Chromosome Fragments Research Articles

Genetic mapping of the wheat leaf rust resistance gene Lr19 and development of translocation lines to break its linkage with yellow pigment.

The leaf rust resistance gene Lr19, which is present on the long arm of chromosome 7E1 in Thinopyrum ponticum, was mapped within a 0.3-cM genetic interval, and translocation lines were developed to break its linkage with yellow pigmentation The leaf rust resistance locus Lr19, which was transferred to wheat (Triticum aestivum) from its relative Thinopyrum ponticum in 1966, still confers broad resistance to most known races of the leaf rust pathogen Puccinia triticina (Pt) worldwide. However, this gene has not previously been fine-mapped, and its tight linkage with a gene causing yellow pigmentation has limited its application in bread wheat breeding. In this study, we genetically mapped Lr19 using a bi-parental population from a cross of two wheat-Th. ponticum substitution lines, the Lr19-carrying line 7E1(7D) and the leaf rust-susceptible line 7E2(7D). Genetic analysis of the F2 population and the F2:3 families showed that Lr19 was a single dominant gene. Genetic markers allowed the gene to be mapped within a 0.3-cM interval on the long arm of Th. ponticum chromosome 7E1, flanked by markers XsdauK3734 and XsdauK2839. To reduce the size of the Th. ponticum chromosome segment carrying Lr19, the Chinese Spring Ph1b mutant was employed to promote recombination between the homoeologous chromosomes of the wheat chromosome 7D and the Th. ponticum chromosome 7E1. Two translocation lines with short Th. ponticum chromosome fragments carrying Lr19 were identified using the genetic markers closely linked to Lr19. Both translocation lines were resistant to 16 Pt races collected throughout China. Importantly, the linkage between Lr19 and yellow pigment content was broken in one of the lines. Thus, the Lr19 linked markers and translocation lines developed in this study are valuable resources in marker-assisted selection as part of common wheat breeding programs.

FANCM interacts with the MHF1-MHF2 complex to limit crossover frequency during rice meiosis.

Crossovers (COs) are necessary for generating genetic diversity that breeders can select, but there are conserved mechanisms that regulate their frequency and distribution. Increasing CO frequency may raise the efficiency of selection by increasing the chance of integrating more desirable traits. In this study, we characterize rice FANCM and explore its functions in meiotic CO control. FANCM mutations do not affect fertility in rice, but they cause a great boost in the overall frequency of COs in both inbred and hybrid rice, according to genetic analysis of the complete set of fancm zmm (hei10, ptd, shoc1, mer3, zip4, msh4, msh5, and heip1) mutants. Although the early homologous recombination events proceed normally in fancm, the meiotic extra COs are not marked with HEI10 and require MUS81 resolvase for resolution. FANCM depends on PAIR1, COM1, DMC1, and HUS1 to perform its functions. Simultaneous disruption of FANCM and MEICA1 synergistically increases CO frequency, but it is accompanied by nonhomologous chromosome associations and fragmentations. FANCM interacts with the MHF complex, and ablation of rice MHF1 or MHF2 could restore the formation of 12 bivalents in the absence of the ZMM gene ZIP4. Our data indicate that unleashing meiotic COs by mutating any member of the FANCM-MHF complex could be an effective procedure to accelerate the efficiency of rice breeding.

Programmed DNA elimination in Mesorhabditis nematodes

Some species undergo programmed DNA elimination (PDE), whereby portions of the genome are systematically destroyed in somatic cells. PDE has emerged independently in several phyla, but its function is unknown. Although the mechanisms are partially solved in ciliates, PDE remains mysterious in metazoans because the study species were not yet amenable to functional approaches. We fortuitously discovered massive PDE in the free-living nematode genus Mesorhabditis, from the same family as C.elegans. As such, these species offer many experimental advantages to start elucidating the PDE mechanisms in an animal. Here, we used cytology to describe the dynamics of chromosome fragmentation and destruction in early embryos. Elimination occurs once in development, at the third embryonic cell division in the somatic blastomeres. Chromosomes are first fragmented during S phase. Next, some of the fragments fail to align on the mitotic spindle and remain outside the re-assembled nuclei after mitosis. These fragments are gradually lost after a few cell cycles. The retained fragments form new mini chromosomes, which are properly segregated in the subsequent cell divisions. With genomic approaches, we found that Mesorhabditis mainly eliminate repeated regions and also about a hundred genes. Importantly, none of the eliminated protein-coding genes are shared between closely related Mesorhabditis species. Our results strongly suggest PDE has not been selected for regulating genes with important biological functions in Mesorhabditis but rather mainly to irreversibly remove repeated sequences in the soma. We propose that PDE may target genes, provided their elimination in the soma is invisible to selection.

An efficient method for targeted cloning of large DNA fragments from Streptomyces.

Cloning of large DNA fragments from microorganisms becomes increasingly important but remains seriously challenging due to the complexity and diversity of genetic background. In particular, the methods with high precision and efficiency are in great need for obtaining intact biosynthetic gene clusters (BGCs) of microbial natural products. Here, we report a new strategy for targeted cloning of large DNA fragments (TCLD) from different bacteria. Using this method, precise cloning of desired E. coli chromosomal fragments up to 201kb was achieved with 53% positive rate. Moreover, its application in cloning of large BGCs with high G + C content and multiple repetitive sequences was also demonstrated, including the 98kb tylosin BGC (tyl), 128kb daptomycin BGC (dpt), and 127kb salinomycin BGC (sal). Subsequently, heterologous expression of the cloned tyl BGC in Streptomyces coelicolor M1146 led to the production of tylosins in the resulting recombinant strains. And also, its introduction into Streptomyces fradiae ATCC 19609, a native producer of tylosin, effectively increased tylosin yield to 230%. Hence, TCLD is a powerful tool for cloning large BGCs and would facilitate the discovery of bioactive substances from microbial resources. KEY POINTS: • TCLD is an efficient method for cloning large DNA fragments. • Repeat sequence-mediated intra-molecular cyclization improves the cloning efficiency. • TCLD combined with scarless editing allows unlimited modifications on BGCs.

Multiple Chromosome Fissions, Including That of the X Chromosome, in Aulacocyclus tricuspis Kaup (Coleoptera, Passalidae) from New Caledonia: Characterization of a Rare but Recurrent Pathway of Chromosome Evolution in Animals.

The male karyotype of Aulacocyclus tricuspis Kaup 1868 (Coleoptera, Scarabaeoidea, Passalidae, Aulacocyclinae) from New Caledonia contains an exceptionally high number of chromosomes, almost all of which are acrocentric (53,X1X2Y). Unlike the karyotypes of other species of the pantropical family Passalidae, which are principally composed of metacentric chromosomes, this karyotype is derived by fissions involving almost all the autosomes after breakage in their centromere region. This presupposes the duplication of the centromeres. More surprising is the X chromosome fragmentation. The rarity of X chromosome fission during evolution may be explained by the deleterious effects of alterations to the mechanisms of gene dosage compensation (resulting from the over-expression of the unique X chromosome in male insects). Herein, we propose that its occurrence and persistence were facilitated by (1) the presence of amplified heterochromatin in the X chromosome of Passalidae ancestor, and (2) the capacity of heterochromatin to modulate the regulation of gene expression. In A. tricuspis, we suggest that the portion containing the X proper genes and either a gene-free heterochromatin fragment or a fragment containing a few genes insulated from the peculiar regulation of the X by surrounding heterochromatin were separated by fission. Finally, we show that similar karyotypes with multiple acrocentric autosomes and unusual sex chromosomes rarely occur in species of Coleoptera belonging to the families Vesperidae, Tenebrionidae, and Chrysomelidae. Unlike classical Robertsonian evolution by centric fusion, this pathway of chromosome evolution involving the centric fission of autosomes has rarely been documented in animals.

P-287 Morphokinetic analysis of early embryos subjected to double stranded DNA damage provides evidence for cell cycle checkpoint activity

Abstract Study question Is there evidence of cell cycle checkpoint activation in preimplantation embryos with double stranded breaks (DSBs) in their DNA, induced using CRISPR? Summary answer Cells with persistent double strand DNA damage exhibit longer timeframes to reach key morphological milestones than those with successful repair, consistent with checkpoint activation. What is known already In most cell types, DNA damage leads to activation of cell cycle checkpoints that halt the cycle while DNA repair is attempted. It has been hypothesised that early embryos lack (or have relaxed) checkpoints, and that this may be necessary to allow the embryo to divide rapidly and synchronously during the first few mitoses. It is thought that maternal (oocyte derived) inhibitors may be responsible for suppressing checkpoints until activation of the embryonic genome. Inadequate checkpoint control may be responsible for the genetic instability and sensitivity to DNA damage seen during early preimplantation stages, which is of clinical importance. Study design, size, duration 84 embryos were generated for research in an IRB approved study. For this purpose, donor oocytes were fertilised with donor sperm using ICSI. 51 of the resulting embryos served as controls, while in the other 33 double strand DNA breaks were created in a highly controlled fashion, directed at specific genomic sites using CRISPR-Cas9 technology. Successfully fertilised oocytes underwent culture in a time-lapse incubator and the duration of key developmental events were carefully timed. Participants/materials, setting, methods Precise induction of DNA damage involved injection of CRISPR-Cas9 ribonuclear complex (RNP), along with the sperm at the time of fertilization (ICSI). All embryos were disaggregated on day-3 and their cells subjected to whole genome amplification. Amplified products underwent low-pass next generation sequencing to detect segmental aneuploidy related to failure of DNA repair, while the site targeted using CRISPR-Cas9 was PCR amplified and sequenced to confirm whether it had successfully undergone repair. Main results and the role of chance Embryos that successfully repaired the induced DNA damage showed timings of pronuclei appearance/disappearance and cell divisions that were indistinguishable from control embryos. Rates of embryo arrest prior to completion of the second mitotic division were also similar between the two groups (25% versus 24%). In contrast, embryos with unresolved DNA damage, as evidenced by the detection of chromosomal fragments involving a breakpoint at the site targeted using CRISPR, were delayed in reaching the same developmental milestones (p < 0.0001 for time to first cleavage division) and displayed a much higher incidence of arrest (63% before the second mitotic division; p = 0.0002). The delay in mitotic progression in blastomeres with DNA damage represents strong evidence that a checkpoint is active in the cells of cleavage stage embryos, sensing double strand DNA breaks and slowing the cell cycle. However, the fact that 36% of embryos with unresolved DNA damage continued to progress, albeit at a slower rate, is consistent with the notion that checkpoint control is less stringent in early human embryos. This relaxation of control is likely to contribute to the genetic instability seen at the cleavage stage, including a risk of unresolved DNA damage and a high frequency of chromosomal malsegregation (causing mosaicism). Limitations, reasons for caution While altered cell cycle timings are consistent with checkpoint activation, other factors could conceivably influence the duration of key morphokinetic events. Complimentary experiments to test the functionality of specific checkpoints and/or the activity of their individual components will be required for definitive proof that embryonic checkpoints are active but weakened. Wider implications of the findings Segmental aneuploidy, micronucleation and mosaicism are frequently seen in human preimplantation embryos and are associated with reduced likelihood of ongoing pregnancy. Such abnormalities are symptomatic of genetic instability associated with excessively permissive checkpoints. These results highlight the need for culture systems that protect embryos from cellular stressors, especially DNA damage. Trial registration number N.A.

QTL Mapping by Chromosome Segment Substitution Lines (CSSLs) Reveals Candidate Gene Controlling Leaf Sucrose Content in Soybean (Glycine max (L.) Merr.)

Understanding the genetic basis of leaf sucrose content can provide a novel way in improving soybean yields. To identify the related QTLs, 190 materials of chromosome fragment substitution lines (CSSLs) were used in this study. The CSSLs were developed from the cross between the cultivated soybean Suinong 14 (SN14) and wild soybean ZYD00006. Only one QTL with a high logarithm of odds (LOD) score was detected in 2021 and 2022 among 3780 bin markers (combined by 580,524 SNPs) distributed in 20 chromosomes. Nine candidate genes were screened and Glyma.14G029100 was considered as the hub gene. A promoter difference and CDS mutant was found among the parents and the reference genome, which lead to the relative transcriptional level difference.. Our results lay the groundwork for further research into its genetic mechanism.

Testing the generalizability of cfDNA fragmentomic features across different studies for cancer early detection

cfDNA fragmentomic features have been used in cancer detection models; however, the generalizability of the models needs to be tested. We proposed a type of cfDNA fragmentomic feature named chromosomal arm-level fragment size distribution (ARM-FSD), evaluated and compared its performance and generalizability for lung cancer and pan-cancer detection with existing cfDNA fragmentomic features (as reference) by using cohorts from different institutions. The ARM-FSD lung cancer model outperformed the reference model by ∼10% when being tested by two external cohorts (AUC: 0.97 vs. 0.86; 0.87 vs. 0.76). For pan-cancer detection, the performance of the ARM-FSD based model is consistently higher than the reference (AUC: 0.88 vs. 0.75, 0.98 vs. 0.63) in a pan-cancer and a lung cancer external validation cohort, indicating that ARM-FSD model produces stable performance across multiple cohorts. Our study reveals ARM-FSD based models have a higher generalizability, and highlights the necessity of cross-study validation for predictive model development.

Multiomics and Multidimensional Testing for Efficacy Monitoring of Patients with Lymphoma

To explore the role of a new blood-based, multiomics and multidimensional method for evaluating the efficacy of patients with lymphoma. 10 ml peripheral blood was extracted from each patient, and the genomic copy number aberrations (CNA) and fragment size (FS) were evaluated by low-depth whole genome sequencing of cfDNA, and the level of a group of plasma tumor marker (PTM) were detected at the same time. The cancer efficacy score (CES) was obtained by standardized transformation of the value of above three numerical indexes, and the changes of CES before and after treatment were compared to evaluate the patient's response to the treatment regimen. A total of 35 patients' baseline data were collected, of which 23 cases (65.7%) had elevated CES values. 18 patients underwent the first time test. The results showed that the CES value of 9 patients with positive baseline CES decreased significantly at the first test, and the efficacy evaluation was PR, which was highly consistent with the imaging evaluation results of the same period. At the same time, the CNA variation spectrum of all patients were evaluated and it was found that 23 patients had partial amplification or deletion of chromosome fragments. The most common amplification site was 8q24.21, which contains important oncogenes such as MYC. The most common deletion sites were 1p36.32, 4q21.23, 6q21, 6q27, 14q32.33, and tumor suppressor-related genes such as PRDM1, ATG5, AIM1, FOXO3 and HACE1 were expressed in the above regions, so these deletions may be related to the occurrence and development of lymphoma. With the advantages of more convenience, sensitivity and non-invasive, this multiomics and multidimensional efficacy detection method can evaluate the tumor load of patients with lymphoma at the molecular level, and make more accurate efficacy evaluation, which is expected to serve the clinic better.

CIP2A and TOPBP1: Molecular lassos that herd pulverized micronuclear chromosomes

Lin etal.1 demonstrate that acentric chromosome fragments generated within micronuclei are tethered by the CIP2A-TOPBP1 complex during mitosis, thus promoting clustered segregation of the fragments to a single daughter cell nucleus and facilitating re-ligation with limited chromosomal scattering and loss.

High-Quality Chromosome-Level Genome Assembly of the Corsac Fox (Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments.

The Corsac fox (Vulpes corsac) is a species of fox distributed in the arid prairie regions of Central and Northern Asia, with distinct adaptations to dry environments. Here, we applied Oxford-Nanopore sequencing and a chromosome structure capture technique to assemble the first Corsac fox genome, which was then assembled into chromosome fragments. The genome assembly has a total length of 2.2 Gb with a contig N50 of 41.62 Mb and a scaffold N50 of 132.2 Mb over 18 pseudo-chromosomal scaffolds. The genome contained approximately 32.67% of repeat sequences. A total of 20,511 protein-coding genes were predicted, of which 88.9% were functionally annotated. Phylogenetic analyses indicated a close relation to the Red fox (Vulpes vulpes) with an estimated divergence time of ~3.7 million years ago (MYA). We performed separate enrichment analyses of species-unique genes, the expanded and contracted gene families, and positively selected genes. The results suggest an enrichment of pathways related to protein synthesis and response and an evolutionary mechanism by which cells respond to protein denaturation in response to heat stress. The enrichment of pathways related to lipid and glucose metabolism, potentially preventing stress from dehydration, and positive selection of genes related to vision, as well as stress responses in harsh environments, may reveal adaptive evolutionary mechanisms in the Corsac fox under harsh drought conditions. Additional detection of positive selection for genes associated with gustatory receptors may reveal a unique desert diet strategy for the species. This high-quality genome provides a valuable resource for studying mammalian drought adaptation and evolution in the genus Vulpes.

An optimal guidance strategy for fire evacuations: A hybrid modeling approach

Evacuation plans are subject to many restrictions in the event of a fire, and unreasonable evacuation guidance methods can affect efficiency and even cause danger. In the current study, we investigate the optimal guidance strategy for fire evacuation to obtain the optimal guider layout and the evacuation paths. The environmental constraints are generated in conjunction with FDS fire simulation to transform the evacuation space into a pseudo-static obstacle grid. A multi-objective model of the guider layout is constructed, and the guider number is used as an optimization variable. The pseudo-static obstacle grid is combined with the exit fluency strategy to plan paths. The evacuation time and cost of the crowd are adopted as two objective functions. Finally, the optimal guider layout is generated by iterative optimization of NSGA-II algorithm with the introduction of a chromosome fragment deletion operator. The simulation results and comparative analysis indicate that the model can improve fire evacuation safety, enhance the utilization and balance of each exit, and reduce evacuation time and resource redundancy.

An Analysis of Genetic Predisposition to Hereditary Catalepsy in a Mouse Model of Neuropsychiatric Disorders Using Whole-Genome Sequencing Data.

Catalepsy is a behavioral condition that is associated with severe psychopathologies, including schizophrenia, depression, and Parkinson's disease. In some mouse strains, catalepsy can be induced by pinching the skin at the scruff of the neck. The main locus of hereditary catalepsy in mice has recently been linked to the 105-115 Mb fragment of mouse chromosome 13 by QTL analysis. We performed whole-genome sequencing of catalepsy-resistant and catalepsy-prone mouse strains in order to pinpoint the putative candidate genes related to hereditary catalepsy in mice. We remapped the previously described main locus for hereditary catalepsy in mice to the chromosome region 103.92-106.16 Mb. A homologous human region on chromosome 5 includes genetic and epigenetic variants associated with schizophrenia. Furthermore, we identified a missense variant in catalepsy-prone strains within the Nln gene. Nln encodes neurolysin, which degrades neurotensin, a peptide reported to induce catalepsy in mice. Our data suggest that Nln is the most probable candidate for the role of major gene of hereditary, pinch-induced catalepsy in mice and point to a shared molecular pathway between catalepsy in mice and human neuropsychiatric disorders.

Antimitotic and genotoxic effect of methanolic extracts of leaves of Peganum harmala L. on the meristematic cells of Allium cepa L.

Medicinal plants are an inexhaustible source of molecules with several biological activities. The main objective of this research was the evaluation of the antimitotic and genotoxic effect by the Allium cepa test of the methanolic extract of the leaves of Peganum harmala, a spontaneous plant from the arid zones of Algeria (Timzerth, Laghouat). Different concentrations (1, 4, 10, and 16 mg∙mL-1) of the extract, as well as two standards (colchicine and quercetin) at 1 mg∙mL-1 concentration were tested. Mitotic index (MI), limit value for cytotoxicity (LVC), phase index (PI), and aberration indexes (AI) were calculated, and different aberrations were identified in treated meristematic onion cells. Statistical analyses by ANOVA and Newman-Keuls test were performed. The results confirmed our previous findings that the methanolic extract has an anti-mitotic effect similar to that of the standards. The increase in extract concentrations was accompanied by a decrease in the various indexes calculated. The extracts blocked mitosis in prophase which was predominantly present, and caused increase in abnormalities, represented by dominant rates of agglutinations, chromosomal fragmentations and binuclear cells. confirmed that the effect was independent of concentrations, though to varying degrees.

A tubule-sheet continuum model for the mechanism of nuclear envelope assembly.

Nuclear envelope (NE) assembly defects cause chromosome fragmentation, cancer, and aging. However, major questions about the mechanism of NE assembly and its relationship to nuclear pathology are unresolved. In particular, how cells efficiently assemble the NE starting from vastly different, cell type-specific endoplasmic reticulum (ER) morphologies is unclear. Here, we identify a NE assembly mechanism, "membrane infiltration," that defines one end of a continuum with another NE assembly mechanism, "lateral sheet expansion," in human cells. Membrane infiltration involves the recruitment of ER tubules or small sheets to the chromatin surface by mitotic actin filaments. Lateral sheet expansion involves actin-independent envelopment of peripheral chromatin by large ER sheets that then extend over chromatin within the spindle. We propose a "tubule-sheet continuum" model that explains the efficient NE assembly from any starting ER morphology, the cell type-specific patterns of nuclear pore complex (NPC) assembly, and the obligatory NPC assembly defect of micronuclei.

Cytogenetic disorders in young cattle vaccinated against trichophytosis

This article continues a series of works by the authors devoted to most of the karyopathological effects of vaccines used in agriculture. The authors of the test cytogenetic analysis of the impact caused by the LTF130 vaccine from an attenuated culture of the fungus Trichophyton verrucosum TF-130 L VGNKI in peripheral blood lymphocytes of healthy 30-day-old healthy Holstein Colonial calves. The experiment was conducted on the material and technical basis of two departments: veterinary genetics and biotechnology, epizootiology and microbiology, FSBEI HE “Novosibirsk State Agrarian University”. The authors found that the spectrum of induced cytogenetic disorders included polyploid, hyper- and hypoploid cells, chromatid and chromosome breaks, and single and paired fragments of chromosomes, regardless of the time since the introduction of the vaccine. They did not differ from the spectrum of spontaneously occurring mutations in this species. It was noted that among cells with a changed number of chromosomes, polyploid cells with tetraploid sets (79.3–91.9%) and aneuploid cells with hypoploid sets (45.7–74.3%) of chromosomes predominated. The authors found a decrease in the frequency of polyploid cells seven days after vaccination of calves against trichophytosis to 1.6%, control - 3.4 ± 0.57% (P < 0.01). An increase in the frequency of hyperploid cells 14 days after vaccination of calves against trichophytosis up to 3.69% was revealed due to trisomy (2.91 ± 0.74%, P < 0.05) and tetrasomy (0.78 ± 0.39%, P < 0.01). An increase in the frequency of cells with chromosome aberrations was found 2 and 7 days after vaccination of calves against trichophytosis, respectively, to 5.74 and 5.24% due to breaks (4.49 ± 1.03 and 3.31 ± 0.66%, P < 0.01–0.01) and paired fragments of chromosomes (1.38 ± 0.43%, Р < 0.05).

Finger printing-RFLP analysis of chromosomal IS6110 insertion sequence and PCR diagnosis of pulmonary tuberculosis, isolated from patients in El Hajeb region of Morocco

Tuberculosis (TB) is one of the contagious diseases caused by M. tuberculosis (MTB) bacteria. Prompt diagnosis is one of the active solutions to control the spread of this infection. Besides, a targeted, specific and non-complex diagnosis can prove promising in this type of epidemic. This study was designed to compare the efficiencies of a diagnosis by Ziehl-Neelsen staining (ZN) and by the polymerase chain reaction (PCR) technique. Samples presented smear-positive pulmonary TB were subjected to Chromosomal restriction fragment length polymorphism of IS6110 (IS6110-RFLP) for fingerprinting profile determination.The results showed that out of 100 sputum samples of suspected case, 53 were positive. Numbers of positive individuals for tuberculosis obtained by the different diagnostic techniques, to know, (ZN staining; culture and PCR) were respectively: 6, 25 and 22. Chromosomal RFLP fingerprinting profile revealed the presence of five different genotypes obtained from seven tested isolates.These results suggest that molecular techniques are alternative tool for fast and specific diagnosis of pulmonary MTB from sputum.

Synthetic maize centromeres transmit chromosomes across generations.

Centromeres are long, often repetitive regions of genomes that bind kinetochore proteins and ensure normal chromosome segregation. Engineering centromeres that function in vivo has proven to be difficult. Here we describe a tethering approach that activates functional maize centromeres at synthetic sequence arrays. A LexA-CENH3 fusion protein was used to recruit native Centromeric Histone H3 (CENH3) to long arrays of LexO repeats on a chromosome arm. Newly recruited CENH3 was sufficient to organize functional kinetochores that caused chromosome breakage, releasing chromosome fragments that were passed through meiosis and into progeny. Several fragments formed independent neochromosomes with centromeres localized over the LexO repeat arrays. The new centromeres were self-sustaining and transmitted neochromosomes to subsequent generations in the absence of the LexA-CENH3 activator. Our results demonstrate the feasibility of using synthetic centromeres for karyotype engineering applications.

Levels and Cytogenotoxicity of Phytochemicals and Heavy Metals in Guava (Psidium guajava L.) Leaves Obtained From Birnin Kebbi, Nigeria

Background: Psidium guajava (guava tree) is widely used in Nigeria to treat diseases. However, a paucity of information exists on the safety of the plant. Objectives: This study determined the safety of P. guajava leaves collected in Birnin Kebbi, Nigeria. Methods: The methanolic extract of the plant’s leaves was subjected to phytochemical and heavy metal screening using standard protocols, and thereafter, subjected to a cytogenetoxicity test using the Allium cepa toxicity assay. Twenty-one A. cepa bulbs divided equally into seven groups were grown over beakers containing distilled water (negative control), formaldehyde (positive control), as well as 0.25, 0.5, 1, 2, and 4 g of the extract, respectively, for five days. The root-tip cells of the A. cepa bulbs were treated and then examined for chromosomal aberrations. Results: The phytochemical screening revealed high levels of saponins, and moderate levels of phenols, tannins, and flavonoids, while quinones and terpenoids were sparingly available. The heavy metal analysis showed non-permissible levels of cadmium and zinc, while two other tested heavy metals (lead and copper) were undetected. Except for the A. cepa treated with 0.25 and 0.5 g, the extract induced dose-dependent root growth and mitotic index inhibition (P<0.05). The extract also induced cytogenetic effects, mainly sticky, vagrant, and fragmented chromosomes as well as anaphase bridges. Conclusions: It can be inferred from the results that low to medium doses of the extract are safe but may elicit harmful effects at high doses. Advice from a phytomedicine or phytotherapy expert should be sought before using it.

Machine learning-aided scoring of synthesis difficulties for designer chromosomes.

Designer chromosomes are artificially synthesized chromosomes. Nowadays, these chromosomes have numerous applications ranging from medical research to the development of biofuels. However, some chromosome fragments can interfere with the chemical synthesis of designer chromosomes and eventually limit the widespread use of this technology. To address this issue, this study aimed to develop an interpretable machine learning framework to predict and quantify the synthesis difficulties of designer chromosomes in advance. Through the use of this framework, six key sequence features leading to synthesis difficulties were identified, and an eXtreme Gradient Boosting model was established to integrate these features. The predictive model achieved high-quality performance with an AUC of 0.895 in cross-validation and an AUC of 0.885 on an independent test set. Based on these results, the synthesis difficulty index (S-index) was proposed as a means of scoring and interpreting synthesis difficulties of chromosomes from prokaryotes to eukaryotes. The findings of this study emphasize the significant variability in synthesis difficulties between chromosomes and demonstrate the potential of the proposed model to predict and mitigate these difficulties through the optimization of the synthesis process and genome rewriting.