Aspects Of Phenotype Research Articles

Psychometric evaluation of the Autism Symptom Dimensions Questionnaire.

To replicate and extend previous psychometric findings for the Autism Symptom Dimensions Questionnaire (ASDQ). Using a cross-sectional design in two samples, including a total of 3366 children and adolescents (aged 2-17 years; 1399 with autism spectrum disorder) and a small case series, factor structure, measurement invariance, reliability, construct validity, screening and diagnostic efficiency, and detection of reliable change were examined for the ASDQ. Strong psychometric properties were observed, including replicable factor structure, strong measurement invariance, adequate-to-excellent scale and conditional reliability, strong convergent and discriminant validity, and good screening efficiency. Importantly, two crucial measurement aspects required for a good treatment outcome measure were found, that is, good test-retest stability and the potential to detect reliable change. As expected for an informant-reported questionnaire, diagnostic efficiency was weak. The ASDQ showed evidence of favorable and well-replicated psychometric properties in two samples. Good screening but weak diagnostic efficiency, coupled with good test-retest stability, suggest that optimal clinical use is in screening and in detailed clinical characterization beyond what is offered by current informant-reported measures, with the potential for monitoring response to intervention. Despite relative brevity, the ASDQ provides good coverage of broad and specific aspects of the autism behavioral phenotype, which is consistent with the criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition.

Association of Physiological Reserve Obtained from Cardiopulmonary Exercise Testing and Frailty with All-Cause Mortality in Hemodialysis Patients.

Potential impairment of exercise capacity is prevalent even in patients undergoing hemodialysis without frailty. Cardiopulmonary exercise testing (CPET) can detect physiological reserves such as cardiopulmonary, muscle, and autonomic function. We hypothesized that these indices could accurately determine the prognosis of patients on hemodialysis and analyzed them based on their relationship to frailty. In this two-center prospective cohort study hemodialysis patients from Japan, participants underwent CPET and physical assessment to evaluate peak oxygen uptake (peak VO2, indicator of exercise capacity), peak work rate (WR, indicator of muscle function), ventilatory equivalent for carbon dioxide (VE/VCO2) slope (indicator of cardiac reserve), heart rate reserve (indicator of chronotropic incompetence), and frailty phenotype. Survival was followed-up for up to 5 years. Data from 189 patients (median [IQR] age: 71 [62, 77] years) were analyzed. All CPET indicators showed a consistent nonlinear relationship with all-cause mortality after adjustment: for peak VO2, hazard ratio [HR] 0.79 [95% CI: 0.71, 0.88], P <0.001; for peak WR, HR 0.95 [95% CI: 0.93, 0.97], P <0.001; for VE/VCO2 slope, HR 1.09 [95% CI: 1.05, 1.13], P <0.001; for heart rate reserve, HR 0.96 [95% CI: 0.93, 0.99], P=0.02). Frailty phenotype was associated with mortality after adjustment (HR 1.73 [95% CI: 1.06, 2.81], P=0.03); however, this association was not statistically significant in the model after adding peak VO2 (P=0.41). Furthermore, in both subgroups with and without frailty, CPET measures were significantly associated with mortality risk (peak VO2, peak WR, and VE/VCO2 slope: P <0.05). The peak VO2 (Δ area under the curve [AUC] 0.09, 95% CI: 0.02, 0.16) or the peak WR (ΔAUC 0.09, 95% CI: 0.02, 0.15) most significantly improved the prognostic accuracy. Results showed the fragile aspect of the frailty phenotype in the hemodialysis population and the superior ability of CPET to indicate death risk complementing that aspect.

Assessing pathogenicity of mismatch repair variants of uncertain significance by molecular tumor analysis

Functional analyses are the main method to classify mismatch repair (MMR) gene variants of uncertain significance (VUSs). However, the pathogenicity remains unclear for many variants because of conflicting results between clinical, molecular, and functional data. In this study, we evaluated whether whole exome sequencing (WES) could add another layer of evidence to elucidate the pathogenicity of MMR variants with conflicting interpretations. WES was performed on formalin-fixed paraffin-embedded tumor tissue of eight patients with a constitutional MMR VUS (seven families), including eight colorectal and two endometrial carcinomas and one ovarian carcinoma. Cell-free CIMRA assays were performed to assign Odds of Pathogenicity to these VUSs. In four families, seven tumors showed MMR deficiency-associated mutational signatures, supporting the pathogenicity of the VUS. Moreover, somatic (second) MMR hits identified in the WES data were found to explain MMR staining patterns when the MMR staining was discordant with the reported germline MMR gene variant. In conclusion, WES did not significantly reclassify VUS in these cases but clarified some phenotypic aspects such as age of onset and explanations in case of discordant MMR stainings.

Cutting the sap: First molecular phylogeny of twig‐girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviours contributed to morphological evolution

AbstractUnderstanding how novel adaptive traits arise, evolve and impact other aspects of an organism's phenotype is a foundational question in evolutionary biology. We explore this by focusing on Onciderini (Coleoptera: Cerambycidae: Lamiinae), a tribe of longhorn beetles commonly referred to as twig girdlers because the females of some species girdle live trees to deposit their eggs. We reconstructed the first time‐calibrated phylogeny of the Onciderini, based on three genetic markers (cytochrome c oxidase subunit 1 ‘cox1’, Wingless ‘Wg’ and carbamoyl‐phosphate synthase domain of the CAD locus ‘CPS’), and used morphometric data, employing multiple models of trait evolution and phylogenetic regressions, to assess whether girdling behaviour predicts head size or head size sexual dimorphism. Our results indicate that onciderines originated c. 49 million years ago ‘Ma’ (95% highest posterior densities ‘HPD’: 44.1–54.57 Ma) and consist of two major lineages, which we formalize as subtribes Hypsiomina and Onciderina. Additionally, our analyses revealed several taxonomic inconsistencies within the tribe, which we rectify by proposing new synonymies, including Jamesia Jekel as a synonym of Hypselomus Perty, Cipriscola Dillon &amp; Dillon of Hypsioma Audinet‐Serville and Psyllotoxus Thomson and Taricanus Thomson as a synonym of Oncideres Lacordaire, and a new combination for Periergates kenjii Nearns &amp; Swift as Oncideres kenjii (Nearns &amp; Swift) comb. nov. Using this new phylogenetic framework, we identified five independent unidirectional origins of girdling behaviour within the tribe. Overall, our results suggest that girdling influences head size evolution in Onciderini, as it is associated with an increase in both male and female head size of girdler species. Despite this, girdling and non‐girdling lineages do not consistently differ in head size sexual dimorphism. This study refines the classification of Onciderini and marks a significant step in understanding the evolutionary dynamics shaping the diversity of twig‐girdler beetles, a group with notable ecological and economic importance.

Acute introduction of monomeric or multimeric α-synuclein induces distinct impacts on synaptic vesicle trafficking at lamprey giant synapses.

Synaptic aggregation of α-synuclein often occurs in Parkinson's disease (PD), dementia with Lewy bodies (DLB) and other synucleinopathies and is associated with cognitive deficits and dementia. Thus, it is important to understand how accumulation of α-synuclein affects synapse structure and function. Native, physiological α-synuclein comprises a mixture of tetramers and related physiological oligomers (60-100kDa) in equilibrium with monomeric α-synuclein. We previously demonstrated that acutely increasing the levels of physiologicalα-synuclein impaired intracellular synaptic vesicle trafficking and produced a pleiotropic phenotype, raising questions about which aspects of the synaptic phenotype were due to multimeric versus monomeric α-synuclein. Here, we address this by taking advantage of the unique features of the lamprey giant reticulospinal (RS) synapse, a vertebrate synapse that is amenable to acute perturbations of presynaptic processes via microinjection of purified proteins. α-Synuclein monomers and multimers were purified from HEK cells and separately introduced to lamprey synapses. Ultrastructural analysis revealed that both multimeric and monomeric α-synuclein impaired intracellular vesicle trafficking, leading to a loss of synaptic vesicles and buildup of endosomes. However, while monomeric α-synuclein additionally induced atypical fusion/fission at the active zone and impaired clathrin-mediated endocytosis, multimeric α-synuclein did not. Conversely, multimeric α-synuclein led to a decrease in synaptic vesicle docking, which was not observed with monomeric α-synuclein. These data provide further evidence that different molecular species of α-synuclein produce distinct and complex impacts on synaptic vesicle trafficking and reveal important insights into the cell biological processes that are affected in PD and DLB. KEY POINTS: α-Synuclein accumulation at synapses is associated with cognitive decline and dementia in Parkinson's disease and other synucleinopathies. We previously showed that acute introduction of excess human brain-derived α-synuclein to lamprey giant synapses caused pleiotropic phenotypes on synaptic vesicle trafficking, probably due to the mixture of molecular species of α-synuclein. Here, we dissected which aspects of the synaptic phenotypes were caused by monomeric (14kDa) or multimeric (60-100kDa) α-synuclein by purifying each molecular species and introducing each one separately to synapses via axonal microinjection. While monomeric α-synuclein inhibited clathrin-mediated synaptic vesicle endocytosis, multimeric α-synuclein primarily impaired endosomal trafficking. These findings reveal that different molecular species of α-synuclein have distinct impacts on synapses, suggesting different cellular and molecular targets.

Sex differences in sleep deficits in mice with an autism-linked Shank3 mutation

BackgroundInsomnia is more prevalent in individuals with Autism Spectrum Disorder (ASD), can worsen core-symptoms and reduces quality of life of both individuals and caregivers. Although ASD is four times more prevalent in males than females, less is known about sex specific sleep differences in autistic individuals. Recent ASD studies suggest that sleep problems may be more severe in females, which aligns with the sex bias seen in insomnia for the general population. We have previously shown that male mice with a mutation in the high confidence ASD gene Shank3, Shank3∆C, recapitulate most aspects of the ASD insomnia phenotype. The objective of the present study was to leverage the Shank3∆C model to investigate sex-specific effects in sleep using polysomnography.MethodsAdult male and female Shank3∆C and wildtype (WT) littermates were first recorded for 24 h of baseline recordings. Subsequently, they were sleep deprived (SD) for five hours via gentle handling and allowed 19 h of recovery sleep to characterize the homeostatic response to SD. Vigilance states (rapid eye movement (REM) sleep, non-rapid eye movement (NREM) sleep and wake) were assigned by manual inspection using SleepSign. Data processing, statistical analysis and visualization were conducted using MATLAB.ResultsSex and genotype effects were found during baseline sleep and after SD. At baseline, male Shank3∆C mice sleep less during the dark period (active phase) while female Shank3∆C mice sleep less during the light period (rest phase) and sleep more during the dark period. Both male and female Shank3∆C mice show reduced spectral power in NREM sleep. We detect a significant effect of sex and genotype in sleep onset latency and homeostatic sleep pressure (sleepiness). In addition, while male Shank3∆C mice fail to increase sleep time following SD as seen in WT, female Shank3∆C mice decrease sleep time.ConclusionsOverall, our study demonstrates sex differences in sleep architecture and homeostatic response to SD in adult Shank3∆C mice. Thus, our study demonstrates an interaction between sex and genotype in Shank3∆C mice and supports the use of the Shank3∆C model to better understand mechanisms contributing to the sex differences in insomnia in ASD in clinical populations.

Genetic And Phenotypic Aspects and Trends of Longevity and Lifetime Production Traits in Friesian Cattle in Egypt

Genetic And Phenotypic Aspects and Trends of Longevity and Lifetime Production Traits in Friesian Cattle in Egypt

Mice with lymphatic dysfunction develop pathogenic lung tertiary lymphoid organs that model an autoimmune emphysema phenotype of COPD.

We have previously shown that mice with a loss of C-type lectin-like type II (CLEC2), which have lymphatic dysfunction due to the role of CLEC2 in platelets for maintaining separation between the venous and lymphatic system, develop lung tertiary lymphoid organ (TLO) formation and lung injury that resembles an emphysema phenotype of chronic obstructive pulmonary disease (COPD). We now sought to investigate whether and how TLOs in these mice may play a pathogenic role in lung injury that is relevant to human disease. We found that inhibiting TLO formation using an anti-CD20 antibody in CLEC2-deficient mice partially blocked the development of emphysema. TLOs in CLEC2-deficient mice were rich in plasma cells and were a source of a broad array of autoantibodies. Chronic cigarette smoke exposure increased the size and number of lung TLOs in CLEC2-deficient mice and was associated with increased markers of antigen presentation and maturation, leading to increased autoantibody deposition. Using lung tissue from patients with COPD, we found an increase in lymphatic markers in patients with an emphysema phenotype and autoreactive TLOs compared with patients with COPD without emphysema that lack prominent TLOs. Taken together, these results demonstrate that emphysema in mice with lymphatic dysfunction can be partially rescued by blocking TLO formation and that these TLOs are the source of autoantibodies that are exacerbated by cigarette smoke. Our work suggests that lymphatic dysfunction in mice may recapitulate some aspects of an autoimmune emphysema phenotype that is seen in a subset of patients with COPD.NEW & NOTEWORTHY The lymphatic vasculature has been implicated in the pathogenesis of lung disease but remains understudied. Here, the authors use a mouse model to show that lymphatic dysfunction leads to a phenotype of emphysema that is characterized by lung tertiary lymphoid organs that are autoreactive and pathogenic. Analysis of human tissue showed increased lymphatic markers in autoimmune emphysema with prominent TLOs, compared with other COPD phenotypes.

Genomics and evolutionary analysis of Chlorella variabilis-infecting viruses demarcate criteria for defining species of giant viruses.

Chloroviruses exhibit a close relationship with their hosts with the phenotypic aspect of their ability to form lytic plaques having primarily guided the taxonomy. However, with the isolation of viruses that are only able to complete their replication cycle in one strain of Chlorella variabilis, systematic challenges emerged. In this study, we described the genomic features of 53 new chlorovirus isolates and used them to elucidate part of the evolutionary history and taxonomy of this clade. Our analysis revealed new chloroviruses with the largest genomes to date (>400 kbp) and indicated that four genomic features are statistically different in the viruses that only infect the Syngen 2-3 strain of C. variabilis (OSy viruses). We found large regions of dissimilarity in the genomes of viruses PBCV-1 and OSy-NE5 when compared with the other genomes. These regions contained genes related to the interaction with the host cell machinery and viral capsid proteins, which provided insights into the evolution of the replicative and structural modules in these giant viruses. Phylogenetic analysis using hallmark genes of Nucleocytoviricota revealed that OSy-viruses evolved from the NC64A-viruses, possibly emerging as a result of the strict relationship with their hosts. Merging phylogenetics and nucleotide identity analyses, we propose strategies to demarcate viral species, resulting in seven new species of chloroviruses. Collectively, our results show how genomic data can be used as lines of evidence to demarcate viral species. Using the chloroviruses as a case study, we expect that similar initiatives will emerge using the basis exhibited here.IMPORTANCEChloroviruses are a group of giant viruses with long dsDNA genomes that infect different species of Chlorella-like green algae. They are host-specific, and some isolates can only replicate within a single strain of Chlorella variabilis. The genomics of these viruses is still poorly explored, and the characterization of new isolates provides important data on their genetic diversity and evolution. In this work, we describe 53 new chlorovirus genomes, including many isolated from alkaline lakes for the first time. Through comparative genomics and molecular phylogeny, we provide evidence of genomic gigantism in chloroviruses and show that a subset of viruses became highly specific for their hosts at a particular point in evolutionary history. We propose criteria to demarcate species of chloroviruses, paving the way for an update in the taxonomy of other groups of viruses. This study is a new and important piece in the complex puzzle of giant algal viruses.

Understanding the chemodiversity of plants: Quantification, variation and ecological function

AbstractPlants produce a great number of phytochemicals serving a variety of different functions. Recently, the chemodiversity of these compounds (i.e., the diversity of compounds produced by a plant) has been suggested to be an important aspect of the plant phenotype that may shape interactions between plants, their environment, and other organisms. However, we lack an agreement on how to quantify chemodiversity, which complicates conclusions about the functional importance of it. Here, we discuss how chemodiversity (deconstructed into components of richness, evenness and disparity) may relate to different ecologically relevant aspects of the phenotype. Then, we systematically review the literature on chemodiversity to examine methodological practices, explore patterns of variability in diversity across different levels of biological organization, and investigate the functional role of this diversity in interactions between plants and other organisms. Overall, the reviewed literature suggests that high chemodiversity is often beneficial for plants, although a heterogeneity of methodological approaches partly limits what general conclusions can be drawn. Importantly, to support future research on this topic, we provide a framework with a decision tree facilitating choices on which measures of chemodiversity are best used in different contexts and outline key questions and avenues for future research. A more thorough understanding of chemodiversity will provide insights into its evolution and functional role in ecological interactions between plants and their environment.

Phenotypical aspects of Culex pipiens biotype pipiens during diapause: Lipid utilization, body size, insemination, and parity

In temperate regions, female Culex pipiens biotype pipiens mosquitoes undergo diapause in winter. Diapausing biotype pipiens mosquitoes are potentially important winter reservoirs for mosquito-borne viruses, such as West Nile virus (WNV), Usutu virus (USUV), and Sindbis virus (SINV). Mosquitoes in diapause have not taken a bloodmeal prior to winter. Therefore, they do not become infected by taking an infectious bloodmeal and as a consequence, vertical transmission is considered the primary mechanism of mosquito-borne virus overwintering. Prior to winter, biotype pipiens mosquitoes build up fat reserves, which they utilize throughout winter. Furthermore, earlier studies have indicated that larger body size is correlated with increased survival during winter. However, not much is known about lipid utilization and body size of wild biotype pipiens mosquitoes in diapause. Therefore, we performed monthly collections of diapausing biotype pipiens mosquitoes in two consecutive winters (2020/2021 and 2021/2022) in bunkers of the New Hollandic Waterline in the Netherlands. Every month, we checked the proportion of inseminated and parous females via microscopy. In addition, we measured wing length as proxy for body size, and assessed total lipid content. Furthermore, we monitored indoor temperature in the overwintering locations. We show that the overwintering sites in our study provide relatively stable environments, in which temperatures rarely drop below 0 °C. The vast majority of biotype pipiens females were inseminated (84.1 %) and nulliparous (97.5 %). We detected differences in body size between but not within the two years of sampling. Additionally, we detected a difference in lipid content between the sampling years. We confirm that the vast majority of diapausing biotype pipiens females are inseminated and nulliparous. This indicates that they did not blood feed prior to winter, which underscores the likeliness of vertical transmission being the primary mechanism behind virus overwintering. The detected difference in body size between years can most likely be attributed to differences in summer conditions the mosquitoes were exposed to as larvae, although this needs confirmation. The difference in lipid depletion could not be explained by differences in climatic conditions. To shed more light on the links between climatic conditions, body size, lipid depletion and the consequences for mosquito population dynamics and arbovirus transmission, future experimental work, for example by arbovirus exposure followed by artificially induced diapause, is desired.

Systemic gene therapy corrects the neurological phenotype in a mouse model of NGLY1 deficiency.

The cytoplasmic peptide:N-glycanase (NGLY1) is ubiquitously expressed and functions as a de-N-glycosylating enzyme that degrades misfolded N-glycosylated proteins. NGLY1 deficiency due to biallelic loss-of-function NGLY1 variants is an ultrarare autosomal recessive deglycosylation disorder with multisystemic involvement; the neurological manifestations represent the main disease burden. Currently, there is no treatment for this disease. To develop a gene therapy, we first characterized a tamoxifen-inducible Ngly1-knockout (iNgly1) C57BL/6J mouse model, which exhibited symptoms recapitulating human disease, including elevation of the biomarker GlcNAc-Asn, motor deficits, kyphosis, Purkinje cell loss, and gait abnormalities. We packaged a codon-optimized human NGLY1 transgene cassette into 2 adeno-associated virus (AAV) capsids, AAV9 and AAV.PHPeB. Systemic administration of the AAV.PHPeB vector to symptomatic iNgly1 mice corrected multiple disease features at 8 weeks after treatment. Furthermore, another cohort of AAV.PHPeB-treated iNgly1 mice were monitored over a year and showed near-complete normalization of the neurological aspects of the disease phenotype, demonstrating the durability of gene therapy. Our data suggested that brain-directed NGLY1 gene replacement via systemic delivery is a promising therapeutic strategy for NGLY1 deficiency. Although the superior CNS tropism of AAV.PHPeB vector does not translate to primates, emerging AAV capsids with enhanced primate CNS tropism will enable future translational studies.

Cockayne syndrome B protein is implicated in transcription and associated chromatin dynamics in homeostatic and genotoxic conditions.

The integrity of the actively transcribed genome against helix-distorting DNA lesions relies on a multilayered cellular response that enhances Transcription-Coupled Nucleotide Excision Repair (TC-NER). When defective, TC-NER is causatively associated with Cockayne-Syndrome (CS), a rare severe human progeroid disorder. Although the presence of unresolved transcription-blocking lesions is considered a driver of the aging process, the molecular features of the transcription-driven response to genotoxic stress in CS-B cells remain largely unknown. Here, an in-depth view of the transcriptional and associated chromatin dynamics that occur in CS-B cells illuminates the role of CSB therein. By employing high-throughput genome-wide approaches, we observed that absence of a functional CSB protein results in a delay in transcription progression, more positioned +1 nucleosomes, and less dynamic chromatin structure, compared to normal cells. We found that early after exposure to UV, CS-B cells released RNA polymerase II (RNAPII) from promoter-proximal pause sites into elongation. However, the magnitude of this response and the progression of RNAPII were reduced compared to normal counterparts. Notably, we detected increased post-UV retainment of unprocessed nascent RNA transcripts and chromatin-associated elongating RNAPII molecules. Contrary to the prevailing models, we found that transcription initiation is operational in CS-B fibroblasts early after UV and that chromatin accessibility showed a marginal increase. Our study provides robust evidence for the role of CSB in shaping the transcription and chromatin landscape both in homeostasis and in response to genotoxic insults, which is independent of its known role in TC-NER, and which may underlie major aspects of the CS phenotype.

Host-driven phenotypic and phenological differentiation in sympatric races of a parasitic plant

Host specificity is a key factor influencing the ecology and evolutionary diversification of parasitic organisms. Host specialisation and geographic isolation are known to lead to the genetic differentiation of allopatric races in parasitic plants. However, how divergence can co-occur in sympatry remains largely unknown. We investigated phenological and phenotypic differentiation and potential reproductive isolation among three sympatric genetic races of Cytinus hypocistis (Cytinaceae) - an extreme endophytic holoparasite with a high degree of host specialisation. We compared spatio-temporal variations in flowering phenology, flower production, floral longevity, floral rewards, and morphology, and conducted inter-race pollinations among three races parasitising Cistus ladanifer, C. salviifolius, and Halimium halimifolium (Cistaceae) in six co-occurring populations. We found that host-defined genetic races differed significantly across multiple phenotypic and phenological aspects – a phenomenon previously overlooked due to the plants’ cryptic morphology. The race parasitising H. halimifolium showed earlier blooming, higher floral display, longer flowers, and higher pollen production and nectar concentration; the race on C. salviifolius showed later flowering, significantly lower floral display and smaller flowers with lower floral rewards; the race on C. ladanifer had intermediate characteristics. Genetic races were interfertile yet may remain differentiated by restricted gene flow and host-driven selection pressures. Together, our data point to a rare case of sympatric divergent evolution hiding in plain sight: apparently morphologically similar co-occurring parasite races can be genetically, phenotypically, and phenologically distinct. This hitherto unreported example of host-driven sympatric diversification challenges how species concepts are applied to cryptic parasitic plant races.

Deep bone oncology Diagnostics: Computed tomography based Machine learning for detection of bone tumors from breast cancer metastasis

PurposeThe objective of this study is to develop a novel diagnostic tool using deep learning and radiomics to distinguish bone tumors on CT images as metastases from breast cancer. By providing a more accurate and reliable method for identifying metastatic bone tumors, this approach aims to significantly improve clinical decision-making and patient management in the context of breast cancer. MethodsThis study utilized CT images of bone tumors from 178 patients, including 78 cases of breast cancer bone metastases and 100 cases of non-breast cancer bone metastases. The dataset was processed using the Medical Image Segmentation via Self-distilling TransUNet (MISSU) model for automated segmentation. Radiomics features were extracted from the segmented tumor regions using the Pyradiomics library, capturing various aspects of tumor phenotype. Feature selection was conducted using LASSO regression to identify the most predictive features. The model’s performance was evaluated using ten-fold cross-validation, with metrics including accuracy, sensitivity, specificity, and the Dice similarity coefficient. ResultsThe developed radiomics model using the SVM algorithm achieved high discriminatory power, with an AUC of 0.936 on the training set and 0.953 on the test set. The model’s performance metrics demonstrated strong accuracy, sensitivity, and specificity. Specifically, the accuracy was 0.864 for the training set and 0.853 for the test set. Sensitivity values were 0.838 and 0.789 for the training and test sets, respectively, while specificity values were 0.896 and 0.933 for the training and test sets, respectively. These results indicate that the SVM model effectively distinguishes between bone metastases originating from breast cancer and other origins. Additionally, the average Dice similarity coefficient for the automated segmentation was 0.915, demonstrating a high level of agreement with manual segmentations. ConclusionThis study demonstrates the potential of combining CT-based radiomics and deep learning for the accurate detection of bone metastases from breast cancer. The high-performance metrics indicate that this approach can significantly enhance diagnostic accuracy, aiding in early detection and improving patient outcomes. Future research should focus on validating these findings on larger datasets, integrating the model into clinical workflows, and exploring its use in personalized treatment planning.

Facing Heavy Metal Stress, What Are the Positive Responses of Melatonin in Plants: A Review

With the growth of the population and the development of modern industry and the economy, the problem of heavy metal pollution in cultivated soil has become increasingly prominent. Moreover, heavy metal poses a serious threat to plant growth due to its characteristics of difficult degradation, high mobility, easy enrichment, and potential toxicity and has become a social topic. Melatonin is a new type of plant hormone widely present in animals, plants, fungi, and bacteria, and its biological role has begun investigated in the last dozen years. Facing heavy metal stress, melatonin can play a pleiotropic role in the physiological processes of plants, such as stress resistance and growth regulation, mitigate the damage caused by stress on plants, and provide a new research idea for alleviating heavy metal stress in plants. From the aspects of the plant phenotype, physiology, element absorption, and molecular structure, this paper, therefore, mainly reviews the effects of melatonin on plants subjected to heavy metal stress and the mechanism of melatonin alleviating heavy metal stress and then puts forward future research directions. This information may be of great significance to the normal growth of crops under heavy metal stress and will provide an important theoretical basis for the genetic improvement of crop resistance in the future.

Exploring the role of FAT genes in Solanaceae species through genome-wide analysis and genome editing.

Plants produce numerous fatty acid derivatives, and some of these compounds have significant regulatory functions, such as governing effector-induced resistance, systemic resistance, and other defense pathways. This study systematically identified and characterized eight FAT genes (Acyl-acyl carrier protein thioesterases), four in the Solanum lycopersicum and four in the Solanum tuberosum genome. Phylogenetic analysis classified these genes into four distinct groups, exhibiting conserved domain structures across different plant species. Promoter analysis revealed various cis-acting elements, most of which are associated with stress responsiveness and growth and development. Micro-RNA (miRNA) analysis identified specific miRNAs, notably miRNA166, targeting different FAT genes in both species. Utilizing clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout, mutant lines for SlFATB1 and SlFATB3 were successfully generated and exhibited diverse mutation types. Biochemical evaluation of selected mutant lines revealed significant changes in fatty acid composition, with linoleic and linolenic acid content variations. The study also explored the impact of FAT gene knockout on tomato leaf architecture through scanning electron microscopy, providing insights into potential morphological alterations. Knocking out of FAT genes resulted in a significant reduction in both trichome and stoma density. These findings contribute to a comprehensive understanding of FAT genes in Solanaceous species, encompassing genetic, functional, and phenotypic aspects.

2-Bromopalmitate treatment attenuates senescence phenotype in human adult cells - possible role of palmitoylation.

Cells may undergo senescence in response to DNA damage, which is associated with cell cycle arrest, altered gene expression and altered cell morphology. Protein palmitoylation is one of the mechanisms by which the DNA damage response is regulated. Therefore, we hypothesized that protein palmitoylation played a role in regulation of the senescent phenotype. Here, we showed that treatment of senescent human vascular smooth muscle cells (VSMCs) with 2-bromopalmitate (2-BP), an inhibitor of protein acyltransferases, is associated with changes in different aspects of the senescent phenotype, including the resumption of cell proliferation, a decrease in DNA damage markers and the downregulation of senescence-associated β-galactosidase activity. The effects were dose dependent and associated with significantly decreased total protein palmitoylation level. We also showed that the senescence-modifying properties of 2-BP were at least partially mediated by the downregulation of elements of DNA damage-related molecular pathways, such as phosphorylated p53. Our data suggest that cell senescence may be regulated by palmitoylation, which provides a new perspective on the role of this posttranslational modification in age-related diseases.

Loss of FMRP affects ovarian development and behaviour through multiple pathways in a zebrafish model of fragile X syndrome.

Fragile X syndrome (FXS) is an inherited neurodevelopmental disorder and the leading genetic cause of autism spectrum disorders. FXS is caused by loss of function mutations in Fragile X mental retardation protein (FMRP), an RNA binding protein that is known to regulate translation of its target mRNAs, predominantly in the brain and gonads. The molecular mechanisms connecting FMRP function to neurodevelopmental phenotypes are well understood. However, neither the full extent of reproductive phenotypes, nor the underlying molecular mechanisms have been as yet determined. Here, we developed new fmr1 knockout zebrafish lines and show that they mimic key aspects of FXS neuronal phenotypes across both larval and adult stages. Results from the fmr1 knockout females also showed that altered gene expression in the brain, via the neuroendocrine pathway contribute to distinct abnormal phenotypes during ovarian development and oocyte maturation. We identified at least three mechanisms underpinning these defects, including altered neuroendocrine signaling in sexually mature females resulting in accelerated ovarian development, altered expression of germ cell and meiosis promoting genes at various stages during oocyte maturation, and finally a strong mitochondrial impairment in late stage oocytes from knockout females. Our findings have implications beyond FXS in the study of reproductive function and female infertility. Dissection of the translation control pathways during ovarian development using models like the knockout lines reported here may reveal novel approaches and targets for fertility treatments.

Endothelial LATS2 is a suppressor of bone marrow fibrosis

Myelofibrosis and osteosclerosis are fibrotic diseases disrupting bone marrow function that occur in various leukemias but also in response to non-malignant alterations in hematopoietic cells. Here we show that endothelial cell–specific inactivation of the Lats2 gene, encoding Hippo kinase large tumor suppressor kinase 2, or overexpression of the downstream effector YAP1 induce myofibroblast formation and lead to extensive fibrosis and osteosclerosis, which impair bone marrow function and cause extramedullary hematopoiesis in the spleen. Mechanistically, loss of LATS2 induces endothelial-to-mesenchymal transition, resulting in increased expression of extracellular matrix and secreted signaling molecules. Changes in endothelial cells involve increased expression of serum response factor target genes, and, strikingly, major aspects of the LATS2 mutant phenotype are rescued by inactivation of the Srf gene. These findings identify the endothelium as a driver of bone marrow fibrosis, which improves understanding of myelofibrotic and osteosclerotic diseases, for which drug therapies are currently lacking.