Identification and characterization of satellite DNAs in two-toed sloths of the genus Choloepus (Megalonychidae, Xenarthra)

Abstract Choloepus, the only extant genus of the Megalonychidae family, is composed of two living species of two-toed sloths: Choloepus didactylus and C. hoffmanni. In this work, we identified and characterized the main satellite DNAs (satDNAs) in the sequenced genomes of these two species. SATCHO1, the most abundant satDNA in both species, is composed of 117 bp tandem repeat sequences. The second most abundant satDNA, SATCHO2, is composed of ~ 2292 bp tandem repeats. Fluorescence in situ hybridization in C. hoffmanni revealed that both satDNAs are located in the centromeric regions of all chromosomes, except the X. In fact, these satDNAs present some centromeric characteristics in their sequences, such as dyad symmetries predicted to form secondary structures. PCR experiments indicated the presence of SATCHO1 sequences in two other Xenarthra species: the tree-toed sloth Bradypus variegatus and the anteater Myrmecophaga tridactyla. Nevertheless, SATCHO1 is present as large tandem arrays only in Choloepus species, thus likely representing a satDNA exclusively in this genus. Our results reveal interesting features of the satDNA landscape in Choloepus species with the potential to aid future phylogenetic studies in Xenarthra and mammalian genomes in general.

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Identification and characterization of normal length nonfluorescent Y chromosomes: cytogenetic analysis, Southern hybridization and non-isotopic in situ hybridization

Human Genetics ◽

10.1007/bf00193576 ◽

1990 ◽

Vol 85 (6) ◽

pp. 569-575 ◽

Cited By ~ 19

Author(s):

Frank Speleman ◽

Bart Van der Auwera ◽

Kathelijne Mangelschots ◽

Miet Vercruyssen ◽

Ton Raap ◽

...

Keyword(s):

In Situ Hybridization ◽

Cytogenetic Analysis ◽

Southern Hybridization ◽

Normal Length ◽

Y Chromosomes ◽

Identification And Characterization

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Identification and Characterization of Four Autophagy-Related Genes That Are Expressed in Response to Hypoxia in the Brain of the Oriental River Prawn (Macrobrachium nipponense)

International Journal of Molecular Sciences ◽

10.3390/ijms20081856 ◽

2019 ◽

Vol 20 (8) ◽

pp. 1856 ◽

Cited By ~ 2

Author(s):

Shengming Sun ◽

Ying Wu ◽

Hongtuo Fu ◽

Xianping Ge ◽

Hongzheng You ◽

...

Keyword(s):

Developmental Stages ◽

Open Reading Frames ◽

Dependent Manner ◽

Macrobrachium Nipponense ◽

Oriental River Prawn ◽

Adverse Environmental Conditions ◽

The Brain ◽

Identification And Characterization

Autophagy is a cytoprotective mechanism triggered in response to adverse environmental conditions. Herein, we investigated the autophagy process in the oriental river prawn (Macrobrachium nipponense) following hypoxia. Full-length cDNAs encoding autophagy-related genes (ATGs) ATG3, ATG4B, ATG5, and ATG9A were cloned, and transcription following hypoxia was explored in different tissues and developmental stages. The ATG3, ATG4B, ATG5, and ATG9A cDNAs include open reading frames encoding proteins of 319, 264, 268, and 828 amino acids, respectively. The four M. nipponense proteins clustered separately from vertebrate homologs in phylogenetic analysis. All four mRNAs were expressed in various tissues, with highest levels in brain and hepatopancreas. Hypoxia up-regulated all four mRNAs in a time-dependent manner. Thus, these genes may contribute to autophagy-based responses against hypoxia in M. nipponense. Biochemical analysis revealed that hypoxia stimulated anaerobic metabolism in the brain tissue. Furthermore, in situ hybridization experiments revealed that ATG4B was mainly expressed in the secretory and astrocyte cells of the brain. Silencing of ATG4B down-regulated ATG8 and decreased cell viability in juvenile prawn brains following hypoxia. Thus, autophagy is an adaptive response protecting against hypoxia in M. nipponense and possibly other crustaceans. Recombinant MnATG4B could interact with recombinant MnATG8, but the GST protein could not bind to MnATG8. These findings provide us with a better understanding of the fundamental mechanisms of autophagy in prawns.

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The identification and characterization of a testis-specific cDNA during spermatogenesis

Cellular & Molecular Biology Letters ◽

10.2478/s11658-006-0008-4 ◽

2006 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Ying Chen ◽

Jiarui Hu ◽

Ping Song ◽

Wuming Gong

Keyword(s):

Experimental Validation ◽

Rna Binding ◽

Pcr Analysis ◽

Splicing Factors ◽

Rt Pcr ◽

Rich Domain ◽

Pachytene Spermatocytes ◽

Identification And Characterization

AbstractUsing bioinformatics and experimental validation, we obtained a cDNA (named srsf) which was exclusively expressed in the mouse testes. RT-PCR analysis showed that srsf mRNA was not expressed in the gonad during the sex determination period or during embryogenesis. In developing mouse tests, srsf expression was first detected on post-natal day 10, reached its highest level on day 23, and then reduced to and remained at a moderate level throughout adulthood. In situ hybridization analysis demonstrated that srsf mRNA was expressed in pachytene spermatocytes and round spermatids in the testes. The predicted protein contains one RNA-binding domain (RBD) and a serine-arginine rich domain (RS), which are characterized by some splicing factors of SR family members. These findings indicate that srsf may play a role during spermatogenesis.

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In situ identification and characterization of the microbial community structure of full-scale enhanced biological phosphorous removal plants in Japan

Water Research ◽

10.1016/j.watres.2005.05.015 ◽

2005 ◽

Vol 39 (13) ◽

pp. 2901-2914 ◽

Cited By ~ 94

Author(s):

Man-Tak Wong ◽

Takashi Mino ◽

Robert J. Seviour ◽

Motoharu Onuki ◽

Wen-Tso Liu

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Full Scale ◽

Phosphorous Removal ◽

Identification And Characterization

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Diverse origins of high copy tandem repeats in grass genomes

10.7287/peerj.preprints.2314 ◽

2016 ◽

Author(s):

Paul Bilinski ◽

Yonghua Han ◽

Matthew B Hufford ◽

Anne Lorant ◽

Pingdong Zhang ◽

...

Keyword(s):

Tandem Repeat ◽

Tandem Repeats ◽

High Throughput Sequencing ◽

De Novo ◽

Repetitive Sequences ◽

Read Mapping ◽

Hybridization Data ◽

Centromeric Repeat ◽

Tandem Repeat Sequences

In studying genomic architecture, highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Here, we utilize sequence assembly and read mapping to identify and quantify the genomic abundance of different tandem repeat sequences. Previous research has posited that the highest abundance tandem repeat in eukaryotic genomes is often the centromeric repeat, and we pair our bioinformatic pipeline with fluorescent in-situ hybridization data to test this hypothesis. We find that de novo assembly and bioinformatic filters can successfully identify repeats with homology to known tandem repeats. Fluorescent in-situ hybridization, however, shows that de novo assembly fails to identify novel centromeric repeats, instead identifying other potentially important repetitive sequences. Together, our results test the applicability and limitations of using de novo repeat assembly of tandem repeats to identify novel centromeric repeats. Building on our findings of genomic composition, we also set forth a method for exploring the repetitive regions of non-model genomes whose diversity limits the applicability of established genetic resources.

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Identification and characterization of epitopes shared between the mycobacterial 65-kilodalton heat shock protein and the actively secreted antigen 85 complex: their in situ expression on the cell wall surface of Mycobacterium leprae.

Infection and Immunity ◽

10.1128/iai.60.11.4517-4527.1992 ◽

1992 ◽

Vol 60 (11) ◽

pp. 4517-4527 ◽

Cited By ~ 7

Author(s):

A Rambukkana ◽

P K Das ◽

J D Burggraaf ◽

W R Faber ◽

P Teeling ◽

...

Keyword(s):

Cell Wall ◽

Heat Shock ◽

Heat Shock Protein ◽

Mycobacterium Leprae ◽

Wall Surface ◽

Antigen 85 ◽

Identification And Characterization

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Identification and Characterization of a Rhodopsin Kinase Gene in the Suckers of Octopus vulgaris: Looking around Using Arms?

Biology ◽

10.3390/biology10090936 ◽

2021 ◽

Vol 10 (9) ◽

pp. 936

Author(s):

Al-Sayed Al-Soudy ◽

Valeria Maselli ◽

Stefania Galdiero ◽

Michael J. Kuba ◽

Gianluca Polese ◽

...

Keyword(s):

3D Structure ◽

Complete Characterization ◽

Octopus Vulgaris ◽

Kinase Gene ◽

Light Sensing ◽

Rhodopsin Kinase ◽

First Time ◽

Identification And Characterization

In their foraging behavior octopuses rely on arm search movements outside the visual field of the eyes. In these movements the environment is explored primarily by the suckers that line the entire length of the octopus arm. In this study, for the first time, we report the complete characterization of a light-sensing molecule, Ov-GRK1, in the suckers, skin and retina of Octopus vulgaris. We sequenced the O. vulgaris GRK1 gene, defining a phylogenetic tree and performing a 3D structure model prediction. Furthermore, we found differences in relative mRNA expression in different sucker types at several arm levels, and localized it through in situ hybridization. Our findings suggest that the suckers in octopus arms are much more multimodal than was previously shown, adding the potential for light sensing to the already known mechanical and chemical sensing abilities.

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Stability of tandem repeats in the Drosophila melanogaster Hsr-omega nuclear RNA.

Genetics ◽

10.1093/genetics/139.4.1611 ◽

1995 ◽

Vol 139 (4) ◽

pp. 1611-1621 ◽

Cited By ~ 1

Author(s):

N C Hogan ◽

F Slot ◽

K L Traverse ◽

J C Garbe ◽

W G Bendena ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Tandem Repeats ◽

Repeat Unit ◽

Nucleotide Substitutions ◽

Satellite Dnas ◽

Tandem Repeat Sequences ◽

Nuclear Rna ◽

Minimum Number ◽

Flanking Regions ◽

New Alleles

Abstract The Drosophila melanogaster Hsr-omega locus produces a nuclear RNA containing > 5 kb of tandem repeat sequences. These repeats are unique to Hsr-omega and show concerted evolution similar to that seen with classical satellite DNAs. In D. melanogaster the monomer is approximately 280 bp. Sequences of 19 1/2 monomers differ by 8 +/- 5% (mean +/- SD), when all pairwise comparisons are considered. Differences are single nucleotide substitutions and 1-3 nucleotide deletions/insertions. Changes appear to be randomly distributed over the repeat unit. Outer repeats do not show the decrease in monomer homogeneity that might be expected if homogeneity is maintained by recombination. However, just outside the last complete repeat at each end, there are a few fragments of sequence similar to the monomer. The sequences in these flanking regions are not those predicted for sequences decaying in the absence of recombination. Instead, the fragmentation of the sequence homology suggests that flanking regions have undergone more severe disruptions, possibly during an insertion or amplification event. Hsr-omega alleles differing in the number of repeats are detected and appear to be stable over a few thousand generations; however, both increases and decreases in repeat numbers have been observed. The new alleles appear to be as stable as their predecessors. No alleles of less than approximately 5 kb nor more than approximately 16 kb of repeats were seen in any stocks examined. The evidence that there is a limit on the minimum number of repeats is consistent with the suggestion that these repeats are important in the function of the unusual Hsr-omega nuclear RNA.

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Multiparametric MRI for Localized Prostate Cancer: Lesion Detection and Staging

BioMed Research International ◽

10.1155/2014/684127 ◽

2014 ◽

Vol 2014 ◽

pp. 1-11 ◽

Cited By ~ 4

Author(s):

Daniel J. A. Margolis

Keyword(s):

Prostate Cancer ◽

Functional Imaging ◽

Systematic Approach ◽

Multiparametric Mri ◽

Lesion Detection ◽

Prostate Capsule ◽

Identification And Characterization ◽

Cancer Lesion

Multiparametric MRI of the prostate combines high-resolution anatomic imaging with functional imaging of alterations in normal tissue caused by neoplastic transformation for the identification and characterization ofin situprostate cancer. Lesion detection relies on a systematic approach to the analysis of both anatomic and functional imaging using established criteria for the delineation of suspicious areas. Staging includes visual and functional analysis of the prostate “capsule” to determine ifin situdisease is, in fact, organ-confined, as well as the evaluation of pelvic structures including lymph nodes and bones for the detection of metastasis. Although intertwined, the protocol can be optimized depending on whether lesiondetectionorstagingis of the highest priority.

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