keyword
https://read.qxmd.com/read/37841687/glutamatergic-synaptic-deficits-in-the-prefrontal-cortex-of-the-ts65dn-mouse-model-for-down-syndrome
#21
JOURNAL ARTICLE
Aurore Thomazeau, Olivier Lassalle, Olivier J Manzoni
Down syndrome (DS), the most prevalent cause of intellectual disability, stems from a chromosomal anomaly resulting in an entire or partial extra copy of chromosome 21. This leads to intellectual disability and a range of associated symptoms. While there has been considerable research focused on the Ts65Dn mouse model of DS, particularly in the context of the hippocampus, the synaptic underpinnings of prefrontal cortex (PFC) dysfunction in DS, including deficits in working memory, remain largely uncharted territory...
2023: Frontiers in Neuroscience
https://read.qxmd.com/read/37761920/origins-of-east-caucasus-gene-pool-contributions-of-autochthonous-bronze-age-populations-and-migrations-from-west-asia-estimated-from-y-chromosome-data
#22
JOURNAL ARTICLE
Anastasia Agdzhoyan, Nasib Iskandarov, Georgy Ponomarev, Vladimir Pylev, Sergey Koshel, Vugar Salaev, Elvira Pocheshkhova, Zhaneta Kagazezheva, Elena Balanovska
The gene pool of the East Caucasus, encompassing modern-day Azerbaijan and Dagestan populations, was studied alongside adjacent populations using 83 Y-chromosome SNP markers. The analysis of genetic distances among 18 populations ( N = 2216) representing Nakh-Dagestani, Altaic, and Indo-European language families revealed the presence of three components (Steppe, Iranian, and Dagestani) that emerged in different historical periods. The Steppe component occurs only in Karanogais, indicating a recent medieval migration of Turkic-speaking nomads from the Eurasian steppe...
September 9, 2023: Genes
https://read.qxmd.com/read/37745315/unique-territorial-and-sub-chromosomal-organization-revealed-in-the-holocentric-moth-bombyx-mori
#23
J Gil, L F Rosin, E Navarrete, N Chowdhury, S Abraham, G Cornilleau, E P Lei, J Mozziconacci, L A Mirny, H Muller, I A Drinnenberg
The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and different types of domains, including topologically associated domains (TADs). Yet, most of these concepts derive from analyses of organisms with monocentric chromosomes. Here we describe the 3D genome architecture of an organism with holocentric chromosomes, the silkworm Bombyx mori . At the genome-wide scale, B. mori chromosomes form highly separated territories and lack substantial trans contacts...
September 16, 2023: bioRxiv
https://read.qxmd.com/read/37735233/homeology-of-sex-chromosomes-in-amazonian-harttia-armored-catfishes-supports-the-x-fission-hypothesis-for-the-x-1-x-2-y-sex-chromosome-system-origin
#24
JOURNAL ARTICLE
Francisco de Menezes Cavalcante Sassi, Alexandr Sember, Geize Aparecida Deon, Thomas Liehr, Niklas Padutsch, Osvaldo Takeshi Oyakawa, Marcelo Ricardo Vicari, Luiz Antonio Carlos Bertollo, Orlando Moreira-Filho, Marcelo de Bello Cioffi
The Neotropical monophyletic catfish genus Harttia represents an excellent model to study karyotype and sex chromosome evolution in teleosts. Its species split into three phylogenetic clades distributed along the Brazilian territory and they differ widely in karyotype traits, including the presence of standard or multiple sex chromosome systems in some members. Here, we investigate the chromosomal rearrangements and associated synteny blocks involved in the origin of a multiple X1 X2 Y sex chromosome system present in three out of six sampled Amazonian-clade species...
September 21, 2023: Scientific Reports
https://read.qxmd.com/read/37723501/tlr8-escapes-x-chromosome-inactivation-in-human-monocytes-and-cd4-t-cells
#25
JOURNAL ARTICLE
Ali Youness, Claire Cenac, Berenice Faz-López, Solange Grunenwald, Franck J Barrat, Julie Chaumeil, José Enrique Mejía, Jean-Charles Guéry
BACKGROUND: Human endosomal Toll-like receptors TLR7 and TLR8 recognize self and non-self RNA ligands, and are important mediators of innate immunity and autoimmune pathogenesis. TLR7 and TLR8 are, respectively, encoded by adjacent X-linked genes. We previously established that TLR7 evades X chromosome inactivation (XCI) in female immune cells. Whether TLR8 also evades XCI, however, has not yet been explored. METHOD: In the current study, we used RNA fluorescence in situ hybridization (RNA FISH) to directly visualize, on a single-cell basis, primary transcripts of TLR7 and TLR8 relative to X chromosome territories in CD14+ monocytes and CD4+ T lymphocytes from women, Klinefelter syndrome (KS) men, and euploid men...
September 18, 2023: Biology of Sex Differences
https://read.qxmd.com/read/37702976/patterns-of-genetic-differentiation-imply-distinct-phylogeographic-history-of-the-mosquito-species-anopheles-messeae-and-anopheles-daciae-in-eurasia
#26
JOURNAL ARTICLE
Ilya I Brusentsov, Mikhail I Gordeev, Andrey A Yurchenko, Dimitriy A Karagodin, Anton V Moskaev, James M Hodge, Vladimir A Burlak, Gleb N Artemov, Anuarbek K Sibataev, Norbert Becker, Igor V Sharakhov, Elina M Baricheva, Maria V Sharakhova
Detailed knowledge of phylogeography is important for control of mosquito species involved in the transmission of human infectious diseases. Anopheles messeae is a geographically widespread and genetically diverse dominant vector of malaria in Eurasia. A closely related species, An. daciae, was originally distinguished from An. messeae based on five nucleotide substitutions in its ribosomal DNA (rDNA). However, the patterns of phylogeographic history of these species in Eurasia remain poorly understood...
September 13, 2023: Molecular Ecology
https://read.qxmd.com/read/37603403/the-dynamic-role-of-cohesin-in-maintaining-human-genome-architecture
#27
JOURNAL ARTICLE
Abhishek Agarwal, Sevastianos Korsak, Ashutosh Choudhury, Dariusz Plewczynski
Recent advances in genomic and imaging techniques have revealed the complex manner of organizing billions of base pairs of DNA necessary for maintaining their functionality and ensuring the proper expression of genetic information. The SMC proteins and cohesin complex primarily contribute to forming higher-order chromatin structures, such as chromosomal territories, compartments, topologically associating domains (TADs) and chromatin loops anchored by CCCTC-binding factor (CTCF) protein or other genome organizers...
August 21, 2023: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://read.qxmd.com/read/37589106/evaluation-of-the-complex-use-of-plant-test-systems-to-determine-the-nature-and-intensity-of-the-mutagenic-background-of-the-environment
#28
JOURNAL ARTICLE
Liubov S Shvets, Nataliia I Frych, Nataliia V Dovganych, Larysa Y Kovalchuk, Oksana H Popadynets, Taras L Kotyk, Nadiya S Tokaruk
OBJECTIVE: Aim: A comprehensive evaluation of the effectiveness of the use of plant test-systems as biological objects for the identification of the specifitown of the effect of mutagens on the hereditary apparatus. PATIENTS AND METHODS: Materials and methods: With the use of test-systems (determination of the gonadotoxitown of plant pollen grains, the Allium cepa-test and the use of celandine greater Chelidonium majus as an accumulative phytoindicator) was analyzed the ecological situation of the areas in Ivano-Frankivsk region...
2023: Polski Merkuriusz Lekarski: Organ Polskiego Towarzystwa Lekarskiego
https://read.qxmd.com/read/37566037/the-material-properties-of-the-cell-nucleus-a-matter-of-scale
#29
REVIEW
Maud Hertzog, Fabian Erdel
Chromatin regulatory processes physically take place in the environment of the cell nucleus, which is filled with the chromosomes and a plethora of smaller biomolecules. The nucleus contains macromolecular assemblies of different sizes, from nanometer-sized protein complexes to micrometer-sized biomolecular condensates, chromosome territories, and nuclear bodies. This multiscale organization impacts the transport processes within the nuclear interior, the global mechanical properties of the nucleus, and the way the nucleus senses and reacts to mechanical stimuli...
July 28, 2023: Cells
https://read.qxmd.com/read/37563441/transcription-and-replication-meet-the-silent-x-chromosome-territory
#30
JOURNAL ARTICLE
Frederic Zimmer, M Felicia Basilicata, Claudia Isabelle Keller Valsecchi
No abstract text is available yet for this article.
August 2023: Nature Structural & Molecular Biology
https://read.qxmd.com/read/37537310/long-range-gene-regulation-in-hormone-dependent-cancer
#31
REVIEW
Theophilus T Tettey, Lorenzo Rinaldi, Gordon L Hager
The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts...
October 2023: Nature Reviews. Cancer
https://read.qxmd.com/read/37532989/sequential-viral-introductions-and-spread-of-ba-1-across-pakistan-provinces-during-the-omicron-wave
#32
JOURNAL ARTICLE
Ali Raza Bukhari, Javaria Ashraf, Akbar Kanji, Yusra Abdul Rahman, Nídia S Trovão, Peter M Thielen, Maliha Yameen, Samiah Kanwar, Waqasuddin Khan, Furqan Kabir, Muhammad Imran Nisar, Brian Merritt, Rumina Hasan, David Spiro, Zeba Rasmussen, Uzma Bashir Aamir, Zahra Hasan
BACKGROUND: COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan. METHODS: We studied 276,525 COVID-19 cases and 1,031 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees. RESULTS: The highest case numbers and deaths were recorded in Sindh and Punjab, the most populous provinces in Pakistan...
August 3, 2023: BMC Genomics
https://read.qxmd.com/read/37504615/the-effect-of-chromosomes-on-courtship-behavior-in-sibling-species-of-the-drosophila-virilis-group
#33
JOURNAL ARTICLE
Elena G Belkina, Dmitry G Seleznev, Svetlana Yu Sorokina, Alex M Kulikov, Oleg E Lazebny
Prezygotic isolation mechanisms, particularly courtship behavior, play a significant role in the formation of reproductive barriers. The action of these mechanisms leads to the coexistence of numerous closely related insect species with specific adaptations in a shared or adjacent territory. The genetic basis of these mechanisms has been studied using closely related Drosophila species, such as the D. virilis group. However, the investigation of individual courtship behavior elements has been limited until recently, and the effect of genotype on the species-specific features of courtship as a whole has not been thoroughly examined...
July 5, 2023: Insects
https://read.qxmd.com/read/37467757/fundamental-insights-into-the-correlation-between-chromosome-configuration-and-transcription
#34
REVIEW
Swayamshree Senapati, Inayat Ullah Irshad, Ajeet K Sharma, Hemant Kumar
Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression...
August 4, 2023: Physical Biology
https://read.qxmd.com/read/37457299/chromosome-conformation-capture-technologies-as-tools-to-detect-structural-variations-and-their-repercussion-in-chromatin-3d-configuration
#35
REVIEW
Aura Stephenson-Gussinye, Mayra Furlan-Magaril
3D genome organization regulates gene expression in different physiological and pathological contexts. Characterization of chromatin structure at different scales has provided information about how the genome organizes in the nuclear space, from chromosome territories, compartments of euchromatin and heterochromatin, topologically associated domains to punctual chromatin loops between genomic regulatory elements and gene promoters. In recent years, chromosome conformation capture technologies have also been used to characterize structural variations (SVs) de novo in pathological conditions...
2023: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/37426677/three-dimensional-genome-structure-and-function
#36
REVIEW
Hao Liu, Hsiangyu Tsai, Maoquan Yang, Guozhi Li, Qian Bian, Gang Ding, Dandan Wu, Jiewen Dai
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated...
August 2023: MedComm
https://read.qxmd.com/read/37386239/recent-advances-in-chromosome-capture-techniques-unraveling-3d-genome-architecture-in-germ-cells-health-and-disease
#37
REVIEW
Nuruliarizki Shinta Pandupuspitasari, Faheem Ahmed Khan, Chunjie Huang, Azhar Ali, Muhammad Rizwan Yousaf, Farwa Shakeel, Ezi Masdia Putri, Windu Negara, Anis Muktiani, Bambang Waluyo Hadi Eko Prasetiyono, Limbang Kustiawan, Dimar Sari Wahyuni
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis...
June 29, 2023: Functional & Integrative Genomics
https://read.qxmd.com/read/37384527/early-chromosome-condensation-by-xist-builds-a-repeat-rna-density-that-facilitates-gene-silencing
#38
JOURNAL ARTICLE
Melvys Valledor, Meg Byron, Brett Dumas, Dawn M Carone, Lisa L Hall, Jeanne B Lawrence
XIST RNA triggers chromosome-wide gene silencing and condenses an active chromosome into a Barr body. Here, we use inducible human XIST to examine early steps in the process, showing that XIST modifies cytoarchitecture before widespread gene silencing. In just 2-4 h, barely visible transcripts populate the large "sparse zone" surrounding the smaller "dense zone"; importantly, density zones exhibit different chromatin impacts. Sparse transcripts immediately trigger immunofluorescence for H2AK119ub and CIZ1, a matrix protein...
June 28, 2023: Cell Reports
https://read.qxmd.com/read/37368581/individual-risk-assessment-for-population-living-on-the-territories-long-term-polluted-by-organochlorine-pesticides
#39
JOURNAL ARTICLE
Aleksandr Garshin, Nazym Altynova, Erika Djangalina, Ozada Khamdiyeva, Gulminyam Baratzhanova, Anar Tolebaeva, Zhasulan Zhaniyazov, Elmira Khussainova, Céline Cakir-Kiefer, Stefan Jurjanz, Matthieu Delannoy, Leyla Djansugurova
The long-term storage of unutilized pesticides raised new problems of long-term environmental contamination. The study presents the results of surveying 151 individuals in 7 villages living close to pesticide-contaminated localities. All individuals have been surveyed concerning their consumption habits and lifestyle characteristics. An assessment of the general exposure risks of the local population was carried out using the analysis of pollutants in food products and the average levels of their consumption in the region...
May 25, 2023: Toxics
https://read.qxmd.com/read/37335489/visualizing-chromosome-territories-and-nuclear-architecture-of-large-plant-genomes-using-alien-introgressions
#40
JOURNAL ARTICLE
Kateřina Perničková, David Kopecký
Visualization of chromosome territories is a challenging task in plant genomes due to the lack of chromosome-specific probes, especially in species with large genomes. On the other hand, combination of flow sorting, genomic in situ hybridization (GISH), confocal microscopy, and employment of software for 3D modeling enables to visualize and characterize chromosome territories (CT) in interspecific hybrids. Here, we describe the protocol for the analysis of CTs in wheat-rye and wheat-barley hybrids, including amphiploids and introgression forms, where a pair of chromosomes or chromosome arms from one species is introgressed into the genome of another species...
2023: Methods in Molecular Biology
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