scholarly journals Insights into the Karyotype Evolution of Charinidae, the Early-Diverging Clade of Whip Spiders (Arachnida: Amblypygi)

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3233
Author(s):  
Azucena Claudia Reyes Lerma ◽  
František Šťáhlavský ◽  
Michael Seiter ◽  
Leonela Zusel Carabajal Paladino ◽  
Klára Divišová ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Karyotype Evolution ◽  
Gradual Reduction ◽  
Wide Range ◽  
The Family ◽  
Heteromorphic Sex Chromosomes ◽  
Pericentric Inversions ◽  
Low Diversity ◽  
Insight Into

Whip spiders (Amblypygi) represent an ancient order of tetrapulmonate arachnids with a low diversity. Their cytogenetic data are confined to only a few reports. Here, we analyzed the family Charinidae, a lineage almost at the base of the amblypygids, providing an insight into the ancestral traits and basic trajectories of amblypygid karyotype evolution. We performed Giemsa staining, selected banding techniques, and detected 18S ribosomal DNA and telomeric repeats by fluorescence in situ hybridization in four Charinus and five Sarax species. Both genera exhibit a wide range of diploid chromosome numbers (2n = 42–76 and 22–74 for Charinus and Sarax, respectively). The 2n reduction was accompanied by an increase of proportion of biarmed elements. We further revealed a single NOR site (probably an ancestral condition for charinids), the presence of a (TTAGG)n telomeric motif localized mostly at the chromosome ends, and an absence of heteromorphic sex chromosomes. Our data collectively suggest a high pace of karyotype repatterning in amblypygids, with probably a high ancestral 2n and its subsequent gradual reduction by fusions, and the action of pericentric inversions, similarly to what has been proposed for neoamblypygids. The possible contribution of fissions to charinid karyotype repatterning, however, cannot be fully ruled out.

scholarly journals Monocentric chromosomes in Juncus (Juncaceae) and implications for the chromosome evolution of the family

2019 ◽  
Vol 191 (4) ◽  
pp. 475-483 ◽  
Author(s):  
Marcelo Guerra ◽  
Tiago Ribeiro ◽  
Leonardo P Felix
Keyword(s):  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Chromosome Evolution ◽  
Holocentric Chromosomes ◽  
Mitotic Chromosomes ◽  
Restricted Area ◽  
Rdna Sites ◽  
The Family ◽  
Meiotic Analyses

Abstract Holocentric chromosomes are rare among angiosperms, but have been suggested to be shared by all or most of the species of Cyperaceae and Juncaceae. However, no clear demonstration of the centromere type in Juncus, the largest genus of Juncaceae, has so far been published. Thus, we conducted a detailed chromosomal investigation of four Juncus spp. aiming to identify their centromere type. Mitotic chromosomes were analysed using the fluorochromes CMA and DAPI, fluorescent in situ hybridization (FISH) with rDNA probes and immunodetection of histones H3 phosphorylated at serine 10 (H3-S10ph) and H2A phosphorylated at threonine 133 (H2A-T133ph). DAPI-stained chromosomes of all species displayed typical primary constrictions, which were not related to AT-poor CMA+ heterochromatin or rDNA sites (usually negatively stained with DAPI). Immunodetection with H3-S10ph and H2A-T133ph revealed hyperphosphorylation of pericentromeric and centromeric regions, respectively, in a restricted area, as observed in monocentric chromosomes. Meiotic analyses in J. microcephalus showed no indication of inverted meiosis, commonly found in plants with holocentric chromosomes. Since the species investigated here belong to four different sections of Juncus and all of them display typical monocentric chromosomes, it seems that this kind of centromere is common in the genus and may represent the standard centromere organization for Juncus. If Juncus has monocentric chromosomes, there is no reason to hypothesize that other genera of Juncaceae for which centromeres have not been carefully investigated have holocentric chromosomes.

Detection of fatty acid beta-oxidizing syntrophic bacteria by fluorescence in situ hybridization

2006 ◽  
Vol 54 (2) ◽  
pp. 33-39 ◽  
Author(s):  
R.J. Menes ◽  
D. Travers
Keyword(s):  
In Situ Hybridization ◽  
Fatty Acid ◽  
Fluorescence In Situ Hybridization ◽  
Upflow Anaerobic Sludge Blanket ◽  
Anaerobic Sludge ◽  
Enrichment Cultures ◽  
The Family ◽  
Syntrophic Bacteria ◽  
Anaerobic Sludge Blanket

A new 16S rRNA-targeted oligonucleotide probe, specific for the cluster of fatty acid β-oxidizing syntrophic bacteria of the family Syntrophomonadaceae was designed for fluorescence in situ hybridization. This probe was evaluated with target as well as non-target cultures. Moreover this probe was assessed with butyrate and oleate degrading enrichment cultures and methanogenic sludges from full-scale plants. The results showed that the probe revealed the presence of fatty acid β-oxidizing syntrophic bacteria in some of the samples analyzed. However, cell quantification was possible only in enrichment cultures and in a flocculent sludge from a reactor that treats lipid-rich wastewaters, but not in methanogenic granular sludges from upflow anaerobic sludge blanket reactors.

Karyotype Evolution in Harvestmen of the Suborder Cyphophthalmi (Opiliones)

2016 ◽  
Vol 148 (2-3) ◽  
pp. 227-236 ◽  
Author(s):  
Hana Svojanovská ◽  
Petr Nguyen ◽  
Matyáš Hiřman ◽  
Ivan H. Tuf ◽  
Rodzay Abdul Wahab ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Ribosomal Rna ◽  
Chromosome Pair ◽  
Karyotype Evolution ◽  
Rdna Locus ◽  
Ancestral Karyotype ◽  
Rdna Probe ◽  
Basal Group ◽  
Rna Genes

The morphologically uniform suborder Cyphophthalmi represents a basal group of harvestmen (Opiliones). As such, it plays an important role in the reconstruction of the karyotype evolution within this arachnid order. The cytogenetic analysis of 6 representatives of the suborder Cyphophthalmi, namely Miopsalis sp. (2n = 30; Stylocellidae), Austropurcellia arcticosa (Cantrell, 1980) (2n = 30; Pettalidae), Parapurcellia amatola de Bivort & Giribet, 2010 (2n = 32; Pettalidae), Paramiopsalis aff. ramulosus Juberthie, 1962 (2n = 28; Sironidae), Cyphophthalmus duricorius Joseph, 1868 (2n = 24; Sironidae), and Siro carpaticus Rafalski, 1956 (2n = 52; Sironidae) was performed. Fluorescence in situ hybridization with 18S rDNA probe was used to analyze the distribution of major ribosomal RNA genes in harvestmen. We confront the obtained cytogenetic data with current hypotheses on cyphophthalmid phylogeny to reconstruct their karyotype evolution. We conclude that the ancestral karyotype of harvestmen consisted of 2n = 30 elements with 1 chromosome pair bearing terminal rDNA clusters. The rDNA locus was multiplicated in the evolution of Cyphophthalmi. However, decreases as well as increases in the number of chromosomes have been detected in the karyotype evolution of Cyphophthalmi. Our data thus reveal unexpected diversity in cyphophthalmid karyotypes.

Identification of the E3900 family, a second family of rye B chromosome specific repeated sequences

Genome ◽  
1993 ◽  
Vol 36 (4) ◽  
pp. 706-711 ◽  
Author(s):  
Richard Blunden ◽  
Timothy J. Wilkes ◽  
John W. Forster ◽  
Mar M. Jimenez ◽  
Michael J. Sandery ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Secale Cereale ◽  
Repeated Sequence ◽  
B Chromosome ◽  
Repeated Sequences ◽  
Genomic Hybridization ◽  
The Family

A second family of highly repeated sequences has been identified on the B chromosome of rye (Secale cereale). The E3900 family was detected as a variant band in EcoRI digests of +B DNA. A clone of the basic repeat of the family was obtained, and the organization of the family was investigated by genomic hybridization. The E3900 family has no apparent homology to the A chromosome sequences of rye or other members of the Gramineae. The family has been localized by in situ hybridization to the end of the long arm of the rye B chromosome. The previously characterized E1100 sequence shows in situ hybridization to the same location as the E3900 family. These results are discussed in light of current theories of the origin of B chromosomes.Key words: B chromosome, Secale cereale, repeated sequence, cloning, in situ hybridization.

Differential sensitivity of 16S rRNA targeted oligonucleotide probes used for fluorescence in situ hybridization is a result of ribosomal higher order structure

1996 ◽  
Vol 42 (10) ◽  
pp. 1061-1071 ◽  
Author(s):  
Marc E. Frischer ◽  
Peter J. Floriani ◽  
Sandra A. Nierzwicki-Bauer
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
Fluorescence In Situ Hybridization ◽  
Differential Sensitivity ◽  
Probe Design ◽  
Oligonucleotide Probes ◽  
Whole Cells ◽  
Gene Probes ◽  
Wide Range

The use of 16S rRNA targeted gene probes for the direct analysis of microbial communities has revolutionized the field of microbial ecology, yet a comprehensive approach for the design of such probes does not exist. The development of 16S rRNA targeted oligonucleotide probes for use with fluorescence in situ hybridization (FISH) procedures has been especially difficult as a result of the complex nature of the rRNA target molecule. In this study a systematic comparison of 16S rRNA targeted oligonucleotide gene probes was conducted to determine if target location influences the hybridization efficiency of oligonucleotide probes when used with in situ hybridization protocols for the detection of whole microbial cells. Five unique universal 12-mer oligonucleotide sequences, located at different regions of the 16S rRNA molecule, were identified by a computer-aided sequence analysis of over 1000 partial and complete 16S rRNA sequences. The complements of these oligomeric sequences were chemically synthesized for use as probes and end labeled with either [γ-32P] ATP or the fluorescent molecule tetramethylrhodamine-5/-6. Hybridization sensitivity for each of the probes was determined by hybridization to heat-denatured RNA immobilized on blots or to formaldehyde fixed whole cells. All of the probes hybridized with equal efficiency to denatured RNA. However, the probes exhibited a wide range of sensitivity (from none to very strong) when hybridized with whole cells using a previously developed FISH procedure. Differential hybridization efficiencies against whole cells could not be attributed to cell wall type, since the relative probe efficiency was preserved when either Gram-negative or -positive cells were used. These studies represent one of the first attempts to systematically define criteria for 16S rRNA targeted probe design for use against whole cells and establish target site location as a critical parameter in probe design.Key words: 16S rRNA, oligonucleotide probes, in situ hybridization.

scholarly journals High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

2016 ◽  
Vol 113 (50) ◽  
pp. 14456-14461 ◽  
Author(s):  
Jeffrey R. Moffitt ◽  
Junjie Hao ◽  
Dhananjay Bambah-Mukku ◽  
Tian Lu ◽  
Catherine Dulac ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Single Molecule ◽  
High Performance ◽  
Detection Efficiency ◽  
Tissue Samples ◽  
Spatially Resolved ◽  
Wide Range ◽  
Cellular Context ◽  
Target Binding

Highly multiplexed single-molecule FISH has emerged as a promising approach to spatially resolved single-cell transcriptomics because of its ability to directly image and profile numerous RNA species in their native cellular context. However, background—from off-target binding of FISH probes and cellular autofluorescence—can become limiting in a number of important applications, such as increasing the degree of multiplexing, imaging shorter RNAs, and imaging tissue samples. Here, we developed a sample clearing approach for FISH measurements. We identified off-target binding of FISH probes to cellular components other than RNA, such as proteins, as a major source of background. To remove this source of background, we embedded samples in polyacrylamide, anchored RNAs to this polyacrylamide matrix, and cleared cellular proteins and lipids, which are also sources of autofluorescence. To demonstrate the efficacy of this approach, we measured the copy number of 130 RNA species in cleared samples using multiplexed error-robust FISH (MERFISH). We observed a reduction both in the background because of off-target probe binding and in the cellular autofluorescence without detectable loss in RNA. This process led to an improved detection efficiency and detection limit of MERFISH, and an increased measurement throughput via extension of MERFISH into four color channels. We further demonstrated MERFISH measurements of complex tissue samples from the mouse brain using this matrix-imprinting and -clearing approach. We envision that this method will improve the performance of a wide range of in situ hybridization-based techniques in both cell culture and tissues.

Chromosome Banding and 18S rDNA in situ Hybridization Analysis of Seven Species of the Family Achiridae (Teleostei: Pleuronectiformes)

Genetica ◽  
2005 ◽  
Vol 125 (2-3) ◽  
pp. 125-132 ◽  
Author(s):  
Marisa Fagundes Carvalho de Azevedo ◽  
Claudio Oliveira ◽  
Belén G. Pardo ◽  
Paulino Martínez ◽  
Fausto Foresti
Keyword(s):  
In Situ Hybridization ◽  
18S Rdna ◽  
Chromosome Banding ◽  
Hybridization Analysis ◽  
The Family

scholarly journals How to distinguish between different cell lineages sharing common markers using combinations of double in-situ-hybridization and immunostaining in avian embryos: CXCR4-positive mesodermal and neural crest-derived cells

2020 ◽  
Vol 155 (1) ◽  
pp. 145-155 ◽  
Author(s):  
Imadeldin Yahya ◽  
Marion Böing ◽  
Beate Brand-Saberi ◽  
Gabriela Morosan-Puopolo
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Embryonic Development ◽  
Neural Crest ◽  
Expression Patterns ◽  
Simultaneous Detection ◽  
Neural Crest Cells ◽  
Cell Lineages ◽  
Wide Range

AbstractCell migration plays a crucial role in early embryonic development. The chemokine receptor CXCR4 has been reported to guide migration of neural crest cells (NCCs) to form the dorsal root ganglia (DRG) and sympathetic ganglia (SG). CXCR4 also plays an important part during the formation of limb and cloacal muscles. NCCs migration and muscle formation during embryonic development are usually considered separately, although both cell lineages migrate in close neighbourhood and have markers in common. In this study, we present a new method for the simultaneous detection of CXCR4, mesodermal markers and NCCs markers during chicken embryo developmental stages HH18–HH25 by combining double whole-mount in situ hybridization (ISH) and immunostaining on floating vibratome sections. The simultaneous detection of CXCR4 and markers for the mesodermal and neural crest cells in multiple labelling allowed us to compare complex gene expression patterns and it could be easily used for a wide range of gene expression pattern analyses of other chicken embryonic tissues. All steps of the procedure, including the preparation of probes and embryos, prehybridization, hybridization, visualization of the double labelled transcripts and immunostaining, are described in detail.

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