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We analyze multiplexed fluorescence in situ hybridization (m-FISH) data for human and mouse cell lines. The m-FISH technique uses fluorescently-labeled single-stranded probes which hybridize to specific chromosomal regions, thereby allowing the measurement of the spatial positions of up to ∼ 100 tagged sites for several thousands of interphase chromosomes. Our analysis focuses on a wide range of different cell lines and two distinct organisms and provides a unified picture of chromatin structure for scales ranging from 5 kb (kilobases) up to 2 Mb (megabases), thus covering a genomic region of almost three orders of magnitude. Confirming recent analysis [Remini et al., Phys. Rev. E 109, 024408 (2024)], we show that there are two characteristic arrangements of chromatin referred to as phase α (crumpled globule) and phase β (looped domain) and discuss the physical properties of these phases. We show that a simple heterogeneous random walk model captures the main behavior observed in experiments and brings considerable insights into chromosomal structure. [ABSTRACT FROM AUTHOR]

Lung cancer is one of the most common cancers in humans. However, there is still a need to understand the underlying mechanisms of a normal cell developing into a cancer cell. Here, we develop the chromosome dynamic structural model and quantify the important characteristics of the chromosome structural ensemble of the normal lung cell and the lung cancer A549 cell. Our results demonstrate the essential relationship among the chromosome ensemble, the epigenetic marks, and the gene expressions, which suggests the linkage between chromosome structure and function. The analysis reveals that the lung cancer cell may have a higher level of relative ensemble fluctuation (micro CFI) and a higher degree of phase separation between the two compartments than the normal lung cell. In addition, the significant conformational "switching off" events (from compartment A to B) are more than the significant conformational "switching on" events during the lung cancerization. We identify "nucleation seeds" or hot spots in chromosomes, which initiate the transitions and determine the mechanisms. The hot spots and interaction network results reveal that the lung cancerization process (from normal lung to A549) and the reversion process have different mechanisms. These investigations have revealed the cell fate determination mechanism of the lung cancer process, which will be helpful for the further prevention and control of cancers. [ABSTRACT FROM AUTHOR]

KIFC1 is a motor protein of the Kinesin family and it is involved in spindle apparatus assembly, chromosome arrangement, and microfilament-mediated biological processes in mitosis. However, the specific function of KIFC1 in pig oocytes remains unclear. Here, in order to explore the function of KIFC1 in porcine oocytes, the AZ82 inhibitor was used to inhibit the activity of KIFC1. Our results showed when KIFC1 was inhibited, the polar body extrusion rate was obviously decreased, indicating that KIFC1 plays a crucial role in porcine oocytes. We next measured the spindle structure and chromosome arrangement via immunofluorescent staining and found both the rates of abnormal spindle and chromosome disorder increased significantly. By further analyzing the causes of the abnormal spindle, we found the acetylation of tubulin was disrupted. In addition, we also found the spindle position was impaired after KIFC1 inhibition, declaring the spindle migration was affected. Further analysis found cortex actin decreased and cytoplasmic actin increased after KIFC1 inhibition. In summary, we found that KIFC1 played a critical role in porcine oocytes maturation by controlling spindle apparatus via mediating the acetylation of microtubule and regulating the spindle migration via affecting actin dynamics. [ABSTRACT FROM AUTHOR]

The role of chromatin remodelers (CRs) during mitosis to facilitate DNA–protein interactions for cell division has been extensively studied, whereas their significance in meiosis-specific events is poorly understood. Studies of meiosis in various model systems have revealed essential roles of CRs in meiotic recombination, chromosome segregation, and transcription regulation. CRs have essential roles in meiotic recombination (e.g., Spo11-mediated double-stranded breaks, strand invasion, crossover formation, and synapsis of homologous chromosomes) in yeast, mice, and plants. CRs also have essential roles in meiotic chromosome segregation, such as spindle assembly and centromere function. In Saccharomyces cerevisiae , CRs regulate transcription switching during meiosis to produce 5′ extended transcripts (long undecoded transcript isoforms) of ~190 genes. In eukaryotic cells, DNA is wrapped around histone octamers to compact the genome. Although such compaction is required for the precise segregation of the genome during cell division, it restricts the DNA–protein interactions essential for several cellular processes. During meiosis, a specialized cell division process that produces gametes, several DNA–protein interactions are crucial for assembling meiosis-specific chromosome structures, meiotic recombination, chromosome segregation, and transcriptional regulation. The role of chromatin remodelers (CRs) in facilitating DNA–protein transactions during mitosis is well appreciated, whereas how they facilitate meiosis-specific processes is poorly understood. In this review, we summarize experimental evidence supporting the role of CRs in meiosis in various model systems and suggest future perspectives to advance the field. [ABSTRACT FROM AUTHOR]

3D organization of the genome plays a critical role in regulating gene expression. How 3D-genome organization differs among different cell types and relates to cell type-dependent transcriptional regulation remains unclear. Here, we used genome-scale DNA and RNA imaging to investigate 3D-genome organization in transcriptionally distinct cell types in the mouse cerebral cortex. We uncovered a wide spectrum of differences in the nuclear architecture and 3D-genome organization among different cell types, ranging from the size of the cell nucleus to higher-order chromosome structures and radial positioning of chromatin loci within the nucleus. These cell type-dependent variations in nuclear architecture and chromatin organization exhibit strong correlations with both the total transcriptional activity of the cell and transcriptional regulation of cell type-specific marker genes. Moreover, we found that the methylated DNA binding protein MeCP2 promotes active-inactive chromatin segregation and regulates transcription in a nuclear radial position-dependent manner that is highly correlated with its function in modulating active-inactive chromatin compartmentalization. [ABSTRACT FROM AUTHOR]

Telomeres are terminal protective chromosome structures. Genetic variants in genes coding for proteins required for telomere maintenance cause rare, life-threatening Telomere Biology Disorders (TBDs) such as dyskeratosis congenita, aplastic anemia or pulmonary fibrosis. The more frequently used mice strains have telomeres much longer than the human ones which question their use as in vivo models for TBDs. One mice model with shorter telomeres based on the CAST/EiJ mouse strain carrying a mutation in the Terc gene, coding for the telomerase RNA component, has been studied in comparison with C57BL/6J mice, carrying the same mutation and long telomeres. The possible alterations produced in lungs and the haematopoietic system, frequently affected in TBD patients, were determined at different ages of the mice. Homozygous mutant mice presented a very shortened life span, more notorious in the short-telomeres CAST/EiJ strain. The lungs of mutant mice presented a transitory increase in fibrosis and a significant decrease in the relative amount of the alveolar epithelial type 2 cells from six months of age. This decrease was larger in mutant homozygous animals but was also observed in heterozygous animals. On the contrary the expression of the senescence-related protein P21 increased from six months of age in mutant mice of both strains. The analysis of the haematopoietic system indicated a decrease in the number of megakaryocyte-erythroid progenitors in homozygous mutants and an increase in the clonogenic potential of bone marrow and LSK cells. Bone marrow cells from homozygous mutant animals presented decreasing in vitro expansion capacity. The alterations observed are compatible with precocious ageing of lung alveolar cells and the bone marrow cells that correlate with the alterations observed in TBD patients. The alterations seem to be more related to the genotype of the animals that to the basal telomere length of the strains although they are more pronounced in the short-telomere CAST/EiJ-derived strain than in C57BL/6J animals. Therefore, both animal models, at ages over 6–8 months, could represent valuable and convenient models for the study of TBDs and for the assay of new therapeutic products. [ABSTRACT FROM AUTHOR]

Human endogenous retroviruses (HERV) represent nearly 8% of the human genome. Of these, HERV-K subtype HML-2 is a transposable element that plays a critical role in embryonic development and in the pathogenesis of several diseases. Quantification and characterization of these multiple HML-2 insertions in the human chromosome has been challenging due to their size, sequence homology with each other, and their repetitive nature. We examined a cohort of 222 individuals for HML-2 proviruses 6q14.1 and 7p22.1a, two loci that are capable of producing full-length viral proteins and have been previously implicated in several cancers, autoimmune disorders and neurodegenerative diseases, using long-read DNA sequencing. While the reference genome for both regions suggests these two loci are structurally dissimilar, we found that for both loci about 5% of individuals have a unique tandem repeat-like sequence (three long terminal repeat sequences sandwiching two internal, potentially protein coding sequences), while most individuals have a standard proviral structure (one internal region sandwiched by two long terminal repeats). Moreover, both proviruses can make full-length, or nearly full-length, HERV-K proteins in multiple transcription orientations. The amino acid sequences from different loci in the same transcriptional orientation share sequence homology with each other. These results demonstrate a clear, previously unreported, relationship between HML-2 loci 6q14.1 and 7p22.1a and highlight the utility of long-read sequencing to study repetitive elements. Future studies need to determine if these polymorphisms determine genetic susceptibility to diseases that are associated with them. [ABSTRACT FROM AUTHOR]

Anaphase is tightly controlled spatiotemporally to ensure proper separation of chromosomes. 1,2,3 The mitotic spindle, the self-organized microtubule structure driving chromosome segregation, scales in size with the available cytoplasm. 4,5,6,7 Yet, the relationship between spindle size and chromosome movement remains poorly understood. Here, we address this relationship during the cleavage divisions of the Drosophila blastoderm. We show that the speed of chromosome separation gradually decreases during the four nuclear divisions of the blastoderm. This reduction in speed is accompanied by a similar reduction in spindle length, ensuring that these two quantities are tightly linked. Using a combination of genetic and quantitative imaging approaches, we find that two processes contribute to controlling the speed at which chromosomes move in anaphase: the activity of molecular motors important for microtubule depolymerization and sliding and the cell cycle oscillator. Specifically, we found that the levels of multiple kinesin-like proteins important for microtubule depolymerization, as well as kinesin-5, contribute to setting the speed of chromosome separation. This observation is further supported by the scaling of poleward flux rate with the length of the spindle. Perturbations of the cell cycle oscillator using heterozygous mutants of mitotic kinases and phosphatases revealed that the duration of anaphase increases during the blastoderm cycles and is the major regulator of chromosome velocity. Thus, our work suggests a link between the biochemical rate of mitotic exit and the forces exerted by the spindle. Collectively, we propose that the cell cycle oscillator and spindle length set the speed of chromosome separation in anaphase. • Chromosome separation speed decreases over the four Drosophila blastoderm cycles • Anaphase spindle length reduction correlates with decreased chromosome speed • Microtubule-depolymerizing and -sliding motors regulate chromosome velocity • The cell cycle oscillator sets anaphase duration, impacting chromosome velocity Xu et al. investigate how the speed of chromosome separation is regulated during the cleavage divisions of the Drosophila blastoderm. They find that spindle length and the cell cycle oscillator jointly control the velocity of chromosome movement in anaphase. [ABSTRACT FROM AUTHOR]

Mutations in the TP53 gene and chromosomal instability (CIN) are two of the most common alterations in cancer. CIN, marked by changes in chromosome numbers and structure, drives tumor development, but is poorly tolerated in healthy cells, where developmental and tissue homeostasis mechanisms typically eliminate cells with chromosomal abnormalities. Mechanisms that allow cancer cells to acquire and adapt to CIN remain largely unknown. Tumor suppressor protein p53, often referred to as the "guardian of the genome", plays a critical role in maintaining genomic stability. In cancer, CIN strongly correlates with TP53 mutations, and recent studies suggest that p53 prevents the propagation of cells with abnormal karyotypes arising from mitotic errors. Furthermore, p53 dysfunction is frequent in cells that underwent whole-genome doubling (WGD), a process that facilitates CIN onset, promotes aneuploidy tolerance, and is associated with poor patient prognosis across multiple cancer types. This review summarizes current insights into p53's role in protecting cells from chromosome copy number alterations and discusses the implications of its dysfunction for the adaption and propagation of cancer cells. [ABSTRACT FROM AUTHOR]

Biomolecular condensates (BMCs) represent a group of organized and programmed systems that participate in gene transcription, chromosome organization, cell division, tumorigenesis, and aging. However, the understanding of BMCs in terms of internal organizations and external regulations remains at an early stage. Recently, novel approaches such as synthetic biology have been used for de novo synthesis of BMCs. These synthesized BMCs (SBMCs) driven by phase separation adeptly resemble the self-assembly and dynamics of natural BMCs, offering vast potentials in basic and applied research. This review introduces recent progresses in phase separation-induced SBMCs, attempting to elaborate on the intrinsic principles and regulatory methodologies used to construct SBMCs. Furthermore, the scientific applications of SBMCs are illustrated, as indicated by the studies of chromosome structure, pathogenesis, biomanufacturing, artificial cell design, and drug delivery. The controllable SBMCs offer a powerful tool for understanding metabolic regulations, cellular organizations, and disease-associated protein aggregations, raising both opportunities and challenges in the future of biomaterial, biotechnology, and biomedicine. [ABSTRACT FROM AUTHOR]

Understanding genetic structure and chromosomal characteristics is essential for developing effective breeding programmes and improving plant species. This research compared karyotypic features of 10 plant populations of Populus euphratica from various regions of Iran. Fresh roots grown from cuttings of the populations were used to get metaphase cells. Then several chromosomal parameters were recorded and analysed using a nested statistical model. All the studied populations were diploid, with 2 n = 38 chromosomes, consisting of medium and sub-medium chromosome types. Significant differences (P ⩽ 0.01) were observed between the plant populations in chromosomal dimensions and arm ratios, suggesting chromosomal rearrangements. Chromosome lengths in the studied populations ranged from 0.69 to 3.38 μm. Intra-chromosomal index (A 1) showed clear asymmetrical differences between the plant populations. Furthermore, using Stebbins's standards, the studied populations classified as 1A and 1B classes, demonstrated more asymmetry than those categorized as 1B and 2B, respectively. Cytological differences between the plant populations, collected from different parts of the country, showed that chromosome structural rearrangements are responsible for the speciation and adaption of the species against the mentioned variable ecological conditions and play a key role in response to diverse climatic and geographical conditions. [ABSTRACT FROM AUTHOR]

Fennel is a member of the Apiaceae family native to the Mediterranean area. The last taxonomic revision recognizes two species of fennel, Anethum foeniculum and Anethum piperitum corresponding, respectively, to the taxa previously classified as Foeniculum vulgare subsp. vulgare and Foeniculum vulgare subsp. piperitum. In recent years research has dedicated interest to fennel, considering both its agronomic and pharmaceutical aspects but largely overlooking its cytogenetic characteristics. To fill this gap, the chromosome structure of A. foeniculum and A. piperitum was examined by applying a combination of FISH (Fluorescence In Situ Hybridization), GISH (Genomic In Situ Hybridization) and DAPI (4′-6-diamidino-2-phenylindole) banding techniques. The FISH experiments revealed a similar distribution pattern of rDNA sites and telomeric repeats in both fennel species. An in-depth view of the chromosome structure of A. piperitum and A. foeniculum was obtained using the self-GISH procedure which revealed repetitive DNA sequences located in the centromeric and terminal regions of all chromosomes. The correspondence of s-GISH signals with DAPI banding suggests that these sequences are the principal component of the heterochromatin of fennel. These results could constitute the basic references for further molecular cytogenetic analyses to shed light on the evolutionary and taxonomic aspects of fennel. [ABSTRACT FROM AUTHOR]

Refactoring the genetic code can optimize gene expression, distinguish synthetic from natural genomes, and enable strains to prevent viral infections and genetic information leakage. The artificial design of noncoding regions can enhance genome stability and flexibility while ensuring the functionality of the genome. Genome reduction can provide a new approach for exploring genome components and their interactions, thereby enabling a more comprehensive understanding of the genome. Modification of the 3D structure of synthetic chromosomes enables the regulation of gene expression without modifying the DNA sequence. Genome design is the foundation of genome synthesis, which provides a new platform for deepening our understanding of biological systems by exploring the fundamental components and structure of the genome. Artificial genome designs can endow unnatural genomes with desired functions. We provide a comprehensive overview of genome design principles ranging from DNA sequences to the 3D structure of chromosomes. Furthermore, we highlight applications of genome design in gene expression, genome structure, genome function, and biocontainment, and discuss the potential of artificial intelligence (AI) in genome design. [ABSTRACT FROM AUTHOR]

Karyotyping is a study of chromosomes to identify various chromosomal aberrations related to structure and number. Chromosome image analysis involves challenging issues related to overlapping and touching of chromosomes. Chromosome segmentation and classification generally focus on separating overlapping and touching chromosomes. The analysis methods start from conventional image processing methods to advanced machine learning techniques. These methods are broadly classified into low-level and high-level methods. The low-level methods are thresholding-based approaches, edge detection, feature extraction techniques like active contours and watershed approaches and machine learning for classification. The high-level methods are deep learning algorithms like convolutional neural networks (CNNs), U-Net, autoencoder architectures. These methods help in improving accuracy and automate the process of chromosome segmentation and classification. High-level approaches can handle complexity in chromosome overlaps which provides better segmentation results. The approach learns complicated patterns and structures of chromosome images, which helps in achieving better classification accuracy. The challenges are: (i) working on large and annotated dataset for training deep learning models and (ii) suffer issues with new dataset even in they perform better during training phase. The solution for all these can be a hybrid approach that combines conventional method with modern approaches. This survey gives readers a basic understanding of automated karyotyping and future direction in this domain. [ABSTRACT FROM AUTHOR]

Background: Chickens and ducks are vital sources of animal protein for humans. Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species, highlighting the need for more comprehensive genomes. The bird genome has more than tens of microchromosomes, but comparative genomics, annotations, and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies. We aim to complete the chicken and duck genomes, recover missing genes, and reveal common and unique chromosomal features between birds. Results: The near telomere-to-telomere genomes of Silkie Gallus gallus and Mallard Anas platyrhynchos were successfully assembled via multiple high-coverage complementary technologies, with quality values of 36.65 and 44.17 for Silkie and Mallard, respectively; and BUSCO scores of 96.55% and 96.97% for Silkie and Mallard, respectively; the mapping rates reached over 99.52% for both assembled genomes, these evaluation results ensured high completeness and accuracy. We successfully annotated 20,253 and 19,621 protein-coding genes for Silkie and Mallard, respectively, and assembled gap-free sex chromosomes in Mallard for the first time. Comparative analysis revealed that microchromosomes differ from macrochromosomes in terms of GC content, repetitive sequence abundance, gene density, and levels of 5mC methylation. Different types of arrangements of centromeric repeat sequence centromeres exist in both Silkie and the Mallard genomes, with Mallard centromeres being invaded by CR1. The highly heterochromatic W chromosome, which serves as a refuge for ERVs, contains disproportionately long ERVs. Both Silkie and the Mallard genomes presented relatively high 5mC methylation levels on sex chromosomes and microchromosomes, and the telomeres and centromeres presented significantly higher 5mC methylation levels than the whole genome. Finally, we recovered 325 missing genes via our new genomes and annotated TNFA in Mallard for the first time, revealing conserved protein structures and tissue-specific expression. Conclusions: The near telomere-to-telomere assemblies in Mallard and Silkie, with the first gap-free sex chromosomes in ducks, significantly enhanced our understanding of genetic structures in birds, specifically highlighting the distinctive chromosome features between the chicken and duck genomes. This foundational work also provides a series of newly identified missing genes for further investigation. [ABSTRACT FROM AUTHOR]

T cell activation is accompanied by extensive changes in epigenome. However, the high-ordered chromatin organization underpinning CD8+ T cell activation is not fully known. Here, we show extensive changes in the three-dimensional genome during CD8+ T cell activation, associated with changes in gene transcription. We show that CD8+ T-cell-specific deletion of Trim28 in mice disrupts autocrine IL-2 production and leads to impaired CD8+ T cell activation in vitro and in vivo. Mechanistically, TRIM28 binds to regulatory regions of genes associated with the formation of chromosomal loops during activation. At the loop anchor regions, TRIM28-occupancy overlaps with that of CTCF, a factor known for defining the boundaries of topologically associating domains and for forming of the loop anchors. In the absence of Trim28, RNA Pol II and cohesin binding to these regions diminishes, and the chromosomal structure required for the active state is disrupted. These results thus identify a critical role for TRIM28-dependent chromatin topology in gene transcription in activated CD8+ T cells. TRIM28 is known to recruit chromatin modifiers to its target regions to co-regulate gene expression in multiple cell types. Here authors show that in CD8+ T cells, TRIM28 is an integrant part of the larger-scale chromatin architecture that characterises the activated functional state but dispensable for CD8 T cell maturation. [ABSTRACT FROM AUTHOR]

An important part of UAV technological development consists of improvements in the scope of path planning. Different choices can be made in path planning according to operational priorities, it may be preferred to reach the destination as fast as possible or to increase the airtime by compromising speed. For every speed and altitude that the UAV can fly; fuel data of cruise, climb and descent phases are used in the path planning algorithm. Thus, economical and airtime-maximizing paths could be produced on the basis of performance characteristics compatible with the kinematic constraints customized for the UAV. In this study, Cellular (cGA) and Segmented Cellular Genetic Algorithm (scGA) are proposed. The novel overprotective algorithm which has a fixed initial population and segmented chromosome structure achieves a high convergence speed to optimal solution and can generate paths which have 5.2 times higher fitness value on average compared with a conventional Genetic Algorithm (GA). It has been seen that scGA improves the initial population in terms of the best solutions 1.9 times and the general population 5.8 times better compared with GA. [ABSTRACT FROM AUTHOR]

Radiation-resistant Deinococcus radiodurans is an extremophilic microorganism capable of withstanding high levels of ionizing radiation and chemical mutagens. It possesses remarkable DNA repair capability and serves as a model organism for studying stress resistance mechanisms. However, our understanding of the spatial chromosome organization of this species remains limited. In this study, we employed chromosome conformation capture (3C) technology to determine the 3D genome structure of D. radiodurans and to further investigate the changes of chromosome conformation induced by ultraviolet (UV) irradiation. We observed that UV irradiation reduced short-range chromosome interactions, and smaller chromosomal interaction domains (CIDs) merged to form larger CIDs. Integrating transcriptomic data analysis, we found that the majority of upregulated differentially expressed genes were significantly enriched near specific CID boundaries. Specifically, we comprehensively elucidated that the nucleoidassociated protein DrEbfC as a global regulatory factor for gene expression, may modulate the efficiency of relevant metabolic pathways by altering the local chromosome structure, thereby influencing the physiological state of the bacterium. Overall, our study revealed the chromosome conformations of D. radiodurans under different conditions and offered valuable insights into the molecular response mechanism of this extremophile to survival stresses. [ABSTRACT FROM AUTHOR]

Simple Summary: Dairy cows are essential for milk production, but their productive lifespan—how long they stay healthy and productive—has not increased in recent years. This has led to concerns about animal welfare, environmental sustainability, and farm profitability. Scientists are searching for ways to predict which calves will have longer, healthier lives. One idea is to measure telomeres: tiny structures at the ends of chromosomes that shorten as animals age. In this study, we measured the telomere length of newborn dairy calves and investigated if it could predict their lifespan, milk production, or reproductive performance. We found that telomere length did not predict how long the cows lived or how much milk they produced. However, calves with the longest telomeres were less efficient at producing milk fat and protein. Interestingly, these calves also required fewer inseminations and had slightly longer intervals between calvings, suggesting a possible link to reproductive performance. While telomere length alone may not be a reliable predictor of lifespan or productivity, it could help us better understand the biology of aging and reproduction in dairy cows. Future research could provide more insights into how this information could improve animal welfare and farming efficiency. Telomere length (TL) has gained attention as a biomarker for longevity and productivity in dairy cattle. This study explored the association between neonatal TL in Holstein calves and lifetime parameters (lifespan, milk production, and reproduction). Blood samples were collected from 210 calves (≤10d old) across four dairy farms in Flanders, Belgium. Telomere length was measured using qPCR and analyzed as a continuous variable and across three groups: the 10% shortest, the 10% longest, and the remaining 80%. Survival analyses showed no association between TL and lifespan (p = 0.1) or TL groups (p = 0.8). Similarly, TL showed no significant association with production traits. However, categorical analyses revealed that calves with the longest TL had lower lifetime fat (p = 0.01) and protein yields (p = 0.01) than those with the shortest TL. Reproductive analyses showed cows in the long TL group required fewer inseminations per lactation (p = 0.02) and exhibited longer calving intervals (p = 0.05). These findings suggest that while neonatal TL may not predict productive lifespan, it may provide insight into reproductive efficiency. Future studies should prioritize longitudinal assessments of TL dynamics to better understand their interactions with management practices and application in herd improvement. [ABSTRACT FROM AUTHOR]

The rise of induced pluripotent stem cells (iPSCs) technology has ushered in a landmark shift in the study of hereditary diseases. However, there is a scarcity of reports that offer a comprehensive and objective overview of the current state of research at the intersection of iPSCs and hereditary diseases. Therefore, this study endeavors to categorize and synthesize the publications in this field over the past decade through bibliometric methods and visual knowledge mapping, aiming to visually analyze their research focus and clinical trends. The English language literature on iPSCs and hereditary diseases, published from 2014 to 2023 in the Web of Science Core Collection (WoSCC), was examined. The CiteSpace (version 6.3.R1) software was utilized to visualize and analyze country/region, institution, scholar, co-cited authors, and co-cited journals. Additionally, the co-occurrence, clustering, and bursting of co-cited references were displayed. Analysis of 347 articles that met the inclusion criteria revealed a steady increase in the number of published articles and citation frequency in the field over the past decade. With regard to the countries/regions, institutions, scholars, and journals where the articles were published, the highest numbers were found in the USA, the University of California System, Suren M. Zakian, and Stem Cell Research, respectively. The current research is focused on the construction of disease models, both before and after correction, as well as drug target testing for single-gene hereditary diseases. Chromosome transplantation genomic therapy for hereditary diseases with abnormal chromosome structures may emerge as a future research hotspot in this field. [ABSTRACT FROM AUTHOR]

Pulp polyp is often eliminated as dental waste. Pulp polyp cells were reported to have high proliferation activity which might be comprised of stem cells. However, little has been known on the presence of stem cells in the pulp polyp. Moreover, pulp polyp cells might contain chromosomal abnormality. The present study was conducted to investigate the presence of pulp polyp stem cells, which could later be propagated and confirmed as normal/non-pathogenic cells using karyotype analysis. Collected pulp polyps were minced, enzymatically digested, and cultured. Expression of mesenchymal stem cell (MSC) markers on pulp polyp cells were analyzed using flow cytometry. Multilineage differentiation capacity was assessed by culturing the cells in osteogenic, chondrogenic, and adipogenic differentiation media. Genomic stability of the cells was evaluated with G-banded and molecular karyotype analyses. Pulp polyp cells appeared as fibroblasts-like cells. The cells were positive for cluster of differentiation (CD)105, CD90, and CD73, and negative for CD45, CD34, CD11b, CD19, and human leukocyte antigen (HLA)-DR. The cells were capable of osteogenic, chondrogenic, and adipogenic differentiation. G-banded karyotype analysis showed that there was no abnormality in the number or structure of chromosomes in pulp polyp-derived MSCs (PP-MSCs). Molecular karyotype analysis revealed that all copy number variations identified in PP-MSCs were not pathogenic. PP-MSCs, which fulfill the minimal criteria for MSCs and are proven to have normal karyotype, have been successfully established. PP-MSCs might be a promising and safe candidate that can be considered for pulp-dentin complex regeneration. [ABSTRACT FROM AUTHOR]

Abstract Single-cell chromosome conformations vary significantly among individual cells. We introduce a two-step dimensionality reduction method for density-based, unsupervised clustering of single-cell 3D chromosome structures from simulations or multiplexed 3D-FISH imaging. Our method clusters up to half of all structures into 5–12 prevalent conformational states per chromosome. These states are distinguished by subdivisions into chromosome territory domains, whose boundary locations influence subnuclear positions and speckle associations of certain genes and establish long-range structural variations of more than 10 Mb. Territory domain boundaries are found at few sequence locations, shared among cell types and often situated at syntenic breakpoints.

Amphotericin B (AmB) is a potent antifungal and antiparasitic medication that exerts its action by disrupting the cell membrane of the leishmanial parasite, leading to its death. Understanding the genetic alterations induced by Amphotericin B is crucial for gaining insights into drug resistance mechanisms and developing more effective treatments against Leishmania infections. As a new Leishmania species, the molecular response of Leishmania orientalis to anti-leishmanial drugs has not been fully explored. In this study, Leishmania orientalis strain PCM2 culture was subjected to AmB exposure at a concentration of 0.03 uM over 72 hours compared to the control. The genomic alteration and transcriptomic changes were investigated by utilising the whole genome and RNA sequencing methods, followed by the analysis of single nucleotide polymorphisms (SNPs), differential gene expression, and chromosomal copy number variations (CNVs) assessed using read depth coverage (RDC) values across the entire genome. The chromosomal CNV analysis showed no significant difference between L. orientalis from the control and AmB-treated groups. The distribution of SNPs displayed notable variability, with higher SNP incidence in the control group compared to the AmB-treated group. Gene ontology analysis unveiled functions of the SNPs -associated genes involved in transporter function, genetic precursor synthesis, and purine nucleotide metabolism. Notably, the impact of AmB treatment on the L. orientalis gene expression profiles exhibited diverse expressional alterations, particularly the downregulation of pivotal genes such as the tubulin alpha chain gene. The intricate interplay between SNPs and gene expression alterations might underscore the complex regulatory networks underlying the AmB resistance of L. orientalis strain PCM2. Author summary: Leishmaniasis is a neglected tropical disease caused by parasites of the Leishmania genus, and treatments often rely on drugs like Amphotericin B (AmB). This study focuses on Leishmania orientalis, a newly recognized species, to better understand its molecular responses to AmB, which could shed light on drug resistance mechanisms. Using advanced genomic and transcriptomic techniques, the authors analyzed how L. orientalis responds to AmB treatment over 72 hours. Interestingly, while there were no significant changes in chromosomal structure, the authors observed differences in single nucleotide polymorphisms (SNPs) and gene expression patterns. The control group showed more genetic variability than the treated group, and several key genes involved in critical cellular functions were downregulated after treatment. These findings suggest that L. orientalis might regulate its genetic and molecular machinery in complex ways to survive drug exposure. By unraveling these mechanisms, this research contributes to understanding Leishmania biology and supports the development of more effective treatments for this neglected disease. [ABSTRACT FROM AUTHOR]

Growing evidence indicates that the deterioration of egg quality caused by postovulatory ageing significantly hampers embryonic development. However, the molecular mechanisms by which postovulatory ageing leads to a decline in oocyte quality have not been fully characterized. In this study, we observed an accelerated decay of maternal mRNAs through RNA‐seq analyses in postovulatory‐aged (PostOA) oocytes. We noted that these downregulated mRNAs should be degraded during the 2‐cell stage. Proteomic analyses revealed that the degradation of maternal mRNAs is associated with the accumulation of DCP1A. The injection of exogenous Dcp1a mRNA or siRNA into MII stage oocytes proved that DCP1A could accelerate the degradation of maternal mRNAs. Additionally, we also found that SPDL1 is crucial for maintaining spindle/chromosome structure and chromosome euploidy in PostOA oocytes. Spdl1‐mRNA injection remarkably recovered the meiotic defects in PostOA oocytes. Collectively, our findings provide valuable insights into the molecular mechanisms underlying postovulatory ageing. [ABSTRACT FROM AUTHOR]

The R-loop is a common transcriptional by-product that consists of an RNA-DNA duplex joined to a displaced strand of genomic DNA. While the effects of R-loops on health and disease are well established, there is still an incomplete understanding of the cellular processes responsible for their removal from eukaryotic genomes. Here, we show that a core regulator of chromosome architecture --the Smc5/6 complex-- plays a crucial role in the removal of R-loop structures formed during gene transcription. Consistent with this, budding yeast mutants defective in the Smc5/6 complex and enzymes involved in R-loop resolution show strong synthetic interactions and accumulate high levels of RNA-DNA hybrid structures in their chromosomes. Importantly, we demonstrate that the Smc5/6 complex acts on specific types of RNA-DNA hybrid structures in vivo and promotes R-loop degradation by the RNase H2 enzyme in vitro. Collectively, our results reveal a crucial role for the Smc5/6 complex in the removal of toxic R-loops formed at highly transcribed genes and telomeres. [ABSTRACT FROM AUTHOR]

Determining or assigning the sex of a newborn baby can be a complicated matter. Those with a male chromosomal structure may look like a typical woman, and those with a female chromosomal structure may look like a typical male, or people may have ambiguous external genitalia. The phenomenon referred to by terms such as Disorders of Sex Development (DSD), hermaphroditism, and intersexuality has become a subject of interdisciplinary inquiry, engaging fields such as medicine, theology, law, philosophy, and ethics. This article discusses disorders of sex development according to Islamic bioethics. The aim of the article is to reveal Islam's ethical approach to disorders of sex development through the example of Islamic law. Disorders of sex development have been carefully addressed by Islamic jurists since the early periods, and ethical values were also considered in regulating rulings for individuals with DSD. Considering that ethical discussions about disorders of sex development are shaped according to the medical conjuncture of each period, the ethical approach to DSD in classical Islamic law was shaped in the context of protecting human dignity and privacy. For example, in cases where it is necessary to look at the external genital organs of a person with DSD, it was decided to purchase a concubine (jariya). Considering that according to Islamic law, the marriage of an individual with DSD whose sex has not been assigned is not allowed, it is aimed to protect the human dignity and privacy of the individuals with DSD by assigning the task of sex assignment and circumcision to the concubine. According to classical Islamic law, the two institutions that create privacy for looking at the external genital organs of the opposite sex are marriage and having a concubine. These Islamic rulings may imply that, depending on the medical conditions of the period, the ethical approach to DSD in classical Islamic law was shaped mostly to prevent psychological complications. Over time, with advancements in medicine allowing for the removal of tissues associated with the opposite sex from the bodies of individuals with DSD, a significant shift occurred in Islamic ethical values. In this context, contemporary Islamic jurists have focused on ethical values such as the Islamic rulings of sex correction surgeries, the evidence for permissibility (halal status) of these surgeries, the necessary parameters for the religious legitimacy of these procedures, and the doctrine of informed consent. In other words, the ethical approach, which initially focused on preventing psychological complications, evolved into the development of standards of medical care for DSD. This shift in the ethical approach of Islamic law regarding disorders of sex development emphasizes the importance of the medical context in the ethical discussions surrounding DSD. While contemporary Islamic jurists were investigating the ruling of sex correction operations, they questioned whether there was a medical indication for surgical interventions performed under DSD conditions. Contemporary Islamic jurists who accept disorders of sex development (DSD) as an anomaly occurring during the prenatal period have ruled that sex correction surgeries are permissible (halal) as part of medical treatment. They have used some evidence to achieve this result: these surgical operations are considered part of medical treatment; they do not cause deformity to the body, thus not violating the dignity of the human body, and they align with the higher interests (maslahahs) of preserving life and lineage. However, sex correction operations are not considered unlimitedly halal in Islamic ethics. A number of parameters have been established to ensure the Islamic legitimacy of sex correction operations. For example, in order to perform sex correction operations, parameters required, such as the sex must be definitively unclear, there must be a medical indication for the surgery, and the operation should be considered a last resort. In contemporary Islamic ethics, the doctrine of informed consent is highly valued in sex correction surgeries. In this context, contemporary Islamic jurists demand that, regardless of the outcome, the physician must completely inform the individual with DSD or, if the individual is incompetent, his/her parents. Thus, it may be said that the autonomy of individuals with DSD is valued as an extension of the principle of informed consent in Islamic ethics. As a result, this article argues that ethical values have been considered in regulating religious rulings related to disorders of sex development in Islamic law since its early periods. It positions the shifts in the ethical approach under DSD conditions in classical and contemporary Islamic law within the context of the changing medical conjuncture. [ABSTRACT FROM AUTHOR]

Chromosomal instability (CIN), characterized by fluctuations in chromosome number or structure within cells, stands out as a hallmark of cancer, enabling tumors to thrive in hostile conditions. CIN serves as a driver of genetic diversity, giving rise to clonal heterogeneity (CH). Emerging evidence points to a potential correlation between CIN, CH, and the prognosis of breast cancer (BC) patients, especially in tumors exhibiting overexpression of the human epidermal growth factor receptor 2 (HER2+). However, our understanding of the role of CIN in other subtypes of BC is limited. Furthermore, it remains unclear whether CIN levels above a certain threshold in BC tumors could adversely affect tumor growth, or if lower to moderate levels of CIN might be associated with a more favorable prognosis for BC patients compared to elevated levels. Elucidating these relationships could significantly influence risk assessment and the formulation of future therapeutic approaches targeting CIN in BC. This study aimed to assess CIN and CH in tumor tissue samples obtained from Colombian patients diagnosed with luminal A, luminal B, HER2+, or triple-negative BC, and compare them with established clinicopathological parameters. The findings of this study indicate that BC patients exhibit intermediate CIN, high CH, and stable aneuploidy. All these characteristics were found to be related to clinicopathological features. Our results suggest that the identification of CIN, CH, and aneuploidy could improve cancer risk stratification, which could help to clarify the prediction of clinical outcomes and guide personalized therapeutic strategies for patients with different BC subtypes. [ABSTRACT FROM AUTHOR]

Chromosomal abnormalities (CAs) are changes in the number or structure of chromosomes, manifested as alterations in the total number of chromosomes or as structural abnormalities involving the loss, duplication, or rearrangement of chromosomal segments. CAs can be inherited or can occur spontaneously, leading to congenital malformations and genetic diseases. CAs associated with cardiovascular diseases cause structural or functional alterations of the heart, affecting the cardiac chambers, valves, coronary arteries, aorta, and cardiac conduction, thus increasing the likelihood of arrhythmias, cardiac arrest, and sudden cardiac death (SCD). An early diagnosis and the adequate management of chromosomal abnormalities associated with cardiovascular diseases are essential to prevent SCD, which is a serious public health problem today. In our review, we analyzed the structural and functional CAs responsible for congenital heart disease (CHD) that increase the risk of SCD and analyzed the prevention strategies to be implemented to reduce SCD. [ABSTRACT FROM AUTHOR]

This study addresses the challenges in the early diagnosis of deep infiltrating endometriosis (DIE) by exploring the potential role of the deubiquitinating enzyme USP14. By analyzing the GSE141549 dataset from the Gene Expression Omnibus (GEO) database, using bioinformatics methods and three machine learning algorithms (LASSO, Random Forest, and Support Vector Machine), the key feature gene USP14 was identified. The results indicated that USP14 is significantly upregulated in DIE and exhibits good predictive value (AUC = 0.786). Further analysis revealed the important role of USP14 in muscle function, cellular growth factor response, and maintenance of chromosome structure, and its close association with various immune cell functions. Immunohistochemical staining confirmed the high expression of USP14 in DIE tissues. This study provides a new molecular target for the early diagnosis of DIE, which holds significant clinical implications and potential application value. [ABSTRACT FROM AUTHOR]

Introduction: Transient neonatal diabetes mellitus (TNDM) is a heterogeneous subtype of neonatal diabetes that usually presents within the first days or weeks of life, spontaneously remits in infancy, but can recur in childhood or adolescence as a permanent form of diabetes. Approximately 70% of TNDM cases are due to overexpression of genes at chromosome 6q24 (6q24‐TNDM) caused by one of three potential mechanisms: paternal uniparental disomy (pUPD6), paternal duplication, or hypomethylation of the maternal allele. Our aim was to further elucidate the clinical characteristics of a relatively large group of individuals with this rare condition. Methods: Participants with a genetically confirmed diagnosis of 6q24‐TNDM were identified through the University of Chicago Monogenic Diabetes Registry. Some participants had testing done on a clinical basis, with the remainder having received research‐based genetic testing. Clinical information was extracted from survey responses and medical records. Results: There were 33 participants with 6q24‐TNDM (58% were male). Eight (24%) had hypomethylation of the maternal allele, seven (21%) had paternal duplication, 17 (52%) had pUPD6, and one individual had 6q24 hypomethylation of unknown etiology. The median age of initial diabetes presentation was 2 days (n = 33). Remission occurred at a median age of 3 months (n = 28). The median age of relapse was 14 years (range 12–31 years, n = 9). The majority (71%) of participants were born small for gestational age and 32% of participants were born before 37 weeks gestation. The most common extra‐pancreatic features were umbilical hernia (22%, n = 6/27), macroglossia (56%, n = 15/27), and speech pathologies (36%, n = 10/28). No significant differences in clinical characteristics were identified across the three genetic etiologies (pUPD6, paternal duplication, maternal hypomethylation). Conclusions: Clinical characteristics were not different across underlying genetic mechanism groups, suggesting that genetic testing is required to definitively determine the mechanism and diagnosis of 6q24‐TNDM. Clarification of the specific underlying mechanism is strongly encouraged to clarify recurrence risk, but whether these subcategories may have other clinically relevant differences remains to be elucidated. Early assessment for speech therapy should be considered for this patient population. We recommend that patients in remission be equipped to check blood glucose levels as needed, such as during illness, and should continue seeing a diabetes provider at least occasionally, especially around the time of puberty and thereafter. [ABSTRACT FROM AUTHOR]

Natural selection in the cave habitat has resulted in unique phenotypic traits (including pigmentation loss and ocular degeneration) in the Mexican tetra Astyanax mexicanus, considered a model species for evolutionary research. A. mexicanus has a karyotype of 2n = 50 chromosomes, and long-read sequencing and quantitative trait linkage maps (QTLs) have completely reconstructed the reference genome at the chromosomal level. In the current work, we performed whole chromosome isolation by microdissection and total amplification using DOP-PCR and Whole Chromosome Painting (WCP), followed by sequencing on the Illumina NextSeq platform, to investigate the microstructure of the large and conserved metacentric chromosome 1 of A. mexicanus. The sequences aligned to linkage block 3 of the reference genome, as determined by processing the reads with the DOPseq pipeline and characterizing the satellites with the TAREAN program. In addition, part of the sequences was anchored in linkage blocks that have not yet been assigned to the chromosomes. Furthermore, fluorescence in situ hybridization using WCP 1 carried out in other nearby species revealed a high degree of chromosome conservation, which allows us to hypothesize a common origin of this element. The physical mapping of the repetitive marker sequences provided a micro- and macrostructural overview and confirmed their position in chromosome pair 1. These sequences can serve as comparative tools for understanding the evolution and organization of this chromosome in other species of the family in future studies. [ABSTRACT FROM AUTHOR]

Every cell must solve the problem of how to fold its genome. We describe how the folded state of chromosomes is the result of the combined activity of multiple conserved mechanisms. Homotypic affinity-driven interactions lead to spatial partitioning of active and inactive loci. Molecular motors fold chromosomes through loop extrusion. Topological features such as supercoiling and entanglements contribute to chromosome folding and its dynamics, and tethering loci to sub-nuclear structures adds additional constraints. Dramatically diverse chromosome conformations observed throughout the cell cycle and across the tree of life can be explained through differential regulation and implementation of these basic mechanisms. We propose that the first functions of chromosome folding are to mediate genome replication, compaction, and segregation and that mechanisms of folding have subsequently been co-opted for other roles, including long-range gene regulation, in different conditions, cell types, and species. All cells must fold their chromosomes. The combined action of a small set of conserved molecular and biophysical mechanisms fold chromosomes in a variety of ways across the cell cycle and tree of life. We are increasingly understanding more about how chromosome structure relates to genome functions. [ABSTRACT FROM AUTHOR]

Simple Summary: ASPM is a gene involved in cell division, and recent research shows that it plays an important role in breast cancer (BC). This study looked at large datasets of BC patients to see how ASPM is linked to tumor growth and patient outcomes. We found that patients with higher levels of ASPM had more aggressive forms of cancer and poorer chances of survival. This suggests that ASPM may be useful as a marker to predict how aggressive the BC is and how well it will respond to treatment. These findings could guide future research and potentially lead to new treatments targeting ASPM in cancer. Background: Assembly factor for spindle microtubules (ASPM) has gained significant attention in cancer research due to its association with tumor growth and progression. Through the analysis of large-scale genomic datasets, ASPM has been identified as the top upregulated gene in breast cancer (BC), characterized by high proliferation. This multicohort study aimed to investigate the clinicopathological and prognostic significance of ASPM mRNA and protein expression in BC. Methods: ASPM mRNA expression was assessed using the Cancer Genome Atlas (TCGA) BC cohort and has been further validated in the Molecular Taxonomy of BC International Consortium (METABRIC) (n = 1980), The Uppsala cohort (n = 249), in addition to the combined multicentric cohort (n = 7252). ASPM protein expression was evaluated in a large BC cohort (n = 1300) using immunohistochemistry. The correlations between ASPM expression, clinicopathological parameters, molecular subtypes and outcome were assessed. The response to taxane treatment was compared to the clinical prognosis of ASPM using the ROC plotter. Results: High ASPM mRNA and protein expression were significantly associated with aggressive BC features and poor survival across all cohorts. The association with poor outcomes was maintained in the adjuvant chemotherapy and radio-therapy-treated patients. Responders to taxane treatment showed significantly elevated ASPM levels compared to non-responders. Conclusions: High ASPM expression predicts poor prognosis in BC. It may play a role in treatment resistance within a specific subgroup of patients. Further clinical trials are warranted to explore the potential of ASPM as a target for therapeutic interventions in cancer. [ABSTRACT FROM AUTHOR]

Chicory (Cichorium intybus L., 2n = 18), belonging to the Asteraceae family, exhibits significant edible, medicinal, and pasture values. Moderate research has been performed on identifying Chicory species' chromosomes using fluorescence in situ hybridization (FISH) and C-banding. Detailed karyotype comparisons with chromosome nomenclature have not yet been performed for Chicory and similar species. In this study, the tandem repeats (TRs) were predicted and mapped to chromosomal regions based on released C. intybus L. ASM2352571 genome assembly v1, and then compared to the genome of Lettuce (Lactuca sativa L.). Nine new oligo probes were then developed and employed for karyotypic investigation of endive, Lettuce, and Chicory mitotic metaphase using non-denaturing FISH (ND-FISH). By combining the conserved oligo probes for 5S rDNA and 18S rDNA with the unique ND-FISH signals of new TR-oligo probes, we can develop a high-resolution standard karyotype for the cultivars of Lettuce and Chicory. The occurrence of chromosome structure variations from the natural population of Chicory and Lettuce was also revealed by ND-FISH with multiple oligo probes. The current observation of the karyotype differences and divergences of Lactuca and Cichorium and the genomic research offers crucial information about the Asteraceae family's genetic diversity, chromosomal dynamics, and evolutionary routes. [ABSTRACT FROM AUTHOR]

Background: As the inflorescence of wheat, spike architecture largely determines grain productivity. Dissecting the genetic basis for the spike morphology of wheat can contribute to the designation of ideal spike morphology to improve grain production. Results: The present study characterizes a dense spike1 (ds1) mutant, derived from Nongda3753, induced by EMS treatment, which exhibits a dense spike and reduced plant height. Through bulked segregant analysis sequencing (BSA-Seq) of two segregating populations, ds1 was mapped to the short arm of chromosome 7B. Further genotypic and phenotypic analyses of the residual heterozygous lines from F3 to F6 of Yong3002×ds1 revealed that there was a 0-135 Mb deletion in chromosome 7B associated with the dense spike phenotype. The reads count analysis of the two bulks in BSA-Seq, along with the cytological analysis of ds1, ND3753, NIL-ds1 and NIL-Y3002, confirmed that the partial unidirectional translocation of 5AL (543–713 Mb) to 7BS (0-135 Mb) exists in ds1. This translocation led to an increase in both copy number and expression of the Q gene, which is one of the reasons for the dense spike phenotype observed in ds1. Conclusion: Partial unidirectional translocation from 5AL to 7BS was identified in the EMS-induced mutant ds1, which exhibits dense spike phenotype. This research illustrates the effect of one chromosome structure variation on wheat spike morphology, and provides new materials with several chromosome structure variations for future wheat breeding. [ABSTRACT FROM AUTHOR]

Although multiplexed DNA fluorescence in situ hybridization (FISH) enables tracking the spatial localization of thousands of genomic loci using probes within individual cells, the high rates of undetected probes impede the depiction of 3D chromosome structures. Current data imputation methods neither utilize single‐cell Hi‐C data, which elucidate 3D genome architectures using sequencing nor leverage multimodal RNA FISH data that reflect cell‐type information, limiting the effectiveness of these methods in complex tissues such as the mouse brain. To this end, a novel multiplexed DNA FISH imputation method named ImputeHiFI is proposed, which fully utilizes the complementary structural information from single‐cell Hi‐C data and the cell type signature from RNA FISH data to obtain a high‐fidelity and complete spatial location of chromatin loci. ImputeHiFI enhances cell clustering, compartment identification, and cell subtype detection at the single‐cell level in the mouse brain. ImputeHiFI improves the recognition of cell‐type‐specific loops in three high‐resolution datasets. In short, ImputeHiFI is a powerful tool capable of imputing multiplexed DNA FISH data from various resolutions and imaging protocols, facilitating studies of 3D genome structures and functions. [ABSTRACT FROM AUTHOR]

The sugarcane aphid, Melanaphis sacchari , is an agricultural pest that causes damage to plants in the Poaceae (the grasses) family, such as sorghum and sugarcane. In this study, we used nanopore long reads and a high-throughput chromosome conformation capture chromatin interaction maps to generate a chromosome-level assembly with a total length of 356.1 Mb, of which 85.5% (304.6 Mb) is contained within the 3 autosomes and the X chromosome. Repetitive sequences accounted for 16.29% of the chromosomes, and a total of 12,530 protein-coding genes were annotated, achieving 95.8% Benchmarking Universal Single-Copy Ortholog gene completeness. This offered a substantial improvement compared with previous low-quality genomic resources. A phylogenomic analysis by comparing M. sacchari with 24 published aphid genomes representing 3 aphid tribes revealed that M. sacchari belonged to the tribe Aphidini and maintained a conserved chromosome structure with other Aphidini species. The high-quality genomic resources reported in this study are useful for understanding the evolution of aphid genomes and studying pest management of M. sacchari. [ABSTRACT FROM AUTHOR]

The three‐dimensional architecture of the bacterial chromosome is intertwined with genome processes such as transcription and replication. Conspicuously so, that the structure of the chromosome permits accurate prediction of active genome processes. Although appreciation of this interplay has developed rapidly in the past two decades, our understanding of this subject is still in its infancy, with research primarily focusing on how the process of transcription regulates and is regulated by chromosome structure. Here, we summarize the latest developments in the field with a focus on the interplay between chromosome structure and transcription in Escherichia coli (E. coli) as mediated by H‐NS—a model nucleoid structuring protein. We describe how the organization of chromosomes at the global and local scales is dependent on transcription, and how transcription is regulated by chromosome structure. Finally, we take note of studies that highlight our limited knowledge of structure‐function relationships in the chromosome, and we point out research tracks that will improve our insight in the topic. [ABSTRACT FROM AUTHOR]

Flavopiridol (FP) is a plant-derived flavonoidis and used to treat cancers, fungal infections and inflammation-related diseases. However, it is not clear whether it has side effects on the female reproductive system. In this study, we aimed to investigate the toxic effects and potential underlying mechanisms of FP on oocyte maturation and cumulus cell expansion in mice. Cumulus-oocyte complexes (COCs) were cultured in vitro with FP of gradient concentration (50–1000 nM), according to the plasma concentration of FP in the clinical trial. The maturation rate and cumulus expansion index of oocytes were counted and studied by immunofluorescence staining, qRT-PCR, oocyte chromosome preparation and so on. The results showed that the FP-exposed COCs inhibited the oocyte maturation and cumulus cell expansion, leading to cell apoptosis in a dose dependent way. Oocytes exposed to 500 nM FP showed abnormalities in the spindle structure and chromosome arrangement, ultimately leading to the oocyte maturation arrest and aneuploidy. This may be due to the excessive oxidative stress caused by mitochondrial membrane potential damage and mislocalization. Therefore, when FP is used for cancer treatment, its side effects on the female reproductive system should be seriously considered. • Flavopiridol exposure leads to a decrease in the maturation rate of mouse oocytes. • Flavopiridol causes oxidative stress and mitochondrial dysfunction. • Flavopiridol causes abnormal spindle structure and chromosome arrangement. [ABSTRACT FROM AUTHOR]

Genetic linkage maps are valuable resources for investigating chromosomal structure, quantifying karyotype, estimating recombination rates, and improving preexisting genome assemblies. Comparative linkage mapping, in turn, broadens our understanding of the phylogenetic history of these genomic features. Through an assessment of synteny (the conservation of gene order on homologous chromosomes in different species) and variation in recombination rate, we can begin to understand how genomic features change during the evolution of distinct species. Here, we construct high-density genetic linkage maps for 3 Vespidae wasp species from the Vespula genus: Vespula consobrina, Vespula pensylvanica, and Vespula vidua to investigate shared genomic architecture between these 3 yellowjacket wasp species. We show that these species exhibit high levels of collinearity, often in chromosome-length blocks of synteny, with some evidence for small interchromosomal rearrangements. We also identify 2 "inversions" in all 3 species that are likely artifacts from the genome assembly process. In addition, we map genome-wide recombination rates and reveal the recombination landscape to be highly variable on intrachromosomal, interchromosomal, and interspecific scales. Genome-wide recombination rates are high for all three Vespula species, (V. pensylvanica: 22.7 cM/Mb, V. consobrina: 24.3 cM/Mb, and V. vidua: 24.7 cM/Mb), which is consistent with findings of high recombination rates for other eusocial species. Our high-quality linkage maps will be resources for ongoing evolutionary genetics studies interested in the genome evolution of social wasps. [ABSTRACT FROM AUTHOR]

Eleocharis vivipara, an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C3 photosynthesis underwater and C4 photosynthesis on land. However, the absence of genomic data has hindered its utility for evolutionary and genetic research. Here, we present a high‐quality genome for E. vivipara, representing the first chromosome‐level genome for the Eleocharis genus, with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes. Its Hi–C pattern, chromosome clustering results, and one‐to‐one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n = 4x = 20. Phylogenetic analysis suggests that E. vivipara diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), and underwent a whole‐genome duplication (WGD) about 3.5 Mya. Numerous fusion and fission events were identified between the chromosomes of E. vivipara and its close relatives. We demonstrate that E. vivipara has holocentromeres, a chromosomal feature which can maintain the stability of such chromosomal rearrangements. Experimental transplantation and cross‐section studies showed its terrestrial culms developed C4 Kranz anatomy with increased number of chloroplasts in the bundle sheath (BS) cells. Gene expression and weighted gene co‐expression network analysis (WGCNA) showed overall elevated expression of core genes associated with the C4 pathway, and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency. We found evidence of mixed nicotinamide adenine dinucleotide ‐ malic enzyme and phosphoenolpyruvate carboxykinase type C4 photosynthesis in E. vivipara, and hypothesize that the evolution of C4 photosynthesis predates the WGD event. The mixed type is dominated by subgenome A and supplemented by subgenome B. Collectively, our findings not only shed light on the evolution of E. vivipara and karyotype within the Cyperaceae family, but also provide valuable insights into the transition between C3 and C4 photosynthesis, offering promising avenues for crop improvement and breeding. [ABSTRACT FROM AUTHOR]

Chromosome structural variations (SVs), such as deletion, duplication, inversion, and translocation, are important contributors to genetic diversification and crop improvement. Using genome editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated nuclease (Cas9), desired SVs involving large DNA fragments have been created in rice (Oryza sativa L.), maize (Zea mays L.), and Arabidopsis (Arabidopsis thaliana L.). However, it is still uncertain whether the size of DNA fragment involved could be a prohibiting factor to generate Cas9‐mediated SVs. In this study, we constructed five CRISPR/Cas9 vectors, each expressing two single‐guide RNAs (sgRNAs), to cut two sites spacing at 0.5, 5, 10, 20, and 30 Mb on rice chromosome 4 (Chr4), respectively. Meanwhile, another CRISPR/Cas9 vector cutting two sites, one on Chr4 and the other on Chr1, was also constructed for creation of chromosomal translocation between Chr1 and Chr4. These vectors were transfected into rice protoplasts by polyethylene glycol–mediated transformation. Specific primers were designed to detect desired SV events. The results showed that all designed SVs could be effectively generated by CRISPR/Cas9 in rice protoplasts. This study suggested that the size of DNA fragment involved is unlikely a prohibiting factor for creation of desired SV events. Core Ideas: Deletion, duplication, and inversion events were generated in rice protoplasts by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated nuclease 9 (Cas9).Translocation events were generated in rice protoplasts by CRISPR/Cas9.The size of DNA fragment involved is unlikely a limiting factor for creation of desired structural variation events. Plain Language Summary: This study focuses on using CRISPR/Cas9 genome editing tools to create specific structural variations (SVs) in rice chromosomes. SVs are changes in the structure of chromosomes, like deletions, duplications, inversions, and translocations, which can contribute to genetic diversity and crop improvement. This study aimed to determine if the size of the DNA fragment involved in the SV creation using CRISPR/Cas9 is a limiting factor. Cas9 vectors were designed and constructed to target different distances on the same chromosome and even between different chromosomes. When these vectors were transfected into rice protoplasts, the desired SVs were readily detected, suggesting that the size of the DNA fragment involved was not a limiting factor in creating SVs using CRISPR/Cas9. This result has important implications for genetic engineering and crop improvement, as it opens up new possibilities for creating desired genetic changes in crops. [ABSTRACT FROM AUTHOR]

Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide. Life history traits including polyphagy, haplodiploidy, inbreeding polygyny, and symbiosis with fungi contribute to their dispersal and impact. Species vary in their interactions with host trees, with many attacking stressed or recently dead trees, such as the globally distributed Euwallacea similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering our understanding of their invasive capabilities as well as modern control measures, surveillance, and management. Using a combination of long and short read sequencing platforms, we assembled and annotated high quality (BUSCO > 98% complete) pseudo-chromosome-level genomes for these species. Comparative macrosynteny analysis identified an increased number of pseudo-chromosome scaffolds in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and to the management of these invasive pests. [ABSTRACT FROM AUTHOR]

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens' genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage an innovative, multi-genome method to construct and annotate the first pangenome graph of an oomycete plant pathogen. We expand on this approach by analysing the graph and creating synteny based single-copy orthogroups for all genes. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, virulence related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens. Author summary: Plant pathogens are known to evolve rapidly and overcome disease resistance of newly introduced crop varieties. This swift adaptation is visible in the genomes of these pathogens, which can be highly variable. Such genomic variation cannot be captured with contemporary comparative genomic methods that rely on a single reference genome or focus solely on protein coding genes. To overcome these limitations and compare multiple genomes in a robust and scalable method, we constructed the first pangenome graph for an oomycete filamentous plant pathogen with six telomere-to-telomere genome assemblies of Peronospora effusa. This high-resolution pangenomic framework enabled detailed comparisons of the genomes at any level, from the nucleotide to the chromosome, and for any subset of protein-coding genes or transposable elements, to discover novel biology and potential mechanisms for the rapid evolution of this devastating pathogen. [ABSTRACT FROM AUTHOR]

Recent studies showed an interphase chromosome architecture—a specific coiled nucleosome structure—derived from cryopreserved EM tomograms, and dispersed throughout the nucleus. The images were computationally processed to fill in the missing wedges of data caused by incomplete tomographic tilts. The resulting structures increased z-resolution enabling an extension of the proposed architecture to that of mitotic chromosomes. Here, we provide additional insights into the chromosome architecture that was recently published [M. Elbaum et al., Proc. Natl. Acad. Sci. U.S.A. 119, e2119101119 (2022)]. We build on the defined chromosomes time-dependent structures in an effort to probe their dynamics. Variants of the coiled chromosome structures, possibly further defining specific regions, are discussed. We propose, based on generalized specific uncoiling of mitotic chromosomes in telophase, large-scale reorganization of interphase chromosomes. Chromosome territories, organized as micron-sized small patches, are constructed, satisfying complex volume considerations. Finally, we unveiled the structures of replicated coiled chromosomes, still attached to centromeres, as part of chromosome architecture. [ABSTRACT FROM AUTHOR]

Background: Spermidine (SPD) is an intermediate compound in the polyamine metabolism which takes critical part in a variety of cellular processes. In particular, it has been reported to exert anti-aging effects, suppress the age-related diseases, and extend lifespan across species. However, whether it has the favorable influence on the quality of postovulatory aged oocytes remains elusive. Methods: Immunostaining and fluorescence intensity measurement were used to evaluate the effects of postovulatory aging and SPD supplementation on the oocyte fragmentation, spindle/chromosome structure, actin polymerization, dynamics of cortical granules (CGs) and ovastacin, mitochondrial distribution and function, as well as autophagy levels. In addition, in vitro sperm binding assay and in vitro fertilization (IVF) experiment were applied to assess the impacts of postovulatory aging and SPD supplementation on the sperm binding ability and fertilization capacity of oocytes. Results: Here, we showed that supplementation of SPD during postovulatory aging could relieve the deterioration of porcine oocytes. Specifically, we found that postovulatory aging impaired the oocyte quality by damaging the morphological integrity of oocytes, maintenance of spindle/chromosome structure, and dynamics of actin cytoskeleton. Postovulatory aging also weakened the sperm binding ability and fertilization capacity of oocytes by compromising the distribution pattern of CGs and their content ovastacin. Notably, supplementation of SPD attenuated these defects in postovulatory aged porcine oocytes via strengthening mitochondrial function, eliminating excessive reactive oxygen species (ROS), inhibiting apoptosis, and enhancing autophagy levels. Conclusion: Altogether, our findings demonstrate that SPD supplementation is a feasible approach to ameliorate the quality of postovulatory aged oocytes, which can be potentially applied to the human assisted reproductive technology (ART) and in vitro production of animal embryos. [ABSTRACT FROM AUTHOR]

Background: Chromosome organization plays an important role in biological processes such as replication, regulation, and transcription. One way to study the relationship between chromosome structure and its biological functions is through Hi-C studies, a genome-wide method for capturing chromosome conformation. Such studies generate vast amounts of data. The problem is exacerbated by the fact that chromosome organization is dynamic, requiring snapshots at different points in time, further increasing the amount of data to be stored. We present a novel approach called the High-Efficiency Contact Matrix Compressor (HiCMC) for efficient compression of Hi-C data. Results: By modeling the underlying structures found in the contact matrix, such as compartments and domains, HiCMC outperforms the state-of-the-art method CMC by approximately 8% and the other state-of-the-art methods cooler, LZMA, and bzip2 by over 50% across multiple cell lines and contact matrix resolutions. In addition, HiCMC integrates domain-specific information into the compressed bitstreams that it generates, and this information can be used to speed up downstream analyses. Conclusion: HiCMC is a novel compression approach that utilizes intrinsic properties of contact matrix, such as compartments and domains. It allows for a better compression in comparison to the state-of-the-art methods. HiCMC is available at https://github.com/sXperfect/hicmc. [ABSTRACT FROM AUTHOR]

The long genomic DNA molecules in eukaryotes are fragile and prone to entanglement, and must be tightly folded to fit into the micrometric dimensions of mitotic chromosomes. Histones transform the monotonous linear structure of double‐helical DNA into a chromatin filament formed by many nucleosomes. A physically consistent model for the packaging of the chromatin filament must be compatible with all the constraints imposed by the structural properties of chromosomes. It has to be compatible with 1) the high concentration of DNA and the elongated cylindrical shape of chromosomes and 2) the known self‐associative properties of chromatin, and also with 3) an effective protection of chromosomal DNA from topological entanglement and mechanical breakage. The multilayer chromosome model, in which a repetitive weak interaction between nucleosomes at the nanoscale produces the stacking of many chromatin layers, is compatible with all these constraints. The self‐organization of the multilayer structure of the whole chromosome is consistent with current knowledge of the self‐assembly of micrometric structures from different repetitive building blocks. The multilayer model justifies the geometry of chromosome bands and translocations, and is compatible with feasible physical mechanisms for the control of gene expression, and for DNA replication, repair, and segregation to daughter cells. [ABSTRACT FROM AUTHOR]