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opencc-by-4.0Jun 2022View details →

miR-126 promotes M1 to M2 macrophage phenotype switching via VEGFA and KLF4

Background. Macrophage polarization and microRNA play crucial roles in the development of atherosclerosis (AS). The M1 macrophage phenotype contributes to the formation of plaques, while the M2 macrophage phenotype resolves inflammation and promotes tissue repair. MiR-126 has been found to play a role in regulating macrophage polarization in the context of AS. However, the exact mechanism of miR-126 requires further research. Methods. The foam cell model was established by stimulating THP-1 with oxidized low-density lipoprotein (ox-LDL). We transfected foam cells with miR-126 mimic and its negative control. The transfection of miR-126 was implemented by riboFECT CP transfection kit. The levels of miR-126 and M1/M2 associated genes in foam cells were quantified using reverse transcription-quantitative PCR (RT-qPCR). Additionally, the expressions of CD86+ and CD206+ cells in foam cells were determined by flow cytometry. Western blotting and RT-qPCR were used to determine the protein and mRNA levels of the vascular endothelial growth factor A (VEGFA) and the transcriptional regulator Krüppel-like factor 4 (KLF4), respectively. Additionally, we detected endothelial cell migration after co-culturing endothelial cells and macrophages. MG-132 was used to indirectly activate the expression of VEGFA, and the expression of KLF4 was also evaluated. Results. The activation of apoptosis and production of foam cells were boosted by the addition of ox-LDL. We transfected foam cells with miR-126 mimic and its negative control and observed that miR-126 greatly suppressed foam cell development and inhibited phagocytosis. Moreover, it caused pro-inflammatory M1 macrophages to switch to the anti-inflammatory M2 phenotype. This was reflected by the increase in anti-inflammatory gene expression and the decrease in pro-inflammatory gene expression. Additionally, miR-126 dramatically decreased the expressions of VEGFA and KLF4. The protein-protein interaction network analysis showed a significantly high correlation between miR-126, VEGFA, and KLF4. MiR-126 may also promote EC migration by activating macrophage PPAR γ expression and effectively suppressing macrophage inflammation. MG-132 indirectly activated the expression of VEGFA, and the expression of KLF4 also significantly increased, which indicates a direct or indirect relationship between VEGFA and KLF4. Conclusion. Our study shows that miR-126 can reverse ox-LDL-mediated phagocytosis and apoptosis in macrophages. Consequently, the potential role of miR-126 was manifested in regulating macrophage function and promoting vascular endothelial migration.

opencc-zeroFeb 2023View details →

Anticipatory plasticity: frog embryos respond to environmental cues by producing an adaptive phenotype at hatching

Developmental plasticity can occur at any life stage, but a context in which it might be crucial is when individuals that produce specific phenotypes early in development gain a competitive advantage at a later life stage. Here we asked if pre-hatching (embryonic) exposure to a nutrient-rich resource can impact hatchling morphology in tadpoles of Mexican spadefoot toads, Spea multiplicata. Induction of a distinctive carnivore morph can occur when a tadpole eats live fairy shrimp. We investigated whether cues from fairy shrimp, detected as embryos, determine hatchling morphology in a manner allowing individuals to take advantage of this nutritious resource. We found that hatchlings with embryonic exposure to shrimp were larger and had larger jaw muscles––traits that increase their ability to compete for shrimp. Thus, embryos can assess and respond to environmental cues by producing preemptive resource-use phenotypes. Such anticipatory plasticity may be an important but understudied form of developmental plasticity.

opencc-zeroFeb 2023View details →

Extraction of clinical phenotypes for Alzheimer disease dementia from clinical notes using natural language processing

Objectives There is much interest in utilizing clinical data for developing prediction models for Alzheimer disease (AD) risk, progression, and outcomes. Existing studies have mostly utilized curated research registries, image analysis, and structured Electronic Health Record (EHR) data. However, much critical information resides in relatively inaccessible unstructured clinical notes within the EHR. Materials and Methods We developed a natural language processing (NLP)-based pipeline to extract AD-related clinical phenotypes, documenting strategies for success and assessing the utility of mining unstructured clinical notes. We evaluated the pipeline against gold-standard manual annotations performed by two clinical dementia experts for AD-related clinical phenotypes including medical comorbidities, biomarkers, neurobehavioral test scores, behavioral indicators of cognitive decline, family history, and neuroimaging findings. Results Documentation rates for each phenotype varied in the structured versus unstructured EHR. Inter-annotator agreement was high (Cohen's kappa = 0.72–1) and positively correlated with the NLP-based phenotype extraction pipeline's performance (average F1-score = 0.65-0.99) for each phenotype. Discussion We developed an automated NLP-based pipeline to extract informative phenotypes that may improve the performance of eventual machine-learning predictive models for AD. In the process, we examined documentation practices for each phenotype relevant to the care of AD patients and identified factors for success. Conclusion Success of our NLP-based phenotype extraction pipeline depended on domain-specific knowledge and focus on a specific clinical domain instead of maximizing generalizability.

opencc-zeroDec 2022View details →

High heterogeneity in genomic differentiation between phenotypically divergent songbirds: A test of mitonuclear co-introgression

Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression—a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.

opencc-by-4.0Dec 2022View details →

Functional and molecular characterization of suicidality factors using phenotypic and genome-wide data

GWAS summary statistics for Functional and molecular characterization of suicidality factors using phenotypic and genome-wide data published in Molecular Psychiatry by Quintero Reis A, Newton BA, Kessler R, Polimanti R, and Wendt FR.

dataset related to article: " Cerebrospinal fluid neuropathological biomarkers in beta-propeller protein-associated neurodegeneration, with complicated parkinsonian phenotype"

analysis sanger electropherograms in the patient's in .abi format and segregation in the family (mother; father and sister

Datset related to article "DUPLICATION OF EXONS 15 AND 16 IN MATRIN-3: A PHENOTYPE BRIDGING AMYOTROPHIC LATERAL SCLEROSIS AND IMMUNE-MEDIATED DISORDERS"

NGS analysis performed at Fondazione Besta carried out as part of the study reported at title

dataset relate to article: "Functional Characterization of Two Variants at the Intron 6-Exon 7 Boundary of the KCNQ2 Potassium Channel Gene Causing Distinct Epileptic Phenotypes"

Sequencing Analysis performed at Fondazione Besta and carried out as part of the study mentioned at title

Datset related to article "G507D MUTATION IN FUS GENE CAUSES FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS WITH A SPECIFIC GENOTYPE-PHENOTYPE CORRELATION"

NGS_analysis performed at Fondazione Besta carried out as part of the study reported at title

opencc-zeroFeb 2023View details →

Data from: The CellPhe toolkit for cell phenotyping using time-lapse imaging and pattern recognition

With phenotypic heterogeneity in whole cell populations widely recognised, the demand for quantitative and temporal analysis approaches to characterise single cell morphology and dynamics has increased. We present CellPhe, a pattern recognition toolkit for the unbiased characterisation of cellular phenotypes within time-lapse videos. CellPhe imports tracking information from multiple segmentation and tracking algorithms to provide automated cell phenotyping from different imaging modalities, including fluorescence. To maximise data quality for downstream analysis, our toolkit includes automated recognition and removal of erroneous cell boundaries induced by inaccurate tracking and segmentation. We provide an extensive list of features extracted from individual cell time series, with custom feature selection to identify variables that provide the greatest discrimination for the analysis in question. Using ensemble classification for accurate prediction of cellular phenotype and clustering algorithms for the characterisation of heterogeneous subsets, we validate and prove adaptability using different cell types and experimental conditions.

Dataset related to article"G507D MUTATION IN FUS GENE CAUSES FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS WITH A SPECIFIC GENOTYPE-PHENOTYPE CORRELATION"

NGS Analyses of patients included in the study reported at title followed at Fondazione Besta

opencc-by-4.0Mar 2023View details →

Medication and condition codes used to develop a computable phenotype for Crohn's Disease incident cases

Lists of medication and condition concepts used for Crohn's disease incident case phenotyping as described in my Master's Thesis "Machine Learning Based Prediction of Incident Cases of Crohn’s Disease Using Electronic Health Records From a Large Integrated Health System". <ul> <li>ibd_medication.csv contains medication names, OMOP Concept IDs, RxNorm codes and a flag indicating whether the medication is IBD-specific (i.e., antibiotics and glucocorticoides are marked as unspecific)</li> <li>ibd_conditions.csv contains condition names, OMOP Concept IDs, SNOMED CT codes and a categorical column indicating whether the condition refers to Crohn's Disease (CD), Ulcerative Colitis (UC), or Inflammatory bowel disease unclassified (IBD-U)</li> <li>ibd_symptoms.csv contains symptom names, OMOP Concept IDs, containing symptom group categories, and a flag indicating whether the symptom was added because it is a SNOMED CT descendent code of another code on the list. The list was created based on the IBD symptoms Read Code list provided by Blackwell et. al, 2021, doi:10.1093/ecco-jcc/jjaa146</li> </ul> IBD, Inflammatory Bowel Disease; OMOP, Observational Medical Outcomes Partnership; SNOMED CT, Systematized Nomenclature of Medicine Clinial Terms.

opencc-zeroMar 2023View details →

Data for: Decoupling of sexual signals and their underlying morphology facilitates rapid phenotypic diversification

How novel phenotypes evolve is challenging to imagine because traits are often underlain by numerous integrated phenotypic components, and changes to any one form can disrupt the function of the entire module. Yet novel phenotypes do emerge, and research on adaptive phenotypic evolution suggests that complex traits can diverge while either maintaining existing form-function relationships or through innovations that alter form-function relationships. How these alternate routes contribute to sexual signal evolution is poorly understood, despite the role of sexual signals in generating biodiversity. In Hawaiian populations of the Pacific field cricket, male song attracts both female crickets and a deadly acoustically orienting parasitoid fly. In response to this conflict between natural and sexual selection, male crickets have evolved altered wing morphologies multiple times, resulting in loss and dramatic alteration of sexual signals. More recently, we and others have observed a radical increase in sexual signal variation and the underlying morphological structures that produce song. We conducted the first combined analysis of form (wing morphology), function (emergent signal), and receiver responses to characterize novel variation, test alternative hypotheses about form-function relationships (Form-Function Continuity vs. Form-Function Decoupling) and investigate underlying mechanistic changes and fitness consequences of novel signals. We identified three sound-producing male morphs (one previously undescribed, named "rattling") and found that relationships between morphology and signals have been rewired (Form-Function Decoupling), rapidly and repeatedly, through the gain, loss, and alteration of morphological structures, facilitating the production of signals that exist in novel phenotypic space. By integrating across a hierarchy of phenotypes, we uncovered divergent morphs with unique solutions to the challenge of attracting mates while evading fatal parasitism.

opencc-by-4.0Mar 2023View details →

Spring temperature drives phenotypic selection on plasticity of flowering time

Data on field observations of flowering time and fitness of the perennial forest herb Lathyrus vernus and on spring temperature from weather station data. The dataset includes 22 years of data (1987–1996 and 2006–2017) from a L. vernus population located in a deciduous forest in Tullgarn, SE Sweden (58.9496 N, 17.6097 E). It includes records from 837 individuals (607 from 1987 to 1996, and 230 from 2006 to 2017), and from 2478 flowering events. The dataset includes the following variables: year: year of the recording id_nr: numeric plant id id: unique plant id (combination of numeric plant id and period) fcode: flowering code (1 if the plant flowered on that year, 0 if not) FFD: First Flowering Date n_fl: number of flowers n_fr: number of fruits totseed: total number of seeds intactseed: total number of intact seeds (not damaged by seed predator beetles) shoot_vol: shoot volume period: old (1987–1996) or new (2006–2017) n_years_fl_fitness: number of years when data on flowering and fitness is available n_years_study: number of years when the plant was included in the study mean_4: Average daily mean temperature of April (calculated from nearby meteorological station data) cmean_4: Mean-centred average daily mean temperature of April

FIG. 4. — A in The use of photographic color information for highthroughput phenotyping of pigment composition in Agarophyton vermiculophyllum (Ohmi) Gurgel, J.N.Norris & Fredericq

FIG. 4. — A, After color correction procedures, color values estimated for four areas on the color card (i.e., black, white, red, and blue swatches) included in each photograph showed no significant differences among light condition groups (shapes); B, After color correction using values standardized using a color card, color traits (RGB values analyzed with PCA) were more similar within thallus (numbered clusters) than among light conditions (shapes), with a few exceptions. C, Centroids estimated for each thallus (numbered clusters) and light condition (shape and color) combination showed that some light conditions could be effectively standardized with color correction procedures (e.g. blue, direct sunlight, and white light), whereas thalli photographed under other conditions showed different color profiles even after correction (e.g. indirect sunlight (triangles), and to a lesser extend yellow light (boxed Xs).

FIG. 2 in The use of photographic color information for highthroughput phenotyping of pigment composition in Agarophyton vermiculophyllum (Ohmi) Gurgel, J.N.Norris & Fredericq

FIG. 2. — Principal components of variation for: A, R, G, and B values; B, pigment variables. Arrow directions indicate the association of each variable to PC 1 and PC 2. Arrow length indicates the relative strength of the contribution of each variable. Point color reflects the average color of each thallus; C, the major axis of variation in pigments (PC1) is best predicted by a combination of color PC1 and PC2. The dashed line represents predicted values when PC2 is low, compared to when PC2 is high (solid line); D, pigment variation along PC2 is best predicted by color variation along PC2.

FIG. 1 in The use of photographic color information for highthroughput phenotyping of pigment composition in Agarophyton vermiculophyllum (Ohmi) Gurgel, J.N.Norris & Fredericq

FIG. 1. — Agarophyton vermiculophyllum color variation. Photographs used for color information arranged (from top left) in rank order of increasing hue value. Lower right panel shows the color of the average RGB values estimated from each image. Labels indicated the region and site of origin for each thallus. Diameter of dish in each image is 100 mm.

FIG. 3 in The use of photographic color information for highthroughput phenotyping of pigment composition in Agarophyton vermiculophyllum (Ohmi) Gurgel, J.N.Norris & Fredericq

FIG. 3. — Examples of images taken of the same thallus and color card under five light conditions (left column), and those same images after white balancing (right column). Width of the color card in each image is 178 mm.

opencc-by-4.0Apr 2023View details →

Structural colour in the bacterial domain: the ecogenomics of an optical phenotype

Structural colour  is an optical phenomena resulting from light interacting with nanostructured materials. Although structural colour is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here we collected and sequenced a set of 87 structurally coloured bacterial isolates, and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two dimensional packing capable of producing SC. Genome-wide association approaches were used to identify genes associated with structural colour. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilisation and metabolism, were found to be involved. Using this information, we constructed a classifier to predict structural colour directly from bacterial genome sequences, validated it by scoring 100 strains that were not involved in creating the structural colour classifier, and predicted that photonic structures are widely distributed within Gram-negative bacteria. Analysis of over 13 thousand assembled metagenomes predicted that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides the first large-scale ecogenomics view of structural colour in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.