bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copper trafficking inTrypanosoma cruzi: the transcriptional response of candidates to balance toxicity and recruitment
Authors: Merli Marcelo L. , Mediavilla María G. , Zhu Xinyu , Cobine Paul A. , Cricco Julia A. 
Published: April 2024

AbstractTrypanosoma cruzi(Chagas disease) depends on acquiring nutrients and cofactors, like copper (Cu), from its hosts. Cu is essential for aerobic organisms, but it can also be toxic, so its transport and storage must be regulated. In the present study, we characterized the effects of changes in Cu availability on growth, intracellular ion content, and oxygen consumption. Our results show that Cu is essential for epimastigote proliferation and for metacyclogenesis, while intracellular amastigotes suffered from Cu stress during infection. We identify several genes potentially involved in Cu metabolism among which orthologs of the conserved P-type Cu ATPases involved in Cu export and loading of secreted enzymes were found and namedTcCuATPase.TcCuATPase transcription is regulated during infective stages and by Cu availability in epimastigotes. No homologs were identified for the high affinity importer CTR1 instead we propose that the iron transportTcIT a ZIP family transporter is involved in Cu uptake based on its transcriptional response to Cu. Further canonical Cu targets (based on homology to yeast and mammals) such as the iron reductaseTcFR and the cupro-oxidaseTcFet3 are up regulated during infective stages and under intracellular Cu stress. We also demonstrated that Cu, iron, and heme metabolisms are related. In sum, Cu metabolism is essential inT. cruzilife cycle. Even though cytosolic Cu-chaperons are still missing, we propose a model for Cu transport and intracellular distribution inT. cruziincluding conserved factors such asTcCuATPase and others such asTcFR andTcIT playing novel functions.
Free fatty acid receptor 4 in cardiac myocytes ameliorates ischemic cardiomyopathy
Authors: Zhang Michael J. , Karachenets Sergey , Gyberg Dylan J. , Puccini Sara , Healy Chastity L. , Wu Steven C. , Shearer Gregory C. , O’Connell Timothy D. 
Published: April 2024

AbstractAimsFree fatty acid receptor 4 (Ffar4) is a receptor for long-chain fatty acids that attenuates heart failure driven by increased afterload. Recent findings suggest that Ffar4 prevents ischemic injury in brain, liver, and kidney, and therefore, we hypothesized that Ffar4 would also attenuate cardiac ischemic injury.Methods and ResultsUsing a mouse model of ischemia-reperfusion (I/R), we found that mice with systemic deletion of Ffar4 (Ffar4KO) demonstrated impaired recovery of left ventricular systolic function post-I/R with no effect on initial infarct size. To identify potential mechanistic explanations for the cardioprotective effects of Ffar4, we performed bulk RNAseq to compare the transcriptomes from wild-type (WT) and Ffar4KO infarcted myocardium 3-days post-I/R. In the Ffar4KO infarcted myocardium, gene ontology (GO) analyses revealed augmentation of glycosaminoglycan synthesis, neutrophil activation, cadherin binding, extracellular matrix, rho signaling, and oxylipin synthesis, but impaired glycolytic and fatty acid metabolism, cardiac repolarization, and phosphodiesterase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated impaired AMPK signaling and augmented cellular senescence in the Ffar4KO infarcted myocardium. Interestingly, phosphodiesterase 6c (PDE6c), which degrades cGMP, was the most upregulated gene in the Ffar4KO heart. Further, the soluble guanylyl cyclase stimulator, vericiguat, failed to increase cGMP in Ffar4KO cardiac myocytes, suggesting increased phosphodiesterase activity. Finally, cardiac myocyte-specific overexpression of Ffar4 prevented systolic dysfunction post-I/R, defining a cardioprotective role of Ffa4 in cardiac myocytes.ConclusionsOur results demonstrate that Ffar4 in cardiac myocytes attenuates systolic dysfunction post-I/R, potentially by attenuating oxidative stress, preserving mitochondrial function, and modulation of cGMP signaling.
Modeling With Uncertainty Quantification Identifies Essential Features of a Non-Canonical Algal Carbon-Concentrating Mechanism
Authors: Steensma Anne K. , Kaste Joshua A.M. , Heo Junoh , Orr Douglas J. , Sung Chih-Li , Shachar-Hill Yair , Walker Berkley J. 
Published: April 2024

AbstractThe thermoacidophilic red algaCyanidioschyzon merolaesurvives its challenging environment likely in part by operating a carbon-concentrating mechanism (CCM). Here, we demonstrated thatC. merolae’s cellular affinity for CO2is stronger than its rubisco affinity for CO2. This provided further evidence thatC. merolaeoperates a CCM while lacking structures and functions characteristic of CCMs in other organisms. To test how such a CCM could function, we created a mathematical compartmental model of a simple CCM distinct from those previously described in detail. The results supported the feasibility of this proposed minimal and non-canonical CCM inC. merolae. To facilitate robust modeling of this process, we incorporated new physiological and enzymatic data into the model, and we additionally trained a surrogate machine-learning model to emulate the mechanistic model and characterized the effects of model parameters on key outputs. This parameter exploration enabled us to identify model features that influenced whether the model met experimentally-derived criteria for functional carbon-concentration and efficient energy usage. Such parameters included cytosolic pH, bicarbonate pumping cost and kinetics, cell radius, carboxylation velocity, number of thylakoid membranes, and CO2membrane permeability. Our exploration thus suggested that a novel CCM could exist inC. merolaeand illuminated essential features necessary for CCMs to function.SignificanceCarbon-concentrating mechanisms (CCMs) are processes which boost photosynthetic efficiency. By developing modeling approaches to robustly describe CCMs in organisms where biochemical data is limited, such as extremophile algae, we can better understand how organisms survive environmental challenges. We demonstrate an interdisciplinary modeling approach which efficiently sampled from large parameter spaces and identified features (e.g., compartment permeability, pH, enzyme characteristics) which determine the function and energy cost of a simple CCM. This approach is new to compartmental photosynthetic modeling, and could facilitate effective use of models to inform experiments and rational engineering. For example, engineering CCMs into crops may improve agricultural productivity, and could benefit from models defining the structural and biochemical features necessary for CCM function.
Conditionalnmy-1andnmy-2alleles establish that non-muscle myosins are required for lateC. elegansembryonic elongation
Authors: Molnar Kelly , Suman Shashi Kumar , Eichelbrenner Jeanne , Plancke Camille N. , Robin François B. , Labouesse Michel 
Published: April 2024

ABSTRACTThe elongation ofC. elegansembryos allows examination of mechanical interactions between adjacent tissues. Muscle contractions during late elongation induce the remodelling of epidermal circumferential actin filaments through mechanotransduction. We investigated the possible role of the non-muscle myosins NMY-1 and NMY-2 in this process usingnmy-1andnmy-2thermosensitive alleles. Our findings suggest these myosins act redundantly in late elongation, and that they are involved in the multi-step process of epidermal remodeling. When inactivated, NMY-1 was seen to form protein aggregates.
On-farm biomass recycling with biostimulant Re-Gen increases corn yields in multi-year farm trials
Authors: Gibson William S , Ziobron Amy S , Olson Noah E , Neher Deborah A , Smith Charles F , Holden Victoria I 
Published: April 2024

AbstractThe United States produced 15.1 billion bushels of corn for grain in 2023, relying on harmful synthetic chemicals such as fertilizer and pesticides to ensure high yields. This dependency on agrochemicals has negatively impacted the environment and soil microbiome, therefore, there is a need to rebuild soil health by implementing regenerative agricultural practices. One increasingly utilized regenerative practice is the application of biostimulants, or microbial inoculants that can rebuild soil health and productivity. A multi-year corn trial was conducted to quantify the impact of Re-Gen, a biostimulant invented to degrade woody biomass and increase nutrient bioavailability in the soil, to increase corn yield at a dairy farm in Ferrisburgh, Vermont. Over the two-year trial, Re-Gen application on corn stover and cover crop residues increased corn bushels per acre by 24% and increased tons of corn silage per acre by 12.5-30%, depending on the field. Soil nutrient analysis and plant tissue analysis showed increased nutrients, particularly in one trial field. Multi-year Re-Gen application showed increased monetary value, indicating that the effects of Re-Gen do not diminish with multiple applications. Further investigation into the mechanism suggests that increased phosphatase production stimulated by Re-Gen could contribute to increased phosphorus bioavailability in the soil and uptake in the tissue, potentially increasing yields. These results highlight the potential for Re-Gen to foster regenerative agriculture processes while also increasing yield and, therefore, revenue for corn farmers in the United States.
On the critical concentration for net assembly of dynamically unstable polymers
Authors: Mullins R. Dyche 
Published: April 2024

AbstractCytoskeletal and cytomotive filaments are protein polymers that move molecular cargo and organize cellular contents in all domains of life. A key parameter describing the self-assembly of many of these polymers —including actin filaments and microtubules— is the minimum concentration required for polymer formation. This ‘critical concentration for net assembly’ (ccN) is easy to calculate for eukaryotic actins but more difficult for dynamically unstable filaments such as microtubules and some bacterial polymers. To better understand how cells (especially bacteria) regulate assembly of dynamically unstable polymers I investigate the microscopic parameters that influence their critical concentrations. Assuming simple models for spontaneous nucleation and catastrophe I derive expressions for the monomer-polymer balance. In the absence of concentration-dependent rescue, fixed catastrophe rates do not produce clear critical concentrations. In contrast, simple ATP-/GTP-cap models with concentration-dependent catastrophe rates, generate phenomenological critical concentrations that increase linearly with the rate of nucleotide hydrolysis and decrease logarithmically with the rate of spontaneous nucleation.
Relationship between Striatal Connectivity and Apathy during Phosphodiesterase 10 Inhibition in Schizophrenia
Authors: Omlor Wolfgang , Cecere Giacomo , Huang Gao-Yang , Rabe Finn , Kallen Nils , Kirschner Matthias , Surbeck Werner , Burrer Achim , Spiller Tobias , Garibaldi George , Holiga Štefan , Dukart Juergen , Umbricht Daniel , Homan Philipp 
Published: April 2024

AbstractNegative symptoms in schizophrenia remain a challenge with limited therapeutic strategies. The novel compound RG7203 promotes reward learning via dopamine D1-dependent signaling and therefore holds promise to improve especially the apathy dimension of negative symptoms. When tested as add-on to antipsychotic medication apathy did not change significantly with RG7203 versus placebo. However, the response varied across patients, and a subset showed clinically relevant improvement of apathy. It remains unclear if these interindividual differences are related to neurobiological correlates. Due to the predominant binding of RG7203 in the striatum, we asked how apathy changes with RG7203 are related to changes in cortico-striatal connectivity. We focused on cortico-striatal circuits that have been associated with apathy and previously showed connectivity alterations in schizophrenia. In a double-blind, 3-way randomized crossover study, resting state functional magnetic resonance imaging was acquired in 24 individuals with schizophrenia following a 3-week administration of placebo, 5mg or 15mg of RG7203 as add-on to antipsychotics. We found that 5mg or 15mg of RG7203 did not lead to significant changes in striatal connectivity. However, changes in the apathy response across individuals were reflected by striatal connectivity changes. Apathy improvement with 5mg RG7203 vs. placebo was associated with increased connectivity between ventral caudate (vCaud) and paracingulate gyrus (PCG) as well as anterior cingulate cortex (ACC). The same trend was observed for 15mg RG7203 vs. placebo. Importantly, such associations were not observed for the negative symptom dimension of expressive deficits. These findings suggest that the relationship between vCaud-PCG/ACC connectivity and apathy response with RG7203 should be further explored in larger clinical studies. Replication and further elaboration of these findings could help to advance biologically informed treatment options for negative symptoms.
RNA complexes with nicks and gaps: thermodynamic and kinetic effects of coaxial stacking and dangling ends
Authors: Todisco Marco , Radakovic Aleksandar , Szostak Jack W. 
Published: April 2024

ABSTRACTMultiple RNA strands can interact in solution and assume a large variety of configurations dictated by their potential for base pairing. Although duplex formation from two complementary oligonucleotides has been studied in detail, we still lack a systematic characterization of the behavior of higher order complexes. Here we focus on the thermodynamic and kinetic effects of an upstream oligonucleotide on the binding of a downstream oligonucleotide to a common template, as we vary the sequence and structure of the contact interface. We show that coaxial stacking in RNA is well correlated with but much more stabilizing than helix propagation over an analogous intact double helix step (median Δ Δ G37°C≈ 1.7 kcal/mol). Consequently, approximating coaxial stacking in RNA with the helix propagation term leads to large discrepancies between predictions and our experimentally determined melting temperatures, with an offset of ≈ 10°C. Our kinetic study reveals that the hybridization of the downstream probe oligonucleotide is impaired (lowerkon) by the presence of the upstream oligonucleotide, with the thermodynamic stabilization coming entirely from an extended lifetime (lowerkoff) of the bound downstream oligonucleotide, which can increase from seconds to months. Surprisingly, we show that the effect of nicks is dependent on the length of the stacking oligonucleotides, and we discuss the binding of ultrashort (1 ∼ 4 nt) oligonucleotides that are relevant in the context of the origin of life. The thermodynamic and kinetic data obtained in this work allow for the prediction of the formation and stability of higher order multi-stranded complexes.Graphic entry for the Table of Contents (TOC)
Development of the ULK1-Recruiting Chimeras (ULKRECs) to enable proximity-induced and ULK1-dependent degradation of mitochondria
Authors: Zaman Niyaz , Aley Natasha , Pingitore Valeria , Selwood David L , Ketteler Robin 
Published: April 2024

ABSTRACTTargeted protein degradation (TPD) has opened new opportunities to investigate signalling pathways as a research tool, and as a unique therapeutic strategy using bifunctional chimeric small molecules, with candidate molecules in clinical trials for the treatment of breast cancer and prostate cancer. Most current TPD approaches use the 26S proteasomal machinery via PROteolysis TArgeting Chimeras (PROTACs), however, new emerging strategies using the autophagy system, termed AUtophagy TArgeting Chimeras (AUTACs) expand on the degrader arsenal and repertoire of targets that can be degraded. This includes non-protein molecules such as lipid droplets, organelles, insoluble protein aggregates as well as typical TPD targets, soluble intracellular proteins. AUTACs were proposed to operate by binding the target of interest (TOI) and linking it to an autophagy cargo protein (LC3 or p62), tethering the TOI into forming autophagosomes. In this study, we designed an alternative strategy for AUTACs, reasoning that the local recruitment and activation of ULK1 is sufficient to induce the formation of an autophagosome at the site of recruitment. As a proof of concept, we used an ULK1 agonist linked to a mitochondrial targeting ligand and termed these chimeric molecules ULK1-Recruiting Chimeras (ULKRECs). We show that local activation of ULK1 by ULKRECs at the outer mitochondrial membrane (OMM) induces mitophagy, further enhanced by mitochondrial insult. Using Parkinson’s disease (PD) patient-derived fibroblasts, we show the ULKRECs induce mitophagy independently of the PRKN/PINK axis, components required to signal for canonical mitophagy in response to stressors and often dysfunctional in many neurological diseases. We propose that ULKRECs are a novel class of degraders that have potential as unique therapeutics for diseases where dysfunctional mitophagy plays a key role in disease pathology and progression.
SMG1:SMG8:SMG9-complex integrity maintains robustness of nonsense-mediated mRNA decay
Authors: Kueckelmann Sabrina , Theunissen Sophie , Lackmann Jan-Wilm , Franitza Marek , Becker Kerstin , Boehm Volker , Gehring Niels H. 
Published: April 2024

AbstractNonsense-mediated mRNA decay (NMD) is a translation-dependent mRNA turnover pathway, which degrades transcripts containing premature termination codons. SMG1-mediated phosphorylation of the key NMD factor UPF1 is essential for NMD initiation and regulated by SMG9 and the C-terminus of SMG8. However, their specific roles in NMD regulation within intact cells remain partially understood. Here, we deleted the C-terminus of en-dogenous SMG8 in human cultured cells, which resulted in unchanged NMD activity. Cell lines lacking SMG8 and SMG9 showed slight NMD inhibition and unchanged UPF1 phosphorylation levels, but were sensitized to treatment with a SMG1 inhibitor (SMG1i). Transcriptome-wide analysis revealed the upregulation of NMD-annotated transcripts, which corresponded to synergistic effects of SMG1i concentration and SMG8 and SMG9 knock-out conditions. Moreover, the UPF1 interactome showed enrichment of various NMD factors in SMG8 or SMG9 knock-out cells and following SMG1i treatment, suggesting an accumulation of stalled NMD complexes at various stages of the NMD process. Together, our work uncovers important roles of SMG8 and SMG9 in maintaining NMD robustness in human cells.
Human adherent cortical organoids in a multiwell format
Authors: Kroeg Mark van der , Bansal Sakshi , Unkel Maurits , Smeenk Hilde , Kushner Steven A. , de Vrij Femke M.S. 
Published: April 2024

SummaryIn the growing diversity of human iPSC-derived models of brain development, we present here a novel method that exhibits 3D cortical layer formation in a highly reproducible topography of minimal dimensions. The resulting adherent cortical organoids develop by self-organization after seeding frontal cortex patterned iPSC-derived neural progenitor cells in 384-well plates during eight weeks of differentiation. The organoids have stereotypical dimensions of 3 × 3 × 0.2 mm, contain multiple neuronal subtypes, astrocytes and oligodendrocyte lineage cells, and are amenable to extended culture for at least 10 months. Longitudinal imaging revealed morphologically mature dendritic spines, axonal myelination, and robust neuronal activity. Moreover, adherent cortical organoids compare favorably to existing brain organoid models on the basis of robust reproducibility in obtaining topographically-standardized singular radial cortical structures and circumvent the internal necrosis that is common in free-floating cortical organoids. The adherent human cortical organoid platform holds considerable potential for high-throughput drug discovery applications, neurotoxicological screening, and mechanistic pathophysiological studies of brain disorders.
Ultrastructural Dynamics of Dopaminergic Presynaptic Release Sites revealed by Cryo-correlative Light and Electron Microscopy
Authors: Lycas Matthew Domenic , Morado Dustin R. , Gether Ulrik , Briggs John A.G. , Erlendsson Simon 
Published: April 2024

AbstractDopaminergic neurons are fundamental in governing motivation, movement, and many aspects of cognition. The targeted modulation of dopaminergic signaling serves as a cornerstone in developing therapeutic interventions for conditions such as Parkinson’s disease, schizophrenia, and addiction. Despite the pivotal role of dopaminergic neurons, the ultrastructure and associated dynamics of dopaminergic synapses remain poorly understood. Here, we develop and utilize a cryo-correlative light and electron microscopy process chain to investigate the micro- to nanoscale architecture and organelle content of dopaminergic presynaptic release sites. Using cryo electron tomography, we identify several protein complexes crucial to dopaminergic function and we utilize subtomogram averaging to resolvein situassemblies of the TRiC/CCT chaperone and vacuolar-type ATPase. Lastly, we find that pharmacological treatments using either dopamine or the dopamine D2 receptor antagonist, haloperidol, bidirectionally modulate vesicular content, mitochondrial size and calcium phosphate deposition. These findings contribute to our general understanding of the composition and ultrastructural dynamics of dopaminergic presynaptic release sites and provide a methodological platform for further studies of the structure and cell biology of dopaminergic neurons and their responses.
Inhibitory control of locomotor statistics in walkingDrosophila
Authors: Gattuso Hannah C. , van Hassel Karin A. , Freed Jacob D. , Nuñez Kavin M. , de la Rea Beatriz , May Christina E. , Ermentrout G. Bard , Victor Jonathan D. , Nagel Katherine I. 
Published: April 2024

AbstractIn order to forage for food, many animals regulate not only specific limb movements but the statistics of locomotor behavior over time, switching between long-range dispersal and localized search depending on resource availability. How pre-motor circuits regulate such locomotor statistics is not clear. Here we analyze and model locomotor statistics in walkingDrosophila, and their modulation by attractive food odor. Odor evokes three motor regimes in flies: baseline walking, upwind running during odor, and search behavior following odor loss. During search behavior, we find that flies adopt higher angular velocities and slower ground speeds, and tend to turn for longer periods of time in one direction. We further find that flies spontaneously adopt periods of different mean ground speed, and that these changes in state influence the length of odor-evoked runs. We next developed a simple model of neural locomotor control that suggests that contralateral inhibition plays a key role in regulating the statistical features of locomotion. As the fly connectome predicts decussating inhibitory neurons in the lateral accessory lobe (LAL), a pre-motor structure, we gained genetic access to a subset of these neurons and tested their effects on behavior. We identified one population of neurons whose activation induces all three signature of search and that bi-directionally regulates angular velocity at odor offset. We identified a second group of neurons, including a single LAL neuron pair, that bi-directionally regulate ground speed. Together, our work develops a biologically plausible computational architecture that captures the statistical features of fly locomotion across behavioral states and identifies potential neural substrates of these computations.