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The three-dimensional (3D) structure of chromosomes is of great significance to ensure that the genome performs various functions (e.g., gene expression) correctly and replicates and separates correctly in mitosis. Since the emergence of Hi-C in 2009, a new experimental technique in molecular biology, researchers have been paying more and more attention to the reconstruction of chromosome 3D structure. To reconstruct the 3D structure of chromosomes based on Hi-C experimental data, many algorithms have been proposed, among which ShRec3D is one of the most outstanding. In this article, an iterative ShRec3D algorithm is presented to greatly improve the native ShRec3D algorithm. Experimental results show that our algorithm can significantly promote the performance of ShRec3D, and this improvement is applicable to almost all data noise range and signal coverage range, so it is universal. [ABSTRACT FROM AUTHOR]

Simple Summary: The experimental/pathological observation of genome chaos (including massive and large-scale translocations, chromothripsis, and polyploidy cancer cells) highlighted the importance of genome reorganization in evolution. Recent advances in sequencing and bioinformatic analysis have highlighted such chromosomal diversity. The evolution of the genome has been studied in the field of macroevolution and speciation as well as in the context of cancer and tumor progression. Evolution is inherent to adaptation to the environment and preparing for future pressure to initiate survival. Human cells are plastic, and several mechanisms are involved in sporadic timing in view of generating genomic diversity under normal conditions, such as during gametogenesis or during pathology like cancer. Interestingly, patterns of chromosomal instability are strikingly similar in evolution and in cancer. Here we will discuss some events leading to several varieties of chromosomal patterns, from cancer to speciation, and discuss the disease associated with chromosomal instability. The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression. [ABSTRACT FROM AUTHOR]

To study the effects of gamma radiation on tea seed germination, morphological changes, and genetic variation by using gamma radiation. Fresh Tea seed material were irradiated with twenty different doses of gamma radiation such as 0, 2, 4, 6, 8, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80 90, 100, 200, 500 and 1000 Gy from Cobalt 60Co source from Regional Nuclear Agriculture Research Center, Bidhan Chandra Krishi Viswavidyalaya (BCKV), West Bengal, in between 2019 and 2020. The growth behavior of tea seedling was recorded under varying levels of gamma radiation and its performance at nursery stages. It was observed seed irradiated with doses from 35 Gy to 100 Gy could germinate but could not survive beyond five (05) months. When treated with higher doses as 200 Gy, 500 Gy and 1000 Gy, no seed germination takes places due to possible damages occur in the DNA structure. Screening of growth characteristics of tea plant generally monitored by the characteristics like plant height, number of leaves, number of primary branches, base diameter, and total leaf area of plants and we found that these characteristics significantly increased with the progress of time and increasing levels of gamma radiation; however, the plant height showed decreasing trend with the increasing levels of gamma radiation, which could be due to the change in chromosomal structure and genetic alteration. After 90 weeks of planting, the plant height, no. of primary branches, the number of leaves, plant base diameter, and total leaf area per plant recorded were 36.42 cm, 1/plant, 7.11/plant, 0.62 c.m, 22.92 cm2/plant respectively under the radiation level 30 Gy, whereas the corresponding figures of the above parameters at the control treatment were 85.32 cm, 1/plant, 18.84/plant, 1.18 c.m and 26.68 cm2/plant, respectively. The total plant height, no. of primary branches, the number of leaves, plant base diameter, and total leaf area per plant were significantly influenced by the rising levels of gamma radiation (up to 100 Gy), finally, after 90 weeks of planting, the maximum no. of branching was observed in the treatment of 8 Gy, 10 Gy and 15 Gy respectively. The study reveals a hitherto open the possibility of using gamma radiation on tea plant for creation of variation in the tea seed planting materials. Further studies on mutation using tea planting materials would give an insight into its mutable gene behavior. [ABSTRACT FROM AUTHOR]

Optimization using genetic algorithms (GA) is a well-known strategy in several scientific disciplines. The crossover is an essential operator of the genetic algorithm. It has been an active area of research to develop sustainable forms for this operand. In this work, a new crossover operand is proposed. This operand depends on giving an elicited description for the chromosome with a new structure for alleles of the parents. It is suggested that each allele has two attitudes, one attitude differs contrastingly with the other, and both of them complement the allele. Thus, in case where one attitude is good, the other should be bad. This is suitable for many systems which contain admired parameters and unadmired parameters. The proposed crossover would improve the desired attitudes and dampen the undesired attitudes. The proposed crossover can be achieved in two stages: The first stage is a mating method for both attitudes in one parent to improving one attitude at the expense of the other. The second stage comes after the first improvement stage for mating between different parents. Hence, two concurrent steps for improvement would be applied. Simulation experiments for the system show improvement in the fitness function. The proposed crossover could be helpful in different fields, especially to optimize routing algorithms and network protocols, an application that has been tested as a case study in this work. [ABSTRACT FROM AUTHOR]

Background: Optical genome mapping (OGM) has developed into a highly promising method for detecting structural variants (SVs) in human genomes. Complex chromosomal rearrangements (CCRs) and cryptic translocations are rare events that are considered difficult to detect by routine cytogenetic methods. In this study, OGM was applied to delineate the precise chromosomal rearrangements in three cases with uncertain or unconfirmed CCRs detected by conventional karyotyping and one case with a cryptic translocation suggested by fetal chromosomal microarray analysis (CMA). Results: In the three cases with CCRs, OGM not only confirmed or revised the original karyotyping results but also refined the precise chromosomal structures. In the case with a suspected translocation not detected by karyotyping, OGM efficiently identified the cryptic translocation and defined the genomic breakpoints with relatively high accuracy. Conclusions: Our study confirmed OGM as a robust alternative approach to karyotyping for the detection of chromosomal structural rearrangements, including CCRs and cryptic translocations. [ABSTRACT FROM AUTHOR]

We tackle here genomic mechanisms of a rapid onset and recovery from anosmia—a potential diagnostic indicator for early-stage COVID-19 infection. Based on previous observations on how olfactory receptor (OR) gene expression is regulated via chromatin structure in mice, we hypothesized that the disruption of the OR gene expression and, respectively, deficiency of the OR function can be caused by chromatin reorganization taking place upon SARS-CoV-2 infection. We obtained chromatin ensemble reconstructions from COVID-19 patients and control samples using our original computational framework for the whole-genome 3D chromatin ensemble reconstruction. Specifically, we used megabase-scale structural units and effective interactions between them obtained in the Markov State modelling of the Hi-C contact network as an unput in the stochastic embedding procedure of the whole-genome 3D chromatin ensemble reconstruction. We have also developed here a new procedure for analyzing fine structural hierarchy with (sub)TAD-size units in local chromatin regions, which we apply here to parts of chromosomes containing OR genes and corresponding regulatory elements. We observed structural modifications in COVID-19 patients on different levels of chromatin organization, from the alteration of whole genome structure and chromosomal intermingling to reorganization of contacts between chromatin loops at the level of topologically associating domains. While complementary data on known regulatory elements point to potential pathology-associated changes within the overall picture of chromatin alterations, further investigation using additional epigenetic factors mapped on 3D reconstructions with improved resolution will be required for better understanding of anosmia caused by SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

Objectives To elucidate the role of a novel carbapenem-hydrolysing class D β-lactamase (RAD-1) from Riemerella anatipestifer. Methods We applied WGS and bioinformatic analysis to screen putative β-lactamase genes in R. anatipestifer SCVM0004. A putative class D β-lactamase gene was cloned into pET24a and transferred into Escherichia coli BL21 (DE3) for antibiotic susceptibility determination and protein purification. Meanwhile, the purified native protein was used to determine the enzymatic activities. Results A class D β-lactamase, RAD-1, was identified in the genome of R. anatipestifer SCVM0004. It was distinct from all characterized class D β-lactamases (≤42% amino acid sequence identity). Searching in GenBank showed that bla RAD-1 was widely disseminated among R. anatipestifer. Genomic environment analysis indicated that the chromosomal structures of bla RAD-1-located regions were relatively conserved. Expression of RAD-1 in E. coli results in elevated MICs for various β-lactam antibiotics, including penicillins, extended-spectrum cephalosporins, a monobactam and carbapenems. Moreover, kinetic analysis of purified RAD-1 revealed: (i) high-level activity against penicillins; (ii) highest affinity for carbapenems; (iii) moderate hydrolysis of extended-spectrum cephalosporins and a monobactam; and (iv) no activity for oxacillin and cefoxitin. Conclusions This study identified a novel chromosomally located class D carbapenemase RAD-1 (Bush–Jacoby functional group 2def) in R. anatipestifer SCVM0004. Moreover, bioinformatic analysis confirmed that the RAD-1 was widely prevalent and conserved in R. anatipestifer. [ABSTRACT FROM AUTHOR]

The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome's dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration. [ABSTRACT FROM AUTHOR]

• ERGamp is a unique driver of myeloid malignancy with a signature genetic profile with loss of 5q, chromothripsis and TP53 loss of function variants. • Chromosome structure with copy number analysis (CNA) and loss of heterozygosity (LOH) should be standard of care to risk stratify myeloid malignancies. ETS-related gene (ERG) amplification, observed in 4–6% of acute myeloid leukemia (AML), is associated with unfavorable prognosis. To determine coincident effects of additional genomic abnormalities in AML with ERG amplification (ERG amp), we examined 11 ERG amp cases of 205 newly diagnosed AML using chromosomal microarray analysis and next generation sequencing. ERG amp cases demonstrated a distinct pattern of high genetic complexity: loss of 5q, chromothripsis and TP53 loss of function variants. Remarkably, allelic TP53 loss or loss of heterozygosity (LOH) co-occurring with TP53 inactivating mutation dramatically effected ERG amp tumor patient outcome. In the presence of homozygous TP53 loss of function, ERG amp patients demonstrated no response to induction chemotherapy with median overall survival (OS) of 3.8 months (N = 9). Two patients with heterozygous loss of TP53 function underwent alloSCT without evidence of relapse at one year. Similarly, a validation TCGA cohort, 6 of the 8 ERG amp cases with TP53 loss of function demonstrated median OS of 2.5 months. This suggests that with TP53 mutant ERG amp AML, successive loss of the second TP53 allele, typically by 17p deletion or LOH identifies a specific high-risk subtype of AML patients who are resistant to standard induction chemotherapy and need novel approaches to avert the very poor prognosis. [ABSTRACT FROM AUTHOR]

Simple Summary: R-loops, also referred to as RNA: DNA hybrids, are tripartite structures formed when a single-stranded RNA molecule forms a complex with a double-stranded DNA duplex via homology-directed base pairing. Many cellular functions are thought to be mediated by R-loops, including gene regulation, DNA replication, chromatin patterning, and DNA repair. R-loops are common and dynamic structures that account for up to 5% of mammalian genomes. In this review, we present an updated review of R-loops at a specific locus, telomeres. We summarize recent advances in the protein factors that regulate the formation and resolution of R-loops at telomeres. We also discuss the role of persistent or unscheduled R-loops in promoting genome and telomere instability and their links to human diseases. Telomeric repeat containing RNA (TERRA) is transcribed from subtelomeric regions to telomeres. TERRA RNA can invade telomeric dsDNA and form telomeric R-loop structures. A growing body of evidence suggests that TERRA-mediated R-loops are critical players in telomere length homeostasis. Here, we will review current knowledge on the regulation of R-loop levels at telomeres. In particular, we will discuss how the central player TERRA and its binding proteins modulate R-loop levels through various mechanisms. We will further provide an overview of the consequences of TERRA-mediated persistent or unscheduled R-loops at telomeres in human ALT cancers and other organisms, with a focus on telomere length regulation after replication interference-induced damage and DNA homologous recombination-mediated repair. [ABSTRACT FROM AUTHOR]

The histone‐like protein HU plays a diverse role in bacterial physiology from the maintenance of chromosome structure to the regulation of gene transcription. HU binds DNA in a sequence‐non‐specific manner via two distinct binding modes: (i) random binding to any DNA through ionic bonds between surface‐exposed lysine residues (K3, K18, and K83) and phosphate backbone (non‐specific); (ii) preferential binding to contorted DNA of given structures containing a pair of kinks (structure‐specific) through conserved proline residues (P63) that induce and/or stabilize the kinks. First, we show here that the P63‐mediated structure‐specific binding also requires the three lysine residues, which are needed for a non‐specific binding. Second, we demonstrate that substituting P63 to alanine in HU had no impact on non‐specific binding but caused differential transcription of diverse genes previously shown to be regulated by HU, such as those associated with the organonitrogen compound biosynthetic process, galactose metabolism, ribosome biogenesis, and cell adhesion. The structure‐specific binding also helps create DNA supercoiling, which, in turn, may influence directly or indirectly the transcription of other genes. Our previous and current studies show that non‐specific and structure‐specific HU binding appear to have separate functions‐ nucleoid architecture and transcription regulation‐ which may be true in other DNA‐binding proteins. [ABSTRACT FROM AUTHOR]

'Niagara Steck' and 'Niagara Variegada' are two grapevine varieties that arose spontaneously as somatic mutants of 'Niagara Rosada'. Berries characterize 'Niagara Steck' at young stages exhibiting a remarkable brown reticulated structure on the epidermis which develops into a brown-bronze russet-like structure as the berries ripe. The mature berries have strongly acidic flesh. 'Niagara Variegada' shows notable variegation in leaves and berries. Meiotic studies were carried out to ascertain if the mutant phenotypes could be related to any change in chromosome number, structure or other irregularity. Floral buds of both varieties at different developmental stages were collected and fixed for cytological analyses. Chromosome counts at diakinesis/metaphase I showed n=19 bivalents for both varieties. Univalent, trivalent, tetravalent chromosomes or chain configuration were not recorded ruling out the possibility of any alteration in the chromosome number or structure in both mutant varieties. However, low percentages of meiotic irregularities were recorded such as chromosome stickiness, laggards, non-oriented chromosomes, precocious chromosome segregation, tetrads with one microcyte, microspore fusion, and tetrad degeneration. The total percentage of abnormalities was higher in 'Niagara Variegada' (19.68%) than in 'Niagara Steck' (14.40%) which may have contributed to a lower percentage of pollen fertility (79.80%) when compared to 'Steck' (90.74%). The aforementioned varieties can be propagated by hardwood cuttings and constitute an interesting option for ornamentation of home backyards, patios, and gardens with the advantage that 'Niagara Variegada' bearing sweet edible berries. [ABSTRACT FROM AUTHOR]

• Chromosome numbers and structures of both sensitive and resistant MCF-7 cells are extremely heterogeneous according to the conventional karyotyping. • Copy numbers of numerous genes were affected by the resistance to doxorubicin in MCF-7 cells. • Altered gene copy numbers were proportional to resistance status. • DNA microarray could be a powerful tool for the evaluation of the cancer drug resistance. Elimination of cytotoxic effect in cells with multidrug resistance (MDR) phenotype is a situation that is gradually acquired over time and develops through multiple pathways resulting in global phenotypic changes of cells. Although molecular background of the resistance phenotype has widely been studied in the gene expression level, segmental and gene copy number variations (CNVs) have limitedly been documented. Thus, in the present study, we aimed to analyze the CNVs using DNA microarray in the sensitive and two doxorubicin-resistant MCF-7 breast cancer cell lines which had different resistance indices. In the present study, we performed conventional karyotyping and array comparative genomic hybridization (aCGH). Then, results of aCGH data were studied with genomic profiling, comparison analysis and ideogram plotting to evaluate genomic profiles, and the loss and gains of heterozygosity profiles. Next, gene lists for each cell line were compared with the 66-breast cancer-related genes and the multidrug resistance-related genes. aCGH analyses showed that CNV profiles and the copy number of specific genes were dramatically different between these three cell lines. Totally, 6212, 6558, and 11,201 genes were found to be altered in MCF-7, MCF-7/400DOX, and MCF-7/1000DOX genomes, respectively. Amongst the MCF-7/1000DOX had the highest number of altered genes, and doxorubicin resistance may cause differential chromosomal changes depending on the resistance status. DNA microarray would be one of the informative methods used in the studies on the cancer drug resistance in addition to transcriptomic and proteomic level high throughput analysis to define molecular mechanisms of the resistance status. [ABSTRACT FROM AUTHOR]

The physical organization and properties of chromatin within the interphase nucleus are intimately linked to a wide range of functional DNA-based processes. In this context, interphase chromatin mechanics — that is, how chromatin, physically, responds to forces — is gaining increasing attention. Recent methodological advances for probing the force–response of chromatin in cellulo open new avenues for research, as well as new questions. This review discusses emerging views from these approaches and others, including recent in vitro single-molecule studies of cohesin and condensin motor activities, providing insights into physical and material aspects of chromatin, its plasticity in the context of functional processes, its nonequilibrium or 'active matter' properties, and the importance of factors such as chromatin fiber tension and stiffness. This growing field offers exciting opportunities to better understand the interplay between interphase chromosome structure, dynamics, mechanics, and functions. [ABSTRACT FROM AUTHOR]

• PICH maintains chromosome stability. • PICH acts as the tension recognizer to facilitate the resolution of UFBs. • PICH facilitates tumorigenesis. Genomic instability is regarded as a hallmark of cancer cells. It can be presented in many ways, among which chromosome instability has received attention. Ultrafine anaphase bridges are a type of chromatin bridges, the untimely resolution of which can also lead to chromosome instability. PICH can play a role in maintaining chromosome stability by regulating chromosome morphology and resolving ultrafine anaphase bridges. Recently, PICH has been found to be overexpressed in various cancers. Overexpression of PICH is related to the proliferation of tumors and poor prognosis. In this article, we consider that PICH can maintain genomic stability by regulating appropriate chromosome structure, ensuring proper chromosome segregation, and facilitating replication fork reversal. We summarize how PICH regulates chromosome stability, how PICH resolves Ultrafine anaphase bridges with other proteins, and how PICH promotes tumor progression. [ABSTRACT FROM AUTHOR]

Cuscuta gronovii Willd., a member of the Convolvulaceae family, is noted for its potential medicinal and nutritional benefits. In this study, we utilized a combination of Illumina and Oxford Nanopore sequencing technologies to successfully assemble the complete circular mitochondrial genome (mitogenome) of C. gronovii. The mitogenome, spanning 304,467 base pairs, includes 54 genes: 33 protein-coding genes, three ribosomal RNA (rRNA) genes, and 18 transfer RNA (tRNA) genes. Beyond its primary circular structure, we discovered and validated several alternative genomic conformations, driven by five specific repeat sequences. Three inverted repeats were found to initiate rearrangements, resulting in the creation of seven distinct chromosomal structures, while two direct repeats split a larger molecule into two subgenomic entities. We also mapped 421 RNA editing sites across the protein-coding sequences, influencing 33 protein-coding genes with varying distribution, particularly noting high frequencies in the nad 4 and ccm B genes. Sixteen of these RNA editing sites were experimentally validated through PCR amplification and Sanger sequencing, confirming their presence with 100 % accuracy. This research not only introduces the first mitochondrial genome of C. gronovii but also highlights its complex conformational variability induced by repeat-mediated recombination, providing a valuable genomic resource for further molecular breeding efforts and phylogenetic evolution within the genus Cuscuta. • Cuscuta gronovii has the largest plant mitochondrial genome currently available. • The mitochondrial genome of Cuscuta gronovii has 6 circular chromosomes and 1 linear chromosome. • Cuscuta gronovii has a close genetic relationship with Cuscuta campestris but its collinearity is very low. [ABSTRACT FROM AUTHOR]

Abstract Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie biological processes such as chromosomal segregation and the regulation of gene expression. We present a new tool called Genome Decomposition Analysis (GDA) that characterises genome architectures and acts as an accessible approach for discovering hidden features of a genome assembly. With the imminent deluge of high-quality genome assemblies from projects such as the Darwin Tree of Life and the Earth BioGenome Project, GDA has been designed to facilitate their exploration and the discovery of novel genome biology. We highlight the effectiveness of our approach in characterising the genome architectures of single-celled eukaryotic parasites from the phylum Apicomplexa and show that it scales well to large genomes.

Aimee Jaramillo-Lambert, an Assistant Professor at the University of Delaware, was awarded the Society for Developmental Biology 2023 Elizabeth D. Hay New Investigator Award for her research in developmental biology. In an interview, she discusses her interest in science, her career path, and her research on sexual reproduction in Caenorhabditis elegans. She also highlights the importance of mentorship and her work in diversity, equity, and inclusion. Her research focuses on studying chromosome structure during meiosis and the proteins provided by sperm during fertilization and egg activation. Jaramillo-Lambert emphasizes the use of biophysics in the field and the challenges of transitioning to a group leader role. She also discusses the importance of mentorship in academia and her involvement in diversity initiatives. [Extracted from the article]

Simple Summary: Oligometastatic disease is a condition in oncology where cancer affects only a few distant sites. It is associated with a low-burden spread and a more favorable prognosis compared to polymetastatic disease. Recent studies have identified specific molecular and genetic features that underlie the oligometastatic phenotype, including reduced cancer cell migration and invasion ability, and an enhanced immune response in the metastatic microenvironment. Understanding these characteristics could suggest innovative personalized therapies and contribute to improving the understanding of complex cancer–host relationships. This scoping review highlights new clinical, biological, and methodological challenges that characterize this fascinating field from a modern and innovative perspective. By shedding light on the unique features of oligometastatic disease, we aim to promote the development of more effective and tailored treatments for patients with this condition. Some cancer patients display a less aggressive form of metastatic disease, characterized by a low tumor burden and involving a smaller number of sites, which is referred to as "oligometastatic disease" (OMD). This review discusses new biomarkers, as well as methodological challenges and perspectives characterizing OMD. Recent studies have revealed that specific microRNA profiles, chromosome patterns, driver gene mutations (ERBB2, PBRM1, SETD2, KRAS, PIK3CA, SMAD4), polymorphisms (TCF7L2), and levels of immune cell infiltration into metastases, depending on the tumor type, are associated with an oligometastatic behavior. This suggests that OMD could be a distinct disease with specific biological and molecular characteristics. Therefore, the heterogeneity of initial tumor burden and inclusion of OMD patients in clinical trials pose a crucial methodological question that requires responses in the near future. Additionally, a solid understanding of the molecular and biological features of OMD will be necessary to support and complete the clinical staging systems, enabling a better distinction of metastatic behavior and tailored treatments. [ABSTRACT FROM AUTHOR]

Meiotic recombination not only maintains the stability of the chromosome structure but also creates genetic variations for adapting to changeable environments. A better understanding of the mechanism of crossover (CO) patterns at the population level is useful for crop improvement. However, there are limited cost-effective and universal methods to detect the recombination frequency at the population level in Brassica napus. Here, the Brassica 60K Illumina Infinium SNP array (Brassica 60K array) was used to systematically study the recombination landscape in a double haploid (DH) population of B. napus. It was found that COs were unevenly distributed across the whole genome, and a higher frequency of COs existed at the distal ends of each chromosome. A considerable number of genes (more than 30%) in the CO hot regions were associated with plant defense and regulation. In most tissues, the average gene expression level in the hot regions (CO frequency of greater than 2 cM/Mb) was significantly higher than that in the regions with a CO frequency of less than 1 cM/Mb. In addition, a bin map was constructed with 1995 recombination bins. For seed oil content, Bin 1131 to 1134, Bin 1308 to 1311, Bin 1864 to 1869, and Bin 2184 to 2230 were identified on chromosomes A08, A09, C03, and C06, respectively, which could explain 8.5%, 17.3%, 8.6%, and 3.9% of the phenotypic variation. These results could not only deepen our understanding of meiotic recombination in B. napus at the population level, and provide useful information for rapeseed breeding in the future, but also provided a reference for studying CO frequency in other species. [ABSTRACT FROM AUTHOR]

Three Ogataea minuta var. minuta strains have been deposited as NBRC 0975, NBRC 10402, and NBRC 10746 in the National Institute of Technology and Evaluation (NITE) Biological Resource Center (NBRC) collection. We investigated the ability to produce secretory proteins and several genotypic and phenotypic characteristics in order to select the best strain for heterologous protein expression. NBRC 10746 showed the best performance as evaluated by Cypridina noctiluca luciferase expression. Subsequently, clone #5–30 named tat06213, which was obtained by single-colony isolation from NBRC 10746, was established as a promising host for heterologous protein expression. To deepen our understanding of the characteristics of O. minuta var. minuta strains, sequence analysis of the D1/D2 domain of large subunit rRNA was conducted and the resulting phylogenetic tree derived from the D1/D2 domain showed that NBRC 10402 and NBRC 10746 were grouped into a different cluster far from NBRC 0975. Furthermore, a chromosome structure topology with electrophoretic karyotype and AOX1 loci analyzed by pulsed-field gel electrophoresis with Southern blotting showed different chromosome patterns and AOX1 -hybridization loci among the strains. Additionally, the sequences of the promoter regions of the cloned AOX1 genes were not identical among the three strains. These findings might explain the differences in heterologous protein expression among the tested O. minuta var. minuta strains. [ABSTRACT FROM AUTHOR]

Telomeres are nucleoprotein structures at eukaryotic chromosome termini. Their stability is preserved by a six-protein complex named shelterin. Among these, TRF1 binds telomere duplex and assists DNA replication with mechanisms only partly clarified. Here we found that poly (ADP-ribose) polymerase 1 (PARP1) interacts and covalently PARylates TRF1 in S-phase modifying its DNA affinity. Therefore, genetic and pharmacological inhibition of PARP1 impairs the dynamic association of TRF1 and the bromodeoxyuridine incorporation at replicating telomeres. Inhibition of PARP1 also affects the recruitment of WRN and BLM helicases in TRF1 containing complexes during S-phase, triggering replication-dependent DNA-damage and telomere fragility. This work unveils an unprecedented role for PARP1 as a "surveillant" of telomere replication, which orchestrates protein dynamics at proceeding replication fork. The poly (ADP-ribose) polymerase (PARP1) interacts with the telomere factor TRF1 and loss of PARP1 results in telomere fragility and impairment of helicases -TRF1 complex assembly. [ABSTRACT FROM AUTHOR]

Telomeres are structures made of DNA, proteins and RNA found at the ends of eukaryotic linear chromosomes. These dynamic nucleoprotein structures protect chromosomal tips from end-to-end fusions, degradation, activation of damage checkpoints and erroneous DNA repair events. Telomeres were thought to be transcriptionally silent regions because of their constitutive heterochromatin signature until telomeric long non-coding RNAs (LncRNAs) were discovered. One of them, TERRA (TElomeric Repeat-containing RNA), starts in the subtelomeric regions towards the chromosome ends from different telomeres and has been extensively studied in many evolutionarily distant eukaryotes. Changes in TERRA's expression can lead to telomeric dysfunction, interfere with the replicative machinery and impact telomere length. TERRA also co-localizes in vivo with telomerase, and can form RNA:DNA hybrid structures called R-loops, which have been implicated in the onset of senescence and the alternative lengthening of telomere (ALT) pathway. Yet, the molecular mechanisms involving TERRA, as well as its function, remain elusive. Here, we review the current knowledge of TERRA transcription, structure, expression, regulation and its multiple telomeric and extra-telomeric functions in the budding yeast Saccharomyces cerevisiae. [ABSTRACT FROM AUTHOR]

Chromosomal instability (CIN) has become a topic of great interest in recent years, not only for its implications in cancer diagnosis and prognosis but also for its role as an enabling feature and central hallmark of cancer. CIN describes cell-to-cell variation in the number or structure of chromosomes in a tumor population. Although extensive research in recent decades has identified some associations between CIN with response to therapy, specific associations with other hallmarks of cancer have not been fully evidenced. Such associations place CIN as an enabling feature of the other hallmarks of cancer and highlight the importance of deepening its knowledge to improve the outcome in cancer. In addition, studies conducted to date have shown paradoxical findings about the implications of CIN for therapeutic response, with some studies showing associations between high CIN and better therapeutic response, and others showing the opposite: associations between high CIN and therapeutic resistance. This evidences the complex relationships between CIN with the prognosis and response to treatment in cancer. Considering the above, this review focuses on recent studies on the role of CIN in cancer, the cellular mechanisms leading to CIN, its relationship with other hallmarks of cancer, and the emerging therapeutic approaches that are being developed to target such instability, with a primary focus on breast cancer. Further understanding of the complexity of CIN and its association with other hallmarks of cancer could provide a better understanding of the cellular and molecular mechanisms involved in prognosis and response to treatment in cancer and potentially lead to new drug targets. [ABSTRACT FROM AUTHOR]

Decreased oocyte quality and compromised embryo development are particularly prevalent in older females, but the aging-related cellular processes and effective ameliorative approaches have not been fully characterized. Intermittent fasting (IF) can help improve health and extend lifespan; nevertheless, how it regulates reproductive aging and its mechanisms remain unclear. We used naturally aged mice to investigate the role of IF in reproduction and found that just one month of every-other-day fasting was sufficient to improve oocyte quality. IF not only increased antral follicle numbers and ovulation but also enhanced oocyte meiotic competence and embryonic development by improving both nuclear and cytoplasmic maturation in maternally aged oocytes. The beneficial effects of IF manifested as alleviation of spindle structure abnormalities and chromosome segregation errors and maintenance of the correct cytoplasmic organelle reorganization. Moreover, single-cell transcriptome analysis showed that the positive impact of IF on aged oocytes was mediated by restoration of the nicotinamide adenine dinucleotide (NAD+)/Sirt1-mediated antioxidant defense system, which eliminated excessive accumulated ROS to suppress DNA damage and apoptosis. Collectively, these findings suggest that IF is a feasible approach to protect oocytes against advanced maternal age-related oxidation damage and to improve the reproductive outcomes of aged females. [Display omitted] • Female reproductive aging is associated with oocytes oxidative stress. • Intermittent fasting promotes both nuclear and cytoplasmic maturation in maternal aged oocytes. • Intermittent fasting reverses the declining quality of maternally aged oocytes. • Intermittent fasting alleviates the ROS-induced oxidative stress and DNA damage. • Intermittent fasting improving the endogenous cellular antioxidant defenses. [ABSTRACT FROM AUTHOR]

Multiprocessor systems with parallel computing play an important role in data processing. Considering the optimal use of existing computing systems, scheduling on parallel systems has gained great significance. Usually, a sequential program to run on parallel systems is modeled by a task graph. Because scheduling of task graphs onto processors is considered the most crucial NP-complete problem, many attempts have been made to find the most approximate optimal scheduling using genetic algorithms. Its chromosomal representation largely influences the performance of the genetic algorithm. The chromosomal structure used in the existing genetic algorithms does not entirely scan the solution space. As a result, these algorithms fail to produce an appropriate schedule frequently. To overcome this constraint, the present study proposed a new method for constructing chromosomal representation. The proposed approach was divided into three phases: ranking, clustering, and cluster scheduling, where a genetic algorithm schedules clusters. To optimize the proposed genetic algorithm's performance, it was equipped with four heuristic principles: load balancing, reuse of idle time, task duplication, and critical path. Finally, by comparing the obtained results for 6 task graphs in 3 types, the amount of optimization was equal to the results of previous best algorithm, but in the other 3 types, the amount of optimization was a value between 4.25 and 6.88%. [ABSTRACT FROM AUTHOR]

The "genomic shock" hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession "Bhyb26." We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species' similarity in transposable element load may account for the subtlety of the observed genome dominance. [ABSTRACT FROM AUTHOR]

Summary: Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter‐specific, and inter‐ploidy admixture of its genome and lack of in depth genome‐wide inheritance and comparative structural studies.Here we describe a new high‐quality, phased, chromosome‐scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high‐density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species.Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr‐6 and one of chr‐10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter‐crossable wild diploid species.These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this crop. [ABSTRACT FROM AUTHOR]

Constitutive-heterochromatin placement in the genome affects chromosome structure by occupying centromeric areas and forming large blocks. To investigate the basis for heterochromatin variation in the genome, we chose a group of species with a conserved euchromatin part: the genus Martes [stone marten (M. foina, 2n = 38), sable (M. zibellina, 2n = 38), pine marten (M. martes, 2n = 38), and yellow-throated marten (M. flavigula, 2n = 40)]. We mined the stone marten genome for the most abundant tandem repeats and selected the top 11 macrosatellite repetitive sequences. Fluorescent in situ hybridization revealed distributions of the tandemly repeated sequences (macrosatellites, telomeric repeats, and ribosomal DNA). We next characterized the AT/GC content of constitutive heterochromatin by CDAG (Chromomycin A3-DAPI-after G-banding). The euchromatin conservatism was shown by comparative chromosome painting with stone marten probes in newly built maps of the sable and pine marten. Thus, for the four Martes species, we mapped three different types of tandemly repeated sequences critical for chromosome structure. Most macrosatellites are shared by the four species with individual patterns of amplification. Some macrosatellites are specific to a species, autosomes, or the X chromosome. The variation of core macrosatellites and their prevalence in a genome are responsible for the species-specific variation of the heterochromatic blocks. [ABSTRACT FROM AUTHOR]

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We use data-driven physical simulations to study the three-dimensional architecture of the Aedes aegypti genome. Hi-C maps exhibit both a broad diagonal and compartmentalization with telomeres and centromeres clustering together. Physical modeling reveals that these observations correspond to an ensemble of 3D chromosomal structures that are folded over and partially condensed. Clustering of the centromeres and telomeres near the nuclear lamina appears to be a necessary condition for the formation of the observed structures. Further analysis of the mechanical properties of the genome reveals that the chromosomes of Aedes aegypti, by virtue of their atypical structural organization, are highly sensitive to the deformation of the nuclei. This last finding provides a possible physical mechanism linking mechanical cues to gene regulation. Within the nucleus, the genome of eukaryotes folds into partially organized three-dimensional structures specific to each organism. Here the authors perform physical simulations to study the genome architecture of Aedes aegypti, which reveal an ensemble of 3D chromosomal structures that are folded over and partially condensed, resembling liquid crystalline properties. [ABSTRACT FROM AUTHOR]

Simple Summary: Human DNA is ~2 m long, but is efficiently packaged in cell nucleus that is a million times smaller. The concerted action of several enzymes enables this packaging through hierarchical folding of DNA. These enzymes deposit unique marks on the DNA and DNA-binding proteins collectively called the histone code. The histone code determines when and how a segment of DNA will open and be expressed. Pathogenic changes or mutations in the proteins produced by the cells alter this expression pattern. Here, we discuss how these mutations affect DNA packaging in cancer establishment, diversification, and therapeutic resistance. We also document available therapeutic approaches aimed at DNA packaging in cancer and the direction in which current research is heading. A hallmark of cancers is uncontrolled cell proliferation, frequently associated with an underlying imbalance in gene expression. This transcriptional dysregulation observed in cancers is multifaceted and involves chromosomal rearrangements, chimeric transcription factors, or altered epigenetic marks. Traditionally, chromatin dysregulation in cancers has been considered a downstream effect of driver mutations. However, here we present a broader perspective on the alteration of chromatin organization in the establishment, diversification, and therapeutic resistance of cancers. We hypothesize that the chromatin organization controls the accessibility of the transcriptional machinery to regulate gene expression in cancerous cells and preserves the structural integrity of the nucleus by regulating nuclear volume. Disruption of this large-scale chromatin in proliferating cancerous cells in conventional chemotherapies induces DNA damage and provides a positive feedback loop for chromatin rearrangements and tumor diversification. Consequently, the surviving cells from these chemotherapies become tolerant to higher doses of the therapeutic reagents, which are significantly toxic to normal cells. Furthermore, the disorganization of chromatin induced by these therapies accentuates nuclear fragility, thereby increasing the invasive potential of these tumors. Therefore, we believe that understanding the changes in chromatin organization in cancerous cells is expected to deliver more effective pharmacological interventions with minimal effects on non-cancerous cells. [ABSTRACT FROM AUTHOR]

Background: Gossypium barbadense L. Pima cotton is known for its resistance to Fusarium wilt and for producing fibers of superior quality highly prized in the textile market. We report a high-quality genome assembly and annotation of Pima-S6 cotton and its comparison at the chromosome and protein level to other ten Gossypium published genome assemblies. Results: Synteny and orthogroup analyses revealed important differences on chromosome structure and annotated proteins content between our Pima-S6 and other publicly available G. barbadense assemblies, and across Gossypium assemblies in general. Detailed synteny analyses revealed chromosomal rearrangements between Pima-S6 and other Pima genomes on several chromosomes, with three major inversions in chromosomes A09, A13 and D05, raising questions about the true chromosome structure of Gossypium barbadense genomes. Conclusion: Analyses of the re-assembled and re-annotated genome of the close relative G. barbadense Pima 3–79 using our Pima-S6 assembly suggest that contig placement of some recent G. barbadense assemblies might have been unduly influenced by the use of the G. hirsutum TM-1 genome as the anchoring reference. The Pima-S6 reference genome provides a valuable genomic resource and offers new insights on genomic structure, and can serve as G. barbadense genome reference for future assemblies and further support FOV4-related studies and breeding efforts. [ABSTRACT FROM AUTHOR]

Molecular cytogenetic and cytogenomic studies have made a contribution to genetics of epilepsy. However, current genomic research of this devastative condition is generally focused on the molecular genetic aspects (i.e. gene hunting, detecting mutations in known epilepsy-associated genes, searching monogenic causes of epilepsy). Nonetheless, chromosomal abnormalities and copy number variants (CNVs) represent an important part of genetic defects causing epilepsy. Moreover, somatic chromosomal mosaicism and genome/chromosome instability seem to be a possible mechanism for a wide spectrum of epileptic conditions. This idea becomes even more attracting taking into account the potential of molecular neurocytogenetic (neurocytogenomic) studies of the epileptic brain. Unfortunately, analyses of chromosome numbers and structure in the affected brain or epileptogenic brain foci are rarely performed. Therefore, one may conclude that cytogenomic area of genomic epileptology is poorly researched. Accordingly, molecular cytogenetic and cytogenomic studies of the clinical cohorts and molecular neurocytogenetic analyses of the epileptic brain appear to be required. Here, we have performed a theoretical analysis to define the targets of the aforementioned studies and to highlight future directions for molecular cytogenetic and cytogenomic research of epileptic disorders in the widest sense. To succeed, we have formed a consortium, which is planned to perform at least a part of suggested research. Taking into account the nature of the communication, "cytogenomic epileptology" has been introduced to cover the research efforts in this field of medical genomics and epileptology. Additionally, initial results of studying cytogenomic variations in the Russian neurodevelopmental cohort are reviewed with special attention to epilepsy. In total, we have concluded that (i) epilepsy-associated cytogenomic variations require more profound research; (ii) ontological analyses of epilepsy genes affected by chromosomal rearrangements and/or CNVs with unraveling pathways implicating epilepsy-associated genes are beneficial for epileptology; (iii) molecular neurocytogenetic (neurocytogenomic) analysis of postoperative samples are warranted in patients suffering from epileptic disorders. [ABSTRACT FROM AUTHOR]

Cytogenetics of five species of Murdannia (Commelinaceae) from North-eastern Thailand were conducted. The result revealed that the diploid chromosome number (2n) and karyotype formula were as follow: M. edulis (Stokes) Faden; 2n = 20 (12 m + 4sm + 4st), M. loriformis (Hassk.) R.S.Rao & Kammathy; 2n = 18 (4 m + 10sm + 4st), M. madica (Lour.) D.Y.Hong; 2n = 22 (8 m + 8sm + 6st), M. nudiflora (L.) Brenan; 2n = 22 (14 m + 6sm + 2st) and M. spectabilis (Kurz) Faden; 2n = 20 (8 m + 8sm + 4st). The fundamental numbers (NF) of all species were 40, 36, 44, 44 and 40, respectively. The diploid chromosome numbers from root tips of M. edulis, M. madica and M. spectabilis were studied for the first time. Moreover, four species, M. edulis, M. madica, M. nudiflora and M. spectabilis had new reported of their NF, karyotype formula and total chromosome length. Furthermore, the karyotype structure and total chromosome length of the four species in this study differed from previous studies. The cytogenetic characterization including chromosome number, NF and karyotype of five Murdannia species in this study can be used for classification. [ABSTRACT FROM AUTHOR]

Variation in chromosome structure is a central source of DNA damage and DNA damage response, together representinga major hallmark of chromosomal instability. Cancer cells under selective pressure of therapy use DNA damage and DNA damage response to produce newfunctional assets as an evolutionary mechanism. Recent efforts to understand DNA damage/chromosomal instability and elucidate its role in initiation or progression of cancer have also disclosed its vulnerabilities represented by inappropriate DNA damage response, chromatin changes, andinflammation. Understanding these vulnerabilities can provide important clues for predicting treatment response and for the development of novel strategies that prevent the emergence of therapy resistant tumors. [ABSTRACT FROM AUTHOR]

Lipopolysaccharide (LPS), a significant virulence factor of gram-negative bacteria, adversely affects female reproduction, especially the maturation and early embryonic development of oocytes, through inducing of inflammatory and oxidative stress-associated toxic responses. Resveratrol (Res), a potent antioxidant, exhibits many beneficial effects on the maturation and developmental competence of oocytes. However, it is unclear whether Res can restore LPS-induced defects in the maturation of oocytes during meiosis. In this study, we used porcine oocytes to explore the protective effects of Res and its underlying mechanism against the toxic impacts of LPS exposure on meiotic maturation and developmental competence of oocytes during meiosis. The oocytes were randomly assigned to a control, LPS-exposed or Res-supplemented group. Nuclear and cytoplasmic maturation was assessed after 26 h (MI) or 44 h (MII) of in vitro maturation (IVM). Our results showed that 10 µM Res significantly improved the rates of oocyte maturation and blastocyst formation after exposure to 15 µg/mL LPS. In addition, Res preserved the normal spindle/chromosome structure and maintained acetylated tubulin levels, actin polymerization and cortical granules (CGs) distribution. Additionally, Res protected mitochondrial content and function, scavenges reactive oxygen species (ROS), and reduced DNA damage and apoptosis in LPS-exposed oocytes. Furthermore, inhibition of SIRT1 by its specific inhibitor EX527 suppressed the recovery of ROS levels, mitochondrial content, and spindle/chromosome structure by Res supplementation. In summary, this study shows that Res can alleviate the impacts of LPS-induced toxicity on meiosis in porcine oocytes by upregulating SIRT1, which ameliorates oxidative stress and increasing mitochondrial content. • Resveratrol protects against the porcine oocyte meiotic defects induced by lipopolysaccharide. • Resveratrol scavenges the ROS levels, maintains mitochondrial content and function in LPS-induced porcine oocytes. • Resveratrol scavenges the accumulated ROS and increases mitochondrial content through SIRT1 upregulation. [ABSTRACT FROM AUTHOR]

Simple Summary: The wide-ranging Eurasian species Zootoca vivipara (Lichtenstein, 1823), of the family Lacertidae (Reptilia), is a rare species within the family, possessing multiple sex chromosomes (male Z1Z2Z1Z2/Z1Z2W female). In addition, the intense reorganization of this W sex chromosome is accompanied by active subspeciation and the formation of 4–5 cryptic taxa. In the females of two cryptic forms having a similar system of multiple sex chromosomes (Z1Z2W) but with different morphology, the cytogenetic and specific genomic structures of the W sex chromosome's early oogenesis and meiosis have standard occurrence. Despite the ambiguous behavior of the three presumed sex chromosomes at the early stages of meiotic prophase I, variability in their number of bivalents and chromosomes and significant disturbances in chromosome segregation have not been discovered. Because in Z. vivipara the W sex chromosome, unlike all the other chromosomes, does not have several identified SINE-Zv and TE elements, we may assume that the specific genomic structure of this chromosome may be one of the factors ensuring meiotic stability in the cryptic taxa of the species with the multiple sex chromosomes. The question of female meiotic drive in the meiosis of the cryptic forms of the Z. vivipara complex is still obscure. This brief review is focused on the viviparous lizard Zootoca vivipara (Lichtenstein, 1823), of the family Lacertidae, which possesses female heterogamety and multiple sex chromosomes (male 2n = 36, Z1Z1Z2Z2/Z1Z2W, female 2n = 35, with variable W sex chromosome). Multiple sex chromosomes and their changes may influence meiosis and the female meiotic drive, and they may play a role in reproductive isolation. In two cryptic taxa of Z. vivipara with different W sex chromosomes, meiosis during early spermatogenesis and oogenesis proceeds normally, without any disturbances, with the formation of haploid spermatocytes, and in female meiosis with the formation of synaptonemal complexes (SCs) and the lampbrush chromosomes. In females, the SC number was constantly equal to 19 (according to the SC length, 16 SC autosomal bivalents plus three presumed SC sex chromosome elements). No variability in the chromosomes at the early stages of meiotic prophase I, and no significant disturbances in the chromosome segregation at the anaphase–telophase I stage, have been discovered, and haploid oocytes (n = 17) at the metaphase II stage have been revealed. There should be a factor/factors that maintain the multiple sex chromosomes, their equal transmission, and the course of meiosis in these cryptic forms of Z. vivipara. [ABSTRACT FROM AUTHOR]

The common bean (Phaseolus vulgaris L.), whose annual production is 26 million tons worldwide, is one of the main sources of protein and is known as one of the most important food sources. In this study, the karyotype variations and the genome size of four common bean genotypes in Turkey were investigated to determine whether the geographic variables in these regions affected the genome size and the karyotype parameters. In addition, it is known that as that the cytological and chromosomal parameters change under the influence of the climatic conditions of each region, appropriate and stable cytological methods for each plant facilitate and enable the determination of the chromosomal structure and the identification of specific chromosomes in the genotypes of the relevant region. Correct and valuable information such as this enables breeders and researchers to determine the correct shape and actual size of chromosomes. The genome size of the genotypes was measured with a flow cytometer, and chromosome analyses were performed with the squash method. For each genotype, the karyotype parameters, such as the number of somatic chromosomes, the Mean Total Chromosome Length (MTCL), the Mean Centromere Index (MCI), and the Mean Arm Ratio (MAR), were measured. The results showed that the highest and the lowest amounts of DNA per nucleus (3.28 pg and 1.49 pg) were observed in the Bitlis and Elaziğ genotypes. In addition, all genotype chromosome numbers were counted to be 2n = 2x = 22. The Mean Total Chromosome Length varied from 15.65 µm in Elaziğ to 34.24 µm in the Bitlis genotype. The Mean Chromosome Length ranged between 1.42 µm and 3.11 µm in the Elaziğ and Bitlis genotypes. The Hakkari and Van genotypes consist of eleven metacentric chromosomes, while the Bitlis and Elaziğ genotypes consist of ten metacentric chromosomes and one sub-metacentric chromosome. However, the Mean Centromere Index and Arm Ratio differed considerably among the genotypes. The highest (46.88) and the lowest (43.18) values of the Mean Centromere Index were observed in the Hakkari and Elaziğ genotypes, respectively. On the other hand, the lowest (1.15) and the highest (1.36) values of the Mean Arm Ratio were obtained in the Bitlis and Elaziğ genotypes, respectively. Eventually, intraspecies variations in genome size and chromosomal parameters were observed, and it was determined that the changes in nuclear DNA content and different chromosomal parameters among the four Phaseolus genotypes from four different regions of Turkey indicate the effect of climate change in the regions on these parameters. Such information in these areas can be used as useful information for the improvement of this plant and breeding programs. [ABSTRACT FROM AUTHOR]

The quality of post-ovulatory oocytes deteriorates over time, impacting the outcome of early embryonic development during human ART. We and other groups have found that NAD+, a prominent redox cofactor and enzyme substrate, decreases in both aging ovaries and oocytes. In this study, we found that the NAD+ levels decreased in the post-ovulatory mouse oocytes during in vitro culture and this decrease was partly prevented by NR supplementation. NR treatmenty restored MII oocyte quality and enhanced the early embryonic development potential of post-ovulatory oocytes via alleviating mitochondrial dysfunction and maintaining normal spindle/chromosome structure. Also, treatment with NR decreased ROS levels and reduced DNA damage and apoptosis in post-ovulatory oocytes. Taken together, our findings indicated that NR supplementation increases the oocyte quality and early embryonic development potential in post-ovulatory oocytes which could potentially increase the success rate of ART. [ABSTRACT FROM AUTHOR]

With the gradual increase of commercial banks and the expansion of their branches, the demand for cash transportation inflates sharply, bringing opportunities to the business development of Cash-In-Transit (CIT) sectors. However, the branches are often distributed in densely populated areas where traffic jams occur from time to time, which poses a severe challenge to the route planning of CIT vehicles. In addition, risk factors need to be considered during the optimization process because the goods transported belong to valuables. In order to effectively deal with the routing problem of CIT sectors, this paper established a bi-objective model and a goal programming model of Risk-Constrained Multi Depot Vehicle Routing Problems (RCMDVRPs) using real-time traffic data. Based on the traditional genetic algorithm, a Hybrid Genetic Algorithm with Intensification procedures (HGAI) is proposed to solve the goal programming model by using a three-level linked list structure to express chromosomes visually. Then, a new Self-constrained Hybrid Genetic Algorithm (SHGA) is designed for the bi-objective model. Besides, an online path updating strategy is developed to guide remote vehicles against time-dependent traffic flows. Finally, the HGAI is performed on benchmark instances to verify its accuracy. Experimental results of performance test show that the algorithm can achieve a gap of about 3% compared with the Best Known Result (BKR). The results of a case study also show that the two models and the corresponding algorithms are feasible and can be used to solve large-scale problems according to the special preferences and goals of decision-makers. [ABSTRACT FROM AUTHOR]

X chromosome inactivation (XCI) equalizes X-linked gene expression between sexes. B cells exhibit dynamic XCI, with Xist RNA/heterochromatic marks absent on the inactive X (Xi) in naive B cells but returning following mitogenic stimulation. The impact of dynamic XCI on Xi structure and maintenance was previously unknown. Here, we find dosage compensation of the Xi with state-specific XCI escape genes in naive and in vitro-activated B cells. Allele-specific OligoPaints indicate similar Xi and active X (Xa) territories in B cells that are less compact than in fibroblasts. Allele-specific Hi-C reveals a lack of TAD-like structures on the Xi of naive B cells and stimulation-induced alterations in TAD-like boundary strength independent of gene expression. Notably, Xist deletion in B cells changes TAD boundaries and large-scale Xi compaction. Altogether, our results uncover B cell-specific Xi plasticity, which could underlie sex-biased biological mechanisms., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2025 The Author(s). Published by Elsevier Inc. All rights reserved.)

Proper segregation of homologous chromosomes during meiosis requires crossovers that are tightly regulated by the chromosome structure. PDHA2 is the testis-specific paralog of PDHA1, a core subunit of pyruvate dehydrogenase. However, its role during spermatogenesis is unclear. We show that PDHA2 knockout results in male infertility in mice, but meiotic DSBs in spermatocytes occur normally and are efficiently repaired. Detailed analysis reveals that mid/late recombination intermediates are moderately reduced, resulting in fewer crossovers and many chromosomes without a crossover. Furthermore, defective chromosome structure is observed, including aberrant histone modifications, defective chromosome ends, precocious release of REC8 from chromosomes and fragmented chromosome axes after pachytene. These defects contribute to the failure of pyruvate conversion to acetyl-CoA, resulting in decreased acetyl-CoA and precursors for metabolites and energy in the absence of PDHA2. These findings reveal the important functions of PDHA2 in ensuring proper crossover formation and in modulating chromosome structure during spermatogenesis., (© 2025 The Author(s). Cell Proliferation published by Beijing Institute for Stem Cell and Regenerative Medicine and John Wiley & Sons Ltd.)

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., Competing Interests: Declarations. Ethical approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: F.A. is shareholder of EarlyDiagnostics. The other authors declare that they have no competing interests., (© 2025. The Author(s).)

Hi-C is a powerful method for obtaining genome-wide chromosomal structural information. The typical Hi-C analysis utilizes a two-dimensional (2D) contact matrix, which poses challenges for quantitative comparisons, visualizations, and integrations across multiple datasets. Here, we present a protocol for extracting one-dimensional (1D) features from chromosome structure data by HiC1Dmetrics. Leveraging these 1D features enables integrated analysis of Hi-C and epigenomic data., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Tamias sibiricus is regarded as one predominant scatter-hoarder that stores their food items both in small scattered caches and underground larder-hoards. This unique behavior, though providing essential seed dispersal services for many plant species worldwide, relies highly on accurate spatial memory and acute sense of olfaction. Here, we assembled a chromosome-scale genome of T. sibiricus using Illumina sequencing, PacBio sequencing and chromosome structure capture technique. The genome was 2.64 Gb in size with scaffold N50 length of 172.61 Mb. A total of 2.59 Gb genome data was anchored and orientated onto 19 chromosomes (ranging from 28.70 to 222.90 Mb) with a mounting rate of up to 98.03%. Meanwhile, 25,311 protein-coding genes were predicted with an average gene length of 32,936 bp, and 94.73% of these genes were functionally annotated. This reference genome will be a valuable resource for in-depth studies on basic biological possess and environmental adaptation of the Siberian chipmunk, as well as promoting comparative genomic analyses with other species within Rodentia. [ABSTRACT FROM AUTHOR]

BACKGROUND: Telomeres form special structures at the end of chromosomes in human cells, which have special functions and show a very close relationship with biological aging. Exercise can improve the activity of telomerases and protect the structure of telomeres, thus affecting human health. Shorter telomeres increase the incidence of diseases and decrease the survival rate. Therefore, telomeres are often considered as biological markers of cell aging and the “biological clock” that triggers aging. OBJECTIVE: Based on the relationship between telomeres and aging, to summarize and analyze the effect of exercise on telomeres and telomerases and to explore the mechanism of telomerase retardation by exercise, so as to provide theoretical basis and reference for anti-aging and health promotion by exercises. METHODS: We searched for relevant articles in CNKI, PubMed and Web of Science databases using the keywords of “telomeres, telomerase, exercise, senescence” in Chinese and English, and conducted preliminary screening of titles and abstracts according to inclusion criteria. After reading the full text, a total of 89 documents were included for further analysis. RESULTS AND CONCLUSION: Different exercises have different effects on telomeres. Exercise is positively correlated with telomere length, uncorrelated with telomere length, and has inverted U-shaped relationship with telemeter length. Exercise and telomerase activity are age-deviated. Suitable exercises can slow down the speed of telomere shortening, prevent the excessive consumption of telomeres, delay or prevent the occurrence of age-related diseases, and prolong life, but the mechanism has not been fully clarified. [ABSTRACT FROM AUTHOR]

Background: Anopheles cell lines are used in a variety of ways to better understand the major vectors of malaria in sub-Saharan Africa. Despite this, commonly used cell lines are not well characterized, and no tools are available for cell line identification and authentication. Methods: Utilizing whole genome sequencing, genomes of 4a-3A and 4a-3B 'hemocyte-like' cell lines were characterized for insertions and deletions (indels) and SNP variation. Genomic locations of distinguishing sequence variation and species origin of the cell lines were also examined. Unique indels were targeted to develop a PCR-based cell line authentication assay. Mitotic chromosomes were examined to survey the cytogenetic landscape for chromosome structure and copy number in the cell lines. Results: The 4a-3A and 4a-3B cell lines are female in origin and primarily of Anopheles coluzzii ancestry. Cytogenetic analysis indicates that the two cell lines are essentially diploid, with some relatively minor chromosome structural rearrangements. Whole-genome sequence was generated, and analysis indicated that SNPs and indels which differentiate the cell lines are clustered on the 2R chromosome in the regions of the 2Rb, 2Rc and 2Ru chromosomal inversions. A PCR-based authentication assay was developed to fingerprint three indels unique to each cell line. The assay distinguishes between 4a-3A and 4a-3B cells and also uniquely identifies two additional An. coluzzii cell lines tested, Ag55 and Sua4.0. The assay has the specificity to distinguish four cell lines and also has the sensitivity to detect cellular contamination within a sample of cultured cells. Conclusions: Genomic characterization of the 4a-3A and 4a-3B Anopheles cell lines was used to develop a simple diagnostic assay that can distinguish these cell lines within and across research laboratories. A cytogenetic survey indicated that the 4a-3A and Sua4.0 cell lines carry essentially normal diploid chromosomes, which makes them amenable to CRISPR/Cas9 genome editing. The presented simple authentication assay, coupled with screening for mycoplasma, will allow validation of the integrity of experimental resources and will promote greater experimental reproducibility of results. [ABSTRACT FROM AUTHOR]

Background: Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal structural unit. During evolution, these are conserved based on checking synteny block cross species. Are there common TAD patterns across species or cell lines? Results: To address the above question, we propose a novel task—TAD recognition—as opposed to traditional TAD identification. Specifically, we treat Hi-C maps as images, thus re-casting TAD recognition as image pattern recognition, for which we use a convolutional neural network and a residual neural network. In addition, we propose an elegant way to generate non-TAD data for binary classification. We demonstrate deep learning performance which is quite promising, AUC > 0.80, through cross-species and cell-type validation. Conclusions: TADs have been shown to be conserved during evolution. Interestingly, our results confirm that the TAD recognition model is practical across species, which indicates that TADs between human and mouse show common patterns from an image classification point of view. Our approach could be a new way to identify TAD variations or patterns among Hi-C maps. For example, TADs of two Hi-C maps are conserved if the two classification models are exchangeable. [ABSTRACT FROM AUTHOR]

Plant evolution has been a complex process involving hybridization and polyploidization making understanding the origin and evolution of a plant's genome challenging even once a published genome is available. The oilseed crop, Camelina sativa (Brassicaceae), has a fully sequenced allohexaploid genome with 3 unknown ancestors. To better understand which extant species best represent the ancestral genomes that contributed to C. sativa's formation, we sequenced and assembled chromosome level draft genomes for 4 diploid members of Camelina: C. neglecta C. hispida var. hispida, C. hispida var. grandiflora, and C. laxa using long and short read data scaffolded with proximity data. We then conducted phylogenetic analyses on regions of synteny and on genes described for Arabidopsis thaliana, fromacross each nuclear genome and the chloroplasts to examine evolutionary relationships within Camelina and Camelineae. We conclude that C. neglecta is closely related to C. sativa's sub-genome 1 and that C. hispida var. hispida and C. hispida var. grandiflora are most closely related to C. sativa's sub-genome 3. Further, the abundance and density of transposable elements, specifically Helitrons, suggest that the progenitor genome that contributed C. sativa's sub-genome 3 maybe more similar to the genome of C. hispida var. hispida than that of C. hispida var. grandiflora. These diploid genomes show few structural differences when compared to C. sativa's genome indicating little change to chromosome structure following allopolyploidization. This work also indicates that C. neglecta and C. hispida are important resources for understanding the genetics of C. sativa and potential resources for crop improvement. [ABSTRACT FROM AUTHOR]