Genetic manipulation of the genes for clonal seeds results in sterility in cotton.

BACKGROUND: Heterosis is a common phenomenon in plants and has been extensively applied in crop breeding. However, the superior traits in the hybrids can only be maintained in the first generation but segregate in the following generations. Maintaining heterosis in generations has been challenging but highly desirable in crop breeding. Recent study showed that maternally produced diploid seeds could be achieved in rice by knocking out three meiosis related genes, namely REC8, PAIR1, OSD1 to create MiMe in combination with egg cell specific expression of BBM transcription factor, a technology called clonal seeds. Interestingly, there has been very limited reports indicating the feasibility of this approach in other crops. RESULTS: In this study, we aimed to test whether clonal seeds could be created in cotton. We identified the homologs of the three meiosis related genes in cotton and used the multiplex CRISPR/Cas9 gene editing system to simultaneously knock out these three genes in both A and D sub-genomes. More than 50 transgenic cotton plants were generated, and fragment analysis indicated that multiple gene knockouts occurred in the transgenic plants. However, all the transgenic plants were sterile apparently due to the lack of pollen. Pollination of the flowers of the transgenic plants using the wild type pollens could not generate seeds, an indication of defects in the formation of female sexual cells in the transgenic plants. In addition, we generated transgenic cotton plants expressing the cotton BBM gene driven by the Arabidopsis egg cell specific promoter pDD45. Two transgenic plants were obtained, and both showed severely reduced fertility. CONCLUSIONS: Overall, our results indicate that knockout of the clonal seeds related genes in cotton causes sterility and how to manipulate genes to create clonal seeds in cotton requires further research.

Aged rather than pristine polyvinyl chloride microplastic affect the development and structure of Vallisneria natans population.

A large number of microplastics have been discharged into freshwater ecosystems, where they age and are deposited in the sediment, posing a risk to primary producers, such as submerged macrophytes. Many macrophytes benefit from clonal integration, which lets the population work as a 'macro' organism. Nonetheless, little is known about the differences in phytotoxicity between aged and pristine microplastics, particularly for clonal populations of macrophytes. In this study, we showed that UV-aging changes the characteristics of polyvinyl chloride microplastics (PVC-MPs). Aged PVC-MPs possessed higher hydrophilicity, less chlorine and crystallinity, and more severe toxicity. The pristine PVC-MPs did not affect Vallisneria natans, while the aged PVC-MPs significantly affected the development and structure of the clonal population. The severely aged PVC-MPs reduced the relative growth rate of V. natans by 26 % at the population level. Furthermore, the mother plant (ortet) and offspring (ramet) responded differently to the aged PVC-MPs. A trade-off was observed between the growth rate and stress resistance in the ortets. The ortets increased investment in the root part to tolerate stress when facing exposure to microplastics. In contrast, the ramets were less resistant, as shown by shorter roots, and lower leaf chlorophyll, carbon, and nitrogen concentrations. Notably, the growth of the ramets was maintained and the investments in stolon structure by the ortets were not lessened. The ortet sacrificed itself for the continuation of the ramet. This clonal integration may safeguard V. natans survival and compensate for vegetative expansion. This study sheds new light on how macrophytes respond to microplastics at the clonal population level and provides direct evidence that existing studies may have underestimated the toxic effect of microplastics in freshwater ecosystems.

ICESp1109, a novel hybrid Integrative Conjugative Element of macrolide-resistant Streptococcus pyogenes serotype M77 collected between 2003 and 2017 in Poland.

OBJECTIVES: Genetic characterization of the antibiotic resistance determinants and associated mobile genetic elements (MGEs) among Streptococcus pyogenes [Group A streptococci (GAS)] clinical isolates of an M77 serotype collected in Poland between 2003 and 2017. METHODS: The genomes of 136 M77 GAS isolates were sequenced using Illumina, and selected with long-read approach (Oxford Nanopore). Whole genome sequences were analyzed to determine the presence of macrolide resistance determinants, and their genetic context. RESULTS: The strains used in the study were collected in the two multicenter surveys from in- and outpatients. Sequencing data analysis revealed that all strains carried the tet(O) gene (100%, N=136). They were classified as a single sequence type ST63. For erythromycin resistance, the unique determinant was erm(TR) detected in 76.5% (N=104) isolates. A single appearance of tet(M) and erm(B) on Tn3872 was noticed. The mefA, mefE, and msr(D) genes were detected in neither of the genomes. This correlated with the detected strain phenotypes - 11 exhibited cMLSB, 93 - iMLSB, and no M phenotype.The erm(TR) gene was predominantly (N=74) found within a novel hybrid Integrative Conjugative Element composed of the ICESp1108-like sequence and ICESp2906 variant which was then named ICESp1109. However, in strains isolated before 2008, erm(TR) was located within ICESp2905 (N=27). The erm(TR) gene was detected within stand-alone ICESp1108-like sequences in 3 strains. CONCLUSIONS: Based on phylogenetic analysis results the clonal dissemination of the macrolide-resistant S. pyogenes M77/ST63 strain with hybrid ICESp1109 was observed between 2008 and 2017. ICESp1109 is the novel hybrid ICE in Gram-positive bacteria.

Factor H binding protein (FHbp): An evaluation of genotypic diversity across Neisseria meningitidis serogroups.

Neisseria meningitidis serogroups A, B, C, W, X, and Y cause invasive meningococcal disease (IMD) worldwide. Factor H binding protein (FHbp), a key meningococcal virulence factor, is an antigen included in both licensed meningococcal serogroup B (MenB) vaccines. This review examines the biology and epidemiology of FHbp and assesses the ability and potential of FHbp vaccine antigens to protect against IMD. Using evidence from the literature and the contemporary PubMLST database, we discuss analyses of MenB genotypes on the representation of the most prevalent multilocus sequence typing (MLST)/clonal complexes, FHbp subfamily distribution, and FHbp and porin A (PorA) variants. We further discuss that the similar genotypes, distribution, and diversity of FHbp variant types have remained stable over long time periods, supporting the potential for FHbp-containing, protein-based vaccines to protect against IMD, including MenB-FHbp (Trumenba®), which contains two lipidated FHbp antigens (one each from both FHbp subfamilies: A and B).

[Aberrant mitochondrial dynamics in myeloid neoplasms].

Age-related clonal hematopoiesis and myeloid malignancies arise from hematopoietic stem cells and progenitors with genetic abnormalities. Advances in next-generation sequencing technology have led to the identification of a wide variety of genetic alterations involved in disease onset. However, it remains unclear how diverse genetic alterations, lacking disease specificity, lead to the development of myeloid malignancies and the progression of clonal hematopoiesis. Mitochondrial abnormalities and their roles in various pathological conditions such as aging, inflammation, neurological diseases, cardiac diseases, and cancer have recently been revealed, and have garnered attention as new therapeutic targets. This review focuses on regulation of mitochondrial dynamics and outlines the role of mitochondria in myeloid malignancies and clonal hematopoiesis.

Simultaneous clonal spread of NDM-1-producing Pseudomonas aeruginosa ST773 from Ukrainian patients in the Netherlands and Spain.

Objectives: We describe the clonal spread of New Delhi metallo-ß-lactamase (NDM) 1-producing Pseudomonas aeruginosa isolates belonging to the ST773 clone in Spain and the Netherlands, associated with the transfer of Ukrainian patients during the war. Methods: Between March and December 2022, nine NDM-1-producing P. aeruginosa ST773 isolates were recovered from nine Ukrainian patients evacuated to two Spanish (n = 3) and five Dutch (n = 6) hospitals. Antimicrobial susceptibility testing was studied (Sensititre, Microscan, EUCAST-2023). Whole genome sequencing (Illumina, Oxford-Nanopore) was used to analyze the genetic relatedness, the resistome, and the prophage content. Results: All NDM-1-producing P. aeruginosa ST773 isolates exhibited resistance to all tested antimicrobials except colistin, aztreonam, and cefiderocol. Genomic analysis revealed that all isolates had an identical resistome and a chromosomally encoded integrative conjugative element carrying the bla NDM-1 gene. The core genome multilocus sequence typing and core genome single nucleotide polymorphisms analysis showed highly related isolates, irrespective of country of isolation, distant from other NDM-1-ST773 P. aeruginosa not collected in Ukraine. Both analysis revealed two closely related clusters, spanning the Spanish and Dutch isolates. In addition, a high content of prophages was identified in all strains, most of them in more than one isolate simultaneously, regardless of their origin country. Moreover, an identical phage tail-like bacteriocin cluster was identified in all NDM-1-ST773 P. aeruginosa. Conclusions: We report a clonal dissemination of NDM-producing P. aeruginosa ST773 to the Netherlands and Spain associated with patients from Ukraine. Our work highlights the importance of genomic surveillance and to understand the dynamics of resistance in multidrug-resistant bacteria after the transfer of patients from conflict zones. International collaboration is crucial to address global antimicrobial resistance.

Epstein-Barr virus-positive, primary cutaneous marginal zone lymphoma, with transformation: Case report and review of the literature.

Epstein-Barr Virus (EBV) positive primary cutaneous marginal zone lymphoma (PCMZL) is uncommon and subsequent transformation is rare. METHODS: We report a patient with EBV positive PCMZL with subsequent transformation to plasmablastic lymphoma and review the literature for transformed PCMZL to assess clinical and pathologic characteristics. In the case we describe, the patient presented with multifocal PCMZL, developed large B cell transformation with plasmacytic differentiation, followed by plasmablastic transformation (PBL), and ultimately died of disease progression despite multiple lines of therapy. Past history was significant for psoriatic arthritis (multiple prior lines of immunomodulatory therapy). The lymphomas and non-involved bone marrow share the same somatic DNMT3A and TET2 mutations, suggesting clonal relatedness and an association with clonal hematopoiesis (CH). RESULTS: Eighteen cases complied the cohort (seventeen cases from the literature and the case reported herein). Nearly half of the eighteen cases of PCMZL with transformation died of progressive disease (44%). Transformed cases were more commonly seen in patients with >2 sites at initial diagnosis. EBV was assessed in 5 patients, 3 were positive (all died of disease). Two patients with NGS studies demonstrated TET2 and DNMT3A mutations. CONCLUSIONS: Transformation of EBV positive PCMZL appears to be a poor prognostic indicator, with our reported case being the first well defined case transformed to PBL, suspected to arise from myeloid-CH.

IgG-k/IgG-λ Para-Osseous Plasmacytoma Relapsed as Soft-Tissue Plasmacytoma with IgA-k Immunophenotype: A Case Report and Review of the Literature on Related Biochemical Aspects.

Neoplastic plasma cells (PCs) proliferation at anatomic sites dislocated from the bone marrow (BM) or their contiguous growth from osseous lesions that disrupt the cortical bone is termed extramedullary multiple myeloma (EMD). EMD still remains challenging from a therapeutic and biological perspective. Pathogenesis has not been completely clarified, and it is generally associated with high-risk cytogenetics (HRCAs). In order to emphasize the clinical and biochemical complexity of this disease, we have decided to describe the case of a patient affected by relapsed-refractory (RR) EMD, which presented as para-osseous plasmacytoma with a bi-phenotypical immunoglobulin (Ig) component and lately relapsed as soft-tissue plasmacytoma with a total immunophenotype switch. We have also hypothesized a correlation between Ig patterns and prognosis and suggested the possible inclusion of these biochemical features in the general risk assessment.

Clonal Evolution in 207 Cases of Refractory or Relapsed Acute Myeloid Leukemia.

Clonal evolution (CE) is a driving force behind the development and progression of acute myeloid leukemia (AML). Advances in molecular and cytogenetic assays have improved the depth and breadth of detection of CE in AML, which is defined here as a detected change in cytogenetic or molecular profile at relapsed or refractory (RR) disease. In this study, we demonstrate the clinical impact of CE in a cohort of patients with RR AML treated between 2013 and 2023. We discovered CE is significantly more frequent in relapsed disease (58.2%, [46.6%, 69.2%]) than in refractory disease (21.1%, [14.4%, 29.2%], p < 0.001). CE negatively impacts prognosis when detected by conventional karyotyping in refractory disease (4.2 vs. 13.9 months, p < 0.011). In contrast with prior literature, CE had no impact on overall survival if detected in relapsed disease. Surprisingly, those who achieved negative measurable residual disease (MRD) were no more likely to eliminate their original clone than those who did not (p = 1). We found several cytogenetic and molecular signatures which may predispose to CE: aberrations of chromosome 17, trisomy 8, TP53, KRAS, and FLT3-TKD. Finally, physicians were less likely to retreat those with CE with IC after receiving IC as first-line therapy (35.0% vs. 70.9%, p = 0.004). This study illustrates the role of CE in chemotherapy-resistant AML; we identify unique cytogenetic and molecular signatures that define a subset of patients associated with a dismal prognosis. As next-generation sequencing panels expand and new methods to characterize cytogenetic abnormalities emerge, our findings establish a basis for future studies investigating the prognostic and therapeutic impact of CE.

Clonal hematopoiesis of indeterminate potential and cardiovascular disease: Pathogenesis, clinical presentation, and future directions.

Clonal hematopoiesis of indeterminate potential (CHIP) is a well-studied phenomenon in hematologic malignancies. With advancements in gene sampling and analysis and the use of large cohort studies, CHIP has recently been linked to cardiovascular disease (CVD). The relationship between CHIP and CVD appears to be bidirectional, with traditional risk factors for cardiovascular disease increasing the mutation burden in CHIP, and CHIP itself effecting the incidence or prognosis of a variety of CVD. The purpose of this review is to understand the epidemiology, risk factors, and pathogenesis of CHIP in the context of various CVD conditions.

Association Between Clonal Hematopoiesis and Left Ventricular Reverse Remodeling in Nonischemic Dilated Cardiomyopathy.

Although clonal hematopoiesis of indeterminate potential (CHIP) is an adverse prognostic factor for atherosclerotic disease, its impact on nonischemic dilated cardiomyopathy (DCM) is elusive. The authors performed whole-exome sequencing and deep target sequencing among 198 patients with DCM and detected germline mutations in cardiomyopathy-related genes and somatic mutations in CHIP driver genes. Twenty-five CHIP driver mutations were detected in 22 patients with DCM. Ninety-two patients had cardiomyopathy-related pathogenic mutations. Multivariable analysis revealed that CHIP was an independent risk factor of left ventricular reverse remodeling, irrespective of known prognostic factors. CHIP exacerbated cardiac systolic dysfunction and fibrosis in a DCM murine model. The identification of germline and somatic mutations in patients with DCM predicts clinical prognosis.

[Clonal evolution in myeloproliferative neoplasms].

Recent advances in sequencing technologies have clarified the driver gene landscape in Philadelphia chromosomenegative (Ph-) myeloproliferative neoplasms (MPNs) and progressed understanding of MPN pathogenesis. Beyond mutations in the main three drivers of MPN, namely JAK2, MPL and CALR, somatic mutations in the epigenetic regulators and RNA splicing factors have been identified and their association with transformation to myelofibrosis and acute myeloid leukemia have been determined. Clonal expansion of hematopoietic cells with driver mutations (clonal hematopoiesis) has been detected in healthy individuals, especially in elderly people. In MPN patients, however, initial driver mutations such as those in JAK2 and DNMT3A have been shown to be acquired in utero or during childhood. In this review, I will summarize the recent findings about clonal evolution in MPN and the role of driver mutations.

Ultralow-dose irradiation enables engraftment and intravital tracking of disease initiating niches in clonal hematopoiesis.

Recent advances in imaging suggested that spatial organization of hematopoietic cells in their bone marrow microenvironment (niche) regulates cell expansion, governing progression, and leukemic transformation of hematological clonal disorders. However, our ability to interrogate the niche in pre-malignant conditions has been limited, as standard murine models of these diseases rely largely on transplantation of the mutant clones into conditioned mice where the marrow microenvironment is compromised. Here, we leveraged live-animal microscopy and ultralow dose whole body or focal irradiation to capture single cells and early expansion of benign/pre-malignant clones in the functionally preserved microenvironment. 0.5 Gy whole body irradiation (WBI) allowed steady engraftment of cells beyond 30 weeks compared to non-conditioned controls. In-vivo tracking and functional analyses of the microenvironment showed no change in vessel integrity, cell viability, and HSC-supportive functions of the stromal cells, suggesting minimal inflammation after the radiation insult. The approach enabled in vivo imaging of Tet2+/- and its healthy counterpart, showing preferential localization within a shared microenvironment while forming discrete micro-niches. Notably, stationary association with the niche only occurred in a subset of cells and would not be identified without live imaging. This strategy may be broadly applied to study clonal disorders in a spatial context.

Unraveling the occurrence of hyperhydricity in oil palm somatic embryos during somatic embryogenesis process.

The propagation of oil palm through somatic embryogenesis is the most effective method of cloning this palm tree; however, in vitro cultivation can lead to abnormalities in plant tissue, such as hyperhydricity. The present study aimed to evaluate the difference in anatomical, morphological, and histochemical characteristics, and gene expression in normal (Nm) and hyperhydric (Hh) somatic embryos of oil palm. For this purpose, Nm and Hh somatic embryos were collected from the differentiation medium and were submitted to anatomical and histochemical analyses to assess the nucleus/cytoplasm ratio (toluidine blue), starch (Lugol), and proteins (XP), as well as ultrastructural analyses via transmission electron microscopy. Additionally, gene expression analyses were performed to gain a better understanding on the molecular aspect of hyperhydric abnormality. A higher quantity of differentiated Nm somatic embryos per explant was observed, with a germination rate close to zero in Hh somatic embryos. Additionally, a higher accumulation of proteins and starch was found in Nm somatic embryos when compared to Hh embryos. It was also noted that in Nm somatic embryos, protein reserves were primarily located in the proximal region (embryonic axis), whereas starch reserves were mainly accumulated in the distal region of the somatic embryos. Hh somatic embryos exhibit insignificant starch reserves, and a greater number of intercellular spaces were observed compared to Nm somatic embryos. However, some Hh somatic embryos displayed histochemical characteristics similar to Nm, which could explain the occurrence of reversions from the Hh state to the Nm state observed in this study. Regarding molecular analyses, the gene expression results obtained showed that out of the 19 genes analyzed, 17 were upregulated in hyperhydric embryos when compared to the control condition (normal somatic embryos). Genes involved in stress response, energy metabolism, defense, membrane transport, hormonal regulation, and development were positively regulated, especially those involved in ethylene synthesis and energetic metabolism. To the best of our knowledge, this is the first in-depth study addressing hyperhydricity in oil palm during somatic embryogenesis.

Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations.

Population bottlenecks can impact the rate of adaptation in evolving populations. On the one hand, each bottleneck reduces the genetic variation that fuels adaptation. On the other hand, each founder that survives a bottleneck can undergo more generations and leave more descendants in a resource-limited environment, which allows surviving beneficial mutations to spread more quickly. A theoretical model predicted that the rate of fitness gains should be maximized using ~8-fold dilutions. Here we investigate the impact of repeated bottlenecks on the dynamics of adaptation using numerical simulations and experimental populations of Escherichia coli. Our simulations confirm the model's prediction when populations evolve in a regime where beneficial mutations are rare and waiting times between successful mutations are long. However, more extreme dilutions maximize fitness gains in simulations when beneficial mutations are common and clonal interference prevents most of them from fixing. To examine these predictions, we propagated 48 E. coli populations with 2-, 8-, 100-, and 1000-fold dilutions for 150 days. Adaptation began earlier and fitness gains were greater with 100- and 1000-fold dilutions than with 8-fold dilutions, consistent with the simulations when beneficial mutations are common. However, the selection pressures in the 2-fold treatment were qualitatively different from the other treatments, violating a critical assumption of the model and simulations. Thus, varying the dilution factor during periodic bottlenecks can have multiple effects on the dynamics of adaptation caused by differential losses of diversity, different numbers of generations, and altered selection.

Effects of soil microplastic heterogeneity on plant growth vary with species and microplastic types.

Microplastics are heterogeneously distributed in soils. However, it is unknown whether soil microplastic heterogeneity affects plant growth and root foraging responses and whether such effects vary with plant species and microplastic types. We grew each of seven herbaceous species (Platycodon grandiflorus, Trifolium repens, Portulaca oleracea, Medicago sativa, Taraxacum mongolicum, Perilla frutescenst, and Paspalum notatum) in heterogeneous soil (patches without microplastics and patches with 0.2 % microplastics) and homogeneous soil (patches with 0.1 % microplastics). Three microplastic types were tested: polypropylene (PP), polyacrylonitrile (PAN), and polyester (PET). P. frutescens showed no response to soil microplastic heterogeneity. For P. grandiflora, microplastic heterogeneity tended to decrease its biomass (total, shoot and root) when the microplastic was PAN and also shoot biomass when it was PET, but had no effect when it was PP. For T. repens, microplastic heterogeneity promoted biomass when PAN was used, decreased total and root biomass when PET was used, but showed no effect when PP was used. Microplastic heterogeneity increased biomass of P. oleracea and decreased that of M. sativa when PET was used, but had no effect when PP or PAN was used. For T. mongolicum, microplastic heterogeneity reduced biomass when the microplastic was PAN, tended to increase total and root biomass when it was PP, but showed no effect when it was PET. For P. notatum, microplastic heterogeneity increased biomass when the microplastic was PP, decreased it when PET was used, but had no effect when PAN was used. However, biomass of none of the seven species showed root foraging responses at the patch level. Therefore, soil microplastic heterogeneity can influence plant growth, but such effects depend on species and microplastic types and are not associated with root foraging. Our findings highlight the roles of soil microplastic heterogeneity, which may influence species interactions and community structure and productivity.