bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intermediate Filaments Associate with Aggresome-like Structures in ProteostressedC. elegansNeurons and Influence Large Vesicle Extrusions as Exophers
Authors: Arnold Meghan Lee , Cooper Jason , Androwski Rebecca , Ardeshna Sohil , Melentijevic Ilija , Smart Joelle , Guasp Ryan J. , Nguyen Ken C.Q. , Bai Ge , Hall David H. , Grant Barth D. , Driscoll Monica 
Published: August 2022

AbstractUnder conditions of proteostasis disequilibrium, neurons can enhance intracellular and extracellular protective mechanisms to guard against neurotoxicity. In mammals, an intracellular response to severe proteostasis imbalance that results from proteosome inhibition is the formation of juxtanuclear intermediate filament-surrounded, aggregate-filled aggresomes, which sequester threatening aggregates for later disposal via lysosomal degradation. Highly proteo-stressed neurons can also engage the assistance of neighboring cells in aggregate removal by loading threatening materials into large exopher vesicles that are transferred to neighboring cells for remote degradation of contents, a process that has been suggested to be analogous to the process that enables aggregate spreading in the human brain in neurodegenerative disease. InC. elegansthese large extruded vesicles are called exophers.Here we document that players involved in aggresome biology are required for the elimination of potentially deleterious materials in neuronal exophers. We show that in proteostressedC. eleganstouch receptor neurons, intermediate filament proteins IFD-1 and IFD-2 can assemble into juxtanuclear structures with multiple molecular and cellular characteristics of mammalian aggresomes. IFD-concentrating structures depend upon orthologs of mammalian adapter proteins, dynein motors, and microtubule integrity for aggregate collection into juxtanuclear compartments where they associate with ubiquitinated and neurotoxic polyglutamine expansion proteins. Strikingly, disruption of aggresome-decoration genes encoding IFDs or disruption of the BAG/14-3-3/Hsc70 adapter that promote aggregate loading of aggresome-like organelles, lowers exopher production via a cell autonomous mechanism. Although aggresome-like structures are not mandatory exopher cargo, IFD compartments can be extruded from neurons in exophers, revealing a previously unreported strategy to eliminate neuronal aggresome-like organelles via transfer to neighboring cells. Human IF neurofilament light chain hNFL can partially substitute forC. elegansIFD-2 proteins in promoting exopher production, indicating conservation of the capacity of intermediate filaments to influence neuronal aggregate extrusions across phyla. In sum, we identify a requirement for specific intermediate filaments, counterparts of human biomarkers of neuronal injury and disease and major components of Parkinson’s disease Lewy bodies, inC. elegansneuronal aggresome-like organelle formation and large vesicle exopher extrusion from stressed neurons.
CAMSAP-driven microtubule release from γ-TuRC and its regulation by nucleation-promoting factors
Authors: Rai Dipti , Hua Shasha , Monster Jooske L. , Stucchi Riccardo , Stecker Kelly , Zhang Yaqian , Katrukha Eugene A. , Altelaar Maarten , Wieczorek Michal , Jiang Kai , Akhmanova Anna 
Published: August 2022

Abstractγ-tubulin ring complex (γ-TuRC) is the major microtubule-nucleating factor. After nucleation, microtubules can be released from γ-TuRC and stabilized by other proteins, such as CAMSAPs, but the biochemical cross-talk between minus-end regulation pathways is poorly understood. Here, we reconstituted this process in vitro using purified components. We found that all CAMSAP proteins could bind to the minus-ends of γ-TuRC-attached microtubules. CAMSAP2 and CAMSAP3, which decorate and stabilize growing minus ends, but not the minus-end tracking protein CAMSAP1 induced microtubule release from γ-TuRC. CDK5RAP2, a γ-TuRC-interactor, and CLASP2, a regulator of microtubule growth, stimulated γ-TuRC-dependent microtubule nucleation, but only CDK5RAP2 inhibited CAMSAP-driven microtubule detachment by suppressing CAMSAP binding to γ-TuRC-anchored minus ends. CDK5RAP2 also improved γ-TuRC selectivity for 13-rather than 14-protofilament microtubules in microtubule-capping assays. Our results support a model whereby CAMSAPs exploit an imperfect attachment between γ-TuRC and the nucleated microtubule to promote minus-end elongation and release, whereas CDK5RAP2 improves the fit between γ-TuRC and 13-protofilament microtubules and enhances nucleation.
Design of extended metal-binding β-sandwiches from de novo immunoglobulin domains
Authors: Roel-Touris Jorge , Nadal Marta , Marcos Enrique 
Published: August 2022

ABSTRACTThe antigen binding sites of antibodies, and derivatives such as scFvs, consist of an immunoglobulin structural framework that anchors hypervariable loops, and that is arranged as a dimer of β-sandwiches (from the heavy and light chains) packing face-to-face. Yet, the naturally occurring dimer orientation of antibodies is not well suited for engineering rigid single-chain formats of increased stability and solubility, which are two key limitations of engineered antibodies. In this work, we computationally designed an extended 12-stranded β-sandwich as a rigid single-chain dimer of de novo immunoglobulin domains interacting through an alternative edge-to-edge arrangement. The extended β-sandwich was found to be hyperstable and structurally accurate as confirmed through X-ray crystallography. We functionalized this design by inserting a long EF-hand calcium-binding motif into the β-hairpin bridge between both domains, showing high metal-binding affinity while remaining soluble and stable in solution. Finally, we propose a few designs with two EF-hand motifs in either or the same side of the scaffold with high-confidence structure predictions; altogether suggesting the robustness and versatility of our scaffold to harbor long functional loops. Our extended β-sandwiches are structurally divergent to natural antibodies and open new avenues for incorporating multiple loop binding sites either for increased or bispecific activities.
Mitochondrial uncouplers impair human sperm motility without altering ATP content
Authors: Skinner Will M. , Petersen Natalie T. , Unger Bret , Tang Shaogeng , Tabarsi Emiliano , Lamm Julianna , Jalalian Liza , Smith James , Bertholet Ambre M. , Xu Ke , Kirichok Yuriy , Lishko Polina V. 
Published: August 2022

AbstractSperm motility is necessary for successful fertilization, but there remains controversy about whether human sperm motility is primarily powered by glycolysis or oxidative phosphorylation. To evaluate the plausibility of reducing human sperm mitochondrial ATP production as an avenue for contraceptive development, we treated human sperm with small-molecule mitochondrial uncouplers, which reduce mitochondrial membrane potential by inducing passive proton flow, and evaluated the effects on a variety of physiological processes that are critical for fertilization. We also sought to clarify the subcellular localization of Adenosine Nucleotide Translocator 4 (ANT4), a gamete-specific protein that has been suggested as a contraceptive target. We determined that ANT4 is mitochondrially localized, that induced mitochondrial uncoupling can be partially mediated by the ANT family, and that two uncouplers, Niclosamide Ethanolamine and BAM15, significantly decreased sperm progressive motility. However, these uncouplers did not reduce sperm ATP content or impair other physiological processes, implying that human sperm can rely on glycolysis for ATP production in the absence of functional mitochondria. Thus, since certain mitochondrial uncouplers impair motility through ATP-independent mechanisms, they could be useful ingredients in on-demand, vaginally-applied contraceptives. However, systemically delivered contraceptives that target sperm mitochondria to reduce their ATP production would need to be paired with sperm-specific glycolysis inhibitors.Significance StatementDevelopment of novel contraceptives is critical, since half of all pregnancies are still unplanned, even in developed countries. This high unplanned pregnancy rate contributes to a wide variety of social, environmental, and ecological problems. Impairing human sperm is a way to develop male and unisex contraceptives, but much remains unknown about these unique cells. Here we settle a long-running debate about human sperm metabolism, finding that human sperm can maintain their ATP levels without mitochondrial oxidative phosphorylation. This finding will help focus future contraceptive development efforts. We also identify the potential use of an FDA-approved compound (Niclosamide) as a motility-impairing ingredient in spermicides and correct the misunderstood subcellular localization of an existing contraceptive target, Adenosine Nucleotide Translocator 4.
CRHR1-mediated Akt activation involves endocytosis and soluble adenylyl cyclase activity
Authors: dos Santos Claro Paula A. , Armando Natalia G. , Attorresi Alejandra , Lindl Karen E. , Silbermins Micaela , Inda Carolina , Silberstein Susana 
Published: August 2022

ABSTRACTCorticotropin-releasing hormone receptor 1 (CRHR1) signaling initiates at the cell membrane and continues after receptor internalization. A sustained cAMP generation after ligand-activated CRHR1 endocytosis supported by the soluble adenylyl cyclase (sAC) is required for the G protein-independent phase of ERK1/2 phosphorylation in neuronal cells. Here, we report that Akt is activated by CRHR1 stimulation in a mechanism dependent on the endosomal cAMP production by sAC activity. Moreover, AktS473 phosphorylation profile was distinct to that of phospho-ERK1/2 revealing a crosstalk between these pathways. We found that the CRHR1 activation of PI3K/Akt pathway is required for a full ERK1/2 activation but negatively regulates the cAMP response and CREB phosphorylation downstream CRHR1 stimulation. Immunofluorescence colocalization analysis revealed that activated CRHR1 transits to early (Rab5) and recycling (Rab11) endosomes. Additionally, CRHR1 colocalized with two Rab5 effectors, APPL1 and EEA1. shRNA mediated knockdown uncovered a role of these proteins in CRHR1 signaling. APPL1 silencing led to a decrease in pAktS473 levels without affecting ERK1/2 activation, whereas EEA1 depletion had the opposite effect, suggesting that CRHR1 intracellular signaling diversity may be achieved through different signaling platforms.
Serum response factor reduces gene expression noise and confers cell state stability
Authors: Zhang Jian , Hu Xiao , Wu Qiao , Guo Shangqin 
Published: August 2022

AbstractThe role of serum response factor (Srf), a central mediator of actin dynamics and mechanical signaling, in cell identity regulation is debated to be either a cell identity stabilizer or destabilizer. We thus investigated the role of Srf in cell fate stability using mouse pluripotent stem cells, one of the very few cell types that can tolerate null Srf. Despite the fact that serum-containing cultures yield heterogeneous gene expression, deletion of Srf in mouse pluripotent stem cells leads to further exacerbated cell state heterogeneity. The exaggerated heterogeneity is not only detectible as increased lineage priming, but also as the 2C-like cell state. Thus, pluripotent cells explore more variety of cellular states in both directions of development surrounding naïve pluripotency, a behavior that is constrained by Srf. These results support that Srf functions as a cell state stabilizer, providing rationale for its functional perturbation in cell fate engineering and pathological intervention.
Transient glycolytic complexation of arsenate enhances resistance in the enteropathogen Vibrio cholerae
Authors: Bueno Emilio , Pinedo Víctor , Shinde Dhananjay D. , Mateus André , Typas Athanasios , Savitski Mikhail M , Thomas Vinai C. , Cava Felipe 
Published: August 2022

AbstractThe ubiquitous presence of toxic arsenate (AsV) in the environment has virtually raised mechanisms of resistance in all living organisms. Generally, bacterial detoxification of AsV relies on its reduction to arsenite (AsIII) by ArsC, followed by the export of AsIII by ArsB. However, how pathogenic species resist this metalloid remains largely unknown. Here, we found that V. cholerae, the etiologic agent of the diarrheal disease cholera, outcompetes other enteropathogens when grown on millimolar concentrations of AsV. To do so, V. cholerae uses, instead of ArsCB, the AsV-inducible vc1068-1071 operon (renamed var for vibrio arsenate resistance), which encodes the arsenate repressor ArsR, an alternative glyceraldehyde-3-phosphate dehydrogenase, a putative phosphatase, and the AsV transporter ArsJ. In addition to Var, V. cholerae induces oxidative stress- related systems to counter ROS production caused by intracellular AsV. Characterization of the var mutants suggested these proteins function independently from one another and play critical roles in preventing deleterious effects on the cell membrane potential and growth derived from the accumulation AsV. Mechanistically, we demonstrate that V. cholerae complexes AsV with the glycolytic intermediate 3-phosphoglycerate into 1-arseno-3-phosphoglycerate (1As3PG). We further show that 1As3PG is not transported outside the cell; instead, it is subsequently dissociated to enable extrusion of free AsV through ArsJ. Collectively, we propose the formation of 1As3PG as a transient metabolic storage of AsV to curb the noxious effect of free AsV. This study advances our understanding of AsV resistance in bacteria and underscores new points of vulnerability that might be an attractive target for antimicrobial interventions.
Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains
Authors: Wang Jing Yang (John) , Khmelinskaia Alena , Sheffler William , Miranda Marcos C. , Antanasijevic Aleksandar , Borst Andrew J. , Torres Susana Vazquez , Shu Chelsea , Hsia Yang , Nattermann Una , Ellis Daniel , Walkey Carl , Ahlrichs Maggie , Chan Sidney , Kang Alex , Nguyen Hannah , Sydeman Claire , Sankaran Banumathi , Wu Mengyu , Bera Asim K. , Carter Lauren , Fiala Brooke , Murphy Michael , Baker David , Ward Andrew B. , King Neil P. 
Published: August 2022

AbstractComputationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. Retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the novel nanoparticles we describe may be broadly useful in biotechnological applications.
Probability Ramp Control reduces the number of sessions required to find an acceptable dose of succinylcholine during Electroconvulsive Therapy - an in silico analysis
Authors: Mandel Jeff E 
Published: August 2022

AbstractIntroductionElectroconvulsive Therapy may be utilized in as many as 76,000 cases annually in the US, with the majority of cases employing succinylcholine. The reported dose spans the range of 0.29 - 2.1 mg/kg, and while motor seizures only last 36 ± 6 seconds, the duration of paralysis extends to 310 ± 38 seconds. While a model of succinylcholine pharmacokinetics/pharmacodynamics exists, this has not been employed to facilitate dose selection in clinical practice. Probability ramp control was investigated for this purpose.MethodsTwo approaches to dose finding were implemented. The first was an optimized Up-Down Method (UDM) that utilized an initial bolus, an adjustment dose, and a decrement to decrease the adjustment when crossing the target of 95% twitch depression. The second utilized probability ramp control (PRC) comprised of an infusion sequence that stopped when 95% twitch depression was obtained, a model that mapped the times for onset and offset of blockade to a subsequent bolus, and an adjustment dose to refine this dose when needed. Two populations of 10000 randomly parameterized models were developed from published data to train and evaluate the performance. Performance was assessed with a fuzzy classifier that segmented outcomes into three sets – LOW, HIGH, and SUCCESS. A loss function was developed that determined the number of sessions required to bring all models to SUCCESS. The probability distributions were compared using the Kolmogorov-Smirnov 2 sample test, with P<0.001 considered significant.ResultsOptimal values for the UDM parameters BOLUS, ADJUSTMENT, and DECREMENT were 0.7834 mg/kg, 0.3334 mg/kg, and 0.4056. Optimal values for the PRC SEQUENCE were 0.2663 mg/kg/min for 3 minutes followed by 0.7028 mg/kg/min. A fourth order polynomial MODEL produced estimates of the bolus that brought 99% of models to SUCCESS on the second session, while UDM required 6 sessions to achieve 99% SUCCESS. The probability distributions were distinct with P<<0.001.DiscussionPRC was able to correctly produce SUCCESS in significantly fewer sessions than UDM. Additionally, PRC is easy to implement and allows pooling of results from multiple clinicians. The performance of PRC in clinical use for ECT will require further study.Key PointsQuestionCan probability ramp control reduce the number of ECT sessions with suboptimal succinylcholine dosing?FindingsProbability ramp control found the correct dose in two sessions in 99% of simulations, compared to six sessions for the Up-Down Method.MeaningProbability ramp control is a more efficient method for finding the appropriate dose of succinylcholine for repeated sessions of ECT.
Cortical Dynein Drives Centrosome Clustering in Cells with Centrosome Amplification
Authors: Mercadante Dayna L. , Aaron William A. , Olson Sarah D. , Manning Amity L. 
Published: August 2022

AbstractDuring cell division, the microtubule nucleating and organizing organelle, known as the centrosome, is critical for the formation of the mitotic spindle. In cells with two centrosomes, each centrosome functions as an anchor point for microtubules, leading to the formation of a bipolar spindle and progression through a bipolar cell division. When extra centrosomes are present, multipolar spindles form and the parent cell may divide into more than two daughter cells. Cells that are born from multipolar divisions are not viable and hence clustering of extra centrosomes and progression to a bipolar division are critical determinants of viability in cells with extra centrosomes. We combine experimental approaches with computational modeling to define a role for cortical dynein in centrosome clustering. We show that centrosome clustering fails and multipolar spindles dominate when cortical dynein distribution or activity is experimentally perturbed. Our simulations further reveal that centrosome clustering is sensitive to the distribution of dynein on the cortex. Together, these results indicate that dynein’s cortical localization alone is insufficient for effective centrosome clustering and instead, dynamic relocalization of dynein from one side of the cell to the other throughout mitosis promotes timely clustering and bipolar cell division in cells with extra centrosomes.
Influence of Zr content on immersion and electrochemical corrosion behavior of as-cast TiZr alloys
Authors: Zhao Suli , Liu Shuguang , Liu Yaqing , Liu Xuan , Xu Kuixue , Shi Chunbao , Jiang Qing 
Published: August 2022

Purpose
The purpose of this paper is to study the influence of Zr content on immersion and electrochemical corrosion behavior of Zr-containing Ti-based (TiZr) alloys.

Design/methodology/approach
The phase analysis of as-cast TχZAB alloys was carried out using X-ray diffraction. The microstructure of corrosion surfaces of the samples was observed using optical metallographic microscopy and scanning electron microscopy, equipped with energy dispersive spectroscopy.

Findings
The immersion test reveals that the corrosion is alleviated in the presence of a high amount of Zr, whereas pitting corrosion occurs when the Zr content is up to 40 Wt.%. Furthermore, the electrochemical analysis demonstrates that the corrosion resistance TiZr alloys is improved with increasing Zr content.

Originality/value
The TiZr alloys are promising candidates for high-end applications because of their excellent comprehensive properties. These alloys are usually used in marine or other harsh corrosive environments; therefore, it is essential to study their corrosion behavior.
Development of a novel supervisory controller on a parallel-hybrid powertrain for small unmanned aerial systems
Authors: Fouellefack Lionel Dongmo , Smith Lelanie , Kruger Michael 
Published: August 2022

Purpose
A hybrid-electric unmanned aerial vehicle (HE-UAV) model has been developed to address the problem of low endurance of a small electric UAV. Electric-powered UAVs are not capable of achieving a high range and endurance due to the low energy density of its batteries. Alternatively, conventional UAVs (cUAVs) using fuel with an internal combustion engine (ICE) produces more noise and thermal signatures which is undesirable, especially if the air vehicle is required to patrol at low altitudes and remain undetected by ground patrols. This paper aims to investigate the impact of implementing hybrid propulsion technology to improve on the endurance of the UAV (based on a 13.6 kg UAV).

Design/methodology/approach
A HE-UAV model is developed to analyze the fuel consumption of the UAV for given mission profiles which were then compared to a cUAV. Although, this UAV size was used as reference case study, it can potentially be used to analyze the fuel consumption of any fixed wing UAV of similar take-off weight. The model was developed in a Matlab-Simulink environment using Simulink built-in functionalities, including all the subsystem of the hybrid powertrain. That is, the ICE, electric motor, battery, DC-DC converter, fuel system and propeller system as well as the aerodynamic system of the UAV. In addition, a ruled-based supervisory controlled strategy was implemented to characterize the split between the two propulsive components (ICE and electric motor) during the UAV mission. Finally, an electrification scheme was implemented to account for the hybridization of the UAV during certain stages of flight. The electrification scheme was then varied by changing the time duration of the UAV during certain stages of flight.

Findings
Based on simulation, it was observed a HE-UAV could achieve a fuel saving of 33% compared to the cUAV. A validation study showed a predicted improved fuel consumption of 9.5% for the Aerosonde UAV.

Originality/value
The novelty of this work comes with the implementation of a rule-based supervisory controller to characterize the split between the two propulsive components during the UAV mission. Also, the model was created by considering steady flight during cruise, but not during the climb and descend segment of the mission.