bluuebunny/crossref_metadata_2025 huggingface dataset:
In planta genome editing with CRISPR/Cas9 ribonucleoproteins
Authors: Kumagai Yuya , Liu Yuelin , Hamada Haruyasu , Luo Weifeng , Zhu Jianghui , Kuroki Misa , Nagira Yozo , Taoka Naoaki , Kato Etsuko , Imai Ryozo
Published: June 2021

In planta genome editing represents an attractive approach to engineering crops/varieties that are recalcitrant to culture-based transformation methods. Here, we report the direct delivery of CRISPR/Cas9 ribonucleoproteins into the shoot apical meristem using in planta particle bombardment and introduction of a semidwarf1 (sd1)-orthologous mutation into wheat. The triple knockout tasd1 mutant of an elite wheat variety reduced culm length by 10% without a reduction in yield.
Similar neural networks respond to coherence during comprehension and production of discourse
Authors: Morales Matías , Patel Tanvi , Tamm Andres , Pickering Martin J. , Hoffman Paul
Published: June 2021

When comprehending discourse, listeners engage default mode regions associated with integrative semantic processing to construct a situation model of its content. We investigated how similar networks are engaged when we produce, as well as comprehend, discourse. During fMRI, participants spoke about a series of specific topics and listened to discourse on other topics. We tested how activation was predicted by natural fluctuations in the global coherence of the discourse, i.e., the degree to which utterances conformed to the expected topic. The neural correlates of coherence were similar across speaking and listening, particularly in default mode regions. This network showed greater activation when less coherent speech was heard or produced, reflecting updating of mental representations when discourse did not conform to the expected topic. In contrast, regions that exert control over semantic activation showed task-specific effects, correlating negatively with coherence during listening but not during production. Participants who showed greater activation in left inferior prefrontal cortex also produced more coherent discourse, suggesting a specific role for this region in goal-directed regulation of speech content. Results suggest strong correspondence of discourse representations during speaking and listening. However, they indicate that the semantic control network plays different roles in comprehension and production.
Human gut Bacteroides uniformis utilizes mixed linked β- glucans via an alternative strategy
Authors: Singh Ravindra Pal , Thakur Raksha , Kumar Gulshan
Published: June 2021

Human gut microbial communities have a tremendous impact on well-being of the human health by producing myriad of metabolites. Polysaccharide utilizing capability of these microbial communities is a key driving force in shaping the composition of gut microbiota. Previous studies suggest that genes responsible for β- glucans utilizing in Bacteroides are present in a polysaccharide utilization locus (PUL). However, recent observations show that Bacteroides uniformis lacks such PUL archetypal organisation for efficient utilization of pustulan (β1-6) and mixed linkage (β1-4/ β1-3) glucans, and its mechanism is yet to be studied. Here, we first used BuGH16 for production of important two mixed linked β- glucan-oligosaccharides, and then demonstrate kinetics of the BuGH3MLG. The B. uniformis JCM13288T coordinates between PUL associated glycoside hydrolase (GH)-16 and distantly localised bespoke GH 3 (BuGH3MLG) for efficient utilization of mixed linkage (β1-4/ β1-3) glucans. BuGH3MLG found to be cleaved β1-4, β1-3 and β1-6 glucan-oligosaccharides. Such understanding of glycan utilization mechanism of human gut bacterial communities is crucial for development of nutraceutical therapy and improving health of human being.
Ectosomes and exosomes are distinct proteomic entities that modulate spontaneous activity in neuronal cells
Authors: Brás Inês Caldeira , Khani Mohammad Hossein , Riedel Dietmar , Parfentev Iwan , Gerhardt Ellen , Christoph van Riesen  , Urlaub Henning , Gollisch Tim , Outeiro Tiago Fleming
Published: June 2021

Extracellular vesicles (EVs) are important mediators in intercellular communication. However, understanding the biological origin and functional effects of EVs subtypes has been challenging due to the moderate differences in their physical properties and absence of reliable markers. Here, we characterize the proteomes of ectosomes and exosomes using an improved differential ultracentrifugation protocol and quantitative proteomics. Cytoskeleton and glycolytic proteins are distinctively present in ectosomes, while endosomal sorting complexes proteins and tetraspanins are enriched in exosomes. Furthermore, annexin-A2 was identified as a specific marker for ectosomes derived from cell media and human cerebrospinal fluid. Expression of EGFP as a cytosolic reporter leads to its incorporation in EVs and enables their imaging with higher resolution. Importantly, ectosomes and exosomes internalization in neuronal cells results in the modulation of neuronal spontaneous activity. Our findings suggest that EVs cargoes reflect core intracellular processes, and their functional properties might regulate basic biological and pathological processes.
Integrating T-cell receptor and transcriptome for large-scale single-cell immune profiling analysis
Authors: Drost Felix , An Yang , Dratva Lisa M , Lindeboom Rik GH , Haniffa Muzlifah , Teichmann Sarah A , Theis Fabian , Lotfollahi Mohammad , Schubert Benjamin
Published: June 2021

Recent advancements in single-cell immune profiling that enable the measurement of the transcriptome and T-cell receptor (TCR) sequences simultaneously have emerged as a promising approach to study immune responses at cellular resolution. Yet, combining these different types of information from multiple datasets into a joint representation is complicated by the unique characteristics of each modality and the technical effects between datasets. Here, we presentmvTCR, a multimodal generative model to learn a unified representation across modalities and datasets for joint analysis of single-cell immune profiling data. We show thatmvTCRallows the construction of large-scale and multimodal T-cell atlases by distilling modality-specific properties into a shared view, enabling unique and improved data analysis. Specifically, we demonstratedmvTCR’spotential by revealing and separating SARS-CoV-2-specific T-cell clusters from bystanders that would have been missed in individual unimodal data analysis. Finally,mvTCRcan enable automated analysis of new datasets when combined with transfer-learning approaches.

Overall,mvTCRprovides a principled solution for standard analysis tasks such as multimodal integration, clustering, specificity analysis, and batch correction for single-cell immune profiling data.
AFEchidna is an R package for genetic evaluation of plant and animal breeding datasets
Authors: Zhang Weihua , Wei Ruiyan , Liu Yan , Lin Yuanzhen
Published: June 2021

Progeny tests play important roles in plant and animal breeding programs, and mixed linear models are usually performed to estimate variance components of random effects, estimate the fixed effects (Best Linear Unbiased Estimates, BLUEs) and predict the random effects (Best Linear Unbiased Predictions, BLUPs) via restricted maximum likehood (REML) methods in progeny test datasets. The current pioneer software for genetic assessment is ASReml, but it is commercial and expensive. Although there is free software such as Echidna or the R package sommer, the Echidna syntax is complex and the R package functionality is limited. Therefore, this study aims to develop an R package named AFEchidna based on Echidna software. The mixed linear models are conveniently implemented for users through the AFEchidna package to solve variance components, genetic parameters and the BLUP values of random effects, and the batch analysis of multiple traits, multiple variance structures and multiple genetic parameters can be also performed, as well as comparison between different models and genomic BLUP analysis. The AFEchidna package is free, please email us (yzhlinscau@163.com) to get a copy if reader is interested for it. The AFEchidna package is developed to expand free genetic assessment software with the expectation that its efficiency could be close to the commercial software.
Chilean blind spots in soil biodiversity and ecosystem function research
Authors: Marín César , Rubio Javiera , Godoy Roberto
Published: June 2021

Soil harbor up to a quarter of the world’s biodiversity, contributing to many ecosystem functions. It is of great importance to identify distribution patterns of soil organisms and their ecosystem functions to support their conservation and policy building. This has been recently analyzed at macroecological scales, but analyses at national/local scales are scarce. Here we identify and analyze the blind spots in soil taxa and ecosystem functioning data in continental Chile, through a Web of Science articles (1945-2020) search, and focusing on ten soil taxonomic groups and four ecosystem functions (nutrient cycling, decomposition, water infiltration, soil respiration). A total of 741 sampling sites were obtained from 239 articles. In 49.25% of the sites soil biodiversity was studied, while this percentage was 32.65% for ecosystem functions; in 18.10% of the sites both soil biodiversity and ecosystem functions were investigated at the same time, a surprisingly high percentage compared to global studies. By far, Bacteria/Fungi and nutrient cycling were the most investigated taxa and function, respectively. There is a significant number of soil taxa (Acari, Collembola, Nematoda, Formicoidea, Protista, Rotifera) represented by just a few sites concentrated in specific Chilean regions. Places like the central regions, the Atacama desert, and the Valdivian temperate forests present a proliferation of studies on soil Fungi, Bacteria, and nutrient cycling, reflecting historical interests of established research groups. Based on this research, we are identifying the causes of the data blind spots and invite the Chilean soil ecology community to propose ideas on how to fill them.
Mutant strains of Escherichia coli lacking global regulators, arcA and fis, demonstrate better growth fitness by pathway reprogramming under acetate metabolism
Authors: Jindal Shikha , Iyer Mahesh S. , Jyoti Poonam , Masakapalli Shyam Kumar , Venkatesh K.V.
Published: June 2021

Global regulatory transcription factors play a significant role in controlling microbial metabolism under genetic and environmental perturbations. A systems-level effect of carbon sources such as acetate on microbial metabolism under disrupted global regulators has not been well established. Acetate is one of the substrates available in a range of nutrient niches such as the mammalian gut and high-fat diet. Therefore, investigating the study on acetate metabolism is highly significant. It is well known that the global regulators arcA and fis regulate acetate uptake genes in E. coli under glucose condition. In this study, we deciphered the growth and flux distribution of E.coli transcription regulatory knockout mutants ΔarcA, Δfis and double deletion mutant, ΔarcAfis under acetate using 13C-Metabolic Flux Analysis which has not been investigated before. We observed that the mutants exhibited an expeditious growth rate (~1.2-1.6 fold) with a proportionate increase in acetate uptake rates compared to the wild-type. 13C-MFA displayed the distinct metabolic reprogramming of intracellular fluxes, which conferred an advantage of faster growth with better carbon usage in all the mutants. Under acetate metabolism, the mutants exhibited higher fluxes in the TCA cycle (~18-90%) and lower gluconeogenesis flux (~15-35%) with the proportional increase in growth rate. This study reveals a novel insight by stating the sub-optimality of the wild-type strain grown under acetate substrate aerobically. These mutant strains efficiently oxidize acetate to acetyl-CoA and therefore are potential candidates that can serve as a precursor for the biosynthesis of isoprenoids, biofuels, vitamins and various pharmaceutical products.

Importance

Unravelling the role of global regulatory genes on microbial metabolism of substrates available in various growth niche is important. Studies have shown that the global transcriptional regulators arcA and fis, under glucose availability, suppress the acetate uptake genes indicating a link between nutrient source and gene regulatory control. This work is focused on deciphering the influence of these regulators on acetate metabolism in E.coli. Growth studies using knockout strains (ΔarcA, Δfis and ΔarcAfis) and 13C Metabolic flux analysis defined precise metabolic phenotypes under acetate metabolism. Interestingly, the mutants showed metabolic readjustment to facilitate optimal biomass requirements and a better balance between energy and precursor synthesis, resulting in better growth, which lacked in the wild-type strain. The outcomes of this study will be leveraged in understanding the regulatory control under various nutrient shifts.
High affinity FcγR activating function depends on IRAP+endosomal-signaling platforms
Authors: Benadda Samira , Nugues Mathilde , Bens Marcelle , De Luca Mariacristina , Pellé Olivier , Monteiro Renato C. , Evnouchidou Irini , Saveanu Loredana
Published: June 2021

Although endocytosis of cell surface receptors is generally thought to terminate the signaling, for some receptors, endocytosis sustains signaling. We wondered if endosomal signaling participates to the function of the receptors for Fc immunoglobulin fragments (FcRs) that are highly internalized after their activation. We demonstrate here that four different FcRs follow distinct endocytic pathways after activation. While FcαRI is internalized into lysosomes, FcγRIIA is internalized and partially retained in early endosomes, whereas the inhibitory receptor FcγRIIB is internalized in endosomes decorated by the autophagy marker LC3. Interestingly, the high affinity FcγRI is internalized in specialized endosomal compartments described by the Insulin Responsive AminoPeptidase (IRAP), where it remains associated with the active form of the signaling kinase Syk. Our results show that FcγRI has the ability to build endosomal-signaling platforms, which depend on the presence of IRAP and Rab14. Destabilization of the endosomal signaling platforms compromised the ability of peritoneal macrophages to kill tumor cells by antibody-dependent cell mediated cytotoxicity, indicating that FcγRI endosomal signaling is required for the therapeutic action of anti-tumor monoclonal antibodies.

One sentence summary

Binding of immune complexes to FcγRI receptor leads to receptor internalization and sustained signaling from endosomes described by the Insulin Responsive AminoPeptidase and the small GTPase Rab14.
Directed Evolution of AAV Targeting Primate Retina by Intravitreal Injection Identifies R100, a Variant Demonstrating Robust Gene Delivery and Therapeutic Efficacy in Non-Human Primates
Authors: Kotterman Melissa , Beliakoff Ghezal , Croze Roxanne , Vazin Tandis , Schmitt Christopher , Szymanski Paul , Leong Meredith , Quezada Melissa , Holt Jenny , Barglow Katherine , Hassanipour Mohammad , Schaffer David , Francis Peter , Kirn David
Published: June 2021

Targeted AAV vectors are needed for safe and efficient delivery to and transduction of specific tissue target(s) in patients. Effective intravitreal delivery for retina gene therapy is not feasible with wildtype AAV. We employed directed evolution in nonhuman primates (NHP) to discover an AAV variant (R100) for intravitreal treatment of multiple target cells in the primate retina. R100 demonstrated superior transduction of human retinal cells compared to wildtype AAV. Furthermore, three R100-based gene therapeutics demonstrated safety, delivery, and durable pan-retinal expression of intracellular or secreted transgenes throughout the NHP retina following intravitreal administration. Finally, efficacy of R100-mediated delivery of therapeutic transgenes was demonstrated in patient-derived retinal cells (monogenic diseases) and in an NHP model of pathogenic retinal angiogenesis.
Temporal-spectral signaling of sensory information and expectations in the cerebral processing of pain
Authors: Nickel Moritz M. , Tiemann Laura , Hohn Vanessa D. , May Elisabeth S. , Ávila Cristina Gil , Eippert Falk , Ploner Markus
Published: June 2021

The perception of pain is shaped by somatosensory information about threat. However, pain is also influenced by an individual’s expectations. Such expectations can result in clinically relevant modulations and abnormalities of pain. In the brain, sensory information, expectations (predictions), and discrepancies thereof (prediction errors) are signaled by an extended network of brain areas. These brain areas generate evoked potentials and oscillatory responses at different latencies and frequencies. Recent evidence has provided first insights into how oscillatory responses at different frequencies signal predictions and prediction errors. However, a comprehensive picture of how evoked and oscillatory brain responses signal sensory information, predictions, and prediction errors in the processing of pain is lacking so far. We therefore built upon a neuroimaging study which investigated the spatial signalling of sensory information, predictions and predictions errors in the processing of pain (Geuter et al., 2017). To complement and extend this study, we applied brief painful stimuli to 48 healthy human participants and independently modulated sensory information (stimulus intensity) and expectations of pain intensity while measuring brain activity using electroencephalography (EEG). Pain ratings confirmed that pain intensity was shaped by both sensory information and expectations. In contrast, Bayesian analyses revealed that stimulus-induced EEG responses at different latencies (the N1, N2, and P2 components) and frequencies (alpha, beta, and gamma oscillations) were shaped by sensory information but not by expectations. Expectations, however, shaped alpha and beta oscillations before the painful stimuli. These findings indicate that commonly analyzed EEG responses to painful stimuli are more involved in signaling sensory information than in signaling expectations or mismatches of sensory information and expectations. Moreover, they indicate that the effects of expectations on pain are served by brain mechanisms which differ from those conveying effects of sensory information on pain.
Asymmetric peptidoglycan editing generates the curvature of predatory bacteria, optimizing invasion and replication within a spherical prey niche
Authors: Banks Emma J. , Valdivia-Delgado Mauricio , Biboy Jacob , Wilson Amber , Cadby Ian T. , Vollmer Waldemar , Lambert Carey , Lovering Andrew L. , Sockett R. Elizabeth
Published: June 2021

The vibrioid predatory bacterium Bdellovibrio bacteriovorus secretes prey wall-modifying enzymes to invade and replicate within the periplasm of Gram-negative prey bacteria. Studying self-modification of predator wall peptidoglycan during predation, we discover that Bd1075 generates self-wall curvature by exerting LD-carboxypeptidase activity in the vibrioid B. bacteriovorus strain HD100 as it grows inside spherical prey. Bd1075 localizes to the outer curved face of B. bacteriovorus, in contrast to most known shape-determinants. Asymmetric protein localization is determined by the novel function of a nuclear transport factor 2-like (NTF2) domain at the protein C-terminus. The solved structure of Bd1075 is monomeric, with key differences to other LD-carboxypeptidases. Rod-shaped Δbd1075 mutants invade prey more slowly than curved wild-type predators, and stretch and deform the invaded prey cell from within. Vibrioid morphology increases the evolutionary fitness of wild predatory bacteria, facilitating efficient prey invasion and intracellular growth of curved predators inside a spherical prey niche.
New Drosophila models to uncover the intrinsic and extrinsic factors mediating the toxicity of the human prion protein
Authors: Myers Ryan R. , Sanchez-Garcia Jonatan , Leving Daniel C. , Fernandez-Funez Pedro
Published: June 2021

Misfolded conformations of the prion protein (PrP) are responsible for devastating neurological disorders in humans and mammals. An unresolved problem is unraveling the mechanisms governing PrP conformational dynamics, misfolding, and the cellular mechanism leading to neurodegeneration. The variable susceptibility of mammals to prion diseases can be exploited to understand the conformational dynamics of PrP. Here we present a new fly model expressing human PrP with robust phenotypes in brain neurons and the eye. Using comparable attP2 insertions, we demonstrate the heightened toxicity of human PrP compared to that of mouse and hamster PrP along with a specific interaction with the amyloid-beta peptide. Using this new highly toxic new model, we started to uncover the intrinsic (sequence / structure) and extrinsic (interactions) factors regulating PrP toxicity. As extrinsic factors, we describe the importance of the PERK - ATF4 branch of the unfolded protein response as a key cellular mechanism mediating the toxicity of human PrP. For intrinsic factors, we introduced point mutations in human PrP (N159D, D167S, N174S) that were partially protective, revealing its high propensity to misfold into toxic conformations.
Unprecedented incidence ofTrypanosoma cruziinfections in a cohort of dogs directly detected through longitudinal tracking at multi-dog kennels, Texas, USA
Authors: Busselman Rachel E. , Meyers Alyssa C. , Zecca Italo B. , Auckland Lisa D. , Castro Andres H. , Dowd Rebecca E. , Curtis-Robles Rachel , Hodo Carolyn L. , Saunders Ashley B. , Hamer Sarah A.
Published: June 2021

Canine Chagas disease, caused by the protozoan parasiteTrypanosoma cruzi, is increasingly recognized as a health concern for dogs in the USA, and infected dogs may signal geographic regions of risk for human disease. Dogs living in multi-dog kennel environments where triatomine vectors are endemic may be at high risk for infection. We monitored a cohort of 64T. cruzi-infected and uninfected dogs from across 10 kennels in Texas, USA, to characterize changes in infection status over time. We used robust diagnostic criteria in which reactivity on multiple independent platforms was required to be considered positive. Among the 30 dogs enrolled as serologically- and/or PCR-positive, all but one dog showed sustained positiveT. cruzidiagnostic results over time. Among the 34 dogs enrolled as serologically- and PCR-negative, 10 newT. cruziinfections were recorded over a 12-month period. The resulting incidence rate was 30.7T. cruziinfections per 100 dogs per year. This study highlights the risk ofT.cruziinfection to dogs in kennel environments, despite multiple vector control methods employed by kennel owners. To protect both dog and human health, there is an urgent need to develop more integrated vector control methods as well as prophylactic and curative antiparasitic treatment options forT. cruziinfection in dogs.
Characterization of novel competitive inhibitors of P. falciparum cGMP-dependent protein kinase
Authors: Eck Tyler , de Souza Mariana Laureano , Yadav Bheemanaboina Rammohan R. , Chakrasali Ramappa , Kreiss Tamara , Siekierka John J. , Rotella David P. , Bhanot Purnima , Goodey Nina M.
Published: June 2021

P. falciparum cGMP-dependent protein kinase (PfPKG) is an enticing anti-malarial drug target. Structurally novel isoxazole-based compounds were shown to be ATP competitive inhibitors of PfPKG. Isoxazoles 3 and 5 had Ki values of 0.7 ± 0.2 and 2.3 ± 0.9 nM, respectively, that are comparable to a known standard, 4-[2-(4-fluorophenyl)-5-(1-methylpiperidine-4-yl)-1H pyrrol-3-yl] pyridine (1.4 ± 0.5 nM). They also exhibited excellent selectivity for PfPKG over the human ortholog and the gatekeeper mutant T618Q PfPKG, which mimics the less accessible binding site of the human ortholog. The human ortholog’s larger binding site volume was predicted to explain the selectivity of the inhibitors for the P. falciparum enzyme. Analogs 4 and 6 were at least 20-fold less potent compared to 3 and 5, suggesting that removing the carbonyl group in 3 or altering the diethylamino moiety in 5 reduced affinity.
Non-Newtonian Blood Rheology Impacts Left Atrial Stasis in Patient-Specific Simulations
Authors: Gonzalo A. , García-Villalba M. , Rossini L. , Durán E. , Vigneault D. , Martínez-Legazpi P. , Flores O. , Bermejo J. , McVeigh E. , Kahn A. M. , del Alamo J. C.
Published: June 2021

The lack of mechanically effective contraction of the left atrium (LA) during atrial fibrillation (AF) disturbs blood flow, increasing the risk of thrombosis and ischemic stroke. Thrombosis is most likely in the left atrial appendage (LAA), a small narrow sac where blood is prone to stagnate. Slow flow promotes the formation of erythrocyte aggregates in the LAA, also known as rouleaux, causing viscosity gradients that are usually disregarded in patient-specific simulations. To evaluate these non-Newtonian effects, we built atrial models derived from 4D computed tomography scans of patients and carried out computational fluid dynamics simulations using the Carreau-Yasuda constitutive relation. We examined six patients, three of whom had AF and LAA thrombosis or a history of transient ischemic attacks (TIAs). We modeled the effects of hematocrit and rouleaux formation kinetics by varying the parameterization of the Carreau-Yasuda relation and modulating non-Newtonian viscosity changes based on residence time. Comparing non-Newtonian and Newtonian simulations indicates that slow flow in the LAA increases blood viscosity, altering secondary swirling flows and intensifying blood stasis. While some of these effects can be subtle when examined using instantaneous metrics like shear rate or kinetic energy, they are manifested in the blood residence time, which accumulates over multiple heartbeats. Our data also reveal that LAA blood stasis worsens when hematocrit increases, offering a potential new mechanism for the clinically reported correlation between hematocrit and stroke incidence. In summary, we submit that hematocrit-dependent non-Newtonian blood rheology should be considered in calculating patient-specific blood stasis indices by computational fluid dynamics.
Genetic evidence for environment-dependent hybrid incompatibilities in threespine stickleback
Authors: Thompson Ken A. , Peichel Catherine L. , Rennison Diana J. , McGee Matthew D. , Albert Arianne Y. K. , Vines Timothy H. , Greenwood Anna K. , Wark Abigail R. , Brandvain Yaniv , Schumer Molly , Schluter Dolph
Published: June 2021

Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are ‘intrinsic’, meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis are scarce. In this article, we compiled genetic data for F2hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatusL.) that were born and raised in either the field (semi-natural experimental ponds) or the laboratory (aquaria). We tested for differences in excess heterozygosity between these two environments at ancestry informative loci—a genetic signature of selection against incompatibilities. We found that excess ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Previous results from F1 hybrids in the field suggest that pond-specific (single-locus) heterosis is unlikely to explain this finding. Our study suggests that, in stickleback, a coarse signal of environment-dependent hybrid incompatibilities is reliably detectable and that extrinsic incompatibilities have evolved before intrinsic incompatibilities.
Protection of the prodomain α1-helix correlates with latency in the transforming growth factor-β family
Authors: Le Viet Q. , Zhao Bo , Iacob Roxana E. , Tian Yuan , Toohey Cameron , Engen John R. , Springer Timothy A.
Published: June 2021

The 33 members of the transforming growth factor beta (TGF-β) family are fundamentally important for organismal development and homeostasis. Family members are synthesized and secreted as pro-complexes of prodomains that are non-covalently bound to the growth factor (GF). The pro-complexes of some members are latent and require activation steps to release the GF for signaling. Why some members are latent while others are non-latent is incompletely understood, but crystal structures and hydrogen-deuterium exchange (HDX) of four family members have begun to unravel how latency is regulated. Here, we extend this understanding by comparing pro-complex conformation in negative stain EM (nsEM) and HDX of ActA, BMP7, BMP9, BMP10, GDF8, TGF-β1, and TGF-β2. nsEM revealed that family members varied in either adopting cross-armed, open-armed, or V-armed configurations. Latency was achieved in both cross-armed and V-armed but not open-armed conformations. HDX revealed remarkably varying patterns of exchange between family members, consistent with large prodomain sequence divergence. We observed a strong correlation between latency and protection of the prodomain α1-helix from exchange, which in latent members coincided with greater buried surface area of the α1-helix and more hydrogen and cation-pi bonds from the prodomain fastener and GF to the α1-helix. Strong sequence conservation of the α1-helix and fastener only in latent members suggests that similar interactions are conserved and sufficient to confer latency. Moreover, most members exhibited rapid exchange in the unstructured “association region” at the prodomain N-terminus, highlighting their availability for interacting with factors that may regulate latency and extracellular storage.
Identification and characterization of novel proteins from Arizona bark scorpion venom that inhibit Nav1.8, a voltage-gated sodium channel regulator of pain signaling
Authors: Abd El-Aziz Tarek Mohamed , Xiao Yucheng , Kline Jake , Gridley Harold , Heaston Alyse , Linse Klaus D. , Ward Micaiah J. , Rokyta Darin R. , Stockand James D. , Cummins Theodore R. , Fornelli Luca , Rowe Ashlee H.
Published: June 2021

The voltage-gated sodium channel Nav1.8 is linked to neuropathic and inflammatory pain, highlighting the potential to serve as a drug target. However, the biophysical mechanisms that regulate Nav1.8 activation and inactivation gating are not completely understood. Progress has been hindered by a lack of biochemical tools for examining Nav1.8 gating mechanisms. Arizona bark scorpion (Centruroides sculpturatus) venom proteins inhibit Nav1.8 and block pain in grasshopper mice (Onychomys torridus). These proteins provide tools for examining Nav1.8 structure-activity relationships. To identify proteins that inhibit Nav1.8 activity, venom samples were fractioned using liquid chromatography (reversed phase and ion exchange). A recombinant Nav1.8 clone expressed in ND7/23 cells was used to identify subfractions that inhibited Nav1.8 Na+ current. Mass spectrometry-based bottom-up proteomic analyses identified unique peptides from inhibitory subfractions. A search of the peptides against the AZ bark scorpion venom gland transcriptome revealed four novel proteins between 40 and 60% conserved with venom proteins from scorpions in four genera (Centruroides, Parabuthus, Androctonus, and Tityus). Ranging from 63 to 82 amino acids, each primary structure includes 8 cysteines and a “CXCE” motif where X = an aromatic residue (tryptophan, tyrosine or phenylalanine). Electrophysiology data demonstrated that the inhibitory effects of bioactive subfractions can be removed by hyperpolarizing the channels, suggesting that proteins may function as gating modifiers as opposed to pore blockers.
WMW-A: Rank-based two-sample independent test for smallsample sizes through an auxiliary sample
Authors: Guo Yin , Li Limin
Published: June 2021

Two-sample independent test methods are widely used in case-control studies to identify significant changes or differences, for example, to identify key pathogenic genes by comparing the gene expression levels in normal and disease cells. However, due to the high cost of data collection or labelling, many studies face the small sample problem, for which the traditional two-sample test methods often lose power. We propose a novel rank-based nonparametric test method WMW-A for small sample problem by introducing a three-sample statistic through another auxiliary sample. By combining the case, control and auxiliary samples together, we construct a three-sample WMW-A statistic based on the gap between the average ranks of the case and control samples in the combined samples. By assuming that the auxiliary sample follows a mixed distribution of the case and control populations, we analyze the theoretical properties of the WMW-A statistic and approximate the theoretical power. The extensive simulation experiments and real applications on microarray gene expression data sets show the WMW-A test could significantly improve the test power for two-sample problem with small sample sizes, by either available unlabelled auxiliary data or generated auxiliary data.
Photoinactivation of Catalase Sensitizes Wide-Ranging Bacteria to ROS-Producing Agents and Immune Cells
Authors: Dong Pu-Ting , Jusuf Sebastian , Hui Jie , Zhan Yuewei , Zhu Yifan , Liu George Y. , Cheng Ji-Xin
Published: June 2021

Bacteria have evolved to cope with the detrimental effects of reactive oxygen species (ROS) using their essential molecular components. Catalase, a heme-containing tetramer protein expressed universally in most of the aerobic bacteria, plays an indispensable role in scavenging excess hydrogen peroxide (H2O2). Here, through utilization of wild-type and catalase-deficient mutants, we identified catalase as an endogenous therapeutic target of 400-420 nm blue light. Catalase residing in bacteria could be effectively inactivated by blue light, subsequently rendering the pathogens extremely vulnerable to H2O2and H2O2-producing agents. As a result, photoinactivation of catalase and H2O2synergistically eliminate a wide range of catalase-positive planktonic bacteria andP. aeruginosainside biofilms. In addition, photoinactivation of catalase is shown to facilitate macrophages to defend against intracellular pathogens. The antimicrobial efficacy of catalase photoinactivation is further validated using aPseudomonas aeruginosa-induced mice abrasion model. Taken together, our findings offer a catalase-targeting phototherapy against multidrug-resistant bacterial infections.
Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state
Authors: Daniel Bence , Belk Julia A. , Meier Stefanie L. , Chen Andy Y. , Sandor Katalin , Qi Yanyan , Kitano Hugo , Wheeler Joshua R. , Foster Deshka S. , Januszyk Michael , Longaker Michael T. , Chang Howard Y. , Satpathy Ansuman T.
Published: June 2021

Cell cycle (CC) is a fundamental biological process with robust, cyclical gene expression programs to facilitate cell division. In the immune system, a productive immune response requires the expansion of pathogen-responsive cell types, but whether CC also confers unique gene expression programs that inform the subsequent immunological response remains unclear. Here we demonstrate that single macrophages adopt different plasticity states in CC, which is a major source of heterogeneity in response to polarizing cytokines. Specifically, macrophage plasticity to interferon gamma (IFNG) is substantially reduced, while interleukin 4 (IL-4) can induce S-G2/M-biased gene expression. Additionally, IL-4 polarization shifts the CC-phase distribution of the population towards G2/M phase, providing a mechanism for reduced IFNG-induced repolarization. Finally, we show that macrophages express tissue remodeling genes in the S-G2/M-phases of CC, that can be also detectedin vivoduring muscle regeneration. Therefore, macrophage inflammatory and regenerative responses are gated by CC in a cyclical phase-dependent manner.

Highlights

Single-cell chromatin maps reveal heterogeneous macrophage polarization states

Cell cycle coincides with heterogeneity and alters macrophage plasticity to polarizing cytokines

Macrophage polarization is a cell cycle phase-dependent immunological process

S-G2/M-biased gene expression is linked to tissue remodeling and detected in proliferating macrophages during muscle regeneration
Pre-existing anxiety, depression, and neurological disability is associated with long COVID: A prospective and longitudinal cohort of the United Kingdom Multiple Sclerosis Register
Authors: Garjani Afagh , Middleton Rodden M , Nicholas Richard , Evangelou Nikos
Published: June 2021

Objectives

To assess the prevalence of long COVID among people with multiple sclerosis (MS) and its predictors, including their pre-COVID-19 functional status.

Design

Community-based prospective and longitudinal cohort study

Setting

The United Kingdom (UK) MS Register (UKMSR) COVID-19 study

Participants

A national cohort of people with MS and COVID-19

Main outcome measures

Participants used the online questionnaire-based platform of the UKMSR to update their COVID-19 symptoms, recovery status, and duration of symptoms for those who had fully recovered. Questionnaires were date-stamped for estimation of COVID-19 symptom duration for those who had not recovered at their last follow-up. The UKMSR holds demographic and up-to-date clinical data on participants as well as their web-based Expanded Disability Status Scale (a measure of physical disability in MS) and Hospital Anxiety and Depression Scale scores. The association between these factors and recovery from COVID-19 was assessed using multivariable Cox regression analysis.

Results

Out of 7,977 people with MS who participated in the UKMSR COVID-19 study, 599 had COVID-19 and updated their recovery status prospectively. At least 181 participants (31.1%) had long-standing COVID-19 symptoms for ≥4 weeks and 76 (13.1 %) for ≥12 weeks. Participants with higher levels of pre-COVID-19 physical disability, participants with anxiety and/or depression prior to COVID-19 onset, and women were less likely to report recovery from COVID-19.

Conclusions

Long COVID appears to disproportionately affect people with pre-existing mental health problems or physical disabilities. As post-COVID-19 rehabilitation services are being developed, individualised pathways should be considered to accommodate the needs of these vulnerable populations.

Trial Registration

ClinicalTrials.gov: NCT04354519
mOTUpan: a robust Bayesian approach to leverage metagenome assembled genomes for core-genome estimation
Authors: Buck Moritz , Mehrshad Maliheh , Bertilsson Stefan
Published: June 2021

Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome assembled genomes (MAGs) or single-cell assembled genomes (SAGs). While this expanded diversity can provide novel insights about microbial population structure, most tools available for core-genome estimation are overly sensitive to genome completeness. Consequently a major portion of the huge phylogenetic diversity uncovered by environmental genomics approaches remain excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core-genome for sets of genomes of highly diverse completeness range. The likelihood for each gene-cluster to belong to core- or accessory-genome is estimated by computing the probability of its presence/absence pattern in the target set of genomes. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates as state-of-the-art tools Roary and PPanGGoLiN for high-quality genomes and outperforms them at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.
Coupling of pupil- and neuronal population dynamics reveals diverse influences of arousal on cortical processing
Authors: Pfeffer Thomas , Keitel Christian , Kluger Daniel S. , Keitel Anne , Russmann Alena , Thut Gregor , Donner Tobias H. , Gross Joachim
Published: June 2021

Fluctuations in arousal, controlled by subcortical neuromodulatory systems, continuously shape cortical state, with profound consequences for information processing. Yet, how arousal signals influence cortical population activity in detail has so far only been characterized for a few selected brain regions. Traditional accounts conceptualize arousal as a homogeneous modulator of neural population activity across the cerebral cortex. Recent insights, however, point to a higher specificity of arousal effects on different components of neural activity and across cortical regions. Here, we provide a comprehensive account of the relationships between fluctuations in arousal and neuronal population activity across the human brain. Exploiting the established link between pupil size and central arousal systems, we performed concurrent magnetoencephalographic (MEG) and pupillographic recordings in a large number of participants, pooled across three laboratories. We found a cascade of effects relative to the peak timing of spontaneous pupil dilations: Decreases in low-frequency (2-8 Hz) activity in temporal and lateral frontal cortex, followed by increased high-frequency (>64 Hz) activity in mid-frontal regions, followed by monotonic and inverted-U relationships with intermediate frequency-range activity (8-32 Hz) in occipito-parietal regions. Pupil-linked arousal also coincided with widespread changes in the structure of the aperiodic component of cortical population activity, indicative of changes in the excitation-inhibition balance in underlying microcircuits. Our results provide a novel basis for studying the arousal modulation of cognitive computations in cortical circuits.
Flexible encoding of objects and space in single cells of the dentate gyrus
Authors: GoodSmith Douglas , Kim Sang Hoon , Puliyadi Vyash , Ming Guo-li , Song Hongjun , Knierim James J. , Christian Kimberly M.
Published: June 2021

The hippocampus is involved in the formation of memories that require associations among stimuli to construct representations of space and the items and events within that space. Neurons in the dentate gyrus (DG), an initial input region of the hippocampus, have robust spatial tuning, but it is unclear how nonspatial information may be integrated with spatially modulated firing at this stage. We recorded from the DG of 21 adult mice as they foraged for food in an environment that contained discrete objects. By classifying recorded DG cells into putative granule cells and mossy cells, we examined how the addition or displacement of objects affected the spatial firing of these DG cell types. We found DG cells with multiple firing fields at a fixed distance and direction from objects (landmark vector cells) as well as cells that exhibited localized changes in spatial firing when objects in the environment were manipulated. When mice were exposed to a second environment with the same objects, DG spatial maps were completely reorganized, suggesting standard global remapping, and a largely different subset of cells responded to object manipulations. Together, these data reveal the capacity of DG cells to detect small changes in the environment, while preserving a stable spatial representation of the overall context.
The NLRP3/eIF2 axis drives cell cycle progression in acute myeloid leukemia
Authors: Luciano Michela , Blöchl Constantin , Vetter Julia , Urwanisch Laura , Neuper Theresa , Elmer Dominik P. , Bauer Renate , Dang Hieu-Hoa , Strandt Helen , Neureiter Daniel , Krenn Peter , Tesanovic Suzana , Rieser Sebastian , Bergsleitner Olivia , Zell Lukas , Binder Stephanie , Schaller Susanne , Strunk Dirk , Pleyer Lisa , Greil Richard , Winkler Stephan , Hartmann Tanja N. , Huber Christian G. , Aberger Fritz , Horejs-Hoeck Jutta
Published: June 2021

Aberrant activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome mediates numerous inflammatory diseases. Oncogenes can activate the NLRP3 inflammasome and thereby promote myeloproliferative neoplasia, suggesting a crucial role of NLRP3 in the malignant transformation of hematopoietic cells. Here, we show that bone marrow-derived mononuclear cells of AML patients display enhanced expression of NLRP3, IL-1β and IL-18 and that high-level expression of NLRP3 is linked to poor survival of AML patients. Pharmacological and genetic inhibition of NLRP3 inflammasome activation attenuated cell proliferation of MOLM-13 AML cells in vitro. In vivo, genetic inhibition of NLRP3 in MOLM-13 AML cells resulted in reduced engraftment potential in xenografts, along with reduced splenomegaly and organ infiltration. Differential proteomic analysis revealed the eIF2 pathway as potential target of NLRP3 in AML, with a significant increase of eIF2α phosphorylation upon NLRP3 inhibition. NLRP3 inhibition also caused a strong decrease in cyclin – dependent kinases CDK4 and CDK6, accompanied by an upregulation of the CDK inhibitor p21 (CDKN1A) and a marked arrest of cell cycle progression in the G0/G1 phase, consistent with the role of eIF2α phosphorylation as negative cell cycle regulator.

Taken together, we show that inhibition of the NLRP3 inflammasome reduces AML cell proliferation by promoting eIF2α phosphorylation, which in turn enhances the expression of cell cycle arrest genes such as p21. Thus, the study uncovers the NLRP3/eIF2 axis as new driver of AML proliferation and proposes a novel therapeutic treatment of AML by targeted inhibition of NLRP3 activation.
The contribution of the European LIFE program to mitigate damages caused by large carnivores in Europe
Authors: Oliveira Teresa , Treves Adrian , López-Bao José Vicente , Krofel Miha
Published: June 2021

Governments around the world invest considerable resources to reduce damages caused by large carnivores on human property. To use these investments more efficiently and effectively, we need to understand which interventions successfully prevent such damages and which do not. In the European Union, the LIFE program represents by far the largest financial instrument to help EU Member States with the implementation of conservation activities, including mitigation of damages caused by large carnivores. However, we currently lack information about the effectiveness of this funding program in reducing carnivore damages. We reviewed 135 LIFE projects dealing with large carnivores between 1992 and 2019 to provide an overview of the use of damage prevention methods and evaluate their functional and perceived effectiveness. Methods evaluated ranged from non-lethal and lethal interventions, to information dissemination and compensation schemes. The largest number of the projects was focused on grey wolf (Canis lupus) and brown bears (Ursus arctos) in the Mediterranean countries and in Romania. Electric fences were reported as the most successful method for reducing damages by large carnivores, and most of the non-lethal methods used showed at least moderate effectiveness. However, standards of measuring and reporting effectiveness were in general relatively low, which limits our ability to measure actual impact. Therefore we urge project managers and evaluators to improve these standards, as well as the dissemination of the project results. We provide a list of recommendations for improving measuring and reporting success of implemented interventions for the benefit of future projects aimed to reduce damages caused by wildlife.

Article impact statement

Electric fences were reported as the most effective method to prevent large-carnivore damages and are recommended for future use.