bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeting B and T lymphocyte attenuator regulates lupus disease development in NZB/W mice
Authors: Gherardi Léa , Aubergeon Lucie , Sayah Mélanie , Fauny Jean-Daniel , Dumortier Hélène , Monneaux Fanny
Published: June 2024

B and T Lymphocyte Attenuator (BTLA) is a co-inhibitory receptor expressed by most immune cells, playing a role in negatively regulating immune responses. Studies in MRL/lpr lupus mice deficient for BTLA, indicate that BTLA has a protective role in lupus. We have previously shown an altered BTLA expression by regulatory T cells and an impaired capacity of BTLA to inhibit CD4+T cell activation in lupus patients. In this study, we thoroughly analyzed BTLA expression and function in the NZB/W lupus-mouse model. We found that diseased NZB/W mice exhibit a BTLA expression and function pattern similar to that observed in lupus patients, emphasizing the importance of this mouse model in evaluating the therapeutic potential of targeting BTLA. Administration of a monoclonal anti-BTLA antibody (clone 6F7, which displays agonist propertiesex vivo) into pre-diseased NZB/W mice resulted in a delayed onset of proteinuria, limited kidney damages and an increased survival rate compared to isotype-treated mice. This beneficial effect was associated with a decrease in circulating B cell frequency and required continuous exposure to the antibody. Regarding its mode of action, we demonstrated that the 6F7 antibody is not a depleting antibody and does not block HVEM binding to BTLA, but instead induces BTLA down modulation, leading to a selective reduction of follicular B cell numbers, and exhibitsin vivoagonist activity. Overall, our data confirm the involvement of BTLA in lupus pathogenesis and provide the first evidence that BTLA is a potential therapeutic target for the treatment of lupus.
DockQ v2: Improved automatic quality measure for protein multimers, nucleic acids, and small molecules
Authors: Mirabello Claudio , Wallner Björn
Published: June 2024

It is important to assess the quality of modeled biomolecules to benchmark and assess the performance of different prediction methods. DockQ has emerged as the standard tool for assessing the quality of protein interfaces in model structures against given references. However, as predictions of large multimers with multiple chains become more common, there is a need to update DockQ with more functionality for robustness and speed. Moreover, as the field progresses and more methods are released to predict interactions between proteins and other types of molecules, such as nucleic acids and small molecules, it becomes necessary to have a tool that can assess all types of interactions. Here, we present a complete reimplementation of DockQ in pure Python. The updated version of DockQ is more portable, faster and introduces novel functionalities, such as automatic DockQ calculations for multiple interfaces and automatic chain mapping with multi-threading. These enhancements are designed to facilitate comparative analyses of protein complexes, particularly large multi-chain complexes. Furthermore, DockQ is now also able to score interfaces between proteins, nucleic acids, and small molecules.

Code

https://wallnerlab.org/DockQ
Predicting metal-protein interactions using cofolding methods: Status quo
Authors: Dürr Simon L. , Rothlisberger Ursula
Published: June 2024

Metals play important roles for enzyme function and many therapeutically relevant proteins. Despite the fact that the first drugs developed via computer aided drug design were metalloprotein inhibitors, many computational pipelines for drug discovery still discard metalloproteins due to the difficulties of modelling them computationally. New “cofolding” methods such as AlphaFold3 (AF3) (Abramson et al., 2024) and RoseTTAfold-AllAtom (RFAA) (Krishna et al., 2024) promise to improve this issue by being able to dock small molecules in presence of multiple complex cofactors including metals or covalent modifications. Here, we analyze the current status for metal ion prediction using these methods. We find that currently only AF3 provides realistic predictions for metal ions, RFAA in contrast does perform worse than more specialized models such as AllMetal3D in predicting the location of metal ions accurately. We find that AF3 predictions are consistent with expected physico-chemical trends/intuition whereas RFAA often also predicts unrealistic metal ion locations.
Contributions of action potentials to scalp EEG: theory and biophysical simulations
Authors: Brake Niklas , Khadra Anmar
Published: June 2024

Differences in the apparent 1/f component of neural power spectra require correction depending on the underlying neural mechanisms, which remain incompletely understood. Past studies suggest that neuronal spiking produces broadband signals and shapes the spectral trend of invasive macroscopic recordings, but it is unclear to what extent action potentials (APs) influence scalp EEG. Here, we combined biophysical simulations with statistical modelling to examine the amplitude and spectral content of scalp potentials generated by the electric fields from spiking activity. We found that under physiological conditions, synchronized aperiodic spiking can account for at most 1% of the spectral density observed in EEG recordings, suggesting that the EEG spectral trend reflects only external noise at high frequencies. Indeed, by analyzing previously published data from pharmacologically paralyzed subjects, we confirmed that the EEG spectral trend is entirely explained by synaptic timescales and electromyogram contamination. We also investigated rhythmic EEG generation, finding that APs can generate narrowband power between approximately 60 and 600 Hz, thus reaching frequencies much faster than the timescales of excitatory synaptic currents. Our results imply that different spectral detrending strategies are required for high frequency oscillations compared to slower synaptically generated EEG rhythms.
Obg-like ATPase 1 Genetic Deletion Leads to Dilated Cardiomyopathy in Mice and Structural Changes in Drosophila Heart
Authors: Dubey Praveen K , Singh Sarojini , Khalil Hussain , Kommini Goutham K , Bhat Krishna Moorthi , Krishnamurthy Prasanna
Published: June 2024

Cardiomyopathy, disease of the heart muscle, is a significant contributor to heart failure. The pathogenesis of cardiomyopathy is multifactorial and involves genetic, environmental, and lifestyle factors. Identifying and characterizing novel genes that contribute to cardiac pathophysiology are crucial for understanding cardiomyopathy and effective therapies.

In this study, we investigated the role of a novel gene,Obg-like ATPase 1(Ola1), in cardiac pathophysiology using a cardiac-specific knockout mouse model as well as a Drosophila model. Our previous work demonstrated that OLA1 modulates the hypertrophic response of cardiomyocytes through the GSK-beta/beta-catenin signaling pathway. Furthermore, recent studies have suggested that OLA1 plays a critical role in organismal growth and development. For example,Ola1null mice exhibit increased heart size and growth retardation. It is not known, however, if loss of function forOla1leads to dilated cardiomyopathy.

We generated cardiac-specificOla1knockout mice (OLA1-cKO) to evaluate the role of OLA1 in cardiac pathophysiology. We found thatOla1-cKO in mice leads to dilated cardiomyopathy (DCM) and left ventricular (LV) dysfunction. These mice developed severe LV dilatation, thinning of the LV wall, reduced LV function, and, in some cases, ventricular wall rupture and death. In Drosophila, RNAi-mediated knock-down specifically in developing heart cells led to the change in the structure of pericardial cells from round to elongated, and abnormal heart function. This also caused significant growth reduction and pupal lethality. Thus, our findings suggest that OLA1 is critical for cardiac homeostasis and that its deficiency leads to dilated cardiomyopathy and dysfunction. Furthermore, our study highlights the potential of theOla1gene as a therapeutic target for dilated cardiomyopathy and heart failure.
DrugGym: A testbed for the economics of autonomous drug discovery
Authors: Retchin Michael , Wang Yuanqing , Takaba Kenichiro , Chodera John D.
Published: June 2024

Drug discovery is stochastic. The effectiveness of candidate compounds in satisfying design objectives is unknown ahead of time, and the tools used for prioritization—predictive models and assays—are inaccurate and noisy. In a typical discovery campaign, thousands of compounds may be synthesized and tested before design objectives are achieved, with many others ideated but deprioritized. These challenges are well-documented, but assessing potential remedies has been difficult. We introduceDrugGym, a frame-work for modeling the stochastic process of drug discovery. Emulating biochemical assays with realistic surrogate models, we simulate the progression from weak hits to sub-micromolar leads with viable ADME. We use this testbed to examine how different ideation, scoring, and decision-making strategies impact statistical measures of utility, such as the probability of program success within predefined budgets and the expected costs to achieve target candidate profile (TCP) goals. We also assess the influence of affinity model inaccuracy, chemical creativity, batch size, and multi-step reasoning. Our findings suggest that reducing affinity model inaccuracy from 2 to 0.5 pIC50 units improves budget-constrained success rates tenfold. DrugGym represents a realistic testbed for machine learning methods applied to the hit-to-lead phase. Source code is available atwww.drug-gym.org.
A glial circadian gene expression atlas reveals cell type and disease-specific reprogramming in response to amyloid pathology or aging
Authors: Sheehan Patrick W. , Fass Stuart , Sapkota Darshan , Kang Sylvia , Hollis Henry C. , Lawrence Jennifer H. , Anafi Ron C. , Dougherty Joseph D. , Fryer Jon D. , Musiek Erik S.
Published: June 2024

While circadian rhythm disruption may promote neurodegenerative disease, how aging and neurodegenerative pathology impact circadian gene expression patterns in different brain cell types is unknown. Here, we used translating ribosome affinity purification methods to define the circadian translatomes of astrocytes, microglia, and bulk cerebral cortex, in healthy mouse brain and in the settings of amyloid-beta plaque pathology or aging. Our data reveal that glial circadian translatomes are highly cell type-specific and exhibit profound, context-dependent reprogramming of rhythmic transcripts in response to amyloid pathology or aging. Transcripts involved in glial activation, immunometabolism, and proteostasis, as well as nearly half of all Alzheimer Disease (AD)-associated risk genes, displayed circadian oscillations, many of which were altered by pathology. Amyloid-related differential gene expression was also dependent on time of day. Thus, circadian rhythms in gene expression are cell- and context dependent and provide important insights into glial gene regulation in health, AD, and aging.
Targeting Unique Ligand Binding Domain Structural Features Downregulates DKK1 in Y537S ESR1 Mutant Breast Cancer Cells
Authors: Young Kristen S , Hancock Govinda R , Fink Emma C , Zigrossi Alexandra , Flowers Brenna , Cooper D A , Ngyuen V T , Martinez Millie , Mon Khin Su , Bosland Maarten C , Zak David , Runde Austin P , Sharifi Marina N , Kastrati Irida , Minh David , Kregel Steven , Fanning Sean W
Published: June 2024

Resistance to endocrine therapies remains a major clinical hurdle in breast cancer. Mutations to estrogen receptor alpha (ERα) arise after continued therapeutic pressure. Next generation selective estrogen receptor modulators and degraders/downregulators (SERMs and SERDs) show clinical efficacy, but responses are often non-durable. A tyrosine to serine point mutation at position 537 in the ERα ligand binding domain (LBD) is among the most common and most pathogenic alteration in this setting. It enables endocrine therapy resistance by superceding intrinsic structural-energetic gatekeepers of ER hormone-dependence, it enhances metastatic burden by enabling neomorphic ER-dependent transcriptional programs, and it resists SERM and SERD inhibition by reducing their binding affinities and abilities to antagonize transcriptional coregulator binding. However, a subset of SERMs and SERDs can achieve efficacy by adopting poses that force the mutation to engage in a new interaction that favors the therapeutic receptor antagonist conformation. We previously described a chemically unconventional SERM, T6I-29, that demonstrates significant anti-proliferative activities in Y537S ERα breast cancer cells. Here, we use a comprehensive suite of structural-biochemical, in vitro, and in vivo approaches to better T6I-29′s activities in breast cancer cells harboring Y537S ERα. RNA sequencing in cells treated with T6I-29 reveals a neomorphic downregulation of DKK1, a secreted glycoprotein known to play oncogenic roles in other cancers. Importantly, we find that DKK1 is significantly enriched in ER+ breast cancer plasma compared to healthy controls. This study shows how new SERMs and SERDs can identify new therapeutic pathways in endocrine-resistant ER+ breast cancers.
IL1A enhances TNF-induced retinal ganglion cell death
Authors: Andersh Katherine M. , MacLean Michael , Howell Gareth R. , Libby Richard T.
Published: June 2024

Glaucoma is a neurodegenerative disease that leads to the death of retinal ganglion cells (RGCs). A growing body of literature suggests a role for neuroinflammation in RGC death after glaucoma-relevant insults. For instance, it was shown that deficiency of three proinflammatory cytokines, complement component 1, subcomponent q (C1q), interleukin 1 alpha (Il1a), and tumor necrosis factor (Tnf), resulted in near complete protection of RGCs after two glaucoma-relevant insults, optic nerve injury and ocular hypertension. While TNF and C1Q have been extensively investigated in glaucoma-relevant model systems, the role of IL1A in RGC is not as well defined. Thus, we investigated the direct neurotoxicity of IL1A on RGCs in vivo. Intravitreal injection of IL1A did not result in RGC death at either 14 days or 12 weeks after insult. Consistent with previous studies, TNF injection did not result in significant RGC loss at 14 days but did after 12 weeks. Interestingly, IL1A+TNF resulted in a relatively rapid RGC death, driving significant RGC loss two weeks after injection. JUN activation and SARM1 have been implicated in RGC death in glaucoma and after cytokine insult. Using mice deficient in JUN or SARM1, we show RGC loss after IL1A+TNF insult is JUN-independent and SARM1-dependent. Furthermore, RNA-seq analysis showed that RGC death by SARM1 deficiency does not stop the neuroinflammatory response to IL1A+TNF. These findings indicate that IL1A can potentiate TNF-induced RGC death after combined insult is likely driven by a SARM1-dependent RGC intrinsic signaling pathway.
Precise cell recovery by cell nucleus united transcript (CellCUT) for enhanced spatial transcriptomics
Authors: Hong Bei , Zeng Bo , Feng Huimin , Liu Zeyuan , Ni Qi , Wang Wei , Li Mayuqing , Yang Meng , Wang Mengdi , Sun Le , Zhong Suijuan , Wu Qian , Wang Xiaoqun
Published: June 2024

Cell segmentation is the first step in parsing spatial transcriptomic data, often a challenging task. Existing cell segmentation methods do not fully leverage spatial cues between nuclear images and transcripts, tending to produce undesirable cell profiles for densely packed cells. Here, we propose CellCUT to perform cell segmentation and transcript assignment without additional manual annotations. CellCUT provides a flexible computational framework that maintains high segmentation accuracy across diverse tissues and spatial transcriptomics protocols, showing superior capabilities compared to state-of-the-art methods. CellCUT is a robust model to deal with undesirable data such as low contrast intensity, localized absence of transcripts, and blurred images. CellCUT supports a human-in-the-loop workflow to enhance its generalizability to customized datasets. CellCUT identifies subcellular structures, enabling insights at both the single-cell and subcellular levels.
Dihydromyricetin promotes GLP-1 secretion to improve insulin resistance via “gut microbiota-CDCA”
Authors: Li Pengfei , Zhang Yong , Lang Hedong , Hou Pengfei , Yao Yu , Zhang Ruiliang , Wang Xiaolan , Zhang QianYong , Mi Mantian , Yi Long
Published: June 2024

Dihydromyricetin (DHM) is a polyphenolic phytochemical found mainly in plants such asAmpelopsis grossedentata,which has beneficial effects on insulin resistance. However, the specific mechanism has not been clarified. In this study, C57BL/6 mice were exposed to a high-fat diet (HFD) for eight weeks. DHM could improve insulin resistance via enhancing the incretin effect. DHM increased serum GLP-1 by improving intestinal GLP-1 secretion and inhibiting GLP-1 decomposition, associated with the alteration of intestinal intraepithelial lymphocytes (IELs) proportions and decreased expression of CD26 in IELs and TCRαβ+CD8αβ+IELs in HFD-induced mice. Meanwhile, DHM could ameliorate GLP-1 level and insulin resistance by modulation of gut microbiota and the metabolites, particularly the regulation of intestinal bile acid CDCA content, followed by the inhibition of FXR expression in intestinal L cells as well as increased Gcg mRNA expression and the secretion of GLP-1. These findings clarify the role of the “gut microbiota-CDCA” pathway in the improvement of intestinal GLP-1 levels in HFD-induced mice by DHM administration, providing a new pharmacological target for the prevention of insulin resistance.
A temporally restricted function of the Dopamine receptor Dop1R2 during memory formation
Authors: Kaldun Jenifer C. , Fritsch Cornelia , Komarov Nikita , Sprecher Simon G.
Published: June 2024

Dopamine is a crucial neuromodulator, which is involved in many brain processes, including learning and the formation of memories. Dopamine acts through multiple receptors and controls an intricate signaling network to regulate different tasks. While the diverse functions of dopamine are intensely studied, the interplay and role of the distinct dopamine receptors to regulate different processes is less well understood. An interesting candidate is the dopamine receptor Dop1R2 (also known as Damb), as it could connect to different downstream pathways. Dop1R2 is reported to be involved in forgetting and memory maintenance, however, the circuits requiring the receptors are unknown. To study Dop1R2 and its role in specific spatial and temporal contexts, we generated a conditional knock-out line using the CRISPR-Cas9 technique. Two FRT sites were inserted, allowing flippase-mediated excision of the dopamine receptor in neurons of interest. To study the function of Dop1R2, we knocked it out conditionally in the Mushroom body ofDrosophila melanogaster, a well-studied brain region for memory formation. We show that Dop1R2 is required for later memory forms but not for short-term memories for both aversive and appetitive memories. Moreover, Dop1R2 is specifically required in the the α/β-lobe and the α’/β’-lobe but not in the γ-lobe of the Mushroom body. Our findings show a spatially and temporally restricted role of Dop1R2 in the process of memory formation highlighting the differential requirement of receptors during distinct phases of learning.
Emergence of activation or repression in transcriptional control under a fixed molecular context
Authors: Martinez-Corral Rosa , Friedrich Dhana , Frömel Robert , Velten Lars , Gunawardena Jeremy , DePace Angela H.
Published: June 2024

For decades, studies have noted that transcription factors (TFs) can behave as either activators or repressors of different target genes. More recently, evidence suggests TFs can act on transcription simultaneously in positive and negative ways. Here we use biophysical models of gene regulation to define, conceptualize and explore these two aspects of TF action: “duality”, where TFs can be overall both activators and repressors at the level of the transcriptional response, and “coherent and incoherent” modes of regulation, where TFs act mechanistically on a given target gene either as an activator or a repressor (coherent) or as both (incoherent). For incoherent TFs, the overall response depends on three kinds of features: the TF’s mechanistic effects, the dynamics and effects of additional regulatory molecules or the transcriptional machinery, and the occupancy of the TF on DNA. Therefore, activation or repression can be tuned by just the TF-DNA binding affinity, or the number of TF binding sites, given an otherwise fixed molecular context. Moreover, incoherent TFs can cause non-monotonic transcriptional responses, increasing over a certain concentration range and decreasing outside the range, and we clarify the relationship between non-monotonicity and common assumptions of gene regulation models. Using the mammalian SP1 as a case study and well controlled, synthetically designed target sequences, we find experimental evidence for incoherent action and activation, repression or non-monotonicity tuned by affinity. Our work highlights the importance of moving from a TF-centric view to a systems view when reasoning about transcriptional control.
Bio-inspired augmented reality: an interactive, digital twin ofC. elegans
Authors: Sacristán Daniel , Jenderny Sebastian , Hövel Philipp , Albers Christian , Beyer Isabella , Ochs Karlheinz
Published: June 2024

This work presents a digital twin of the nematodeCaenorhabditis elegans(C. elegans), an organism whose biology has been extensively studied. The digital twin can emulate neuronal activity and the corresponding muscle activity, and performs basic locomotion movement. The underlying mathematical model ofC. eleganscan be realized directly as an electronic circuit and is additionally implemented as a ready-to-use simulation in software. We implemented the digital twin in augmented reality (AR) as a novel format that extends the content of a traditional paper with an interactive visualization in the real world. The figures in the paper are the anchor point for the AR that can be accessed by the readers via an open-source app, which is freely available for tablets, phones, and AR glasses. This enables immersive experiences of the three-dimensional visualization in the real world from a perspective chosen by the reader, supplementing the traditional, flat figure layout of the paper. For researchers, the digital twin further provides a useful tool that is highly relevant and versatile for future developments. At the same time, its manifold possibilities for scientific outreach also aim at making the topic more engaging for a broader audience.
Folding of mRNA-DNA origami for controlled translation and viral vector packaging
Authors: Seitz Iris , Saarinen Sharon , Wierzchowiecka Julia , Cornelissen Jeroen J. L. M. , Linko Veikko , Kostiainen Mauri A.
Published: June 2024

mRNA is an important molecule in vaccine development and treatment of genetic disorders. Its capability to hybridize with DNA oligonucleotides in a programmable manner facilitates the formation of RNA-DNA origami structures, which can possess a well-defined morphology and serve as rigid supports for mRNA delivery. However, to date, compre- hensive studies on the requirements for efficient folding of mRNA into distinct mRNA-DNA structures while preserving its translation func- tionality remain elusive. Here, we systematically investigate the impact of design parameters on the folding of protein-encoding mRNA into mRNA-DNA origami structures and demonstrate the importance of the availability of ribosome-binding sequences on the translation effi- ciency. Furthermore, these hybrid structures can be encapsulated inside virus capsids for protecting them against nuclease degradation and also for enhancing their cellular uptake. This multicomponent system therefore showcases a modular and versatile nanocarrier. Our work pro- vides valuable insight into the design of mRNA-DNA origami structures contributing to the development of mRNA-based gene delivery platforms.
Sympathetic innervation of interscapular brown adipose tissue is not a predominant mediator of oxytocin-elicited reductions of body weight and adiposity in male diet-induced obese mice
Authors: Edwards Melise M. , Nguyen Ha K. , Dodson Andrew D. , Herbertson Adam J. , Wolden-Hanson Tami , Wietecha Tomasz , Honeycutt Mackenzie K. , Slattery Jared D. , O’Brien Kevin D. , Graham James L. , Havel Peter J. , Mundinger Thomas O. , Sikkema Carl , Peskind Elaine R. , Ryu Vitaly , Taborsky Gerald J. , Blevins James E.
Published: June 2024

Previous studies indicate that CNS administration of oxytocin (OT) reduces body weight in high fat diet-induced obese (DIO) rodents by reducing food intake and increasing energy expenditure (EE). We recently demonstrated that hindbrain (fourth ventricular [4V]) administration of OT elicits weight loss and elevates interscapular brown adipose tissue temperature (TIBAT, a surrogate measure of increased EE) in DIO mice. What remains unclear is whether OT-elicited weight loss requires increased sympathetic nervous system (SNS) outflow to IBAT. We hypothesized that OT-induced stimulation of SNS outflow to IBAT contributes to its ability to activate BAT and elicit weight loss in DIO mice. To test this hypothesis, we determined the effect of disrupting SNS activation of IBAT on the ability of 4V OT administration to increase TIBATand elicit weight loss in DIO mice. We first determined whether bilateral surgical SNS denervation to IBAT was successful as noted by ≥ 60% reduction in IBAT norepinephrine (NE) content in DIO mice. NE content was selectively reduced in IBAT at 1-, 6- and 7-weeks post-denervation by 95.9±2.0, 77.4±12.7 and 93.6±4.6% (P<0.05), respectively and was unchanged in inguinal white adipose tissue, pancreas or liver. We subsequently measured the effects of acute 4V OT (1, 5 µg ≈ 0.99, 4.96 nmol) on TIBATin DIO mice following sham or bilateral surgical SNS denervation to IBAT. We found that the high dose of 4V OT (5 µg ≈ 4.96 nmol) elevated TIBATsimilarly in sham mice as in denervated mice. We subsequently measured the effects of chronic 4V OT (16 nmol/day over 29 days) or vehicle infusions on body weight, adiposity and food intake in DIO mice following sham or bilateral surgical denervation of IBAT. Chronic 4V OT reduced body weight by 5.7±2.23% and 6.6±1.4% in sham and denervated mice (P<0.05), respectively, and this effect was similar between groups (P=NS). OT produced corresponding reductions in whole body fat mass (P<0.05). Together, these findings support the hypothesis that sympathetic innervation of IBAT is not necessary for OT-elicited increases in BAT thermogenesis and reductions of body weight and adiposity in male DIO mice.
Femtosecond X-ray snapshots reveal correlated displacements of specific distal atoms in a protein crystal
Authors: Gagnér Viktor Ahlberg , Jensen Maja , Olsson Torbjörn Nur , Sánchez Juan Cabello , Bengtsson Åsa U. J. , Ekström J. Carl , Zhang Zhedong , Jurgilaitis Andrius , Kroon David , Pham Van-Thai , Checchia Stefano , Coudert-Alteirac Hélène , Rodilla Helena , Stake Jan , Zhaunerchyk Vitali , Friedman Ran , Larsson Jörgen , Mezzasalma Stefano A. , Katona Gergely
Published: June 2024

Protein dynamics is shaped by interactions between thermal fluctuations, external forces, and molecular structures. Thermal fluctuations have high frequencies and are hence very challenging to quantify. We were able to record femtosecond X-ray diffraction snapshots and determine atomic displacements of crystalline bovine trypsin atoms either in the native steady state or in a transient state initiated by a short THz pulse, the results of which were interpreted with numerical simulations. In the absence of THz pulses, specific distal atoms exhibited correlated movements. Under the influence of THz fields, numerical simulations demonstrated a slight enhancement of displacement correlations. The experimental results revealed a contrasting response to short THz pulses, where the measured displacements were not solely determined by the atom position, but also influenced by the atomic type. These findings call for a reinterpretation of the dynamic properties inherent in folded protein structures and the physical principles behind the formation of protein assemblies. To this end, a theoretical model was developed for lattice deformations and local excitations entraining a (squeezed) coherent steady state, explaining the emergence of atom correlations. The model accounts for the magnitudes of atomic displacements and fluctuations through a balance between harmonic and anharmonic coupling forces.
A Self-Supervised Learning Approach for High Throughput and High Content Cell Segmentation
Authors: Lam Van , Byers Jeff M. , Robitaille Michael , Kaler Logan , Christodoulides Joseph A. , Raphael Marc P.
Published: June 2024

In principle, AI-based algorithms should enable rapid and accurate cell segmentation in high-throughput settings. However, reliance on large datasets, human input, and computational expertise, along with issues of limited generalizability and the necessity for specialized training are notable drawbacks of nominally “automated” segmentation tools. To overcome this roadblock, we introduce an innovative, user-friendly self-supervised learning method (SSL) for pixel classification that requires no dataset-specific modifications or curated labelled data sets, thus providing a more streamlined cell segmentation approach for high-throughput and high-content research. We demonstrate that our algorithm meets the criteria of being fully automated with versatility across various magnifications, optical modalities and cell types. Moreover, our SSL algorithm is capable of identifying complex cellular structures and organelles which are otherwise easily missed, thereby broadening the machine learning applications to high-content imaging. Our SSL technique displayed consistent F1 scores across segmented images, with scores ranging from 0.831 to 0.876, outperforming the popular Cellpose algorithm, which showed greater variance in F1 scores from 0.645 to 0.8815, mainly due to errors in segmentation. On average, our SSL method achieved an F1 score of 0.852 ±0.017, exceeding Cellpose’s average of 0.804 ±0.08. This novel SSL method not only advances segmentation accuracy but also minimizes the need for extensive computational expertise and data security concerns, making it easier for biological researchers to incorporate automated segmentation into their studies.
Artificial Intelligence driven Benchmarking Tool for Emission Reduction in Canadian Dairy Farms
Authors: Parmar Pratik Mukund , Bi Hangqing , Neethirajan Suresh
Published: June 2024

This study develops an Artificial Intelligence-driven benchmarking tool to reduce methane emissions in Canadian dairy farms, responding to the urgent need to mitigate environmental impacts from agriculture. Utilizing a comprehensive dataset from over 1000 dairy farms and processors across Canada, combined with satellite-driven methane emission data, we apply advanced machine learning technologies and data analytics, including geospatial analysis and time series forecasting. This approach identifies critical emission hotspots and temporal trends. We tested several predictive models—ARIMA, LSTM, GBR, and PROPHET—with the LSTM model showing the greatest accuracy in forecasting emissions, demonstrated by the lowest Root Mean Squared Error (RMSE) of 15.40. Our results highlight the transformative potential of AI tools in agricultural environmental management by providing dairy farmers and policymakers with precise, real-time emission insights. This facilitates informed decision-making and the implementation of effective emission reduction strategies. This study not only advances understanding of emission dynamics in dairy farming but also underscores the role of technology in sustainable agricultural practices and achieving environmental targets consistent with global agreements.
SLO2.1/NALCN Functional Complex Activity in Mouse Myometrial Smooth Muscle Cells During Pregnancy
Authors: Ferreira Juan J. , Kent Lindsey N. , McCarthy Ronald , Butler Alice , Ma Xiaofeng , Peramsetty Nikita , Amazu Chinwendu , Zhang Alexander , Whitter Grace C. , England Sarah K. , Santi Celia M.
Published: June 2024

At the end of pregnancy, the uterus transitions from a quiescent to a highly contractile state. This is partly due to depolarization of the resting membrane potential in uterine (myometrial) smooth muscle cells (MSMCs). Experiments with human MSMCs showed that the membrane potential is regulated by a functional complex between the sodium (Na+)-activated potassium (K+) channel SLO2.1 and the Na+Leak Channel Non-Selective (NALCN). In human MSMCs, Na+entering through NALCN activates SLO2.1, leading to K+efflux, membrane hyperpolarization (cells become more negative inside), and reduced contractility. Decreased SLO2.1/NALCN activity results in reduced K+efflux, leading to membrane depolarization, Ca2+influx via voltage-dependent calcium channels, and increased MSMC contractility. However, all of these experiments were performed with MSMCs isolated from women at term, so the role of the SLO2.1/NALCN complex early in pregnancy was speculative. To address this question here, we examined the role of the SLO2.1/NALCN complex in regulating mouse MSMC membrane potential across pregnancy. We report thatSlo2.1andNalcnexpression change along pregnancy, being more highly expressed in MSMCs from non-pregnant and early pregnant mice than in those from late-pregnant mice.

Functional studies revealed that SLO2.1 channels mediate a significant portion of the K+current in mouse MSMCs, particularly in cells from non-pregnant and early pregnant mice. Activation of SLO2.1 by Na+influx through NALCN led to membrane hyperpolarization in MSMCs from early pregnancy but not in MSMCs from later pregnancy. Moreover, we found that the NALCN/SLO2.1 complex regulates intracellular Ca2+responses more in MSMCs from non-pregnant and early pregnancy mice than in MSMCs from late pregnancy. Together, these findings reveal that the SLO2.1/NALCN functional complex is conserved between mouse and humans and functions throughout pregnancy. This work could open avenues for targeted pharmacological interventions in pregnancy-related complications.
Solu – a Cloud Platform for Real-Time Genomic Pathogen Surveillance
Authors: Moilanen Timo J , Visuri Kerkko , Lehtinen Jonatan , Ortega Sanz Irene , Steenwyk Jacob L. , Sihvonen Samuel
Published: June 2024

Background: Genomic surveillance is extensively used for tracking public health outbreaks and healthcare-associated pathogens. Despite advancements in bioinformatics pipelines, there are still significant challenges in terms of infrastructure, expertise, and security when it comes to continuous surveillance. The existing pipelines often require the user to set up and manage their own infrastructure and are not designed for continuous surveillance that demands integration of new and regularly generated sequencing data with previous analyses. Additionally, academic projects often do not meet the privacy requirements of healthcare providers. Results: We present Solu, a cloud-based platform that integrates genomic data into a real-time, privacy-focused surveillance system. Evaluation: Solu's accuracy for taxonomy assignment, antimicrobial resistance genes, and phylogenetics, was comparable to established pathogen surveillance pipelines. In some cases, Solu identified antimicrobial resistance genes that were previously undetected. Together, these findings demonstrate the efficacy of our platform. Conclusions: By enabling reliable, user-friendly, and privacy-focused genomic surveillance, Solu has the potential to bridge the gap between cutting-edge research and practical, widespread application in healthcare settings. The platform is available for free academic use at platform.solugenomics.com.
L-Arginine and asymmetric dimethylarginine (ADMA) transport across the mouse blood-brain and blood-CSF barriers: evidence of saturable transport at both interfaces and CNS to blood efflux
Authors: Fidanboylu Mehmet , Thomas Sarah Ann
Published: June 2024

L-Arginine is the physiological substrate for the nitric oxide synthase (NOS) family, which synthesises nitric oxide (NO) in endothelial and neuronal cells. NO synthesis can be inhibited by endogenous asymmetric dimethylarginine (ADMA). NO has explicit roles in cellular signalling and vasodilation. Impaired NO bioavailability represents the central feature of endothelial dysfunction associated with vascular diseases. Interestingly, dietary supplementation withL-arginine has been shown to alleviate endothelial dysfunctions caused by impaired NO synthesis. In this study the transport kinetics of [3H]-arginine and [3H]-ADMA into the central nervous system (CNS) were investigated using physicochemical assessment and thein situbrain/choroid plexus perfusion technique in anesthetized mice. Results indicated thatL-arginine and ADMA are tripolar cationic amino acids and have a gross charge at pH 7.4 of 0.981.L-Arginine (0.00149±0.00016) has a lower lipophilicity than ADMA (0.00226±0.00006) as measured using octanol-saline partition coefficients. Thein situperfusion studies revealed that [3H]-arginine and [3H]-ADMA can cross the blood-brain barrier (BBB) and the blood-CSF barrier. [3H]-Arginine (11.6nM) and [3H]-ADMA (62.5nM) having unidirectional transfer constants (Kin) into the frontal cortex of 5.84±0.86 and 2.49±0.35 μl.min-1.g-1, respectively, and into the CSF of 1.08±0.24 and 2.70±0.90 μl.min-1.g-1, respectively. In addition, multiple-time uptake studies revealed the presence of CNS-to-blood efflux of ADMA. Self- and cross-inhibition studies indicated the presence of transporters at the BBB and the blood-CSF barriers for both amino acids, which were shared to some degree. Importantly, these results are the first to demonstrate: (i) saturable transport of [3H]-ADMA at the blood-CSF barrier (choroid plexus) and (ii) a significant CNS to blood efflux of [3H]-ADMA. Our results suggest that the arginine paradox, in other words the clinical observation that NO-deficient patients respond well to oral supplementation withL-arginine even though the plasma concentration is easily sufficient to saturate endothelial NOS, could be related to ADMA transport.
Serotonin-2B receptor (5-HT2BR) expression and binding in the brain of ageing APPswe/PS1de9transgenic mice and in human Alzheimer’s Disease brain tissue
Authors: Anzalone Marco , Karam Sarmad A. , Briting Sanne R. R. , Petersen Sussanne , Thomsen Majken B. , Landau Anne M. , Finsen Bente , Metaxas Athanasios
Published: June 2024

Although evidence of dysregulation in central serotonergic signaling is widespread in Alzheimer’s disease (AD), relatively little is known about the specific involvement of the serotonin-2B receptor (5-HT2BR) subtype. Here, we assessed 5-HT2BR expression and binding in brain tissue fromAPPswe/PS1dE9transgenic (TG) mice and AD patients. 5-HT2BR mRNA was measured by RT-qPCR in 3-to >18-month-old TG and wild-type (WT) littermate mice (n=3-8), and in middle frontal gyrus samples from female, AD and control subjects (n=7-10). The density of 5-HT2BRs was measured by autoradiography using 1 nM [3H]RS127445 and 1 μM LY266097. In both mouse and human samples, 5-HT2BR mRNA was detectable after 33 amplification cycles. Levels in WT mice, not TG mice, increased with age, and were higher in AD patients compared to control subjects. [3H]RS127445 binding was low in the mouse brain, detected after 3 months of age. 5-HT2BR density was overall lower in the hippocampus of TG compared to WT mice. Specific binding was too low to be reliably quantified in the human samples. These data provide evidence of a different 5-HT2BR expression and binding in theAPPswe/PS1dE9TG model of AD and AD patients. Studies investigating the functional involvement of the 5-HT2BR in AD are warranted.
Arterial effects of anthracycline: structural and inflammatory assessments in non-human primates and lymphoma patients using18F-FDG positron emission tomography
Authors: Rankin Stephen , Fountain Caitlin , Gemmell Alastair J , Quinn Daire , Henderson Alasdair , McClure John , Small Sandy , Venugopal Balaji , McKay Pamela , Slomka Piotr J , Colville David , Petrie Mark C , Meléndez Giselle C. , Lang Ninian N
Published: June 2024

Background

Anthracyclines, such as doxorubicin, are important anti-cancer therapies but are associated with arterial injury. Histopathological insights have been limited to small animal models and the role of inflammation in the arterial toxic effects of anthracycline is unclear in humans. Our aims were: 1) To evaluate aortic media fibrosis and injury in non-human primates treated with anthracyclines; 2) To assess the effect of anthracycline on aortic inflammation in patients treated for lymphoma.

Methods

1) African Green monkeys (AGM) received doxorubicin (30–60 mg/m2/biweekly IV, cumulative dose: 240 mg/m2). Blinded histopathologic analyses of collagen deposition and cell vacuolization in the ascending aorta were performed 15 weeks after the last doxorubicin dose and compared to 5 age- and gender-matched healthy, untreated AGMs. 2) Analysis of the thoracic aorta of patients with diffuse large B-cell lymphoma (DLBCL), at baseline and after doxorubicin exposure, was performed using18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) in this observational study. The primary outcome was change in maximal tissue-to-background ratio (TBRmax) of the thoracic aorta from baseline to their end-of-treatment clinical PET/CT.

Results

In AGMs, doxorubicin exposure was associated with greater aortic fibrosis (collagen deposition: doxorubicin cohort 6.23±0.88% vs. controls 4.67±0.54%; p=0.01) and increased intracellular vacuolization (doxorubicin 66.3 ± 10.1 vs controls 11.5 ± 4.2 vacuoles/field, p<0.0001) than untreated controls.

In 101 patients with DLBCL, there was no change in aortic TBRmax after anthracycline exposure (pre-doxorubicin TBRmax 1.46±0.16 vs post-doxorubicin TBRmax 1.44±0.14, p=0.14). The absence of change in TBRmax was consistent across all univariate analyses.

Conclusions

In a large animal model, anthracycline exposure was associated with aortic fibrosis. In patients with lymphoma, anthracycline exposure was not associated with aortic inflammation.Further research is required to elucidate the mechanisms of anthracycline-related vascular harm.
Residual immunity and seasonality of an epidemic
Authors: Chen Siyu , Sankoff David
Published: June 2024

We present a dynamical model of the onset and severity of cyclical epidemic disease taking account only of seasonal boosts of antibody during the infectious season and residual immunity remaining from one season to the next. We also compile data from public health sources on the annual number of cases of influenza A and peak infectivity month over a quarter century. In these data, we discover that there is a negative correlation between the change in number of cases from one year to the next and the shift of peak infectivity month between the two seasons, although this does not extend to a prediction of epidemic timing or case number based on the the previous season’s statistics. Simulating the mathematical model, we discover that there is also a negative correlation between the change in titer from one season to the next and the shift of peak infectivity month between the two seasons, suggesting that the empirical results can be explained by our minimal boost-and-wane model. In addition, the model predicts that suppressing the epidemic for one season, or witnessing a strong surge for one season, both have lasting effects for a number of successive seasons.
Evaluation of Acute Myeloid Leukemia Genomes using Genomic Proximity Mapping
Authors: Yeung Cecilia CS , Eacker Stephen M. , Sala-Torra Olga , Beppu Lan , Woolston David W. , Liachko Ivan , Malig Maika , Stirewalt Derek , Fang Min , Radich Jerald
Published: June 2024

Background

Cytogenetic analysis encompasses a suite of standard-of-care diagnostic testing methods that is routinely applied in cases of acute myeloid leukemia (AML) to assess chromosomal changes that are clinically relevant for risk classification and treatment decisions.

Objective

In this study, we assess the use of Genomic Proximity Mapping (GPM) for cytogenomic analysis of AML diagnostic specimens for detection of cytogenetic risk variants included in the European Leukemia Network (ELN) risk stratification guidelines.

Methods

Archival patient samples (N=48) from the Fred Hutchinson Cancer Center leukemia bank with historical clinical cytogenetic data were processed for GPM and analyzed with the CytoTerra® cloud-based analysis platform.

Results

GPM showed 100% concordance for all specific variants that have associated impacts on risk stratification as defined by ELN 2022 criteria, and a 72% concordance rate when considering all variants reported by the FH cytogenetic lab. GPM identified 39 additional variants, including variants of known clinical impact, not observed by cytogenetics.

Conclusions

GPM is an effective solution for the evaluation of known AML-associated risk variants and a source for biomarker discovery.
Diabetes mellitus is associated with a shared hyper-inflammatory immune response in melioidosis and tuberculosis patients: an observational case-control study
Authors: Rongkard Patpong , Kronsteiner Barbara , Eckold Clare , Jenjaroen Kemajittra , Chumseng Suchintana , Chamnan Parinya , Ali Mohammad , Marchi Emanuele , Limmathurotsakul Direk , Chantratita Narisara , West Timothy Eoin , Gharib Sina A. , Cliff Jacqueline M. , Day Nicholas P.J. , Klenerman Paul , Dunachie Susanna J.
Published: June 2024

Background: Melioidosis is a serious infection caused by the bacterium Burkholderia pseudomallei with a case fatality rate of up to 40% in Northeast Thailand. Diabetes increases the risk of developing melioidosis by 12-fold. A similar, but less marked, relationship with diabetes is seen in tuberculosis (TB) patients, with a 3-fold increased risk of developing TB in people with diabetes. However, the mechanisms underlying increased susceptibility are not fully understood. Methods: 81 acute melioidosis patients from Northeast Thailand and 151 TB patients from South Africa, Indonesia, Romania and Peru alongside uninfected control cohorts were studied by whole blood RNA sequencing. Both supervised and unsupervised data analysis approaches were performed including differential gene expression (DGE) analysis, pathway analyses, and weighted gene co-expression network analysis (WGCNA). Results: Diabetes status was associated with a hyper-inflammatory response to both melioidosis and TB, with increased neutrophil and platelet degranulation, and exaggerated activation of coagulation and scavenger activation pathways, alongside decreased phosphoinositide-3-kinase protein kinase B (P13K-Akt) signalling. In melioidosis, changes with diabetes were subtle but also included increased tumour necrosis factor (TNF) signalling via nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) and enhancement of endoplasmic reticulum stress and unfolded protein responses. Diabetes-related changes were more distinct in TB, with marked reduction of interferon signalling responses. Conclusion: Diabetes is associated with enhanced non-specific inflammatory responses in both melioidosis and TB and an impaired interferon-mediated response to TB, with implications for future host-directed therapies.