bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimized Protein–Excipient Interactions in the Martini 3 Force Field
Authors: Prass Tobias M. , Lindorff-Larsen Kresten , Garidel Patrick , Blech Michaela , Schäfer Lars V.
Published: December 2024

The high doses of drugs required for biotherapeutics, such as monoclonal antibodies (mAbs), and the small volumes that can be administered to patients by subcutaneous injections pose challenges due to high concentration formulations. The addition of excipients, such as arginine and glutamate, to high concentration protein formulations can increase solubility and reduce the tendency of protein particle formation. Molecular dynamics (MD) simulations can provide microscopic insights into the mode of action of excipients in mAb formulations but require large system sizes and long time scales that are currently beyond reach at the fully atomistic level. Computationally efficient coarse-grained models such as the Martini 3 force field can tackle this challenge but require careful parametrization, testing, and validation. This study extends the popular Martini 3 force field towards realistic protein–excipient interactions of arginine and glutamate excipients, using the Fab domains of the therapeutic mAbs trastuzumab and omalizumab as model systems. A novel all-atom to coarse-grained mapping of the amino acid excipients is introduced, which explicitly captures the zwitterionic character of the backbone. The Fab–excipient interactions of arginine and glutamate are characterized concerning molecular contacts with the Fabs at the single-residue level. The Martini 3 simulations are compared with results from all-atom simulations as a reference. Our findings reveal an overestimation of Fab–excipient contacts with the default interaction parameters of Martini 3, suggesting a too strong attraction between protein residues and excipients. Therefore, we reparametrized the protein–excipient interaction parameters in Martini 3 against all-atom simulations. The excipient interactions obtained with the new Martini 3 mapping and Lennard-Jones (LJ) interaction parameters, coined Martini 3-exc, agree closely with the all-atom reference data. This work presents an improved parameter set for mAb-arginine and mAb-glutamate interactions in the Martini 3 coarse-grained force field, a key step towards large-scale coarse-grained MD simulations of high-concentration mAb formulations and the stabilizing effects of excipients.
Effect of MisMatch Repair Deficiency on metastasis occurrence modelized in a syngeneic mouse model
Authors: Laplante Pierre , Rosa Reginaldo , Nebot-Bral Laetitia , Goulas Jordane , Nikolaev Sergey , Silvin Aymeric , Kannouche Patricia L
Published: December 2024

Mismatch repair deficiency leads to high mutation rates and microsatellite instability (MSI-H), associated with immune infiltration and responsiveness to immunotherapies. In early stages, MSI-H tumors generally have a better prognosis and lower metastatic potential than microsatellite-stable (MSS) tumors, especially in colorectal cancer. However, in advanced stages, MSI-H tumors lose this survival advantage for reasons that remain unclear. We developed a syngeneic mouse model of MSI cancer by knocking out the MMR geneMsh2in the metastatic 4T1 breast cancer cell line. This model mirrored genomic features of MSI-H cancers and showed reduction in metastatic incidence compared to their MSS counterparts. In MSI-H tumors, we observed an enrichment of immune gene-signatures that negatively correlated with metastasis incidence. Importantly, a hybrid epithelial-mesenchymal signature, related to aggressiveness was detected only in metastatic MSI-H tumors which may explain the worse outcomes after recurrence of MSI tumors compared to MSS. Interestingly, we identified immature myeloid cells at primary and metastatic sites in MSI-H tumor-bearing mice, suggesting that MMR deficiency elicits specific immune responses beyond T-cell activation.

Significance

A novel syngeneic mouse model of MSI cancer demonstrates that the immune system regulates MSI cancer cell dissemination, offering an important tool to model advanced stages of human MSI-driven disease.
Mavacamten facilitates myosin head ON-to-OFF transitions and shortens thin filament length in relaxed skeletal muscle
Authors: Kuehn Michel N. , Engels Nichlas M. , Nissen Devin L. , Freundt Johanna K. , Ma Weikang , Irving Thomas C. , Linke Wolfgang A. , Hessel Anthony L.
Published: December 2024

The first-in-its-class cardiac drug mavacamten reduces the proportion of so-called ON-state myosin heads in relaxed sarcomeres, altering contraction performance. However, mavacamten is not completely specific to cardiac myosin and can also affect skeletal muscle myosin, an important consideration since mavacamten is administered orally and so will also be present in skeletal tissue. Here, we studied the effect of mavacamten on skeletal muscle structure using small-angle X-ray diffraction. Mavacamten treatment reduced the proportion of ON myosin heads but did not eliminate the molecular underpinnings of length-dependent activation, demonstrating similar effects to those observed in cardiac muscle. These findings provide valuable insights for the potential use of mavacamten as a tool to study muscle contraction across striated muscle.
The relationship between sexual dimorphism and intersex correlation: do models support intuition?
Authors: Puixeu Gemma , Hayward Laura Katharine
Published: December 2024

That a high genetic correlation between the sexes (rfm) constrains the evolution of sexual dimorphism and that they should negatively correlate with one another, are assumptions commonly made in the field of sex-specific adaptation. While some empirical observations support a general negative relationship, the mechanisms underlying this pattern and the conditions under which it arises are poorly understood. Concretely, two primary hypotheses are often invoked: first, that traits with ancestrally lowrfmare less constrained in their ability to respond to sex-specific selection and thus evolve to be more dimorphic; second, that sex-specific selection acts to reducerfm. However, no model to date has formalized these hypotheses and tested the conditions in which they hold. Here, we develop models of sex-specific stabilizing selection, mutation and drift to explore various scenarios potentially generating a negative correlation between intersex correlation and sexual dimorphism, with a focus on testing the common hypotheses. We recover the classical result that, with an infinite population size,rfmand sexual dimorphism are independent at equilibrium. Further, we show that this independence is maintained with a finite population; and this is in spite of the fact that, as we demonstrate, genetic drift generates nonzero sexual dimorphism even when selection between the two sexes is identical. Moreover, we demonstrate that the two common hypotheses only imply a negative association if additional assumptions are made. Specifically, that 1) some traits are sex-specifically adapting under directional selection, and 2) this sex-specific adaptation favours increased dimorphism more often than decreased dimorphism. These results provide, to our knowledge, the first mechanistic framework for understanding the conditions under which a negative correlation between intersex correlation and sexual dimorphism may arise. They also offer a compelling explanation for the inconsistent empirical evidence observed in nature, highlighting the importance of context-specific factors in shaping this relationship.
Translocation of effector proteins into plant cells by the flax rust pathogenMelampsora lini
Authors: Zhang Xiaoxiao , Catanzariti Ann-Maree , Lawrence Gregory J. , Gan Pamela H. P. , Jones David A. , Dodds Peter N. , Rathjen John P.
Published: December 2024

During infection, rust fungi secrete effector proteins into host plant cells from haustoria to aid their colonisation. How rust effectors are secreted from the haustorium and delivered into the cytoplasm of host cells remains poorly understood. We used anAgrobacterium-mediated transformation procedure to generate stable transgenic flax rust strains expressing the effectors AvrM and AvrP123 fused to yellow fluorescent protein (YFP). We showed that both AvrM-YFP and AvrP123-YFP fusion proteins were secreted by the fungus into the extrahaustorial matrix (EHMx); however only AvrM-YFP was delivered into host cells, triggering a typical resistance phenotype in plants carrying the corresponding resistance (R)geneM. The signal peptide of AvrM was sufficient to direct YFP secretion into the EHMx; however, delivery into the host cell required a larger 105 amino acid N-terminal fragment of AvrM. These results indicate that translocation of this protein into the host cell from the EHMx is a separate process from secretion into the EHMx and requires a signal present in AvrM between amino acids 34 and 105. This is in contrast to previous observations of AvrM localisation after transient expression in plants, highlighting the necessity for analysis in the natural infection system.
ARBEL: A Machine Learning Tool with Light-Based Image Analysis for Automatic Classification of 3D Pain Behaviors
Authors: Barkai Omer , Zhang Biyao , Lenfers Turnes Bruna , Arab Maryam , Yarmolinsky David A , Zhang Zihe , Barrett Lee B , Woolf Clifford J
Published: December 2024

A detailed analysis of pain-related behaviors in rodents is essential for exploring both the mechanisms of pain and evaluating analgesic efficacy. With the advancement of pose-estimation tools, automatic single-camera video animal behavior pipelines are growing and integrating rapidly into quantitative behavioral research. However, current existing algorithms do not consider an animal’s body-part contact intensity with- and distance from- the surface, a critical nuance for measuring certain pain-related responses like paw withdrawals (‘flinching’) with high accuracy and interpretability. Quantifying these bouts demands a high degree of attention to body part movement and currently relies on laborious and subjective human visual assessment. Here, we introduce a supervised machine learning algorithm, ARBEL: Automated Recognition of Behavior Enhanced with Light, that utilizes a combination of pose estimation together with a novel light-based analysis of body part pressure and distance from the surface, to automatically score pain-related behaviors in freely moving mice in three dimensions. We show the utility and accuracy of this algorithm for capturing a range of pain-related behavioral bouts using a bottom-up animal behavior platform, and its application for robust drug-screening. It allows for rapid objective pain behavior scoring over extended periods with high precision. This open-source algorithm is adaptable for detecting diverse behaviors across species and experimental platforms.
Quantitative analysis of gas chromatography-coupled electroantennographic detection (GC-EAD) of plant volatiles by insects
Authors: Byers Kelsey J.R.P. , Jacobs Robert N.
Published: December 2024

Premise

Plant-interacting insects receive plant volatile signals through their antennae, and voltage changes across an antenna exposed to volatile stimuli can be measured to determine if insects can perceive them, often by coupling gas chromatography to electroantennographic detection (GC-EAD). Current methods for analysing GC-EAD data rely onqualitativeobservation, rather than usingquantitativeanalysis, and are thus prone to bias.

Methods and Results

We developed a novelquantitativemethodology for analysis of GC-EAD data using a signal processing technique on EAD data to compare responses of hawkmoths and bumble bees to a library of common floral volatiles. Responses varied between species and sexes and these responses were in some cases affected by compound type or modification.

Conclusions

Our novel GC-EAD analysis technique is robust to baseline drift and low signal:noise ratios commonly found in GC-EAD data, and provides a way forward for quantitative studies of plant volatile-mediated plant-insect interactions.
An exploratory study of urinary proteome in trigeminal neuralgia
Authors: Wei Lilong , Wang Haitong , Zhou Yun , Wu Jianqiang , Zhan Yuliang , Cao Yongtong , Gao Youhe
Published: December 2024

Trigeminal neuralgia (TN) is a neurological disorder characterized by severe pain, with a complex pathogenesis that seriously affects the quality of life of patients. Urinary proteomics has shown great potential in disease research. The aim of this study is to explore the diagnostic and therapeutic value of urine proteomics in TN. The urine of 10 cases of TN and 11 healthy individuals were studied using liquid chromatography-mass spectrometry (LC-MS) proteomics technology. Group analysis and one to many individual analysis strategies were used in quantitative analysis. A total of 2620 proteins were identified in group analysis, of which 1865 were quantifiable proteins. The majority of specimens in each group could be distinguished by unsupervised clustering analysis of urine proteome. The biological processes of immune response regulation signal pathway, immune response, natural killer cell activation, fatty acid transport, and natural killer cell inhibition signal pathway, as well as the KEGG pathway of antigen processing and presentation and natural killer cell-mediated cytotoxicity, were significantly enriched in the comparison between the two populations. An individual analysis revealed that there were more significantly different proteins among individuals, with 15 proteins identified in at least 9 different patients. The urinary proteome provided molecular characteristics of urinary proteins for patients with TN, describing the changes that occur in the patient’s body. The strong enrichment of its immune response might be related to the onset of the disease, providing new directions for immune related treatment of the disease; the significant differential proteins could become potential disease markers for disease diagnosis and treatment evaluation.
Next Generation Evidence: High-Precision Information Retrieval for Rapid Clinical Guideline Updates
Authors: Borchert Florian , Wullenweber Paul , Oeser Annika , Kreuzberger Nina , Karge Torsten , Langer Thomas , Skoetz Nicole , Wieler Lothar H. , Schapranow Matthieu-P. , Arnrich Bert
Published: December 2024

Delays in translating new medical evidence into clinical practice hinder patient access to the best available treatments. Our data reveals an average delay of nine years from the initiation of human research to its adoption in clinical guidelines, with 1.7–3.0 years lost between trial publication and guideline updates. A substantial part of these delays stems from slow, manual processes in updating clinical guidelines, which rely on time-intensive evidence synthesis workflows. The Next Generation Evidence (NGE) system addresses this challenge by harnessing state-of-the-art biomedical Natural Language Processing (NLP) methods. This novel system integrates diverse evidence sources, such as clinical trial reports and digital guidelines, enabling automated, data-driven analyses of the time it takes for research findings to inform clinical practice. The NGE system accelerates guideline updates by employing precision-focused literature search filters tailored specifically for guideline maintenance. In benchmarking against two German oncology guidelines, these filters demonstrate exceptional precision in identifying pivotal publications for guideline updates. By streamlining evidence synthesis, NGE has the potential to deliver faster updates, improve guideline responsiveness, and enhance patient access to state-of-the-art treatments.
Risk Factors for Suicidal Behavior in Youth and the Impact of SARS-CoV-2 Infection: A Retrospective Case-Control Study
Authors: Heslin Kathleen P. , Montero Michelle , Faraone Stephen V. , Zhang-James Yanli
Published: December 2024

Background

Suicide and self-harm remain critical concerns in youth. This study compares patients with and without suicidality or self-harm (SOSH), suicidality (SI/SA), and COVID-19 to investigate 53 pre-existing risk factors associated with suicidality in patients with and without COVID-19.

Methods

A retrospective case-control study was conducted using TriNetX data from 111,631,250 patients across 78 healthcare networks. This study included patients aged 0-21 with any healthcare visit between January 20, 2020, and May 11, 2023.

Outcomes

Comparison groups shared many risk factors, with specific differences. Children with SOSH and COVID-19 had higher odds of support group problems, personality disorder, thyroid disorders, and insomnia; children with SOSH without COVID-19 had higher odds of upbringing problems, anxiety and nonpsychotic disorders, sleep disorders, and autism. Adolescents with SOSH and COVID-19 had higher odds of parent-child conflict; adolescents with SOSH without COVID-19 had higher odds of education and literacy problems. Children with SI/SA and COVID-19 had higher odds of support group problems, personality disorders, and asthma; children with SI/SA without COVID-19 had higher odds of autism. Adolescents with SI/SA and COVID-19 had higher odds of asthma. The effect size of COVID-19 was not significant. SOSH was associated with increased odds of prior SARS-CoV-2 infection in children (OR 2.42) and adolescents (OR 1.88).

Interpretation

This study confirms known SOSH risk factors and demonstrates their association with suicidality. We observed a significant association between SOSH and preceding SARS-CoV-2 infection. This underscores the need to focus on suicide risk in youth affected by COVID-19.
Complexity of Coronary Disease and a Genetic Risk Profile in Patients with Type 2 Diabetes in Colombia
Authors: Giraldo-Gonzalez German Camilo , Fuentes Jheyson Jair , Sepúlveda-Arias Juan Carlos , Castaño Carlos Eduardo
Published: December 2024

Background

Coronary artery disease (CAD) remains a leading cause of mortality in patients with type 2 diabetes (T2DM). Both conditions share genetic and environmental etiologies, making T2DM a unique risk factor for CAD. Despite advancements, no highly accurate genetic or clinical prediction models exist to identify patients at high risk for complex coronary disease.

Methods

A cross-sectional genetic epidemiology study was conducted at a cardiovascular center in Manizales, Colombia, involving 106 T2DM patients with documented coronary heart disease (CHD). Genetic analysis focused on 11 single nucleotide polymorphisms (SNPs) using polymerase chain reaction (PCR) and TaqMan assays. Clinical and genetic data were analyzed to assess associations with CAD complexity, defined as monovascular (one vessel) or polyvascular (≥2 vessels) involvement. Statistical methods included bivariate analyses, binary logistic regression, and Bonferroni correction for significance.

Results

Among participants (mean age 68.1 ± 8.3 years; 53.7% male), 33 had monovascular disease, and 73 had polyvascular disease. Male sex (p = 0.016) and a significant genetic profile (PRP-5: rs1412830-CDKN2A/B, rs2074192-ACE2, rs4420638-APOE, rs646776-CELSR2, rs7903146-TCF7L2) were associated with polyvascular disease. PRP-5 demonstrated an odds ratio (OR) of 5.2 (p = 0.007) for complex CAD. Other metabolic and clinical parameters showed no significant differences between genetic risk groups.

Conclusions

This study identifies a polygenic risk profile (PRP-5) associated with complex CAD in T2DM patients, independent of traditional clinical factors. These findings support the hypothesis of genetic contributions to CAD severity and suggest the need for longitudinal studies to evaluate this risk profile’s clinical utility. As the first cohort-based genetic study in Hispanoamerica, it highlights the high prevalence of relevant alleles in this population and provides a foundation for future research into personalized cardiovascular risk stratification.

Subject Áreas

genetics, cardiometabolic disease, Type 2 diabetes, coronary disease, cardiovascular diseases, polymorphism, single nucleotide.
Dynamic Regulation OF The Chromatin Environment By Ash1L Modulates Human Neuronal Structure And Function
Authors: Jhanji Megha , Ward Joseph A. , Leung Calvin S. , Krall Colleen L. , Ritchie Foster D. , Guevara Alexis , Vestergaard Kai , Yoon Brian , Amin Krishna , Berto Stefano , Liu Judy , Lizarraga Sofia B.
Published: December 2024

Precise regulation of the chromatin environment through post-translational histone modification modulates transcription and controls brain development. Not surprisingly, mutations in a large number of histone-modifying enzymes underlie complex brain disorders. In particular, the histone methyltransferase ASH1L modifies histone marks linked to transcriptional activation and has been implicated in multiple neuropsychiatric disorders. However, the mechanisms underlying the pathobiology of ASH1L-asociated disease remain underexplored. We generated human isogenic stem cells with a mutation in ASH1L’s catalytic domain. We find that ASH1L dysfunction results in reduced neurite outgrowth, which correlates with alterations in the chromatin profile of activating and repressive histone marks, as well as the dysregulation of gene programs important for neuronal structure and function implicated in neuropsychiatric disease. We also identified a novel regulatory node implicating both the SP andKrüppel-like families of transcription factors and ASH1L relevant to human neuronal development. Finally, we rescue cellular defects linked to ASH1L dysfunction by leveraging two independent epigenetic mechanisms that promote transcriptional activation. In summary, we identified an ASH1L-driven epigenetic and transcriptional axis essential for human brain development and complex brain disorders that provide insights into future therapeutic strategies for ASH1L-related disorders.
Identification of Inhibitors ofChikungunyavirus nsP2 ATPase
Authors: Navarro Hernan , Scott John E. , Smith Ginger R. , Ghiabi Pegah , Gibson Elisa , Loppnau Peter , Harding Rachel J. , Hossain Mohammad Anwar , Bose Muthu Ramalingam , Pearce Kenneth H. , Merten Eric M. , Willson Timothy M. , Brown Peter J.
Published: December 2024

Non-structural protein 2 (nsP2), which plays an essential role in replication of CHIKV, contains a protease, helicase, and methyltransferase-like domain. We executed a simple a screen using malachite green to detect compounds that decreased ATP hydrolysis and tested a library of diverse compounds to find inhibitors of CHIKV nsP2 helicase.
Mapping the canine microbiome: Insights from the Dog Aging Project
Authors: Bamberger Tal , Muller Efrat , Algavi Yadid M. , Greenier Ashlee , Adjangba Christine , Slikas Elizabeth , Brassington Layla , Mariner Blaise , McCoy Brianah , Harrison Benjamin R. , Partida-Aguilar Maria , Marye Abbey , Harris Adam , Rout Emily ,   DAP Consortium, Avery Anne , Promislow Daniel E.L. , Snyder-Mackler Noah , Borenstein Elhanan
Published: December 2024

Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, the largest population-wide study of the canine gut microbiome to date. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with comprehensive phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as diet, health, and living conditions. Our analyses identify various factors associated with microbiome composition. In addition, we find a gradual shift in microbiome composition with age, which allows us to develop a novel metagenomics-based “clock” to predict biological aging based on microbial signatures. Overall, these findings provide an unprecedented and detailed understanding of the role the microbiome plays in our four-legged companions, offering both potential applications in veterinary medicine and an exciting model for aging research.
Female budgerigars prefer males with foraging skills that differ from their own
Authors: Zou Yuqi , Song Zitan , Chen Jiani , Sun Yuehua , Griesser Michael
Published: December 2024

Foraging skills influence food intake and may therefore also play a role in mate choice decision. Previous empirical work has shown that individuals benefit from being in groups that include individuals with a variety of foraging skills as this increases foraging success. This idea, formalized in the skill-pool hypothesis, may extend to mate choice. Diverse foraging skills can expand the foraging niche of a pair and benefit offspring through enhanced parental provisioning, and exposure to a broader foraging skillset. To test this idea, we trained captive female and male budgerigars to solve one of two different novel foraging puzzle boxes. Then, females simultaneously observed two males that could solve either the same or the other box, and assessed female preferences in a binary mate choice apparatus. Females preferred males with foraging skills that differed from their own, independent of the skill type and the number of times males solved the foraging puzzle. These findings show that foraging skills can influence social preferences, including in a mate choice context, and support intraspecific diversity in foraging skills.
Control of mitochondrial dynamics by dPGC1 limits Yorkie-induced oncogenic growth inDrosophila
Authors: Sew Wei Qi Guinevere , Li Zhiquan , Rasmussen Lene Juel , Herranz Héctor
Published: December 2024

Mitochondrial function and dynamics are crucial for maintaining cellular homeostasis and overall health. Disruptions in these processes can lead to various diseases, including cancer. The Hippo signaling pathway, a universal growth regulator, plays central roles in cancer through its main effector, the Yes-associated protein (YAP), known as Yorkie (Yki) inDrosophila. Yki upregulation drives benign tissue overgrowth inDrosophilaimaginal discs. Our research demonstrates that the conserved metabolic regulator dPGC1 limits Yki-driven tissue hyperplasia and maintains tissue homeostasis in vivo. Yki upregulation and dPGC1 depletion lead to tumors characterized by enlarged and hyperfused mitochondria, a condition both necessary and sufficient for Yki-driven oncogenic growth. Our findings demonstrate that mitochondrial hyperfusion elevates the levels of the cell cycle regulator Cyclin E, which is crucial for tumor development. Our findings identify dPGC1 as a context-dependent tumor suppressor that coordinates mitochondrial dynamics and cell cycle regulation in response to oncogene activation. Defects in these processes are commonly found in cancer cells, highlighting major implications for cancer development in humans.
Characterizing vascular function in mouse models of Alzheimer’s disease, atherosclerosis, and mixed Alzheimer’s and atherosclerosis
Authors: Eyre Beth , Shaw Kira , Drew Dave , Rayson Alexandra , Shabir Osman , Lee Llywelyn , Francis Sheila , Berwick Jason , Howarth Clare
Published: December 2024

Significance

Alzheimer’s disease does not occur in isolation and there are many comorbidities associated with the disease – especially diseases of the vasculature. Atherosclerosis is a known risk factor for the subsequent development of Alzheimer’s disease, therefore understanding how both diseases interact will provide a greater understanding of co-morbid disease progression and aid the development of potential new treatments.

Aim

The current study characterizes hemodynamic responses and cognitive performance in APP/PS1 Alzheimer’s mice, atherosclerosis mice, and a mixed disease group (APP/PS1 & atherosclerosis) between the ages of 9 and 12 months.

Approach

Whisker-evoked hemodynamic responses and recognition memory were assessed in awake mice, immunohistochemistry to assess amyloid pathology, and histology to characterize atherosclerotic plaque load.

Results

We observed hemodynamic deficits in atherosclerosis mice (vs Alzheimer’s, mixed disease or wild-type mice), with reduced short-duration stimulus-evoked hemodynamic responses occurring when there was no concurrent locomotion during the stimulation period. Mixed Alzheimer’s and atherosclerosis models did not show differences in amyloid beta coverage in the cortex or hippocampus or atherosclerotic plaque burden in the aortic arch vs relevant Alzheimer’s or atherosclerosis controls. Consistent with the subtle vascular deficits and no pathology differences, we also observed no difference in performance on the novel object recognition task across groups.

Conclusions

These results emphasize the importance of experimental design for characterizing vascular function across disease groups, as locomotion and stimulus duration impacted the ability to detect differences between groups. Whilst atherosclerosis did reduce hemodynamic responses, these were recovered in the presence of co-occurring Alzheimer’s disease which may provide targets for future studies to explore the potentially contrasting vasodilatory mechanisms these diseases impact.
The marine wormCapitella teletais sensitive to neurochemical manipulation, as revealed via a novel high-throughput behavioural tool
Authors: Hendershot Maxwell , Thompson William Andrew , Ramos Andrea Murillo , Bradshaw Olivia , Wilson Joanna Y.
Published: December 2024

Anthropogenic impacts have led to increases in contaminants in marine habitats. The presence of compounds such as pharmaceuticals, personal care products, and pesticides is a concern, as these compounds have been shown to act as neurochemicals in aquatic organisms. However, screens of the multitude of chemicals found environmentally have yet to be carried out.Capitella teletaare marine annelid polychaete worms that live in the sediment of estuarian environments, acting as ecosystem engineers for marine habitats. This study aimed to develop a behaviour tool to identify neurochemical pathways involved in controlling locomotion that could be applied to screen the impacts of toxicants in the environment using this key invertebrate species at multiple life stages. Adult and juvenile life stages (2 weeks post-emergence) ofCapitella teletawere observed in Petri dishes (adults only) or 6-well plates (adults and juveniles), and conserved behavioural responses were isolated, such as their velocity, distance travelled, the time to reach the edge of the arena, and time spent at the periphery. We exposed juvenile and adult worms to nicotine (acetylcholine agonist) as a proof of concept. We noted similar disruptions to locomotion at both life stages, with low doses of nicotine stimulating movement and higher doses reducing locomotion. From here, we exposed juvenile worms to fluoxetine (serotonin reuptake inhibitor), phenobarbital (GABA agonist), and apomorphine (dopamine agonist). The behaviour of juvenile worms can be altered by exposure to fluoxetine, phenobarbital, and apomorphine. Fluoxetine and phenobarbital exposure reduces movement at high doses, but fluoxetine influences the amount of time at the periphery of the arena. Apomorphine produced modest changes in locomotion compared to other chemicals tested. Genome searching, as well as transcriptomics, were used to confirm the presence of neurochemical pathways inCapitella teleta. Our results demonstrate thatCapitella teletais a viable model for behavioural work, that several neurochemical pathways contribute to locomotory behaviour, and that this assay may be useful as a screen for contaminants found in marine habitats.
Single cell migration along and against confined haptotactic gradients
Authors: Fortunato Isabela Corina , Brückner David B. , Grosser Steffen , Rossetti Leone , Bosch-Padrós Miquel , Trebicka Jonel , Roca-Cusachs Pere , Sunyer Raimon , Hannezo Edouard , Trepat Xavier
Published: December 2024

Directed cell migration along gradients of extracellular matrix (ECM) density –a process called haptotaxis– plays a central role in morphogenesis, the immune response, and cancer invasion. It is commonly assumed that cells respond to these gradients by migrating directionally towards the regions of highest ligand density. In contrast with this view, here we show that cells exposed to micropatterned fibronectin gradients exhibit a complex repertoire of trajectories, including directed haptotactic migration up the gradient but also linear oscillations and circles with extended periods of migration down the gradient. To explain this behavior, we developed a biophysical model of haptotactic cell migration based on a coarse-grained molecular clutch model coupled to persistent stochastic polarity dynamics. While initial haptotactic migration is explained by the differential friction at the front and back of the cell, the observed complex trajectories over longer time scales arise from the interplay between differential friction, persistence, and physical confinement. Overall, our study reveals that confinement and persistence modulate the ability of cells to sense and respond to haptotactic cues and provides a framework to understand how cells navigate complex environments.
KIF3C Regulates Bergmann Glia Density and Patterning during Cerebellar Development
Authors: Waas Bridget , Allen Benjamin L.
Published: December 2024

Kinesin-2 motors have been demonstrated to regulate Hedgehog (HH) signaling, particularly within the developing cerebellum (Spassky et al., 2008; Waas et al., 2024). KIF3A/KIF3B are required for ciliogenesis in mice, and loss of this motor complex results in cerebellar hypoplasia due to lack of mitogenic response of HH-responsive cerebellar granule neural progenitors (CGNPs). Homodimeric KIF17 regulates HH-dependent CGNP proliferation through regulating levels of SHH and GLI3 but is not required for ciliogenesis in the developing cerebellum. Germline deletion ofKif3chas previously been reported to have no effect on embryonic development or gross cerebellar morphology in adult mice (Yang et al., 2001). Examination of these mice during neonatal development reveal cerebellar hypoplasia due to reduced CGNP proliferation inKif3cmutant mice. While decreased CGNP proliferation is often associated with reduced Hedgehog (HH) signaling, we did not detect a change in the levels of HH signaling inKif3c-/-cerebella. However, we observed Bergmann glia density and localization is altered inKif3cmutants, a phenotype consistent with disrupted Notch signaling. Further, we detected reduced expression ofHes1inKif3c-/-cerebella. Altogether, these data demonstrate KIF3C is required for proper cerebellar development but in a HH-independent manner.

Highlights

Kif3cis widely expressed in developing cerebellum

KIF3C regulates cerebellar size, but in a HH-independent manner

Kif3c-/-mice have increased BG density and abnormal spatial patterning
Voluntary locomotion induces an early and remote hemodynamic decrease in the large cerebral veins
Authors: Eyre Beth , Shaw Kira , Francis Sheila , Howarth Clare , Berwick Jason
Published: December 2024

Significance

Behavior regulates dural and cerebral vessels, with spontaneous locomotion inducing dural vessel constriction and increasing stimulus-evoked cerebral hemodynamic responses. It is vital to investigate the function of different vascular network components, surrounding and within the brain, to better understand the role of the neurovascular unit in health and neurodegeneration.

Aim

We characterized locomotion-induced hemodynamic responses across vascular compartments of the whisker barrel cortex: artery, vein, parenchyma, draining and meningeal vein.

Approach

Using 2D-OIS, hemodynamic responses during locomotion were recorded in 9–12-month-old awake mice: wild-type, Alzheimer’s disease (AD), atherosclerosis or mixed (atherosclerosis/AD) models. Within somatosensory cortex, responses were taken from pial vessels inside the whisker barrel region ([WBR]: “whisker artery” and “whisker vein”), a large vein from the sagittal sinus adjacent to the WBR (draining vein), and meningeal vessels from the dura mater (which do not penetrate cortical tissue).

Results

We demonstrate that locomotion evokes an initial decrease in total hemoglobin (HbT) within the draining vein before the increase in HbT within WBR vessels. The locomotion event size influences the magnitude of the HbT increase in the pial vessels of the WBR, but not of the early HbT decrease within the draining veins. Following locomotion onset, an early HbT decrease was also observed in the overlying meningeal vessels, which unlike within the cortex did not go on to exceed baseline HbT levels during the remainder of the locomotion response. We show that locomotion-induced hemodynamic responses are altered in disease in the draining vein and whisker artery, suggesting this could be an important neurodegeneration biomarker.

Conclusion

This initial reduction in HbT within the draining and meningeal veins potentially serves as a ‘space saving’ mechanism, allowing for large increases in cortical HbT associated with locomotion. Given this mechanism is impacted by disease it may provide an important target for vascular-based therapeutic interventions.
Analysis of FAIMS for the Study of Affinity-Purified Protein Complexes Using the Orbitrap Ascend Tribrid Mass Spectrometer
Authors: Goswami Pratik , Cesare Joe , Rekowski Michaella , Clark Zachary , Thornton Janet , Washburn Michael
Published: December 2024

In this study, we analyzed the combination of affinity purification mass spectrometry (AP-MS) with high-field asymmetric waveform ion mobility spectrometry (FAIMS), integrated between nanoLC-MS and an Orbitrap Ascend Tribrid Mass Spectrometer. Our primary objective was to evaluate the application of the FAIMS interface for detecting affinity purified SAP25 protein complexes with enhanced sensitivity and robustness. As a result, we observed that nanoLC-FAIMS-MS (with FAIMS) significantly improved the sensitivity and detection limits at the protein level, peptide level and significantly reduced chemical contaminants compared to nanoLC-MS alone without FAIMS (No FAIMS). This FAIMS configuration resulted in 42% and 92% increases for the total proteins and unique proteins, respectively, and 44% and 88% increases for total peptides and unique peptides compared to the No FAIMS configuration. Our in-depth comparison of FAIMS and No FAIMS shows that FAIMS outperforms by significantly reducing the missing value by <15% in datasets and plays a significant role in filtering chemical contaminants. Our findings highlight the potential of FAIMS with Orbitrap Ascend Tribrid Mass Spectrometer to enhance the depth of AP-MS analysis. The data were deposited with the MASSIVE repository with the identifier MSV000096548.
Modest functional diversity decline and pronounced composition shifts of microbial communities in a uranium-contaminated aquifer
Authors: Fan Yupeng , Wang Dongyu , Yang Joy X. , Ning Daliang , He Zhili , Zhang Ping , Rocha Andrea M. , Xiao Naijia , Michael Jonathan P. , Walker Katie F. , Joyner Dominique C. , Pan Chongle , Adams Michael W. W. , Fields Matthew W. , Alm Eric J. , Stahl David A. , Hazen Terry C. , Adams Paul D. , Arkin Adam P. , Zhou Jizhong
Published: December 2024

Background

Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated bacterial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (<3).

Results

Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy.

Conclusions

Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection.
Origin of Chromosome 12 Trisomy Surge in Human Induced Pluripotent Stem Cells (iPSCs)
Authors: Narozna Maria , Latham Megan C , Gorbsky Gary J
Published: December 2024

Cultured pluripotent stem cells are unique in being the only fully diploid immortal human cell lines. However, during continued culture, they acquire significant chromosome abnormalities. Chromosome 12 trisomy is the most common whole-chromosome abnormality found during culture of human induced pluripotent stem cells (iPSCs). The conventional paradigm is that trisomy 12 occurs very rarely but provides a proliferative advantage, enabling these cells to outcompete the diploid. Here, we challenge this prevailing model by demonstrating that trisomy 12 arises simultaneously in a very high percentage of diploid cells. Using a single cell line that reproducibly undergoes transition from diploid to trisomy 12, we found that proliferation differences alone do not account for the rapid dominance of trisomic cells. Through careful mapping by fluorescent in-situ hybridization, we identified critical transition passages where trisomic cells first appeared and swiftly gained dominance. Remarkably, single trisomic cells repeatedly emerged de novo from diploid parents. Delving deeper, we discovered an extremely high incidence of chromosome 12 anaphase bridging exclusively during transition passages, along with overrepresentation of chromosome 12 chromatids in micronuclei. These micronuclei fail to replicate during S phase. Subsequently, when these micronucleated cells enter mitosis they contain an unreplicated chromosome 12 chromatids. We also found that nearly 20% of the shorter p arms of chromosome 12 but not the longer q arms exhibited loss of subtelomeric repeats during transition passages. Chromosome 12p arms were exclusively responsible for the bridging observed in anaphase cells. Our findings unveil a novel mechanism of whole-chromosome instability in human stem cells, where chromosome 12p arm-specific segregation errors occur simultaneously in a high percentage of cells. The slight yet significant growth advantage of trisomy 12 cells allows them to persist and eventually dominate the population. Our findings detailing this novel interpretation of the origin of chromosome instability in cultured of human stem cells may have broad implications for understanding the genesis of aneuploidy across diverse biological systems.
The complete genome sequence of the crayfish pathogen CandidatusParacoxiella cheracisn.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family
Authors: Ingle Danielle J. , Walsh Calum J. , Samuel Genevieve R. , Wick Ryan R. , Davidovich Nadav , Fiocchi Eleonora , Judd Louise M. , Elliman Jennifer , Owens Leigh , Stinear Timothy P. , Basso Andrea , Pretto Tobia , Newton Hayley J.
Published: December 2024

The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever,Coxiella burnetii, represents the best characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the previously referred to as CandidatusCoxiella cheraxirepresents a novel genus within this family, herein denoted CandidatusParacoxiella cheracis. Interestingly, we demonstrate that CandidatusP. cheracisencodes for a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen. In silico analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologues of several importantC. burnetiieffectors including a homologue of CpeB that was demonstrated to be a Dot/Icm substrate inC. burnetii.

IMPORTANCE

Using long-read sequencing technology we have uncovered the full genome sequence of CandidatusParacoxiellacheracis, a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insight into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. CandidatusP. cheracisalso represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. CandidatusP. cheracispossesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology manipulating effector proteins.
Spatiochemical Investigation of Potential Biocontrol Agents AgainstPhytophthora capsiciInfection in Tomato
Authors: Robinson Jamille Y. , Shepard Hawkins S. , Ambachew Daniel , Eyegheleme Peter J. , May Jody C. , Mmbaga Margaret T. , McLean John A.
Published: December 2024

Biological control agents can offer an eco-friendly and more sustainable alternative to conventional chemical pesticides, providing protection against destructive pathogens, such asPhytophthora capsici,while reducing potential environmental harm associated with synthetic pesticide use in agricultural production systems. This work demonstrates the biocontrol effectiveness of variousBacillusspecies, includingBacillus vallismortis,Bacillus amyloliquefaciens, Bacillus thuringiensis,andBacillus subtilis, against the widespread plant pathogen,Phytophthora capsici. Our studies showed thatBacillus thuringiensisandBacillus subtilispromote plant growth and provide protection againstPhytophthora capsiciin bothin vitroandin vivogreenhouse studies, whileBacillus vallismortisandBacillus amyloliquefacienswere effectivein vitrobut notin vivo. Specifically,Bacillus thuringiensiswas observed to both hinder the growth ofPhytophthora capsiciand enhance plant resilience to this oomycete pathogen. To probe the molecular interactions between biocontrol agent and pathogen, a dual culture ofBacillus thuringiensisandPhytophthora capsiciwas analyzedin situusing a mass spectrometry imaging workflow that implemented desorption electrospray ionization. This imaging approach spatially investigated the complex biochemical interactions that serve as the molecular foundation for the effectiveness of these biological control agents in crop protection, including antagonistic interactions that may be fundamental to their method of action. Herein, we demonstrate the benefits of biological control agent application in tomato cultivation, including enhanced pathogen control and plant growth, and showcase the strengths of desorption electrospray ionization-mass spectrometry imaging when applied to the spatially-resolved molecular characterization of agriculturally relevant microorganisms.