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Jimenez, J.

Publications and source records attributed to Jimenez, J..

At least 19 recordsLinked to original sources

Continent-wide calibration of camera-trap metrics reveals low population densities in the European wildcat

Effective conservation depends on demographic metrics that reliably reflect species status, particularly population abundance. For elusive species occurring at low densities, however, such metrics remain difficult to obtain. Spatial capture-recapture (SCR) models are the standardized approach for estimating density in marked populations, but their data requirements, especially the need for multiple spatial recaptures across individuals, often limit applicability in small or data-poor populations. This constraint has resulted in knowledge gaps for some of the most vulnerable species, undermining evidence-based conservation planning and management. Using camera-trap data and SCR-derived density estimates from data-rich populations, we evaluated alternative, less data-demanding metrics and tested the hypothesis: Space to Event (STE), Mean Local Abundance (MLA), and Relative Abundance Index (RAI) exhibit predictable relationships with SCR-derived density; if supported, these metrics can reliably estimate density in populations where SCR models cannot be implemented. We applied this framework to the European wildcat (Felis silvestris), an elusive small felid with highly fragmented populations across Europe, for which density estimates are largely lacking despite growing conservation concern. Across 21 study areas spanning most of the species range, our results indicate that European wildcats generally occur at lower densities than previously reported. SCR-derived estimates (n=10) averaged 10.32 {+/-} 11.56 inds/100km2, while STE enabled density estimation in five additional data-poor areas (mean 5.52 {+/-} 5.33 inds/100km2). STE showed a strong linear relationship with SCR-derived density (R2=0.98), supporting its use as a viable alternative when SCR is infeasible, although it tended to underestimate compared to SCR, especially at higher densities. In contrast, MLA and RAI showed weaker and non-linear relationships with SCR-derived density (R2=0.65), indicating substantially lower explanatory power and suggesting their estimates are more strongly influenced by confounding processes. By explicitly calibrating alternative metrics across a wide density gradient throughout most of the species distribution, this study provides a transferable methodological framework for estimating density in low-density wildlife populations and the first continent-wide, standardized density assessment of a carnivore species. From a management perspective, our findings identify populations that may be most vulnerable, particularly those with the lowest densities, and highlight the need to prioritize absolute abundance monitoring.

ecology↗

Novel substrate affinity of FaCCR1 and FaCCR1/FaOCT4 expression control the content of medium-chain esters in strawberry fruit

Fruit flavor and aroma are influenced by the sugars-to-acid ratio and most importantly by the specific profile and abundance of volatile organic compounds (VOCs). While over 550 VOCs have been identified in strawberry fruit, fewer than 20 are believed to be key for aroma, being esters the major components. A major and stable quantitative trait locus (QTL) explaining a large percentage (40%) of phenotypic variation for several medium-chain esters (MCE) was mapped at about 19 Mb in chromosome 6A using both a biparental population and genome-wide association studies (GWAS). Using a combination of genetic mapping, global transcriptomic studies of bulked contrasting lines, and in vivo and in silico functional analyses, we identified the cinnamoyl Co-A reductase FaCCR1(6A) and the organic cation/carnitine transporter FaOCT4(6A) as underlying genes. Subcellular localization experiments indicated that FaCCR1(6A) and FaOCT4(6A) localize at the cytosol and tonoplast membrane respectively. Transient overexpression of FaCCR1(6A) and FaOCT4(6A) in fruits resulted in a significant increase in MCE content. Despite the well-described function of CCRs in the biosynthesis of monolignols, in vitro enzymatic assays and molecular docking revealed that FaCCR1(6A) also presents high affinity for MCE precursors, indicating a previously unidentified function of this protein in volatile biosynthesis. Based in our findings, we have developed a predictive KASP assay in FaOCT4(6A) for selecting superior cultivars with enhanced fruit aroma.

plant biology↗

How many (distinguishable) classes can we identify in Single Particle Analysis?

Heterogeneity in cryoEM is essential for capturing macromolecule structural variability, reflecting their functional states and biological significance. However, estimating heterogeneity remains challenging due to particle misclassification and algorithmic biases, which can lead to reconstructions that blend distinct conformations or fail to resolve subtle differences. Furthermore, the low signal-to-noise ratio (SNR) inherent in cryo-EM data makes it nearly impossible to detect minute structural changes, as noise often obscures subtle variations in macromolecular projections. In this paper, we investigate the use of p-values associated with the null hypothesis that the observed classification differs from a random partition of the input dataset, thereby providing a statistical framework for determining the number of distinguishable classes present in a given dataset.

molecular biology↗

Distinct representations of an anxiogenic environment in different cell types of the ventral hippocampus

In addition to its role in episodic memory and spatial navigation, the hippocampus has also been found to influence mood-related disorders such as anxiety and depression. These seemingly distinct roles are consistent with a functional dissociation between the two anatomical poles of the hippocampus: whereas the dorsal portion of the hippocampus in rodents is necessary for spatial tasks, the ventral portion controls affective behaviors. We have recently found that neurons in the ventral, but not dorsal, CA1 area of mice encode anxiety-related information (i.e. are "anxiety cells") in diverse defensive and exploratory behaviors. Still it is unclear how general threat-related information is computed within the hippocampal circuit. In this work, we have examined how distinct hippocampal subregions and cell types encode anxiety-related information by imaging calcium activity in large populations of genetically-defined neurons in the ventral hippocampus while mice explore the elevated plus maze (EPM), a conflict-based anxiety test. We compared the neural encoding of task-related features within the ventral CA1 (vCA1) and ventral dentate gyrus (vDG) regions in order to examine the emergence of anxiety-related activity through the hippocampal circuit. We found that granule cells (vGCs) of the vDG represented similar valence information to neurons in vCA1 in the form of arm-type specific encoding in the EPM, which suggests that encoding of anxiety-related features is already present at this first stage of hippocampal processing. When compared with ventral granule cells (vGCs), ventral mossy cells (vMCs) underlying the DG had stronger spatial encoding and less valence encoding, suggesting that they may be more functionally connected with the highly spatially sensitive dorsal hippocampus. Together these findings will help to understand the encoding of anxiety-related information in the hippocampus and how it relates to neural circuit defects in mood-related disorders.

neuroscience↗

Nuclear Speckle Dynamics are Controlled by Polyphosphate Inhibition of CLK Proteins

Nuclear speckles (NS) are membrane-less nuclear organelles that act as critical hubs for pre-mRNA splicing. Defects in splicing are linked to several human diseases, including cancer, Alzheimers disease, and dystrophies. While CLK kinases regulate the mobilization of splicing factors from NS, the molecular mechanisms underlying NS assembly and dissolution remain unclear. Using an adaptation of the Biotinylation by Antibody Recognition (BAR) technique, we identify polyphosphate (polyP) as a novel and essential regulator of NS dynamics. Polyphosphate, a highly conserved polyanion composed of a chain of phosphate molecules, is involved in several functions in mammalian cells. Here, we show that polyP interacts with the NS core component SRRM2, and polyP depletion disrupts NS organization releasing splicing factors into the nucleoplasm. RNA-seq analysis reveals that polyP depletion increases exon inclusion, particularly in long genes with multiple exons, highlighting its role in splicing regulation. Mechanistically, we demonstrate that polyP acts as a physiological inhibitor of CLK3 kinase, preventing the phosphorylation of SR proteins and thereby maintaining NS stability. Our findings not only expand our understanding of NS biology but also provide new insights into the polyP involvement in splicing-related diseases. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/633116v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1dc44b6org.highwire.dtl.DTLVardef@2339e4org.highwire.dtl.DTLVardef@ade454org.highwire.dtl.DTLVardef@69482b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

A key role of the EMC complex for mitochondrial respiration and quiescence in fission yeasts

In eukaryotes, oxygen consumption is mainly driven by the respiratory activity of mitochondria, which generates most of the cellular energy that sustains life. This parameter provides direct information about mitochondrial activity of all aerobic biological systems. Using the Seahorse analyzer instrument, we show here that deletion of the oca3/emc2 gene (oca3{Delta}) encoding the Emc2 subunit of the ER membrane complex (EMC), a conserved chaperone/insertase which aids membrane protein biogenesis in the ER, severely affects oxygen consumption rates and quiescence survival in Schizosaccharomyces pombe yeast cells. Remarkably, the respiratory defects of the oca3{Delta} mutation (EMC dysfunction) is rescued synergistically by the disruption of ergosterol biosynthesis (erg5{Delta}) and the action of the membrane fluidizing agent tween 20, suggesting a direct role of membrane fluidity and sterols composition in mitochondrial respiration in the fission yeast.

cell biology↗

Unveiling miR-451a and miR-142-3p as Prognostic Markers in NSCLC via sEV Liquid Biopsy

Despite advancements in personalized cancer therapies, platinum-based chemotherapy remains the cornerstone for treating solid tumors, including Non-Small Cell Lung Cancer (NSCLC). The integration of novel immunotherapies with platinum compounds has shown promising outcomes for the treatment of advanced disease. However, a significant proportion of patients experience therapeutic failure due to innate or acquired resistance. Thus, identifying molecular profiles and biomarkers to monitor patient progress and treatment response is crucial for tailoring therapeutic strategies. Small extracellular vesicle (sEV)-based liquid biopsy emerges as a promising non-invasive method for cancer management. sEVs play a critical role in cell communication and provide molecular insights into the tumor environment. In this study, we characterized the microRNome content of sEVs from cisplatin-resistant and -sensitive cancer cells using small-RNA sequencing. We identified and validated three miRNAs in two cohorts of 78 and 49 patients treated with either chemotherapy alone or chemo-immunotherapy, respectively, analyzed via liquid biopsy, differentiating NSCLC patients based on progression and overall survival. Notably, miR-451a emerged as a prognostic marker for chemo and chemo-immunotherapy, while miR-142-3p was identified for the first time as a potential prognostic marker specifically for stage IV patients, irrespective of the treatment. The combination of miR-451, miR-142-3p, and miR-55745, a novel miRNA identified from our miRNome screening, serves as a valuable biomarker for both cisplatin and chemo-immunotherapy treatment responses. This study underscores the role of sEVs in acquired cisplatin resistance and introduces novel miRNA-sEV biomarkers for managing NSCLC progression.

cancer biology↗

EMC regulates cell membrane fluidity to facilitate biogenesis of membrane proteins

The EMC complex is a highly conserved transmembrane chaperone located in the endoplasmic reticulum (ER). This complex has been associated in humans with sterol homeostasis and a myriad of different cellular activities, making the mechanism of EMC functionality enigmatic. Using fission yeast, we demonstrate that EMC assists biogenesis of the sterol transfer protein Lam6/Ltc1 at the ER-Plasma membrane and ER-Mitochondria contact sites. Cells losing EMC function sequester unfolded Lam6/Ltc1 and other proteins at the mitochondrial matrix, driving to surplus ergosterol, cold-sensitive growth and mitochondrial disfunctions. Remarkably, inhibition of the ergosterol biosynthesis, but also fluidization of cell membranes to counteract its rigidizing effects, reduce the ER-unfolded protein response and rescue growth and mitochondrial defects in EMC-deficient cells. These results indicate that EMC-assisted biogenesis of Lam6/Ltc1 provides, through ergosterol homeostasis, optimal membrane fluidity to facilitate biogenesis of other ER-membrane proteins. HIGHLIGHTS- Lam6/Ltc1 requires EMC for localization at ER-Plasma membrane and ER-Mitochondria contact sites. - EMC-driven biogenesis of Lam6/Ltc1 is involved in membrane fluidity homeostasis. - EMC-deficient cells accumulate misfolded proteins in the mitochondrial matrix. - Cell membrane fluidization alleviates the ER-misfolded proteins response and rescues growth and mitochondrial defects of EMC-deficient cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=139 HEIGHT=200 SRC="FIGDIR/small/618411v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@17be2aborg.highwire.dtl.DTLVardef@5e7465org.highwire.dtl.DTLVardef@12bafccorg.highwire.dtl.DTLVardef@1229b81_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic representation of EMC-membrane fluidity homeostasis connecting protein folding and mitochondrial activity.

cell biology↗

Microplate micromilling: A customizable platform to support the prototyping, development and testing of microphysiological culture models

The development of microphysiological cell culture models (MPMs) that align with the throughput demands of drug and chemical testing are needed to help reduce animal testing, aide in the discovery of new drugs, and identify harmful chemical exposures. To address this need, we have developed a process for rapid prototyping MPM devices using computer numerical control (CNC) micromilling of commercially available microplates. Microchannels are cut out of the existing microplate structure and ports are drilled into the bottom of the wells to interface the wells. To test versatility and benchmark to another rapid-prototyping approach, we manufactured common microfluidic features into microplates using four different CNC mills as well as a 3D printer. Cell viability was assessed for polystyrene (PS) well plates and two 3D printed resins (MED610 and VeroClear) with the PS showing >2.5-fold increase in cell growth after three days. Machines were tested on their ability to create common device features including a traditional microfluidic device as well as a custom design incorporating complex geometries. Features were measured by confocal microscopy. We found that features including 1000{micro}m ports, 800{micro}m microchannels, 200{micro}m phase-guides, and 500{micro}m post arrays were machined and the range of CVs for features were 1.02-4.42, 1.32-3.50, 2.34-16.58, 6.25-16.40 respectively, while the 3D printed features exhibited maximal CVs of 20.98, 11.68, 23.60, and 10.01 for the same features. Predictably, more expensive machines generally showed higher accuracy and lower variation, but many features could be created accurately and precisely by inexpensive (<$3000) machines facilitating the broader use of this technology to create a user customizable platform to support the prototyping, development, and testing of human relevant models with broad applications across the life sciences. Graphical abstractMultiple CNC mills are assessed on accuracy and precision of microfluidic features of interest for microphysiological model development creation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/615399v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1be08eorg.highwire.dtl.DTLVardef@33b0a4org.highwire.dtl.DTLVardef@192167borg.highwire.dtl.DTLVardef@200b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

CD40 is an immune checkpoint regulator that potentiates myocardial inflammation through activation and expansion of CCR2+ macrophages and CD8 T-cells

Novel immune checkpoint therapeutics including CD40 agonists have tremendous promise to elicit antitumor responses in patients resistant to current therapies. Conventional immune checkpoint inhibitors (PD-1/PD-L1, CTLA-4 antagonists) are associated with serious adverse cardiac events including life-threatening myocarditis. However, little is known regarding the potential for CD40 agonists to trigger myocardial inflammation or myocarditis. Here, we leveraged genetic mouse models, single cell sequencing, and cell depletion studies to demonstrate that an anti-CD40 agonist antibody reshapes the cardiac immune landscape through activation of CCR2+ macrophages and subsequent recruitment of effector memory CD8 T-cells. We identify a positive feedback loop between CCR2+ macrophages and CD8 T-cells driven by IL12b, TNF, and IFN-{gamma} signaling that promotes myocardial inflammation and show that prior exposure to CD40 agonists sensitizes the heart to secondary insults and accelerates LV remodeling. Collectively, these findings highlight the potential for CD40 agonists to promote myocardial inflammation and potentiate heart failure pathogenesis.

immunology↗

Prenatal VEGF Nano-Delivery Reverses Congenital Diaphragmatic Hernia-Associated Pulmonary Abnormalities

RationaleCongenital diaphragmatic hernia (CDH) results in lung hypoplasia. In severe cases, tracheal occlusion (TO) can be offered to promote lung growth. However the benefit is limited, and novel treatments are required to supplement TO. Vascular endothelial growth factor (VEGF) is downregulated in animal models of CDH and could be a therapeutic target, but its role in human CDH is not known. ObjectivesTo investigate whether VEGF supplementation could be a suitable treatment for CDH-associated lung pathology. MethodsFetal lungs from CDH patients were used to determine pulmonary morphology and VEGF expression. A novel human ex vivo model of fetal lung compression recapitulating CDH features was developed and used to determine the effect of exogenous VEGF supplementation (Figure 1A). A nanoparticle-based approach for intra-pulmonary delivery of VEGF was developed by conjugating it on functionalized nanodiamonds (ND-VEGF) and was tested in experimental CDH in vivo. O_FIG O_LINKSMALLFIG WIDTH=138 HEIGHT=200 SRC="FIGDIR/small/581170v1_fig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@2ba882org.highwire.dtl.DTLVardef@4413d2org.highwire.dtl.DTLVardef@17155aborg.highwire.dtl.DTLVardef@1af7c73_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1C_FLOATNO (A) Schematic of the study design based on the analysis of the early-stage CDH fetal lung sections to assess early hypoplasia and VEGF impairment. In parallel, a human compression-based CDH model will be developed to validate the CDH phenotype and test a therapeutical approach to rescue lung hypoplasia. (B) H&E analysis of 18 and 22 pcw post-mortem CDH human lung tissue reveals impaired epithelial development compared to control healthy tissue at matching developmental stages. Scale bar 100m. (C) Morphometric analysis of CDH and healthy lung tissue at 18-22 pcw reveals decreased values of volume densities of air space (Vair%) and corresponding higher values of volume densities of alveolar septa (Vsep%) in CDH tissues compared to healthy tissue at the same developmental stages. A similar trend can be observed for the mean linear intercept of air space (Lma%) and its corresponding mean linear intercept of septal thickness (Lmw%). (D) Histologic analysis of VEGFA, KDR, Ki67 and NKX2-1 markers in normal and CDH fetal lung tissue at 18 and 22 pcw. Scale bar 100m. (E) Quantification of epithelial VEGFA and KDR expression reported in D shows a significant decrease for both markers in CDH compared to healthy samples. Correspondingly, the percentage of Ki67-positive epithelial cells is significantly lower in CDH compared to healthy samples, with no significant differences in the number of NKX2-1-positive cells. ***<p=0.001. (F) Immunofluorescence analysis of ECAD in normal and CDH fetal lung tissue at 18 and 22 pcw. Scale bar 100m. (G) Quantification of epithelial nuclear density based on results in Figure F shows no significant differences between CDH and healthy tissue. C_FIG Measurements and Main ResultsVEGF expression was downregulated in distal pulmonary epithelium of human CDH fetuses in conjunction with attenuated cell proliferation. The compression model resulted in impaired branching morphogenesis similar to CDH and downregulation of VEGF expression in conjunction with reduced proliferation of terminal bud epithelial progenitors; these could be reversed by exogenous supplementation of VEGF. Prenatal delivery of VEGF with the ND-VEGF platform in CDH fetal rats resulted in lung growth and pulmonary arterial remodelling that was complementary to that achieved by TO alone with appearances comparable to healthy controls. ConclusionsThis innovative approach could have a significant impact on the treatment of CDH.

bioengineering↗

The HCM-Linked Mutation Arg92Leu in TNNT2 Allosterically Alters the cTnC-cTnI Interface and Disrupts the PKA-mediated Regulation of Myofilament Relaxation

BackgroundImpaired left ventricular relaxation, high filling pressures, and dysregulation of Ca2+ homeostasis are common findings contributing to diastolic dysfunction in hypertrophic cardiomyopathy (HCM). Studies have shown that impaired relaxation is an early observation in the sarcomere-gene-positive preclinical HCM cohort which suggests potential involvement of myofilament regulators of relaxation. Yet, a molecular level understanding of mechanism(s) at the level of the myofilament is lacking. We hypothesized that mutation-specific, allosterically mediated, changes to the cardiac troponin C-cardiac troponin I (cTnC-cTnI) interface can account for the development of early-onset diastolic dysfunction via decreased PKA accessibility to cTnI. MethodsHCM mutations R92L-cTnT (Arg92Leu) and {Delta}160E-cTnT (Glu160 deletion) were studied in vivo, in vitro, and in silico via 2D echocardiography, western blotting, ex vivo hemodynamics, stopped-flow kinetics, time resolved fluorescence resonance energy transfer (TR-FRET), and molecular dynamics simulations. ResultsThe HCM-causative mutations R92L-cTnT and {Delta}160E-cTnT result in different time-of-onset of diastolic dysfunction. R92L-cTnT demonstrated early-onset diastolic dysfunction accompanied by a localized decrease in phosphorylation of cTnI. Constitutive phosphorylation of cTnI (cTnI-D23D24) was sufficient to recover diastolic function to Non-Tg levels only for R92L-cTnT. Mutation-specific changes in Ca2+ dissociation rates associated with R92L-cTnT reconstituted with cTnI-D23D24 led us to investigate potential involvement of structural changes in the cTnC-cTnI interface as an explanation for these observations. We probed the interface via TR-FRET revealing a repositioning of the N-terminus of cTnI, closer to cTnC, and concomitant decreases in distance distributions at sites flanking the PKA consensus sequence. Implementing TR-FRET distances as constraints into our atomistic model identified additional electrostatic interactions at the consensus sequence. ConclusionThese data indicate that the early diastolic dysfunction observed in a subset of HCM is likely attributable to structural changes at the cTnC-cTnI interface that impair accessibility of PKA thereby blunting {beta}-adrenergic responsiveness and identifying a potential molecular target for therapeutic intervention.

biophysics↗

Expansion of Disease Specific Cardiac Macrophages in Immune Checkpoint Inhibitor Myocarditis

BackgroundImmune checkpoint inhibitors (ICIs), antibodies targeting PD-1/PD-L1 or CTLA4 have revolutionized cancer management but are associated with devastating immune-related adverse events (irAEs) including myocarditis. The main risk factor for ICI myocarditis is the use of combination PD-1 and CTLA4 inhibition. ICI-myocarditis is often fulminant and is pathologically characterized by myocardial infiltration of T lymphocytes and macrophages. While much has been learned regarding the role of T-cells in ICI-myocarditis, little is understood regarding the identity, transcriptional diversity, and functions of infiltrating macrophages. MethodsWe employed an established murine ICI myocarditis model (Ctla4+/-Pdcd1-/- mice) to explore the cardiac immune landscape using single-cell RNA-sequencing, immunostaining, flow cytometry, in situ RNA hybridization and molecular imaging and antibody neutralization studies. ResultsWe observed marked increases in CCR2+ monocyte-derived macrophages and CD8+ T-cells in this model. The macrophage compartment was heterogeneous and displayed marked enrichment in an inflammatory CCR2+ subpopulation highly expressing Cxcl9, Cxcl10, Gbp2b, and Fcgr4 that originated from CCR2+ monocytes. Importantly, a similar macrophage population expressing CXCL9, CXCL10, and CD16 (human homologue of mouse FcgR4) was found selectively expanded in patients with ICI myocarditis compared to other forms of heart failure and myocarditis. In silico prediction of cell-cell communication suggested interactions between T-cells and Cxcl9+Cxcl10+ macrophages via IFN-{gamma} and CXCR3 signaling pathways. Depleting CD8+T-cells, macrophages, and blockade of IFN-{gamma} signaling blunted the expansion of Cxcl9+Cxcl10+macrophages in the heart and attenuated myocarditis suggesting that this interaction was necessary for disease pathogenesis. ConclusionThese data demonstrate that ICI-myocarditis is associated with the expansion of a specific population of IFN-{gamma} induced inflammatory macrophages and suggest the possibility that IFN-{gamma} blockade may be considered as a treatment option for this devastating condition.

immunology↗

BiFCo: Visualising cohesin assembly/disassembly cycle in living cells.

Cohesin is a ring-shaped protein complex highly conserved in evolution that is composed in all eukaryotes of at least two SMC proteins (Structural Maintenance of Chromosomes) SMC1 and SMC3 in humans (Psm1 and Psm3 in fission yeast), and the kleisin RAD21 (Rad21 in fission yeast). Mutations in its components or its regulators cause genetic syndromes (known as cohesinopathies) and several types of cancer. It has been shown in a number of organisms that only a small fraction of each subunit is assembled into complexes. Therefore, the presence of an excess of soluble components hinders dynamic chromatin loading/unloading studies using fluorescent fusions in vivo. Here, we present a system based on bimolecular fluorescent complementation in the fission yeast Schizosaccharomyces pombe, named Bi-molecular Fluorescent Cohesin (BiFCo) that selectively excludes signal from individual proteins to allow monitoring the complex assembly/disassembly within a physiological context during a whole cell cycle in living cells. This system may be expanded and diversified in different genetic backgrounds and other eukaryotic models, including human cells.

cell biology↗

Prospective Motion Correction and Automatic Segmentation of Penetrating Arteries in Phase Contrast MRI at 7 T

PurposeTo develop a prospective motion correction (MC) method for phase contrast (PC) MRI of penetrating arteries (PA) in centrum semiovale at 7 T and evaluate its performance using automatic PA segmentation. MethodsHead motion was monitored and corrected during the scan based on fat navigator images. Two convolutional neural networks (CNN) were developed to automatically segment PAs and exclude surface vessels. Real-life scans with MC and without MC (NoMC) were performed to evaluate the MC performance. Motion score was calculated from the range of translational and rotational motion parameters. MC vs NoMC pairs were divided according to their score differences into groups with similar, less, or more motions during MC. Data reacquisition was also performed to evaluate whether it can further improve PA visualization. ResultsIn the group with similar motion, more PA counts (NPA) were obtained with MC in 9 (60%) cases, significantly more than the number of cases (1) with less PAs (p = 0.011; binomial test). In the group with less motion during MC, MC images had more or similar NPA in all cases, while in the group with more motion during MC, the numbers of cases with less and more NPA during MC were not significantly different (3 vs 0). Data reacquisition did not further increase NPA. CNNs had higher sensitivity (0.85) and accuracy (Dice coefficient 0.85) of detecting PAs than a threshold based method. ConclusionsProspective MC and CNN based segmentation improved the visualization and delineation of PAs in PC MRI at 7 T.

bioengineering↗

ToxCast chemical library screen identifies diethanolamine as an activator of Wnt signaling

Numerous autism spectrum disorder (ASD) risk genes are associated with Wnt signaling, suggesting that brain development may be especially sensitive to genetic perturbation of this pathway. Additionally, valproic acid, which modulates Wnt signaling, increases risk for ASD when taken during pregnancy. We previously found that an autism-linked gain-of-function UBE3AT485A mutant construct hyperactivated canonical Wnt signaling, providing a genetic means to elevate Wnt signaling above baseline levels. To identify environmental use chemicals that enhance or suppress Wnt signaling, we screened the ToxCast Phase I and II libraries in cells expressing this autism linked UBE3AT485 gain-of-function mutant construct. Using structural comparisons, we identify classes of chemicals that stimulated Wnt signaling, including ethanolamines, as well as chemicals that inhibited Wnt signaling, such as agricultural pesticides, and synthetic hormone analogs. To prioritize chemicals for follow-up, we leveraged predicted human exposure data, and identified diethanolamine (DEA) as a chemical that both stimulates Wnt signaling in UBE3AT485A-transfected cells and has a high potential for prenatal exposure in humans. DEA also enhanced proliferation in two primary human neural progenitor cell lines. Overall, this study identifies chemicals with the potential for human exposure that influence Wnt signaling in human cells.

molecular biology↗

Multimodal memory T cell profiling identifies a reduction in a polyfunctional Th17 state associated with tuberculosis progression

Mycobacterium tuberculosis (M.tb) results in 10 million active tuberculosis (TB) cases and 1.5 million deaths each year1, making it the worlds leading infectious cause of death2. Infection leads to either an asymptomatic latent state or TB disease. Memory T cells have been implicated in TB disease progression, but the specific cell states involved have not yet been delineated because of the limited scope of traditional profiling strategies. Furthermore, immune activation during infection confounds underlying differences in T cell state distributions that influence risk of progression. Here, we used a multimodal single-cell approach to integrate measurements of transcripts and 30 functionally relevant surface proteins to comprehensively define the memory T cell landscape at steady state (i.e., outside of active infection). We profiled 500,000 memory T cells from 259 Peruvians > 4.7 years after they had either latent M.tb infection or active disease and defined 31 distinct memory T cell states, including a CD4+CD26+CD161+CCR6+ effector memory state that was significantly reduced in patients who had developed active TB (OR = 0.80, 95% CI: 0.73-0.87, p = 1.21 x 10-6). This state was also polyfunctional; in ex vivo stimulation, it was enriched for IL-17 and IL-22 production, consistent with a Th17-skewed phenotype, but also had more capacity to produce IFN{gamma} than other CD161+CCR6+ Th17 cells. Additionally, in progressors, IL-17 and IL-22 production in this cell state was significantly lower than in non-progressors. Reduced abundance and function of this state may be an important factor in failure to control M.tb infection.

immunology↗

A positively selected, common, missense variant in FBN1 confers a 2.2 centimeter reduction of height in the Peruvian population

Peruvians are among the shortest people in the world. To understand the genetic basis of short stature in Peru, we examined an ethnically diverse group of Peruvians and identified a novel, population-specific, missense variant in FBN1 (E1297G) that is significantly associated with lower height in the Peruvian population. Each copy of the minor allele (frequency = 4.7%) reduces height by 2.2 cm (4.4 cm in homozygous individuals). This is the largest effect size known for a common height-associated variant. This variant shows strong evidence of positive selection within the Peruvian population and is significantly more frequent in Native American populations from coastal regions of Peru compared to populations from the Andes or the Amazon, suggesting that short stature in Peruvians is the result of adaptation to the coastal environment. One Sentence SummaryA mutation found in Peruvians has the largest known effect on height for a common variant. This variant is specific to Native American ancestry.

genomics↗