Biology subjects

Roy, M.

Publications and source records attributed to Roy, M..

At least 19 recordsLinked to original sources

bioRxiv2026

A comprehensive physiological dataset of pain and aversive modalities for pain biomarkers research

While progress has been made in identifying pain biomarkers using neuroimaging, the development of reliable EEG-based biomarkers remains challenging, limited by small sample sizes and the lack of adequate control conditions. We present a comprehensive dataset from 125 pain-free adults, comprising electroencephalogram (EEG) recordings, and behavioural, sociodemographic, and psychological data. Galvanic skin response and electrocardiogram data were also recorded in a subset of participants (n = 76). Participants received two sustained painful stimulations (thermal, chemical) and two sustained aversive non-painful stimulations (auditory, taste), each delivered twice (with and without continuous intensity ratings). Data are provided in Brain Imaging Data Structure format, where all physiological, stimulus-related, and behavioural data are synchronized within the EEG data files for easy access and analysis. Technical validation confirmed data integrity, with spectral and physiological analyses showing responses associated with stimulus intensity and subjective pain/unpleasantness levels. By providing multimodal physiological data across painful and non-painful aversive conditions, this initiative represents a valuable resource for developing or validating biomarkers and exploring the multidimensional nature of pain perception.

neuroscience↗

bioRxiv2026

Thioesterase modulates antibacterial Type VI secretion system via alteration in oxidative stress responses in Burkholderia

Bacteria utilize specialized protein secretion systems, particularly the type VI secretion system (T6SS), to dominate interbacterial competitions and kill the prey bacteria in a contact-dependent manner. Here, we report that disruption of the thioesterase gene encoded in the gramibactin (a bacterial siderophore) biosynthetic gene cluster activates the T6SS in the Burkholderia gladioli strain NGJ1, even in the absence of prey. The thioesterase mutant exhibits enhanced antibacterial activity, and ectopic expression of the gene complements the phenotype. Notably, thio mutant as well as thioesterase-complement strains show enhanced sensitivity to oxidative stress. The qRT-PCR analysis showed that the thio mutant had upregulated expression of RpoN1, a sigma factor, which positively regulates T6SS functions. We demonstrate that rpoN1 mutant is hypersensitive to oxidative stress and defective in T6SS activation, whereas overexpression of RpoN1 enhances oxidative stress tolerance in NGJ1 and activates T6SS. We propose that, during interbacterial conflicts encountered during plant colonization, NGJ1 faces an oxidative-stress-enriched environment that modulates thioesterase expression, induces RpoN1, and activates T6SS. Overall, our study exemplifies the broader physiological role of Thioesterase in maintaining intracellular ROS homeostasis in bacteria and stimulating antibacterial activity.

microbiology↗

bioRxiv2026

Long-read, whole-genome sequencing and chemotherapy response of two patient-derived organoids from a TP53- and KRAS-mutant ovarian carcinoma

Patient-derived organoids (PDOs) have transformed translational cancer research, allowing tractable models that better represent clinical features than traditional immortalized cell lines. Here we describe two PDOs with differential responses to carboplatin derived from sequential ascites fluid collections from a patient with high-grade mullerian carcinoma, that could not be further subclassified on the omental biopsy. Uterine origin was clinically excluded by pelvic imaging/CT scan of the uterus and absence of vaginal bleeding. Successful derivation from independent collections enabled comparison of intra-patient heterogeneity across sequential ascites samples and demonstrates that PDO efficiency rate is at least partly patient-specific or tumor-dependent. We performed long-read whole genome sequencing on the two PDOs, OC104 and OC109, to better characterize the structural variant landscape while also obtaining information on single nucleotide variants and DNA methylation. In addition to confirming single nucleotide variants noted in clinical sequencing (TP53, KRAS, SPOP, PPP2R1A, KMT2D), we identified additional variants in TSC2, NCOR2, and CTNNA2 that are predicted to be likely pathogenic. The spectrum of mutations, particularly the coincident KRAS and TP53, highlighted unexpected overlap with ovarian mucinous carcinoma. We also identified larger insertions and deletions that result in non-synonymous variants in MUC5AC, TPRX1, and BMX, as well as four translocation events, including two that could not have been resolved with short-read sequencing. Differentially methylated promoters between the two PDOs include 201 oncogenes and tumor suppressor genes, with HNF1A, MSI2, and SETBP1 having methylation directions consistent with these genes roles in platinum response differences observed between the PDOs. Notably, the clonal nature of PDOs produced from two samples taken one week apart is important for the field to appreciate, particularly since they have clonal differences in platinum response. The temporal differences in clonality may indicate a limitation of low volume sampling, however may provide opportunity to longitudinally predict clinical outcomes. We also demonstrate the ability of long-read sequencing to add detail into the genomics and epigenetics of ovarian cancer.

cancer biology↗

bioRxiv2026

Increased perceived effort during contralateral thermal heat pain is not explained by increased intracortical and corticospinal inhibition.

BackgroundPain influences motor function and has been proposed to reduce corticospinal and intracortical excitability. At the same time, performance can be maintained during pain, at the cost of increased perceived effort, a centrally generated signal reflecting resource engagement. Here, we tested whether contralateral thermal heat pain-related changes in corticospinal and intracortical excitability contribute to increased effort perception. MethodsIn this preregistered transcranial magnetic stimulation (TMS) study, twenty-one healthy participants received single and paired pulse TMS at rest and during submaximal isometric right wrist flexions performed at 20% maximal peak force. Trials were conducted under a control condition or during contralateral thermal stimulation (painful or non-painful warm) applied to the left forearm. After each contraction, participants rated the intensity of their perceived effort. Corticospinal and intracortical excitability of the right wrist flexor was assessed at rest and during submaximal contractions. ResultsContralateral heat pain significantly increased perceived effort compared with the control and warm conditions. Contralateral heat pain did not reduce corticospinal or intracortical excitability. Conversely, contralateral heat pain increased corticospinal excitability, reflected primarily in decreased cortical silent period duration. Perceived effort was associated with the subjective experience of pain rather than with TMS-derived variables. ConclusionsThese findings suggest that increased effort during contralateral heat pain cannot be attributed to inhibition of the primary motor cortex or the corticospinal pathway. The higher perceived effort in the presence of contralateral heat pain likely reflects the cognitive cost of pain rather than alterations in the transmission of the motor command.

neuroscience↗

bioRxiv2026

RNA Organelles in DNA-based Artificial Cells Provide Spatial Aptamer Functions and Enhanced Signal Processing

Naturally occurring biomolecular condensates orchestrate key cellular processes by creating spatially distinct reaction environments, yet engineering synthetic condensates that combine structural programmability with spatioselectively encoded function remains challenging. Here we report multiphase DNA-RNA artificial cells (ACs) that embed functional RNA condensates as organelle-like compartments within programmable DNA core-shell ACs. A single thermal assembly protocol yields three-phase ACs comprising a glassy RNA core organelle embedded in a liquid-like DNA compartment, surrounded by a crosslinked DNA shell. The RNA organelles contain aptamer function, enabling selective protein recruitment and small-molecule activation, while the DNA scaffold provides independent addressability, regulates RNA-condensate size and enhances resistance to serum-mediated degradation. We further show that RNA chemistry can be used to adjust environmental responsiveness: unmodified RNA organelles undergo rapid degradation in serum and release captured protein cargo, whereas 2'-fluoro-modified RNA organelles remain stable for at least 24 h. Finally, by coupling transcriptional modules localized in the DNA core to cell-free protein translation in the surrounding medium, we establish sender-receiver communication between AC populations and self-actuating signal processing within individual DNA-RNA ACs. These results establish hybrid nucleic-acid ACs as programmable, spatially organized systems that couple compartment architecture, RNA molecular recognition and biochemical communication. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/733869v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@23ee9org.highwire.dtl.DTLVardef@1706336org.highwire.dtl.DTLVardef@181a241org.highwire.dtl.DTLVardef@1c374d8_HPS_FORMAT_FIGEXP M_FIG C_FIG Multiphase DNA-RNA artificial cells integrate a protective DNA shell, a transcriptionally active DNA core, and a functional RNA organelle. Spatial compartmentalization enables signal generation, external protein expression, and selective recapture via RNA aptamers.

Synthetic Biology↗

bioRxiv2026

Facing pain is effortful: key role of the supplementary motor area and anterior midcingulate cortex

Pain captures attention and interferes with executive and motor processes. In the presence of pain, increasing effort may represent a compensatory mechanism to counteract pain-related disruption and maintain task performance. In this preregistered fMRI study, we investigated neural mechanisms underlying preserved task performance during pain and increased perceived effort. Forty right-handed participants performed a visuomotor force-matching task consisting of isometric handgrip contractions at a low and high force levels under individually calibrated painful or non-painful thermal stimulation. Thermal stimulation was applied to the left forearm, and participants rated the intensity of perceived effort after each isometric contraction. Maintaining task performance under pain was associated with increased perceived effort and recruited brain regions involved in pain modulation and cognitive control. Region-of-interest analysis showed perceived effort was consistently linked to decreased anterior midcingulate cortex activity, whereas supplementary motor area contributions varied depending on its role in motor execution or pain processing. Across experimental condition, motor, pain-modulatory and cognitive-control regions were associated with effort perception. Independently of condition, effort perception was modulated by ventromedial prefrontal cortex and ventral striatum. These findings indicate that effort perception is a complex phenomenon reflecting brain activity within areas involved in motor, executive and valuation processes. Significance StatementThis study advances our understanding of the neural mechanisms underlying task performance under pain and increased effort perception. Brain activity was measured during a visuomotor force-matching task performed in the presence or absence of pain. By contrasting task-related activity between painful and non-painful conditions, we identified regions associated with cognitive control and pain modulation involved in preserving task performance under pain. By correlating activity in regions of interest with ratings of perceived effort, we demonstrated the involvement of the supplementary motor area and midcingulate cortex in effort perception. These findings suggest that additional neural resources are recruited to maintain performance during pain and that the supplementary motor area and midcingulate cortex contribute to heightening the effort experienced.

neuroscience↗

bioRxiv2026

Maintaining performance under pain is effortful: experimental and computational evidence

Pain creates a competing demand on attention, though its impact on performance remains debated. Motivational intensity theory predicts that resource reallocation can preserve output until motivational or capacity limits are reached. Forty adults took part in two preregistered experiments. They completed parallel cognitive (choice reaction, n=20) and motor (isometric hand grip, n=20) tasks at three difficulty levels while receiving warm, low, or high pain heat stimulation on the opposite forearm. Across both domains, participants maintained performance despite painful stimulation. This preservation, however, relied on increased effort mobilization: perceived effort rose with pain intensity, while pain perception decreased during motor and cognitive task execution. Trial wise computational modelling revealed that perceived effort was better predicted by subjective pain experience than by stimulus temperature, supporting a compensatory regulatory mechanism. Thus, maintained performance under pain reflects active resource allocation via effort, generalizable across cognitive and motor domains, but achieved at the cost of increased perceived effort.

neuroscience↗

bioRxiv2026

Early Colonic and Microbial Responses Precede Hyperphagia in Short Bowel Syndrome: Insights from a Rat Model

BackgroundShort bowel syndrome (SBS) resulting from extensive small bowel resection is characterized by severe malabsorption and represents the leading cause of intestinal failure. Although spontaneous intestinal adaptation can partially restore nutrient absorption, the temporal coordination and hierarchy of the adaptive mechanisms involved--particularly those linking the gut microbiota, enteroendocrine function, hyperphagia, and intestinal remodeling-- remain incompletely understood. MethodsWe investigated the kinetics of spontaneous intestinal adaptation in a rat model mimicking type 2 SBS over a 28-day postoperative period. Body weight, food intake, gastrointestinal transit, fecal losses, intestinal morphology, enteroendocrine hormone secretion, hypothalamic neuropeptide expression, and gut microbiota composition were assessed longitudinally in SBS and SHAM-operated rats. ResultsExtensive small bowel resection induced marked early weight loss, accelerated intestinal transit, diarrhea, and increased fecal energy losses that persisted throughout the follow-up. Profound gut microbiota remodeling occurred as early as day 7, remained largely stable thereafter, and was characterized by reduced diversity and enrichment in Lactobacillaceae and Enterobacteriaceae. Early elongation of remaining colon and epithelial remodeling were observed, preceding the jejunal hyperplasia, which became evident from day 14 onward. Enteroendocrine adaptation was marked by an early increase in plasma peptide YY levels, whereas glucagon-like peptide-1 showed a modest response. Food intake was increased in SBS rats from day 7 onward, and hyperphagia developed gradually and reached a plateau by the end of the third postoperative week, in parallel with increased hypothalamic AgRP levels and reduced POMC levels. No significant improvement of intestinal transit and fecal energy losses was observed during the study period. ConclusionIntestinal adaptation to extensive resection follows a time-dependent sequence in which early gut microbiota remodeling and colonic adaptation precede hyperphagia and small intestinal remodeling. These findings highlight the gut microbiota and the colon as central components of the early post-resection adaptation and potential therapeutic targets in SBS.

pathology↗

bioRxiv2025

Colitis-primed circulating T cells drive small intestinal barrier function through Nod2, microbiota and myosin light chain kinase-dependent mechanisms

Inflammatory bowel diseases (IBD), including Crohns disease (CD) and ulcerative colitis (UC), are characterized by intestinal inflammation and barrier dysfunction. While disruption of the intestinal barrier contributes to the pathogenesis of IBD, yet how colonic inflammation alters small intestinal homeostasis remains poorly defined. Here, we demonstrate that three models of colitis, including 2,4,6-Trinitrobenzenesulfonic acid (TNBS), Dextran Sulfate Sodium (DSS), and oxazolone, induce paracellular barrier dysfunction in the small intestine, with model-specific immune profiles. Th1/Th17-skewed responses (TNBS and DSS) were associated with microbiota-dependent upregulation of myosin light chain kinase (MLCK), ROR{gamma}t CD4 T cell expansion, and elevated expression of Nod2, which was not observed under Th2-dominant (oxazolone) conditions. Inhibition of MLCK restored barrier function and suppressed inflammation in a CD4 T cell-dependent manner. Using Nod2-deficient and 2939insC mutant mice, we showed Nod2 as a critical regulator of small intestinal permeability during colitis. Bone marrow chimeras revealed compartment-specific roles of Nod2, with non-hematopoietic Nod2 sufficient to preserve epithelial integrity, while hematopoietic Nod2 expression is required to limit cytokine-mediated inflammation. Moreover, MLCK inhibition ameliorated intestinal lesions only in mice with Nod2 deficiency in the hematopoietic compartment. Finally, microbiota transfer experiments ruled out a causal role for dysbiosis in driving small intestinal permeability defects in Nod2-deficient mice. These findings uncover a Nod2-MLCK-CD4 T cell axis linking colonic inflammation to small intestinal barrier dysfunction and highlight distinct immune-epithelial-microbial mechanisms shaping intestinal homeostasis during colitis. Graphical AbstractCirculating ROR{gamma}t Foxp3- CD4 T cells from mice with TNBS- or DSS-induced colitis increase small intestinal permeability by promoting cytokine secretion that enhances MLCK activity. This effect is attenuated by Nod2 activation. Specifically, Nod2 expression in hematopoietic cells reduces cytokine secretion and permeability, while activation of Nod2 in non-hematopoietic cells alone is sufficient to prevent increased permeability by directly regulating MLCK activity, independently of cytokine influence. Moreover, the absence of Nod2 is associated with inflammatory lesions in the small intestine of TNBS-treated mice.

immunology↗

bioRxiv2025

Accurate PROTAC targeted degradation prediction with DegradeMaster

MotivationProteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that can degrade undruggable protein of interest (POI) by recruiting E3 ligases and hijacking the ubiquitin-proteasome system. Some efforts have been made to develop deep learning-based approaches to predict the degradation ability of a given PROTAC. However, existing deep learning methods either simplify proteins and PROTACs as 2D graphs by disregarding crucial 3D spatial information or exclusively rely on limited labels for supervised learning without considering the abundant information from unlabeled data. Nevertheless, considering the potential to accelerate drug discovery, it is critical to develop more accurate computational methods for PROTAC-targeted protein degradation prediction. ResultsThis study proposes DegradeMaster, a semi-supervised E(3)-equivariant graph neural network-based predictor for targeted degradation prediction of PROTACs. DegradeMaster leverages an E(3)-equivariant graph encoder to incorporate 3D geometric constraints into the molecular representations and utilises a memory-based pseudo-labeling strategy to enrich annotated data during training. A mutual attention pooling module is also designed for interpretable graph representation. Experiments on both supervised and semi-supervised PROTAC datasets demonstrate that DegradeMaster outperforms state-of-the-art baselines, with substantial improvement of AUROC by 10.5%. Case studies show DegradeMaster achieves 88.33% and 77.78% accuracy in predicting the degradability of VZ185 candidates on BRD9 and ACBI3 on KRAS mutants. Visualization of attention weights on 3D molecule graph demonstrates that DegradeMaster recognises linking and binding regions of warhead and E3 ligands and emphasizes the importance of structural information in these areas for degradation prediction. Together, this shows the potential for cutting-edge tools to highlight functional PROTAC components, thereby accelerating novel compound generation. AvailabilityThe source code and datasets are available at https://github.com/Jackson117/DegradeMaster and https://zenodo.org/records/14715718.

bioinformatics↗

bioRxiv2024

Comparative analysis of dietary iron deprivation and supplementation in a murine model of colitis

Inflammatory bowel diseases are chronic inflammatory conditions with growing prevalence in western populations. Iron is an essential component of erythrocytes hemoglobin. Under the influence of elevated hepcidin production, iron is sequestered in cells during inflammation which, in turn, leads to iron restriction for red blood cells synthesis. As a consequence, iron deficiency and anemia of inflammation are the most prevalent extraintestinal complications in IBD patients. Patients are thus treated with oral iron supplements that have limited efficacy as iron absorption is blunted during intestinal inflammation. Moreover, iron supplementation can cause intestinal complications and previous studies have shown that iron supplementation worsens the inflammatory response. However, a comparative analysis of the effects of low, adequate and high dietary iron content matching iron the supplementation given to patients has not been performed in mice. We therefore tested the impact of dietary iron deprivation and supplementation in a murine model of colitis induced by dextran sodium sulfate. We found that both dietary iron deprivation and supplementation were accompanied by a more severe inflammation with earlier signs of gastrointestinal bleeding compared to mice fed an iron adequate diet. The manipulation of dietary iron led to a comparable oxidative stress and a pronounced dysbiosis in the colon of control mice that differed depending on the dietary iron content. Analysis of these dysbiosis is in line with a pronounced susceptibility to colonic inflammation thus questioning the benefit/risk balance of oral iron supplementation for IBD patients.

pathology↗

bioRxiv2024

Two strains of Toscana virus show different virulence and replication capacity in mice and cell culture models

Toscana virus (TOSV), belonging to Phenuiviridae family, is circulating in most Mediterranean countries and is transmitted to humans by infected female sand flies. While most infections are asymptomatic, TOSV is considered as a leading cause of meningitis and encephalitis in humans during summer. Three TOSV genotypes (named A, B, and C) have been identified, although no virus strain belonging to lineage C has been isolated so far. To date, the relationship between TOSV genetic diversity and viral pathogenicity or replication capacity remains unknown. This study aimed to compare two TOSV strains from either lineage A (TOSV-A) or B (TOSV-B) in several cell culture and two mouse models. We showed that TOSV-A replicated more efficiently in BSR and A549 cells while TOSV-B had a replication advantage in human induced pluripotent stem cells differentiated in neural cells and LL-5 sand fly cells. In vivo, we were unable to detect any virus in the brains of immunocompetent C57BL/6JRj mice infected with either strain of TOSV. On the contrary, we showed that TOSV-A disseminated to the central nervous system of 129/Sv ifnar -/- mice unlike TOSV-B, despite higher viremia of TOSV-B and a greater dissemination of this strain in other organs. The reasons for these differences are not yet known, although we showed that the presence of TOSV neutralizing antibodies in serum was slightly delayed in TOSV-A-infected mice. Altogether, the data presented in this study provide new avenues to study TOSV-induced pathogenesis and ultimately unveil molecular viral determinants modulating TOSV replication capacity. Author SummaryToscana virus is a sand fly-borne phlebovirus with tropism for the human central nervous system (CNS) and the causal agent of aseptic meningitis and encephalitis during summer in countries surrounding the Mediterranean Sea. The pathogenesis induced by TOSV is still poorly understood as well as the correlation between TOSV genetic diversity and viral pathogenicity or replication capacity. In this study, we characterised two TOSV strains belonging to two different genetic lineages (named A and B) in several in vitro, ex vivo and in vivo models of infection. We showed that the biological properties of these two strains is strikingly different and, importantly, we identified 129/Sv ifnar -/- mice as a suitable model to study the mechanism of TOSV invasion of the CNS and viral pathogenesis. Our comparative study also highlights the importance of strengthening our efforts to identify molecular viral determinants modulating TOSV-induced pathogenesis and vector transmission, in order to better characterise the epidemiological risk posed by circulating strains.

microbiology↗

bioRxiv2024

Proteostasis and metabolic dysfunction in a distinct subset of storage-induced senescent erythrocytes targeted for clearance

Although refrigerated storage slows the metabolism of volunteer donor RBCs, cellular aging still occurs throughout this in vitro process, which is essential in transfusion medicine. Storage-induced microerythrocytes (SMEs) are morphologically-altered senescent RBCs that accumulate during storage and which are cleared from circulation following transfusion. However, the molecular and cellular alterations that trigger clearance of this RBC subset remain to be identified. Using a staining protocol that sorts long-stored SMEs (i.e., CFSEhigh) and morphologically-normal RBCs (CFSElow), these in vitro aged cells were characterized. Metabolomics analysis identified depletion of energy, lipid-repair, and antioxidant metabolites in CFSEhigh RBCs. By redox proteomics, irreversible protein oxidation primarily affected CFSEhigh RBCs. By proteomics, 96 proteins, mostly in the proteostasis family, had relocated to CFSEhigh RBC membranes. CFSEhigh RBCs exhibited decreased proteasome activity and deformability; increased phosphatidylserine exposure, osmotic fragility, and endothelial cell adherence; and were cleared from the circulation during human spleen ex vivo perfusion. Conversely, molecular, cellular, and circulatory properties of long-stored CFSElow RBCs resembled those of short-stored RBCs. CFSEhigh RBCs are morphologically and metabolically altered, have irreversibly oxidized and membrane-relocated proteins, and exhibit decreased proteasome activity. In vitro aging during storage selectively alters metabolism and proteostasis in SMEs, targeting these senescent cells for clearance.

cell biology↗

bioRxiv2024

Passive infusion of an S2-Stem broadly neutralizing antibody protects against SARS-CoV-2 infection and lower airway inflammation in rhesus macaques

The continued evolution of SARS-CoV-2 variants capable of subverting vaccine and infection-induced immunity suggests the advantage of a broadly protective vaccine against betacoronaviruses ({beta}-CoVs). Recent studies have isolated monoclonal antibodies (mAbs) from SARS-CoV-2 recovered-vaccinated donors capable of neutralizing many variants of SARS-CoV-2 and other {beta}-CoVs. Many of these mAbs target the conserved S2 stem region of the SARS-CoV-2 spike protein, rather the receptor binding domain contained within S1 primarily targeted by current SARS-CoV-2 vaccines. One of these S2-directed mAbs, CC40.8, has demonstrated protective efficacy in small animal models against SARS-CoV-2 challenge. As the next step in the pre-clinical testing of S2-directed antibodies as a strategy to protect from SARS-CoV-2 infection, we evaluated the in vivo efficacy of CC40.8 in a clinically relevant non-human primate model by conducting passive antibody transfer to rhesus macaques (RM) followed by SARS-CoV-2 challenge. CC40.8 mAb was intravenously infused at 10mg/kg, 1mg/kg, or 0.1 mg/kg into groups (n=6) of RM, alongside one group that received a control antibody (PGT121). Viral loads in the lower airway were significantly reduced in animals receiving higher doses of CC40.8. We observed a significant reduction in inflammatory cytokines and macrophages within the lower airway of animals infused with 10mg/kg and 1mg/kg doses of CC40.8. Viral genome sequencing demonstrated a lack of escape mutations in the CC40.8 epitope. Collectively, these data demonstrate the protective efficiency of broadly neutralizing S2-targeting antibodies against SARS-CoV-2 infection within the lower airway while providing critical preclinical work necessary for the development of pan-{beta}-CoV vaccines. AUTHOR SUMMARYIn this study, we explore the development of a broadly protective vaccine against betacoronaviruses ({beta}-CoVs), including SARS-CoV-2. We focused on monoclonal antibodies (mAbs) from individuals who recovered-vaccinated donors capable of neutralizing many variants of SARS-CoV-2 and other {beta}-CoVs. Unlike current vaccines that target the S1 region of the virus, these mAbs target a highly conserved S2 region of the spike protein. One antibody, CC40.8, showed promising results in small animal models. To further test its effectiveness, we infused CC40.8 into rhesus macaques at different doses and then challenged them with SARS-CoV-2. We found that higher doses of CC40.8 significantly reduced viral loads and inflammation in the lower airway. Additionally, there were no escape mutations in the targeted region, suggesting that the virus could not easily evade the antibody. Our findings highlight the potential of S2-targeting antibodies to protect against SARS-CoV-2 and support the development of vaccines that can broadly protect against various {beta}-CoVs. Conflicting InterestsRA, TFR, and DRB are listed as inventors on pending patent applications describing the SARS-CoV-2 and HCoV-HKU1 S cross-reactive antibodies. DRB and RA are listed as inventors on a pending patent application describing the S2 stem epitope immunogens identified in this study. DRB is a consultant for IAVI. All other authors declare that they have no competing interests. ONE SENTENCE SUMMARYPan-beta-coronavirus neutralizing mAb CC40.8 reduces SARS-CoV-2 viral loads and inflammation within the lower airway of infected rhesus macaques and provides pre-clinical support for S2-directed immunization strategies.

immunology↗

bioRxiv2024

Collective responses of flocking sheep to a herding dog

Across taxa, group-living organisms exhibit collective escape responses to stimuli varying from mild stress to predatory pressures. How exactly does information flow among group members leading to a collective escape remains an open question. Here we study the collective responses of a flock of sheep to a shepherd dog in a driving task between well-defined target points. We collected highresolution spatio-temporal data from 14 sheep and the dog, using Ultra Wide Band tags attached to each individual. Through the time delay analysis of velocity correlations, we identify a hierarchy among sheep in terms of directional influence. Notably, the average spatial position of a sheep along the front-back axis of the groups velocity strongly correlates with its impact on the collective movement. Our findings demonstrate that, counter-intuitively, directional information on shorter time scales propagates from the front of the group towards the rear, and that the dog exhibits adaptive movement adjustments in response to the flocks dynamics. Furthermore, we show that a simple shepherding model can capture key features of the collective response of the sheep flocks. In conclusion, our study reveals novel insights on how directional information propagates in escaping animal groups.

animal behavior and cognition↗

bioRxiv2024

Functional diversity in the Hsp60 of Sulfolobus acidocaldarius: mosaic of Group I and Group II chaperonin

External stress can disrupt protein homeostasis in organisms, necessitating the involvement of heat shock proteins (Hsps) to restore equilibrium and ensure survival. Unlike other organisms, the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius lacks Hsp100, Hsp90, and Hsp70, possessing only two small heat shock proteins (Hsp14 and Hsp20) and one group II chaperonin, Hsp60. This raises questions about how protein substrates are protected and transferred to Hsp60 for refolding without other chaperones. Our study focused on ATP-dependent Hsp60 in S. acidocaldarius, revealing its formation of oligomeric structures in the presence of ATP. While ATP hydrolysis is not essential for oligomer formation and lid closure, it is crucial for Hsp60s chaperone activity, effectively folding stress-denatured substrate proteins by stabilizing their folded conformations. The mechanism involves hydrophobic recognition of unfolded substrates, encapsulating and releasing them in a more folded state. Negatively charged inner surface of the ring seems to be responsible for driving the folding of the substrate. Importantly, Hsp14 was found to transfer substrate proteins to Hsp60{beta}, orchestrating their refolding into an active state. Beyond protein folding, Hsp60{beta} protects the membrane under stress, contributing to maintaining membrane rigidity. Hsp60 exhibits nested cooperativity in ATPase activity, adapting to ATP concentration changes and interestingly Hsp60{beta} and Hsp60{beta} complex shows a mosaic behaviour during ATP hydrolysis belonging to both group I and group II chaperonin respectively. In conclusion, our study provides insights into the intricate mechanisms employed by Hsp60 in S. acidocaldarius to maintain protein homeostasis. It offers a comprehensive understanding of Hsp60s role in the heat shock response pathway, shedding light on fundamental cellular processes in extremophilic archaea.

biochemistry↗

bioRxiv2023

Modulating Subjective Pain Perception with Decoded MNI-space Neurofeedback

Pain is a complex emotional experience that still remains challenging to manage. Previous functional magnetic resonance imaging (fMRI) studies have associated pain with distributed patterns of brain activity (i.e., brain decoders), but it is still unclear whether these observations reflect causal mechanisms. To address this question, we devised a new neurofeedback approach leveraging real-time decoding of fMRI data to test if modulating pain-related multivoxel fMRI patterns could lead to changes in subjective pain experience. We first showed that subjective pain ratings can indeed be accurately predicted using a real-time decoding approach based on the stimulus intensity independent pain signature (SIIPS) and the neurologic pain signature (NPS). Next, we trained participants in a double-blinded decoded fMRI neurofeedback experiment to up- or down-regulate the SIIPS. Our results indicate that participants can learn to down-regulate the expression of SIIPS independently from NPS expression. Importantly, the success of this neurofeedback training was associated with the perceived intensity of painful stimulation following the intervention. Taken together, these results indicate that closed-loop brain imaging can be efficiently conducted using a priori fMRI decoders of pain, potentially opening up a new range of applications for decoded neurofeedback, both for clinical and basic science purposes.

neuroscience↗

bioRxiv2023

Efficient Prohibitin 2 exposure during mitophagy depends on Voltage-dependent anion-selective channel protein 1.

Autophagic elimination of depolarized mitochondria (mitophagy) depends on Ubiquitin proteasome complex to expose the inner mitochondrial membrane-resident protein-Prohibitin 2 (PHB2). This uncovering facilitates its interaction with autophagosomal membrane-associated protein LC3. It remains unclear whether PHB2 is uncovered randomly through mitochondrial rupture sites. Prior knowledge and initial screening indicated that Voltage-dependent anion-selective channel protein 1 (VDAC1) might play a role in this process. Through in vitro biochemical assays and imaging, we have found that VDAC1-PHB2 interaction increases during mitochondrial depolarization. Subsequently, this interaction enhances the efficiency of PHB2 exposure and mitophagy. To investigate the relevance in vivo, we utilized a Porin (equivalent to VDAC1) knockout Drosophila line. Our findings demonstrate that during rotenone-induced mitochondrial stress, Porin is essential for PHB2 exposure, PHB2-LC3 interaction, and mitophagy. This study highlights that VDAC1 predominantly synchronizes efficient PHB2 exposure through mitochondrial rupture sites during mitophagy. These findings may provide insights to understand progressive neurodegeneration.

cell biology↗