bluuebunny/crossref_metadata_2025 huggingface dataset:
A quantitative analysis of Alzheimer’s Disease and construction of an early Alzheimer’s detection deep learning system (EADDLS) using MRI data via machine learning along with ADmod: spatiotemporal-aware brain-amyloidβ growth model, using deep encoder-decoder networks about MRI
Authors: Mohanty Naitik B , Sarmadi Morteza
Published: August 2024

Alzheimer’s disease (AD) presents a significant societal challenge, with no current cure and an increasing prevalence among older adults. This study addresses the pressing need for early detection by harnessing the potential of machine learning applied to longitudinal MRI data. The dataset, sourced from the Open Access Series of Imaging Studies (OASIS) project, comprises MRI records of 150 subjects aged 60 to 96, each scanned at least once. Notably, 72 subjects were classified as ‘Nondemented,’ 64 as ‘Demented,’ and 14 underwent a transition from ‘Nondemented’ to ‘Demented,’ forming the ‘Converted’ category. What we propose is to develop a machine learning sound model capable of predicting the progression of mild cognitive impairment, leveraging key biomarkers extracted from MRI data. The chosen biomarkers include years of education (EDUC), socioeconomic status (SES), Mini-Mental State Examination (MMSE), Clinical Dementia Rating (CDR), Estimated Total Intracranial Volume (eTIV), Normalized Whole Brain Volume (nWBV), and Atlas Scaling Factor (ASF). Prior work in the field is referenced, highlighting studies that predominantly focused on raw MRI data analysis. In contrast, this study introduces a unique approach by utilizing a curated set of biomarkers, allowing for a more targeted and potentially interpretable model. Machine learning models such as Logistic Regression, Support Vector Machine, Decision Tree, Random Forest Classifier, and AdaBoost are employed, with performance measured using established metrics. Information about severity and state are stored during the EADDLS module and used for ADmod. ADmod uses the stored MRI data during the EADDLS module to model the growth of amyloid β build-up in the brain using convolution, resulting in both generalizable approaches and patient-specific approaches. There have been numerous mathematical instantiations to model amyloid β build-up using partial differential equations (or PDEs), these however have remained unincorporated due to prolonged runtimes and storage limitations along with those of pre-set conditions. We propose a novel amyloid β growth model using deep encoder-decoder networks in conjunction with convolution. The study contributes to the growing body of research in early Alzheimer’s detection, offering insights, results, and a discussion of limitations. The conclusion outlines a unique approach, emphasizes the practical implementation of the proposed model, acknowledges limitations, and suggests avenues for further research. Early detection of AD can significantly better the patient’s quality of care and lead to future preventative or risk assessment measures.
Refining gene delivery to skeletal muscle with a dual-strategy approach of muscle-tropic AAV capsids and muscle-specific promoters
Authors: Darbey Annalucia , Jin Wenanlan , Greensmith Linda , Sleigh James N. , Counsell John , Fratta Pietro
Published: August 2024

Viral vector technologies based on adeno-associated virus (AAV) have demonstrated promising ability to deliver genetic cargo to a range of organsin vivo,with several novel candidates showing clinical efficacy in human trials over the past decade. However, naturally occurring AAV serotypes are limited in their ability to target skeletal muscle, an important gene therapy target for many neuromuscular disorders. This means that high doses of AAV are often required to achieve therapeutically effective doses in muscle. To overcome this, novel AAV vector capsids have been engineered by inserting targeting peptides into the AAV9 capsid variable region VIII (VRIII) to achieve greater muscle transduction efficiency. Here we describe investigation of a newly reported capsid, called MyoAAV1A combined with clinically validated muscle-specific promoters. We profiled the efficiency ofin vivodelivery to murine skeletal muscle and found that the optimal combination of MyoAAV1A capsid with MHCK7 promoter maintains transgene expression in skeletal muscle, and reduces expression in off-target tissues, particularly the liver. This highlights a promising capsid-promoter combination to progress in further preclinical research for skeletal muscle gene therapy.

Graphical abstract
Localizedin vivoprodrug activation using radionuclides
Authors: Quintana J.M. , Jiang F. , Kang M. , Valladolid Onecha V. , Könik A. , Qin L. , Rodriguez V.E. , Hu H. , Borges N. , Khurana I. , Banla L.I. , Le Fur M. , Caravan P. , Schuemann J. , Bertolet A. , Weissleder R. , Miller M.A. , Ng T.S.C.
Published: August 2024

Radionuclides used for imaging and therapy can show high molecular specificity in the body with appropriate targeting ligands. We hypothesized that local energy delivered by molecularly targeted radionuclides could chemically activate prodrugs at disease sites while avoiding activation in off-target sites of toxicity. As proof-of-principle, we tested whether this strategy of “RAdionuclideinducedDrugEngagement forRelease” (RAiDER) could locally deliver combined radiation and chemotherapy to maximize tumor cytotoxicity while minimizing exposure to activated chemotherapy in off-target sites.

Methods

We screened the ability of radionuclides to chemically activate a model radiation-activated prodrug consisting of the microtubule destabilizing monomethyl auristatin E caged by a radiation-responsive phenyl azide (“caged-MMAE”) and interpreted experimental results using the radiobiology computational simulation suite TOPAS-nBio. RAiDER was evaluated in syngeneic mouse models of cancer using fibroblast activation protein inhibitor (FAPI) agents99mTc-FAPI-34 and177Lu-FAPI-04, the prostate-specific membrane antigen (PSMA) agent177Lu-PSMA-617, combined with caged-MMAE or caged-exatecan. Biodistribution in mice, combined with clinical dosimetry, estimated the relationship between radiopharmaceutical uptake in patients and anticipated concentrations of activated prodrug using RAiDER.

Results

RAiDER efficiency varied by 250-fold across radionuclides (99mTc>177Lu>64Cu>68Ga>223Ra>18F), yielding up to 1.22µM prodrug activation per Gy of exposure from99mTc. Computational simulations implicated low-energy electron-mediated free radical formation as driving prodrug activation. Clinically relevant radionuclide concentrations chemically activated caged-MMAE restored its ability to destabilize microtubules and increased its cytotoxicity by up to 600-fold compared to non-irradiated prodrug. Mice treated with99mTc-FAPI-34 and caged-MMAE accumulated up to 3000× greater concentrations of activated MMAE in tumors compared to other tissues. RAiDER with99mTc-FAPI-34 or177Lu-FAPI-04 delayed tumor growth, while monotherapies did not (P<0.03). Clinically-guided dosimetry suggests sufficient radiation doses can be delivered to activate therapeutically meaningful levels of prodrug.

Conclusion

This proof-of-concept study shows that RAiDER is compatible with multiple radionuclides commonly used in nuclear medicine and has the potential to improve the efficacy of radiopharmaceutical therapies to treat cancer safely. RAiDER thus shows promise as an effective strategy to treat disseminated malignancies and broadens the capability of radiopharmaceuticals to trigger diverse biological and therapeutic responses.

Abstract Figure
Engineered human iPS cell models reveal altered podocytogenesis and glomerular capillary wall in CHD-associatedSMAD2mutations
Authors: Bhattacharya Rohan , Ward Tarsha , Kalejaiye Titilola D. , Mishra Alekshyander , Leeman Sophia , Arzaghi Hamidreza , Seidman Jonathan G. , Seidman Christine E. , Musah Samira
Published: August 2024

Early developmental programming involves extensive cell lineage diversification through shared molecular signaling networks. Clinical observations of congenital heart disease (CHD) patients carryingSMAD2genetic variants revealed correlations with multi-organ impairments at the developmental and functional levels. For example, many CHD patients present with glomerulosclerosis, periglomerular fibrosis, and albuminuria. Still, it remains largely unknown whetherSMAD2variants associated with CHD can directly alter kidney cell fate, tissue patterning, and organ-level function. To address this question, we engineered human iPS cells (iPSCs) and organ-on-a-chip systems to uncover the role of pathogenicSMAD2variants in kidney podocytogenesis. Our results show that abrogation ofSMAD2causes altered patterning of the mesoderm and intermediate mesoderm (IM) cell lineages, which give rise to nearly all kidney cell types. Upon further differentiation of IM cells, the mutant podocytes failed to develop arborizations and interdigitations. A reconstituted glomerulus-on-a-chip platform exhibited significant proteinuria as clinically observed in glomerulopathies. This study implicates CHD-associatedSMAD2mutations in kidney tissue malformation and provides opportunities for therapeutic discovery in the future.
Dynamics of Bagaza, West Nile, and Usutu viruses in Portugal revealed by long-term serological surveillance in red-legged partridges, 2018-2022
Authors: Fontoura-Gonçalves Catarina , Llorente Francisco , Pérez-Ramírez Elisa , Jiménez-Clavero Miguel Ángel , Costa João Basso , de Mello Gonçalo , Gonçalves David , Alves Paulo Célio , Höfle Ursula , Queirós João
Published: August 2024

Background

Bagaza virus (BAGV) emerged in Portugal in 2021. BAGV and other flaviviruses such as West Nile virus (WNV) and Usutu virus (USUV) represent emerging threats in Europe, yet uncertainties persist regarding their epidemiological status in Portugal.

Aim

This study aimed to elucidate the epidemiological dynamics of BAGV, WNV, and USUV in Portugal using the red-legged partridge (Alectoris rufa) as a susceptible bird model species.

Methods

Serum samples collected from a partridge population in Southern Portugal, between 2018 and 2022, were analysed to characterize exposure to flaviviruses through enzyme-linked immunosorbent assay (ELISA; n=468) and virus neutralization test (VNT; n=433).

Results

ELISA test revealed an average seroprevalence of 58.1% for WNV and WNV-cross-reacting antibodies between 2018 and 2022, while 66.3% of individuals tested positive using VNT: 28.8% specific for WNV, 8.1% for BAGV, 2.1% for USUV and 27.2% for “undetermined flaviviruses”. BAGV seroprevalence was first detected in October 2021 (8.7%), alongside an outbreak detection, peaking in November 2021 (26.3%) and persisting until October 2022 (2.3%). WNV antibodies were detected throughout all sampling periods, with the highest seroprevalence in October 2020 (44.8%). USUV seroprevalence was detected until the BAGV outbreak in 2021, peaking in October 2020 (6.9%).

Conclusion

Long-term serological surveillance of partridges revealed endemic circulation of WNV and sporadic circulation of BAGV and USUV in Portugal. Notably, the highest WNV seroprevalence coincided with the human WNV outbreak in southern Spain in the summer of 2020, highlighting the role of red-legged partridges in the transmission/maintenance cycle and as sentinels of flaviviruses circulation.
Expression quantitative trait locus mapping in recombinant gametes using single nucleus RNA sequencing
Authors: Parker Matthew T. , Amar Samija , Campoy José A. , Krause Kristin , Tusso Sergio , Marek Magdalena , Huettel Bruno , Schneeberger Korbinian
Published: August 2024

Phenotypic differences between individuals of a species are often caused by differences in gene expression, which are in turn caused by genetic variation. Expression quantitative trait locus (eQTL) analysis is a methodology by which we can identify such causal variants. Scaling eQTL analysis is costly due to the expense of generating mapping populations, and the collection of matched transcriptomic and genomic information. We developed a rapid eQTL analysis approach using single-cell/nucleus RNA sequencing of gametes from a small number of heterozygous individuals. Patterns of inherited polymorphisms are used to infer the recombinant genomes of thousands of individual gametes and identify how different haplotypes correlate with variation in gene expression. Applied to Arabidopsis pollen nuclei, our approach uncovers bothcis- andtrans-eQTLs, ultimately mapping variation in a master regulator of sperm cell development that affects the expression of hundreds of genes. This establishes snRNA-sequencing as a powerful, cost-effective method for the mapping of meiotic recombination, addressing the scalability challenges of eQTL analysis and enabling eQTL mapping in specific cell-types.
Diseases and invasive species have synergistic effects with other anthropogenic threats on the functional and phylogenetic diversity in Testudines and Crocodilia
Authors: Rodriguez-Caro Roberto C. , Gumbs Rikki , Gracia Eva , Blomberg Simon P , Cayuela Hugo , Grace Molly K , Carmona Carlos Perez , Perez-Mendoza Hibraim Adan , Gimenez Andres , Davis Katrina J , Salguero-Gomez Rob
Published: August 2024

Understanding how multiple threats interact is crucial for the prioritization of conservation measures. Here, we investigate how interactions between six common threats (climate change, habitat disturbance, global trade, overconsumption, pollution, and emerging diseases/invasive species) affect the functional and phylogenetic diversity of 230 species of Testudines and 21 of Crocodilia. We classify two-way threat interactions into additive, synergistic, and antagonistic according to their effects on functional and phylogenetic diversity. Most threat interactions are antagonistic, the effect of threats jointly is lower than the sum of the effects of threats separately. However, we find that the interaction between emerging diseases or invasive species with other threats has synergistic and additive effects, meaning that the combined effects are greater or equal to the effects of threats separately. Our work can help target conservation strategies and detect key places to address multiple threats when they appear together.
Physiological and Molecular Responses of Projected Future Temperatures on Potato Tuberization
Authors: Guillemette Abigail M. , Casanova Guillian Hernández , Hamilton John P. , Pokorná Eva , Dobrev Petre I. , Motyka Václav , Rashotte Aaron M. , Leisner Courtney P.
Published: August 2024

Potato (Solanum tuberosumL.) is one of the most important food crops globally and is especially vulnerable to heat stress. Significant knowledge gaps remain however, in our understanding of the developmental mechanisms associated with tuber responses to heat stress. This study uses whole-plant physiology, transcriptomics, and hormone profiling to gain insights into the mechanisms associated with heat stress impacts on potato tuber development. When plants were grown in projected future temperature conditions, levels of abscisic acid (ABA) were significantly decreased in leaf and tuber tissues while rates of leaf carbon assimilation and stomatal conductance were not significantly affected. While plants grown in elevated temperature conditions initiated more tubers on average per plant, there was a significant decrease (66%) in mature tubers at final harvest. We hypothesize that reduced tuber yields at elevated temperatures are not due to reductions in tuber initiation, but due to impaired tuber filling. Transcriptomic analysis found significant changes in transcript expression for genes related to response to ABA, heat and auxin biosynthetic process. The known tuberization repressor genes SELF PRUNING 5G (StSP5G) and CONSTANS-LIKE1 (StCOL1) were found to be differentially expressed in tubers grown in elevated temperatures. IDENTITY OF TUBER 1 (StIT1) and TIMING OF CAB EXPRESSION 1 (StTOC1) are other known tuberization genes that displayed distinct expression patterns in elevated versus ambient temperatures but were not differentially expressed. This work highlights potential gene targets and key developmental stages associated with tuberization to development more heat tolerant potatoes.
Mastering Artifact Correction in Neuroimaging Analysis: A Retrospective Approach
Authors: Oliveira Alícia , Cepa Beatriz , Brito Cláudia , Sousa António
Published: August 2024

The correction of artifacts in Magnetic Resonance Imaging (MRI) is increasingly relevant as voluntary and involuntary artifacts can hinder data acquisition. Reverting from corrupted to artifact-free images is a complex task. Deep Learning (DL) models have been employed to preserve data characteristics and to identify and correct those artifacts. We proposeMOANA, a novel DL-based solution to correct artifacts in multi-contrast brain MRI scans.MOANAoffers two models: the simulation and the correction models. The simulation model introduces perturbations similar to those occurring in an exam while preserving the original image as ground truth; this is required as publicly available datasets rarely have motion-corrupted images. It allows the addition of three types of artifacts with different degrees of severity. The DL-based correction model adds a fourth contrast to state-of-the-art solutions while im-proving the overall performance of the models.MOANAachieved the highest results in the FLAIR contrast, with a Structural Similarity Index Measure (SSIM) of 0.9803 and a Normalized Mutual Information (NMI) of 0.8030. With this, theMOANAmodel can correct large volumes of images in less time and adapt to different levels of artifact severity, allowing for better diagnosis.
The intrinsic dimension of gene expression during cell differentiation
Authors: Biondo Marta , Cirone Niccolò , Valle Filippo , Lazzardi Silvia , Caselle Michele , Osella Matteo
Published: August 2024

Waddington’s epigenetic landscape has long served as a conceptual framework for understanding cell fate decisions. The landscape’s geometry encodes the molecular mechanisms that guide the gene expression profiles of uncommitted cells toward terminally differentiated cell types. In this study, we demonstrate that applying the concept of intrinsic dimension to single-cell transcriptomic data can effectively capture trends in expression trajectories, supporting this framework. This approach allows us to define a robust cell potency score without relying on prior biological information. By analyzing an extensive collection of datasets from various species, experimental protocols, and differentiation processes, we validate our method and successfully reproduce established hierarchies of cell type potency.
Paradoxical SERCA dysregulation contributes to atrial fibrillation in a model of diet-induced obesity
Authors: Ponce-Balbuena Daniela , Tyrrell Daniel J. , Cruz-Cortés Carlos , Guerrero-Serna Guadalupe , Da Rocha Andre Monteiro , Herron Todd J. , Song Jianrui , Raza Danyal S. , Anumonwo Justus , Goldstein Daniel R. , Espinoza-Fonseca L. Michel
Published: August 2024

Obesity is a major risk factor for atrial fibrillation (AF) the most common serious cardiac arrhythmia, but the molecular mechanisms underlying diet-induced AF remain unclear. In this study, we subjected mice to a chronic high-fat diet and acute sympathetic activation (‘two-hit’ model) to study the mechanisms by which diet-induced obesity promotes AF. Surface electrocardiography revealed that diet-induced obesity and sympathetic activation synergize during intracardiac tachypacing to induce AF. At the cellular level, diet-induced obesity and acute adrenergic stimulation facilitate the formation of delayed afterdepolarizations in atrial myocytes, implicating altered Ca2+dynamics as the underlying cause of AF. We found that diet-induced obesity does not alter the expression of major Ca2+-handling proteins in atria, including the sarcoplasmic reticulum Ca2+-ATPase (SERCA), a major component of beat-to-beat Ca2+cycling in the heart. Paradoxically, obesity reduces phospholamban phosphorylation, suggesting decreased SERCA activity, yet atrial myocytes from obese mice showed a significantly increased Ca2+transient amplitude and SERCA-mediated Ca2+uptake. Adrenergic stimulation further increases the Ca2+transient amplitude but does not affect Ca2+reuptake in atrial myocytes from obese mice. Transcriptomics analysis showed that a high-fat diet prompts upregulation of neuronatin, a protein that has been implicated in obesity and is known to stimulate SERCA activity. We propose a mechanism in which obesity primes SERCA for paradoxical activation, and adrenergic stimulation facilitates AF conversion through a Ca2+-induced Ca2+release gain in atrial myocytes. Overall, this study links obesity, altered Ca2+signaling, and AF, and targeting this mechanism may prove effective for treating obesity-induced AF.
Bridging tuning and invariance with equivariant neuronal representations
Authors: Hoeller Judith , Zhong Lin , Pachitariu Marius , Romani Sandro
Published: August 2024

As we move through the world, we see the same visual scenes from different perspectives. Although we experience perspective deformations, our perception of a scene remains stable. This raises the question of which neuronal representations in visual brain areas are perspective-tuned and which are invariant. Focusing on planar rotations, we introduce a mathematical framework based on the principle of equivariance, which asserts that an image rotation results in a corresponding rotation of neuronal representations, to explain how the same representation can range from being fully tuned to fully invariant. We applied this framework to large-scale simultaneous neuronal recordings from four visual cortical areas in mice, where we found that representations are both tuned and invariant but become more invariant across higher-order areas. While common deep convolutional neural networks show similar trends in orientation-invariance across layers, they are not rotation-equivariant. We propose that equivariance is a prevalent computation of populations of biological neurons to gradually achieve invariance through structured tuning.
OXPHOS TARGETING OF MYCN-AMPLIFIED NEUROBLASTOMA
Authors: Epp Soraya , Egan Donagh , Poon Evon , Abdul Aziz Amirah Adlina , Wynne Kieran , Halasz Melinda , Kolch Walter
Published: August 2024

Abstract/Summary

High risk - neuroblastoma (HR-NB) is a pediatric solid tumor with high lethality. Half of HR-NB are driven by MYCN gene amplification (MNA). These HR-NBs require high dosage chemotherapy and often relapse. Moreover, current therapies can cause severe long-term side effects and new therapies are urgently needed. This study investigates a novel therapeutic approach targeting the metabolic vulnerabilities of MNA NB cells. We discovered that Diphenyleneiodonium chloride (DPI), an inhibitor of flavoprotein enzymes and mitochondrial complex I, synergizes with mitoquinone mesylate (MitoQ), a mitochondria-targeted antioxidant in 2D and 3Din vitromodels of NB. Similarly to DPI, MitoQ affects MNA cells in a MYCN-dependent way, being more toxic when MYCN levels are high. Furthermore, low nanomolar concentrations of MitoQ significantly decrease MYCN protein expression and induce differentiation of MNA cells. The DPI and MitoQ combination further synergizes with vincristine, a chemotherapeutic agent used in NB treatment. Phosphoproteomics and proteomics analysis suggests that the drug combination induces MNA NB cell death by arresting the cell cycle and inhibiting oxidative phosphorylation (OXPHOS) in the mitochondria. Thus, interference with mitochondrial metabolism may represent an effective strategy to enhance the activity of chemotherapeutic drugs in MNA-NB.
VSTM2L protects prostate cancer cells against ferroptosis via inhibiting VDAC1 oligomerization and maintaining mitochondria homeostasis
Authors: Yang Juan , Lu Xiao , Hao Jing-Lan , Li Lan , Ruan Yong-Tong , An Xue-Ni , Dong Xiao-Ming , Gao Ping
Published: August 2024

Mitochondria play a critical role in initiating and amplifying ferroptosis. VDAC1 embedded in the mitochondrial outer membrane, exerts a crucial role in regulation of ferroptosis. However, the mechanisms of VDAC1 oligomerization in regulating ferroptosis are not well elucidated. Here, we identified that VSTM2L, a novel VDAC1 binding protein, is positively associated with prostate cancer (PCa) progression, and a key regulator of ferroptosis. Moreover, VSTM2L knockdown in PCa cells enhanced the sensibility of RSL3-induced ferroptosis. Mechanistically, VSTM2L forms complex with VDAC1 and HK2, enhancing their binding affinity and preventing VDAC1 oligomerization, thereby inhibiting ferroptosis and maintaining mitochondria homeostasisin vitroandin vivo. Collectively, our findings reveal a pivotal role for VSTM2L in driving ferroptosis resistance and highlight its potential as a ferroptosis-inducing therapeutic target for the treatment of PCa.
WITHDRAWN: A preliminary investigation of a soluble dietary fibre and mineral formulation on post-prandial glucose regulation and satiation
Authors: Haynes Michael
Published: August 2024

Withdrawal statement

The authors have withdrawn this manuscript because of conflicts of interest. This involves coauthor contributions and Optibiotix awareness/ agreement for their product use in this study. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
From messy chemistry to ecology: autocatalysis and heritability in prebiotically plausible chemical systems
Authors: Sokolskyi Tymofii , Zuviria Bruno Cuevas , Gargulak Sydney , Allen Esau , Baum David
Published: August 2024

A key question in origins-of-life research, is whether heritability, and thus evolution, could have preceded genes. Out-of-equilibrium chemical reaction networks with multiple autocatalytic motifs may provide chemical “memory” and serve as units of heritability, but experimental validation is lacking. We established conditions that may be conducive to the emergence of heritable variation and developed methods to search for heritability and autocatalysis. We prepared a food set (FS) of three organic species, three inorganic salts and pyrite. We conducted a serial dilution experiment where FS was incubated for 24 hours, after which a 20% fraction was transferred into freshly prepared FS that went through the same procedure, repeated for 10 generations. To serve as controls, we also incubated the fresh solutions in each generation. We compared the chemical composition of transfer vials and no-transfer controls using liquid chromatography-mass spectrometry (LCMS), with metrics adapted from ecology and evolutionary biology. While variability was high, focusing on a subset of chemicals with more consistent patterns revealed evidence of heritable variation among vials. Using rule-based chemical reaction network inference, constrained by the LCMS data, we identified a plausible FS-driven chemical reaction network that was found to contain numerous autocatalytic cycles.
From Virtual Screens to Cellular Target Engagement: New Small Molecule Ligands for the Immune Checkpoint LAG-3
Authors: Fuchs Natalie , Calvo-Barreiro Laura , Talagayev Valerij , Pach Szymon , Wolber Gerhard , Gabr Moustafa T.
Published: August 2024

Herein, we performed a virtual screening study to discover new scaffolds for small molecule-based ligands of the immune checkpoint lymphocyte-activation gene 3 (LAG-3). Molecular dynamics (MD) simulations using the LAG-3 structure revealed two putative binding sites for small molecules: the antibody interface and a lipophilic canyon. A 3D pharmacophore screening resulted in the identification of potential ligands for these binding sites and afforded a library of 25 compounds. We then evaluated the screening hits for LAG-3 binding via microscale thermophoresis (MST) and surface plasmon resonance (SPR). Our biophysical screening identified two binders withKDvalues in the low micromolar range, compounds 3 (antibody interface) and25(lipophilic canyon). Furthermore, we investigated the ability of LAG-3 hits to en-gage LAG-3 on a cellular level using a cellular thermal shift assay (CETSA), where compound3emerged as a promising candidate for future development.
ERBB2/HOXB13co-amplification with interstitial deletion ofBRCA1defines a unique subset of breast cancers
Authors: Mitsiades Irene Rin , Onozato Maristela , John Iafrate A. , Hicks Daniel , Sgroi Dennis C. , Rheinbay Esther
Published: August 2024

Background

TheHOXB13/IL17BRgene expression biomarker has been shown to predict response to adjuvant and extended endocrine therapy in patients with early-stage ER+ HER2- breast tumors.HOXB13gene expression is the primary determinant driving the prognostic and endocrine treatment-predictive performance of the biomarker. Currently, there is limited data onHOXB13expression in HER2+ and ER- breast cancers. Herein, we studied the expression ofHOXB13in large cohorts of HER2+ and ER- breast cancers.

Methods

We investigated gene expression, genomic copy number, mutational signatures, and clinical outcome data in the TGGA and METABRIC breast cancer cohorts. Genomic-based gene amplification data was validated with tri-colored fluorescencein situhybridization.

Results

In the TCGA breast cancer cohort,HOXB13gene expression was significantly higher in HER2+ versus HER2- breast cancers, and its expression was also significantly higher in the ER- versus ER+ breast cancers.HOXB13is frequently co-gained or co-amplified withERBB2. Joint copy gains ofHOXB13andERBB2occurred with low-level co-gains or high-level co-amplifications (co-amp), the latter of which is associated with an interstitial deletion that includes the tumor suppressorBRCA1.ERBB2/HOXB13co-amp tumors with interstitialBRCA1loss exhibit a mutational signature associated with APOBEC deaminase activity, and copy number signatures associated with chromothripsis and genomic instability. AmongERBB2-amplified tumors of different tissue origins,ERBB2/HOXB13co-amp with aBRCA1loss appeared to be unique to breast cancer. Lastly, patients withERBB2/HOXB13co-amplified andBRCA1lost tumors displayed a significantly shorter progression-free survival (PFS) than those withERBB2-only amplifications. The difference in PFS was restricted to the ER- subset patients and this difference in PFS was not solely driven byHOXB13gene expression.

Conclusions

HOXB13is frequently co-gained withERBB2at both low-copy number level or as complex high-level amplification with relativeBRCA1loss.ERBB2/HOXB13amplified,BRCA1-lost tumors are strongly enriched in breast cancer, and patients with such breast tumors experience a shortened PFS.
Geometry representations along visual pathways in human spatial navigation
Authors: Zeng Taiping , Cai Ming Bo
Published: August 2024

The representation of geometric structures in the environments is key to self-localization during human spatial navigation. Its spatial organization in the visual system is not fully characterized. Using brain activity from 20 participants watching videos from identical realistic virtual environments under different weather and lighting conditions, we found a compact representation of scene geometric structures encoded in a large network of brain regions, allowing for reconstructing depth. It forms a continuous map composed of three parallel pathways that we jointly coin as ”geometry visual pathways”, starting from the primary visual cortex: the dorsal and medial pathways end in the intraparietal areas, while the ventral pathway arrives at the hippocampus via the parahippocampal gyrus. Furthermore, road types, a more abstract representation of geometry, are encoded in overlapping pathways ex-cluding early visual cortex (V1, V2, V3). The geometry visual pathways provide new insights into the traditional dichotomy between ”what” and ”where” pathways.
TAM receptors mediate the Fpr2-driven pain resolution and fibrinolysis after nerve injury
Authors: Hartmannsberger Beate , Ben-Kraiem Adel , Kramer Sofia , Guidolin Carolina , Kazerani Ida , Doppler Kathrin , Thomas Dominique , Gurke Robert , Sisignano Marco , Kalelkar Pranav P. , García Andrés J. , Monje Paula V. , Nusrat Asma , Brack Alexander , Krug Susanne M. , Sommer Claudia , Rittner Heike L.
Published: August 2024

Nerve injury causes neuropathic pain and multilevel nerve barrier disruption. Nerve barriers consist of perineurial, endothelial, and myelin barriers. So far, it is unclear whether resealing nerve barriers fosters pain resolution and recovery. To this end, we analysed the nerve barrier property portfolio, pain behaviour battery, and lipidomics for precursors of specialized pro-resolving meditators (SPMs) and their receptors in chronic constriction injury of rat sciatic nerve to identify targets for pain resolution by resealing the selected nerve barriers. Of the three nerve barriers – perineurium, capillaries, and myelin – only capillary tightness specifically against larger molecules, such as fibrinogen, recuperated with pain resolution. Fibrinogen immunoreactivity was not only elevated in rats at the time of neuropathic pain but also in nerve biopsies from patients with (but not without) painful polyneuropathy indicating that sealing of the vascular barrier might be novel approach in pain treatment. 15R-HETE (hydroxyeicosatetraenoic acid), a precursor of aspirin-triggered lipoxin A4, were specifically upregulated at the beginning of pain resolution. Repeated local application of resolvin D1-laden nanoparticles or Fpr2 agonists sex-independently resulted in accelerated pain resolution and fibrinogen removal. Clearing macrophages (Cd206)and fibrinolytic pathways (Plat)were also induced while inflammation (Tnfα)and inflammasomes (Nlrp3)were unaffected by this treatment. Blocking TAM receptors (Tyro3, Axl, and Mer) and tyrosine kinase receptors linking haemostasis and inflammation completely inhibited all the effects. In summary, nanoparticles can be used as transporters for fleeting lipids, such as SPMs, and therefore expand the array of possible therapeutic agents. Thus, the Fpr2-Cd206-TAM receptor axis may be a suitable target for strengthening the capillary barrier, removing endoneurial fibrinogen, and boosting pain resolution in patients with chronic neuropathic pain.
A Small Interfering Peptide Potentiates AMPA Receptor Diffusional Trapping and Prevents Social-Isolation-Induced Forgetting of Fear Memory
Authors: Gundersen Jens Edvard Trygstad , Wu Xinrong , Song Jiaxing , Yao Jingyu , Nesbø Håvard Håvardsholm , Pokharna Aditya , Mergiya Tadiwos Feyissa , Liu Huadong , Sun Suya , Greger Ingo , Wang Changhe , Xu Nan-jie , Bramam Clive R , Zhang Hongyu
Published: August 2024

Regulation and dysregulation of AMPA receptor (AMPAR) diffusional trapping at synapses are critical for synaptic efficacy and are implicated in various neurological and neuropsychiatric disorders. However, the limited availability of reliable tools to modulate this process hinders our ability to explore its role in both physiological conditions and disease, as well as in drug development. In this study, we designed and characterized a 21-amino-acid trans-activator of transcription (TAT)-fused peptide that mimics the binding region of the transmembrane AMPAR regulatory proteins (TARPs) C-tail to the activity-regulated cytoskeleton-associated protein (Arc/Arg3.1) N-lobe. Acute intrahippocampal infusion of this peptide enhanced perforant path-evoked synaptic transmission in the rat dentate gyrus (DG) in vivo, likely by strengthening the interaction between TARP and postsynaptic density protein 95 (PSD-95), a mechanism crucial for the synaptic anchoring of AMPARs. Additionally, the peptide also slowed AMPAR lateral diffusion and blocked KCl-induced AMPAR endocytosis, likely by enhancing the diffusional trapping of AMPARs at the synapse. Remarkably, a 7-day peptide infusion prevented social-isolation-induced forgetting of fear memory. Our findings suggest that targeting AMPAR diffusional trapping, particularly through disrupting the TARP-Arc N-lobe interaction, could hold promise as a therapeutic approach for neurological and neuropsychiatric disorders associated with impaired AMPAR synaptic retention.
Twisted Sister1: an agravitropic mutant of bread wheat (Triticum aestivum) with altered root and shoot architectures
Authors: Zeng Deying , Peng Jiayu , Zhang Lan , Hayden Mathew J. , Rathjen Tina M. , Zhu Bo , Zeng Zixian , Delhaize Emmanuel
Published: August 2024

We identified a mutant of hexaploid wheat (Triticum aestivum) with impaired responses to gravity. The mutant namedTwisted Sister1(TS1) had agravitropic roots that were often twisted along with altered shoot phenotypes. Roots ofTS1were insensitive of externally applied auxin with the genetics and physiology suggestive of a mutatedAUX/IAAtranscription factor gene. Hexaploid wheat possesses over eightyAUX/IAAgenes and sequence information did not identify an obvious candidate. Bulked segregant analysis of an F2population mapped the mutation to chromosome 5A and subsequent mapping located the mutation to a 41 Mbp region. RNA-seq identified theTraesCS5A03G0149800gene encoding a TaAUX/IAA protein to be mutated in the highly conserved domain II motif. We confirmedTraesCS5A03G0149800as underlying the mutant phenotype by generating transgenicArabidopsis thaliana. Analysis of RNA-seq data suggested broad similarities between Arabidopsis and wheat for the role ofAUX/IAAgenes in gravity responses. Here we show that the sequenced wheat genome along with previous knowledge largely from the model species Arabidopsis, gene mapping, RNA-seq and expression in Arabidopsis have enabled cloning of a key wheat gene defining plant architecture.
Learning in single cells: biochemically-plausible models of habituation
Authors: Eckert Lina , Vidal-Saez Maria Sol , Zhao Ziyuan , Garcia-Ojalvo Jordi , Martinez-Corral Rosa , Gunawardena Jeremy
Published: August 2024

The ability to learn is typically attributed to animals with brains. However, the apparently simplest form of learning, habituation, in which a steadily decreasing response is exhibited to a repeated stimulus, is found not only in animals but also in single-cell organisms and individual mammalian cells. Habituation has been codified from studies in both invertebrate and vertebrate animals, as having ten characteristic hallmarks, seven of which involve a single stimulus. Here, we show by mathematical modelling that simple molecular networks, based on plausible biochemistry with common motifs of negative feedback and incoherent feedforward, can robustly exhibit all single-stimulus hallmarks. The models reveal how the hallmarks arise from underlying properties of timescale separation and reversal behaviour of memory variables and they reconcile opposing views of frequency and intensity sensitivity expressed within the neuroscience and cognitive science traditions. Our results suggest that individual cells may exhibit habituation behaviour as rich as that in multi-cellular animals with central nervous systems and that the relative simplicity of the biomolecular level may enhance our understanding of the mechanisms of learning.
Improved Degradome Sequencing Protocol via Reagent Recycling from sRNAseq Library Preparations
Authors: Puchta-Jasińska Marta , Groszyk Jolanta , Boczkowska Maja
Published: August 2024

Background

One of the key elements in the analysis of gene expression and its post-translational regulation is miRNAs. Degradome-seq analyses are performed to analyze the cleavage of target RNAs in the transcriptome. In this work, an improved library preparation protocol for degradome sequencing is presented. The developed protocol improves the efficiency of library preparation in degradome-seq analysis used to identify microRNA targets, reduces the time of library preparation and lowers the cost of purchasing reagents..

Results

The aim of this study was the development of an efficient protocol for the construction of degradome sequencing libraries using residual reagents from the sRNA-seq library preparation kit. To this end, modified primers and adaptors were designed. The library purification step based on automated electrophoresis and high-resolution agarose was modified and optimized in the presented protocol. Size standards of 60 and 65 bp were developed. They were prepared for precise band excision from the gel. Cloning to plasmid and sequencing of the inserted fragment, i.e., a fragment from the degradome library, verified the correctness of the library preparation using the developed protocol.

Conclusion

The developed protocol allowed the construction and sequencing of degradome libraries even from RNA samples with low RIN. It significantly reduces the cost of library construction. This is due to the use of residues from the sRNA-seq library kit. The precision of the excised fragment after electrophoresis performed during the procedure to isolate fragments of the correct length is significantly improved by the use of additional size markers. Compared to previously used methods, optimizing the purification method of degradom-seq libraries allowed to increase the yield of fragments obtained. Notably, the time required for the entire library preparation protocol does not exceed three days, also a significant time savings.
Optimized semi-specific PCR amplification using arbitrarily degenerate primer for genome-wide genotyping and its application in peanut genetic diversity study
Authors: Zhao Sheng , Wang Yue , Zhang Xuejiao , Xie Shuxian , Chen Haotian , Yan Yiming , Gu Jiaqi , Chen Peng , Chang Yuxiao , Xu Zhijun
Published: August 2024

Cultivated peanut (Arachis hypogaeaL.) is an important legume crop with a large genome size but a limited genetic diversity. Evaluating the genetic variation among diverse peanut germplasms using genome-wide molecular markers is an effective strategy to explore its genetic diversity and thereby facilitate peanut improvement. In this study, we introduced a novel whole-genome genotyping (WGG) technique named dRAPD-seq (degenerate Random Amplification Polymorphic DNA and sequencing), which relies on semi-specific PCR amplification by arbitrarily degenerate (AD) primer and next-generation sequencing (NGS), and demonstrated its robust reproducibility and high accuracy. Subsequently, we applied dRAPD-seq to investigate the genetic relatedness within a population of 101 diverse peanut accessions and identified a low genetic diversity among these accessions. Our phylogenetic tree, population structure analyses, and principal component analysis (PCA) indicated that this population could be clustered into three subpopulations, largely corresponding to three botanical types. In conclusion, this research not only introduced a cost-effective and easy-to-conduct WGG method but also provided valuable insights for utilizing these peanut accessions in future breeding programs.
Decoding the Dewlap: Multiple signals in females and males of a gliding lizard
Authors: Sharma Avantika Deep , Sridharan Aravind , Isvaran Kavita
Published: August 2024

Social interactions across taxa are often mediated through multiple signals. Studies examining the maintenance of multiple signals are mostly focused on males and often fail to capture female signalling diversity and strategies. In the recent decade, there has been a surge in the documentation of female signalling, however, our understanding of the functional relevance of multiple signals in females still lags behind. In this study, we examined multiple signals in females of an arboreal gliding lizard,Draco dussumieri, and compared them to those in males. We specifically tested the relative role of the backup signal and the multiple receiver hypotheses in the maintenance of multiple signals in both sexes. FemaleD.dussumieriused a variety of signals to socially interact with conspecifics, especially using their dewlap. The signalling repertoire of females was as diverse as that of males, although the relative use of the signals varied. In females, a few signals seem to be maintained by the backup signal hypothesis, with limited support for the multiple receiver hypothesis as well. For males too, both mechanisms appeared to maintain multiple signals. Interestingly, for some signals, the sexes differed in the context in which they used a given signal. Overall, these findings highlight the functional role of multiple signals in females, which can differ from that observed in males. Therefore, traits conventionally considered male-exclusive when also examined in females can provide finer insights into trait function and evolution.
Diagnosis of celiac disease on a gluten-free diet: a multicenter prospective quasi-experimental clinical study
Authors: Gómez-Aguililla Sara , Farrais Sergio , López-Palacios Natalia , Arau Beatriz , Senosiain Carla , Corzo María , Fernandez-Jimenez Nora , Ruiz-Carnicer Ángela , Fernández-Bañares Fernando , González-García Bárbara P. , Tristán Eva , Montero-Calle Ana , Garranzo-Asensio María , Casado Isabel , Pujals Mar , Hernández Juana María , Infante-Menéndez Jorge , Roy Garbiñe , Sousa Carolina , Núñez Concepción
Published: August 2024

Background

Diagnosing celiac disease (CD) in individuals adhering to a gluten-free diet (GFD) presents significant challenges. Current guidelines recommend a gluten challenge (GC) lasting at least 6-8 weeks, which has several limitations.

Objectives

This study compares four approaches previously proposed for diagnosing CD on a GFD: IL-2 serum levels, gut-homing CD8+T cells, %TCRγδ+intraepithelial lymphocytes (IELs), andUBE2L3gene expression. Additionally, we evaluated the CD8+T-cell based method with a 3-day GC against the standard GC protocol.

Methods

We conducted a multicenter prospective quasi-experimental clinical study. Two subsets of individuals were considered: 1) 20 patients with CD and 15 non-CD controls previously diagnosed, to evaluate the first aim; 2) 45 individuals with uncertain diagnosis who were on a GFD and required GC following current clinical guidelines, to assess the second aim. All participants underwent a 3-day GC (10 g gluten/day).

Results

Among CD patients and non-CD controls, the sensitivity and specificity of IL-2, gut-homing CD8+T cells, andUBE2L3were 82.4% and 83.3%, 88.2% and 100%, and 52.9% and 100%, respectively. The percentage of TCRγδ+IELs showed 88.2% sensitivity. In the uncertain diagnosis group, a CD8+T-cell positive response was observed in 8 of the 45 subjects.

Conclusion

The percentage of TCRγδ+IELs and the gut-homing CD8+T-cell assay are promising diagnostic methods for CD on a GFD. Notably, the CD8+T-cell assay provides a consistent and reliable alternative to the extended GC, eliminating the need for the invasive procedures to obtain duodenal samples and the prolonged gluten ingestion.