bluuebunny/crossref_metadata_2025 huggingface dataset:
Secondary structure determines electron transport in peptides
Authors: Samajdar Rajarshi , Meigooni Moeen , Yang Hao , Li Jialing , Liu Xiaolin , Jackson Nicholas E. , Mosquera Martín A. , Tajkhorshid Emad , Schroeder Charles M.
Published: February 2024

Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, non-equilibrium Green’s function-density functional theory (NEGF-DFT) calculations, and unsupervised machine learning to understand the role of primary amino acid sequence and secondary structure on charge transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn) and a low-conductance state occurring for extended peptide structures. Conformer selection for the peptide structures is rationalized using principal component analysis (PCA) of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonably good agreement with experiments. Projected density of states (PDOS) calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides new avenues for understanding the electronic properties of longer peptides or proteins.

Significance Statement

Electron transport in proteins serves as a biological power line that fuels cellular activities such as respiration and photosynthesis. Within cells, proteins act as conduits, shuttling electrons through a series of reactions and pathways to generate proton gradients and to fuel ATP synthesis. Despite recent progress, the mechanisms underlying the flow of energy in protein complexes are not fully understood. Here, we study electron transport in peptides at the single-molecule level by combining experiments and molecular modeling. Our results reveal two distinct molecular sub-populations underlying electron transport that arise due to the flexibility of peptide backbones and the ability to fold into compact structures. This work provides a basis for understanding energy flow in larger proteins or biomolecular assemblies.
Information structure of heterogeneous criticality in a fish school
Authors: Niizato Takayuki , Sakamoto Kotaro , Mototake Yoh-ichi , Murakami Hisashi , Tomaru Takenori
Published: February 2024

The integrated information theory (IIT) measures the degree of consciousness in living organisms from an information-theoretic perspective. This theory can be extended to general systems such as those measuring criticality. Herein, we applied the IIT to actual collective behaviour (Plecoglossus altivelis). We found that the group integrity (i.e., Φ) could be maximised in the critical state and that several levels of criticalities existed in a group as subgroups. Furthermore, these fragmented critical groups coexisted with traditional criticality as a whole. The distribution of high-criticality subgroups was heterogeneous in terms of time and space. In particular, the core fish in the high-criticality group tended to be unaffected by internal and external stimulation, in contrast to those in the low-criticality group. The results of this study are consistent with previous interpretations of critical phenomena and provide a new interpretation of the detailed dynamics of an empirical critical state.
The Strongest Protein Binder is Surprisingly Labile
Authors: Fernandez-Calvo Alba , Reifs Antonio , Saa Laura , Cortajarena Aitziber L. , Sancho David De , Perez-Jimenez Raul
Published: February 2024

Bacterial adhesins are cell-surface proteins that anchor to the cell wall of the host, thus initiating infection. The initial step in infection is precisely the binding to fibrinogen (Fg) from human tissue, after which bacteria can colonize the heart valves by the formation of biofilms. The study of this family of proteins is hence essential to develop new strategies to fight bacterial infections. In the case ofStaphylococcus aureus, there exists a type of adhesins known as Microbial Surface Components Recognizing Adhesive Matrix Molecules (MSCRAMMs). Here, we focus on one of them, the Clumping Factor A (ClfA), which has been found to bind Fg through the dock-lock-latch (DLL) mechanism. Interestingly, it has recently been discovered that MSCRAMMs proteins employ a catch-bond to withstand forces exceeding 2 nN, making this type of interaction as mechanically strong as a covalent bond. However, whether this strength is an evolved feature characteristic of the bacterial protein or is typical only of the interaction with its partner is not known. Here we combine single-molecule force spectroscopy (smFS), biophysical binding assays and molecular simulations to study the intrinsic mechanical strength of ClfA. We find that despite the extremely high forces required to break its interactions with Fg, ClfA is not by itself particularly strong, in the absence of its human target. Integrating the results from both theory and experiments we dissect contributions to the mechanical stability of this protein.
Guidelines for QSM phantom production and evaluation of candidate phantom materials
Authors: Hooper Padriac , Jin Jin , O’Brien Kieran , Tourell Monique , Robinson Simon Daniel , Barth Markus
Published: February 2024

Purpose

Quantitative susceptibility mapping (QSM) is an MR technique that depicts and precisely quantifies spatial biodistributions from MR phase images. Recently, QSM has gained much uptake as method for mapping iron and identifying calcium. However, QSM as a quantitative method needs an objective reference to assess its accuracy. Here we present guidelines for reproducible workflows for QSM phantom design and production to help standardization efforts and provide characterizations and recommendations for iron- and calcium-based materials given the repeatability and reproducibility.

Methods

5 concentrations of 4 materials (USPIO, ferritin, calcium chloride, calcium carbonate) were imaged with a multi-echo gradient-echo acquisition at 3 and 7 Tesla. Magnetic susceptibility and R2* relaxivity as well as intra-session, inter-session repeatability, inter-scanner reproducibility and molar susceptibility by QSM were quantified.

Results

The QSM measurements of USPIO had a moderate to good inter-session repeatability. The molar susceptibility was approximately 2.45 times larger at 3 T compared to 7 T. The QSM measurements of ferritin had excellent inter-session repeatability. The molar susceptibility was approximately 4 % larger at 3 T compared to 7 T. The QSM measurements of calcium chloride had excellent inter-session repeatability and excellent inter-scanner reproducibility. The QSM measurements of calcium carbonate had a good to excellent inter-session repeatability and an excellent inter-scanner reproducibility.

Conclusion

This work reveals ferritin and calcium chloride to be the most repeatable and reproducible iron-and calcium-based materials for QSM, respectively. A detailed methodology for phantom production, concentration ranges, visual analysis and statistical analysis are provided.
Transcriptome sequencing and bioinformatics analysis of kidney tissue in a tree shrew model of calcium oxalate nephrolithiasis
Authors: Wang Guang , Huang Ziye , Wu Yuyun , Xu Rui , Li Jiongming
Published: February 2024

Background

Kidney stones, predominantly composed of calcium oxalate, are a prevalent and recurrent urological condition. Given their high incidence and recurrence rates, understanding their pathogenesis and identifying effective treatment strategies are imperative.

Methods

In this study, we established a calcium oxalate nephrolithiasis model using tree shrews, a primate-like animal species. When compared to commonly used rodent models (rats and mice), the tree shrew model demonstrated superior reproducibility and relevance. And leveraging transcriptome sequencing and comprehensive bioinformatics analysis.

Results

we identified 1,927 differentially expressed genes, including 1,450 upregulated and 476 downregulated genes. Furthermore, we annotated these genes to 41 KEGG enriched pathways and 1,413 GO enrichments, encompassing 1276 Biological Processes, 72 Cellular Components, and Molecular Functions. Notably, we prioritized the top 50 core genes that could potentially underlie the pathogenesis of calcium oxalate nephrolithiasis.

Conclusions

Our findings establish the tree shrew as a relevant model for studying kidney stone formation and provide valuable insights into the underlying molecular mechanisms. These insights hold promise for the development of novel therapeutic strategies to address this significant health burden.
QM/MM simulations of EFGR with afatinib reveal the role of theβ-dimethylaminomethyl substitution
Authors: Ma Shuhua , Patel Heeral , Peeples Craig A. , Shen Jana
Published: February 2024

Acrylamides are the most commonly used warheads of targeted covalent inhibitors (TCIs) directed at cysteines; however, the reaction mechanisms of acrylamides in proteins remain controversial, particularly for those involving protonated or unreactive cysteines. Using the combined semiempirical quantum mechanics (QM)/molecular mechanics (MM) free energy simulations, we investigated the reaction between afatinib, the first TCI drug for cancer treatment, and Cys797 in the EGFR kinase. Afatinib contains aβ-dimethylaminomethyl (β-DMAM) substitution which has been shown to enhance the intrinsic reactivity and potency against EGFR for related inhibitors. Two hypothesized reaction mechanisms were tested. Our data suggest that Cys797 becomes deprotonated in the presence of afatinib and the reaction proceeds via a classical Michael addition mechanism, with Asp800 stabilizing the ion-pair reactant stateβ-DMAM+/C797−and the transition state of the nucleophilic attack. Our work elucidates an important structure-activity relationship of acrylamides in proteins.
Human lymphoid-neutrophil/monocyte restriction co-ordinately activates increased proliferation despite parallel heterogeneity in transcriptional changes
Authors: Wang Fangwu , Gonzalez Laura , Hammond Colin , Hirst Martin , Simons Benjamin D. , Eaves Connie
Published: February 2024

Recent studies indicate the human lympho-myeloid restriction process to be a different and more heterogeneous one than historically inferred. Here we describe the development of bulk and clonal culture systems that efficiently support early B-lymphoid differentiation and their use to identify biological and molecular changes that accompany their initial restriction from subsets of CD34+ human cord blood cells with lympho-myeloid-limited potential. Analyses of the changes observed revealed the acquisition of B-lymphoid- and neutrophil/monocyte (NM)-restricted properties are accompanied by a concomitantly accelerated and lineage-shared cell cycling activity and loss of self-renewal properties. Parallel, single-cell transcriptome analysis identified reduced expression of multiple self-renewal-associated genes and an accompanying heterogeneous activation of lineage-regulatory modules during the production of B, NM and dendritic cell precursors. These results uncover a connected regulation of lineage-shared proliferation control with persistent heterogeneity in the biological and transcriptional changes in the same cells undergoing B and NM lineage restriction.
Personalized composite scaffolds for accelerated cell- and growth factor-free craniofacial bone regeneration
Authors: Kim Mirae , Collins Caralyn P. , Liu Yugang , Tsal Hsiu-Ming , Ahn Yujin , Wang Xinlong , Song Joseph W. , Duan Chongwen , Sun Cheng , Yi Zhu , He Tong-Chuan , Reid Russell R. , Ameer Guillermo A.
Published: February 2024

Approaches to regenerating bone often rely on the integration of biomaterials and biological signals in the form of cells or cytokines. However, from a translational point of view, these approaches face challenges due to the sourcing and quality of the biologic, unpredictable immune responses, complex regulatory paths, and high costs. We describe a simple manufacturing process and a material-centric 3D-printed composite scaffold system (CSS) that offers distinct advantages for clinical translation. The CSS comprises a 3D-printed porous polydiolcitrate-hydroxyapatite composite elastomer infused with a polydiolcitrate-graphene oxide hydrogel composite. Using a continuous liquid interface production 3D printer, we fabricate a precise porous ceramic scaffold with 60% hydroxyapatite content resembling natural bone. The resulting scaffold integrates with a thermoresponsive hydrogel composite, customizablein situto fit the defect. This hybrid phasic porous CSS mimics the bone microenvironment (inorganic and organic) while allowing independent control of each material phase (rigid and soft). The CSS stimulates osteogenic differentiationin vitroandin vivo. Moreover, it promotes M2 polarization and blood vessel ingrowth, which are crucial for supporting bone formation. Our comprehensive micro-CT analysis revealed that within 4 weeks in a critical-size defect model, the CSS accelerated ECM deposition (8-fold) and mineralized osteoid (69-fold) compared to the untreated. Our material-centric approach delivers impressive osteogenic properties and streamlined manufacturing advantages, potentially expediting clinical application for bone reconstruction surgeries.
Investigating the use of odour and colour foraging cues by rosy-faced lovebirds (Agapornis roseicollis) using deep-learning based behavioural analysis
Authors: Wai Tsang Winson King , Kei Poon Emily Shui , Newman Chris , Buesching Christina D. , Sin Simon Yung Wa
Published: February 2024

Olfaction and vision can play important roles in optimizing foraging decisions of birds, enabling them to maximize their net rate of energy intake while searching for, handling, and consuming food. Parrots have been used extensively in avian cognition research, and some species use olfactory cues to find food. Here we pioneered machine learning analysis and pose-estimation with convolutional neural networks (CNNs) to elucidate the relative importance of visual and olfactory cues for informing foraging decisions in the rosy-faced lovebird (Agapornis roseicollis) as a non-typical model species. In a binary choice experiment, we used markerless body pose tracking to analyse bird response behaviours. Rosy-faced lovebirds quickly learnt to discriminate the feeder provisioned with food by forming an association with visual (red/green papers) but not olfactory (banana/almond odour) cues. When visual cues indicated the provisioned and empty feeders, feeder choice was more successful, choice latency shorter, and interest in the empty feeder significantly lower. This demonstrates that visual cues alone are sufficient to inform lovebird foraging decisions without needing to use olfactory cues, suggesting that selection has not driven olfactory-based foraging in lovebird evolution.
A Novel Support Vector Machine-Based One-Day, Single-Dose Prediction Model of Genotoxic Hepatocarcinogenicity in Rats
Authors: Gi Min , Suzuki Shugo , Kanki Masayuki , Yokohira Masanao , Tsukamoto Tetsuya , Fujioka Masaki , Vachiraarunwong Arpamas , Qiu Guiyu , Guo Runjie , Wanibuchi Hideki
Published: February 2024

The development of a rapid and accurate model for determining the genotoxicity and carcinogenicity of chemicals is crucial for effective cancer risk assessment, and it also contributes to cancer prevention. This study aims to develop a one-day, single-dose model for identifying genotoxic hepatocarcinogens (GHCs) in rats. Microarray gene expression data from the livers of rats administered a single dose of 58 compounds, including 5 GHCs, was obtained from the Open TG-GATEs database and used for the identification of marker genes and the construction of a predictive classifier to identify GHCs in rats. We identified 10 gene markers commonly responsive to all 5 GHCs and used them to construct a support vector machine-based predictive classifier. This classifier effectively distinguishes GHCs from other compounds, demonstrating 100% sensitivity and over 96% specificity. To further assess the model’s effectiveness and reliability, we conducted multi-institutional one-day single oral administration studies on rats. These studies examined 64 compounds, including 23 GHCs, with gene expression data of the marker genes obtained via quantitative PCR (qPCR) 24 hours after a single oral administration. Our results demonstrate that qPCR analysis is an effective alternative to microarray analysis. The GHC predictive model showed high accuracy and reliability, achieving a sensitivity of 91% (21/23) and a specificity of 93% (38/41) across multiple validation studies in three institutions. In conclusion, the present one-day single oral administration model proves to be a reliable and highly sensitive tool for identifying GHCs and is anticipated to be a valuable tool in identifying and screening potential GHCs.
YAP promotes chromosomal instability by transcriptionally activating AJUBA through its super enhancer in breast cancer
Authors: Huang Qingwen , Zhang Rui , Meng Weijian , Dong Hongliang , Qi Zhihong , Chen Zhuo , Liu Liang , Shen Jie , Xie Daxing
Published: February 2024

Chromosomal instability (CIN) has been proven to be a fundamental property of cancer and a key underlying mechanism of tumorigenesis and progression. Still, relatively few studies have revealed the mechanism of this process. In this research, we identified the core Hippo component, YAP, played a crucial role in CIN formation in breast cancer. Using public ChIP-seq data and bioinformatic analysis, we found YAP could transcriptionally induce spindle assembly checkpoint, AJUBA, via TEAD, then activate AJUBA-AURKA signaling. Abolish AJUBA-AURKA axis could reverse YAP-induced CIN formation and aberrant mitosis. Mechanically, YAP/TEAD complex could accumulate to the super enhancer region of AJUBA, thus significantly induced its expression, and subsequently promoted AURKA auto-phosphorylating. These findings revealed a novel cross-talk between Hippo and AJUBA-AURKA signaling, and provided a new insight in CIN formation in breast cancer.
Chromosomal inversions harbour excess mutational load in the coral,Acropora kenti,on the Great Barrier Reef
Authors: Zhang Jia , Schneller Nadja M. , Field Matt A. , Chan Cheong Xin , Miller David J. , Strugnell Jan M. , Riginos Cynthia , Bay Line , Cooke Ira
Published: February 2024

The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here we show that the reef-building coral,Acropora kenti(syn. tenuis) harbors at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions.

Based on their high minor allele frequency, uniform distribution across habitats, and elevated genetic load, we propose that these inversions inA. kentiare likely to be under balancing selection. An excess of SNPs with high impact on protein coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future.
Effects of tenascin-C on dental pulp tissue in micein vivoand on the proliferation and differentiation of dental pulp stem cells into odontoblasts and calcificationin vitro
Authors: Kojima Kentaro , Akashi Yoshihiko , Nakajima Kei , Kokubun Katsutoshi , Shintani Seikou , Matsuzaka Kenichi
Published: February 2024

This study aimed to investigate the effects of tenascin-C (TN-C) on dental pulp tissue and on dental pulp stem cells (DPSCs). In in vivo studies, A collagen sponge with phosphate-buffered saline (PBS) for the control group or with TN-C for the experimental group was placed over the dental pulp of mice. The root pulp was excised at 7 and 21 days postoperatively and was observed microscopically using HE staining and immunohistochemistry. Inflammatory cells were found in the entire pulp tissue in the control group but no inflammatory cells were identified in the pulp tissue in the TN-C-treated experimental group. Further, nestin-positive cells at 7 days and dentin sialophosphoprotein (DSPP)-positive cells at 21 days were seen in the experimental group. In in vitro studies, DPSCs were cultured in a medium with or without TN-C, after which the proliferation rate of DPSCs was measured mRNA expression levels were examined using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and the formation of calcified nodules was investigated using alizarin red staining. The cell proliferation rate was not significantly different between the experimental and control groups. The expression of nestin mRNA on day 7 was significantly higher in the experimental group than in the control group (P<0.05), but the expression of osteocalcin (OCN) mRNA was significantly higher in the control group than in the experimental group (P<0.05). More calcified nodules formed in the control group than in the experimental group. These results suggest that TN-C regulates inflammation during the healing process in the dental pulp and induces the differentiation of dental pulp into odontoblast-like cells. Further, TN-C promotes the early differentiation of DPSCs into odontoblast-like cells, which suggests that TN-C may further contribute to the inhibition of excessive dentin formation.
Cas9 nickase-mediated contraction of CAG/CTG repeats at multiple disease loci
Authors: Murillo Alvaro , Alpaugh Melanie , Larin Meghan , Randall Emma L. , Heraty Laura , Durairaj Ruban Rex , Aston Alys N. , Taylor Alysha S. , Monteys Alex Mas , Stöberl Nina , Heuchan Aeverie E. R. , Aeschlimann Pascale , Bhattacharyya Soumyasree , Allen Nicholas D. , Puymirat Jack , Davidson Beverly L. , Cicchetti Francesca , Lelos Mariah , Dion Vincent
Published: February 2024

Expanded CAG/CTG repeats cause at least 15 different neurodegenerative and neuromuscular diseases that all remain without an effective disease modifying treatment. Because the size of the repeat tract accounts for the majority of the variation in disease severity, contracting them presents an attractive therapeutic avenue. Here, we show that the CRISPR-Cas9 nickase targeting the CAG/CTG repeat itself leads to efficient contractions in Huntington’s disease patient-derived neurons and astrocytes, as well as in myotonic dystrophy type 1 patient-derived neurons. Using single-cell DNA sequencing, PCR-free whole genome sequencing, and targeted long-read sequencing of theHTTlocus, we found no off-target mutations above background in neurons and astrocytes. Furthermore, we delivered the Cas9 nickase and sgRNA stereotactically to a mouse model of Huntington’s disease using adeno-associated viruses, and found contractions accumulating in over half of the infected cells over a period of 5 months. We also found that the Cas9 nickase was prone to silencing, further improving the safety of the approach. Our results provide the proof of concept for using the Cas9 nickase to contract the repeat tract safely in multiple cell types and diseases.
The SUMOylation inhibitor TAK-981 (Subasumstat) triggers IFN-I-dependent activation of Natural Killer cells against Acute Myeloid Leukemias
Authors: Hallal Rawan , De Toledo Marion , Tempé Denis , Zemiti Sara , Coënon Loïs , Gitenay Delphine , George Simon , Bonnet Sarah , Gabellier Ludovic , Cartron Guillaume , Pelegrin Mireia , Villalba Martin , Bossis Guillaume
Published: February 2024

Natural Killer (NK) cells play a pivotal role in mounting an anti-cancer immune response. Patients with diminished NK cells number and activity face less favorable prognosis. Promising therapeutic strategies include the adoptive transfer of NK cells or the reactivation of patients’ own NK cells. TAK-981, a first-in-class inhibitor of SUMOylation undergoing phase I/II clinical trials for cancer, is emerging as an immunomodulatory drug. Here, we demonstrate that TAK-981 activates NK cells from healthy donors and patients with Acute Myeloid Leukemia (AML), a cancer with very poor prognosis. TAK-981 heightens their degranulation capacity, secretion of inflammatory cytokines (IFN-γ, TNF-α, FasL), and cytotoxicity against AML cells.In vivo, TAK-981 also enhances the anti-leukemic activity ofex-vivoexpanded human NK cells. At the molecular level, TAK-981 first inducesIFNB1gene in NK cells, leading to the secretion of type I Interferon (IFN-I), which binds to the Interferon receptor IFNAR. This induces Interferon-Stimulated Genes (ISG) and activates NK cellsin vitroandin vivo. Finally, TAK-981 stimulates IFN-I secretion by monocytes, which contributes to the activation of NK cellsin trans. Altogether, targeting SUMOylation could be a promising strategy to reactivate AML patients’ NK cells and enhance the efficiency of NK cells-based therapies.

Abstract Figure
A circadian transcriptional sub-network andEARLY FLOWERING 3control timing of senescence and grain nutrition in bread wheat
Authors: Buckley Christopher R. , Boyte Joshua M. , Albiston Robert L. , Hyles Jessica , Beasley Jesse T , Johnson Alexander AT , Trevaskis Ben , Fournier-Level Alexandre , Haydon Michael J.
Published: February 2024

Circadian clocks control daily and seasonal timing of physiology and development. Because of their influence on photoperiodic flowering, variants in circadian clock genes have been selected for phenology during domestication of cereal crops. To explore the potential impact of this genetic variation on circadian-regulated traits, we investigated the relationship of the circadian clock and leaf senescence in hexaploid bread wheat. Phenotyping of a collection of elite wheat cultivars identified significant variation in circadian rhythms which was associated with timing of senescence and nutrient mobilisation efficiency. RNA sequencing revealed substantial reorganisation of the circadian-regulated transcriptome during senescence and a transcriptional sub-network representing a link between the circadian oscillator and regulators of leaf senescence. We used genotypes of multiple circadian clock genes to assign cultivars to ‘chronotypes’, which could be used to predict circadian-regulated phenotypes. This identified a deletion variant ofEARLY FLOWERING 3-D1 (ELF3-D1)attributed to a phenology locus,Earliness per se (Eps-D1),and we used near-isogenic lines (NILs) to show that it affects timing of senescence and grain protein content (GPC). Thus, there are potential consequences of circadian clock genes selected for phenology on other valuable crop traits.
Molecular dynamics simulations reveal molecular mechanisms for the gain and loss of function effects of fourSCN2Avariants
Authors: Bhattarai Nisha , Montanucci Ludovica , Brünger Tobias , Pérez-Palma Eduardo , Martin William , Smith Iris Nira , Eng Charis , Cheng Feixiong , Helbig Ingo , Møller Rikke S , Brunklaus Andreas , Schorge Stephanie , Lal Dennis
Published: February 2024

SCN2Agene disorders cover a wide range of medical conditions, from epileptic encephalopathies to neurodevelopmental disorders. The variants of these disorders, studied through electrophysiology, show complex behaviors that go beyond simple classification as either gain or loss of function. In our study, we simulated the biophysical effects of variants (R937C,V208E,S1336Y, andR853Q) to understand their impact. Our findings reveal that all these variants negatively affect the structural stability of the gene, withR937Cbeing the most unstable. Specifically,R937Cdisrupts important charged interactions affecting sodium ion flow, whileS1336Yintroduces a new interaction that impacts the channel’s inactivation gate. Conversely, the variantsV208EandR853Q, which are located in the voltage-sensing domains, have opposite effects:R853Qincreases compactness and interaction, whereasV208Eshows a decrease. Our computer-based method offers a scalable way to gain crucial insights into how genetic variants influence channel dysfunction and contribute to neurodevelopmental disorders.

AUTHOR SUMMARY

Despite numerous advancements in computational methods for predicting variant pathogenicity in theSCN2Agene, understanding the precise biophysical molecular mechanisms associated with each variant at the atomic level remains a challenge. Presently, variants are predominantly categorized as either gain or loss of function, often overlooking critical structural details associated with these variants. This study focuses on elucidating the molecular mechanisms linked to the four most commonSCN2Avariants using all-atom molecular dynamics simulations, employing three replicas for each system. Our findings offer insights into the potential mechanisms underlying these four variants, thereby providing explanations for the observed electrophysiological outcomes. This investigation significantly contributes to enhancing our comprehension of howSCN2Avariants manifest in various diseases. It underscores the importance of unraveling the biophysical properties underlying potential disease mechanisms, which could potentially enhance diagnostic and therapeutic strategies for patients afflicted withSCN2A-related disorders.
Functional avidity of anti-B7H3 CAR-T constructs predicts antigen density thresholds for triggering effector function
Authors: Barisa Marta , Zappa Elisa , Muller Henrike , Shah Rivani , Buhl Juliane , Draper Benjamin , Himsworth Courtney , Bowers Chantelle , Munnings-Tomes Sophie , Nicolaidou Marilena , Morlando Sonia , Birley Katie , Leboreiro-Babe Clara , Vitali Alice , Privitera Laura , O’Sullivan Kyle , Greppi Ailsa , Buschhaus Magdalena , Román Mario Barrera , de Blank Sam , van den Ham Femke , van ‘t Veld Brenna R. , Ferry Gabrielle , Donovan Laura K. , Chesler Louis , Molenaar Jan , Drost Jarno , Rios Anne , Chester Kerry , Wienke Judith , Anderson John
Published: February 2024

Chimeric Antigen receptor T cell (CAR-T) treatments for solid cancers have been compromised by limited expansion and survival in the tumor microenvironment following interaction with antigen-expressing target cells. Using B7H3 as a model antigen with broad clinical applicability, we evaluated the relationship between the antibody/antigen affinity of three clinical candidate binders and the three following functional characteristics: functional avidity, prolonged cytotoxicity in tumoroid re-stimulation assays, andin vivoanti-tumoral responses. BEHAV3D video-microscopy assessed distinct CAR-T cell behaviors at single cell resolution. T cell exhaustion did not dictate effector function. Rather, we demonstrated a threshold avidity of CAR-T / tumor cell interaction, characterized by longer cumulative CD8+CAR-T / tumor target interaction times, and required for adequate CAR-T cell expansion to result in sustained tumor control upon re-challenge. These results provide new insights into design of CAR-T cells for antigen-dim cell targeting, and avoidance of antigen-dim tumor relapse.
Importance of environmental signals for proper cardiac morphological development in Atlantic salmon
Authors: Vindas Marco A. , Engdal Vilde Arntzen , Kavaliauskiene Simona , Folkedal Ole , Höglund Erik , Moyano Marta , Øverli Øyvind , Frisk Michael , Johansen Ida B.
Published: February 2024

The hearts of salmonids display remarkable plasticity, adapting to various environmental factors that influence cardiac function and demand. For instance, in response to cold temperature, the salmonid heart undergoes growth and remodeling to counterbalance the reduced contractile function associated with dropping temperatures. Alongside heart size, the distinct pyramidal shape of the wild salmonid heart is essential for optimal cardiac performance, yet the environmental drivers behind this optimal cardiac morphology remain to be fully understood. Intriguingly, farmed salmonids often have rounded, asymmetrical ventricles and misaligned bulbi from an early age. These deformities are noteworthy given that farmed salmon are often not exposed to natural cues, such as a gradual temperature increase and changing day lengths, during critical developmental stages. In this study, we investigated whether natural environmental conditions during early life stages are pivotal for proper cardiac morphology. Atlantic salmon were raised under simulated natural conditions (low temperature with a natural photoperiod; SIMNAT) and compared with those reared under simulated farming conditions (SIMFARM). Our findings reveal that the ventricle shape and bulbus alignment in SIMNAT fish closely resemble those of wild salmon, while functional analyses indicate significant differences between SIMNAT and SIMFARM hearts, suggesting diastolic dysfunction and higher cardiac workload in SIMFARM hearts. These findings highlight the profound influence of environmental factors such as water temperature and photoperiod on the structural development of the salmonid heart, underscoring the importance of early environmental conditions for cardiac health.
The DC1 domain protein Vacuoleless Gametophytes regulates stamen development in Arabidopsis
Authors: Amigo Natalia L. , Arias Leonardo A. , Marchetti Fernanda , D’Ippólito Sebastián , Cascallares Milagros , Lorenzani Salvador , Frik Jesica , Lombardo María Cristina , Terrile María Cecilia , Casalongue Claudia A. , Pagnussat Gabriela C. , Fiol Diego F.
Published: February 2024

Vacuoleless Gametophytes (VLG) is a DC1 domain protein that was initially characterized as essential for early female and male gametophytes development in Arabidopsis. However, VLG expression was also detected in stamens, pistils and other sporophytic tissues, implying a broader role for this protein. As homozygous insertional VLG lines resulted unviable, we generated Arabidopsis amiRNAVLGknock-down plants to study the role of VLG in sporophyte development. The phenotypic characterization ofVLGknock-down plants showed reduced seed set and indehiscent anthers with shorter filaments and stigma exsertion. Moreover, amiRNAVLGknock-down plants displayed unbroken stomia and septa, markedly reduced endothecium lignification, diminished ROS accumulation, and lower transcript levels of genes involved in jasmonic acid and lignin biosynthesis. The indehiscent phenotype was rescued by exogenous application of either jasmonic acid or H2O2. Altogether, our results suggest that VLG is involved in lignin and jasmonic acid biosynthesis pathways, and that proper levels of VLG are required in the process that leads to stomium breakage and anther dehiscence. Our findings shed light on the mechanisms underlying stamen development and provide new insights into the roles of a DC1 domain protein in plant reproduction.

Key Message

Vacuoleless Gametophytes participates in anther dehiscence through a process that involves JA, ROS and lignin accumulation.
Transcriptional profiling sheds light on the fibrotic aspects of idiopathic subglottic tracheal stenosis
Authors: Direder Martin , Laggner Maria , Copic Dragan , Klas Katharina , Bormann Daniel , Schweiger Thomas , Hoetzenecker Konrad , Aigner Clemens , Ankersmit Hendrik Jan , Mildner Michael
Published: February 2024

1

Idiopathic subglottic stenosis (ISGS) is a rare fibrotic disease of the upper trachea with an unknown pathomechanism. It typically affects adult Caucasian female patients, leading to severe airway constrictions caused by progressive scar formation and inflammation with clinical symptoms of dyspnoea, stridor and potential changes to the voice. Endoscopic treatment frequently leads to recurrence, whereas surgical resection and reconstruction provides excellent long-term functional outcome. This study aimed to identify so far unrecognized pathologic aspects of ISGS using single cell RNA sequencing. Our scRNAseq analysis uncovered the cellular composition of the subglottic scar tissue, including the presence of a pathologic, profibrotic fibroblast subtype and the presence of Schwann cells in a profibrotic state. In addition, a pathology-associated increase of plasma cells was identified. Using extended bioinformatics analyses, we decoded pathology-associated changes of factors of the extracellular matrix. Our data identified ongoing fibrotic processes in ISGS and provide novel insights on the contribution of fibroblasts, Schwann cells and plasma cells to the pathogenesis of ISGS. This knowledge could impact the development of novel approaches for diagnosis and therapy of ISGS.
Epigenetic histone modifications H3K36me3 and H4K5/8/12/16ac induce open polynucleosome conformations via different mechanisms
Authors: Lin Yi-Yun , Müller Peter , Karagianni Evdoxia , Vanderlinden Willem , Lipfert Jan
Published: February 2024

Nucleosomes are the basic compaction unit of chromatin and nucleosome structure, and their higher-order assemblies regulate genome accessibility. Many post-translational modifications alter nucleosome dynamics, nucleosome-nucleosome interactions, and ultimately chromatin structure and gene expression. Here, we investigate the role of two post-translational modifications associated with actively transcribed regions, H3K36me3 and H4K5/8/12/16ac, in the contexts of tri-nucleosome arrays that provide a tractable model system for quantitative single-molecule analysis, while enabling us to probe nucleosome-nucleosome interactions. Direct visualization by AFM imaging reveals that H3K36me3 and H4K5/8/12/16ac nucleosomes adopt much more open and loose conformations than unmodified nucleosomes. Similarly, magnetic tweezers force spectroscopy shows a reduction in DNA outer turn wrapping and nucleosome-nucleosome interactions for the modified nucleosomes. The results suggest that for H3K36me3 the increased breathing and outer DNA turn unwrapping seen in mononucleosomes propagates to more open conformations in nucleosome arrays. In contrast, the even more open structures of H4K5/8/12/16ac nucleosome arrays do not appear to derive from the dynamics of the constituent mononucleosomes, but are driven by reduced nucleosome-nucleosome interactions, suggesting that stacking interaction can overrule DNA breathing of individual nucleosomes. We anticipate that our methodology will be broadly applicable to reveal the influence of other post-translational modifications and action of nucleosome remodelers.
Free radical production induced by visible light in live fruit flies
Authors: Daplan Ekin , Turin Luca
Published: February 2024

Visible light triggers free radical production in alive and intactDrosophila melanogaster. We exposed fruit flies to red (613-631 nm), green (515-535 nm), and blue (455-475 nm) light while we monitored changes in unpaired electron content with an electron spin resonance spectrometer (ESR/EPR). The immediate response to light is a rapid increase in spin content lasting approximately 10 seconds followed by a slower, linear increase for approximately 170 seconds. When the light is turned off, the spin population promptly decays with a similar time course, though never fully returning to baseline. The magnitude and time course of the spin production depends on the wavelength of the light. Initially, we surmised that eumelanin might be responsible for the spin change because of its documented ability for visible light absorption and its highly stable free radical content. To explore this, we utilized different fruit fly strains with varying eumelanin content and clarified the relation of melanin types with the spin response. Our findings revealed that flies with darker cuticle have at least three-fold more unpaired electrons than flies with yellow cuticle. However, to our surprise, the increase in unpaired electron population by light was not drastically different amongst the genotypes. This suggests that light-induced free radical production may not exclusively rely on the presence of black melanin, but may instead be dependent on light effects on quinone-based cuticular polymers.
TIRR regulates mRNA export and association with P bodies in response to DNA damage
Authors: Glossop Michelle S , Chelysheva Irina , Ketley Ruth F , Alagia Adele , Gullerova Monika
Published: February 2024

To ensure the integrity of our genetic code, a coordinated network of signalling and repair proteins known as the DNA damage response (DDR) detects and repairs DNA insults, the most toxic being double-stranded breaks (DSBs). Tudor interacting repair regulator (TIRR) is a key factor in DSB repair, acting through its interaction with p53 binding protein 1 (53BP1). TIRR is also an RNA-binding protein, yet its role in RNA regulation during the DNA damage response remains elusive. Here we show that TIRR selectively binds to a subset of mRNAs in response to DNA damage with preference for transcripts encoding transcription factors and RNA polymerase II (RNAPII) transcription regulators. Upon DNA damage, TIRR interacts with the nuclear export protein Exportin-1 (XPO1), through its nuclear export sequence (NES). Furthermore, TIRR plays a crucial role in modulation of RNA processing bodies (P bodies/PBs). TIRR itself and TIRR-bound RNA co-localises with PBs, and TIRR depletion results in nuclear RNA retention and impaired PB formation. Finally, the role of TIRR in RNA export contributes to efficient DNA damage response. This work reveals intricate involvement of TIRR in orchestrating mRNA nuclear export and storage within PBs, emphasizing its significance in the regulation of RNA-mediated DNA damage response.
Developmental synchrony and extraordinary multiplication rates in pathogenic organisms
Authors: Greischar Megan A. , Childs Lauren M.
Published: February 2024

The multiplication rates of pathogenic organisms influence disease progression, efficacy of immunity and therapeutics, and potential for within-host evolution. Thus, accurate estimates of multiplication rates are essential for biological understanding. We recently showed that common methods for inferring multiplication rates from malaria infection data substantially overestimate true values (i.e., under simulated scenarios), providing context for extraordinarily large estimates in human malaria parasites. A key unknown is whether this bias arises specifically from malaria parasite biology or represents a broader concern. Here we identify the potential for biased multiplication rate estimates across pathogenic organisms with different developmental biology by generalizing a within-host malaria model. We find that diverse patterns of developmental sampling bias—the change in detectability over developmental age—reliably generate overestimates of the fold change in abundance, obscuring not just true growth rates but potentially even whether populations are expanding or declining. This pattern emerges whenever synchrony, the degree to which development is synchronized across the population of pathogenic organisms comprising an infection, decays with time. Only with simulated increases in synchrony do we find noticeable underestimates of multiplication rates. Obtaining robust estimates of multiplication rates may require accounting for diverse patterns of synchrony in pathogenic organisms.

Subjects

computational biology, theoretical biology, ecology, developmental biology
Tertiary lymphoid structure-related immune infiltrates in NSCLC tumor lesions correlate with low tumor-reactivity of TIL products
Authors: Castenmiller Suzanne M. , Kanagasabesan Nandhini , Guislain Aurélie , Nicolet Benoît P. , van Loenen Marleen M. , Monkhorst Kim , Veenhof Alexander A.F.A. , Smit Egbert F. , Hartemink Koen J. , Haanen John B.A.G. , de Groot Rosa , Wolkers Monika C.
Published: February 2024

Adoptive transfer of tumor infiltrating lymphocytes (TIL therapy) has shown great potential for the treatment of solid cancers, including non-small cell lung cancer (NSCLC). However, not all patients benefit from this therapy, and the parameters that define the likelihood of TIL products to be tumor reactive are to date unknown. Defining prognostic markers that correlate with high level of tumor-reactivity is key for achieving better tailored immunotherapies.

To determine whether the composition of immune cell infiltrates correlates with the tumor-reactivity of expanded TIL products, we employed multi-parameter flow cytometry to characterize the immune cell infiltrates from 26 early-stage, and 20 late-stage NSCLC tumor lesions. Unbiased flow cytometry analysis with Cytotree and Spearman’s Rank Correlation was used to correlate immune infiltrates with the expansion rate, immune cell activation and T cell differentiation state, and the anti-tumor response of TIL products generated from the same lesions.

The composition of tumor immune infiltrates was highly variable between patients, irrespective of the disease stage. High percentages of B cell infiltrates positively correlated with the presence of conventional CD4+T cells, and an overall increase of naïve T cell infiltrates. In contrast, high B cell infiltrates negatively correlated with the tumor-reactivity of expanded TIL products, as defined by cytokine production upon exposure to autologous tumor digest. Tumors with high B cell infiltrates contained IgD+BCL6+B cells and CXCR5+BLC6+CD4+T cell infiltrates and an increased percentage of naïve CD8+T cells, indicative of the presence of tertiary lymphoid structures (TLS) in tumors with high B cell infiltrates.

This study reveals that the composition of immune cell infiltrates in NSCLC tumors associates with the functionality of expanded TIL products from NSCLC tumor lesions. Importantly, the tumor-responsiveness of TIL products negatively correlated with the presence of TLS-associated immune infiltrates in tumors. Our finding may thus help improve patient selection for TIL therapy.