bluuebunny/crossref_metadata_2025 huggingface dataset:
Reactive Postural Responses Predict Risk For Acute Musculoskeletal Injury In Collegiate Athletes
Authors: Morris Amanda , Fino Nora F. , Pelo Ryan , Cushman Daniel M. , Monson Nicholas E. , Jameson Trevor , Dibble Leland E. , Fino Peter C.
Published: September 2022

Identifying risk factors for musculoskeletal (MSK) injury is critical to maintain the health and safety of athletes. While current tests consider isolated assessments of function or subjective ratings, objective tests of reactive postural responses, especially when in cognitively demanding scenarios, may better identify risk of MSK injury than traditional tests alone.

Objectives

To examine if objective assessments of reactive postural responses, quantified using wearable inertial measurement units, are associated with the risk for acute lower extremity MSK injuries in collegiate athletes.

Design

Prospective survival analysis

Methods

191 Division I NCAA athletes completed an instrumented version of a modified Push and Release (I-mP&R) test at the beginning of their competitive season. The I-mP&R was performed with eyes closed under single- and dual-task (concurrent cognitive task) conditions. Inertial measurement units recorded acceleration and angular velocity data that was used to calculate time to stability (TTS). Acute lower extremity MSK injuries were tracked from first team activity for six months. Cox proportional hazard models were used to determine if longer times to stability were associated with faster time to injury.

Results

Longer TTS was associated with increased risk of injury; every 250 ms increase in dual-task median TTS was associated with a 37% increased risk of acute, lower-extremity MSK injury.

Conclusion

Tests of reactive balance, particularly under dual-task conditions, may be able to identify athletes at risk of acute lower extremity MSK injury. Clinically-feasible, instrumented tests of reactive should be considered in assessments for prediction and prevention of MSK injury in collegiate athletes.
Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA
Authors: Lisius Grace , Duttagupta Radha , Ahmed Asim A. , Hensley Matthew , Al-Yousif Nameer , Lu Michael , Bain William , Shah Faraaz , Schaefer Caitlin , Qin Shulin , Wang Xiaohong , Zhang Yingze , Mitchell Kevin J. , Hughes Ellen K. , Jacobs Jana L. , Naqvi Asma , Haidar Ghady , Mellors John W. , Methé Barbara , McVerry Bryan J. , Morris Alison , Kitsios Georgios D.
Published: September 2022

Background

Secondary infection (SI) diagnosis in COVID-19 is challenging, due to overlapping clinical presentations, practical limitations in obtaining samples from the lower respiratory tract (LRT), and low sensitivity of microbiologic cultures.

Research Question

Can metagenomic sequencing of plasma microbial cell-free DNA (mcfDNA-Seq) help diagnose SIs complicating COVID-19?

Study Design and Methods

We enrolled 42 inpatients with COVID-19 classified as microbiologically-confirmed SI (Micro-SI, n=8), clinically-diagnosed SI (Clinical-SI, n=13, i.e. empiric antimicrobials), or no clinical suspicion for SI (No-Suspected-SI, n=21) at time of enrollment. From baseline and follow-up plasma samples (days 5 and 10 post-enrollment), we quantified mcfDNA for all detected microbes by mcfDNA sequencing and measured nine host-response biomarkers. From LRT samples among intubated subjects, we quantified bacterial burden with 16S rRNA gene quantitative PCR.

Results

We performed mcfDNA-Seq in 82 plasma samples. Sequencing was successful in 60/82 (73.2%) samples, which had significantly lower levels of human cfDNA than failed samples (p<0.0001). McfDNA detection was significantly higher in Micro-SI (15/16 [94%]) compared to Clinical-SI samples (8/14 [57%], p=0.03), and unexpectedly common in No-Suspected-SI samples (25/30 [83%]), similar to detection rate in Micro-SI. We detected culture-concordant mcfDNA species in 13/16 Micro-SI samples (81%) and mcfDNA levels tracked with SI outcome (resolution or persistence) under antibiotic therapy. McfDNA levels correlated significantly with LRT bacterial burden (r=0.74, p=0.02) as well as plasma biomarkers of host response (white blood cell count, IL-6, IL-8, and SPD, all p<0.05). Baseline mcfDNA levels were predictive of worse 90-day survival (hazard ratio 1.30 [1.02-1.64] for each log10 mcfDNA, p=0.03).

Interpretation

High circulating levels of mcfDNA in a substantial proportion of patients with COVID-19 without clinical suspicion for SI suggest that SIs may often remain undiagnosed. McfDNA-Seq, when clinically available, can offer a non-invasive diagnostic tool for pathogen identification, with prognostic value on host inflammatory response and clinical outcomes.
How short decoding times, stimulus dimensionality and spontaneous activity constrain the shape of tuning curves: A speed-accuracy trade-off
Authors: Lenninger Movitz , Skoglund Mikael , Herman Pawel , Kumar Arvind
Published: September 2022

According to the efficient coding hypothesis, sensory neurons are adapted to provide maximal information about the environment given some biophysical constraints. Early sensory neurons modulate their average firing rates in response to some features of the external stimulus, creating tuned responses. In early visual areas, these modulations (or tunings) are predominantly single-peaked. However, periodic tuning, as exhibited by grid cells, has been linked to a significant increase in decoding performance. Does this imply that the tuning curves in early visual areas are sub-optimal? We argue that the time scale at which neurons encode information is imperative to understanding the relative advantages of single-peaked and periodic tuning curves. Because, if decoding ability scales differently with time for the different shapes of tuning curves, the time scale at which the neurons operate becomes critical. Here, we show that the possibility of catastrophic (large) errors due to overlapping neural responses for distinct stimulus conditions creates a trade-off between decoding time and decoding ability. Unfortunately, standard theoretical measures such as Fisher information do not capture these errors. We investigate how (very) short decoding times and stimulus dimensionality affect the optimal shape of tuning curves for stimuli with finite domains. In particular, we focus on the spatial periods of the tuning curves (or the number of “peaks”) for a class of circular tuning curves. We show a general trend for minimal decoding time, i.e., the shortest decoding time required to produce a statistically reliable signal, to increase with increasing Fisher information implying a trade-off between accuracy and speed. This trade-off is reinforced whenever the stimulus dimensionality is high or there is ongoing activity. Thus, given constraints on processing speed, we present normative arguments for the existence of single-peaked, rather than a periodic, tuning organization observed in early visual areas.
G protein-coupled Receptor Contributions to Wing Growth and Morphogenesis inDrosophila melanogaster
Authors: Huizar Francisco J. , Kumar Nilay , Unger Maria , Velagala Vijay , Wu Qinfeng , Brodskiy Pavel A. , Zartman Jeremiah J.
Published: September 2022

The development of multicellular organisms relies on a symphony of spatiotemporally coordinated signals that regulate gene expression. G protein-coupled receptors (GPCRs) are the largest group of transmembrane receptors that play a pivotal role in transducing extracellular signals into physiological outcomes. Emerging research has implicated neurotransmitter GPCRs, classically associated with communication in neuronal tissues, as regulators of pattern formation and morphogenesis. However, how these receptors interact amongst themselves and signaling pathways to regulate organogenesis is still poorly understood. To address this gap, we performed a systematic RNA interference (RNAi)-based screening of 111 GPCRs along with 8 Gα, 3 Gβ, and 2 Gγprotein subunits inDrosophila melanogaster. We performed a coupled, machine learning-based quantitative and qualitative analysis to identify both severe and more subtle phenotypes. Of the genes screened, 25 demonstrated at least 60% penetrance of severe phenotypes with several of the most severe phenotypes resulting from the knockdown of neuropeptide and neurotransmitter GPCRs that were not known previously to regulate epithelial morphogenesis. Phenotypes observed in positive hits mimic phenotypic manifestations of diseases caused by dysregulation of orthologous human genes. Quantitative reverse transcription polymerase chain reaction and meta-analysis of RNA expression validated positive hits. Overall, the combined qualitative and quantitative characterization of GPCRs and G proteins identifies an extensive set of GPCRs involved in regulating epithelial morphogenesis and relevant to the study of a broad range of human diseases.
Individual differences in neural event segmentation of continuous experiences
Authors: Sava-Segal Clara , Richards Chandler , Leung Megan , Finn Emily S.
Published: September 2022

Event segmentation is a spontaneous part of perception, important for processing continuous information and organizing it into memory. While neural and behavioral event segmentation show a degree of inter-subject consistency, meaningful individual variability exists atop these shared patterns. Here we characterized individual differences in the location of neural event boundaries across four short movies that evoked variable interpretations. Event boundary alignment across subjects followed a posterior-to-anterior gradient that was tightly correlated with the rate of segmentation: slower-segmenting regions that integrate information over longer time periods showed more individual variability in boundary locations. This relationship held irrespective of the stimulus, but the degree to which boundaries in particular regions were shared versus idiosyncratic depended on certain aspects of movie content. Furthermore, this variability was behaviorally significant in that similarity of neural boundary locations during movie-watching predicted similarity in how the movie was ultimately remembered and appraised. In particular, we identified a subset of regions in which neural boundary locations are both aligned with behavioral boundaries during encoding and predictive of stimulus interpretation, suggesting that event segmentation may be a mechanism by which narratives generate variable memories and appraisals of stimuli.
Characterizing the differential distribution and targets of Sumo paralogs in the mouse brain
Authors: Suk Terry R. , Nguyen Trina T. , Fisk Zoe A. , Mitkovski Miso , Geertsma Haley M. , Parmasad Jean-Louis A. , Heer Meghan M. , Callaghan Steve M. , Brose Nils , Tirard Marilyn , Rousseaux Maxime W.C.
Published: September 2022

SUMOylation is an evolutionarily conserved and essential mechanism whereby Small Ubiquitin Like Modifiers, or SUMO proteins (Sumo in mice), are covalently bound to protein substrates in a highly dynamic and reversible manner. SUMOylation is involved in a variety of basic neurological processes including learning and memory, and central nervous system development, but is also linked with neurological disorders. However, studying SUMOylation in vivo remains challenging due to limited tools to study Sumo proteins and their targets in their native context. More complexity arises from the fact that Sumo1 and Sumo2 are ∼50% homologous, whereas Sumo2 and Sumo3 are nearly identical and indistinguishable with antibodies. While Sumo paralogues can compensate for one another’s loss, Sumo2 is highest expressed and only paralog essential for embryonic development making it critical to uncover roles specific to Sumo2 in vivo. To further examine the roles of Sumo2, and to begin to tease apart the redundancy and similarity between key Sumo paralogs, we generated (His6-)HA epitope-tagged Sumo2 knock-in mouse alleles, expanding the current Sumo knock-in mouse tool-kit comprising of the previously generated His6-HA-Sumo1 knock-in model. Using these HA-Sumo mouse lines, we performed whole brain imaging and mapping to the Allen Brain Atlas to analyze the relative distribution of the Sumo1 and Sumo2 paralogues in the adult mouse brain. We observed differential staining patterns between Sumo1 and Sumo2, including a partial localization of Sumo2 in nerve cell synapses of the hippocampus. Combining immunoprecipitation with mass spectrometry, we identified native substrates targeted by Sumo1 or Sumo2 in the mouse brain. We validated select hits using proximity ligation assays, further providing insight into the subcellular distribution of neuronal Sumo2-conjugates. These mouse models thus serve as valuable tools to study the cellular and biochemical roles of SUMOylation in the central nervous system.
Local and long-distance inputs dynamically regulate striatal acetylcholine during decision making
Authors: Chantranupong Lynne , Beron Celia C. , Zimmer Joshua A. , Wen Michelle J. , Wang Wengang , Sabatini Bernardo L.
Published: September 2022

Within the basal ganglia, striatal dopamine (DA) and acetylcholine (Ach) are essential for the selection and reinforcement of motor actions and decision making. In vitro studies have revealed a circuit local to the striatum by which each of these two neurotransmitters directly regulates release of the other. Ach, released by a unique population of cholinergic interneurons (CINs), drives DA release via direct axonal depolarization. In turn, DA inhibits CIN activity via dopamine D2 receptors (D2R). Whether and how this circuit contributes to striatal function in vivo remains unknown. To define the in vivo role of this circuit, we monitored Ach and DA signals in the ventrolateral striatum of mice performing a reward-based decision-making task. We establish that DA and Ach exhibit multiphasic and anticorrelated transients that are modulated by decision history and reward outcome. However, CIN perturbations reveal that DA dynamics and reward-prediction error encoding do not require Ach release by CINs. On the other hand, CIN-specific deletion of D2Rs shows that DA inhibits Ach levels in a D2R-dependent manner, and loss of this regulation impairs decision-making. To determine how other inputs to striatum shape Ach signals, we assessed the contribution of projections from cortex and thalamus and found that glutamate release from both sources is required for Ach release. Altogether, we uncover a dynamic relationship between DA and Ach during decision making and reveal modes of CIN regulation by local DA signals and long-range cortical and thalamic inputs. These findings deepen our understanding of the neurochemical basis of decision making and behavior.
Stu2 has an essential kinetochore role independent of regulating microtubule dynamics
Authors: Abouelghar Ahmed , Carrier Joseph S. , Torvi Julia R. , Jenson Erin , Jones Chloe , Gangadharan Binnu , Geyer Elisabeth A. , Rice Luke M. , Lagesse Brent , Barnes Georjana , Miller Matthew P.
Published: September 2022

ch-TOG family proteins, including the budding yeast Stu2, are essential for spindle formation and chromosome segregation. Such functions depend on an array of activities ranging from microtubule nucleation, polymerization and depolymerization, to conferring tension sensitivity to kinetochores. This functional diversity makes it challenging to dissect these various functions and understand their relative importance. Here, we developed separation-of-function mutants and used artificial tethering tools to elucidate several important mechanistic insights into Stu2’s essential role. We show that Stu2’s microtubule polymerization activity depends on its basic linker region but is surprisingly dispensable for viability; that in fact, Stu2 carries out an essential kinetochore-associated function; and finally, that Stu2’s precise location within the kinetochore is critical for its function, suggesting a spatial separation mode of action may underlie its ability to confer tension sensitivity. Our findings highlight the significance of Stu2’s kinetochore role and provide insights into the molecular mechanisms by which it performs its various functions.
How enhancers regulate wavelike gene expression patterns: Novel enhancer prediction and live reporter systems identify an enhancer associated with the arrest of pair-rule waves in the short-germ beetleTribolium
Authors: Mau Christine , Rudolf Heike , Strobl Frederic , Schmid Benjamin , Regensburger Timo , Palmisano Ralf , Stelzer Ernst , Taher Leila , El-Sherif Ezzat
Published: September 2022

A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called ‘enhancers’. Much of our models of how enhancers work rely on the assumption that genes are activatedde novoas stable domains across embryonic tissues. Such view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of theDrosophilaembryo, where indeed gene expression domains seem to arise more or less stably. However, careful analysis of gene expressions in other model systems (including the AP patterning in vertebrates and short-germ insects like the beetleTribolium castaneum) painted a different, very dynamic view of gene regulation, where genes are oftentimes expressed in a wavelike fashion. How such gene expression waves are mediated at the enhancer level is so far unclear. Here we establish the AP patterning of the short-germ beetleTriboliumas a model system to study dynamic and temporal pattern formation at the enhancer level. To that end, we established an enhancer prediction system inTriboliumbased on time- and tissue-specific ATAC-seq and an enhancer live reporter system based on MS2 tagging. Using this experimental framework, we discovered severalTriboliumenhancers, and assessed the spatiotemporal activities of some of them in live embryos. We found our data consistent with a model in which the timing of gene expression during embryonic pattern formation is mediated by a balancing act between enhancers that induce rapid changes in gene expressions (that we call ‘dynamic enhancers’) and enhancers that stabilizes gene expressions (that we call ‘static enhancers’).
4EBP1/2 support tumorigenicity and cell survival during energetic stress by translationally regulating fatty acid synthesis
Authors: Levy Tal , Voeltzke Kai , Hauffe Laura , Alasad Khawla , Snaebjörnsson Marteinn , Marciano Ran , Scharov Katerina , Planque Mélanie , Vriens Kim , Christen Stefan , Funk Cornelius M , Hassiepen Christina , Kahler Alisa , Heider Beate , Picard Daniel , Lim Jonathan KM , Bas Zuelal , Bendrin Katja , Vargas-Toscano Andres , Kahlert Ulf , Remke Marc , Elkabets Moshe , Grünewald Thomas GP , Reichert Andreas S. , Fendt Sarah-Maria , Schulze Almut , Reifenberger Guido , Rotblat Barak , Leprivier Gabriel
Published: September 2022

Energetic stress compels cells to evolve adaptive mechanisms to maintain homeostasis. Here, we report that the negative regulators of mRNA translation initiation eukaryotic initiation factor 4E binding proteins 1/2 (4EBP1/2) are essential to promote the survival of mammalian cells and budding yeast under glucose starvation. Functionally, 4EBP1/2 inhibit fatty acid synthesis upon energetic stress via repression of Acetyl-CoA Carboxylase Alpha (ACACA) mRNA translation, sparing NADPH, to maintain intracellular redox balance. This has important relevance in cancers, as we uncovered that oncogene-transformed cells and glioma cells exploit the 4EBP1/2 regulation of ACACA expression and redox balance to combat energetic stress, thereby supporting transformation and tumorigenicity in vitro and in vivo. Clinically, high EIF4EBP1 (encoding 4EBP1) expression is associated with poor outcomes in several cancer types, including glioma. Our data reveal that 4EBP1/2 are conserved mediators of the survival response to energetic stress which are exploited by cancer cells for metabolic adaptation.
ATFS-1 regulates peroxisome assembly genes and protects both mitochondria and peroxisomes during peroxin perturbations
Authors: Shpilka Tomer , Naresh Nandhitha Uma , Du YunGuang , Watts Jennifer L. , Haynes Cole M.
Published: September 2022

Peroxisome biogenesis disorders lead to a myriad of clinical manifestations, among which is the dysfunction of the mitochondria. Mitochondria dysfunction is typically sensed by the UPRmt, a broad protective transcriptional response governed by the transcription factor ATFS-1. Here, we investigated the role of the UPRmt during peroxisomal stress. We show that mutations or knockdown of peroxins, the genes required for peroxisome assembly, lead to mitochondria dysfunction and the induction of the UPRmt in C.elegans. The UPRmt induced the transcription of the mitochondrial outer membrane translocase mspn-1 (ATAD-1), that in turn alleviated mitochondrial stress most likely by extracting mislocalized proteins. Importantly, ATFS-1 regulated the transcription of peroxins and the peroxisomal transporter pmp-4. A prx-5 loss of function strain induced a retrograde response that resulted in the transcriptional induction of peroxins, peroxisomal transporters, chaperons and proteases. And was dependent on ATFS-1 and on the peroxisome proliferator activator receptor alpha, NHR-49. Knockout of atfs-1 during peroxisomal stress resulted in severe developmental delays, import defects to peroxisomes and the appearance of large peroxisomal structures. We propose that ATFS-1 regulates the biogenesis of peroxisomes and protects the organism by alleviating the stress of both peroxisomes and mitochondria during peroxisomal stress.
Bone marrow hemogenic endothelial cells contribute multilineage hematopoietic progenitors in adult mice
Authors: Feng Jing-Xin , Yang Mei-Ting , Li Caiyi C. , Livák Ferenc , Abdelmaksoud Abdalla , Wang Dunrui , Tosato Giovanna
Published: September 2022

During development, hematopoietic stem/progenitor cells (HSPCs) originate from a subset of hemogenic endothelial cells (ECs) through a process of endothelial-to-hematopoietic transition (EHT). This process is temporally restricted to short developmental windows and generates HSPC with distinct capabilities for hematopoiesis. Although it is generally thought that adult hematopoiesis is sustained by HSCs derived from hemogenic endothelium during development, some observations point to EHT persistence in the late fetus/perinatally. Here we use lineage tracking and bioinformatics analysis to assess the presence of hemogenic endothelial cells in the adult mouse. Our analysis identifies a subset of bone marrow-resident adult endothelial cells, characterized by the expression of VE-Cadherin and the transcription factor RUNX1, that produce CD45+ hematopoietic cells. This EHT generates hematopoietic progenitors, and mature myeloid and lymphoid cells in the adult mouse. Our results reveal the identification of a distinct source of adult blood.
A novel overlapping geneazyx-1affects the translation of zyxin inC. elegans
Authors: Parmar Bhavesh S. , Geens Ellen , Vandewyer Elke , Kieswetter Amanda , Ludwig Christina , Temmerman Liesbet
Published: September 2022

Overlapping genes are widely prevalent, however, their expression and consequences are poorly understood. Here, we describe and functionally characterize a novelzyx-1overlapping gene,azyx-1, with distinct regulatory functions inC. elegans. We observed conservation of alternative open reading frames overlapping the 5’ region of zyxin family members in several animal species, and find shared sites ofazyx-1and zyxin proteoform expression inC. elegans. In line with a standard ribosome scanning model, our results supportcisregulation ofzyx-1long isoform(s) by upstream initiatingazyx-1a. Moreover, we report on a rare observation oftransregulation ofzyx-1byazyx-1, with evidence of increased ZYX-1 uponazyx-1overexpression. Our results suggest a dual role forazyx-1in influencingzyx-1proteoform heterogeneity and highlights its impact onC. elegansmuscular integrity and locomotion.
Intrinsic reward-like dopamine and acetylcholine dynamics in striatum
Authors: Krok Anne C. , Mistry Pratik , Li Yulong , Tritsch Nicolas X.
Published: September 2022

External rewards like food and money are potent modifiers of behavior1,2. Pioneering studies established that these salient sensory stimuli briefly interrupt the tonic cell-autonomous discharge of neurons that produce the neuromodulators dopamine (DA) and acetylcholine (ACh): midbrain DA neurons (DANs) fire a burst of action potentials that broadly elevates DA levels in striatum3-5 at the same time as striatal cholinergic interneurons (CINs) produce a characteristic pause in firing6-8. These phasic responses are thought to create unique, temporally-limited conditions that motivate action and promote learning9-14. However, the dynamics of DA and ACh outside explicitly-rewarded situations remain poorly understood. Here we show that extracellular levels of DA and ACh fluctuate spontaneously in the striatum of mice and maintain the same temporal relationship as that evoked by reward. We show that this neuromodulatory coordination does not arise from direct interactions between DA and ACh within striatum. Periodic fluctuations in ACh are instead controlled by glutamatergic afferents, which act to locally synchronize spiking of striatal cholinergic interneurons. Together, our findings reveal that striatal neuromodulatory dynamics are autonomously organized by distributed extra-striatal afferents across behavioral contexts. The dominance of intrinsic reward-like rhythms in DA and ACh offers novel insights for explaining how reward-associated neural dynamics emerge and how the brain motivates action and promotes learning from within.
Low noise HRTFs and delay line corrections are detrimental to the prediction of ITD discrimination thresholds from environmental statistics
Authors: Gutiérrez Camperos Maria Juliana , Gonçalves Thaís Caroline , Marin Bóris , Pavão Rodrigo
Published: September 2022

Interaural Time Difference (ITD) is the main cue for azimuthal auditory perception in humans. ITDs at each frequency contribute differently to azimuth discrimination, which can be quantified by their azimuthal Fisher Information. Consistently, human ITD discrimination thresholds are predicted by the azimuthal information. However, this prediction is poor for frequencies below 500 Hz. Such poor prediction could be ascribed to the strategy of quantifying azimuthal information using HRTFs obtained in unnaturalistic anechoic chambers or by using a direct method which does not incorporate the delay lines proposed by the Jeffress-Colburn model. In the present study, we obtained ITD discrimination thresholds from extensive sampling across frequency and ITD, and applied multiple strategies for quantifying azimuthal information. These strategies employed HRTFs obtained in realistic and anechoic chambers, with and without considering delay lines. We found that ITD discriminability thresholds across the complete range of frequencies are better predicted by azimuthal information conveyed by ITD cues when (1) we use naturalistic high-noise HRTFs, and (2) ITD delay compensation is not applied. Our results support that auditory perception is shaped by natural environments, which include high reverberation in low frequencies. Moreover, we also suggest that delay lines are not a crucial feature for determining ITD discrimination thresholds in the human auditory system.

GRAPHICAL ABSTRACT
Dual role of brain endothelial Gpr126 in blood-brain barrier development and ischemic stroke
Authors: Kakogiannos Nikolaos , Scalise Anna Agata , Martini Emanuele , Maderna Claudio , Magni Serena , Gullotta Giorgia Serena , Lampugnani Maria Grazia , Iannelli Fabio , Beznoussenko Galina V. , Mironov Alexander A. , Cerutti Camilla , Bentley Katie , Philippides Andrew , Zanardi Federica , Bacigaluppi Marco , Martino Gianvito , Dejana Elisabetta , Giannotta Monica
Published: September 2022

The blood–brain barrier (BBB) acquires unique properties for regulation of the neuronal function during development. The genesis of the BBB coupled with angiogenesis is orchestrated by the Wnt/β-catenin signaling pathway. Aside from the importance of Wnt/β-catenin signaling, the molecular mechanisms that regulate these processes are poorly understood. Here, we identify the brain endothelial adhesion G-protein–coupled receptor Gpr126 as a novel target gene of Wnt/β-catenin signaling that is required for postnatal BBB development, and its expression is detrimental for ischemic stroke in adults. We show that Gpr126 expression is high in mouse brain endothelium during BBB formation, but decreases in the adult. Inactivation of Gpr126 in postnatal endothelial cells results in vessel enlargement and impairs acquisition of the BBB characteristics, such as increased neurovascular permeability, and reduced basement membrane protein deposition and pericyte coverage. Mechanistically, Gpr126 is required during developmental angiogenesis to promote endothelial cell migration, acting via an interaction between Lrp1 and α3β1-integrin, which couples vessel morphogenesis to BBB formation. Interestingly, in adult mice with an established BBB, the lack of Gpr126 expression in acute ischemic stroke is protective and coupled with reduced microglia activation, which contributes to an improved neurological outcome. These data identify Gpr126 as a promising therapeutic target to treat ischemic stroke.
A small-molecule myosin inhibitor as a targeted multi-stage antimalarial
Authors: Trivedi Darshan V. , Karabina Anastasia , Bergnes Gustave , Racca Alice , Wander Heba , Jung Seongwon , Mittal Nimisha , Huijs Tonnie , Ouchida Stephanie , Ruijgrok Paul V. , Song Dan , Wittlin Sergio , Mukherjee Partha , Chakraborty Arnish , Winzeler Elizabeth A. , Burrows Jeremy N. , Laleu Benoît , Spudich Annamma , Ruppel Kathleen , Dechering Koen , Nag Suman , Spudich James A.
Published: September 2022

Malaria is a devastating disease that resulted in an estimated 627,000 deaths in 2020. About 80% of those deaths were among children under the age of five. Our approach is to develop small molecule inhibitors against cytoskeletal targets that are vital components of parasite function, essential at multiple stages of parasite infection, can be targeted with high specificity, and are highly druggable. Here we describe KNX-115, which inhibits purifiedPlasmodium falciparummyosin A (PfMyoA) actin-activated ATPase with a potency in the 10s of nanomolar range and >50-fold selectivity against cardiac, skeletal, and smooth muscle myosins. KNX-115 inhibits the blood and liver stages ofPlasmodiumwith an EC50of about 100 nanomolar, with negligible liver cell toxicity. In addition, KNX-115 inhibits sporozoite cell traversal and blocks the gametocyte to oocyst conversion in the mosquito. KNX-115 displays a similar killing profile to pyrimethamine and parasites are totally killed after 96 hours of treatment. In line with its novel mechanism of action, KNX-115 is equally effective at inhibiting a panel ofPlasmodiumstrains resistant to experimental and marketed antimalarials.In vitroevolution data likely suggests a refractory potential of KNX-115 in developing parasite resistance.
An unwanted association: the threat to papaya crops by a novel potexvirus in northwest Argentina
Authors: Mederos Dariel Cabrera , Debat Humberto , Torres Carolina , Portal Orelvis , Zapata Margarita Jaramillo , Trucco Verónica , Flores Ceferino , Ortiz Claudio , Badaracco Alejandra , Acuña Luis , Nome Claudia , Quito-Ávila Diego , Bejerman Nicolás , Collazo Onias Castellanos , Sánchez-Rodríguez Aminael , Giolitti Fabián
Published: September 2022

An emerging virus isolated from papaya (Carica papaya) crops in northwestern (NW) Argentina was sequenced and characterized using next-generation sequencing. The resulting genome is 6,667-nt long and encodes five open reading frames in an arrangement typical of other potexviruses. This virus appears to be a novel member within the genus Potexvirus. Blast analysis of RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes showed the highest amino acid sequence identity (67% and 71%, respectively) with pitaya virus X. Based on nucleotide sequence similarity and phylogenetic analysis, the name papaya virus X is proposed for this newly characterized potexvirus that was mechanically transmitted to papaya plants causing chlorotic patches and severe mosaic symptoms. RT-PCR based detection of papaya virus X (PapVX) revealed that it is widely present in papaya crops from NW Argentina. The prevalence of PapVX, which seems to be restricted to the NW region of Argentina, and the fact that it has only been detected in this region could be associated with a recent emergence or adaptation of this virus to papaya in NW Argentina.
The imprinted Mir483 is a growth suppressor and metabolic regulator functioning through IGF1
Authors: Sandovici Ionel , Fernandez-Twinn Denise S. , Campbell Niamh , Cooper Wendy N. , Sekita Yoichi , Zvetkova Ilona , Ferland-McCollough David , Prosser Haydn M. , Oyama Lila M. , Cimadomo Danilo , de Queiroz Karina Barbosa , Cheuk Cecilia S.K. , Smith Nicola M. , Kay Richard G. , Hoelle Katharina , Smith Noel H. , Geyer Stefan H. , Reissig Lukas F. , Weninger Wolfgang J. , Siddle Kenneth , Willis Anne E. , Bushell Martin , Ozanne Susan E. , Constância Miguel
Published: September 2022

Mir483 is a conserved and highly expressed microRNA in placental mammals, embedded within the Igf2 gene. Here, we uncover the control mechanisms and physiological functions of Mir483 in vivo, by generating constitutive loss-of-function and over-expressing mice. Mir483 expression is imprinted and dependent on the Igf2 promoters and Igf2/H19 imprinting control region. Over-expression of Mir483 causes severe mid-gestation fetal, but not placental, growth restriction, and late lethality. Fetal death is prevented by restoring Mir483 to endogenous levels using an inducible transgenic system. Continuous postnatal Mir483 over-expression induces growth stunting, elevated hepatic lipid content, increased adiposity, reduced local and systemic IGF1 levels and increased GH. The growth phenotypes are rescued by IGF1 infusion. Our findings provide evidence for a novel functional antagonism between a growth-suppressor microRNA and its growth-promoter host gene, and suggest that Mir483 evolved to limit excessive tissue growth through repression of IGF ligand signalling.
Acetylation of a fungal effector that translocates host PR1 facilitates virulence
Authors: Li Jingtao , Ma Xiaoying , Wang Chenyang , Liu Sihui , Yu Gang , Gao Mingming , Qian Hengwei , Liu Mengjie , Luisi Ben F. , Gabriel Dean W. , Liang Wenxing
Published: September 2022

Pathogens utilize a panoply of effectors to manipulate plant defense. However, despite their importance, relatively little is actually known about regulation of these virulence factors. Here, we show that the effector FolSvp1, secreted from fungal pathogenFusarium oxysporumf. sp.lycopersici(Fol) directly binds and translocates the tomato pathogenesis-related protein1, SlPR1, from the apoplast outside the plasma membrane to the host nucleus via its nuclear localization signal. Relocation of SlPR1 abolishes generation of the defense signaling peptide, CAPE1, from its C-terminus, and as a consequence, facilitates pathogen invasion of plants. The action of FolSvp1 requires covalent modification by acetylation for full virulence in host tomato tissues. The modification is catalyzed by theFolFolArd1 lysine acetyltransferase prior to secretion. Addition of an acetyl group to one residue, K167, prevents ubiquitination-dependent degradation of FolSvp1 in bothFoland plant cells with different mechanisms, allowing it to function normally in fungal invasion. Either inactivation of FolSvp1 or removal of the acetyl group on K167 leads to impaired pathogenicity ofFol. These findings indicate that acetylation can regulate the stability of effectors of fungal plant pathogens with impact on virulence.
Accurate prediction of nucleic acid and protein-nucleic acid complexes using RoseTTAFoldNA
Authors: Baek Minkyung , McHugh Ryan , Anishchenko Ivan , Baker David , DiMaio Frank
Published: September 2022

Protein-nucleic acid complexes play critical roles in biology. Despite considerable recent advances in protein structure prediction, the prediction of the structures of protein-nucleic acid complexes without homology to known complexes is a largely unsolved problem. Here we extend the RoseTTAFold end-to-end deep learning approach to modeling of nucleic acid and protein-nucleic acid complexes. We develop a single trained network, RoseTTAFoldNA, that rapidly produces 3D structure models with confidence estimates for protein-DNA and protein-RNA complexes, and for RNA tertiary structures. In all three cases, confident predictions have considerably higher accuracy than current state of the art methods. RoseTTAFoldNA should be broadly useful for modeling the structure of naturally occurring protein-nucleic acid complexes, and for designing sequence specific RNA and DNA binding proteins.
STAT3 promotes RNA polymerase III-directed transcription by controlling the miR-106a-5p/TP73 axis
Authors: Zhang Cheng , Zhao Shahsha , Deng Huan , Zhang Shihua , Wang Juan , Song Xiaoye , Yu Deen , Zhang Yue , Deng Wensheng
Published: September 2022

Abstracts

Deregulation of Pol III products causes a range of diseases, including neural diseases and cancers. However, the pathways and factors that control Pol III-directed transcription have yet to be elucidated. Here, we show that STAT3 positively regulates the activities of Pol III-dependent transcription and cancer cell growth. RNA-seq analysis revealed that STAT3 inhibits the expression of TP73, a member of the p53 family. We found that TP73 is not only required for the regulation of Pol III-directed transcription mediated by STAT3 but also independently suppresses the synthesis of Pol III products. Mechanistically, TP73 can disrupt the assembly of TFIIIB subunits and inhibit their occupancies at Pol III target loci by interacting with TFIIB subunit TBP. MiR-106a-5p can activate Pol III-directed transcription by targeting the TP73 mRNA 3’ UTR to reduce TP 73 expression. We show that STAT3 activates the expression of miR-106a-5p by binding to the microRNA promoter, indicating that miR-106a-5p links STAT3 to TP73 and Pol III transcription. Collectively, these findings indicate that STAT3 functions as a positive regulator in Pol III-directed transcription by controlling the miR-106a-5p/TP73 axis.
Does Functional Recovery Imply Stable Circuitry in the Spinal Animal?
Authors: Refy Omar , Geyer Hartmut
Published: September 2022

Spinal animals can regain locomotor function through gait training. However, the neural processes involved in this recovery are poorly understood. Here we use computer simulation to address if the reorganization of spinal circuits associated with the functional recovery leads to meaningful, stable circuitry function. Specifically, we develop a neuromuscular model of a spinalized rat whose circuitry can adapt based on two alternative Hebbian learning strategies, one designed to guide the circuitry back to its normal pre-injury state and the other designed to destabilize it and drive it into saturation. Exposing the model to simulated gait training, we find that both strategies lead to recovery of locomotor function as defined by the outcome measures reported in studies with spinal rats. If anything, the results obtained with the destabilizing learning strategy seem to agree more with animal observations, since it produces similarly excessive amplitudes in muscle activity. Our results suggest that gait training of spinalized animals does not necessarily effect a meaningful recovery of their spinal circuitry function. More experimental work should be directed to clarify this point, as it may have grave implications for the potential of gait rehabilitation in patients with motor complete injuries of the spinal cord.
Silicon as a microfluidic material for imaging and incubation of droplets
Authors: Lobato-Dauzier Nicolas , Deteix Robin , Gines Guillaume , Baccouche Alexandre , Hapsianto Benediktus Nixon , Okumura Shu , Mariette Guilhem , Belharet Djaffar , Queste Samuel , Jalabert Laurent , Denoual Matthieu , Rondelez Yannick , Toshiyoshi Hiroshi , Fujita Hiroyuki , Kim Soo Hyeon , Fujii Teruo , Genot Anthony J.
Published: September 2022

Droplet microfluidics has become a powerful tool in life sciences, underlying digital assays, single-cell sequencing or directed evolution, and it is making foray in physical sciences as well. Imaging and incubation of droplets are crucial, yet they are encumbered by the poor optical, thermal and mechanical properties of PDMS - thede factomaterial for microfluidics. Here we show that silicon is an ideal material for droplet chambers. Si chambers pack droplets in a crystalline and immobile monolayer, are immune to evaporation or sagging, boost the number of collected photons, and tightly control the temperature field sensed by droplets. We use the mechanical and optical benefits of Si chambers to image ∼1 million of droplets from a multiplexed digital assay - with an acquisition rate similar to the best in-line methods. Lastly, we demonstrate their applicability with a demanding assay that maps the thermal dependence of Michaelis-Menten constants with an array of ∼150,000. The design of the Si chambers is streamlined to avoid complicated fabrication and improve reproducibility, which makes Silicon a complementary material to PDMS in the toolbox of droplet microfluidics.

Significance Statement

As the technological engine behind single-cell sequencing and digital assays, droplets microfluidics has revolutionized life science and molecular diagnosis, and is making foray into physical sciences as well. Observing droplets in a controlled manner is becoming crucial, but PDMS - thede factomaterial of microfluidics – hampers imaging and incubation. Here we revisit silicon as a microfluidic material and show that its superior mechanical, optical and thermal performances improve the throughput and operation of droplets assay.
GLKs directly regulate carotenoid biosynthesis via interacting with GBFs in nuclear condensates in plants
Authors: Sun Tianhu , Zeng Shaohua , Wang Xin , Owens Lauren A. , Fe Zhangjun , Zhao Yunde , Mazourek Michael , Giovannoni James G. , Li Li
Published: September 2022

Carotenoids are vital photosynthetic pigments for plants and provide essential nutrients for humans. However, our knowledge of the regulatory control of carotenoid biosynthesis remains limited. Golden2-like transcription factors (GLKs) are widely recognized as essential and conserved factors for chloroplast development and the major regulators of chlorophyll biosynthesis. Yet the molecular mechanisms by which GLKs transcriptionally activate their target genes are unclear. Here, we report that GLKs directly regulate carotenoid biosynthesis in a G-box Binding Factor (GBF)-dependent manner. Bothin vitroandin vivostudies reveal that GLKs physically interact with GBFs. Through the direct binding of GBFs to the G-box motif, the GLK-GBF regulatory module transcriptionally activatesphytoene synthase(PSY), the gene encoding the rate-limiting enzyme for carotenoid biosynthesis. The ability ofGLKsto promote carotenoid and chlorophyll biosynthesis is greatly diminished in the Arabidopsisgbf1/2/3triple knockout mutants, showing the requirement of GBFs for GLK function. GLKs and GBFs form liquid-liquid phase separation-mediated nuclear condensates as the compartmented and concentrated transcriptional complexes. Our findings uncover a novel and conserved regulatory module for photosynthetic pigment biosynthesis through formation of GLK-GBF transcriptional complexes and nuclear biomolecular condensates in plants.

One-sentence summary

GLKs transcriptionally regulate photosynthetic pigment synthesis in a GBF-dependent manner and are associated with the formation of phase separation-mediated nuclear condensates.
Thyroid Ablation Alters Passive Stiffness and Swimming Kinematics in Zebrafish
Authors: Parikh Pranav , Nguyen Stacy , McMenamin Sarah , Kenaley Christopher P.
Published: September 2022

Locomotion behavior is ultimately determined by the integration between active and passive tissues of an organism, but little is known about how these properties develop or are maintained. In this study, we used zebrafish (Danio rerio) to address the effects of a developmental hormone on morphogenesis and mechanical integration during swimming. We analyzed common kinematic variables and estimated intervertebral joint (IVJ) stiffness of zebrafish reared under different thyroid hormone profiles (euthyroid and hypothyroid) swimming during two different forward speeds, 5 and 10 BL·s−1. We found that zebrafish reared under hypothyroid conditions swam with higher trailing-edge amplitude, a larger amplitude envelope, longer propulsive wavelengths, and lower values of lateral strain in posterior regions at both speeds. IVJ second moment area about the bending axis was greater in the TH-, a result of a change in vertebral shape compared to wildtype fish. We conclude that thyroid hormone contributes to axial design during development and therefore has an important role in determining flexural stiffness and the swimming behaviors that are affected by this important property.
Dynamic fluctuations in ascending heart–to–brain communication under mental stress
Authors: Candia-Rivera Diego , Norouzi Kian , Ramsøy Thomas Zoëga , Valenza Gaetano
Published: September 2022

Dynamical information exchange between central and autonomic nervous systems, as referred to functional brain–heart interplay, occurs during emotional and physical arousal. It is well documented that physical and mental stress lead to sympathetic activation. Nevertheless, the role of autonomic inputs in nervous-system-wise communication under mental stress is yet unknown. In this study, we estimated the causal and bidirectional neural modulations between EEG oscillations and peripheral sympathetic and parasympathetic activities using a recently proposed computational framework for a functional brain–heart interplay assessment, namely the sympathovagal synthetic data generation model. Mental stress was elicited in 37 healthy volunteers by increasing their cognitive demands throughout three tasks associated with increased stress levels. Stress elicitation induced an increased variability in sympathovagal markers, as well as increased variability in the directional brain–heart interplay. The observed heart–to–brain interplay was primarily from sympathetic activity targeting a wide range of EEG oscillations, whereas variability in the efferent direction seemed mainly related to EEG oscillations in the gamma band. These findings extend current knowledge on stress physiology, which mainly referred to top-down neural dynamics. Our results suggest that mental stress may not cause an increase in sympathetic activity exclusively as it initiates a dynamic fluctuation within brain-body networks including bidirectional interactions at a brain–heart level. We conclude that directional brain–heart interplay measurements may provide suitable biomarkers for a quantitative stress assessment and bodily feedback may modulate the perceived stress caused by increased cognitive demand.