bluuebunny/crossref_metadata_2025 huggingface dataset:
A tool for federated training of segmentation models on whole slide images
Authors: Lutnick Brendon , Manthey David , Becker Jan U. , Zuckerman Jonathan E. , Rodrigues Luis , Jen Kuang Yu. , Sarder Pinaki
Published: August 2021

The largest bottleneck to the development of convolutional neural network (CNN) models in the computational pathology domain is the collection and curation of diverse training datasets. Training CNNs requires large cohorts of image data, and model generalizability is dependent on training data heterogeneity. Including data from multiple centers enhances the generalizability of CNN based models, but this is hindered by the logistical challenges of sharing medical data. In this paper we explore the feasibility of training our recently developed cloud-based segmentation tool (Histo-Cloud) using federated learning. We show that a federated trained model to segment interstitial fibrosis and tubular atrophy (IFTA) using datasets from three institutions is comparable to a model trained by pooling the data on one server when tested on a fourth (holdout) institution’s data. Further, training a model to segment glomeruli for a federated dataset (split by staining) demonstrates similar performance.
Physicochemical and Pharmacokinetic Properties Determining Drug Detection in Skin
Authors: Bittremieux Wout , Advani Rohit S. , Jarmusch Alan K. , Aguirre Shaden , Lu Aileen , Dorrestein Pieter C. , Tsunoda Shirley M.
Published: August 2021

Chemicals, including some systemically administered xenobiotics and their biotransformations, can be detected noninvasively using skin swabs and untargeted metabolomics analysis. We sought to understand the principal drivers that determine whether a drug taken orally or systemically is likely to be observed on the epidermis by using a random forest classifier to predict which drugs would be detected on the skin. A variety of molecular descriptors describing calculated properties of drugs, such as measures of volume, electronegativity, bond energy, and electrotopology, were used to train the classifier. The mean area under the ROC curve was 0.71 for predicting drug detection on the epidermis, and the SHapley Additive exPlanations model interpretation technique was used to determine the most relevant molecular descriptors. Based on the analysis of 2,561 FDA approved drugs, we predict that therapeutic drug classes such as nervous system drugs are more likely to be detected on the skin. Detecting drugs and other chemicals noninvasively on the skin using untargeted metabolomics could be a useful clinical advancement in therapeutic drug monitoring, adherence, and health status.
Long-term p21 and p53 trends regulate the frequency of mitosis events and cell cycle arrest
Authors: Tran Anh Phong , Tralie Christopher J. , Moosmüller Caroline , Belkhatir Zehor , Reyes José , Levine Arnold J. , Deasy Joseph O. , Tannenbaum Allen R.
Published: August 2021

1

Radiation exposure of healthy cells can halt cell cycle temporarily or permanently. In this work, two single cell datasets that monitored the time evolution of p21 and p53, one subjected to gamma irradiation and the other to x-ray irradiation, are analyzed to uncover the dynamics of this process. New insights into the biological mechanisms were found by decomposing the p53 and p21 signals into transient and oscillatory components. Through the use of dynamic time warping on the oscillatory components of the two signals, we found that p21 signaling lags behind its lead signal, p53, by about 3.5 hours with oscillation periods of around 6 hours. Additionally, through various quantification methods, we showed how p21 levels, and to a lesser extent p53 levels, dictate whether the cells are arrested in their cell cycle and how fast these cells divide depending on their long-term trend in these signals.
Bryophyte spermiogenesis occurs through multimode autophagic and nonautophagic degradation
Authors: Norizuki Takuya , Minamino Naoki , Tsukaya Hirokazu , Ueda Takashi
Published: August 2021

Mitochondria change their morphology in response to developmental and environmental cues. During sexual reproduction, bryophytes produce spermatozoids with two mitochondria in the cell body. Although intensive morphological analyses have been conducted thus far, how this fixed number of mitochondria is realized remains unknown. Here, we investigated how mitochondria are reorganized during spermiogenesis in Marchantia polymorpha. We found that the mitochondrial number is reduced to one through fission followed by autophagic degradation during early spermiogenesis, and then the posterior mitochondrion arises by fission of the anterior mitochondrion. Autophagy is also responsible for the removal of other organelles, including peroxisomes, but these other organelles are removed at distinct developmental stages from mitochondrial degradation. We also found that spermiogenesis involves nonautophagic organelle degradation. Our findings highlight the dynamic reorganization of mitochondria, which is regulated distinctly from that of other organelles, and multiple degradation mechanisms operate in organelle remodeling during spermiogenesis in M. polymorpha.
New insights into antimalarial chemopreventive activity of antifolates
Authors: Pethrak Chatpong , Posayapisit Navaporn , Pengon Jutharat , Suwanakitti Nattida , Saeung Atiporn , Shorum Molnipha , Aupalee Kittipat , Taai Kritsana , Yuthavong Yongyuth , Kamchonwongpaisan Sumalee , Jupatanakul Natapong
Published: August 2021

Antifolates targeting dihydrofolate reductase (DHFR) are antimalarial compounds that have long been used for malaria treatment and chemoprevention (inhibition of infection from mosquitoes to humans). Despite their extensive applications, the thorough understanding of antifolate activity against hepatic malaria parasites, especially resistant parasites, have yet to be achieved. Using a transgenic P. berghei harboring quadruple mutant dhfr from P. falciparum (Pb::Pfdhfr-4M), we demonstrate that quadruple mutations on Pfdhfr confer complete chemoprevention resistance to pyrimethamine, the previous generation of antifolate, but not a new class of antifolate designed to overcome the resistance such as P218. Detailed investigation to pin-point stage-specific chemoprevention further demonstrated that it is unnecessary for the drug to be present throughout hepatic development. The drug is most potent against the developmental stages from early hepatic trophozoite to late hepatic trophozoite, but is not effective at inhibiting sporozoite and early hepatic stage development from sporozoite to early trophozoite. Our data shows that P218 also inhibited the late hepatic stage development, from trophozoite to mature schizonts to a lesser extent. With a single dose of 15 mg/kg, P218 prevented infection from up to 25,000 pyrimentamine-resistant sporozoites, a number equal to thousands of infectious mosquito bites. Additionally, the hepatic stage of malaria parasite is much more susceptible to antifolates than the asexual blood stage. This study provides important insights into the activity of antifolates, as a chemopreventive therapeutic which could lead to a more efficient and cost effective treatment regime.
Algorithm for the Quantitation of Variants of Concern for Rationally Designed Vaccines Based on the Isolation of SARS-CoV-2 Hawaiʻi Lineage B.1.243
Authors: Maison David P. , Ching Lauren L. , Cleveland Sean B. , Tseng Alanna C. , Nakano Eileen , Shikuma Cecilia M. , Nerurkar Vivek R.
Published: August 2021

SARS-CoV-2 worldwide emergence and evolution has resulted in variants containing mutations resulting in immune evasive epitopes that decrease vaccine efficacy. We acquired clinical samples, analyzed SARS-CoV-2 genomes, used the most worldwide emerged spike mutations from Variants of Concern/Interest, and developed an algorithm for monitoring the SARS-CoV-2 vaccine platform. The algorithm partitions logarithmic-transformed prevalence data monthly and Pearson’s correlation determines exponential emergence. The SARS-CoV-2 genome evaluation indicated 49 mutations. Nine of the ten most worldwide prevalent (>70%) spike protein changes have r-values >0.9. The tenth, D614G, has a prevalence >99% and r-value of 0.67. The resulting algorithm is based on the patterns these ten substitutions elucidated. The strong positive correlation of the emerged spike protein changes and algorithmic predictive value can be harnessed in designing vaccines with relevant immunogenic epitopes. SARS-CoV-2 is predicted to remain endemic and continues to evolve, so must SARS-CoV-2 monitoring and next-generation vaccine design.
A neural circuit architecture for rapid behavioral flexibility in goal-directed navigation
Authors: Dan Chuntao , Hulse Brad K. , Kappagantula Ramya , Jayaraman Vivek , Hermundstad Ann M.
Published: August 2021

Anchoring goals to spatial representations enables flexible navigation in both animals and artificial agents. However, using this strategy can be challenging in novel environments, when both spatial and goal representations must be acquired quickly and simultaneously. Here, we propose a framework for howDrosophilause their internal representation of head direction to build a goal heading representation upon selective thermal reinforcement. We show that flies in a well-established operant visual learning paradigm use stochastically generated fixations and directed saccades to express heading preferences, and that compass neurons, which represent flies’ head direction, are required to modify these preferences based on reinforcement. We describe how flies’ ability to quickly map their surroundings and adapt their behavior to the rules of their environment may rest on a behavioral policy whose parameters are flexible but whose form and dependence on head direction and goal representations are genetically encoded in the modular structure of their circuits. Using a symmetric visual setting, which predictably alters the dynamics of the head direction system, enabled us to describe how interactions between the evolving representations of head direction and goal impact behavior. We show how a policy tethered to these two internal representations can facilitate rapid learning of new goal headings, drive more exploitative behavior about stronger goal headings, and ensure that separate learning processes involved in mapping the environment and forming goals within that environment remain consistent with one another. Many of the mechanisms we outline may be broadly relevant for rapidly adaptive behavior driven by internal representations.
Identification and comparative analysis of long non-coding RNAs in the brain of fire ant queens in two different reproductive states
Authors: Tsai Cheng-Hung , Lin Tzu-Chieh , Chang Yi-Hsien , Tsai Huai-Kuang , Huang Jia-Hsin
Published: August 2021

Background

Many long non-coding RNAs (lncRNAs) have been extensively identified in many higher eukaryotic species. The function of lncRNAs has been reported to play important roles in diverse biological processes, including developmental regulation and behavioral plasticity. However, there are no reports of systematic characterization of long non-coding RNAs in the fire ant Solenopsis invicta.

Results

In this study, we performed a genome-wide analysis of lncRNAs in the brains of S. invicta from RNA-seq. In total, 1,393 novel lncRNA transcripts were identified in the fire ant. In contrast to the annotated lncRNA transcripts having at least two exons, novel lncRNAs are monoexonic transcripts with a shorter length. Besides, the transcriptome from virgin alate and dealate mated queens were analyzed and compared. The results showed 295 differentially expressed mRNA genes (DEGs) and 65 differentially expressed lncRNA genes (DELs) between virgin and mated queens, of which 17 lncRNAs were highly expressed in the virgin alates and 47 lncRNAs were highly expressed in the mated dealates. By identifying the DEL:DEG pairs with high association in their expression (Spearman’s |rho| > 0.8 and p-value < 0.01), many DELs were co-regulated with DEGs after mating. Furthermore, several remarkable lncRNAs (MSTRG.6523, MSTRG.588, and nc909) that were found to associate with particular coding genes may play important roles in the regulation of brain gene expression in reproductive transition in fire ants.

Conclusion

This study provides the first genome-wide identification of S. invicta lncRNAs in the brains in different reproductive states and will contribute to a fuller understanding of the transcriptional regulation underpinning reproductive changes.
THE TRANSCRIPTIONAL RESPONSE TO OXIDATIVE STRESS IS INDEPENDENT OF STRESS-GRANULE FORMATION
Authors: Singh Amanjot , Kandi Arvind Reddy , Jayaprakashappa Deepa , Thuery Guillaume , Purohit Devam J , Huelsmeier Joern , Singh Rashi , Pothapragada Sai Shruti , Ramaswami Mani , Bakthavachalu Baskar
Published: August 2021

Cells respond to stress with translational arrest, robust transcriptional changes, and transcription-independent formation of mRNP assemblies termed stress granules (SGs). Despite considerable interest in the role of SGs in oxidative, unfolded-protein, and viral stress responses, whether and how SGs contribute to stress-induced transcription has not been rigorously examined. To address this issue, we characterized transcriptional changes in Drosophila S2 cells induced by acute oxidative-stress and assessed how these were altered under conditions that disrupted SG assembly. Sodium-arsenite stress for 3 hours predominantly resulted in the induction or upregulation of stress-responsive mRNAs whose levels peaked during cell recovery after stress cessation. The stress-transcriptome is enriched in mRNAs coding for protein chaperones, including HSP70 and low molecular-weight heat shock proteins, glutathione transferases, and several non-coding RNAs. Oxidative stress also induced prominent cytoplasmic stress granules that disassembled 3-hours after stress cessation. As expected, RNAi-mediated knockdown of the conserved G3BP1/ Rasputin protein inhibited stress-granule assembly. However, this disruption had no significant effect on the stress-induced transcriptional response or stress-induced translational arrest. Thus, SG assembly and stress-induced effects on gene expression appear to be driven by distinctive signaling processes. We suggest that while SG assembly represents a fast, transient mechanism, the transcriptional response enables a slower, longer-lasting mechanism for adaptation to and recovery from cell stress.
Trait empathy modulates music-related functional connectivity
Authors: Moorthigari Vishnu , Carlson Emily , Toiviainen Petri , Vuust Peter , Brattico Elvira , Alluri Vinoo
Published: August 2021

It has been well established through behavioural studies that empathy significantly influences music perception. Such individual differences typically manifest as variability in whole brain functional connectivity patterns. To date, nobody has examined the modulatory effect of empathy on functional connectivity patterns during continuous music listening. In the present study, we seek to investigate the global and local connectivity patterns of 36 participants whose fMRI scanning was done by employing the naturalistic paradigm wherein they listened to a continuous piece of music. We used graph-based measures of functional connectivity to identify how cognitive and affective components of empathy modulate functional connectivity. Partial correlation between Eigenvector centrality and measures of empathy showed that cognitive empathy is associated with higher centrality in the sensorimotor regions responsible for motor mimicry while affective empathy showed higher centrality in regions related to auditory affect processing. We furthermore identified a left-hemispheric dominance in the modulatory effect of affective empathy particularly in the Orbitofrontal cortex and the temporal pole. Results are discussed in relation to various theoretical models of empathy and music cognition.
Deep Bayesian networks for uncertainty estimation and adversarial resistance of white matter hyperintensity segmentation
Authors: Forooshani Parisa Mojiri , Biparva Mahdi , Ntiri Emmanuel E. , Ramirez Joel , Boone Lyndon , Holmes Melissa F. , Adamo Sabrina , Gao Fuqiang , Ozzoude Miracle , Scott Christopher J.M. , Dowlatshahi Dar , Lawrence-Dewar Jane M. , Kwan Donna , Lang Anthony E. , Marcotte Karine , Leonard Carol , Rochon Elizabeth , Heyn Chris , Bartha Robert , Strother Stephen , Tardif Jean-Claude , Symons Sean , Masellis Mario , Swartz Richard H. , Moody Alan , Black Sandra E. , Goubran Maged
Published: August 2021

White matter hyperintensities (WMH) are frequently observed on structural neuroimaging of elderly populations and are associated with cognitive decline and increased risk of dementia. Many existing WMH segmentation algorithms produce suboptimal results in populations with vascular lesions or brain atrophy, or require parameter tuning and are computationally expensive. Additionally, most algorithms do not generate a confidence estimate of segmentation quality, limiting their interpretation. MRI-based segmentation methods are often sensitive to acquisition protocols, scanners, noise-level, and image contrast, failing to generalize to other populations and out-of-distribution datasets. Given these concerns, we propose a novel Bayesian 3D Convolutional Neural Network (CNN) with a U-Net architecture that automatically segments WMH, provides uncertainty estimates of the segmentation output for quality control and is robust to changes in acquisition protocols. We also provide a second model to differentiate deep and periventricular WMH. 432 subjects were recruited to train the CNNs from four multi-site imaging studies. A separate test set of 158 subjects was used for evaluation, including an unseen multi-site study. We compared our model to two established state-of-the-art techniques (BIANCA and DeepMedic), highlighting its accuracy and efficiency. Our Bayesian 3D U-Net achieved the highest Dice similarity coefficient of 0.89 ± 0.08 and the lowest modified Hausdorff distance of 2.98 ± 4.40 mm. We further validated our models highlighting their robustness on ‘clinical adversarial cases’ simulating data with low signal-to-noise ratio, low resolution, and different contrast (stemming from MRI sequences with different parameters). Our pipeline and models are available at:https://hypermapp3r.readthedocs.io
L-DOPA enhances hippocampal direction signals in younger and older adults
Authors: Koch Christoph , Bäuchl Christian , Glöckner Franka , Riedel Philipp , Petzold Johannes , Smolka Michael , Li Shu-Chen , Schuck Nicolas W.
Published: August 2021

Previous studies indicate a role of dopamine in hippocampus-dependent spatial navigation. Although neural representations of direction are an important aspect of spatial cognition, it is not well understood whether dopamine directly affects these representations, or only impacts other aspects of spatial brain function. Moreover, both dopamine and spatial cognition decline sharply during age, raising the question which effect dopamine has on directional signals in the brain of older adults. To investigate these questions, we used a double-blind cross-over L-DOPA/Placebo intervention design in which 43 younger and 37 older adults navigated in a virtual spatial environment while undergoing functional magnetic resonance imaging (fMRI). We studied the effect of L-DOPA, a DA precursor, on fMRI activation patterns that encode spatial walking directions that have previously been shown to lose specificity with age. This was done in predefined regions of interest, including the early visual cortex, retrosplenial cortex, and hippocampus. Classification of brain activation patterns associated with different walking directions was improved in the hippocampus and the retrosplenial cortex following L-DOPA administration. This suggests that DA enhances the specificity of neural representations of walking direction in these areas. In the hippocampus these results were found in both age groups, while in the RSC they were only observed in younger adults. Taken together, our study provides evidence for a mechanistic link between DA and the specificity of neural responses during spatial navigation.

Significance Statement

The sense of direction is an important aspect of spatial navigation, and neural representations of direction can be found throughout a large network of space-related brain regions. But what influences how well these representations track someone’s true direction? Using a double-blind cross-over L-DOPA/Placebo intervention design, we find causal evidence that the neurotransmitter dopamine impacts the fidelity of direction selective neural representations in the human hippocampus and retrosplenial cortex. Interestingly, the effect of L-DOPA was either equally present or even smaller in older adults, despite the well-known age related decline of dopamine. These results provide novel insights into how dopamine shapes the neural representations that underlie spatial navigation.
Perinatal Inflammation Disturbs Secondary Germinal Zone Neurogenesis and Gliogenesis Producing Deficits in Sociability
Authors: Velloso Fernando Janczur , Wadhwa Anna , Kumari Ekta , Carcea Ioana , Gunal Ozlem , Levison Steven W.
Published: August 2021

Epidemiologic studies have demonstrated that infections during pregnancy increase the risk of offspring developing Schizophrenia, Autism, Depression and Bipolar Disorder and have implicated interleukin-6 (IL-6) as a causal agent. However, other cytokines have been associated with psychiatric disorders; therefore, it remains to be established whether elevating IL-6 is sufficient to alter the trajectory of neural development. Furthermore, most rodent studies have manipulated the maternal immune system at mid-gestation, which affects the stem cells and progenitors in both the primary and secondary germinal matrices. Therefore, a question that remains to be addressed is whether elevating IL-6 when the secondary germinal matrices are most active will affect brain development. Here, we have increased IL-6 from postnatal days 3-6, when the secondary germinal matrices are rapidly expanding. Using Nestin-CreERT2 fate mapping we show that this transient increase in IL-6 decreased neurogenesis in the dentate gyrus of the dorsal hippocampus, reduced astrogliogenesis in the prefrontal cortex and amygdala and decreased oligodendrogenesis in the body and splenium of the corpus callosum all by ∼50%. Moreover, the IL-6 treatment elicited behavioral changes classically associated with neurodevelopmental disorders. As adults, IL-6 injected male mice lost social preference in the social approach test, spent ∼30% less time socially engaging with sexually receptive females and produced ∼50% fewer ultrasonic vocalizations during mating. They also engaged ∼50% more time in self-grooming behavior and had an increase in inhibitory avoidance. Altogether, these data provide new insights into the biological mechanisms linking perinatal immune activation to complex neurodevelopmental brain disorders.

Significance statement

In these studies, we doubled circulating IL-6 levels in mice from postnatal days 3-6 to test the hypothesis that this would be sufficient to disturb neural development. More specifically, we hypothesized that IL-6 would affect postnatal neural stem cell and progenitor expansion and specification. We show that this transient increase in IL-6 decreases the numbers of granule neurons in the dorsal hippocampus, astrocytes in the prefrontal cortex and amygdala and oligodendrocytes in the corpus callosum. Importantly, this transient increase in IL-6 changes the sociability, communication and repetitive behaviors of the treated mice as adults, which are core symptoms pertinent to several neurodevelopmental psychiatric disorders.
Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L
Authors: Wani Gulzar A. , Sprenger Hans-Georg , Ndoci Kristiano , Chandragiri Srikanth , Acton Richard James , Schatton Désirée , Kochan Sandra M.V. , Sakthivelu Vignesh , Jevtic Milica , Seeger Jens M. , Müller Stefan , Giavalisco Patrick , Rugarli Elena I. , Motori Elisa , Langer Thomas , Bergami Matteo
Published: August 2021

The transition between quiescence and activation in neural stem and progenitor cells (NSPCs) is coupled to reversible changes in energy metabolism with key implications for life-long NSPC self-renewal and neurogenesis. How this metabolic plasticity is ensured between NSPC activity states is unclear. We found that a state-dependent rewiring of the mitochondrial proteome by the peptidase YME1L is required to preserve NSPC self-renewal in the adult brain. YME1L-mediated proteome rewiring regulates the rate of fatty acid oxidation (FAO) for replenishing Krebs cycle intermediates and dNTP precursors, which are required to sustain NSPC amplification. Yme1l deletion irreversibly shifts the metabolic profile of NSPCs away from a FAO-dependent state resulting in defective self-renewal, premature differentiation and NSPC pool depletion. Our results disclose an important role for YME1L in coordinating the switch between metabolic states of NSPCs and suggest that NSPC fate is regulated by compartmentalized changes in protein network dynamics.
Subpopulations of soluble, misfolded proteins commonly bypass chaperones: How it happens at the molecular level
Authors: Halder Ritaban , Nissley Daniel A. , Sitarik Ian , O’Brien Edward P.
Published: August 2021

Subpopulations of soluble, misfolded proteins can bypass chaperones within cells. The scope of this phenomenon and the lifetimes of these states have not been experimentally quantified, and how such misfolding happens at the molecular level is poorly understood. We address the first issue through a meta-analysis of the experimental literature. We find that in all quantitative protein refolding-function studies, there is always a subpopulation of soluble but misfolded and less-functional protein that does not fold in the presence of one or more chaperones. This subpopulation ranges from 8% to 50% of the soluble protein molecules in solution. Fitting the experimental time traces to a kinetic model, we find these chaperone-bypassing misfolded states take months or longer to fold and function in the presence of different chaperones. We next addressed how, at the molecular level, some misfolded proteins can evade chaperones by simulating six different proteins interacting withE. coli’s GroEL and HtpG chaperones when those proteins are in folded, unfolded, or long-lived, soluble, misfolded states. We observe that both chaperones strongly bind the unfolded state and weakly bind the folded and misfolded states to a similar degree. Thus, these chaperones cannot distinguish between the folded and long-lived misfolded states of these proteins. A structural analysis reveals the misfolded states are highly similar to the native state – having a similar size, amount of exposed hydrophobic surface area, and level of tertiary structure formation. These results demonstrate thatin vitroit is common for appreciable subpopulations of proteins to remain misfolded, soluble, and evade the refolding action of chaperones for very long times. Further, these results suggest that this happens because these misfolded subpopulations are near-native and therefore interact with chaperones to a similar extent as properly folded proteins. More broadly, these results indicate a mechanism in which long-time scale changes in protein structure and function can persist in cells because some protein’s non-native states can bypass components of the proteostasis machinery.

TEASER

Near-native, misfolded protein conformations explain why some soluble proteins fail to refold in the presence of chaperones.
A genealogical estimate of genetic relationships
Authors: Fan Caoqi , Mancuso Nicholas , Chiang Charleston W.K.
Published: August 2021

The application of genetic relationships among individuals, characterized by a genetic relationship matrix (GRM), has far-reaching effects in human genetics. However, the current standard to calculate the GRM generally does not take advantage of linkage information and does not reflect the underlying genealogical history of the study sample. Here, we propose a coalescent-informed framework to infer the expected relatedness between pairs of individuals given an ancestral recombination graph (ARG) of the sample. Through extensive simulations we show that the eGRM is an unbiased estimate of latent pairwise genome-wide relatedness and is robust when computed using genealogies inferred from incomplete genetic data. As a result, the eGRM better captures the structure of a population than the canonical GRM, even when using the same genetic information. More importantly, our framework allows a principled approach to estimate the eGRM at different time depths of the ARG, thereby revealing the time-varying nature of population structure in a sample. When applied to genotyping data from a population sample from Northern and Eastern Finland, we find that clustering analysis using the eGRM reveals population structure driven by subpopulations that would not be apparent using the canonical GRM, and that temporally the population model is consistent with recent divergence and expansion. Taken together, our proposed eGRM provides a robust tree-centric estimate of relatedness with wide application to genetic studies.
DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity
Authors: Ochmann Sarah E. , Joshi Himanshu , Büber Ece , Franquelim Henri G. , Stegemann Pierre , Saccà Barbara , Keyser Ulrich F. , Aksimentiev Aleksei , Tinnefeld Philip
Published: August 2021

Signal transmission in neurons goes along with changes in the transmembrane potential. To report them, different approaches including optical voltage-sensing dyes and genetically encoded voltage indicators have evolved. Here, we present a DNA nanotechnology-based system. Using DNA origami, we incorporate and optimize different properties such as membrane targeting and voltage sensing modularly. As a sensing unit, we use a hydrophobic red dye anchored to the membrane and an anionic green dye at the DNA connecting the DNA origami and the membrane dye anchor. Voltage-induced displacement of the anionic donor unit is read out by changes of Fluorescence Resonance Energy Transfer (FRET) of single sensors attached to liposomes. They show a FRET change of ∼5% for ΔΨ=100 mV and allow adapting the potential range of highest sensitivity. Further, the working mechanism is rationalized by molecular dynamics simulations. Our approach holds potential for the application as non-genetically encoded sensors at membranes.
Interaction between spike protein of SARS-CoV-2 and human virus receptor ACE2 using two-color fluorescence cross-correlation spectroscopy
Authors: Fujimoto Ai , Yidan Lyu , Kinjo Masataka , Kitamura Akira
Published: August 2021

Infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), is initiated by the interaction between a receptor protein, angiotensin-converting enzyme type 2 (ACE2) on the cell surface, and the viral spike (S) protein. This interaction is similar to the mechanism in SARS-CoV, a close relative of SARS-CoV-2, which was identified in 2003. Drugs and antibodies that inhibit the interaction between ACE2 and S proteins could be key therapeutic methods for preventing viral infection and replication in COVID-19. Here, we demonstrate the interaction between human ACE2 and a fragment of the S protein (S1 subunit) derived from SARS-CoV-2 and SARS-CoV using two-color fluorescence cross-correlation spectroscopy (FCCS), which can detect the interaction of fluorescently labeled proteins. The S1 subunit of SARS-CoV-2 interacted in solution with soluble ACE2, which lacks a transmembrane region, more strongly than that of SARS-CoV. Furthermore, one-to-one stoichiometry of the two proteins during the interaction was indicated. Thus, we propose that this FCCS-based interaction detection system can be used to analyze the interaction strengths of various mutants of the S1 subunit that have evolved during the worldwide pandemic, and also offers the opportunity to screen and evaluate the performance of drugs and antibodies that inhibit the interaction.
CRISPR activation screening identifies VGLL3 and GATA2 as transcriptional regulators of PD-L1
Authors: Wijdeven Ruud H. , Cabukusta Birol , Qiu Xueer , Borras Daniel M. , Liang Yun , Neefjes Jacques
Published: August 2021

The PD-L1/2 – PD-1 immune checkpoint is essential for the proper induction of peripheral tolerance and limits autoimmunity, whereas tumor cells exploit their expression to promote immune evasion. Many different cell types express PD-L1/2, either constitutively or upon stimulation, but the factors driving this expression are often not defined. Here, using genome-wide CRISPR-activation screening, we identified three factors that upregulate PD-L1 expression; GATA2, MBD6, and VGLL3. GATA2 and VGLL3 act as transcriptional regulators and their expression induced PD-L1 in many different cell types. Conversely, loss of VGLL3 impaired IFNγ-induced PD-L1/2 expression in keratinocytes. Mechanistically, by performing a second screen to identify proteins acting together with VGLL3, we found that VGLL3 forms a complex with TEAD1 and RUNX1/3 to drive expression of PD-L1/2. Collectively, our work identified a new transcriptional network controlling PD-L1/2 expression and suggests that VGLL3, in addition to its known role in the expression of pro-inflammatory genes, can balance inflammation by upregulating the anti-inflammatory factors PD-L1 and PD-L2.
Aβ toxicity rescued by protein retention in the ER
Authors: Catterson James H , Minkley Lucy , Aspe Salomé , Judd-Mole Sebastian , Moura Sofia , Dyson Miranda C , Rajasingam Arjunan , Woodling Nathaniel S , Atilano Magda L , Ahmad Mumtaz , Durrant Claire S , Spires-Jones Tara L , Partridge Linda
Published: August 2021

Accumulation of Aβ in the brain is one of the hallmarks of Alzheimer’s disease (AD). In the adult Drosophila brain, human Aβ over-expression is toxic and leads to deterioration of climbing ability and shortened lifespan. However, it remains unknown if Aβ is inherently toxic or if it triggers toxic downstream pathways that lead to neurodegeneration. Here, we describe a novel, and previously unidentified, protective role of intracellular laminin chain accumulation. Despite high Aβ levels, over-expression of the extracellular matrix protein subunit Laminin B1 (LanB1) resulted in a robust rescue of toxicity, highlighting a potential protective mechanism of resistance to Aβ. Over-expression of other Laminin subunits and a Collagen IV subunit also significantly rescued Aβ toxicity, while combining LanB1 with these subunits led to an even larger rescue. Imaging revealed that LanB1 was retained in the ER but had no effect on the secretion of Aβ into the extracellular milieu. LanB1 rescued toxicity independently of the IRE1α/XBP1-mediated branch of the ER stress response. Interestingly, over-expression of ER-targeted GFP also rescued Aβ toxicity, indicating a potentially broader benefit of ER protein retention. Finally, in proof-of-principle lentiviral transduction experiments using murine organotypic hippocampal slice cultures, over-expression of mouse Lamb1 resulted in ER-retention in transduced cells, highlighting a conserved mechanism. Typically, retention of proteins in the ER is detrimental to cellular health, but in the context of neuronal Aβ toxicity it may prove to be beneficial and a new therapeutic avenue for AD.
How the insect central complex could coordinate multimodal navigation
Authors: Sun Xuelong , Yue Shigang , Mangan Michael
Published: August 2021

The central complex of the insect midbrain is thought to coordinate insect guidance strategies. Computational models can account for specific behaviours but their applicability across sensory and task domains remains untested. Here we assess the capacity of our previous model explaining visual navigation to generalise to olfactory navigation and its coordination with other guidance in flies and ants. We show that fundamental to this capacity is the use of a biologically-realistic neural copy-and-shift mechanism that ensures sensory information is presented in a format compatible with the insect steering circuit regardless of its source. Moreover, the same mechanism is shown to transfer cues from unstable/egocentric to stable/geocentric frames of reference providing a first account of the mechanism by which foraging insects robustly recover from environmental disturbances. We propose that these circuits can be flexibly repurposed by different insect navigators to address their unique ecological needs.
Macrophages in the reticuloendothelial system inhibit the propagation phase of mouse apolipoprotein A-II amyloidosis
Authors: Miyahara Hiroki , Dai Jian , Li Ying , Xiaoran Cui , Takeuchi Hibiki , Hachiya Naomi , Kametani Fuyuki , Yazaki Masahide , Mori Masayuki , Higuchi Keiichi
Published: August 2021

Amyloidosis refers to a group of degenerative diseases that are characterized by the deposition of misfolded protein fibrils in various organs. Deposited amyloid may be removed by a phagocyte-dependent innate immune system; however, the precise mechanisms during disease progression remain unclear. We herein investigated the properties of macrophages that contribute to amyloid degradation and disease progression using transmissible apolipoprotein A-II amyloidosis model mice. Intravenously injected AApoAII amyloid was efficiently engulfed by reticuloendothelial macrophages in the liver and spleen and disappeared by 24 h. While cultured murine macrophages degraded AApoAII via the endosomal-lysosomal pathway, AApoAII fibrils reduced cell viability and phagocytic capacity. Furthermore, the depletion of reticuloendothelial macrophages prior to the induction of AApoAII markedly increased hepatic and splenic AApoAII deposition. These results highlight the physiological role of reticuloendothelial macrophages against inter-individual amyloid propagation and suggest the maintenance of phagocytic integrity as a therapeutic strategy to inhibit disease progression.
Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites
Authors: Lansink Lianne I.M. , Engel Jessica A. , Lee Hyun Jae , Soon Megan S.F. , Williams Cameron G. , SheelaNair Arya , Pernold Clara P.S. , Laohamonthonkul Pawat , Akter Jasmin , Stoll Thomas , Hill Michelle M. , Talman Arthur M. , Russell Andrew , Lawniczak Mara , Davenport Miles P. , Khoury David S. , Haque Ashraful
Published: August 2021

Maturation rate of malaria parasites within red blood cells (RBC) can be influenced by host nutrient status or circadian rhythm. Here, we observed in mice that systemic host inflammation, induced by lipopolysaccharide (LPS) conditioning or ongoing acute malaria infection, slowed the progression of a single cohort of parasites from one generation of RBC to the next. LPS-conditioning and acute infection both triggered substantial changes to the metabolomic composition of plasma in which parasites circulated. This altered plasma directly slowed parasite maturation in a manner that could not be rescued by supplementation, consistent with the presence of inhibitory factors. Single-cell transcriptomic assessment of mixed parasite populations, exposed to a short period of systemic host inflammation in vivo, revealed specific impairment in the transcriptional activity and translational capacity of trophozoites compared to rings or schizonts. Thus, we provide in vivo evidence of transcriptomic and phenotypic plasticity of asexual blood-stage Plasmodium parasites when exposed to systemic host inflammation.
Transcription factor-based transdifferentiation of human embryonic to trophoblast stem cells
Authors: Balestrini Paula A , Abdelbaki Ahmed , McCarthy Afshan , Devito Liani , Senner Claire E , Chen Alice E , Munusamy Prabhakaran , Blakeley Paul , Elder Kay , Snell Phil , Christie Leila , Serhal Paul , Odia Rabi A , Sangrithi Mahesh , Niakan Kathy K , Fogarty Norah ME
Published: August 2021

During the first week of development, human embryos form a blastocyst comprised of an inner cell mass and trophectoderm (TE) cells, the latter of which are progenitors of placental trophoblast. Here we investigated the expression of transcripts in the human TE from early to late blastocyst stages. We identified enrichment of transcription factors GATA2, GATA3, TFAP2C and KLF5 and characterised their protein expression dynamics across TE development. By inducible overexpression and mRNA transfection we determined that these factors, together with MYC, are sufficient to establish induced trophoblast stem cells (iTSCs) from primed human embryonic stem cells. These iTSCs self-renew and recapitulate morphological characteristics, gene expression profiles, and directed differentiation potential similar to existing human TSCs. Systematic omission of each, or combinations of factors, revealed the critical importance of GATA2 and GATA3 for iTSC transdifferentiation. Altogether, these findings provide insights into the transcription factor network that may be operational in the human TE and broaden the methods for establishing cellular models of early human placental progenitor cells, which may be useful in the future to model placental-associated diseases.
The interferon-rich skin environment regulates Langerhans cell ADAM17 to promote photosensitivity in lupus
Authors: Li Thomas M. , Zyulina Victoria , Seltzer Ethan S. , Dacic Marija , Chinenov Yurii , Daamen Andrea R. , Veiga Keila R. , Schwartz Noa , Oliver David J. , Lora Jose , Jabbari Ali , Liu Yong , Shipman William D. , Ambler William G. , Taber Sarah F. , Onel Karen B. , Zippin Jonathan H. , Rashighi Mehdi , Krueger James G. , Anandasabapathy Niroshana , Rogatsky Inez , Blobel Carl P. , Lipsky Peter E. , Lu Theresa T.
Published: August 2021

Background

The autoimmune disease lupus erythematosus (lupus) is characterized by photosensitivity, where even ambient ultraviolet radiation (UVR) exposure inflames skin. Beneficial effects of anifrolumab (anti-interferon α/breceptor (anti-IFNAR)) on lupus skin disease support a pathogenic role for IFN-I, but mechanistic understanding is limited. We have shown that Langerhans cell (LC) dysfunction contributes to photosensitivity. Healthy LCs act via a disintegrin and metalloprotease 17 (ADAM17) to release epidermal growth factor receptor (EGFR) ligands that limit UVR-induced keratinocyte apoptosis and photosensitivity. However, LC ADAM17 activity is reduced in non-lesional lupus model skin, and data point to reduced LC-mediated protection in human lupus. Here, we asked about the role of the IFN-rich lupus skin environment in LC dysfunction and the implications of this regulation for photosensitivity.

Methods

Gene expression patterns in non-lesional skin from human lupus and multiple murine models were examined. We used MRL/lpr, B6.Sle1yaa, and imiquimod models of lupus inin vivostudies to assess the role of IFN-I in LC ADAM17 dysfunction and photosensitivity.

Results

We show a shared IFN-rich environment in non-lesional skin across human and murine model systems, that IFN-I inhibits LC ADAM17 activity, and that anti-IFNAR in lupus models restores LC ADAM17 function and reduces photosensitivity in EGFR and LC ADAM17-dependent manners. Reactive oxygen species (ROS) can mediate ADAM17 activity, and we show reduced LC ROS expression in lupus models that is restored by anti-IFNAR.

Conclusions

Our findings suggest that IFN-I promotes photosensitivity by causing LC ADAM17 dysfunction and that anifrolumab ameliorates lupus skin disease at least in part by restoring LC function. This work provides insight into IFN-I-mediated disease mechanisms, LC regulation, and a mechanism of action for anifrolumab in lupus.
TGF-β1 drives Th9 but not Treg cells upon allergen exposure
Authors: Musiol Stephanie , Alessandrini Francesca , Jakwerth Constanze A. , Chaker Adam M. , Schneider Evelyn , Guerth Ferdinand , Ghiordanescu Ileana , Ullmann Julia T. , Kau Josephine , Plaschke Mirjam , Haak Stefan , Buch Thorsten , Schmidt-Weber Carsten B. , Zissler. Ulrich M.
Published: August 2021

TGF-β1 is known to have a pro-inflammatory impact by inducing Th9 cells, while it also induces anti-inflammatory Treg cells (Tregs). In the context of allergic airway inflammation (AAI) its dual role can be of critical importance in influencing the outcome of the disease. Here we demonstrate that TGF-β acts in AAI by driving effector T cells into Th9 cells, while Tregs differentiate independently. Induction of experimental AAI and airway hyperreactivity in a mouse model with inducible genetic ablation of the TGFβ-receptor 2 (TGFBR2) on CD4+T cells significantly reduced the disease phenotype. Further, it blocked the induction of Th9 cell frequencies, but increased Treg cells. To translate these findings into a human clinically relevant context, Th9 and Treg cells were quantified both locally in induced sputum and systemically in blood of allergic rhinitis and asthma patients with or without allergen-specific immunotherapy (AIT). Natural allergen exposure induced local and systemic Th2, Th9 cell and reduced Tregs, while therapeutic allergen exposure by AIT suppressed Th2 and Th9 cell frequencies along with TGF-β and IL-9 secretion. Altogether, these findings support that neutralization of TGF-β represents a viable therapeutic option in allergy and asthma, not posing the risk of immune dysregulation by impacting Tregs.
Quantitative Phosphoproteomic Analyses Identify STK11IP as a Lysosome-Specific Substrate of mTORC1 that Regulates Lysosomal Acidification
Authors: Zi Zhenzhen , Zhang Zhuzhen , Feng Qiang , Kim Chiho , Scherer Philipp E. , Gao Jinming , Levine Beth , Yu Yonghao
Published: August 2021

The evolutionarily conserved serine/threonine kinase mTORC1 is a central regulator of cell growth and proliferation. mTORC1 is activated on the lysosome surface. However, once mTORC1 is activated, it is unclear whether mTORC1 phosphorylates local lysosomal proteins to regulate specific aspects of lysosomal biology. Through cross-reference analyses of lysosome proteomic with mTORC1-regulated phosphoproteomic, we identified STK11IP as a novel lysosome-specific substrate of mTORC1. mTORC1 directly phosphorylates STK11IP at S404. Knockout of STK11IP led to a robust increase of autophagosome-lysosome fusion and autophagy flux. Dephosphorylation of STK11IP at S404 represses the role of STK11IP as an autophagy inhibitor. Mechanistically, STK11IP binds to V-ATPase, and regulates the activity of V-ATPase. Knockout of STK11IP protects mice from fasting and Methionine and Choline-Deficient Diet (MCD) diet induced fatty liver. Thus, our study demonstrates that STK11IP phosphorylation represents a novel mechanism for mTORC1 to regulate lysosomal acidification, and points to STK11IP as a promising therapeutic target for the amelioration of diseases with aberrant autophagy signaling.