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Frontiers in Big Data 2024plant is a complex system that is sensible to environmental factors such as water supply, pH, temperature, light, radiation, impurities, and nutrient availability. It...
plant is a complex system that is sensible to environmental factors such as water supply, pH, temperature, light, radiation, impurities, and nutrient availability. It can be used as a biomonitor for environmental changes; however, the bioassays are time-consuming and have a strong human interference factor that might change the result depending on who is performing the analysis. We have developed computer vision models to study color variations from clone 4430 plant stamen hair cells, which can be stressed due to air pollution and soil contamination. The study introduces a novel dataset, Trad-204, comprising single-cell images from clone 4430, captured during the stamen-hair mutation bioassay (Trad-SHM). The dataset contain images from two experiments, one focusing on air pollution by particulate matter and another based on soil contaminated by diesel oil. Both experiments were carried out in Curitiba, Brazil, between 2020 and 2023. The images represent single cells with different shapes, sizes, and colors, reflecting the plant's responses to environmental stressors. An automatic classification task was developed to distinguishing between blue and pink cells, and the study explores both a baseline model and three artificial neural network (ANN) architectures, namely, TinyVGG, VGG-16, and ResNet34. revealed sensibility to both air particulate matter concentration and diesel oil in soil. The results indicate that Residual Network architecture outperforms the other models in terms of accuracy on both training and testing sets. The dataset and findings contribute to the understanding of plant cell responses to environmental stress and provide valuable resources for further research in automated image analysis of plant cells. Discussion highlights the impact of turgor pressure on cell shape and the potential implications for plant physiology. The comparison between ANN architectures aligns with previous research, emphasizing the superior performance of ResNet models in image classification tasks. Artificial intelligence identification of pink cells improves the counting accuracy, thus avoiding human errors due to different color perceptions, fatigue, or inattention, in addition to facilitating and speeding up the analysis process. Overall, the study offers insights into plant cell dynamics and provides a foundation for future investigations like cells morphology change. This research corroborates that biomonitoring should be considered as an important tool for political actions, being a relevant issue in risk assessment and the development of new public policies relating to the environment.
PubMed: 38812700
DOI: 10.3389/fdata.2024.1384240 -
Polish Journal of Pathology : Official... 2024Small cell lung carcinoma (SCLC) is characterized by rapid growth and an aggressive clinical course. Standard therapy regimes have limited effects on disease course;...
Small cell lung carcinoma (SCLC) is characterized by rapid growth and an aggressive clinical course. Standard therapy regimes have limited effects on disease course; therefore the prognosis of SCLC is poor. In the current study, the frequency of programmed death ligand 1 (PD-L1) expression in SCLC and its correlation with clinico-pathological features were evaluated. The study included 100 cases of SCLC wherein testing for PD-L1 was done with the SP263 clone on the Ventana benchmark XT system. Cases with > 1% PD-L1 expression in tumour cells or immune cells were categorized as positive. PD-L1 expression was identified in 14% of cases using the cut-off of ≥ 1%. The tumour proportion score was 10% and the immune proportion score was 9.78% using a cut-off of ≥ 1%. PD-L1 positive expression was more frequent in the male population with age > 40 years. All the patients with positive PD-L1 expression were smokers. In the PD-L1 positive group, presence of necrosis was identified in 71.4% of cases and when compared with the PD-L1 negative subgroup this finding was statistically significant (p = 0.010). Personalized targeted therapy for cases of SCLC is still under evaluation. The use of immunotherapeutic targets, such as PD-L1, may help to define a new treatment strategy for SCLC. Development of new treatment strategies may improve prognosis and survival.
Topics: Humans; B7-H1 Antigen; Male; Small Cell Lung Carcinoma; Female; Middle Aged; Lung Neoplasms; Adult; Aged; Biomarkers, Tumor; Aged, 80 and over; Immunohistochemistry; Prognosis
PubMed: 38808606
DOI: 10.5114/pjp.2024.136281 -
PloS One 2024Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and...
Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and to reprogram cells by combining these parts in new ways. Historically, many genetic parts on plasmids were copied and reused without routinely checking their DNA sequences. With the widespread use of high-throughput DNA sequencing technologies, we now know that plasmids often contain variants of common genetic parts that differ slightly from their canonical sequences. Because the exact provenance of a genetic part on a particular plasmid is usually unknown, it is difficult to determine whether these differences arose due to mutations during plasmid construction and propagation or due to intentional editing by researchers. In either case, it is important to understand how the sequence changes alter the properties of the genetic part. We analyzed the sequences of over 50,000 engineered plasmids using depositor metadata and a metric inspired by the natural language processing field. We detected 217 uncatalogued genetic part variants that were especially widespread or were likely the result of convergent evolution or engineering. Several of these uncatalogued variants are known mutants of plasmid origins of replication or antibiotic resistance genes that are missing from current annotation databases. However, most are uncharacterized, and 3/5 of the plasmids we analyzed contained at least one of the uncatalogued variants. Our results include a list of genetic parts to prioritize for refining engineered plasmid annotation pipelines, highlight widespread variants of parts that warrant further investigation to see whether they have altered characteristics, and suggest cases where unintentional evolution of plasmid parts may be affecting the reliability and reproducibility of science.
Topics: Plasmids; Genetic Engineering; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Mutation; Base Sequence; Sequence Analysis, DNA
PubMed: 38805426
DOI: 10.1371/journal.pone.0304164 -
Antibodies (Basel, Switzerland) May 2024CD99 was demonstrated to be a potential target for antibody therapy on T-acute lymphoblastic leukemia (T-ALL). The ligation of CD99 by certain monoclonal antibodies...
CD99 was demonstrated to be a potential target for antibody therapy on T-acute lymphoblastic leukemia (T-ALL). The ligation of CD99 by certain monoclonal antibodies (mAbs) induced T-ALL apoptosis. However, the molecular basis contributing to the apoptosis of T-ALL upon anti-CD99 mAb engagement remains elusive. In this study, using our generated anti-CD99 mAb clone MT99/3 (mAb MT99/3), mAb MT99/3 engagement strongly induced apoptosis of T-ALL cell lines, but not in non-malignant peripheral blood cells. By transcriptome analysis, upon mAb MT99/3 ligation, 13 apoptosis-related genes, including FOS, TNF, FASLG, BCL2A1, JUNB, SOCS1, IL27RA, PTPN6, PDGFA, NR4A1, SGK1, LPAR5 and LTB, were significantly upregulated. The epitope of CD99 recognized by mAb MT99/3 was then identified as the VDGENDDPRPP at residues 60-70 of CD99, which has never been reported. To the best of our knowledge, this is the first transcriptome data conducted in T-ALL with anti-CD99 mAb engagement. These findings provide new insights into CD99 implicated in the apoptosis of T-ALL. The identification of a new epitope and apoptosis-related genes that relate to the induction of apoptosis by mAb MT99/3 may serve as a new therapeutic target for T-ALL. The anti-CD99 mAb clone MT99/3 might be a candidate for further development of a therapeutic antibody for T-ALL therapy.
PubMed: 38804310
DOI: 10.3390/antib13020042 -
BMC Bioinformatics May 2024Cancers are spatially heterogenous, thus their clonal evolution, especially following anti-cancer treatments, depends on where the mutated cells are located within the...
BACKGROUND
Cancers are spatially heterogenous, thus their clonal evolution, especially following anti-cancer treatments, depends on where the mutated cells are located within the tumor tissue. For example, cells exposed to different concentrations of drugs, such as cells located near the vessels in contrast to those residing far from the vasculature, can undergo a different evolutionary path. However, classical representations of cell lineage trees do not account for this spatial component of emerging cancer clones. Here, we propose routines to trace spatial and temporal clonal evolution in computer simulations of the tumor evolution models.
RESULTS
The LinG3D (Lineage Graphs in 3D) is an open-source collection of routines (in MATLAB, Python, and R) that enables spatio-temporal visualization of clonal evolution in a two-dimensional tumor slice from computer simulations of the tumor evolution models. These routines draw traces of tumor clones in both time and space, and may include a projection of a selected microenvironmental factor, such as the drug or oxygen distribution within the tumor, if such a microenvironmental factor is used in the tumor evolution model. The utility of LinG3D has been demonstrated through examples of simulated tumors with different number of clones and, additionally, in experimental colony growth assay.
CONCLUSIONS
This routine package extends the classical lineage trees, that show cellular clone relationships in time, by adding the space component to show the locations of cellular clones within the 2D tumor tissue patch from computer simulations of tumor evolution models.
Topics: Clonal Evolution; Humans; Neoplasms; Computer Simulation; Software
PubMed: 38802748
DOI: 10.1186/s12859-024-05813-7 -
Turkish Journal of Haematology :... May 2024It has been shown that clonal mutations occur in hematopoietic stem cells with advancing age and increase the risk of death due to atherosclerotic vascular diseases,...
OBJECTIVE
It has been shown that clonal mutations occur in hematopoietic stem cells with advancing age and increase the risk of death due to atherosclerotic vascular diseases, just like in myeloproliferative neoplasms. It is known that endothelial cells (EC) and hematopoietic stem cells develop from a common stem cell called hemangioblast in early embryonic period. However, the presence of hemangioblast in the postnatal period is controversial. In this study, JAK2 gene variants was examined in patients with atherosclerotic carotid disease and without any hematological malignancy.
MATERIALS AND METHODS
Ten consecutive patients (8 men and 2 women) with symptomatic atherosclerotic carotid stenosis were included in this study. EC (CD31+CD45-) were separated from tissue samples taken by carotid endarterectomy. JAK2 variants was examined in EC, peripheral blood mononuclear cells and oral epithelial cells of the patients with next generation sequencing.
RESULTS
The median age of the patients was 74 (58-80) and the median BMI was 24,44 (18,42-30,85) kg/m2. Smoking history was present in 50%, hypertension in 80%, diabetes in 70%, and ischemic heart disease in 70% of the patients. JAK2V617F mutation was detected in peripheral blood mononuclear cells in three out of 10 patients, two of them also had JAK2V617F mutation in their EC. JAK2V617F mutation was not found in oral epithelial cells in any of the patients.
CONCLUSION
In this study, for the first time in the literature, we showed that JAK2V617F mutation was found somatically in both peripheral blood cells and EC in patients with atherosclerosis. This finding may support that EC and hematopoietic cells originate from a common clone or that the somatic mutation can be transmitted to EC by other mechanisms. Examining the molecular and functional changes caused by JAK2V617F mutation in EC may help open a new avenue for treating atherosclerosis.
PubMed: 38801025
DOI: 10.4274/tjh.galenos.2024.2024.0161 -
Frontiers in Microbiology 2024Porcine Reproductive and Respiratory Syndrome virus (PRRSV) causes high abortion rates in gestating sows and stillbirths, as well as high piglet mortality, seriously...
INTRODUCTION
Porcine Reproductive and Respiratory Syndrome virus (PRRSV) causes high abortion rates in gestating sows and stillbirths, as well as high piglet mortality, seriously jeopardizing the pig industry in China and worldwide.
METHODS
In this study, an infectious clone containing the full-length genome of NADC34-like PRRSV was constructed for the first time using reverse genetic techniques. The gene was amplified segmentally onto a plasmid, transfected into BHK-21 cells, and the transfected supernatant was harvested and transfected into PAM cells, which showed classical cytopathic effects (CPE).
RESULTS
The virus rJS-KS/2021 was successfully rescued which could be demonstrated by Western Blot and indirect immunofluorescence assays. Its growth curve was similar to the original strain. Replace the 5'UTR and 3'UTR of rJS-KS/2021 with 5'UTR and 3'UTR of HP-PRRSV (strain SH1) also failed to propagate on MARC-145.
DISCUSSION
In this study, an infectious clone of NADC34-like was constructed by reverse genetics, replacing the UTR and changing the cellular tropism of the virus. These findings provide a solid foundation for studying the recombination of different PRRSVs and the adaption of PRRSVs on MARC-145 in the future.
PubMed: 38800747
DOI: 10.3389/fmicb.2024.1359970 -
Journal of Oral and Maxillofacial... 2024Programmed cell death ligand 1 (PD L1) is a transmembrane protein that is highly expressed in neoplastic cells. Therapy with immune checkpoint inhibitors target...
Immunohistochemical study of Programmed Cell Death Ligand 1 (PDL1) expression by combined positive score using 22C3 clone in head and neck squamous cell carcinomas, its correlation with clinicopathological features and outcome.
CONTEXT
Programmed cell death ligand 1 (PD L1) is a transmembrane protein that is highly expressed in neoplastic cells. Therapy with immune checkpoint inhibitors target PD-1/PD-L1 blockade-inducing tumour regression. Immunohistochemistry (IHC) for PD-L1 expression enables patient selection for immunotherapy and can be considered as a potential predictive biomarker for immunotherapy in head and neck squamous cell carcinoma (HNSCC).
AIMS
To determine the PDL1 expression in HNSCC, to correlate with clinicopathological features and outcome.
SETTINGS AND DESIGN
We retrospectively analysed 59 cases of HNSCC at our Tertiary Hospital between January 2017 and November 2018 and followed up until death/Nov 2022 for Overall survival.
METHODS AND MATERIAL
IHC analysis of PD-L1 using Combined Positive Score (CPS) with antibody clone 22C3 in 59 cases of HNSCC was performed. PD-L1 expression was correlated with clinicopathological features and outcomes.
STATISTICAL ANALYSIS USED
Pearson Chi-square test was used to analyse the correlation between PD-L1 expression and clinicopathological parameters using SPSS20.0. Survival curves were calculated by Kaplan-Meier method, and differences were analysed by log-rank test.
RESULTS
A total of 25 cases (42.4%) had positive PDL expression (CPS ≥1). 16/25 cases (27.1%) belonged to CPS (≥1, <10). An almost-perfect interobserver agreement was noted by two pathologists for PD-L1 IHC expression. No statistically significant correlation was noted between PD-L1 score and clinicopathologic features.
CONCLUSIONS
Detection of PD-L1 status gives further insight into frequency of PD-L1 expression in Indian HNSCC patients to possibly improve clinical treatment strategies, ensuring that our patients get the maximum therapeutic benefit of immunotherapy.
PubMed: 38800420
DOI: 10.4103/jomfp.jomfp_339_23 -
Frontiers in Immunology 2024Macrophage function is determined by microenvironment and origin. Brain and retinal microglia are both derived from yolk sac progenitors, yet their microenvironments...
INTRODUCTION
Macrophage function is determined by microenvironment and origin. Brain and retinal microglia are both derived from yolk sac progenitors, yet their microenvironments differ. Utilizing single-cell RNA sequencing (scRNA-seq) data from mice, we tested the hypothesis that retinal and brain microglia exhibit distinct transcriptional profiles due to their unique microenvironments.
METHODS
Eyes and brains from 2-4 month wildtype mice were combined (20 eyes; 3 brains) to yield one biologically diverse sample per organ. Each tissue was digested into single cell suspensions, enriched for immune cells, and sorted for scRNA-seq. Analysis was performed in Seurat v3 including clustering, integration, and differential expression. Multi-parameter flow cytometry was used for validation of scRNA-seq results. Lymphocytic choriomeningitis virus (LCMV) Clone 13, which produces a systemic, chronic, and neurotropic infection, was used to validate scRNA-seq and flow cytometry results .
RESULTS
Cluster analysis of integrated gene expression data from eye and brain identified 6 microglial clusters. Differential expression analysis revealed that eye microglia were enriched for more pro-inflammatory processes including antigen processing via MHC class I (14.0-fold, and ) and positive regulation of T-cell immunity (8.4-fold) compared to brain microglia. Multi-parameter flow cytometry confirmed that retinal microglia expressed 3.2-fold greater H2-Db and 263.3-fold more H2-Kb than brain microglia. On Day 13 and 29 after LCMV infection, CD8 T-cell density was greater in the retina than the brain.
DISCUSSION
Our data demonstrate that the microenvironment of retina and brain differs, resulting in microglia-specific gene expression changes. Specifically, retinal microglia express greater MHC class I by scRNA-seq and multi-parameter flow cytometry, resulting in a possibly enhanced capability to stimulate CD8 T-cell inflammation during LCMV infection. These results may explain tissue-specific differences between retina and brain during systemic viral infections and CD8 T-cell driven autoimmune disease.
Topics: Animals; Microglia; Mice; Retina; Brain; Mice, Inbred C57BL; Lymphocytic choriomeningitis virus; Histocompatibility Antigens Class I; T-Lymphocytes; Inflammation; Lymphocytic Choriomeningitis; Single-Cell Analysis; CD8-Positive T-Lymphocytes; Transcriptome
PubMed: 38799448
DOI: 10.3389/fimmu.2024.1399989 -
BioRxiv : the Preprint Server For... May 2024Within a given tissue, the stem cell niche provides the microenvironment for stem cells suitable for their self-renewal. Conceptually, the niche space constrains the...
Within a given tissue, the stem cell niche provides the microenvironment for stem cells suitable for their self-renewal. Conceptually, the niche space constrains the size of a stem-cell pool, as the cells sharing the niche compete for its space. It has been suggested that either neutral- or non-neutral-competition of stem cells changes the clone dynamics of stem cells. Theoretically, if the rate of asymmetric division is high, the stem cell competition is limited, thus suppressing clonal expansion. However, the effects of asymmetric division on clone dynamics have never been experimentally tested. Here, using the germline stem cell (GSC) system, as a simple model of the in-vivo niche, we examine the effect of division modes (asymmetric or symmetric) on clonal dynamics by combining experimental approaches with mathematical modeling. Our experimental data and computational model both suggest that the rate of asymmetric division is proportional to the time a stem cell clone takes to expand. Taken together, our data suggests that asymmetric division is essential for maintaining the genetic variation of stem cells and thus serves as a critical mechanism for safeguarding fertility over the animal age or preventing multiple disorders caused by the clonal expansion of stem cells.
PubMed: 38798517
DOI: 10.1101/2024.05.16.594576