bluuebunny/crossref_metadata_2025 huggingface dataset:
Does over-reliance on auditory feedback cause disfluency? An fMRI study of induced fluency in people who stutter
Authors: Meekings Sophie , Jasmin Kyle , Lima Cesar , Scott Sophie
Published: November 2020

This study tested the idea that stuttering is caused by over-reliance on auditory feedback. The theory is motivated by the observation that many fluency-inducing situations, such as synchronised speech and masked speech, alter or obscure the talker’s feedback. Typical speakers show ‘speaking-induced suppression’ of neural activation in superior temporal gyrus (STG) during self-produced vocalisation, compared to listening to recorded speech. If people who stutter over-attend to auditory feedback, they may lack this suppression response. In a 1.5T fMRI scanner, people who stutter spoke in synchrony with an experimenter, in synchrony with a recording, on their own, in noise, listened to the experimenter speaking and read silently. Behavioural testing outside the scanner demonstrated that synchronising with another talker resulted in a marked increase in fluency regardless of baseline stuttering severity. In the scanner, participants stuttered most when they spoke alone, and least when they synchronised with a live talker. There was no reduction in STG activity in the Speak Alone condition, when participants stuttered most. There was also strong activity in STG in response to the two synchronised speech conditions, when participants stuttered least, suggesting that either stuttering does not result from over-reliance on feedback, or that the STG activation seen here does not reflect speech feedback monitoring. We discuss this result with reference to neural responses seen in the typical population.
Naturalistic spatiotemporal stimulus modulation during epiretinal stimulation increases the persistence of retinal ganglion cell responsivity
Authors: Chenais Naïg Aurélia Ludmilla , Leccardi Marta Jole Ildelfonsa Airaghi , Ghezzi Diego
Published: November 2020

Objective

Retinal stimulation in blind patients evokes the sensation of discrete points of light called phosphenes, which allows them performing visual guided tasks, such as orientation, navigation, object recognition, object manipulation and reading. However, the clinical benefit of artificial vision in profoundly blind patients is still tenuous, as several engineering and biophysical obstacles keep it away from natural perception. The relative preservation of the inner retinal neurons in hereditary degenerative retinal diseases, such as retinitis pigmentosa, supports artificial vision through the network-mediated stimulation of retinal ganglion cells. However, the response of retinal ganglion cells to repeated electrical stimulation rapidly declines, primarily because of the intrinsic desensitisation of their excitatory network. In patients, upon repetitive stimulation, phosphenes fade out in less than half of a second, which drastically limits the understanding of the percept.

Approach

A more naturalistic stimulation strategy, based on spatiotemporal modulation of electric pulses, could overcome the desensitisation of retinal ganglion cells. To investigate this hypothesis, we performed network-mediated epiretinal stimulations paired to electrophysiological recordings in retinas explanted from both male and female retinal degeneration 10 mice.

Main results

The results showed that the spatial and temporal modulation of the network-mediated epiretinal stimulation prolonged the responsivity of retinal ganglion cells from 400 ms up to 4.2 s.

Significance

A time-varied, non-stationary and interrupted stimulation of the retinal network, mimicking involuntary microsaccades, might reduce the fading of the visual percept and improve the clinical efficacy of retinal implants.
Only the fastest corticospinal fibers contribute to beta corticomuscular coherence
Authors: Ibáñez J. , Del Vecchio A. , Rothwell J. C. , Baker S. N. , Farina D.
Published: November 2020

A common way to study human corticospinal transmission is with transcranial magnetic stimulation. However, this is biased to activity in the fastest conducting axons. It is unclear whether conclusions obtained in this context are representative of volitional activity in mild-to-moderate contractions. A possible alternative to overcome this limitation is to study the corticospinal transmission of endogenously generated brain activity. Here we study the transmission speeds of cortical beta rhythms travelling to the muscles during steady contractions. To do this, we introduce new methods to improve delay estimates in the corticomuscular transmission of beta rhythms, and which we validate both in simulations and experimentally. Applying these approaches to experimental data from humans, we show that corticomuscular beta transmission delays are only 1-2ms longer than expected from the fastest corticospinal pathway. Simulations using realistic distributions of the conduction velocities for descending axons projecting to lower motoneurons suggest two scenarios that can explain these results: either a very small fraction of only the fastest corticospinal axons selectively transmit beta activity, or else the entire pool does. The implications that these two scenarios have for our understanding of corticomuscular interactions are discussed in the final part of this manuscript.

SIGNIFICANCE

We present and validate an improved methodology to measure the delay in the transmission of cortical beta activity to tonically active muscles. The estimated corticomuscular beta transmission delays which this yields are remarkably similar to those expected from transmission in the fastest corticospinal axons. A simulation of beta transmission along a pool of corticospinal axons using a realistic distribution of fiber diameters suggests two possible mechanisms by which fast corticomuscular transmission is achieved: either a very small fraction of descending axons transmits beta activity to the muscles or, alternatively, the entire population does and natural cancellation of slow channels occurs due to the distribution of axon diameters in the corticospinal tract.
Patterns of MHC-dependent sexual selection in a free-living population of sheep
Authors: Huang Wei , Pilkington Jill G. , Pemberton Josephine M.
Published: November 2020

The MHC is one of the most polymorphic gene clusters in vertebrates and play an essential role in adaptive immunity. Apart from pathogen-mediated selection, sexual selection can also contribute to the maintenance of MHC diversity. MHC-dependent sexual selection could occur via several mechanisms but at present there is no consensus as to which of these mechanisms are involved and their importance. Previous studies have often suffered from limited genetic and behavioural data and small sample size, and were rarely able to examine all the mechanisms together, determine whether signatures of MHC-based non-random mating are independent of genomic effects or differentiate whether MHC-dependent sexual selection takes place at the pre- or post-copulatory stage. In this study, we use Monte Carlo simulation to investigate evidence for non-random MHC-dependent mating patterns by all three mechanisms in a free-living population of Soay sheep. Using 1710 sheep diplotyped at the MHC class IIa region and genome-wide SNPs, together with field observations of consorts, we found sexual selection against a particular haplotype in males at the pre-copulatory stage and sexual selection against female MHC heterozygosity during the rut. We also found MHC-dependent disassortative mating at the post-copulatory stage, along with strong evidence of inbreeding avoidance at both stages. However, results from generalized linear mixed models suggest that the pattern of MHC-dependent disassortative mating could be a by-product of inbreeding avoidance. Our results therefore suggest that while multiple apparent mechanisms of non-random mating with respect to the MHC may occur, some of them have alternative explanations.
Deletion ofLetmd1leads to the disruption of mitochondrial function in brown adipose tissue
Authors: Song Runjie , Du Yaqi , Li Peng , Liu Huijiao , Zheng Han , Lu Xiaohui , Wang Shenghong , Zhou Lijun , Rahman Nafis A , Wołczyński Sławomir , Kretowski Adam , Ren Fazheng , Li Xiru , Li Xiangdong
Published: November 2020

Human cervical cancer oncogene (HCCR-1), also named as LETMD1, is a LETM-domain containing outer mitochondrial membrane protein which plays an important role in the carcinogenesis of cancers. Surprisingly, we found that loss ofLetmd1in mice leads to multiply severe abnormities, such as the brown adipose tissue (BAT) whitening, disruption of thermogenesis, cold-induced death, diet-induced obesity, hyperglycinemia and insulin resistance. Mechanistically, deletion ofLetmd1in BAT causes the reduction of mitochondrial calcium ion, which in turn results in the suppressed fission of mitochondria, and ultimately leads to the depletion ofUcp1-mediated BAT heat production. This study indicates that LETMD1 plays a crucial role in controlling BAT thermogenesis and energy homeostasis by regulating mitochondrial structures and functions, and also provides a novel insight for the clinical biomarker and therapeutical target of oncogene for the metabolic disorders.

Highlights

Letmd1is an oncogene and also highly expressed in brown adipose tissue (BAT) of human and mice.

Loss ofLetmd1leads to BAT whitening, diet-induced obesity, hyperglycemia and insulin resistant.

Letmd1knockout causes the disruption of thermogenesis and death at 4°C exposure.

Deletion ofLetmd1results in mitochondrial calcium homeostasis disorders.

Graphic abstract
Computing the Orientational-Average of Diffusion-Weighted MRI Signals: A Comparison of Different Techniques
Authors: Afzali Maryam , Knutsson Hans , Özarslan Evren , Jones Derek K
Published: November 2020

Numerous applications in diffusion MRI, from multi-compartment modeling to power-law analyses, involves computing the orientationally-averaged diffusion-weighted signal. Most approaches implicitly assume, for a given b-value, that the gradient sampling vectors are uniformly distributed on a sphere (or ‘shell’), computing the orientationally-averaged signal through simple arithmetic averaging. One challenge with this approach is that not all acquisition schemes have gradient sampling vectors distributed over perfect spheres (either by design, or due to gradient non-linearities). To ameliorate this challenge, alternative averaging methods include: weighted signal averaging; spherical harmonic representation of the signal in each shell; and using Mean Apparent Propagator MRI (MAP-MRI) to derive a three-dimensional signal representation and estimate its ‘isotropic part’. This latter approach can be applied to all q-space sampling schemes, making it suitable for multi-shell acquisitions when unwanted gradient non-linearities are present.

Here, these different methods are compared under different signal-to-noise (SNR) realizations. With sufficiently dense sampling points (61points per shell), and isotropically-distributed sampling vectors, all methods give comparable results, (accuracy of MAP-MRI-based estimates being slightly higher albeit with slightly elevated bias as b-value increases). As the SNR and number of data points per shell are reduced, MAP-MRI-based approaches give pronounced improvements in accuracy over the other methods.
Cell cycle lengths of stem cells and their lineage from cellular demography
Authors: Gadre Purna , Nitsure Nitin , Mazumdar Debasmita , Gupta Samir , Ray Krishanu
Published: November 2020

Adult stem cells and their transit-amplifying (TA) progeny dynamically alter their proliferation rates to maintain tissue homeostasis. To test how the division rates of stem cell and TA cells affect tissue growth and differentiation, we developed a computation strategy which estimates the average cell cycle lengths/lifespans of germline stem cells (GSCs) and their TA progeny from cellular demography. Analysis of the wild-type data fromDrosophilatestis using this method indicated anomalous changes in lifespans during the germline transit-amplification with a nearly 1.3-fold increase after the first division and about a 2-fold decrease in the subsequent stage. Genetic perturbations altering the cell cycle rates of GSC and its immediate daughter, the gonialblast (GB), proportionately changed the rates of subsequent TA divisions. Notably, a nearly 2-fold increase or decrease in the total TA duration did not alter the induction of meiosis after four mitotic cycles. Altogether, these results suggest that the rates of GSC and GB divisions can adjust the rates of subsequent divisions and the onset of differentiation.

Significance Statement

Dynamic regulation of the proliferation rate of stem cells and their transit-amplifying daughters maintains tissue homeostasis in different conditions such as tissue regeneration, aging, and hormonal imbalance. Previous studies suggested that a molecular clock in the stem cell progeny determines the timing of differentiation. This work shows that alterations of the rates of stem cell divisions, as well as that of its progeny, could override the differentiation clock in theDrosophilatestis, and highlights a possible mechanism of fine-tuning the transit-amplification program under different conditions such as tissue damage, aging, and hormonal inputs. Also, the method developed for this study could be adapted to estimate lineage expansion plasticity from demographic changes in other systems.

Highlights

Determination of cellular lifespan during transit-amplification from demography

Lifespans of Drosophila male germline cells changes anomalously during the TA

Lifespan changes of germline stem cells readjust that of the progeny cells

Anomalous lifespan expansion midway through TA precedes the Bam onset
Spatial structure of natural boxwood and the invasive box tree moth can promote coexistence
Authors: Ledru Léo , Garnier Jimmy , Gallet Christiane , Noûs Camille , Ibanez Sébastien
Published: November 2020

In the absence of top-down and bottom-up controls, herbivores eventually drive themselves to extinction by ex-hausting their host plants. Poorly mobile herbivores may experiment only local disappearance, because they can recolonize intact plant patches elsewhere, leaving time to previously over-exploited patches to regrow. However most herbivores such as winged insects are highly mobile, which may prevent the formation of spatial heterogeneity.

We test if long-distance dispersal can preclude coexistence using the invasion of box tree moth (Cydalima perspectalis) in Europe as a model system. We build a lattice model and estimate the parameters with a combination of field measurements, experimental data and literature sources. Space corresponds either to a realistic boxwood landscape in the Alps, or to theoretical landscapes of various sizes.

We find that both species persist under a large range of realistic parameter values, despite a severe reduction in boxwood biomass, with an alternation of outbreaks and near-to-extinction moth densities. Large landscapes are necessary for coexistence, allowing the formation of spatial structure. Slow plant regrowth combined with long-distance dispersal could drive moths to extinction, because of resources depletion at the global scale even without a complete synchronization of the local dynamics. The spatial dynamics leads to formation of small plant patches evenly distributed in the landscape, because of a combination of local plant dispersal and global indirect competition between plants through their positive effect on moth population size. Coexistence is favored by such heterogeneous landscapes, because empty patches increase moth mortality during dispersal: the system thus creates its own stability conditions.
A neural turning point - the EEG P3 component tracks unfolding changes of mind
Authors: Parés-Pujolràs Elisabeth , Hatchuel Jeremy , Haggard Patrick
Published: November 2020

The ability to change one’s mind is a key feature of human cognition. Yet, the neural mechanisms underpinning our capacity to change our minds remain poorly understood. Here, we investigated the neural correlates of evidence accumulation and changes of mind in a two-step sequential sampling task. Participants provided a first, quick guess regarding the relative frequencies of target letters in a visual stream, followed by a slower, more deliberate decision. We found that the P3 amplitude evoked by successive target letters tracks an internal signed decision variable and predicts choices on a single-trial level. Moreover, this neural decision variable offers new insights into the dynamics of changes of mind. In particular, we show that the start of evidence accumulation after the early decision constitutes a neural turning point: the P3 evoked by the first letter contrary to the initial decision can be used to predict subsequent changes of mind. Our results highlight a critical interaction between the processing of external evidence and endogenous modulations of decisional parameters that facilitate reversing an original decision.
A short course of Tofacitinib sustains the immunoregulatory effect of CTLA4-Ig in presence of inflammatory cytokines and promotes long-term survival of murine cardiac allografts
Authors: Iglesias Marcos , Khalifian Saami , Oh Byoung Chol , Zhang Yichuan , Miller Devin , Beck Sarah , Brandacher Gerald , Raimondi Giorgio
Published: November 2020

Costimulation blockade-based regimens are a promising strategy for management of transplant recipients. However, maintenance immunosuppression via CTLA4-Ig monotherapy is characterized by high frequency of rejection episodes. Recent evidence suggests that inflammatory cytokines contribute to alloreactive T cell activation in a CD28-independent manner, a reasonable contributor to the limited efficacy of CTLA4-Ig. In this study, we investigated the possible synergism of a combined short-term inhibition of cytokine signaling and CD28 engagement on the modulation of rejection. Our results demonstrate that the JAK/STAT inhibitor Tofacitinib restored the immunomodulatory effect of CTLA4-Ig on mouse alloreactive T cells in presence of inflammatory cytokines. Tofacitinib exposure conferred dendritic cells with a tolerogenic phenotype reducing their cytokine secretion and costimulatory molecules expression. JAK inhibition also directly affected T cell activation. In vivo, the combination of CTLA4-Ig and Tofacitinib induced long-term survival of heart allografts and, importantly, it was equally effective when using grafts subjected to prolonged ischemia. Transplant survival correlated with a reduction in effector T cells and intragraft accumulation of regulatory T cells. Collectively, our studies demonstrate a powerful synergism between CTLA4-Ig and Tofacitinib and suggest their combined use is a promising strategy for improved management of transplanted patients.
No preference for prosocial ‘helping’ behavior in rats with concurrent social interaction opportunities
Authors: Heslin Kelsey A. , Brown Michael F.
Published: November 2020

‘Helping behavior’ tasks are proposed to assess prosocial or ‘empathic’ behavior in rodents. This paradigm characterizes the behavior of subject animals presented with the opportunity to release a conspecific from a distressing situation. Previous studies found a preference in rats for releasing restrained or distressed conspecifics over other controls (e.g., empty restrainers or inanimate objects). An empathy account was offered to explain the observed behaviors, claiming subjects were motivated to reduce the distress of others based on a rodent homologue of empathy. An opposing account attributes all previous results to subjects seeking social-contact. To dissociate these two accounts for helping behavior, we presented subject rats with three simultaneous choice alternatives: releasing a restrained conspecific, engaging a non-restrained conspecific, or not socializing. Subjects showed an initial preference for socializing with the non-restrained conspecific, and no preference for helping. This result contradicts the empathy account, but is consistent with the social-contact account of helping behavior.
Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing
Authors: Mulroney Logan , Wulf Madalee G. , Schildkraut Ira , Tzertzinis George , Buswell John , Jain Miten , Olsen Hugh , Diekhans Mark , Corrêa Ivan R. , Akeson Mark , Ettwiller Laurence
Published: November 2020

Nanopore sequencing devices read individual RNA strands directly. This facilitates identification of exon linkages and nucleotide modifications; however, using conventional methods the 5′ and 3′ ends of poly(A) RNA cannot be identified unambiguously. This is due in part to the architecture of the nanopore/enzyme-motor complex, and in part to RNA degradation in vivo and in vitro that can obscure transcription start and end sites. In this study, we aimed to identify individual full-length human RNA isoform scaffolds among ∼4 million nanopore poly(A)-selected RNA reads. First, to identify RNA strands bearing 5′ m7G caps, we exchanged the biological cap for a modified cap attached to a 45-nucleotide oligomer. This oligomer adaptation method improved 5′ end sequencing and ensured correct identification of the 5′ m7G capped ends. Second, among these 5′-capped nanopore reads, we screened for ionic current signatures consistent with a 3′ polyadenylation site. Combining these two steps, we identified 294,107 individual high-confidence full-length RNA scaffolds, most of which (257,721) aligned to protein-coding genes. Of these, 4,876 scaffolds indicated unannotated isoforms that were often internal to longer, previously identified RNA isoforms. Orthogonal data confirmed the validity of these high-confidence RNA scaffolds.
Efficient and precise single-cell reference atlas mapping with Symphony
Authors: Kang Joyce B. , Nathan Aparna , Zhang Fan , Millard Nghia , Rumker Laurie , Moody D. Branch , Korsunsky Ilya , Raychaudhuri Soumya
Published: November 2020

Recent advances in single-cell technologies and integration algorithms make it possible to construct comprehensive reference atlases encompassing many donors, studies, disease states, and sequencing platforms. Much like mapping sequencing reads to a reference genome, it is essential to be able to map query cells onto complex, multimillion-cell reference atlases to rapidly identify relevant cell states and phenotypes. We present Symphony (https://github.com/immunogenomics/symphony), an algorithm for building integrated reference atlases of millions of cells in a convenient, portable format that enables efficient query mapping within seconds. Symphony localizes query cells within a stable low-dimensional reference embedding, facilitating reproducible downstream transfer of reference-defined annotations to the query. We demonstrate the power of Symphony by (1) mapping a multi-donor, multi-species query to predict pancreatic cell types, (2) localizing query cells along a developmental trajectory of human fetal liver hematopoiesis, and (3) inferring surface protein expression with a multimodal CITE-seq atlas of memory T cells.
Deep Learning-based Ligand Design using Shared Latent Implicit Fingerprints from Collaborative Filtering
Authors: Srinivas Raghuram , Verma Niraj , Kraka Elfi , Larson Eric C.
Published: November 2020

In their previous work, Srinivas et al.1 have shown that implicit fingerprints capture ligands and proteins in a shared latent space, typically for the purposes of virtual screening with collaborative filtering models applied on known bioactivity data. In this work, we extend these implicit fingerprints/descriptors using deep learning techniques to translate latent descriptors into discrete representations of molecules (SMILES), without explicitly optimizing for chemical properties. This allows the design of new compounds based upon the latent representation of nearby proteins, thereby encoding drug-like properties including binding affinities to known proteins. The implicit descriptor method does not require any fingerprint similarity search, which makes the method free of any bias arising from the empirical nature of the fingerprint models. 1 We evaluate the properties of the novel drugs generated by our approach using physical properties of drug-like molecules and chemical complexity. Additionally, we analyze the reliability of the biological activity of the new compounds generated using this method by employing models of protein ligand interaction, which assists in assessing the potential binding affinity of the designed compounds. We find that the generated compounds exhibit properties of chemically feasible compounds and are likely to be excellent binders to known proteins. Furthermore, we also analyze the diversity of compounds created using the Tanimoto distance and conclude that there is a wide diversity in the generated compounds.

Graphical TOC Entry
A conserved ubiquitin- and ESCRT-dependent pathway to regulate human lysosomal membrane proteins
Authors: Zhang Weichao , Yang Xi , Chen Liang , Liu Yun-Yu , Venkatarangan Varsha , Reist Lucas , Hanson Phyllis , Xu Haoxing , Wang Yanzhuang , Li Ming
Published: November 2020

The lysosome is an essential organelle to recycle cellular materials and maintain nutrient homeostasis, but the mechanism to down-regulate lysosomal membrane proteins is poorly understood. In this study, we developed a cycloheximide chase assay to measure the half-lives of ~30 human lysosomal membrane proteins, and identified RNF152 as a short-lived protein. The degradation of RNF152 depends on ubiquitin and the endosomal sorting complexes required for transport (ESCRT) machinery. Ubiquitinated RNF152 is sorted and internalized by the ESCRT machinery into the lysosomal lumen for degradation. Strikingly, when expressed in budding yeast, human RNF152 is also degraded by the vacuole (yeast lysosome) in an ESCRT-dependent manner. Thus, our study uncovered a conserved mechanism to down-regulate lysosome membrane proteins.
A modified fluctuation test for elucidating drug resistance in microbial and cancer cells
Authors: Bokes Pavol , Singh Abhyudai
Published: November 2020

Clonal populations of microbial and cancer cells are often driven into a drug-tolerant persister state in response to drug therapy, and these persisters can subsequently adapt to the new drug environment via genetic and epigenetic mechanisms. Estimating the frequency with which drug-tolerance states arise, and its transition to drug-resistance, is critical for designing efficient treatment schedules. Here we study a stochastic model of cell proliferation where drug-tolerant persister cells transform into a drug-resistant state with a certain adaptation rate, and the resistant cells can then proliferate in the presence of the drug. Assuming a random number of persisters to begin with, we derive an exact analytical expression for the statistical moments and the distribution of the total cell count (i.e., colony size) over time. Interestingly, for Poisson initial conditions the noise in the colony size (as quantified by the Fano factor) becomes independent of the initial condition and only depends on the adaptation rate. Thus, experimentally quantifying the fluctuations in the colony sizes provides an estimate of the adaptation rate, which then can be used to infer the starting persister numbers from the mean colony size. Overall, our analysis introduces a modification of the classical Luria–Delbrück experiment, also called the “Fluctuation Test”, providing a valuable tool to quantify the emergence of drug resistance in cell populations.
The ant fungus garden acts as an external digestive system
Authors: Caraballo-Rodríguez Andrés Mauricio , Puckett Sara P. , Kyle Kathleen E. , Petras Daniel , da Silva Ricardo , Nothias Louis-Félix , Ernst Madeleine , van der Hooft Justin J.J. , Tripathi Anupriya , Wang Mingxun , Balunas Marcy J. , Klassen Jonathan L. , Dorrestein Pieter C.
Published: November 2020

Most animals digest their food within their own bodies, but some do not. Many species of ants grow fungus gardens that pre-digest food as an essential step of the ants’ nutrient uptake. To better understand this digestion process, we generated a 3D molecular map of anAtta texanafungus garden, revealing chemical modifications mediated by the fungus garden as plant material passes through.
Dynamic tracing using ultra-bright labelling and multi-photon microscopy identifies endothelial uptake of poloxamer 188 coated poly(lactic-co-glycolic acid) nano-carriersin vivo
Authors: Khalin Igor , Severi Caterina , Heimburger Doriane , Wehn Antonia , Hellal Farida , Reisch Andreas , Klymchenko Andrey S. , Plesnila Nikolaus
Published: November 2020

Poly(lactic-co-glycolic acid) (PLGA)-based drug formulations are approved for the use in humans, however, the potential of PLGA to design nanoparticles (NPs) and target the central nervous system remains to be exploited.

The aim of the current study was design PLGA NPs, loading them with bulky fluorophores thereby increasing single particle fluorescence to a level visible byin vivomicroscopy, and investigate their brain biodistribution. We developed, highly fluorescent 70 nm PLGA NPs significantly brighter then quantum dots enabling their visualization by intravital real-time 2-photon microscopy. We found that PLGA NPs coated with pluronic F-68 (PF-68) had a substantially longer plasma half-life than uncoated NPs and were taken up by cerebro-vascular endothelial cells. High resolution confocal microscopy revealed that coated PLGA NPs were present in late endothelial endosomes of cerebral vessels within 1 hour after systemic injection and were more readily taken up by endothelial cells in peripheral organs.

The current data suggest that PF-68 coated PLGA NPs are taken up by mouse cerebral and peripheral endothelial cellsin vivo. The combination of ultra-bright NPs andin vivoimaging may thus represent a promising approach to reduce the gap between development and clinical application of nanoparticle-based drug carriers.
Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation
Authors: Haase Robert , Jain Akanksha , Rigaud Stéphane , Vorkel Daniela , Rajasekhar Pradeep , Suckert Theresa , Lambert Talley J. , Nunez-Iglesias Juan , Poole Daniel P. , Tomancak Pavel , Myers Eugene W.
Published: November 2020

Modern life science relies heavily on fluorescent microscopy and subsequent quantitative bio-image analysis. The current rise of graphics processing units (GPUs) in the context of image processing enables batch processing large amounts of image data at unprecedented speed. In order to facilitate adoption of this technology in daily practice, we present an expert system based on the GPU-accelerated image processing library CLIJ: The CLIJ-assistant keeps track of which operations formed an image and suggests subsequent operations. It enables new ways of interaction with image data and image processing operations because its underlying GPU-accelerated image data flow graphs (IDFGs) allow changes to parameters of early processing steps and instantaneous visualization of their final results. Operations, their parameters and connections in the IDFG are stored at any point in time enabling the CLIJ-assistant to offer an undo-function for virtually unlimited rewinding parameter changes. Furthermore, to improve reproducibility of image data analysis workflows and interoperability with established image analysis platforms, the CLIJ-assistant can generate code from IDFGs in programming languages such as ImageJ Macro, Java, Jython, JavaScipt, Groovy, Python and C++ for later use in ImageJ, Fiji, Icy, Matlab, QuPath, Jupyter Notebooks and Napari. We demonstrate the CLIJ-assistant for processing image data in multiple scenarios to highlight its general applicability. The CLIJ-assistant is open source and available online:https://clij.github.io/assistant/
Human hepatocyte PNPLA3 148M exacerbates rapid non-alcoholic steatohepatitis development in chimeric mice
Authors: Kabbani Mohammad , Michailidis Eleftherios , Steensels Sandra , Fulmer Clifton G. , Luna Joseph M. , Le Pen Jérémie , Tardelli Matteo , Razooky Brandon , Ricardo-Lax Inna , Zou Chenhui , Zeck Briana , Stenzel Ansgar F. , Quirk Corrine , Foquet Lander , Ashbrook Alison W. , Schneider William M. , Belkaya Serkan , Lalazar Gadi , Liang Yupu , Pittman Meredith , Devisscher Lindsey , Suemizu Hiroshi , Theise Neil D. , Chiriboga Luis , Cohen David E. , Copenhaver Robert , Grompe Markus , Meuleman Philip , Ersoy Baran A. , Rice Charles M. , de Jong Ype P.
Published: November 2020

Advanced non-alcoholic fatty liver disease (NAFLD) is a rapidly emerging global health problem associated with pre-disposing genetic polymorphisms, most strikingly an isoleucine to methionine substitution in patatin-like phospholipase domain-containing protein 3 (PNPLA3-I148M). Here, we study how human hepatocytes with PNPLA3 148I and 148M variants engrafted in the livers of chimeric mice respond to a hypercaloric Western-style diet. As early as 4 weeks, mice developed dyslipidemia, impaired glucose tolerance, and steatohepatitis selectively in the human graft, followed by pericellular fibrosis after 8 weeks of hypercaloric feeding. The PNPLA3 148M variant, either from a homozygous 148M human donor or overexpressed in a homozygous 148I donor background, caused widespread microvesicular steatosis and even more severe steatohepatitis. We conclude that PNPLA3 148M in human hepatocytes exacerbates NAFLD. These models will facilitate mechanistic studies into human genetic variants associated with advanced fatty liver diseases.
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Authors: Beghini Francesco , McIver Lauren J. , Blanco-Míguez Aitor , Dubois Leonard , Asnicar Francesco , Maharjan Sagun , Mailyan Ana , Thomas Andrew Maltez , Manghi Paolo , Valles-Colomer Mireia , Weingart George , Zhang Yancong , Zolfo Moreno , Huttenhower Curtis , Franzosa Eric A. , Segata Nicola
Published: November 2020

Culture-independent analyses of microbial communities have advanced dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1,262 metagenomes) and IBD (1,635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4,077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbeRuminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.
Biological autoluminescence for assessing oxidative processes in yeast cell cultures
Authors: Vahalová Petra , Červinková Kateřina , Cifra Michal
Published: November 2020

Nowadays, modern medicine is looking for new, more gentle, and more efficient diagnostic methods. A pathological state of an organism is often closely connected with increased amount of reactive oxygen species. They can react with biomolecules and subsequent reactions can lead to very low endogenous light emission (biological autoluminescence -BAL). This phenomenon can be potentially used as a non-invasive and low-operation-cost tool for monitoring oxidative stress during diseases. To contribute to the understanding of the parameters affecting BAL, we analyzed the BAL from yeastSaccharomyces cerevisiaeas a representative eukaryotic organism. The relationship between the BAL intensity and the amount of reactive oxygen species that originates as a result of the Fenton reaction as well as correlation between spontaneous BAL and selected physical and chemical parameters (pH, oxygen partial pressure, and cell concentration) during cell growth were established. Our results contribute to real-time non-invasive methodologies for monitoring oxidative processes in biomedicine and biotechnology.
ATP triggers macropinocytosis that internalizes and is regulated by PANX1
Authors: Boyce Andrew K.J. , van der Slagt Emma , Sanchez-Arias Juan C. , Swayne Leigh Anne
Published: November 2020

Macropinocytosis is an endocytic process that allows cells to respond to changes in their environment by internalizing nutrients and cell surface proteins, as well as modulating cell size. Here, we identify that adenosine triphosphate (ATP) triggers macropinocytosis in murine neuroblastoma cells, thereby internalizing the ATP release channel pannexin 1 (PANX1) while concurrently increasing cross-sectional cellular area. Amiloride, a potent inhibitor of macropinocytosis-associated GTPases, abolished ATP-induced PANX1 internalization and cell area expansion. Transient expression of the GTP-hydrolysis resistant GTPase ARF6 Q67L led to increased PANX1 internalization and increased cell area equivalent to levels seen with ATP stimulation. Mutation of an extracellular tryptophan (W74) in PANX1 abolished ATP-evoked cell area enlargement suggesting that PANX1 regulates this form of macropinocytosis. This novel role of PANX1 in macropinocytosis could be particularly important for disease states implicating PANX1, such as cancer, where ATP can act as a purinergic regulator of cell growth/metastasis and as a supplementary energy source following internalization.
Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains
Authors: Hung Po-Hsiang , Liao Chia-Wei , Ko Fu-Hsuan , Tsai Huai-Kuang , Leu Jun-Yi
Published: November 2020

Enhanced phenotypic diversity increases the likelihood of a population surviving catastrophic conditions. It has been suggested that Hsp90, an essential molecular chaperone in eukaryotes, can suppress (i.e., buffer) or enhance (i.e., potentiate) the effects of genetic variation, enabling organisms to adjust their levels of phenotypic diversity in response to environmental cues. Many Hsp90-interacting proteins are involved in signaling transduction pathways and transcriptional regulation. However, it remains unclear if Hsp90-dependent differential gene expression is common in natural populations. By examining the gene expression profiles of five diverse yeast strains, we identified many genes exhibiting Hsp90-dependent strain-specific differential expression. We employed an analysis pipeline to identify transcription factors (TFs) potentially contributing to variable expression. We found that upon Hsp90 inhibition or heat stress, activities or abundances of Hsp90-dependent TFs varied among strains, resulting in differential strain-specific expression of their target genes, which consequently led to phenotypic diversity. We provide evidence that individual populations can readily display specific Hsp90-dependent gene expression, suggesting that the evolutionary impacts of Hsp90 are widespread in nature.

Highlights

Hsp90-dependent gene expression varies among different yeast strains.

Hsp90 differentially influences transcriptional activity or protein abundances of transcription factors among yeast strains.

Differential strain-specific gene expression is correlated with phenotypic variations upon Hsp90 inhibition.

Hsp90-mediated strain-specific regulation manifests under environmental stress.
Anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) potency of Mefloquine as an entry inhibitor in vitro
Authors: Shionoya Kaho , Yamasaki Masako , Iwanami Shoya , Ito Yusuke , Fukushi Shuetsu , Ohashi Hirofumi , Saso Wakana , Tanaka Tomohiro , Aoki Shin , Kuramochi Kouji , Iwami Shingo , Takahashi Yoshimasa , Suzuki Tadaki , Muramatsu Masamichi , Takeda Makoto , Wakita Takaji , Watashi Koichi
Published: November 2020

Coronavirus disease 2019 (COVID-19) has caused serious public health, social, and economic damage worldwide and effective drugs that prevent or cure COVID-19 are urgently needed. Approved drugs including Hydroxychloroquine, Remdesivir or Interferon were reported to inhibit the infection or propagation of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), however, their clinical efficacies have not yet been well demonstrated. To identify drugs with higher antiviral potency, we screened approved anti-parasitic/anti-protozoal drugs and identified an anti-malarial drug, Mefloquine, which showed the highest anti-SARS-CoV-2 activity among the tested compounds. Mefloquine showed higher anti-SARS-CoV-2 activity than Hydroxychloroquine in VeroE6/TMPRSS2 and Calu-3 cells, with IC50= 1.28 μM, IC90= 2.31 μM, and IC99= 4.39 μM in VeroE6/TMPRSS2 cells. Mefloquine inhibited viral entry after viral attachment to the target cell. Combined treatment with Mefloquine and Nelfinavir, a replication inhibitor, showed synergistic antiviral activity. Our mathematical modeling based on the drug concentration in the lung predicted that Mefloquine administration at a standard treatment dosage could decline viral dynamics in patients, reduce cumulative viral load to 7% and shorten the time until virus elimination by 6.1 days. These data cumulatively underscore Mefloquine as an anti-SARS-CoV-2 entry inhibitor.
Detecting flying insects using mega-nets and meta-barcoding
Authors: Svenningsen Cecilie S. , Frøslev Tobias Guldberg , Bladt Jesper , Pedersen Lene Bruhn , Larsen Jonas Colling , Ejrnæs Rasmus , Fløjgaard Camilla , Hansen Anders Johannes , Heilmann-Clausen Jacob , Dunn Robert R. , Tøttrup Anders P.
Published: November 2020

Insect diversity and abundance are increasingly reported as being under pressure. However, monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect diversity across a large spatial scale within a limited time period.

During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples were processed with a DNA metabarcoding protocol to estimate taxonomic composition, and the results were compared to known flying insect diversity and occurrence data.

We detected 15 out of 19 flying insect orders present in Denmark. Diptera. Psocoptera and Thysanoptera were overrepresented, while Hymenoptera, Coleoptera, Lepidoptera, Trichoptera, Odonata, Neuroptera and Plecoptera were underrepresented, compared to Danish estimates. We detected 319 species not known for Denmark. Our results indicate that this method can assess the flying insect fauna to a wide extent, but may be, like other methods, biased towards certain insect orders. Furthermore, car net sampling and DNA metabarcoding can update species records for Denmark while preserving specimens for natural history collections.
A Unique Renal Architecture inTribolium castaneumInforms the Evolutionary Origins of Systemic Osmoregulation in Beetles
Authors: Koyama Takashi , Naseem Muhammad Tayyib , Kolosov Dennis , Vo Camilla Trang , Mahon Duncan , Jakobsen Amanda Sofie Seger , Jensen Rasmus Lycke , Denholm Barry , O’Donnell Michael , Halberg Kenneth Agerlin
Published: November 2020

Maintaining internal salt and water balance in response to fluctuating external conditions is essential for animal survival. This is particularly true for insects as their high surface-to-volume ratio makes them highly susceptible to osmotic stress. However, the cellular and hormonal mechanisms that mediate the systemic control of osmotic homeostasis in beetles (Coleoptera), the largest group of insects, remain largely unidentified. Here, we demonstrate that eight neurons in the brain of the red flour beetleTribolium castaneumrespond to internal changes in osmolality by releasing diuretic hormone (DH) 37 and DH47 – homologues of vertebrate corticotropinreleasing factor (CRF) hormones – to control systemic water balance. Knockdown of the gene encoding the two hormones (Urinate, Urn8) reduces renal secretion and restricts organismal fluid loss, whereas injection of DH37 or DH47 reverses these phenotypes. We further identify a novel CRF-like receptor, Urinate Receptor (Urn8R), which is exclusively expressed in a unique secondary cell (SC) in the beetle renal organs, as underlying this response. Activation of Urn8R increases K+secretion specifically through SCs, creating a lumen-positive transepithelial potential that drives fluid secretion. Together, these data show that beetle renal organs operate by fundamentally different mechanism than those of other insects. Finally, we adopt a fluorescent labelling strategy to identify the evolutionary origin of this unusual renal architecture within the large Order of Coleoptera. Our work thus uncovers an important homeostatic program that is key to maintaining osmotic control in beetles, which evolved in parallel to the radiation of the higher beetle families.

Significance Statement

Beetles are the most diverse animal group on the planet. Their evolutionary success suggests unique physiological adaptations in overcoming water stress, yet the mechanisms underlying this ability are unknown. Here we use molecular genetic, electrophysiology and behavioral studies to show that a group of brain neurons responds to osmotic disturbances by releasing diuretic hormones that regulate salt and water balance. These hormones bind to their receptor exclusively localized to a unique secondary cell in the renal organs to modulate fluid secretion and organismal water loss. This renal architecture, common to all higher beetle families, is novel within the insects, and provides an important clue to the evolutionary success of the beetles in colonizing an astounding range of habitats on Earth.
Deciphering the genetic basis of wheat seminal root anatomy uncovers ancestral axial conductance alleles
Authors: Hendel Elisha , Bacher Harel , Oksenberg Adi , Walia Harkamal , Schwartz Nimrod , Peleg Zvi
Published: November 2020

Root axial conductance which describes the ability of water to pass throw the xylem, contributes to the rate of water uptake from the soil throughout the whole plant lifecycle. In a rainfed wheat agro-system, grain-filling is typically occurring during declining water availability (i.e. terminal drought). Therefore, preserving soil water moisture during grain filling could serve as a key adaptive trait. We hypothesized that lower wheat root axial conductance can promote higher yields under terminal drought. A segregating population derived from a cross between durum wheat and its direct progenitor wild emmer wheat was used to underpin the genetic basis of seminal root architectural and functional traits. We detected 75 QTL associated with seminal roots morphological, anatomical, and physiological traits, with several hotspots harboring co-localized QTL. We further validated the axial conductance and central metaxylem QTL using wild introgression lines. Field-based characterization of genotypes with contrasting axial conductance suggested the contribution of low axial conductance as a mechanism for water conservation during grain filling and consequent increase in grain size and yield. Our findings underscore the potential of introducing wild alleles to reshape the wheat root system architecture for greater adaptability under changing climate.