bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal Decline of Exercise Capacity in Male and Female Mice
Authors: Pajski Megan L. , Maroto Rosario , Byrd Chris , Graber Ted G. 
Published: July 2024

AbstractThe population of older adults is exponentially expanding. Alongside aging comes the onset of chronic disease, decline of functional capacity, and reduced quality of life. Thus, this population increase will stress the capacity and financial viability of health and long-term care systems. Developing pre-clinical models for age-related functional decline is imperative to advancing therapies that extend healthspan and prolong independence. Previously in a cross-sectional study, we established a powerful composite scoring system we termed CFAB (comprehensive functional assessment battery). CFAB measures physical function and exercise capacity using well-validated determinants to measure overall motor function, fore-limb strength, four-limb strength/endurance, aerobic capacity, and volitional exercise/activity rate. In the current work, we used CFAB to track cohorts of male and female C57BL/6 mice over the lifespan (measuring CFAB at 6, 12, 18, 24, and 28 months of age). Overall, we found statistically significantly declining function as the mice aged, with some differences between males and females in trajectory and slope. We also determined that body mass changes presented differently between sexes, and tracked body composition (fat percentage, using magnetic resonance imagery) in females. In a subset of mice, we trackedin vivocontractile physiology noting declines in plantar flexor maximum isometric torque. In summary, our data suggest that males and females declined at different rates. We confirmed the efficacy of CFAB to track longitudinal changes in exercise capacity and physical fitness in both males and females, further validating the system to track age-related functional decline.
Galanin receptor 1 expressing neurons in hippocampal-prefrontal circuitry modulate goal directed attention and impulse control
Authors: Messanvi Fany , Visocky Vladimir , Senneca Carolyn , Berkun Kathleen , Taori Maansi , Bradley Sean P. , Wang Huikun , Tejeda Hugo , Chudasama Yogita 
Published: July 2024

AbstractWhile amino acid neurotransmitters are the main chemical messengers in the brain, they are co-expressed with neuropeptides which are increasingly recognized as modulators of cognitive pathways. For example, the neuropeptide galanin has been implicated in a wide range of pathological conditions in which frontal and temporal structures are compromised. In a recent study in rats, we discovered that direct pharmacological stimulation of galanin receptor type 1 (GalR1) in the ventral prefrontal cortex (vPFC) and ventral hippocampus (vHC) led to opposing effects on attention and impulse control behavior. In the present study, we investigate how subtypes of neurons expressing GalR1 in these two areas differentially contribute to these behaviors. We first establish that GalR1 is predominantly expressed in glutamatergic neurons in both the vPFC and HC. We develop a novel viral approach to gain genetic access to GalR1-expressing neurons and demonstrate that optogenetic excitation of GalR1 expressing neurons in the vPFC, but not vHC, selectively disrupts attention in a complex behavioral task. Finally, using fiber photometry, we measure the bulk calcium dynamics in GalR1-expressing neurons during the same task to demonstrate opposing activity in vPFC and vHC. These results are consistent with our previous work demonstrating differential behavioral effects induced by GalR1 activating in vPFC and vHC. These results indicate the distinct neuromodulatory and behavioral contributions of galanin mediated by subclasses of neurons in the hippocampal and prefrontal circuitry.
Efficientin situepitope tagging of rice genes by nuclease-mediated prime editing
Authors: Li Xueqi , Zhang Sujie , Wang Chenyang , Ren Bin , Yan Fang , Li Shaofang , Spetz Carl , Huang Jinguang , Zhou Xueping , Zhou Huanbin 
Published: July 2024

AbstractIn situepitope tagging is crucial for probing gene expression, protein localization, and the dynamics of protein interactions within their natural cellular context. However, the practical application of this technique in plants presents considerable hurdles. Here, we comprehensively explore the potential of the CRISPR/Cas nuclease-mediated prime editing and different DNA repair pathways in epitope tagging of endogenous rice genes. We find that SpCas9 nuclease/microhomology-mediated end joining (MMEJ)-based prime editing strategy (termed NM-PE) facilitates more straightforward and efficient gene tagging compared to the conventional and other derivative PE method. Furthermore, the PAM-flexible SpRY and ScCas9 nucleases-based prime editors have been engineered and implemented for the tagging of endogenous genes with diverse epitopes, significantly broadening the applicability of NM-PE in rice. Moreover, NM-PE has been successfully adopted in simultaneous tagging ofOsMPK1andOsMPK13in rice plants with c-Myc and HA tags, respectively. Taken together, our results indicate great potential of the NM-PE toolkit in the targeted gene tagging for Rice Protein Tagging Project, gene function study and genetic improvement.
Mechanical problem solving in mice
Authors: Boon Marcus N. , Andresen Niek , Traverso Soledad , Meier Sophia , Schuessler Friedrich , Hellwich Olaf , Lewejohann Lars , Thöne-Reineke Christa , Sprekeler Henning , Hohlbaum Katharina 
Published: July 2024

AbstractRecent advances in automated tracking tools have sparked a growing interest in studying naturalistic behavior. Yet, traditional decision-making tasks remain the norm for assessing learning behavior in neuroscience. We introduce an alternative sequential decision-making task for studying mouse behavior. It consists of an open-source, 3D-printed “lockbox”, a mechanical riddle that requires four different mechanisms to be solved in sequence to obtain a reward. During the task, the mice move around freely, allowing the expression of complex behavioral patterns. We observed that mice willingly engage in the task and learn to solve it in only a few trials. To analyze how the mice solved the task, we recorded their behavior in a multi-camera setup and developed a custom data analysis pipeline to automatically detect the interactions of the mice with the different lockbox mechanisms for a large corpus of video footage (>300h, 12 mice). The pipeline allows us to further delineate why mouse performance increases over trials. Our analyses suggest that this is not due to an increased interaction time with the task or the acquisition of a smart solution strategy, but primarily due to habituation to the lockbox. Lockboxes may hence be a promising approach to study both abstract sequential decision making and low-level motor learning in a single task that can be rapidly learned by mice.
Enhanced RNAi does not provide efficient innate antiviral immunity in micein vivo
Authors: Kulmann Marcos Iuri Roos , Taborska Eliska , Benköova Brigita , Palus Martin , Drobek Ales , Horvat Filip , Pasulka Josef , Malik Radek , Salyova Eva , Hönig Vaclav , Pellerova Michaela , Borsanyiova Maria , Stepanek Ondrej , Bopegamage Shubhada , Ruzek Daniel , Svoboda Petr 
Published: July 2024

AbstractIn RNA interference (RNAi), long double-stranded RNA (dsRNA) is cleaved by Dicer endonuclease into small RNA interfering RNAs (siRNAs), which guide degradation of complementary RNAs. While RNAi mediates antiviral innate immunity in plants and many invertebrates, vertebrates adopted sequence-independent response and their Dicer produces siRNAs inefficiently because it is adapted to process small hairpin microRNA precursors in the gene-regulating microRNA pathway. Mammalian RNAi is thus a rudimentary pathway of unclear significance. To investigate its antiviral potential, we modified mouse Dicer locus to express a truncated variant (DicerΔHEL1) known to stimulate RNAi. Next, we analyzed how DicerΔHEL1/wtmice respond to four RNA viruses: Coxsackievirus B3 (CVB3) and encephalomyocarditis virus (ECMV) fromPicornaviridae; tick-borne encephalitis virus (TBEV) fromFlaviviridae; and lymphocytic choriomeningitis virus (LCMV) fromArenaviridae. Increased Dicer activity in DicerΔHEL1/wtmice did not elicit any antiviral effect. supporting insignificant antiviral function of endogenous mammalian RNAiin vivo. However, we also report that sufficiently high expression of DicerΔHEL1suppressed LCMV in embryonic stem cells and in a transgenic mouse model. Altogether, mice with increased Dicer activity offer a new benchmark for identifying and studying viruses susceptible to mammalian RNAiin vivo.
Evidence for an efferent-based prediction contributing to implicit motor adaptation
Authors: Szarka Annika , Kim Hyosub E. , Inglis J. Timothy , Chua Romeo 
Published: July 2024

AbstractModels of sensorimotor adaptation have proposed that implicit adaptation is driven by error signals created by discrepancies between various sensory information sources. While proprioception has been suggested as a critical source for the error signals driving adaptation, the role of an efferent-based motor prediction has largely been neglected. In this study, we examined the effect of dissociating the afferent and efferent information available during implicit adaptation. Participants moved a visual cursor towards targets by applying horizontal forces to a stationary handle at a central home location. During perturbation trials, the cursor followed an invariant path rotated relative to the target. Participants were instructed to ignore this task-irrelevant cursor feedback and to isometrically “reach” towards the target. Participants implicitly adapted in the isometric task, even when the hand never actually moved to the target. Moreover, the level of adaptation surpassed that of a typical clamped reaching paradigm by nearly twofold. This was confirmed in a secondary experiment where participants performed actual reaching movements and demonstrated significantly less adaptation. Our findings suggest that while afferent proprioceptive feedback of hand position around the target most likely plays a role in adaptation, it is not necessary to induce adaptation.
Oxidation of Four Monoterpenoid Indole Alkaloid Classes by Three Cytochrome P450 Monooxygenases fromTabernaemontana litoralis
Authors: Mai Zhan , Kim Kyunghee , Richardson Matthew Bailey , Deschênes Daniel André Ramey , Garza-Garcia Jorge Jonathan Oswaldo , Shahsavarani Mohammadamin , Perley Jacob Owen , Njoku Destiny Ichechi , Deslongchamps Ghislain , De Luca Vincenzo , Qu Yang 
Published: July 2024

AbstractCytochrome P450 monooxygenases (CYPs) are well known for their ability to catalyze diverse oxidation reactions, playing a significant role in the biosynthesis of various natural products. In the realm of monoterpenoid indole alkaloids (MIAs), one of the largest groups of alkaloids in nature, CYPs are integral to reactions such as hydroxylation, epoxidation, ring opening, ring rearrangement, and aromatization, contributing to the extensive diversification of these compounds. In this study, we investigate the transcriptome, metabolome, and MIA biosynthesis inTabernaemontana litoralis(milky way tree), a prolific producer of rare pseudoaspidosperma-type MIAs. Alongside known pseudoaspidosperma biosynthetic genes, we identify and characterize three new CYPs that facilitate regio- and stereospecific oxidation of four MIA skeletons: iboga, aspidosperma, pseudoaspidosperma, and quebrachamine. Notably, the tabersonine 14,15-β-epoxidase catalyzes the formation of pachysiphine, the stereoisomer of 14,15-α-epoxytabersonine (lochnericine) found inCatharanthus roseus(Madagascar periwinkle) roots. The pseudovincadifformine 18-hydroxylase is the first CYP identified to modify a pseudoaspidosperma skeleton. Additionally, we demonstrate that the enzyme responsible for C10-hydroxylation of the iboga MIA coronaridine also catalyzes the same reaction on voaphylline, which bears a quebrachamine skeleton. With the discovery of a new MIA, 11-hydroxypseudovincadifformine, this study provides a comprehensive understanding of MIA biosynthesis and diversification inT. litoralis, highlighting its potential for further exploration.
Genetic diversity analysis of main agronomic traits and ISSR markers in 35 ornamental rape germplasm resources
Authors: Xia Mang , Chen Meizhu , Dong Xiaoxiao , Chen Jingdong , Cheng Miao , Wan Heping , Dong Yuanhuo , Zeng Changli , Dai Xigang 
Published: July 2024

AbstractRape (Brassica napusL.) is a major oil crop in our country, valued for its oil and ornamental uses. This study analyzed 35 ornamental rape germplasm resources from different origins to examine differences in agronomic traits and molecular markers. Nine agronomic traits were assessed in the field for variability, correlation, principal component analysis, and cluster analysis. Genetic diversity was analyzed using microsatellite (ISSR) markers and the unweighted pair group method with arithmetic mean (UPGMA). Our findings revealed a notable average coefficient of variation of 22.59% across the nine agronomic traits, with flower color exhibiting the highest variability and corolla width the least. The observed range of variation spanned from 9.24% to 83.38%, the correlation among these traits was generally low, with a mere 13.9% demonstrating significant correlations. The four principal components accounted for an impressive 84.62% of the cumulative contribution rate, while the genetic similarity, as gauged by eight ISSR primers, varied from 0.675 to 0.980. Most strikingly, we observed that plants from the same geographical region displayed molecular-level differences, underscoring the rich genetic diversity inherent in the 35 ornamental rape resources under study. Employing UPGMA cluster analysis on the primary agronomic traits and ISSR molecular markers, the 35 ornamental rape resources were categorized into seven and four distinct groups, respectively. Although the clustering outcomes from these two methodologies did not align perfectly, they served to complement each other. Collectively, these insights offer a theoretical framework for the innovation of ornamental rape germplasm resources and the cultivation of novel varieties.
Appendage regeneration requires IMPDH2 and creates a sensitized environment for enzyme filament formation
Authors: McCartney Morgan E. , Wheeler Gavin M. , O’Neill Audrey G. , Patel Jeet H. , Litt Zoey R. , Calise S. John , Kollman Justin M. , Wills Andrea E. 
Published: July 2024

SummaryRegeneration of lost tissue requires biosynthesis of metabolites needed for cell proliferation and growth. Among these are the critical purine nucleotides ATP and GTP. The abundance and balance of these purines is regulated by inosine monophosphate dehydrogenase 2 (IMPDH2), which catalyzes the committing step of GTP synthesis. IMPDH2 assembles into filaments that resist allosteric inhibition under conditions of high GTP demand. Here we asked whether IMPDH2 is required in the highly proliferative context of regeneration, and whether its assembly into filaments takes place in regenerating tissue. We find that inhibition of IMPDH2 leads to impaired tail regeneration and reduced cell proliferation in the tadpoleXenopus tropicalis. We find that both endogenous and fluorescent fusions of IMPDH2 robustly assemble into filaments throughout the tadpole tail, and that the regenerating tail creates a sensitized condition for filament formation. These findings clarify the role of purine biosynthesis in regeneration and reveal that IMPDH2 enzyme filament formation is a biologically relevant mechanism of regulation in vertebrate regeneration.Graphical Abstract
Methods for detecting “missing” dimensions in genetic covariance matrices
Authors: Dochtermann Ned A. 
Published: July 2024

AbstractBlows and Hoffmann (2005) and others have suggested that low levels of genetic variation in some dimensions of an additive genetic variance-covariance matrix (G) will be detectable as eigenvalues approaching zero. These dimensions may be indicative of trade-offs (Blows and Hoffmann 2005) or, potentially, of “holes” in fitness landscapes (Dochtermann et al. 2023).However, because the estimation ofGtypically constrains variances to be positive, and matrices to therefore be positive definite, “approaching zero” is challenging to statistically define. It is, therefore, not currently clear how to statistically identify dimensions with effectively zero variances. Being able to identify dimensions ofGwith variances approaching zero would improve our ability to understand trade-offs which, typically and inappropriately, focus on the signs of bivariate correlations (Houle 1991). Viable approaches would also allow better understanding of the structure ofGand the evolutionary processes that have shapedGacross taxa.Mezey and Houle (2005) and Kirkpatrick and Lofsvold (1992) used matrix rank to determine if there were dimensions lacking variation. Rank is the number of eigenvalues for a matrix that are greater than zero. If aG’s rank is less than its dimensionality, this would be evidence that there are dimensions without variation. However, most contemporary analysis procedures force estimates ofGto be positive semi-definite. Consequently, estimatedGs will not have eigenvalues of 0 or negative. Therefore, the estimated eigenvalues on their own will not allow the identification of absolute constraints (sensu(Houle 2001)) or more generally dimensions lacking variation. One alternative would be to compare the eigenvalues of observed matrices to those of random matrices and, if there were dimensions with less variation than expected by chance, this comparison could be used to identify dimensions in which evolution is constrained.If trade-offs or landscape holes result in dimensions ofGthat have minimal variance, we would expect that the associated eigenvalues exhibit less variation than expected by chance. Here, I tested whether the distribution of eigenvalues from randomly generated correlated matrices can be used for such testing.
Topological mixing and irreversibility in animal chromosome evolution
Authors: Schultz Darrin T. , Blümel Arno , Destanović Dalila , Sarigol Fatih , Simakov Oleg 
Published: July 2024

Abstract/Summary ParagraphAnimal chromosomes can persist with recognizable homology over hundreds of millions of years, in spite of homology-obfuscating processes such as chromosomal fusion and translocation. The frequency and pace of these major genome structural changes are unknown, and it remains unclear whether or how they impact long-term genome evolution. Here, we compare whole chromosomal sequences of 3,631 genomes from 2,291 species spanning all major animal clades and show that animal karyotypes evolve primarily via karyotype contraction, associated with increased rates of chromosomal fusion-with-mixing and dispersion that largely obey chromosomal algebra1, or karyotype expansion, which breaks up ancestral linkage groups and forms new chromosomal elements via non-algebraic changes. We show that chromosomal changes can be associated with major extinction events. Using a multi-scale encoding of pan-animal genome homology and a manifold representation of genomic changes, we find that genome evolution is not only driven by changes at the chromosomal level, but that subchromosomal mixing and irreversibility define clade-specific evolution. Using this ‘evolutionary genome topology’ approach, we calculate extrema of irreversible genomic configurations and identify species that occupy intermediate manifold positions, providing evidence for distinct macro-evolutionary trajectories. We propose that investigation of mixed state accumulation around important gene loci (such as Hox) will be crucial in capturing and further study of clade-specific regulatory innovations.
Nuclear Argonaute protein NRDE-3 switches small RNA partners during embryogenesis to mediate temporal-specific gene regulatory activity
Authors: Chen Shihui , Phillips Carolyn M. 
Published: July 2024

AbstractRNA interference (RNAi) is a conserved gene regulation mechanism that utilizes the Argonaute protein and their associated small RNAs to exert regulatory function on complementary transcripts. While the majority of germline-expressed RNAi pathway components reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here we find that the small RNA biogenesis machinery is spatially and temporally organized during embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. We also observe that many other RNAi factors form foci in embryonic cells distinct from “SIMR granules”, including the Argonaute protein CSR-1, underscoring a potential role for cytoplasmic concentrates of RNAi factors to promote gene regulation in embryos. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. Prior work has shown that NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.
A modular system to label endogenous presynaptic proteins using split fluorophores inC. elegans
Authors: Kurashina Mizuki , Snow Andrew W. , Mizumoto Kota 
Published: July 2024

AbstractVisualizing the subcellular localization of presynaptic proteins with fluorescent proteins is a powerful tool to dissect the genetic and molecular mechanisms underlying synapse formation and patterning in live animals. Here, we utilize split green and red fluorescent proteins to visualize the localization of endogenously expressed presynaptic proteins at a single neuron resolution inCaenorhabditis elegans.By using CRISPR/Cas9 genome editing, we generated a collection ofC. elegansstrains in which endogenously expressed presynaptic proteins (RAB-3/Rab3, CLA-1/Piccolo, SYD-2/Liprin-α, UNC-10/RIM and ELKS-1/ELKS) are tagged with tandem repeats of GFP11and/or wrmScarlet11. We show that the expression of wrmScarlet1-10and GFP1-10under neuron-specific promoters can robustly label presynaptic proteins in different neuron types. We believe that combinations of knock-in strains and wrmScarlet1-10and GFP1-10plasmids are a versatile modular system to examine the localization of endogenous presynaptic proteins in any neuron type.