bioinformatics-machine-learning-identification-pulmonary-hypertension

Bioinformatics and Machine-Learning Identification of Pulmonary Hypertension Biomarkers and Candidate Therapeutic Compounds

This study aimed to identify pulmonary hypertension (PH)-associated molecular biomarkers and candidate small-molecule compounds using public ...

Huaihua University

In order to analyze the conservation of maize centromeric satellite DNA (CentC) and centromeric retrotransposon (CRM) in the subspecies and relatives of Zea mays, dual fluorescence in situ hybridization (FISH) was used to detect the existence and distribution of the above two repetitive sequences in Zea mays ssp. mexicana, Z. diploperennis, Z. perennis, Tripsacum dactyloides, Coix lacryma-jobi, and Sorghum bicolor. In Z. mays ssp. mexicana, Z. diploperennis, and Z. perennis, both CentC and CRM probes produced strong or relatively strong signals in the centromeric regions of all chromosomes. There was an obvious variation in the intensity of hybridization signals on different chromosomes, indicating that different centromeres have different amounts of CentC and CRM sequences. In some centromeres, the intensity of CentC signals differed from that of CRM signals and was free from overlapping. In T. dactyloides, only weak CentC and CRM signals were detected in the centromeric regions of most chromosomes, while in C. lacryma-jobi and S. bicolor only relatively strong or strong CRM signals primarily located in the centromeric regions were detected. This result indicates that CentC is highly conserved among the subspecies of Z. mays and the species of Zea, and has high conservation in Tripsacum, a genus that is most closely related to Zea, and CRM is conserved among the species of grass family either closely or distantly related to Zea.

[Detection of maize centromeric repeats in the relatives of maize using fluorescence in situ hybridization].

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Using ITS sequence of nine species to identify counterfeiting medicine and analyse phylogenetic of Asparagus.

[Comparison of rDNA internal transcribed spacer sequences in asparagus].

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[Comparaison des ADNr interne transcrit des s&eacute;quences de l&#39;espaceur en asperge].

Verwenden die Sequenz von neun Arten Ermittlung F&auml;lschungen Medizin und Spargel phylogenetische analyse.

[Vergleich der internen rDNA transkribiert Spacer-Sequenzen in Spargel].

Utilizzando la sua sequenza di nove specie di identificare contraffazione medicina e analisi filogenetica degli asparagi.

[Confronto di rDNA interna trascritto sequenze distanziale in asparagi].

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Usando su secuencia de nueve especies para identificar la falsificaci&oacute;n de medicamentos y an&aacute;lisis filogen&eacute;tico de esp&aacute;rragos.

[Comparaci&oacute;n del rDNA interno transcrito secuencias del espaciador en esp&aacute;rragos].

The two cultivated  (Adanson, 1763) species,  (N. J. von Jacquin, 1788) A. P. de Candolle, 1825 and  (Linnaeus, 1753) A. P. de Candolle, 1825 are closely related based on morphological and molecular phylogenetic data. However, the similarities and differences in genome organization between them have not been evaluated at molecular cytogenetic level. Here, detailed karyotypes of both species were constructed using combined PI and DAPI (CPD) staining, rDNA-FISH and self-genomic  hybridization (sGISH). For further comparison, comparative genomic  hybridization (cGISH) and sequence analysis of 5S rDNA were applied. Their chromosomes were accurately identified by sGISH and rDNA-FISH signals. Both species had the karyotype formula 2n = 22 = 18m + 4m-SAT, but the karyotype of  was shorter and more asymmetric than that of . They displayed similar CPD bands at all 45S rDNA sites and centromeres.  had ten centromeric 5S rDNA loci and two SC (secondary constriction)-associated 45S rDNA loci.  had nine centromeric and one interstitial 5S loci, two SC-associated and one proximal 45S loci. Their sGISH signal patterns displayed both basic similarities and distinct differences. Reciprocal cGISH generated prominent signals in all pericentromeric regions and 45S sites. There was lower level of sequence identity of the non-transcribed spacer between their 5S rDNA repeats. These data confirmed the evolutionary closeness between  and  and demonstrated obvious differentiation between their genomes, and supported the opinion that  is more advanced in evolution than .

Molecular cytogenetic characterization and comparison of the two cultivated  species (Fabaceae).

To extend our knowledge on karyotype variation of the genus  Savi, 1824, the chromosomal organization of rRNA genes and fluorochrome banding patterns of five wild  species were studied. Sequential combined PI (propidium iodide) and DAPI (4',6-diamidino-2-phenylindole) (CPD) staining and fluorescence  hybridization (FISH) with 5S and 45S rDNA probes were used to analyze the karyotypes of  (Jacquin, 1771) Bentham, 1959,  (Linnaeus, 1753) A. Richard, 1845,  (Roxburgh, 1832) Ohwi & H. Ohashi, 1969,  (Linnaeus, 1753) Verdcourt, 1968, and  (Linnaeus, 1753) Verdcourt,1970. For further phylogenetic analysis, genomic  hybridization (GISH) with the genomic DNA of  (Thunberg, 1794) Ohwi & H.Ohashi, 1969 onto the chromosomes of five wild  species was also performed. Detailed karyotypes were established for the first time using chromosome measurements, fluorochrome bands, and rDNA-FISH signals. All species had chromosome number 2n = 2x = 22, and symmetrical karyotypes that composed of only metacentric or metacentric and submetacentric chromosomes. CPD staining revealed all 45S rDNA sites in the five species analyzed, (peri)centromeric GC-rich heterochromatin in ,  and , interstitial GC-rich and pericentromeric AT-rich heterochromatin in . rDNA-FISH revealed two 5S loci in  and one 5S locus in the other four species; one 45S locus in  and , two 45S loci in  and , and five 45S loci in . The karyotypes of the studied species could be clearly distinguished by the karyotypic parameters, and the patterns of the fluorochrome bands and the rDNA sites, which revealed high interspecific variation among the five species. The  genomic DNA probe produced weak signals in all proximal regions of  and all (peri)centromeric regions of . The combined data demonstrate that distinct genome differentiation has occurred among the five species during evolution. The phylogenetic relationships between the five wild species and related cultivated species of  are discussed based on our present and previous molecular cytogenetic data.

Comparative molecular cytogenetic characterization of five wild  species (Fabaceae).

To have an insight into the karyotype variation of eight Cucurbitaceae crops including  Linnaeus, 1753,  Linnaeus, 1753,  (Thunberg, 1794) Matsumura et Nakai, 1916,  (Thunberg, 1784) Cogniaux, 1881,  Linnaeus, 1753,  (Linnaeus, 1753) Roemer, 1846, Lagenariasicerariavar.hispida (Thunberg, 1783) Hara, 1948 and  Duchesne ex Poiret, 1819, well morphologically differentiated mitotic metaphase chromosomes were prepared using the enzymatic maceration and flame-drying method, and the chromosomal distribution of heterochromatin and 18S-5.8S-26S rRNA genes (45S rDNA) was investigated using sequential combined PI and DAPI (CPD) staining and fluorescence  hybridization (FISH) with 45S rDNA probe. Detailed karyotypes were established using the dataset of chromosome measurements, fluorochrome bands and rDNA FISH signals. Four karyotype asymmetry indices, CV, CV, M and Stebbins' category, were measured to elucidate the karyological relationships among species. All the species studied had symmetrical karyotypes composed of metacentric and submetacentric or only metacentric chromosomes, but their karyotype structure can be discriminated by the scatter plot of M vs. CV. The karyological relationships among these species revealed by PCoA based on , 2, TCL, M, CV and CV was basically in agreement with the phylogenetic relationships revealed by DNA sequences. CPD staining revealed all 45S rDNA sites in all species, (peri)centromeric GC-rich heterochromatin in , , ,  and , terminal GC-rich heterochromatin in . DAPI counterstaining after FISH revealed pericentromeric DAPI heterochromatin in . rDNA FISH detected two 45S loci in five species and five 45S loci in three species. Among these 45S loci, most were located at the terminals of chromosome arms, and a few in the proximal regions. In , individual chromosomes can be precisely distinguished by the CPD band and 45S rDNA signal patterns, providing an easy method for chromosome identification of cucumber. The genome differentiation among these species was discussed in terms of genome size, heterochromatin, 45S rDNA site, and karyotype asymmetry based on the data of this study and previous reports.

﻿Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH.

Hybridization is considered as an important model of speciation, but the evolutionary process of natural hybridization is still poorly characterized in Lycoris. To reveal the phylogenetic relationship of two new putative natural hybrids in Lycoris, morphological, karyotypic and chloroplast genomic data of four Lycoris species were analyzed in this study.

Reciprocal natural hybridization between Lycoris aurea and Lycoris radiata (Amaryllidaceae) identified by morphological, karyotypic and chloroplast genomic data.

To characterize the chromosomes of the four species of  Miller, 1754, used in traditional Chinese medicine,  Hua, 1892,  Collett et Hemsley, 1890,  (Miller, 1768) Druce, 1906, and  Redouté, 1811, and have an insight into the karyotype variation of the genus , fluorescence  hybridization (FISH) with 5S and 45S rDNA oligonucleotide probes was applied to analyze the karyotypes of 9 populations of the four species. Detailed molecular cytogenetic karyotypes of the 9 populations were established for the first time using the dataset of chromosome measurements and FISH signals of 5S and 45S rDNA. Four karyotype asymmetry indices, CV, CV, M and Stebbins' category, were measured to elucidate the asymmetry of the karyotypes and karyological relationships among species. Comparison of their karyotypes revealed distinct variations in the karyotypic parameters and rDNA patterns among and within species. The basic chromosome numbers detected were  = 9, 11 and 13 for ,  = 15 for ,  = 10 and 11 for , and  = 12 for . The original basic chromosome numbers of the four species were inferred on the basis of the data of this study and previous reports. All the 9 karyotypes were of moderate asymmetry and composed of metacentric, submetacentric and subtelocentric chromosomes or consisted of two of these types of chromosomes. Seven populations have one locus of 5S rDNA and two loci of 45S rDNA, and two populations added one 5S or 45S locus. The karyological relationships among the four species revealed by comparison of rDNA patterns and PCoA based on , 2, TCL, CV, M and CV were basically accordant with the phylogenetic relationships revealed by molecular phylogenetic studies. The mechanisms of both intra- and inter-specific dysploidy in  were discussed based on the data of this study and literature.

﻿Molecular cytogenetic characterization of 9 populations of four species in the genus  (Asparagaceae).

The complexity of the classification of the genus  necessitates further molecular cytogenetic research to clarify the karyotype differentiation and chromosome evolution among species, validate the existing classification, and help resolve ongoing classification disputes. In this study, the chromosomes of eleven species of , encompassing main medicinal and edible lilies in China as well as seven species endemic to southwest and central China, were characterized using fluorescence  hybridization (FISH) with 5S and 35S rDNA oligonucleotide probes. Quantitative molecular cytogenetic karyotypes were established using the dataset of chromosome measurements and FISH signals. Karyotype asymmetry indices were calculated to assess their karyotype asymmetry and infer their karyological relationships. Karyotype structures could be differentiated through the scatter plot of M versus CV. FISH results revealed 1–2 5S rDNA loci and 2–6 35S rDNA loci across the examined species, with most 35S loci associated with secondary constrictions. Comparative analysis of rDNA patterns, combined with PCoA based on , 2, TCL, M, CV and CV provided insights into the evolutionary relationships among these species. Our findings provide cytogenetic support for the taxonomic validity of subset.  6a in the most recent revised classification of .

Article	Year
[Detection of maize centromeric repeats in the relatives of maize using fluorescence in situ hybridization]. Yi chuan = Hereditas\| PubMed ID: 20233704	2010
[Comparison of rDNA internal transcribed spacer sequences in asparagus]. Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials\| PubMed ID: 21355188	2010
Molecular cytogenetic characterization and comparison of the two cultivated species (Fabaceae). Comparative cytogenetics\| PubMed ID: 29114355	2017
Comparative molecular cytogenetic characterization of five wild species (Fabaceae). Comparative cytogenetics\| PubMed ID: 32676173	2020
Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH. Comparative cytogenetics\| PubMed ID: 37305810	2023
Reciprocal natural hybridization between Lycoris aurea and Lycoris radiata (Amaryllidaceae) identified by morphological, karyotypic and chloroplast genomic data. BMC plant biology\| PubMed ID: 38163886	2024
Molecular cytogenetic characterization of 9 populations of four species in the genus (Asparagaceae). Comparative cytogenetics\| PubMed ID: 38798789	2024
Comparative karyotype analysis of eleven species of Lilium from China using FISH with rDNA oligo-probes. Scientific reports\| PubMed ID: 41702966	2026

Xianghui Jiang

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