B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription

B chromosomes (Bs) are highly polymorphic additional chromosomes in the genomes of many species. Due to the dispensability of Bs and the lack of noticeable phenotypic effects in their carriers, they were considered genetically inert for a long time. Recent studies on Bs in Apodemus flavicollis revealed their genetic composition, potential origin, and spatial organization in the interphase nucleus. Surprisingly, the genetic content of Bs in this species is preserved in all studied samples, even in geographically distinct populations, indicating its biological importance. Using RT-PCR we studied the transcription activity of three genes (Rraga, Haus6, and Cenpe) previously identified on Bs in A. flavicollis. We analysed mRNA isolated from spleen tissues of 34 animals harboring different numbers of Bs (0–3). The products of transcriptional activity of the analysed sequences differ in individuals with and without Bs. We recorded B-genes and/or genes from the standard genome in the presence of Bs, showing sex-dependent higher levels of transcriptional activity. Furthermore, the transcriptional activity of Cenpe varied with the age of the animals differently in the group with and without Bs. With aging, the amount of product was only found to significantly decrease in B carriers. The potential biological significance of all these differences is discussed in the paper.

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New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis

Cells ◽

10.3390/cells10071819 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1819

Author(s):

Tatyana Karamysheva ◽

Svetlana Romanenko ◽

Alexey Makunin ◽

Marija Rajičić ◽

Alexey Bogdanov ◽

...

Keyword(s):

In Situ Hybridization ◽

Sex Chromosomes ◽

Interphase Nucleus ◽

Spatial Organization ◽

Three Dimensional ◽

Dna Probes ◽

B Chromosomes ◽

Apodemus Flavicollis ◽

Yellow Necked Mouse

The gene composition, function and evolution of B-chromosomes (Bs) have been actively discussed in recent years. However, the additional genomic elements are still enigmatic. One of Bs mysteries is their spatial organization in the interphase nucleus. It is known that heterochromatic compartments are not randomly localized in a nucleus. The purpose of this work was to study the organization and three-dimensional spatial arrangement of Bs in the interphase nucleus. Using microdissection of Bs and autosome centromeric heterochromatic regions of the yellow-necked mouse (Apodemus flavicollis) we obtained DNA probes for further two-dimensional (2D)- and three-dimensional (3D)- fluorescence in situ hybridization (FISH) studies. Simultaneous in situ hybridization of obtained here B-specific DNA probes and autosomal C-positive pericentromeric region-specific probes further corroborated the previously stated hypothesis about the pseudoautosomal origin of the additional chromosomes of this species. Analysis of the spatial organization of the Bs demonstrated the peripheral location of B-specific chromatin within the interphase nucleus and feasible contact with the nuclear envelope (similarly to pericentromeric regions of autosomes and sex chromosomes). It is assumed that such interaction is essential for the regulation of nuclear architecture. It also points out that Bs may follow the same mechanism as sex chromosomes to avoid a meiotic checkpoint.

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Chromatin loop anchors contain core structural components of the gene expression machinery in maize

BMC Genomics ◽

10.1186/s12864-020-07324-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Stéphane Deschamps ◽

John A. Crow ◽

Nadia Chaidir ◽

Brooke Peterson-Burch ◽

Sunil Kumar ◽

...

Keyword(s):

Gene Expression ◽

High Resolution ◽

Transcriptional Activity ◽

Spatial Organization ◽

Regulatory Elements ◽

Open Chromatin ◽

Maize Genome ◽

Chromatin Loop ◽

Structural Components ◽

Chromatin Loops

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.

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Overview of Safety Measures at Selected Airports during the COVID-19 Pandemic

Sustainability ◽

10.3390/su13158499 ◽

2021 ◽

Vol 13 (15) ◽

pp. 8499

Author(s):

Monika Blišťanová ◽

Michaela Tirpáková ◽

Ľubomíra Brůnová

Keyword(s):

Time Frame ◽

Organizational Changes ◽

Rt Pcr ◽

Final Phase ◽

Chain Reaction ◽

Scoring Method ◽

Safety Measures ◽

Long Time ◽

Polymerase Chain ◽

Cleaning And Disinfection

The year 2020 was very challenging for the whole world, given the outbreak of the ongoing coronavirus-related pandemic, and was marked in particular by overcoming new hitherto unknown obstacles. For air transport, in particular, airlines stopped flying altogether and were forced to ground hundreds of planes worldwide involuntarily. Airports had to close their terminals for a long time, wholly suspend operations, and its resumption required significant organizational changes. This article summarizes the measures related to the COVID-19 pandemic adopted by airports to minimize the risk of spreading the disease. The article focuses on countermeasures and their implementation at selected airports in a specific time frame and airports’ behavior during a pandemic which varies depending on country and time of the year. The results demonstrated that steps being taken at airports include the use of face coverings or masks, social distance, enhanced cleaning and disinfection, or temperature checks and/or symptoms (fever, loss of smell, chills, cough, shortness of breath), RT-PCR (reverse transcription-polymerase chain reaction) screening and data collection with health declaration. These measures have now become an essential standard for the operation of airports and can, therefore, be used to assess the level of airport safety achieved. In the final phase, the article evaluates the level of achieved airport safety based on the proposed scoring method.

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Spatial organization of fibroblast and spermatocyte nuclei with different B-chromosome content in Korean field mouse, Apodemus peninsulae (Rodentia, Muridae)

Genome ◽

10.1139/gen-2017-0029 ◽

2017 ◽

Vol 60 (10) ◽

pp. 815-824 ◽

Cited By ~ 4

Author(s):

Tatyana V. Karamysheva ◽

Anna A. Torgasheva ◽

Yaroslav R. Yefremov ◽

Anton G. Bogomolov ◽

Thomas Liehr ◽

...

Keyword(s):

Laser Scanning ◽

Spatial Organization ◽

Constitutive Heterochromatin ◽

B Chromosome ◽

B Chromosomes ◽

Laser Scanning Microscopy ◽

Field Mouse ◽

Apodemus Peninsulae ◽

Basic Set ◽

Korean Field Mouse

Korean field mouse (Apodemus peninsulae) shows a wide variation in the number of B chromosomes composed of constitutive heterochromatin. For this reason, it provides a good model to study the influence of the number of centromeres and amount of heterochromatin on spatial organization of interphase nuclei. We analyzed the three-dimensional organization of fibroblast and spermatocyte nuclei of the field mice carrying a different number of B chromosomes using laser scanning microscopy and 3D fluorescence in situ hybridization. We detected a co-localization of the B chromosomes with constitutive heterochromatin of the chromosomes of the basic set. We showed a non-random distribution of B chromosomes in the spermatocyte nuclei. Unpaired B chromosomes showed a tendency to occur in the compartment formed by the unpaired part of the XY bivalent.

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Cloning, Sequencing, and the Expression of the Elusive Sarcomeric TPM4α Isoform in Humans

Molecular Biology International ◽

10.1155/2016/3105478 ◽

2016 ◽

Vol 2016 ◽

pp. 1-11 ◽

Cited By ~ 3

Author(s):

Dipak K. Dube ◽

Syamalima Dube ◽

Lynn Abbott ◽

Ruham Alshiekh-Nasany ◽

Charles Mitschow ◽

...

Keyword(s):

Mass Spectrometry ◽

Western Blot ◽

Human Heart ◽

Amino Acid Sequences ◽

Rt Pcr ◽

Adult Heart ◽

Qrt Pcr ◽

Long Time ◽

Alternate Promoters ◽

Computational Analyses

In mammals, tropomyosin is encoded by four known TPM genes (TPM1, TPM2, TPM3, and TPM4) each of which can generate a number of TPM isoforms via alternative splicing and/or using alternate promoters. In humans, the sarcomeric isoform(s) of each of the TPM genes, except for the TPM4, have been known for a long time. Recently, on the basis of computational analyses of the human genome sequence, the predicted sequence of TPM4α has been posted in GenBank. We designed primer-pairs for RT-PCR and showed the expression of the transcripts of TPM4α and a novel isoform TPM4δ in human heart and skeletal muscle. qRT-PCR shows that the relative expression of TPM4α and TPM4δ is higher in human cardiac muscle. Western blot analyses using CH1 monoclonal antibodies show the absence of the expression of TPM4δ protein (~28 kDa) in human heart muscle. 2D western blot analyses with the same antibody show the expression of at least nine distinct tropomyosin molecules with a mass ~32 kD and above in adult heart. By Mass spectrometry, we determined the amino acid sequences of the extracted proteins from these spots. Spot “G” reveals the putative expression of TPM4α along with TPM1α protein in human adult heart.

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Do B chromosomes affect morphometric characters in yellow-necked mice Apodemus flavicollis (Rodentia, Mammalia)?

ACTA THERIOLOGICA ◽

10.4098/at.arch.00-14 ◽

2000 ◽

Vol 45 ◽

pp. 129-135 ◽

Cited By ~ 9

Author(s):

Jelena Blagojević ◽

Mladen Vujošević

Keyword(s):

B Chromosomes ◽

Apodemus Flavicollis ◽

Morphometric Characters

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miR-509-5p Inhibits the Proliferation and Invasion of Osteosarcoma by Targeting TRIB2

BioMed Research International ◽

10.1155/2019/2523032 ◽

2019 ◽

Vol 2019 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Jiekun Guo ◽

Qiang Wu ◽

Xiaoming Peng ◽

Bin Yu

Keyword(s):

Tumor Suppressor ◽

Cell Lines ◽

Transcriptional Activity ◽

Preventive Intervention ◽

Suppressor Gene ◽

Rt Pcr ◽

Malignant Bone Tumors ◽

Direct Target ◽

Proliferation And Invasion

Osteosarcoma (OS) is one of the most common malignant bone tumors in adolescents with a poor prognosis. Though miR-509-5p has been reported as a tumor suppressor in several human cancers, the role of miR-509-5p in OS remains unclear. In this study, our result of real-time PCR (RT-PCR) showed that the expression of miR-509-5p was significantly decreased in OS tissues and cell lines. Overexpression of miR-509-5p significantly suppressed cell proliferation and invasion in OS cell lines. Moreover, we identified tribbles homolog 2 (TRIB2) as the direct target of miR-509-5p. Knockdown of TRIB2 could inhibit the malignant capacity of OS cells. At last, we reported that TRIB2 could inhibit the bioactivity of the tumor suppressor gene p21 via blocking its transcriptional activity. Collectively, our study revealed that miR-509-5p functions as a tumor suppressor by targeting TRIB2 in OS and thus could affect the activity of p21, suggesting that miR-509-5p is a novel preventive intervention for OS patients.

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Differential distribution of ERα and ERβ mRNA in intrauterine tissues of the pregnant rhesus monkey

AJP Cell Physiology ◽

10.1152/ajpcell.2000.278.1.c190 ◽

2000 ◽

Vol 278 (1) ◽

pp. C190-C198 ◽

Cited By ~ 17

Author(s):

Wen Xuan Wu ◽

Xiao Hong Ma ◽

Gordon C. S. Smith ◽

Peter W. Nathanielsz

Keyword(s):

Endothelial Cells ◽

Estrogen Receptor ◽

Smooth Muscle ◽

Sequence Analysis ◽

Cesarean Section ◽

Rhesus Monkey ◽

Biological Significance ◽

Rt Pcr ◽

Differential Distribution ◽

Term Labor

Two estrogen receptor (ER) isoforms, ERα and ERβ, have been described. However, no information is available in any species regarding the comparison of ERα and ERβ levels in pregnant intrauterine tissues. We investigated 1) distribution of ERα and ERβ mRNA in myometrium, amnion, choriodecidua, and placenta; 2) their abundance in intrauterine tissues at term not in labor (NIL) and in spontaneous term labor (STL); and 3) immunolocalization of ERα and ERβ in pregnant rhesus monkey myometrium. Myometrium, amnion, choriodecidua, and placenta were obtained at cesarean section from monkeys in STL at 156–166 days gestational age (GA) ( n = 4) and from control monkeys NIL at 140–152 days GA ( n = 4). RT-PCR was conducted to determine ERα and ERβ and glyceraldehyde-3-phosphate dehydrogenase mRNA abundance in four intrauterine tissues of the pregnant rhesus monkey. The cloned ERβ PCR fragment was subjected to sequence analysis. ERα and ERβ were localized in the myometrium by immunohistochemistry. We demonstrated that 1) rhesus monkey ERβ shares >97% identity with human ERβ in the region sequenced; 2) both ERs were expressed in myometrium, amnion, and choriodecidua but not in placenta in the current study; 3) ERα and ERβ were differentially distributed in myometrium and amnion; 4) ERα and ERβ were immunolocalized in myometrial smooth cells and smooth muscle and endothelial cells of the myometrial blood vessels. The biological significance of these quantitative differences in ER subtypes merits further study.

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The Social and Genetic Structure of a Natural Colony of House Mice, Mus musculus, at Healesville WildlifeSanctuary

Australian Journal of Zoology ◽

10.1071/zo9830155 ◽

1983 ◽

Vol 31 (2) ◽

pp. 155 ◽

Cited By ~ 38

Author(s):

GR Singleton

Keyword(s):

Genetic Structure ◽

Life Span ◽

Social Organization ◽

Turnover Rate ◽

Spatial Organization ◽

House Mice ◽

Genetic Composition ◽

Short Life ◽

Short Life Span ◽

The Social

A 2-year program monitored the spatial organization, genetic structure and turnover rate of an unconfined commensal colony of mice. Four demes (social breeding units) were identified; each usually consisted of one or two males and two or three females. Demes were detected simultaneously in adjoining cages of an aviary (one deme per cage). Movement between demes was rare and the life span of a deme ranged from 2 to 7 months. The adult members of each deme had genotypes compatible to the majority of the young captured in the respective cage of the aviary at the time of residence of the deme. Taken in isolation, these results suggest that social behaviour would have a major impact on the genetic structure of the aviary population. When viewed over the main breeding season, the short life span of a deme and the genetic differences between demes indicate that social organization probably had only a temporary effect on the genetic composition of the aviary population.

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