bluuebunny/crossref_metadata_2025 huggingface dataset:
Caveolin-1 and mechanical stress control the release of a pro-metastatic subpopulation of small extracellular vesicles
Authors: Saquel Cristian , Gracia Celine , Viaris de Lesegno Christine , Verweij Frederik , Urena-Martin Carlos , Raposo Graça , Lamaze Christophe
Published: September 2024

Extracellular vesicles are lipid-enclosed vesicles released by most cells and are present in all human bodily fluids. EVs carry genetic material and proteins, which can be transferred to other cells, generating various biological effects. Caveolin-1 (Cav1) is a key structural protein of the small invaginations of the plasma membrane known as caveolae, which function as mechano-sensors and membrane tension buffering devices. Elevated levels of Cav1 have been detected in EVs from patients with advanced cancer. Given the importance of mechanical forces within the tumor microenvironment, we investigated the potential role of caveolae and Cav1 in regulating EV dynamics and cancer progression under mechanical stress. Our study revealed that different types of mechanical stress significantly induce the release of EVs from several cancer cell lines. These EVs were characterized as exosomes enriched for Cav1. Notably, we found that functional Cav1 was essential for the stress-induced increase in EV production. Lipidomic and proteomic analyses showed differences in the composition of EVs between WT and Cav1-deficient cells and between resting cells and cells subjected to mechanical stress. Additionally, EVs isolated from mechanically stressed cells were shown to promote enhanced migration and invasion of cancer cells in a Cav1-dependent manner. Altogether, our data uncover a new role for Cav1 in mediating cell-to-cell communication and promoting the acquisition of metastatic traits through the mechanical regulation of EV production and dynamics.
An antibiotic that mediates immune destruction of senescent cancer cells
Authors: Casagrande Raffi Gabriele , Chen Jian , Feng Xuezhao , Chen Zhen , Lieftink Cor , Deng Shuang , Mo Jinzhe , Zeng Chuting , Steur Marit , Wang Jing , Bleijerveld Onno B. , Hoekman Liesbeth , van der Wel Nicole , Wang Feng , Beijersbergen Roderick , Zheng Jian , Bernards Rene , Wang Liqin
Published: September 2024

Drugs that eliminate senescent cells, senolytics, can be powerful when combined with pro-senescence cancer therapies. Using a CRISPR/Cas9-based genetic screen, we identify here SLC25A23 as a vulnerability of senescent cancer cells. Suppressing SLC25A23 disrupts cellular calcium homeostasis, impairs oxidative phosphorylation and interferes with redox signaling, leading to death of senescent cells. These effects can be replicated by salinomycin, a cation ionophore antibiotic. Salinomycin prompts a PANoptosis-like cell death in senescent cells, including apoptosis and two forms of immunogenic cell death: necroptosis and pyroptosis. Notably, we observed that salinomycin treatment or SLC25A23 suppression elevates reactive oxygen species, upregulating death receptor 5 via JNK pathway activation. We show that a combination of a DR5 agonistic antibody and salinomycin is a robust senolytic cocktail. We provide evidence that this drug combination provokes a potent NK and CD8+ T cell mediated immune destruction of senescent cancer cells, mediated by the pyroptotic cytokine IL18.

Significance

The efficacy of multiple cancer drugs is limited by the induction of senescence, which enables cancer cells to evade cell death. We uncover here a new selective vulnerability of senescent cancer cells and we show that this vulnerability can be targeted with a commonly-used antibiotic. We show that a combination of senescence-inducing therapy, combined with this antibiotic causes a highly immunogenic cell death phenotype that further stimulates potent immune destruction of senescent cancer cells.
On the equivalence between agent-based and continuum models for cell population modeling. Application to glioblastoma evolution in microfluidic devices
Authors: Arroyo-Vázquez Raquel B. , Pérez-Aliacar Marina , Ayensa-Jiménez Jacobo , Doblaré Manuel
Published: September 2024

Abstract

Mathematical models are invaluable tools for understanding the mechanisms and interactions that control the behavior of complex systems. Modeling a problem as cancer evolution includes many coupled phenomena being therefore impossible to obtain sufficient experimental results to fully evaluate all possible conditions. In this work, we focus on Agent-Based Models (ABMs), as these models allow to obtain more complete and interpretable information at the individual level than other types ofin silicomodels. However, ABMs, need many parameters, requiring more information at the cellular and environmental levels to be calibrated. To overcome this problem we propose a complementary approach to traditional calibration methods. We used existent continuum models able to reproduce experimental data, validated and with fitted parameters, to establish relationships between parameters of both, continuum and agent-based models, to simplify and improve the process of adjusting the parameters of the ABM. With this approach, it is possible to bridge the gap between both kinds of models, allowing to work with them simultaneously and take advantage of the benefits of each of them.

To illustrate this methodology, the evolution of glioblastoma (GB) is modeled as an example of application. The resulting ABM obtains very similar results to those previously obtained with the continuum model, replicating the main histopathological features (the formation of necrotic cores and pseudopalisades) appearing in several different in vitro experiments in microfluidic devices, as we previously obtained with continuum models. However, ABMs have additional advantages: since they also incorporates the inherent random effects present in Biology, providing a more natural explanation and a deeper understanding of biological processes. Moreover, additional relevant phenomena can be easily incorporated, such as the mechanical interaction between cells or with the environment, angiogenic processes and cell concentrations far from the continuum requirement as happens, for intance, with immune cells.
RepeatParam: Algorithm for Parameterising Repeat Proteins and Analysis of Repeat Protein Architectures
Authors: Pretorius Daniella , Murray James W.
Published: September 2024

Motivation

Tandem repeat proteins consist of repetitive sequence and structure motifs and have diverse roles in Nature for molecular recognition and signalling. The architecture of repeat proteins can be described using simple helical parameters. Understanding these structural features can inform both the function of these proteins and be used to parametrically design new proteins. Despite their importance, no existing program is capable of completely parameterising repeat proteins.

Results

Here we describe a novel repeat protein parameterisation algorithm, RepeatParam, and a comprehensive repeat protein dataset. RepeatParam determines a helix that defines the global protein architecture and a superhelix that describes the relationship between consecutive repeats. We analyse the relationships between helical parameters and families of different repeat proteins.

Availability

https://github.com/dpretorius/repeat-protein-parameterisation
Expression, purification, and characterization of diacylated Lipo-YcjN fromEscherichia coli
Authors: Treviño Matthew A. , Amankwah Kofi , Fernandez Daniel , Weston Scott , Stewart Claire J. , Gallardo Jaime Morales , Shahgholi Mona , Sharaf Naima G.
Published: September 2024

YcjN is a putative substrate-binding protein expressed from a cluster of genes involved in carbohydrate import and metabolism inEscherichia coli. Here, we determine the crystal structure of YcjN to a resolution of 1.95 Å, revealing that its three-dimensional structure is similar to substrate binding proteins in subcluster D-I, which includes the well-characterized maltose binding protein (MBP). Furthermore, we found that recombinant overexpression of YcjN results in the formation of a lipidated form of YcjN that is posttranslationally diacylated at cysteine 21. Comparisons of size-exclusion chromatography profiles and dynamic light scattering measurements of lipidated and non-lipidated YcjN proteins suggest that lipidated YcjN aggregates in solution via its lipid moiety. Additionally, bioinformatic analysis indicates that YcjN-like proteins may exist in both Bacteria and Archaea, potentially in both lipidated and non-lipidated forms. Together, our results provide a better understanding of the aggregation properties of recombinantly expressed bacterial lipoproteins in solution and establish a foundation for future studies that aim to elucidate the role of these proteins in bacterial physiology.
Modeling of Non-invasive Cell Membrane Potential Measurement: LTSpice Simulation and Machine Learning Analysis
Authors: Ma Xiaofeng
Published: September 2024

This paper presents a novel simulation approach using electric pulses to measure cell membrane potential. The primary objective was to develop a non-invasive method for accurately assessing membrane potential without altering the cell membrane or its internal components. Traditional techniques, such as voltage-sensitive dyes, often require cell incubation, which can affect membrane properties and reduce measurement accuracy. To overcome these limitations, we modeled the cell as two series-connected capacitors with a negative potential between them. By manipulating this negative potential and analyzing the charge and discharge characteristics, simulations conducted with LTspice demonstrated the feasibility of predicting membrane potential based on these characteristics.

We tested 202 groups with various capacitor combinations and measured four key parameters related to charge and discharge currents: maximum current, minimum current, total charge time, and total discharge time. Using the XGBRegressor model, we achieved a strong fit with an R2score of 0.9. This indicates a robust correlation between the measured charge and discharge characteristics and the internal potential of the cell. Our findings suggest that accurate measurement of cell membrane potential is possible by attaching an electrode to the cell without disrupting membrane integrity. Thus, this simulation-based approach offers a promising and non-invasive alternative for measuring cell membrane potential.
Mechanisms of traditional Chinese medicine in modulating cardiac microvascular endothelial cells in various injury models: A comprehensive systematic review
Authors: Zhou Huiwen , Liu Hongxu , Li Xiang , Shang Juju , Chen Jiaping , Zong Huiqi
Published: September 2024

Background

The structural and functional failure of cardiac microvascular endothelial cells (CMECs) is a primary contributor to coronary microvascular dysfunction (CMD). Traditional Chinese medicine (TCM) has been identified as a potential therapeutic approach for preserving CMECs and mitigating CMD.

Objective

This systematic review aims to present the latest evidence on TCM intervention mechanisms in CMECs under diverse injury models.

Methods

This systematic review was performed following the parameters of the PRISMA statement (Preferred Reporting Items for Systematic Reviews and Meta-Analysis). A comprehensive literature search was conducted using PubMed, Embase, Web of Science, Scopus, China National Knowledge Infrastructure and China Biology Medicine disc. Reference lists of selected articles were reviewed to identify relevant studies. The search was not limited by year and was conducted solely in English. Eligible studies comprised publications describing in vitro studies that presented the latest evidence on TCM intervention mechanisms in CMECs under diverse injury models.

Results

A total of 63 papers were included in this study. According to the cell processing approach, 19 studies on ischemia or hypoxic injury models, 16 studies on Ischemia/reperfusion (I/R) or hypoxia/reoxygenation (H/R) injury models, 10 studies on inflammatory injury models, 5 studies on metabolic injury models, 3 studies on angiotensin II injury models, and 10 studies on other models. TCM exhibits structural and functional intervention capabilities in diverse damage conditions of CMECs. Its mechanism of action involves antioxidant, anti-apoptotic, anti-inflammatory effects, as well as regulation of energy metabolism through signaling pathways such as HIF-1α/VEGF, PI3K/AKT, MAPK, and NF-κB.

Conclusions

The CCM and its constituents modulate CMECs through multiple signaling pathways in response to various injury models, thereby conferring protection on the coronary microcirculation.

Graphical Abstract
A novel mechanism for the uptake of enterobactin-chelated ferric ions by the mitochondria and subsequent reduction to ferrous ions inside
Authors: Dutta Abeg , Parthasarathy Anutthaman , Ganesh Pandian Namasivayam
Published: September 2024

Conventional knowledge of mitochondrial iron metabolism talks about the export of iron in its doubly charged state once it is reduced inside the cell until it reaches the mitochondria. At physiological oxygen tension and pH 7.4, the comparatively soluble Fe(II) is easily available. Fe(III) hydrolyses to generate insoluble ferric hydroxides. Iron must be regularly chaperoned because of its near insolubility and potential toxicity due to redox activity. All tissues pick up iron through the binding of transferrin (Tf) to the transferrin receptor 1 (TfR1), followed by the complex’s internalisation through receptor-mediated endocytosis. The low pH created by the operation of a proton pump within the endosome reduces Tf’s affinity for iron. Importantly, the TfR1 promotes iron escape from Tf in the pH range (pH 5-5.5) reached by the endosome. A "trap," such as pyrophosphate, is neededin vitrofor iron release from Tf. However, a physiological chelator that can play this role has not yet been discovered. Fe(III) is hypothesised to be reduced to Fe(II) in erythroid cells by a ferrireductase known as the six-transmembrane epithelial antigen of the prostate 3 in the endosomal membrane after being released from Tf in the endosome. Following this, the divalent metal transporter-1 (DMT1) transports Fe(II) through the endosomal membrane and, it is generally accepted that this generates the cytosolic labile or chelatable iron pool. This reservoir of iron is believed to provide the metal for metabolic requirements, including as iron intake by the mitochondrion for haem and ISC synthesis, as well as storage in the cytosolic protein ferritin. The possibility of Fe(III) entering the mitochondria has not been explored before. A series of dockings shows that binding of the alpha subunit to a complex of Fe(III) with enterobactin is as stable as the binding with of the same chelator with Fe(II). Enterobactin is a bacterial iron chelator thought to play an integral role in host iron metabolism. Our results suggest an interesting possibility of iron being trafficked to the mitochondria as Fe(III). We propose a potential mechanism of Fe(III) trafficking and subsequent reduction to Fe(II) inside the mitochondria.
Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation
Authors: Guang Xuanmin , Yang Jingnan , Zhang Shilai , Guo Fei , Li Linzhou , Lian Xiaoping , Zeng Tao , Cai Chongyang , Liu Fushu , Li Zhihao , Hu Yangzi , Fang Dongming , He Weiming , Sahu Sunil Kumar , Li Wangsheng , Lu Haorong , Li Yuxiang , Liu Huan , Xu Xun , Gu Ying , Hu Fengyi , Dong Yuliang , Wei Tong
Published: September 2024

Rice (Oryza sativa) is one of the most important staple food crops worldwide, and its wild relatives serve as an important gene pool in its breeding. Compared with cultivated rice species, African wild rice (Oryza longistaminata) has several advantageous traits, such as resistance to increased biomass production, clonal propagation via rhizomes, and biotic stresses. However, previousO. longistaminatagenome assemblies have been hampered by gaps and incompleteness, restricting detailed investigations into their genomes. To streamline breeding endeavors and facilitate functional genomics studies, we generated a 343-Mb telomere-to-telomere (T2T) genome assembly for this species, covering all telomeres and centromeres across the 12 chromosomes. This newly assembled genome has markedly improved over previous versions. Comparative analysis revealed a high degree of synteny with previously published genomes. A large number of structural variations were identified between theO. longistaminataandO. sativa. A total of 2,466 segmentally duplicated genes were identified and enriched in cellular amino acid metabolic processes. We detected a slight expansion of some subfamilies of resistance genes and transcription factors. This newly assembled T2T genome ofO. longistaminataprovides a valuable resource for the exploration and exploitation of beneficial alleles present in wild relative species of cultivated rice.
Efficiently Constructing Complete Genomes with CycloneSEQ to Fill Gaps in Bacterial Draft Assemblies
Authors: Liang Hewei , Wang Mengmeng , Hu Tongyuan , Wang Haoyu , He Wenxin , Ju Yanmei , Guo Ruijin , Chen Junyi , Guo Fei , Zeng Tao , Dong Yuliang , Wang Bo , Liu Chuanyu , Jin Xin , Zhang Wenwei , Zou Yuanqiang , Xu Xun , Xiao Liang
Published: September 2024

Background

Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, favored for their low cost and high accuracy. However, these methods often produce fragmented draft genomes, hindering comprehensive bacterial function analysis. CycloneSEQ, a novel long-read sequencing platform developed by BGI-Research, its sequencing performance and assembly improvements has been evaluated.

Findings

Using CycloneSEQ long-read sequencing, the type strain produced long reads with an average length of 11.6 kbp and an average quality score of 14.4. After hybrid assembly with short reads data, the assembled genome exhibited an error rate of only 0.04 mismatches and 0.08 indels per 100 kbp compared to the reference genome. This method was validated across 9 diverse species, successfully assembling complete circular genomes. Hybrid assembly significantly enhances genome completeness by using long reads to fill gaps and accurately assemble multi-copy rRNA genes, which unable be achieved by short reads solely. Through data subsampling, we found that over 500 Mbp of short-read data combined with 100 Mbp of long-read data can result in a high-quality circular assembly. Additionally, using CycloneSEQ long reads effectively improves the assembly of circular complete genomes from mixed microbial communities.

Conclusions

CycloneSEQ’s read length is sufficient for circular bacterial genomes, but its base quality needs improvement. Integrating DNBSEQ short reads improved accuracy, resulting in complete and accurate assemblies. This efficient approach can be widely applied in microbial sequencing.
Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV
Authors: Karia Dimple , Koh Adrian F. , Yang Wen , Cushing Victoria I. , Basanta Benjamin , Mihaylov Daniel B. , Khavnekar Sagar , Vyroubal Ondřej , Malínský Miloš , Sháněl Ondřej , Doležal Vojtěch , Plitzko Juergen M. , Yu Lingbo , Lander Gabriel C. , Aricescu A. Radu , Greber Basil J. , Kotecha Abhay
Published: September 2024

Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by providing high-resolution insights into biological macromolecules. Here, we present sub-3 Å resolution structures determined using the 100 keV Tundra cryogenic transmission electron microscope (cryo-TEM), equipped with the newly developed Falcon C direct electron detector (DED). Our results demonstrate that this lower voltage microscope, when combined with advanced electron optics and detectors, can achieve high-resolution reconstructions that were previously only attainable with higher voltage systems. The implementation of an extreme-brightness field emission gun (XFEG) and an SP-TWIN objective lens significantly enhanced the spatial and temporal coherence of the system. Furthermore, the semi-automated sample loader minimized contamination and drift, allowing extended data collection sessions without manual intervention. The high detective quantum efficiency (DQE) of Falcon C further improved the signal-to-noise ratio, which is critical for achieving high-resolution structures. We validated the performance of this microscope by determining the structures of various biological samples, including apoferritin, T20S proteasome, GABAAreceptor, haemoglobin, and human transthyretin ranging in size from 440 kDa to 50 kDa. The highest resolutions achieved were 2.1 Å for apoferritin, 2.7 Å for the 20S proteasome, 2.8 Å for the GABAA receptor, 5.0 Å for haemoglobin, and 3.5 Å for transthyretin. We also explored a larger specimen, a 3.9 MDa Adeno-associated virus (AAV9) capsid and resolved it a 2.8 Å. This work highlights the potential of 100 keV TEMs to make high-resolution cryo-EM more accessible to the structural biology community. Furthermore, it sets a precedent for the use of lower voltage TEMs in routine cryo-EM studies, not only for screening grids for single particle analysis but also for achieving high-resolution structures of protein samples.
H/ACA snoRNP guides ribosomal RNA subdomain folding in a satellite particle before joining the core 90S pre-ribosome
Authors: Fischer Paulina , Thoms Matthias , Lau Benjamin , Denk Timo , Kuvshinova Maria , Berninghausen Otto , Flemming Dirk , Hurt Ed , Beckmann Roland
Published: September 2024

During synthesis, modification and maturation of the ribosomal RNA, correct subdomain folding without additional guidance poses a major challenge. An essential H/ACA snoRNP, snR30, was observed to be outsourced from the core of the 90S, the earliest known pre-ribosome, to form a "satellite particle". This particle interacts with the so-called 18S rRNA platform subdomain, guiding its independent folding through localized structural interactions. Once this subdomain achieves its proper conformation, it is integrated into the core pre-ribosome, contributing to the overall maturation of the 18S rRNA. By temporarily segregating the folding process within a specialized satellite particle, the correct assembly of individual components is facilitated, thereby reducing the risk of errors during the complex process of ribosome assembly. In a broader sense, molecular outsourcing in cellular processes, where transient subcomplexes handle specific tasks before rejoining the main assembly line, can enhance efficiency and accuracy of complex molecular processes like ribosome biogenesis.
In Vivo Optical Clearing of Mammalian Brain
Authors: Franzesi Giovanni Talei , Gupta Ishan , Hu Ming , Piatkevich Kiryl , Yildirim Murat , Zhao Jian-Ping , Eom Minho , Han Seungjae , Park Demian , Andaraarachchi Himashi , Li Zhaohan , Greenhagen Jesse , Islam Amirul Muhammad , Vashishtha Parth , Yaqoob Zahid , Pak Nikita , Wissner-Gross Alexander D , Martin-Alarcon Daniel A. , Veinot Jonathan J. , So Peter T. C. , Kortshagen Uwe , Yoon Young-Gyu , Sur Mriganka , Boyden Edward S.
Published: September 2024

Established methods for imaging the living mammalian brain have, to date, taken the brain’s optical properties as fixed; we here demonstrate that it is possible to modify the optical properties of the brain itself to significantly enhance at-depth imaging while preserving native physiology. Using a small amount of any of several biocompatible materials to raise the refractive index of solutions superfusing the brain prior to imaging, we could increase several-fold the signals from the deepest cells normally visible and, under both one-photon and two-photon imaging, visualize cells previously too dim to see. The enhancement was observed for both anatomical and functional fluorescent reporters across a broad range of emission wavelengths. Importantly, visual tuning properties of cortical neurons in awake mice, and electrophysiological properties of neurons assessedex vivo, were not altered by this procedure.
Human and bats genome robustness under COSMIC mutational signatures
Authors: Song Joon-Hyun , Zeng Ying , Davalos Liliana M , MacCarthy Thomas , Larijani Mani , Damaghi Mehdi
Published: September 2024

Carcinogenesis is an evolutionary process, and mutations can fix the selected phenotypes in selective microenvironments. Both normal and neoplastic cells are robust to the mutational stressors in the microenvironment to the extent that secure their fitness. To test the robustness of genes under a range of mutagens, we developed a sequential mutation simulator, Sinabro, to simulate single base substitution under a given mutational process. Then, we developed a pipeline to measure the robustness of genes and cells under those mutagenesis processes. We discovered significant human genome robustness to the APOBEC mutational signature SBS2, which is associated with viral defense mechanisms and is implicated in cancer. Robustness evaluations across over 70,000 sequences against 41 signatures showed higher resilience under signatures predominantly causing C-to-T (G-to-A) mutations. Principal component analysis indicates the GC content at the codon's wobble position significantly influences robustness, with increased resilience noted under transition mutations compared to transversions. Then, we tested our results in bats at extremes of the lifespan-to-mass relationship and found the long-lived bat is more robust to APOBEC than the short-lived one. By revealing APOBEC as the prime driver of robustness in the human (and other mammalian) genome, this work bolsters the key potential role of APOBECs in carcinogenesis, as well as evolved countermeasures to this innate mutagenic process. It also provides the baseline of the human and bat genome robustness under mutational processes associated with cancer.
DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning
Authors: Savojardo Castrense , Manfredi Matteo , Martelli Pier Luigi , Casadio Rita
Published: September 2024

The knowledge of protein stability upon residue variation is an important step for functional protein design and for understanding how protein variants can promote disease onset. Computational methods are important to complement experimental approaches and allow a fast screening of large datasets of variations. In this work we present DDGemb, a novel method combining protein language model embeddings and transformer architectures to predict protein ΔΔG upon both single- and multi-point variations. DDGemb has been trained on a high-quality dataset derived from literature and tested on available benchmark datasets of single- and multi-point variations. DDGemb performs at the state of the art in both single- and multi-point variations.
Connecting crowns: Analyzing morphological covariation in the modern human postcanine dentition
Authors: Šimková Petra G. , Krenn Viktoria A. , Fornai Cinzia , Wurm Lisa , Halász Vanda , Lidinsky Dominika , Weber Gerhard W.
Published: September 2024

Morphological covariation within the modern human postcanine dentition remains an open field of study. Analysis of covariation patterns of the three-dimensional (3D) shape between different tooth types has been seldom conducted, but it is relevant for the advancement of human biology and evolution, as well as dental anthropology, phylogeny, and medicine. Here, we analysed 3D shape covariation of the postcanine dentition (excluding third molars), both within and between dental arches using geometric morphometrics (GM). Based on high-resolution (µCT) scans of 526 teeth from 136 individuals we found high pairwise correlation in tooth pairs within the dental arches (lower P3 and P4, r1= 0.89; upper P3 and P4, r1= 0.81; upper M1 and M2, r1= 0.86). The correlation values between antagonists varied notably from the highest value detected between upper and lower M1s (r = 0.9), to the lowest between upper P4s and lower M1s (r = 0.58). Of all analysed tooth types, only the upper M1s showed moderate to high correlation in every pair analysis. Noticeably, unusually high covariation was detected between some of the tooth type pairs that do not articulate in a normal dentition (e.g., lower P3 and upper M2, r1= 0.88). Furthermore, a relatively high covariation was found in the pairs of lower P4s and M1s (r1= 0.79), and upper P4s and M1s (r1= 0.77), which are the only tooth type pairs of the postcanine dentition belonging to different tooth classes (premolars and molars, respectively) and still serving similar masticatory functions.

This study points to the fact that higher morphological integration seems to characterize teeth within the same dental arch rather than between antagonistic teeth. With this study, we provided an overview of pairwise correlations and strength of covariation between different tooth types. This information might inform future studies aimed at understanding developmental, phylogenetic, and functional aspects of the human postcanine dentition, including possible phenotype-genotype associations. However, with this study being the first one performed on a 3D sample of this size, we also report on obstacles and peculiarities that have been determined.
The Protein Design Archive (PDA): insights from 40 years of protein design
Authors: Chronowska Marta , Stam Michael James , Woolfson Derek N , Di Costanzo Luigi F , Wood Christopher W
Published: September 2024

The field of protein design has changed dramatically over the last 40 years, with a range of methods developing from rational design to more recent data-driven approaches. While considerable insight could be gained from analysing designed proteins, there is no single resource that brings together all the relevant data, making it difficult to identify current challenges and opportunities within the field. Here we present the Protein Design Archive, a website and database of designed proteins. Using the database, we performed systematic analysis that reveals a rapid increase in the number and complexity of designs over time and uncovers biases in their amino-acid usage and secondary structure content. Finally, sequence- and structure-based analysis demonstrates the breadth and novelty of designs within the archive. The PDA will be a valuable resource for guiding development of protein design, helping the field reach its potential. The PDA is available freely and without registration at https://pragmaticproteindesign.bio.ed.ac.uk/pda/.
Virus-like particle-based vaccines targeting theAnophelesmosquito salivary protein, TRIO
Authors: Francian Alexandra , Flores-Garcia Yevel , Powell John R. , Petrovsky Nikolai , Zavala Fidel , Chackerian Bryce
Published: September 2024

Malaria is a highly lethal infectious disease caused byPlasmodiumparasites. These parasites are transmitted to vertebrate hosts when mosquitoes of theAnophelesgenus probe for a blood meal. Sporozoites, the infectious stage ofPlasmodium, transit to the liver within hours of injection into the dermis. Vaccine efforts are hindered by the complexity of the parasite’s lifecycle and the speed at which the infection is established in the liver. In an effort to enhance immunity againstPlasmodium, we produced a virus-like particle (VLP)-based vaccine displaying an epitope of TRIO, anAnophelessalivary protein which has been shown to enhance mobility and dispersal of sporozoites in the dermis. Previous work demonstrated that passive immunization with TRIO offered protection from liver infection and acted synergistically with aPlasmodiumtargeted vaccine. Immunization of mice with TRIO VLPs resulted in high-titer and long-lasting antibody responses that did not significantly drop for over 18 months post-immunization. TRIO VLPs were similarly immunogenic when combined with an anti-malaria vaccine targeting the L9 epitope of thePlasmodium falciparumcircumsporozoite protein.However, when used in a malaria challenge mouse model, TRIO VLPs only provided modest protection from infection and did not boost the protection provided by L9 VLPs.
The Nuclear and Mitochondrial Genomes ofAmoebophryasp. exKarlodinium veneficum
Authors: DeMontigny Wesley , Bachvaroff Tsvetan
Published: September 2024

Dinoflagellates are a diverse group of microplankton that include free-living, symbiotic, and parasitic species.Amoebophrya, a basal lineage of parasitic dinoflagellates, infects a variety of marine microorganisms, including harmful-bloom-forming algae. Although there are currently three publishedAmoebophryagenomes, this genus has considerable genomic diversity. We add to the growing genomic data forAmoebophryawith an annotated genome assembly forAmoebophryasp. exKarlodinium veneficum. This species appears to translate all three canonical stop codons contextually. Stop codons are present in the open reading frames of about half of the predicted gene models, including genes essential for cellular function. The in-frame stop codons are likely translated by suppressor tRNAs that were identified in the assembly. We also assembled the mitochondrial genome, which has remained elusive in the previousAmoebophryagenome assemblies. The mitochondrial genome assembly consists of many fragments with high sequence identity in the genes but low sequence identity in intergenic regions. Nuclear and mitochondrially-encoded proteins indicate thatAmoebophryasp. exK. veneficumdoes not have a bipartite electron transport chain, unlike previously analyzedAmoebophryaspecies. This study highlights the importance of analyzing multiple genomes from highly diverse genera such asAmoebophrya.

This new long-read assembly demonstrates the remarkable diversity found withinAmoebophrya. Despite being assigned the rank of genus, the available genome assemblies indicate significant variation in gene content, AT content, genetic codes, and potentially mitochondrial biology. Furthermore, this study contributes to the expanding list of organisms that contextually translate all three canonical stop codons. Although the mechanisms underlying such a genetic code remain elusive, the relative ease of culturingAmoebophryasuggests it may be useful as a model organism for future research on this subject.
A dopamine-dependent mechanism for reward-induced modification of fear memories
Authors: Kong Mi-Seon , Jo Yong S. , Sethi Ekayana , Pyeon Gyeong Hee , Zweifel Larry S.
Published: September 2024

A positive mental state has been shown to modulate fear-related emotions associated with the recall of fear memories. These, and other observations suggest the presence of central brain mechanisms for affective states to interact. The neurotransmitter dopamine is important for both reward- and fear-related processes, but it is unclear whether dopamine contributes to such affective interactions. Here, we show that precisely timed reward-induced activation of dopamine neurons in mice potently modifies fear memories and enhances their extinction. This reward-based switch in fear states is associated with changes in dopamine release and dopamine-dependent regulation of fear encoding in the central amygdala (CeA). These data provide a central mechanism for reward-induced modification of fear states that have broad implications for treating generalized fear disorders.

Reward-induced dopamine release in the central amygdala switches fear states and modifies fear encoding.
The effect of glucose restriction on cancer cell contractility: A threshold response in U-87 glioma
Authors: Kong Albert , Pallaoro Alessia , Yapp Donald , Elfring Gwynn J. , Bacca Mattia
Published: September 2024

Cells rely on contractility to proliferate, and cancerous ones exhibit an increased glucose dependence. It is therefore hypothesized that glucose restriction can mitigate cancer cell proliferation by ’stunting’ their contractility. However, glucose-restriction studies have mostly been based on experiments that have yielded conflicting results; some cells become less contractile under glucose-restriction, intuitively, while, others become surprisingly more contractile. Active mechanistic modeling may prove fruitful in resolving these conflicts. In this study, we develop a model for glucose-mediated cell contractility to capture the mechanical implications of glucose restriction. The model is calibrated on cell contraction data taken from 2D-cultured glioma cells, laying on a collagen substrate. The model predicts the existence of a critical level of glucose restriction that must be exceeded for contractility to be affected, and this is validated by our experiments. Our model provides an initial step toward a fundamental understanding of the metabolic implications of cell contractility, particularly in the context of glucose restriction: an essential step in cancer studies.

significance

This study advances our understanding of how glucose restriction affects cancer cell contractility, an essential factor in cell proliferation. Our findings reveal that cells require severe glucose deprivation before exhibiting reduced contractility, highlighting a threshold response. This indicates that the cytoskeleton, a key structural component, remains active until a significant reduction in energy supply forces the cell into a lower energy state. These insights provide critical knowledge about the metabolic hierarchy within cells, contributing to the broader study of cancer metabolism and potential therapeutic strategies aimed at disrupting cellular energy pathways.
Paired C-type lectin receptors mediate specific recognition of divergent oomycete pathogens inC. elegans
Authors: Liu Kenneth , Grover Manish , Trusch Franziska , Vagena-Pantoula Christina , Ippolito Domenica , Barkoulas Michalis
Published: September 2024

Innate immune responses can be initiated through the detection of pathogen or damage-associated molecular patterns by host receptors that are often present on the surface of immune cells. While certain invertebrates likeCaenorhabditis eleganslack professional immune cells, they still respond to infection in a pathogen-specific manner. It has been debated for years whether homologues of the canonical pathogen recognition receptors are also functioning in the nematode. Here we show that C-type lectin receptors mediate species-specific recognition of divergent oomycetes inC. elegans.A CLEC-27/CLEC-35 pair is essential for recognition of the oomyceteMyzocytiopsis humicola, while a CLEC-26/CLEC-36 pair is required for detection ofHaptoglossa zoospora.Bothclecpairs are transcriptionally regulated through a shared promoter by the conserved PRD-like homeodomain transcription factor CEH-37/OTX2 and act in sensory neurons and the anterior intestine to trigger a protective immune response in the epidermis. This system enables redundant tissue sensing of oomycete threats through canonical CLEC receptors and host defense via cross-tissue communication.

Highlights

A CLEC-27/CLEC-35 pair is required for recognition of the oomyceteMyzocytiopsis humicola

A CLEC-26/CLEC-36 pair is required for recognition of the oomyceteHaptoglossa zoospora

Both CLEC pairs are co-regulated by the homeodomain transcription factor CEH-37/OTX2

Both CLEC pairs function redundantly in sensory neurons and the intestine for host defense
Early Events in G-quadruplex Folding Captured by Time-Resolved Small-Angle X-Ray Scattering
Authors: Monsen Robert C. , Sabo T. Michael , Gray Robert , Hopkins Jesse B. , Chaires Jonathan B.
Published: September 2024

Time-resolved small-angle X-ray experiments (TR-SAXS) are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in G4 folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 20.6 to 12.6 Å. The collapse is monophasic and is complete in less than 600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, to show that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method (EOM) analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.
Structural basis of the excitatory amino acid transporter 3 substrate recognition
Authors: Qiu Biao , Boudker Olga
Published: September 2024

Excitatory amino acid transporters (EAATs) reside on cell surfaces and uptake substrates, including L-glutamate, L-aspartate, and D-aspartate, using ion gradients. Among five EAATs, EAAT3 is the only isoform that can efficiently transport L-cysteine, a substrate for glutathione synthesis. Recent work suggests that EAAT3 also transports the oncometabolite R-2-hydroxyglutarate (R-2HG). Here, we examined the structural basis of substrate promiscuity by determining the cryo-EM structures of EAAT3 bound to different substrates. We found that L-cysteine binds to EAAT3 in thiolate form, and EAAT3 recognizes different substrates by fine-tuning local conformations of the coordinating residues. However, using purified human EAAT3, we could not observe R-2HG binding or transport. Imaging of EAAT3 bound to L-cysteine revealed several conformational states, including an outward-facing state with a semi-open gate and a disrupted sodium-binding site. These structures illustrate that the full gate closure, coupled with the binding of the last sodium ion, occurs after substrate binding. Furthermore, we observed that different substrates affect how the transporter distributes between a fully outward-facing conformation and intermediate occluded states on a path to the inward-facing conformation, suggesting that translocation rates are substrate-dependent.
Grb2 Phosphorylation Antagonizes EGFR-driven Ras Activation by Interfering with Condensate Assembly
Authors: Phan Henry T. , Lin Chun-Wei , Stinger Brittany L. , DeGrandchamp Joseph B. , Nugent Lew L.J. , Huang Serena J. , Groves Jay T.
Published: September 2024

Upon ligand binding, the kinase domain of EGFR phosphorylates multiple tyrosine residues on the receptor cytoplasmic tail through a trans-autophosphorylation process. Phosphotyrosine sites on activated receptors recruit Grb2, which further recruits SOS to initiate downstream signaling by activating Ras. Multivalent binding between SOS and Grb2, as well as direct Grb2:Grb2 interactions, contribute to formation of a protein condensate of activated EGFR. The condensed state of EGFR facilitates autoinhibition release in SOS and exerts regulatory control over signal propagation from activated EGFR to Ras. While kinase activity of EGFR is an essential driver of this signaling process, phosphorylation at residue Y160 on Grb2 blocks Grb2:Grb2 binding and can interfere with EGFR condensation. Here, using a reconstituted system, we examine how titrating kinase activity in the EGFR system can both promote and inhibit signal output to Ras. The results reveal how effects of tyrosine kinase inhibition can, under some circumstances, promote Ras activation by inhibiting negative feedback through Grb2 phosphorylation and disruption of a Grb2 SH2/SH3 dimer interface.

Statement of Significance

Activated EGFR forms a biomolecular condensate, via linkage of multiple EGFR through Grb2 and SOS, and the condensation state of EGFR influences signal propagation to Ras. While tyrosine phosphorylation is a critical step in EGFR activation, phosphorylation of Grb2 can have an inhibitory effect on EGFR condensation and subsequent Ras activation. Under some conditions, kinase inhibition can promote signaling from EGFR to Ras.
Coat protein of TCV suppresses RNA decay via ubiquitination and autophagy pathways to facilitate viral infection
Authors: Wu Kunxin , Xie Qiuxian , Liu Xueting , Fu Yan , Li Shuxia , Yu Xiaoling , Li Wenbin , Zhao Pingjuan , Ren Yanli , Ruan Meng Bin , Zhang Xiuchun
Published: September 2024

RNA decay is a pervasive process in eukaryotic cells. Viruses utilize the host cell's intracellular machinery to gain access to essential molecules and subcellular structures required for infection during the pathogenesis process. The study demonstrates that turnip crinkle virus (TCV) infection enhances the expression of Arabidopsis Dcp1 (AtDcp1), which negatively regulates the accumulation of TCV RNA, indicating its involvement in antiviral defense. Nevertheless, TCV circumvents the antiviral defense based on RNA decay, as indicated by the capsid protein (CP) of TCV stabilizing the known nonsense-mediated RNA decay targeted transcripts. In vivo, CP physically interacts with AtDcp1, promoting AtDcp1 degradation via ubiquitination and autophagy pathways. This is evidenced by the observation that the degradation is inhibited by both 26S proteasome and autophagy inhibitors. Furthermore, CP elevates the polyubiquitination of Dcp1-Flag and the quantity of pre-autophagosome or autophagosome structures. These data indicate that CP suppresses RNA decay by interacting with AtDcp1 and mediating its degradation through the 26S proteasome and autophagy pathways, effectively subduing antiviral RNA decay. This study uncovers a previously unidentified virulence strategy in the ongoing conflict between plants and viruses.
Molecular Evolution of Gustatory Receptors in theAnopheles gambiaeComplex
Authors: Popkin-Hall Zachary R. , Slotman Michel A.
Published: September 2024

Background

Mosquitoes in theAnopheles(An.)gambiaespecies complex are major vectors ofPlasmodium falciparummalaria. One reason for this is the high anthropophily of the constituent speciesAn. coluzzii,An. gambiaesensu stricto, andAn. arabiensis. In contrast, their sister speciesAn. quadriannulatusis highly zoophilic.Anophelesmosquitoes largely rely on chemical cues for host-seeking, which are primarily detected by four chemosensory gene families: olfactory receptors (Ors), ionotropic receptors (Irs), gustatory receptors (Grs), and odorant binding proteins (Obps). Genes from these families that have been implicated in host adaptation show evidence of positive selection in other insect species, including other mosquitoes. As such, we analyzed the molecular evolutionary patterns of the gustatory receptors within theAnopheles gambiaecomplex, with a particular interest in identifyingGrsthat show evidence of positive selection in highly anthropophilic species.

Results

We identified sixteenGrsthat show evidence of potential positive selection using the McDonald-Kreitman test, including four putative sugar receptors and twoGrswith unknown ligands that are relatively highly expressed in chemosensory organs of eitherAn. coluzziiorAn. quadriannulatus. In addition, we identified twelveGrsthat show evidence of potential purifying selection using the McDonald-Kreitman test, and twelveGrsthat may have experienced a selective sweep using the DH test, including three putative sugar receptors and the carbon dioxide receptorGr24. We also identified both positive and purifying selection in the coastal speciesAn. melas(West Africa) andAn. merus(East Africa).

Conclusions

Our results, together with transcriptomic data, identify fourGrsas possible candidates for involvement in the evolution of vertebrate host preference in theAn. gambiaecomplex, as may have occurred in theAn. farauticomplex. They also point to sugar receptors as playing a role in recent adaptation of some of these species. As the vast majority ofGrshave unknown functions and much is still unknown about the role ofGrsin these species, a more complete interpretation of our data necessitates further characterization of these genes.