bluuebunny/crossref_metadata_2025 huggingface dataset:
Signaling through the Dystrophin Glycoprotein Complex affects the stress-dependent transcriptome in Drosophila
Authors: Carney Travis D , Hebalkar Rucha Y , Edeleva Evgeniia , Çiçek Ibrahim Ömer , Shcherbata Halyna R
Published: June 2022

The Dystrophin Glycoprotein Complex (DGC) is a cell membrane-spanning complex that links the extracellular matrix with the intracellular cytoskeleton. Deficiencies in the DGC in humans cause muscular dystrophies (MDs), a group of inherited, incurable disorders associated with heterogeneous muscle, brain, and eye anomalies. To advance disease diagnostics and develop new treatment strategies, it is essential to understand the genetic pathways that are perturbed by DGC mutations and the mechanisms underlying these pathologies. Stresses such as nutrient deprivation and aging cause a reduction of muscle mass can be exacerbated by a reduced content of the DGC in membranes, whose integrity is vital for muscle health and function. This illustrates that the DGC plays a role in stress-response pathways. Therefore, it is important to investigate the influence of stress not only on healthy individuals but also on the wellbeing of MD patients. Moreover, the DGC has also emerged as an integral component in multiple signaling pathways, demonstrating an important yet poorly understood connection between intercellular forces and regulation of gene expression and illustrating the importance of understanding DGC-related transcriptional effects. Here, we utilize a Drosophila model to investigate the transcriptomic changes in mutants of four different DGC components under unstressed, temperature-stressed, and starvation-stressed conditions. Our analysis reveals a group of genes that exhibit DGC-dependent gene regulation. We identify large groups of genes that are differentially regulated in response to either temperature or starvation stress. Importantly, we also identify groups of genes with expression patterns dependent on the DGC signaling pathway for a proper stress response. This work reveals a novel function of the DGC in stress-response signaling. The view of the DGC as a regulatory unit involved in the stress response will give new insights into the etiology of symptoms of MDs and possible directions of symptomatic treatment and relief, and it will ultimately aid in a better understanding of DGC signaling and regulation under normal and stress conditions.
Benefits of individualized brain anatomies and EEG electrode positions for auditory cortex localization
Authors: Ignatiadis Karolina , Barumerli Roberto , Tóth Brigitta , Baumgartner Robert
Published: June 2022

Due to its high temporal resolution and non-invasive nature, electroencephalography (EEG) is considered a method of great value for the field of auditory cognitive neuroscience. In performing source space analyses, localization accuracy poses a bottleneck, which precise forward models based on individualized attributes such as subject anatomy or electrode locations aim to overcome. Yet acquiring anatomical images or localizing EEG electrodes requires significant additional funds and processing time, making it an oftentimes inaccessible asset. Neuroscientific software offers template solutions, on which analyses can be based. For localizing the source of auditory evoked responses, we here compared the results of employing such template anatomies and electrode positions versus the subject-specific ones, as well as combinations of the two. All considered cases represented approaches commonly used in electrophysiological studies. We considered differences between two commonly used inverse solutions (dSPM, sLORETA) and targeted the primary auditory cortex; a notoriously small cortical region that is located within the lateral sulcus, thus more prone to errors in localization. Through systematical comparison of the outcomes in terms of auditory activity attributes and leakage quantification, we assessed how the individualization steps impacted the analyses outcomes. Both electrode locations as well as subject anatomies were found to have an effect, which though varied based on the configuration considered. When comparing the inverse solutions, we moreover found that dSPM more consistently benefited from individualization of subject characteristics. Based on the scientific question considered, our results may be used to facilitate the planning of auditory neuroscientific experiments in terms of expected infrastructure, personnel and funds.
Isolation of a novel heterodimeric PSII complex via strep-tagged PsbO
Authors: Lambertz Jan , Meier-Credo Jakob , Kucher Svetlana , Bordignon Enrica , Langer Julian D. , Nowaczyk Marc M.
Published: June 2022

The multi-subunit membrane protein complex Photosystem II (PSII) catalyzes the light-driven oxidation of water and with this the initial step of photosynthetic electron transport in plants, algae, and cyanobacteria. Its biogenesis is coordinated by a network of auxiliary proteins that facilitate the stepwise assembly of individual subunits and cofactors, forming various intermediate complexes until fully functional mature PSII is present at the end of the process. In the current study, we purified PSII complexes from a mutant line of the thermophilic cyanobacterium Thermosynechococcus vestitus BP-1 in which the extrinsic subunit PsbO, characteristic for active PSII, was fused with an N-terminal Twin-Strep-tag. Three distinct PSII complexes were separated by ion-exchange chromatography after the initial affinity purification. Two complexes differ in their oligomeric state (monomeric and dimeric) but share the typical subunit composition of mature PSII. They are characterized by the very high oxygen-evolving activity of approx. 6,000 µmol O2· (mg Chl·h)-1. Analysis of the third (heterodimeric) PSII complex revealed lower oxygen-evolving activity of approx. 3,000 µmol O2· (mg Chl·h)-1 and manganese content of 2.7 (± 0.2) per reaction center compared to 3.7 (± 0.2) of fully active PSII. Mass spectrometry and time-resolved fluorescence spectroscopy further indicated that PsbO is partially replaced by Psb27 in this PSII fraction, thus implying a role in the repair of the complex.
Analyzing single-cell bisulfite sequencing data withMethSCAn
Authors: Kremer Lukas P. M. , Braun Martina M. , Ovchinnikova Svetlana , Küchenhoff Leonie , Cerrizuela Santiago , Martin-Villalba Ana , Anders Simon
Published: June 2022

Single-cell bisulfite sequencing (scBS) is a technique that enables the assessment of DNA methylation at single-base pair and single-cell resolution. The analysis of large datasets obtained from scBS requires preprocessing to reduce data size, improve signal-to-noise ratio, and provide interpretability. Typically, this is achieved by dividing the genome into large tiles and averaging the methylation signals within each tile.

Here, we demonstrate that this coarse-graining approach can lead to signal dilution. As an alternative, we propose improved strategies to identify more informative regions for methylation quantification, and a more accurate quantitation method than simple averaging. Our approach enables better discrimination of cell types and other features of interest and reduces the need for large numbers of cells. We also present an approach to detect differentially methylated regions (DMRs) between groups of cells, and demonstrate its ability to identify biologically meaningful regions that are associated with genes involved in the core functions of specific cell types.

To facilitate the analysis of scBS data, we have developed a software tool calledMeth-SCAnthat implements these methods and provides additional functionality.
Sensory input to cortex encoded on low-dimensional periphery-correlated subspaces
Authors: Barreiro Andrea K , Fontenele Antonio J , Ly Cheng , Raju Prashant , Gautam Shree Hari , Shew Woodrow L
Published: June 2022

As information about the world is conveyed from the sensory periphery to central neural circuits, it mixes with complex ongoing cortical activity. How do neural populations keep track of sensory signals, separating them from noisy ongoing activity? Here we show that sensory signals are encoded more reliably in certain low-dimensional subspaces. These coding subspaces are defined by correlations between neural activity in primary sensory cortex and upstream sensory brain regions; the most correlated dimensions were best for decoding. We analytically show that these correlation-based coding subspaces improve, reaching optimal limits (without an ideal observer) as noise correlations between cortex and upstream regions are reduced. We show that this principle generalizes across diverse sensory stimuli in the olfactory system and the visual system of awake mice. Our results demonstrate an algorithm the cortex may use to multiplex different functions, processing sensory input in low dimensional subspaces separate from other ongoing functions.

Significance statement

Traditionally, primary sensory cortex was thought to have one job – processing sensory signals. As technical advances allow more holistic measurements of the brain and body in action, it has become clear that primary sensory cortex is involved with many other aspects of brain function, not just dealing with sensory input. How can a single neural circuit juggle multiple jobs simultaneously? Here we use numerical, analytical, and experimental methods to demonstrate an algorithm the brain may use to solve this problem by separating different jobs into different subspaces defined by correlations between primary sensory cortex and the brain regions that source the sensory input signals.
Solution structure and synaptic analyses reveal determinants of bispecific T cell engager potency
Authors: Leithner Alexander , Staufer Oskar , Mitra Tanmay , Liberta Falk , Valvo Salvatore , Kutuzov Mikhail , Dada Hannah , Spaeth Jacob , Zhou Sally , Schiele Felix , Reindl Sophia , Nar Herbert , Hoerer Stefan , Crames Maureen , Comeau Stephen , Young David , Low Sarah , Jenkins Edward , Davis Simon J. , Klenerman David , Nixon Andrew , Pefaur Noah , Wyatt David , Dushek Omer , Kasturirangan Srinath , Dustin Michael L.
Published: June 2022

Bispecific T-cell engagers (TcEs) link T cell receptors to tumor-associated antigens on cancer cells, forming cytotoxic immunological synapses (IS). Close membrane-to-membrane contact (≤13 nm) has been proposed as a key mechanism of TcE function. To investigate this and identify potential additional mechanisms, we compared four immunoglobulin G1-based (IgG1) TcE Formats (A-D) targeting CD3ε and Her2, designed to create varying intermembrane distances (A<B<C<D). Small-angle X-ray scattering (SAXS) and modelling of the conformational states of isolated TcEs and TcE-antigen complexes predicted close-contacts (≤13 nm) for Formats A and B and far-contacts (≥18 nm) for Formats C and D. In supported lipid bilayer (SLB) model interfaces, Formats A and B recruited, whereas Formats C and D repelled, CD2-CD58 interactions. Formats A and B also excluded bulky Quantum dots more effectively. SAXS also revealed that TcE-antigen complexes formed by Formats A and C were less flexible than complexes formed by Formats B and D. Functional data with Her2-expressing tumor cells showed cytotoxicity, surface marker expression and cytokine release following the order A>B=C>D. In a minimal system for IS formation on SLBs, TcE performance followed the trend A=B=C>D. Addition of close-contact requiring CD58 co-stimulation revealed phospholipase C-γ activation matching cytotoxicity with A>B=C>D. Our findings suggest that, when adhesion is equivalent, TcE potency is determined by two parameters: contact distance and flexibility. Both the close/far-contact formation axis and the low/high flexibility axis significantly impact TcE potency, explaining the similar potency of Format B (close-contact/high flexibility) and C (far-contact/low flexibility).

Significance statement

Bispecific T-cell engagers (TcEs) are immunotherapeutic drugs that trigger the destruction of cancer cells by linking T cells to cancer cell through specific surface molecules (antigens). We designed a series of TcEs with varying distances between their binding sites and flexibilities of the TcE-antigen complexes. By combining structural and functional analyses, we confirmed close-contact formation between T cells and cancer cells as a critical determinant, mediated by co-activating receptors. Furthermore, we also identified molecular flexibility of the TcE-antigen complex as a further critical parameter for TcE potency. These findings provide novel insights into TcE function and highlight the importance of both parameters for future research and the design of improved immunotherapies.
qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data
Authors: Queme Bryan , Braisted John C. , Dranchak Patricia , Inglese James
Published: June 2022

High throughput screening (HTS) is widely used in drug discovery and chemical biology to identify and characterize agents having pharmacologic properties often by evaluation of large chemical libraries. Standard HTS data can be simply plotted as an x-y graph usually represented as % activity of a compound tested at a single concentration vs compound ID, whereas quantitative HTS (qHTS) data incorporates a third axis represented by concentration. By virtue of the additional data points arising from the compound titration and the incorporation of logistic fit parameters that define the concentration-response curve, such as EC50 and Hill slope, qHTS data has been challenging to display on a single graph. Here we provide a flexible solution to the rapid plotting of complete qHTS data sets to produce a 3-axis plot we call qHTS Waterfall Plots. The software described here can be generally applied to any 3-axis dataset and is available as both an R package and an R shiny application.
Brain-Controlled Electrical Stimulation Restores Continuous Finger Function
Authors: Nason-Tomaszewski Samuel R. , Mender Matthew J. , Kennedy Eric , Lambrecht Joris M. , Kilgore Kevin L. , Chiravuri Srinivas , Kumar Nishant Ganesh , Kung Theodore A. , Willsey Matthew S. , Chestek Cynthia A. , Patil Parag G.
Published: June 2022

Brain-machine interfaces have shown promise in extracting upper extremity movement intention from the thoughts of nonhuman primates and people with tetraplegia. Attempts to restore a user’s own hand and arm function have employed functional electrical stimulation (FES), but most work has restored discrete grasps. Little is known about how well FES can control continuous finger movements. Here, we use a low-power brain-controlled functional electrical stimulation (BCFES) system to restore continuous volitional control of finger positions to a monkey with a temporarily paralyzed hand. In a one-dimensional, continuous, finger-related target acquisition task, the monkey improved his success rate to 83% (1.5s median acquisition time) when using the BCFES system during temporary paralysis from 8.8% (9.5s median acquisition, equivalent to chance) when attempting to use his temporarily paralyzed hand. With two monkeys under general anesthesia, we found FES alone could control the monkeys’ fingers to rapidly reach targets in a median 1.1s but caused oscillation about the target. Finally, when attempting to perform a virtual two-finger continuous target acquisition task in brain-control mode following temporary hand paralysis, we found performance could be completely recovered by executing recalibrated feedback-intention training one time following temporary paralysis. These results suggest that BCFES can restore continuous finger function during temporary paralysis using existing low-power technologies and brain-control may not be the limiting performance factor in a BCFES neuroprosthesis.
Evaluation of OCT biomarker changes in treatment-naive neovascular AMD using a deep semantic segmentation algorithm
Authors: Asani Ben , Holmberg Olle , Schiefelbein Johannes B , Hafner Michael , Herold Tina , Spitzer Hannah , Siedlecki Jakob , Kern Christoph , Kortuem Karsten U. , Frishberg Amit , Theis Fabian J. , Priglinger Siegfried G
Published: June 2022

Purpose

To determine real life quantitative changes in OCT biomarkers in a large set of treatment naive patients undergoing anti-VEGF therapy. For this purpose, we devised a novel deep learning based semantic segmentation algorithm providing, to the best of our knowledge, the first benchmark results for automatic segmentation of 11 OCT features including biomarkers that are in line with the latest consensus nomenclature of the AAO for age-related macular degeneration (AMD).

Design

Retrospective study.

Participants

Segmentation algorithm training set of 458 volume scans as well as single scans from 363 treatment naive patients for the analysis.

Methods

Training of a Deep U-net based semantic segmentation ensemble algorithm leveraging multiple deep convolutional neural networks for state of the art semantic segmentation performance as well as analyzing OCT features prior to, after 3 and 12 months of anti-VEGF therapy.

Main outcome measures

F1 score for the segmentation efficiency and the quantified volumes of 11 OCT features.

Results

The segmentation algorithm achieved high F1 scores of almost 1.0 for neurosensory retina and subretinal fluid on a separate hold out test set with unseen patients. The algorithm performed worse for subretinal hyperreflective material and fibrovascular PED, on par with drusenoid PED and better in segmenting fibrosis. In the evaluation of treatment naive OCT scans, significant changes occurred for intraretinal fluid (mean: 0.03µm3to 0.01µm3, p<0.001), subretinal fluid (0.08µm3to 0.01µm3, p<0.001), subretinal hyperreflective material (0.02µm3to 0.01µm3, p<0.001), fibrovascular PED (0.12µm3to 0.09µm3, p=0.02) and central retinal thickness C0 (225.78µm3to 169.40µm3).The amounts of intraretinal fluid, fibrovascular PED and ERM were predictive of poor outcome.

Conclusions

The segmentation algorithm allows efficient volumetric analysis of OCT scans. Anti-VEGF therapy provokes most potent changes in the first 3 months and afterwards only acts as a stabilizing agent. Furthermore, a gradual loss of RPE hints at a progressing decline of visual acuity even beyond month 12. Additional research is required to understand how these accurate OCT predictions can be leveraged for a personalized therapy regimen.

Précis

Novel high performance segmentation algorithm shows most volumetric changes under anti-VEGF therapy in oct biomarkers occur in the first 3 months. Afterwards the injections seem only to serve as a stabilizing agent.
Predicting SARS-CoV-2 variant spread in a completely seropositive population using semi-quantitative antibody measurements in blood donors
Authors: Buss Lewis F , Prete Carlos A , Whittaker Charles , Salomon Tassila , Oikawa Marcio K. , Pereira Rafael H. M. , Moura Isabel C. G. , Delerino Lucas , Franca Rafael F. O. , Miyajima Fabio , Mendrone-Junior Alfredo , de Almeida Neto César , Salles Nanci A. , Ferreira Suzete C. , Fladzinski Karine A. , de Souza Luana M. , Schier Luciane K. , Inoue Patricia M. , Xabregas Lilyane A. , Crispim Myuki A. E. , Fraiji Nelson , Carlos Luciana M. B. , Pessoa Veridiana , Ribeiro Maisa A. , de Souza Rosenvaldo E. , Cavalcante Anna F. , Valença Maria I. B. , da Silva Maria V. , Lopes Esther , Filho Luiz A. , Mateos Sheila O. G. , Nunes Gabrielle T. , Schlesinger David , da Silva Sônia Mara Nunes , Silva-Junior Alexander L. , Castro Marcia C , Nascimento Vítor H. , Dye Christopher , Busch Michael P , Faria Nuno R , Sabino Ester C
Published: June 2022

Background

SARS-CoV-2 serologic surveys estimate the proportion of the population with antibodies against historical variants which nears 100% in many settings. New analytic approaches are required to exploit the full information in serosurvey data.

Method

Using a SARS-CoV-2 anti-Spike (S) protein chemiluminescent microparticle assay, we attained a semi-quantitative measurement of population IgG titres in serial cross-sectional monthly samples of routine blood donations across seven Brazilian state capitals (March 2021-November 2021). In an ecological analysis (unit of analysis: age-city-calendar month) we assessed the relative contributions of prior attack rate and vaccination to antibody titre in blood donors. We compared blood donor anti-S titre across the seven cities during the growth phase of the Delta variant of concern (VOC) and use this to predict the resulting age-standardized incidence of severe COVID-19 cases.

Results

On average we tested 780 samples per month in each location. Seroprevalence rose to >95% across all seven capitals by November 2021. Driven proximally by vaccination, mean antibody titre increased 16-fold over the study. The extent of prior natural infection shaped this process, with the greatest increases in antibody titres occurring in cities with the highest prior attack rates. Mean anti-S IgG was a strong predictor (adjusted R2 =0.89) of the number of severe cases caused by the Delta VOC in the seven cities.

Conclusions

Semi-quantitative anti-S antibody titres are informative about prior exposure and vaccination coverage and can inform on the potential impact of future SARS-CoV-2 variants.

In the face of near 100% SARS-CoV-2 seroprevalence, we show that average semi-quantitative anti-S titre predicted the extent of the Delta variant’s spread in Brazil. This is a valuable metric for future seroprevalence studies.
White matter microstructure in face and body networks predicts facial expression and body posture perception across development
Authors: Ward Isobel L. , Raven Erika P. , de la Rosa Stephan , Jones Derek K. , Teufel Christoph , von dem Hagen Elisabeth
Published: June 2022

Facial expression and body posture recognition have protracted developmental trajectories. Interactions between face and body perception, such as the influence of body posture on facial expression perception, also change with development. While the brain regions underpinning face and body processing are well-defined, little is known about how white-matter tracts linking these regions relate to perceptual development. Here, we obtained complementary diffusion magnetic resonance imaging (MRI) measures (fractional anisotropy FA, spherical mean), and a quantitative MRI myelin-proxy measure (R1), within white-matter tracts of face- and body-selective networks in children and adolescents and related these to perceptual development. In tracts linking occipital and fusiform face areas, facial expression perception was predicted by age-related microstructural development, as measured byand R1, as well as age-independent individual differences in microstructure, as measured by FA. Tract microstructure linking the body region in posterior superior temporal sulcus with anterior temporal lobe (ATL) was related to the influence of body on facial expression perception, supporting ATL as a site of face and body network convergence. Overall, our results highlight age-dependent and age-independent constraints that white-matter microstructure poses on perceptual abilities during development and the importance of complementary microstructural measures in linking brain structure and behaviour.
Axo-vascular coupling mediated by oligodendrocytes
Authors: Restrepo Alejandro , Trevisiol Andrea , Restrepo-Arango Camilo , Depp Constanze , Sasmita Andrew Octavian , Keller Annika , Tzvetanova Iva D. , Hirrlinger Johannes , Nave Klaus-Armin
Published: June 2022

The high energy requirements of the cortical gray matter are met by the precise cooperation of neurons, glia, and vascular cells in a process known as neurovascular coupling (NVC). In contrast, the existence and significance of NVC in white matter (WM) are still debated and basic regulatory mechanisms are unknown. We recently discovered that oligodendrocytes sense the spiking axons’ activity via NMDA receptors and regulate their cell surface expression of glucose transporter GLUT1 allowing an increase in glycolytic metabolism that enables lactate release to metabolically support the axons. Here, we show for the mouse optic nerve (ON), a model WM tract, that the vascular support is also dynamically controlled. Axonal spiking activity induces small vessel dilations which are sustained for more than 20 minutes upon the ending of electrical stimulation. Pharmacological inhibition shows that the electrically evoked dilation is mediated by the prostaglandin E2 receptor EP4 and can be modulated by the oxygen concentration, as has been shown in the grey matter. Importantly, we found in ONs from conditional mouse mutants that oligodendroglial NMDA receptors are required for this type of neurovascular response, demonstrating a critical role of oligodendrocytes in coupling axonal activity to pericyte function. Reminiscent of NVC in cortical slices, the “axo-vascular” response is slower and may represent a more rudimentary form of neurovascular coupling.
Sequence-independent substrate selection by the eukaryotic wobble base deaminase ADAT2/3 involves multiple protein domains and distortion of the tRNA anticodon loop
Authors: Dolce Luciano G. , Zimmer Aubree A. , Tengo Laura , Weis Félix , Rubio Mary Anne T. , Alfonzo Juan D. , Kowalinski Eva
Published: June 2022

The essential deamination of adenosine A34 to inosine at the wobble base is the individual tRNA modification with the greatest effects on mRNA decoding, empowering a single tRNA to translate three different codons. To date, many aspects of how eukaryotic deaminases specifically select their multiple substrates remain unclear. Here, using cryo-EM, we present the first structure of a eukaryotic ADAT2/3 deaminase bound to a full-length tRNA, revealing that the enzyme distorts the anticodon loop, but in contrast to the bacterial enzymes, selects its substrate via sequence-independent contacts of eukaryote-acquired flexible or intrinsically unfolded motifs distal from the conserved catalytic core. A novel gating mechanism for substrate entry to the active site is identified. Our multi-step tRNA recognition model yields insights into how RNA editing by A34 deamination evolved, shaped the genetic code, and directly impacts the eukaryotic proteome.
Invasive alien insects represent a clear but variable threat to biodiversity
Authors: Clarke David A. , McGeoch Melodie A.
Published: June 2022

Invasive alien insects as a driver of biodiversity change are an important yet understudied component of the general threat of biological invasions. The environmental impacts of invasive alien insects are varied and widespread, with evidence to suggest that an insect species global maximum impact is likely to increase in severity as it increases its non-native distribution. Two potential explanations are that large geographic distributions include environmental heterogeneity and increase resource availability, or that there are intrinsic factors of widely-spread species that also facilitate greater impacts. Determining which explanation is more likely, and developing a more comprehensive and general understanding of the environmental impacts of invasive alien species, can be assisted by addressing the information shortfalls highlighted in this research.
The effect ofDrosophila attP40background on the glomerular organization of Or47b olfactory receptor neurons
Authors: Duan Qichen , Estrella Rachel , Carson Allison , Chen Yang , Volkan Pelin C.
Published: June 2022

Bacteriophage integrase-directed insertion of transgenic constructs into specific genomic loci has been widely used byDrosophilacommunity. TheattP40landing site located on the second chromosome gained popularity because of its high inducible transgene expression levels. Here, unexpectedly, we found that homozygousattP40chromosome disrupts normal glomerular organization of Or47b olfactory receptor neuron (ORN) class inDrosophila. This effect is not likely to be caused by the loss of function ofMsp300, where theattP40docking site is inserted. Moreover, the attP40background seems to genetically interact with the second chromosomeOr47b-GAL4driver, which results in a similar glomerular defect. Whether the ORN phenotype is caused by the neighboring genes aroundMsp300locus in the presence ofattP40-based insertions or a second unknown mutation in theattP40background remains elusive. Our findings tell a cautionary tale about using this popular transgenic landing site, highlighting the importance of rigorous controls to rule out theattP40landing site-associated background effects.
Single cell preparations ofMycobacterium tuberculosisdamage the mycobacterial envelope and disrupt macrophage interactions
Authors: Mittal Ekansh , Roth Andrew T. , Seth Anushree , Singamaneni Srikanth , Beatty Wandy , Philips Jennifer A.
Published: June 2022

For decades, investigators have studied the interaction ofMycobacterium tuberculosis(Mtb) with macrophages, which serve as a major cellular niche for the bacilli. Because Mtb are prone to aggregation, investigators rely on varied methods to disaggregate the bacteria for these studies. Here, we examined the impact of routinely used preparation methods on bacterial cell envelop integrity, macrophage inflammatory responses, and intracellular Mtb survival. We found that both gentle sonication and filtering damaged the mycobacterial cell envelope and markedly impacted the outcome of macrophage infections. Unexpectedly, sonicated bacilli were hyperinflammatory, eliciting dramatically higher TLR2-dependent gene expression and elevated secretion of IL-1β and TNF-α. Despite evoking enhanced inflammatory responses, sonicated bacilli replicated normally in macrophages. In contrast, Mtb that had been passed through a filter induced little inflammatory response, and they were attenuated in macrophages. Previous work suggests that the mycobacterial cell envelope lipid, phthiocerol dimycocerosate (PDIM), dampens macrophage inflammatory responses to Mtb. However, we found that the impact of PDIM depended on the method used to prepare Mtb. In conclusion, widely used methodologies to disaggregate Mtb may introduce experimental artifacts in Mtb-host interaction studies, including alteration of host inflammatory signaling, intracellular bacterial survival, and interpretation of bacterial mutants.
Fatty acid desaturation by stearoyl-CoA desaturase-1 controls regulatory T cell differentiation and autoimmunity
Authors: Grajchen Elien , Loix Melanie , Baeten Paulien , Côrte-Real Beatriz F. , Hamad Ibrahim , Haidar Mansour , Dehairs Jonas , Broos Jelle Y. , Ntambi James M. , Zimmermann Robert , Breinbauer Rolf , Stinissen Piet , Hellings Niels , Kooij Gijs , Giera Martin , Swinnen Johannes V. , Broux Bieke , Kleinewietfeld Markus , Hendriks Jerome J.A. , Bogie Jeroen F.J.
Published: June 2022

The imbalance between pathogenic and protective T cell subsets is a cardinal feature of autoimmune disorders such as multiple sclerosis (MS). Emerging evidence indicates that endogenous and dietary-induced changes in fatty acid metabolism have a major impact on both T cell fate and autoimmunity. To date, however, the molecular mechanisms that underlie the impact of fatty acid metabolism on T cell physiology and autoimmunity remain poorly understood. Here, we report that stearoyl-CoA desaturase-1 (SCD1), an enzyme essential for the desaturation of fatty acids and highly regulated by dietary factors, acts as an endogenous brake on regulatory T cell (Treg) differentiation and augments autoimmunity in an animal model of MS. Guided by RNA sequencing and lipidomics analysis, we found that absence ofScd1promotes hydrolysis of triglycerides and phosphatidylcholine through adipose triglyceride lipase (ATGL). ATGL-dependent release of docosahexaenoic acid enhanced Treg differentiation by activating the nuclear receptor peroxisome proliferator-activated receptor gamma. Our findings identify fatty acid desaturation by SCD1 as an essential determinant of Treg differentiation and autoimmunity, with potentially broad implications for the development of novel therapeutic strategies and dietary interventions for autoimmune disorders.
A multivariate brain signature for reward
Authors: Speer Sebastian P.H. , Keysers Christian , Smidts Ale , Boksem Maarten A.S. , Wager Tor D. , Gazzola Valeria
Published: June 2022

The processing of rewards and losses are crucial for learning to adapt to an ever changing environment. Dysregulated reward processes are prevalent in mental health and substance use disorders. While many human brain measures related to reward have been based on activity in individual brain regions, recent studies indicate that many affective and motivational processes are encoded in distributed systems that span multiple regions. Consequently, decoding these processes using individual regions yields small effect sizes and limited reliability, whereas predictive models based on distributed patterns yield much larger effect sizes and excellent reliability. To create such a predictive model for the processes of rewards and losses, from now on termed the Brain Reward Signature (BRS), we trained a LASSO-PCR model to predict the signed magnitude of monetary rewards and losses on the Monetary Incentive Delay task (MID; N = 39) and achieved a high significant decoding performance (92% for decoding rewards versus losses). We subsequently demonstrate the generalizability of our signature on another version of the MID in a different sample (92% decoding accuracy for rewards versus losses; N = 12) and on a gambling task from a large sample (73% decoding accuracy for rewards versus losses, N = 1084) from the Human Connectome Project. Lastly, we also provided preliminary evidence for specificity to rewarding outcomes by illustrating that the signature map generates estimates that significantly differ between rewarding and negative feedback (92% decoding accuracy) but do not differ for conditions that differ in disgust rather than reward in a novel Disgust-Delay Task (N = 39). We thus created a BRS that can be used to make specific, generalizable and reproducible predictions about brain responses to rewards and losses.
Temporal and spatial frameworks supporting plant responses to vegetation proximity
Authors: Pastor-Andreu Pedro , Moreno-Romero Jordi , Urdin-Bravo Mikel , Palau-Rodriguez Julia , Paulisic Sandi , Kastanaki Elizabeth , Vives-Peris Vicente , Gomez-Cadenas Aurelio , Rodríguez-Villalón Antía , Martínez-García Jaime F.
Published: June 2022

After perception of vegetation proximity by the phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the Shade Avoidance Syndrome (SAS). The shade-induced de-repression of active phytochrome B (phyB) releases the repression imposed over the PHYTOCHROME INTERACTING FACTORs (PIFs). InArabidopsis thalianaseedlings, this mechanism triggers rapid and massive changes in gene expression, increases auxin production in a SHADE AVOIDANCE 3-dependent manner and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5 (HY5), also participate in the shade regulation of the hypocotyl elongation response repressing it. However, it is less clear how phyA and HY5 interact with PIFs to regulate this response. Our physiological, genetic, cell biology and transcriptomic analyses showed that these components are organized in two main branches, and incorporate into the model for the regulation of shade-induced hypocotyl elongation the temporal and spatial functional importance of the various SAS regulators analyzed in here. They also indicated that PIFs and HY5, belonging to separate branches, target common genes whose expression is rapidly modulated by shade. This transcriptional relationship, however, changes after longer shade-treatments, suggesting that it is a dynamic convergence point to modulate the hypocotyl elongation.
Understanding molecular mechanisms and predicting phenotypic effects of pathogenic tubulin mutations
Authors: Attard Thomas , Welburn Julie P.I. , Marsh Joseph
Published: June 2022

Cells rely heavily on microtubules for several processes, including cell division and molecular trafficking. Mutations in the different tubulin-α and -β proteins that comprise microtubules have been associated with various diseases and are often dominant, sporadic and congenital. While the earliest reported tubulin mutations affect neurodevelopment, mutations are also associated with other disorders such as bleeding disorders and infertility. We performed a systematic survey of tubulin mutations across all isotypes in order to improve our understanding of how they cause disease, and increase our ability to predict their phenotypic effects. Both protein structural analyses and computational variant effect predictors were very limited in their utility for differentiating between pathogenic and benign mutations. This was even worse for those genes associated with non-neurodevelopmental disorders. We selected tubulin-α and -β disease mutations that were most poorly predicted for experimental characterisation. These mutants co-localise to the mitotic spindle in HeLa cells, suggesting they may exert dominant-negative effects by altering microtubule properties. Our results show that tubulin mutations represent a blind spot for current computational approaches, being much more poorly predicted than mutations in most human disease genes. We suggest that this is likely due to their strong association with dominant-negative and gain-of-function mechanisms.
Genetic parameters for resistance to gastrointestinal nematodes in sheep: a meta-analysis
Authors: Hayward Adam D.
Published: June 2022

Gastrointestinal nematodes (GIN) are damaging parasites of global sheep populations. The key weapons in fighting GIN have been anthelmintic drugs, but the emergence of drug-resistant parasites has meant that alternative control methods are needed. One of these alternatives is to breed for enhanced host resistance to GIN, and decades of research have estimated the genetic contribution to different measures of resistance to GIN and their genetic correlations with other desirable performance traits. It is clear that parasite resistance is a heritable trait that can be selected for. Despite this consensus, estimates of both heritability of resistance and genetic correlations with other traits vary widely between studies, and the reasons for this variation have not been examined. This study provides a comprehensive and quantitative meta-analysis of genetic parameters for resistance to GIN in sheep, including measures of worm burden (faecal egg counts, FEC), anti-parasite immunity (GIN-specific antibodies), and parasite-induced pathology (FAMACHA© scores). Analysis of 591 heritability estimates from 121 studies revealed a global heritability estimate for resistance to GIN of 0.25 (95%CI = 0.22 – 0.27) that was stable across breeds, ages, geographical location and analytical methods. Meanwhile, analysis of 559 genetic correlations from 54 studies revealed that resistance to GIN overall has a positive genetic correlation of +0.10 (95%CI = 0.02 – 0.19) with performance traits, and that this was consistent across breeds, ages, sexes and analytical methods. Importantly, the direction of the genetic correlation varied with the resistance trait measured: while FEC and FAMACHA© scores were favourably correlated with performance traits, adaptive immune markers were unfavourably correlated, suggesting that selection for enhanced immune responses to GIN could reduce animal performance. Overall, the results suggest that breeding for resistance to GIN should continue to form part of integrated management programs to reduce the impact of parasites on health and performance, but that selection for enhanced immune responses should be avoided.
Identification of secreted proteins by comparison of protein abundance in conditioned media and cell lysates
Authors: Abbineni Prabhodh S. , Tang Vi T. , Veiga Leprevost Felipe da , Basrur Venkatesha , Xiang Jie , Nesvizhskii Alexey I. , Ginsburg David
Published: June 2022

Analysis of the full spectrum of secreted proteins in cell culture is complicated by leakage of intracellular proteins from damaged cells. To address this issue, we compared the abundance of individual proteins between the cell lysate and the conditioned medium, reasoning that secreted proteins should be relatively more abundant in the conditioned medium. Marked enrichment for signal-peptide-bearing proteins with increasing conditioned media to cell lysate ratio, as well loss of this signal following brefeldin A treatment, confirmed the sensitivity and specificity of this approach. The subset of proteins demonstrating increased conditioned media to cell lysate ratio in the presence of Brefeldin A identified candidates for unconventional secretion via a pathway independent of ER to Golgi trafficking.
Quantitative mapping of synaptic periactive zone architecture and organization
Authors: Del Signore Steven J. , Mitzner Margalit G. , Silveira Anne M. , Fai Thomas G. , Rodal Avital A.
Published: June 2022

1.

Following exocytosis at active zones, synaptic vesicle membranes and membrane-bound proteins must be recycled. The endocytic machinery that drives this recycling accumulates in the periactive zone (PAZ), a region of the synapse adjacent to active zones, but the organization of this machinery within the PAZ, and how PAZ composition relates to active zone release properties remains unknown. The PAZ is also enriched for cell adhesion proteins, but their function at these sites is poorly understood. Here, using Airyscan and STED imaging ofDrosophilasynapses, we develop a quantitative framework describing the organization and ultrastructure of the PAZ. Different endocytic proteins localize to distinct regions of the PAZ, suggesting that sub-domains are specialized for distinct biochemical activities, stages of membrane remodeling, or synaptic functions. We find that the accumulation and distribution of endocytic but not adhesion PAZ proteins correlate with the abundance of the scaffolding protein Bruchpilot at active zones - a structural correlate of release probability. These data suggest that endocytic and exocytic activities are spatially correlated. Taken together, our results provide a new approach to quantify synaptic architecture and identify novel relationships between the exocytic and endocytic apparatus at the synapse.
Experiments on osmotically driven flow in idealized elastic membranes
Authors: Nakad Mazen , Domec Jean-Christophe , Sevanto Sanna , Katul Gabriel
Published: June 2022

The phloem provides a pathway for products of photosynthesis to be transported to different parts of the plant for consumption or storage. The Münch pressure flow hypothesis (PFH) is considered the leading framework to mathematically represent this transport. It assumes that osmosis provides the necessary pressure differences to drive the fluid flow and sucrose within the phloem. Mathematical models utilizing the PFH approximate the phloem by a relatively rigid semi-permeable tube. However, the phloem consists of living cells that contract and expand in response to pressure fluctuations. The effect of membrane elasticity on osmotically driven sucrose front speed has rarely been considered and frames the scope here. Laboratory experiments were conducted to elucidate the elastic-to-plastic pressure-deformation relation in membranes and their effect on sucrose front speeds. It is demonstrated that membrane elasticity acts to retard the sucrose front speed. The retardation emerges because some of the osmotic pressure performs mechanical work to expand the membrane instead of pressurizing water. These results offer a novel perspective about the much discussed presence of sieve plates through-out the phloem acting as structural dampers.
The phoenix hypothesis of speciation
Authors: Yamaguchi Ryo , Wiley Bryn , Otto Sarah P.
Published: June 2022

Genetic divergence among allopatric populations builds reproductive isolation over time and is thought to be the major mechanism underlying the formation of new species. This process is accelerated when populations face a changing environment, but abrupt change also places populations at risk of extinction. Here we use simulations of Fisher’s geometric model with explicit population dynamics to explore the genetic changes that occur in the face of extreme environmental changes to which populations must adapt or go extinct. We show that evolutionary rescue leads to the fixation of mutations whose effects are larger on average and that these mutations are more likely to lead to reproductive isolation, compared with populations not at risk of extinction. We refer to the formation of new species from the ashes of populations in decline as the phoenix hypothesis of speciation. The phoenix hypothesis predicts more substantial hybrid fitness breakdown among populations surviving a higher extinction risk. The hypothesis was supported when many loci underlie adaptation. When, however, there was only a small number of potential rescue mutations, we found that mutations fixed in different populations were more likely to be identical, with parallel changes reducing isolation. With a limited genomic potential for adaptation, we find support for a modified version of the phoenix hypothesis where reproductive isolation builds fastest in populations subject to an intermediate extinction risk. While processes driving extinction lead to the loss of lineages with deep evolutionary histories, they may also generate new taxa, albeit taxa with minimal genetic differences.
Epigenetic reprogramming of melanoma cell state through fatty acid β-oxidation and Toll-like receptor 4 signaling
Authors: Huang Ting-Hsiang , Ma Yilun , Montal Emily , Suresh Shruthy , Tagore Mohita M. , Corbin Alexandra , Lumaquin Dianne , Campbell Nathaniel R. , Baggiolini Arianna , Koche Richard P. , White Richard M.
Published: June 2022

Tumor cells respond to a host of factors from the local microenvironment. Microenvironmental fatty acids can be used by melanoma cells for fuel, but their effects on transcription and epigenetics are still unclear. Here, we show that the fatty acid β-oxidation (FAO) pathway integrates signaling and epigenetics to drive melanoma progression. Using transgenic zebrafish and human cell lines, we find that octanoate, a medium-chain fatty acid, increases tumorigenesis. Octanoate is metabolized via the FAO/ACLY axis into acetyl-CoA, leading to increased histone acetylation. Transcriptomic and epigenetic analyses demonstrate a convergence of inflammatory gene signatures in octanoate-treated melanoma cells. This signature is mediated by TLR4/MyD88 signaling, which is activated by saturated fatty acids like octanoate. Genetic inactivation of either FAO enzymes or TLR4/MyD88 inhibits alterations in histone acetylation, and rescues octanoate-tumor promoting effects. Together, these data demonstrate clear evidence linking fatty acid metabolism and epigenetics to melanoma pathogenesis through TLR4 signaling.