bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extraction of bouton-like structures from neuropil calcium imaging data
Authors: Fukumasu Kazushi , Nose Akinao , Kohsaka Hiroshi 
Published: May 2021

AbstractThe neuropil, the plexus of axons and dendrites, plays a critical role in operating the circuit processing of the nervous system. Revealing the spatiotemporal activity pattern within the neuropil would clarify how the information flows throughout the nervous system. However, calcium imaging to examine the circuit dynamics has mainly focused on the soma population due to their discrete distribution. The development of a methodology to analyze the calcium imaging data of a densely packed neuropil would provide us with new insights into the circuit dynamics. Here, we propose a new method to decompose calcium imaging data of the neuropil into populations of bouton-like synaptic structures with a standard desktop computer. To extract bouton-like structures from calcium imaging data, we introduced a new type of modularity, a widely used quality measure in graph theory, and optimized the clustering configuration by a simulated annealing algorithm, which is established in statistical physics. To assess this method’s performance, we conducted calcium imaging of the neuropil of Drosophila larvae. Based on the obtained data, we established artificial neuropil imaging datasets. We applied the decomposition procedure to the artificial and experimental calcium imaging data and extracted individual bouton-like structures successfully. Based on the extracted spatiotemporal data, we analyzed the network structure of the central nervous system of fly larvae and found it was scale-free. These results demonstrate that neuropil calcium imaging and its decomposition could provide new insight into our understanding of neural processing.
Strategy for detecting off-target sites in genome-edited rice
Authors: Narushima Jumpei , Kimata Shinya , Shiwa Yuh , Gondo Takahiro , Akimoto Satoru , Soga Keisuke , Yoshiba Satoko , Nakamura Kosuke , Shibata Norihito , Kondo Kazunari 
Published: May 2021

ABSTRACTGenome-editing using the CRISPR-Cas9 system can substantially accelerate crop breeding. Because off-target editing is the main problem with this system, a reliable method for comprehensively detecting off-target sites is required for the editing of food crop genomes. However, a method that accurately predicts off-target sites has not been established. In this study, we performed a SITE-Seq analysis to predict potential off-target sites. SITE-Seq is an unbiased method applicable for the in vitro detection of double-strand breaks (DSBs). To analyze SITE-Seq data, we developed a novel Galaxy system, which can perform simple and reproducible analyses without a command line operation. We conducted a SITE-Seq analysis of a rice genome modified by OsFH15 gRNA-Cas9, and identified 41 DSB sites in the annotated regions. Amplicon-sequencing revealed mutations at one off-target site in the genome-edited rice. The presence of an uncommon protospacer adjacent motif (NTG PAM) likely makes this off-target site difficult to identify using in silico methods. Of the six tested programs, only CRISPRdirect predicted this off-target site, but it also predicted 6,080 off-target sites in total. These results suggest the SITE-Seq method presented herein can efficiently predict off-target sites and is useful for assessing the safety of genome-edited food.
Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle
Authors: Ham Daniel J. , Börsch Anastasiya , Chojnowska Kathrin , Lin Shuo , Leuchtmann Aurel B. , Ham Alexander S. , Thürkauf Marco , Delezie Julien , Furrer Regula , Burri Dominik , Sinnreich Michael , Handschin Christoph , Tintignac Lionel A. , Zavolan Mihaela , Mittal Nitish , Rüegg Markus A. 
Published: May 2021

AbstractAs global life expectancy continues to climb, maintaining skeletal muscle function is increasingly essential to ensure a good life quality for aging populations. Calorie restriction (CR) is the most potent and reproducible intervention to extend health and lifespan, but is largely unachievable in humans. Therefore, identification of “CR mimetics” has received much attention. CR targets nutrient-sensing pathways centering on mTORC1. The mTORC1 inhibitor, rapamycin, has been proposed as a potential CR mimetic and is proven to counteract age-related muscle loss. Therefore, we tested whether rapamycin acts via similar mechanisms as CR to slow muscle aging. Contrary to our expectation, long-term CR and rapamycin-treated geriatric mice display distinct skeletal muscle gene expression profiles despite both conferring benefits to aging skeletal muscle. Furthermore, CR improved muscle integrity in a mouse with nutrient-insensitive sustained muscle mTORC1 activity and rapamycin provided additive benefits to CR in aging mouse muscles. Therefore, RM and CR exert distinct, compounding effects in aging skeletal muscle, opening the possibility of parallel interventions to counteract muscle aging.
Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA barcoding and molecular phylogenetic reconstruction
Authors: Katoh Takehiro K. , Chen Ji-Min , Yang Jin-Hua , Zhang Guang , Wang Lu , Suwito Awit , Toda Masanori J. , Zhang Ya-Ping , Gao Jian-Jun 
Published: May 2021

AbstractThe genus Dichaetophora is currently comprised of 67 formally described species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. In the present study, we challenged to delimit species from a huge amount of samples of Dichaetophora and allied taxa (the genus Mulgravea and the subgenus Dudaica of Drosophila) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, which were tentatively classified into the species groups of Dichaetophora, Mulgravea and Dudaica based on the morphological diagnoses for these supraspecific taxa. Then, we selected representative specimen(s) for each morpho-species and subjected them to barcoding of COI (the cytochrome c oxidase subunit I gene) sequences. The applied ABGD (automatic barcode gap discovery) algorithm estimated a total of 222 MOTUs (molecular operational taxonomic units). Although most of the morpho-species were recognized as individual MOTUs, some others were divided into multiple MOTUs or combined into a single MOTU, suggesting the existence of cryptic sibling species, subspecies or intraspecific genetic varieties. Out of the 222 MOTUs, 88 representing the supraspecific taxa of Dichaetophora, Mulgravea and Dudaica were selected, along with 33 species from major genera and subgenera of Drosophila in the tribe Drosophilini, as in-group (four species from the tribe Colocasiomyini as out-group) for phylogenetic reconstruction. We analyzed a dataset of concatenated nucleotide sequences of 12 nuclear gene markers by the maximum likelihood and Bayesian inference methods. As a result, the three focal taxa (i.e., Dichaetophora, Mulgravea and Dudaica) formed a clade, which we called the “pan-Dichaetophora”. Within this large clade, the agbo, tenuicauda, sinensis and trilobita groups of Dichaetophora, Mulgravea and Dudaica were recovered as monophyletic groups, but Dichaetophora and its acutissima group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped MOTUs of Dichaetophora. Thus, the present study has uncovered some problems in the taxonomy of the pan-Dichaetophora. Solving such problems will be challenged in Part II of this serial work.
Network instability dynamics drive a transient bursting period in the developing hippocampus in vivo
Authors: Graf Jürgen , Rahmati Vahid , Majoros Myrtill , Witte Otto W. , Geis Christian , Kiebel Stefan J. , Holthoff Knut , Kirmse Knut 
Published: May 2021

AbstractSpontaneous correlated activity is a universal hallmark of immature neural circuits. However, the cellular dynamics and intrinsic mechanisms underlying network burstiness in the intact developing brain are largely unknown. Here, we use two-photon Ca2+ imaging to comprehensively map the developmental trajectories of spontaneous network activity in hippocampal area CA1 in vivo. We unexpectedly find that network burstiness peaks after the developmental emergence of effective synaptic inhibition in the second postnatal week. We demonstrate that the enhanced network burstiness reflects an increased functional coupling of individual neurons to local population activity. However, pairwise neuronal correlations are low, and network bursts (NBs) recruit CA1 pyramidal cells in a virtually random manner. Using a dynamic systems modeling approach, we reconcile these experimental findings and identify network bi-stability as a potential regime underlying network burstiness at this age. Our analyses reveal an important role of synaptic input characteristics and network instability dynamics for NB generation. Collectively, our data suggest a mechanism, whereby developing CA1 performs extensive input-discrimination learning prior to the onset of environmental exploration.
Resolving the molecular architecture of the photoreceptor active zone by MINFLUX nanoscopy
Authors: Grabner Chad P. , Jansen Isabelle , Neef Jakob , Weiss Tobias , Schmidt Roman , Riedel Dietmar , Wurm Christian A. , Moser Tobias 
Published: May 2021

AbstractCells assemble macromolecular complexes into scaffoldings that serve as substrates for catalytic processes. Years of molecular neurobiology indicate that neurotransmission depends on such optimization strategies, yet the molecular topography of the presynaptic Active Zone (AZ) where transmitter is released upon synaptic vesicle (SV) fusion remains to be visualized. Therefore, we implemented MINFLUX optical nanoscopy to resolve the AZ of rod photoreceptors. To facilitate MINFLUX nanoscopy of the AZ, we developed and verified an immobilization technique, we name Heat Assisted Rapid Dehydration (HARD). Here fresh retinal slices are directly stamped onto glass coverslips yielding a single layer of rod AZs. These AZs exhibited excellent labeling efficiency and minimal signal redundancy in the Z-direction. Our data indicate that the SV release site is a molecular complex of bassoon-Rab3-binding molecule 2 (RIM2)-ubMunc13-2-CAST. The complexes are serially duplicated longitudinally, and reflected in register along the axis of symmetry of the synaptic ribbon.One sentence summaryStructural motifs formed by active zone proteins at the photoreceptor synapse.
Single-cell Transcriptomic Profiling Unveils Cardiac Cell-type Specific Response to Maternal Hyperglycemia Underlying the Risk of Congenital Heart Defects
Authors: Manivannan Sathiyanarayanan , Mansfield Corrin , Zhang Xinmin , Kodigepalli Karthik. M. , Majumdar Uddalak , Garg Vidu , Basu Madhumita 
Published: May 2021

AbstractCongenital heart disease (CHD) is the most prevalent structural malformations of the heart affecting ∼1% of live births. To date, both damaging genetic variations and adverse environmental exposure such as maternal diabetes have been found to cause CHD. Clinical studies show ∼fivefold higher risk of CHD in the offspring of mothers with pregestational diabetes. Maternal pregestational diabetes affects the gene regulatory networks key to proper cardiac development in the fetus. However, the cell-type specificity of these gene regulatory responses to maternal diabetes and their association with the observed cardiac defects in the fetuses remains unknown. To uncover the transcriptional responses to maternal diabetes in the early embryonic heart, we used an established murine model of pregestational diabetes. In this model, we have previously demonstrated an increased incidence of CHD. Here, we show maternal hyperglycemia (matHG) elicits diverse cellular responses during heart development by single-cell RNA-sequencing in embryonic hearts exposed to control and matHG environment. Through differential gene-expression and pseudotime trajectory analyses of this data, we identified changes in lineage specifying transcription factors, predominantly affecting Isl1+ second heart field progenitors and Tnnt2+ cardiomyocytes with matHG. Using in vivo cell-lineage tracing studies, we confirmed that matHG exposure leads to impaired second heart field-derived cardiomyocyte differentiation. Finally, this work identifies matHG-mediated transcriptional determinants in cardiac cell lineages elevate CHD risk and show perturbations in Isl1-dependent gene-regulatory network (Isl1-GRN) affect cardiomyocyte differentiation. Functional analysis of this GRN in cardiac progenitor cells will provide further mechanistic insights into matHG-induced severity of CHD associated with diabetic pregnancies.
Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered tropical birds
Authors: Costantini Maria S. , Medeiros Matthew C.I. , Crampton Lisa H. , Reed Floyd A. 
Published: May 2021

AbstractThe gut microbiome of an animal has a strong influence on the health, fitness, and behavior of its host, and is thus a critical component of the animal itself. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawai‘i, several threats have caused widespread population declines of Hawaiian honeycreepers (subfamily Carduelinae). These threats, and the environmental changes that result, can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, no previous study has explored the natural patterns of the gut microbiome of a honeycreeper species in the wild. This project used amplicon-based sequencing of the 16S rRNA gene to characterize the gut microbiome of two critically endangered species of Hawaiian honeycreepers. The two species differed significantly in both alpha and beta diversity. Intraspecific variation of the gut microbiome among individual birds was a major factor. However, small but significant differences also exist between sampling location and sexes. This baseline knowledge will help inform management decisions for these honeycreeper species both in their native habitats and in captivity.
Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat
Authors: Zheng Zhi-Zhong , Hua Rong , Xu Guo-Qiang , Yang Hui , Shi Peng 
Published: May 2021

AbstractThe naked mole-rats (Heterocephalus glaber, NMRs) and the blind mole-rats (Spalax galili, BMRs) are representative subterranean rodents that evolved many extraordinary traits, including hypoxia tolerance, longevity and cancer resistance. Although a batch of candidate loci responsible for these intriguing traits have been uncovered by genomic studies, many of them are limited to functional modifications of intact genes and little is known about the contributions of other genetic makeups. Here, to address this issue, we focused on gene losses (unitary pseudogenes) and systematically analyzed gene losses in NMRs and BMRs, as well as their respective terrestrial relatives, guinea pigs and rats, in a genome-wide scale. 167, 139, 341 and 112 pseudogenes were identified in NMRs, BMRs, guinea pigs and rats, respectively. Functional enrichment analysis identified 4 shared and 2 species-specific enriched functional groups (EFGs) in subterranean lineages. The pseudogenes in these EFGs might be associated with either regressive (e.g. visual system) or adaptive (e.g. altered DNA damage response) traits. In addition, several pseudogenes including TNNI3K and PDE5A, might be associated with their specific cardiac features observed in subterranean linages. Furthermore, we observed 20 convergent gene losses in NMRs and BMRs. Given that the functional investigations of these genes are generally scarce, we provided functional evidence that independent loss of TRIM17 in NMRs and BMRs might be beneficial for neuronal survival under hypoxia, supporting the positive role of eliminating TRIM17 function in hypoxia adaptation. We also demonstrated that pseudogenes, together with positively selected genes, reinforced subterranean adaptations cooperatively. Overall, our study provides new insights into the molecular underpinnings of subterranean adaptations and highlights the importance of gene losses in mammalian evolution.
Molecular mechanisms of sperm motility are conserved in a basal metazoan
Authors: Speer Kelsey F. , Allen-Waller Luella , Novikov Dana R. , Barott Katie L. 
Published: May 2021

AbstractEfficient and targeted sperm motility is essential for animal reproductive success. Studies in mammals and echinoderms have uncovered a highly conserved signaling mechanism in which sperm motility is stimulated by pH-dependent activation of the cAMP-producing enzyme soluble adenylyl cyclase (sAC). However, the presence of this pathway in basal metazoans has, until now, been unexplored. Here we found that cytoplasmic alkalinization induced a rapid burst of cAMP signaling and the full activation of motility in sperm from the reef-building coral Montipora capitata. Coral sperm expressed sAC in the flagellum, midpiece, and acrosomal regions, indicating that this molecular pH sensor may play a role in regulating mitochondrial respiration and flagellar beating. In bilaterians, sAC is a central node of a broader pH-dependent signaling pathway that alters cellular behavior in response to changes to the extracellular environment. We present transcript-level evidence that a homologous pathway is present in coral sperm, including the Na+/H+ exchanger SLC9C1, protein kinase A, and the CatSper Ca2+ channel conserved even in mammalian sperm. Our discovery of this pathway in a basal metazoan species highlights the ancient origin of the pH-sAC-cAMP signaling node in sperm physiology and suggests that it may be present in many other marine invertebrate taxa for which sperm motility mechanisms remain unexplored. These results emphasize our need to better understand the role of pH-dependent signaling in marine reproductive success, particularly as worsening ocean acidification and warming due to climate change continue to impair the physiology of corals and other marine invertebrates.Statement of significanceReef-building corals are the keystone species of the world’s most biodiverse yet threatened marine ecosystems. Corals reproduce by broadcast spawning, making the ability of their sperm to swim through the water column essential for fertilization. However, little is known about the mechanisms that regulate coral sperm motility. Here we found that elevated intracellular pH promotes the production of the second messenger cAMP in coral sperm and triggers the onset of motility. This study reveals the deep conservation of a sperm activation pathway from humans to corals, presenting the first comprehensive examination of the molecular mechanisms regulating sperm motility in an ancestral animal. These results are critical for understanding the resilience of this sensitive life stage to a changing marine environment.
Astrocyte GluN2C NMDA receptors control basal synaptic strengths of hippocampal CA1 pyramidal neurons in thestratum radiatum
Authors: Chipman Peter H. , Fernandez Alejandra Pazo , Fung Chi Chung Alan , Tedoldi Angelo , Kawai Atsushi , Gautam Sunita Ghimire , Kurosawa Mizuki , Abe Manabu , Sakimura Kenji , Fukai Tomoki , Goda Yukiko 
Published: May 2021

SummaryExperience-dependent plasticity is a key feature of brain synapses for which neuronal N-Methyl-D-Aspartate receptors (NMDARs) play a major role, from developmental circuit refinement to learning and memory. Astrocytes also express NMDARs although their exact function has remained controversial. Here we identify a circuit function for GluN2C NMDAR, a subtype highly expressed in astrocytes, in layer-specific tuning of synaptic strengths in mouse hippocampal CA1 pyramidal neurons. Interfering with astrocyte NMDAR or GluN2C NMDAR activity reduces the range of presynaptic strength distribution specifically in thestratum radiatuminputs without an appreciable change in the mean presynaptic strength. Mathematical modeling shows that narrowing of the width of presynaptic release probability distribution compromises the expression of long-term synaptic plasticity. Our findings suggest a novel feedback signaling system that uses astrocyte GluN2C NMDARs to adjust basal synaptic weight distribution of Schaffer collateral inputs, which in turn impacts computations performed by the CA1 pyramidal neuron.
Synthetic antigen-presenting cells reveal the diversity and functional specialisation of extracellular vesicles composing the fourth signal of T cell immunological synapses
Authors: Céspedes Pablo F. , Jainarayanan Ashwin , Fernández-Messina Lola , Saliba David G. , Valvo Salvatore , Kvalvaag Audun , Chen Lina , Kurz Elke , Ganskow Charity , Colin-York Huw , Fritzsche Marco , Peng Yanchun , Dong Tao , Johnson Errin , Siller-Farfán Jesús A. , Dushek Omer , Sezgin Erdinc , Peacock Ben , Law Alice , Aubert Dimitri , Engledow Simon , Attar Moustafa , Hester Svenja , Fischer Roman , Sánchez-Madrid Francisco , Dustin Michael L. 
Published: May 2021

ABSTRACTThe T cell Immunological Synapse (IS) is a pivotal hub for the regulation of adaptive immunity by endowing the exchange of information between cells engaged in physical contacts. Beyond the integration of antigen (signal one), co-stimulation (signal two), and cytokines (signal three), the IS facilitates the delivery of T-cell effector assemblies including supramolecular attack particles (SMAPs) and extracellular vesicles (EVs). How these particulate outputs differ among T -cell subsets and how subcellular compartments and signals exchanged at the synapse contribute to their composition is not fully understood. Here we harnessed bead-supported lipid bilayers (BSLBs) as a tailorable and versatile technology for the study of synaptic particle biogenesis and composition in different T-cell subsets, including CART. These synthetic antigen-presenting cells (APCs) facilitated the characterisation of trans-synaptic vesicles (tSV) as a heterogeneous population of EVs comprising among others PM-derived synaptic ectosomes and CD63+exosomes. We harnessed BSLB to unveil the factors influencing the vesicular release of CD40L, as a model effector, identifying CD40 trans presentation, T-cell activation, ESCRT upregulation/recruitment, antigen density/potency, co-repression by PD-1 ligands, and its processing by ADAM10 as major determinants. Further, BSLB made possible the comparison of microRNA (miR) species associated with tSV and steadily released EVs. Altogether, our data provide evidence for a higher specialisation of tSV which are enriched not only in effector immune receptors but also in miR and RNA-binding proteins. Considering the molecular uniqueness and functional complexity of the tSV output, which is also accompanied by SMAPs, we propose their classification as signal four.Graphical abstractHighlightsBead Supported Lipid Bilayers (BSLB) reconstituting antigen-presenting cells support synapse assembly by T cells and the release of effector particles.BSLB facilitate the dissection of the cellular machineries and synapse composition shaping the released tSV.tSV and their steadily released counterparts have a different composition. TSV show a higher enrichment of effectors including immune receptors, miR, RNA- and other nucleic acid-binding proteins, than EVs.