bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pairing to the microRNA 3′ region occurs through two alternative binding modes, with affinity shaped by nucleotide identity as well as pairing position
Authors: McGeary Sean E. , Bisaria Namita , Bartel David P. 
Published: April 2021

ABSTRACTMicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2–8), preferences of the miRNA 3′ region are poorly understood, due to the sparsity of measured affinities for the many pairing possibilities. We used RNA bind-n-seq with purified AGO2–miRNA complexes to measure relative affinities of >1,000 3′-pairing architectures for each miRNA. In some cases, optimal 3′ pairing increased affinity by >500-fold. Some miRNAs had two high-affinity 3′-pairing modes—one of which included additional nucleotides bridging seed and 3′ pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3′ pairing is determined for each miRNA.HIGHLIGHTSRNA bind-n-seq reveals relative affinities of >1,000 3′-pairing architecturesTwo distinct 3′-binding modes can enhance affinity, by >500-fold in some instancesG and oligo(G/C) residues help define the miRNA 3′ segment most critical for pairingSeed mismatch identity can influence the contribution of compensatory 3′ pairing
α3β4* Nicotinic acetylcholine receptors strongly modulate the excitability of VIP neurons in the mouse inferior colliculus
Authors: Rivera-Perez Luis M. , Kwapiszewski Julia T. , Roberts Michael T. 
Published: April 2021

AbstractThe inferior colliculus (IC), the midbrain hub of the central auditory system, receives extensive cholinergic input from the pontomesencephalic tegmentum. Activation of nicotinic acetylcholine receptors (nAChRs) in the IC can alter acoustic processing and enhance auditory task performance. However, how nAChRs affect the excitability of specific classes of IC neurons remains unknown. Recently, we identified vasoactive intestinal peptide (VIP) neurons as a distinct class of glutamatergic principal neurons in the IC. Here, in experiments using male and female mice, we show that cholinergic terminals are routinely located adjacent to the somas and dendrites of VIP neurons. Using whole-cell electrophysiology in brain slices, we found that acetylcholine drives surprisingly strong and long-lasting excitation and inward currents in VIP neurons. This excitation was unaffected by the muscarinic receptor antagonist atropine. Application of nAChR antagonists revealed that acetylcholine excites VIP neurons mainly via activation of α3β4* nAChRs, a nAChR subtype that is rare in the brain. Furthermore, we show that cholinergic excitation is intrinsic to VIP neurons and does not require activation of presynaptic inputs. Lastly, we found that low frequency trains of acetylcholine puffs elicited temporal summation in VIP neurons, suggesting that in vivo-like patterns of cholinergic input can reshape activity for prolonged periods. These results reveal the first cellular mechanisms of nAChR regulation in the IC, identify a functional role for α3β4* nAChRs in the auditory system, and suggest that cholinergic input can potently influence auditory processing by increasing excitability in VIP neurons and their postsynaptic targets.Key points summaryThe inferior colliculus (IC), the midbrain hub of the central auditory system, receives extensive cholinergic input and expresses a variety of nicotinic acetylcholine receptor (nAChR) subunits.In vivo activation of nAChRs alters the input-output functions of IC neurons and influences performance in auditory tasks. However, how nAChR activation affects the excitability of specific IC neuron classes remains unknown.Here we show in mice that cholinergic terminals are located adjacent to the somas and dendrites of VIP neurons, a class of IC principal neurons.We find that acetylcholine elicits surprisingly strong, long-lasting excitation of VIP neurons and this is mediated mainly through activation of α3β4* nAChRs, a subtype that is rare in the brain.Our data identify a role for α3β4* nAChRs in the central auditory pathway and reveal a mechanism by which cholinergic input can influence auditory processing in the IC and the postsynaptic targets of VIP neurons.
From Structure to Sequence: Identification of polyclonal antibody families using cryoEM
Authors: Antanasijevic Aleksandar , Bowman Charles A. , Kirchdoerfer Robert N. , Cottrell Christopher A. , Ozorowski Gabriel , Upadhyay Amit A. , Cirelli Kimberly M. , Carnathan Diane G. , Enemuo Chiamaka A. , Sewall Leigh M. , Nogal Bartek , Zhao Fangzhu , Groschel Bettina , Schief William R. , Sok Devin , Silvestri Guido , Crotty Shane , Bosinger Steven E. , Ward Andrew B. 
Published: April 2021

AbstractOne of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and bioinformatic approach to directly assign the heavy and light chains, identify complementarity-determining regions and discover sequences from cryoEM density maps of serum-derived polyclonal antibodies bound to an antigen. When combined with next generation sequencing of immune repertoires we were able to specifically identify clonal family members, synthesize the monoclonal antibodies and confirm that they interact with the antigen in a manner equivalent to the corresponding polyclonal antibodies. This structure-based approach for identification of monoclonal antibodies from polyclonal sera opens new avenues for analysis of immune responses and iterative vaccine design.Graphical AbstractOne Sentence SummaryCryoEM and next generation sequencing were used to identify monoclonal antibodies elicited by HIV Env vaccine candidates.
Single-cell immune profiling with TCR clonotype barcoding identifies biomarker signatures that predict response to immune checkpoint blockade
Authors: Lee Dean , Fulton Ross , Manne Monika , Schweizer Liang , Raue Andreas 
Published: April 2021

AbstractThe identification of predictive biomarkers for patient treatment response is urgently needed to increase the probability of success of existing and novel experimental therapies. Single-cell profiling has provided novel biological insights into drug responses in the tumor microenvironment, but its potential for biomarker discovery has not been fully explored for therapeutic purposes. We describe a novel approach to discover predictive response biomarkers from single-cell data from a small patient cohort using the T cell receptor sequence intrinsic to each T cell to match clonotypes between pre- and post-treatment tumor samples. As a result, we have identified a predictive gene expression signature for immune checkpoint blockade and validated its predictive performance using data from three larger clinical studies. Our results demonstrated that applying clonotyping with single-cell genomic profiling is a promising novel approach for biomarker identification that does not require data collected from large patient cohorts. This could increase success rates, reduce clinical trial size, and significantly impact future clinical developments of immunomodulatory therapeutics.
Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution
Authors: Monberg Maria E. , Geiger Heather , Lee Jaewon J. , Sharma Roshan , Semaan Alexander , Bernard Vincent , Swartzlander Daniel B. , Stephens Bret M. , Chen Ken , Katz Matthew HG , Robine Nicolas , Guerrero Paola A. , Maitra Anirban 
Published: April 2021

AbstractIntratumoral heterogeneity (ITH) is a hallmark of cancer. The advent of single-cell technologies has helped uncover ITH in a high-throughput manner in different cancers across varied contexts. Here we apply single-cell sequencing technologies to reveal striking ITH in assumptively oligoclonal pancreatic ductal adenocarcinoma (PDAC) cell lines. Our findings reveal a high degree of both genomic and transcriptomic heterogeneity in established and globally utilized PDAC cell lines, custodial variation induced by growing apparently identical PDAC cell lines in different laboratories, and profound transcriptomic shifts in transitioning from 2D to 3D spheroid growth models. Our findings also call into question the validity of widely available immortalized, non-transformed pancreatic lines as contemporaneous “control” lines in experiments. Further, while patient-derived organoid (PDOs) are known to reflect the cognatein vivobiology of the parental tumor, we identify transcriptomic shifts duringex vivopassage that might hamper their predictive abilities over time. The impact of these findings on rigor and reproducibility of experimental data generated using established preclinical PDAC models between and across laboratories is uncertain, but a matter of concern.
Non-clinical evidence supports anti-inflammatories as more effective medication than antihistamines against tarantula local effects envenomation
Authors: Alves Bruno Ricardo , Sutti Rafael , da Silva Pedro Ismael , Bertani Rogerio , Santos-Junior Jair Guilherme , Rocha e Silva Thomaz Augusto Alves , Linardi Alessandra 
Published: April 2021

AbstractBackgroundTarantulas are the most common invertebrates pets, especially in North America and Europe. The most commercialized genera are from Southern Asia and tropical Americas, represented byVitalius, found in Southeastern Brazil, andBrachypelma, common in Mexican desert. Bites by these spiders in humans occurs during manipulation and generally result in clinical manifestations such local pain, erythema and oedema, with the possibility of secondary local infection. Hence, the cases are usually treated with prescription free drugs such as antihistamines and anti-inflammatories.MethodsIn this work, we investigated the post treatment with commercial nonsteroidal and steroidal anti-inflammatories and anti-histamines administered by oral and intraperitoneal routes on rat paw oedema induced by venoms ofV. dubiusandB. smithi. Hydroplethysmometer standard oedema measurement and Evans blue extravasation were performed. Dose standardization experiments showed that theV. dubiusis more potent thanB. smithi, and doses were established at 30 μg/paw and 60 μg/paw respectively.ResultsThe oral post-administration of ketoprofen (non-selective cyclooxygenase inhibitor) and prednisolone (steroidal anti-inflammatory) markedly reduced a paw oedema evoked by onlyV. dubiusvenom, but loratadine (H1-antihistamine) had negligible effect on rat paw oedema induced by both venoms. Intraperitoneal administration, ketoprofen (20 mg Kg−1) and loratadine (5 mg Kg−1) reduced the rat paw oedema induced byV. dubiusandB. smithiwhile methylprednisolone (10 mg Kg−1) only inhibited the oedema induced byV. dubius.ConclusionThese results suggest that the pos-treatment with nonsteroidal and steroidal anti-inflammatory drugs are more potent than antihistamines in attenuating the local effect induced byV. dubiusandB. smithivenoms.
Selective prefrontal-amygdala circuit interactions underlie social and nonsocial valuation in rhesus macaques
Authors: Pujara Maia S. , Ciesinski Nicole K. , Reyelts Joseph F. , Rhodes Sarah E.V. , Murray Elisabeth A. 
Published: April 2021

AbstractLesion studies in macaques suggest dissociable functions of the orbitofrontal cortex (OFC) and medial frontal cortex (MFC), with OFC being essential for goal-directed decision making and MFC supporting social cognition. Bilateral amygdala damage results in impairments in both of these domains. There are extensive reciprocal connections between these prefrontal areas and the amygdala; however, it is not known whether the dissociable roles of OFC and MFC depend on functional interactions with the amygdala. To test this possibility, we compared the performance of male rhesus macaques (Macaca mulatta) with crossed surgical disconnection of the amygdala and either MFC (MFC x AMY,n=4) or OFC (OFC x AMY,n=4) to a group of unoperated controls (CON,n=5). All monkeys were assessed for their performance on two tasks to measure: (1) food-retrieval latencies while viewing videos of social and nonsocial stimuli in a test of social interest, and (2) object choices based on current food value using reinforcer devaluation in a test of goal-directed decision making. Compared to the CON group, the MFC x AMY group, but not the OFC x AMY group, showed significantly reduced food-retrieval latencies while viewing videos of conspecifics, indicating reduced social valuation and/or interest. By contrast, on the devaluation task, group OFC x AMY, but not group MFC x AMY, displayed deficits on object choices following changes in food value. These data indicate that the MFC and OFC must functionally interact with the amygdala to support normative social and nonsocial valuation, respectively.Significance StatementAscribing value to conspecifics (social) vs. objects (nonsocial) may be supported by distinct but overlapping brain networks. Here we test whether two nonoverlapping regions of the prefrontal cortex, the medial frontal cortex and the orbitofrontal cortex, must causally interact with the amygdala to sustain social valuation and goal-directed decision making, respectively. We found that these prefrontal-amygdala circuits are functionally dissociable, lending support for the idea that medial frontal and orbital frontal cortex make independent contributions to cognitive appraisals of the environment. These data provide a neural framework for distinct value assignment processes and may enhance our understanding of the cognitive deficits observed following brain injury or in the development of mental health disorders.
Visual detection of binary, ternary, and quaternary protein-protein interactions in fission yeast by Pil1 co-tethering assay
Authors: Yu Zhong-Qiu , Liu Xiao-Man , Zhao Dan , Xu Dan-Dan , Du Li-Lin 
Published: April 2021

AbstractProtein-protein interactions are vital for executing nearly all cellular processes. To facilitate the detection of protein-protein interactions in living cells of the fission yeastSchizosaccharomyces pombe, here we present an efficient and convenient method termed the Pil1 co-tethering assay. In its basic form, we tether a bait protein to mCherry-tagged Pil1, which forms cortical filamentary structures, and examine whether a GFP-tagged prey protein colocalizes with the bait. We demonstrate that this assay is capable of detecting pairwise protein-protein interactions of cytosolic proteins, transmembrane proteins, and nuclear proteins. Furthermore, we show that this assay can be used for detecting not only binary protein-protein interactions, but also ternary and quaternary protein-protein interactions. Using this assay, we systematically characterized the protein-protein interactions in the Atg1 complex and in the phosphatidylinositol 3-kinase (PtdIns3K) complexes and found that Atg38 is incorporated into the PtdIns3K complex I via an Atg38-Vps34 interaction. Our data show that this assay is a useful and versatile tool and should be added to the routine toolbox of fission yeast researchers.
The second wave of SARS-CoV-2 infections and COVID-19 deaths in Germany – driven by values, social status and migration background? A county-scale explainable machine learning approach
Authors: Doblhammer Gabriele , Reinke Constantin , Kreft Daniel 
Published: April 2021

ABSTRACTThere is a general consensus that SARS-CoV-2 infections and COVID-19 deaths have hit lower social groups the hardest, however, for Germany individual level information on socioeconomic characteristics of infections and deaths does not exist. The aim of this study was to identify the key features explaining SARS-CoV-2 infections and COVID-19 deaths during the upswing of the second wave in Germany.We considered information on COVID-19 diagnoses and deaths from 1. October to 15. December 2020 on the county-level, differentiating five two-week time periods. We used 155 indicators to characterize counties in nine geographic, social, demographic, and health domains. For each period, we calculated directly age-standardized COVID-19 incidence and death rates on the county level. We trained gradient boosting models to predict the incidence and death rates with the 155 characteristics of the counties for each period. To explore the importance and the direction of the correlation of the regional indicators we used the SHAP procedure. We categorized the top 20 associations identified by the Shapley values into twelve categories depicting the correlation between the feature and the outcome.We found that counties with low SES were important drivers in the second wave, as were those with high international migration and a high proportion of foreigners and a large nursing home population. During the period of intense exponential increase in infections, the proportion of the population that voted for the Alternative for Germany (AfD) party in the last federal election was among the top characteristics correlated with high incidence and death rates.We concluded that risky working conditions with reduced opportunities for social distancing and a high chronic disease burden put populations in low-SES counties at higher risk of SARS-CoV-2 infections and COVID-19 deaths. In addition, noncompliance with Corona measures and spill-over effects from neighbouring counties increased the spread of the virus. To further substantiate this finding, we urgently need more data at the individual level.
Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast
Authors: Kalita R. , Flanagan W. , Lightley J. , Kumar S. , Alexandrov Y. , Garcia E. , Hintze M. , Barkoulas M , Dunsby C. , French P.M.W. 
Published: April 2021

AbstractWe present a robust, low-cost single-shot implementation of differential phase microscopy utilising a polarisation-sensitive camera to simultaneously acquire 4 images from which the phase gradients and quantitative phase image can be calculated. This polarisation-resolved differential phase contrast (pDPC) microscopy technique can be interleaved with single-shot imaging polarimetry.
A Paradigm Free Regularization Approach to Recover Brain Activation from Functional MRI Data
Authors: Costantini Isa , Deriche Rachid , Deslauriers-Gauthier Samuel 
Published: April 2021

AbstractContextFunctional MRI is a non-invasive imaging technique that provides an indirect view into brain activity, via the blood-oxygen-level-dependent (BOLD) response. In particular, resting-state fMRI poses challenges to the recovery of brain activity without prior knowledge on the experimental paradigm, as it is the case for task-fMRI. Conventional methods to infer brain activity from the fMRI signals, for example the general linear model (GLM), require the knowledge of the experimental paradigm to define regressors and estimate the contribution of each voxel’s time course to the task. To overcome this limitation, approaches to deconvolve the BOLD response and recover the underlying neural activation without a priori information on the task have been proposed. State-of-the-art techniques, and in particular the Total Activation (TA), formulates the deconvolution as an optimization problem with decoupled spatial and temporal regularization terms. This increases the number of hyperparameters to be set and requires an optimization strategy that alternates between the constraints.ApproachIn this work, we propose a paradigm-free regularization algorithm named Paradigm-Free fMRI (PF-fMRI) that is applied on the 4-D fMRI image, acting simultaneously in the 3-D space and 1-D time dimensions. Based on the idea that large image variations should be preserved as they occur during brain activation, whereas small variations considered as noise should be removed, the PF-fMRI applies an anisotropic regularization, thus recovering the location and the duration of brain activation.ResultsUsing the experimental paradigm as ground truth, the PF-fMRI is validated on synthetic and real task-fMRI data from 51 subjets, and its performance is compared to the TA. Results show higher correlations of the recovered time-courses with the ground truth compared to the TA and lower computational times. In addition, we show that the PF-fMRI recovers activity that agrees with the GLM, without requiring or using any knowledge of the experimental paradigm.
Behavior-dependent spatial maps enable efficient theta phase coding
Authors: Parra-Barrero Eloy , Diba Kamran , Cheng Sen 
Published: April 2021

AbstractNavigation through space involves learning and representing relationships between past, current and future locations. In mammals, this might rely on the hippocampal theta phase code, where in each cycle of the theta oscillation, spatial representations start behind the animal’s location and then sweep forward. However, the exact relationship between phase and represented and true positions remains unclear. Developing a quantitative framework for the theta phase code, we formalize two previous notions: in spatial sweeps, different phases of theta encode positions at fixed distances behind or ahead of the animal, whereas in temporal sweeps, they encode positions reached at fixed time intervals into the past or future. These two schemes predict very different position representations during theta depending on the animal’s running speed. Paradoxically, in some studies sweep length has been shown to increase proportionally with running speed, consistent with temporal sweeps, whereas in other studies individual place field parameters such as field size and phase precession slope were shown to remain constant with speed, consistent with spatial sweeps. Here, we introduce a third option: behavior-dependent sweeps, according to which sweep length and place field properties vary across the environment depending on the running speed characteristic of each location. Analyzing single-cell and population variables in parallel in recordings from rat CA1 place cells and comparing them to model simulations, we show that behavior-dependent sweeps uniquely account for all relevant variables. This coding scheme combines features and advantages of both spatial and temporal sweeps, revealing an efficient hippocampal code.SignificanceTo learn the structure of the world and the consequences of our actions, information about the past must be carried through to the present and linked to what is currently happening. To plan, desired future states and the predicted outcomes of actions must be represented. In mammals, including humans, hippocampal neurons are thought to encode such representations of past, present and future states at different phases of the theta oscillation. However, the precise hippocampal phase code remains unknown. We show that two previous ideas are incompatible with each other and with rat experimental data. So, we propose a new coding scheme that synthesizes features from both ideas and accounts for all relevant observations.