bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryo-FIB workflow for imaging brain tissue viain situcryo-electron microscopy
Authors: Ning Jiying , Glausier Jill R. , Hsieh Chyongere , Schmelzer Thomas , Buck Silas A. , Franks Jonathan , Hampton Cheri M. , Lewis David A. , Marko Michael , Freyberg Zachary 
Published: February 2023

AbstractCryo-electron microscopy (cryo-EM) enables the study of protein complexes, cytoskeletal elements, and organelles in three dimensions without the use of chemical fixation. Most cryo-EM studies focus on vitreously frozen individual cells separated from their native tissue contexts. This reliance on imaging of single cells is primarily due to technical challenges associated with preparing fresh tissue sections at a thinness sufficient for visualization via cryo-EM. Highly heterogenous and specialized tissues, such as brain, are especially affected by this limitation as the cellular, subcellular, and synaptic milieus can significantly vary across neuroanatomical locations. To address this limitation, we established new instrumentation and a workflow that consists of: 1) high-pressure freezing of fresh brain tissue; 2) tissue trimming followed by cryo-focused ion beam milling via the H-bar approach to generate ultrathin lamellae; and 3) cryo-EM imaging. Here, we apply this workflow to visualize the fine ultrastructural details of organelles, as well as cytoskeletal and synaptic elements that comprise the cortical neuropil within fresh, unfixed mouse brain tissue. Moreover, we present initial studies that apply principles of the above workflow to the analysis of postmortem human brain tissue. Overall, our work integrates the strengths of cryo-electron microscopy and tissue-based approaches to produce a generalizable workflow capable of visualizing subcellular structures within complex tissue environments.
Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryo-electron microscopy
Authors: Watkins Maxwell B. , Wang Haoyue , Burnim Audrey , Ando Nozomi 
Published: February 2023

AbstractCobalamin-dependent methionine synthase (MetH) catalyzes the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate (CH3-H4folate) using the unique chemistry of its cofactor. In doing so, MetH links the cycling ofS-adenosylmethionine with the folate cycle in one-carbon metabolism. Extensive biochemical and structural studies onEscherichia coliMetH have shown that this flexible, multi-domain enzyme adopts two major conformations to prevent a futile cycle of methionine production and consumption. However, as MetH is highly dynamic as well as both a photosensitive and oxygen-sensitive metalloenzyme, it poses special challenges for structural studies, and existing structures have necessarily come from a “divide and conquer” approach. In this study, we investigateE. coliMetH and a thermophilic homolog fromThermus filiformisusing small-angle X-ray scattering (SAXS), single-particle cryo-electron microscopy (cryo-EM), and extensive analysis of the AlphaFold2 database to present the first structural description of MetH in its entirety. Using SAXS, we describe a common resting-state conformation shared by both active and inactive oxidation states of MetH and the roles of CH3-H4folate and flavodoxin in initiating turnover and reactivation. By combining SAXS with a 3.6-Å cryo-EM structure of theT. filiformisMetH, we show that the resting-state conformation consists of a stable arrangement of the catalytic domains that is linked to a highly mobile reactivation domain. Finally, by combining AlphaFold2-guided sequence analysis and our experimental findings, we propose a general model for functional switching in MetH.
Life history and cancer in birds: clutch size predicts cancer
Authors: Kapsetaki Stefania E. , Compton Zachary , Dolan Jordyn , Harris Valerie K. , Rupp Shawn M. , Duke Elizabeth G. , Harrison Tara M. , Aksoy Selin , Giraudeau Mathieu , Vincze Orsolya , McGraw Kevin J. , Aktipis Athena , Tollis Marc , Boddy Amy M. , Maley Carlo C. 
Published: February 2023

AbstractCancer is a disease that affects nearly all multicellular life, including birds. However, little is known about what factors explain the variance in cancer prevalence among species. Litter size is positively correlated with cancer prevalence in managed species of mammals, and larger body size, but not incubation or nestling period, is linked to tumor prevalence in wild birds. Also, birds that produce more elaborate sexual traits are expected to have fewer resources for cancer defenses and thus higher cancer prevalence. In this study, we examined whether cancer prevalence is associated with a wide variety of life history traits (clutch size, incubation length, body mass, lifespan, and the extent of sexual dimorphism) across 108 species of managed birds in 25 different zoological facilities, sanctuaries, and veterinary clinics. We found that clutch size was positively correlated with cancer and neoplasia (both benign and malignant) prevalence, even after controlling for body mass. Cancer prevalence was not associated with incubation length, body mass, lifespan, or sexual dimorphism. The positive correlations of clutch size with cancer prevalence and neoplasia prevalence suggest that there may be life-history trade-offs between reproductive investment and somatic maintenance (in the form of cancer prevention mechanisms) in managed birds.
Insecticidal Efficacy of Selected Botanicals on three species of Adult Mosquitoes in Osogbo, Osun State, Nigeria
Authors: Ademodi P.K. , Busari L.O. , Iwalewa Z.O. , Fasasi K.A 
Published: February 2023

AbstractThe present study investigated the insecticidal potency of phytochemicals from three indigenous botanicals namelyMoringa oleifera(Drumstick tree),Vernonia amygdalina(Bitter leaf) andOcimum gratissimum(Scent leaf) against adult mosquitoes of theAnophelesspecies,Aedesspecies andCulexspecies cum their larval habitats.Collection of the mosquito larval was made after scouting and identifying their breeding sites using scoops, plastic containers, sieves etc. Larva collection was done in the wet season (April to October) while the collected larva were conveyed to the laboratory and reared until they emerged into adults. A bioassay comprising twenty five adult mosquitoes from each of the three adult mosquito species were exposed to the botanicals at three different concentrations (5g/10ml, 10g/10ml and 15g/10ml) to assess their insecticidal potency which was measured through their knockdown rate (kdr) and mortality rate. The kdr were recorded at intervals for an hour while the mortality rates were recorded after 24hours of exposure.A total of 400 mosquito larva were collected and five larval habitat encountered. The three botanicals showed insecticidal potency against the adult mosquito species. However,O. gratissimumhad the highest potency at 15g/10ml againstAnopheles(46%) andCulex(34%) species respectively (p □ 0.05).Aedes sppwas resistant to the botanicals which may be due to a resistance barrier mechanism inAedes sppthat the botanicals lack the ability to break.The botanicals could be adopted in the control of adult mosquitoes as they are biodegradable, eco-friendly and economical in contrast to synthetic insecticides with a view to consolidating global efforts on mosquito-borne diseases control and elimination with little or no human or environmental hazard.
Somatotopic organization among parallel sensory pathways that promote a grooming sequence inDrosophila
Authors: Eichler Katharina , Hampel Stefanie , Alejandro-García Adrián , Calle-Schuler Steven A. , Santana-Cruz Alexis , Kmecova Lucia , Blagburn Jonathan M. , Hoopfer Eric D. , Seeds Andrew M. 
Published: February 2023

AbstractMechanosensory neurons located across the body surface respond to tactile stimuli and elicit diverse behavioral responses, from relatively simple stimulus location-aimed movements to complex movement sequences. How mechanosensory neurons and their postsynaptic circuits influence such diverse behaviors remains unclear. We previously discovered thatDrosophilaperform a body location-prioritized grooming sequence when mechanosensory neurons at different locations on the head and body are simultaneously stimulated by dust (Hampel et al., 2017; Seeds et al., 2014). Here, we identify nearly all mechanosensory neurons on theDrosophilahead that individually elicit aimed grooming of specific head locations, while collectively eliciting a whole head grooming sequence. Different tracing methods were used to reconstruct the projections of these neurons from different locations on the head to their distinct arborizations in the brain. This provides the first synaptic resolution somatotopic map of a head, and defines the parallel-projecting mechanosensory pathways that elicit head grooming.
Spatial omics imaging of fresh-frozen tissue and routine FFPE histopathology on a single cancer needle core biopsy: freezing device and multimodal workflow
Authors: Rittel Miriam F. , Schmidt Stefan , Weis Cleo-Aron , Birgin Emrullah , van Marwick Björn , Rädle Matthias , Diehl Steffen J. , Rahbari Nuh , Marx Alexander , Hopf Carsten 
Published: February 2023

ABSTRACTComplex molecular alterations underlying cancer pathophysiology are intensely studied with omics methods using bulk tissue extracts. For spatially resolved tissue diagnostics using needle biopsy cores, however, histopathological analysis using stained FFPE tissue and immuno-histochemistry (IHC) of few marker proteins is currently the main clinical focus. Today, spatial omics imaging using MSI or IRI are emerging diagnostic technologies for identification and classification of various cancer types. However, to conserve tissue-specific metabolomic states, fast, reliable and precise methods for preparation of fresh-frozen (FF) tissue sections are crucial. Such methods are often incompatible with clinical practice, since spatial metabolomics and routine histopathology of needle biopsies currently require two biopsies for FF and FFPE sampling, respectively. Therefore, we developed a device and corresponding laboratory and computational workflows for multimodal spatial omics analysis of fresh-frozen, longitudinally sectioned needle biopsies to accompany standard FFPE histopathology on the same biopsy core. As proof-of-concept, we analyzed surgical human liver cancer specimen by IRI and MSI with precise co-registration and, following FFPE processing, by sequential clinical pathology analysis on the same biopsy core. This workflow allowed spatial comparison between different spectral profiles and alterations in tissue histology, as well as direct comparison to histological diagnosis without the need of an extra biopsy.SIMPLE SUMMARYRoutine clinical approaches for cancer diagnosis demand fast, cost-efficient, and reliable methods, and their implementation within clinical settings. Currently, histopathology is the golden standard for tissue-based clinical diagnosis. Recently, spatially resolved molecular profiling techniques like mass spectrometry imaging (MSI) or infrared spectroscopy imaging (IRI) have increasingly contributed to clinical research, e.g., by differentiation of cancer subtypes using molecular fingerprints. However, adoption of the corresponding workflows in clinical routine remains challenging, especially for fresh-frozen tissue specimen. Here, we present a novel device based on 3D-printing technology, which facilitates sample preparation of needle biopsies for correlated clinical tissue analysis. It enables combination of MSI and IRI on fresh-frozen clinical samples with histopathological examination of the same needle core after formalin-fixation and paraffin-embedding (FFPE). This device and workflow can pave the way for a more profound understanding of biomolecular processes in cancer and, thus, aid more accurate diagnosis.Abstract Figure
IN SITU IMAGING OF RETINAL CALCIUM DYNAMICS IN AWAKE ANIMALS
Authors: Wang Yixiang , Su Ashley , Jin Jialin , Barson Daniel , Crair Michael 
Published: February 2023

AbstractMammalian vision starts in the retina. The study of retinal circuitsin vivois essential for comprehending retinal neural dynamics under physiological conditions. While several transpupillary retina imaging techniques have been utilized in anesthetized animals, thein situimaging of retinal activity in awake animals has been more difficult to accomplish. These limits have frustrated crucial scientific inquiries, such as how visual processing in the retina is modulated by behavior. In this study, we present novel experimental approaches that stabilize the eye to accessin situretinal dynamics with optical techniques in awake mice. Our findings demonstrate that this method can be utilized to: 1) image neural activity in distinct cell types across multiple ages, 2) record meso-scale (e.g. spontaneous retinal waves) or cellular retinal dynamics, 3) study retina functional connectivityin vivo, and 4) pharmacologically manipulate retinal activity. We applied these novel approaches to demonstrate that retinal activity is strongly modulated by movement through H1R-dependent histaminergic transmission in vivo, even at the amacrine cell level. These methods are suitable to simultaneously record retinal and brain activity dynamics or to investigate retinal responses to patterned visual stimuli, making accessible fundamental questions about visual processing that have previously been very challenging to achieve.
Integrative analysis ofin vitrostrategies to induce human vascularized cerebral organoids using single-cell RNA sequencing data
Authors: Sato Yuya , Asahi Toru , Kataoka Kosuke 
Published: February 2023

AbstractCerebral organoids are three-dimensionalin vitrocultured brains that mimic the function and structure of the human brain. One of the major challenges for cerebral organoids is the lack of functional vasculature. Without perfusable vessels, oxygen and nutrient supplies may be insufficient for long-term culture, hindering the investigation of the neurovascular interactions. Recently, several strategies for the vascularization of human cerebral organoids have been reported. However, the generalizable trends and variability among different strategies are unclear due to the lack of a comprehensive characterization and comparison of these vascularization strategies. In this study, we aimed to explore the effect of different vascularization strategies on the nervous system and vasculature in human cerebral organoids. We integrated single-cell RNA sequencing data of multiple vascularized and vascular organoids and fetal brains from publicly available datasets and assessed the protocol-dependent and culture-day-dependent effects on the cell composition and transcriptomic profiles in neuronal and vascular cells. We revealed the similarities and uniqueness of multiple vascularization strategies and demonstrated the transcriptomic effects of vascular induction on neuronal and mesodermal-like cell populations. Moreover, our data suggested that the interaction between neurons and mesodermal-like cell populations is important for the cerebrovascular-specific profile of endothelial-like cells. This study highlights the current challenges to vascularization strategies in human cerebral organoids and offers a benchmark for the future fabrication of vascularized organoids.
Genomic, genetic and phylogenetic evidence for a new falcon species using chromosome-level genome assembly of the gyrfalcon and population genomics
Authors: Al-Ajli Farooq Omar , Formenti Giulio , Fedrigo Olivier , Tracey Alan , Sims Ying , Howe Kerstin , Al-Karkhi Ikdam M. , Althani Asmaa Ali , Jarvis Erich D. , Rahman Sadequr , Ayub Qasim 
Published: February 2023

AbstractThe taxonomic classification of a falcon population found in the Altai region in Asia has been heavily debated for two centuries and previous studies have been inconclusive, hindering a more informed conservation approach. Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 44 falcons from different species and populations, including “Altai” falcons, we analyzed their population structure, admixture patterns and demographic history. We find that the Altai falcons are genomically mosaic of saker and gyrfalcon ancestries, and carry distinct W- and mitochondrial-haplotypes that cluster with the lanner falcon. The Altai haplotype diverged 422,000 years ago from the ancestor of sakers and gyrfalcons, both of which, in turn, split 109,000 years ago. The Altai W chromosome includes coding variants that may influence important structural, behavioral and reproductive traits. These findings support the designation of Altai falcons as a distinct falcon species (Falco altaicus).
Temporal modification of H3K9/14ac and H3K4me3 histone marks mediates mechano-responsive gene expression during the accommodation process in poplar
Authors: Ghosh Ritesh , Roué Juliette , Franchel Jérôme , Paul Amit , Leblanc-Fournier Nathalie 
Published: February 2023

ABSTRACTPlants can attenuate their molecular response to repetitive mechanical stimulation as a function of their mechanical history. For instance, a single bending of stem is sufficient to attenuate the gene expression in poplar plants to the subsequent mechanical stimulation, and the state of desensitization can last for several days. The role of histone modifications in memory gene expression and modulating plant response to abiotic or biotic signals is well known. However, such information is still lacking to explain the attenuated expression pattern of mechano-responsive genes in plants under repetitive stimulation. Using poplar as a model plant in this study, we first measured the global level of H3K9/14ac and H3K4me3 marks in the bent stem. The result shows that a single mild bending of the stem for 6 seconds is sufficient to alter the global level of the H3K9/14ac mark in poplar, highlighting the fact that plants are extremely sensitive to mechanical signals. Next, we analyzed the temporal dynamics of these two active histone marks at attenuated (PtaZFP2, PtaXET6, andPtaACA13) and non-attenuated (PtaHRD) mechano-responsive loci during the desensitization and resensitization phases. Enrichment of H3K9/14ac and H3K4me3 in the regulatory region of attenuated genes correlates well with their transient expression pattern after the first bending. Moreover, the levels of H3K4me3 correlate well with their expression pattern after the second bending at desensitization (3 days after the first bending) as well as resensitization (5 days after the first bending) phases. On the other hand, H3K9/14ac status correlates only with their attenuated expression pattern at the desensitization phase. The expression efficiency of the attenuated genes was restored after the second bending in the histone deacetylase inhibitor-treated plants. While both histone modifications contribute to the expression of attenuated genes, mechanostimulated expression of the non-attenuatedPtaHRDgene seems to be H3K4me3 dependent.
Correlative super-resolution analysis of cardiac calcium sparks and their molecular origins in health and disease
Authors: Hurley Miriam E. , White Ed , Sheard Thomas M.D. , Steele Derek , Jayasinghe Izzy 
Published: February 2023

AbstractRapid release of calcium from internal stores via ryanodine receptors (RyRs) is one of the fastest types of cytoplasmic second messenger signalling in excitable cells. In the heart, rapid summation of the elementary events of calcium release, calcium sparks, determine the contraction of the myocardium. Recent advances in super-resolution microscopy methods have revealed complex clustering patterns of RyRs at single-channel resolution. Here, we have experimentally correlated sub-sarcolemmal spontaneous calcium sparks in rat right ventricular myocytes with the underlying nanoscale sub-sarcolemmal RyR patterns resolved with super-resolution DNA-PAINT microscopy. Local functional groupings and clustering patterns of RyR were sampled by the location and the two-dimensional area of each calcium spark to reveal a steep dependence of the integral of a calcium spark on the sum of the local RyRs. Visualisation of recurring spark sites showed evidence of repeated and triggered saltatory activation of multiple local RyR clusters. In similar myocytes taken from rats with induced right ventricular failure, RyR clusters themselves showed a dissipated morphology and fragmented (smaller) clusters. The failing myocytes featured greater heterogeneity in both the spark properties and the relationship between the integral of the calcium spark and the local ensemble of RyRs. Whilst fragmented (smaller) RyR clusters were rarely observed to directly underlying the larger sparks or the recurring spark sites, local interrogation of the channel-to-channel distances confirmed a clear link between the positions of each calcium spark and the tight non-random clustering of the local RyRs in both healthy and failing ventricles.
Specific guidelines for time and space of multisensory plasticity in the superior colliculus
Authors: Wang Linghong , Han Yaxin , Sun Zhe , Ouyang Biao , Dong Chao 
Published: February 2023

AbstractThe potential to combine facts from exceptional senses, and thereby facilitate detecting and localizing events, commonly develops regularly in cat superior colliculus (SC) neurons. Multisensory integration in SC neurons depends on the spatial and temporal relationships of cross-modal cues. Here, we reveal that the parallel process of short-term plasticity during adulthood that would adapt multisensory integration to reliable changes in environmental conditions. The short-term experience altered the temporal preferences of SC neurons, this short-term plasticity was limited to changes in cross-modal timing (a factor commonly induced by events at different distances from the receiver. Nonetheless the plasticity was no evident in response to changes in cross-modal spatial configuration.
CVD-associated SNPs with regulatory potential drive pathologic non-coding RNA expression
Authors: Zhu Chaonan , Baumgarten Nina , Wu Meiqian , Wang Yue , Das Arka Provo , Kaur Jaskiran , Ardakani Fatemeh Behjati , Duong Thanh Thuy , Pham Minh Duc , Duda Maria , Dimmeler Stefanie , Yuan Ting , Schulz Marcel H. , Krishnan Jaya 
Published: February 2023

AbstractBackgroundCardiovascular diseases (CVDs) are the leading cause of death worldwide. Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) appearing in non-coding genomic regions in CVDs. The SNPs may alter gene expression by modifying transcription factor (TF) binding sites and lead to functional consequences in cardiovascular traits or diseases. To understand the underlying molecular mechanisms, it is crucial to identify which variations are involved and how they affect TF binding.MethodsThe SNEEP (SNP exploration and analysis using epigenomics data) pipeline was used to identify regulatory SNPs, which alter the binding behavior of TFs and link GWAS SNPs to their potential target genes for six CVDs. The human induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs), monoculture cardiac organoids (MCOs) and self-organized cardiac organoids (SCOs) were used in the study. Gene expression, cardiomyocyte size and cardiac contractility were assessed.ResultsBy using our integrative computational pipeline, we identified 1905 regulatory SNPs in CVD GWAS data. These were associated with hundreds of genes, half of them non-coding RNAs (ncRNAs), suggesting novel CVD genes. We experimentally tested 40 CVD-associated non-coding RNAs, among them RP11-98F14.11, RPL23AP92, IGBP1P1, and CTD-2383I20.1, which were upregulated in hiPSC-CMs, MCOs and SCOs under hypoxic conditions. Further experiments showed that IGBP1P1 depletion rescued expression of hypertrophic marker genes, reduced hypoxia-induced cardiomyocyte size and improved hypoxia-reduced cardiac contractility in hiPSC-CMs and MCOs.ConclusionsIGBP1P1 is a novel ncRNA with key regulatory functions in modulating cardiomyocyte size and cardiac function in our disease models. Our data suggest ncRNA IGBP1P1 as a potential therapeutic target to improve cardiac function in CVDs.