bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection, spread and phylogeny of meticillin-resistant Staphylococcus aureus sequence type 45 in Taiwan
Authors: Huang Yhu-Chering , Chen Chih-Jung , Lauderdale Tsai-Ling Yang
Published: April 2021

Meticillin-resistant

Staphylococcus aureus

(MRSA) sequence type (ST) 45 was reported in the literature to have been first identified in 2006 in Taiwan. The present study was carried out to explore and trace the emergence, transmission and evolutional dynamics of MRSA ST45 in Taiwan. We identified MRSA ST45 isolates retrospectively from two collections of MRSA isolates, namely TSAR (Taiwan Surveillance of Antimicrobial Resistance) surveys and the CGMH (Chang Gung Memorial Hospital)-based laboratory collection. Representative ST45 isolates were selected for whole-genome sequencing (WGS) analysis. A total of 9554 MRSA isolates was included in this study. Among the 3766 MRSA isolates biennially collected from TSAR surveys between 1998 and 2014, ST45 accounted for 133 (3.53 %) MRSA isolates, was first identified in 2004, and the prevalence rate peaked in 2010 (up to 10.77 %). Among the 5788 MRSA isolates collected between 1995 and 2017 by the CGMH-based laboratory, 257 isolates (4.44 %) were characterized as ST45, with most identified from nursing homes since 2012. Of the 75 isolates randomly selected for WGS, two clades were identified. The major clade, clade II, comprised 63 isolates and was phylogenetically relatively close to those isolates identified from Singapore. All but one of the isolates in clade I, the minor clade, were identified from non-Taiwanese people, mostly from newly recruited foreign workers in 2017, and were phylogenetically relatively close to one isolate from the USA (CA-347). Conclusively, the emergence of MRSA ST45 strain in Taiwan can be traced back to 2004 and the strain is connected to South-East Asian countries. Since its emergence, transmission and spread of MRSA ST45 has occurred in Taiwan.
Broadly-reactive IgG responses to heterologous H5 prime-boost influenza vaccination are shaped by antigenic relatedness to priming strains
Authors: Wang Jiong , Li Dongmei , Perry Sheldon , Hilchey Shannon P. , Wiltse Alexander , Treanor John J. , Sangster Mark Y. , Zand Martin S.
Published: April 2021

Prime-boost vaccinations of humans with different H5 strains have generated broadly protective antibody levels. However, the effect of an individual’s H5 exposure history on antibody responses to subsequent H5 vaccination is poorly understood. To investigate this, we analyzed the IgG response to H5 A/Indonesia/5/2005 (Ind05) vaccination in three cohorts: (1) a double primed group that received two H5 vaccinations: A/Vietnam/203/2004 (Vie04) 5 years ago and A/Hong Kong/156/1997 (HK97) 11 years ago, (2) a single primed group that received Vie04 5 years ago, and (3) an H5-naïve group that received two doses of the Ind05 vaccine 28 days apart. Hemagglutinin (HA)-reactive IgG levels were estimated by multiplex assay against an HA panel that included 21 H5 strains and 9 other strains representing H1, H3, H7, and H9 subtypes. Relative HA antibody landscapes were generated to quantitatively analyze the magnitude and breadth of antibody binding after vaccination. We found that short-interval prime-boosting with the Ind05 in the naïve group generated a low anti-H5 response. Both primed groups generated robust antibody responses reactive to a broad range of H5 strains after boosting with Ind05; IgG antibody levels persisted longer in subjects who had been double primed years ago. Notably, the IgG responses were strongest against the first priming H5 strain, that reflecting influenza virus immune imprinting. Finally, the broad anti-H5 IgG response was stronger against strains having a small antigenic distance to the initial priming strain.

IMPORTANCE

The antigenic shift and draft of hemagglutinin (HA) in influenza viruses is accepted as one of the major reasons for immune evasion. The analysis of B cell immune responses to influenza infection and vaccination is complicated by the impact of exposure history and antibody cross-reaction between antigenically similar influenza strains. To assist in such analyses, the influenza “antibody landscape” method has been used to analyze and visualize the relationship of antibody mediated immunity to the antigenic distance between influenza strains. In this study, we describe a “relative antibody landscape” method, calculating the antigenic distance between the vaccine influenza strain and other H5 strains, and using this relative antigenic distance to plot with the anti-H5 IgG levels post-vaccination. This new method quantitatively estimates and visualizes the correlation between the humoral response to a particular influenza strain, and the antigenic distance to other strains. Our findings demonstrate the effect of H5 exposure history on H5 vaccine responses quantified by the relative antibody landscape method.
Inhaled budesonide for COVID-19 in people at higher risk of adverse outcomes in the community: interim analyses from the PRINCIPLE trial
Authors:   PRINCIPLE Collaborative Group, Yu Ly-Mee , Bafadhel Mona , Dorward Jienchi , Hayward Gail , Saville Benjamin R , Gbinigie Oghenekome , Van Hecke Oliver , Ogburn Emma , Evans Philip H , Thomas Nicholas PB , Patel Mahendra G , Berry Nicholas , Detry Michelle A. , Saunders Christina T. , Fitzgerald Mark , Harris Victoria , de Lusignan Simon , Andersson Monique I , Barnes Peter J , Russell Richard EK , Nicolau Dan V , Ramakrishnan Sanjay , Hobbs FD Richard , Butler Christopher C
Published: April 2021

BACKGROUND

Inhaled budesonide has shown efficacy for treating COVID-19 in the community but has not yet been tested in effectiveness trials.

METHODS

We performed a multicenter, open-label, multi-arm, adaptive platform randomized controlled trial involving people aged ≥65 years, or ≥50 years with comorbidities, and unwell ≤14 days with suspected COVID-19 in the community (PRINCIPLE). Participants were randomized to usual care, usual care plus inhaled budesonide (800µg twice daily for 14 days), or usual care plus other interventions. The co-primary endpoints are time to first self-reported recovery, and hospitalization/death related to COVID-19, both measured over 28 days from randomisation and analysed using Bayesian models.

RESULTS

The trial opened on April 2, 2020. Randomization to inhaled budesonide began on November 27, 2020 and was stopped on March 31, 2021 based on an interim analysis using data from March 4, 2021. Here, we report updated interim analysis data from March 25, 2021, at which point the trial had randomized 4663 participants with suspected COVID-19. Of these, 2617 (56.1%) tested SARS-CoV-2 positive and contributed data to this interim budesonide primary analysis; 751 budesonide, 1028 usual care and 643 to other interventions. Time to first self-reported recovery was shorter in the budesonide group compared to usual care (hazard ratio 1.208 [95% BCI 1.076 – 1.356], probability of superiority 0.999, estimated benefit [95% BCI] of 3.011 [1.134 – 5.41] days). Among those in the interim budesonide primary analysis who had the opportunity to contribute data for 28 days follow up, there were 59/692 (8.5%) COVID-19 related hospitalizations/deaths in the budesonide group vs 100/968 (10.3%) in the usual care group (estimated percentage benefit, 2.1% [95% BCI −0.7% – 4.8%], probability of superiority 0.928).

CONCLUSIONS

In this updated interim analysis, inhaled budesonide reduced time to recovery by a median of 3 days in people with COVID-19 with risk factors for adverse outcomes. Once 28 day follow up is complete for all participants randomized to budesonide, final analyses of time to recovery and hospitalization/death will be published. (Funded by the National Institute of Health Research/ United Kingdom Research Innovation [MC_PC_19079]; PRINCIPLE ISRCTN number, ISRCTN86534580.)
Quantatitive Analysis of Conserved Sites on the SARS-CoV-2 Receptor-Binding Domain to Promote Development of Universal SARS-Like Coronavirus Vaccines
Authors: Wang Siling , Wu Dinghui , Xiong Hualong , Wang Juan , Tang Zimin , Chen Zihao , Wang Yizhen , Zhang Yali , Ying Dong , Lin Xue , Liu Chang , Guo Shaoqi , Tian Weikun , Lin Yajie , Zhang Xiaoping , Yuan Quan , Yu Hai , Zhang Tianying , Zheng Zizheng , Xia Ningshao
Published: April 2021

Although vaccines have been successfully developed and approved against SARS-CoV-2, it is still valuable to perform studies on conserved antigenic sites for preventing possible pandemic-risk of other SARS-like coronavirus in the future and prevalent SARS-CoV-2 variants. By antibodies obtained from convalescent COVID-19 individuals, receptor binding domain (RBD) were identified as immunodominant neutralizing domain that efficiently elicits neutralizing antibody response with on-going affinity mature. Moreover, we succeeded to define a quantitative antigenic map of neutralizing sites within SARS-CoV-2 RBD, and found that sites S2, S3 and S4 (new-found site) are conserved sites and determined as subimmunodominant sites, putatively due to their less accessibility than SARS-CoV-2 unique sites. P10-6G3, P07-4D10 and P05-6H7, respectively targeting S2, S3 and S4, are relatively rare antibodies that also potently neutralizes SARS-CoV, and the last mAbs performing neutralization without blocking S protein binding to receptor. Further, we have tried to design some RBDs to improve the immunogenicity of conserved sites. Our studies, focusing on conserved antigenic sites of SARS-CoV-2 and SARS-CoV, provide insights for promoting development of universal SARS-like coronavirus vaccines therefore enhancing our pandemic preparedness.
Luminal Flow Actuation Generates Coupled Shear and Strain in a Microvessel-on-Chip
Authors: Dessalles Claire A. , Ramón-Lozano Clara , Babataheri Avin , Barakat Abdul I.
Published: April 2021

In the microvasculature, blood flow-derived forces are key regulators of vascular structure and function. Consequently, the development of hydrogel-based microvessel-on-chip systems that strive to mimic the in vivo cellular organization and mechanical environment has received great attention in recent years. However, despite intensive efforts, current microvessel- on-chip systems suffer from several limitations, most notably failure to produce physiologically relevant wall strain levels. In this study, a novel microvessel-on-chip based on the templating technique and using luminal flow actuation to generate physiologically relevant levels of wall shear stress and circumferential stretch is presented. Normal forces induced by the luminal pressure compress the surrounding soft collagen hydrogel, dilate the channel, and create large circumferential strain. The fluid pressure gradient in the system drives flow forward and generates realistic pulsatile wall shear stresses. Rigorous characterization of the system reveals the crucial role played by the poroelastic behavior of the hydrogel in determining the magnitudes of the wall shear stress and strain. The experimental measurements are combined with an analytical model of flow in both the lumen and the porous hydrogel to provide an exceptionally versatile user manual for an application-based choice of parameters in microvessels-on-chip. This unique strategy of flow actuation adds a dimension to the capabilities of microvessel-on-chip systems and provides a more general framework for improving hydrogel-based in vitro engineered platforms.

Abstract Figure
Rapid appetitive transitions are sculpted by amygdala to accumbens pathways
Authors: Millan E. Zayra , Lim Jun Hua , Power John M. , McNally Gavan P.
Published: April 2021

Foraging, pursuit, and predation rapidly transition into behavioral quiescence during reward capture and consumption. While appetitive-consummatory dissociations are embedded at both psychological and neural levels, the mechanisms controlling switches or transitions between appetitive seeking and consummatory behaviors remain poorly understood. Here we identify the BLA→AcbSh pathway as critical to these transitions by showing that this pathway inhibits the appetitive seeking response in the presence of consummatory demands. Using an appetitive cue-discrimination task in male rats, we show that reward delivery is a significant driver of seeking inhibition and that a BLA→AcbSh pathway mediates this inhibition. This role in suppressing seeking responses during periods of consumption was not due to a general suppression of behavior because responding to other cues during the same test was unaffected. Moreover, it was specific to the BLA→AcbSh pathway, because the contribution of the BLA→AcbC pathway to appetitive switching was distinct and modest. State-dependent silencing of BLA→AcbSh revealed that the modulation of seeking before and after reward delivery are co-dependent. Finally, we found that BLA terminals in AcbSh have functional connectivity to LH-projecting AcbSh neurons, thereby identifying a BLA→AcbSh→LH pathway as a putative route for the rapid regulation of appetitive behaviors. Taken together, these findings suggest that the BLA→AcbSh pathway is a core component of an appetitive switching system, recruited under conditions requiring rapid or dynamic shifts in appetitive behavior, and that this pathway enables these shifts by actively inhibiting seeking.

Significance statement

Foraging, pursuit, and predation quickly transition into behavioral quiescence during reward capture and consumption. These transitions are critical for flexible and responsive sequences of behavior. Here we show that behavioral transitions are actively controlled at the limbic-striatal interface. We identify reward receipt as a proximal trigger for transition between reward seeking and taking, we identify active inhibition as the functional operation of this transition, and we identify the basolateral amygdala→accumbens shell pathway as critical to this functional operation.
The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding
Authors: Breimann Laura , Morao Ana Karina , Kim Jun , Jimenez David Sebastian , Maryn Nina , Bikkasani Krishna , Carrozza Michael J , Albritton Sarah E , Kramer Maxwell , Street Lena Annika , Cerimi Kustrim , Schumann Vic-Fabienne , Bahry Ella , Preibisch Stephan , Woehler Andrew , Ercan Sevinç
Published: April 2021

Condensin is a multi-subunit SMC complex that binds to and compacts chromosomes. Here we addressed the regulation of condensin binding dynamics usingC. eleganscondensin DC, which represses X chromosomes in hermaphrodites fordosagecompensation. We established fluorescence recovery after photobleaching (FRAP) using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes its binding. Next, we performed FRAP in the background of several chromatin modifier mutants that cause varying degrees of X-chromosome derepression. The greatest effect was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of condensin DC reduced from ∼30% to 10%. In contrast, a catalytic mutant ofdpy-21did not regulate condensin DC mobility. Hi-C data in thedpy-21null mutant showed little change compared to wild type, uncoupling Hi-C measured long-range DNA contacts from transcriptional repression of the X chromosomes. Together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.
The neural correlates of semantic and grammatical encoding during sentence production in a second language: evidence from an fMRI study using syntactic priming
Authors: Nakagawa Eri , Koike Takahiko , Sumiya Motofumi , Shimada Koji , Makita Kai , Yoshida Haruyo , Yokokawa Hirokazu , Sadato Norihiro
Published: April 2021

Japanese English learners have difficulty speaking Double Object (DO; give B A) than Prepositional Object (PO; give A to B) structures which neural underpinning is unknown. In speaking, syntactic and phonological processing follow semantic encoding, conversion of non-verbal mental representation into a structure suitable for expression. To test whether DO difficulty lies in linguistic or prelinguistic process, we conducted functional magnetic resonance imaging. Thirty participants described cartoons using DO or PO, or simply named them. Greater reaction times and error rates indicated DO difficulty. DO compared with PO showed parieto-frontal activation including left inferior frontal gyrus, reflecting linguistic process. Psychological priming in PO produced immediately after DO and vice versa compared to after control, indicated shared process between PO and DO. Cross-structural neural repetition suppression was observed in occipito-parietal regions, overlapping the linguistic system in pre-SMA. Thus DO and PO share prelinguistic process, whereas linguistic process imposes overload in DO.
The TIR-NBS-LRR protein CSA1 is required for autoimmune cell death in Arabidopsis pattern recognition co-receptorbak1andbir3mutants
Authors: Schulze Sarina , Yu Liping , Ehinger Alexandra , Kolb Dagmar , Saile Svenja C. , Stahl Mark , Franz-Wachtel Mirita , Li Lei , Kasmi Farid El , Cevik Volkan , Kemmerling Birgit
Published: April 2021

The BRI1-associated kinase BAK1/SERK3 is a positive regulator of multiple leucine rich receptor kinase-mediated signaling pathways including pattern triggered immunity (PTI). Absence or overexpression of BAK1 leads to spontaneous cell death formation. BAK1-interacting receptors (BIR) constitutively interact with BAK1, and plants lacking or overexpressing BIR proteins phenocopy the cell death symptoms observed inbak1knock outs or overexpressors. In the interactome of BIR3, the TIR-NBS-LRR protein CONSTITUTIVE SHADE-AVOIDANCE 1 (CSA1) was identified by mass spectrometry. CSA1 physically interacts with BIR proteins and can be detected in complexes with BAK1. Direct interaction was shown only for CSA1 with BIR proteins but not BAK1. Double mutantbak1 bir3genotypes develop strong dwarfism and cell death symptoms that are dependent on EDS1 and salicylic acid. Loss of CSA1 blocksbak1andbak1 bir3-mediated cell death formation thus demonstrating that CSA1 is causal for this type of cell death. We propose that CSA1 guards BIR proteins and initiates autoimmune cell death that is observed when BAK1 BIR complexes are impaired. Our findings reveal how cell death in the absence of BAK1 and BIR3 is executed and links BAK1, a common co-receptor of many pattern recognition receptors, to NLR proteins typically implicated in effector-triggered immunity.
Continuous Theta Burst Stimulation to the Secondary Visual Cortex at 80% Active Motor Threshold Does Not Impair Central Vision in Humans During a Simple Detection Task
Authors: Lasagna Carly A. , Taylor Stephan F. , Lee Taraz G. , Rutherford Saige , Greathouse Tristan , Gu Pan , Tso Ivy F.
Published: April 2021

Continuous theta burst stimulation (cTBS) is a powerful form of repetitive transcranial magnetic stimulation capable of suppressing cortical excitability for up to 50 min. A growing number of studies have applied cTBS to the visual cortex in human subjects to investigate the neural dynamics of visual processing, but few have specifically examined its effects on central vision, which has crucial implications for safety and inference on downstream cognitive effects. The present study assessed the safety of offline, neuronavigated cTBS to V2 by examining its effects on central vision performance. In this single-blind, randomized sham-controlled, crossover study, 17 healthy adults received cTBS (at 80% active motor threshold) and sham to V2 1–2 weeks apart. Their central vision (≤8°) was tested at 1-min (T1) and again at 50-min (T50) post-stimulation. Effects of condition (cTBS vs. sham) and time (T1 vs. T50) on accuracy and reaction time were examined using Bayes factor. Bayes factor results suggested that cTBS did not impair stimulus detection over the entire central visual field nor subfields at T1 or T50. Our results offer the first explicit evidence supporting that cTBS applied to V2 does not create blind spots in the central visual field in humans during a simple detection task. Any subtler changes to vision and downstream visual perception should be investigated in future studies.
A muscle-related contractile tissue specified by myocardin-related transcription factor activity in Porifera
Authors: Colgren J. , Nichols S.A.
Published: April 2021

Muscle-based movement is a hallmark of animal biology, but the evolutionary origins of myocytes – the cells that comprise muscle tissues – are unknown. Sponges (Porifera) provide an opportunity to reconstruct the earliest periods of myocyte evolution. Although sponges are believed to lack muscle, they are capable of coordinated whole-body contractions that purge debris from internal water canals. This behavior has been observed for decades, but their contractile tissues remain uncharacterized; it is an open question whether they have affinity to muscle or non-muscle contractile tissues in other animals. Here, we characterize the endothelial-like lining of water canals (the endopinacoderm) as a primary contractile tissue in the spongeEphydatia muelleri. We find tissue-wide organization of contractile actin-bundles that contain striated-muscle myosin II and transgelin, and that contractions are regulated by the release of internal Ca2+stores upstream of the myosin-light-chain-kinase (MLCK) pathway. Further, we show that the endopinacoderm is developmentally specified by myocardin-related transcription factor (MRTF) as part of an environmentally-inducible transcriptional complex that otherwise is known to function in muscle development, plasticity, and regeneration in other animals. We conclude that both muscle tissues and the endopinacoderm evolved from a common, multifunctional contractile tissue in the animal stem-lineage. Furthermore, as an actin-regulated force-sensor, MRTF-activity offers a mechanism for how water canals dynamically remodel in response to flow and can re-form normally from stem-cells in the absence of the intrinsic positional cues characteristic of embryogenesis in other animals.
Reduction of bundle sheath size boosts cyclic electron flow in C4Setaria viridisacclimated to low light
Authors: Bellasio Chandra , Ermakova Maria
Published: April 2021

When C4leaves are exposed to low light, CO2concentration in the bundle sheath (BS) cells decreases, causing an increase in photorespiration relative to assimilation, and a consequent reduction in biochemical efficiency. These effects can be mitigated by complex acclimation syndromes, which are of primary importance for crop productivity, but not well studied. We unveil an acclimation strategy involving regulation of electron transport processes. Firstly, we characterise anatomy, gas-exchange and electron transport of C4Setaria viridisgrown under low light. Through a purposely developed biochemical model, we resolve the photon fluxes and reaction rates to explain how the concerted acclimation strategies sustain photosynthetic efficiency. Our results show that a smaller BS in low light-grown plants limited leakiness (the ratio of CO2leak rate out of the BS over the rate of supply via C4acid decarboxylation) but sacrificed light harvesting and ATP production. To counter ATP shortage and maintain high assimilation rates, plants facilitated light penetration through the mesophyll and upregulated cyclic electron flow in the BS. This shade tolerance mechanism based on optimisation of light reactions is potentially more efficient than the known mechanisms involving the rearrangement of carbon metabolism, and can potentially lead to innovative strategies for crop improvement.

Significance

We mechanistically link the optical cross-section of leaf compartments with the rate of electron transport, the engagement of cyclic electron flow, the relative rate of ATP and NADPH generation, and fluxes through the carbon metabolism. The striking capacity ofSetaria viridisto counter the decrease in light absorption in the bundle sheath with an increase of cyclic electron flow presents perhaps the most efficient mechanism of shade acclimation.
Respiratory dysfunctions in two rodent models of chronic epilepsy and acute seizures and their link with brainstem serotonin system
Authors: Kouchi Hayet , Ogier Michaël , Dieuset Gabriel , Morales Anne , Georges Béatrice , Rouanet Jean-Louis , Martin Benoît , Ryvlin Philippe , Rheims Sylvain , Bezin Laurent
Published: April 2021

Patients with drug-resistant epilepsy can experience respiratory alterations notably during seizures. The mechanisms underlying this long-term alteration of respiratory function remain unclear. This study aimed at determining in rats whether epilepsy is associated with alterations of both the respiratory function and brainstem serotonin (5-HT) system. Epilepsy was triggered by pilocarpine-inducedstatus epilepticusin rats. 30-50% of epileptic (EPI) rats exhibited sharp decrease of oxygen consumption (SDOC), low metabolic rate of oxygen and slow regular ventilation; these rats were called EPI/SDOC+ rats. These alterations were only detected in rats with chronic epilepsy, independent of behavioral seizures, persisted over the time, and were not associated with death. In these rats, 5-HT fiber density in the nucleustractus solitariuswas below that of control and EPI/SDOC-rats. Both EPI/SDOC+ rats and DBA/2 mice presenting with fatal respiratory arrest following an audiogenic-induced seizure, a model of sudden and expected death in epilepsy, had increased transcript levels of tryptophan hydroxylase 2 (p<0.001 for both strains) and 5-HT presynaptic transporter (rats: p=0.003; mice: p=0.001). Thus, our data support that 5-HT alterations are associated with chronic and acute epilepsy-related respiratory dysfunctions.
Hsp40s display class-specific binding profiles, serving complementary roles in the prevention of tau amyloid formation
Authors: Irwin Rose , Faust Ofrah , Petrovic Ivana , Wolf Sharon Grayer , Hofmann Hagen , Rosenzweig Rina
Published: April 2021

The microtubule-associated protein, tau, is the major subunit of neurofibrillary tangles, forming insoluble, amyloid-type aggregates associated with neurodegenerative conditions, such as Alzheimer’s disease. Tau aggregation, however, can be prevented in the cell by a class of proteins known as molecular chaperones, which play important roles in maintaining protein homeostasis. While numerous chaperones are known to interact with tau, though, little is known about the detailed mechanisms by which these prevent tau aggregation. Here, we describe the effects of the ATP-independent Hsp40 chaperones, DNAJA2 and DNAJB1, on tau amyloid fiber formation and compare these to the well-studied small heat shock protein HSPB1. We find that each chaperone prevents tau aggregation differently, by interacting with distinct sets of tau species along the aggregation pathway and thereby affecting their incorporation into fibers. Whereas HSPB1 only binds tau monomers, DNAJB1 and DNAJA2 recognize aggregation-prone tau conformers and even mature fibers, thus efficiently preventing formation of tau amyloids. In addition, we find that both Hsp40s bind tau seeds and fibers via their C-terminal domain II (CTDII), with DNAJA2 being further capable of recognizing tau monomers by a second, different site in CTDI. These results provide important insight into the molecular mechanism by which the different members of the Hsp40 chaperone family counteract the formation, propagation, and toxicity of tau aggregates. Furthermore, our findings highlight the fact that chaperones from different families and different classes play distinct, but complementary roles in preventing pathological protein aggregation.
Predictors of genomic differentiation within a hybrid taxon
Authors: Cuevas Angelica , Eroukhmanoff Fabrice , Ravinet Mark , Særtre Glenn-Peter , Runemark Anna
Published: April 2021

Hybridization is increasingly recognized as an important evolutionary force. Novel genetic methods now enable us to address how the genomes of parental species are combined to build hybrid genomes. However, we still do not know the relative importance of contingencies, genome architecture and local selection in shaping hybrid genomes. Here, we take advantage of the genetically divergent island populations of Italian sparrow on Crete, Corsica and Sicily to investigate the predictors of genomic variation within a hybrid taxon. We test if differentiation is affected by recombination rate, selection, or variation in ancestry proportion from each parent species. We find that the relationship between recombination rate and differentiation is less pronounced within hybrid lineages than between the parent species, as expected if purging of minor parent ancestry in low recombination regions reduces the variation available for differentiation. In addition, we find that differentiation between islands is correlated with differences in selection in two out of three comparisons. Patterns of within-island selection are correlated across all islands, suggesting that shared selection may mould genomic differentiation. The best predictor of strong differentiation within islands is the degree of differentiation from house sparrow, and hence loci with Spanish sparrow ancestry may vary more freely. Jointly, this suggests that constraints and selection interact in shaping the genomic landscape of differentiation in this hybrid species.
Including random effects in statistical models in ecology: fewer than five levels?
Authors: Gomes Dylan G.E.
Published: April 2021

As generalized linear mixed-effects models (GLMMs) have become a widespread tool in ecology, the need to guide the use of such tools is increasingly important. One common guideline is that one needs at least five levels of a random effect. Having such few levels makes the estimation of the variance of random effects terms (such as ecological sites, individuals, or populations) difficult, but it need not muddy one’s ability to estimate fixed effects terms – which are often of primary interest in ecology. Here, I simulate ecological datasets and fit simple models and show that having too few random effects terms does not influence the parameter estimates or uncertainty around those estimates for fixed effects terms. Thus, it should be acceptable to use fewer levels of random effects if one is not interested in making inference about the random effects terms (i.e. they are ‘nuisance’ parameters used to group non-independent data). I also use simulations to assess the potential for pseudoreplication in (generalized) linear models (LMs), when random effects are explicitly ignored and find that LMs do not show increased type-I errors compared to their mixed-effects model counterparts. Instead, LM uncertainty (and p values) appears to be more conservative in an analysis with a real ecological dataset presented here. These results challenge the view that it is never appropriate to model random effects terms with fewer than five levels – specifically when inference is not being made for the random effects, but suggest that in simple cases LMs might be robust to ignored random effects terms. Given the widespread accessibility of GLMMs in ecology and evolution, future simulation studies and further assessments of these statistical methods are necessary to understand the consequences of both violating and blindly following simple guidelines.
An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput screens
Authors: Coukos Robert , Yao David , Sanchez Mateo I. , Strand Eric T. , Weissman Jonathan S. , Bassik Michael C. , Ting Alice Y.
Published: April 2021

The trafficking of specific protein cohorts to the correct subcellular location at the correct time is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or FACS. To broadly empower the study of protein trafficking processes with gene perturbation, we developed a genetically-encoded molecular tool named HiLITR. HiLITR converts protein colocalization into proteolytic release of a membrane-anchored transcription factor, which drives the expression of a chosen reporter gene. Using HiLITR in combination with FACS-based CRISPRi screening in human cell lines, we identify genes that influence the trafficking of mitochondrial and ER tail-anchored proteins. We show that loss of the SUMO E1 component SAE1 results in the mislocalization and destabilization of mitochondrial tail-anchored proteins. We also demonstrate a distinct regulatory role for EMC10 in the ER membrane complex, opposing the transmembrane-domain insertion activity of the complex. Through transcriptional integration of complex cellular functions, HiLITR expands the scope of biological processes that can be studied by genetic perturbation screening technologies.
Recurring adaptive introgression of a supergene variant that determines social organization
Authors: Stolle Eckart , Pracana Rodrigo , López-Osorio Federico , Priebe Marian K. , Hernández Gabriel Luis , Castillo-Carrillo Claudia , Arias Maria Cristina , Paris Carolina Ivon , Bollazzi Martin , Priyam Anurag , Wurm Yannick
Published: April 2021

Introgression has been proposed as an essential source of adaptive genetic variation. However, a key barrier to adaptive introgression is that recombination can break down combinations of alleles that underpin many traits. This barrier might be overcome in supergene regions, where suppressed recombination leads to joint inheritance across many loci. Here, we study the evolution of a large supergene region that determines a major social and ecological trait inSolenopsisfire ants: whether colonies have one queen or multiple queens. Using coalescent-based phylogenies built from the genomes of 365 haploid fire ant males, we show that the supergene variant responsible for multiple-queen colonies evolved in one species and repeatedly spread to other species through introgressive hybridization. This finding highlights how supergene architecture can enable a complex adaptive phenotype to recurrently permeate species boundaries.
Energy expenditure does not explain step length-width choices during walking
Authors: Antos Stephen A. , Kording Konrad P. , Gordon Keith E.
Published: April 2021

Healthy young adults have a most preferred walking speed, step length, and step width that are close to energetically optimal. However, people can choose to walk with a multitude of different step lengths and widths, which can vary in both energy expenditure and preference. Here we further investigate step length-width preferences and their relationship to energy expenditure. In line with a growing body of research, we hypothesized that people’s preferred stepping patterns would not be fully explained by metabolic energy expenditure. To test this hypothesis we used a two-alternative forced-choice paradigm. Fifteen participants walked on an oversized treadmill. Each trial participants experienced two stepping patterns and then chose the pattern they preferred. Over time, we adapted the choices such that there was 50% chance of choosing one pattern over another (equally preferred). If people’s preferences are based solely on metabolic energy expenditure, then these equally preferred stepping patterns should have equal energy expenditure. We found that energy expenditure differed across equally preferred step length-width patterns (p < 0.001). On average, longer steps with higher energy expenditures were preferred over shorter and wider steps with lower energy expenditures (p < 0.001). We also asked participants to rank a set of shorter, wider, and longer steps from most preferred to least preferred, and from most energy expended to least energy expended. Only 7/15 participants had the same rankings for their preferences and perceived energy expenditure. Our results suggest that energy expenditure is not the only factor influencing a person’s conscious gait choices.
CRISPR Knock-in Designer: automatic oligonucleotide design software to introduce point mutations using CRISPR/Cas9
Authors: Prykhozhij Sergey V. , Rajan Vinothkumar , Ban Kevin , Berman Jason N.
Published: April 2021

Knock-in of precise point mutations into protein-coding genes has been one of the earliest and most important applications of Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9. The ability to perform such precise gene editing is crucial to interrogate the function of specific protein residues and to create models of human diseases caused by protein amino acid changes. The homologous protein residues can be mutated in model animal species, and the consequences of these mutations can be studied, leading to a better understanding of the disease in question. Design of point mutation knock-in strategies has been a combination of manual steps assisted by several computational tools resulting in a time-consuming process and preventing a single rapid and integrated solution. We have therefore designed CRISPR Knock-in Designer, which can perform rapid and automatic design of point mutation knock-in DNA oligonucleotides upon provision of the mutation, a guide RNA, and essential identifier or sequence information. The tool supports most experimentally established CRISPR types and has multiple options for the resulting oligonucleotides to satisfy the needs of most users. We also provide allele-specific PCR-based and restriction enzyme-based genotyping strategies as part of the program output. CRISPR Knock-in Designer adjusts to the genomic context of any target codon and tries to design knock-in strategies when a codon straddles two exons, a situation we explored in whole genomes of several model species. CRISPR Knock-in Designer output can also be adapted for use with some of the newer Prime Editing design tools to facilitate the introduction of a specific mutation sequence using this advanced technology.
Detection of sleep apnea from single-channel electroencephalogram (EEG) using an explainable convolutional neural network
Authors: Barnes Lachlan D , Lee Kevin , Kempa-Liehr Andreas W , Hallum Luke E
Published: April 2021

Sleep apnea (SA) is a common disorder involving the cessation of breathing during sleep. It can cause daytime hypersomnia, accidents, and, if allowed to progress, serious, chronic conditions. Continuous positive airway pressure is an effective SA treatment. However, long waitlists impede timely diagnosis; overnight sleep studies involve trained technicians scoring a polysomnograph, which comprises multiple physiological signals including multi-channel electroencephalography (EEG). Therefore, it is important to develop simplified and automated approaches to detect SA. We have developed an explainable convolutional neural network (CNN) to detect SA from single-channel EEG recordings which generalizes across subjects. The network architecture consisted of three convolutional layers. We tuned hyperparameters using the Hyperband algorithm, optimized parameters using Adam, and quantified network performance with subjectwise 10-fold cross-validation. Our CNN performed with an accuracy of 76.7% and a Matthews correlation coefficient (MCC) of 0.54. This performance was reliably above the conservative baselines of 50% (accuracy) and 0.0 (MCC). To explain the mechanisms of our trained network, we used critical-band masking (CBM): after training, we added bandlimited noise to test recordings; we parametrically varied the noise band center frequency and noise intensity, quantifying the deleterious effect on performance. We reconciled the effects of CBM with lesioning, wherein we zeroed the trained network’s 1st-layer filter kernels in turn, quantifying the deleterious effect on performance. These analyses indicated that the network learned frequency-band information consistent with known SA biomarkers, specifically, delta and beta band activity. Our results indicate single-channel EEG may have clinical potential for SA diagnosis.
Single-cell atlas of progressive supranuclear palsy reveals a distinct hybrid glial cell population
Authors: Sharma Abhijeet , Song Won-Min , Farrell Kurt , Whitney Kristen , Zhang Bin , Crary John F. , Pereira Ana C.
Published: April 2021

Progressive supranuclear palsy (PSP) is a neurodegenerative disorder whose molecular complexity at a single cell level has not been evaluated. Here we analyzed 45,559 high quality nuclei from the subthalamic nucleus and associated basal ganglia regions from post-mortem human PSP brains with varying degrees of tau pathology compared to controls (n=3 per group). We identified novel astrocyte-oligodendrocyte hybrid cell populations that overexpress neurotropic factors in conjunction with suppression of the unfolded protein response pathway. Notably, trajectory analysis identified subpopulations of hybrid cells with distinct astrocytic, oligodendrocytic and hybrid molecular states that change from a neuroprotective hybrid cell to an astrocytic cell with impaired homeostatic function in PSP. Our single nucleus transcriptomic data provides insights into the cell-type-specific contributions to the disease for investigating the molecular and cellular basis of PSP.
Structural Insights Into the Initiation and Elongation of Ubiquitination by Ubr1
Authors: Pan Man , Zheng Qingyun , Wang Tian , Liang Lujun , Mao Junxiong , Zuo Chong , Ding Ruichao , Ai Huasong , Xie Yuan , Si Dong , Yu Yuanyuan , Liu Lei , Zhao Minglei
Published: April 2021

The N-end rule pathway was one of the first ubiquitin (Ub)-dependent degradation pathways to be identified. Ubr1, a single-chain E3 ligase, targets proteins bearing a destabilizing residue at the N-terminus (N-degron) for rapid K48-linked ubiquitination and proteasome-dependent degradation. How Ubr1 catalyses the initiation of ubiquitination on the substrate and elongation of the Ub chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here, we report the cryo-electron microscopy structures of two complexes representing the initiation and elongation intermediates of Ubr1 captured using chemical approaches. In these two structures, Ubr1 adopts different conformations to facilitate the transfer of Ub from Ubc2 to either an N-degron peptide or a monoubiquitinated degron. These structures not only reveal the architecture of the Ubr1 complex but also provide mechanistic insights into the initiation and elongation steps of ubiquitination catalysed by Ubr1.
Nanoscale 3D DNA tracing in single human cells visualizes loop extrusion directly in situ
Authors: Beckwith K.S. , Ødegård-Fougner Ø. , Morero N.R. , Barton C. , Schueder F. , Tang W. , Alexander S. , Peters J-M. , Jungmann R. , Birney E. , Ellenberg J.
Published: April 2021

The spatial organization of the genome is essential for its functions, including gene expression, DNA replication and repair, as well as chromosome segregation. Biomolecular condensates and loop extrusion have been proposed as the principal driving forces that underlie the formation of chromatin compartments and topologically associating domains, respectively. However, whether the actual 3D-fold of DNA in single cells is consistent with these mechanisms has been difficult to address in situ. Here, we present LoopTrace, a workflow for nanoscale 3D imaging of the genome sequence in structurally well-preserved nuclei in single human cells. Tracing the in situ structure of DNA in thousands of individual cells reveals that genomic DNA folds as a flexible random coil in the absence of loop extruding enzymes such as Cohesin. In the presence of Cohesin and its boundary factor CTCF, reproducibly positioned loop structures dominate the folds, while Cohesin alone leads to randomly positioned loops. The 3D structure and size variability of DNA loops we observe in a large number of single cells allow us to formulate a data-constrained computational model of genomic DNA folding that explains how sparse and dynamic loops in single cells lead to the emergence of compact topological domains in averages of cell populations.
Direct neural evidence for the contrastive roles of the complementary learning systems in adult acquisition of native vocabulary
Authors: Gore Katherine R. , Woollams Anna M. , Bruehl Stefanie , Halai Ajay D. , Lambon Ralph Matthew A.
Published: April 2021

The Complementary Learning Systems (CLS) theory provides a powerful framework for considering the acquisition, consolidation and generalisation of new knowledge. We tested this proposed neural division of labour in adults through an investigation of the consolidation and long-term retention of newly-learned native vocabulary with post-learning functional neuroimaging. Newly-learned items were compared to two conditions: (i) previously known items to highlight the similarities and differences with established vocabulary; and (ii) unknown/untrained items to provide a control for non-specific perceptual and motor-speech output. Consistent with the CLS, retrieval of newly-learned items was supported by a combination of regions associated with episodic memory (including left hippocampus) and the language-semantic areas that support established vocabulary (left inferior frontal gyrus and left anterior temporal lobe). Furthermore, there was a shifting division of labour across these two networks in line with the items’ consolidation status; faster naming was associated with more activation of language-semantic areas and lesser activation of episodic memory regions. Hippocampal activity during naming predicted more than half the variation in naming retention six months later.
Dynein activation in vivo is regulated by the nucleotide states of its AAA3 domain
Authors: Qiu Rongde , Zhang Jun , Rotty Jeremy D. , Xiang Xin
Published: April 2021

Cytoplasmic dynein is activated by dynactin and cargo adapters in vitro, and the activation also needs LIS1 (Lissencephaly 1) in vivo. How this process is regulated remains unclear. Here we found inAspergillus nidulansthat a dynein AAA4 arginine-finger mutation bypasses the requirement of LIS1 for dynein activation driven by the early endosomal adapter HookA. As the AAA4 arginine-finger is implicated in AAA3 ATP hydrolysis, we examined AAA3 mutants defective in ATP binding and hydrolysis respectively. Astonishingly, blocking AAA3 ATP hydrolysis allows dynein activation by dynactin in the absence of LIS1 or HookA. As a consequence, dynein accumulates at microtubule minus ends while early endosomes stay near the plus ends. On the other hand, blocking AAA3 ATP binding abnormally prevents LIS1 from being dissociated from dynein upon motor activation. Thus, the AAA3 ATPase cycle regulates the coordination between dynein activation and cargo binding as well as the dynamic dynein-LIS1 interaction.