bluuebunny/crossref_metadata_2025 huggingface dataset:
Unleashing the secrets of plant-fungal interactions using a transformation-free confocal staining technique that supports AI-assisted quantitative analysis
Authors: Nelson Ashley C. , Kariyawasam Gayan , Wyatt Nathan A. , Li Jinling , Haueisen Janine , Stukenbrock Eva H. , Borowicz Pawel , Liu Zhaohui , Friesen Timothy L.
Published: October 2023

Laser scanning confocal microscopy’s ability to generate high-contrast 3D images has become essential to studying plant-fungal interactions. Techniques such as visualization of native fluorescence, fluorescent protein tagging of microbes, GFP/RFP-fusion proteins, and fluorescent labelling of plant and fungal proteins have been widely used to aid in these investigations. Use of fluorescent proteins have several pitfalls including variability of expressionin plantaand the requirement of gene transformation. Here we used the unlabeled pathogensParastagonospora nodorum,Pyrenophora teresf.teres, andCercospora beticolainfecting wheat, barley, and sugar beet respectively, to show the utility of a staining and imaging technique that uses propidium iodide (PI), which stains RNA and DNA, and wheat germ agglutinin labeled with fluorescein isothiocyanate (WGA-FITC), which stains chitin, to visualize fungal colonization of plants. This method relies on the use of KOH to remove the cutin layer of the leaf, increasing its permeability. This permeability allows the staining solution to penetrate and efficiently bind to its targets, resulting in a consistent visualization of cellular structures. We have also used this staining technique in conjunction with machine learning to analyze fungal volume, which indicates the fitness of the pathogenin planta, as well as quantifying nuclear breakdown, an early indicator of programmed cell death (PCD). This technique is simple to use, robust, consistent across host species, and can be applied to any plant-fungal interaction. Therefore, this technique can be used to characterize model systems as well as non-model interactions where transformation is not routine.
Detecting and quantifying heterogeneity in susceptibility using contact tracing data
Authors: Tuschhoff Beth M. , Kennedy David A.
Published: October 2023

The presence of heterogeneity in susceptibility, differences between hosts in their likelihood of becoming infected, can fundamentally alter disease dynamics and public health responses, for example, by changing the final epidemic size, the duration of an epidemic, and even the vaccination threshold required to achieve herd immunity. Yet, heterogeneity in susceptibility is notoriously difficult to detect and measure, especially early in an epidemic. Here we develop a method that can be used to detect and estimate heterogeneity in susceptibility given contact by using contact tracing data, which is typically collected early in the course of an outbreak. This approach provides the capability, given sufficient data, to estimate and account for the effects of this heterogeneity before they become apparent during an epidemic. It additionally provides the capability to analyze the wealth of contact tracing data available for previous epidemics and estimate heterogeneity in susceptibility for disease systems in which it has never been estimated previously. The premise of our approach is that highly susceptible individuals become infected more often than less susceptible individuals, and so individuals not infected after appearing in contact networks should be less susceptible than average. This change in susceptibility can be detected and quantified when individuals show up in a second contact network after not being infected in the first. To develop our method, we simulated contact tracing data from artificial populations with known levels of heterogeneity in susceptibility according to underlying discrete or continuous distributions of susceptibilities. We analyzed this data to determine the parameter space under which we are able to detect heterogeneity and the accuracy with which we are able to estimate it. We found that our power to detect heterogeneity increases with larger sample sizes, greater heterogeneity, and intermediate fractions of contacts becoming infected in the discrete case or greater fractions of contacts becoming infected in the continuous case. We also found that we are able to reliably estimate heterogeneity and disease dynamics. Ultimately, this means that contact tracing data alone is sufficient to detect and quantify heterogeneity in susceptibility.
Predicting Small Molecule Ligand – RNA Binding Pocket Binding Modes Using Metadynamics
Authors: Bai Zhixue , Chen Alan
Published: October 2023

Understanding the structural dynamics of how small molecule ligand recognize its RNA binding pocket is always a crucial determinant in pharmaceutical research. Molecular dynamics (MD) simulation is often used to interpretate this process at atomic resolution. However, the insurmountable high energy barriers in the binding pathway results in the nonergodic dynamics for unbiased MD sampling. To address this limitation, we applied well-tempered metadynamics coupled with upper wall restrain in this work, therefore providing an novel modeling approach for sampling the multiple state transitions during this binding process and probing the most energy favorable binding modes through two-dimensional free energy landscape reconstructed by incorporating couple possible hydrogen binding interactions between small molecule ligand and its RNA binding pocket as collective variables (CVs). Our computational predictions of binding modes for all five cases studied are in quantitative agreement with structures solved by X-ray crystallography or NMR with RMSD less than 2.0 Å. In addition, we presented the first molecular dynamics binding pathway and binding mechanism for the three cases of in vitro selected RNA aptamer. Our study demonstrated that metadynamics can be applied to effectively sampling state transitions of ligand binding events. By coupling with upper wall restrain, we have enabled fast free energy profile calculation and binding mode prediction for small molecule-RNA binding process, facilitating RNA-ligand binding investigation. This method therefore could be much-needed in computer-aided drug design pipelines of RNA-targeted small molecule compounds.

Abstract Figure
A Systematic Review of Evidence Behind the CDC Guidelines for Indoor Lightning Safety
Authors: Brown Elissa , Haslam Alyson , Prasad Vinay
Published: October 2023

Objective

To assess the evidence underlying the Centers for Disease Control and Prevention (CDC) indoor safety guidance for lightning storms.

Design

Systematic Review of peer-reviewed literature.

Setting

Google Scholar, PubMed, and Web of Science (through 2023).

Participants

Reports of indoor death or injury from lightning strike.

Main outcome measures

The number of deaths and injuries from lightning-related activities.

Results

A majority of the 15 articles identified were retrospective reviews of data from death certificates, medical records, and newspaper reports; 5 articles were based on single case reports. Reports of injuries from lightning while indoors are exceedingly rare; death from lightning while indoors is essentially non-existent in modern times. No evidence exists that supports the given advice.

Conclusions

Current U.S. lightning avoidance tips may inadvertently portray indoor spaces as unsafe, despite their protective advantage. Guidelines should place less emphasis on indoor situations and highlight controllable risks, such as behavior in outdoor and recreation situations.
Daytime broadcast spawning in crypticPocilloporaspecies at Mo’orea, French Polynesia
Authors: Harnay P , Turner AM , Burgess SC , Putnam HM
Published: October 2023

Knowledge of when corals release gametes is fundamentally important for understanding reef ecology and evolution, but further research is needed to document patterns at the species level and in a broader range of taxa. In Mo’orea (17°32′S 149°50′W), French Polynesia, when corals were decimated by crown-of-thorns and a cyclone between 2007-2010,Pocillopora spp.recruitment primarily drove reef recovery over the following decade. Furthermore, recent research has identified that the Pocillopora community is composed of six morphologically-cryptic species. Spawning times at the genetically-verified species level at Mo’orea are undocumented in the scientific literature. To address this gap, we conducted in situ surveys ofPocillopora spp.over a total of 89 days during September 2022 - January 2023 and October 2023 - January 2024. For corals observed spawning, we used molecular analysis of mtORF and PocHistone markers to identify corals to species. We documented the synchronized lagoon level spawning ofP. meandrina2-3 days following the full moon in December 2022 (06:16-06:32, 06:21-06:35), and of a few colonies in October of 2023 (06:22-06:38) and a single colony in November 2022 (06:32). In contrast, sister speciesP. verrucosaandP. tuahiniensisspawned around the new moons in November and December of 2023. These species’ spawning overlapped one day after the new moon, butP. verrucosatended to release on the new moon and earlier in the day (∼05:45 - 06:15), whereasP. tuahiniensistended to release 1 - 3 days after the new moon and later in the day (∼06:30 - 06:50), We observed only one colony ofP. cf. effusaspawning (+3 days after new moon ∼06:30 - 06:50). Collectively, these first reported observations provide an initial documentation ofPocilloporaspawning in Mo’orea (to our knowledge), expanding on indigenous knowledge and increasing capacity to study the essential, yet environmentally sensitive, process of coral reproduction for critical reef building species in French Polynesia.
Afanc: a Metagenomics Tool for Variant Level Disambiguation of NGS Datasets
Authors: Morris Arthur V. , Price Anna , Connor Tom
Published: October 2023

Genomics is amongst the most powerful tools available for mounting a clinical response to infectious disease. The accurate and precise taxonomic evaluation of pathogens is essential when building a picture of pathogenicity, virulence, transmission, and drug resistance. Carrying out such profiling in a high throughput manner necessitates the development of reliable bioinformatic tools. Here we present Afanc, a novel metagenomic profiler which is sensitive down to species and strain level taxa, and capable of elucidating the complex pathogen profile of compound datasets. We compared Afanc against currently available cutting edge profilers using 3 datasets: single species read sets simulated from the full Mycobacteriaceae taxonomic landscape; compound read sets containing multiple Mycobacteriaceae species and variants; and real data covering the majority of theM. tuberculosislineage taxonomic space. Afanc outperformed all profilers, both generic and Mycobacteriaceae specific, across all tested fields. As a species agnostic profiler, we predict that Afanc will be of great utility when carrying out highly specific and sensitive pathogen profiling of clinical datasets. Such analyses are essential in advising both the clinical response to an individual disease case, and in forming the foundation of epidemiological surveys.
Bacteroidesis increased in an autism cohort and induces autism-relevant behavioral changes in mice in a sex-dependent manner
Authors: Carmel Julie , Ghanayem Nasreen , Mayouf Rasha , Saleev Natalia , Chaterjee Ipsita , Getselter Dmitriy , Tiknonov Evgeny , Turjeman Sondra , Shaalan Mounia , Khatib Saleh , Kuzminsky Alla , Kevtani-Friedman Neta , Kronos Tanya , Bretler Tali , Koren Omry , Elliott Evan
Published: October 2023

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition which is defined by decreased social communication and the presence of repetitive or stereotypic behaviors. Recent evidence has suggested that the gut-brain axis may be important in neurodevelopment in general and may play a role in ASD in particular. Here, we present a study of the gut microbiome in 96 individuals diagnosed with ASD in Israel, compared to 42 neurotypical individuals. We determined differences in alpha and beta diversity in the microbiome of individuals with ASD and demonstrated that the phylum Bacteroidetes and genusBacteroideswere the most significantly over-represented in individuals with ASD. To understand the possible functional significance of these changes, we treated newborn mice withBacteroides fragilisat birth.B. fragilis-treated male mice displayed social behavior dysfunction, increased repetitive behaviors and gene expression dysregulation in the prefrontal cortex, while female mice did not display behavioral deficits. These findings suggest that overabundance ofBacteroides, particularly in early life, may have functional consequences for individuals with ASD.
Serum Lipidome Profiling Reveals a Distinct Signature of Ovarian Cancer in Korean Women
Authors: Sah Samyukta , Bifarin Olatomiwa O. , Moore Samuel G. , Gaul David A. , Chung Hyewon , Cho Hanbyoul , Cho Chi-Heum , Kim Jae-Hoon , Kim Jaeyeon , Fernández Facundo M.
Published: October 2023

Distinguishing ovarian cancer (OC) from other gynecological malignancies remains a critical unmet medical need with significant implications for patient survival. However, non-specific symptoms along with our lack of understanding of OC pathogenesis hinder its diagnosis, preventing many women from receiving appropriate medical assistance. Accumulating evidence suggests a link between OC and deregulated lipid metabolism. Most studies, however, are limited by small sample size, particularly for early-stage cases. Furthermore, racial/ethnic differences in OC survival and incidence have been reported, yet most of the studies consist largely of non-Hispanic white women or women with European ancestry. Studies of more diverse racial/ethnic populations are needed to make OC diagnosis and prevention more inclusive. Here, we profiled the serum lipidome of 208 OC, including 93 patients with early-stage OC, and 117 non-OC (other gynecological malignancies) patients of Korean descent. Serum samples were analyzed with a high-coverage liquid chromatography high-resolution mass spectrometry platform, and lipidome alterations were investigatedviastatistical and machine learning approaches. Results show that lipidome alterations unique to OC were present in Korean women as early as when the cancer is localized, and those changes increase in magnitude as the diseases progresses. Analysis of relative lipid abundances revealed specific patterns for various lipid classes, with most classes showing decreased abundance in OC in comparison to other gynecological diseases. Machine learning methods selected a panel of 17 lipids that discriminated OC from non-OC cases with an AUC of 0.85 for an independent test set. This study provides a systemic analysis of lipidome alterations in human OC, specifically in Korean women, emphasizing the potential of circulating lipids in distinguishing OC from non-OC conditions.
Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion
Authors: Yuan Tianyu , Yan Hao , Li Kevin C. , Surovtsev Ivan , King Megan C. , Mochrie Simon G. J.
Published: October 2023

Inhomogeneous patterns of enhanced chromatin-chromatin contacts within 10-100 kb-sized regions of the genome are a generic feature of chromatin spatial organization. These features, termed topologically associating domains (TADs), have led to the loop extrusion factor (LEF) model, where TADs arise from loop extrusion by cohesin complexes. Currently, our ability to model TADs relies on the observation that in vertebrates TAD boundaries are correlated with DNA sequences that bind CTCF, which therefore is inferred to block loop extrusion. However, although TADs feature prominently in their Hi-C maps, non-vertebrate eukaryotes either do not express CTCF or show few TAD boundaries that correlate with CTCF sites. In all of these organisms, the counterparts of CTCF remain unknown, frustrating comparisons between Hi-C data and simulations. To extend the LEF model across the tree of life, here, we propose theconserved-current loop extrusion (CCLE) modelthat interprets loop-extruding cohesin as a nearly-conserved probability current. From cohesin ChIP-seq data alone, we thus derive a position-dependent loop extrusion rate, allowing for a modified paradigm for loop extrusion, that goes beyond solely discrete, localized barriers to also include loop extrusion rates that vary more continuously across the genome. To demonstrate its utility in organisms lacking CTCF, we applied the CCLE model to the Hi-C maps of interphaseSchizosaccharomyces pombe, as well as to those of meiotic and mitoticSaccharomyces cerevisiae. In all cases, even though their Hi-C maps appear quite different, the model accurately predicts the TAD-scale Hi-C maps. It follows that loop extrusion by cohesin is indeed the primary mechanism underlying TADs in these systems. CCLE allows us to obtain loop extrusion parameters such as the LEF density and processivity, which compare well to independent estimates. The model also provides new insights intoin vivoLEF composition and function.
Calcium Sulfate Microparticle Size Modification for Improved Alginate Hydrogel Fabrication and Its Application in 3D Cell Culture
Authors: Kim Joo Ho , Iyer Siddharth , Tessman Christian , Lakshman Shashank Vummidi , Kang Heemin , Gu Luo
Published: October 2023

Calcium ion-crosslinked alginate hydrogels are widely used as a materials system for investigating cell behavior in 3D environmentsin vitro. Suspensions of calcium sulfate particles are often used as the source of Ca2+to control the rate of gelation. However, the instability of calcium sulfate suspensions can increase chances of reduced homogeneity of the resulting gel and requires researcher’s proficiency. Here, we show that ball-milled calcium sulfate microparticles with smaller sizes can create more stable crosslinker suspensions than unprocessed or simply autoclaved calcium sulfate particles. In particular, 15 µm ball-milled calcium sulfate microparticles result in gels that are more homogeneous with a balanced gelation rate, which facilitates fabrication of gels with consistent mechanical properties and reliable performance for 3D cell culture. Overall, these microparticles represent an improved method for alginate hydrogel fabrication that can increase experimental reliability and quality for 3D cell culture.
Switching Neuron Contributions to Second Network Activity
Authors: Fahoum Savanna-Rae H , Blitz Dawn M
Published: October 2023

Network flexibility is important for adaptable behaviors. This includes neuronal switching, where neurons alter their network participation, including changing from single-to dual-network activity. Understanding the implications of neuronal switching requires determining how a switching neuron interacts with each of its networks. Here, we tested 1) whether “home” and second networks, operating via divergent rhythm generation mechanisms, regulate a switching neuron, and 2) if a switching neuron, recruited via modulation of intrinsic properties, contributes to rhythm or pattern generation in a new network. Small, well-characterized feeding-related networks (pyloric, ∼1 Hz; gastric mill, ∼0.1 Hz) and identified modulatory inputs make the isolated crab (Cancer borealis) stomatogastric nervous system (STNS) a useful model to study neuronal switching. In particular, the neuropeptide Gly1-SIFamide switches the lateral posterior gastric (LPG) neuron (2 copies) from pyloric-only to dual-frequency pyloric/gastric mill (fast/slow) activity via modulation of LPG intrinsic properties. Using current injections to manipulate neuronal activity, we found that gastric mill, but not pyloric, network neurons regulated the intrinsically generated LPG slow bursting. Conversely, selective elimination of LPG from both networks using photoinactivation revealed that LPG regulated gastric mill neuron firing frequencies but was not necessary for gastric mill rhythm generation or coordination. However, LPG alone was sufficient to produce a distinct pattern of network coordination. Thus, modulated intrinsic properties underlying dual-network participation may constrain which networks can regulate switching neuron activity. Further, recruitment via intrinsic properties may occur in modulatory states where it is important for the switching neuron to actively contribute to network output.

New and Noteworthy

We used small, well-characterized networks to investigate interactions between rhythmic networks and neurons that switch their network participation. For a neuron switching into dual-network activity, only the second network regulated its activity in that network. Additionally, the switching neuron was sufficient but not necessary to coordinate second network neurons, and regulated their activity levels. Thus, regulation of switching neurons may be selective, and a switching neuron is not necessarily simply a follower in additional networks.
Discovery of a new activator of Slack potassium channels with robust efficacy in models of histamine-independent and chronic itch
Authors: Balzulat Annika , Zhu W. Felix , Flauaus Cathrin , Hernandez-Olmos Victor , Heering Jan , Sethumadhavan Sunesh , Dubiel Mariam , Frank Annika , Menge Amelie , Hebchen Maureen , Metzner Katharina , Lu Ruirui , Lukowski Robert , Ruth Peter , Knapp Stefan , Müller Susanne , Steinhilber Dieter , Hänelt Inga , Stark Holger , Proschak Ewgenij , Schmidtko Achim
Published: October 2023

Various disorders are accompanied by histamine-independent itching, which is often resistant to the currently available therapies. In this study, we hypothesized that pharmacological activation of Slack (Kcnt1, KNa1.1), a potassium channel highly expressed in itch-sensitive sensory neurons, has therapeutic potential for the treatment of itching. Based on the Slack-activating antipsychotic drug, loxapine, we designed a series of new derivatives with improved pharmacodynamic and pharmacokinetic profiles that enabled us to validate Slack as a pharmacological targetin vivo. One of these new Slack activators, compound 6, exhibited negligible dopamine D2and D3receptor binding, unlike loxapine. We found that compound 6 displayed potent on-target antipruritic activity in multiple mouse models of acute histamine-independent and chronic itch without motor side effects. These properties make compound 6 a lead molecule for the development of new antipruritic therapies targeting Slack.
Unravelling the origins of boldness: A common garden experiment with cave fish (Barbatula barbatula)
Authors: Jolles Jolle W. , Böhm Alexander , Brinker Alexander , Behrmann-Godel Jasminca
Published: October 2023

Many animals show an aversion to bright, open spaces, with significant variability seen across species, populations, and individuals within populations. Although there is much interest in the underlying causes of this behaviour, few studies have been able to systematically isolate the role of heritable and environmental effects. Here we addressed this gap using a common garden experiment with cave fish. Specifically, we bred and cross-bred cave loaches (Barbatula barbatula) in the lab, raised the offspring in complete darkness or normal light conditions, and studied their light avoidance behaviour. Cave fish spent much more time in a light area and ventured further out, while surface fish spent considerable time on the edge between light and dark areas. Hybrids behaved most similarly to cave fish. Light treatment and eye size and quality only had a modest effect. Our results suggest light avoidance behaviour of cave fish has a heritable basis and is fundamentally linked to increased boldness rather than reduced vision, which is likely adaptive given the complete lack of macropredators in the cave environment. Our study provides novel experimental insights into the behavioural divergence of cave fish and contributes to our broader understanding of the evolution of boldness and behavioural adaptation.
Human brain representations of internally generated outcomes of approximate calculation revealed by ultra-high-field brain imaging
Authors: Czajko Sébastien , Vignaud Alexandre , Eger Evelyn
Published: October 2023

Much of human culture’s advanced technology owes its existence to the ability to mentally manipulate quantities. Neuroscience has described the brain regions overall recruited by numerical tasks and the neuronal codes representing individual quantities during perceptual tasks. Nevertheless, it remains unknown how quantity representations are combined or transformed during mental computations and how specific quantities are coded in the brain when generated as the result of internal computations rather than evoked by a stimulus. Here, we imaged the brains of adult human subjects at 7 Tesla during an approximate calculation task designed to disentangle in- and outputs of the computation from the operation itself. While physically presented sample numerosities were distinguished in activity patterns along the dorsal visual pathway and within frontal and occipito-temporal regions, a representation of the internally generated result was most prominently detected in higher order regions such as angular gyrus and lateral prefrontal cortex. Behavioral precision in the task was related to cross-decoding performance between sample and result representations in medial IPS regions. This suggests the transformation of sample into result may be carried out within dorsal stream sensory-motor integration regions, and resulting outputs maintained for task purposes in higher-level regions in a format possibly detached from sensory-evoked inputs.
TheRAD51paralogueHvXRCC2regulates meiosis and recombination in barley
Authors: Colas Isabelle , Macaulay Malcolm , Arrieta Mikel , Schreiber Miriam , Orr Jamie , Sandhu Amritpal , Augustine Anu , Targońska-Karasek Małgorzata , Armstrong Susan J , Waugh Robbie , Ramsay Luke
Published: October 2023

Using a positional candidate-gene approach we show that semi-steriledesynaptic8mutants are associated with deletions in or complete knockout of the barley homolog ofXRCC2(X-Ray Repair Cross Complementing 2). In barleyXRCC2mutants, the initial meiotic progression is normal, albeit with a small delay in initiation, with completion of synapsis. However, the absence ofHvXRCC2subsequently leads to a dramatic reduction in the number of crossovers, chromosome mis-segregation, and infertility, suggesting thatHvXRCC2plays a major role in recombination. This mutant phenotype is congruent with that reported in mammalian studies but contrasts with theXRCC2mutant in Arabidopsis which is fertile, exhibits normal chromosome pairing and correct chromosome segregation, and is associated with an increased rate of crossovers. This indicates that theXRCC2mutant phenotype in Arabidopsis is not representative of all plants and thatXRCC2is not a good candidate for the modulation of recombination in barley.

Highlight

The mutants of the barley homolog ofXRCC2exhibit delays in replication leading to defective meiosis, altered RAD51 orthologue behaviour, and significant reduction in the number of crossovers as in canonical mammalianXRCC2mutants but unlike those in Arabidopsis.
The SAM Domain of EphA2 Inhibits Ligand-Independent Clustering and Activation
Authors: Shi Xiaojun , Lingerak Ryan , Shrestha Pravesh , Buck Matthias , Wang Bing-Cheng , Smith Adam W.
Published: October 2023

Eph receptors are the largest family of receptor tyrosine kinases (RTKs). They play a role in the pathogenesis of various diseases including cancer, atherosclerosis, fibrosis, infectious diseases, diseases of the central nervous system and age-related cataract. EphA2 has attracted much attention over the years owing to its dysregulation in many diseases. Previous studies have revealed the unique molecular organizations of Eph receptors, and particularly EphA2, into large clusters of receptor-ligand complexes. One unique feature of Eph receptors is a C-terminal sterile alpha motif (SAM) domain, which has been proposed to alter dimerization and kinase activity in EphA2. However, the precise role of the SAM domain in regulating the function and oligomerization state of EphA2 has not been reported. Here we apply a time-resolve fluorescence spectroscopy, PIE-FCCS, to characterize the oligomerization state of EphA2 in live cells and determine the role of the SAM domain. We deleted the SAM domain in the context of full length EphA2 and an intracellular domain (ICD) construct to assess the effect of the SAM domain on oligomerization state, kinase activity, and cellular behavior. Overall, we find that the SAM domain inhibits ligand-independent clustering and kinase activity in both full-length EphA2 and the isolated ICD construct at the cell membrane. These results are consistent with the autoinhibitory features of the C-terminal tail of EGFR and may help resolve the allosteric regulation of other RTKs.
Ly6G+Granulocytes-derived IL-17 limits protective host responses and promotes tuberculosis pathogenesis
Authors: Sharma Priya , Sharma Raman Deep , Das Mrinmoy , Sarkar Binayak , Singh Lakshyaveer , Jain Neharika , Chaturvedi Shivam , Mehra Lalita , Rathee Aditya , Sharma Shilpa , Foo Shihui , Lee Andrea , kumar N Pavan , Das Prasenjit , Viswanathan Vijay , Kornfeld Hardy , Howland Shanshan W. , Babu Subash , Nandicoori Vinay , Singhal Amit , Kumar Dhiraj
Published: October 2023

The protective correlates ofMycobacterium tuberculosis(Mtb) infection-elicited host immune responses are incompletely understood. Here, we report pro-pathogenic crosstalk involving Ly6G+granulocytes (Ly6G+Gra), IL-17 and COX2. We show that in the lungs ofMtb-infected wildtype mice, either BCG-vaccinated or not, most intracellular bacilli are Ly6G+Gra-resident four weeks post-infection onwards. In the genetically susceptibleIFNγ−/−mice, excessive Ly6G+Gra infiltration correlates with severe bacteraemia. Neutralizing IL-17 (anti-IL17mAb) and COX2 inhibition by celecoxib reverse Ly6G+Gra infiltration, associated pathology and death inIFNγ−/−mice. Surprisingly, Ly6G+Gra also serves as the major source of IL-17 in the lungs ofMtb-infected WT orIFNγ−/−mice. The IL-17-COX2-Ly6G+Gra interplay also operates in WT mice. Inhibiting RORγt, the key transcription factor for IL-17 production or COX2, reduces the bacterial burden in Ly6G+Gra, leading to reduced bacterial burden and pathology in the lungs of WT mice. In theMtb-infected WT mice, COX2 inhibition abrogates IL-17 levels in the lung homogenates and significantly enhances BCG’s protective efficacy, mainly by targeting the Ly6G+Gra-residentMtbpool. Furthermore, in pulmonary TB patients, high neutrophil count and IL-17 correlated with adverse treatment outcomes. Together, our results suggest that IL-17 and PGE2 are the negative correlates of protection, and we propose targeting the pro-pathogenic IL-17-COX2-Ly6G+Gra axis for TB prevention and therapy.
Concordant dynamic changes of global network properties in the frontoparietal and limbic compartments: an EEG study
Authors: Lee Tien-Wen , Tramontano Gerald , Hinrichs Clay
Published: October 2023

Introduction

Despite its complexity, deciphering nodal interaction is imperative to understanding a neural network. Network interaction is an even more complicated topic that must be addressed. This study aimed to examine the relationship between the brain waves of two canonical brain structures, i.e., the frontoparietal and limbic compartments, during a resting state.

Methods

Electroencephalography (EEG) of 51 subjects in eye-closed condition was analyzed, and the eLORETA method was applied to convert the signals from the scalp to the brain. By way of community detection, representative neural nodes and the associated mean activities were retrieved. Total and lagged coherences were computed to indicate functional connectivity between those neural nodes. Two global network properties were elucidated based on the connectivity measures, i.e., global efficiency and mean functional connectivity strength. The temporal correlation of the global network indices between the two studied networks was explored.

Results

It was found that there was a significant trend of positive correlation across the four metrics (lagged vs. total coherence x global efficiency vs. average connectivity). In other words, when the neural interaction in the FP network was stronger, so did that in the limbic network, and vice versa. Notably, the above interaction was not spectrally specific and only existed at a finer temporal scale (under hundreds of milliseconds level).

Conclusion

The concordant change in network properties indicates an intricate balance between FP and LM compartments. Possible mechanisms and implications for the findings are discussed.
Biomarker discovery in progressive supranuclear palsy from human cerebrospinal fluid using mass spectrometry-based proteomics
Authors: Jang Yura , Oh Sungtaek , Hall Anna J. , Zhang Zhen , Tropea Thomas F. , Chen-Plotkin Alice , Rosenthal Liana S. , Dawson Ted M. , Na Chan Hyun , Pantelyat Alexander Y.
Published: October 2023

Progressive supranuclear palsy (PSP) is a neurodegenerative disorder that is often misdiagnosed as Parkinson’s Disease (PD) because of shared symptoms. PSP is characterized by the accumulation of tau protein in specific brain regions, which results in loss of balance, gaze impairment, and dementia. Diagnosing PSP is often challenging, and there’s a significant demand for reliable biomarkers. However, existing biomarkers, including tau protein and neurofilament light chain (NfL) levels in cerebrospinal fluid (CSF), show inconsistencies in distinguishing PSP from other neurodegenerative disorders. To overcome these limitations, we conducted a comprehensive proteome analysis for CSF samples from 40 PSP, 40 PD, and healthy controls (HC) using the tandem mass tag-based quantification method, identifying 3,653 unique proteins. Our statistical analysis identified 190, 152, and 247 differentially expressed proteins when comparing PSP vs. HC, PSP vs. PD, and PSP against both PD and HC, respectively. Gene set enrichment analysis and interactome analysis conducted with the differentially expressed proteins in PSP CSF indicated that most of them were implicated in cell adhesion, cholesterol metabolism, and glycan biosynthesis. Cell-type enrichment analysis revealed that neuronally-derived proteins were predominant among the differentially expressed proteins. Potential biomarker classification performance showed that ATP6AP2 (reduced in PSP) had the highest AUC (0.922), followed by NEFM, EFEMP2, LAMP2, CHST12, FAT2, B4GALT1, LCAT, CBLN3, FSTL5, ATP6AP1, and GGH. This is the first large-scale mass spectrometry-based proteome analysis to discover CSF PSP biomarkers differentiating from both controls and PD, thereby laying a foundation for further development and validation.
Variants in theDDX6-CXCR5autoimmune disease risk locus influence the regulatory network in immune cells and salivary gland
Authors: Wiley Mandi M. , Khatri Bhuwan , Joachims Michelle L. , Tessneer Kandice L. , Stolarczyk Anna M. , Rasmussen Astrid , Anaya Juan-Manuel , Aqrawi Lara A. , Bae Sang-Cheol , Baecklund Eva , Björk Albin , Brun Johan G. , Bucher Sara Magnusson , Dand Nick , Eloranta Maija-Leena , Engelke Fiona , Forsblad-d’Elia Helena , Fugmann Cecilia , Glenn Stuart B. , Gong Chen , Gottenberg Jacques-Eric , Hammenfors Daniel , Imgenberg-Kreuz Juliana , Jensen Janicke Liaaen , Johnsen Svein Joar Auglænd , Jonsson Malin V. , Kelly Jennifer A. , Khanam Sharmily , Kim Kwangwoo , Kvarnström Marika , Mandl Thomas , Martín Javier , Morris David L. , Nocturne Gaetane , Norheim Katrine Brække , Olsson Peter , Palm Øyvind , Pers Jacques-Olivier , Rhodus Nelson L. , Sjöwall Christopher , Skarstein Kathrine , Taylor Kimberly E. , Tombleson Phil , Thorlacius Gudny Ella , Venuturupalli Swamy , Vital Edward M. , Wallace Daniel J , Grundahl Kiely M. , Radfar Lida , Brennan Michael T. , James Judith A. , Scofield R. Hal , Gaffney Patrick M. , Criswell Lindsey A. , Jonsson Roland , Appel Silke , Eriksson Per , Bowman Simon J. , Omdal Roald , Rönnblom Lars , Warner Blake M. , Rischmueller Maureen , Witte Torsten , Farris A. Darise , Mariette Xavier , Shiboski Caroline H. ,   Sjögren’s International Collaborative Clinical Alliance (SICCA), Wahren-Herlenius Marie , Alarcón-Riquelme Marta E. ,   PRECISESADS Clinical Consortium, Ng Wan-Fai ,   UK Primary Sjögren’s Syndrome Registry, Sivils Kathy L. , Guthridge Joel M. , Adrianto Indra , Vyse Timothy J. , Tsao Betty P. , Nordmark Gunnel , Lessard Christopher J.
Published: October 2023

Fine mapping and bioinformatic analysis of theDDX6-CXCR5genetic risk association in Sjögren’s Disease (SjD) and Systemic Lupus Erythematosus (SLE) identified five common SNPs with functional evidence in immune cell types: rs4938573, rs57494551, rs4938572, rs4936443, rs7117261. Functional interrogation of nuclear protein binding affinity, enhancer/promoter regulatory activity, and chromatin-chromatin interactions in immune, salivary gland epithelial, and kidney epithelial cells revealed cell type-specific allelic effects for all five SNPs that expanded regulation beyond effects onDDX6andCXCR5expression. Mapping the local chromatin regulatory network revealed several additional genes of interest, includinglnc-PHLDB1-1. Collectively, functional characterization implicated the risk alleles of these SNPs as modulators of promoter and/or enhancer activities that regulate cell type-specific expression ofDDX6,CXCR5, andlnc-PHLDB1-1, among others. Further, these findings emphasize the importance of exploring the functional significance of SNPs in the context of complex chromatin architecture in disease-relevant cell types and tissues.
Deep-seain situand laboratory proteomics provide insights into the sulfur metabolism of a novel deep-sea bacterium,Pseudodesulfovibrio serpenssp. nov.
Authors: Wang Chong , Zheng Rikuan , Sun Chaomin
Published: October 2023

Sulfate-reducing bacteria (SRB) are ubiquitously distributed across various biospheres and play key roles in global sulfur cycles. However, few deep-sea SRB have been cultivated and studiedin situ, limiting our understanding of the true metabolism of SRB in the deep biosphere. Here, we firstly clarified the high abundance of SRB in deep-sea cold seep sediments and successfully isolated a sulfate-reducing bacterium (strain zrk46). Our genomic, physiological and phylogenetic analyses indicate that strain zrk46 is a novel species, which we propose asPseudodesulfovibrio serpens. Based on the combined results from growth assays and proteomic analyses, we found that supplementation with sulfate (SO42-), thiosulfate (S2O32-), or sulfite (SO32-) promoted the growth of strain zrk46 by facilitating energy production through the dissimilatory sulfate reduction with the auxiliary functions of heterodisulfide reductases, ferredoxins, and nitrate reduction associated proteins, which were coupled with the oxidation of environmental organic matter in both laboratory and deep-seain situconditions. Moreover, metatranscriptomic results confirmed the dissimilatory sulfate reduction of deep-sea SRB in deep-sea environment, which might be coupled to the methane oxidation of anaerobic methanotrophic archaea (ANME-2) through direct interspecies electron transfer via cytochromes.

IMPORTANCE

The deep-sea cold seep sediments were ideal habitats for uncovering diverse metabolisms of SRB. Unfortunately, the paucity of SRB isolates has limited further insights into their physiological and metabolic features as well as ecological roles. In the present study, we demonstrated the high abundance of SRB in the deep-sea cold seep sediments and isolated a sulfate-reducing bacterium. Our results demonstrate that the existence of dissimilatory sulfate reduction of strain zrk46 in both laboratory and deep-seain situenvironments, accompanied by the auxiliary effect of heterodisulfide reductases, ferredoxins, and nitrate reduction associated proteins. Our findings also unravel that the sulfate reduction of deep-sea SRB inin situenvironment might be coupled to the methane oxidation of ANME-2. Overall, these findings expand our understanding of deep-sea SRB, while highlighting their importance for deep-sea elemental cycles.
Systematic analysis of transcription factor combinatorial binding uncovers TEAD1 as an antagonist of tissue-specific transcription factors in human organogenesis
Authors: Garcia-Mora Araceli , Mallen Joshua , Zarrineh Peyman , Hanley Neil , Gerrard Dave , Bobola Nicoletta
Published: October 2023

Gene expression is largely controlled by transcription factors (TFs), which bind to enhancers in combination with other TFs in a mechanism known as combinatorial binding. While combinatorial binding is well established, a comprehensive view of tissue-specific TF combinations at active enhancers during human embryonic development is still lacking. Using a two-step pipeline to detect co-occurring TF motifs in developmental enhancers across 11 human embryonic tissues, we found that motifs recognized by ubiquitous TF families, including TEAD, TALE, ETS, and STAT, are enriched near tissue-specific sequence signatures in developmental enhancers across multiple tissues. In human heart enhancers, TEAD and GATA motifs frequently co-occur, and in the developing mouse heart TEAD1 and GATA4 co-occupy a set of genomic regions, which are also preferentially bound by CHD4, a component of the NuRD complex involved in transcriptional repression. Consistently, TEAD1 attenuates enhancer activation in vitro, with this repressive effect dependent on tissue-specific activators. Overall, our findings reveal universal patterns of TF connectivity within organ-specific transcriptional networks and highlight a broad, previously unrecognized role for TEAD in coordinating organ growth and differentiation across multiple tissues.
Intensity-dependent effects of tDCS on motor learning are related to dopamine
Authors: Leow Li-Ann , Jiang Jiaqin , Bowers Samantha , Zhang Yuhan , Dux Paul E , Filmer Hannah L
Published: October 2023

Non-invasive brain stimulation techniques, such as transcranial direct current stimulation (tDCS), are popular methods for inducing neuroplastic changes to alter cognition and behaviour. One challenge for the field is to optimise stimulation protocols to maximise benefits. For this to happen, we need a better understanding ofhowstimulation modulates cortical functioning/behaviour. To date, there is increasing evidence for a dose-response relationship between tDCS and brain excitability, however how this relates to behaviour is not well understood. Even less is known about the neurochemical mechanisms which may drive the dose-response relationship between stimulation intensities and behaviour. Here, we examine the effect of three different tDCS stimulation intensities (1mA, 2mA, 4mA anodal motor cortex tDCS) administered during the explicit learning of motor sequences. Further, to assess the role of dopamine in the dose-response relationship between tDCS intensities and behaviour, we examined how pharmacologically increasing dopamine availability, via 100mg of levodopa, modulated the effect of stimulation on learning. In the absence of levodopa, we found that 4mA tDCS improved and 1mA tDCS impaired acquisition of motor sequences relative to sham stimulation. Conversely, levodopa reversed the beneficial effect of 4mA tDCS. This effect of levodopa was no longer evident at the 48-hour follow-up, consistent with previous work characterising the persistence of neuroplastic changes in the motor cortex resulting from combining levodopa with tDCS. These results provide the first direct evidence for a role of dopamine in the intensity-dependent effects of tDCS on behaviour.
Retinoic Acid Boosts HIV-1 Replication in MacrophagesviaCCR5/SAMHD1-Dependent and mTOR-Modulated Mechanisms
Authors: Dias Jonathan , Cattin Amélie , Goulet Jean-Philippe , Fert Augustine , Raymond Marchand Laurence , Wiche Salinas Tomas Raul , Ngassaki Yoka Christ-Dominique , Moreira Gabriel Etiene , Caballero Edwin Ramon , Routy Jean-Pierre , Ancuta Petronela
Published: October 2023

The intestinal environment facilitates HIV-1 infectionviamechanisms involving the gut-homing elixir retinoic acid (RA), which transcriptionally reprograms CD4+T-cells for increased HIV-1 permissiveness. Consistently, colon-infiltrating CD4+T-cells carry replication-competent viral reservoirs in people living with HIV-1 (PLWH) receiving antiretroviral therapy (ART). Intriguingly, integrative infection in colon macrophages, a pool replenished by circulating monocytes, represents a rare event in ART-treated PLWH, thus questioning on HIV-1 permissiveness in gut-resident macrophages. Here, we demonstrate that RA significantly boosts R5 but not X4 HIV-1 replication in monocyte-derived macrophages (MDMs). RNA-Sequencing, Gene Set Variation Analysis, and HIV interactor NCBI database interrogation, revealed RA- mediated transcriptional reprogramming associated with metabolic/inflammatory processes and HIV-1 resistance/dependency factors. Functional validations pointed to mechanisms of RA action, including CCR5 upregulation and SAMHD1 phosphorylation under the control of mTOR. These results support a model in which intestinal MDM contribute to viral replication/dissemination before ART and upon treatment interruption in mTOR-sensitive manner.Figure 1:
Glial activity load on PET (GALP) reveals persistent ‘smoldering’ inflammation in MS despite disease modifying treatment: [F-18]PBR06 study
Authors: Singhal Tarun , Cicero Steven , Rissanen Eero , Ficke John Hunter , Kukreja Preksha , Vaquerano Steven , Glanz Bonnie , Dubey Shipra , Sticka William , Seaver Kyle , Kijewski Marie , Callen Alexis M. , Chu Renxin , Carter Kelsey , Silbersweig David , Chitnis Tanuja , Bakshi Rohit , Weiner Howard L
Published: October 2023

Introduction

Cortical grey (CoGM) and white matter (WM) microglial activation (MA) is involved in the pathogenesis of multiple sclerosis (MS). [F-18]PBR06 positron emission tomography (PET) targeting 18kilodalton-translocator protein (TSPO) can detect abnormal MA in MS.

Aims and Objectives

The goal of this study is to determine the effect of disease modifying treatment (DMT) efficacy on modulating the extent and clinical and radiological correlates of MA in MS patients.

Methods

Thirty [F-18]PBR06 PET scans were performed in 22 MS patients (13 RR, 9 SP, mean age 46±14 years, 15 females, median EDSS 3.5, mean T25FW 7.2±4.6s) and 8 healthy controls (HC). Individualized z-score maps of brain parenchymal MA were generated by voxel-by-voxel comparison between each subject’s PET SUVR images and a HC dataset. Logarithmically transformed ‘Glial activity load on PET’ scores (calculated as the sum of voxel-by-voxel z-scores ≥4 in CoGM and WM regions), ‘lnGALP’, were compared between MS subjects on DMT with high efficacy (HT; including rituximab, ocrelizumab, natalizumab and fingolimod, n=13) versus those on no or lower efficacy treatment (LT; including glatiramer acetate and interferons), and correlated with clinical measures and cortical thickness (measured using Freesurfer). p<0.05 was considered statistically significant.

Results

CoGM and WM lnGALP scores were higher in MS vs. HCs (10.0±1.5 vs. 7.5±1.5 and 9.8±1.5 vs. 6.6±2.4, both p<0.01) and were inversely correlated with cortical thickness across groups (r=-0.44 and - 0.48, both p<0.05, n=30). In HT-MS group, CoGM and WM lnGALP was significantly lower as compared to LT-MS group (9.1±1.0 vs. 11.3±1.1 and 9.1±1.3 vs. 10.8±1.4, p=0.000075 and 0.006) but remained abnormally higher than in HC group (p=0.006 and 0.02, respectively). Within HT-MS patients, CoGM lnGALP scores were higher in SP vs. RR subgroups (p=0.008), correlated positively with EDSS, T25FW, fatigue scores and serum GFAP levels (r=0.65,0.79, 0.75 and 0.67, all p<0.05), and inversely with cortical thickness (r=-0.66, p=0.01).

Conclusions

High-efficacy DMTs decrease, but do not normalize, CoGM and WM MA in MS patients. Such “residual” MA in CoGM is associated with clinical disability, symptom severity and cortical degeneration. Individualized mapping of TSPO-PET using [F-18]PBR06 can potentially serve as an imaging biomarker for evaluating emerging therapies targeting MA in MS patients who are worsening despite high-efficacy DMTs.