bluuebunny/crossref_metadata_2025_split huggingface dataset:
Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization
Authors: Deogharia Manisha , Agrawal Akanksha , Shi Miusi , Jain Abhinav K , McHugh Kevin J. , Altamirano Francisco , Marian A J , Gurha Priyatansh 
Published: April 2023

RationaleHuman pluripotent stem cell-derived CMs (iPSC-CMs) are a valuable tool for disease modeling, cell therapy and to reconstruct the CM maturation process and identify, characterize factors that regulate maturation. The transition from immature fetal to adult CM entails coordinated regulation of the mature gene programming, which is characterized by the induction of myofilament and OXPHOS gene expression among others. Recent studies inDrosophila,C. elegans,and C2C12 myoblast cell lines have implicated the histone H3K4me3 demethylase KDM5 and its homologs, as a potential regulator of developmental gene program and mitochondrial function. We speculated that KDM5 may potentiate the maturation of iPSC-CMs by targeting a conserved epigenetic program that encompass mitochondrial OXPHOS and other CM specific maturation genes.ObjectivesThe purpose of this study is to determine the role of KDM5 in iPSC-CM maturation.Methods and ResultsImmunoblot analysis revealed that KDM5A, B, and C expression was progressively downregulated in postnatal cardiomyocytes and absent in adult hearts and CMs. Additionally, KDM5 proteins were found to be persistently expressed in iPSC-CMs up to 60 days after the onset of myogenic differentiation, consistent with the immaturity of these cells. Inhibition of KDM5 by KDM5-C70 -a pan-KDM5 inhibitor-resulted in differential regulation of 2,372 genes including upregulation of Fatty acid oxidation (FAO), OXPHOS, and myogenic gene programs in iPSC-CMs. Likewise, genome-wide profiling of H3K4me3 binding sites by the CUT&RUN assay revealed enriched H3K4me3 peaks at the promoter regions of FAO, OXPHOS, and sarcomere genes. Consistent with the chromatin and gene expression data, KDM5 inhibition led to increased expression of multiple sarcomere proteins, enhanced myofibrillar organization and improved calcium handling. Furthermore, inhibition of KDM5 increased H3K4me3 deposits at the promoter region of theESRRAgene, which is known to regulate OXPHOS and cardiomyocyte maturation, and resulted in its increased RNA and protein levels. Finally, KDM5 inhibition increased baseline, peak, and spare oxygen consumption rates in iPSC-CMs.ConclusionsKDM5 regulates the maturation of iPSC-CMs by epigenetically regulating the expression of ESRRA, OXPHOS, FAO, and sarcomere genes and enhancing myofibril organization and mitochondrial function.
Molecular profiling of high-level athlete skeletal muscle after acute exercise – a systems biology approach
Authors: Reitzner Stefan M , Emanuelsson Eric B , Arif Muhammad , Kaczkowski Bogumil , Kwon Andrew TJ , Mardinoglu Adil , Arner Erik , Chapman Mark A. , Sundberg Carl Johan 
Published: April 2023

SUMMARYLife-long high-level exercise training leads to improvements in physical performance and multi-tissue adaptation following changes in molecular pathways. While skeletal muscle baseline differences between exercise-trained and untrained individuals have been previously investigated, it remains unclear how acute exercise multi-omics are influenced by training history. We recruited and extensively characterized 24 individuals categorized as endurance athletes, strength athletes or control subjects. Multi-omics profiling was performed from skeletal muscle before and at three time-points after endurance or resistance exercise sessions. Timeseries multi-omics analysis revealed distinct differences in molecular processes such as fatty- and amino acid metabolism and for transcription factors such as HIF1A and the MYF-family between both exercise history and acute form of exercise. Furthermore, we found a “transcriptional specialization effect” by transcriptional narrowing and intensification. Finally, we performed multi-omics network analysis and clustering, providing a novel resource of skeletal muscle transcriptomic and metabolomic profiling in highly trained and untrained individuals.
Sucrose phosphorylase fromAlteromonas mediterranea: structural insight into the regioselective α-glucosylation of (+)-catechin
Authors: Goux Marine , Demonceaux Marie , Hendrickx Johann , Solleux Claude , Lormeau Emilie , Fredslund Folmer , Tezé David , Offmann Bernard , André-Miral Corinne 
Published: April 2023

AbstractSucrose phosphorylases, through transglycosylation reactions, are interesting enzymes that can transfer regioselectively glucose from sucrose, the donor substrate, onto acceptors like flavonoids to form glycoconjugates and hence modulate their solubility and bioactivity. Here, we report for the first time the structure of sucrose phosphorylase from the marine bacteriaAlteromonas mediterranea(AmSP) and its enzymatic properties. Kinetics of sucrose hydrolysis and transglucosylation capacities on (+)-catechin were investigated. Wild-type enzyme (AmSP-WT) displayed high hydrolytic activity on sucrose and was devoid of transglucosylation activity on (+)-catechin. Two variants,AmSP-Q353F andAmSP-P140D catalysed the regiospecific transglucosylation of (+)-catechin: 89% of a novel compound (+)-catechin-4′-O-α-D-glucopyranoside (CAT-4’) for AmSP-P140D and 92% of (+)-catechin-3′-O-α-D-glucopyranoside (CAT-3’) for AmSP-Q353F. The compound CAT-4’ was fully characterized by NMR and mass spectrometry. An explanation for this difference in regiospecificity was provided at atomic level by molecular docking simulations:AmSP-P140D was found to preferentially bind (+)-catechin in a mode that favours glucosylation on its hydroxyl group in position 4’ while the binding mode in AmSP-Q353F favoured glucosylation on its hydroxyl group in position 3’.
A bioorthogonal antibody-based chemically-induced-dimerization switch for therapeutic application
Authors: Martinko Alexander J. , Tran Hai L. , Simonds Erin F. , Cooke Allison L. , Huang Zhong , Raguveer Sruthi , Agullet Judit Pina , Prasad Suchitra , Going Catherine , Marshall Lisa , Park Timothy , Banerjee Sunandan , Macdonald Ramsay , Jian Mike , Ng Kenneth , Palakodaty Akhila , Kaur Manpreet , Ponce Alberto , Tabrizi Mohammad , Hill Zachary B. 
Published: April 2023

AbstractWe present the Indinavir Ligand Induced Transient Engagement switch (IDV LITE Switch), a fully synthetic Chemically Induced Dimerization (CID) system wherein two humanized antibody fragments are heterodimerized by the antiviral drug indinavir. The IDV LITE Switch represents the first CID system made from fully humanized protein components and dimerized by a clinically approved small molecule drug lacking a mammalian target, making it an ideal bioorthogonal molecular switch for application in small-molecule controlled therapeutics.
Cryo-EM structure of the human cardiac myosin filament
Authors: Dutta Debabrata , Nguyen Vu , Campbell Kenneth S. , Padrón Raúl , Craig Roger 
Published: April 2023

AbstractPumping of the heart is powered by filaments of the motor protein myosin, which pull on actin filaments to generate cardiac contraction. In addition to myosin, the filaments contain cardiac myosin-binding protein C (cMyBP-C), which modulates contractility in response to physiological stimuli, and titin, which functions as a scaffold for filament assembly1. Myosin, cMyBP-C and titin are all subject to mutation, which can lead to heart failure. Despite the central importance of cardiac myosin filaments to life, their molecular structure has remained a mystery for 60 years2. Here, we have solved the structure of the main (cMyBP-C-containing) region of the human cardiac filament to 6 Å resolution by cryo-EM. The reconstruction reveals the architecture of titin and cMyBP-C for the first time, and shows how myosin’s motor domains (heads) form 3 different types of motif (providing functional flexibility), which interact with each other and with specific domains of titin and cMyBP-C to dictate filament architecture and regulate function. A novel packing of myosin tails in the filament backbone is also resolved. The structure suggests how cMyBP-C helps generate the cardiac super-relaxed state3, how titin and cMyBP-C may contribute to length-dependent activation4, and how mutations in myosin and cMyBP-C might disrupt interactions, causing disease5, 6. A similar structure is likely in vertebrate skeletal myosin filaments. The reconstruction resolves past uncertainties, and integrates previous data on cardiac muscle structure and function. It provides a new paradigm for interpreting structural, physiological and clinical observations, and for the design of potential therapeutic drugs.
deMULTIplex2: robust sample demultiplexing for scRNA-seq
Authors: Zhu Qin , Conrad Daniel N. , Gartner Zev J. 
Published: April 2023

AbstractSingle-cell sample multiplexing technologies function by associating sample-specific barcode tags with cell-specific barcode tags, thereby increasing sample throughput, reducing batch effects, and decreasing reagent costs. Computational methods must then correctly associate cell-tags with sample-tags, but their performance deteriorates rapidly when working with datasets that are large, have imbalanced cell numbers across samples, or are noisy due to cross-contamination among sample tags - unavoidable features of many real-world experiments. Here we introduce deMULTIplex2, a mechanism-guided classification algorithm for multiplexed scRNA-seq data that successfully recovers many more cells across a spectrum of challenging datasets compared to existing methods. deMULTIplex2 is built on a statistical model of tag read counts derived from the physical mechanism of tag cross-contamination. Using generalized linear models and expectation-maximization, deMULTIplex2 probabilistically infers the sample identity of each cell and classifies singlets with high accuracy. Using Randomized Quantile Residuals, we show the model fits both simulated and real datasets. Benchmarking analysis suggests that deMULTIplex2 outperforms existing algorithms, especially when handling large and noisy single-cell datasets or those with unbalanced sample compositions.
A system of feed-forward cerebellar circuits that extend and diversify sensory signaling
Authors: Hariani Harsh N. , Algstam A. Brynn , Candler Christian T. , Witteveen Isabelle F. , Sidhu Jasmeen K. , Balmer Timothy S. 
Published: April 2023

ABSTRACTSensory signals are processed by the cerebellum to coordinate movements. Numerous cerebellar functions are thought to require the maintenance of a sensory representation that extends beyond the input signal. Granule cells receive sensory input, but they do not prolong the signal and are thus unlikely to maintain a sensory representation for much longer than the inputs themselves. Unipolar brush cells (UBCs) are excitatory interneurons that project to granule cells and transform sensory input into prolonged increases or decreases in firing, depending on their ON or OFF UBC subtype. Further extension and diversification of the input signal could be produced by UBCs that project to one another, but whether this circuitry exists is unclear. Here we test whether UBCs innervate one another and explore how these small networks of UBCs could transform spiking patterns. We characterized two transgenic mouse lines electrophysiologically and immunohistochemically to confirm that they label ON and OFF UBC subtypes and crossed them together, revealing that ON and OFF UBCs innervate one another. A Brainbow reporter was used to label UBCs of the same ON or OFF subtype with different fluorescent proteins, which showed that UBCs innervate their own subtypes as well. Computational models predict that these feed-forward networks of UBCs extend the length of bursts or pauses and introduce delays—transformations that may be necessary for cerebellar functions from modulation of eye movements to adaptive learning across time scales.SIGNIFICANCE STATEMENTThe cerebellum is essential for the accurate performance of behaviors ranging in complexity from stabilizing an image on the retina to playing a piano or performing a gymnastics routine. Cerebellar dysfunction disrupts the ability to produce smooth movements and leads to a disorder called ataxia. Damage to the vestibular cerebellum occurs in various disorders including medulloblastoma and leads to nystagmus, involuntary movements of the eyes that prevent normal vision. Treating disorders of motor control such as nystagmus, requires a better understanding of how representations of movements are maintained in the firing patterns of neurons in the cerebellar circuit. Here we use transgenic mice to label a type of neuron called the unipolar brush cell and revealed that these cells innervate one another and are likely to increase the length and diversity of spiking patterns in the cerebellum. These transformations may be necessary for numerous functions from controlling eye movements to learning new behaviors.
Cooperative dynamics of DNA grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami
Authors: Lak Aidin , Wang Yihao , Kolbeck Pauline J. , Pauer Christoph , Chowdhury Mohammad Suman , Cassani Marco , Ludwig Frank , Viereck Thilo , Selbach Florian , Tinnefeld Philip , Schilling Meinhard , Liedl Tim , Tavacoli Joe , Lipfert Jan 
Published: April 2023

ABSTRACTMagnetic nanoparticles (MNPs) enable unique capabilities for biosensing and actuation via coupling to DNA origami, yet how DNA grafting density affects their dynamics and accessibility remains poorly understood. Here, we demonstrate functionalization of MNPs with single-stranded DNA (ssDNA) via click chemistry conjugation with tunable grafting density. Several complementary methods show that particle translational and rotational dynamics exhibit a sigmoidal dependence on ssDNA grafting density. At low densities ssDNA strands are coiled and cause small changes to particle dynamics, while at high densities they form polymer brushes that cooperatively change particle dynamics. Intermediate ssDNA densities show the highest magnetic biosensing sensitivity for detection of target nucleic acids. Finally, we demonstrate that MNPs with high grafting densities are required to efficiently couple them to DNA origami. These results together establish ssDNA grafting density as a critical parameter for functionalization of MNPs for use in a broad range of applications.
Maturation-Dependent Changes in the Structure and Seeding Capacity of Aβ42 Amyloid Fibrils
Authors: Miller Alyssa , Chia Sean , Klimont Ewa , Knowles Tuomas P.J. , Vendruscolo Michele , Ruggeri Francesco Simone 
Published: April 2023

AbstractMany proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases, and can be exploited to develop versatile functional biomaterials. Thus, amyloid aggregation has been widely studied, shedding light on the properties of fibrils and their intermediates. A question that remains open concerns the microscopic processes that underlie the long-time behaviour of the fibrillar assemblies. Here, we use atomic force microscopy to observe that the fibrils undergo a maturation process, with an increase in both fibril length and thickness, and a change in the cross-β sheet content. These changes affect the ability of the fibrils to catalyse the formation of new aggregates through secondary nucleation. The identification of these changes helps us understand the fibril maturation processes, facilitate the targeting of amyloid fibrils in drug discovery, and offer insight into the development of biocompatible and sustainable protein based materials.
Optogenetic-Induced Muscle Loading Leads to Mechanical Adaptation of the Achilles Tendon Enthesis in Mice
Authors: Ganji Elahe , Lamia Syeda N. , Stepanovich Matthew , Whyte Noelle , Abraham Adam C. , Killian Megan L. 
Published: April 2023

AbstractThe growth of the skeleton depends on the transmission of contractile muscle forces from tendon to bone across the extracellular matrix-rich enthesis. Loss of muscle loading leads to significant impairments in enthesis development. However, little is known about how the enthesis responds to increased loading during postnatal growth. To study the cellular and matrix adaptations of the enthesis in response to increased muscle loading, we used optogenetics to induce skeletal muscle contraction and unilaterally load the Achilles tendon and enthesis in young (i.e., during growth) and adult (i.e., mature) mice. In young mice, daily bouts of unilateral optogenetic loading led to expansion of the calcaneal apophysis and growth plate, as well as increased vascularization of the normally avascular enthesis. Daily loading bouts, delivered for 3 weeks, also led to a mechanically weaker enthesis with increased molecular-level accumulation of collagen damage in young mice. However, adult mice did not exhibit impaired mechanical properties or noticeable structural adaptations to the enthesis. We then focused on the transcriptional response of the young tendon and bone following optogenetic-induced loading. After 1 or 2 weeks of loading, we identified, in tendon, transcriptional activation of canonical pathways related to glucose metabolism (glycolysis) and inhibited pathways associated with cytoskeletal remodeling (e.g., RHOA and CREB signaling). In bone, we identified activation of inflammatory signaling (e.g., NFkB and STAT3 signaling) and inhibition of ERK/MAPK and PTEN signaling. Thus, we have demonstrated the utility of optogenetic-induced skeletal muscle contraction to elicit structural, functional, and molecular adaptation of the enthesisin vivoespecially during growth.
Genome-wide gene birth-death dynamics are associated with diet breadth variation in Lepidoptera
Authors: Dort Hanna , Bijl Wouter van der , Wahlberg Niklas , Nylin Sören , Wheat Christopher W. 
Published: April 2023

ABSTRACTComparative analyses of gene birth-death dynamics (GBDD) have the potential to reveal gene families that played an important role in the evolution of morphological, behavioral, or physiological variation. Here, we used whole genomes of 30 species of butterflies and moths to identify GBDD among the Lepidoptera that are associated with specialist or generalist feeding strategies. Our work advances this field by using a uniform set of annotated proteins for all genomes, investigating associations while correcting for phylogeny, and assessing all gene familes rather thana priorisubsets. We discovered that the sizes of several important gene families (e.g., those associated with pesticide resistance, xenobiotic detoxification, and/or protein digestion) are significantly correlated with diet breadth. We also found 12 gene families showing significant shifts in GBDD at the butterfly (Papilionoidea) crown node, the most notable of which was a family of pheromone receptors that underwent a contraction potentially linked with a shift to visual-based mate recognition. Our findings highlight the importance of uniform annotations, phylogenetic corrections and unbiased gene family analyses in generating a list of candidate genes that warrant further exploration.Significance StatementGene duplications and gene deaths are important for the development of novel traits, but their study is often complicated by methodological issues, such as input data coming from different sources with different biases. Here, we address many of these issues in an analysis of gene duplication and death across 30 species of moths by using standardized, genome-wide input data. Importantly, our analysis uses a model that can correlate gene family sizes with any quantitative trait, while also accounting for relatedness between species. Using this model, we provide novel evolutionary insights by showing that the sizes of several important gene families are correlated with increases or decreases in the number of host plant orders that Lepidoptera eat.
Environmental conditions predetermine innate antioxidants pool in sea oat (Uniola paniculataL.) seeds
Authors: Egesa Andrew Ogolla , Pérez Héctor E. , Begcy Kevin 
Published: April 2023

ABSTRACTBackground and AimsSecondary metabolites such as antioxidants are critical components that protect seeds from stress damage during seed development, desiccation, and ex-situ storage. Antioxidants are essential determinants of seed quality, longevity, and persistence. Understanding the environmental factors that regulate the accumulation, content, and function of antioxidant pools in sea oat seeds is critical for gene banking and understanding the environmental impacts on seed quality.MethodsGermination, viability, and Trolox Equivalent Antioxidant Capacity (TEAC) were analyzed on seeds from 18 sea oat populations from the US Atlantic and Gulf of Mexico coasts. We first assessed baseline TEAC, followed by TEAC performed on imbibed seeds for 36 hours at 35/25 °C during the day and night, respectively. Then, we analyzed the relationship of the antioxidant pools from these 18 sea oat populations to sampling site environmental classifications.Key ResultsHigher baseline antioxidants were common in regions with extreme environmental conditions corresponding to sea oat populations growing at latitudinal extremes characterized by warmer and colder temperatures. Baseline antioxidants did not correlate with prevailing seed germination. However, higher concentrations of antioxidants following imbibition were associated with poor seed germination in warmer conditions.ConclusionsOur results indicate that climatic conditions and environmental components associated with temperatures and precipitation may largely influence the innate pool of antioxidants in sea oat seeds. Also, a high amount of antioxidants following sea oat seeds imbibition suggest seed damage or poor viability influenced by environmental stress conditions during seed development.
Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins
Authors: Mathony Jan , Aschenbrenner Sabine , Becker Philipp , Niopek Dominik 
Published: April 2023

AbstractDomain insertion engineering is a promising approach to recombine the functions of evolutionarily unrelated proteins. Insertion of light-switchable receptor domains into a selected effector protein, for instance, can yield allosteric effectors with light-dependent activity. However, the parameters that determine domain insertion tolerance are poorly understood.Here, we used an unbiased screen to systematically assess the domain insertion permissibility of several evolutionary unrelated proteins. Training machine learning models on the resulting data allowed us to dissect features informative for domain insertion tolerance and revealed sequence conservation statistics as the strongest indicators of suitable insertion sites. Finally, extending our experimental pipeline towards the identification of switchable hybrids resulted in opto-chemogenetic derivatives of the transcription factor AraC that function as single-protein Boolean logic gates. Our study reveals determinants of domain insertion tolerance and facilitates the engineering of switchable proteins with unique mechanistic properties.