, while for the design, thickness, and content of the book shows an agreeable attitude. The conclusion is that (1) Still found the behavior of tourists in mountain climbing that is not environmentally friendly, (2) The responsible tourism practices of mountaineering that includes pre-ascending, ascent, and post-ascent, not well implemented by tourists, and (3) The responsible tourism practices guidebook still lack both technical and substance. Keywords: responsible tourism, mountain hiking, guidebook, tourist behavior

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