bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of long-term care facility size on preparedness and adherence to infection prevention and control guidance for the mitigation of COVID-19
Authors:   Adherence to COVID-19 guidance, Wachholz Patrick Alexander , de Melo Ruth Caldeira , Jacinto Alessandro Ferrari , Villas Boas Paulo Jose Fortes
Published: June 2021

Aim

To evaluate the preparedness and adherence of Brazilian long-term care facilities (LTCFs) to the World Health Organization (WHO) infection prevention and control (IPC) guidance and examine the association of LTCF size with adherence to recommendations.

Methods

We conducted a cross-sectional study of LTCF managers for 12 consecutive weeks from May 5, 2020. We developed and pre-tested a 46-item questionnaire based on WHO IPC guidance that included multiple-choice and dichotomous questions as well as an open-ended question on the main difficulties encountered by the facility in tackling the pandemic. Using a global adherence score based on the adoption of 20 recommendations, we classified preparedness as (1)excellentfor LTCFs following ≥14 recommendations, (2)goodfor those following 10-13 recommendations, and (3)poorfor those following <10 recommendations. LTCF size was established as small, medium, and large according to a 2-step cluster analysis of the number of residents as a continuous variable. We used descriptive statistics and chi-square tests at a 5% significance level.

Results

Of 362 facilities included in the study, 308 (85.1%) adhered to 14 or more recommendations; 3 were classified as poorly adherent. Regarding LTCF size, we found a lower adherence to screening visitors for COVID-19 signs and symptoms (p=0.037) and to isolating patients until they have 2 negative laboratory tests (p=0.032) in larger facilities than in medium and small facilities.

Conclusions

Preparedness for mitigating COVID-19 in Brazilian LTCFs was considered excellent for most of the proposed recommendations, regardless of LTCF size. Difficulties and problems with infrastructure and/or resident care were much less commonly reported than those related to maintenance of a sufficient stock of materials, workforce management, and financial distress.
Interferon-stimulated and metallothionein-expressing macrophages are associated with acute and chronic allograft dysfunction after lung transplantation
Authors: Moshkelgosha Sajad , Duong Allen , Wilson Gavin , Andrews Tallulah , Berra Gregory , Renaud-Picard Benjamin , Liu Mingyao , Keshavjee Shaf , MacParland Sonya , Yeung Jonathan , Martinu Tereza , Juvet Stephen
Published: June 2021

Lung transplant (LT) recipients experience episodes of immune-mediated acute lung allograft dysfunction (ALAD). ALAD episodes are a risk factor for chronic lung allograft dysfunction (CLAD), the major cause of death after LT. We have applied single-cell RNA sequencing (scRNAseq) to bronchoalveolar lavage (BAL) cells from stable and ALAD patients and to cells from explanted CLAD lung tissue to determine key cellular elements in dysfunctional lung allografts, with a focus on macrophages. We identified two alveolar macrophage (AM) subsets uniquely represented in ALAD. Using pathway analysis and differentially expressed genes, we annotated these as pro-inflammatory interferon-stimulated gene (ISG) and metallothionein-mediated inflammatory (MT) AMs. Functional analysis of an independent set of AMsin vitrorevealed that ALAD AMs exhibited a higher expression of CXCL10, a marker of ISG AMs, and increased secretion of pro-inflammatory cytokines compared to AMs from stable patients. Using publicly available BAL scRNAseq datasets, we found that ISG and MT AMs are associated with more severe inflammation in COVID-19 patients. Analysis of cells from four explanted CLAD lungs revealed similar macrophage populations. Using a single nucleotide variation calling algorithm, we also demonstrated contributions of donor and recipient cells to all AM subsets early post-transplant, with loss of donor-derived cells over time. Our data reveals extensive heterogeneity among lung macrophages after LT and indicates that specific sub-populations may be associated with allograft dysfunction, raising the possibility that these cells may represent important therapeutic targets.
Viral transduction and the dynamics of bacterial adaptation
Authors: Cherabier Philippe , Méléard Sylvie , Ferrière Régis
Published: June 2021

Transduction - horizontal gene transfer (HGT) by viruses - is an important macroevolutionary force in prokaryotes, contributing to functional innovation and lineage diversification. In contrast, the role that transduction plays in bacterial microevolutionary adaptation is poorly known. By facilitating the transfer of beneficial alleles between host cells, transduction may accelerate adaptation. But transduction also carries the risk of transferring deleterious alleles, which, in addition to the demographic cost of viral infection, may hinder adaptation. Here we resolve the conflicting effects of transduction on bacterial adaptation in a simple eco-evolutionary model for large populations characterized by a quantitative (resource-use) trait with a single evolutionary optimum. Our model focuses on generalized transduction by virulent phages. Away from the optimum, the effect of transferring beneficial alleles dominates and transduction tends to accelerate adaptation. Close to the optimum, transduction generates a large amount of stochasticity in the population adaptive trajectory, thus hindering adaptation. Under disruptive selection, transduction may either limit (as sexual recombination would) or promote phenotypic diversification, or drive ‘transient optimization’ whereby phenotypic subpopulations recurrently visit the optimum. Our modeling framework paves the way to study complex adaptive feedbacks between bacterial hosts and phages generated by the combination of deterministic and stochastic effects of transduction.
Identification of enamel knot gene signature within the developing mouse molar
Authors: Winchester Emma Wentworth , Cotney Justin
Published: June 2021

In most mammals, the primary teeth developin uteroand the cells capable of contributing to hard surface regeneration are lost before tooth eruption. These cells differentiate through a series of reciprocal induction steps between the epithelium and mesenchyme, initially orchestrated by an epithelial signaling center called the enamel knot. While the factors secreted by this structure are of interest to the dental regeneration and development communities, its small size makes it difficult to isolate for analysis. Here we describe our work to identify the enamel knot from whole E14 molars using publicly available scRNA-seq data. We identified 335 genes differentially expressed in the enamel knot compared to the surrounding tissues, including known enamel knot marker genes. We validated expression of the most highly enriched enamel knot marker genes and identified 42 novel marker genes of the enamel knot which provide excellent targets for future dental regeneration investigations.
I, We, andThey: A Linguistic and Narrative Exploration of the Authorship Process
Authors: Konopasky Abigail , O’Brien Bridget C. , Artino Anthony R. , Driessen Erik W. , Watling Christopher J. , Maggio Lauren A.
Published: June 2021

Introduction

While authorship plays a powerful role in the academy, research indicates many authors engage in questionable practices like honorary authorship. This suggests that authorship may be acontested spacewhere individuals must exerciseagency--a dynamic and emergent process, embedded in context--to negotiate potentially conflicting norms among published criteria, disciplines, and informal practices. This study explores how authors narrate their own and others’ agency in making authorship decisions.

Method

We conducted a mixed-methods analysis of 24 first authors’ accounts of authorship decisions on a recent multi-author paper. Authors included 14 females and 10 males in health professions education (HPE) from U.S. and Canadian institutions (10 assistant, 6 associate, and 8 full professors). Analysis took place in three phases: (1) linguistic analysis of grammatical structures shown to be associated with agency (coding for main clause subjects and verb types); (2) narrative analysis to create a “moral” and “title” for each account; and (3) integration of (1) and (2).

Results

Participants narrated other authors most frequently as main clause subjects (n= 191), then themselves (I;n= 151), inanimate nouns (it, the paper;n= 146), and author team (we;n= 105). Three broad types of agency were narrated:distributed(n= 15 participants), focusing on how resources and work were spread across team members;individual(n= 6), focusing on the first author’s action; andcollaborative(n= 3), focusing on group actions. These three types of agency contained four sub-types, e.g., supported, contested, task-based, negotiated.

Discussion

This study highlights the complex and emergent nature of agency narrated by authors when making authorship decisions. Published criteria offer us starting point--thestated rulesof the authorship game; this paper offers us a next step--theenactedandnarrated approachto the game.
Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE
Authors: Phongpreecha Thanaphong , Gajera Chandresh R. , Liu Candace C. , Vijayaragavan Kausalia , Chang Alan L. , Becker Martin , Fallahzadeh Ramin , Fernandez Rosemary , Postupna Nadia , Sherfield Emily , Tebaykin Dmitry , Latimer Caitlin , Shively Carol A. , Register Thomas C. , Craft Suzanne , Montine Kathleen S. , Fox Edward J. , Poston Kathleen L. , Dirk Keene C. , Angelo Michael , Bendall Sean C. , Aghaeepour Nima , Montine Thomas J.
Published: June 2021

Synaptic molecular characterization is limited for Alzheimer’s disease (AD). We used mass cytometry to quantify 38 probes in approximately 17 million single synaptic events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), non-human primates (NHP), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice synaptic events. Clustering and pattern identification of human synapses showed expected disease-specific differences, like increased hippocampal pathologic tau in AD and reduced caudate dopamine transporter in LBD, and revealed novel findings including increased hippocampal CD47 and lowered DJ1 in AD and higher ApoE in AD dementia. Our results were independently supported by multiplex ion beam imaging of intact tissue.
Neuronal Activity in Dorsal Anterior Cingulate Cortex during Economic Choices under Variable Action Costs
Authors: Cai Xinying , Padoa-Schioppa Camillo
Published: June 2021

The role of the dorsal anterior cingulate cortex (ACCd) in decision making has often been discussed but remains somewhat unclear. On the one hand, numerous studies implicated this area in decisions driven by effort or action cost. On the other hand, work on economic choices between goods (under fixed action costs) found that neurons in ACCd encoded only post-decision variables. To advance our understanding of the role played by this area in decision making, we trained monkeys to choose between different goods (juice types) offered in variable amounts and with different action costs. Importantly, the task design dissociated computation of the action cost from planning of any particular action. Neurons in ACCd encoded the chosen value and the binary choice outcome in several reference frames (chosen juice, chosen cost, chosen action). Thus, this area provided a rich representation of post-decision variables. In contrast, neurons in ACCd did not represent pre-decision variables such as individual offer values in any reference frame. Hence, ongoing decisions are unlikely guided by ACCd. Conversely, neuronal activity in this area might inform subsequent choices.
Phase-separated stress granules and processing bodies are compromised in Myotonic Dystrophy Type 1
Authors: Gulyurtlu Selma , Magon Monika S , Guest Patrick , Papavasiliou Panagiotis P , Prescott Alan R , Sleeman Judith E
Published: June 2021

RNA regulation in mammalian cells requires complex physical compartmentalisation using structures thought to be formed by liquid-liquid phase separation. Disruption of these structures is implicated in numerous degenerative diseases. Myotonic Dystrophy Type 1 (DM1) is a multi-systemic trinucleotide repeat disorder resulting from a CTG expansion in the dystonia myotonica protein kinase gene (DMPK). The cellular hall-mark of DM1 is the formation of nuclear foci containing expanded DMPK RNA (CUGexp). We report here the deregulation of stress granules and processing bodies (P-bodies), two cytoplasmic structures key for mRNA regulation, in cell culture models of DM1. Alterations to the rates of formation and dispersal of stress granules suggest an altered ability to respond to stress associated with DM1, while changes to the structure and dynamics of stress granules and P-bodies suggest that a more widespread alteration to the biophysical properties of cellular structures may be a consequence of the presence of CUGexp RNA.
Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques
Authors: Ge Yunhui , Wych David C. , Samways Marley L. , Wall Michael E. , Essex Jonathan W. , Mobley David L.
Published: June 2021

1

Water often plays a key role in protein structure, molecular recognition, and mediating protein-ligand interactions. Thus, free energy calculations must adequately sample water motions, which often proves challenging in typical MD simulation timescales. Thus, the accuracy of methods relying on MD simulations ends up limited by slow water sampling. Particularly, as a ligand is removed or modified, bulk water may not have time to fill or rearrange in the binding site. In this work, we focus on several molecular dynamics (MD) simulation-based methods attempting to help rehydrate buried water sites: BLUES, using nonequilibrium candidate Monte Carlo (NCMC); grand, using grand canonical Monte Carlo (GCMC); and normal MD. We assess the accuracy and efficiency of these methods in rehydrating target water sites. We selected a range of systems with varying numbers of waters in the binding site, as well as those where water occupancy is coupled to the identity or binding mode of the ligand. We analyzed rehydration of buried water sites in binding pockets using both clustering of trajectories and direct analysis of electron density maps. Our results suggest both BLUES and grand enhance water sampling relative to normal MD and grand is more robust than BLUES, but also that water sampling remains a major challenge for all of the methods tested. The lessons we learned for these methods and systems are discussed.
Deep learning trained on H&E tumor ROIs predicts HER2 status and Trastuzumab treatment response in HER2+ breast cancer
Authors: Farahmand Saman , Fernandez Aileen I , Ahmed Fahad Shabbir , Rimm David L. , Chuang Jeffrey H. , Reisenbichler Emily , Zarringhalam Kourosh
Published: June 2021

The current standard of care for many patients with HER2-positive breast cancer is neoadjuvant chemotherapy in combination with anti-HER2 agents, based on HER2 amplification as detected by in situ hybridization (ISH) or protein immunohistochemistry (IHC). However, hematoxylin & eosin (H&E) tumor stains are more commonly available, and accurate prediction of HER2 status and anti-HER2 treatment response from H&E would reduce costs and increase the speed of treatment selection. Computational algorithms for H&E have been effective in predicting a variety of cancer features and clinical outcomes, including moderate success in predicting HER2 status. In this work, we present a novel convolutional neural network (CNN) approach able to predict HER2 status with increased accuracy over prior methods. We trained a CNN classifier on 188 H&E whole slide images (WSIs) manually annotated for tumor regions of interest (ROIs) by our pathology team. Our classifier achieved an area under the curve (AUC) of 0.90 in cross-validation of slide-level HER2 status and 0.81 on an independent TCGA test set. Within slides, we observed strong agreement between pathologist annotated ROIs and blinded computational predictions of tumor regions / HER2 status. Moreover, we trained our classifier on pre-treatment samples from 187 HER2+ patients that subsequently received trastuzumab therapy. Our classifier achieved an AUC of 0.80 in a five-fold cross validation. Our work provides an H&E-based algorithm that can predict HER2 status and trastuzumab response in breast cancer at an accuracy that is better than IHC and may benefit clinical evaluations.
Practical observations on the use of fluorescent reporter systems in C. difficile
Authors: Oliveira Paiva Ana M. , Friggen Annemieke H. , Douwes Roxanne , Wittekoek Bert , Smits Wiep Klaas
Published: June 2021

Objectives

Fluorescence microscopy is a valuable tool to study a broad variety of bacterial cell components and dynamics thereof. For Clostridioides difficile, the fluorescent proteins CFPopt, mCherryOpt and phiLOV2.1, and the self-labelling tags SNAPCd and HaloTag, hereafter collectively referred as fluorescent systems, have been described to explore different cellular pathways. In this study, we sought to characterize previously used fluorescent systems in C. difficile cells.

Methods

We performed single cell analyses using fluorescence microscopy of exponentially growing C. difficile cells harbouring different fluorescent systems, either expressing these separately in the cytosol or fused to the C-terminus of HupA, under defined conditions.

Results

We show that the intrinsic fluorescence of C. difficile cells increases during growth, independent from sigB or spo0A. However, when C. difficile cells are exposed to environmental oxygen autofluorescence is enhanced.

Cytosolic overexpression of the different fluorescent systems alone, using the same expression signals, showed heterogeneous expression of the fluorescent systems. High levels of mCherryOpt were toxic for C. difficile cells limiting the applicability of this fluorophore as a transcriptional reporter. When fused to HupA, C. difficile histone-like protein, the fluorescent systems behaved similarly and did not affect the HupA overproduction phenotype.

Conclusions

The present study compares several commonly used fluorescent systems for application as transcriptional or translational reporters in microscopy and summarizes the limitations and key challenges for live-cell imaging of C. difficile. Due to independence of molecular oxygen and fluorescent signal, SNAPCd appears the most suitable candidate for live-cell imaging in C. difficile to date.

Abstract Figure
Oscillations and variability in neuronal systems: interplay of autonomous transient dynamics and fast deterministic fluctuations
Authors: Pena Rodrigo F. O. , Rotstein Horacio G.
Published: June 2021

Neuronal systems are subject to rapid fluctuations both intrinsically and externally. These fluctuations can be disruptive or constructive. We investigate the dynamic mechanisms underlying the interactions between rapidly fluctuating signals and the intrinsic properties of the target cells to produce variable and/or coherent responses. We use linearized and non-linear conductance-based models and piecewise constant (PWC) inputs with short duration pieces. The amplitude distributions of the constant pieces consist of arbitrary permutations of a baseline PWC function. In each trial within a given protocol we use one of these permutations and each protocol consists of a subset of all possible permutations, which is the only source of uncertainty in the protocol. We show that sustained oscillatory behavior can be generated in response to various forms of PWC inputs independently of whether the stable equilibria of the corresponding unperturbed systems are foci or nodes. The oscillatory voltage responses are amplified by the model nonlinearities and attenuated for conductance-based PWC inputs as compared to current-based PWC inputs, consistent with previous theoretical and experimental work. In addition, the voltage responses to PWC inputs exhibited variability across trials, which is reminiscent of the variability generated by stochastic noise (e.g., Gaussian white noise). Our analysis demonstrates that both oscillations and variability are the result of the interaction between the PWC input and the target cell’s autonomous transient dynamics with little to no contribution from the dynamics in vicinities of the steady-state, and do not require input stochasticity.
Nutrient-dependent allometric plasticity in a male-diphenic mite
Authors: Rhebergen Flor T. , Stewart Kathryn A. , Smallegange Isabel M.
Published: June 2021

Male secondary sexual traits often scale allometrically with body size. These allometries can be variable within species, and may shift depending on environmental conditions such as food quality. Such allometric plasticity has been hypothesized to initiate local adaptation and evolutionary diversification of scaling relationships, but is under-recorded, and its eco- evolutionary effects are not well understood. Here, we test for allometric plasticity in the bulb mite (Rhizoglyphus robini) in which large males tend to develop as armed adult fighters with thickened third legs, while small males become adult scramblers without thickened legs. We first examined the ontogenetic timing for size- and growth-dependent male morph determination, using experimentally amplified fluctuations in growth rate throughout juvenile development. Having established that somatic growth and body size determine male morph expression immediately before metamorphosis, we examined whether the relationship between adult male morph and size at metamorphosis shifts with food quality. We found that the threshold body size for male morph expression shifts towards lower values with deteriorating food quality, confirming food-dependent allometric plasticity. Such allometric plasticity may allow populations to track prevailing nutritional conditions, potentially facilitating rapid evolution of allometric scaling relationships.
Functional regulatory variants implicate distinct transcriptional networks in dementia
Authors: Cooper Yonatan A. , Davis Jessica E. , Kosuri Sriram , Coppola Giovanni , Geschwind Daniel H.
Published: June 2021

Predicting functionality of noncoding variation is one of the major challenges in modern genetics. We employed massively parallel reporter assays to screen 5,706 variants from genome-wide association studies for both Alzheimer’s disease (AD) and Progressive Supranuclear Palsy (PSP). We identified 320 functional regulatory polymorphisms (SigVars) comprising 27 of 34 unique tested loci, including multiple independent signals across the complex 17q21.31 region. We identify novel risk genes includingPLEKHM1in PSP andAPOC1in AD, and perform gene-editing to validate four distinct causal loci, confirming complement 4 (C4A) as a novel genetic risk factor for AD. Moreover, functional variants preferentially disrupt transcription factor binding sites that converge on enhancers with differential cell-type specific activity in PSP and AD, implicating a neuronalSP1-driven regulatory network in PSP pathogenesis. These analyses support a novel mechanism underlying noncoding genetic risk, whereby common genetic variants drive disease risk via their aggregate activity on specific transcriptional programs.

One Sentence Summary

High-throughput functional analysis of GWAS loci reveals cell-type specific regulatory networks that mediate genetic risk for dementia.
Distinct gene expression dynamics in developing and regenerating limbs
Authors: Sinigaglia Chiara , Almazán Alba , Sémon Marie , Gillet Benjamin , Hughes Sandrine , Edsinger Eric , Averof Michalis , Paris Mathilde
Published: June 2021

Regenerating animals have the ability to reproduce organs that were originally generated in the embryo and subsequently lost due to injury. Understanding whether the process of regeneration mirrors development is an open question in most regenerative species. Here we take a transcriptomics approach to examine to what extent leg regeneration shows the same temporal patterns of gene expression as leg development in the embryo, in the crustacean Parhyale hawaiensis. We find that leg development in the embryo shows stereotypic temporal patterns of gene expression. In contrast, global patterns of gene expression during leg regeneration show a high degree of variation, related to the physiology of individual animals. A major driver of this variation is the molting cycle. After dissecting the transcriptional signals of individual physiology from regeneration, we obtain temporal signals that mark distinct phases of leg regeneration. Comparing the transcriptional dynamics of development and regeneration we find that, although both processes use largely the same genes, the temporal patterns in which these gene sets are deployed are different and cannot be systematically aligned.

HIGHLIGHTS

Single-limb data on transcriptional dynamics of leg development and regeneration

Developing embryonic legs show stereotypic transcriptional profiles

Regenerating leg transcriptomes show a high degree on individual variation

Regenerating leg transcriptomes are influenced by adult physiology, especially molting

Regenerating leg transcriptomes reveal distinct phases of leg regeneration

Leg development and regeneration use overlapping sets of genes in different temporal patterns
MetA is a ‘thermal fuse’ that arrests growth and protects Escherichia coli at elevated temperatures
Authors: Schink Severin , Gough Zara , Biselli Elena , Huiman Mariel Garcia , Chang Yu-Fang , Basan Markus , Gerland Ulrich
Published: June 2021

Adaptive stress resistance in microbes is mostly attributed to the expression of stress response genes, such as heat shock proteins, which prevent deterioration of cellular material. Here, we report a novel response of E. coli to heat stress: induction of a growth-arrested state, caused by degradation of an enzyme in the methionine biosynthesis pathway (MetA). While MetA degradation is detrimental for proliferation, we show that the resulting growth arrest has a direct benefit for survival at high temperatures; it protects cells when temperatures rise beyond 50°C, increasing the survival chances by over 1000-fold. Using a combination of experiments and mathematical modelling, we show that degradation of MetA leads to the coexistence of growing and non-growing cells, allowing microbes to bet-hedge between continued growth if conditions remain bearable and survival if conditions worsen. We test our model experimentally and verify quantitatively how protein expression, degradation rates and environmental stresses affect the partitioning between growing and non-growing cells. Because growth arrest can be abolished with simple mutations, such as point mutations of MetA and knock-outs of proteases, we interpret the breakdown of methionine synthesis as a system that has evolved to disintegrate at high temperature and shut off growth, analogous to ‘thermal fuses’ used in engineering to shut off electricity when the device could be damaged by overheating.
Distributional reinforcement learning in prefrontal cortex
Authors: Muller Timothy H. , Butler James L. , Veselic Sebastijan , Miranda Bruno , Behrens Timothy E.J. , Kurth-Nelson Zeb , Kennerley Steven W.
Published: June 2021

Prefrontal cortex is crucial for learning and decision-making. Classic reinforcement learning (RL) theories centre on learning the expectation of potential rewarding outcomes and explain a wealth of neural data in prefrontal cortex. Distributional RL, on the other hand, learns the full distribution of rewarding outcomes and better explains dopamine responses. Here we show distributional RL also better explains prefrontal cortical responses, suggesting it is a ubiquitous mechanism for reward-guided learning.
Targeting a proteolytic neo-epitope of CUB-domain containing protein 1 in RAS-driven cancer
Authors: Lim Shion A. , Zhou Jie , Martinko Alexander J. , Wang Yung-Hua , Filippova Ekaterina V. , Steri Veronica , Wang Donghui , Remesh Soumya G. , Liu Jia , Hann Byron , Kossiakoff Anthony A. , Evans Michael J. , Leung Kevin K. , Wells James A.
Published: June 2021

A central challenge for any therapeutic is targeting diseased over normal cells. Proteolysis is frequently upregulated in disease and can generate proteoforms with unique neo-epitopes. We hypothesize that targeting proteolytic neo-epitopes can enable more effective and safer treatments, reflecting a conditional layer of disease-specific regulation. Here, we characterized the precise proteolytic isoforms of CUB domain containing protein 1 (CDCP1), a protein overexpressed and specifically cleaved in RAS-driven cancers. We validated that the N-terminal and C-terminal fragments of CDCP1 remain associated after proteolysis in vitro and on the surface of pancreatic cancer cells. Using a differential phage display strategy, we generated exquisitely selective recombinant antibodies that target cells harboring cleaved CDCP1 and not the full-length form using antibody-drug conjugates or a bi-specific T-cell engagers. We show tumor-specific localization and anti-tumor activity in a syngeneic pancreatic tumor model having superior safety profiles compared to a pan-CDCP1-targeting antibody. Our studies show proteolytic neo-epitopes can provide an orthogonal “AND” gate for disease-specific targeting.

One-Sentence Summary

Antibody-based targeting of neo-epitopes generated by disease-associated proteolysis improves the therapeutic index
FlyPhoneDB: An integrated web-based resource for cell-cell communication prediction in Drosophila
Authors: Liu Yifang , Hu Yanhui , Li Joshua Shing Shun , Rodiger Jonathan , Comjean Aram , Attrill Helen , Antonazzo Giulia , Brown Nicholas H. , Perrimon Norbert
Published: June 2021

Multicellular organisms rely on cell-cell communication to exchange information necessary for developmental processes and metabolic homeostasis. Cell-cell communication pathways can be inferred from transcriptomic datasets based on ligand-receptor (L-R) expression. Recently, data generated from single cell RNA sequencing (scRNA-seq) have enabled L-R interaction predictions at an unprecedented resolution. While computational methods are available to infer cell-cell communication in vertebrates such a tool does not yet exist for Drosophila. Here, we generated a high confidence list of L-R pairs for the major fly signaling pathways and developed FlyPhoneDB, a quantification algorithm that calculates interaction scores to predict L-R interactions between cells. At the FlyPhoneDB user interface, results are presented in a variety of tabular and graphical formats to facilitate biological interpretation. To demonstrate that FlyPhoneDB can effectively identify active ligands and receptors to uncover cell-cell communication events, we applied FlyPhoneDB to Drosophila scRNA-seq data sets from adult midgut, abdomen, and blood, and demonstrate that FlyPhoneDB can readily identify previously characterized cell-cell communication pathways. Altogether, FlyPhoneDB is an easy-to-use framework that can be used to predict cell-cell communication between cell types from scRNA-seq data in Drosophila.
A functional network signature in the developing cerebellum: evidence from a preclinical model of autism
Authors: Soria-Ortiz María Berenice , Martínez-Torres Ataúlfo , Reyes-Haro Daniel
Published: June 2021

Autism spectrum disorders (ASD) are pervasive neurodevelopmental conditions detected during childhood when delayed language onset and social deficits are observed. Children diagnosed with ASD frequently display sensorimotor deficits associated with the cerebellum, suggesting a dysfunction of synaptic circuits. Astroglia are part of the tripartite synapses and postmortem studies reported an increased expression of the glial fibrillary acidic protein (GFAP) in the cerebellum of ASD patients. Astroglia respond to neuronal activity with calcium transients that propagate to neighboring cells, resulting in a functional network response known as a calcium wave. This form of intercellular signaling is implicated in proliferation, migration, and differentiation of neural precursors. Prenatal exposure to valproate (VPA) is a preclinical model of ASD in which premature migration and excess of apoptosis occur in the internal granular layer (IGL) of the cerebellum during the early postnatal period. In this study we tested calcium wave propagation in the IGL of mice prenatally exposed to VPA. Sensorimotor and social deficits were observed and IGL depolarization evoked a calcium wave with astrocyte recruitment. The calcium wave propagation, initial cell recruitment, and mean amplitude of the calcium transients increased significantly in VPA-exposed mice compared to the control group. Astrocyte recruitment was significantly increased in the VPA model, but the mean amplitude of the calcium transients was unchanged. Western blot and histological studies revealed an increased expression of GFAP and higher astroglial density. We conclude that the functional network of the IGL is remarkably augmented in the preclinical model of autism.
Suv420 enrichment at the centromere limits Aurora B localization and function
Authors: Herlihy Conor P , Hahn Sabine , Hermance Nicole M , Crowley Elizabeth A , Manning Amity L
Published: June 2021

Centromere structure and function are defined by the epigenetic modification of histones at centromeric and pericentromeric chromatin. The constitutive heterochromatin found at pericentromeric regions is highly enriched for H3K9me3 and H4K20me3. While mis-expression of the methyltransferase enzymes, Suv39 and Suv420, that regulate these marks are common in disease, the consequences of such changes are not well understood. Our data show that increased centromere localization of Suv39 and Suv420 suppress centromere transcription and compromise localization of the mitotic kinase Aurora B: decreasing microtubule dynamics and compromising chromosome alignment and segregation. We find that inhibition of Suv420 methyltransferase activity partially restores Aurora B localization to centromeres and that restoration of the Aurora B-containing CPC to the centromere is sufficient to suppress mitotic errors that result when Suv420/H4K20me3 is enriched at centromeres. Consistent with a role for Suv39 and Suv420 in negatively regulating Aurora B, high expression of these enzymes corresponds with increased sensitivity to Aurora kinase inhibition in cancer cells suggesting that increased H3K9 and H4K20 methylation may be an underappreciated source of chromosome missegregation in cancer.
The IL-33-ILC2 pathway protects from amebic colitis
Authors: Uddin Md Jashim , Leslie Jhansi L. , Burgess Stacey L. , Oakland Noah , Thompson Brandon , Abhyankar Mayuresh , Frisbee Alyse , Donlan Alexandra N , Kumar Pankaj , Petri William A
Published: June 2021

Entamoeba histolytica is a pathogenic protozoan parasite that causes intestinal colitis, diarrhea, and in some cases, liver abscess. Through transcriptomics analysis, we observed that E. histolytica infection was associated with increased expression of IL-33 mRNA in both the human and murine colon. IL-33, the IL-1 family cytokine, is released after cell injury to alert the immune system of tissue damage during infection. Treatment with recombinant IL-33 protected mice from amebic infection and colonic tissue damage; moreover, blocking IL-33 signaling made mice more susceptible to infection and weight loss. IL-33 limited the recruitment of inflammatory immune cells and decreased the pro-inflammatory cytokine IL-6 in the colon. Type 2 immune responses, which are known to be involved in tissue repair, were upregulated by IL-33 treatment during amebic infection. Interestingly, administration of IL-33 protected RAG2-/- mice but not RAG2-/-γc-/- mice, demonstrating that IL-33 mediated protection occurred in the absence of T or B cells but required the presence of innate lymphoid cells (ILCs). IL-33 induced recruitment of ILC2 but not ILC1 and ILC3 in RAG2-/- mice. Adoptive transfer of ILC2s to RAG2-/-γc-/- mice restored IL-33 mediated protection. These data reveal that the IL-33-ILC2 pathway is an important host defense mechanism against amebic colitis.
Computational fluid dynamics provide evidence for a compensatory suction feeding like effect in the predatory strike of dragonfly larvae
Authors: Koehnsen Alexander , Brede Martin , Gorb Stanislav N , Büsse Sebastian
Published: June 2021

Most fast-moving aquatic predators face the challenge of bow wave formation. Water in front of the predator alarms or even displaces the prey. To mitigate the formation of such a bow wave, a strategy aiming at pressure reduction via suction has evolved convergently in several animal groups: compensatory suction feeding. The aquatic larvae of dragonflies and damselflies (Insecta: Odonata) are likely to face this challenge as well. They capture prey underwater using a fast-moving raptorial appendage, the so-called prehensile labial mask. Within dragonflies (Odonata: Anisoptera) two basic shapes of the prehensile labial mask have evolved, with an either flat and slender or concave distal segment. While the former is a pure grasping device, the latter is also capable of scooping up smaller prey and retaining it inside the cavity by arrays of bristle-like structures. The hydrodynamics of the prehensile labial mask was previously unknown. We used computational fluid dynamic (CFD) simulations of the distal segment of the mask, to investigate for the first time how different shapes of the mask impact their function. Our results suggest that both shapes are highly streamlined and generate a low-pressure area, likely leading to an effect analogous to compensatory suction feeding. This presents a vivid example of how convergent evolution enables very different animal groups to successfully deal with the challenges of their environment. It may also be an interesting concept for technical application in small scale grasping devices; e.g. for simple sampling mechanisms in small-sized autonomous underwater vehicles (μAUVs).
Low-dose fluvoxamine modulates endocytic trafficking of SARS-CoV-2 spike protein: a potential mechanism for anti-COVID-19 protection by antidepressants
Authors: Glebov Oleg O
Published: June 2021

Commonly prescribed antidepressants may be associated with protection against severe COVID-19, with one drug (fluvoxamine) currently undergoing a Phase 3 clinical trial. The mechanism of their action, however, remains unknown. Here, I investigated the effect of fluvoxamine on membrane trafficking of the SARS-CoV-2 spike protein and its cell host receptor ACE2 in HEK293T cells. A sub-therapeutic concentration (80 nM) of fluvoxamine rapidly upregulated fluid-phase endocytosis, resulting in enhanced accumulation of the spike-ACE2 complex in enlarged early endosomes. Diversion of endosomal trafficking may provide a simple cell biological mechanism consistent with the protective effect of antidepressants against COVID-19, highlighting their therapeutic and prophylactic potential.
Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery
Authors: Voss Gjendine , Edsjö Anders , Bjartell Anders , Ceder Yvonne
Published: June 2021

Even though microRNAs have been viewed as promising biomarkers for years, their clinical implementation is still lagging far behind. This is in part due to the lack of RT-qPCR technologies that can differentiate between microRNA isoforms. For example, A-to-I editing of microRNAs through adenosine deaminase acting on RNA (ADAR) enzymes can affect their expression levels and functional roles, but editing isoform-specific assays are not commercially available. Here, we describe RT-qPCR assays that are specific for editing isoforms, using microRNA-379 (miR-379) as a model. The assays are based on two-tailed RT-qPCR, and we show them to be compatible both with SYBR Green and hydrolysis-based chemistries, as well as with both qPCR and digital PCR. The assays could readily detect different miR-379 editing isoforms in various human tissues. We found that the miR-379 editing frequency was higher in prostate cancer samples compared to benign prostatic hyperplasia samples. Furthermore, decreased expression of unedited miR-379, but not edited miR-379, was associated with treatment resistance, metastasis and shorter overall survival. Taken together, this study presents the first RT-qPCR assays that were demonstrated to distinguish A-to-I-edited microRNAs, and shows that they can be useful in the identification of biomarkers that previously have been masked by other isoforms.

Graphical abstract
RHBDL4 protects against endoplasmic reticulum stress by regulating the morphology and distribution of ER sheets
Authors: Lastun Viorica L. , Levet Clémence , Freeman Matthew
Published: June 2021

In metazoans, the architecture of the endoplasmic reticulum (ER) differs between cell types, and undergoes major changes through the cell cycle and according to physiological needs. Although much is known about how the different ER morphologies are generated and maintained, especially the ER tubules, how context dependent changes in ER shape and distribution are regulated and the factors involved are less characterized. Here, we show that RHBDL4, an ER-resident rhomboid protease, modulates the shape and distribution of the ER, especially under conditions that require rapid changes in the ER sheet distribution, including ER stress. RHBDL4 interacts with CLIMP-63, a protein involved in ER sheet stabilisation, and with the cytoskeleton. Mice lacking RHBDL4 are sensitive to ER stress and develop liver steatosis, a phenotype associated with unresolved ER stress. Our data introduce a new physiological role of RHBDL4 and also imply that this function does not require its enzymatic activity.
Complete metamorphosis and microbiota turnover in insects
Authors: Manthey Chrisitin , Johnston Paul , Rolff Jens
Published: June 2021

The insects constitute the majority of animal diversity. Most insects are holometabolous: during complete metamorphosis their bodies are radically re-organized. This re-organization poses a significant challenge to the gut microbiota, as the gut is replaced during pupation, a process that does not occur in hemimetabolous insects. In holometabolous hosts, it offers the opportunity to decouple the gut microbiota between the larval and adult life stages resulting in high beta diversity whilst limiting alpha diversity. Here we studied 18 different herbivorous insect species from 5 orders of holometabolous and 3 orders of hemimetabolous insects. Comparing larval and adult specimens, we find a much higher beta-diversity and hence microbiota turnover in holometabolous insects compared to hemimetabolous insects. Alpha diversity did not differ between holo-and hemimetabolous insects nor between developmental stages within these groups. Our results support the idea that pupation offers the opportunity to change the gut microbiota and hence facilitates ecological niche shifts. This effect of niche shift facilitation could explain a selective advantage of the evolution of complete metamorphosis, which is a defining trait of the most speciose insect taxon, the holometabola.
The SARS-CoV-2 nucleocapsid protein associates with the replication organelles before viral assembly at the Golgi/ERGIC and lysosome-mediated egress
Authors: Scherer Katharina M. , Mascheroni Luca , Carnell George W. , Wunderlich Lucia C. S. , Makarchuk Stanislaw , Brockhoff Marius , Mela Ioanna , Fernandez-Villegas Ana , Barysevich Max , Stewart Hazel , Sans Maria Suau , George Charlotte L. , Lamb Jacob R. , Kaminski-Schierle Gabriele S. , Heeney Jonathan L. , Kaminski Clemens F.
Published: June 2021

Despite being the target of extensive research efforts due to the COVID-19 pandemic, relatively little is known about the dynamics of SARS-CoV-2 replication within cells. We investigate and characterise the tightly orchestrated sequence of events during different stages of the infection cycle by visualising the spatiotemporal dynamics of the four structural proteins of SARS-CoV-2 at high resolution. The nucleoprotein is expressed first and accumulates around folded ER membranes in convoluted layers that connect to viral RNA replication foci. We find that of the three transmembrane proteins, the membrane protein appears at the Golgi apparatus/ERGIC before the spike and envelope proteins. Relocation of the lysosome marker LAMP1 towards the assembly compartment and its detection in transport vesicles of viral proteins confirm an important role of lysosomes in SARS-CoV-2 egress. These data provide new insights into the spatiotemporal regulation of SARS-CoV-2 assembly, and refine current understanding of SARS-CoV-2 replication.
Tensor Decomposition-based Unsupervised Feature Extraction Succeeded in Identification of Differentially Expressed Transcripts from Redundantde novoTranscriptome ofPlanarian
Authors: Kashima Makoto , Kumagai Nobuyoshi , Hirata Hiromi , Taguchi Y-h.
Published: June 2021

RNA-Seq data analysis of non-model organisms is often difficult because of the lack of a well-annotated genome. However, in non-model organisms, contigs can be generated byde novoassembling. This can result in a large number of transcripts, making it difficult to easily remove redundancy. A large number of transcripts can also lead to difficulty in the recognition of differentially expressed transcripts (DETs) between more than two experimental conditions, becauseP-values must be corrected by considering multiple comparison corrections whose effect is enhanced as the number of transcripts increases. Heavily correctedP-values often fail to take sufficiently smallP-values as significant. In this study, we applied a recently proposed tensor decomposition (TD)-based unsupervised feature extraction (FE) to the RNA-seq data obtained for a non-model organism, planarianDugesia japonica; Although we used de novo assembled transcriptome reference with high redundancy, we successfully obtained a larger number of transcripts whose expression was altered between normal and defective samples as well as during time development than those identified by a conventional method. TD-based unsupervised FE is expected to be an effective tool that can identify a substantial number of DETs, even when a poorly annotated genome is available.
Effect of Substrate Stiffness on Human Intestinal Enteroids Infectivity by Enteroaggregative Escherichia coli
Authors: Swaminathan Ganesh , Kamyabi Nabiollah , Carter Hannah , Rajan Anubama , Karandikar Umesh , Criss Zachary , Shroyer Noah Freeman , Robertson Matthew , Coarfa Cristian , Huang Chenlin , Shannon Tate , Tadros Madeleine , Estes Mary , Maresso Anthony , Grande-Allen Kathryn Jane
Published: June 2021

Human intestinal enteroids (HIE) models have contributed significantly to our understanding of diarrheal diseases and other intestinal infections, but their routine culture conditions fail to mimic the mechanical environment of the native intestinal wall. Because the mechanical characteristics of the intestine significantly alter how pathogens interact with the intestinal epithelium, we used different concentrations of polyethylene glycol (PEG) to generate soft (~2 kPa), medium (~10 kPa), and stiff (~100 kPa) hydrogel biomaterial scaffolds. The height of HIEs cultured in monolayers atop these hydrogels was 18 μm whereas HIEs grown on rigid tissue culture surfaces (with stiffness in the GPa range) were 10 μm. Substrate stiffness also influenced the amount of enteroaggregative E. coli (EAEC strain 042) adhered to the HIEs. We quantified a striking difference in adherence pattern; on the medium and soft gels, the bacteria formed clusters of >100 and even >1000 on both duodenal and jejunal HIEs (such as would be found in biofilms), but did not on glass slides and stiff hydrogels. All hydrogel cultured HIEs showed significant enrichment for gene and signaling pathways related to epithelial differentiation, cell junctions and adhesions, extracellular matrix, mucins, and cell signaling compared to the HIEs cultured on rigid tissue culture surfaces. Collectively, these results indicate that the HIE monolayers cultured on the hydrogels are primed for a robust engagement with their mechanical environment, and that the soft hydrogels promote the formation of larger EAEC aggregates, likely through an indirect differential effect on mucus.