bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncoupling the CRMP2-CaV2.2 interaction reduces pain-like behavior in a preclinical osteoarthritis model
Authors: Allen Heather N. , Hestehave Sara , Duran Paz , Nelson Tyler S. , Khanna Rajesh
Published: June 2024

Osteoarthritis (OA) represents a significant pain challenge globally, as current treatments are limited and come with substantial and adverse side effects. Voltage-gated calcium channels have proved to be pharmacologically effective targets, with multiple FDA-approved CaV2.2 modulators available for the treatment of pain. Although effective, drugs targeting CaV2.2 are complicated by the same obstacles facing other pain therapeutics-invasive routes of administration, narrow therapeutic windows, side effects, and addiction potential. We have identified a key regulator of CaV2.2 channels, collapsing response mediator protein 2 (CRMP2), that allows us to indirectly regulate CaV2.2 expression and function. We developed a peptidomimetic modulator of CRMP2, CBD3063, that effectively reverses neuropathic and inflammatory pain without negative side effects by reducing membrane expression of CaV2.2. Using a rodent model of OA, we demonstrate the intraperitoneal administration of CBD3063 alleviates both evoked and non-evoked behavioral hallmarks of OA pain. Further, we reveal that CBD3063 reduces OA-induced increased neural activity in the parabrachial nucleus, a key supraspinal site modulating the pain experience. Together, these studies suggest CBD3063 is an effective analgesic for OA pain.
Recycling Materials for Sustainable DNA Origami Manufacturing
Authors: Neuhoff Michael J. , Wang Yuchen , Vantangoli Nicholas J. , Poirier Michael G. , Castro Carlos E. , Pfeifer Wolfgang G.
Published: June 2024

DNA origami nanotechnology has great potential in multiple fields including biomedical, biophysical, and nanofabrication applications. However, current production pipelines lead to single-use devices incorporating a small fraction of initial reactants, resulting in a wasteful manufacturing process. Here, we introduce two complementary approaches to overcome these limitations by recycling the strand components of DNA origami nanostructures (DONs). We demonstrate reprogramming entire DONs into new devices, re-using scaffold strands. We validate this approach by reprogramming DONs with complex geometries into each other, using their distinct geometries to verify successful scaffold recycling. We reprogram one DON into a dynamic structure and show both pristine and recycled structures display similar properties. Second, we demonstrate the recovery of excess staple strands post-assembly and fold DONs with these recycled strands, showing these structures exhibit the expected geometry and dynamic properties. Finally, we demonstrate the combination of both approaches, successfully fabricating DONs solely from recycled DNA components.
Social learning of navigational routes in tandem running acorn ants (Temnothorax nylanderi)
Authors: Colomer-Vilaplana Aina , Williams Tara , Glaser Simone M. , Grüter Christoph
Published: June 2024

Tandem running in ants is a form of social learning that involves an informed leader guiding a naïve nestmate to a valuable resource, such as a nest site or a food source. Little is currently known about what tandem followers learn and how socially acquired navigational information affects future trips. While some studies suggest that tandem followers learn the resource position but not the route taken by the tandem pair to reach the resource, more recent evidence contradicts this view. We studied tandem running in foraging acorn antsTemnothorax nylanderiand provide evidence that tandem followers socially learn routes from their leaders and later use these routes when travelling between their nest and a food source. Followers that became tandem leaders themselves then guided their follower along the same routes in 90% of tandem runs, demonstrating that navigational information can spread in a forager population through sequential social learning. Ants increased their travelling speed, but not path straightness over successive trips. We also found that ants needed less time on subsequent trips if they experienced longer-lasting tandem runs, suggesting that longer lasting tandem runs allow followers to learn routes more efficiently. Adding visual cues did not affect most of the quantified variables, and we currently know little about the cues used byT. nylanderiduring navigation. We discuss how the visual environment inhabited by different species might affect the importance of route learning during tandem running.
Evaluation of the adaptability of cassava genotypes in three different agro-ecological zones of Gabon
Authors: Effa Effa Branly Wilfrid , Moto Rostand Abaga , Zeh Nguema Yves Landry , Ifada Anaclé , Demikoyo Kanghou Dick Sadler , Guibinga Stéphane Mibemu , Akoubou Sidoine , Ngouang Louis Clotaire
Published: June 2024

Cassava is a staple food in over twenty African countries, including Gabon. However, current production cannot meet the needs of the Gabonese people. Studies are being carried out to find ways of increasing national production throughout the country. Our study of sixteen cassava genotypes planted in different agro-ecological zones of Gabon focuses on three quantitative variables: number of lobes per leaf, petiole length and plant height at the vegetative stage. This study was carried out to see which introduced cassava genotypes were adapted to environments with different rainfall levels.
Identification of 5mC within heterogenous tissue usingde-novosomatic mutations
Authors: Wilcox Justin Jon Schader , Foucault Quentin Jean Robert , Gossmann Toni Ingolf
Published: June 2024

Tissues represent a fundamental evolutionary interface at the junction of genotype and phenotype. Indeed, gene regulation often occurs at the tissue level and manifests itself through tissue-specific epigenetic modifications. Studies investigating tissue epigenetics are limited by access to pure tissues. Tissues not only differ epigenetically, they are also subject to genetic differentiation through somatic mutations. As somatic mutations follow predictable patterns of inheritance, the application of population genomic approaches to inter- and intra-tissue variation could allow for the efficient detection of epigenetic modifications, even when tissue samples are convoluted. Here, we present an approach that usesde-novosomatic mutations to deconvolute 5mC methylation patterns through analysis of shifts in tissue-specific allele frequencies. We use simulations and bisulfite sequencing data to show that somatic mutations are common and detectable in next-generation sequencing data. We then use changes in mutation frequencies to accurately derive the proportional tissue of origin along a gradient ofin silicosubsamples of mixed-tissue bisulfite reads. We confirm that mixed tissues bias estimates of methylation levels and prevent detection of methylation differences at high levels of mixture. Our derived estimates of tissue contamination allow for unbiased and accurate deconvolution of mixed-tissue methylations in CpG and non-CpG context. We are ultimately able to recover 15-30% of differentially-methylated sites, and approximately 40-90% of differentially-methylated CpG islands and gene bodies in any cytosine context at contamination levels up to 90%. Our findings highlight the utility of population genomic approaches across scales, and expand the accessibility of epigenetics studies within evolutionary biology.
Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing
Authors: Fendler Nikole L. , Ly Jimmy , Welp Luisa , Urlaub Henning , Vos Seychelle M.
Published: June 2024

The eukaryotic microrchidia (MORC) protein family are DNAgyrase,Hsp90, histidinekinase, MutL(GHKL)-type ATPases involved in gene expression regulation and chromatin compaction. The molecular mechanisms underlying these activities are incompletely understood. Here we studied the full-length human MORC2 protein biochemically. We identified a DNA binding site in the C-terminus of the protein, and we observe that this region is heavily phosphorylated in cells. Phosphorylation of MORC2 reduces its affinity for DNA and appears to exclude the protein from the nucleus. We observe that DNA binding by MORC2 reduces its ATPase activity and that MORC2 can topologically entrap multiple DNA substrates between its N-terminal GHKL and C-terminal coiled coil 3 dimerization domains. Finally, we observe that the MORC2 C-terminal DNA binding region is required for gene silencing in cells. Together, our data provide a model to understand how MORC2 engages with DNA substrates to mediate gene silencing.
Large Language Model Uncertainty Measurement and Calibration for Medical Diagnosis and Treatment
Authors: Savage Thomas , Wang John , Gallo Robert , Boukil Abdessalem , Patel Vishwesh , Ahmad Safavi-Naini Seyed Amir , Soroush Ali , Chen Jonathan H
Published: June 2024

Introduction

The inability of Large Language Models (LLMs) to communicate uncertainty is a significant barrier to their use in medicine. Before LLMs can be integrated into patient care, the field must assess methods to measure uncertainty in ways that are useful to physician-users.

Objective

Evaluate the ability for uncertainty metrics to quantify LLM confidence when performing diagnosis and treatment selection tasks by assessing the properties of discrimination and calibration.

Methods

We examined Confidence Elicitation, Token Level Probability, and Sample Consistency metrics across GPT3.5, GPT4, Llama2 and Llama3. Uncertainty metrics were evaluated against three datasets of open-ended patient scenarios.

Results

Sample Consistency methods outperformed Token Level Probability and Confidence Elicitation methods. Sample Consistency by Sentence Embedding achieved the highest discrimination performance (ROC AUC 0.68–0.79) with poor calibration, while Sample Consistency by GPT Annotation achieved the second-best discrimination (ROC AUC 0.66-0.74) with more accurate calibration. Nearly all uncertainty metrics had better discriminative performance with diagnosis rather than treatment selection questions. Furthermore, verbalized confidence (Confidence Elicitation) was found to consistently over-estimate model confidence.

Conclusions

Sample Consistency is the most effective method for estimating LLM uncertainty of the metrics evaluated. Sample Consistency by Sentence Embedding can effectively estimate uncertainty if the user has a set of reference cases with which to re-calibrate their results, while Sample Consistency by GPT Annotation is more effective method if the user does not have reference cases and requires accurate raw calibration. Our results confirm LLMs are consistently over-confident when verbalizing their confidence through Confidence Elicitation.
Bone marrow S-phase is Associated with Risk assessment and Shows Differential Correlation with levels of CD34+Blasts and CD16−Granulocytes in Patients with Myelodysplastic syndromes
Authors: Azoulay David , Paz Avigail , Stemer Galia
Published: June 2024

Introduction

Including of proliferative parameters in the routine clinical flow-cytometry (FC) workup may be important for better evaluation of prognosis and risk assessment in patients with myelodysplastic syndromes (MDS). However, supportive data are still contradicting.

Aim

To assess the levels of FC based proliferative parameters in patients with MDS using propidium Iodide, and to study their correlation with risk assessment and the incidences of CD34+blasts and CD16-and CD16+granulocytes.

Methods

Data was retrospectively collected and analysed from 40 specimens of bone marrow (BM) aspiration of MDS patients, 14 specimens of hypocellular BM with no evidence of malignancy, and 16 specimens of reactive BM as determined by pathological examination. IPSS-R scores were calculated for MDS patients then divided to high-risk (IPSS-R score >4.5) and low-risk (IPSS-R score <3). The levels of proliferative parameters and their correlation with incidence of CD34+blasts and CD16-and CD16+granulocytes were compared between high and low risk MDS patients.

Results

MDS and reactive BM specimens showed similar whole sample S-phase percentage that was significantly higher than hypocellular BM specimens. As compared to MDS, reactive BM show a greater S-phase percentage in the erythroid fraction. In MDS, the whole sample S-phase percentage was significantly high in a subset of high-risk patients. Increased S-phase percentage in these patients was attributed to high S-phase percentage in granulocytes and monocytes. S-phase percentage correlated with the level of CD34+blasts in the low-risk group but not in the high-risk group. In contrast to CD34+blasts, the S-phase percentage correlated with the level of CD16-granulocytes in the high-risk group but not in the low-risk group.

Conclusions

Our observations confirm the association of increased proliferative parameters and adverse prognosis in MDS, and suggest differential proliferation pattern of CD34+and CD16-granulocytes in low and high-risk MDS patients.
Impact of Effective Refractory Period Personalization on Arrhythmia Vulnerability in Patient-Specific Atrial Computer Models
Authors: Díaz Patricia Martínez , Dasí Albert , Goetz Christian , Unger Laura , Haas Annika , Luik Armin , Rodríguez Blanca , Dössel Olaf , Loewe Axel
Published: June 2024

Background and Aims

The effective refractory period is one of the main electrophysiological properties governing arrhythmia maintenance, yet effective refractory period personalisation is rarely performed when creating patient-specific computer models of the atria to inform clinical decision-making. The aim of this study is to evaluate the impact of incorporating clinical effective refractory period measurements when creatingin silicopersonalised models on arrhythmia vulnerability.

Methods

Clinical effective refractory period measurements were obtained in seven patients from multiple locations in the atria. The atrial geometries from the electroanatomical mapping system were used to generate personalised anatomical atrial models. To reproduce patient-specific refractory period measurements, the Courtemanche cellular model was gradually reparameterised from control conditions to a setup representing atrial fibrillation-induced remodelling. Four different modelling approaches were compared: homogeneous (A), heterogeneous (B), regional (C), and continuous (D) distribution of effective refractory period. The first two configurations were non-personalised based on literature data, the latter two were personalised based on patient measurements. We evaluated the effect of each modelling approach by quantifying arrhythmia vulnerability and tachycardia cycle length. We performed a sensitivity analysis to assess the influence of effective refractory period measurement uncertainty on arrhythmia vulnerability.

Results

The mean vulnerability was 3.4±4.0%, 7.7±3.4%, 9.0±5.1%, 7.0±3.6% for scenarios A to D, respectively. The mean tachycardia cycle length was 167.1±12.6ms, 158.4±27.5ms, 265.2±39.9ms, and 285.9±77.3ms for scenarios A to D, respectively. Incorporating perturbations to the measured effective refractory period in the range of 2, 5, 10 and 20ms, had an impact on the vulnerability of the model of 5.8±2.7%, 6.1±3.5%, 6.9±3.7%, 5.2±3.5%, respectively.

Conclusion

Increased dispersion of the effective refractory period had a greater effect on reentry dynamics than on mean vulnerability values. The incorporation of personalised effective refractory period in the form of gradients had a greater impact on vulnerability than had a homogeneously reduced effective refractory period. Effective refractory period measurement uncertainty up to 20ms slightly influences arrhythmia vulnerability. Electrophysiological personalisation of atrialin silicomodels appears essential and warrants confirmation in larger cohorts.
Socioeconomic Inequalities in the Visual Assessment of Older Adults with Cataracts in Peru
Authors: Intimayta-Escalante Claudio , Vitteri-Soto Gino
Published: June 2024

Introduction

In Peru, one in six adults over 50 years old has cataracts. This proportion increases due to the lack of routine visual assessments among older adults. Therefore, the objective of this research was to evaluate the socioeconomic inequalities in visual assessments among older adults with cataracts in Peru.

Methods

This analytical cross-sectional study was conducted using data from the Demographic and Family Health Survey in Peru from 2013 to 2023. Socioeconomic conditions such as gender, age, educational level, wealth quintile, area or place of residence, health insurance status, and comorbidities were evaluated. Inequalities were estimated using the concentration index (CI) and Erreyger’s modification (ECI).

Results

Of the 6,367 older adults with cataracts included in the study, 93.1% (95%CI: 92.2–93.9) had a visual assessment. The average age of the participants was 76.7 years, with over half of them being women (56.2%). Conditions such as educational level, wealth quintile, area or place of residence, and comorbidities mediated differences in the proportion of adults with cataracts who had visual assessments (p<0.001). Adults without education (ECI: -0.16), residents of rural areas (ECI: -0.41), or those outside Lima (ECI: -0.51) exhibited greater inequalities in receiving visual assessments.

Conclussion

Among older adults with cataracts, living in rural areas or outside Lima and having a low educational level were identified as key factors mediating greater inequality in visual assessments.
Cardiovascular outcomes in adult patients with atrial septal defect: a nationwide population-based study
Authors: Lee Jue Seong , Park Man Young , Jung Jin-Man , Shin Hong Ju
Published: June 2024

Background

The beneficial effects of atrial septal defect (ASD) closure on cardiovascular events and mortality in adults remain undetermined. Therefore, this study aimed to investigate the long-term effects of different ASD closure methods on cardiovascular events in adults.

Methods

A retrospective analysis was conducted using data obtained from the Korean National Health Insurance Service from 2002 to 2020, focusing on patients aged ≥20 years diagnosed with ASD based on the codes provided by the Tenth revision of International Classification of Diseases codes between 2004 and 2015. Participants were categorized into the observation, device closure, and surgery groups. Propensity score matching (PSM) of variables such as sex, age, comorbidities, and medications was employed at a 2:1:1 ratio to mitigate imbalances among the groups. The Cox proportional hazards model was utilized to compare the occurrence of major adverse cardiovascular events (MACE), including stroke, myocardial infarction (MI), coronary revascularization, and all-cause death, and each individual component among the three groups.

Results

In total, 20,643 patients with ASD were included in this study. After PSM, there were 6,636 in the observation group and 3,318 each in the device closure and surgery group. Over a 5-year follow-up period, the adjusted hazard ratios for MACE were significantly lower in the surgery (0.72; 95% CI: 0.66–0.79) and device closure groups (0.85; 95% CI: 0.78–0.92) than in the observation group. Beneficial effects on stroke and all-cause mortality were observed in both intervention groups. Additionally, a beneficial effect on coronary revascularization was observed in the surgery group, whereas the impact on MI was not significantly different between the groups.

Conclusions

ASD closure, whether by surgery or using a device, is associated with a decreased incidence of cardiovascular outcomes in adults. The benefits on cardiovascular outcomes vary with the type of closure method, underscoring the need for a tailored approach to manage ASD in adults.

Clinical Perspectives

What is new?

Compared with no intervention, surgery exhibited a more beneficial effect in terms of MACE, followed by device closure.

Device closure appears to be more beneficial in terms of all-cause death.

Surgery reduced the occurrence of coronary revascularization.

What are the clinical implications?

Cardiovascular preventive effects after ASD closure (through surgery or device) were observed in adult patients with ASD when compared to the untreated individuals.

The benefits on cardiovascular outcomes vary with the type of closure method, underscoring the need for a tailored approach to manage ASD in adults.
Prevalence of Depression in pre- and post-operative CABG (Coronary Artery Bypass Graft) patients
Authors: Tariq Maheen , Mazhar Ismail , Rai Mir Muhammad , Khan Qudsia Umaira , Daniyal Muhammad , Faisal Danyal
Published: June 2024

Depression in post-surgical patients is a common occurrence. It is likely to occur in cardiac surgery like Coronary Artery Bypass Grafting. This condition could significantly prolong recovery time and could result in complications. Therefore, this study aimed to study the prevalence of Post-Operative Depression amongst Coronary Artery Bypass Graft patients. The undertaken research was conducted amongst patients who had undergone CABG at CMH Lahore and Punjab Institute of Cardiology. A survey was conducted on a sample size of 150 patients, out of which 147 gave consent to participation. The sample size was calculated using WHO Formula. The severity of depression was analyzed through questions in the Becks Depression Inventory. Data was analyzed using SPSS software (25.0 version). Out of 147 patients, 110 were males and 37 were females. The results depicted greater depression amongst females than in males both pre-operatively and post-operatively, with a mean score of 1.41 and 1.08 respectively. A significant difference (p<0.01) was obtained between the correlation of Pre-Operative Scores (in percentages and frequency) and Post-Operative Scores (in percentages and frequency). An insignificant difference (p=0.125) was obtained between the correlation between Preoperative Scores and Gender. A greater Mean Score (1.41) was seen in females, indicating more post-operative depression than males (1.05). An insignificant difference (p=0.239) was obtained between the correlation between Preoperative Scores and Gender. A greater Mean Score (1.08) was seen in females, indicating more post-operative depression than males (0.84). The study concluded that the prevalence of postoperative depression among patients was not significant.
STIPS algorithm enables tracking labyrinthine patterns and reveals distinct rhythmic dynamics of actin microridges
Authors: Bhavna Rajasekaran , Sonawane Mahendra
Published: June 2024

Tracking and motion analyses of semi-flexible biopolymer networks from time-lapse microscopy images are important tools that enable quantitative measurements to unravel dynamical and mechanical properties of biopolymers in living tissues important for understanding their organization and function. Biopolymer networks pose tracking challenges as they exhibit continuous stochastic transitions in the form of merges/splits resulting in local neighborhood rearrangements over short time/length scales. We propose the STIPS algorithm (SpatioTemporalInformation onPixelSubsets) that tracks merging/splitting events in self-organizing patterning systems, by creating pixel subsets to link trajectories across consecutive frames. We demonstrate our method on actin-enriched protrusions, the ‘microridges’ that form dynamic labyrinthine patterns on outer surfaces of squamous cell epithelia, mimicking ‘active Turing-patterns’. We uncovered two distinct actomyosin based rhythmic dynamics within neighboring cells; common pulsatile mechanism between 2-5.9 mins period governing both fusion and fission contributing to pattern maintenance and cell area pulses predominantly exhibiting ∼10 mins period.
Alarm functions of PD-1+ brain resident memory T cells
Authors: Musial Shawn C. , Kleist Sierra A. , Degefu Hanna N. , Ford Myles A. , Chen Tiffany , Isaacs Jordan F. , Boussiotis Vassiliki A. , Skorput Alexander G. J. , Rosato Pamela C.
Published: June 2024

Resident memory T cells (TRM) have been described in barrier tissues as having a ‘sensing and alarm’ function where, upon sensing cognate antigen, they alarm the surrounding tissue and orchestrate local recruitment and activation of immune cells. In the immunologically unique and tightly restricted CNS, it remains unclear if and how brain TRM, which express the inhibitory receptor PD-1, alarm the surrounding tissue during antigen re-encounter. Here, we reveal that TRMare sufficient to drive the rapid remodeling of the brain immune landscape through activation of microglia, DCs, NK cells, and B cells, expansion of Tregs, and recruitment of macrophages and monocytic dendritic cells. Moreover, we report that while PD-1 restrains granzyme B expression by reactivated brain TRM, it has no effect on cytotoxicity or downstream alarm responses. We conclude that TRMare sufficient to trigger rapid immune activation and recruitment in the CNS and may have an unappreciated role in driving neuroinflammation.
ERH Enables Early Embryonic Differentiation and Overlays H3K9me3 Heterochromatin on a Cryptic Pluripotency H3K9me3 Landscape in Somatic Cells
Authors: Katznelson Andrew , Hernandez Blake , Fahning Holly , Tapia Kylea , Burton Adam , Zhang Jingchao , Torres-Padilla Maria-Elena , Plachta Nicolas , Zaret Kenneth S. , McCarthy Ryan L.
Published: June 2024

Enhancer of Rudimentary Homolog (ERH) is an evolutionarily conserved protein originally characterized in fission yeast1and recently shown to maintain H3K9me3 in human fibroblasts2. Here, we find that ERH depletion in fibroblasts reverts the H3K9me3 landscape to an embryonic stem cell (ESC) state and enables activation of naïve and pluripotency genes and transposable elements during induced pluripotent stem cell (iPSC) reprogramming. We find that ERH similarly represses totipotent and alternative lineage programs during mouse preimplantation development and is required for proper segregation of the inner cell mass and trophectoderm cell lineages. During human ESC differentiation into germ layer lineages, ERH silences naïve and pluripotency genes, transposable elements, and alternative lineage somatic genes. As in fission yeast, we find that mammalian ERH interacts with RNA-binding proteins to engage and repress its chromatin targets. Our findings reveal a fundamental role for ERH in cell fate specification via the initiation and maintenance of early developmental gene repression.
Evolutionary genomics of a zoonotic parasite across the Neotropical Realm
Authors: Heeren Senne , Sanders Mandy , Shaw Jeffrey Jon , Brandão-Filho Sinval Pinto , Boité Mariana Côrtes , Cantanhêde Lilian Motta , Chourabi Khaled , Maes Ilse , Llanos-Cuentas Alejandro , Arevalo Jorge , Marco Jorge D. , Lemey Philippe , Cotton James A. , Dujardin Jean-Claude , Cupolillo Elisa , Van den Broeck Frederik
Published: June 2024

The Neotropical realm, one of the most biodiverse regions on Earth, houses a broad range of zoonoses that pose serious public health threats. Protozoan parasites of theLeishmania(Viannia)braziliensisspecies complex cause zoonotic leishmaniasis in Latin America with clinical symptoms ranging from simple cutaneous to destructive, disfiguring mucosal lesions. We present the first comprehensive genome-wide continental study including 257 cultivated isolates representing most of the geographical distribution of this major human pathogen. TheL. braziliensisspecies complex is genetically highly heterogeneous, consisting of divergent parasite groups that are associated with different environments and vary greatly in diversity. Apart from several small ecologically isolated groups with little diversity, our sampling identifies two major parasite groups, one associated with the Amazon and the other with the Atlantic Forest biomes. These groups show different recombination histories, as suggested by high levels of heterozygosity and effective population sizes in the Amazonian group in contrast to high levels of linkage and clonality in the Atlantic group. We argue that these differences are linked to strong eco-epidemiological differences between the two regions. In contrast to geographically focused studies, our study provides a broad understanding of the molecular epidemiology of zoonotic parasites circulating in tropical America.
Location of NMDARs and co-agonist control the generation of bursts in nigral dopamine neurons
Authors: Ringlet Sofian , Motta Zoraide , Vandries Laura , Seutin Vincent , Jehasse Kevin , Caldinelli Laura , Pollegioni Loredano , Engel Dominique
Published: June 2024

NMDA receptor activation in pars compacta substantia nigra dopamine neurons is central to the generation of bursting activity, a key signal temporally associated to movement initiation. The site of the NMDAR pool (synaptic and/or extrasynaptic) as well as the identity of the co-agonist involved in the ignition of this phasic activity remains unknown. Usingex vivoelectrophysiological recordings, we demonstrate that NMDARs located outside synapses are preponderant for this firing. This pool of receptors is recruited during intense synaptic activity via spillover of glutamate and require the binding of NMDAR co-agonist glycine for their full activation. Synaptic NMDARs are not directly involved in bursting and are activated by D-serine, a distinct co-agonist. Location dependency of NMDARs and co-agonist underlying burst generation may serve as a guideline in understanding the physiological role of dopamine neurons in health and disease.

Teaser

Extrasynaptic NMDARs recruited by spillover and glycine allow the generation of bursts in dopamine neurons.
DNA binding is rate-limiting for natural transformation
Authors: Ellison Taylor J. , Ellison Courtney K.
Published: June 2024

Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet determining how different factors universally contribute to or limit this process across species has remained challenging. Here we show thatAcinetobacter baylyi, the most naturally transformable species, is highly transformable due to its ability to robustly bind nonspecific DNA via a dedicated orphan minor pilin, FimT. We show that, compared to its homologues,A. baylyiFimT contains multiple positively charged residues that additively promote DNA binding efficiency. Expression ofA. baylyiFimT in a closely relatedAcinetobacterpathogen is sufficient to substantially improve its capacity for natural transformation, demonstrating that T4P-DNA binding is a rate-limiting step in this process. These results demonstrate the importance of T4P-DNA binding efficiency in driving natural transformation, establishing a key factor limiting horizontal gene transfer.

Importance

Natural transformation is a multi-step, broadly conserved mechanism for horizontal gene transfer in which bacteria take up exogenous DNA from the environment and integrate it into their genome by homologous recombination. A complete picture of the factors that limit this behavior remain unclear due to variability between bacterial systems. In this manuscript, we provide clear and direct evidence that DNA binding by type IV pili prior to DNA uptake is a rate-limiting step of natural transformation. We show that increasing DNA binding in antibiotic resistant Acinetobacter pathogens can boost their transformation rates by 100-fold. In addition to expanding our understanding of the factors that limit transformation in the environment, these results will also contribute to a deeper understanding of the spread of antibiotic resistance genes in relevant human pathogens.
Structures of the human transcription factor brachyury offer insights into DNA recognition, and identify small molecule binders for the development of degraders for cancer therapy
Authors: Newman Joseph A , Gavard Angeline E , Imprachim Nergis , Aitkenhead Hazel , Sheppard Hadley E. , Clarke Paul A. , Hossain Mohammad Anwar , Temme Louisa , Oh Hans J. , Wells Carrow I. , Davis-Gilbert Zachary W. , Workman Paul , Gileadi Opher , Drewry David H.
Published: June 2024

The transcription factor brachyury is a member of the T-Box family of transcription factors. It is active during embryogenesis and is required for the formation of the posterior mesoderm and the notochord in vertebrates. Aside from its role in embryogenesis, brachyury plays an essential role in tumour growth of the rare chordoma bone cancer and is implicated in other solid tumours. Given that brachyury is minimally expressed in healthy tissues, these findings suggest that brachyury is a potential therapeutic target in cancer. Unfortunately, as a ligandless transcription factor, brachyury has historically been considered undruggable. To investigate direct targeting of brachyury by small molecules, we initially determined the structure of human brachyury both in complex with its cognate DNA and in the absence of DNA. Analysis of these structures provided insights into brachyury DNA binding and the structural context of the G177D variant which is strongly associated with chordoma risk. We used these structures to perform a crystallographic fragment screen of brachyury and identify hotspot regions on numerous pockets on the brachyury surface. Finally, we have performed follow-up chemistry on fragment hits and describe the structure-based progression of a thiazole-containing chemical series. Excitingly, we have produced brachyury binders with low µM potency that can serve as starting point for further medicinal chemistry efforts. These data show that brachyury is ligandable and provides an example of how crystallographic fragment screening may be used to find ligands to target protein classes that are traditionally difficult to address using other approaches.
Vasopressin differentially modulates the excitability of rat olfactory bulb neuron subtypes
Authors: Suyama Hajime , Bianchini Gaia , Lukas Michael
Published: June 2024

Vasopressin (VP) is essential for social memory already at the level of the olfactory bulb (OB), and OB VP cells are activated by social interaction. However, it remains unclear how VP modulates olfactory processing to enable enhanced discrimination of very similar odors, e.g., rat body odors. So far, it has been shown that VP reduces firing rates in mitral cells (MCs) during odor presentationin-vivoand decreases the amplitudes of olfactory nerve-evoked excitatory postsynaptic potentials (ON-evoked EPSPs) in external tufted cellsin-vitro. We performed whole-cell patch-clamp recordings and population Ca2+imaging on acute rat OB slices. We recorded ON-evoked EPSPs as well as spontaneous inhibitory postsynaptic currents (IPSCs) from two types of projection neurons, middle tufted cells (mTCs) and MCs. VP bath-application reduced the amplitudes of ON-evoked EPSPs and the frequencies of spontaneous IPSCs in mTCs but did not change those in MCs. Therefore, we analyzed ON evoked-EPSPs in inhibitory interneurons, i.e., periglomerular cells (PGCs) and granule cells (GCs), to search for the origin of increased inhibition in mTCs. However, VP did not increase the amplitudes of evoked EPSPs in either type of interneurons. We next performed two-photon population Ca2+imaging in the glomerular layer and the superficial GC layer of responses to stronger ON stimulation than during patch-clamp experiments that should evoke action potentials in the measured cells. We observed that VP application increased ON-evoked Ca2+influx in juxtaglomerular cell and GC somata and decreased it in the intraglomerular neuropil. Thus, our findings indicate inhibition by VP on projection neurons via strong ON input-mediated inhibitory interneuron activity.
Shedding Light onH. pyloriDetection: A Fusion Protein Approach Unveiled through LIPS Method
Authors: Farzanfar Seyedeh Mahsa , Asad Sedigheh
Published: June 2024

The Luciferase Immunoprecipitation Systems (LIPS) method serves as a highly sensitive approach for quantitatively detecting antibodies to antigens, offering potential in identifying viral and bacterial infections. However, the substantial size of the luciferase-antigen fusion protein presents challenges in both production and folding. An alternative strategy employing epitopes rather than full length antigenic protein may circumvent issues associated with recombinant expression.Helicobacter pylori, a gram-negative bacterium, poses a risk of gastric cancer if untreated over time. This study focuses on the recombinant production of a fusion protein comprising in silico designed antigenic epitopes from theH. pyloriurease protein and luciferase, aiming to reduce the fusion protein’s size and thus augment its expression in theE. colisystem. By employing bioinformatic analysis, sequences encoding the antigenic regions were pinpointed and subsequently amplified via PCR. A luciferase-linker-epitope construct was devised and constructed accordingly. TheE. coliBl21 (DE3) strain was utilized to express the recombinant chimeric protein, which was subsequently purified to achieve a state of homogeneity. The molecular weight of the fusion protein was estimated to be 75 kilodalton. Verification of the chimeric protein’s proper folding and functionality was confirmed, as evidenced by a bioluminescence assay yielding an emission of 13.7 × 106(RLU/s). Furthermore, western blot analysis authenticated the fusion protein’s capability to bind specifically toH. pyloriantibodies. These findings underscore the potential of the resultant protein as a promising candidate forH. pyloridetection while also streamlining the recombinant production of LIPS fusion proteins.

Key Points

Epitope-driven protein design boostsE. coliexpression for LIPS advancement.

ImprovedH. pyloridetection aids early gastric cancer identification.
Characterization of the calmodulin-like protein family inChara brauniiand their conserved interaction with the calmodulin-binding transcription activator family
Authors: Symonds Kyle , Wali Udo , Duff Liam , Snedden Wayne A.
Published: June 2024

Calcium sensor proteins play important roles by detecting changes in intracellular calcium and relaying that information onto downstream targets through protein-protein interaction. Very little is known about calcium sensors from plant species that predate land colonization and the evolution of embryophytes. Here, we examined the genome of the multicellular algae,Chara braunii, for orthologs to the evolutionarily-conserved calcium sensor calmodulin (CaM), and for CaM-like proteins (CMLs). We identified one CaM and eight CML isoforms which rang in size from 16.4 to 21.3 kDa and are predicted to have between two to four calcium-binding (EF-hand) domains. Using recombinant protein, we tested whether CbCaM and CbCMLs1-7 possess biochemical properties of typical calcium sensors. CbCaM and the CbCMLs all displayed high-affinity calcium binding with estimated globalKDvalues in the physiological µM range. In response to calcium binding, CbCaM and the CbCMLs exhibited varying degrees of increase in exposed hydrophobicity, suggesting different calcium-induced conformational changes occur among isoforms. We found many examples of putative CaM targets encoded in theC. brauniigenome and explored the ability of CbCaM and CbCMLs to interactin plantawith a representative putative target, aC. brauniiCaM-binding transcription factor (CbCAMTA1). CbCaM, CbCML2, and CbCML4 associated with the C-terminal region of CbCAMTA1. Collectively, our data support the hypothesis that complex calcium signaling and sensing networks involving CaM and CMLs evolved early in the green lineage. Similarly, it seems likely that calcium-mediated regulation of transcription occurs inC. brauniivia CAMTAs and is an ancient trait predating embryophytic emergence.

Highlights

Although calmodulin (CaM) and calmodulin-like (CML) proteins are well studied in vascular plants, little is known about their orthologs in ancient lineages. We characterized CaM and CMLs fromChara braunii, and assessed their ability to bind a representative target protein, a calmodulin-binding transcription factor, CbCAMTA1.
Dupilumab dampens mucosal type 2 response during acetylsalicylic acid challenge in N-ERD patients
Authors: Eckl-Dorna J. , Morgenstern C. , Poglitsch K. , Arnoldner T. , Gangl K. , Bartosik T. , Campion N.J. , Tu A. , Stanek V. , Schneider S. , Bangert C.
Published: June 2024

Rationale

Non-steroidal anti-inflammatory drug-exacerbated respiratory disease (N-ERD) is characterized by the clinical triad of hypersensitivity to NSAIDs, nasal polyposis, and asthma. The cells and mediators causing acute symptoms when driving the hypersensitivity reaction to acetylsalicylic acid (ASA) ingestion, remain poorly defined.

Objectives

To investigate the dynamics of nasal mediators during ASA provocation in N-ERD patients before and twenty-four weeks after therapy with the IL-4 receptor alpha-blocking antibody dupilumab.

Methods

Nasal mucosal lining fluids of patients with N-ERD, chronic rhinosinusitis patients with nasal polyp (CRSwNP) and healthy disease controls were collected at selected time points up to two hours after ASA provocation. Analysis of thirty-three different inflammatory mediators as well as transcriptomic profiling was performed. In N-ERD patients, provocation was repeated after twenty-four weeks of dupilumab therapy.

Measurements and Main Results

Sixty minutes after provocation with ASA, N-ERD patients showed a significant increase in type 2 associated cytokines (i.e., TSLP, IL-5, and eotaxin-3) as compared to the other patient groups. This effect was diminished after twenty-four weeks of dupilumab therapy and was independent of the development of ASA tolerance. Transcriptomics revealed dampened upregulation of type 2 associated pathways genes (i.e.,AREG) as well as enhanced downregulation of lipid (i.e.,ALOX15) and peroxisome metabolisms (i.e.,NOS2) at ASA provocation after dupilumab therapy.

Conclusions

Treatment with dupilumab leads to reduced nasal type 2 cytokine secretion and distinct changes in transcriptomic profile during ASA provocation, but changes in type 2 mediators show no association with tolerance development.
Production of the
ΞN
dibaryon as a weakly bound system in
pp
collisions
Authors: Wu Tian-Chen , Hosaka Atsushi , Geng Li-Sheng
Published: June 2024

The ΞN interaction plays an important role in understanding the long-anticipated H dibaryon. Recent lattice QCD calculations verified the attractive nature of the ΞN interaction. On the other hand, whether it is strong enough to generate a bound state remains inconclusive. In this work, assuming it can generate a weakly bound state, we study the yields of the ΞN dibaryon for different binding energies in pp collisions at 7 TeV using the coalescence model and the transport model PACIAE. The yields are estimated first numerically and then analytically, adopting a Yukawa-type wave function. In particular, we find that in the weak binding limit, there exists a universal relation between the yield and the binding energy, valid for pp collisions.

Published by the American Physical Society
2024
Decoding the
B→Kνν
excess at Belle II: Kinematics, operators, and masses
Authors: Fridell Kåre , Ghosh Mitrajyoti , Okui Takemichi , Tobioka Kohsaku
Published: June 2024

An excess in the branching fraction for B+→K+νν recently measured at Belle II may be a hint of new physics. We perform thorough likelihood analyses for different new physics scenarios such as B→KX with a new invisible particle X, or B→Kχχ through a scalar, vector, or tensor current with χ being a new invisible particle or a neutrino. We find that vector-current three-body decay with mX≃0.6 GeV—which may be dark matter—is most favored, while two-body decay with

m

X

≃

2

 

 

GeV

is also competitive. The best-fit branching fractions for the scalar and tensor cases are a few times larger than for the two-body and vector cases. Past measurements provide further discrimination, although the best-fit parameters stay similar.

Published by the American Physical Society
2024
Fully
ab-initio
all-electron calculation of dark matter-electron scattering in crystals with evaluation of systematic uncertainties
Authors: Dreyer Cyrus E. , Essig Rouven , Fernandez-Serra Marivi , Singal Aman , Zhen Cheng
Published: June 2024

We calculate target-material responses for dark matter–electron scattering at the all-electron level using atom-centered Gaussian basis sets. The all-electron effects enhance the material response at high momentum transfers from dark matter to electrons, q≳O(10αme), compared to calculations using conventional plane wave methods, including those used in ; this enhances the expected event rates at energy transfers E≳10  eV, especially when scattering through heavy mediators. We carefully test a range of systematic uncertainties in the theory calculation, including those arising from the choice of basis set, exchange-correlation functional, number of unit cells in the Bloch sum, k-mesh, and neglect of scatters with very high momentum transfers. We provide state-of-the-art crystal form factors, focusing on silicon and germanium. Our code and results are made publicly available as a new tool, called (“”).

Published by the American Physical Society
2024
Optimizing fictitious states for Bell inequality violation in bipartite qubit systems with applications to the
tt¯
system
Authors: Cheng Kun , Han Tao , Low Matthew
Published: June 2024

There is a significant interest in testing quantum entanglement and Bell inequality violation in high-energy experiments. Since the analyses in high-energy experiments are performed with events statistically averaged over phase space, the states used to determine observables depend on the choice of coordinates through an event-dependent basis and are thus not genuine quantum states, but rather “fictitious states.” We find that the basis which diagonalizes the spin-spin correlations is optimal for constructing fictitious states to test the violation of Bell’s inequality. This result is applied directly to the bipartite qubit system of a top and antitop produced at a hadron collider. We show that the beam axis is the optimal basis choice near the tt¯ threshold production for measuring Bell inequality violation, while at high transverse momentum the basis that aligns along the momentum direction of the top is optimal.

Published by the American Physical Society
2024
Rotating metrics and new multipole moments from scattering amplitudes in arbitrary dimensions
Authors: Gambino Claudio , Pani Paolo , Riccioni Fabio
Published: June 2024

We compute the vacuum metric generated by a generic rotating object in arbitrary dimensions up to third post-Minkowskian order by computing the classical contribution of scattering amplitudes describing the graviton emission by massive spin-1 particles up to two loops. The solution depends on the mass, angular momenta, and on up to two parameters related to generic quadrupole moments. In D=4 spacetime dimensions, we recover the vacuum Hartle-Thorne solution describing a generic spinning object to second order in the angular momentum, of which the Kerr metric is a particular case obtained for a specific mass quadrupole moment dictated by the uniqueness theorem. At the level of the effective action, the case of minimal couplings corresponds to the Kerr black hole, while any other mass quadrupole moment requires nonminimal couplings. In D>4, the absence of black-hole uniqueness theorems implies that there are multiple spinning black hole solutions with different topology. Using scattering amplitudes, we find a generic solution depending on the mass, angular momenta, the mass quadrupole moment, and a new stress quadrupole moment which does not exist in D=4. As special cases, we recover the Myers-Perry and the single-angular-momentum black ring solutions, to third and first post-Minkowksian order, respectively. Interestingly, at variance with the four-dimensional case, none of these solutions corresponds to the minimal coupling in the effective action. This shows that, from the point of view of scattering amplitudes, black holes are the “simplest” general relativity vacuum solutions only in D=4.

Published by the American Physical Society
2024