Biological Characteristics Research Articles

Identification of genetic subtypes in follicular lymphoma

Follicular lymphoma (FL) exhibits considerable variability in biological features and clinical trajectories across patients. To dissect the diversity of FL, we utilized a Bernoulli mixture model to identify genetic subtypes in 713 pre-treatment tumor tissue samples. Our analysis revealed the existence of five subtypes with unique genetic profiles that correlated with clinicopathological characteristics. The clusters were enriched in specific mutations as follows: CS (CREBBP and STAT6), TT (TNFAIP3 and TP53), GM (GNA13 and MEF2B), Q (quiescent, for low mutation burden), and AR (mutations of mTOR pathway-related genes). The subtype Q was enriched for patients with stage I disease and associated with a lower proliferative history than the other subtypes. The AR subtype was unique in its enrichment for IgM-expressing FL cases and was associated with advanced-stage and more than 4 nodal sites. The existence of subtypes was validated in an independent cohort of 418 samples from the GALLIUM trial. Notably, patients assigned to the TT subtype consistently experienced inferior progression-free survival when treated with immunochemotherapy. Our findings offer insight into core pathways distinctly linked with each FL cluster and are expected to be informative in the era of targeted therapies.

LncRNA PCIF1 promotes aerobic glycolysis in A549/DDP cells by competitively binding miR-326 to regulate PKM expression

ObjectiveUtilizing transcriptome analysis to investigate the mechanisms and therapeutic approaches for cisplatin resistance in non-small cell lung cancer (NSCLC). MethodsFirstly, the biological characters of A549 cells and A549/DDP cells were detected by RNA sequencing, CCK-8 and hippocampal energy analyzer. Then, the differential Genes were functionally enriched by GO and KEGG and the competitive endogenous RNA network map was constructed. Finally, the effects of the predicted biogenesis pathway on the biological functions of A549/DDP cells were verified by in vitro and in vivo experiments. ResultThe differentially transcribed genes of A549 and A549/DDP cells were analyzed by enrichment analysis and cell biological characteristics detection. The results showed that A549/DDP cells showed significantly increased resistance to cisplatin, glucose metabolism signaling pathway and glycolysis levels compared with A549 cells. Among glycolysis-related transcription genes, PKM had the most significant difference Fold Change is 8. LncRNA PCIF1 is a new marker of A549/DDP cells and can be used as a molecular sponge to regulate the expression of PKM. LncRNA PCIF1 targets miR-326 to induce PKM expression, promote glycolysis level, and enhance the resistance of A549/DDP cells to cisplatin. ConclusionLncRNA PCIF1 as biomarkers of A549/DDP cells, higher expression can induce the PKM, promote cell glycolysis, lead to the occurrence of cisplatin resistance. LncRNA PCIF1 can be considered as a potential target for treating cisplatin-resistant NSCLC.

Insights into non-coding RNAS: biogenesis, function and their potential regulatory roles in acute kidney disease and chronic kidney disease.

Noncoding RNAs (ncRNAs) have emerged as pivotal regulators of gene expression, and have attracted significant attention because of their various roles in biological processes. These molecules have transcriptional activity despite their inability to encode proteins. Moreover, research has revealed that ncRNAs, especially microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are linked to pervasive regulators of kidney disease, including anti-inflammatory, antiapoptotic, antifibrotic, and proangiogenic actions in acute and chronic kidney disease. Although the exact therapeutic mechanism of ncRNAs remains uncertain, their value in treatment has been studied in clinical trials. The numerous renal diseases and the beneficial or harmful effects of NcRNAs on the kidney will be discussed in this article. Afterward, exploring the biological characteristics of ncRNAs, as well as their purpose and potential contributions to acute and chronic renal disease, were explored. This may offer guidance for treating both acute and long-term kidney illnesses, as well as insights into the potential use of these indicators as kidney disease biomarkers.

Study on the relationship between net primary productivity and site quality in Japanese larch plantations in mountainous areas of eastern Liaoning

Plantation forests enhance carbon storage in terrestrial ecosystems in China. Larix kaempferi (Lamb.) Carrière (Lamb.) (Larix olgensis Henry) is the main species for afforestation in the eastern Liaoning Province. Therefore, it is important to understand the correlation between the site class and carbon sink potential of Larix kaempferi plantations in Liaoning Province for afforestation and carbon sink in this area. The model was fitted using three classical theoretical growth equations: the Richards model, the Korf model, and the Hossfeld model. This study used the forest resource inventory data for management in Liaoning Province in 2011 to build six dynamic height-age models for a Larix kaempferi plantation in Dandong City regardless of base-age. The optimal model derived by the generalized algebraic difference approach (GADA) method was compared with the model derived by the algebraic difference approach (ADA) method. The superiority of GADA was demonstrated by comparison. The Levenberg-Marquardt algorithm was used to fit the model. The statistical and biological characteristics were considered synthetically when comparing the models. The best model was screened out by statistical analysis and graphic analysis. The results show that the differential height-age model derived from Richards equation can well explain the growth process of Larix kaempferi in Dandong City, Liaoning Province under different conditions. The site index model based on Richards equation and derived by GADA was used to calculate the site class of a Larix kaempferi plantation in Dandong City. The net primary productivity (NPP) value from the past ten years was extracted from the MOD17A3HGF data set. Spearman correlation analysis and Kendall correlation analysis were used to show that there is a significant positive correlation between NPP value and site class of Larix kaempferi plantation in Dandong City. Among them, the highest growth occurred in 2016; NPP increased by about 3.914 gC/m2/year for every two increases in height-age grade; the lowest increase in NPP was in 2014; NPP increased by about 2.113 gC/m2/year for every two increases in height-age grade; and for every two increases in height-age grade in the recent ten years, the average NPP value increased by about 2.731 gC/m2/year.

Pediatric Hemispheric High-Grade Gliomas and H3.3-G34 Mutation: A Review of the Literature on Biological Features and New Therapeutic Strategies

Pediatric high-grade glioma (pHGG) encompasses a wide range of gliomas with different genomic, epigenomic, and transcriptomic features. Almost 50% of pHGGs present a mutation in genes coding for histone 3, including the subtype harboring the H3.3-G34 mutation. In this context, histone mutations are frequently associated with mutations in TP53 and ATRX, along with PDGFRA and NOTCH2NL amplifications. Moreover, the H3.3-G34 histone mutation induces epigenetic changes in immune-related genes and exerts modulatory functions on the microenvironment. Also, the functionality of the blood–brain barrier (BBB) has an impact on treatment response. The prognosis remains poor with conventional treatments, thus eliciting the investigation of additional and alternative therapies. Promising molecular targets include PDGFRA amplification, BRAF mutation, EGFR amplification, NF1 loss, and IDH mutation. Considering that pHGGs harboring the H3.3-G34R mutation appear to be more susceptible to immunotherapies (ITs), different options have been recently explored, including immune checkpoint inhibitors, antibody mediated IT, and Car-T cells. This review aims to summarize the knowledge concerning cancer biology and cancer-immune cell interaction in this set of pediatric gliomas, with a focus on possible therapeutic options.

Biological features and quality comprehensive analysis of twelve germplasm resources of the genus Allium from Tibet

IntroductionAllium is important vegetables and seasonings in China, Tibet is rich in unique resources of the genus Allium, but lacks development and utilization.MethodsWe compared the biological features and comprehensively evaluating the quality of twelve germplasm resources of the genus Allium collected from Tibet.ResultsThe results revealed that nine germplasm resources were bolting and bloom normally except for SC015, SC019, and SC048, all twelve germplasm resources were able to vegetative growth. The individual differences in moisture, soluble sugar, and protein content among the twelve germplasm resources were relatively small, with pyruvic acid content ranging from 0.11 to 1.12 mg/g and a large variation coefficient. A total of 8 categories and 97 volatile compounds were detected in twelve germplasm resources, the majority possessed the highest proportions of aldehydes and organosulfur compounds, but there were certain differences between the different Allium species. Additionally, 11 to 16 types of free amino acids were present in all germplasm resources, proline exhibited the highest content. The total content of essential and non-essential amino acids in SC009 was the highest. Carbon (C) accounted for the largest proportion of all elements, and the contents of other mineral elements varied greatly among the different plants.ConclusionIn conclusion, combined with biological performance and comprehensive evaluation of quality, SC009 is the excellent germplasm resource suitable for growth and capable of reproduction with good quality. These results improved the exploitation and utilization of the genus Allium in Tibet, as well as provided germplasm resources for high-quality breeding of the genus Allium.

Progressive Multifocal Leukoencephalitis of the Immunocompromised Subject: A Case Report from Zinder National Hospital

Progressive multifocal leukoencephalitis (PML) is a rare opportunistic infection of HIV-infected individuals. It is a viral infection caused by the John Cunningham (JC) virus, which occurs during the AIDS stage. An elderly patient immunosuppressed by HIV for more than 5 years presented to the HNZ SMIT with headache, vomiting, visual disturbances, speech disorders and numbness of the limbs, all of which had been evolving in a febrile context for more than seven months. Neurological examination revealed left hemiparesis, frontal syndrome, temporal syndrome and homolateral hemianopia. Cerebral computed tomography revealed multiple lesions of leukoencephalitis. PCR revealed JC virus. The patient was put on corticosteroids, rehydration and nursing care. The course was marked by a progressive deterioration in the patient's neurological condition, culminating in death. We report the clinical, biological and CT features of this progressive multifocal leukoencephalitis.

A targeted gene phylogenetic framework to investigate diversification in the highly diverse yet geographically restricted red devil spiders (Araneae, Dysderidae).

The family Dysderidae is a highly diverse group of nocturnal ground-dwelling and active-hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased-80% of its 644 documented species belong to just two genera, Dysdera (326) and Harpactea (211). Dysderidae provides an excellent study case for evolutionary and ecological research. It includes cases of trophic specialization, which are uncommon among spiders, and exhibit other remarkable biological (e.g. holocentric chromosomes), behavioural (e.g. cryptic female choice), evolutionary (e.g. adaptive radiation) and ecological features (e.g. recurrent colonization of the subterranean environment). The lack of a quantitative hypothesis on its phylogenetic structure has hampered its potential as a testing ground for evolutionary, biogeographical and ecological hypotheses. Here, we present the results of a target, multi-locus phylogenetic analysis, using mitochondrial (cox1, 16s and 12s) and nuclear genes (h3, 28s and 18s), of the most exhaustive taxonomic sample within Dysderidae (104 spp.) to date and across related families (Synspermiata) (83 spp.). We estimate divergence times using a combination of fossil and biogeographic node calibrations and use this timeline to identify shifts in diversification rates. Our results support the monophyly of the Dysderidae subfamilies Rhodinae and Dysderinae but reject Harpacteinae as currently defined. Moreover, the clades recovered within Harpacteinae do not support its current taxonomy. The origin of the family most likely post-dated the break-up of Pangea, and cave colonization may be older than previously considered. After correcting for the taxonomic artefacts, we identified a significant shift in diversification rates at the base of the genus Dysdera. Although the unique coexistence of specialist and generalist diets within the lineage could be suggested as the potential driver for the rate acceleration, further quantitative analyses would be necessary to test this hypothesis.

Assessing a respiratory toxic infectious bronchitis virus (IBV) strain: isolation, identification, pathogenicity, and immunological failure insights.

Infectious bronchitis virus (IBV) is caused by avian coronavirus and poses a global economic threat to the poultry industry. In 2023, a highly pathogenic IBV strain, IBV/CN/GD20230501, was isolated and identified from chickens vaccinated with IBV-M41 in Guangdong, China. This study comprehensively investigated the biological characteristics of the isolated IBV strain, including its genotype, whole genome sequence analysis of its S1 gene, pathogenicity, host immune response, and serum non-targeted metabolomics. Through the analysis of the S1 gene sequence, serum neutralization tests, and comparative genomics, it was proven that IBV/CN/GD20230501 belongs to the GI-I type of strain and is serotype II. One alanine residue in the S1 subunit of the isolated strain was mutated into serine, and some mutations were observed in the ORF1ab gene and the terminal region of the genome. Animal challenge experiments using the EID50 and TCID50 calculations showed that IBV/CN/GD20230501 possesses strong respiratory pathogenicity, with early and long-term shedding of viruses and rapid viral spread. Antibody detection indicated that chickens infected with IBV/CN/GD20230501 exhibited delayed expression of early innate immune genes, while those infected with M41 showed rapid gene induction and effective viral control. Metabolomics analysis demonstrated that this virus infection led to differential expression of 291 ions in chicken serum, mainly affecting the citric acid cycle (tricarboxylic acid cycle).IMPORTANCEThis study identified an infectious bronchitis virus (IBV) strain isolated from vaccinated chickens in an immunized population that had certain sequence differences compared to IBV-M41, resulting in significantly enhanced pathogenicity and host defense. This strain has the potential to replace M41 as a more suitable challenge model for drug research. The non-targeted metabolomics analysis highlighting the citric acid cycle provides a new avenue for studying this highly virulent strain.

Constructing and Validating Estimation Models for Individual-Tree Aboveground Biomass of Salix suchowensis in China

Biomass serves as a crucial indicator of plant productivity, and the development of biomass models has become an efficient way for estimating tree biomass production rapidly and accurately. This study aimed to develop a rapid and accurate model to estimate the individual aboveground biomass of Salix suchowensis. Growth parameters, including plant height (PH), ground diameter (GD), number of first branches (NFB), number of second branches (NSB) and aboveground fresh biomass weight (FW), were measured from 892 destructive sample trees. Correlation analysis indicated that GD had higher positive correlations with FW than PH, NFB and NSB. According to the biological features and field observations of S. suchowensis, the samples were classified into three categories: single-stemmed type, first-branched type and second-branched type. Based on the field measurement data, regression models were constructed separately between FW and each growth trait (PH, GD, NFB and NSB) using linear and nonlinear regression functions (linear, exponential and power). Then, multiple power regression and multiple linear regression were conducted to estimate the fresh biomass of three types of S. suchowensis. For the single-stemmed plant type, model M1 with GD as the single parameter had the highest adj R2, outperforming the other models. Among the 16 constructed biomass-estimating equations for the first-branched plant type, model M32 FW = 0.010371 × PH1.15862 × GD1.250581 × NFB0.190707 was found to have the best fit, with the highest coefficient of determination (adj R2 = 0.6627) and lowest Akaike Information Criterion (AIC = 5997.3081). When it comes to the second-branched plant type, the best-fitting equation was proved to be the multiple power model M43 with PH, GD, NFB and NSB as parameters, which had the highest adj R2 value and best-fitting effect. The stability and reliability of the models were confirmed by the F-test, repeated k-fold cross-validation and paired-sample t-tests. The models developed in this study could provide efficient tools for accurately estimating the total aboveground biomass for S. suchowensis at individual tree levels. The results of this study could also be useful for optimizing the economic productivity of shrub willow plantations.

Retracted] Effects of RUNX3 mediated Notch signaling pathway on biological characteristics of colorectal cancer cells

Retracted] Effects of RUNX3 mediated Notch signaling pathway on biological characteristics of colorectal cancer cells

Продуктивные особенности коров голштинской породы разных генетических линий

Abstract. The purpose of the study is to investigate the productive features of Holstein cows of different genetic lines. Methods. The research was carried out in two breeding enterprises of the Sverdlovsk region on the livestock of Holstein cows. Groups of animals were formed by the method of pairs of analogues, taking into account the age of animals in lactation, physiological condition, live weight, lines of breeding bulls. The coefficient of milk content was estimated by the calculation method. The lactose, fat and protein content in milk was determined using a “Bentley 150” device. Somatic cells were determined on the “Somatos-M” device. Bacterial contamination was studied using a reductase assay. Prolactin was determined by enzyme immunoassay, cortisol by immunochemiluminescent method. Results. In terms of milk yield for 305 days of lactation and protein content in milk, Montwick Chieftain cows had an advantage with a significant difference between the groups (P < 0.05). The animals of the Reflection Sovering line were the best in terms of fat content, the difference between the groups was insignificant. The lowest content of somatic cells in milk and bacterial contamination was found in animals of the Reflection Sovering and Vis Back Idial lines. The best indicators of the leukocyte profile were determined in animals of the Vis Back Idial and Montwick Chieftain lines. In terms of glucose and total protein content in the blood, cows of the Montwick Chieftain line had an advantage, in terms of the amount of urea, animals of the Montwick Chieftain and Vis Back Idial line affiliation. The highest level of total lipids in the blood is typical for cows of the Reflection Sovering line. Scientific novelty. The research results indicate the relationship of biological characteristics and milk productivity with different lines of breeding bulls. The leukocyte profile of this herd of cows of different genetic lines in breeding enterprises of the Sverdlovsk region was studied for the first time. Practical significance. The results of the research can be used in breeding enterprises in order to increase the milk productivity of cows.

Characterizing relationships between T-cell inflammation and outcomes in patients with high-risk neuroblastoma according to mesenchymal and adrenergic signatures.

Recent insights have identified adrenergic (ADRN) and mesenchymal (MES) cell lineages as distinct biologic cell types and T-cell inflammation as a prognostic marker in neuroblastoma. We hypothesized that elucidating unique and overlapping aspects of these biologic features could serve as novel biomarkers for informing ongoing efforts to improve therapeutic approaches for children with high-risk neuroblastoma. We identified lineage-specific, single-stranded super-enhancers to define ADRN and MES specific genes. Publicly available RNA-seq of diagnostic tumor biopsies was used in Discovery and Validation cohorts. Each tumor was assigned a relative MES score and T-cell-inflamed (TCI) score. Survival was assessed using the Kaplan-Meier method, and differences were assessed by the log-rank test. Inflammation scores were correlated with MES scores and anticorrelated with MYCN-amplification in both cohorts. Among patients with high-risk, ADRN tumors, those with TCI tumors had superior overall survival to those with non-inflamed tumors. A similar, but non-significant, trend was observed in the Validation cohort. Conversely, there was no difference according to TCI status in the MES cohort in either the Discover or Validation Cohorts. High inflammation scores were correlated with improved survival in some patients with high-risk, ADRN but not MES neuroblastoma. Our findings bolster support for further developing T-cell based immunotherapy-based approaches for children with high-risk neuroblastoma of varying MES and ADRN expression.

25 Enrichment of tertiary lymphoid structures provides novel insight into mediators of anti-tumor immune activity in sarcomatoid renal cell carcinoma

Abstract Background Renal cell carcinoma (RCC) comprises various histological subtypes, with clear cell RCC (ccRCC) being the most prevalent histotype. RCC with sarcomatoid features (sRCC) is a unique kidney cancer subtype associated with aggressive biological features and poor clinical outcomes that can arise from multiple RCC histologies, most commonly ccRCC. While clinically aggressive, sRCC paradoxically has also demonstrated preferential responsiveness to immune checkpoint blockade (ICB) therapies in subgroup analyses of multiple phase III trials. However, the mediators of this immune sensitivity are largely unknown. We therefore applied transcriptomic techniques to identify orchestrators of immune activity within the sRCC tumor microenvironment (TME). Methods Nephrectomy specimens from patients with sRCC and ccRCC were procured for single cell RNA sequencing (scRNAseq). Clustering and dimensionality reduction were performed, and cell populations were annotated based on expression of canonical lineage markers. Immune populations (CD8+ T cells, CD4+ T cells, B/plasma cells, myeloid cells) were computationally extracted and differential gene expression between sRCC- and ccRCC-derived cells within each subpopulation was performed. Gene expression programs enriched in sRCC samples by scRNAseq were validated on publicly available bulk gene expression data comparing sRCC to ccRCC. Spatial transcriptomics were performed on sRCC tumor sections using the 10X Visium platform. Results Across 18 RCC specimens (10 sRCC; 8 ccRCC), 73,123 cells were analyzed by scRNAseq. Within the CD8+ T cell compartment, CXCL13 was the most significantly enriched nuclear-encoded gene in sRCC samples (log 2-fold change=1.29; q<0.001). CXCL13 was also significantly enriched in CD4+ T cells from sRCC (q<0.001), suggesting enhanced presence of follicular T cells within the sRCC TME. As follicular T cells function in support of B cells, we next interrogated the B lymphocyte population. sRCC samples were enriched for mature B cell and plasma cells, with a five-fold increase in the relative abundance of plasma cells compared to ccRCC samples. Immune deconvolution of patient-derived RNA sequencing from the IMmotion 151 trial revealed a significant increase in the predicted proportion of B lymphocytes (including plasma cells) within the sRCC TME relative to ccRCC (p=0.034). Further, over 20 B lymphocyte activation and maturation pathways were consistently enriched (q<0.25) in sRCC across clinical datasets (Javelin101, CheckMate, and TCGA KIPAN), including Signaling by the B Cell Receptor, Positive Regulation of B Cell Activation, and Immunoglobulin Production Involved in Immunoglobulin Mediated Immune Response, amongst others. B lymphocytes mediate anti-tumor immunity through antibody dependent cellular cytotoxicity (ADCC), and thus the phagocytic effectors of ADCC were interrogated. Myeloid populations differentially expressed FCγR3A in sRCC vs ccRCC (q<0.001), which was recapitulated in bulk gene expression populations (q=0.002, 0.12, and 1.08x10-4 in Javelin101, CheckMate, and TCGA cohorts, respectively). Given the enrichment of follicular T cell and differentiated B lymphocyte programs, we explored the presence of tertiary lymphoid structures (TLS) in sRCC. Two distinct TLS signatures – the 12 Chemokine Score and the TLS Imprint Signature – were significantly enriched in sRCC vs ccRCC across RCC patient datasets (Figure 1). Furthermore, spatial transcriptomics were applied to H&E slides of sRCC to successfully identify the presence of TLS by expression of TLS-associated genes adjacent to sarcomatoid regions. Conclusions TLS, which have previously been associated with response to ICB in RCC (Meylan et al. Immunity. 2022), are transcriptomically enriched for in sRCC, paralleling an observed increase in CXCL13-expressing T cells and differentiated B lymphocytes. Together, TLS and their constituents offer a previously unexplored mediator of immunosurveillance in the sRCC TME that may underlie the paradoxical responsiveness to ICB seen within this population clinically.

Population characteristic of torpedo scad (Megalaspis cordyla Linnaeus, 1758) in the Lampung Bay: Size structure, growth type, and condition factor

Megalaspis cordyla, locally known as ikan bekre, stands as a crucial economic species commonly consumed by the people of Lampung. The escalating demand for this fish has significant implications for increased fishing activities, potentially impacting its population. This research aimed to explore the biological characteristics of M. cordyla landed at the Lempasing Fishing Port, Bandar Lampung, providing fundamental insights for fisheries resource management in the waters of Lampung Bay. Using a quantitative descriptive method, the sampled fish has been analyzed to get size structure, growth type, and fish condition factors based on length and weight data collected from M. cordyla landed weekly. Between April and June 2022, a total of 300 samples were collected, with length ranging from 230 to 430 mm TL, with the largest count (77 individuals) in the 314-334 mm interval. M. cordyla has an allometric negative growth pattern in Lampung Bay, with a growth coefficient (b) value of 2.47. Fish condition factor values ranged from 0.71 to 1.33, with June having the highest average value of 1.03. This information contributes greatly to a better understanding and long-term planning for the management of this fish population.Keywords: Allometric; Condition Factor; Length-Weight Relationship; Pelagic Fish; Aquatic Resources Management

The Effects of Different Developmental Stages on Bone Regeneration of Periodontal Ligament Stem Cells and Periodontal Ligament Cell Sheets In Vitro and Vivo.

Periodontal ligament stem cells (PDLSCs) have broad applications in tissue engineering and regeneration. However, the function of PDLSCs changes in different microenvironments. This study aimed to explore the effects of different developmental stages on the biological characteristics of PDLSCs. Here, PDLSCs were successfully cultured from the periodontal tissues of various groups, including a group with immature roots, a young group with mature roots, and an aging group with mature roots. By comparing the results of the three experimental groups, we found that the donors with immature roots exhibited the best proliferative ability and osteogenic differentiation, while the aging group demonstrated the worst proliferation. The trend for adipogenic differentiation was the opposite to that for osteogenic differentiation. The cell sheet and in vivo experiments revealed that in the immature root group, the cells produced more extracellular matrix (ECM) and new bone and better absorbed the implant materials. These results indicate that PDLSCs perform various functions at different stages of development. In clinical applications of PDLSCs for periodontal regeneration, donors with incompletely developed roots have stronger biological characteristics.

Biological and Molecular Characterization of the Cucumber Mosaic Virus Infecting Purple Coneflowers in China

Purple coneflower (Echinacea purpurea L.), which is a perennial herbaceous plant belonging to the Asteraceae family, is extensively cultivated because of its medicinal applications. However, in Hohhot, Inner Mongolia, China, purple coneflowers in the field exhibited symptoms such as mottle, mosaic, and crinkle. This study aimed to explore the biological and molecular characteristics of the cucumber mosaic virus (CMV) infecting the purple coneflowers in China. We observed isometric particles approximately 30 nm in diameter in the symptomatic leaf specimens. Infection with the CMV was confirmed via high-throughput sequencing and RT-PCR validation. Mechanical inoculation assays demonstrated that the CMV-SGJ isolate could infect both Nicotiana benthamiana and Nicotiana tabacum. Three viral genomic components were identified: RNA1 with 3321 nucleotides, RNA2 with 3048 nucleotides, and RNA3 with 2209 nucleotides. Phylogenetic analysis revealed that the CMV-SGJ isolate clustered into phylogenetic subgroup IA, exhibiting a nucleotide identity of 92.2–95% with subgroup IA CMV isolates in GenBank. This report is the first documentation of the complete genome of the CMV infecting purple flowers in China.

Simulated herbicide mixtures delay both specialist monogenic and generalist polygenic resistance evolution in weeds.

Evolution of herbicide-resistant weed populations is a major challenge to world food production. Using different herbicides in rotation and/or using different herbicides together as mixtures are strategies that may delay the selection of resistance. This study used simulation modelling to investigate whether mixtures and rotations can delay the selection of both generalist polygenic and specialist monogenic herbicide resistance, and whether these strategies are more likely to lead to the selection of generalist resistance in weed types with varying biological characteristics. Our simulations suggest that well-designed effective herbicide mixtures should delay evolution of both polygenic and monogenic resistance better than rotations and single herbicides across all weed types. Both mixture and rotation strategies increased the likelihood of polygenic resistance compared to single-herbicide use, and the likelihood of polygenic resistance increased as the fecundity and competitiveness of the weed increased. Whether monogenic or polygenic resistance occurred in each case depended most on the relative initial allele frequencies. We did not find that herbicide mixtures were more likely than rotations to lead to the selection of generalist polygenic resistance. The simulated efficacy of mixtures over rotations decreased if components were used at reduced rates or when individual components had already been used solo. Herbicide rotations and particularly well-designed mixtures should delay evolution of both polygenic and monogenic resistance, especially if used as part of an effective integrated weed management programme. However, herbicide mixtures and rotations may also increase the risk that resistance will be generalist polygenic rather than specialist monogenic. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Predicting the ER Status Using the Gene Expression Profiles

Breast cancer is the most frequently diagnosed malignancy among women globally, making it the leading cause of cancer incidence worldwide. This type of cancer is particularly challenging due to its high degree of molecular heterogeneity, with many different subtypes exhibiting distinct genetic and biological characteristics. Estrogen receptors (ERs) play a crucial role in breast cancer by acting as receptors for the hormone estrogen, often referred to as the hormone receptor (HR). The presence or absence of ERs, known as ER status, significantly impacts treatment decisions, making accurate prediction of ER status essential for personalized treatment plans. Various methods have been proposed in the literature to predict ER status based on gene expression profiles using microarray genome-wide gene expression profiling. The issue of class imbalance, indicated by a notable variation in the number of samples per class and the curse of dimensionality, is a significant concern with microarray datasets. This paper introduces a novel technique, Fuzzy XGBoost, to predict ER status in breast cancer cases while addressing the class imbalance problem. The proposed algorithm enhances the traditional XGBoost method by incorporating fuzzy logic principles, improving its robustness, computational power, and accuracy in handling imbalanced datasets. Our research demonstrates the effectiveness of the proposed Fuzzy XGBoost algorithm in accurately predicting ER status across multiple gene expression profile datasets. This approach not only contributes to advancements in breast cancer treatment but also showcases the power of computational methods in bioinformatics. We evaluate our method using four datasets: GSE2990, GSE3494, GSE6532, and GSE7390, achieving predictive accuracies of 100%, 92%, 100%, and 96%, respectively. The successful application of Fuzzy XGBoost in this context highlights its potential for broader use in bioinformatics, where leveraging computational power to address challenges such as imbalanced data is critical for predictive accuracy and personalized treatment. DOI: https://doi.org/10.52783/pst.619

Carbon quantum dots for the diagnosis and treatment of ophthalmic diseases.

Carbon quantum dots (CQDs), an emerging nanomaterial, are gaining attention in ophthalmological applications due to their distinctive physical, chemical, and biological characteristics. For example, their inherent fluorescent capabilities offer a novel and promising alternative to conventional fluorescent dyes for ocular disease diagnostics. Furthermore, because of the excellent biocompatibility and minimal cytotoxicity, CQDs are well-suited for therapeutic applications. In addition, functionalized CQDs can effectively deliver drugs to the posterior part of the eyeball to inhibit neovascularization. This review details the use of CQDs in the management of ophthalmic diseases, including various retinal diseases, and ocular infections. While still in its initial phases within ophthalmology, the significant potential of CQDs for diagnosing and treating eye conditions is evident.