keyword
https://read.qxmd.com/read/38416776/whole-cell-reconstructions-of-leishmania-mexicana-through-the-cell-cycle
#1
JOURNAL ARTICLE
Molly Hair, Ryuji Yanase, Flávia Moreira-Leite, Richard John Wheeler, Jovana Sádlová, Petr Volf, Sue Vaughan, Jack Daniel Sunter
The unicellular parasite Leishmania has a precisely defined cell architecture that is inherited by each subsequent generation, requiring a highly coordinated pattern of duplication and segregation of organelles and cytoskeletal structures. A framework of nuclear division and morphological changes is known from light microscopy, yet this has limited resolution and the intrinsic organisation of organelles within the cell body and their manner of duplication and inheritance is unknown. Using volume electron microscopy approaches, we have produced three-dimensional reconstructions of different promastigote cell cycle stages to give a spatial and quantitative overview of organelle positioning, division and inheritance...
February 28, 2024: PLoS Pathogens
https://read.qxmd.com/read/38266035/a-genome-wide-comprehensive-analysis-of-nucleosome-positioning-in-yeast
#2
JOURNAL ARTICLE
Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar
In eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as transcription and DNA repair. Despite strong efforts to study nucleosome positioning using Next Generation Sequencing (NGS) data, the mechanism of their collective arrangement along the gene body remains poorly understood. Here, we classify nucleosome distributions of protein-coding genes in Saccharomyces cerevisiae according to their profile similarity and analyse their differences using functional Principal Component Analysis...
January 24, 2024: PLoS Computational Biology
https://read.qxmd.com/read/38132714/cytology-techniques-can-provide-insight-into-human-placental-structure-including-syncytiotrophoblast-nuclear-spatial-organisation
#3
JOURNAL ARTICLE
Cassie Fives, André Toulouse, Louise Kenny, Therese Brosnan, Julie McCarthy, Brendan Fitzgerald
The aim of this study was to provide the first systematic description of human placental cytology appearances and to investigate syncytiotrophoblast nuclear organisation patterns using cytology techniques. Term placentas from normal pregnancies were sampled using fine-needle aspiration (FNA) and direct scrapes. Standard histological examination was also performed to exclude pathological changes in the placentas being studied. Both Papanicolaou-stained cytospin preparations and air-dried Giemsa slides from FNA provided high-quality material for cytological assessment with good cellularity...
December 15, 2023: Journal of Developmental Biology
https://read.qxmd.com/read/38131168/molecular-analysis-of-xpo1-inhibitor-and-gemcitabine-nab-paclitaxel-combination-in-kpc-pancreatic-cancer-mouse-model
#4
JOURNAL ARTICLE
Md Hafiz Uddin, Mohammad Najeeb Al-Hallak, Husain Yar Khan, Amro Aboukameel, Yiwei Li, Sahar F Bannoura, Gregory Dyson, Seongho Kim, Yosef Mzannar, Ibrahim Azar, Tanya Odisho, Amr Mohamed, Yosef Landesman, Steve Kim, Rafic Beydoun, Ramzi M Mohammad, Philip A Philip, Anthony F Shields, Asfar S Azmi
BACKGROUND: The majority of pancreatic ductal adenocarcinoma (PDAC) patients experience disease progression while on treatment with gemcitabine and nanoparticle albumin-bound (nab)-paclitaxel (GemPac) necessitating the need for a more effective treatment strategy for this refractory disease. Previously, we have demonstrated that nuclear exporter protein exportin 1 (XPO1) is a valid therapeutic target in PDAC, and the selective inhibitor of nuclear export selinexor (Sel) synergistically enhances the efficacy of GemPac in pancreatic cancer cells, spheroids and patient-derived tumours, and had promising activity in a phase I study...
December 2023: Clinical and Translational Medicine
https://read.qxmd.com/read/37377734/the-courtship-choreography-of-homologous-chromosomes-timing-and-mechanisms-of-dsb-independent-pairing
#5
REVIEW
Mireia Solé, Álvaro Pascual, Ester Anton, Joan Blanco, Zaida Sarrate
Meiosis involves deep changes in the spatial organisation and interactions of chromosomes enabling the two primary functions of this process: increasing genetic diversity and reducing ploidy level. These two functions are ensured by crucial events such as homologous chromosomal pairing, synapsis, recombination and segregation. In most sexually reproducing eukaryotes, homologous chromosome pairing depends on a set of mechanisms, some of them associated with the repair of DNA double-strand breaks (DSBs) induced at the onset of prophase I, and others that operate before DSBs formation...
2023: Frontiers in Cell and Developmental Biology
https://read.qxmd.com/read/37202403/autophagy-receptor-ndp52-alters-dna-conformation-to-modulate-rna-polymerase-ii-transcription
#6
JOURNAL ARTICLE
Ália Dos Santos, Daniel E Rollins, Yukti Hari-Gupta, Hannah McArthur, Mingxue Du, Sabrina Yong Zi Ru, Kseniia Pidlisna, Ane Stranger, Faeeza Lorgat, Danielle Lambert, Ian Brown, Kevin Howland, Jesse Aaron, Lin Wang, Peter J I Ellis, Teng-Leong Chew, Marisa Martin-Fernandez, Alice L B Pyne, Christopher P Toseland
NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters...
May 18, 2023: Nature Communications
https://read.qxmd.com/read/37082862/evidence-for-low-nanocompaction-of-heterochromatin-in-living-embryonic-stem-cells
#7
JOURNAL ARTICLE
Claire Dupont, Dhanvantri Chahar, Antonio Trullo, Thierry Gostan, Caroline Surcis, Charlotte Grimaud, Daniel Fisher, Robert Feil, David Llères
Despite advances in the identification of chromatin regulators and genome interactions, the principles of higher-order chromatin structure have remained elusive. Here, we applied FLIM-FRET microscopy to analyse, in living cells, the spatial organisation of nanometre range proximity between nucleosomes, which we called "nanocompaction." Both in naive embryonic stem cells (ESCs) and in ESC-derived epiblast-like cells (EpiLCs), we find that, contrary to expectations, constitutive heterochromatin is much less compacted than bulk chromatin...
April 21, 2023: EMBO Journal
https://read.qxmd.com/read/36587785/temporal-evolution-of-plutonium-concentrations-and-isotopic-ratios-in-the-ukedo-takase-rivers-draining-the-difficult-to-return-zone-in-fukushima-japan-2013-2020
#8
JOURNAL ARTICLE
Aurélie Diacre, Thomas Chalaux, Soazig Burban, Caroline Gauthier, Amélie Hubert, Anne-Claire Humbert, Irène Lefevre, Anne-Laure Fauré, Fabien Pointurier, Olivier Evrard
In 2011, the Fukushima Dai-Ichi Nuclear Power Plant (FDNPP) accident released significant quantities of radionuclides into the environment. Japanese authorities decided to progressively reopen the Difficult-To-Return Zone after the decontamination of priority reconstruction zones. These areas include parts of the initially highly contaminated municipalities located to the north of the FDNPP, including Namie Town, an area drained by the Ukedo and Takase Rivers. Eleven years after the accident, research focused on the spatial distribution of plutonium (Pu) and radiocesium (Cs) isotopes at contrasted individual locations...
December 29, 2022: Environmental Pollution
https://read.qxmd.com/read/36292757/episomes-and-transposases-utilities-to-maintain-transgene-expression-from-nonviral-vectors
#9
REVIEW
Florian Kreppel, Claudia Hagedorn
The efficient delivery and stable transgene expression are critical for applications in gene therapy. While carefully selected and engineered viral vectors allowed for remarkable clinical successes, they still bear significant safety risks. Thus, nonviral vectors are a sound alternative and avoid genotoxicity and adverse immunological reactions. Nonviral vector systems have been extensively studied and refined during the last decades. Emerging knowledge of the epigenetic regulation of replication and spatial chromatin organisation, as well as new technologies, such as Crispr/Cas, were employed to enhance the performance of different nonviral vector systems...
October 16, 2022: Genes
https://read.qxmd.com/read/35027552/genomic-loci-mispositioning-in-tmem120a-knockout-mice-yields-latent-lipodystrophy
#10
JOURNAL ARTICLE
Rafal Czapiewski, Dzmitry G Batrakou, Jose I de Las Heras, Roderick N Carter, Aishwarya Sivakumar, Magdalena Sliwinska, Charles R Dixon, Shaun Webb, Giovanna Lattanzi, Nicholas M Morton, Eric C Schirmer
Little is known about how the observed fat-specific pattern of 3D-spatial genome organisation is established. Here we report that adipocyte-specific knockout of the gene encoding nuclear envelope transmembrane protein Tmem120a disrupts fat genome organisation, thus causing a lipodystrophy syndrome. Tmem120a deficiency broadly suppresses lipid metabolism pathway gene expression and induces myogenic gene expression by repositioning genes, enhancers and miRNA-encoding loci between the nuclear periphery and interior...
January 13, 2022: Nature Communications
https://read.qxmd.com/read/34322871/pgc-1%C3%AE-regulates-myonuclear-accretion-after-moderate-endurance-training
#11
JOURNAL ARTICLE
Edmund Battey, Regula Furrer, Jacob Ross, Christoph Handschin, Julien Ochala, Matthew J Stroud
The transcriptional demands of skeletal muscle fibres are high and require hundreds of nuclei (myonuclei) to produce specialised contractile machinery and multiple mitochondria along their length. Each myonucleus spatially regulates gene expression in a finite volume of cytoplasm, termed the myonuclear domain (MND), which positively correlates with fibre cross-sectional area (CSA). Endurance training triggers adaptive responses in skeletal muscle, including myonuclear accretion, decreased MND sizes and increased expression of the transcription co-activator peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α)...
January 2022: Journal of Cellular Physiology
https://read.qxmd.com/read/32859945/surveillance-of-cohesin-supported-chromosome-structure-controls-meiotic-progression
#12
JOURNAL ARTICLE
Maikel Castellano-Pozo, Sarai Pacheco, Georgios Sioutas, Angel Luis Jaso-Tamame, Marian H Dore, Mohammad M Karimi, Enrique Martinez-Perez
Chromosome movements and programmed DNA double-strand breaks (DSBs) promote homologue pairing and initiate recombination at meiosis onset. Meiotic progression involves checkpoint-controlled termination of these events when all homologue pairs achieve synapsis and form crossover precursors. Exploiting the temporo-spatial organisation of the C. elegans germline and time-resolved methods of protein removal, we show that surveillance of the synaptonemal complex (SC) controls meiotic progression. In nuclei with fully synapsed homologues and crossover precursors, removing different meiosis-specific cohesin complexes, which are individually required for SC stability, or a SC central region component causes functional redeployment of the chromosome movement and DSB machinery, triggering whole-nucleus reorganisation...
August 28, 2020: Nature Communications
https://read.qxmd.com/read/32788229/chromosome-nuclear-envelope-tethering-a-process-that-orchestrates-homologue-pairing-during-plant-meiosis
#13
REVIEW
Adél Sepsi, Trude Schwarzacher
During prophase I of meiosis, homologous chromosomes pair, synapse and exchange their genetic material through reciprocal homologous recombination, a phenomenon essential for faithful chromosome segregation. Partial sequence identity between non-homologous and heterologous chromosomes can also lead to recombination (ectopic recombination), a highly deleterious process that rapidly compromises genome integrity. To avoid ectopic exchange, homology recognition must be extended from the narrow position of a crossover-competent double-strand break to the entire chromosome...
August 12, 2020: Journal of Cell Science
https://read.qxmd.com/read/32571970/location-specific-cell-identity-rather-than-exposure-to-gi-microbiota-defines-many-innate-immune-signalling-cascades-in-the-gut-epithelium
#14
JOURNAL ARTICLE
Ozge Kayisoglu, Franziska Weiss, Carolin Niklas, Isabella Pierotti, Malvika Pompaiah, Nina Wallaschek, Christoph-Thomas Germer, Armin Wiegering, Sina Bartfeld
OBJECTIVE: The epithelial layer of the GI tract is equipped with innate immune receptors to sense invading pathogens. Dysregulation in innate immune signalling pathways is associated with severe inflammatory diseases, but the responsiveness of GI epithelial cells to bacterial stimulation remains unclear. DESIGN: We generated 42 lines of human and murine organoids from gastric and intestinal segments of both adult and fetal tissues. Genome-wide RNA-seq of the organoids provides an expression atlas of the GI epithelium...
April 2021: Gut
https://read.qxmd.com/read/32300614/quantifying-nuclear-wide-chromatin-compaction-by-phasor-analysis-of-histone-f%C3%A3-rster-resonance-energy-transfer-fret-in-frequency-domain-fluorescence-lifetime-imaging-microscopy-flim-data
#15
JOURNAL ARTICLE
Zhen Liang, Jieqiong Lou, Lorenzo Scipioni, Enrico Gratton, Elizabeth Hinde
The nanometer spacing between nucleosomes throughout global chromatin organisation modulates local DNA template access, and through continuous dynamic rearrangements, regulates genome function [1]. However, given that nucleosome packaging occurs on a spatial scale well below the diffraction limit, real time observation of chromatin structure in live cells by optical microscopy has proved technically difficult, despite recent advances in live cell super resolution imaging [2]. One alternative solution to quantify chromatin structure in a living cell at the level of nucleosome proximity is to measure and spatially map Förster resonance energy transfer (FRET) between fluorescently labelled histones - the core protein of a nucleosome [3]...
June 2020: Data in Brief
https://read.qxmd.com/read/31626286/topological-data-analysis-quantifies-biological-nano-structure-from-single-molecule-localization-microscopy
#16
JOURNAL ARTICLE
Jeremy A Pike, Abdullah O Khan, Chiara Pallini, Steven G Thomas, Markus Mund, Jonas Ries, Natalie S Poulter, Iain B Styles
MOTIVATION: Localization microscopy data is represented by a set of spatial coordinates, each corresponding to a single detection, that form a point cloud. This can be analyzed either by rendering an image from these coordinates, or by analyzing the point cloud directly. Analysis of this type has focused on clustering detections into distinct groups which produces measurements such as cluster area, but has limited capacity to quantify complex molecular organization and nano-structure...
March 1, 2020: Bioinformatics
https://read.qxmd.com/read/31492900/importin-%C3%AE-karyopherin-%C3%AE-1-modulates-mitotic-microtubule-function-and-taxane-sensitivity-in-cancer-cells-via-its-nucleoporin-binding-region
#17
JOURNAL ARTICLE
Annalisa Verrico, Paola Rovella, Laura Di Francesco, Michela Damizia, David Sasah Staid, Loredana Le Pera, M Eugenia Schininà, Patrizia Lavia
The nuclear transport receptor importin-β/karyopherin-β1 is overexpressed in cancers that display genomic instability. It is regarded as a promising cancer target and inhibitors are being developed. In addition to its role in nucleo-cytoplasmic transport, importin-β regulates mitosis, but the programmes and pathways in which it operates are defined only in part. To unravel importin-β's mitotic functions we have developed cell lines expressing either wild-type or a mutant importin-β form in characterised residues required for nucleoporin binding...
January 2020: Oncogene
https://read.qxmd.com/read/31075125/non-invasive-faecal-sampling-reveals-spatial-organization-and-improves-measures-of-genetic-diversity-for-the-conservation-assessment-of-territorial-species-caucasian-lynx-as-a-case-species
#18
JOURNAL ARTICLE
Deniz Mengüllüoğlu, Jörns Fickel, Heribert Hofer, Daniel W Förster
The Caucasian lynx, Lynx lynx dinniki, has one of the southernmost distributions in the Eurasian lynx range, covering Anatolian Turkey, the Caucasus and Iran. Little is known about the biology and the genetic status of this subspecies. To collect baseline genetic, ecological and behavioural data and benefit future conservation of L. l. dinniki, we monitored 11 lynx territories (396 km2) in northwestern Anatolia. We assessed genetic diversity of this population by non-invasively collecting 171 faecal samples and trapped and sampled 12 lynx individuals using box traps...
2019: PloS One
https://read.qxmd.com/read/29626665/ethiopian-highlands-as-a-cradle-of-the-african-fossorial-root-rats-genus-tachyoryctes-the-genetic-evidence
#19
JOURNAL ARTICLE
Radim Šumbera, Jarmila Krásová, Leonid A Lavrenchenko, Sewnet Mengistu, Afework Bekele, Ondřej Mikula, Josef Bryja
Root-rats of the genus Tachyoryctes (Spalacidae) are subterranean herbivores occupying open humid habitats in the highlands of Eastern Africa. There is strong disagreement about species diversity of the genus, because some authors accept two species, while others more than ten. Species with relatively high surface activity, the giant root-rat Tachyoryctes macrocephalus, which is by far largest member of the genus, and the more fossorial African root-rat Tachyoryctes splendens, which eventually has been divided up to 12-13 species, represent two major morphological forms within the genus...
September 2018: Molecular Phylogenetics and Evolution
https://read.qxmd.com/read/29141034/structure-of-the-human-chromosome-interaction-network
#20
JOURNAL ARTICLE
Sergio Sarnataro, Andrea M Chiariello, Andrea Esposito, Antonella Prisco, Mario Nicodemi
New Hi-C technologies have revealed that chromosomes have a complex network of spatial contacts in the cell nucleus of higher organisms, whose organisation is only partially understood. Here, we investigate the structure of such a network in human GM12878 cells, to derive a large scale picture of nuclear architecture. We find that the intensity of intra-chromosomal interactions is power-law distributed. Inter-chromosomal interactions are two orders of magnitude weaker and exponentially distributed, yet they are not randomly arranged along the genomic sequence...
2017: PloS One
keyword
keyword
20829
1
2
Fetch more papers »
Fetching more papers... Fetching...
Remove bar
Read by QxMD icon Read
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"

We want to hear from doctors like you!

Take a second to answer a survey question.