Search

Crossover recombination is a hallmark of meiosis that holds the paternal and maternal chromosomes (homologs) together for their faithful segregation, while promoting genetic diversity of the progeny. The pattern of crossover is mainly controlled by the architecture of the meiotic chromosomes. Environmental factors, especially temperature, also play an important role in modulating crossovers. However, it is unclear how temperature affects crossovers. Here, we examined the distribution of budding yeast axis components (Red1, Hop1, and Rec8) and the crossover-associated Zip3 foci in detail at different temperatures, and found that both increased and decreased temperatures result in shorter meiotic chromosome axes and more crossovers. Further investigations showed that temperature changes coordinately enhanced the hyperabundant accumulation of Hop1 and Red1 on chromosomes and the number of Zip3 foci. Most importantly, temperature-induced changes in the distribution of axis proteins and Zip3 foci depend on changes in DNA negative supercoils. These results suggest that yeast meiosis senses temperature changes by increasing the level of negative supercoils to increase crossovers and modulate chromosome organization. These findings provide a new perspective on understanding the effect and mechanism of temperature on meiotic recombination and chromosome organization, with important implications for evolution and breeding. [ABSTRACT FROM AUTHOR]

In eukaryotes, maintenance of heterochromatin structure that represses gene expression during cell proliferation is essential for guaranteeing cell identity. However, how heterochromatin is maintained and transmitted to the daughter cells remains elusive. In this study, we constructed a reporter system to study the maintenance of heterochromatin in the subtelomeric region of the fission yeast, Schizosaccharomyces pombe. We demonstrated that once subtelomeric heterochromatin was established, it tended to be maintained as a metastable structure through cell proliferation. Using this system, we screened an S. pombe genome‐wide gene deletion library for subtelomeric heterochromatin maintenance factors and identified 57 genes related to various cellular processes, in addition to well‐characterized heterochromatin factors. We focused on Mrc1Claspin, a mediator of DNA replication checkpoint. We found that Mrc1 maintains heterochromatin structure not only at the subtelomeres but also at the pericentromeres and mating‐type regions. Furthermore, we showed that Mrc1 is required for the localization of Snf2/Hdac‐containing Repressor Complex (SHREC) and the maintenance of hypoacetylation state of histone H3K14. This study complements the recent discoveries that Mrc1 functions as a histone H3‐H4 chaperone in heterochromatin maintenance. [ABSTRACT FROM AUTHOR]

Background: The high-value aryl tetralin lignan (+)-pinoresinol is the main precursor of many plant lignans including (-)-podophyllotoxin, which is used for the synthesis of chemotherapeutics. As (-)-podophyllotoxin is traditionally isolated from endangered and therefore limited natural sources, there is a particular need for biotechnological production. Recently, we developed a reconstituted biosynthetic pathway from (+)-pinoresinol to (-)-deoxypodophyllotoxin, the direct precursor of (-)-podophyllotoxin, in the recombinant host Escherichia coli. However, the use of the expensive substrate (+)-pinoresinol limits its application from the economic viewpoint. In addition, the simultaneous expression of multiple heterologous genes from different plasmids for a multi-enzyme cascade can be challenging and limits large-scale use. Results: In this study, recombinant plasmid-free E. coli strains for the multi-step synthesis of pinoresinol from ferulic acid were constructed. To this end, a simple and versatile plasmid toolbox for CRISPR/Cas9-assisted chromosomal integration has been developed, which allows the easy transfer of genes from the pET vector series into the E. coli chromosome. Two versions of the developed toolbox enable the efficient integration of either one or two genes into intergenic high expression loci in both E. coli K-12 and B strains. After evaluation of this toolbox using the fluorescent reporter mCherry, genes from Petroselinum crispum and Zea mays for the synthesis of the monolignol coniferyl alcohol were integrated into different E. coli strains. The product titers achieved with plasmid-free E. coli W3110(T7) were comparable to those of the plasmid-based expression system. For the subsequent oxidative coupling of coniferyl alcohol to pinoresinol, a laccase from Corynebacterium glutamicum was selected. Testing of different culture media as well as optimization of gene copy number and copper availability for laccase activity resulted in the synthesis of 100 mg/L pinoresinol using growing E. coli cells. Conclusions: For efficient and simple transfer of genes from pET vectors into the E. coli chromosome, an easy-to-handle molecular toolbox was developed and successfully tested on several E. coli strains. By combining heterologous and endogenous enzymes of the host, a plasmid-free recombinant E. coli growing cell system has been established that enables the synthesis of the key lignan pinoresinol. [ABSTRACT FROM AUTHOR]

ABSTRACT Spiders are a hyperdiverse taxon and among the most abundant predators in nearly all terrestrial habitats. Their success is often attributed to key developments in their evolution such as silk and venom production and major apomorphies such as a whole‐genome duplication. Resolving deep relationships within the spider tree of life has been historically challenging, making it difficult to measure the relative importance of these novelties for spider evolution. Whole‐genome data offer an essential resource in these efforts, but also for functional genomic studies. Here, we present de novo assemblies for three spider species: Ryuthela nishihirai (Liphistiidae), a representative of the ancient Mesothelae, the suborder that is sister to all other extant spiders; Uloborus plumipes (Uloboridae), a cribellate orbweaver whose phylogenetic placement is especially challenging; and Cheiracanthium punctorium (Cheiracanthiidae), which represents only the second family to be sequenced in the hyperdiverse Dionycha clade. These genomes fill critical gaps in the spider tree of life. Using these novel genomes along with 25 previously published ones, we examine the evolutionary history of spidroin gene and structural hox cluster diversity. Our assemblies provide critical genomic resources to facilitate deeper investigations into spider evolution. The near chromosome‐level genome of the ‘living fossil’ R. nishihirai represents an especially important step forward, offering new insights into the origins of spider traits. [ABSTRACT FROM AUTHOR]

The article considers the distribution and mechanisms of the meiotic drive as a phenomenon manifested in unequal transmission of gene alleles and/or homologous chromosomes into gametes during meiosis. The meiotic drive has been studied in the most detail in Drosophila, mice, corn, and ascomycete fungi of the genera Neurospora and Podospora. The consequence of the meiotic drive is a shift in the frequencies of alleles in the gene pool and the maintenance of nonadaptive traits in the population. [ABSTRACT FROM AUTHOR]

Objective: Characterization of the multidrug resistance (MDR) region in P. aeruginosa strain PA59 revealed the presence of antibiotic resistance genes, including blaIMP-45 and blaVIM-2, within a complex genetic landscape of mobile genetic elements. Methods: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) strains were isolated from Shanghai Changhai Hospital. Polymerase chain reaction (PCR) was used to detect the β-lactamase genes in the isolated strains. Strains carrying two or more genes were subjected to whole-genome sequencing (WGS) and in-depth bioinformatics analysis. Results: A total of 94 CRPA strains were isolated, among which PA59 was determined to carry blaIMP-45 and blaVIM-2 genes. Compared with single-gene positive or other blaIMP and blaVIM dual-gene positive strains reported, PA59 exhibited a broader range of drug resistance. We discovered a multidrug resistant (MDR)–related region composed of various mobile elements in the PA59 chromosome. This region carried many resistance genes, including the target genes blaIMP-45 and blaVIM-2. By further comparing the mobile elements GI13 and Ph08, we speculated that this integron structure carrying blaIMP-45 and blaVIM-2 was initially integrated into the genomic island or prophage, forming a more complex genetic structure, and then further integrated into the PA59 chromosome through plasmids. Phylogenetic tree analysis showed limited sequence similarity between PA59 and other CRPA strains. Conclusions: This study identified PA59 as the first reported P. aeruginosa strain carrying both blaIMP-45 and blaVIM-2 on the chromosome. The assembly and annotation of the PA59 genome provide valuable insights into the genomic diversity and gene content of this clinically important pathogen, aiding the development of effective strategies against antibiotic resistance. [ABSTRACT FROM AUTHOR]

Mammalian oocytes undergo a long‐term meiotic arrest that can last for almost the entire reproductive lifespan. This arrest occurs after DNA replication and is prolonged with age, which poses a challenge to oocytes in maintaining replication‐dependent chromosomal proteins required for the completion of meiosis. In this study, we show that chromosomal histones are reduced with age in mouse oocytes. Both types of histone H3 variants, replication‐dependent H3.1/H3.2 and replication‐independent H3.3, decrease with age. Aging‐associated histone reduction is associated with transcriptomic features that are caused by genetic depletion of histone H3.3. Neither the genetic reduction of chromosomal H3.1/H3.2 nor H3.3 accelerates the aging‐associated increase in premature chromosome separation that causes meiotic segregation errors. We suggest that aging‐associated reduction of chromosomal histones is linked to several transcriptomic abnormalities but does not significantly contribute to errors in meiotic chromosome segregation during the reproductive lifespan of mice. [ABSTRACT FROM AUTHOR]

Proteus mirabilis, a gram‐negative bacterium, poses a significant public health threat due to its multidrug‐resistant (MDR) characteristics. Here, for the first time, we report the isolation and comprehensive genome analysis of an MDR strain, P. mirabilis KUST‐1312, obtained from migratory birds in Yunnan Province, China. A total of 65 samples, including migratory bird feces, soil, and water from Dianchi Lake, were collected. Standard microbiological techniques were employed to isolate the P. mirabilis KUST‐1312 strain from these samples. Genomic sequencing was conducted using a hybrid assembly strategy, combining Illumina and Oxford nanopore sequencing technologies. Phenotypic testing revealed the MDR nature of P. mirabilis KUST‐1312, displaying resistance to various antibiotics except gentamicin and Cefotaxime. Notably, 15 antimicrobial resistance genes (ARGs), including aph(3′)‐Ia, cat, tet(J), bleO, dfrA12, aadA2, AAC(3)‐IId, bla-TEM-1B, erm(42),aph(6)‐Id, blaPER-1, sul2, aph(3′')‐Ib(2copies), and aph(3′)‐VIb, were identified on a single chromosome. These 15 ARGs were dispersed along three MDR regions, and the boundaries of these regions were consistently flanked by copies of insertion sequences and also contained other genetic elements. Phylogenetic analysis revealed the close relation of P. mirabilis KUST‐1312 with environmental and clinical isolates reported from other continents rather than with Asian isolates. In conclusion, this study reports the first‐ever isolation of an MDR P. mirabilis KUST‐1312 strain from migratory birds globally, particularly in China. There is a need to explore further its prevalence in detail in various ecological niches, including migratory birds. [ABSTRACT FROM AUTHOR]

The proper control of mitosis depends on the ubiquitin-mediated degradation of the right mitotic regulator at the right time. This is effected by the Anaphase Promoting Complex/Cyclosome (APC/C) ubiquitin ligase that is regulated by the Spindle Assembly Checkpoint (SAC). The SAC prevents the APC/C from recognising Cyclin B1, the essential anaphase and cytokinesis inhibitor, until all chromosomes are attached to the spindle. Once chromosomes are attached, Cyclin B1 is rapidly degraded to enable chromosome segregation and cytokinesis. We have a good understanding of how the SAC inhibits the APC/C, but relatively little is known about how the APC/C recognises Cyclin B1 as soon as the SAC is turned off. Here, by combining live-cell imaging, in vitro reconstitution biochemistry, and structural analysis by cryo-electron microscopy, we provide evidence that the rapid recognition of Cyclin B1 in metaphase requires spatial regulation of the APC/C. Using fluorescence cross-correlation spectroscopy, we find that Cyclin B1 and the APC/C primarily interact at the mitotic apparatus. We show that this is because Cyclin B1, like the APC/C, binds to nucleosomes, and identify an 'arginine-anchor' in the N-terminus as necessary and sufficient for binding to the nucleosome. Mutating the arginine anchor on Cyclin B1 reduces its interaction with the APC/C and delays its degradation: cells with the mutant, non-nucleosome-binding Cyclin B1 become aneuploid, demonstrating the physiological relevance of our findings. Together, our data demonstrate that mitotic chromosomes promote the efficient interaction between Cyclin B1 and the APC/C to ensure the timely degradation of Cyclin B1 and genomic stability. Synopsis: How the anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase initiates Cyclin B1 degradation as soon as the spindle assembly checkpoint is switched off remains mysterious. This work reveals chromosomes as the crucial platform for inactivating the major mitotic kinase Cyclin B1-CDK1. Cyclin B1 binds to nucleosomes through an 'arginine anchor' motif in its amino terminus. APC/C binds to nucleosomes through an arginine anchor in its APC3 subunit. Fluorescence cross-correlation shows that the APC/C primarily binds Cyclin B1 at chromosomes. Preventing Cyclin B1 chromosome binding by arginine anchor mutations interferes with its binding to the APC/C and delays its degradation by several minutes, leading to aneuploidy. Chromosomes are the crucial platform for timely inactivation of CDK1-Cyclin B1, the major kinase that keeps cells in mitosis. [ABSTRACT FROM AUTHOR]

The long arm of the Y chromosome (Yq) contains many amplified and palindromic sequences that are prone to self-reorganization during spermatogenesis, and tiny submicroscopic segmental deletions in the proximal Yq are called Y chromosome microdeletions (YCM). A retrospective study was conducted on male infertility patients of Zhuang ethnicity who presented at Reproductive Medical Center of Nanning between January 2015 and May 2023. Seminal fluid was collected for standard examination. YCM were detected by using a combination of multiplex PCR and agarose gel electrophoresis. Preparation of peripheral blood chromosomes and karyotyping of chromosomes was performed. 147 cases (9.22%) of YCM were detected in 1596 male infertility patients of Zhuang ethnicity. Significant difference was found in the detection rate of YCM between the azoospermia group and the oligospermia group (P < 0.001). Of all types of YCM, the highest detection rate was AZFc (n = 83), followed by AZFb + c (n = 28). 264 cases (16.54%) of sex chromosomal aberrations were detected. The most prevalent karyotype was 47, XXY (n = 202). The detection rate of sex chromosomal aberrations in azoospermia group was higher than that in severe oligospermia group and oligospermia group, and the differences were significant (P < 0.001). 28 cases (1.57%) of autosomal aberrations and 105 cases (6.58%) of chromosomal polymorphism were identified. The current research has some limitations due to the lack of normal men as the control group but suggests that YCM and chromosomal aberrations represent key genetic factors influencing spermatogenesis in infertile males of Zhuang ethnicity in Guangxi. [ABSTRACT FROM AUTHOR]

Summary: Ultraviolet (UV) radiation influences development and genome stability in organisms; however, its impact on meiosis, a special cell division essential for the delivery of genetic information across generations in eukaryotes, has not yet been elucidated.In this study, by performing cytogenetic studies, we reported that UV radiation does not damage meiotic chromosome integrity but attenuates centromere‐mediated chromosome stability and induces unreduced gametes in Arabidopsis thaliana.We showed that functional centromere‐specific histone 3 (CENH3) is required for obligate crossover formation and plays a role in the protection of sister chromatid cohesion under UV stress. Moreover, we found that UV specifically alters the orientation and organization of spindles and phragmoplasts at meiosis II, resulting in meiotic restitution and unreduced gametes. We determined that UV‐induced meiotic restitution does not rely on the UV Resistance Locus8‐mediated UV perception and the Tapetal Development and Function1‐ and Aborted Microspores‐dependent tapetum development, but possibly occurs via altered JASON function and downregulated Parallel Spindle1.This study provides evidence that UV radiation influences meiotic genome stability and gametophytic ploidy consistency in flowering plants. [ABSTRACT FROM AUTHOR]

Quinoa is emerging as a key seed crop for global food security due to its ability to grow in marginal environments and its excellent nutritional properties. Because quinoa is partially allogamous, we have developed quinoa inbred lines necessary for molecular genetic analysis. Our comprehensive genomic analysis showed that the quinoa inbred lines fall into three genetic subpopulations: northern highland, southern highland, and lowland. Lowland and highland quinoa are the same species, but have very different genotypes and phenotypes. Lowland quinoa has relatively small grains and a darker grain color, and is widely tested and grown around the world. In contrast, the white, large-grained highland quinoa is grown in the Andean highlands, including the regionwhere quinoa originated, and is exported worldwide as high-quality quinoa. Recently, we have shown that viral vectors can be used to regulate endogenous genes in quinoa, paving the way for functional genomics to reveal the diversity of quinoa. However, although a high-quality assembly has recently been reported for a lowland quinoa line, genomic resources of the quality required for functional genomics are not available for highland quinoa lines. Here we present high-quality chromosome-level genome assemblies for two highland inbred quinoa lines, J075 representing the northern highland line and J100 representing the southern highland line, using PacBio HiFi sequencing and dpMIG-seq. In addition, we demonstrate the importance of verifying and correcting reference-based scaffold assembly with other approaches such as linkage maps. The assembled genome sizes of J075 and J100 are 1.29 and 1.32 Gb,with contigs N50 of 66.3 and 12.6Mb, andscaffoldN50of 71.2 and70.6Mb, respectively, comprising 18 pseudochromosomes. The repetitive sequences of J075 and J100 represent 72.6% and 71.5% of the genome, the majority of which are long terminal repeats, representing 44.0% and 42.7% of the genome, respectively. The de novo assembled genomes of J075 and J100 were predicted to contain 65,303 and 64,945 protein-coding genes, respectively. The high quality genomes of these highland quinoa lines will facilitate quinoa functional genomics research on quinoa and contribute to the identification of key genes involved in environmental adaptation and quinoa domestication. [ABSTRACT FROM AUTHOR]

Summary: A new species, Cyclamen brulloi, is described and illustrated from Sicily (Italy). This is an Autumn flowering species belonging to Cyclamen subg. Cyclamen and it is currently restricted to some localities of western Sicily, where it grows on carbonatic rocks and in rocky crevices. This taxon shows close relationships both with C. hederifolium and C. africanum. However, several morphological and karyological features are clearly different. Morphology, pollen grain micromorphology, karyology (2n = 4x = 68), ecology, conservation status and taxonomic relationships of the new taxon with the most allied species are presented. [ABSTRACT FROM AUTHOR]

The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here, we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories—high and low rearrangement—largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion, or rapid, all-encompassing changes over short evolutionary timescales. [ABSTRACT FROM AUTHOR]

Objectives: The mechanisms underlying chromosomally encoded colistin resistance in Escherichia coli remain insufficiently investigated. In this study, we investigated the contribution of various pmrB mutations from E. coli clinical isolates to colistin resistance. Methods: The resistance mechanisms in eight mcr-negative colistin-resistant E. coli isolates obtained from a nationwide surveillance program in Taiwan using recombinant DNA techniques and complementary experiments were investigated. The minimal inhibitory concentrations (MICs) of colistin in the recombinant strains were compared with those in the parental strains. The expression levels of pmrA and pmrK (which are part of the pmrCAB and pmrHFIJKLM operons associated with colistin resistance) were measured using reverse transcription-quantitative real-time polymerase chain reaction. Results: In the complementation experiments, various mutated pmrB alleles from the eight mcr-negative colistin-resistant E. coli strains were introduced into an ATCC25922 mutant with a PmrB deletion, which resulted in colistin resistance. The MIC levels of colistin in the most complemented strains were comparable to those of the parental colistin-resistant strains. Increased expression levels of pmrA and pmrK were consistently detected in most complemented strains. The impact for colistin resistance was confirmed for various novel amino acid substitutions, P94L, G19E, L194P, L98R and R27L in PmrB from the parental clinical strains. The detected amino acid substitutions are distributed in the different functional domains of PmrB. Conclusions: Colistin resistance mediated by amino acid substitutions in PmrB is a major chromosomally encoded mechanism in E. coli of clinical origin.

This case report delves into the complexities surrounding Edwards syndrome (Trisomy 18), a chromosomal abnormality stemming from meiotic disjunction. Initially reported in 1960, Edwards syndrome is the second most prevalent autosomal trisomy following Down syndrome, affecting between 1 in 3500 and 1 in 7000 individuals, with a slight male predominance. The majority of cases involve parents under 30 years old. A review of 152 cases demonstrates a myriad of anomalies, including severe intellectual deficits, congenital heart problems and distinct facial features. This report aims to enhance understanding of Edwards syndrome by presenting a comprehensive case study detailing the diagnosis and distinctive clinical features of a newborn with Trisomy 18. This case report helps in understanding the complexity of genetics and clinical manifestations, highlighting the importance of prenatal diagnosis and counseling, multidisciplinary care approaches, parental decision-making, palliative care and the need for further research. The case report underscores the necessity for heightened public awareness and support for affected families. This study contributes to the body of knowledge regarding Trisomy 18, fostering a more compassionate and informed approach to managing this challenging genetic disorder, ultimately aiming to improve the quality of life for those affected by Edwards syndrome.

Chromosomal abnormalities are a common cause of human miscarriage but rarely reported in any other species. As a result, there are currently inadequate animal models available to study this condition. Horses present one potential model since mares receive intense gynecological care. This allowed us to investigate the prevalence of chromosomal copy number aberrations in 256 products of conception (POC) in a naturally occurring model of pregnancy loss (PL). Triploidy (three haploid sets of chromosomes) was the most common aberration, found in 42% of POCs following PL over the embryonic period. Over the same period, trisomies and monosomies were identified in 11.6% of POCs and subchromosomal aberrations in 4.2%. Whole and subchromosomal aberrations involved 17 autosomes, with chromosomes 3, 4, and 20 having the highest number of aberrations. Triploid fetuses had clear gross developmental anomalies of the brain. Collectively, data demonstrate that alterations in chromosome number contribute to PL similarly in women and mares, with triploidy the dominant ploidy type over the key period of organogenesis. These findings, along with highly conserved synteny between human and horse chromosomes, similar gestation lengths, and the shared single greatest risk for PL being advancing maternal age, provide strong evidence for the first animal model to truly recapitulate many key features of human miscarriage arising due to chromosomal aberrations, with shared benefits for humans and equids. [ABSTRACT FROM AUTHOR]

Plasmids incur a fitness cost that has the potential to restrict the dissemination of resistance in bacterial pathogens. However, bacteria can overcome this disadvantage by compensatory evolution to maintain their resistance. Compensatory evolution can occur via both chromosomes and plasmids, but there are a few reviews regarding this topic, and most of them focus on plasmids. In this review, we provide a comprehensive overview of the currently reported mechanisms underlying compensatory evolution on chromosomes and plasmids, elucidate key targets regulating plasmid fitness cost, and discuss future challenges in this field. We found that compensatory evolution on chromosomes primarily arises from mutations in transcriptional regulatory factors, whereas compensatory evolution of plasmids predominantly involves three pathways: plasmid copy number regulation, conjugation transfer efficiency, and expression of antimicrobial resistance (AMR) genes. Furthermore, the importance of reasonable selection of research subjects and effective integration of diverse advanced research methods is also emphasized in our future study on compensatory mechanisms. Overall, this review establishes a theoretical framework that aims to provide innovative ideas for minimizing the emergence and spread of AMR genes. [ABSTRACT FROM AUTHOR]

In this manuscript we reported the results of our studies concerning the response of vibration bands in deoxyribonucleic acid region in neuronal-like cells under exposure to static and 50 Hz electromagnetic fields using Fourier Transform Infrared spectroscopy. This technique was chosen because it is able to detect alteration of vibration bands of chemical compounds even induced by small stress agents. The aim of this study was to investigate the response of chromatin and chromosome to low intensity electromagnetic fields at values similar to manmade electromagnetic fields. The phosphate bands of asymmetric and symmetric stretching mode (representative of deoxyribonucleic acid spectral region) were observed to decrease after 3 h exposure at 1 mT (both static and 50 Hz magnetic field). Prolonging time exposure or increasing the intensity of applied magnetic field induced a low increasing in intensity of these vibration bands. This finding can be explaining assuming that chromatin uncoiling occurred at low intensity of the field and that increasing time exposure or magnetic field intensity caused an increasing of the torque on chromosome inducing an alignment along the direction of the field. [ABSTRACT FROM AUTHOR]

The genus Hedysarum L. (Fabaceae) includes about 200 species of annual and perennial herbs distributed in Asia, Europe, North Africa, and North America. Many species of this genus are valuable medicinal, melliferous, and forage resources. In this review, we consider the taxonomic history of the genus Hedysarum, the chromosomal organization of the species from the sections Hedysarum and Multicaulia, as well as phylogenetic relationships between these sections. According to morphological, genetic, and phylogenetic data, the genus Hedysarum is divided into three main sections: Hedysarum (= syn. Gamotion), Multicaulia, and Stracheya. In species of this genus, two basic chromosome numbers, x = 7 (section Hedysarum) and x = 8 (sections Multicaulia and Stracheya), were determined. The systematic positions of some species within the sections are still uncertain due to their morphological similarities. The patterns of distribution of molecular chromosomal markers (45S rDNA, 5S rDNA, and different satellite DNAs) in karyotypes of various Hedysarum species made it possible to determine their ploidy status and also specify genomic relationships within the sections Hedysarum and Multicaulia. Recent molecular phylogenetic studies clarified significantly the taxonomy and evolutionary development of the genus Hedysarum. [ABSTRACT FROM AUTHOR]

In papillary renal neoplasm with reverse polarity (PRNRP), the status of chromosomal copy number alterations, especially chromosomes 7/17 gain and chromosome Y loss, has remained controversial. In the literatures, there is a discrepancy among the results of chromosomal alteration in PRNRP depending on the analytical methods. Here, we comprehensively analyzed the status of chromosomal abnormalities in PRNRP. Nineteen PRNRP cases were analyzed by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), five of which were additionally subjected to array-based comparative genomic hybridization (aCGH) analysis. Fifteen cases of PRCC were used as controls. From the aCGH results, no genome copy number abnormalities were found in the five PRNRP cases. By FISH, numbers of nuclei with abnormal chromosomal signals in PRNRP (centromere 7 gain: 11–21% of nuclei, centromere 17 gain: 11% of nuclei, centromere Y loss: 14–31% of nuclei) were similar to those in non-neoplastic tubular cells (centromere 7 gain: 11–15% of nuclei, centromere 17 gain: 12–15% of nuclei, centromere Y loss: 13–45% of nuclei). c-MET immunohistochemical overexpression, a substitute marker for chromosome 7 trisomy, was observed in 0 of 19 PRNRP cases, consistent with the analyses by aCGH and NGS regarding chromosome 7 gain. Taken together, the frequency of chromosomal alterations in PRNRP is similar to that in non-neoplastic tubular cells, and lower than that in PRCC. Our data suggest that PRNRP has a different tumorigenesis and is a distinct entity from PRCC. [ABSTRACT FROM AUTHOR]

Chromosomal structural variations (SVs) are linked to a wide range of phenotypes and arise due to disruptions during DNA replication, which can affect gene function within the SV regions. This case report details a patient diagnosed with neurodevelopmental delay. Detailed investigation through array comparative genomic hybridization revealed two pathogenic SVs on chromosome 1, which align with a 1p36 microdeletion, and a microduplication at 2p35.3, the latter being classified as a variant of unknown significance. The patient’s clinical presentation is consistent with the 1p36 deletion syndrome, characterized by specific developmental delays and physical anomalies. Further genetic analysis suggests that these terminal rearrangements might stem from an unbalanced translocation between the short arms of chromosomes 1 and 2. This case underscores the complexity of interpreting multiple concurrent SVs and their cumulative effect on phenotype. Ongoing research into such chromosomal abnormalities will enhance our understanding of their clinical manifestations and guide more targeted therapeutic strategies. [ABSTRACT FROM AUTHOR]

Among the repetitive elements, satellite DNA (SatDNA) emerges as extensive arrays of highly similar tandemly repeated units, spanning megabases in length. Given that the satDNA PboSat01-176, previously characterized in P. boiei, prompted our interest for having a high abundance in P. boiei and potential for centromeric satellite, here, we employed various approaches, including low coverage genome sequencing, followed by computational analysis and chromosomal localization techniques in four Proceratophrys species and, investigating the genomic presence and sharing, as well as its potential for chromosomal centromere marker in Proceratophrys frog species. Our findings demonstrate that PboSat01-176 exhibits high abundance across all four Proceratophrys species, displaying distinct characteristics that establish it as the predominant repetitive DNA element in these species. The satellite DNA is prominently clustered in the peri/centromeric region of the chromosomes, particularly in the heterochromatic regions. The widespread presence of PboSat01-176 in closely related Proceratophrys species reinforces the validity of the library hypothesis for repetitive sequences. Thus, this study highlighted the utility of the satDNA family PboSat01-176 as a reliable centromeric marker in Proceratophrys species, with potential to be applied in other species of anuran amphibians. The observed sharing and maintenance of this sequence within the genus suggest possibilities for future research, particularly through expanded sampling to elucidate parameters that underlie the library hypothesis and the evolutionary dynamics of satDNA sequences. [ABSTRACT FROM AUTHOR]

Simple Summary: In the species-diverse butterfly genus Polyommatus, speciation is often driven by rapid changes in chromosome number and structure, resulting in cryptic species. These cryptic species are morphologically similar, but usually can be recognized relatively easily using chromosomal markers. In this work, we show that similar chromosome numbers can independently evolve in different phylogenetic lineages, resulting in species that are difficult to distinguish using routine cytogenetic techniques. We also demonstrate that the combined analysis of chromosomes and mitochondrial DNA barcodes is a simple and effective tool for identifying such cryptic species. The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77–79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73–75), P. demavendi antonius, subsp. nov. (n = 71–73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29–34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis. [ABSTRACT FROM AUTHOR]

The sclerotia of Wolfiporia hoelen (Fr.) Y.C. Dai & V. Papp is an important traditional Chinese medicine with diverse pharmacological properties. This study utilized a combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing to generate a high-quality chromosome-level genome assembly of a W. hoelen strain Minling A5. There were 112 contigs in the genome, with 62.95 Mb in total length and 4.21 Mb in length for the contig N50. The average GC content was 51.89%. Based on Hi-C data, we corrected the CCS data and scaffolded them into 14 pseudo-chromosomes. The genome contained 44.37% repetitive sequences and 12,670 protein-coding genes, 86.53% (10,963) of which could be functionally annotated in at least one of the KOG, GO, Pfam, Swissprot, TrEMBL, NR, and KEGG databases. In addition, 240 transfer RNAs, 97 ribosomal RNAs, and 103 other non-coding RNAs were identified in the W. hoelen genome. A total of 755 pseudogenes were also identified, with an average length of 2665.51 bp. Further, there were 398, 100, 2837, 519, and 2068 genes annotated by CAZymes, TCDB, PHI, P450, and DFVF databases, respectively. One notable attribute of W. hoelen is its capacity to thrive in a substrate of fresh pine sawdust. Through an analysis of the growth on various pure wood sawdust culture media, we found that the growth of W. hoelen and Sparassis latifolia on pine sawdust was similar to that on broad-leaved wood sawdust, while the growth of Pleurotus ostreatus, P. eryngii, and Cyclocybe aegerita was slower than that on broad-leaved wood sawdust. By the functional annotation analysis of orthogroups in these five mushroom-forming fungi, it was determined that 645 orthogroups were specifically common in W. hoelen and S. latifolia. The genes in these specific orthogroups were significantly enriched in 12 pathways, including steroid biosynthesis, biosynthesis of antibiotics, and tyrosine metabolism. The high-quality genome and comparative genome analysis results significantly contribute to advancing our foundational knowledge of W. hoelen biology, while also offering valuable insights for the development of innovative biotechnological approaches aimed at enhancing the efficient and sustainable utilization of Pinus. [ABSTRACT FROM AUTHOR]

A Gram-negative, aerobic, rod-shaped, non-motile, yellow-pigmented bacterium, KMM 9835T, was isolated from the sediment sample obtained from the Amur Bay of the Sea of Japan seashore, Russia. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences positioned the novel strain KMM 9835T in the genus Mariniflexile as a separate line sharing the highest 16S rRNA gene sequence similarities of 96.6% and 96.2% with Mariniflexile soesokkakense RSSK-9T and Mariniflexile fucanivorans SW5T, respectively, and similarity values of <96% to other recognized Mariniflexile species. The average nucleotide identity and digital DNA–DNA hybridization values between strain KMM 9835T and M. soesokkakense KCTC 32427T, Mariniflexile gromovii KCTC 12570T, M. fucanivorans DSM 18792T, and M. maritimum M5A1MT were 83.0%, 82.5%, 83.4%, and 78.3% and 30.7%, 29.6%, 29.5%, and 24.4%, respectively. The genomic DNA GC content of strain KMM 9835T was 32.5 mol%. The dominant menaquinone was MK-6, and the major fatty acids were iso-C15:0, iso-C15:1ω10c, and C15:0. The polar lipids of strain KMM 9835T consisted of phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, and six unidentified lipids. A pan-genome analysis showed that the KMM 9835T genome encoded 753 singletons. The annotated singletons were more often related to transport protein systems (SusC), transcriptional regulators (AraC, LytTR, LacI), and enzymes (glycosylases). The KMM 9835T genome was highly enriched in CAZyme-encoding genes, the proportion of which reached 7.3%. Moreover, the KMM 9835T genome was characterized by a high abundance of CAZyme gene families (GH43, GH28, PL1, PL10, CE8, and CE12), indicating its potential to catabolize pectin. This may represent part of an adaptation strategy facilitating microbial consumption of plant polymeric substrates in aquatic environments near shorelines and freshwater sources. Based on the combination of phylogenetic and phenotypic characterization, the marine sediment strain KMM 9835T (=KCTC 92792T) represents a novel species of the genus Mariniflexile, for which the name Mariniflexile litorale sp. nov. is proposed. [ABSTRACT FROM AUTHOR]

Background: The clinical features of Turner syndrome (TS) involve multiple organ system dysplasia, among which growth retardation and gonadal dysplasia are the most important clinical phenotypes. Methods: G banding karyotype analysis, chromosome microarray (CMA), and fluorescence in situ hybridization (FISH) were used for prenatal diagnosis of fetal chromosomes. Results: The result of fetal chromosome karyotype analysis was 46,XX. CMA showed arr[GRCh38]Xp22.33 p22.13(251888_18176046)x1,Xq27.1q28(140998347_156003433)x3. FISH indicated that the short arm end fragment of X chromosome was monomer and the long arm end fragment was trisomy. Conclusions: The fetal chromosome karyotype was normal, but CMA indicated that there was deletion and duplication of X chromosome. FISH verified the CMA results, locating the deletion and duplication fragments. CMA and FISH make up for the shortcomings of chromosome karyotype analysis technique. It is suggested that multiple detection methods should be applied in genetic prenatal diagnosis [ABSTRACT FROM AUTHOR]

Psocodean species are emerging as significant sanitary and stored‐product pests, posing threats to human health and global food security. Out of an estimated 10 000 species, the whole genome sequences of only 4 species have been published. Genomic resources are crucial for establishing effective pest control and enhancing our understanding of the evolution of psocodean species. In this study, we employed Illumina and PacBio sequencing along with Hi‐C scaffolding techniques to generate a chromosome‐level genome assembly for the parthenogenetic booklouse Liposcelis bostrychophila. The assembled genome of this booklouse measures 291.67 Mb in length and comprises 9 chromosomes. Notably, the genome of L. bostrychophila exhibits a high level of heterozygosity and features a distinctive nonhomologous chromosome. This heterozygous characteristic of the parthenogenetic booklouse genome may arise from high mutation rates, based on genomic variations analysis across multiple generations. Our analysis revealed significantly expanded gene families, primarily associated with the detoxification and feeding habits of L. bostrychophila. These include integument esterases (ESTs), ATP‐binding cassette (ABC) transporter genes and gustatory receptors (GRs). The high‐quality genome sequence of L. bostrychophila provides valuable resources for further study on the molecular mechanisms of stress resistance. It enables researchers to identify crucial functional genes and facilitates research on the population genetics, evolution and phylogeny of booklice. [ABSTRACT FROM AUTHOR]

T-DNA transformation is prevalent in Arabidopsis research and has expanded to a broad range of crops and model plants. While major progress has been made in optimizing the Agrobacterium -mediated transformation process for various species, a variety of pitfalls associated with the T-DNA insertion may lead to the misinterpretation of T-DNA mutant analysis. Indeed, secondary mutagenesis either on the integration site or elsewhere in the genome, together with epigenetic interactions between T-DNA inserts or frequent genomic rearrangements, can be tricky to differentiate from the effect of the knockout of the gene of interest. These are mainly the case for genomic rearrangements that become balanced in filial generations without consequential phenotypical defects, which may be confusing particularly for studies that aim to investigate fertility and gametogenesis. As a cautionary note to the plant research community studying gametogenesis, we here report an overview of the consequences of T-DNA-induced secondary mutagenesis with emphasis on the genomic imbalance on gametogenesis. Additionally, we present a simple guideline to evaluate the T-DNA-mutagenized transgenic lines to decrease the risk of faulty analysis with minimal experimental effort. [ABSTRACT FROM AUTHOR]

Hybrid parthenogenetic animals are an exceptionally interesting model for studying the mechanisms and evolution of sexual and asexual reproduction. A diploid parthenogenetic lizard Darevskia unisexualis is a result of an ancestral cross between a maternal species Darevskia raddei nairensis and a paternal species Darevskia valentini and presents a unique opportunity for a cytogenetic and computational analysis of a hybrid karyotype. Our previous results demonstrated a significant divergence between the pericentromeric DNA sequences of the parental Darevskia species; however, an in‐depth comparative study of their pericentromeres is still lacking. Here, using target sequencing of microdissected pericentromeric regions, we reveal and compare the repertoires of the pericentromeric tandem repeats of the parental Darevskia lizards. We found species‐specific sequences of the major pericentromeric tandem repeat CLsat, which allowed computational prediction and experimental validation of fluorescent DNA probes discriminating parental chromosomes within the hybrid karyotype of D. unisexualis. Moreover, we have implemented a generalizable computational method, based on the optimization of the Levenshtein distance between tandem repeat monomers, for finding species‐specific fluorescent probes for pericentromere staining. In total, we anticipate that our comparative analysis of Darevskia pericentromeric repeats, the species‐specific fluorescent probes that we found and the pipeline that we developed will form a basis for the future detailed cytogenomic studies of a wide range of natural and laboratory hybrids. Research Highlights: We computationally predicted and experimentally verified fluorescent DNA probes discriminating parental pericentromeric subgenomes in a hybrid parthenogenetic lizard Darevskia unisexualis. We implemented our prediction method as a species‐agnostic Nextflow pipeline. [ABSTRACT FROM AUTHOR]

Histone and non-histone proteins play key roles in the activation and repression of genes. In addition to experimental studies of their regulation of gene expression, molecular modeling at the nucleosome, chromatin, and chromosome levels can contribute insights into the molecular mechanisms involved. In this review, we provide an overview for protein-bound chromatin modeling, and describe how our group has integrated protein binding into genome systems across the scales, from all-atom to coarse-grained models, using explicit to implicit descriptions. We describe the associated applications to protein binding effects and biological mechanisms of genome folding and gene regulation. We end by illustrating the application of machine learning tools like AlphaFold2 to proteins relevant to chromatin systems. [ABSTRACT FROM AUTHOR]

The article analyzes data on the production of new intergenomic hybrids involving the species Gossypium thurberi Tod., Gossypium raimondii Ulbr., Gossypium arboreum L., Gossypium hirsutum L., Gossypium barbadense L., belonging to genome groups D1, D5 A2 cotton and presents the results of some cytological studies of the resulting hybrids. As a result of experiments using the method of interspecific hybridization, an amphidiploid {[(G. thurberi Tod. × G. raimondii Ulbr.) × G. arboreum L.] × G. hirsutum L.} with a complex genetic basis was obtained. Based on the hybridization of the resulting amphidiploid with cultivars of the species G. barbadense L. and G. hirsutum L., interspecific complex hybrids were synthesized, including 4 species with hybridization of 46.7-55.1% and including 5 species with hybridization of 24.6-31.3%.By interspecific hybridization and backcrosses, valuable source material for the cotton breeding has been created. Valuable introgressed lines having high productivity and high quality, which are at various stages of testing have been realized. Cytological analysis of the hybrids revealed that they were true interspecific crosses. Observations of meiotic metaphase chromosomes indicated the degree of relatedness between species.

The interaction between lamin A and the cytoplasmic skeleton plays a key role in maintaining nuclear mechanical properties. However, the effect of destruction of the cytoplasmic skeleton on the 3D submicroscopic structure of lamin A has not been elucidated. In this study, we developed an image quantization algorithm to quantify changes in the submicroscopic structure of the intact lamin A 3D network within the nucleus. We used blebbistatin or nocodazole to disrupt the fibrillar structure of F-actin or tubulin, respectively, and then quantified changes in the lamin A super-resolution network structure, the morphological and mechanical properties of the nucleus and the spatial distribution of chromosomes. Ultimately, we found for the first time that disruption of the cytoplasmic skeleton changes the lamin A submicroscopic network and nuclear structural characteristics. In summary, this study contributes to understanding the trans-nuclear membrane interaction characteristics of lamin A and the cytoplasmic skeleton.

Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.

Abstract Background Uniparental disomy is the inheritance of a homologous chromosome pair or part of homologous chromosomes from only one parent. However, the clinical significance of uniparental disomy and the difference among the prognosis of involvement of different chromosomes remain unclear. Objective To assess the associated prenatal ultrasound presentations and clinical outcomes of uniparental disomy on different chromosomes and to analyze the relationship between prenatal ultrasound markers and clinical outcomes. Study design We retrospectively analyzed data from fetuses with uniparental disomy diagnosed using chromosome microarray analysis with the Affymetrix CytoScan HD array at our institution between January 2013 and September 2022. The relationship between prenatal ultrasound findings, the involved chromosome(s), and clinical outcomes was evaluated. Results During the study period, 36 fetuses with uniparental disomy were diagnosed, and two cases were excluded for non-available postnatal data. Finally, 34 fetuses were included in our study, of which 30 (88.2%) had uniparental disomy occurring on a single chromosome, while four (11.8%) were identified with uniparental disomy on different chromosomes. The most frequently involved chromosomes were chromosomes 16, X and 2, which presented in 8 (23.5%), 5 (14.7%) and 4 (11.8%), respectively. Prenatal ultrasound abnormalities were detected in 21 fetuses, with the most common category being multiple abnormalities (12 (57.1%)). Fetal growth restriction was identified in 14 (41.2%) fetuses, all of which coexisted with other abnormal findings. The rate of adverse perinatal outcomes in patients with uniparental disomy and fetal abnormalities was significantly higher than those without abnormalities (76.2% versus 15.4%, P = 0.002). The incidence of fetal or neonatal death was significantly higher in fetuses with fetal growth restriction than those without (85.7% versus 30.0%, P = 0.004). Conclusions The prognosis of fetuses with uniparental disomy combined with fetal abnormalities, especially fetal growth restriction, was much poorer than those without.

Abstract Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive analysis. High accuracy base calling was assessed with Guppy version 4.0.11. Filtlong and NanoPlot were used for filtering and visualizing the FASTQ data. Flye (2.8.1) was used for de novo assembly analysis. Variant calls and consensus sequences were created using Medaka. The annotation of the genome was elaborated by DFAST. The assembled genome and annotation were tested using Busco and CheckM. Herein, we found that the highest similarity of the BBR56 isolate was 98.37% with the 16 S rRNA gene sequence of P. viridis G-1387. The genome size was 5.5 Mb and included chromosome 1 (4.2 Mbp) and chromosome 2 (1.3 Mbp), which encoded 61 pseudogenes, 4 noncoding RNAs, 113 tRNAs, 31 rRNAs, 4,505 coding DNA sequences, 4 clustered regularly interspaced short palindromic repeats, 4,444 coding genes, and a GC content of 49.5%. The sequence of the whole genome of P. viridis BBR56 was uploaded to GenBank under the accession numbers CP072425–CP072426, biosample number SAMN18435505, and bioproject number PRJNA716373. The sequence read archive (SRR14179986) was successfully obtained from NCBI for BBR56 raw sequencing reads. Digital DNA–DNA hybridization results showed that the genome of BBR56 had the potential to be a new species because no other bacterial genomes were similar to the sample. Biosynthetic gene clusters (BGCs) were assessed using BAGEL4 and the antiSMASH bacterial version. The genome harbored diverse BGCs, including genes that encoded polyketide synthase, nonribosomal peptide synthase, RiPP-like, NRP-metallophore, hydrogen cyanide, betalactone, thioamide-NRP, Lant class I, sactipeptide, and prodigiosin. Thus, BBR56 has considerable potential for further exploration regarding the use of its secondary metabolite products in the human and fisheries sectors.

Abstract Background The current understanding of acquired chromosomal colistin resistance mechanisms in Enterobacterales primarily involves the disruption of the upstream PmrAB and PhoPQ two-component system (TCS) control caused by mutations in the regulatory genes. Interestingly, previous studies have yielded conflicting results regarding the interaction of regulatory genes related to colistin resistance in Escherichia coli, specifically those surrounding PhoPQ and PmrAB TCS. Results In our study, we focused on two clinical non-mcr colistin-resistant strains of E. coli, TSAREC02 and TSAREC03, to gain a better understanding of their resistance mechanisms. Upon analysis, we discovered that TSAREC02 had a deletion (Δ27–45) in MgrB, as well as substitutions (G206R, Y222H) in PmrB. On the other hand, TSAREC03 exhibited a long deletion (Δ84–224) in PhoP, along with substitutions (M1I, L14P, P178S, T235N) in PmrB. We employed recombinant DNA techniques to explore the interaction between the PhoPQ and PmrAB two-component systems (TCSs) and examine the impact of the mutated phoPQ and pmrB genes on the minimum inhibitory concentrations (MICs) of colistin. We observed significant changes in the expression of the pmrD gene, which encodes a connector protein regulated by the PhoPQ TCS, in the TSAREC02 wild-type (WT)-mgrB replacement mutant and the TSAREC03 WT-phoP replacement mutant, compared to their respective parental strains. However, the expressions of pmrB/pmrA, which reflect PmrAB TCS activity, and the colistin MICs remained unchanged. In contrast, the colistin MICs and pmrB/pmrA expression levels were significantly reduced in the pmrB deletion mutants from both TSAREC02 and TSAREC03, compared to their parental strains. Moreover, we were able to restore colistin resistance and the expressions of pmrB/pmrA by transforming a plasmid containing the parental mutated pmrB back into the TSAREC02 and TSAREC03 mutants, respectively. Conclusion While additional data from clinical E. coli isolates are necessary to validate whether our findings could be broadly applied to the E. coli population, our study illuminates distinct regulatory pathway interactions involving colistin resistance in E. coli compared to other species of Enterobacterales. The added information provided by our study contribute to a deeper understanding of the complex pathway interactions within Enterobacterales.

Abstract Background Chromosome is one of the most fundamental part of cell biology where DNA holds the hierarchical information. DNA compacts its size by forming loops, and these regions house various protein particles, including CTCF, SMC3, H3 histone. Numerous sequencing methods, such as Hi-C, ChIP-seq, and Micro-C, have been developed to investigate these properties. Utilizing these data, scientists have developed a variety of loop prediction techniques that have greatly improved their methods for characterizing loop prediction and related aspects. Results In this study, we categorized 22 loop calling methods and conducted a comprehensive study of 11 of them. Additionally, we have provided detailed insights into the methodologies underlying these algorithms for loop detection, categorizing them into five distinct groups based on their fundamental approaches. Furthermore, we have included critical information such as resolution, input and output formats, and parameters. For this analysis, we utilized the GM12878 Hi-C datasets at 5 KB, 10 KB, 100 KB and 250 KB resolutions. Our evaluation criteria encompassed various factors, including memory usages, running time, sequencing depth, and recovery of protein-specific sites such as CTCF, H3K27ac, and RNAPII. Conclusion This analysis offers insights into the loop detection processes of each method, along with the strengths and weaknesses of each, enabling readers to effectively choose suitable methods for their datasets. We evaluate the capabilities of these tools and introduce a novel Biological, Consistency, and Computational robustness score ( $$BCC_{score}$$ B C C score ) to measure their overall robustness ensuring a comprehensive evaluation of their performance.

Cellular behavior is continuously influenced by mechanical forces. These forces span the cytoskeleton and reach the nucleus, where they trigger mechanotransduction pathways that regulate downstream biochemical events. Therefore, the nucleus has emerged as a regulator of cellular response to mechanical stimuli. Cell cycle progression is regulated by cyclin-CDK complexes. Recent studies demonstrated these biochemical pathways are influenced by mechanical signals, highlighting the interdependence of cellular mechanics and cell cycle regulation. In particular, the transition from G2 to mitosis (G2-M) shows significant changes in nuclear structure and organization, ranging from nuclear pore complex (NPC) and nuclear lamina disassembly to chromosome condensation. The remodeling of these mechanically active nuclear components indicates that mitotic entry is particularly sensitive to forces. Here, we address how mechanical forces crosstalk with the nucleus to determine the timing and efficiency of the G2-M transition. Finally, we discuss how the deregulation of nuclear mechanics has consequences for mitosis.

Objective To analyze the chromosomal abnormalities in villus tissue of missed abortion patients with different assisted reproductive techniques.Methods A total of 260 missed abortion patients admitted to the hospital from July 2019 to July 2023 who received assisted conception were selected as the assisted conception group.According to the different assisted reproductive techniques, they were divided into the in-vitro fertilization (IVF) group (135 cases),the artificial fertilization (AIH) group (45 cases) and the intracytoplasmic sperm injection (ICSI) group (80 cases). And a total of 42 missed abortion patients with natural conception were selected as the control group, and the chorionic tissue of the patients in each group was collected.The chromosome copy number variation (CNV) and abnormal number of chromosomes were observed by high-throughput sequencing.Results There was no significant difference in chromosome abnormality detection rate, CNV abnormality rate and number abnormality type between the assisted conception group and the control group (P＞0.05). There was no significant difference in chromosome abnormality detection rate, CNV abnormality rate and number abnormality type in the IVF group compared with the AIH group and the ICSI group (P＞0.05). In the assisted conception group, 16/22/21-trisomy abnormalities were predominant in the patients with abnormal chromosome numbers, while ditrisomy abnormalities were predominant in 48,XX+3,+18,48,XXY,+21,and X monomer abnormalities were all 45,X.Among the patients with triploid abnormalities, five patients were 69,XXY and two patients were 69,XXX.There was no significant difference in the distribution of abnormal karyotypes among all the groups (P＞0.05). Conclusion Assisted reproductive technology does not increase the risk of chromosomal abnormalities, and the distribution of abnormal chromosome karyotypes has nothing to do with the assisted reproductive technology method, and the assisted conception method can be selected according to the overall situation of the patient. [ABSTRACT FROM AUTHOR]

Background and Aims Despite chromosomal evolution being one of the major drivers of diversification in plants, we do not yet have a clear view of how new chromosome rearrangements become fixed within populations, which is a crucial step forward for understanding chromosomal speciation. Methods In this study, we test the role of genetic drift in the establishment of new chromosomal variants in the context of hybrid dysfunction models of chromosomal speciation. We genotyped 178 individuals from seven populations (plus 25 seeds from one population) across the geographical range of Carex helodes (Cyperaceae). We also characterized karyotype geographical patterns of the species across its distribution range. For one of the populations, we performed a detailed study of the fine-scale, local spatial distribution of its individuals and their genotypes and karyotypes. Key Results Synergistically, phylogeographical and karyotypic evidence revealed two main genetic groups: southwestern Iberian Peninsula vs. northwestern African populations; and within Europe our results suggest a west-to-east expansion with signals of genetic bottlenecks. Additionally, we inferred a pattern of descending dysploidy, plausibly as a result of a west-to-east process of post-glacial colonization in Europe. Conclusions Our results give experimental support to the role of geographical isolation, drift and inbreeding in the establishment of new karyotypes, which is key in the speciation models of hybrid dysfunction. [ABSTRACT FROM AUTHOR]