bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct Synaptic Transfer Functions in Same-Type Photoreceptors
Authors: Schröder Cornelius , Oesterle Jonathan , Berens Philipp , Yoshimatsu Takeshi , Baden Tom
Published: February 2021

Many sensory systems use ribbon-type synapses to transmit their signals to downstream circuits. The properties of this synaptic transfer fundamentally dictate which aspects in the original stimulus will be accentuated or suppressed, thereby partially defining the detection limits of the circuit. Accordingly, sensory neurons have evolved a wide variety of ribbon geometries and vesicle pool properties to best support their diverse functional requirements. However, the need for diverse synaptic functions does not only arise across neuron types, but alsowithin. Here we show that UV-cones, a single type of photoreceptor of the larval zebrafish eye, exhibit striking differences in their synaptic ultrastructure and consequent calcium to glutamate transfer function depending on their location in the eye. We arrive at this conclusion by combining serial section electron microscopy and simultaneous “dual-colour” 2-photon imaging of calcium and glutamate signals from the same synapsein vivo. We further use the functional dataset to fit a cascade-like model of the ribbon synapse with different vesicle pool sizes, transfer rates and other synaptic properties. Exploiting recent developments in simulation-based inference, we obtain full posterior estimates for the parameters and compare these across different retinal regions. The model enables us to extrapolate to new stimuli and to systematically investigate different response behaviours of various ribbon configurations. We also provide an interactive, easy-to-use version of this model as an online tool. Overall, we show that already on the synaptic level of single neuron types there exist highly specialized mechanisms which are advantageous for the encoding of different visual features.
Projecting ancient ancestry in modern-day Arabians and Iranians: a key role of the past exposed Arabo-Persian Gulf on human migrations
Authors: Ferreira Joana C. , Alshamali Farida , Montinaro Francesco , Cavadas Bruno , Torroni Antonio , Pereira Luisa , Raveane Alessandro , Fernandes Veronica
Published: February 2021

Arabian Peninsula is strategic for investigations centred on the structuring of the modern human population in the three main groups, in the awake of the out-of-Africa migration. Despite the poor climatic conditions for recovery of ancient DNA human evidence in Arabia, the availability of genomic data from neighbouring ancient specimens and of informative statistical tools allow better modelling the ancestry of these populations. We applied this approach to a dataset of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking west Arabia with Levant, and east Arabia with Iran and Caucasus. East Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for possible bias due to recent sub-Saharan African input in their genomes. Not surprisingly, east Arabians were also the ones with higher similarity with Iberomaurusians, who were so far the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans that diverged from the common European-East Asian pool before 50 thousand years ago, and before the later interbred with Neanderthals. Our results are strong evidence to include the exposed basin of the Arabo-Persian Gulf as possible home of basal Eurasians, to be investigated further on namely by searching ancient Arabian human specimens.
An ultrasensitive GRAB sensor for detecting extracellular ATPin vitroandin vivo
Authors: Wu Zhaofa , He Kaikai , Chen Yue , Li Hongyu , Pan Sunlei , Li Bohan , Liu Tingting , Wang Huan , Du Jiulin , Jing Miao , Li Yulong
Published: February 2021

The purinergic transmitter ATP (adenosine 5’-triphosphate) plays an essential role in both the central and peripheral nervous systems, and the ability to directly measure extracellular ATP in real time will increase our understanding of its physiological functions. We developed an ultrasensitiveGPCRActivation‒Based ATP sensor called GRABATP1.0, with a robust fluorescence response to extracellular ATP when expressed in several cell types. This sensor has sub-second kinetics, ATP affinity in the range of tens of nanomolar, and can be used to localize ATP release with subcellular resolution. Using this sensor, we monitored ATP release under a variety ofin vitroandin vivoconditions, including primary hippocampal neurons, a zebrafish model of injury-induced ATP release, and LPS-induced ATP-release events in individual astrocytes in the mouse cortex measured usingin vivotwo-photon imaging. Thus, the GRABATP1.0sensor is a sensitive, versatile tool for monitoring ATP release and dynamics under both physiological and pathophysiological conditions.
Disrupted circadian core-clock oscillations in Type 2 Diabetes are linked to altered rhythmic mitochondrial metabolism
Authors: Gabriel Brendan M. , Altıntaş Ali , Smith Jonathon A.B. , Sardon-Puig Laura , Zhang Xiping , Basse Astrid L. , Laker Rhianna C. , Gao Hui , Liu Zhengye , Dollet Lucile , Treebak Jonas T. , Zorzano Antonio , Huo Zhiguang , Rydén Mikael , Lanner Johanna T. , Esser Karyn A. , Barrès Romain , Pillon Nicolas J. , Krook Anna , Zierath Juleen R.
Published: February 2021

Circadian rhythms are generated by an auto-regulatory feedback loop composed of transcriptional activators and repressors. Disruption of circadian rhythms contributes to Type 2 diabetes (T2D) pathogenesis. We elucidated whether altered circadian rhythmicity of clock genes is associated with metabolic dysfunction in T2D. Transcriptional cycling of core clock genesARNTL, CLOCK,CRY1andNR1D1was altered in skeletal muscle from individuals with T2D and this was coupled with reduced number and amplitude of cycling genes and disturbed circadian oxygen consumption. Mitochondrial associated genes were enriched for differential circadian amplitudes in T2D, and positively correlated with insulin sensitivity. ChIP- sequencing identified CLOCK and BMAL1 binding to circadian mitochondrial genes associated with insulin sensitivity, implicating regulation by the core clock. Mitochondria disruption altered core-clock gene expression and free-radical production, phenomena that were restored by resveratrol treatment. We identify bi-directional communication between mitochondrial function and rhythmic gene expression, processes which are disturbed in diabetes.
Selection of active defensive behaviors relies on extended amygdala dopamine D2 receptors
Authors: Castell Laia , Gall Valentine Le , Cutando Laura , Puighermanal Emma , Jercog Daniel , Tarot Pauline , Tassou Adrien , Harrus Anne-Gabrielle , Rubinstein Marcelo , Nouvian Régis , Rivat Cyril , Herry Cyril , Valjent Emmanuel
Published: February 2021

The ability to efficiently switch from one defensive strategy to another maximizes an animal’s chance of survival. Here, we demonstrate that the selection of active defensive behaviors requires the coordinated activation of dopamine D2 receptor (D2R) signaling within the central extended amygdala (EA) comprising the nucleus accumbens, the oval bed nucleus stria terminals and the central amygdala. We find that discriminative learning between predictive and non-predictive threat auditory stimuli is unaltered in mice carrying a temporally-controlled deletion of D2R within output neurons of the EA. In contrast, intact EA D2R signaling is required for active avoidance learning and innate flight responses triggered by a visual threat stimulus (looming). Consequently, conditional D2R knockout mice biased defensive responses toward passive defensive strategies. Altogether, these findings identify EA D2R signaling as an important mechanism by which DA regulates the switch from passive to active defensive behaviors, regardless whether of learned or innate threat.
Rapid adaptation and remote delivery of undergraduate research training during the COVID 19 Pandemic
Authors: Yowler Joanna Yang , Knier Kit , WareJoncas Zachary , Ehlers Shawna L. , Ekker Stephen C. , Reyes Fabiola Guasp , Horazdovsky Bruce F. , Mueller Glenda , Gomez Adriana Morales , Sood Amit , Sussman Caroline R. , Scholl Linda M. , Weavers Karen M. , Pierret Chris
Published: February 2021

COVID-19 continues to alter daily life around the globe. Education is particularly affected by shifts to distance learning. This change has poignant effects on all aspects of academic life, including the consequence of increased mental stress reported specifically for students. COVID-19 cancellations of many summer fellowships and internships for undergraduates across the country increased students’ uncertainty about their educational opportunities and careers. When the pandemic necessitated elimination of on-campus programming at Mayo Clinic, a new program was developed for remote delivery. Summer Foundations in Research (SFIR) was drafted around 4 aims: 1) support the academic trajectory gap in research science created by COVID-19; 2) build sustainable scientific relationships with mentors, peers, and the community; 3) create opportunities for participants to share and address concerns with their own experiences in the pandemic; and 4) provide support for individual wellbeing. SFIR included research training, but also training in communication through generative Dialogue and resilience through Amit Sood’s SMART program. 170 participants were followed for outcomes in these spaces. Knowledge of and interest in careers involving biomedical research rose significantly following SFIR. Participants’ mean confidence levels in 12 Key areas of research rose between 0.08 to 1.32 points on a 7-point scale. The strongest gains in mean confidence levels were seen in designing a study and collaborating with others. SFIR participants demonstrated gains in perceived happiness, and measured resilience and a reduction in stress. Participants’ qualitative responses indicated exceptionally positive mentor relationships and specific benefit of both the SMART program and Dialogue.
Efficient Agony Based Transfer Learning Algorithms for Survival Forecasting
Authors: Tamaskar Abhinav , Bannon James , Mishra Bud
Published: February 2021

Progression modeling is a mature subfield of cancer bioinformatics, but it has yet to make a proportional clinical impact. The majority of the research in this area has focused on the development of efficient algorithms for accurately reconstructing sequences of (epi)genomic events from noisy data. We see this as the first step in a broad pipeline that will translate progression modeling to clinical utility, with the subsequent steps involving inferring prognoses and optimal therapy programs for different cancers and using similarity in progression to enhance decision making. In this paper we take some initial steps in completing this pipeline. As a theoretical contribution, we introduce a polytime-computable pairwise distance between progression models based on the graph-theoretic notion of “agony”. Focusing on a particular progression model we can then use this agony distance to cluster (dis)similarities viamulti-dimensional scaling. We recover known biological similarities and dissimilarities. Finally, we use the agony distance to automate transfer learning experiments and show a large improvement in the ability to forecast time to death.
Binocular vs. monocular recovery experience differentially promote recovery from visual deficits in a mouse model of amblyopia
Authors: Martinez Jessy D. , Donnelly Marcus J. , Popke Donald S. , Torres Daniel , Sheskey Sarah , Clawson Brittany C. , Jiang Sha , Aton Sara J.
Published: February 2021

Altered visual experience during monocular deprivation (MD) profoundly changes in ocular dominance (OD) in the developing primary visual cortex (V1). MD-driven changes in OD are an experimental model of amblyopia, where early-life alterations in vision lead visual disruption in adulthood. Current treatments for amblyopia include patching of the dominant eye, and more recently-developed binocular therapies. However, the relative impact of monocular vs. binocular recovery experiences on recovery of function in V1 is not well understood. Using single-unit recording, we compared how binocular recovery [BR] or reverse occlusion [RO] of identical duration and content affects OD and visual response recovery in mouse binocular V1 after a period of MD. We also tested how BR and RO affected MD-driven alterations of parvalbumin expression, and visually-driven expression of cFos in parvalbumin-positive and negative neurons. Finally, we tested how BR and RO affected recovery of normal visual acuity for the two eyes in the context of visually-driven behavior. We find that BR is quantitatively superior with respect to normalization of V1 neurons’ OD, visually-driven cFos expression, and visual acuity for the two eyes. However, MD-driven changes in the firing rate and response properties of V1 principal neuron and fast-spiking interneuron populations do not recover fully after either BR or RO. Binocular matching of orientation preference also remains disrupted in V1 neurons after both forms of recovery experience. Thus BR and RO, analogs of differing treatment regimens for amblyopia, differentially impact various aspects of visual recovery in a mouse model for amblyopia.

Significance Statement

Amblyopia resulting from altered childhood eye function is a leading cause of lifelong vision loss. Treatment typically involves patching of the dominant eye (forcing monocular visual experience), and produces only partial recovery of vision. Using a well-established mouse model of amblyopia, we directly compared how two types of visual experiences influence recovery of visual function. Our findings suggest that binocular vs. monocular visual experience differentially effect restoration of normal visual responses in cortical neurons, visually-driven neuronal gene expression, and visual acuity. Understanding how the quality of recovery experience impacts visual system recovery in amblyopia should provide critical insights for clinical strategies for its treatment.
Progranulin promotes immune evasion of pancreatic adenocarcinoma through regulation of MHCI expression
Authors: Cheung Phyllis F , Yang JiaJin , Krengel Kirsten , Althoff Kristina , Yip Chi Wai , Siu Elaine HL , Ng Linda WC , Lang Karl S , Cham Lamin , Engel Daniel R , Soun Camille , Cima Igor , Scheffler Björn , Striefler Jana K , Sinn Marianne , Bahra Marcus , Pelzer Uwe , Oettle Helmut , Markus Peter , Smeets Esther MM , Aarntzen Erik HJG , Savvatakis Konstantinos , Liffers Sven-Thorsten , Neander Christian , Bazarna Anna , Zhang Xin , Merkler Doron , Paschen Annette , Crawford Howard C. , Chan Anthony WH , Cheung Siu Tim , Siveke Jens T
Published: February 2021

Immune evasion is indispensable for cancer initiation and progression, although its underlying mechanisms in pancreatic ductal adenocarcinoma (PDAC) remain elusive. Here, we unveiled a cancer cell-autonomous function of PGRN in driving immune evasion in primary PDAC. Tumor- but not macrophage-derived PGRN was associated with poor overall survival in PDAC. Multiplex immunohistochemistry revealed low MHC class I (MHCI) expression and lack of CD8+ T cells infiltration in PGRN-high tumors. Inhibition of PGRN abrogated autophagy-dependent MHCI degradation and restored MHCI expression on PDAC cells. Antibody-based blockade of PGRN in a genetic PDAC mouse model remarkably decelerated tumor initiation and progression. Notably, tumors expressing LCMV-gp33 as model antigen were sensitized towards cytotoxic gp33-TCR transgenic T cells upon anti-PGRN antibody treatment. Overall, our study uncovered an unprecedented role of tumor-derived PGRN in regulating immunogenicity of primary PDAC.

STATEMENT OF SIGNIFICANCE

Immune evasion is a key property of PDAC, rendering it refractory to immunotherapy. Here we demonstrate that tumor-derived PGRN promotes autophagy-dependent MHCI degradation, while anti-PGRN increases intratumoral CD8 infiltration and blocks tumor progression. With recent advances in T cell-mediated approaches, PGRN represents a pivotal target to enhance tumor antigen-specific cytotoxicity.
Examining the quality and fertilization competence of bovine ejaculate with low progressive motility – should we give it a chance?
Authors: Li Y. , Kalo D. , Komsky-Elbaz A. , Zeron Y. , Roth Z.
Published: February 2021

Spermatozoa progressive motility is positively correlated with fertilization competence. Bulls’ ejaculates with progressive motility lower than 50% are routinely rejected through the process of straw preparation, designated for artificial insemination of dairy cows. We examined the quality and fertility competence of ejaculates with relative low progressive motility (55–60%, n = 5; control) with those of very low progressive motility i.e. below the lower threshold, (20-45%, n = 5; rejected). Analysis revealed a lower volume for the control vs. rejected samples. Dip-Quick staining revealed a higher proportion of spermatozoa with abnormal morphology in the rejected group, in particular those with detached heads. Activation of spermatozoa with calcium ionophore, resulted by a lower proportion of activated spermatozoa in the rejected group. In addition, a higher proportion of spermatozoa with DNA damage were recorded in the rejected vs. the control samples. Following in-vitro fertilization, the proportion of oocytes that developed to the 2- and 4-cell stage embryos did not differ between groups. However, the proportion of embryos that further developed to blastocysts, was higher in the control group. Transcript abundance of selected genes in the blastocysts and the apoptotic index did not differ between groups, suggesting that the forming blastocysts were of the same quality. It is suggested that in specific cases, for example genetically superior bulls, ejaculates with very low progressive motility can be used forin vitroproduction of embryo. Furtherin vivoexaminations, i.e. artificial insemination or transferring of embryos derived from these inferior ejaculates, might clarified this point.
Determinants of ligand-functionalized DNA nanostructure-cell interactions
Authors: Cremers Glenn A.O. , Rosier Bas J.H.M. , Meijs Ab , Tito Nicholas B. , van Duijnhoven Sander M.J. , van Eenennaam Hans , Albertazzi Lorenzo , de Greef Tom F.A.
Published: February 2021

Synthesis of ligand-functionalized nanomaterials with control over size, shape and ligand orientation, facilitates the design of tailored nanomedicines for therapeutic purposes. DNA nanotechnology has emerged as a powerful tool to rationally construct two- and three-dimensional nanostructures, enabling site-specific incorporation of protein ligands with control over stoichiometry and orientation. To efficiently target cell surface receptors, exploration of the parameters that modulate cellular accessibility of these nanostructures is essential. In this study we systematically investigate tunable design parameters of antibody-functionalized DNA nanostructures binding to therapeutically relevant receptors. We show that, although the native affinity of antibody-functionalized DNA nanostructures remains unaltered, the absolute number of bound surface receptors is lower compared to soluble antibodies and is mainly governed by nanostructure size and DNA handle location. The obtained results provide key insights in the ability of ligand-functionalized DNA nanostructures to bind surface receptors and yields design rules for optimal cellular targeting.
Csf1r-GCaMP5 Reporter Mice Reveal Immune Cell Communication in Vitro and in Vivo
Authors: Taghdiri N , Calcagno D , Fu Z , Huang K , Kohler RH , Weissleder R , Coleman TP , Kevin KR
Published: February 2021

Interconnected cells are responsible for emergent functions ranging from cognition in the brain to cyclic contraction in the heart. In electrically excitable cells, methods for studying cell communication are highly advanced, but in non-excitable cells, generalized methods for studying cell communication are less mature. Immune cells have generally been classified as non-excitable cells with diverse pathophysiologic roles that span every tissue in the body, yet little is known about their interconnectedness because assays are destructive and have low temporal resolution. In this work, we hypothesize that non-excitable immune cells are functionally interconnected in previously unrecognized cell communication networks. To test the hypothesis, we created a hematopoietic calcium reporter mouse (Csf1r-Cre × GCaMP5) and non-destructively quantified the spatiotemporal dynamics of intracellular calciumin vitroandin vivo.In vitro, bone marrow derived macrophages calcium reporters reveal that fatal immune stimulatory DNA-sensing induces rapid intercellular communication to neighboring cells.In vivo, using intravital microscopy through a dorsal window chamber in the context of MC38-H2B-mCherry tumors, Csf1r-GCaMP5 reporters exhibit spatiotemporal dynamics consistent with cell communication. We present a theoretical framework and analysis pipeline for identifying spatiotemporal locations of “excess synchrony” of calcium spiking as a means of inferring previously unrecognized cell communication events. Together, these methods provide a toolkit for investigating known and as-yet-undiscovered cell communication eventsin vitroandin vivo.
A 48-Channel Receive Array Coil for Mesoscopic Diffusion-Weighted MRI of Humanex vivoBrain Imaging on the 3T Connectome Scanner
Authors: Scholz Alina , Etzel Robin , May Markus W , Mahmutovic Mirsad , Tian Qiyuan , Ramos-Llordén Gabriel , Bilgiç Berkin , Witzel Thomas , Stockmann Jason P , Mekkaoui Choukri , Wald Lawrence L , Huang Susie Y , Yendiki Anastasia , Keil Boris
Published: February 2021

In vivodiffusion-weighted magnetic resonance imaging is limited in signal-to-noise-ratio (SNR) and acquisition time, which constrains spatial resolution to the macroscale regime.Ex vivoimaging, which allows for arbitrarily long scan times, is critical for exploring human brain structure in the mesoscale regime without loss of SNR. Standard head array coils designed for patients are sub-optimal for imagingex vivowhole brain specimens. The goal of this work was to design and construct a 48-channelex vivowhole brain array coil for high-resolution and highb-value diffusion-weighted imaging on a 3T Connectome scanner. The coil was validated with bench measurements and characterized by imaging metrics on an agar brain phantom and anex vivohuman brain sample. The two-segment coil former was constructed for a close fit to a whole human brain, with small receive elements distributed over the entire brain. Imaging tests including SNR and G-factor maps were compared to a 64-channel head coil designed forin vivouse. There was a 2.9-fold increase in SNR in the peripheral cortex and a 1.3-fold gain in the center when compared to the 64-ch head coil. The 48-channelex vivowhole brain coil also decreases noise amplification in highly parallel imaging, allowing acceleration factors of approximately one unit higher for a given noise amplification level. The acquired diffusion-weighted images in a wholeex vivobrain specimen demonstrate the applicability of the developed coil for high-resolution and highb-value diffusion-weightedex vivobrain MRI studies.
Quantitative analysis of neuronal mitochondrial movement reveals patterns resulting from neurotoxicity of rotenone and 6-hydroxydopamine
Authors: Simões Rui F. , Pino Rute , Moreira-Soares Maurício , Kovarova Jaromira , Neuzil Jiri , Travasso Rui , Oliveira Paulo J. , Cunha-Oliveira Teresa , Pereira Francisco B.
Published: February 2021

Alterations in mitochondrial dynamics, including their trafficking, can present early manifestation of neuronal degeneration. However, current methodologies used to study mitochondrial trafficking events rely on parameters that are mostly altered in later stages of neurodegeneration. Our objective was to establish a reliable computational methodology to detect early alterations in neuronal mitochondrial trafficking. We propose a novel quantitative analysis of mitochondria trajectories based on innovative movement descriptors, including straightness, efficiency, anisotropy, and kurtosis. Using biological data from differentiated SH-SY5Y cells treated with mitochondrial toxicants 6-hydroxydopamine and rotenone, we evaluated time and dose-dependent alterations in trajectory descriptors. Mitochondrial movement was analyzed by total internal reflection fluorescence microscopy followed by computer modelling to describe the process. The stacks of individual images were analyzed by an open source MATLAB algorithm (www.github.com/kandelj/MitoSPT) and to characterize mitochondria trajectories, we used the Python package trajpy (https://github.com/ocbe-uio/trajpy/). Our results confirm that this computational approach is effective and accurate in order to study mitochondrial motility and trajectories in the context of healthy and diseased neurons in different stages.
Bacteriophage self-counting in the presence of viral replication
Authors: Coleman Seth , Yao Tianyou , Nguyen Thu Vu Phuc , Golding Ido , Igoshin Oleg
Published: February 2021

When host cells are in low abundance, temperate bacteriophages opt for dormant (lysogenic) infection. Phage lambda implements this strategy by increasing the frequency of lysogeny at higher multiplicity of infection (MOI). However, it remains unclear how the phage reliably counts infecting viral genomes even as their intracellular number increases due to replication. By combining theoretical modeling with single-cell measurements of viral copy number and gene expression, we find that, instead of hindering lambda’s decision, replication facilitates it. In a nonreplicating mutant, viral gene expression simply scales with MOI rather than diverging into lytic (virulent) and lysogenic trajectories. A similar pattern is followed during early infection by wildtype phage. However, later in the infection, the modulation of viral replication by the decision genes amplifies the initially modest gene expression differences into divergent trajectories. Replication thus ensures the optimal decision—lysis upon single-phage infection, lysogeny at higher MOI.
Prolonged epigenetic and synaptic plasticity alterations following single exposure to a psychedelic in mice
Authors: de la Fuente Revenga Mario , Zhu Bohan , Guevara Christopher A. , Naler Lynette B. , Saunders Justin M. , Zhou Zirui , Toneatti Rudy , Sierra Salvador , Wolstenholme Jennifer T. , Beardsley Patrick M. , Huntley George W. , Lu Chang , González-Maeso Javier
Published: February 2021

Clinical evidence suggests a potential therapeutic effect of classic psychedelics for the treatment of depression. The most outstanding and distinct characteristic is the rapid and sustained antidepressant action with one single exposure to the drug. However, the biological substrates and key mediators of psychedelics’ enduring action remain unknown. Here, we show that a single administration of the psychedelic DOI produced fast-acting effects on frontal cortex dendritic spine structure and acceleration of fear extinction via the 5-HT2Areceptor. Additionally, a single dose of DOI led to changes in chromatin organization particularly at enhancer regions of genes involved in synaptic assembly that stretched for days after the psychedelic exposure. DOI-induced alterations in neuronal epigenome overlapped with genetic loci associated with schizophrenia, depression and attention deficit hyperactivity disorder. Together, these data support the notion that epigenetic-driven changes in synaptic plasticity operate as the mechanistic substrate of psychedelic’s long-lasting antidepressant action but also warn on the limitations in individuals with underlying risk for psychosis.
Rats spontaneously perceive global motion direction of drifting plaids
Authors: Matteucci Giulio , Zattera Benedetta , Marotti Rosilari Bellacosa , Zoccolan Davide
Published: February 2021

Computing global motion direction of extended visual objects is a hallmark of primate high-level vision. Although neurons selective for global motion have also been found in mouse visual cortex, it remains unknown whether rodents can combine multiple motion signals into global, integrated percepts. To address this question, we trained two groups of rats to discriminate either gratings (G group) or plaids (i.e., superpositions of gratings with different orientations; P group) drifting horizontally along opposite directions. After the animals learned the task, we applied a visual priming paradigm, where presentation of the target stimulus was preceded by the brief presentation of either a grating or a plaid. The extent to which rat responses to the targets were biased by such prime stimuli provided a measure of the spontaneous, perceived similarity between primes and targets. We found that gratings and plaids, when uses as primes, were equally effective at biasing the perception of plaid direction for the rats of the P group. Conversely, for G group, only the gratings acted as effective prime stimuli, while the plaids failed to alter the perception of grating direction. To interpret these observations, we simulated a decision neuron reading out the representations of gratings and plaids, as conveyed by populations of either component or pattern cells (i.e., local or global motion detectors). We concluded that the findings for the P group are highly consistent with the existence of a population of pattern cells, playing a functional role similar to that demonstrated in primates. We also explored different scenarios that could explain the failure of the plaid stimuli to elicit a sizable priming magnitude for the G group. These simulations yielded testable predictions about the properties of motion representations in rodent visual cortex at the single-cell and circuitry level, thus paving the way to future neurophysiology experiments.
Reconstitution of ultrawide DNA origami pores in liposomes for transmembrane transport of macromolecules
Authors: Fragasso Alessio , Franceschi Nicola De , Stömmer Pierre , van der Sluis Eli O. , Dietz Hendrik , Dekker Cees
Published: February 2021

Molecular traffic across lipid membranes is a vital process in cell biology that involves specialized biological pores with a great variety of pore diameters, from fractions of a nanometer to >30 nm. Creating artificial membrane pores covering similar size and complexity will aid the understanding of transmembrane molecular transport in cells, while artificial pores are also a necessary ingredient for synthetic cells. Here, we report the construction of DNA origami nanopores that have an inner diameter as large as 30 nm. We developed new methods to successfully insert these ultrawide pores into the lipid membrane of giant unilamellar vesicles (GUVs) by administering the pores concomitantly with vesicle formation in an inverted-emulsion cDICE technique. The reconstituted pores permit the transmembrane diffusion of large macromolecules such as folded proteins, which demonstrates the formation of large membrane-spanning open pores. The pores are size selective as dextran molecules with a diameter up to 22 nm can traverse the pores, whereas larger dextran molecules are blocked. By FRAP measurements and modelling of the GFP influx rate, we find that up to hundreds of pores can be functionally reconstituted into a single GUV. Our technique bears great potential for applications across different fields from biomimetics, synthetic biology, to drug delivery.
Modeling host-associating microbes under selection
Authors: Bansept Florence , Obeng Nancy , Schulenburg Hinrich , Traulsen Arne
Published: February 2021

The concept of fitness is often reduced to a single component, such as the replication rate in a given habitat. For species with complex life cycles, this can be an unjustified oversimplification, as every step of the life cycle can contribute to reproductive success in a specific way. In particular, this applies to microbes that spend part of their life cycles associated to a host,i.e.in a microbiota. In this case, there is a selection pressure not only on the replication rates, but also on the phenotypic traits associated to migrating from the external environment to the host and vice-versa. Here, we investigate a simple model of a microbial population living, replicating, migrating and competing in and between two compartments: a host and its environment. We perform a sensitivity analysis on the global growth rate to determine the selection gradient experienced by the microbial population. We focus on the direction of selection at each point of the phenotypic space, defining an optimal way for the microbial population to increase its fitness. We show that microbes can adapt to the two-compartment life cycle through either changes in replication or migration rates, depending on the initial values of the traits, the initial distribution of the population across the compartments, the intensity of competition, and the time scales involved in the life cycle versus the time scale of adaptation (which determines the adequate probing time to measure fitness). Overall, our model provides a conceptual framework to study the selection on microbes experiencing a host-associated life cycle.
Cyclophilin A regulates protein phase separation and mitigates haematopoietic stem cell aging
Authors: Maneix Laure , Iakova Polina , Moree Shannon E. , King Jordon C.K. , Sykes David B. , Hill Cedric T. , Saez Borja , Spooner Eric , Krause Daniela S. , Sahin Ergun , Berk Bradford C. , Scadden David T. , Catic André
Published: February 2021

Loss of protein quality is a driving force of aging1. The accumulation of misfolded proteins represents a vulnerability for long-lived cells, such as haematopoietic stem cells. How these cells, which have the ability to reconstitute all haematopoietic lineages throughout life2, maintain their regenerative potential and avert the effects of aging is poorly understood. Here, we determined the protein content in haematopoietic stem and progenitor cells to identify prevalent chaperones that support proteome integrity. We identified Peptidyl-Prolyl Isomerase A (PPIA or Cyclophilin A) as the dominant cytosolic foldase in this cell population. Loss of PPIA accelerated aging in the mouse stem cell compartment. In an effort to define targets of PPIA, we found that RNA- and DNA-binding proteins are common substrates of this chaperone. These proteins are enriched in intrinsically disordered regions (IDRs), which can catalyse protein condensation3. Isomerized target prolines are almost exclusively located within IDRs. We discovered that over 20% of PPIA client proteins are known to participate in liquid-liquid phase separation, enabling the formation of supramolecular membrane-less organelles. Using the poly-A binding protein PABPC1 as an example, we demonstrate that PPIA promotes phase separation of ribonucleoprotein particles, thereby increasing cellular stress resistance. Haematopoietic stem cell aging is associated with a decreased expression of PPIA and reduced synthesis of intrinsically disordered proteins. Our findings link the ubiquitously expressed chaperone PPIA to phase transition and identify macromolecular condensation as a potential determinant of the aging process in haematopoietic stem cells.
Automatic recognition of macaque facial expressions for detection of affective states
Authors: Morozov Anna , Parr Lisa , Gothard Katalin , Paz Rony , Pryluk Raviv
Published: February 2021

Internal affective states produce external manifestations such as facial expressions. In humans, the Facial Action Coding System (FACS) is widely used to objectively quantify the elemental facial action-units (AUs) that build complex facial expressions. A similar system has been developed for macaque monkeys - the Macaque Facial Action Coding System (MaqFACS); yet unlike the human counterpart, which is already partially replaced by automatic algorithms, this system still requires labor-intensive coding. Here, we developed and implemented the first prototype for automatic MaqFACS coding. We applied the approach to the analysis of behavioral and neural data recorded from freely interacting macaque monkeys. The method achieved high performance in recognition of six dominant AUs, generalizing between conspecific individuals (Macaca mulatta) and even between species (Macaca fascicularis). The study lays the foundation for fully automated detection of facial expressions in animals, which is crucial for investigating the neural substrates of social and affective states.
Elementary growth modes/vectors and minimal autocatalytic sets for kinetic/constraint-based models of cellular growth
Authors: Müller Stefan
Published: February 2021

Elementary vectors are fundamental objects in polyhedral geometry. In metabolic pathway analysis, elementary vectors range from elementary flux modes (of the flux cone) and elementary flux vectors (of a flux polyhedron) via elementary conversion modes (of the conversion cone) to minimal cut sets (of a dual polyhedron) in computational strain design.

To better understand cellular phenotypes with optimal (or suboptimal) growth rate, we introduce and analyze classes of elementary vectors for models of cellular growth.Growth modes(GMs) only depend on stoichiometry, but not on growth rate or concentrations; they are elements of the growth cone.Elementarygrowth modes (EGMs) are conformally nondecomposable GMs; unlike elementary flux modes, they are not support-minimal, in general. Most importantly, every GM can be written as a conformal sum of EGMs.Growth vectors(GVs) andelementarygrowth vectors (EGVs) also depend on growth rate, concentrations, and linear constraints; they are elements of a growth polyhedron. Again, every GV can be written as a conformal sum of EGVs. To relate the new concepts to other branches of theory, we defineautocatalyticGMs and the corresponding(minimal) autocatalytic setsof reactions.

As a case study, we consider whole cell models (simple kinetic models of self-fabrication). First, we use EGMs to derive an upper bound for growth rate that only depends on enzyme kinetics. Next, we study growth rate maximization (via control parameters for ribosome kinetics). In particular, we analyzegrowth states(GSs) andelementarygrowth states (EGSs) as introduced in [de Groot et al, 2020]. Unlike EGMs, EGSs depend on (metabolite) concentrations and growth rate. Most importantly, (i) we show that EGSs are support-minimal, (ii) we give a simple proof for the fact that maximum growth rate is attained at an EGS, and (iii) we show that, at every optimal EGS, the ribosome capacity constraint is active. Finally, we determine the dependence of EGSs on growth rate, and we study the relation between EGSs and minimal autocatalytic sets, EGMs, and elementary flux modes. Along the way, we point out (and resolve) mathematical issues in [de Groot et al, 2020].
Towards a systematic characterization of protein complex function: a natural language processing and machine-learning framework
Authors: Sharma Varun S. , Fossati Andrea , Ciuffa Rodolfo , Buljan Marija , Williams Evan G. , Chen Zhen , Shao Wenguang , Pedrioli Patrick G.A. , Purcell Anthony W. , Rodríguez Martínez María , Song Jiangning , Manica Matteo , Aebersold Ruedi , Li Chen
Published: February 2021

It is a general assumption of molecular biology that the ensemble of expressed molecules, their activities and interactions determine biological processes, cellular states and phenotypes. Quantitative abundance of transcripts, proteins and metabolites are now routinely measured with considerable depth via an array of “OMICS” technologies, and recently a number of methods have also been introduced for the parallel analysis of the abundance, subunit composition and cell state specific changes of protein complexes. In comparison to the measurement of the molecular entities in a cell, the determination of their function remains experimentally challenging and labor-intensive. This holds particularly true for determining the function of protein complexes, which constitute the core functional assemblies of the cell. Therefore, the tremendous progress in multi-layer molecular profiling has been slow to translate into increased functional understanding of biological processes, cellular states and phenotypes. In this study we describe PCfun, a computational framework for the systematic annotation of protein complex function using Gene Ontology (GO) terms. This work is built upon the use of word embedding— natural language text embedded into continuous vector space that preserves semantic relationships— generated from the machine reading of 1 million open access PubMed Central articles. PCfun leverages the embedding for rapid annotation of protein complex function by integrating two approaches: (1) an unsupervised approach that obtains the nearest neighbor (NN) GO term word vectors for a protein complex query vector, and (2) a supervised approach using Random Forest (RF) models trained specifically for recovering the GO terms of protein complex queries described in the CORUM protein complex database. PCfun consolidates both approaches by performing the statistical test for the enrichment of the top NN GO terms within the child terms of the predicted GO terms by RF models. Thus, PCfun amalgamates information learned from the gold-standard protein-complex database, CORUM, with the unbiased predictions obtained directly from the word embedding, thereby enabling PCfun to identify the potential functions of putative protein complexes. The documentation and examples of the PCfun package are available athttps://github.com/sharmavaruns/PCfun. We anticipate that PCfun will serve as a useful tool and novel paradigm for the large-scale characterization of protein complex function.
Modeling the SARS-CoV-2 nsp1–5’-UTR complex via extended ensemble simulations
Authors: Sakuraba Shun , Qilin Xie , Kasahara Kota , Iwakiri Junichi , Kono Hidetoshi
Published: February 2021

Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks translation of host mRNAs in SARS-CoV-2-infected cells. Although it is known that SARS-CoV-2’s own RNA evades nsp1’s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results showed that the stem loop structure of the SARS-CoV-2 RNA 5’-untranslated region (SL1) is recognized by both nsp1’s globular region and intrinsically disordered region. The recognition presumably enables selective translation of viral RNAs. Cluster analysis of the binding mode and detailed analysis of the binding poses revealed several residues involved in the SL1 recognition mechanism. The simulation results imply that the nsp1 C-terminal helices are lifted from the 40Sribosome upon the binding of SL1 to nsp1, unblocking translation of the viral RNA.
Domestication effects on immune response: comparison of cell-mediated immune competence in wild and domesticated Bengalese finch
Authors: Suzuki Kenta , Okanoya Kazuo
Published: February 2021

Domesticated Bengalese finch (Lonchura striatavar.domestica)lack natural selection pressures and consequently have more complex songs and altered behavioural and psychological traits when compared to their wild ancestor, the white-rumpud munia (Lonchura striata). Clarifying the sexual traits and life history trade-offs in Bengal finches will be help to improve our understanding of the evolution of complex songs and domesticated traits. Here, we have assessed the immune competence of the Bengalese finch and the white-rumped munia using phytohemagglutinin (PHA) tests to create an index of cell-mediated immune responses. We found that the Bengalese finch had a significantly larger immunocompetence than the white-rumped munia, indicating that they devote more resources to both immunity and reproduction. Thus, there is no trade-off but a positive relationship between immunocompetence and reproductive traits, which may be related to the release from natural selection pressures. These results will be useful in understanding the mechanisms by which domestication-induced changes due to a lack of natural selection pressure affect behavioural and physiological changes.
Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells
Authors: Mira-Bontenbal Hegias , Tan Beatrice , Gontan Cristina , Goossens Sander , Boers R.G. , Boers J. , Dupont Catherine , van Royen Martin , van IJcken Wilfred , French Pim , Bedalov Toni , Gribnau Joost
Published: February 2021

Rett Syndrome is a neurodevelopmental disorder in girls that is caused by heterozygous inactivation of the chromatin remodeler geneMECP2. Rett Syndrome may therefore be treated by reactivation of the wild type copy ofMECP2from the inactive X chromosome. Most studies that modelMecp2reactivation have used mouse fibroblasts rather than neural cells, which would be critical for phenotypic reversal, and rely on fluorescent reporters that lack adequate sensitivity. Here, we present a mouse model system for monitoring Mecp2 reactivation that is more sensitive and versatile than any bioluminescent and fluorescent system currently available. The model consists of neural stem cells derived from female mice with a dual reporter system where MECP2 is fused to NanoLuciferase and TdTomato on the inactive X chromosome. We show by bioluminescence and fluorescence thatMecp2is synergistically reactivated by 5-Aza treatment andXistknockdown. As expected, other genes on the inactive X chromosome are also reactivated, the majority of which overlaps with genes reactivated early during reprogramming of mouse embryonic fibroblasts to iPSCs. Genetic and epigenetic features such as CpG density, SINE elements, distance to escapees and CTCF binding are consistent indicators of reactivation, whereas different higher order chromatin areas are either particularly prone or resistant to reactivation. Our MeCP2 reactivation monitoring system thereby suggests that genetic and epigenetic features on the inactive X chromosome affect reactivation of its genes, irrespective of cell type or procedure of reactivation.