bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of smaller classes on infection-related school absence: Evidence from the Project STAR randomized controlled trial
Authors: von Hippel Paul T.
Published: May 2021

In an effort to reduce viral transmission, many schools are planning to reduce class size if they have not reduced it already. Yet the effect of class size on transmission is unknown. To determine whether smaller classes reduce school absence, especially when community disease prevalence is high, we merge data from the Project STAR randomized class size trial with influenza and pneumonia data from the 122 Cities Mortality Reporting System on deaths from pneumonia and influenza.

Project STAR was a block-randomized trial that followed 10,816 Tennessee schoolchildren from kindergarten in 1985-86 through third grade in 1988-89. Children were assigned at random to small classes (13 to 17 students), regular-sized classes (22 to 26 students), and regular-sized class with a teacher’s aide.

Mixed effects regression showed that small classes reduced absence, but not necessarily by reducing infection. In particular, small classes reduced absence by 0.43 days/year (95% CI -0.06 to -0.80,p<0.05), but had no significant interaction with pneumonia and influenza mortality (95% CI -0.27 to +0.30,p>0.90). Small classes, by themselves, may not suffice to reduce the spread of viruses.
Epigenetic predictors of maximum lifespan and other life history traits in mammals
Authors: Li C.Z. , Haghani A. , Robeck T.R. , Villar D. , Lu A.T. , Zhang J. , Faulkes C.G. , Vu H. , Ablaeva J. , Adams D.M. , Ardehali R. , Arneson A. , Baker C.S. , Belov K. , Blumstein D.T. , Bors E.K. , Breeze C.E. , Brooke R.T. , Brown J.L. , Caulton A. , Cavin J.M. , Chatzistamou I. , Chen H. , Chiavellini P. , Choi O.W. , Clarke S. , DeYoung J. , Emmons C.K. , Emmrich S. , Fei Z. , Ferguson S.H. , Finno C.J. , Flower J.E. , Gaillard J.M. , Garde E. , Gladyshev V.N. , Goya R.G. , Hanson M.B. , Haulena M. , Herrick K. , Hogan A.N. , Hogg C.J. , Hore T.A. , Jasinska A.J. , Jones G. , Jourdain E. , Kashpur O. , Katcher H. , Katsumata E. , Kaza V. , Kiaris H. , Kobor M.S. , Kordowitzki P. , Koski W.R. , Larison B. , Lee S.G. , Lehmann M. , Lemaitre J.F. , Levine A.J. , Li C. , Li X. , Lin D.T.S. , Lindemann D.M. , Macoretta N. , Maddox D. , Matkin C.O. , Mattison J.A. , Mergl J. , Meudt J.J. , Montano G.A. , Mozhui K. , Naderi A. , Nagy M. , Narayan P. , Nathanielsz P.W. , Nguyen N.B. , Niehrs C. , Odom D.T. , Ophir A.G. , Ostrander E.A. , O’Tierney Ginn P. , Parsons K.M. , Paul K.C. , Pellegrini M. , Pinho G.M. , Plassais J. , Prado N.A. , Rey B. , Ritz B.R. , Robbins J. , Rodriguez M. , Russell J. , Rydkina E. , Sailer L.L. , Salmon A.B. , Sanghavi A. , Schachtschneider K.M. , Schmitt D. , Schomacher L. , Schook L.B. , Sears K.E. , Seifert A.W. , Shindyapina A.V. , Singh K. , Sinha I. , Snell R.G. , Soltanmohammadi E. , Spangler M.L. , Spriggs M. , Steinman K.J. , Sugrue V.J. , Szladovits B. , Takasugi M. , Teeling E.C. , Van Bonn B. , Vernes S.C. , Vinters H.V. , Wallingford M.C. , Wang N. , Wilkinson G.S. , Williams R.W. , Yang X.W. , Young B.G. , Zhang B. , Zhang Z. , Zhao P. , Zhao Y. , Zhou W. , Zoller J.A. , Ernst J. , Seluanov A. , Raj K. , Gorbunova V. , Horvath S. ,   MAMMALIAN METHYLATION CONSORTIUM
Published: May 2021

Maximum lifespan of a species is the oldest that individuals can survive, reflecting the genetic limit of longevity in an ideal environment. Here we report methylation-based models that accurately predict maximum lifespan (r=0.89), gestational time (r=0.96), and age at sexual maturity (r=0.87), using cytosine methylation patterns collected from over 12,000 samples derived from 192 mammalian species. Our epigenetic maximum lifespan predictor corroborated the extended lifespan in growth hormone receptor knockout mice and rapamycin treated mice. Across dog breeds, epigenetic maximum lifespan correlates positively with breed lifespan but negatively with breed size. Lifespan-related cytosines are located in transcriptional regulatory regions, such as bivalent chromatin promoters and polycomb-repressed regions, which were hypomethylated in long-lived species. The epigenetic estimators of maximum lifespan and other life history traits will be useful for characterizing understudied species and for identifying interventions that extend lifespan.
Relationships between acute race-induced changes in creatine kinase activity and blood plasma myoglobin concentration and race performance in mountain bike and road cyclists
Authors: Hebisz Paulina , Borkowski Jacek , Hebisz Rafał
Published: May 2021

The aim of this study was to determine if the changes in plasma creatine kinase (CK) activity and myoglobin (MB) concentrations as markers of muscle damage differ between competitive road (n = 14) and mountain bike (n = 11) cyclists and if these biochemical markers show a relationship with real-world race performance. CK and MB were measured from blood samples collected 2 hours before race start and 1 hour after race completion and the change in pre- and post-race difference was calculated (ΔCK and ΔMB). An incremental exercise test was used to determine maximal oxygen uptake, maximal aerobic power, and power output at the second ventilatory threshold. Post-race CK and MB increased in the whole group of cyclists. Although the magnitude of change in CK was similar in both road and mountain bike cyclists, only the increase in road cyclists was significant. MB significantly increased only in mountain bike cyclists. Multiple regression analysis revealed a significant association between both road and mountain bike race performance and ΔCK and ΔMB. The other significant predictors for mountain bike race performance were maximal aerobic power (W·kg-1) and power output at the second ventilatory threshold (W·kg-1) and for road race performance both maximal oxygen uptake (l·min-1) and power output at the second ventilatory threshold (W). In conclusion, mountain bike racing was associated with an increase in MB whereas road racing with an increase in CK, with the post-race changes in CK and MB related to race performance as high ΔCK and low ΔMB were obtained by better-performing cyclists.
Metacommunity analyses show increase in ecological specialisation throughout the Ediacaran
Authors: Eden Rebecca , Manica Andrea , Mitchell Emily G.
Published: May 2021

The first animals appear during the late Ediacaran (572 – 541 Ma); an initial diversity increase was followed by a drop, interpreted as catastrophic mass extinction. We investigate the processes underlying these changes using the “Elements of Metacommunity Structure” framework. The oldest metacommunity was characterized by taxa with wide environmental tolerances, and limited specialisation and inter-taxa interactions. Structuring increased in the middle metacommunity, with groups of taxa sharing synchronous responses to environmental gradients, aggregating into distinct communities. This pattern strengthened in the youngest metacommunity, with communities showing strong environmental segregation and depth structure. Thus, metacommunity structure increased in complexity, with increased specialisation and resulting competitive exclusion, not a catastrophic environmental disaster, leading to diversity loss in the terminal Ediacaran, revealing that the complex eco-evolutionary dynamics associated with Cambrian diversification were established in the Ediacaran.
Unsupervised learning for robust working memory
Authors: Gu Jintao , Lim Sukbin
Published: May 2021

Working memory is a core component of critical cognitive functions such as planning and decision-making. Persistent activity that lasts long after the stimulus offset has been considered a neural substrate for working memory. Attractor dynamics based on network interactions can successfully reproduce such persistent activity. However, it suffers from a fine-tuning of network connectivity, in particular, to form continuous attractors suggested for working memory encoding analog signals. Here, we investigate whether a specific form of synaptic plasticity rules can mitigate such tuning problems in two representative working memory models, namely, rate-coded and location-coded persistent activity. We consider two prominent types of plasticity rules, differential plasticity targeting the slip of instant neural activity and homeostatic plasticity regularizing the long-term average of activity, both of which have been proposed to fine-tune the weights in an unsupervised manner. Consistent with the findings of previous works, differential plasticity alone was enough to recover a graded-level persistent activity with less sensitivity to learning parameters. However, for the maintenance of spatially structured persistent activity, differential plasticity could recover persistent activity, but its pattern can be irregular for different stimulus locations. On the other hand, homeostatic plasticity shows a robust recovery of smooth spatial patterns under particular types of synaptic perturbations, such as perturbations in incoming synapses onto the entire or local populations, while it was not effective against perturbations in outgoing synapses from local populations. Instead, combining it with differential plasticity recovers location-coded persistent activity for a broader range of perturbations, suggesting compensation between two plasticity rules.

Author Summary

While external error and reward signals are essential for supervised and reinforcement learning, they are not always available. For example, when an animal holds a piece of information in mind for a short delay period in the absence of the original stimulus, it cannot generate an error signal by comparing its memory representation with the stimulus. Thus, it might be helpful to utilize an internal signal to guide learning. Here, we investigate the role of unsupervised learning for working memory maintenance, which acts during the delay period without external inputs. We consider two prominent classes of learning rules, namely, differential plasticity, which targets the slip of instant neural activity, and homeostatic plasticity, which regularizes the long-term average of activity. The two learning rules have been proposed to fine-tune the synaptic weights without external teaching signals. Here, by comparing their performance under various types of network perturbations, we reveal the conditions under which each rule can be effective and suggest possible synergy between them.
Cortical Oscillatory Dysrhythmias in Visual Snow Syndrome: A MEG Study
Authors: Hepschke Jenny L. , Seymour Robert A , He Wei , Etchell Andrew , Sowman Paul F , Fraser Clare L
Published: May 2021

Visual Snow (VS) refers to the persistent visual experience of static in the whole visual field of both eyes. It is often reported by patients with migraine and co-occurs with conditions like tinnitus and tremor. The underlying pathophysiology of the condition is poorly understood. Previously we hypothesised, that VSS may be characterised by disruptions to rhythmical activity within the visual system1.

To test this, data from 18 patients diagnosed with visual snow syndrome (VSS), and 16 matched controls, were acquired using Magnetoencephalography (MEG). Participants were presented with visual grating stimuli, known to elicit decreases in alpha-band (8-13Hz) power and increases in gamma-band power (40-70Hz).

Data were mapped to source-space using a beamformer. Across both groups, decreased alpha power and increased gamma power localised to early visual cortex. Data from primary visual cortex (V1) were compared between groups. No differences were found in either alpha or gamma peak frequency or the magnitude of alpha power, p>.05. However, compared with controls, our VSS cohort displayed significantly increased V1 gamma power, p=.035. This new electromagnetic finding concurs with previous fMRI and PET findings suggesting that in VSS, the visual cortex is hyper-excitable. The coupling of alpha-phase to gamma amplitude (i.e., phase-amplitude coupling, PAC) within V1 was also quantified. Compared with controls, the VSS group had significantly reduced alpha-gamma PAC, p<.05, indicating a potential excitation-inhibition imbalance in VSS, as well as a potential disruption to top-down “noise-cancellation” mechanisms.

Overall, these results suggest that rhythmical brain activity in primary visual cortex is both hyperexcitable and disorganised in VSS, consistent with visual snow being a condition of thalamocortical dysrhythmia.
Toughening mechanisms for the attachment of architectured materials: The mechanics of the tendon enthesis
Authors: Golman Mikhail , Abraham Adam C. , Kurtaliaj Iden , Marshall Brittany P. , Hu Yizhong Jenny , Schwartz Andrea G. , Guo X. Edward , Birman Victor , Thurner Philipp J. , Genin Guy M. , Thomopoulos Stavros
Published: May 2021

Architectured materials offer tailored mechanical properties but are limited in engineering applications due to challenges in maintaining toughness across their attachments. The enthesis connects tendon and bone, two vastly different architectured materials, and exhibits toughness across a wide range of loadings. Understanding the mechanisms by which this is achieved could inform the development of engineered attachments. Integrating experiments, simulations, and novel imaging that enabled simultaneous observation of mineralized and unmineralized tissues, we identified putative mechanisms of enthesis toughening in a mouse model and then manipulated these mechanisms viain vivocontrol of mineralization and architecture. Imaging uncovered a fibrous architecture within the enthesis that controls trade-offs between strength and toughness.In vivomodels of pathology revealed architectural adaptations that optimize these trade-offs through cross-scale mechanisms including nanoscale protein denaturation, milliscale load-sharing, and macroscale energy absorption. Results suggest strategies for optimizing architecture for tough bimaterial attachments in medicine and engineering.

Teaser

The architecture of the tendon-to-bone attachment is designed for toughness.
Rat sensitivity to multipoint statistics is predicted by efficient coding of natural scenes
Authors: Caramellino Riccardo , Piasini Eugenio , Buccellato Andrea , Carboncino Anna , Balasubramanian Vijay , Zoccolan Davide
Published: May 2021

Efficient processing of sensory data requires adapting the neuronal encoding strategy to the statistics of natural stimuli. Previously, in Hermundstad et al. 2014, we showed that local multipoint correlation patterns that are most variable in natural images are also the most perceptually salient for human observers, in a way that is compatible with the efficient coding principle. Understanding the neuronal mechanisms underlying such adaptation to image statistics will require performing invasive experiments that are impossible in humans. Therefore, it is important to understand whether a similar phenomenon can be detected in animal species that allow for powerful experimental manipulations, such as rodents. Here we selected four image statistics (from single- to four-point correlations) and trained four groups of rats to discriminate between white noise patterns and binary textures containing variable intensity levels of one of such statistics. We interpreted the resulting psychometric data with an ideal observer model, finding a sharp decrease in sensitivity from 2- to 4-point correlations and a further decrease from 4- to 3-point. This ranking fully reproduces the trend we previously observed in humans, thus extending a direct demonstration of efficient coding to a species where neuronal and developmental processes can be interrogated and causally manipulated.
Dissociation in basolateral and central amygdala effective connectivity predicts the stability of emotion-related impulsivity in adolescents with borderline personality symptoms: a resting-state fMRI study
Authors: Hall Nathan T. , Hallquist Michael N.
Published: May 2021

Background

Borderline personality disorder (BPD) is associated with altered activity in the prefrontal cortex (PFC) and amygdala, yet no studies have examined fronto-limbic circuitry in borderline adolescents. Here, we examined the contribution of fronto-limbic connectivity to the longitudinal stability of emotion-related impulsivity (ERI), a key feature of BPD, in symptomatic adolescents and young adults.

Methods

We compared resting-state effective connectivity (EC) in 82 adolescents and emerging adults with and without clinically significant borderline symptoms (n BPD = 40, ages 13-30). Group-specific directed networks were estimated amongst fronto-limbic nodes including PFC, ventral striatum (VS), central amygdala (CeN), and basolateral amygdala (BLA). We calculated directed centrality metrics and examined if these values were associated with initial levels and rates of change in ERI symptoms over a one-year follow-up using latent growth curve models (LGCMs).

Results

In the healthy group, ventromedial prefrontal cortex (vmPFC) and dorsal ACC had a directed influence on CeN and VS respectively. In the borderline group bilateral BLA had a directed influence on CeN, whereas in the healthy group CeN influenced BLA. LGCMs revealed that in borderline adolescents, ERI remained stable across follow-ups. Further, higher output of R CeN in controls was associated with stronger within-person decreases in ERI.

Conclusions

Functional inputs from BLA and vmPFC appear to play competing roles in influencing CeN activity. In borderline adolescents BLA may predominate over CeN activity, while in controls the ability of CeN to conversely influence BLA activity is associated with more rapid reductions in ERI.
An Atlas of Cortical Arealization Identifies Dynamic Molecular Signatures
Authors: Bhaduri Aparna , Sandoval-Espinosa Carmen , Otero-Garcia Marcos , Oh Irene , Yin Raymund , Eze Ugomma C. , Nowakowski Tomasz J. , Kriegstein Arnold R.
Published: May 2021

The human brain is subdivided into distinct anatomical structures. The neocortex, one of these structures, enables higher-order sensory, associative, and cognitive functions, and in turn encompasses dozens of distinct specialized cortical areas. Early morphogenetic gradients are known to establish an early blueprint for the specification of brain regions and cortical areas. Furthermore, recent studies have uncovered distinct transcriptomic signatures between opposing poles of the developing neocortex1. However, how early, broad developmental patterns result in finer and more discrete spatial differences across the adult human brain remains poorly understood2. Here, we use single-cell RNA-sequencing to profile ten major brain structures and six neocortical areas during peak neurogenesis and early gliogenesis. Our data reveal that distinct cell subtypes are predominantly brain-structure specific. Within the neocortex, we find that even early in the second trimester, a large number of genes are differentially expressed across distinct cortical areas in all cell types, including radial glia, the neural progenitors of the cortex. However, the abundance of areal transcriptomic signatures increases as radial glia differentiate into intermediate progenitor cells and ultimately give rise to excitatory neurons. Using an automated, multiplexed single-molecule fluorescentin situhybridization (smFISH) approach, we validated the expression pattern of area-specific neuronal genes and also discover that laminar gene expression patterns are highly dynamic across cortical regions. Together, our data suggest that early cortical areal patterning is defined by strong, mutually exclusive frontal and occipital gene expression signatures, with resulting gradients giving rise to the specification of areas between these two poles throughout successive developmental timepoints.
“Δ133p53α Protects Human Astrocytes from Amyloid-Beta Induced Senescence and Neurotoxicity”
Authors: Ungerleider Kyra , Lissa Delphine , Beck Jessica A. , Horikawa Izumi , Harris Curtis C.
Published: May 2021

Cellular senescence is an important contributor to aging and age-related diseases such as Alzheimer’s disease (AD). Senescent cells are characterized by a durable cell proliferation arrest and the acquisition of a proinflammatory senescence-associated secretory phenotype (SASP), which participates in the progression of neurodegenerative disorders. Clearance of senescent glial cells in an AD mouse model prevented cognitive decline suggesting pharmacological agents targeting cellular senescence might provide novel therapeutic approaches for AD. Δ133p53α, a natural protein isoform of p53, was previously shown to be a negative regulator of cellular senescence in primary human astrocyte, with clinical implications from its diminished expression in brain tissues from AD patients. Here we show that treatment of proliferating human astrocytes with amyloid-beta oligomers (Aβ), an endogenous pathogenic agent of AD, results in reduced expression of Δ133p53α, as well as induces the cells to become senescent and express proinflammatory SASP cytokines such as IL-6, IL-1β and TNFα. Our data suggest that Aβ-induced astrocyte cellular senescence is associated with accelerated DNA damage, and upregulation of full-length p53 and its senescence-inducing target gene p21WAF1. We also show that exogenously enhanced expression of Δ133p53α rescues human astrocytes from Aβ-induced cellular senescence and SASP through both protection from DNA damage and dominantnegative inhibition of full-length p53, leading to inhibition of Aβ-induced, astrocyte-mediated neurotoxicity. The results presented here demonstrate that Δ133p53α manipulation could modulate cellular senescence in the context of AD, possibly opening new therapeutic avenues.

HIGHLIGHTS

Aβ diminishes the expression of the p53 isoform Δ133p53α, and induces cellular senescence, SASP, and DNA damage in human astrocytes.

Δ133p53α protects human astrocytes from Aβ-induced DNA damage and cellular senescence.

Δ133p53α prevents astrocyte-mediated neurotoxicity to neuro-progenitor cells.
An Open–Access Simultaneous Electrocardiogram and Phonocardiogram Database
Authors: Kazemnejad Arsalan , Gordany Peiman , Sameni Reza
Published: May 2021

The electro-phono-cardiogram (EPHNOGRAM) project focused on the development of low-cost and low-power devices for recording simultaneous electrocardiogram (ECG) and phonocardiogram (PCG) data, with auxiliary channels for capturing environmental audio noise, which could be used for PCG quality enhancement through signal processing. The current database, recorded by version 2.1 of the developed hardware, has been acquired from 24 healthy adults aged between 23 and 29 (average: 25.4 ± 1.9 years) in 30 min stress-test sessions during resting, walking, running and biking conditions, using indoor fitness center equipment. The dataset also contains several 30 s sample records acquired during rest conditions. This data is useful for simultaneous multi-modal analysis of ECG and PCG. It provides interesting insights into the inter-relationship between the mechanical and electrical mechanisms of the heart, under rest and physical activity. The database is provided online on PhysioNet.
Correcting for Body Size Variation in Morphometric Analysis
Authors: Chan Kin Onn , Lee Grismer L.
Published: May 2021

Using an allometric growth model to correct for body size variation has been known for many decades to be superior to several other widely used methods such as ratios, analysis of covariance, principal components analysis, and residual analysis. However, this technique remains relatively obscure and rarely applied. We optimize the implementation of this method through a newly developed and easy-to-use R package GroupStruct and use empirical datasets to test its relative efficacy compared to several commonly used methods. Our results demonstrate the superiority of the allometric method and highlights the negative impacts of applying improper body size correction methods.
Subcellular localization of PKA catalytic subunits provides a basis for their distinct functions in the retina
Authors: Roa Jinae N. , Ma Yuliang , Mikulski Zbigniew , Xu Qianlan , Ilouz Ronit , Taylor Susan S. , Skowronska-Krawczyk Dorota
Published: May 2021

PKA signaling is essential for numerous processes but the subcellular localization of specific PKA isoforms has yet to be explored comprehensively in tissues. Expression of the Cβ protein, in particular, has not been mapped previously at the tissue level. In this study we used retina as a window into PKA signaling in the brain and characterized localization of PKA Cα, Cβ, RIIα, and RIIβ subunits. Each subunit presented a distinct localization pattern. Cα and Cβ were localized in all tissue layers, while RIIα and RIIβ were enriched in the photoreceptor cells in contrast to the cell body and retinal portion of retinal ganglion cells. Only Cα was observed in photoreceptor outer segments and the cilia transition zone, while Cβ was localized primarily to mitochondria and was especially prominent in the ellipsoid of the cone cells. In contrast to Cα, Cβ also never colocalized with RIIα or RIIβ. Using BaseScope technology to track expression of the Cβ isoforms we find that Cβ4 and Cβ4ab are prominently expressed and, therefore, likely code for mitochondrial-Cβ proteins. Our data indicates that PKA subunits are functionally nonredundant in the retina and suggesting that Cβ might be important for mitochondrial-associated neurodegenerative diseases previously linked to PKA dysfunction.
Higher concentrations of bacterial enveloped virus Phi6 can protect the virus from environmental decay
Authors: Bangiyev Ronald , Chudaev Maxim , Schaffner Donald W. , Goldman Emanuel
Published: May 2021

Phage Phi6 is an enveloped virus considered as a possible non-pathogenic surrogate for SARS-CoV-2 and other viral pathogens in transmission studies. Higher input amounts of bacteriophage Phi6 are shown to delay and protect the phage from environmental decay, both when the phage are dried in plastic tubes, and when they are stored in saline solution at 4°C. When bacteriophage Phi6 are placed in LB (Luria-Bertani) growth medium prior to placement on the plastic surface, viral recovery is not influenced by the starting concentration. The protection is reflected in longer half-lives of the phage at higher concentrations compared to lower. Because experiments supporting the possibility of fomite transmission of SARS-CoV-2 and other viruses rely upon survival of infectious virus following inoculation of various surfaces, high initial amounts of input virus on a surface may generate artificially inflated survival times compared to realistic lower levels of virus that a subject would normally encounter. This is not only because there are extra half-lives to go through at the higher concentrations, but also because the half-lives themselves are extended at the higher virus concentrations. It is important to design surface drying experiments for pathogens with realistic levels of input virus, and to consider the role of the carrier and matrix if the results are to be clinically relevant.

IMPORTANCE

During the COVID-19 pandemic, a lot of attention has been paid to the environmental decay of SARS-CoV-2 due to proposed transmission of the virus via fomites. However, published experiments have commenced with very high virus titer inoculums, an experimental design not representative of real-life conditions. The study described here evaluated the impact of initial virus titer on environmental decay of an enveloped virus, using a non-pathogenic surrogate for SARS-CoV-2, enveloped bacteriophage Phi6. We establish that higher concentrations of virus can protect the virus from environmental decay, depending on conditions. This has important implications for stability studies of SARS-CoV-2 and other viruses. Our results point to a limitation in the fundamental methodology that has been used to attribute fomite transmission for almost all respiratory viruses.
Prophylactic inhibition of colonization by Streptococcus pneumoniae with the secondary bile acid metabolite deoxycholic acid
Authors: Vidal Jorge E. , Wier Meagan N. , Angulo-Zamudio Uriel , McDevitt Erin , Jop Vidal Ana G. , Alibayov Babek , Scasny Anna , Wong Sandy M. , Akerley Brian J. , McDaniel Larry S.
Published: May 2021

Streptococcus pneumoniae (Spn) colonizes the nasopharynx of children and the elderly but also kills millions worldwide yearly. The secondary bile acid metabolite, deoxycholic acid (DoC), affects the viability of human pathogens but also plays multiple roles in host physiology. We assessed in vitro the antimicrobial activity of DoC and investigated its potential to eradicate Spn colonization using an ex vivo model of human nasopharyngeal colonization and an in vivo mouse model of colonization. At a physiological concentration DoC (0.5 mg/ml; 1.27 mM) killed all tested Spn strains (N=48) two h post-inoculation. The ex-vivo model of nasopharyngeal colonization showed that DoC eradicated colonization by Spn strains as soon as 10 min post-exposure. The mechanism of action did not involve activation of autolysis since the autolysis-defective double mutants ΔlytAΔlytC and ΔspxBΔlctO were as susceptible to DoC as was the wild-type (WT). Oral streptococcal species (N=20), however, were not susceptible to DoC (0.5 mg/ml). Unlike trimethoprim, whose spontaneous resistance frequency (srF) for TIGR4 or EF3030 was ≥1×10−9, no spontaneous resistance was observed with DoC (srF≥1×10−12). Finally, the efficacy of DoC to eradicate Spn colonization was assessed in vivo using a topical route via intranasal (i.n.) administration and as a prophylactic treatment. Mice challenged with Spn EF3030 carried a median of 4.05×105 cfu/ml four days post-inoculation compared to 6.67×104 cfu/ml for mice treated with DoC. Mice in the prophylactic group had a ∼99% reduction of the pneumococcal density (median, 2.61 ×103 cfu/ml). Thus, DoC, an endogenous human bile salt, has therapeutic potential against Spn.
Multi-Factor Authentication of Potential 5’ Splice Sites by the Saccharomyces cerevisiae U1 snRNP
Authors: Hansen Sarah R. , Scalf Mark , Corrêa Ivan R. , Smith Lloyd M. , Hoskins Aaron A.
Published: May 2021

In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5’ splice site (5’ SS) through a combination of base pairing, protein-RNA contacts, and interactions with other splicing factors. Previous studies investigating the mechanisms of 5’ SS recognition have largely been done in vivo or in cellular extracts where the U1/5’ SS interaction is difficult to deconvolute from the effects of trans-acting factors or RNA structure. In this work we used co-localization single-molecule spectroscopy (CoSMoS) to elucidate the pathway of 5’ SS selection by purified yeast U1 snRNP. We determined that U1 reversibly selects 5’ SS in a sequence-dependent, two-step mechanism. A kinetic selection scheme enforces pairing at particular positions rather than overall duplex stability to achieve long-lived U1 binding. Our results provide a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5’ SS and preferentially accumulate at these sequences rather than on close cognates.

IMPACT STATEMENT

The yeast U1 snRNP recognizes multiple features of target RNAs to reversibly identify splicing-competent 5’ splice sites.
Bimodal Endocytic Probe for Three-Dimensional Correlative Light and Electron Microscopy
Authors: Fermie Job , de Jager Leanne , Foster Helen , Veenendaal Tineke , de Heus Cecilia , van Dijk Suzanne , ten Brink Corlinda , Oorschot Viola , Yang Lin , Li Wei , Müller Wally , Howes Stuart , Carter Andrew , Förster Friedrich , Posthuma George , Gerritsen Hans , Klumperman Judith , Liv Nalan
Published: May 2021

Correlative light and electron microscopy (CLEM) can infer molecular, functional and dynamic information to ultrastructure by linking information of different imaging modalities. One of the main challenges, especially in 3D-CLEM, is the accurate registration of fluorescent signals to electron microscopy (EM). Here, we present fluorescent BSA-gold (fBSA-Au), a bimodal endocytic tracer as fiducial marker for 2D and 3D CLEM applications. fBSA-Au consists of colloidal gold (Au) particles stabilized with fluorescent bovine serum albumin (BSA). The conjugate is efficiently endocytosed and distributed throughout the 3D endo-lysosomal network of the cells, and has an excellent visibility both in fluorescence microscopy (FM) and EM. We demonstrate the use of fBSA-Au in several 2D and 3D CLEM applications using Tokuyasu cryosections, resin-embedded material, and cryo-EM. As a fiducial marker, fBSA-Au facilitates rapid registration of regions of interest between FM and EM modalities and enables accurate (50-150 nm) correlation of fluorescence to EM data. Endocytosed fBSA-Au benefits from a homogenous 3D distribution throughout the endosomal system within the cell, and does not obscure any cellular ultrastructure. The broad applicability and visibility in both modalities makes fBSA-Au an excellent endocytic fiducial marker for 2D and 3D (cryo-)CLEM applications.
Latent disease similarities and therapeutic repurposing possibilities uncovered by multi-modal generative topic modeling of human diseases
Authors: Kozawa Satoshi , Yokoyama Hirona , Urayama Kyoji , Tejima Kengo , Doi Hotaka , Sato Thomas N.
Published: May 2021

Human diseases are characterized by multiple features such as their pathophysiological, molecular, and genetic changes. The rapid expansion of such multi-modal disease-omics space provides an opportunity to re-classify diverse human diseases and uncover their latent molecular similarities, which could be exploited to repurpose a therapeutic-target for one disease to another. Herein, we probe this underexplored space by soft-clustering 6,955 human diseases by multi-modal generative topic-modeling. Focusing on chronic kidney disease and myocardial infarction, two most life-threatening diseases, unveiled are their previously underrecognized molecular similarities to neoplasia and mental/neurological-disorders, and 69 repurposable therapeutic-targets for these diseases. Using an edit-distance based pathway-classifier, we also find molecular pathways by which these targets could elicit their clinical effects. Importantly, for the 17 targets, the evidence for their therapeutic usefulness is retrospectively found in the pre-clinical and clinical space, illustrating the effectiveness of the method, and suggesting its broader applications across diverse human diseases.
Astrocyte Ca2+ Signaling is Facilitated in an Scn1a+/− Mouse Model of Dravet Syndrome
Authors: Uchino Kouya , Ikezawa Wakana , Tanaka Yasuyoshi , Deshimaru Masanobu , Kubota Kaori , Watanabe Takuya , Katsurabayashi Shutaro , Iwasaki Katsunori , Hirose Shinichi
Published: May 2021

Dravet syndrome (DS) is an infantile-onset epileptic encephalopathy. More than 80% of DS patients have a heterozygous mutation in SCN1A, which encodes a subunit of the voltage-gated sodium channel, Nav1.1, in neurons. The roles played by astrocytes, the most abundant glial cell type in the brain, have been investigated in the pathogenesis of epilepsy; however, the specific involvement of astrocytes in DS has not been clarified. In this study, we evaluated Ca2+ signaling in astrocytes using genetically modified mice that have a loss-of-function mutation in Scn1a. We found that the slope of spontaneous Ca2+ spiking was increased without a change in amplitude in Scn1a+/− astrocytes. In addition, ATP-induced transient Ca2+ influx and the slope of Ca2+ spiking were also increased in Scn1a+/− astrocytes. These data indicate that perturbed Ca2+ dynamics in astrocytes may be involved in the pathogenesis of DS.
Intratumoural heterogeneity and immune modulation in lung adenocarcinoma of female smokers and never smokers
Authors: Trefzer Timo , Schneider Marc A. , Jechow Katharina , Chua Lorenz , Muley Thomas , Winter Hauke , Kriegsmann Mark , Meister Michael , Eils Roland , Conrad Christian
Published: May 2021

Lung cancer is still the leading cause of cancer death worldwide despite declining smoking prevalence in industrialised countries. Although lung cancer is highly associated with smoking status, a significant proportion of lung cancer cases develop in patients who never smoked, with an observable bias towards female never smokers. A better understanding of lung cancer heterogeneity and immune system involvement during tumour evolution and progression in never smokers is therefore highly warranted. We employed single nucleus transcriptomics of surgical lung adenocarcinoma (LADC) and normal lung tissue samples from patients with or without smoking history. Immune cells as well as fibroblasts and endothelial cells respond to tobacco smoke exposure by inducing a highly inflammatory state in normal lung tissue. In the presence of LADC, we identified differentially expressed transcriptional programmes in macrophages and cancer-associated fibroblasts, providing insight into how the niche favours tumour progression. Within tumours, we distinguished eight subpopulations of neoplastic cells in female smokers and never smokers. Through pseudotemporal ordering, we inferred a trajectory towards two differentiated tumour cell states implicated in cancer progression and invasiveness. A proliferating cell population sustaining tumour growth exhibits differential immune modulating signatures in both patient groups. Our results resolve cellular heterogeneity and immune interactions in LADC, with a special emphasis on female never smokers and implications for the design of therapeutic approaches.
PAK1 and PAK2 in cell metabolism regulation
Authors: Kořánová Tereza , Dvořáček Lukáš , Grebeňová Dana , Röselová Pavla , Obr Adam , Kuželová Kateřina
Published: May 2021

P21-activated kinases (PAKs) regulate processes associated with cytoskeletal rearrangements, such as cell division, adhesion, and migration. The possible regulatory role of PAKs in cell metabolism has not been well explored, but increasing evidence suggests that a cell metabolic phenotype is related to cell interactions with the microenvironment. We analyzed the impact of PAK inhibition by small molecule inhibitors, small interfering RNA, or gene knockout on the rates of mitochondrial respiration and aerobic glycolysis. Pharmacological inhibition of PAK group I by IPA-3 induced a strong decrease in metabolic rates in human adherent cancer cell lines, leukemia/lymphoma cell lines, and primary leukemia cells. The immediate effect of FRAX597, which inhibits PAK kinase activity, was moderate, indicating that PAK nonkinase functions are essential for cell metabolism. Selective downregulation or deletion of PAK2 was associated with a shift toward oxidative phosphorylation. Alternatively, PAK1 knockout resulted in increased glycolysis. However, the overall metabolic capacity was not substantially reduced by PAK1 or PAK2 deletion, possibly due to partial redundancy in PAK1/PAK2 regulatory roles or to activation of other compensatory mechanisms.
A protein-trap allele reveals roles for Drosophila ATF4 in photoreceptor degeneration, oocyte maturation and wing development
Authors: Vasudevan Deepika , Katow Hidetaka , Tang Grace , Ryoo Hyung Don
Published: May 2021

Metazoans have evolved various stress response mechanisms to cope with cellular stress inflicted by external and physiological conditions. The Integrated Stress Response (ISR) is an evolutionarily conserved pathway that mediates adaptation to cellular stress via the transcription factor, ATF4. Loss of function of Drosophila ATF4, encoded by the gene cryptocephal (crc), results in lethality during pupal development. The roles of crc in Drosophila disease models and adult tissue homeostasis thus remain poorly understood. Here, we report that a protein-trap MiMIC insertion in the crc locus generates a crc-GFP fusion protein that allows visualization of crc activity in vivo, and acts as a hypomorphic mutant that uncovers previously unknown roles for crc. Specifically, the crc protein-trap line shows crc-GFP induction in a Drosophila model for Retinitis Pigmentosa (RP). This crc allele renders photoreceptors more vulnerable to age-dependent retinal degeneration. crc mutant adult animals also show greater susceptibility to amino acid deprivation and reduced levels of known crc transcriptional targets. Furthermore, this mutant allele shows defects in wing veins and oocyte maturation, uncovering previously unknown roles for crc in the development of these tissues. Together, our data establish physiological and pathological functions of crc-mediated ISR in adult Drosophila tissues.
CTCF looping is established during gastrulation in medaka embryos
Authors: Nakamura Ryohei , Motai Yuichi , Kumagai Masahiko , Wike Candice L. , Nishiyama Haruyo , Nakatani Yoichiro , Durand Neva C. , Kondo Kaori , Kondo Takashi , Tsukahara Tatsuya , Shimada Atsuko , Cairns Bradley R. , Aiden Erez Lieberman , Morishita Shinichi , Takeda Hiroyuki
Published: May 2021

Chromatin looping plays an important role in genome regulation. However, because ChIP-seq and loop-resolution Hi-C (DNA-DNA proximity ligation) are extremely challenging in mammalian early embryos, the developmental stage at which cohesin-mediated loops form remains unknown. Here, we study early development in medaka (the Japanese killifish, Oryzias latipes) at 12 time points before, during, and after gastrulation (the onset of cell differentiation) and characterize transcription, protein binding, and genome architecture. We find that gastrulation is associated with drastic changes in genome architecture, including the formation of the first loops between sites bound by the insulator protein CTCF and a large increase in the size of contact domains. In contrast, the binding of the CTCF is fixed throughout embryogenesis. Loops form long after genome-wide transcriptional activation, and long after domain formation seen in mouse embryos. These results suggest that, although loops may play a role in differentiation, they are not required for zygotic transcription. When we repeated our experiments in zebrafish, loops did not emerge until gastrulation, that is, well after zygotic genome activation. We observe that loop positions are highly conserved in synteny blocks of medaka and zebrafish, indicating that the 3D genome architecture has been maintained for >110–200 million years of evolution.
Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
Authors: Shirai Kazumasa , Sato Mitsuhiko P. , Nishi Ranko , Seki Masahide , Suzuki Yutaka , Hanada Kousuke
Published: May 2021

DNA methylation is an important factor regulating gene expression in organisms. However, whether DNA methylation plays a key role in adaptive evolution is unknown. Here, we show evidence of naturally selected DNA methylation in Arabidopsis thaliana. In comparison with single nucleotide polymorphisms, three types of methylation—methylated CGs (mCGs), mCHGs, and mCHHs—contributed highly to variable gene expression levels among an A. thaliana population. Such variably expressed genes largely affect a large variation of specialized metabolic quantities. Among the three types of methylations, only mCGs located in promoter regions of genes associated with specialized metabolites show a selective sweep signature in the A. thaliana population. Thus, naturally selected mCGs appear to be key mutations that cause the expressional diversity associated with specialized metabolites during plant evolution.
Red, white and green: environmental communication on wine bottle labels from New York's Hudson River Region
Authors: Visconti Kevin
Published: May 2021

Purpose

New York is the third top wine producing state in America. Competitive wine production across the United States has challenged New York winemakers to secure a place in the domestic market in order to support the long-term viability of the local economy. As businesses of agriculture become increasingly disrupted by the changing natural environment and consumer demand for sustainable products grows, vintners may distinguish themselves through the production and promotion of strategic initiatives on wine bottle labels.

Design/methodology/approach

Fueled by the distinct fields of green marketing and environmental communication, this research investigates the promotion of sustainable practices on wine bottle labels. Through the methodology of content analysis, this project examines all 13 wineries on the Shawangunk Wine Trail located in the Hudson River Region of New York.

Findings

The findings from this study show that less than half of wineries in the sample selection employ environmental marketing as a communication strategy.

Research limitations/implications

This research carries practical, business and social implications for the local Hudson River Region, the larger New York wine industry, and any organization looking to remain viable in a competitive marketplace.

Originality/value

This paper reveals the potential for the Hudson River Region wine industry to promote its “distinctive” and “innovative” environmental philosophy of “terroir driven and sustainably produced” winemaking on wine bottle labels to differentiate themselves in a crowded and expanding marketplace and build a Basis of Legitimacy with consumers.
Numerical investigation of the flow characteristics and permeability of 2D irregular columnar jointed rock masses
Authors: Cheng Zhichao , Wang Huanling , Xu Weiya , Yan Long
Published: May 2021

Purpose

The objective of this paper is to provide a better understanding of the effect of irregular columnar jointed structure on the permeability and flow characteristics of rock masses.

Design/methodology/approach

An efficient numerical procedure is proposed to investigate the permeability and fluid flow in columnar jointed rock masses (CJRMs), of which the columnar jointed networks are generated by a modified constrained centroid Voronoi algorithm according to the field statistical results. The fractures are represented explicitly by using the lower-dimensional zero thickness elements. And the modeling scheme is validated by a benchmark test for flow in fractured porous media. The effective permeability and representative elementary volume (REV) size of CJRMs are estimated using finite element method (FEM). The influences of joint density and variation coefficient of columnar joint structure on the permeability of the rock mass are discussed.

Findings

The simulation results indicate that the permeability is scale-dependent and tends to be stable with increase of model size. The hydraulic REV size is determined as 3.5 m for CJRMs in the present study. Moreover, the joint density is a dominant factor affecting the permeability of CJRMs. The average permeability of columnar jointed structures increases linearly with the joint density under the same REV size, while the influence from the coefficient of variation can be neglected.

Originality/value

The present paper investigates the REV size of the CJRMs and the effect of joint parameters on the permeability. The proposed method and the results obtained are useful on understanding the hydraulic characteristic of the irregular CJRMs in engineering projects.