bluuebunny/crossref_metadata_2025 huggingface dataset:
Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader
Authors: Sarma Roshmi R. , Crossland Michael R. , Eyck Harrison J. F. , DeVore Jayna L. , Edwards Richard J. , Cocomazzo Michael , Zhou Jia , Brown Gregory P. , Shine Richard , Rollins Lee A.
Published: April 2021

In response to novel environments, invasive populations often evolve rapidly. Standing genetic variation is an important predictor of evolutionary response but epigenetic variation may also play a role. Here, we use an iconic invader, the cane toad (Rhinella marina), to investigate how manipulating epigenetic status affects phenotypic traits. We collected wild toads from across Australia, bred them, and experimentally manipulated DNA methylation of the subsequent two generations (G1, G2) through exposure to the DNA methylation inhibitor zebularine and/or conspecific tadpole alarm cues. Direct exposure to alarm cues (an indicator of predation risk) increased the potency of G2 tadpole chemical cues, but this was accompanied by reductions in survival. Exposure to alarm cues during G1 also increased the potency of G2 tadpole cues, indicating intergenerational plasticity in this inducible defence. In addition, the negative effects of alarm cues on tadpole viability (i.e. the costs of producing the inducible defence) were minimized in the second generation. Exposure to zebularine during G1 induced similar intergenerational effects, suggesting a role for alteration in DNA methylation. Accordingly, we identified intergenerational shifts in DNA methylation at some loci in response to alarm cue exposure. Substantial demethylation occurred within thesodium channel epithelial 1 subunit gammagene (SCNN1G) in alarm cue exposed individuals and their offspring. This gene is a key to the regulation of sodium in epithelial cells and may help to maintain the protective epidermal barrier. These data suggest that early life experiences of tadpoles induce intergenerational effects through epigenetic mechanisms, which enhance larval fitness.

This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’
Protein aggregation and the evolution of stress resistance in clinical yeast
Authors: Chen Yiwen R. , Ziv Inbal , Swaminathan Kavya , Elias Joshua E. , Jarosz Daniel F.
Published: April 2021

Protein aggregation, particularly in its prion-like form, has long been thought to be detrimental. However, recent studies have identified multiple instances where protein aggregation is important for normal physiological functions. Combining mass spectrometry and cell biological approaches, we developed a strategy for the identification of protein aggregates in cell lysates. We used this approach to characterize prion-based traits in pathogenic strains of the yeast
Saccharomyces cerevisiae
isolated from immunocompromised human patients. The proteins that we found, including the metabolic enzyme Cdc19, the translation elongation factor Yef3 and the fibrillarin homologue Nop1, are known to assemble under certain physiological conditions. Yet, such assemblies have not been reported to be stable or heritable. Our data suggest that some proteins which aggregate in response to stress have the capacity to acquire diverse assembled states, certain ones of which can be propagated across generations in a form of protein-based epigenetics.

This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’
A Randomized Trial of Otilimab in Severe COVID-19 Pneumonia (OSCAR)
Authors: Patel Jatin , Beishuizen Albertus , Ruiz Xavier Bocca , Boughanmi Hatem , Cahn Anthony , Criner Gerard J , Davy Katherine , de-Miguel-Díez Javier , Fernandes Sofia , François Bruno , Gupta Anubha , Hanrott Kate , Hatlen Timothy , Inman Dave , Isaacs John D , Jarvis Emily , Kostina Natalia , Lacherade Jean-Claude , Martinez-Ayala Pedro , McEvoy Charlene , Muñoz-Bermúdez Rosana , Neisen Jessica , Plantefeve Gaëtan , Schifano Lorrie , Schwab Lee , Shahid Zainab , Shirano Michinori , Smith Julia E. , Sprinz Eduardo , Summers Charlotte , Terzi Nicolas , Tidswell Mark A , Williamson Russell , Wyncoll Duncan , Layton Mark
Published: April 2021

BACKGROUND

Increasing age is a risk factor for COVID-19 severity and mortality; emerging science implicates GM-CSF and dysregulated myeloid cell responses in the pathophysiology of severe COVID-19.

METHODS

We conducted a large, global, double-blind, randomized, placebo-controlled study evaluating a single 90 mg infusion of otilimab (human anti-GM-CSF monoclonal) plus standard of care in adults hospitalized with severe COVID-19 respiratory failure and systemic inflammation, stratified by age and clinical status. Primary outcome was the proportion of patients alive and free of respiratory failure at Day 28; secondary endpoints included all-cause mortality at Day 60.

RESULTS

Overall, 806 patients were randomized (1:1); 71% of patients receiving otilimab were alive and free of respiratory failure at Day 28 versus 67% receiving placebo, although this did not reach statistical significance (model-adjusted difference 5.3% [95% CI −0.8, 11.4]; p=0.09). However, there was a benefit in the pre-defined ≥70-year age group (model-adjusted difference 19.1% [95% CI 5.2, 33.1]; nominal p=0.009); these patients also had a reduction of 14.4% (95% CI 0.9, 27.9%; nominal p=0.04) in model-adjusted all-cause mortality at Day 60. Safety findings were comparable between otilimab and placebo, and consistent with severe COVID-19.

CONCLUSIONS

Although not statistically significant in the overall population, otilimab demonstrated a substantial benefit in patients aged ≥70, possibly reflecting a population that could benefit from therapeutic blocking of GM-CSF in severe COVID-19 where myeloid cell dysregulation is predominant. These findings are being confirmed in a further cohort of patients aged ≥70 in Part 2 of this study. (ClinicalTrials.gov number: NCT04376684).
Signal quality and power spectrum analysis of remote ultra long-term subcutaneous EEG
Authors: Viana Pedro F. , Remvig Line S. , Duun-Henriksen Jonas , Glasstetter Martin , Dümpelmann Matthias , Nurse Ewan S. , Martins Isabel P. , Schulze-Bonhage Andreas , Freestone Dean R. , Brinkmann Benjamin H. , Kjaer Troels W. , Richardson Mark P.
Published: April 2021

Objective

Ultra long-term subcutaneous EEG (sqEEG) monitoring is a new modality with great potential for both health and disease, including epileptic seizure detection and forecasting. However, little is known about the long-term quality and consistency of the sqEEG signal, which is the objective of this study.

Methods

The largest multicenter cohort of sqEEG was analyzed, including fourteen patients with epilepsy and twelve healthy subjects, implanted with a sqEEG device (24/7 EEG™ SubQ), and recorded from 23 to 230 days (median 42 days), with a median data capture rate of 75% (17.9 hours/day). Median power spectral density plots of each subject were examined for physiological peaks, including at diurnal and nocturnal periods. Long-term temporal trends in signal impedance and power spectral features were investigated with subject-specific linear regression models and group-level linear mixed effects models.

Results

sqEEG spectrograms showed an approximately 1/f power distribution. Diurnal peaks in the alpha range (8-13Hz) and nocturnal peaks in the sigma range (12-16Hz) were seen in the majority of subjects. Signal impedances remained low and frequency band powers were highly stable throughout the recording periods.

Significance

The spectral characteristics of minimally-invasive, ultra long-term sqEEG are similar to scalp EEG, while the signal is highly stationary. Our findings reinforce the suitability of this system for chronic implantation on diverse clinical applications, from seizure detection and forecasting to brain-computer interfaces.

Key Points

Subcutaneous EEG shows similar spectral characteristics to scalp EEG

The subcutaneous EEG signal is highly stable throughout weeks and months of recording

Subcutaneous EEG systems are well suited for chronic implantation, for seizure detection and seizure forecasting
Decoding microbiome and protein family linkage to improve protein structure prediction
Authors: Yang Pengshuo , Zheng Wei , Ning Kang , Zhang Yang
Published: April 2021

Information extracted from microbiome sequences through deep-learning techniques can significantly improve protein structure and function modeling. However, the model training and metagenome search were largely blind with low efficiency. Built on 4.25 billion microbiome sequences from four major biomes (Gut, Lake, Soil and Fermentor), we proposed a MetaSource model to decode the inherent link of microbial niches with protein homologous families. Large-scale protein family folding experiments showed that a targeted approach using predicted biomes significantly outperform combined metagenome datasets in both speed of MSA collection and accuracy of deep-learning structure assembly. These results revealed the important link of biomes with protein families and provided a useful bluebook to guide future microbiome sequence database and modeling development for protein structure and function prediction.
Separation of cohorts on the basis of bacterial type IV conjugation systems identified from metagenomic assemblies
Authors: Joris Benjamin R. , Browne Tyler S. , Hamilton Thomas A. , Edgell David R. , Gloor Gregory B.
Published: April 2021

Conjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways which makes precise identification of these systems in metagenomic samples clinically important. Here, we outline two distinct methods to identify conjugative systems in the human gut microbiome. We first show that conjugative systems exhibit strong population and age-level stratification. Additionally, we find that the total relative abundance of all conjugative systems present in a sample is not an informative metric to use, regardless of the method of identifying the systems. Finally, we demonstrate that the majority of assembled conjugative systems are not included within metagenomic bins, and that only a small proportion of the binned conjugative systems are included in “high-quality” metagenomic bins. Our findings highlight that conjugative systems differ between general North Americans and a cohort of North American pre-term infants, revealing a potential use as an age-related biomarker. Furthermore, conjugative systems can distinguish between other geographical-based cohorts. Our findings emphasize the need to identify and analyze conjugative systems outside of standard metagenomic binning pipelines.

Importance

The human gut microbiome is increasingly being associated with human health outcomes through shotgun metagenomic sequencing. The usual approach of metagenomic-level analyses is to bin assembled sequences into approximations of bacterial genomes and perform further investigations on the resultant bins. Here, we show that type IV conjugative systems differ between age and geographically-based cohorts and that these systems are systematically excluded by binning algorithms. We suggest that analysis of type IV conjugative systems should be added to the current metagenomic analysis approaches as they contain much information that could explain differences between cohorts beyond those we investigated.
MVD-Fuse: Detection of White Matter Degeneration via Multi-View Learning of Diffusion Microstructure
Authors: Fadnavis Shreyas , Polosecki Pablo , Garyfallidis Eleftherios , Castro Eduardo , Cecchi Guillermo
Published: April 2021

Detecting neuro-degenerative disorders in early-stage and asymptomatic patients is challenging. Diffusion MRI (dMRI) has shown great success in generating biomarkers for cellular organization at the microscale level using complex biophysical models, but there has never been a consensus on a clinically usable standard model. Here, we propose a new framework (MVD-Fuse) to integrate measures of diverse diffusion models to detect alterations of white matter microstructure. The spatial maps generated by each measure are considered as a different diffusion representation (view), the fusion of these views being used to detect differences between clinically distinct groups. We investigate three different strategies for performing intermediate fusion: neural networks (NN), multiple kernel learning (MKL) and multi-view boosting (MVB). As a proof of concept, we applied MVD-Fuse to a classification of premanifest Huntington’s disease (pre-HD) individuals and healthy controls in the TRACK-ON cohort. Our results indicate that the MVD-Fuse boosts predictive power, especially with MKL (0.90 AUC vs 0.85 with the best single diffusion measure). Overall, our results suggest that an improved characterization of pathological brain microstructure can be obtained by combining various measures from multiple diffusion models.
Factors Affecting Guardians’ Decision Making on Clinic-based Purchase of Children’s Spectacles in Nigeria
Authors: Chan Ving Fai , Yong Ai Chee , Neill Ciaran O’ , Graham Christine , Congdon Nathan , Lohfeld Lynne , Stephan Tai , Ebri Anne Effiom
Published: April 2021

Background

This study aims to understand the key factors influencing guardians’ decisions when purchasing spectacles for their children in semi-urban and urban areas of Cross River State, Nigeria, where a spectacle cross-subsidisation scheme will be implemented.

Methods

This cross-sectional study was conducted among all consecutive guardians visiting the Calabar (urban), Ugep, Ikom and Ogoja (semi-urban) public eye clinics in Cross River State, southern Nigeria, from August 1 to October 31 2019, and whose children had significant refractive errors (myopia ≤-0.50D, hyperopia ≥1.50D, astigmatism >0.75D) and received spectacles. Guardians were interviewed using a questionnaire which included i) close-ended questions on reasons guardians choose to purchase spectacles for their children in eye clinics, ii) guardians’ perceptions of the quality and design of children’s current spectacle, iii) factors most heavily influencing their choice of spectacles for children, and iv) open-ended questions to seek guardians’ suggestions on how to improve the current spectacle range.

Results

All 137 eligible guardians (n=92, 67.2% women) who visited the selected eye clinics participated in the study (response rate=100%), with 109 (79.6%) from semi-urban and 28 (20.4%) attending urban clinics. Guardians from both urban and semi-urban clinics prioritised frame design, quality, and material as the main factors affecting their decision when purchasing spectacles for their children. Female guardians and those with higher incomes were both 1.5 times more likely to emphasise frame quality when describing selection criteria for purchasing spectacles for their children than male guardians (p=0.01) or guardians earning less (p=0.03).

Conclusion

Design, material, and frame quality are key factors influencing guardians when purchasing spectacles for their children in these setting and female guardians or those with higher income prioritise frame quality. This study could guide the planning and implementation of a novel cross-subsidisation scheme in Cross River State.
A multimodal 3D neuro-microphysiological system with neurite-trapping microelectrodes
Authors: Molina-Martínez Beatriz , Jentsch Laura-Victoria , Ersoy Fulya , van der Moolen Matthijs , Donato Stella , Ness Torbjørn V. , Heutink Peter , Jones Peter D. , Cesare Paolo
Published: April 2021

Three-dimensional cell technologies as pre-clinical models are emerging tools for mimicking the structural and functional complexity of the nervous system. The accurate exploration of phenotypes in engineered 3D neuronal cultures, however, demands morphological, molecular and especially functional measurements. Particularly crucial is measurement of electrical activity of individual neurons with millisecond resolution. Current techniques rely on customized electrophysiological recording set-ups, characterized by limited throughput and poor integration with other readout modalities. Here we describe a novel approach, using multiwell glass microfluidic microelectrode arrays, allowing non-invasive electrical recording from engineered 3D neural tissues. We demonstrate parallelized studies with reference compounds, calcium imaging and optogenetic stimulation. Additionally, we show how microplate compatibility allows automated handling and high-content analysis of human induced pluripotent stem cell–derived neurons. This microphysiological platform opens up new avenues for high-throughput studies on the functional, morphological and molecular details of neurological diseases and their potential treatment by therapeutic compounds.
Oncogenic PKA signaling stabilizes MYC oncoproteins via an aurora kinase A-dependent mechanism
Authors: Chan Gary K. L. , Maisel Samantha , Hwang Yeonjoo C. , Wolber Rebecca R. B. , Vu Phuong , Patra Krushna C. , Bouhaddou Mehdi , Kenerson Heidi L. , Yeung Raymond S. , Swaney Danielle L. , Krogan Nevan J. , Turnham Rigney E. , Scott John D. , Riehle Kimberly J. , Bardeesy Nabeel , Gordan John D.
Published: April 2021

Genetic alterations that activate protein kinase A (PKA) signaling are found across many tumor types, but their downstream oncogenic mechanisms are poorly understood. We used global phosphoproteomics and kinome activity profiling to map the conserved signaling outputs driven by diverse genetic changes that activate PKA in human cancer, including melanoma and fibrolamellar carcinoma (FLC). We define two consensus networks of effectors downstream of PKA in cancer models. One is centered on RAS/MAPK components, and a second involves Aurora Kinase A (AURKA). We find that AURKA stabilizes c-MYC and n-MYC protein levels and expression programs in PKA-dependent tumor models, in part via a positive feedback loop mediated by the oncogenic kinase PIM2. This process can be suppressed by conformation-disrupting AURKA inhibitors such as CD-532. Our findings elucidate two independent mechanisms of PKA-driven tumor cell growth and offer insight into drug targets for study in FLC and other PKA-dependent malignancies.
Comparative analysis of molecular representations in prediction of drug combination effects
Authors: Zagidullin B. , Wang Z. , Guan Y. , Pitkänen E. , Tang J.
Published: April 2021

Abstract

Application of machine and deep learning methods in drug discovery and cancer research has gained a considerable amount of attention in the past years. As the field grows, it becomes crucial to systematically evaluate the performance of novel computational solutions in relation to established techniques. To this end we compare rule-based and data-driven molecular representations in prediction of drug combination sensitivity and drug synergy scores using standardized results of 14 throughput screening studies, comprising 64 200 unique combinations of 4 153 molecules tested in 112 cancer cell lines. We evaluate the clustering performance of molecular representations and quantify their similarity by adapting the Centered Kernel Alignment metric. Our work demonstrates that to identify an optimal molecular representation type it is necessary to supplement quantitative benchmark results with qualitative considerations, such as model interpretability and robustness, which may vary between and throughout preclinical drug development projects.

Abstract Figure
Using embedded alginate microparticles to tune the properties ofin situforming poly(N-isopropylacrylamide)-graft-chondroitin sulfate bioadhesive hydrogels for replacement and repair of the nucleus pulposus of the intervertebral disc
Authors: Christiani Thomas , Mys Karen , Dyer Karl , Kadlowec Jennifer , Iftode Cristina , Vernengo Andrea Jennifer
Published: April 2021

Low back pain (LBP) is a major public health issue associated with degeneration of the intervertebral disc (IVD). The early stages of degeneration are characterized by the dehydration of the central, gelatinous portion of the IVD, the nucleus pulposus (NP). One possible treatment approach is to replace the NP in the early stages of IVD degeneration with a hydrogel that restores healthy biomechanics while supporting tissue regeneration. The present study evaluates a novel thermosensitive hydrogel based on poly(N-isopropylacrylamide-graft-chondroitin sulfate) (PNIPAAM-g-CS) for NP replacement. The hypothesis was tested that the addition of freeze-dried, calcium crosslinked alginate microparticles (MPs) to aqueous solutions of PNIPAAm-g-CS would enable tuning of the rheological properties of the injectable solution, as well as the bioadhesive and mechanical properties of the thermally precipitated composite gel. Further, we hypothesized that the composite would support encapsulated cell viability and differentiation. Structure-material property relationships were evaluated by varying MP concentration and diameter. The addition of high concentrations (50 mg/mL) of small MPs (20 ± 6 µm) resulted in the greatest improvement in injectability, compressive mechanical properties, and bioadhesive strength of PNIPAAm-g-CS. This combination of PNIPAAM-g-CS and alginate MPs supported the survival, proliferation, and differentiation of adipose derived mesenchymal stem cells (ADMSCs) towards an NP-like phenotype in the presence of soluble GDF-6. When implantedex vivointo the intradiscal cavity of degenerated porcine IVDs, the formulation restored the compressive and neutral zone (NZ) stiffnesses to intact values and resisted expulsion under lateral bending. Overall, results indicate the potential of the hydrogel composite to serve as a scaffold for supporting NP regeneration. This work uniquely demonstrates that encapsulation of re-hydrating polysaccharide-based MPs may be an effective method for improving key functional properties ofin situforming hydrogels for orthopaedic tissue engineering applications.
Mindfulness Training Alters Resting-State EEG Dynamics in Novice Practitioners via Mindful Breathing and Body-scan
Authors: Hydra Ng Hei-Yin , Wu Changwei W. , Huang Feng-Ying , Cheng Yu-Ting , Guu Shiao-Fei , Huang Chih-Mao , Hsu Chia-Fen , Chao Yi-Ping , Jung Tzyy-Ping , Chuang Chun-Hsiang
Published: April 2021

Mindfulness-based stress reduction (MBSR) has been proven to improve mental health and quality of life. This study examined how mindfulness training and various types of mindfulness practices altered brain activity. Specifically, the spectral powers of scalp electroencephalography (EEG) of the MBSR group who underwent an 8-week mindfulness training—including mindful breathing and body-scan—were evaluated and compared with those of the waitlist controls. Empirical results indicated that the long-term mindfulness intervention effect significantly elevated the resting-state beta powers and reduced resting-state delta powers in both practices; such changes were not observed in the waitlist control. Compared with mindful breathing, body-scanning resulted in an overall decline in EEG spectral powers at both delta and gamma bands among trained participants. Together with our preliminary data of expert mediators, the aforementioned spectral changes were salient after intervention, but mitigated along with expertise. Additionally, after receiving training, the MBSR group’s mindfulness and emotion regulation levels improved significantly, which were correlated with the EEG spectral changes in the theta, alpha, and low-beta bands. This study elaborated the neurophysiological correlates of mindfulness practices, suggesting that MBSR might function as a unique internal processing that involves increased vigilant capability and induces alterations similar to other cognitive training.
Dynamic reconfiguration of macaque brain networks during free-viewing of natural scenes
Authors: Ortiz-Rios Michael , Balezeau Fabien , Haag Marcus , Schmid Michael C. , Kaiser Marcus
Published: April 2021

Natural vision involves the activation of a wide range of higher-level regions processing objects, motion, faces and actions. Here, we pursue a data-driven approach to explore how higher-level visual processes relate to the underlying structural and functional connectivity. Using a free-viewing paradigm in four awake rhesus macaque monkeys, we investigate how different visual scenes change functional connectivity. Additionally, we explore how such functional connectivity, as measured through fMRI, is related to the structural connectivity, as measured through diffusion weighted imaging. At first, we evaluate the consistency of the elicited free-viewing pattern using standard analytical techniques. We also evaluate the underlying structural connectivity via diffusion data by tracking white matter bundle projections from the visual cortex. We then reconstruct free-viewing and structural networks and quantify their properties. Centrality measures over the entire fMRI time-series revealed a consistent functional network engaged during free-viewing that included widespread hub regions across frontal (FEF, 46v), parietal (LIP, Tpt), and occipitotemporal cortex (MT, V4 and TE) among others. Interestingly, a small number of highly-weighted and long-length inter-hemispheric connections indicated the presence of long-range integrative properties during free-viewing. We hypothesized that during free-viewing, networks had the capacity to change their local and distal connections depending on the on-going changes in visual scenes. To capture these network dynamics, we depart from the static modular architecture of the structural networks and demonstrate that hubs in free-viewing networks reorganize according to the presence of objects, motion, and faces in the movie scenes indicating poly-functional properties. Lastly, we compare each NHP subject network and observe high consistency between individuals across the same network type with closer correspondence between structural networks (e.g., diffusion based and those partially assembled from tract-tracing). In summary, our network analyses revealed ongoing changes in large-scale functional organization present during free-viewing in the macaque monkey and highlight the advantages of multi-contrast imaging in awake monkeys for investigating dynamical processes in visual cognition. To further promote the use of naturalistic free-viewing paradigms and increase the development of macaque neuroimaging resources, we share our datasets in the PRIME-DE consortium.
Neural Sources Underlying Visual Word Form Processing as Revealed by Steady State Visual Evoked Potentials (SSVEP)
Authors: Wang Fang , Kaneshiro Blair , Strauber C. Benjamin , Hasak Lindsey , Nguyen Quynh Trang H. , Yakovleva Alexandra , Vildavski Vladimir Y. , Norcia Anthony M. , McCandliss Bruce D.
Published: April 2021

EEG has been central to investigations of the time course of various neural functions underpinning visual word recognition. Recently the steady-state visual evoked potential (SSVEP) paradigm has been increasingly adopted for word recognition studies due to its high signal-to-noise ratio. Such studies, however, have been typically framed around a single source in the left ventral occipitotemporal cortex (vOT). Here, we combine SSVEP recorded from 16 adult native English speakers with a data-driven spatial filtering approach—Reliable Components Analysis (RCA)—to elucidate distinct functional sources with overlapping yet separable time courses and topographies that emerge when contrasting words with pseudofont visual controls. The first component topography was maximal over left vOT regions with an early latency (approximately 180 msec). A second component was maximal over more dorsal parietal regions with a longer latency (approximately 260 msec). Both components consistently emerged across a range of parameter manipulations including changes in the spatial overlap between successive stimuli, and changes in both base and deviation frequency. We then contrasted word-in-nonword and word-in-pseudoword to test the hierarchical processing mechanisms underlying visual word recognition. Results suggest that these hierarchical contrasts fail to evoke a unitary component that might be reasonably associated with lexical access.
Rigidifying ade novoenzyme increases activity and induces a negative activation heat capacity
Authors: Hindson SA , Bunzel HA , Frank B , Svistunenko DA , Williams C , van der Kamp MW , Mulholland AJ , Pudney CR , Anderson JLR
Published: April 2021

Conformational sampling profoundly impacts the overall activity and temperature dependence of enzymes. Peroxidases have emerged as versatile platforms for high value biocatalysis owing to their broad palette of potential biotransformations. Here, we explore the role of conformational sampling in mediating ade novoperoxidase’s activity. We demonstrate that 2,2,2-triflouoroethanol (TFE) affects the equilibrium of enzyme conformational states, tending towards a more globally rigid structure. This is correlated with increases both stability and activity. Notably, these effects are concomitant with the emergence of curvature in the temperature-activity profile, trading off activity gains at ambient temperature with losses at high temperatures. We apply macromolecular rate theory (MMRT) to understand enzyme temperature dependence data. These data point to an increase in protein rigidity associated with a difference in the distribution of protein dynamics between the ground and transition state. We compare the thermodynamics of thede novoenzyme activity to those of a natural peroxidase, horseradish peroxidase. We find that the native enzyme resembles the rigidifiedde novoenzyme in terms of the thermodynamics of enzyme catalysis and the putative distribution of protein dynamics between the ground and transition state. The addition of TFE apparently causes C45 to behave more like the natural enzyme. Our data suggest robust, generic strategies for improving biocatalytic activity by manipulating protein rigidity; for functionalde novoprotein catalysts in particular, this can provide more enzyme-like catalysts without further rational engineering, computational redesign or directed evolution.
Contrasting processing tomato cultivars unlink yield and pollen viability under heat stress
Authors: Miller Golan , Beery Avital , Singh Prashant Kumar , Wang Fengde , Zelingher Rotem , Motenko Etel , Lieberman-Lazarovich Michal
Published: April 2021

The occurring climate change is causing temperature increment in crop production areas worldwide, generating conditions of heat stress that negatively affect crop productivity. Tomato (Solanum lycopersicum), a major vegetable crop, is highly susceptible to conditions of heat stress. When tomato plants are exposed to ambient day/night temperatures that exceed 32°C/20°C respectively during the reproductive phase, fruit set and fruit weight are reduced, leading to a significant decrease in yield. Processing tomato cultivars are cultivated in open fields, where environmental conditions are not controlled, therefore plants are exposed to multiple abiotic stresses, including heat stress. Understanding the physiological response of modern processing tomato cultivars to heat stress may facilitate the development of thermotolerant cultivars. Here, we compared two tomato processing cultivars, H4107 and H9780, that we found to be constantly differing in yield performance. Using field and temperature-controlled greenhouse experiments, we show that the observed difference in yield is attributed to the occurrence of heat stress conditions. In addition, fruit-set and seed production were significantly improved in the thermotolerant cultivar H4107, compared with H9780. Despite the general acceptance of pollen viability as a measure of thermotolerance, there was no difference in the percentage of viable pollen between H4107 and H9780 under either of the conditions tested. Therefore, processing tomato cultivars may present a particular case, in which other factors are central for heat stress tolerance. Our results also demonstrate the value of combining controlled with uncontrolled experimental settings, in order to identify heat stress related responses and facilitate the development of thermotolerant processing tomato cultivars.
How many markers are needed to robustly determine a cell’s type?
Authors: Fischer Stephan , Gillis Jesse
Published: April 2021

Our understanding of cell types has advanced considerably with the publication of single cell atlases. Marker genes play an essential role for experimental validation and computational analyses such as physiological characterization through pathway enrichment, annotation, and deconvolution. However, a framework for quantifying marker replicability and picking replicable markers is currently lacking. Here, using high quality data from the Brain Initiative Cell Census Network (BICCN), we systematically investigate marker replicability for 85 neuronal cell types. We show that, due to dataset-specific noise, we need to combine 5 datasets to obtain robust differentially expressed (DE) genes, particularly for rare populations and lowly expressed genes. We estimate that 10 to 200 meta-analytic markers provide optimal performance in downstream computational tasks. Replicable marker lists condense single cell atlases into interpretable and generalizable information about cell types, opening avenues for downstream applications, including cell type annotation, selection of gene panels and bulk data deconvolution.
Constitutively activeSARM1variants found in ALS patients induce neuropathy
Authors: Bloom A. Joseph , Mao Xianrong , Strickland Amy , Sasaki Yo , Milbrandt Jeffrey , DiAntonio Aaron
Published: April 2021

In response to injury, neurons activate a program of organized axon self-destruction initiated by the NAD+hydrolase SARM1. In healthy neurons SARM1 is autoinhibited, but single amino acid changes can abolish autoinhibition leading to constitutively-active SARM1 enzymes that promote degeneration when expressed in cultured neurons. To investigate whether naturally-occurring human variants might similarly disrupt SARM1 autoinhibition and potentially contribute to risk for neurodegenerative disease, we assayed the enzymatic activity of 29 rareSARM1alleles identified among 8,507 amyotrophic lateral sclerosis (ALS) patients. Ten missense variants or small in-frame deletions exhibit constitutive NADase activity, including more than half of those that are unique to the ALS patients or that occur in multiple patients. Expression of these constitutively active ALS-associated SARM1 alleles in cultured dorsal root ganglion (DRG) neurons is pro-degenerative and cytotoxic. Intrathecal injection of an AAV expressing the commonSARM1reference allele is innocuous to mice, but a construct harboringSARM1V184G, the constitutively active variant found most frequently in the ALS patients, causes axon loss, motor dysfunction, and sustained neuroinflammation. These results implicate rare hypermorphicSARM1alleles as candidate genetic risk factors for ALS and other neurodegenerative conditions.
Spatial genomics maps the structure, character and evolution of cancer clones
Authors: Lomakin Artem , Svedlund Jessica , Strell Carina , Gataric Milana , Shmatko Artem , Park Jun Sung , Ju Young Seok , Dentro Stefan , Kleshchevnikov Vitalii , Vaskivskyi Vasyl , Li Tong , Bayraktar Omer Ali , Moore Luiza , Pinder Sarah , Richardson Andrea L , Campbell Peter J , Gerstung Moritz , Nilsson Mats , Yates Lucy R
Published: April 2021

Subclonality is a universal feature of cancers yet how clones grow, are spatially organised, differ phenotypically or influence clinical outcome is unclear. To address this, we developed base specific in situ sequencing (BaSISS). In fixed tissues, transcripts harbouring clone-defining mutations are detected, converted into quantitative clone maps and characterised through multi-layered data integration. Applied to 8 samples from key stages of breast cancer progression BaSISS localised 1.42 million genotype informative transcripts across 4.9cm2of tissue. Microscopic clonal topographies are shaped by resident tissue architectures. Distinct transcriptional, histological and immunological features distinguish coexistent genetic clones. Spatial lineage tracing temporally orders clone features associated with the emergence of aggressive clinical traits. These results highlight the pivotal role of spatial genomics in deciphering the mechanisms underlying cancer progression.
Extended frontal networks for visual and auditory working memory
Authors: Noyce Abigail L. , Lefco Ray W. , Brissenden James A. , Tobyne Sean M. , Shinn-Cunningham Barbara G. , Somers David C.
Published: April 2021

Working memory (WM) supports the persistent representation of transient sensory information. Visual and auditory stimuli place different demands on WM and recruit different brain networks. Separate auditory- and visual-biased WM networks extend into the frontal lobes, but several challenges confront attempts to parcellate human frontal cortex, including fine-grained organization and between-subject variability. Here, we use differential intrinsic functional connectivity from two visual-biased and two auditory-biased frontal structures to identify additional candidate sensory-biased regions in frontal cortex. We then examine direct contrasts of task fMRI during visual vs. auditory 2-back WM to validate those candidate regions. Three visual-biased and five auditory-biased regions are robustly activated bilaterally in the frontal lobes of individual subjects (N=14, 7 women). These regions exhibit a sensory preference during passive exposure to task stimuli, and that preference is stronger during WM. Hierarchical clustering analysis of intrinsic connectivity among novel and previously identified bilateral sensory-biased regions confirms that they functionally segregate into visual and auditory networks, even though the networks are anatomically interdigitated. We also observe that the fronto-temporal auditory WM network is highly selective and exhibits strong functional connectivity to structures serving non-WM functions, while the fronto-parietal visual WM network hierarchically merges into the multiple-demand cognitive system.
Role of African swine fever virus (ASFV) proteins EP153R and EP402R in reducing viral persistence and virulence from attenuated BeninΔDP148R
Authors: Petrovan Vlad , Rathakrishnan Anusyah , Islam Muneeb , Goatley Lynnette C. , Moffat Katy , Sanchez-Cordon Pedro J. , Reis Ana L. , Dixon Linda K.
Published: April 2021

The limited knowledge on the role of many of the approximately 170 proteins encoded by African swine fever virus restricts progress towards vaccine development. In this study we investigated the effect of deleting combinations of different genes from a previously attenuated virus, BeninΔDP148R on: virus replication in macrophages, virus persistence and clinical signs post immunization, and induction of protection against challenge. Deletion of either EP402R or EP153R genes individually or in combination from BeninΔDP148R did not reduce virus replicationin vitro. However, deletion of EP402R dramatically reduced viral persistencein vivo, whilst maintaining high levels of protection against challenge. The additional deletion of EP153R (BeninΔDP148RΔEP153RΔEP402R) further attenuated the virus and no viremia or clinical signs were observed post immunization. This was associated with decreased protection and detection of moderate levels of challenge virus in blood. Interestingly, the deletion of EP153R alone from BeninΔDP148R did not result in further virus attenuation and a slight increase in virus genome copies in blood was observed at different times post immunization when compared with BeninΔDP148R. These results show that EP402R and EP153R have a synergistic role in promoting viremia, however EP153R alone does not seem to have a major impact on virus levels in blood.
Structural brain connectivity in children with developmental dyscalculia
Authors: Ayyıldız Nazife , Beyer Frauke , Üstün Sertaç , Kale Emre H. , Mançe Çalışır Öykü , Uran Pınar , Öner Özgür , Olkun Sinan , Anwander Alfred , Witte A. Veronica , Villringer Arno , Çiçek Metehan
Published: April 2021

Developmental dyscalculia (DD) is a neurodevelopmental disorder specific to arithmetic learning even with normal intelligence and age-appropriate education. Difficulties often persist from childhood through adulthood. Underlying neurobiological mechanisms of DD, however, are poorly understood. This study aimed to identify possible structural connectivity alterations in DD. We evaluated 10 children withpureDD (11.3 ± 0.7 years) and 16 typically developing (TD) peers (11.2 ± 0.6 years) using diffusion tensor imaging. We first assessed white matter microstructure with tract-based spatial statistics. Then we used probabilistic tractography to evaluate tract lengths and probabilistic connectivity maps in specific regions. At whole brain level, we found no significant microstructural differences in white matter between children with DD and TD peers. Also, seed-based connectivity probabilities did not differ between groups. However, we did find significant differences in regions-of-interest tracts which had previously been related to math ability in children. The major findings of our study were reduced white matter coherence and shorter tract lengths of the left superior longitudinal/arcuate fasciculus and left anterior thalamic radiation in the DD group. Furthermore, lower white matter coherence and shorter pathways corresponded with the lower math performance as a result of the correlation analyses. These results from regional analyses indicate that learning, memory and language-related pathways in the left hemisphere might underlie DD.
Mycobacterial infection of precision cut lung slices reveals that the type 1 interferon pathway is locally induced by Mycobacterium bovis but not M. tuberculosis in different cattle breeds
Authors: Remot Aude , Carreras Florence , Coupé Anthony , Doz-Deblauwe Émilie , Boschiroli ML , Browne John A. , Marquant Quentin , Descamps Delphyne , Archer Fabienne , Aseffa Abrahma , Germon Pierre , Gordon Stephen V. , Winter Nathalie
Published: April 2021

Tuberculosis exacts a terrible toll on human and animal health. WhileMycobacterium tuberculosis(Mtb) is restricted to humans,Mycobacterium bovis(Mb) is present in a large range of mammalian hosts. In cattle, bovine TB (bTB) is a notifiable disease responsible for important economic losses in developed countries and underestimated zoonosis in the developing world. Early interactions that take place between mycobacteria and the lung tissue early after aerosol infection govern the outcome of the disease. In cattle, these early steps remain poorly characterized. The precision-cut lung slice (PCLS) model preserves the structure and cell diversity of the lung. We developed this model in cattle in order to study the early lung response to mycobacterial infection.In situimaging of PCLS infected with fluorescent Mb revealed bacilli in the alveolar compartment, adjacent or inside alveolar macrophages (AMPs) and in close contact with pneumocytes. We analyzed the global transcriptional lung inflammation signature following infection of PCLS with Mb and Mtb in two French beef breeds: Blonde d’Aquitaine and Charolaise. Whereas lungs from the Blonde d’Aquitaine produced high levels of mediators of neutrophil and monocyte recruitment in response to infection, such signatures were not observed in the Charolaise in our study. In the Blonde d’Aquitaine lung, whereas the inflammatory response was highly induced by two Mb strains, AF2122 isolated from cattle in the UK and Mb3601 circulating in France, the response against two Mtb strains, H37Rv the reference laboratory strain and BTB1558 isolated from zebu in Ethiopia, was very low. Strikingly, the type I interferon pathway was only induced by Mb but not Mtb strains indicating that this pathway may be involved in mycobacterial virulence and host tropism. Hence, the PCLS model in cattle is a valuable tool to deepen our understanding of early interactions between lung host cells and mycobacteria. It revealed striking differences between cattle breeds and mycobacterial strains. This model could help deciphering biomarkers of resistanceversussusceptibility to bTB in cattle as such information is still critically needed for bovine genetic selection programs and would greatly help the global effort to eradicate bTB.
Antibody Cocktail Exhibits Broad Neutralization against SARS-CoV-2 and SARS-CoV-2 variants
Authors: Qu Yuanyuan , Zhang Xueyan , Wang Meiyu , Sun Lina , Jiang Yongzhong , Li Cheng , Wu Wei , Chen Zhen , Yin Qiangling , Jiang Xiaolin , Liu Yang , Li Chuan , Li Jiandong , Ying Tianlei , Li Dexin , Zhan Faxian , Wang Youchun , Guan Wuxiang , Wang Shiwen , Liang Mifang
Published: April 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has precipitated multiple variants resistant to therapeutic antibodies. In this study, 12 high-affinity antibodies were generated from convalescent donors in early outbreaks using immune antibody phage display libraries. Of them, two RBD-binding antibodies (F61 and H121) showed high affinity neutralization against SARS-CoV-2, whereas three S2-target antibodies failed to neutralize SARS-CoV-2. Following structure analysis, F61 identified a linear epitope located in residues G446 -S494, which overlapped with angiotensin-converting enzyme 2 (ACE2) binding sites, while H121 recognized a conformational epitope located on the side face of RBD, outside from ACE2 binding domain. Hence the cocktail of the two antibodies achieved better performance of neutralization to SARS-CoV-2. Importantly, F61 and H121 exhibited efficient neutralizing activity against variants B.1.1.7 and B.1.351, those showed immune escape. Efficient neutralization of F61 and H121 against multiple mutations within RBD revealed a broad neutralizing activity against SARS-CoV-2 variants, which mitigated the risk of viral escape. Our findings defined the basis of therapeutic cocktails of F61 and H121 with broad neutralization and delivered a guideline for the current and future vaccine design, therapeutic antibody development, and antigen diagnosis of SARS-CoV-2 and its novel variants.
Image-based phenotypic profiling of a chemogenomic screening library identifies novel druggable targets in the EGFR-pathway
Authors: Tanabe Kenji
Published: April 2021

The gene encoding epidermal growth factor receptor (EGFR) is a major driver gene in cancer. Many drugs targeting EGFR-associated molecules have been developed, yet many have failed in clinical trials due to a lack of efficacy and/or unexpected side effects. In this study, I used image-based phenotypic profiling to screen a pharmacologically active compound library with the aim of identifying new druggable targets in the EGFR pathway. As anticipated, the phenotypic screen identified compounds that produce phenotypes resulting from targeting a known specific molecule or pathway. The assay also showed that compounds with diverse known mechanisms of action produced similar, EGFR-related cellular phenotypes. Biochemical assays revealed that those compounds share a previously unappreciated common target/pathway, showing that the image-based assay can identify new target molecules that are independent of the compound’s known target. Further experiments showed that ROCK1 and PSMD2 are novel druggable targets within the EGFR pathway.