bluuebunny/crossref_metadata_2025 huggingface dataset:
Can static optimization detect changes in peak medial knee contact forces induced by gait modifications?
Authors: Kaneda Janelle M. , Seagers Kirsten A. , Uhlrich Scott D. , Kolesar Julie A. , Thomas Kevin A. , Delp Scott L.
Published: July 2022

Medial knee contact force (MCF) is related to the pathomechanics of medial knee osteoarthritis. However, MCF cannot be directly measured in the native knee, making it difficult for therapeutic gait modifications to target this metric. Static optimization, a musculoskeletal simulation technique, can estimate MCF, but there has been little work validating its ability to detect changes in MCF induced by gait modifications. In this study, we quantified the error in MCF estimates from static optimization compared to measurements from instrumented knee replacements during normal walking and seven different gait modifications. We then identified minimum magnitudes of simulated MCF changes for which static optimization correctly identified the direction of change at least 70% of the time. A full-body musculoskeletal model with a multi-compartment knee and a custom static optimization implementation was used to estimate MCF. Simulations were evaluated using experimental data from three subjects for a total of 115 steps. Static optimization underpredicted the first peak (mean absolute error = 0.16 bodyweights) and overpredicted the second peak (mean absolute error = 0.31 bodyweights) of MCF. Average root mean square error in MCF over stance phase was 0.32 bodyweights. Static optimization detected the direction of change with at least 70% accuracy for early-stance reductions, late-stance reductions, and early-stance increases in peak MCF of 0.10 bodyweights and greater. These results suggest that a simple static optimization approach accurately detects directional effects on early-stance medial knee loading, potentially making it a valuable tool for evaluating the biomechanical efficacy of gait modifications for knee osteoarthritis.
All-optical observation on activity-dependent nanoscale dynamics of myelinated axons
Authors: Kwon Junhwan , Lee Sungho , Jo Yongjae , Choi Myunghwan
Published: July 2022

In the mammalian brain, rapid conduction of neural information is supported by the myelin, whose functional efficacy shows steep dependence on its nanoscale cytoarchitecture. Although previous in vitro studies suggested that neural activity accompanies nanometer-scale cellular deformations, it has remained unexplored whether neural activity can dynamically remodel the myelinated axon due to the technical challenge in observing its nanostructural dynamics in living tissues. To this end, we introduced a novel all-optical approach combining a nanoscale dynamic readout based on spectral interferometry and optogenetic control of neural excitation on a living brain slice preparation. In response to optogenetically evoked neuronal burst firing, the myelinated axons exhibited progressive and reversible spectral redshifts, corresponding to the transient swelling at a subnanometer scale. We further revealed that the activity-dependent nanostructural dynamics was localized to the paranode. In summary, our novel all-optical studies substantiate that myelinated axon exhibits activity-dependent nanoscale swelling, which potentially serves to dynamically tune the transmission speed of neural information.

RESEARCH SUMMARIES

As neural activity involves rapid ion flux across the cell membrane, researchers have long been tried to detect the accompanying nanoscale morphological dynamics. However, measuring the activity-dependent nanostructural dynamics in the living mammalian brain has been an enigma due to the technical limitations. By combining excitatory optogenetics and in situ nanoscale metrology based on spectral interference, we demonstrate the first direct observation that the mammalian axons exhibit transient activity-dependent swelling at subnanometer-scale.
Spindle-dependent memory consolidation in healthy adults: A meta-analysis
Authors: Kumral Deniz , Matzerath Alina , Leonhart Rainer , Schönauer Monika
Published: July 2022

Accumulating evidence suggests a central role for sleep spindles in the consolidation of new memories. However, no metaanalysis of the association between sleep spindles and memory performance has been conducted so far. Here, we report meta-analytical evidence for spindle-memory associations and investigate how multiple factors, including memory type, spindle type, spindle characteristics, and EEG topography affect this relationship. The literature search yielded 53 studies reporting 1427 effect sizes, resulting in a small to moderate effect for the average association. We further found that spindle-memory associations were significantly stronger for procedural memory than for declarative memory. Neither spindle types nor EEG scalp topography had an impact on the strength of the spindle-memory relation, but we observed a distinct functional role of global and fast sleep spindles, especially for procedural memory. We also found a moderation effect of spindle characteristics, with power showing the largest effect sizes. Collectively, our findings suggest that sleep spindles are involved in learning, thereby representing a general physiological mechanism for memory consolidation.

Highlights

Spindle measures showed a small to medium-sized association with memory performance.

This relationship was stronger for procedural memory than declarative memory.

No moderation effects of spindle type and EEG scalp topography have been observed.

Spindle power emerged as the strongest predictors.

Naps showed similar spindle-related consolidation mechanisms to whole-night sleep.
Neuromorphic Model of Hippocampus Place cells using an Oscillatory Interference Technique for Hardware Implementation
Authors: Chen Zhaoqi , Nasrallah Alia , Alemohammad Milad , Furuta Masanori , Etienne-Cummings Ralph
Published: July 2022

In this paper, we propose a simplified and robust model for Place cell generation based on the Oscillatory Interference (OI) model concept. Aiming toward hardware implementation in bio-inspired Simultaneous Localization and Mapping (SLAM) systems for mobile robotics, we base our model on logic operations that reduce its computational complexity. The model compensates for parameter variations in the behaviors of the population of constituent Theta cells, and allows the Theta cells to have square-wave oscillation profiles. The robustness of the model, with respect to mismatch in the Theta cell’s base oscillation frequency and gain—as a function of modulatory inputs—is demonstrated. Place cell composed of 48 Theta cells with base frequency variations with a 25% standard deviation from the mean and a gain error with 20% standard deviation from the mean only result in a 20% deformations within the place field and 0.24% outer side lobes, and an overall pattern with 0.0015 mean squared error on average. We also present how the model can be used to achieve the localization and path-tracking functionalities of SLAM.
Organic electrochemical transistor as an on-site signal amplifier for electrochemical aptamer-based sensing
Authors: Ji Xudong , Lin Xuanyi , Rivnay Jonathan
Published: July 2022

Electrochemical aptamer-based (E-AB) sensors are typically deployed as individual, passive, surface-functionalized electrodes, but they exhibit limited sensitivity especially when the area of the electrode is reduced for miniaturization purposes. We demonstrated that organic electrochemical transistors (OECTs), electrolyte gated tran-istors with volumetric gating, can serve as on-site amplifiers to improve the sensitivity of single electrode-based E-AB sensors. By monolithically integrating an Au working/sensing electrode, on-chip Ag/AgCl reference electrode and Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) counter electrode — also serving as the OECT channel, we can simultaneously perform OECT testing and traditional electroanalytical measurement on E-AB sensors including cyclic voltammetry (CV) and square-wave voltammetry (SWV). This device can directly amplify the current from the E-AB sensor via the in-plane current modulation in the counter electrode/transistor channel. The integrated OECT-based E-AB sensor is able to sense transforming growth factor beta 1 (TGF-β1) with 3 to 4 orders of magnitude enhancement of sensitivity compared to that in a single electrode-based E-AB sensor (292 µA/dec vs. 85 nA/dec for OECT vs. single electrode SWV). This approach is believed to be universal, which can be applied to a wide range of tethered electrochemical reporter-based sensors to enhance sensitivity, aiding in sensor miniaturization and easing the burden on backend signal processing.
Cannabidiol prevents spontaneous fear recovery after extinction and ameliorates stress-induced extinction resistance
Authors: Papagianni Eleni P. , Warren William G. , Cassaday Helen J. , Stevenson Carl W.
Published: July 2022

Cannabidiol, the main non-psychotropic constituent of cannabis, has potential as a treatment for anxiety-related disorders since it reduces learned fear expression and enhances fear extinction. The return of fear over time after successful extinction and stress-induced extinction resistance are potential barriers to the treatment of these disorders with extinction-based psychological therapy. In two experiments using rats subjected to auditory fear conditioning, we determined the effects of systemic cannabidiol treatment on (1) delayed extinction and later spontaneous fear recovery, and (2) extinction resistance caused by immediate extinction (the immediate extinction deficit (IED)). In Experiment 1, cannabidiol was given before delayed extinction occurring 24 hr after conditioning, with extinction recall and spontaneous fear recovery tested drug-free 1 and 21 days after extinction, respectively. We found that cannabidiol had no effect on extinction recall but it prevented spontaneous fear recovery. In Experiment 2, the IED procedure was first validated, with immediate extinction occurring 30 min after conditioning. We confirmed that immediate extinction impaired extinction recall, compared to delayed extinction. Next, cannabidiol was given before immediate or no extinction, with extinction recall tested drug-free the next day. We found that cannabidiol rescued the IED, which did not involve effects on fear memory consolidation. In summary, cannabidiol prevented spontaneous fear recovery after delayed extinction and ameliorated extinction resistance caused by immediate extinction. Although the pharmacological mechanisms underlying these effects remain to be determined, our results add to evidence indicating that cannabidiol might prove useful as an adjunct for potentiating the psychological treatment of anxiety-related disorders.
Evolution of median fin patterning and modularity in living and fossil osteichthyans
Authors: Charest France , Fernández Jorge Mondéjar , Grünbaum Thomas , Cloutier Richard
Published: July 2022

Morphological and developmental similarities, and interactions among developing structures are interpreted as evidences of modularity. Such similarities exist between the dorsal and anal fins of living actinopterygians: (1) both fins differentiate in the same direction [dorsal and anal fin patterning module (DAFPM)], and (2) radials and lepidotrichia differentiate in the same direction [endoskeleton and exoskeleton module (EEM)]. To infer the evolution of these common developmental patternings among osteichthyans, we address (1) the complete description and quantification of the DAFPM and EEM in a living actinopterygian (the rainbow troutOncorhynchus mykiss) and (2) the presence of these modules in fossil osteichthyans (coelacanths, lungfishes, porolepiforms and ‘osteolepiforms’). InOncorhynchus, sequences of skeletal elements are determined based on (1) apparition (radials and lepidotrichia), (2) chondrification (radials), (3) ossification (radials and lepidotrichia), and (4) segmentation plus bifurcation (lepidotrichia). Correlations are then explored between sequences. In fossil osteichthyans, sequences are determined based on (1) ossification (radials and lepidotrichia), (2) segmentation, and (3) bifurcation of lepidotrichia. Segmentation and bifurcation patterns were found crucial for comparisons between living and extinct taxa. Our data suggest that the EEM is plesiomorphic at least for actinopterygians, and the DAFPM is plesiomorphic for osteichthyans, with homoplastic dissociation. Finally, recurrent patterns suggest the presence of a Lepidotrichia Patterning Module (LPM).
GroovDB: A database of ligand-inducible transcription factors
Authors: d’Oelsnitz Simon , Ellington Andrew D.
Published: July 2022

Genetic biosensors are integral to synthetic biology. In particular, ligand-inducible prokaryotic transcription factors are frequently used in high-throughput screening, for dynamic feedback regulation, as multi-layer logic gates, and in diagnostic applications. In order to provide a curated source that users can rely on for engineering applications, we have developed GroovDB (available at https://groov.bio), a Web-accessible database of ligand-inducible transcription factors that contains all information necessary to build chemically-responsive genetic circuits, including biosensor sequence, ligand, and operator data. Ligand and DNA interaction data has been verified against the literature, while an automated data curation pipeline is used to programmatically fetch metadata, structural information, and references for every entry. A custom tool to visualize the natural genetic context of biosensor entries provides additional information that provides potential insights into alternative ligands and systems biology.
Fixing reference errors efficiently improves sequencing results
Authors: Behera S. , LeFaive J. , Orchard P. , Mahmoud M. , Paulin L. F. , Farek J. , Soto D. C. , Parker Stephen C.J. , Smith A. V. , Dennis M. Y. , Zook J. M. , Sedlazeck F.J.
Published: July 2022

The GRCh38 reference is the current standard in human genomics research and clinical applications, but includes errors across 33 protein-coding genes, including 12 with medical relevance. Current studies rely on the correctness of this reference genome and require an accurate and cost-effective way to improve variant calling and expression analysis across these erroneous loci. We identified likely artifacts in GTEx, gnomAD, 1000 Genomes Project, and other important genomic resources leading to wrong interpretations for these genes. Here, we present FixItFelix together with a modified GRCh38 version that improves the subsequent analysis across these genes within minutes for an existing BAM/CRAM file. We showcase these improvements over multi-ethnic control samples across short and long-read DNA-, and RNA-sequencing. Furthermore, applying our approach across thousands of genomes demonstrates improvements for population variant calling as well as eQTL studies. Still, some genes e.g., DUSP22 indicate mixed results due to their complexity.
COVID-19-associated pulmonary aspergillosis in immunocompetent patients: A virtual patient cohort study
Authors: Ribeiro Henrique AL , Scindia Yogesh , Mehrad Borna , Laubenbacher Reinhard
Published: July 2022

Purpose

The opportunistic fungusAspergillus fumigatusinfects the lungs of immunocompromised hosts, including patients undergoing chemotherapy or organ transplantation. More recently however, immunocompetent patients with severe SARS-CoV2 have been reported to be affected by COVID-19 Associated Pulmonary Aspergillosis (CAPA), in the absence of the conventional risk factors for invasive aspergillosis. This paper explores the hypothesis that contributing causes are the destruction of the lung epithelium permitting colonization by opportunistic pathogens. At the same time, the exhaustion of the immune system, characterized by cytokine storms, apoptosis, and depletion of leukocytes may hinder the response toA. fumigatusinfection. The combination of these factors may explain the onset of invasive aspergillosis in immunocompetent patients.

Methods

We used a previously published computational model of the innate immune response to infection withAspergillus fumigatus. Variation of model parameters was used to create a virtual patient population. A simulation study of this virtual patient population to test potential causes for co-infection in immunocompetent patients.

Results

The two most important factors determining the likelihood of CAPA were the inherent virulence of the fungus and the effectiveness of the neutrophil population, as measured by granule half-life and ability to kill fungal cells. Varying these parameters across the virtual patient population generated a realistic distribution of CAPA phenotypes observed in the literature.

Conclusions

Computational models are an effective tool for hypothesis generation. Varying model parameters can be used to create a virtual patient population for identifying candidate mechanisms for phenomena observed in actual patient populations.
No evidence of theory of mind reasoning in the human language network
Authors: Shain Cory , Paunov Alexander , Chen Xuanyi , Lipkin Benjamin , Fedorenko Evelina
Published: July 2022

Language comprehension and the ability to infer others’ thoughts (theory of mind, ToM) are interrelated during development and language use. However, neural evidence that bears on the relationship between language and ToM mechanisms is mixed. Although robust dissociations have been reported in brain disorders, brain activations for contrasts that target language and ToM bear similarities, and some have reported overlap (Deen et al., 2015). We take another look at the language-ToM relationship by evaluating the response of the language network (Fedorenko et al., 2010), as measured with fMRI, to verbal and non-verbal ToM across 151 participants. Individual-subject analyses reveal that all core language regions respond more strongly when participants read vignettes about false beliefs compared to the control vignettes. However, we show that these differences are largely due to linguistic confounds, and no such effects appear in a non-verbal ToM task. These results argue against cognitive and neural overlap between language processing and ToM. In exploratory analyses, we find responses to social processing in the “periphery” of the language network—right hemisphere homotopes of core language areas and areas in bilateral angular gyri—but these responses are not selectively ToM-related and may reflect general visual semantic processing.
NeuVue: A Framework and Workflows for High-Throughput Electron Microscopy Connectomics Proofreading
Authors: Xenes Daniel , Kitchell Lindsey M. , Rivlin Patricia K. , Brodsky Rachel , Gooden Hannah , Joyce Justin , Luna Diego , Norman-Tenazas Raphael , Ramsden Devin , Romero Kevin , Rose Victoria , Villafane-Delgado Marisel , Gray-Roncal William , Wester Brock
Published: July 2022

1.

NeuVue is a software platform created for large-scale proofreading of machine segmentation and neural circuit reconstruction in high-resolution electron microscopy connectomics datasets. The NeuVue platform provides a robust web-based interface for proofreaders to collaboratively view, annotate, and edit segmentation and connectivity data. A backend queuing service organizes proofreader tasks into purpose-driven task types and increases proofreader throughput by limiting proofreader actions to simple, atomic operations. A collection of analytical dashboards, data visualization tools, and Application Program Interface (API) capabilities provide stakeholders real-time access to proofreading progress at an individual proofreader level as well as insights on task generation priorities. NeuVue is agnostic to the underlying data being proofread and improves upon the traditional proofreader experience through quality-of-life features that streamline complex editing operations such as splitting and merging objects in dense nanoscale segmentation.

NeuVue heavily leverages cloud resources to enable proofreaders to simultaneously access and edit data on the platform. Production-quality features such as load-balancing, auto-scaling, and pre-deployment testing are all integrated into the platform’s cloud architecture. Additionally, NeuVue is powered by well-supported open-source connectomics tools from the community such as Neuroglancer, PyChunkedGraph, and Connectomics Annotation Versioning Engine (CAVE). The modular design of NeuVue facilitates easy integration and adoption of useful community tools to allow proofreaders to take advantage of the latest improvements in data visualization, processing, and analysis.

We demonstrate our framework through proofreading of the mouse visual cortex data generated on the IARPA MICrONS Project. This effort has yielded over 40,000 proofreader edits across the 2 petavoxels of “Minnie” neuroimaging data. 44 unique proofreaders of various skill levels have logged a cumulative 3,740 proofreading hours, and we have been able to validate the improved connectivity of thousands of neurons in the volume. With sustained development on the platform, new integrated error detection and error correction capabilities, and continuous improvements to the proofreader model, we believe that the NeuVue framework can enable high-throughput proofreading for large-scale connectomics datasets of the future.
Interpreting single-step genomic evaluations as mixed effects neural networks of three layers: pedigree, genotypes, and phenotypes
Authors: Zhao Tianjing , Cheng Hao
Published: July 2022

The single-step approach has become the most widely-used methodology for genomic evaluations when only a subset of phenotyped individuals in the pedigree are genotyped, where the genotypes for non-genotyped individuals are imputed based on gene contents of genotyped individuals through their pedigree relationships. We proposed a new method named single-step NN-MM to represent the single-step genomic evaluations as mixed effects neural networks of three sequential layers: pedigree, genotypes, and phenotypes, where the gene contents of non-genotyped individuals are sampled based on pedigree, genotypes, and phenotypes. In simulation analysis, the single-step NN-MM had similar or better prediction performance than the conventional single-step approach. In addition to imputation of genotypes using three sources of information including phenotypes, genotypes, and pedigree, single-step NN-MM provides a more flexible framework to allow nonlinear relationships between genotypes and phenotypes, and individuals being genotyped with different SNP panels. The single-step NN-MM has been implemented in a package called “JWAS”.
Phase Heterogeneity in Cholesterol-containing Ternary Phospholipid Lamellar Phases
Authors: Gater Deborah L. , Hughes Keontré I. , Stojanoff Vivian , Isakovic A. F.
Published: July 2022

Pseudo-ternary mixtures of lamellar phase phospholipids (DPPC and brain sphingomyelin with cholesterol) were studied below Tm, while comparing the influence of cholesterol content, temperature and the presence of small quantities of Vitamin D binding protein (DBP) or Vitamin D receptor (VDR). The measurements, conducted by X-ray diffraction (XRD) and nuclear magnetic resonance (NMR), cover a range of cholesterol concentrations (20% mol. wt to 40% mol. wt.) and physiologically relevant temperature range (294 K – 314 K). In addition to rich intra-phase behaviour, data and modelling are used to approximate the lipids’ headgroup location variations under the above-mentioned experimental conditions.
Metabolic network models ofGardnerellapangenome identify interactions in the vaginal environment
Authors: Dillard Lillian R , Glass Emma M , Lewis Amanda L , Thomas-White Krystal , Papin Jason A
Published: July 2022

Gardnerellais the primary pathogenic bacterial genus present in the polymicrobial infection known as bacterial vaginosis (BV). Despite BV’s high prevalence and associated chronic and acute women’s health impacts, theGardnerellapangenome is largely uncharacterized at both the genetic and functional metabolic level. Here, we used genome scale metabolic models to characterizein silicotheGardnerellapangenome metabolic content and assessed metabolic functional capacity within a BV positive cervicovaginal fluid context. Metabolic capacity varied widely across the pangenome, with 38.15% of all reactions as core to the genus, compared to 49.6% of reactions identified as unique to a smaller subset of species. Four genes –gpsA, fas, suhB, psd– were identified as core essential genes, critical forin silicometabolic function of all analyzed bacterial species in theGardnerellagenus. Further understanding of these core essential metabolic functions could inform novel therapeutic strategies to treat BV. These data represent the first metabolic modelling of theGardnerellapangenome and illustrate strain-specific interactions with the vaginal metabolic environment across the pangenome.
Prediction models of bronchopulmonary dysplasia: a systematic review and meta-analysis with validation
Authors: Kwok T’ng Chang , Batey Natalie , Luu Ka Ling , Prayle Andrew , Sharkey Don
Published: July 2022

Introduction

Neonatal bronchopulmonary dysplasia (BPD) is associated with lifelong respiratory and neurological sequalae. Prediction models could identify infants at greatest risk of BPD and allow targeted preventative strategies. We performed a systematic review and meta-analysis with external validation of identified models.

Methods

Studies using predictors available before day 14 of life to predict BPD in very preterm infants were included. Two reviewers assessed 7,628 studies for eligibility. Meta-analysis of externally validated models was followed by validation using 62,864 very preterm infants in England and Wales.

Results

64 studies using 53 prediction models were included totalling 274,407 infants (range 32–156,587/study). 35 (55%) studies predated 2010; 39 (61%) were single-centre studies. 46 (87%) models were developed for the first week of life. Overall, 97% of studies had a high risk of bias, especially in the analysis domain. Internal (25%) and external (30%) validation were performed infrequently in the 44 model derivation studies. Following meta-analysis of 22 BPD and 11 BPD/death composite models, Laughon’s day one model was the most promising in predicting BPD and death with a fair C-statistic of 0.76 (95% CI 0.70–0.81) and good calibration. Six models were externally validated in our cohort with a C-statistic between 0.70 to 0.90 but with poor calibration.

Conclusion

Few BPD prediction models were developed with contemporary populations, underwent external validation, or had calibration and impact analyses. To reduce the adverse impact of BPD, we need contemporary, validated, and dynamic prediction models to allow targeted preventative strategies.

What is the key question?

This review aims to provide a comprehensive assessment of all BPD prediction models developed to address the clinical uncertainty of which predictive model is sufficiently valid and generalisable for use in clinical practice and research.

What is the bottom line?

Published BPD prediction models are mostly outdated, single centre and lack external validation.

Why read on?

Laughon’s 2011 model is the most promising but more robust models, using contemporary data with external validation are needed to support better treatments.
Streptomycin and Pyridomycin drug molecules provide the most potential inhibitors against Rv3871 to cure Tuberculosis
Authors: Bhushan Shikha , Raja Yashpal Singh , Mishra Surya
Published: July 2022

The ESX-1 secretion system of Mycobacterium tuberculosis delivers bacterial virulence factors to host cells during infection. The most abundant factor, the ESAT-6/CFP-10 dimer, is targeted for secretion via a C-terminal signal sequence on CFP-10 that is recognized by the cytosolic ATPase, Rv3871. ATPase that is a component of the ESAT-6/CFP-10 secretion system. ESX locus contains genes encoding conserved secretion machinery components termed EccCb1. these core components are required for ESAT-6/CFP-10 secretion [70, 71]. Rv3871 is a cytoplasmic protein connected with the Rv3870 and encoded by the EccCb1 gene. These proteins supply energy for the secretion process. Each of these ATPases is involved in targeting protein for ESX-1 secretion. EccCb1 binds a seven amino acid C-terminal signal peptide of CFT-10, which is required for secretion of the ESAT-6/CFP-10 complex. In this we target the Rv3871 seven amino acid c-terminal region and block it through multiple drugs so, it cannot be activated by the ATPases and not to supply energy for the secretion protein during infection (Tuberculosis). In the present study we have comparatively studied different Rv3871 inhibitory antagonist drug molecule which could be a potential drug molecule to inhibit ATPases on the Rv3871 molecule that is responsible for the energy supply. We have 16 antagonistic drug molecules as shortlisted based on previous studies, that block the target site on the Rv3871 molecule.
Compositional profiling of EV-lipoprotein mixtures by AFM nanomechanical imaging
Authors: Ridolfi Andrea , Conti Laura , Brucale Marco , Frigerio Roberto , Cardellini Jacopo , Musicò Angelo , Romano Miriam , Zendrini Andrea , Polito Laura , Bergamaschi Greta , Gori Alessandro , Montis Costanza , Barile Lucio , Berti Debora , Radeghieri Annalisa , Bergese Paolo , Cretich Marina , Valle Francesco
Published: July 2022

The widely overlapping physicochemical properties of lipoproteins (LPs) and extracellular vesicles (EVs) represents one of the main obstacles for the isolation and characterization of these pervasive biogenic lipid nanoparticles. We herein present the application of an atomic force microscopy (AFM)-based quantitative morphometry assay to the rapid nanomechanical screening of mixed LPs and EVs samples.

The method can determine the diameter and the mechanical stiffness of hundreds of individual nanometric objects within few hours. The obtained diameters are in quantitative accord with those measured via cryo-electron microscopy (cryo-EM); the assignment of a specific nanomechanical readout to each object enables the simultaneous discrimination of co-isolated EVs and LPs even if they have overlapping size distributions. EVs and all classes of LPs are shown to be characterized by specific combinations of diameter and stiffness, thus making it possible to estimate their relative abundance in EV/LP mixed samples in terms of stoichiometric ratio, surface area and volume. As a side finding, we show how the mechanical behaviour of specific LP classes is correlated to distinctive structural features revealed by cryo-EM. To the best of our knowledge, these results represent the first systematic single-particle mechanical investigation of lipoproteins.

The described approach is label-free, single-step and relatively quick to perform. Importantly, it can be used to analyze samples which prove very challenging to assess with several established techniques due to ensemble-averaging, low sensibility to small particles, or both, thus providing a very useful tool for quickly assessing the purity of EV/LP isolates including plasma- and serum-derived preparations.
Bacterial NLR-related proteins protect against phage
Authors: Kibby Emily M. , Conte Amy N. , Burroughs A. Maxwell , Nagy Toni A. , Vargas Jose A. , Aravind L. , Whiteley Aaron T.
Published: July 2022

Bacteria use a wide range of immune systems to counter phage infection. A subset of these genes share homology with components of eukaryotic immune systems, suggesting that eukaryotes horizontally acquired certain innate immune genes from bacteria. Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat containing gene family (NLRs), are found in bacteria and defend against phages. NACHT proteins are widespread in bacteria, provide immunity against both DNA and RNA phages, and display the characteristic C-terminal sensor, central NACHT, and N-terminal effector modules. Some bacterial NACHT proteins have domain architectures similar to human NLRs that are critical components of inflammasomes. Human disease-associated NLR mutations that cause stimulus-independent activation of the inflammasome also activate bacterial NACHT proteins, supporting a shared signaling mechanism. This work establishes that NACHT module-containing proteins are ancient mediators of innate immunity across the tree of life.
Age-related Macular Degeneration is associated with faster rates of structural brain changes and widespread differences in connectivity
Authors: Stout Jacques A , Dai Rui , Anderson Robert J , Cousins Scott , Zhuang Jie , Lad Eleonora M , Whitaker Diane , Madden David , Potter Guy , Whitson Heather E , Badea Alexandra
Published: July 2022

Age-related macular degeneration (AMD) is a prevalent disease impeding vision. More recently, AMD has also been linked to cognitive impairment, such as deficits in language and memory skills. In order to better understand the extent of AMD-related changes in the whole brain structure and connectivity, we have conducted an MRI diffusion acquisition study on 40 participants (20 diagnosed with AMD and 20 controls). These acquisitions were then performed again in a follow up two years later. We developed novel analysis methods for diffusion based tractography and connectomes to better determine which, if any, brain region connections saw the greatest changes between the AMD and the age-matched control groups. Using voxel-based analysis, we identified atrophy in AMD participants in the cuneate gyrus, which has been associated with vision, and the left superior temporal gyrus, which has been associated with language, while later acquisitions compounded this with a deficiency in the bilateral cingulate gyrus, itself linked to higher cognition and memory. These regional atrophy findings support that people with AMD experience widespread neuronal degradation that is not limited to retinal neurons. Regions that saw drastically lowered fractional anisotropy among AMD vs. control included the visual cortex, such as the bilateral occipital lobe and the frontoparietal cortex. Tensor Network Principal Component Analysis (TN-PCA) isolated lingual and temporal connections as important differentiators of AMD connectomes compared to controls, thus supporting our morphometric and texture findings in regions related to vision, but also connectopathies of language and memory brain regions. Bundle based analyses in baseline data revealed that the lingual gyrus had greater spread of tracts overall in the AMD participants, which may be explained by prior reorganization in this area, demonstrating a connection between retinal health and lingual structure. Moreover, we noted group differences in the interhemispheric temporal connections, and lingual cerebellar connections, supporting extensive downstream effects of vision loss. Our bundle-based analyses expand the toolset available for neuroimaging-based phenotyping, and reveal widespread changes in AMD participants beyond brain regions and tractography networks directly involved in vision processing, including those involved in language and memory.
Potent Bacterial Vaccines Require FcγRIIB-mediated Pathogen Capture by Liver Sinusoidal Endothelium
Authors: Wang Juanjuan , An Haoran , Ding Ming , Liu Yanhong , Wang Shaomeng , Jin Qian , Dong Haodi , Tian Xianbin , Liu Jiankai , Zhang Jingfei , Zhu Tao , Li Junqiang , Shao Zhujun , Briles David E. , Zheng Haifa , Zhang Linqi , Zhang Jing-Ren
Published: July 2022

Certain vaccines are more effective than others against microbial infections, but the molecular mechanisms separating the two types of vaccines are largely undefined. Here, by comparing two vaccines ofStreptococcus pneumoniaewith identical antigens but different efficacies (pneumococcal conjugate vaccine – PCV13 and pneumococcal polysaccharide vaccine – PPV23), we reveal that superior vaccine protection against blood-borne bacteria is primarily achieved by activating pathogen capture of the sinusoidal endothelial cells (ECs) in the liver. Consistent with its superior protection in humans, PCV13 confers a more potent protection than PPV23 against pneumococcal infection in mice.In vivoreal-time imaging and genetic mutagenesis revealed that PCV13 activates both liver ECs and resident macrophages Kupffer cells (KCs) to capture IgG-coated bacteria via IgG Fc gamma receptor (FcγR). In particular, the FcγRIIB-mediated capture by ECs is responsible for PCV13-induced superior protection. In contrast, PPV23 only activates KCs (but not ECs) to achieve a less effective pathogen capture and protection through complement receptor-mediated recognition of IgM- and C3-coated bacteria. These liver-based vaccine protection mechanisms are also found with the vaccines ofNeisseria meningitidisandKlebsiella pneumoniae, another two important invasive human pathogens. Our findings have uncovered a novel EC- and FcγRIIB-mediated mechanism in the liver for more efficacious vaccine protection. These findings can serve asin vivofunctional readouts to evaluate vaccine efficacy and guide the future vaccine development.

One Sentence Summary

Vaccine efficacy is defined by FcγRIIB-mediated capture of antibody-coated bacteria via liver sinusoidal endothelial cells.
Mammalian Pumilio Proteins Control Cellular Morphology, Migration, and Adhesion
Authors: Sternburg Erin L. , Lillibridge Jordan J. , Phandthong Rattapol , Karginov Fedor V.
Published: July 2022

Pumilio proteins are RNA-binding proteins that control mRNA translation and stability by binding to the 3’ UTR of target mRNAs. Mammals have two canonical Pumilio proteins, PUM1 and PUM2, which are known to act in many biological processes, including embryonic development, neurogenesis, cell cycle regulation and genomic stability. Here, we characterized a new role of both PUM1 and PUM2 in regulating cell morphology, migration, and adhesion in T-REx-293 cells, in addition to previously known defects in growth rate. Gene ontology analysis of differentially expressed genes in PDKO cells for both cellular component and biological process showed enrichment in categories related to adhesion and migration. PDKO cells had a collective cell migration rate significantly lower than that of WT cells and displayed changes in actin morphology. In addition, during growth, PDKO cells aggregated into clusters (clumps) due to an inability to escape cell-cell contacts. Addition of extracellular matrix (Matrigel) alleviated the clumping phenotype. Collagen IV (ColIV), a major component of Matrigel, was shown to be the driving force in allowing PDKO cells to monolayer appropriately, however, ColIV protein levels remained unperturbed in PDKO cells. This study characterizes a novel cellular phenotype associated with cellular morphology, migration, and adhesion which can aid in developing better models for PUM function in both developmental processes and disease.
Glucocorticoid signaling mediates CD8+ T cell memory differentiation
Authors: Tehseen Azeez , Kumar Dhaneshwar , Sarkar Roman , Singh Sudhakar , Dubey Abhishek , Sehrawat Sharvan
Published: July 2022

We provide evidence on the TRM potentiation by glucocorticoids in stimulated CD8+ T cells. Signaling via glucocorticoid receptor reciprocally regulated short-lived effector cells and memory precursor effector cells. Influenza A virus infected mice treated transiently with dexamethasone preferentially generated multipotent TRM cells that efficiently responded to the subsequent infection. Compromised memory following abrogation of glucocorticoid signaling further confirmed their role in memory potentiation. Transcriptomic and biochemical analysis of dexamethasone treated cells revealed a metabolic switch to oxidative phosphorylation via an engagement of AMPK signaling due to reduced glucose uptake. These cells exhibited an accumulation of phosphorylated STAT3 and STAT5 to drive memory differentiation. Therefore, glucocorticoids mediate tissue homing memory T cell differentiation.

One-Sentence Summary

Glucocorticoid signaling in responding CD8+ T cells promotes memory differentiation
OpenGenomeBrowser: A versatile, dataset-independent and scalable web platform for genome data management and comparative genomics
Authors: Roder Thomas , Oberhänsli Simone , Shani Noam , Bruggmann Rémy
Published: July 2022

OpenGenomeBrowser is a self-hostable open-source platform that manages access to genomic data and drastically simplifies comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. The largest instance currently contains over 1,400 bacterial genomes. Source code, documentation, tutorials and a demo server are available at opengenomebrowser.github.io.
A Newly Identified Class of Protein Misfolding in All-atom Folding Simulations Consistent with Limited Proteolysis Mass Spectrometry
Authors: Vu Quyen V. , Sitarik Ian , Jiang Yang , Yadav Divya , Sharma Piyoosh , Fried Stephen D. , Li Mai Suan , O’Brien Edward P.
Published: July 2022

Several mechanisms intrinsic to a protein’s primary structure are known to cause monomeric protein misfolding. Coarse-grained simulations, in which multiple atoms are represented by a single interaction site, have predicted a novel mechanism of misfolding exists involving off-pathway, non-covalent lasso entanglements, which are distinct from protein knots and slip knots. These misfolded states can be long-lived kinetic traps, and in some cases are structurally similar to the native state according to those simulations. Here, we examine whether such misfolded states occur in long-time-scale, physics-based all-atom simulations of protein folding. We find they do indeed form, estimate they can persist for weeks, and some have characteristics similar to the native state. Digestion patterns from Limited Proteolysis Mass Spectrometry are consistent with the presence of changes in entanglement in these proteins. These results indicate monomeric proteins can exhibit subpopulations of misfolded, self-entangled states that can explain long-timescale changes in protein structure and functionin vivo.

One-Sentence Summary

Entangled misfolded states form in physics-based all-atom simulations of protein folding and have characteristics similar to the native state.
CRI-SPA – a mating based CRISPR-Cas9 assisted method for high-throughput genetic modification of yeast strain libraries
Authors: Olsson Helén , Cachera Paul , Coumou Hilde , Jensen Mads L. , Sánchez Benjamín J. , Strucko Tomas , van den Broek Marcel , Daran Jean-Marc , Jensen Michael K. , Sonnenschein Nikolaus , Lisby Michael , Mortensen Uffe H.
Published: July 2022

Abstract

Biological functions are orchestrated by intricate networks of interacting genetic elements. Predicting the interaction landscape remains a challenge for systems biology and the identification of phenotypic maximas would be of great benefit to synthetic biology. Thus, new research tools allowing simple and rapid mapping of sequence to function are required to forward these research fields. Here, we describe CRI-SPA, a method allowing the transfer of a chromosomal genetic feature from a donor strain to arrayed strains in large libraries of Saccharomyces cerevisiae. CRI-SPA is based on mating, CRISPR-Cas9-induced gene conversion and Selective Ploidy Ablation and is executed within a week. We demonstrate the power of CRI-SPA by transferring four genes responsible for the production of betaxanthin, a yellow biosensor for the morphine precursor L-DOPA, into each strain of the yeast knock-out collection (≈4800 strains), providing a genome-wide overview of the genetic requirements for betaxanthin production. CRI-SPA is fast, highly reproducible, can be massively parallelized with automation and does not require selection for the transferred genetic feature.
FastCAR: Fast Correction for Ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets
Authors: Berg Marijn , Petoukhov Ilya , van den Ende Inge , Meyer Kerstin B. , Guryev Victor , Vonk Judith M. , Carpaij Orestes , Banchero Martin , Hendriks Rudi W. , van den Berge Maarten , Nawijn Martijn C.
Published: July 2022

Cell type-specific differential gene expression analyses based on single-cell transcriptome datasets are sensitive to the presence of cell-free mRNA in the droplets containing single cells. This so-called ambient RNA contamination may differ between samples obtained from patients and healthy controls. Current ambient RNA correction methods were not developed specifically for single-cell differential gene expression (sc-DGE) analyses and might therefore not sufficiently correct for ambient RNA-derived signals. Here, we show that ambient RNA levels are highly sample-specific. We found that without ambient RNA correction, sc-DGE analyses erroneously identify transcripts originating from ambient RNA as cell type-specific disease-associated genes. We therefore developed a computationally lean and intuitive correction method, Fast Correction for Ambient RNA (FastCAR), optimized for sc-DGE analysis of scRNA-Seq datasets generated by droplet-based methods including the 10XGenomics Chromium platform. FastCAR uses the profile of transcripts observed in libraries that likely represent empty droplets to determine the level of ambient RNA in each individual sample, and then corrects for these ambient RNA gene expression values. FastCAR can be applied as part of the data pre-processing and QC in sc-DGE workflows comparing scRNA-Seq data in a health versus disease experimental design. We compared FastCAR with two methods previously developed to remove ambient RNA, SoupX and CellBender. All three methods identified additional genes in sc-DGE analyses that were not identified in the absence of ambient RNA correction. However, we show that FastCAR performs better at correcting gene expression values attributed to ambient RNA, resulting in a lower frequency of false-positive observations. Moreover, the use of FastCAR in a sc-DGE workflow increases the cell-type specificity of sc-DGE analyses across disease conditions.
Exploring the in-situ evolution of Nitrofurantoin resistance in clinically derived Uropathogenic Escherichia coli isolates
Authors: Vallée Maxime , Harding Chris , Hall Judith , Aldridge Phillip D , Tan Aaron
Published: July 2022

BACKGROUND

Nitrofurantoin has been re-introduced as a first-choice antibiotic to treat uncomplicated acute urinary tract infections in England and Wales. Its mode of action involves initial reduction by nitroreductases, to generate electrophilic intermediates that inhibit protein and nucleic acid synthesis. Highly effective against common uropathogens such as Escherichia coli, its use is accompanied by a low incidence (<10%) of antimicrobial resistance. Resistance to Nitrofurantoin is predominantly via the acquisition of loss-of-function, step-wise mutations in the nitroreductase genes nfsA and nfsB.

OBJECTIVE

To explore the in situ evolution of NitR, longitudinal uropathogenic E. coli isolates recovered from two rUTI patients.

RESULTS

Growth rate analysis identified a 2-10% slower doubling time for Nitrofurantoin resistant strains, but statistically, these data suggested there was no fitness advantage of evolved strains over their sensitive predecessor (ANOVA P-value = 0.13). Genetic manipulation of E. coli to mimic nitrofurantoin resistance evolution, again confirmed no fitness advantages (ANOVA P-value = 0.22). Rather, further analysis argued that a first-step mutant gained a selective advantage, at sub-MIC (4-8 mg/L) nitrofurantoin concentrations.

CONCLUSION

Correlation of these findings to Nitrofurantoin pharmacokinetic data suggests that the low incidence of E. coli NitR, within the community, is driven by urine-based nitrofurantoin concentrations that selectively inhibit the growth of E. coli strains carrying the key first-step loss-of-function mutation.