scholarly journals The Evolutionary Dynamics of Repetitive DNA and Its Impact on the Genome Diversification in the Genus Sorghum

2021 ◽  
Vol 12 ◽  
Author(s):  
Yi-Tzu Kuo ◽  
Takayoshi Ishii ◽  
Jörg Fuchs ◽  
Wei-Hsun Hsieh ◽  
Andreas Houben ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Structural Changes ◽  
Evolutionary Dynamics ◽  
Distinct Species ◽  
Sorghum Halepense ◽  
Fish Analysis ◽  
Potential Contribution ◽  
Chip Sequencing ◽  
Evolutionary Event

Polyploidization is an evolutionary event leading to structural changes of the genome(s), particularly allopolyploidization, which combines different genomes of distinct species. The tetraploid species, Sorghum halepense, is assumed an allopolyploid species formed by hybridization between diploid S. bicolor and S. propinquum. The repeat profiles of S. bicolor, S. halepense, and their relatives were compared to elucidate the repeats’ role in shaping their genomes. The repeat frequencies and profiles of the three diploid accessions (S. bicolor, S. bicolor ssp. verticilliflorum, and S. bicolor var. technicum) and two tetraploid accessions (S. halepense) are similar. However, the polymorphic distribution of the subtelomeric satellites preferentially enriched in the tetraploid S. halepense indicates drastic genome rearrangements after the allopolyploidization event. Verified by CENH3 chromatin immunoprecipitation (ChIP)-sequencing and fluorescence in situ hybridization (FISH) analysis the centromeres of S. bicolor are mainly composed of the abundant satellite SorSat137 (CEN38) and diverse CRMs, Athila of Ty3_gypsy and Ty1_copia-SIRE long terminal repeat (LTR) retroelements. A similar centromere composition was found in S. halepense. The potential contribution of S. bicolor in the formation of tetraploid S. halepense is discussed.

S1 satellite DNA as a taxonomic marker in brown frogs: molecular evidence that Rana graeca graeca and Rana graeca italica are different species

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 63-70 ◽  
Author(s):  
Orfeo Picariello ◽  
Isidoro Feliciello ◽  
Renato Bellinello ◽  
Gianni Chinali
Keyword(s):  
Satellite Dna ◽  
Balkan Peninsula ◽  
Distinct Species ◽  
Molecular Evidence ◽  
Fish Analysis ◽  
Consensus Sequences ◽  
Repeat Sequences ◽  
Italian Apennines ◽  
Taxonomic Marker

The brown frog Rana graeca was believed to be present in two areas, the Balkan Peninsula and the Italian Apennines. We have characterised the S1 satellite DNA family from Rana graeca graeca and compared it with that of Rana graeca italica. On Southern blots, the patterns of S1 satellite DNA bands are very different between Italian and Greek specimens, but homogeneous among various populations of the same taxon. The satellite DNA from the Greek taxon contains two repetitive units (S1a (494 bp) and S1b (363 bp)) that could be sequenced after amplification from genomic DNA to directly yield their consensus sequences in each genome. These consensus sequences were very similar among the Greek populations, but differed either in sequence (in S1a) or in both size and sequence (in S1b) from the corresponding repeats of the Italian taxon. A mechanism of concerted evolution is likely responsible for the high homogeneity of S1a and S1b repeat sequences within each genome and species. The genomic content of S1 satellite DNA was lower in the Greek than in the Italian populations (0.5 vs. 1.9%) and fluorescence in situ hybridization (FISH) analysis showed the S1 satellite on only 4 chromosome pairs in the Greek taxon and on all 13 chromosome pairs in the Italian taxon. The completely different structure and genomic organization of the S1 satellite DNA indicate that the Greek and Italian taxa are distinct species: R. graeca and R. italica.Key words: satellite DNA, DNA sequence, Southern blot, FISH, Rana.

scholarly journals Jacobsen syndrome and neonatal bleeding: report on two unrelated patients

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Gregorio Serra ◽  
Luigi Memo ◽  
Vincenzo Antona ◽  
Giovanni Corsello ◽  
Valentina Favero ◽  
...  
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Comparative Genomic ◽  
Fish Analysis ◽  
Variable Degree ◽  
Jacobsen Syndrome ◽  
Contiguous Gene ◽  
Clinical Consequences ◽  
11Q Deletion

Abstract Introduction In 1973, Petrea Jacobsen described the first patient showing dysmorphic features, developmental delay and congenital heart disease (atrial and ventricular septal defect) associated to a 11q deletion, inherited from the father. Since then, more than 200 patients have been reported, and the chromosomal critical region responsible for this contiguous gene disorder has been identified. Patients’ presentation We report on two unrelated newborns observed in Italy affected by Jacobsen syndrome (JBS, also known as 11q23 deletion). Both patients presented prenatal and postnatal bleeding, growth and developmental delay, craniofacial dysmorphisms, multiple congenital anomalies, and pancytopenia of variable degree. Array comparative genomic hybridization (aCGH) identified a terminal deletion at 11q24.1-q25 of 12.5 Mb and 11 Mb, in Patient 1 and 2, respectively. Fluorescent in situ hybridization (FISH) analysis of the parents documented a de novo origin of the deletion for Patient 1; parents of Patient 2 refused further genetic investigations. Conclusions Present newborns show the full phenotype of JBS including thrombocytopenia, according to their wide 11q deletion size. Bleeding was particularly severe in one of them, leading to a cerebral hemorrhage. Our report highlights the relevance of early diagnosis, genetic counselling and careful management and follow-up of JBS patients, which may avoid severe clinical consequences and lower the mortality risk. It may provide further insights and a better characterization of JBS, suggesting new elements of the genotype-phenotype correlations.

Fluorescent in situ hybridization (FISH): A useful diagnostic tool for childhood conjunctival melanoma

2021 ◽  
pp. 112067212110307
Author(s):  
Raquel María Moral ◽  
Carlos Monteagudo ◽  
Javier Muriel ◽  
Lucía Moreno ◽  
Ana María Peiró
Keyword(s):  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Pediatric Population ◽  
Diagnostic Technique ◽  
Histopathological Diagnosis ◽  
Fish Analysis ◽  
Conjunctival Melanoma ◽  
Adequate Treatment ◽  
First Case

Introduction: Conjunctival melanoma is extremely rare in children and has low rates of resolution. Definitive histopathological diagnosis based exclusively on microscopic findings is sometimes difficult. Thus, early diagnosis and adequate treatment are essential to improve clinical outcomes. Clinical case: We present the first case in which the fluorescent in situ hybridization (FISH) diagnostic technique was applied to a 10-year-old boy initially suspected of having amelanotic nevi in his right eye. Based on the 65% of tumor cells with 11q13 (CCND1) copy number gain and 33% with 6p25 (RREB1) gain as measured by the FISH analysis, and on supporting histopathological findings, the diagnosis of conjunctival melanoma could be made. Following a larger re-excision, adjuvant therapy with Mitomycin C (MMC), cryotherapy and an amniotic membrane graft, the patient has remained disease-free during 9 years of long-term follow-up. Case discussion: Every ophthalmologist should remember to consider and not forget the possibility of using FISH analyses during the differential diagnosis of any suspicious conjunctival lesions. Genetic techniques, such as FISH, have led to great advances in the classification of ambiguous lesions. Evidence-based guidelines for diagnosing conjunctival melanoma in the pediatric population are needed to determine the most appropriate strategy for this age group.

Roughened gold electrode for in situ SERS analysis of structural changes accompanying the doping process of polyaniline in acidic aqueous media

2021 ◽  
Vol 882 ◽  
pp. 115034
Author(s):  
A. El Guerraf ◽  
M. Bouabdallaoui ◽  
Z. Aouzal ◽  
S. Ben Jadi ◽  
N.K. Bakirhan ◽  
...  
Keyword(s):  
Gold Electrode ◽  
Structural Changes ◽  
Aqueous Media

Laboratory Testing for HER2/neu in Breast Carcinoma: An Evolving Strategy to Predict Response to Targeted Therapy

2001 ◽  
Vol 8 (5) ◽  
pp. 415-418 ◽  
Author(s):  
Nils M. Diaz
Keyword(s):  
Targeted Therapy ◽  
Breast Carcinoma ◽  
Gene Amplification ◽  
Laboratory Testing ◽  
False Positives ◽  
Response To Therapy ◽  
Fish Analysis ◽  
Breast Carcinomas ◽  
Testing Strategies

Background Laboratory testing of HER2/neu in breast carcinoma has become vital to patient care following the approval of trastuzumab as the first therapy to target the HER2/neu oncoprotein. Initial clinical trials used immunohistochemistry (IHC) to test for HER2/neu overexpression in order to select patients for therapy. Fluorescence in situ hybridization (FISH), which tests for gene amplification, is more specific and sensitive than IHC when either assay is compared with HER2/neu overexpression as determined by Northern or Western blot analysis. Many weak overexpressors on IHC testing are not gene amplified on FISH analysis. Such weak overexpressors may be considered false-positives and raise the question of how best to test for HER2/neu. Methods The literature was surveyed regarding testing for HER2/neu overexpression in breast carcinomas and alternative testing strategies. Results False-positive results are a significant problem when IHC is exclusively used to test for HER2/neu overexpression. The false-positives are overwhelmingly confined to the group of 2+ positives and do not respond to targeted therapy. In contrast, concordance between IHC and FISH is high when immunostaining is interpreted as either negative or strongly positive (3+). Whereas some recent studies have suggested that FISH may better predict response to anti-HER2/neu therapy than IHC, others have indicated that IHC is as effective a predictor as FISH. IHC is less technically demanding and costly than FISH. Conclusions IHC analysis of HER2/neu in breast carcinoma is a useful predictor of response to therapy with trastuzumab when strongly positive. Negative immunostaining is highly concordant with a lack of gene amplification by FISH. Most weakly positive overexpressors are false-positives on testing with FISH. Thus, screening of breast carcinomas with IHC and confirmation of weakly positive IHC results by FISH is an effective evolving strategy for testing HER2/neu as a predictor of response to targeted therapy.

Evolution of early Eocene Palaeosinopa (Mammalia, Pantolestidae) in the Willwood Formation of the Bighorn Basin, Wyoming

2015 ◽  
Vol 89 (4) ◽  
pp. 665-694 ◽  
Author(s):  
Rachel H. Dunn ◽  
Kenneth D. Rose
Keyword(s):  
Morphological Evolution ◽  
Distal Tibia ◽  
Distinct Species ◽  
Powder River Basin ◽  
Ancestral Population ◽  
Bighorn Basin ◽  
New Material ◽  
Size And Morphology ◽  
Willwood Formation

AbstractSpecies-level diversity and evolution of Palaeosinopa from the Willwood Formation of the Bighorn Basin is reassessed based on substantial new material from the Bighorn, Powder River, and Wind River basins. We recognize three species of Palaeosinopa in the Willwood Formation of the Bighorn Basin: P. lutreola, P. incerta, and P. veterrima. The late Wasatchian species P. didelphoides is not present in the Bighorn Basin. The Willwood species can be differentiated based only on size. P. veterrima is the most common and wide-ranging species and is the most variable in size and morphology: the stratigraphically lowest individuals are smaller, with narrower, more crestiform lower molars; whereas the highest are larger, with wider, more bunodont teeth. Although it could be argued that these represent distinct species, we demonstrate that this morphological evolution occurred as the gradual and mosaic accumulation of features, suggesting in situ anagenetic evolution. The two smaller species are present only low in the section (biochrons Wa0–Wa4) and show no discernable evolution in size or morphology. A new skeleton of Palaeosinopa veterrima from the Willwood Formation is described, and other new postcrania are reported. The skeleton is the oldest associated skeleton of Palaeosinopa known, yet it is remarkably similar to those of younger, more derived pantolestids, the primary disparities being minor differences in proportions of the innominate, femur, and tibia, and co-ossification of the distal tibia and fibula. Either P. incerta or P. lutreola was likely the ancestral population that gave rise to the other Wasatchian Palaeosinopa. Alternatively, P. veterrima may have migrated into the Bighorn Basin from the Powder River Basin.

scholarly journals High temperature structural study of decagonal Al-Cu-Rh quasicrystal.

2014 ◽  
Vol 70 (a1) ◽  
pp. C94-C94
Author(s):  
Pawel Kuczera ◽  
Walter Steurer
Keyword(s):  
Structural Changes ◽  
Configurational Entropy ◽  
Lattice Vibrations ◽  
X Ray Diffraction ◽  
Stabilization Mechanism ◽  
X Ray ◽  
Comparative Structure ◽  
The Stability

The structure of d(ecagonal)-Al-Cu-Rh has been studied as a function of temperature by in-situ single-crystal X-ray diffraction in order to contribute to the discussion on energy or entropy stabilization of quasicrystals (QC) [1]. The experiments were performed at 293 K, 1223 K, 1153 K, 1083 K, and 1013 K. A common subset of 1460 unique reflections was used for the comparative structure refinements at each temperature. The results obtained for the HT structure refinements of d-Al-Cu-Rh QC seem to contradict a pure phasonic-entropy-based stabilization mechanism [2] for this QC. The trends observed for the ln func(I(T1 )/I(T2 )) vs.|k⊥ |^2 plots indicate that the best on-average quasiperiodic order exists between 1083 K and 1153 K, however, what that actually means is unclear. It could indicate towards a small phasonic contribution to entropy, but such contribution is not seen in the structure refinements. A rough estimation of the hypothetic phason instability temperature shows that it would be kinetically inaccessible and thus the phase transition to a 12 Å low T structure (at ~800 K) is most likely not phason-driven. Except for the obvious increase in the amplitude of the thermal motion, no other significant structural changes, in particular no sources of additional phason-related configurational entropy, were found. All structures are refined to very similar R-values, which proves that the quality of the refinement at each temperature is the same. This suggests, that concerning the stability factors, some QCs could be similar to other HT complex intermetallic phases. The experimental results clearly show that at least the ~4 Å structure of d-Al-Cu-Rh is a HT phase therefore entropy plays an important role in its stabilisation mechanism lowering the free energy. However, the main source of this entropy is probably not related to phason flips, but rather to lattice vibrations, occupational disorder unrelated to phason flips like split positions along the periodic axis.

Perspectives on endothelial-to-mesenchymal transition: potential contribution to vascular remodeling in chronic pulmonary hypertension

2007 ◽  
Vol 293 (1) ◽  
pp. L1-L8 ◽  
Author(s):  
Enrique Arciniegas ◽  
Maria G. Frid ◽  
Ivor S. Douglas ◽  
Kurt R. Stenmark
Keyword(s):  
Pulmonary Hypertension ◽  
Smooth Muscle ◽  
Vascular Remodeling ◽  
Serine Proteases ◽  
Structural Changes ◽  
Transforming Growth Factor ◽  
Pulmonary Arteries ◽  
Potential Contribution ◽  
Mesenchymal Transition ◽  
Endothelial Mesenchymal Transition

All forms of pulmonary hypertension are characterized by structural changes in pulmonary arteries. Increased numbers of cells expressing α-smooth muscle (α-SM) actin is a nearly universal finding in the remodeled artery. Traditionally, it was assumed that resident smooth muscle cells were the exclusive source of these newly appearing α-SM actin-expressing cells. However, rapidly emerging experimental evidence suggests other, alternative cellular sources of these cells. One possibility is that endothelial cells can transition into mesenchymal cells expressing α-SM actin and that this process contributes to the accumulation of SM-like cells in vascular pathologies. We review the evidence that endothelial-mesenchymal transition is an important contributor to cardiac and vascular development as well as to pathophysiological vascular remodeling. Recent work has provided evidence for the role of transforming growth factor-β, Wnt, and Notch signaling in this process. The potential roles of matrix metalloproteinases and serine proteases are also discussed. Importantly, endothelial-mesenchymal transition may be reversible. Thus insights into the mechanisms controlling endothelial-mesenchymal transition are relevant to vascular remodeling and are important as we consider new therapies aimed at reversing pulmonary vascular remodeling.

scholarly journals Break–apart interphase fluorescence in situ hybridization assay in papillary thyroid carcinoma: on the road to optimizing the cut-off level for RET/PTC rearrangements

2015 ◽  
Vol 172 (5) ◽  
pp. 571-582 ◽  
Author(s):  
Chiara Colato ◽  
Caterina Vicentini ◽  
Silvia Cantara ◽  
Serena Pedron ◽  
Paolo Brazzarola ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Chromosomal Rearrangements ◽  
Study Cohort ◽  
Fish Analysis ◽  
Papillary Thyroid ◽  
Qrt Pcr ◽  
Molecular Events ◽  
On The Road

ObjectiveChromosomal rearrangements of theRETproto-oncogene is one of the most common molecular events in papillary thyroid carcinoma (PTC). However, their pathogenic role and clinical significance are still debated. This study aimed to investigate the prevalence of RET/PTC rearrangement in a cohort ofBRAFWT PTCs by fluorescencein situhybridization (FISH) and to search a reliable cut-off level in order to distinguish clonal or non-clonal RET changes.DesignFortyBRAFWT PTCs were analyzed by FISH for RET rearrangements. As controls, sixBRAFV600E mutated PTCs, 13 follicular adenomas (FA), and ten normal thyroid parenchyma were also analyzed.MethodsWe performed FISH analysis on formalin-fixed, paraffin-embedded tissue using a commercially available RET break–apart probe. A cut-off level equivalent to 10.2% of aberrant cells was accepted as significant. To validate FISH results, we analyzed the study cohort by qRT-PCR.ResultsSplit RET signals above the cut-off level were observed in 25% (10/40) of PTCs, harboring a percentage of positive cells ranging from 12 to 50%, and in one spontaneous FA (1/13, 7.7%). Overall, the data obtained by FISH matched well with qRT-PCR results. Challenging findings were observed in five cases showing a frequency of rearrangement very close to the cut-off.ConclusionsFISH approach represents a powerful tool to estimate the ratio between broken and non-broken RET tumor cells. Establishing a precise FISH cut-off may be useful in the interpretation of the presence of RET rearrangement, primarily when this strategy is used for cytological evaluation or for targeted therapy.

Sign in / Sign up

Export Citation Format

Share Document