bluuebunny/crossref_metadata_2025 huggingface dataset:
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures
Authors: Carbery Anna , Buttenschoen Martin , Skyner Rachael , von Delft Frank , Deane Charlotte M.
Published: September 2023

Protein-ligand binding site prediction is a useful tool for understanding the functional behaviour and potential drug-target interactions of a novel protein of interest. However, most binding site prediction methods are tested by providing crystallised ligand-bound (holo) structures as input. This testing regime is insufficient to understand the performance on novel protein targets where experimental structures are not available. An alternative option is to provide computationally predicted protein structures, but this is not commonly tested. However, due to the training data used, computationally-predicted protein structures tend to be extremely accurate, and are often biased toward a holo conformation. In this study we describe and benchmark IF-SitePred, a protein-ligand binding site prediction method which is based on the labelling of ESM-IF1 protein language model embeddings combined with point cloud annotation and clustering. We show that not only is IF-SitePred competitive with state-of-the-art methods when predicting binding sites on experimental structures, but it performs better on proxies for novel proteins where low accuracy has been simulated by molecular dynamics. Finally, IF-SitePred outperforms other methods if ensembles of predicted protein structures are generated.
Nutrient availability influencesE. colibiofilm properties and the structure of purified curli amyloid fibers
Authors: Siri Macarena , Vázquéz-Dávila Mónica , Bidan Cécile M.
Published: September 2023

Bacterial biofilms are highly adaptable and resilient to challenges. Nutrient availability can induce changes in biofilm growth, biomass, morphology, architecture and mechanical properties. Bacterial extracellular matrix plays a major role in achieving biofilm stability under different environmental conditions. Curli amyloid fibers are determining for the architecture and stiffness ofE. colibiofilms, but how this major matrix component adapts to different environmental cues remains unclear.

Here, we investigated for the first time the effect of nutrient availability on both i) biofilm materials properties and ii) the structure and properties of curli amyloid fibers extracted from the biofilms. For this, we culturedE. coliW3110, which main matrix component is curli fibers. We quantified the size, mass and water content of the resulting biofilms and estimated their mechanical properties by microindentation. The curli amyloid fibers were then purified from the biofilms and their molecular structure and properties were studied by spectroscopic techniques. Our results show that the availability of nutrients in the substrate influences the yield of curli fibers, their structural composition and chemical stability, and suggest that these molecular features contribute to the stiffness of the biofilms. Biofilms grown on substrates with high nutrient concentration are softer, contain less curli fibers, and these fibers exhibit low β-sheet content and chemical stability.

Our multiscale study sheds new light on the relationship between the molecular structure of bacterial matrix and the macroscopic properties of biofilms. This knowledge will benefit the development of both anti-biofilm strategies and biofilm-based materials.

Graphical abstract
Dynamic atP5CS2 Filament Facilitates Substrate Channeling
Authors: Guo Chen-Jun , Zhang Tianyi , Leng Qingqing , Zhou Xian , Zhong Jiale , Liu Ji-Long
Published: September 2023

In plants, the rapid accumulation of proline is a common response to combat abiotic stress. Delta-1-pyrroline-5-carboxylate synthase (P5CS) is a rate-limiting enzyme in proline synthesis, catalyzing the initial two-step conversion from glutamate to proline. Here, we determine the first structure of plant P5CS. Our results show that Arabidopsis thaliana P5CS2 (atP5CS2) can form enzymatic filaments in a substrate-sensitive manner. The destruction of atP5CS filaments by mutagenesis leads to a significant reduction in enzymatic activity. Furthermore, separate activity tests on two domains reveals that filament-based substrate channeling is essential for maintaining the high catalytic efficiency of atP5CS. Our study demonstrates the unique mechanism for the efficient catalysis of P5CS, shedding light on the intricate mechanisms underlying plant proline metabolism and stress response. Therefore these findings provide potential avenues for crop genetically modified breeding.
Characterization of hybrid hydrogels combining natural polymers
Authors: Taylan Derin , Güneş İlayda , Durukan Emine , Gök Özgül
Published: September 2023

Hydrogels have emerged as an important field of study in biomedical engineering, biomaterials research and soft tissue modeling due to their versatility and customizable structures. They are three-dimensional networks capable of absorbing significant amounts of water and can be chemically or physically bonded, rendering them insoluble. The unique properties of hydrogels, such as excellent biocompatibility, degradation abilities, and ability to form chemical bonds between macromolecules, make them valuable in a variety of applications. One of the main applications of hydrogels is tissue engineering, where they are used in implantation, surgical procedures, targeted drug delivery and tissue regeneration. Hydrogels can act as scaffolds to mimic the properties of natural tissues, including mechanical strength, degradation properties, gel transformation, and swelling. Crosslinking hydrogels with other polymers, both natural and synthetic, allows their degradation rate to be controlled. Composite hydrogels or biohybrid gels offer advantages such as consistent properties between batches and a high degree of control in the manufacturing process. Using different types of polymers, researchers can fine-tune the chemical and physical properties of the resulting hydrogel, which is crucial for certain biomedical applications such as drug delivery, biocompatibility, and mechanical stability. In this study, our aim is to make hybrid hydrogel scaffolds more suitable for biomedical applications, which can show the healing effect of adding natural polymers to the scaffold structure. Our results revealed that the hybrid hydrogel obtained by chemically linking gelatin polymer chains to PEG polymers during crosslinking via UV light provides more advantageous properties in the final hydrogel structure, such as better durability and pore sizes for future cell placement in tissue engineering applications.
Seeding Activity of Skin Misfolded Tau as a Novel Biomarker for Tauopathies
Authors: Wang Zerui , Wu Ling , Gerasimenko Maria , Gilliland Tricia , Shah Zahid Syed Ali , Gunzler Steven A. , Donadio Vincenzo , Liguori Rocco , Xu Bin , Zou Wen-Quan
Published: September 2023

Tauopathies are a group of age-related neurodegenerative diseases with a molecular hallmark of the prion-like propagation and accumulation of pathologically phosphorylated tau protein in the brain. They include Alzheimer’s disease (AD), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and Pick’s disease (PiD). Currently, in the peripheral tissues and body fluids there are no reliable diagnostic biomarkers available that are able to directly reflect the capability of propagation and spreading of the misfolded tau aggregates. Here, we revealed significantly increased amounts of phosphorylated tau in the skin of AD patients compared to those in other tauopathies and normal controls. Moreover, the seed-amplification assay (SAA) by the ultrasensitive real-time quaking-induced conversion (RT-QuIC) displayed that the prion-like seeding activity of pathological tau in the skin of cadavers with neuropathologically confirmed tauopathies including AD, PSP, CBD, PiD was dramatically higher than that in normal controls, yielding 75-80% sensitivity and 95-100% specificity, respectively, depending on different tau substrates used. The increased tau-seeding activity was also observed in biopsy skin samples from living AD and PSP patients. Moreover, analysis of the end products of skin-tau SAA confirmed that the increased seeding activity is accompanied with formation of tau aggregates that are of different physicochemical properties determined by the different tau-substrates used. Our study provides proof-of-concept that the skin tau-SAA can differentiate tauopathies from normal controls, suggesting that the seeding activity of the skin misfolded tau can serve as an accurate diagnostic biomarker of tauopathies.
Neural representations of concrete concepts enable identification of individuals during naturalistic story listening
Authors: Botch Thomas L. , Finn Emily S.
Published: September 2023

Different people listening to the same story may converge upon a largely shared interpretation while still developing idiosyncratic experiences atop that shared foundation. What semantic properties support this individualized experience of natural language? Here, we investigate how the “concreteness” of word meanings — i.e., the extent to which a concept is derived from sensory experience — relates to variability in the neural representations of language. Leveraging a large dataset of participants who each listened to four auditory stories while undergoing functional MRI, we demonstrate that an individual’s neural representations of concrete concepts are reliable across stories and unique to the individual. In contrast, we find that neural representations of abstract concepts are variable both within individuals and across the population. Using natural language processing tools, we show that concrete words exhibit similar neural signatures despite spanning larger distances within a high-dimensional semantic space, which potentially reflects an underlying signature of sensory experience — namely, imageability — shared by concrete words but absent from abstract words. Our findings situate the concrete-abstract semantic axis as a core dimension that supports reliable yet individualized representations of natural language.
Adaptation of RiPCA for the Live-Cell Detection of mRNA-Protein Interactions
Authors: Soueid Dalia M. , Garner Amanda L.
Published: September 2023

RNA-binding proteins (RBPs) act as essential regulators of cell fate decisions through their ability to bind and regulate the activity of cellular RNAs. For protein-coding messenger RNAs (mRNAs), RBPs control the localization, stability, degradation, and ultimately translation of mRNAs to impact gene expression. Disruption of the vast network of mRNA-protein interactions has been implicated in many human diseases, and accordingly, targeting these interactions has surfaced as a new frontier in RNA-targeted drug discovery. To catalyze this new field, methods are needed to enable the detection and subsequent screening of mRNA-RBP interactions, particularly in live cells. Using our laboratory’s RNA-interaction with Protein-mediated Complementation Assay (RiPCA) technology, herein we describe its application to mRNA-protein interactions and present a guide for the development of future RiPCA assays for structurally diverse classes of mRNA-protein interactions.
The Sensation and Pain Rating Scale: easy to use, clear to interpret, and responsive to clinical change
Authors: Madden Victoria J , Kamerman Peter , Leake Hayley B. , Catley Mark J. , Heathcote Lauren C. , Moseley G Lorimer
Published: September 2023

Background

The Sensation and Pain Rating Scale (SPARS) allows rating of non-painful as well as painful percepts. While it performs well in the experimental context, its clinical utility is untested. This prospective, repeated-measures study mixed qualitative and quantitative methods to examine the utility and performance of the SPARS in a clinical context, and to compare it with the widely used 11-point NRS for pain.

Methods

People presenting for outpatient physiotherapy (n = 121) provided ratings on the SPARS and NRS at first consultation, before and after sham and active clinical interventions, and at follow-up consultation. Clinicians (n = 9) reported each scale’s usability and interpretability using Likert-type scales and free text, and answered additional questions with free text. Each data type was initially analysed separately: quantitative data were visualised and the ES II metric was used to estimate SPARS internal responsiveness; qualitative data were analysed with a reflexive inductive thematic approach. Data types were then integrated for triangulation and complementarity.

Results

The SPARS was well received and considered easy to use, after initial familiarisation. Clinicians favoured the SPARS over the NRS for clarity of interpretation and inter-rater reliability. SPARS sensitivity to change was good (ESII=0.9; 95%CI: 0.75-1.10). The greater perceptual range of the SPARS was deemed especially relevant in the later phases of recovery, when pain may recede into discomfort that still warrants clinical attention.

Conclusion

The SPARS is a promising tool for assessing patient percept, with strong endorsement from clinicians for its clarity and superior perceptual scope.

Significance

Clinicians in this mixed-methods study favoured the Sensation and Pain Rating Scale (SPARS) over a 0-10 Numerical Rating Scale for pain because the SPARS provides a clearly labelled range for rating non-painful events, which supports inter-rater reliability and clear interpretation. Clinicians reported rapid adjustment to the SPARS structure. The SPARS had good internal responsiveness to change. The SPARS may be particularly useful as a person recovers from a painful episode, when residual discomfort still requires clinical attention.
Feasibility Study of the CT Clock Tool for Estimating Onset Time of Ischaemic Stroke: Study Protocol
Authors: Mair Grant , Whiteley William , Chappell Francesca , MacRaild Allan , Wardlaw Joanna
Published: September 2023

Ischaemic stroke is a devastating disease with high rates of death and disability affecting ∼100,000 people annually in the UK. Effective treatments are only offered when the time of stroke onset is known and within specific limits. For the 20% where onset time is unknown or delayed, advanced imaging methods can identify people for safe and effective treatment. However, this advanced imaging is not widely available. We have developed a method for identifying patients who can still be treated even without advanced imaging. The CT Clock Tool uses only the non-enhanced CT brain scan, that most patients with stroke receive upon arrival at hospital, to determine whether patients are eligible for treatment.

This project aims to provide the first prospective clinical testing of the CT Clock Tool in a single-centre feasibility analysis. We will recruit patients in the emergency department with ischaemic stroke and obtain consent to use their acute CT brain imaging and other data relating to their care. We will ask treating clinicians to apply our CT Clock Tool method in real time, but we will not alter routine care pathways or otherwise involve patients. We have powered the study to validate previous estimates of the diagnostic accuracy and precision of our method for identifying treatment eligible patients. Results from this project will enable a future definitive randomised-controlled trial, which if successful would allow the routine use of our method anywhere CT brain imaging is available for patients with stroke.
Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant
Authors: Khan Khadija , Lustig Gila , Reedoy Kajal , Jule Zesuliwe , Römer Cornelius , Karim Farina , Ganga Yashica , Bernstein Mallory , Baig Zainab , Mahlangu Boitshoko , Mnguni Anele , Nzimande Ayanda , Stock Nadine , Kekana Dikeledi , Ntozini Buhle , van Deventer Cindy , Marshall Terry , Manickchund Nithendra , Gosnell Bernadett I. , Lessells Richard J. , Abdool Karim Quarraisha , Abdool Karim Salim S. , Moosa Mahomed-Yunus S. , de Oliveira Tulio , von Gottberg Anne , Wolter Nicole , Neher Richard A , Sigal Alex
Published: September 2023

Omicron BA.2.86 subvariant differs from Omicron BA.2 as well as recently circulating variants by over 30 mutations in the spike protein alone. Here we report on the first isolation of the live BA.2.86 subvariant from a diagnostic swab collected in South Africa which we tested for escape from neutralizing antibodies and viral replication properties in cell culture. BA.2.86 did not have significantly more escape than Omicron XBB.1.5 from neutralizing immunity elicited by infection of Omicron subvariants ranging from BA.1 to XBB, either by infection alone or as breakthrough infection in vaccinated individuals. Neutralization escape was present relative to earlier strains: BA.2.86 showed extensive escape both relative to ancestral virus in sera from pre-Omicron vaccinated individuals and relative to Omicron BA.1 in sera from Omicron BA.1 infected individuals. We did not observe substantial differences in viral properties in cell culture relative to XBB.1.5. Both BA.2.86 and XBB.1.5 produced infection foci of similar size, had similar cytopathic effect (both lower than ancestral SARS-CoV-2), and had similar replication dynamics. We also investigated the relationship of BA.2.86 to BA.2 sequences and found that the closest were BA.2 samples from Southern Africa circulating in early 2022. These observations suggest that BA.2.86 is more closely related to sequences from Southern Africa than other regions and so may have evolved there, and that evolution led to escape from neutralizing antibodies similar in scale to recently circulating strains of SARS-CoV-2.
Co-expression in tissue-specific gene networks links genes in cancer-susceptibility loci to known somatic driver genes
Authors: Urzúa-Traslaviña Carlos G. , van Lieshout Tijs , Boulogne Floranne , Domanegg Kevin , Zidan Mahmoud , Bakker Olivier B. , Claringbould Annique , de Ridder Jeroen , Zwart Wilbert , Westra Harm-Jan , Deelen Patrick , Franke Lude
Published: September 2023

Background

The genetic background of cancer remains complex and challenging to integrate. Many somatic mutations in genes are known to cause and drive cancer, while genome-wide association studies (GWAS) of cancer have revealed many germline risk factors associated with cancer. However, the overlap between known somatic driver genes and positional candidate genes from GWAS loci is surprisingly small. We hypothesised that genes from multiple independent cancer GWAS loci should show tissue-specific co-regulation patterns that converge on cancer-specific driver genes.

Results

We studied recent well powered GWAS of breast, prostate, colorectal and skin cancer by estimating co-expression between genes and subsequently prioritising genes that show co- expression with genes mapping within susceptibility loci from cancer GWAS. We observed that the prioritised genes were strongly enriched for cancer drivers defined by COSMIC, intOGen and Dietleinet al. The enrichment of known cancer driver genes was most significant when using co-expression networks derived from non-cancer samples from the relevant tissue of origin.

Conclusion

We show how genes in risk loci identified by cancer GWAS can be linked to known cancer driver genes through tissue-specific co-expression networks. This provides an important explanation for why seemingly unrelated sets of genes that harbour either germline risk factors or somatic mutations can eventually cause the same type of disease.
Clinical predictors of severe forms of influenza A H1N1 in adults and children during the 2009 epidemic in Brazil
Authors: Braga Jose Ueleres
Published: September 2023

The World Health Organization (WHO) raised the global alert level for the A(H1N1) influenza pandemic in June 2009. However, since the beginning of the epidemic, the fight against the epidemic lacked foundations for managing cases to reduce the disease lethality. It was urgent to carry out studies that would indicate a model for predicting severe forms of influenza. This study aimed to identify risk factors for severe forms during the 2009 influenza epidemic and develop a prediction model based on clinical epidemiological data. A case-control of cases notified to the health secretariats of the states of Rio de Janeiro, São Paulo, Minas Gerais, Paraná, and Rio Grande do Sul was conducted. Cases had fever, respiratory symptoms, positive confirmatory test for the presence of the virus associated with one of the three conditions: (i) presenting respiratory complications such as pneumonia, ventilatory failure, severe acute respiratory distress syndrome, sepsis, acute cardiovascular complications or death; or respiratory failure requiring invasive or non-invasive ventilatory support, (ii) having been hospitalized or (iii) having been admitted to an Intensive Care Unit. Controls were individuals diagnosed with the disease on the same date (or same week) as the cases. A total of 1653 individuals were included in the study, (858 cases/795 controls). These participants had a mean age of 26 years, a low level of education, and were mostly female. The most important predictors identified were systolic blood pressure in mmHg, respiratory rate in bpm, dehydration, obesity, pregnancy (in women), and vomiting (in children). Three clinical prediction models of severity were developed, for adults, adult women, and for children. The performance evaluation of these models indicated good predictive capacity. The area values under the ROC curve of these models were 0.89; 0.98 and 0.91 respectively for the model of adults, adult women, and children respectively.
Can routine antenatal data be used to assess HIV antiretroviral therapy coverage among pregnant women? Evaluating the validity of different data sources in the Western Cape, South Africa
Authors: Jacob Nisha , Rice Brian , Heekes Alexa , Johnson Leigh F. , Brinkmann Samantha , Kufa Tendesayi , Boulle Andrew
Published: September 2023

Background

Accurate measurement of antenatal antiretroviral treatment (ART) coverage in pregnancy is imperative in tracking progress towards elimination of vertical HIV transmission. In the Western Cape, South Africa, public-sector individual-level routine data are consolidated from multiple sources, enabling the description of temporal changes in population-wide antenatal antiretroviral coverage. We evaluated the validity of different methods for measuring ART coverage among pregnant women.

Methods

We compared self-reported ART data from a 2014 antenatal survey with laboratory assay data from a sub-sample within the survey population. Thereafter, we conducted a retrospective cohort analysis of all pregnancies consolidated in the Provincial Health Data Centre (PHDC) from January 2011 to December 2020. Evidence of antenatal and HIV care from electronic platforms were linked using a unique patient identifier. ART coverage estimates were triangulated with available antenatal survey estimates, aggregated programmatic data from registers recorded in the District Health Information System (DHIS) and Thembisa modelling estimates.

Results

Self-reported ART in the 2014 sentinel antenatal survey (n=1434) had high sensitivity (83.5%), specificity (94.5%) and agreement (k=0.8) with the gold standard of laboratory analysis of ART. Based on linked routine data, ART coverage by the time of delivery in mothers of live births increased from 67.4% in 2011 to 94.7% by 2019. This pattern of increasing antenatal ART coverage was also seen in the DHIS data, and estimated by the Thembisa model, but was less consistent in the antenatal survey data.

Conclusion

This study is the first in a high-burden HIV setting to compare sentinel ART surveillance data with consolidated individuated administrative data. Although self-report in survey conditions showed high validity, more recent data sources based on self-report and medical records may be uncertain with increasing ART coverage over time. Linked individuated data may offer a promising option for ART coverage estimation with greater granularity and efficiency.
Translational modulation by ISRIB alleviates synaptic and behavioral phenotypes in Fragile X syndrome
Authors: Coulson Rochelle L. , Frattini Valentina , Moyer Caitlin E. , Hodges Jennifer , Walter Peter , Mourrain Philippe , Zuo Yi , Wang Gordon X.
Published: September 2023

Fragile X syndrome (FXS) is caused by the functional loss of Fragile X messenger ribonucleoprotein (FMRP), a translational regulator that binds the transcripts of many proteins involved in synaptic function and plasticity. Dysregulated protein synthesis is a central effect of FMRP loss and to date direct translational modulation has not been leveraged in the treatment of FXS. Thus, we examined the effect of the small molecule translational modulator, Integrated Stress Response Inhibitor (ISRIB), in treating synaptic and behavioral symptoms of FXS. Using a combination of population-level single synapse analysis,in vivotwo-photon microscopy, and behavioral analysis, we revealed a mechanism for the appearance of dense and immature dendritic spines, which are observed in human FXS patients andFmr1knockout (KO) mice. Our data suggest that FMRP loss at the synapse dysregulates synaptic protein abundance and that spines are disproportionately stabilized through increased PSD-95 expression but prevented from maturing through reduced synaptic accumulation of glutamate receptors. ISRIB rescues these molecular and synaptic deficits in FXS and improves social recognition inFmr1KO mice. These findings highlight the therapeutic potential of targeting core translational mechanisms and the differential impact of FMRP on synaptic and cellular function in FXS and neurodevelopmental disorders more broadly.
Evaluating the Utilities of Foundation Models in Single-cell Data Analysis
Authors: Liu Tianyu , Li Kexing , Wang Yuge , Li Hongyu , Zhao Hongyu
Published: September 2023

Foundation Models (FMs) have made significant strides in both industrial and scientific domains. In this paper, we evaluate the performance of FMs for single-cell sequencing data analysis through comprehensive experiments across eight downstream tasks pertinent to single-cell data. Overall, the top FMs include scGPT, Geneformer, and CellPLM by considering model performances and user accessibility among ten single-cell FMs. However, by comparing these FMs with task-specific methods, we found that single-cell FMs may not consistently excel than task-specific methods in all tasks, which challenges the necessity of developing foundation models for single-cell analysis. In addition, we evaluated the effects of hyper-parameters, initial settings, and stability for training single-cell FMs based on a proposedscEvalframework, and provide guidelines for pre-training and fine-tuning, to enhance the performances of single-cell FMs. Our work summarizes the current state of single-cell FMs, points to their constraints and avenues for future development, and offers a freely available evaluation pipeline to benchmark new models and improve method development.
Deep learning-assisted single-molecule detection of protein post-translational modifications with a biological nanopore
Authors: Cao Chan , Magalhães Pedro , Krapp Lucien Fabrice , Bada Juarez Juan F. , Mayer Simon , Rukes Verena , Chiki Anass , Lashuel Hilal A. , Dal Peraro Matteo
Published: September 2023

Protein post-translational modifications (PTMs) play a crucial role in countless biological processes, profoundly modulating protein properties on both the spatial and temporal scales. Protein PTMs have also emerged as reliable biomarkers for several diseases. However, only a handful of techniques are available to accurately measure their levels, capture their complexity at a single molecule level and characterize their multifaceted roles in health and disease. Nanopore sensing provides high sensitivity for the detection of low-abundance proteins, holding the potential to impact single-molecule proteomics and PTM detection in particular. Here, we demonstrate the ability of a biological nanopore, the pore-forming toxin aerolysin, to detect and distinguish α-synuclein-derived peptides bearing single or multiple PTMs, namely phosphorylation, nitration and oxidation occurring at different positions and in various combinations. The characteristic current signatures of the α-synuclein peptide and its PTM variants could be confidently identified using a deep learning model for signal processing. We further demonstrate that this framework can quantify α-synuclein peptides at picomolar concentration and detect the C-terminal peptides generated by digestion of full-length α-synuclein. Collectively, our work highlights the unique advantage of using nanopore as a tool for simultaneous detection of multiple PTMs and paves the way for their use in biomarker discovery and diagnostics.
Detecting rhythmic spiking through the power spectra of point process model residuals
Authors: Cox Karin M. , Kase Daisuke , Znati Taieb , Turner Robert S.
Published: September 2023

Objective. Oscillations figure prominently as neurological disease hallmarks and neuromodulation targets. To detect oscillations in a neuron's spiking, one might attempt to seek peaks in the spike train's power spectral density (PSD) which exceed a flat baseline. Yet for a non-oscillating neuron, the PSD is not flat: The recovery period ("RP", the post-spike drop in spike probability, starting with the refractory period) introduces global spectral distortion. An established "shuffling" procedure corrects for RP distortion by removing the spectral component explained by the inter-spike interval (ISI) distribution. However, this procedure sacrifices oscillation-related information present in the ISIs, and therefore in the PSD. We asked whether point process models (PPMs) might achieve more selective RP distortion removal, thereby enabling improved oscillation detection. Approach. In a novel "residuals" method, we first estimate the RP duration (nr) from the ISI distribution. We then fit the spike train with a PPM that predicts spike likelihood based on the time elapsed since the most recent of any spikes falling within the preceding nrmilliseconds. Finally, we compute the PSD of the model's residuals. Main results. We compared the residuals and shuffling methods' ability to enable accurate oscillation detection with flat baseline-assuming tests. Over synthetic data, the residuals method generally outperformed the shuffling method in classification of true- versus false-positive oscillatory power, principally due to enhanced sensitivity in sparse spike trains. In single-unit data from the internal globus pallidus (GPi) and ventrolateral anterior thalamus (VLa) of a parkinsonian monkey -- in which alpha-beta oscillations (8-30 Hz) were anticipated -- the residuals method reported the greatest incidence of significant alpha-beta power, with low firing rates predicting residuals-selective oscillation detection. Significance. These results encourage continued development of the residuals approach, to support more accurate oscillation detection. Improved identification of oscillations could promote improved disease models and therapeutic technologies.
Dual Role of Neuroplastin in Pancreatic β Cells: Regulating Insulin Secretion and Promoting Islet Inflammation
Authors: Kitamura Rie Asada , Hummel Devynn , Urano Fumihiko
Published: September 2023

Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-resident secretory protein that reduces inflammation and promotes proliferation in pancreatic β cells. Numerous studies have highlighted the potential of MANF as a therapeutic agent for diabetes mellitus (DM), making it essential to understand the mechanisms underlying MANF’s functions. In our previous search for a molecule that mediates MANF signaling, we identified Neuroplastin (NPTN) as a binding partner of MANF that localizes on the cell surface. However, the roles of NPTN in pancreatic β cells remain unclear. In this study, we generated β cell-specificNptnknockout (KO) mice and conducted metabolic characterization. NPTN deficiency improved glucose tolerance by increasing insulin secretion and β cell mass in the pancreas. Moreover, proliferation and mitochondrial numbers in β cells increased inNptnKO islets. These phenotypes resulted from elevated cytosolic Ca2+levels and subsequent activation of downstream molecules. Simultaneously, we demonstrated that NPTN induces the expression of proinflammatory cytokines via the TRAF6-NF-κB axis in β cells. Additionally, NPTN deficiency conferred resistance to STZ-induced diabetic phenotypes. Finally, exogenous MANF treatment in islets or β cells led to similar phenotypes as those observed in NPTN-deficient models. These results indicate that NPTN plays important roles in the regulation of insulin secretion, proliferation, and mitochondrial quantity, as well as pro-inflammatory responses, which are antagonized by MANF treatment. Thus, targeting the MANF-NPTN interaction may lead to a novel treatment for improving β cell functions in diabetes mellitus.

Significance statement

Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-resident small secretory protein that has the potential as therapeutic agent for various diseases related to inflammation and ER stress, such as Type 1 diabetes mellitus. Our work shed light on the roles of a binding partner protein of MANF, Neuroplastin (NPTN), in pancreatic β cells. We demonstrated NPTN regulates Ca2+dynamics as well as inflammation in pancreatic β cells. NPTN deficiency caused improved insulin secretion as well as the resistance to Type 1 diabetic phenotypes. We also found out that MANF treatment leads to similar phenotypes observed in NPTN deficient models through antagonizing NPTN’s functions. Overall, our results provide a new insight into treatment for improving β cell functions in diabetes mellitus.
Nuclear Lipid Droplets Exit to the Cytoplasm: A Novel Mechanism of non-nuclear pore-dependent material exchange
Authors: Jin Yi , Huang Jin , Zhao Zichen , Tan Yanjie , Wu Jian , Ren Zhuqing
Published: September 2023

In cellular biology, the extrusion of large molecular complexes from the nucleus has consistently represented a considerable challenge. In this investigation, we reveal a hitherto unexplored mechanism facilitating the efflux of nuclear lipid droplets (nLDs) from the nucleus directly into the cytoplasm, a process integral to comprehending cellular processes and nuclear dynamics. Through high-throughput sequencing, immunoprecipitation, and immunofluorescence experimentation, we demonstrated that the type I nucleoplasmic reticulum engages with nLDs, enabling the dynamic protein Rab8a’s transfer to the nLDs and fostering their translocation to the nuclear membrane. Phosphorylation of LMNA/C at the S392 site, adjacent to the nLD-nuclear membrane contact site, induces local depolymerization of lamins, creating an aperture that enables gradual nuclear exit of nLDs. Following this, nLDs, carrying DNA fragments, are released into the cytoplasm through budding and subsequently undergo autophagy-mediated degradation. Furthermore, we demonstrate that RhoA-PKC signaling enhances nLD movement and LMNA/C phosphorylation, while its inhibition impedes nuclear nLD efflux. Our groundbreaking investigation illuminates non-nuclear pore-dependent mechanisms of material exchange and offers fresh perspectives on nuclear metabolic pathways.

In Brief

In this study, Jin et al. elucidate a novel mechanism for the expulsion of nuclear lipid droplets (nLDs) from the nucleus. They demonstrate that the activation of RhoA within the nucleus recruits Rab8a to the surface of nLDs. Concurrently, PKC phosphorylation triggers the phosphorylation of LMNA/C at the S392 site, leading to a localized depolymerization of lamins. This creates an aperture that allows for the gradual exit of nLDs from the nucleus. The efflux process of nLDs involves three sequential steps: rupture of the nuclear fibril layer, fusion of nLDs with the inner nuclear membrane (INM), and subsequent fusion with the outer nuclear membrane (ONM). This enables nLDs to enter the cytoplasm, shedding light on a previously unknown process of large molecular entity expulsion from the nucleus.
Molecular model of a bacterial flagellar motorin situreveals a “parts-list” of protein adaptations to increase torque
Authors: Drobnič Tina , Cohen Eli J. , Calcraft Tom , Alzheimer Mona , Froschauer Kathrin , Svensson Sarah , Hoffmann William H. , Singh Nanki , Garg Sriram G. , Henderson Louie , Umrekar Trishant R. , Nans Andrea , Ribardo Deborah , Pedaci Francesco , Nord Ashley L. , Hochberg Georg K. A. , Hendrixson David R. , Sharma Cynthia M. , Rosenthal Peter B. , Beeby Morgan
Published: September 2023

One hurdle to understanding how molecular machines work, and how they evolve, is our inability to see their structuresin situ. Here we describe a minicell system that enablesin situcryogenic electron microscopy imaging and single particle analysis to investigate the structure of an iconic molecular machine, the bacterial flagellar motor, which spins a helical propeller for propulsion. We determine the structure of the high-torqueCampylobacter jejunimotorin situ,including the subnanometre-resolution structure of the periplasmic scaffold, an adaptation essential to high torque. Our structure enables identification of new proteins, and interpretation with molecular models highlights origins of new components, reveals modifications of the conserved motor core, and explain how these structures both template a wider ring of motor proteins, and buttress the motor during swimming reversals. We also acquire insights into universal principles of flagellar torque generation. This approach is broadly applicable to other membrane-residing bacterial molecular machines complexes.
Differential Carbonic Anhydrase Activities Control EBV-Induced B-Cell Transformation and Lytic Cycle Reactivation
Authors: Malik Samaresh , Biswas Joyanta , Sarkar Purandar , Nag Subhadeep , Gain Chandrima , Roy Shatadru Ghosh , Bhattacharya Bireswar , Ghosh Dipanjan , Saha Abhik
Published: September 2023

Epstein-Barr virus (EBV) contributes to ∼1% of all human cancers including several B-cell neoplasms. A characteristic feature of EBV life cycle is its ability to transform metabolically quiescent B-lymphocytes into hyperproliferating B-cell blasts with the establishment of viral latency, while intermittent lytic cycle induction is necessary for the production of progeny virus. Our RNA-Seq analyses of both latently infected naïve B-lymphocytes and transformed B-lymphocytes upon lytic cycle replication indicate a contrasting expression pattern of a membrane-associated carbonic anhydrase isoform CA9, an essential component for maintaining cell acid-base homeostasis. We show that while CA9 expression is transcriptionally activated during latent infection model, lytic cycle replication restrains its expression. Pharmacological inhibition of CA-activity using specific inhibitors retards EBV induced B-cell transformation, inhibits B-cells outgrowth and colony formation ability of transformed B-lymphocytes through lowering the intracellular pH, induction of cell apoptosis and facilitating degradation of CA9 transcripts. Reanalyses of ChIP-Seq data along with utilization of EBNA2 knockout virus and sh-RNA mediated knockdown of CA9 expression we further demonstrate that EBNA2 mediated CA9 transcriptional activation is essential for EBV latently infected B-cell survival. In contrast, during lytic cycle reactivation CA9 expression is transcriptionally suppressed by the key EBV lytic cycle transactivator, BZLF1 through its transactivation domain. Overall, our study highlights the dynamic alterations of CA9 expression and its activity in regulating pH homeostasis act as one of the major drivers for EBV induced B-cell transformation and subsequent B-cell lymphomagenesis.
Poke And Delayed Drink Intertemporal Choice Task (POKE-ADDICT): an open-source behavioral apparatus for intertemporal choice testing in rodents
Authors: Moro Andrea Stefano , Saccenti Daniele , Seccia Alessia , Ferro A Mattia , Malgaroli Antonio , Lamanna Jacopo
Published: September 2023

Advancements in neuroscience research present opportunities and challenges, requiring substantial resources and funding. To address this, we describe here “Poke And Delayed Drink Intertemporal Choice Task (POKE-ADDICT)”, an open-source, versatile, and cost-effective apparatus for intertemporal choice testing in rodents. This allows quantification of delay discounting (DD), a cross-species phenomenon observed in decision making which provides valuable insights into higher-order cognitive functioning. In DD, the subjective value of a delayed reward is reduced as a function of the delay for its receipt. Using our apparatus, we implemented an effective intertemporal choice paradigm for the quantification of DD based on an adjusting delayed amount (ADA) algorithm using mango juice as a reward. Our paradigm requires limited training and can be directly translated to human subjects using monetary rewards. Our apparatus comprises a few 3D-printed parts and inexpensive electrical components, including a Raspberry Pi control unit. Furthermore, it is compatible with severalin vivoprocedures and the use of nose pokes instead of levers allows for faster task learning. Beside the main application described here, the apparatus can be further extended to implement other behavioral tests and protocols, including standard operant conditioning. In conclusion, we describe a versatile and cost-effective design based on Raspberry Pi that can support research in animal behavior, decision making and, more specifically, delay discounting.
Unveiling the ecology, taxonomy and metabolic capabilities of MBA03, a potential key player in anaerobic digestion
Authors: Puchol-Royo Roser , Pascual Javier , Ortega-Legarreta Asier , Otto Pascal , Tideman Jeroen , de Vries Sjoerd-Jan , Abendroth Christian , Tanner Kristie , Porcar Manuel , Latorre-Perez Adriel
Published: September 2023

Biogas, a mix of CO2, CH4and small proportions of other gases, is a biofuel obtained by anaerobic digestion (AD). Biogas production is often considered a black box process, as the role and dynamics of some of the microorganisms involved remain undisclosed. Previous metataxonomic studies in the frame of the MICRO4BIOGAS project (www.micro4biogas.eu) revealed that MBA03, an uncharacterised and uncultured bacterial taxon, was very prevalent and abundant in industrial full-scale AD plants. Surprisingly, no culturable specimen or genome of this taxon has ever been reported, so its role in AD has remained unclear. In the present work, thirty samples derived from anaerobic digesters were sequenced, allowing the reconstruction of 108 metagenome-assembled genomes (MAGs) potentially belonging to MBA03. According to phylogenetic analyses and genomic similarity indices, MBA03 constitutes a new bacterial order, proposed asDarwinibacterialesord. nov., which includesDarwinibacter acetoxidansgen. nov., sp. nov. of the familyDarwinibacteriaceaefam. nov., along withWallacebacter crypticagen. nov., sp. nov. of theWallacebacteriaceaefam. nov. Ecotaxonomic studies determined that AD processes are the main ecological niche ofDarwinibacteriales. Moreover, metabolic predictions identifiedDarwinibacteraceaemembers as putative syntrophic acetate oxidising bacteria (SAOB), as they encode for the reversed Wood-Ljungdahl (W-L) pathway coupled to the glycine cleavage system. This suggests thatDarwinibacteraceaemembers work in collaboration with hydrogenotrophic archaea to produce methane in industrial biogas plants. Overall, our findings presentDarwinibacterialesas a potential key player in anaerobic digestion and pave the way towards the complete characterisation of this newly described bacterial taxa.
Automated workflow for BioID improves reproducibility and identification of protein-protein interactions
Authors: Cirri Emilio , Knaudt Hannah , Fraia Domenico Di , Pömpner Nadine , Rahnis Norman , Heinze Ivonne , Ori Alessandro , Dau Therese
Published: September 2023

Proximity dependent biotinylation is an important method to study protein-protein interactions in cells, for which an expanding number of applications has been proposed. The laborious and time consuming sample processing has limited project sizes so far. Here, we introduce an automated workflow on a liquid handler to process up to 96 samples at a time. The automation does not only allow higher sample numbers to be processed in parallel, but also improves reproducibility and lowers the minimal sample input. Furthermore, we combined automated sample processing with shorter liquid chromatography gradients and data-independent acquisition to increase analysis throughput and enable reproducible protein quantitation across a large number of samples. We successfully applied this workflow to optimise the detection of proteasome substrates by proximity-dependent labelling.
On Global Brain Reconfiguration after Local Manipulations
Authors: Rabuffo Giovanni , Lokossou Houefa-Armelle , Li Zengmin , Ziaee-Mehr Abolfazl , Hashemi Meysam , Quilichini Pascale P , Ghestem Antoine , Arab Ouafae , Esclapez Monique , Verma Parul , Raj Ashish , Gozzi Alessandro , Sorrentino Pierpaolo , Chuang Kai-Hsiang , Perles-Barbacaru Teodora-Adriana , Viola Angèele , Jirsa Viktor K. , Bernard Christophe
Published: September 2023

Understanding how localized brain interventions translate into whole-brain dynamics is crucial for deciphering neural function and tailoring therapeutic strategies. Combining mouse experimental datasets of focal interventions (thalamic lesion and chemogenetic silencing of cortical hubs), we demonstrate both local and global effects. Using whole-brain simulations of experimental data, we not only confirm the distributed nature of local manipulations but also offer mechanistic insights into these processes. Our simulations predict specific alterations in firing rates and spectral characteristics across specific brain networks, leading to structured changes in functional connectivity patterns. Some of these predictions have been empirically validated. Notably, the affected brain subnetworks—and their resultant ‘signatures’ of change—are contingent on the original intervention site, suggesting a method to accurately localize the source of alteration. Our results provide a general framework for interpreting localized intervention effects, offering insights that could refine clinical interventions for focal brain disorders by enabling targeted circuit-level neuromodulation strategies.
Unsupervised identification of internal perceptual states influencing psychomotor performance
Authors: Vardal Ozan , Karapanagiotidis Theodoros , Stafford Tom , Drachen Anders , Wade Alex R.
Published: September 2023

Abstract

When humans perform repetitive tasks over long periods, their performance is not constant. People may drift in and out of states that might be loosely categorised as engagement, disengagement or ‘flow’ and these will be reflected in multiple aspects of their performance (for example, reaction time, accuracy, criteria shifts and potentially longer-term strategy) but until recently it has been challenging to relate these behavioural states to the underlying neural mechanisms that generate them. Here, we took Magnetoencephalograpy recordings of participants performing an engaging task that required rapid, strategic behavioural responses. In this way we acquired both high density neural data and contemporaneous, dense behavioural data. Specifically, participants played a laboratory version of Tetris which collects detailed recordings of player input and game-state throughout performance. We asked whether it was possible to infer the presence of distinct behavioural states from the behavioural data and, if so, whether these states would have distinct neural correlates. We used hidden Markov modelling to segment the behavioural time series into states with unique behavioural signatures, finding that we could identify three distinct and robust behavioural states. We then computed occipital alpha power across each state. These within-participant differences in alpha power were statistically significant, suggesting that individuals shift between behaviourally and neurally distinct states during complex performance, and that visuo-spatial attention change across these states.