bluuebunny/crossref_metadata_2025 huggingface dataset:
Carotid Plaque Diagnosis With 3-Dimensional Computed Tomography Angiography: A Comparison With Magnetic Resonance Imaging–Based Plaque Diagnosis
Authors: Omi Tatsuo , Hayakawa Motoharu , Adachi Kazuhide , Ohba Shigeo , Sadato Akiyo , Hasebe Akiko , Ishihara Takuma , Nakahara Ichiro , Hirose Yuichi
Published: March 2023

Objective

Although a qualitative diagnosis of plaque causing carotid stenosis has been attempted with carotid computed tomography angiography (CaCTA), no clear findings have been reported. We examined the correlation between the plaque CT values and plaque images obtained by magnetic resonance imaging to derive a qualitative diagnosis of the plaque using CaCTA.

Methods

Preoperative CaCTA images acquired from patients stented for carotid stenosis were retrospectively analyzed with respect to magnetization-prepared rapid acquisition with gradient echo and time-of-flight magnetic resonance angiography data. Carotid plaques in the stenosed region were quantified in terms of CT density and the plaque/muscle ratio (magnetization-prepared rapid acquisition with gradient echo), and correlations between these 2 features were determined. Plaques were classified as stable or unstable based on the plaque/muscle ratio, with the smallest plaque/muscle ratio observed among plaques positive for intraplaque hemorrhage set as the cutoff value (1.76).

Results

A total of 165 patients (179 plaques) were included. Perioperative complications included minor stroke (n = 3), major stroke (n = 1, fatal), and hyperperfusion (n = 2). The correlation between CT density and the plaque/muscle ratio was nonlinear (P = 0.0139) and negative (P < 0.0001). The cutoff point (1.76) corresponded to a CT density of 83 HU, supporting this value as a standard reference for plaque stability.

Conclusions

Computed tomography density exhibits a nonlinear (P = 0.0139) and highly negative correlation (P < 0.0001) with the plaque/muscle ratio. Our results demonstrate that plaque characteristics can be meaningfully diagnosed based on CaCTA image data.
A Characterization of Deep Learning Reconstruction Applied to Dual-Energy Computed Tomography Monochromatic and Material Basis Images
Authors: Nikolau Ethan P. , Toia Giuseppe V. , Nett Brian , Tang Jie , Szczykutowicz Timothy P.
Published: March 2023

Objective

Advancements in computed tomography (CT) reconstruction have enabled image quality improvements and dose reductions. Previous advancements have included iterative and model-based reconstruction. The latest image reconstruction advancement uses deep learning, which has been evaluated for polychromatic imaging only. This article characterizes a commercially available deep learning imaging reconstruction applied to dual-energy CT.

Methods

Monochromatic, iodine basis, and water basis images were reconstructed with filtered back projection (FBP), iterative (ASiR-V), and deep learning (DLIR) methods in a phantom experiment. Slice thickness, contrast-to-noise ratio, modulation transfer function, and noise power spectrum metrics were used to characterize ASiR-V and DLIR relative to FBP over a range of dose levels, phantom sizes, and iodine concentrations.

Results

Slice thicknesses for ASiR-V and DLIR demonstrated no statistically significant difference relative to FBP for all measurement conditions. Contrast-to-noise ratio performance for DLIR-high and ASiR-V 40% at 2 mg I/mL on 40-keV images were 162% and 30% higher than FBP, respectively. Task-based modulation transfer function measurements demonstrated no clinically significant change between FBP and ASiR-V and DLIR on monochromatic or iodine basis images.

Conclusions

Deep learning image reconstruction enabled better image quality at lower monochromatic energies and on iodine basis images where image contrast is maximized relative to polychromatic or high-energy monochromatic images. Deep learning image reconstruction did not demonstrate thicker slices, decreased spatial resolution, or poor noise texture (ie, “plastic”) relative to FBP.
Lung Cancer in Lung Transplant Recipients: Clinical, Radiologic, and Pathologic Characteristics and Treatment Outcome
Authors: Tseng Shu-Chi , Gagne Staci M. , Hatabu Hiroto , Lin Gigin , Sholl Lynette M. , Nishino Mizuki
Published: March 2023

Objective

This study aimed to investigate clinical and radiologic characteristics of lung cancer in lung transplant recipients and evaluate the treatment course and prognosis.

Methods

The study included 448 patients who underwent lung transplant between 2005 and 2021. All patients had pretransplant chest computed tomography (CT), 429 patients had posttransplant CT, whereas 19 had no posttransplant CT (median number of posttransplant CT, 6; range, 0–24). Medical records of these patients were reviewed to identify patients who developed lung cancer after lung transplant. Computed tomography and positron emission tomography/CT at the time of lung cancer diagnoses were reviewed to obtain imaging features. Demographics, tumor histology, stages, and survival were compared using Fisher exact test and Wilcoxon rank sum test.

Results

Among 448 lung transplant recipients with a median follow-up of 71.3 months after lung transplant, 15 patients (3.3%) developed posttransplant lung cancer (13 unilateral, 2 bilateral; 10 men, 5 women; median age, 63.1 years; median time from transplantation to cancer diagnosis, 3.1 years). Twelve cancers were in native lung, and 3 were in transplanted lung. The incidence of lung cancer was higher in single lung transplant recipients than in bilateral lung transplant recipients (10.3% vs 0.6%, respectively; P < 0.0001). Imaging manifestations varied according to tumor stages. Among 12 patients treated for lung cancer, 2 patients developed posttreatment acute respiratory distress syndrome. The median survival from cancer diagnosis of cancer was 6.2 months.

Conclusions

Posttransplant lung cancer was noted in 3% of lung transplant recipients and was more common in unilateral transplant recipients. The prognosis upon diagnosis was poor with rapid clinical deterioration and serious posttreatment complications.
Predicting the Risk of Thymic Tumors Using Texture Analysis of Contrast-Enhanced Chest Computed Tomography
Authors: Guo Wei , Liu Jianfang , Wang Xiaohua , Yuan Huishu
Published: March 2023

Objective

This study aimed to explore the value of contrast-enhanced computed tomography texture features for predicting the risk of malignant thymic epithelial tumor.

Methods

Data of 97 patients with pathologically confirmed thymic epithelial tumors treated at in our hospital from March 2015 to October 2021 were retrospectively analyzed. Based on the World Health Organization classification of thymic epithelial tumors, patients were divided into a high-risk group (types B2, B3, and C; n = 45) and a low-risk group (types A, AB, and B1; n = 52). Texture analysis was performed using a first-order, gray-level histogram method. Six features were evaluated: mean, variance, skewness, kurtosis, energy, and entropy. The association between contrast-enhanced computed tomography texture features and the risk of malignancy in thymic epithelial tumors was analyzed. The predictive thresholds of predictive texture features were determined by receiver operating characteristics analysis.

Results

The mean, skewness, and entropy were significantly greater in the high-risk group than in the low-risk group (P < 0.05); however, variance, kurtosis, and energy were comparable in the two groups (P > 0.05). The area under curve of mean, skewness, and entropy was 0.670, 0.760, and 0.880, respectively. The optimal cutoff value of entropy for predicting risk of malignancy was 7.74, with sensitivity, specificity, and accuracy of 80.0%, 80.0%, and 75%, respectively

Conclusions

Contrast-enhanced computed tomography texture features, especially entropy, may be a useful tool to predict the risk of malignancy in thymic epithelial tumors.
Artificial Intelligence–enabled Decision Support in Surgery
Authors: Loftus Tyler J. , Altieri Maria S. , Balch Jeremy A. , Abbott Kenneth L. , Choi Jeff , Marwaha Jayson S. , Hashimoto Daniel A. , Brat Gabriel A. , Raftopoulos Yannis , Evans Heather L. , Jackson Gretchen P. , Walsh Danielle S. , Tignanelli Christopher J.
Published: March 2023

Objective:

To summarize state-of-the-art artificial intelligence–enabled decision support in surgery and to quantify deficiencies in scientific rigor and reporting.

Background:

To positively affect surgical care, decision-support models must exceed current reporting guideline requirements by performing external and real-time validation, enrolling adequate sample sizes, reporting model precision, assessing performance across vulnerable populations, and achieving clinical implementation; the degree to which published models meet these criteria is unknown.

Methods:

Embase, PubMed, and MEDLINE databases were searched from their inception to September 21, 2022 for articles describing artificial intelligence–enabled decision support in surgery that uses preoperative or intraoperative data elements to predict complications within 90 days of surgery. Scientific rigor and reporting criteria were assessed and reported according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guidelines.

Results:

Sample size ranged from 163–2,882,526, with 8/36 articles (22.2%) featuring sample sizes of less than 2000; 7 of these 8 articles (87.5%) had below-average (<0.83) area under the receiver operating characteristic or accuracy. Overall, 29 articles (80.6%) performed internal validation only, 5 (13.8%) performed external validation, and 2 (5.6%) performed real-time validation. Twenty-three articles (63.9%) reported precision. No articles reported performance across sociodemographic categories. Thirteen articles (36.1%) presented a framework that could be used for clinical implementation; none assessed clinical implementation efficacy.

Conclusions:

Artificial intelligence–enabled decision support in surgery is limited by reliance on internal validation, small sample sizes that risk overfitting and sacrifice predictive performance, and failure to report confidence intervals, precision, equity analyses, and clinical implementation. Researchers should strive to improve scientific quality.
Colonoscopic and Clinical Features of Colonic Angiodysplasia: A Study in 54 Patients
Authors: Zhang Chenchen , Wang Yanan , Zhang Dongdong , Li Shuai
Published: March 2023

Objectives:

Colonic angiodysplasia is a rare disease, it is nevertheless a common cause of lower gastrointestinal (GI) bleeding in older adults. The study summarized the colonoscopic and clinical features of colonic angiodysplasia to raise awareness among endoscopists regarding this disease.

Materials and Methods:

We performed a retrospective study of enrolled patients diagnosed with colonic angiodysplasia between September 2013 and April 2022. Clinical and colonoscopic features of the patients with active bleeding were analyzed and compared with those of patients without bleeding. The comparisons were also conducted between the patients with active lower GI bleeding caused by colonic angiodysplasia and those by other diseases.

Results:

In total, 54 eligible patients were included in this study; 55.55% of the participants were aged over 60 years. Ten patients (3 men and 7 women) with colonic angiodysplasia suffered from active lower GI bleeding, which was mainly located in the left and total colon. The patients with type 2 diabetes mellitus, radiotherapy history, antiplatelet drug use, and multiple lesions were more likely to endure lower GI bleeding. The duration between bleeding and admission was longer in the colonic angiodysplasia group than in the other diseases group (P = 0.043). In the colonic angiodysplasia group, bleeding relapsed in 3 patients, and the recurrence rate was higher than in the other diseases group (P < 0.001).

Conclusion:

Endoscopists should perform colonoscopy scrupulously and consider colonic angiodysplasia as a differential diagnosis in patients with lower GI bleeding, especially for older women and adults with chronic diseases, such as type 2 diabetes mellitus.
Lower respiratory tract microbiome composition and community interactions in smokers
Authors: Campos Michael , Cickovski Trevor , Fernandez Mitch , Jaric Melita , Wanner Adam , Holt Gregory , Donna Elio , Mendes Eliana , Silva-Herzog Eugenia , Schneper Lisa , Segal Jonathan , Amador David Moraga , Riveros Juan Daniel , Aguiar-Pulido Vanessa , Banerjee Santanu , Salathe Matthias , Mathee Kalai , Narasimhan Giri
Published: March 2023

The lung microbiome impacts on lung function, making any smoking-induced changes in the lung microbiome potentially significant. The complex co-occurrence and co-avoidance patterns between the bacterial taxa in the lower respiratory tract (LRT) microbiome were explored for a cohort of active (AS), former (FS) and never (NS) smokers. Bronchoalveolar lavages (BALs) were collected from 55 volunteer subjects (9 NS, 24 FS and 22 AS). The LRT microbiome composition was assessed using 16S rRNA amplicon sequencing. Identification of differentially abundant taxa and co-occurrence patterns, discriminant analysis and biomarker inferences were performed. The data show that smoking results in a loss in the diversity of the LRT microbiome, change in the co-occurrence patterns and a weakening of the tight community structure present in healthy microbiomes. The increased abundance of the genus

Ralstonia

in the lung microbiomes of both former and active smokers is significant. Partial least square discriminant and DESeq2 analyses suggested a compositional difference between the cohorts in the LRT microbiome. The groups were sufficiently distinct from each other to suggest that cessation of smoking may not be sufficient for the lung microbiota to return to a similar composition to that of NS. The linear discriminant analysis effect size (LEfSe) analyses identified several bacterial taxa as potential biomarkers of smoking status. Network-based clustering analysis highlighted different co-occurring and co-avoiding microbial taxa in the three groups. The analysis found a cluster of bacterial taxa that co-occur in smokers and non-smokers alike. The clusters exhibited tighter and more significant associations in NS compared to FS and AS. Higher degree of rivalry between clusters was observed in the AS. The groups were sufficiently distinct from each other to suggest that cessation of smoking may not be sufficient for the lung microbiota to return to a similar composition to that of NS.
Predicting High-Risk Fetal Cardiac Disease Anticipated to Need Immediate Postnatal Stabilization and Intervention with Planned Pediatric Cardiac Operating Room Delivery
Authors: Moray Amol , Mugaba Proscovia M. , Joynt Chloe , McBrien Angela , Eckersley Luke , Philipos Ernest , Holinski Paula , Ryerson Lindsay , Coe James Y , Chandra Sujata , Aiken Amanda , Wong Billy , Derbyshire Michele , Lefebvre Maria , Aklabi Mohamed Al , Hornberger Lisa K
Published: March 2023

Background

Distances between delivery centers and cardiac services can make the care of fetuses with cardiac disease(CD) at risk of acute cardiorespiratory instability(ACRI) at birth a challenge. In 2013 we implemented a fetal echocardiography(FE)-based algorithm targeting fetuses considered high-risk for ACRI at ≤2 hours of birth for Caesarian section(CS) delivery in our pediatric cardiac operating room(PCOR) of our children’s hospital. We examine the experience and outcomes of affected newborns.

Methods

We reviewed maternal and postnatal medical records of all fetuses with CD at high-risk for ACRI encountered January 2013-March 2022. Secondary analysis was performed including all fetuses with diagnoses of d-transposition of the great arteries/intact ventricular septum(d-TGA/IVS) and hypoplastic left heart syndrome(HLHS) encountered over the study period.

Results

Forty fetuses were considered high-risk for ACRI: 15 d-TGA/IVS and 7 HLHS with restrictive atrial septum(RAS), 4 absent pulmonary valve syndrome, 3 obstructed anomalous pulmonary veins, 2 severe Ebstein anomaly, 2 thoracic/intracardiac tumors and 7 others. PCOR delivery occurred for 33 but not for 7 (5 d-TGA/IVS, 2 HLHS with RAS). For high-risk cases, FE had a positive predictive value of 50% for intervention/ECMO/death at ≤2 hours and 70% at ≤24 hours. Of “low-risk” cases, 6/46 with d-TGA/IVS and 0/45 with HLHS required intervention at ≤2 hours. FE predicted intervention/ECMO/death at ≤2hours with a sensitivity of 67%, specificity 93%, and positive and negative predictive values of 87% and 87%, respectively, for d-TGA/IVS, and 100%, 95%, 71%, and 100% for HLHS, respectively.

Conclusions

FE predicts need for urgent intervention in majority with d-TGA/IVS and HLHS, and in half of the entire spectrum of high-risk CD.
Effect of cell membrane tension on the lifetime and size of mature clathrin-coated pits and their spatial distribution
Authors: Liu Xinyue , Xi Wang , Gong Xiaobo
Published: March 2023

Clathrin-mediated endocytosis is the most characterized pathway for cells to internalize diverse receptor-bound cargo, such as proteins, nanoparticles, and viruses. However, the effect of membrane tension on clathrin-coated pit (CCP) maturation remains inadequately characterized. This study aimed to determine the effect of membrane tension on CCP maturation both spatially and temporarily, which remains a controversial and elusive issue. We obtained the sizes and spatial distributions of CCPs by the structured illumination microscopy of fixed cells and observed CCP lifetimes in live cells by total internal reflection fluorescence microscopy. The processes of CCP maturation and abortion were reproduced numerically through Monte Carlo simulation. The results showed that the growth time of CCP was more reasonably proportional to its volume rather than its surface area. We further investigated the spatial distribution of the membrane tension and size of CCPs, finding a significant positive correlation between the membrane tension and the size of mature CCPs spatially. This indicates that the CCPs tend to enrich in the highest-tension region, especially the mature ones. These results agreed with our numerical prediction that the CCP structure grew larger to overcome a higher energy barrier caused by higher background cell membrane tension. Our findings enhance the understanding of CCP maturation dynamics and underscore the importance of membrane tension in regulating CCP development.
Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet
Authors: Hoffman Gabriel E. , Lee Donghoon , Bendl Jaroslav , Prashant N.M. , Hong Aram , Casey Clara , Alvia Marcela , Shao Zhiping , Argyriou Stathis , Therrien Karen , Venkatesh Sanan , Voloudakis Georgios , Haroutunian Vahram , Fullard John F. , Roussos Panos
Published: March 2023

Advances in single-cell and -nucleus transcriptomics have enabled generation of increasingly large-scale datasets from hundreds of subjects and millions of cells. These studies promise to give unprecedented insight into the cell type specific biology of human disease. Yet performing differential expression analyses across subjects remains difficult due to challenges in statistical modeling of these complex studies and scaling analyses to large datasets. Our open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. Designed for data from large cohorts, dreamlet is substantially faster and uses less memory than existing workflows, while supporting complex statistical models and controlling the false positive rate. We demonstrate computational and statistical performance on published datasets, and a novel dataset of 1.4M single nuclei from postmortem brains of 150 Alzheimer’s disease cases and 149 controls.
The vasodilator-stimulated phosphoprotein (VASP) supports the conduction of vasodilator signals and NO-induced arteriolar dilations in murine arteriolesin vivo
Authors: Poley Philip , Benz Peter M. , de Wit Cor
Published: March 2023

VASP is a member of the Enabled/VASP protein family that is involved in cortical actin dynamics and may also contribute to the formation of gap junctions. In vessels, gap junctional coupling allows the transfer of signals along the vessel wall and coordinates vascular behavior. Moreover, VASP is reportedly a mediator of NO-induced inhibition of platelet aggregation. Therefore, we hypothesized that VASP exerts also important physiologic functions in arterioles. We examined the spread of vasodilations enabled by gap junctional coupling in endothelial cells as well as NO-induced arteriolar dilations in VASP-deficient mice by intravital microscopy of the microcirculation in a skeletal muscle in anesthetized mice. Conducted dilations were initiated by brief, locally confined stimulation of the arterioles with acetylcholine. The maximal diameters of the arterioles under study ranged from 30 to 40 μm. Brief stimulation with acetylcholine induced a short dilation at the local site that was also observed at remote, upstream sites without an attenuation of the amplitude up to a distance of 1.2 mm in control animals (wild-type). In contrast, remote dilations were reduced in VASP-deficient mice despite a similar local dilation indicating an impairment of conducted dilations. Superfusion of NOdonors induced a concentration-dependent dilation in wild-type mice. However, these dilations were slightly reduced in VASP-deficient animals. In contrast, dilations induced by the endothelial stimulator acetylcholine were fully preserved in VASP-deficient mice. In summary, this study suggests that VASP exerts critical functions in arteriolar diameter control. It is crucial for the conduction of dilator signals along the endothelial cell layer. The impairment possibly reflects a perturbed formation of gap junctions in the endothelial cell membrane. VASP also participates in the full dilatory potential of NOdonors although the effect of its deficiency is only subtle. In contrast, VASP is not required for dilations initiated by endothelial stimulation which are mediated in the murine microcirculation by an EDH-mechanism.
Detecting Material State Changes in the Nucleolus by Label-free Digital Holographic Microscopy
Authors: Zorbas Christiane , Soenmez Aynur , Léger Jean , De Vleeschouwer Christophe , Lafontaine Denis L.J.
Published: March 2023

Ribosome biogenesis is initiated in the nucleolus, a multiphase biomolecular condensate formed by liquid-liquid phase separation. The nucleolus is a powerful disease biomarker and stress biosensor whose morphology reflects its function. Here we have used digital holographic microscopy (DHM), a label-free quantitative phase contrast microscopy technique, to detect nucleoli in adherent and suspension cells. Subtle nucleolar alterations induced by drug treatment or by depletion of ribosomal proteins were efficiently detected by DHM. We trained convolutional neural networks to detect and quantify nucleoli automatically on DHM images of cultured human cells (HeLa). Holograms containing cell optical thickness information allowed us to define a novel nucleolar index which we used to distinguish nucleoli whose material state had been optogenetically modulated. We conclude that DHM is a powerful tool for quantitatively characterizing nucleoli, including material state, without any staining.
Rigid Scaffolds are Promising for Designing Macrocyclic Kinase Inhibitors
Authors: Zhao Zheng , Bourne Philip E.
Published: March 2023

Macrocyclic kinase inhibitors (MKIs) are gaining attention due to their favorable selectivity and potential to overcome drug resistance, yet they remain challenging to design because of their novel structures. To facilitate the design and discovery of MKIs, we investigate MKI rational design starting from initial acyclic compounds by performing microsecond-scale atomistic simulations for multiple MKIs, constructing an MKI database, and analyzing MKIs using hierarchical cluster analysis. Our studies demonstrate that the binding modes of MKIs are like that of their corresponding acyclic counterparts against the same kinase targets. Importantly, within the respective binding sites, the MKI scaffolds retain the same conformations as their corresponding acyclic counterparts, demonstrating the rigidity of scaffolds before and after molecular cyclization. The MKI database includes 641 nanomole-level MKIs from 56 human kinases elucidating the features of rigid scaffolds, and the tendency of core structures among MKIs. Collectively these results and resources can facilitate MKI development.
Does nonlinear blood-brain barrier transport matter for morphine dosing strategies?
Authors: Gülave Berfin , Budda Divakar , Saleh Mohammed AA , van Hasselt JG Coen , de Lange Elizabeth CM
Published: March 2023

Morphine blood-brain barrier (BBB) transport is governed by passive diffusion, active efflux and saturable active influx. These processes may be associated with nonlinear concentration-dependencies which impact plasma and brain extracellular fluid (brainECF) pharmacokinetics of morphine. In this study, we aim to evaluate the impact of nonlinear BBB transport on brainECFpharmacokinetics of morphine and its metabolites for different dosing strategies using a physiologically based pharmacokinetic simulation study. We extended the human physiologically based pharmacokinetic, LeiCNS-PK3.0, model with equations for nonlinear BBB transport of morphine. Simulations for brainECFpharmacokinetics were performed for various dosing strategies: intravenous (IV), oral immediate (IR) and extended release (ER) with dose range of 0.25-150mg and dosing frequencies of 1-6 times daily. The impact of nonlinear BBB transport on morphine CNS pharmacokinetics was evaluated by quantifying (i) the relative brainECFto plasma exposure (AUCu,brainECF/AUCu,Plasma) and (ii) the impact on the peak-to-trough ratio (PTR) of concentration-time profiles in brainECFand plasma. We found that the relative morphine exposure and PTRs are dose dependent for the evaluated dose range. The highest relative morphine exposure value of 1.4 was found for once daily 0.25mg ER and lowest of 0.1 for 6-daily 150mg IV dosing. At lower doses the PTRs were smaller and increased with increasing dose and stabilized at higher doses independent of dosing frequency. Relative peak concentrations of morphine in relation to its metabolites changed with increasing dose. We conclude that nonlinearity of morphine BBB transport affect the relative brainECFexposure and the fluctuation of morphine and its metabolites.

Highlights

Nonlinear transport affects relative morphine exposure in brainECF.

Nonlinear transport affects PK fluctuations of morphine in brainECF.

Nonlinear transport affects brainECFPK relationship of morphine and its metabolites.

Graphical abstract
Sculpting DNA-based synthetic cells through phase separation and phase-targeted activity
Authors: Malouf Layla , Tanase Diana A. , Fabrini Giacomo , Paez-Perez Miguel , Leathers Adrian , Booth Michael J. , Di Michele Lorenzo
Published: March 2023

Synthetic cells, like their biological counterparts, require internal compartments with distinct chemical and physical properties where different functionalities can be localised. Inspired by membrane-less compartmentalisation in biological cells, here we demonstrate how micro-phase separation can be used to engineer heterogeneous cell-like architectures with programmable morphology and compartment-targeted activity. The synthetic cells selfassemble from amphiphilic DNA nanostructures, producing core-shell condensates due to size-induced de-mixing. Lipid deposition and phase-selective etching are then used to generate a porous pseudo-membrane, a cytoplasm analogue, and membrane-less organelles. The synthetic cells can sustain RNA synthesisvia in vitrotranscription, leading to cytoplasm and pseudo-membrane expansion caused by an accumulation of the transcript. Our approach exemplifies how architectural and functional complexity can emerge from a limited number of distinct building blocks, if molecular-scale programmability, emergent biophysical phenomena, and biochemical activity are coupled to mimic those observed in live cells.
Fast or slow? Clock readout sets internal periods
Authors: Holmes Caroline M. , Palmer Stephanie E.
Published: March 2023

Circadian clocks are essential for the function of a wide array of organisms, from cyanobacteria to humans. Despite decades of productive study of these systems, mysteries remain, including why many biological clocks have non-24-hour internal periods. We take a new approach to circadian clocks by focusing on downstream readout of the clock’s state to answer physiologically relevant questions, such as ‘when will the sun rise?’ Using this framework, we show that systematic errors arising from sunrise and sunset prediction can be compensated by having non-24 hour internal periods. We show that this prediction holds in models of cyanobacterial circadian clocks. Finally, we predict latitude-dependant qualitative changes in circadian clock structure and the performance of different clock phenotypes in common laboratory experimental setups.
Spatial-temporal expression analysis of lineage-restricted shell matrix proteins reveals shell field regionalization and distinct cell populations in the slipper snailCrepidula atrasolea
Authors: Lopez-Anido Rebecca N. , Batzel Grant O. , Ramirez Gabriela , Goodheart Jessica A. , Wang Yiqun , Neal Stephanie , Lyons Deirdre C.
Published: March 2023

Molluscs are one of the most morphologically diverse clades of metazoans, exhibiting an immense diversification of calcium carbonate structures, such as the shell. Biomineralization of the calcified shell is dependent on shell matrix proteins (SMPs). While SMP diversity is hypothesized to drive molluscan shell diversity, we are just starting to unravel SMP evolutionary history and biology. Here we leveraged two complementary model mollusc systems,Crepidula fornicataandCrepidula atrasolea, to determine the lineage-specificity of 185CrepidulaSMPs. We found that 95% of the adultC. fornicatashell proteome belongs to conserved metazoan and molluscan orthogroups, with molluscan-restricted orthogroups containing half of all SMPs in the shell proteome. The low number ofC. fornicata-restricted SMPs contradicts the generally-held notion that an animal’s biomineralization toolkit is dominated by mostly novel genes. Next, we selected a subset of lineage-restricted SMPs for spatial-temporal analysis usingin situhybridization chain reaction (HCR) during larval stages inC. atrasolea. We found that 12 out of 18 SMPs analyzed are expressed in the shell field. Notably, these genes are present in 5 expression patterns, which define at least three distinct cell populations within the shell field. These results represent the most comprehensive analysis of gastropod SMP evolutionary age and shell field expression patterns to date. Collectively, these data lay the foundation for future work to interrogate the molecular mechanisms and cell fate decisions underlying molluscan mantle specification and diversification.
LIFR recruits HGF-producing neutrophils to promote liver injury repair and regeneration
Authors: Deng Yalan , Zhao Zilong , Sheldon Marisela , Zhao Yang , Teng Hongqi , Martinez Consuelo , Zhang Jie , Lin Chunru , Sun Yutong , Yao Fan , Zhu Hao , Ma Li
Published: March 2023

The molecular links between tissue repair and tumorigenesis remain elusive. Here, we report that loss of the liver tumor suppressorLifrin mouse hepatocytes impairs the recruitment and activity of reparative neutrophils, resulting in the inhibition of liver regeneration after partial hepatectomy or toxic injuries. On the other hand, overexpression of LIFR promotes liver repair and regeneration after injury. Interestingly, LIFR deficiency or overexpression does not affect hepatocyte proliferationex vivoorin vitro. In response to physical or chemical damage to the liver, LIFR from hepatocytes promotes the secretion of the neutrophil chemoattractant CXCL1 (which binds CXCR2 to recruit neutrophils) and cholesterol in a STAT3-dependent manner. Cholesterol, in turn, acts on the recruited neutrophils to secrete hepatocyte growth factor (HGF) to accelerate hepatocyte proliferation and regeneration. Altogether, our findings reveal a LIFR-STAT3- CXCL1-CXCR2 axis and a LIFR-STAT3-cholesterol-HGF axis that mediate hepatic damage- induced crosstalk between hepatocytes and neutrophils to repair and regenerate the liver.
FBXO38 does not control PD-1 stability
Authors: Dibus Nikol , Salyova Eva , Kolarova Karolina , Pagano Michele , Stepanek Ondrej , Cermak Lukas
Published: March 2023

SKP1-CUL1-F-box protein (SCF) ubiquitin ligases are versatile protein complexes that mediate the ubiquitination of substrates, which are recognized by their F-box-domain- containing subunits1. One of these substrate receptors is FBXO38. Its gene has been found to be mutated in several families with early-onset distal hereditary motor neuronopathy2. SCFFBXO38ubiquitin ligase controls the stability of ZXDB, a nuclear factor associated with the centromeric chromatin protein CENP-B3. Moreover, the loss of FBXO38 results in growth retardation and defect in spermatogenesis characterized by deregulation of the Sertoli cell transcription program and centromere integrity4. A report by Meng et al. proposed that SCFFBXO38regulates the protein levels of the PD-1 inhibitory receptor (also known as CD279, PDCD1) in T cells5. Here, we have re-addressed the conclusions by Meng et al. usingFbxo38KO/KOmice and cell systems. We have found no evidence indicating that FBXO38 controls the abundance and stability of PD-1.
Organization and replicon interactions within the highly segmented genome ofBorrelia burgdorferi
Authors: Ren Zhongqing , Takacs Constantin N. , Brandão Hugo B. , Jacobs-Wagner Christine , Wang Xindan
Published: March 2023

Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated thatB. burgdorferiis polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/SMC. Here, using chromosome conformation capture (Hi-C), we characterized the organization of theB. burgdorferigenome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosomeoriCregion, and a subset of plasmids interact with each other more than with others. We found that SMC and the SMC-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosomeoriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
Sustained activation in basal ganglia and cerebellum after repetitive movement in a non-task-specific dystonia
Authors: Kuster John K , Levenstein Jacob M. , Waugh Jeff , Multhaupt-Buell Trisha J. , Lee Myung Joo , Kim Byoung Woo , Pagnacco Guido , Makhlouf Miriam L. , Sudarsky Lewis R. , Breiter Hans C. , Sharma Nutan , Blood Anne J.
Published: March 2023

We previously observed sustained fMRI BOLD signal in the basal ganglia in focal hand dystonia patients after a repetitive finger tapping task. Since this was observed in a task-specific dystonia, for which excessive task repetition may play a role in pathogenesis, in the current study we asked if this effect would be observed in a focal dystonia (cervical dystonia [CD]) that is not considered task-specific or thought to result from overuse. We evaluated fMRI BOLD signal time courses before, during, and after the finger tapping task in CD patients. We observed patient/control differences in post-tapping BOLD signal in left putamen and left cerebellum during the non-dominant (left) hand tapping condition, reflecting abnormally sustained BOLD signal in CD. BOLD signals in left putamen and cerebellum were also abnormally elevated in CD during tapping itself and escalated as tapping was repeated. There were no cerebellar differences in the previously studied FHD cohort, either during or after tapping. We conclude that some elements of pathogenesis and/or pathophysiology associated with motor task execution/repetition may not be limited to task-specific dystonias, but there may be regional differences in these effects across dystonias, associated with different types of motor control programs.
A beneficial adaptive role for CHOP in driving cell fate selection during ER stress
Authors: Liu Kaihua , Zhao Chaoxian , Adajar Reed C. , DeZwaan-McCabe Diane , Rutkowski D. Thomas
Published: March 2023

Cellular stresses elicit signaling cascades that are capable of either mitigating the inciting dysfunction or initiating cell death. During endoplasmic reticulum (ER) stress, the transcription factor CHOP is widely recognized to promote cell death. However, it is not clear whether CHOP also has a beneficial role during adaptation. Here, we have combined a new, versatile, genetically modifiedChopallele with single cell analysis and with stresses of physiological intensity, to rigorously examine the contribution of CHOP to cell fate. Paradoxically, we found that CHOP promoted death in some cells, but proliferation—and hence recovery—in others. Strikingly, this function of CHOP conferred to cells a stress-specific competitive growth advantage. The dynamics of CHOP expression and UPR activation at the single cell level suggested that CHOP maximizes UPR activation, which in turn favors stress resolution, subsequent UPR deactivation, and proliferation. Taken together, these findings suggest that CHOP’s function can be better described as a “stress test” that drives cells into either of two mutually exclusive fates—adaptation or death—during stresses of physiological intensity.
Non-additive effects of schizophrenia risk genes reflect convergent downstream function
Authors: Deans PJ Michael , Seah Carina , Johnson Jessica , Gonzalez Judit Garcia , Townsley Kayla , Cao Evan , Schrode Nadine , Stahl Eli , O’Reilly Paul , Huckins Laura M. , Brennand Kristen J.
Published: March 2023

Genetic studies of schizophrenia (SCZ) reveal a complex polygenic risk architecture comprised of hundreds of risk variants, the majority of which are common in the population at-large and confer only modest increases in disorder risk. Precisely how genetic variants with individually small predicted effects on gene expression combine to yield substantial clinical impacts in aggregate is unclear. Towards this, we previously reported that the combinatorial perturbation of four SCZ risk genes (“eGenes”, whose expression is regulated by common variants) resulted in gene expression changes that were not predicted by individual perturbations, being most non-additive among genes associated with synaptic function and SCZ risk. Now, across fifteen SCZ eGenes, we demonstrate that non-additive effects are greatest within groups of functionally similar eGenes. Individual eGene perturbations reveal common downstream transcriptomic effects (“convergence”), while combinatorial eGene perturbations result in changes that are smaller than predicted by summing individual eGene effects (“sub-additive effects”). Unexpectedly, these convergent and sub-additive downstream transcriptomic effects overlap and constitute a large proportion of the genome-wide polygenic risk score, suggesting that functional redundancy of eGenes may be a major mechanism underlying non-additivity. Single eGene perturbations likewise fail to predict the magnitude or directionality of cellular phenotypes resulting from combinatorial perturbations. Overall, our results indicate that polygenic risk cannot be extrapolated from experiments testing one risk gene at a time and must instead be empirically measured. By unravelling the interactions between complex risk variants, it may be possible to improve the clinical utility of polygenic risk scores through more powerful prediction of symptom onset, clinical trajectory, and treatment response, or to identify novel targets for therapeutic intervention.
Using LanM Enzymes to Modify Glucagon-Like Peptides 1 and 2 inE.coli
Authors: Larsen Camilla Kjeldgaard , Lindquist Peter , Rosenkilde Mette , Madsen Alice Ravn , Haselmann Kim , Glendorf Tine , Olesen Kjeld , Kodal Anne Louise Bank , Tørring Thomas
Published: March 2023

Selective modification of peptides is often exploited to improve pharmaceutically relevant properties of bioactive peptides like stability, circulation time, and potency. In Nature, natural products belonging to the class of ribosomally synthesized and post-translationally modified peptides (RiPPs) are known to install a number of highly attractive modifications with high selectivity. These modifications are installed by enzymes guided to the peptide by corresponding leader peptides removed as the last step of biosynthesis. Here, we exploit leader peptides and their matching enzymes to investigate the installment of D-Ala post-translationally in a critical position in the hormones, glucagon-like peptides (GLP) 1 and 2. We also offer insight into how precursor peptide design can modulate the modification pattern achieved.
Amino acid usage and tRNA expression underlies proteome adaptation inPlasmodium falciparum
Authors: Li Qian , Vetter Leonie , Veith Ylva , Christ Elena , Végvári Ákos , Sahin Cagla , Ribacke Ulf , Wahlgren Mats , Ankarklev Johan , Larsson Ola , Chan Sherwin Chun-Leung
Published: March 2023

Parasites often depend on metabolic adaptation to the host environment. An adaptive feature of malaria-causing parasites is digestion of hemoglobin (HB) to acquire amino acids (AAs). Here we describe a link between nutrient availability and translation elongation-dependent regulation of gene expression as an adaptive strategy. We show that, unexpectedly, tRNA expression inP. falciparumdoes not match the decoding need as tRNAs decoding AAs that are rare in HB are lowly expressed. This discrepancy renders codons of HB-rare AAs inefficiently decoded and transcripts levels negatively correlated with the requirement of HB-rare AAs for protein synthesis, which are consistent with poor codon optimality causing co-translational mRNA decay. Intriguingly, proliferation-related genes have evolved to require a high level of HB-rare AAs in their encoded proteins, thereby allowing the parasite to control its proliferation by repressing protein synthesis of these genes during nutrient stress. We conclude that the parasite modulates translation elongation by maintaining a discordant tRNA profile as a mechanism to exploit variations in AA-composition among genes as an adaptation strategy.
Aβ*56 is a stable oligomer that correlates with age-related memory loss in Tg2576 mice
Authors: Liu Peng , Lapcinski Ian P. , Shapiro Samantha L. , Kemper Lisa J. , Ashe Karen H.
Published: March 2023

Amyloid-β (Aβ) oligomers consist of fibrillar and non-fibrillar soluble assemblies of the Aβ peptide. Tg2576 human amyloid precursor protein (APP)-expressing transgenic mice modeling Alzheimer’s disease produce Aβ*56, a non-fibrillar Aβ assembly that has been shown by several groups to relate more closely to memory deficits than plaques. Previous studies did not decipher specific forms of Aβ present in Aβ*56. Here, we confirm and extend the biochemical characterization of Aβ*56. We used anti-Aβ(1-x), anti-Aβ(x-40), and A11 anti-oligomer antibodies in conjunction with western blotting, immunoaffinity purification, and size-exclusion chromatography to probe aqueous brain extracts from Tg2576 mice of different ages. We found that Aβ*56 is a ∼56-kDa, SDS-stable, A11-reactive, non-plaque-related, water-soluble, brain-derived oligomer containing canonical Aβ(1-40) that correlates with age-related memory loss. The unusual stability of this high molecular-weight oligomer renders it an attractive candidate for studying relationships between molecular structure and effects on brain function.
Septum site placement inMycobacteria- Identification and Characterization of mycobacterial homologues ofEscherichia coliMinD
Authors: Kishore Vimal , Gaiwala Sharma Sujata S. , Raghunand Tirumalai R.
Published: March 2023

A major virulence trait ofMycobacterium tuberculosis(M. tb) is its ability to enter a dormant state within its human host. Since cell division is intimately linked to metabolic shut down, understanding the mechanism of septum formation and its integration with other events in the division pathway is likely to offer clues to the molecular basis of dormancy. TheM. tbgenome lacks obvious homologues of several conserved cell division proteins, and this study aimed at identifying and functionally characterising mycobacterial homologues of theE.coliseptum site specification protein MinD (EcMinD). Sequence homology based analyses suggested that the genomes of bothM.tband the saprophyteMycobacterium smegmatis(M. smegmatis) encode two putativeEcMinD homologues-Rv1708/MSMEG_3743 and Rv3660c/MSMEG_6171. BothRv1708andMSMEG_3743were observed to fully complement the mini-cell phenotype of theE.coliΔminDEmutantHL1,but the other homologues only partially complemented the mutant phenotype. Over-expression ofMSMEG_3743but notMSMEG_6171inM. smegmatisled to cell elongation and a drastic decrease in CFU counts, indicating the essentiality ofMSMEG_3743in cell-division. Sequence analysis of MSMEG_3743 showed a conserved Walker A motif, the functional role of which was confirmed by a radiolabelled ATPase activity assay. Rv1708 was observed to interact with the chromosome associated proteins ScpA and ParB, pointing to a link between its septum formation role and chromosome segregation. Comparative structural analyses showed Rv1708 to be closer in similarity toEcMinD than Rv3660c. In summary we have demonstrated that Rv1708 and MSMEG_3743 are true mycobacterial homologues ofEcMinD, adding a critical missing piece to the mycobacterial cell division puzzle.