bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of neuromuscular blockade protocols in cynomolgus macaques: monitoring, doses and antagonism
Authors: Letscher Hélène , Lemaitre Julien , Burban Emma , Grand Roger Le , Bruhns Pierre , Relouzat Francis , Gouel-Chéron Aurélie
Published: December 2023

Background

Neuromuscular blocking agents (NMBAs) are a crucial component of anaesthesia and intensive care. NMBAs are a family of molecules defined by their ability to compete with acetylcholine for binding to the acetylcholine receptor at the neuromuscular junction. This functional homology relies on the presence of ammonium groups in all NMBAs that, however, display vastly different chemical structures. Among animal models, non-human primates (NHP) are an essential model for a great diversity of human disease models but remain poorly characterized for the effectiveness of the diverse NMBAs.

Methods

Seven healthy male cynomolgus macaques were randomly assigned to this study. Experiments using macaques were approved by the local ethical committee (CEtEA #44). All animals were anaesthetized according to institutional guidelines, with ketamine and medetomidine, allowing IV line placement and tracheal intubation. Anaesthesia was maintained with isofluorane. Either rocuronium bromine or atracurium besylate was evaluated, with reversal with sugammadex. Monitoring was performed with two devices, TOF-Watch® and ToFscan®, measuring the T4/T1 and the T4/Tref ratios, respectively. Nonparametric Mann-Whitney statistical analyses were done when indicated.

Results

NMBA monitoring required adaptation compared to humans, such as stimulus intensity and electrodes placement, to be efficient and valid in Cynomolgus macaques. When administered, both NMBAs induced deep and persistent neuro-muscular blockade at equivalent doses to clinical doses in humans. Rocuronium-induced profound neuromuscular blockade could be reverted using the cyclodextrin sugammadex’s reversal agent. We report no adverse effects in these models by clinical observation, blood chemistry, or complete blood count.

Conclusion

These results support the use of non-human primate models for neuromuscular blockade monitoring and testing novel NMBA or their reversal agents.
Phase coding in phoneme processing slows with age
Authors: Dapper Konrad , Schirmer Jakob , Rüttiger Lukas , Gaudrain Etienne , Başkent Deniz , Verhulst Sarah , Braun Christoph , Dalhoff Ernst , Wolpert Stehpan M. , Knipper Marlies , Munk Matthias H. J.
Published: December 2023

The comprehension of phonemes is a fundamental component of speech processing which relies on both, temporal fine structure (TFS) and temporal envelope (TE) coding. EEG amplitude in response to phonemes has been identified as indicator of speech performance in hearing aid users. Presbyacusis may also alter neuro-electric responses to phonemes, even with minimally or unaffected hearing thresholds. Elevated speech reception thresholds (SRT) in absence of pure-tone threshold (PTT) elevation suggest central processing deficits. We therefore collected audiometric data (PTT, SRT) and EEG during passive listening in 80 subjects, ranging in age from 18 to 76 years. We confirm phoneme-evoked EEG response amplitude (PEA) as indicator of speech comprehension. Specifically, PEA decreased with elevated SRT, PTT and increased age. As novel observation, we report the temporal delay of phoneme-evoked EEG responses (PED) to increase with age and PTT. The absolute duration of PED, its age-correlation, and the lack of PEA-lateralization combined with the frequency of phoneme stimuli used here suggest a predominantly thalamic generator of phoneme-evoked EEG responses. Hearing loss in extended high-frequencies affects PED more than PEA. In our sample, neural compensation for increased PTT came at the cost of decreased temporal processing speed. Most importantly, PED correlates with SRT and explains SRT-variance in quiet and in ipsilateral noise that PTT cannot. PED was a better predictor of TFS coding in quiet and of TE coding in ipsilateral noise. As PED reflects both TFS and TE coding, thalamic activity may provide integrated information at the gate of neocortex.

Significance Statement

Intact speech comprehension is essential for social participation which protects against depression and dementia. Age-related hearing loss is a growing problem in aging societies, as hearing deficits constitute the third most important modifiable risk factor for cognitive decline. This work uses electrical brain responses to phonemes in a cohort covering age 18 to 76 years. As the temporal delay of phoneme responses showed the most significant correlations with age and high-frequency thresholds, we demonstrated that speed of neural processing seems essential for speech comprehension. The observed neural signals likely originate from thalamus which receives feedback from neocortex and is embedded in cognitive processing. Developing objective markers for speech processing is key for ensuring cognitive fitness in aging.
An exploratory computational analysis in mice brain networks of widespread epileptic seizure onset locations along with potential strategies for effective intervention and propagation control
Authors: Courson Juliette , Quoy Mathias , Timofeeva Yulia , Manos Thanos
Published: December 2023

Mean-field models have been developed to replicate key features of epileptic seizure dynamics. However, the precise mechanisms and the role of the brain area responsible for seizure onset and propagation remain incompletely understood. In this study, we employ computational methods within The Virtual Brain framework and the Epileptor model to explore how the location and connectivity of an Epileptogenic Zone (EZ) in a mouse brain are related to focal seizures (seizures that start in one brain area and may or may not remain localized), with a specific focus on the hippocampal region known for its association with epileptic seizures. We then devise computational strategies to confine seizures (prevent widespread propagation), simulating medical-like treatments such as tissue resection and the application of an anti-seizure drugs or neurostimulation to suppress hyperexcitability. Through selectively removing (blocking) specific connections informed by the structural connectome and graph network measurements or by locally reducing outgoing connection weights of EZ areas, we demonstrate that seizures can be kept constrained around the EZ region. We successfully identified the minimal connections necessary to prevent widespread seizures, with a particular focus on minimizing surgical or medical intervention while simultaneously preserving the original structural connectivity and maximizing brain functionality.
Nutritional characterisation and seasonal variation of goat forages in Central Malawi
Authors: Cooke A. S. , Mvula W. , Nalivata P. , Ventura-Cordero J. , Gwiriri L.C. , Takahashi T. , Morgan E. R. , Lee M. R. F. , Safalaoh A.
Published: December 2023

Goat ownership is prevalent across rural Malawi and provides a vital source of income, nutrition, and food security. However, goat performance is poor, and this presents a risk to individuals and communities who depend on them. Whilst mitigating this through supplementation of persevered forages may be possible, this is a challenge due to limitations of resources and the fact that goats typically free-roam during the dry season. Nutrition is fundamental to health and productivity of any livestock enterprise, it is required to be able to deal with stresses, such as disease, and to enable growth and production. The aim of this study was to characterise the nutritional profile of naturally available forages in Malawi, including the seasonal variation in nutrition. Samples of herbaceous forages and browse were collected over a 17-month period, across four villages (30 farms/smallholders) in Central Malawi. Forages underwent nutritional analysis for crude protein, fibre fractions, and ash/organic matter and NDVI obtained from satellite imagery was used as a measure of forage availability. Forage nutrition and availability were most adequate in the wet season, with higher concentrations of crude protein and a greater availability of herbaceous plants. There were significant differences in low-digestibility fibre fractions between locations, likely due to local factors such as soil and hydrology. The fall in crude protein concentrations from the wet season to the dry season represent a seasonal nutrition-gap which may result in risks to goat health and productivity.
Decoding Pain: Uncovering the Factors that Affect Performance of Neuroimaging-Based Pain Models
Authors: Lee Dong Hee , Lee Sungwoo , Woo Choong-Wan
Published: December 2023

Abstract

Neuroimaging-based pain biomarkers, when combined with machine learning techniques, have demonstrated potential in decoding pain intensity and diagnosing clinical pain conditions. However, a systematic evaluation of how different modeling options affect model performance remains unexplored. This study presents results from a comprehensive literature survey and benchmarking analysis. We conducted a survey of 57 previously published articles that included neuroimaging-based predictive modeling of pain, comparing classification and prediction performance based on the following modeling variables—the levels of data, spatial scales, idiographic vs. population models, and sample sizes. The findings revealed a preference for population-level modeling with brain-wide features, aligning with the goal of clinical translation of neuroimaging biomarkers. However, a systematic evaluation of the influence of different modeling options was hindered by a limited number of independent test results. This prompted us to conduct benchmarking analyses using a locally collected functional Magnetic Resonance Imaging (fMRI) dataset (N= 124) involving an experimental thermal pain task. The results clearly demonstrated that data levels, spatial scales, and sample sizes significantly impact model performance. Specifically, incorporating more pain-related brain regions, increasing sample sizes, and using less data averaging in training while increasing it in testing enhanced performance. These findings provide a useful reference for decision-making in the development of neuroimaging-based biomarkers, highlighting the importance of the careful selection of modeling strategies and options to build better-performing neuroimaging pain biomarkers. These findings offer useful guidance for developing neuroimaging-based biomarkers, underscoring the importance of strategic selection of modeling approaches to build better-performing neuroimaging pain biomarkers.
Pseudo-craniotomy of a whole-brain model reveals tumor-induced alterations to neuronal dynamics in glioma patients
Authors: Alexandersen Christoffer G. , Douw Linda , Zimmermann Mona L.M. , Bick Christian , Goriely Alain
Published: December 2023

Brain tumors can induce pathological changes in neuronal dynamics both on a local and global level. Here, we use a whole-brain modeling approach to investigate these pathological alterations in neuronal activity. By fitting a Hopf whole-brain model to empirical functional connectivity, we demonstrate that phase correlations are largely determined by the ratio of interregional coupling strength and intraregional excitability. Furthermore, we observe considerable differences in interregional-versus-intraregional dynamics between glioma patients and healthy controls, both on an individual and population-based level. In particular, we show that local tumor pathology induces shifts in the global brain dynamics by promoting the contribution of interregional interactions. Our approach demonstrates that whole-brain models provide valuable insights for understanding glioma-associated alterations in functional connectivity.
Diet-induced miRNAs regulate adult neurogenesis and functional activity of nascent neurons in the hypothalamus
Authors: Srinivasan Balakumar , Samaddar Sarbani , Roy Dipanjan , Banerjee Sourav
Published: December 2023

Neurogenesis in the hypothalamus upon high fat diet (HFD) feeding regulates the feeding circuit. HFD induces the neurogenesis of β2 tanycytes in young-adult mice. However molecular mechanisms of tanycytic neurogenesis; and their functional integration into the feeding circuitry are poorly understood. We investigated the role of miRNAs in the regulation of HFD-induced tanycytic neurogenesis. miRNA arrays identified a cohort of HFD-induced, differentially-regulated miRNAs in BrdU+β2-tanycytes. These miRNAs arise from different chromosomes, rather than a single cluster.In siliconetwork analysis on the predicted targets of all five HFD-induced miRNAs and reporter assays identified a subset of targets that influence neurogenesis and neuronal differentiation. HFD-induced miRNAs drive a molecular program leading to the functional integration of nascent neurons; introduction of a miRNA sponge sequestering all five miRNAs abolishes it. Diet-regulated newborn neurons preferentially differentiate into AgRP+ neurons that functionally integrate into the feeding circuit.
Integrative genomics reveals the polygenic basis of seedlessness in grapevine
Authors: Wang Xu , Liu Zhongjie , Zhang Fan , Xiao Hua , Cao Shuo , Xue Hui , Liu Wenwen , Su Ying , Liu Zhenya , Zhong Haixia , Zhang Fuchun , Ahmad Bilal , Long Qiming , Zhang Yingchun , Liu Yuting , Gan Yu , Hou Ting , Jin Zhongxin , Wu Xinyu , Wang Yiwen , Peng Yanling , Zhou Yongfeng
Published: December 2023

Seedlessness is a crucial quality trait in table grape (Vitis viniferaL.) breeding. However, the development of seeds involved intricate regulations, while the polygenic basis of seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative genetics, and integrative genomics to unravel the evolution and polygenic basis of seedlessness in grapes. We generated four haplotype-resolved telomere-to-telomere (T2T) genomes for two seedless grape cultivars, ‘Thompson Seedless’ (TS, syn. ‘Sultania’) and ‘Black Monukka’ (BM). Comparative genomics identified a ∼4.25 Mb hemizygous inversion on Chr10 specific in seedless cultivars, with seedless-associated genesVvTT16andVvSUS2located at breakpoints. Population genomic analyses of 548 grapevine accessions revealed two distinct clusters of seedless cultivars, tracing the origin of the seedlessness trait back to ‘Sultania’. Introgression, rather than convergent selection, shaped the evolutionary history of seedlessness in grape improvement. Genome-wide association study (GWAS) analysis identified 110 quantitative trait loci (QTLs) associated with 634 candidate genes, including novel candidate genes, such as three11S GLOBULIN SEED STORAGE PROTEINand twoCYTOCHROME P450genes, and well-known genes likeVviAGL11. Integrative genomic analyses resulted in 339 core candidate genes categorized into 13 groups related to seed development. Machine learning based genomic selection achieved a remarkable 99% precision in predicting grapevine seedlessness. Our findings highlight the polygenic nature of seedless and provide novel candidate genes for molecular genetics and an effective prediction for seedlessness in grape genomic breeding.
Error-corrected deep targeted sequencing of circulating cell-free DNA from colorectal cancer patients for sensitive detection of circulating tumor DNA
Authors: Frydendahl Amanda , Rasmussen Mads Heilskov , Jensen Sarah Østrup , Henriksen Tenna Vesterman , Demuth Christina , Diekema Mathilde , Ditzel Henrik J. , Wen Sara Witting Christensen , Pedersen Jakob Skou , Dyrskjøt Lars , Andersen Claus Lindbjerg
Published: December 2023

Introduction

Circulating tumor DNA (ctDNA) is a promising biomarker, reflecting the presence of tumor cells. Sequencing-based detection of ctDNA at low tumor fractions is challenging due to the crude error rate of sequencing. To mitigate this challenge, we developed UMIseq, a fixed-panel deep-targeted sequencing approach, which is universally applicable to all colorectal cancer (CRC) patients.

Methods

UMIseq features UMI-mediated error correction, exclusion of mutations related to clonal hematopoiesis, a panel of normals for error modeling, and signal integration from single-nucleotide variations, insertions, deletions, and phased mutations. UMIseq was trained and independently validated on pre-operative (pre-OP) plasma from CRC patients (n=364) and healthy individuals (n=61).

Results

UMIseq displayed an area under the curve surpassing 0.95 for allele frequencies (AF) down to 0.05%. In the training cohort, the pre-OP detection rate reached 80% at 95% specificity, while in the validation cohort, it was 70%. UMIseq enabled the detection of AFs down to 0.004%. To assess the potential for detection of residual disease, 26 post-operative plasma samples from stage III CRC patients were analyzed. Detection of ctDNA was associated with recurrence (p =0.08).

Conclusion

UMIseq demonstrated robust performance with high sensitivity and specificity, enabling the detection of ctDNA at low allele frequencies.
Angiotensin-II drives changes in microglia-vascular interactions in rats with heart failure
Authors: Althammer Ferdinand , Roy Ranjan K. , Kirchner Matthew K. , McGrath Shaina , Lira Elba Campos , Stern Javier E.
Published: December 2023

Activation of microglia, the resident immune cells of the central nervous system, leading to the subsequent release of pro-inflammatory cytokines, has been linked to cardiac remodeling, autonomic disbalance, and cognitive deficits in heart failure (HF). While previous studies emphasized the role of hippocampal Angiotensin II (AngII) signaling in HF-induced microglial activation, unanswered mechanistic questions persist. Evidence suggests significant interactions between microglia and local microvasculature, potentially affecting blood-brain barrier integrity and cerebral blood flow regulation. Still, whether the microglial-vascular interface is affected in the brain during HF remains unknow. Using a well-established ischemic HF rat model, we demonstrate increased vessel-associated microglia (VAM) in HF rat hippocampi, which showed heightened expression of AngII AT1a receptors. Acute AngII administration to sham rats induced microglia recruitment to the perivascular space, along with increased expression of TNFa. Conversely, administering an AT1aR blocker to HF rats prevented the recruitment of microglia to the perivascular space, normalizing their levels to those in healthy rats. These results highlight the critical importance of a rather understudied phenomenon (i.e., microglia-vascular interactions in the brain) in the context of the pathophysiology of a highly prevalent cardiovascular disease, and unveil novel potential therapeutic avenues aimed at mitigating neuroinflammation in cardiovascular diseases.
Conditions for successful nitrogen removal from source-separated urine by partial nitritation/anammox
Authors: Faust Valentin , Markus Philipp , Schielke-Jenni Sarina , Timmer Marijn J. , Paepe Jolien De , Ganigué Ramon , Vlaeminck Siegfried E. , Udert Kai M.
Published: December 2023

Partial nitritation/anammox (PN/A) of source-separated urine is less energy-intensive and potentially cheaper and more environmentally friendly than conventional nitrogen removal from mixed sewage. However, PN/A of undiluted source-separated urine has not yet been established. In this study, the feasibility of PN/A for source-separated urine (total nitrogen ≈ 2 to 3 g-N L-1). To evaluate the influence of different factors, one- and two-stage configurations were operated using different influents, i.e. source-separated urine, synthetic urine, and urine with additional divalent cations. While partial nitritation was successfully achieved in both configurations with digester supernatant and urine, anammox activity was lost shortly after switching from digester supernatant to the urine influents. Toxic organic compounds or pharmaceuticals and the high monovalent to divalent cation ratio were suspected as causes of anammox failure, but were ruled out due to the different reactor configurations and influent compositions tested. Other suspected factors such as COD/N ratio, phosphate and sulfate inhibition, nitrogen compound inhibition, metal inhibition, pH and dissolved oxygen were also systematically excluded. Instead, the high salt concentration in urine compared to the digester supernatant most likely caused the reactor to fail due to the disintegration of large flocs, and the resulting challenge of biomass retention. The shortcomings of the floccular sludge system were overcome by using biofilm carriers, resulting in successful PN/A. This hybrid system ran for 140 days with nitrogen removal rates of up to 1000 mg-N L-1d-1with an average of 410 ± 220 mg-N L-1d-1, and a nitrogen removal efficiency of 93 ± 3% at 30°C.
Trans-synaptic molecular context of NMDA receptor nanodomains
Authors: Anderson Michael C , Dharmasri Poorna A , Damenti Martina , Metzbower Sarah R , Laghaei Rozita , Blanpied Thomas A , Levy Aaron D
Published: December 2023

Tight coordination of the spatial relationships between protein complexes is required for cellular function. In neuronal synapses, many proteins responsible for neurotransmission organize into subsynaptic nanoclusters whose trans-cellular alignment modulates synaptic signal propagation. However, the spatial relationships between these proteins and NMDA receptors (NMDARs), which are required for learning and memory, remain undefined. Here, we mapped the relationship of key NMDAR subunits to reference proteins in the active zone and postsynaptic density using multiplexed super-resolution DNA-PAINT microscopy. GluN2A and GluN2B subunits formed nanoclusters with diverse configurations that, surprisingly, were not localized near presynaptic vesicle release sites marked by Munc13-1. Despite this, we found asubsetof release sites was enriched with NMDARs, and modeling of glutamate release and receptor activation in measured synapses indicated this nanotopography promotes NMDAR activation. This subset of release sites was internally denser with Munc13-1, aligned with abundant PSD-95, and associated closely with specific NMDAR nanodomains. Further, NMDAR activation drove rapid reorganization of this release site/receptor relationship, suggesting a structural mechanism for tuning NMDAR-mediated synaptic transmission. This work reveals a new principle regulating NMDAR signaling and suggests that synaptic functional architecture depends on the assembly of and trans-cellular spatial relationships between multiprotein nanodomains.
Learning a conserved mechanism for early neuroectoderm morphogenesis
Authors: Lefebvre Matthew , Colen Jonathan , Claussen Nikolas , Brauns Fridtjof , Raich Marion , Mitchell Noah , Fruchart Michel , Vitelli Vincenzo , Streichan Sebastian J
Published: December 2023

Morphogenesis is the process whereby the body of an organism develops its target shape. The morphogen BMP is known to play a conserved role across bilaterian organisms in determining the dorsoventral (DV) axis. Yet, how BMP governs the spatio-temporal dynamics of cytoskeletal proteins driving morphogenetic flow remains an open question. Here, we use machine learning to mine a morphodynamic atlas of Drosophila development, and construct a mathematical model capable of predicting the coupled dynamics of myosin, E-cadherin, and morphogenetic flow. Mutant analysis shows that BMP sets the initial condition of this dynamical system according to the following signaling cascade: BMP establishes DV pair-rule-gene patterns that set-up an E-cadherin gradient which in turn creates a myosin gradient in the opposite direction through mechanochemical feedbacks. Using neural tube organoids, we argue that BMP, and the signaling cascade it triggers, prime the conserved dynamics of neuroectoderm morphogenesis from fly to humans.
Evidence of the ability of endocrine disrupting compounds to induce testicular germ cell cancer in humans
Authors: Nicolas Nour , Moison Delphine , Jampy Amandine , Masson Quentin , Dechamps Nathalie , Messiaen Sébastien , Abdallah Sonia , Pozzi-Gaudin Stéphanie , Benachi Alexandra , Ulveling Damien , Francastel Claire , Rouiller-Fabre Virginie , Livera Gabriel , Guerquin Marie-Justine
Published: December 2023

Testicular cancer is an increasing burden in modern societies and the most common malignancy among young adult males. Environment contaminants, especially endocrine disrupting compounds (EDC), may play a significant role in the development of these cancers through epigenetic alterations occurring during fetal and neonatal development. As long-term studies in humans and suitable experimental models with the potential to develop testicular cancer are lacking, no causal link can be established between endocrine disruptor exposure and testicular cancer incidence. Therefore, we developed an experimental model that recapitulates the differentiation of germ cells from primordial germ cells (pluripotency) into spermatocytes (meiosis) by using xenografted human fetal testis combined with germ cell transplantation into adult testis compartments. Using this model, we demonstrate that long-term fetal exposure (until 12 weeks) to a mixture of Di-2-ethylhexylphthalate (DEHP) and Bisphenol A (BPA), two most prevalent plasticizers, could interfere with fetal germ cell differentiation, leading to carcinogenesis and seminomas. Transcriptome, methylome, and histological analyses reveal that BPA/DEHP exposure induced some significant hallmarks of germ cell tumors to occur: persistent pluripotent and proliferative germ cells, global hypomethylation of CpGs in germ cells, abnormal expression of meiotic markers and fibrotic signatures in fetal testis. Additionally, we found that EDC-exposed fetal germ cells were more likely to develop seminoma in a context that allows spermatogenesis to begin. This study proposes the first experimental evidence that EDC exposure can cause long-term, irreversible lesions in fetal germ cells, which then lead to testicular tumorigenesis in adults.
Intensive task-switching training and single-task training differentially affect behavioral and neural manifestations of cognitive control in children
Authors: Schwarze Sina A. , Laube Corinna , Khosravani Neda , Lindenberger Ulman , Bunge Silvia A. , Fandakova Yana
Published: December 2023

The ability to flexibly switch between tasks develops during childhood. Children’s task-switching performance improves with practice, but the underlying processes remain unclear. We used functional magnetic resonance imaging to examine how nine weeks of task-switching training affect performance and task-related activation and functional connectivity. Children (8–11 years) were assigned to one of three groups: intensive task switching (SW; n = 72), intensive single tasking (SI; n = 74), and passive control (n = 41). While mixing costs decreased in both training groups initially, only the SW group maintained these training-related improvements at the end of training. Activation in dorsolateral prefrontal cortex decreased with training, but again only the SW group maintained these activation decreases at the end of training. Condition-specific connectivity increases with task switching became less pronounced with training, especially in the SI group. Lower costs of task switching along with decreased task-related activations suggest increased processing efficiency in frontoparietal regions with training. Intensive task-switching training was associated with sustained changes, possibly facilitated by a greater mismatch between processing supplies and environmental demands. Our findings suggest that experience-dependent changes with intensive task-switching training do not mirror maturational processes but rather facilitate performance via more efficient task processing.
Variation in hemolymph content and properties among three Mediterranean bee species
Authors: Elfar Salma A. , Bahgat Iman M. , Shebl Mohamed A. , Lihoreau Mathieu , Tawfik Mohamed M.
Published: December 2023

Hemolymph, as mediator of immune responses and nutrient circulation, can be used as physiological marker of an insect’s health, environmental quality or ecological adaptations. Recent studies reported intraspecific variation in protein contents and biological activities of the hemolymph of honey bees related to their diet. Here we measured interspecific variation in three common bee species in the Mediterranean Basin with contrasting ecologies:Apis mellifera,Chalicodoma siculum,andXylocopa pubescens. Despite all the bees were collected in the same area, we found important quantitative and qualitative variations of hemolymph extracts across species. Samples ofA. melliferaandC. siculumhad much higher protein concentration, anticancer, antimicrobial and antoxidant activities than samples ofX. pubescens.This first descriptive study suggests life history traits of bee species have strong influences on their hemolymph properties and call for future large scale comparative analyses across more species and geographical areas.
Discovery of novel brain permeable human ACSS2 inhibitors for blocking breast cancer brain metastatic growth
Authors: Esquea Emily , Ciraku Lorela , Young Riley G. , Merzy Jessica , Talarico Alexandra N. , Rashad Adel Ahmed , Cocklin Simon , Simone Nicole L. , Beld Joris , Reginato Mauricio J. , Dick Alexej
Published: December 2023

Breast-cancer brain metastasis (BCBM) poses a significant clinical challenge, resulting in an end-stage diagnosis and hindered by limited therapeutic options. The blood-brain barrier (BBB) acts as an anatomical and physiological hurdle for therapeutic compounds, restricting the effective delivery of therapies to the brain. In order to grow and survive in a nutrient-poor environment, tumors in the brain must adapt to their metabolic needs, becoming highly dependent on acetate. These tumors rely on the conversion of acetate to acetyl-CoA by the enzyme Acetyl-CoA synthetase 2 (ACSS2), a key metabolic enzyme involved in regulating fatty acid synthesis and protein acetylation in tumor cells. ACSS2 has emerged as a crucial enzyme required for the growth of tumors in the brain. Here, we utilized a computational pipeline, combining pharmacophore-based shape screen methodology with ADME property predictions to identify novel brain-permeable ACSS2 inhibitors. From a small molecule library, this approach identified 30 potential ACSS2 binders, from which two candidates, AD-5584 and AD-8007, were validated for their binding affinity, predicted metabolic stability, and, notably, their ability to traverse the BBB. We show that treatment of BCBM cells, MDA-MB-231BR, with AD-5584 and AD-8007 leads to a significant reduction in lipid storage, reduction in colony formation, and increase in cell deathin vitro. Utilizing anex vivoorthotopic brain-slice tumor model, we show that treatment with AD-8007 and AD-5584 significantly reduces tumor size and synergizes with radiation in blocking BCBM tumor growthex vivo.Importantly, we show that following intraperitoneal injections with AD-5584 and AD-8007, we can detect these compounds in the brain, confirming their BBB permeability. Thus, we have identified and validated novel ACSS2 inhibitor candidates for further drug development and optimization as agents for treating patients with breast cancer brain metastasis.
A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression.
Authors: Maritato Rosa , Medugno Alessia , D'Andretta Emanuela , De Riso Giulia , Lupo Mariangela , Botta Salvatore , Marrocco Elena , Renda Mario , Sofia Martina , Mussolino Claudio , Bacci Maria Laura , Surace Enrico Maria
Published: December 2023

The binding affinity of transcription factors (TFs) for their cognate DNA sequences controls gene expression. DNA determines the recruitment and positioning of TFs; whether it plays other roles is unknown. Here we found that the specific 22-bp sequence interposed between the CRX and NRL TFs in the proximal promoter of RHODOPSIN (RHO) largely controls the expression levels of RHO. Mutagenesis of this DNA-linker sequence resulted in wide variation in gene expression. In contrast, reciprocal exchange of human and murine RHO elements conferred species-specific expression levels. Targeting the DNA-linker with equal orthogonal DNA-binding proteins activates or represses RHO expression depending on its orientation relative to CRX and NRL binding sites. We conclude that DNA itself adds to TF activity through a code that determines optimal levels of RHO expression.
Conserved cold tolerance ofRhagoletisspecies from different host fruits, elevations in Colorado, USA
Authors: Lemay Katelyn , Moore Mackenzie , Brown Paige , Gadey Lahari , Ragland Gregory J. , Toxopeus Jantina
Published: December 2023

Understanding and characterizing how insects tolerate low temperatures is important for predicting their overwintering survival and subsequent geographic spread. This study characterized the cold tolerance of two members of theRhagoletisgenus in Colorado, U.S.A. Pupae were collected from infested fruit in late summer and early fall. For the first time, we show that the rosehip flyRhagoletis basiolais freeze-avoidant; overwintering pupae could supercool to temperatures as low as −26°C and survive. Interestingly, the temperature at which ice forms (supercooling point; SCP) did not vary betweenR. basiolaat high (c. 2900 m above sea level) and lower (c. 1650 m a.s.l.) elevations. We also report the apple maggotRhagoletis pomonellainfesting an unusual host fruit, the Dolgo crabapple, in close proximity to infested hawthorn trees.R. pomonellainfesting hawthorn fruits and crabapples had similar SCPs, and survived temperatures as low as −21°C. Pupae from both host fruits also survived prolonged exposure (2 weeks or more) to mild low temperatures (0 to −5°C). Further study into the mechanisms underlying the impressive and conserved cold tolerance ofR. pomonellaandR. basiolais an interesting avenue for future research.
The LH receptor regulates hippocampal spatial memory and restores dendritic spine density in ovariectomized APP/PS1 AD mice
Authors: Mey Megan , Bhatta Sabina , Suresh Sneha , Montero Labrador Luis , Piontkivska Helen , Casadesus Gemma
Published: December 2023

Activation of the luteinizing hormone receptor (LHCGR) rescues spatial memory function and spine density losses associated with gonadectomy and high circulating gonadotropin levels in females. However, whether this extends to the AD brain or the mechanisms that underlie these benefits remain unknown. To address this question, we delivered the LHCGR agonist human chorionic gonadotropin (hCG) intracerebroventricularly (ICV), under reproductively intact and ovariectomized conditions to mimic the post-menopausal state in the APP/PS1mouse brain. Cognitive function was tested using the Morris water maze task, and hippocampal dendritic spine density, Aβ pathology, and signaling changes associated with these endpoints were determined to address mechanisms. Here we show that central LHCGR activation restored function in ovariectomized APP/PS1 female mice to wild-type levels without altering Aβ pathology. LHCGR activation increased hippocampal dendritic spine density regardless of reproductive status, and this was mediated by BDNF-dependent and independent signaling. We also show that ovariectomy in the APP/PS1 brain elicits an increase in peripherally derived pro-inflammatory genes which are inhibited by LHCGR activation. This may mediate reproductive status specific effects of LHCGR agonism on cognitive function and BDNF expression. Together, this work highlights the relevance of the LHCGR on cognition and its therapeutic potential in the “menopausal” AD brain.
hopsy - a methods marketplace for convex polytope sampling in Python
Authors: Paul Richard D. , Jadebeck Johann F. , Stratmann Anton , Wiechert Wolfgang , Nöh Katharina
Published: December 2023

Effective collaboration between developers of Bayesian inference methods and users is key to advance our quantitative understanding of biosystems. We here presenthopsy, a versatile open source platform designed to provide convenient access to powerful Markov chain Monte Carlo sampling algorithms tailored to models defined on convex polytopes (CP). Based on the high-performance C++ sampling libraryHOPS,hopsyinherits its strengths and extends its functionalities with the accessibility of the Python programming language. A versatile plugin-mechanism enables seamless integration with domain-specific models, providing method developers with a framework for testing, benchmarking, and distributing CP samplers to approach real-world inference tasks. We showcasehopsyby solving common and newly composed domain-specific sampling problems, highlighting important design choices. By likeninghopsyto a marketplace, we emphasize its role in bringing together users and developers, where users get access to state-of-the-art methods, and developers contribute their own innovative solutions for challenging domain-specific inference problems.

Availability and Implementation

Sources, documentation and a continuously updated list of sampling algorithms are available athttps://jugit.fz-juelich.de/IBG-1/ModSim/hopsy, with Linux, Windows and MacOS binaries athttps://pypi.org/project/hopsy/.

Contact

k.noeh@fz-juelich.de
Comprehensive analysis of the functional impact of single nucleotide variants of humanCHEK2
Authors: McCarthy-Leo Claire E. , Brush George S. , Pique-Regi Roger , Luca Francesca , Tainsky Michael A. , Finley Russell L.
Published: December 2023

Loss of function mutations in the checkpoint kinase geneCHEK2are associated with increased risk of breast and other cancers. Most of the 3,188 unique amino acid changes that can result from non-synonymous single nucleotide variants (SNVs) ofCHEK2, however, have not been tested for their impact on the function of theCHEK2-enocded protein (CHK2). One successful approach to testing the function of variants has been to test for their ability to complement mutations in the yeast ortholog ofCHEK2,RAD53. This approach has been used to provide functional information on over 100CHEK2SNVs and the results align with functional assays in human cells and known pathogenicity. Here we tested all but two of the 4,887 possible SNVs in theCHEK2open reading frame for their ability to complementRAD53mutants using a novel high throughput technique. Among the non-synonymous changes, 770 were damaging to protein function while 2,417 were tolerated. The results correlate well with previous structure and function data and provide a first or additional functional assay for all the variants of uncertain significance identified in clinical databases. Combined, this approach can be used to help predict the pathogenicity ofCHEK2variants of uncertain significance that are found in patient screening and could be applied to other cancer risk genes.
Harnessing Bilayer Biomaterial Delivery of FTY720 as an Immunotherapy to Accelerate Oral Wound Healing
Authors: Toma Afra I. , Shah Daniel , Roth Daniela , Oliver Piña Jeremie , Hymel Lauren , Turner Thomas , Kamalakar Archana , Liu Ken , Bartsch Perry , Jacobs Leon , D’Souza Rena , Liotta Dennis , Botchwey Edward , Willett Nick J. , Goudy Steven L.
Published: December 2023

Orofacial clefts are the most common craniofacial congenital anomaly. Following cleft palate repair, up to 60% of surgeries have wound healing complications leading to oronasal fistula (ONF), a persistent connection between the roof of the mouth and the nasal cavity. The current gold standard methods for ONF repair use human allograft tissues; however, these procedures have risks of graft infection and/or rejection, requiring surgical revisions. Immunoregenerative therapies present a novel alternative approach to harness the body’s immune response and enhance the wound healing environment. We utilized a repurposed FDA-approved immunomodulatory drug, FTY720, to reduce the egress of lymphocytes and induce immune cell fate switching toward pro-regenerative phenotypes. Here, we engineered a bilayer biomaterial system using Tegaderm™, a liquid-impermeable wound dressing, to secure and control the delivery of FTY720- nanofiber scaffolds (FTY720-NF). We optimized release kinetics of the bilayer FTY720-NF to sustain drug release for up to 7d with safe, efficacious transdermal absorption and tissue biodistribution. Through comprehensive immunophenotyping, our results illustrate a pseudotime pro-regenerative state transition in recruited hybrid immune cells to the wound site. Additional histological assessments established a significant difference in full thickness ONF closure in mice on Day 7 following treatment with bilayer FTY720-NF, compared to controls. These findings demonstrate the utility of immunomodulatory strategies for oral wound healing, better positing the field to develop more efficacious treatment options for pediatric patients.

One Sentence Summary

Local delivery of bilayer FTY720-nanofiber scaffolds in an ONF mouse model promotes complete wound closure through modulation of pro-regenerative immune and stromal cells.
Steroid signaling controls sex-specific development in an invertebrate
Authors: Grmai Lydia , Jimenez Erin , Baxter Kelly , Van Doren Mark
Published: December 2023

In vertebrate sexual development, two important steroid hormones, testosterone and estrogen, regu-late the sex-specific development of many tissues. In contrast, invertebrates utilize a single steroid hormone, ecdysone, to regulate developmental timing in both sexes. However, here we show that in Drosophila melanogaster, sex-specific ecdysone (E) signaling controls important aspects of gonad sexual dimorphism. Rather than being regulated at the level of hormone production, hor-mone activity is regulated cell-autonomously through sex-specific hormone reception. Ecdysone receptor (EcR) expression is restricted to the developing ovary and is repressed in the testis at a time when ecdysone initiates ovary morphogenesis. Interestingly, EcR expression is regulated downstream of the sex determination factor Doublesex (Dsx), the founding member of the Dsx/Mab3 Related Transcription Factor (DMRT) family that regulates gonad development in all animals. E signaling is required for normal ovary development1,2, and ectopic activation of E sig-naling in the testis antagonized stem cell niche identity and feminized somatic support cells, which were transformed into follicle-like cells. This work demonstrates that invertebrates can also use steroid hormone signaling to control sex-specific development. Further, it may help explain recent work showing that vertebrate sexual development is surprisingly cell-autonomous. For example, chickens utilize testosterone and estrogen to control sex-specific development, but when they have a mixture of cells with male and female genotypes, the male cells develop as male and the female cells develop as female despite exposure to the same circulating hormones3. Sex-specific regulation of steroid hormone signaling may well underly such cell-autonomous sexual fate choices in verte-brates as it does in Drosophila.
Atomic context-conditioned protein sequence design using LigandMPNN
Authors: Dauparas Justas , Lee Gyu Rie , Pecoraro Robert , An Linna , Anishchenko Ivan , Glasscock Cameron , Baker D.
Published: December 2023

Protein sequence design in the context of small molecules, nucleotides, and metals is critical to enzyme and small molecule binder and sensor design, but current state-of-the-art deep learning-based sequence design methods are unable to model non-protein atoms and molecules. Here, we describe a deep learning-based protein sequence design method called LigandMPNN that explicitly models all non-protein components of biomolecular systems. LigandMPNN significantly outperforms Rosetta and ProteinMPNN on native backbone sequence recovery for residues interacting with small molecules (63.3% vs. 50.4% & 50.5%), nucleotides (50.5% vs. 35.2% & 34.0%), and metals (77.5% vs. 36.0% & 40.6%). LigandMPNN generates not only sequences but also sidechain conformations to allow detailed evaluation of binding interactions. Experimental characterization demonstrates that LigandMPNN can generate small molecule and DNA-binding proteins with high affinity and specificity.

One-sentence summary

We present a deep learning-based protein sequence design method that allows explicit modeling of small molecule, nucleotide, metal, and other atomic contexts.
Machine learning reveals the diversity of human 3D chromatin contact patterns
Authors: Gilbertson Erin N. , Brand Colin M. , McArthur Evonne , Rinker David C. , Kuang Shuzhen , Pollard Katherine S. , Capra John A.
Published: December 2023

Understanding variation in chromatin contact patterns across human populations is critical for interpreting non-coding variants and their ultimate effects on gene expression and phenotypes. However, experimental determination of chromatin contacts at a population-scale is prohibitively expensive. To overcome this challenge, we develop and validate a machine learning method to quantify the diversity 3D chromatin contacts at 2 kilobase resolution from genome sequence alone. We then apply this approach to thousands of diverse modern humans and the inferred human-archaic hominin ancestral genome. While patterns of 3D contact divergence genome-wide are qualitatively similar to patterns of sequence divergence, we find that 3D divergence in local 1-megabase genomic windows does not follow sequence divergence. In particular, we identify 392 windows with significantly greater 3D divergence than expected from sequence. Moreover, 26% of genomic windows have rare 3D contact variation observed in a small number of individuals. Usingin silicomutagenesis we find that most sequence changes to do not result in changes to 3D chromatin contacts. However in windows with substantial 3D divergence, just one or a few variants can lead to divergent 3D chromatin contacts without the individuals carrying those variants having high sequence divergence. In summary, inferring 3D chromatin contact maps across human populations reveals diverse contact patterns. We anticipate that these genetically diverse maps of 3D chromatin contact will provide a reference for future work on the function and evolution of 3D chromatin contact variation across human populations.
Unsupervised mapping of causal relations between brain and behavior
Authors: Wahle Iman A. , Adolphs Ralph , Tranel Daniel , Boes Aaron , Eberhardt Frederick
Published: December 2023

Studies of patients with focal brain lesions provided the historical foundation for cognitive neuroscience, but how to identify a precise mapping between specific brain regions and the cognitive variables affected remains unclear. The challenge lies both in identifying anatomical regions wherein lesions have a shared causal effect, as well as in the precise delineation of the behavioral outcome. Currently, either the relevant brain region or the dimensionality of the behavior being mapped are pre-specified by the investigators rather than both being informed by optimal brain-behavior relationships. Here we apply a novel data-driven causal aggregation algorithm, Causal Feature Learning (CFL) to tackle this challenge in 520 individuals with focal brain lesions. CFL simultaneously constructs macro-level summaries of the spatial distribution of brain lesions and the itemized responses on psychometric tests to optimally characterize the causal brain-behavior relationships. Focusing on the domains of language, visuospatial ability, and depression, we recapitulate established findings, provide new and more precise anatomical results, and present an aggregation of item-wise data that provides an empirical test of extant behavioral scores and can be used to identify novel, psychologically meaningful factors. Future work could use our approach to construct entirely new psychometric variables that might cut across established categories.