bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATTRv-V30M Type A amyloid fibrils from heart and nerves exhibit structural homogeneity
Authors: Nguyen Binh An , Afrin Shumaila , Yakubovska Anna , Singh Virender , Alicea Jaime Vaquer , Kunach Peter , Singh Preeti , Pekala Maja , Ahmed Yasmin , Fernandez-Ramirez Maria del Carmen , Hernandez Luis O. Cabrera , Pedretti Rose , Bassett Parker , Wang Lanie , Lemoff Andrew , Villalon Layla , Kluve-Beckerman Barbara , Saelices Lorena 
Published: May 2024

AbstractATTR amyloidosis is a systemic disease characterized by the deposition of amyloid fibrils made of transthyretin, a protein integral to transporting retinol and thyroid hormones. Transthyretin is primarily produced by the liver and circulates in blood as a tetramer. The retinal epithelium also secretes transthyretin, which is secreted to the vitreous humor of the eye. Because of mutations or aging, transthyretin can dissociate into amyloidogenic monomers triggering amyloid fibril formation. The deposition of transthyretin amyloid fibrils in the myocardium and peripheral nerves causes cardiomyopathies and neuropathies, respectively. Using cryo-electron microscopy, here we determined the structures of amyloid fibrils extracted from cardiac and nerve tissues of an ATTRv-V30M patient. We found that fibrils from both tissues share a consistent structural conformation, similar to the previously described structure of cardiac fibrils from an individual with the same genotype, but different from the fibril structure obtained from the vitreous humor. Our study hints to a uniform fibrillar architecture across different tissues within the same individual, only when the source of transthyretin is the liver. Moreover, this study provides the first description of ATTR fibrils from the nerves of a patient and enhances our understanding of the role of deposition site and protein production site in shaping the fibril structure in ATTRv-V30M amyloidosis.
Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure
Authors: Zhan Xuan , Deng Liping , Lian Yun , Shu Zhiyu , Xu Yunong , Mai Xinyi , Krishna Manchugondanahalli S. , Xiong Chi , Lu Rongguang , Wang Anni , Bai Shiyao , Xu Yingyi , Ni Jie , Vandana J. Jeya , Wang Zi , Li Yuqing , Sun Dongmei , Huang Shaohui , Liu Jingyan , Cheng Gui-Juan , Wu Song , Chiang Ying-Chih , Stjepanovic Goran , Jiang Cheng , Shao Yong , Chen Gang 
Published: May 2024

ABSTRACTThe small molecule epiberberine (EPI) is a natural alkaloid with versatile bioactivities against several diseases, including cancer and bacterial infection. EPI can induce the formation of a unique binding pocket at the 5′ side of a human telomeric G-quadruplex (HTG) sequence Q4, resulting in a nanomolar binding affinity (KDapproximately 26 nM) with significant fluorescence enhancement upon binding. It is important to understand (1) how EPI binding affects HTG structural stability and (2) how enhanced EPI binding may be achieved through the engineering of the DNA binding pocket. In this work, the EPI binding-induced HTG structure stabilization effect was probed by a peptide nucleic acid (PNA) invasion assay in combination with a series of biophysical techniques. We show that the PNA invasion-based method may be useful for the characterization of compounds binding to DNA (and RNA) structures in physiological conditions without the need to vary the solution temperature or buffer components, which are typically needed for structural stability characterization. Importantly, the combination of theoretical modeling and experimental quantification allows us to successfully engineer the Q4 derivative Q4-ds-A by a simple extension of a duplex structure to Q4 at the 5′ end. Q4-ds-A is a superb EPI binder with aKDof 8 nM, with the binding enhancement achieved through the preformation of a binding pocket and a reduced dissociation rate. The tight binding of Q4 and Q4-ds-A with EPI allows us to develop a novel magnetic bead-based affinity purification system to effectively extract EPI fromRhizoma coptidis(Huang Lian) extracts.
An integrative characterisation of prolinecisandtransconformers in a disordered peptide
Authors: Pettitt Alice J. , Shukla Vaibhav Kumar , Figueiredo Angelo Miguel , Newton Lydia S. , McCarthy Stephen , Tabor Alethea B. , Heller Gabriella T. , Lorenz Christian D. , Hansen D. Flemming 
Published: May 2024

ABSTRACTIntrinsically disordered proteins (IDPs) often contain proline residues, which undergocis/transisomerisation. While molecular dynamics (MD) simulations have the potential to fully characterise the prolinecisandtranssub-ensembles, they are limited by the slow timescales of isomerisation and force field inaccuracies. Nuclear magnetic resonance (NMR) spectroscopy can report on ensemble-averaged observables for both thecisandtransproline states, but a full atomistic characterisation of these sub-ensembles is challenging. Given the importance of prolinecis/transisomerisation for influencing the conformational sampling of disordered proteins, we employed a combination of all-atom MD simulations with enhanced sampling (metadynamics), NMR, and small-angle X-ray scattering (SAXS) to characterise the two sub-ensembles of the ORF6 C-terminal region (ORF6CTR) from SARS-CoV-2 corresponding to the proline-57 (P57)cisandtransstates. We performed MD simulations in three distinct force fields: AMBER03ws, AMBER99SB-disp, and CHARMM36m, which are all optimised for disordered proteins. Each simulation was run for an accumulated time of 180-220 µs until convergence was reached, as assessed by blocking analysis. A good agreement between thecis-P57 populations predicted from metadynamics simulations in AMBER03ws was observed with populations obtained from experimental NMR data. Moreover, we observed good agreement between the radius of gyration predicted from the metadynamics simulations in AMBER03ws and that measured using SAXS. Our findings suggest that both thecis-P57 andtrans-P57 conformations of ORF6CTRare extremely dynamic and that interdisciplinary approaches combining both multi-scale computations and experiments offer avenues to explore highly dynamic states that cannot be reliably characterised by either approach in isolation.SIGNIFICANCEThis study employs MD simulations (with metadynamics), NMR spectroscopy, and SAXS to elucidate the individualcisandtransproline conformations of ORF6CTRfrom SARS-CoV-2. The good agreement on prolinecis/transpopulations observed in experiments (NMR) and those calculated from simulations in the AMBER03ws force field (with SAXS reweighting) showcases the efficiency of this interdisciplinary approach, which can be used to characterise highly dynamic disordered protein states, even for very slow processes. Furthermore, our study emphasises the importance of considering both computational and experimental methodologies to gain a more holistic understanding of highly dynamic proteins. The presented integrative approach sets a precedent for future studies aiming to explore complex and dynamic biological systems with slow transitions such as proline isomerisations.
Automated adjustment of metabolic niches enables the control of natural and engineered microbial co-cultures
Authors: Martinez Juan Andres , Bouchat Romain , Gallet de Saint Aurin Tiphaine , Martínez Luz María , Caspeta Luis , Telek Samuel , Zicler Andrew , Gosset Guillermo , Delvigne Frank 
Published: May 2024

AbstractA lot of attention has been given to the understanding of microbial interactions leading to stable co-cultures, but the resulting technologies have been rarely challenged in dynamic cultivation conditions. In this work, substrate pulsing was performed to promote better control of the metabolic niches corresponding to each species, leading to the continuous co-cultivation of diverse microbial organisms. For this purpose, we used a cell-machine interface relying on automated flow cytometry, allowing to adjust the temporal profile of two metabolic niches according to a rhythm ensuring the successive growth of two species i.e., in our case a yeast and a bacterium. The resulting approach, called Automated Adjustment of Metabolic Niches (AAMN), was successfully employed for stabilizing both cooperative and competitive co-cultures. Additionally, AAMN can be considered as an enabling technology for the deployment of co-cultures in bioprocesses, demonstrated here based on the continuous bioproduction of p-coumaric acid. Taken altogether, the data accumulated suggest that AAMN could be used for a wider range of biological systems, but also to gain fundamental insights about microbial interaction mechanisms.
Predictive Control of Musculotendon Loads Across Fast and Slow-twitch Muscles in a Simulated System with Parallel Actuation
Authors: Nabipour Mahdi , Sawicki Gregory S. , Sartori Massimo 
Published: May 2024

AbstractResearch in lower limb wearable robotic control have largely focused on reducing the metabolic cost of walking or compensating for a portion of the biological joint torque e.g., by applying support proportional to estimated biological joint torques. However, due to different musculotendon unit (MTU) contractile speed properties, less attention has been given to the development of wearable robotic controllers that can steer MTU dynamics directly. Therefore, closed-loop control of MTU dynamics needs to be robust across fiber phenotypes, i.e. ranging from slow type I to fast type IIx in humans. The ability to closed-loop control the in-vivo dynamics of MTUs, could lead to a new class of wearable robots that can provide precise support to targeted MTUs, for preventing onset of injury or to provide precision rehabilitation to selected damaged tissues. In this paper, we introduce a novel closed-loop control framework that utilizes Nonlinear Model Predictive Control (NMPC) to keep the peak Achilles tendon force within predetermined boundaries during diverse range of cyclic force production simulations in the human ankle plantarflexors. This control framework employs a computationally efficient model comprising a modified Hill-type MTU contraction dynamics component and a model of the ankle joint with parallel actuation. Results indicate that the closed-form muscle-actuation model’s computational time is in the order of microseconds and is robust to different muscle contraction velocity properties. Furthermore, the controller achieves tendon force control within a timeframe below 14ms, aligning with the physiological electromechanical delay of the MTU and facilitating its potential for future real-world applications.
Roles of dimeric intermediates in RNA-catalyzed rolling circle synthesis
Authors: Kristoffersen Emil Laust , McRae Ewan K. , Sørensen Niels R. , Holliger Philipp , Andersen Ebbe S. 
Published: May 2024

AbstractThe RNA world hypothesis is supported by the discovery of RNA polymerase ribozymes that can perform RNA-catalyzed RNA replication processes on different RNA templates. Recently, RNA-catalyzed rolling circle synthesis (RCS) on small circular RNA (scRNA) templates has been demonstrated. However, the structural and dynamic properties of scRNA replication and its products and intermediates have never been explored. Here we have used cryogenic electron microscopy (cryo-EM) to characterize products and intermediates relevant for RCS replication and find that these form an unexpectedly diverse group of RNA nanostructures. The main structural motif observed is a fully hybridized dimeric complex composed of two scRNAs and their complement strands resolved to 5.3 Å. Cryo-EM also reveals higher order dimer filaments and dimer assembly intermediates suggesting a mechanism for assembly of the observed complexes. We show that the dimer complexes are stable and inhibit RNA-catalyzed RCS, but can be reactivated by addition of more scRNA templates. We propose that dimer formation may be a general property of RCS replication and speculate that the observed dimers might have benefited a primordial RNA genetic system by providing a stable “storage” form of RNA replication products and by coordinating RNA replication on both scRNA template strands.
ERK inhibits Cic repressor function via multisite phosphorylation
Authors: Paul Sayantanee , Ilkhani Khandan , Strozewski Nathan , Yang Liu , Denberg David W. , Christalin Wootchelmine , Shvartsman Stanislav Y. , Veraksa Alexey 
Published: May 2024

AbstractThe receptor tyrosine kinase (RTK)/Extracellular Signal-Regulated Kinase (ERK) signaling pathway controls cell proliferation, differentiation, and survival. How ERK activation is relayed to its phosphorylation targets is not well understood. The transcriptional repressor Capicua (Cic) has emerged as a key target for ERK-mediated downregulation inDrosophilaand mammals, and mutations in humanCICresult in cancer and neurological diseases. Phosphorylation by ERK is critical for Cic downregulation, but the identities of phosphosites inDrosophilaCic are unknown. Here, we identify sites of phosphorylation in Cic that are directly targeted by ERK and validate their developmental functions in vivo using mutant Cic variants. Cic phosphosites are distributed throughout the length of the protein, and a group of centrally located sites appears to have a primary role in Cic downregulation. Cic mutated in 20 high-confidence sites behaves as a “super-repressor” in vivo that is largely insensitive to ERK-mediated downregulation, despite fully retaining the ability to bind to ERK. No single site is sufficient to turn off Cic activity; instead, we find that ERK must phosphorylate multiple sites in Cic simultaneously to achieve full downregulation. This multisite phosphorylation likely targets phosphodegrons that are recognized by ubiquitin ligases such as Ago/FBXW7 and contributes to Cic degradation. This study advances our understanding of the molecular mechanisms of signal interpretation downstream of the RTK/ERK signaling network.
Enabling functionality and translation fidelity characterization of mRNA-based vaccines with a platform-based, antibody-free mass spectrometry detection approach
Authors: Stiving Alyssa Q. , Roose Benjamin W. , Tubbs Christopher , Haverick Mark , Gruber Ashley , Rustandi Richard R. , Kuiper Jesse , Schombs Matthew , Schuessler Hillary , Li Xuanwen 
Published: May 2024

AbstractThe success of mRNA-based therapeutics and vaccines can be attributed to their rapid development, adaptability to new disease variants, and scalable production. Modified ribonucleotides are often used in mRNA-based vaccines or therapeutics to enhance stability and reduce immunogenicity. However, substituting uridine with N1-methylpseudouridine has recently been shown to result in +1 ribosomal frameshifting that induces cellular immunity to the translated off-target protein. To accelerate vaccine development, it is critical to have analytical methods that can be rapidly brought online to assess the functionality and translation fidelity of mRNA constructs. Here, a platform-based, antibody-free method was developed using cell-free translation (CFT) and liquid chromatography-tandem mass spectrometry (MS) that can detect, characterize, and provide relative quantification of antigen proteins translated from mRNA vaccine drug substance. This workflow enabled the evaluation of mRNA subjected to thermal stress as well as bivalent (i.e., two mRNA encoding different antigen variants) drug substance. Additionally, the MS detection approach exhibited high sensitivity and specificity by accurately identifying all six translated proteins and their relative abundances in a dose-dependent manner following transfection of human cells with a hexavalent mRNA mixture encapsulated in lipid nanoparticles (LNPs), despite significant protein sequence homology. Expanding on these efforts, we show the utility of the CFT-MS approach in identifying the presence and junction of +1 ribosomal frameshifting resulting from N1-methylpseudouridation. Overall, this CFT-MS methodology offers a valuable analytical tool for the development and production of mRNA-based vaccines by facilitating the evaluation of mRNA quality and functionality while ensuring accurate translation of antigen proteins.Abstract Figure
Genetically modifying the protein matrix of macroscopic living materials to control their structure and rheological properties
Authors: Jimenez Esther M. , Nguyen Carlson , Shakeel Ahmad , Tesoriero Robert , Charrier Marimikel , Stull Alanna , Ajo-Franklin Caroline M. 
Published: May 2024

AbstractThe field of engineering living materials (ELMs) seeks to engineer cells to form macroscopic materials with tailorable structures and properties. While centimeter-scale ELMs can be grown fromCaulobacter crescentusengineered to secrete a protein matrix, how the sequence of the protein matrix affects structural and rheological properties remains poorly understood. Here, we explore how changing the elastin-like polypeptide (ELP) length impacts ELM microstructure and viscoelastic behavior. We demonstrate that shortening ELP produces fibers almost 2x thicker than other variants, resulting in a stiffer material at rest. Interestingly, the mid-length ELP forms a complex structure with globules and multidirectional fibers with increased yield stress under flow conditions. Lengthening ELP creates thinner strands between cells with similar storage and loss moduli to the mid-length ELP. This study indicates that sequence-structure-property relationships in these ELMs are complex with few parallels to other biocomposite models. Furthermore, it highlights that fine-tuning genetic sequences can create significant differences in rheological properties, uncovering new design principles of ELMs.
Time of day of infection shapes development of a eukaryotic algal-Nucleocytoviricotavirocell
Authors: Chase Emily E. , Truchon Alexander R. , Creasey Brooke A. , Wilhelm Steven W. 
Published: May 2024

ABSTRACTAureococcus anophagefferensrepresents one component of a model host-virus system (with the “giant virus”Kratosvirus quantuckense). Studies to define its ribocell (uninfected cells) and virocell (virus-infected cells) forms are needed, as both are abundant during algal blooms. A linkage between light-derived energy, virus particle production and virocell formation has been noted. We explored how the time of day (morning, afternoon, late day) of virus-host contact shaped virocell ontogeny. In parallel, we explored the need for light derived energy in this mixotrophic plankter by inhibiting photosystem II (PSII). Using flow cytometry and photochemical assessments, we examined the physiology of infected cells and controls, and estimated virus particle production by virocells. We observed distinct differences between ribocell and virocell response to treatments, including reductions in virus particle production during reduced light (i.e.,duration) and PSII inhibition. Collectively this work demonstrates the importance of light in shaping the fate of infected cells and provides insight into the factors that constrainin situblooms. Most significantly, we show that time of day when a virus and host come into contact influences viral particle production, and therefore bloom dynamics; a factor that needs to be considered in future bloom modeling work.
An integrated microfluidic and fluorescence platform for probing in vivo neuropharmacology
Authors: Piantadosi Sean C , Lee Min‐Kyu , Wu Mingzheng , Huynh Huong , Avila Raudel , Pizzano Carina , Zamorano Catalina A , Wu Yixin , Xavier Rachael , Stanslaski Maria , Kang Jiheon , Thai Sarah , Kim Youngdo , Zhang Jinglan , Huang Yonggang , Kozorovitskiy Yevgenia , Good Cameron H , Banks Anthony R , Rogers John A , Bruchas Michael R. 
Published: May 2024

AbstractNeurotechnologies and genetic tools for dissecting neural circuit functions have advanced rapidly over the past decade, although the development of complementary pharmacological method-ologies has comparatively lagged. Understanding the precise pharmacological mechanisms of neuroactive compounds is critical for advancing basic neurobiology and neuropharmacology, as well as for developing more effective treatments for neurological and neuropsychiatric disorders. However, integrating modern tools for assessing neural activity in large-scale neural networks with spatially localized drug delivery remains a major challenge. Here, we present a dual microfluidic-photometry platform that enables simultaneous intracranial drug delivery with neural dynamics monitoring in the rodent brain. The integrated platform combines a wireless, battery-free, miniaturized fluidic microsystem with optical probes, allowing for spatially and temporally specific drug delivery while recording activity-dependent fluorescence using genetically encoded calcium indicators (GECIs), neurotransmitter sensors GRABNEand GRABDA, and neuropeptide sensors. We demonstrate the performance this platform for investigating neuropharmacological mechanisms in vivo and characterize its efficacy in probing precise mechanistic actions of neuroactive compounds across several rapidly evolving neuroscience domains.
Competition and Integration of Visual and Goal Vector Signals for Spatial Navigation
Authors: Vijayabaskaran Sandhiya , Cheng Sen 
Published: May 2024

AbstractIntegrating different sources of information is essential to successful spatial navigation. For instance, animals must often rely on a combination of visual impressions, self-motion, olfaction, and other signals to navigate to a goal. This is especially important when navigating in uncertain environments, where switching from one source of information to another or integrating multiple sources of information may be required to make navigation decisions. We propose a computational model of the interaction of visual and goal-vector signals based on reinforcement learning and use it to study behavior and spatial representations. Our model demonstrates that the ability to navigate using each information source independently, in addition to integrating them, is crucial to successfully navigating in uncertain environments. Counterintuitively, our model also shows that when one of the signals is removed, navigation may be improved if the remaining signal is reliable and sufficient to navigate, however, this improvement comes at the expense of robustness.
Circadian rhythms mediate malaria transmission potential
Authors: Bento Inês , Parrington Brianna , Pascual Rushlenne , Goldberg Alexander S , Wang Eileen , Liu Hani , Zelle Mira , Takahashi Joseph S , Elias Joshua E , Mota Maria M , Rijo-Ferreira Filipa 
Published: May 2024

AbstractMalaria transmission begins when infected femaleAnophelesmosquitos depositPlasmodiumparasites into the mammalian host’s skin during a bloodmeal. The salivary gland-resident sporozoite parasites migrate to the bloodstream, subsequently invading and replicating within hepatocytes. AsAnophelesmosquitos are more active at night, with a 24-hour rhythm, we investigated whether their salivary glands are under circadian control, anticipating bloodmeals and modulating sporozoite biology for host encounters. Here we show that approximately half of the mosquito salivary gland transcriptome, particularly genes essential for efficient bloodmeals such as anti-blood clotting factors, exhibits circadian rhythmic expression. Furthermore, we demonstrate that mosquitoes prefer to feed during nighttime, with the amount of blood ingested varying cyclically throughout the day. Notably, we show a substantial subset of the sporozoite transcriptome cycling throughout the day. These include genes involved in parasite motility, potentially modulating the ability to initiate infection at different times of day. Thus, although sporozoites are typically considered quiescent, our results demonstrate their transcriptional activity, revealing robust daily rhythms of gene expression. Our findings suggest a circadian evolutionary relationship between the vector, parasite and mammalian host that together modulate malaria transmission.