bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stiffness of primordial germ cells is required for their extravasation in avian embryos
Authors: Saito Daisuke , Tadokoro Ryosuke , Nagasaka Arata , Yoshino Daisuke , Teramoto Takayuki , Mizumoto Kanta , Funamoto Kenichi , Kidokoro Hinako , Miyata Takaki , Tamura Koji , Takahashi Yoshiko 
Published: May 2022

AbstractDuring metastasis intravascularly circulating cancer cells undergo extravasation, which frequently takes place in vascular capillary beds 1–3. It remains poorly understood how the extravasation in the capillary beds is regulated. To address this question, chicken primordial germ cells (PGCs) serve as a powerful model since they circulate in blood stream and extravasate at a specific site of capillary bed near the forming gonad 4–6. The extravasation consists of two steps, the intravascular arrest of cells and their subsequent transmigration through the endothelial lining. We here demonstrate with live imaging at a single cell level in vivo that the arrest of PGCs is predominantly governed by occlusion at a narrow path in the capillary bed. In addition, this occlusion is enabled by a hightened stiffness of the PGCs, revealed by atomic force microscopy indentation analyses. The PGCs’ stiffness is regulated by actin polymerization: inhibition of the actin function causes not only a failure of PGC occlusion in the capillary bed, but also a failure of PGC colonization in the gonads at later stages. Following the occlusion, PGCs reset their stiffness to soften in order to squeeze through the endothelial lining as they transmigrate. The discovery of F-actin-mediated stiffness in pre-extravasating cells provides a model for understanding of dynamic mechanism by which other cells, including metastasizing cancer cells, extravasate in capillary beds.
Chemoenzymatic fluorescence labeling of intercellularly contacting cells using lipidated sortase A
Authors: Yamaguchi Satoshi , Ikeda Ryosuke , Umeda Yuki , Kosaka Takahiro , Yamahira Shinya , Okamoto Akimitsu 
Published: May 2022

AbstractMethods to label intercellular contact attract particular attention due to their potential in cell biological and medical applications through analysis of intercellular communications. In this study, a simple and versatile method for chemoenzymatically labeling the intercellularly contacting cell was developed by using a cell-surface anchoring reagent of poly(ethylene glycol)(PEG)-lipid conjugate. The surfaces of each cell in cell pairs of interest were efficiently decorated with sortase A (SrtA) and triglycine peptide that were lipidated with PEG-lipid, respectively. In the mixture of the two cell populations, the triglycine-modified cells were enzymatically labeled with a fluorescent labeling reagent by contacting with the SrtA-modified cells both on the substrate and in cell suspensions. Such selective labeling of the contacting cells was confirmed by confocal microscopy and flow cytometry. The results show a proof of principle that the present method is a promising tool for selective visualization and quantification of the intercellularly contacting cells among cell mixtures in cell-cell communication analysis.
Molecular architecture of the C. elegans centriole
Authors: Woglar Alexander , Pierron Marie , Schneider Fabian Zacharias , Jha Keshav , Busso Coralie , Gönczy Pierre 
Published: May 2022

AbstractUncovering organizing principles of organelle assembly is a fundamental pursuit in the life sciences. C. elegans was key in identifying evolutionary conserved components governing assembly of the centriole organelle. However, localizing these components with high precision has been hampered by the minute size of the worm centriole, thus impeding understanding of underlying assembly mechanisms. Here, we used Ultrastructure Expansion coupled with STimulated Emission Depletion microscopy (U-Ex-STED), as well as electron microscopy (EM) and tomography (ET), to decipher the molecular architecture of the worm centriole. Achieving an effective lateral resolution of ∼14 nm, we localize centriolar and PeriCentriolar Material (PCM) components in a comprehensive manner with utmost spatial precision. We uncovered that the procentriole assembles from a location on the centriole margin characterized by SPD-2 and ZYG-1 accumulation. Moreover, we found that SAS-6 and SAS-5 are present in the nascent procentriole, with SAS-4 and microtubules recruited thereafter. We registered U-Ex-STED and EM data using the radial array of microtubules, thus allowing us to map each centriolar and PCM protein to a specific ultrastructural compartment. Importantly, we discovered that SAS-6 and SAS-4 exhibit a radial symmetry that is offset relative to microtubules, leading to a chiral centriole ensemble. Furthermore, we establish that the centriole is surrounded by a region from which ribosomes are excluded and to which SAS-7 localizes. Overall, our work uncovers the molecular architecture of the C. elegans centriole in unprecedented detail and establishes a comprehensive framework for understanding mechanisms of organelle biogenesis and function.
Sampling biases obscure the early diversification of the largest living vertebrate group
Authors: Henderson Struan , Dunne Emma M. , Giles Sam 
Published: May 2022

AbstractExtant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet their spatiotemporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of potential biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends and apply richness estimation techniques to a recently-assembled occurrence database for Palaeozoic ray-finned fishes. We reconstruct patterns of local richness of Palaeozoic actinopterygians, alongside sampling standardised estimates of ‘global’ diversity. We identify substantial fossil record biases, such as geographic bias in the sampling of actinopterygian occurrences centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the abundance distributions of occurrences, reflecting past taxonomic practices and historical biases in sampling. Increasing sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the ‘global’ dataset may identify accurate local diversity trends.
The effect of sociality on competitive interactions among birds
Authors: Berberi Ilias , Miller Eliot T. , Dakin Roslyn 
Published: May 2022

ABSTRACTSociality can provide many benefits, including increased foraging success, reproductive opportunities, and defence against predation. How does sociality influence the dominance hierarchies of ecological competitors? Here, we address this question using a large citizen science dataset of competitive interactions among birds foraging at backyard feeders, representing a network of over 55,000 interactions among 68 common species. We first show that species differ in average group size (the number of conspecifics observed together) as a fundamental measure of sociality. When analyzing heterospecific competition, we find that sociality is inversely related to dominance. On average, a single individual from a solitary species is more likely to displace a size-matched opponent than a single individual from a social species. Yet, we find that social species gain an increase in their competitive advantage when in the presence of their conspecifics, which may occur as a result of dynamics within their groups. Finally, we show that more social species have relatively fewer dominance interactions with heterospecifics, and more with conspecifics. Overall, these results demonstrate that sociality can influence competition in ecological networks. More social species have decreased competitive ability as individuals, but they may gain competitive ability in groups.
MRI Guided Fresh Tissue Procurement in Radical Prostatectomy Specimens: An Evolutionary Paradigm
Authors: Freidlin Raiza Z , Garmendia Marcial A , Krynitsky Jonathan , Bastian Cody , Schultz Connor , Custer Julian , Young Sarah , Mehralivand Sherif , Merino Maria J , Valera Vladimir A , Pinto Peter , Turkbey Baris , Peter Choyke L , Pohida Thomas J 
Published: May 2022

AbstractPurposeThe aim of this work is to assess the feasibility of novel targeted methods for fresh tissue procurement that facilitate accurate identification of lesion location and tissue sample extraction in an excised prostate gland, while minimizing the tissue deformation or damage.Methods and ResultsProposed fresh tissue procurement methods are based on utilizing a custom 3D printed patient-specific prostate mold. In the semi-freehand method, the access cut is guided by a set of markers on the bottom of the mold that define the boundary of a lesion in two orthogonal directions. The procurement site is identified by palpation. In the guided cut with-locator card method the procurement sites are identified by a cutout in the locator cards inserted into the access cuts. The two approaches were utilized to procure >50 samples. In the biopsy needle method guiding channels were designed into the prostate mold to procure fresh tissue. This method was used 4 times. Finally, a mixed-reality biopsy needle method was developed for phantom testing.ConclusionsPreliminary results of fresh tissue procurement utilizing novel methods showed improve precision of obtaining cancerous fresh tissue for molecular and genomic cancer research compared to current methods which rely on surgical estimation of lesion location.
Deciphering the Impact of Genetic Variation on Human Polyadenylation
Authors: Linder Johannes , Kundaje Anshul , Seelig Georg 
Published: May 2022

AbstractGenetic variants that disrupt polyadenylation can cause or contribute to genetic disorders. Yet, due to the complex cis-regulation of polyadenylation, variant interpretation remains challenging. Here, we introduce a residual neural network model,APARENT2, that can infer 3’-cleavage and polyadenylation from DNA sequence more accurately than any previous model. This model generalizes to the case of alternative polyadenylation (APA) for a variable number of polyadenylation signals. We demonstrate APARENT2’s performance on several variant datasets, including functional reporter data and human 3’ aQTLs from GTEx. We apply neural network interpretation methods to gain insights into disrupted or protective higher-order features of polyadenylation. We fine-tune APARENT2 on human tissue-resolved transcriptomic data to elucidate tissue-specific variant effects. Finally, we perform in-silico saturation mutagenesis of all human polyadenylation signals and compare the predicted effects of >44 million variants against gnomAD. While loss-of-function variants were generally selected against, we also find specific clinical conditions linked to gain-of-function mutations. For example, using APARENT2’s predictions we detect an association between gain-of-function mutations in the 3’-end and Autism Spectrum Disorder.
Decoding The Nuclear Genome of The Human Pathogen Babesia duncani Shed Light on its Virulence, Drug Susceptibility and Evolution among Apicomplexa
Authors: Lonardi Stefano , Singh Pallavi , Liang Qihua , Vydyam Pratap , Khabirova Eleonora , Fang Tiffany , Gihaz Shalev , Thekkiniath Jose , Munshi Muhammad , Abel Steven , Batugedara Gayani , Gupta Mohit , Lu Xueqing Maggie , Lenz Todd , Chakravarty Sakshar , Cornillot Emmanuel , Hu Yangyang , Ma Wenxiu , Gonzalez Luis Miguel , Sánchez Sergio , Montero Estrella , Estrada Karel , Sánchez-Flores Alejandro , Harb Omar S. , Le Roch Karine G. , Ben Mamoun Choukri 
Published: May 2022

AbstractBabesia species are tick-transmitted apicomplexan pathogens and the causative agents of babesiosis, a malaria-like disease of major medical and veterinary importance. Of the different species of Babesia reported so far, Babesia duncani causes severe to lethal infection in patients. Despite the highly virulent nature of this parasite and the risk it may pose as an emerging pathogen, little is known about its biology, metabolic requirements, and pathogenesis. B. duncani is unique among apicomplexan parasites that infect red blood cells in that it can be continuously cultured in vitro in human erythrocytes but can also infect mice leading to fulminant babesiosis infection and death. Here we have taken advantage of the recent advances in the propagation of this parasite in vitro and in vivo to conduct detailed molecular, genomic and transcriptomic analyses and to gain insights into its biology. We report the assembly, 3D structure, and annotation of the nuclear genome of this parasite as well as its transcriptomic profile and an atlas of its metabolism during its intraerythrocytic life cycle. Detailed examination of the B. duncani genome and comparative genomic analyses identified new classes of candidate virulence factors, suitable antigens for diagnosis of active infection, and several attractive drug targets. Translational analyses and efficacy studies identified highly potent inhibitors of B. duncani thus enriching the pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.
Evolution of thermal performance curves: a meta-analysis of selection experiments
Authors: Malusare Sarthak P. , Zilio Giacomo , Fronhofer Emanuel A. 
Published: May 2022

AbstractTemperatures are increasing due to global changes, putting biodiversity at risk. Organisms are faced with a limited set of options to cope with this situation: adapt, disperse or die. We here focus on the first possibility, more specifically, on evolutionary adaptations to temperature. Ectotherms are usually characterized by a hump-shaped relationship between fitness and temperature, a non-linear reaction norm that is referred to as thermal performance curve (TPC). To understand and predict impacts of global change, we need to know whether and how such TPCs evolve.Therefore, we performed a systematic literature search and a statistical meta-analysis focusing on experimental evolution and artificial selection studies. This focus allows us to directly quantify relative fitness responses to temperature selection by calculating fitness differences between TPCs from ancestral and derived populations after thermal selection.Out of 7561 publications screened, we found 47 studies corresponding to our search criteria representing taxa across the tree of life, from bacteria, to plants and vertebrates. We show that, independently of species identity, the studies we found report a positive response to temperature selection. Considering entire TPC shapes, adaptation to higher temperatures traded off with fitness at lower temperatures, leading to niche shifts. Effects were generally stronger in unicellular organisms. By contrast, we do not find statistical support for the often discussed “Hotter is better” hypothesis.While our meta-analysis provides evidence for adaptive potential of TPCs across organisms, it also highlights that more experimental work is needed, especially for under-represented taxa, such as plants and non-model systems.
Corynebacterium matruchotii fitness enhancement of adjacent streptococci by multiple mechanisms
Authors: Almeida Eric , Puri Surendra , Elangovan Subhashini , Kim Jiyeon , Ramsey Matthew 
Published: May 2022

AbstractPolymicrobial biofilms are present in many environments particularly in the human oral cavity where they can prevent or facilitate the onset of disease. While recent advances have provided a clear picture of both the constituents and their biogeographical arrangement, it is still unclear what mechanisms of interaction occur between individual species in close proximity within these communities. In this study we investigated two mechanisms of interaction between the highly abundant supragingival plaque (SUPP) commensal Corynebacterium matruchotii and Streptococcus mitis which are directly adjacent in vivo. We discovered that C. matruchotii enhanced the fitness of streptococci dependent on its ability to detoxify streptococcal-produced hydrogen peroxide and its ability to oxidize lactate also produced by streptococci. We demonstrate that the fitness of adjacent streptococci was linked to that of C. matruchotii and that these mechanisms support the previously described “corncob” arrangement between these species but that this is favorable only in aerobic conditions. Further we utilized scanning electrochemical microscopy (SECM) to quantify lactate production and consumption between individual bacterial cells for the 1st time, revealing that lactate oxidation provides a fitness benefit to S. mitis and not pH mitigation. This study describes mechanistic interactions between two highly abundant human commensals that can explain their observed in vivo spatial arrangements and suggest a way by which they may help preserve a healthy oral bacterial community.
Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses
Authors: Uyehara Christopher M. , Leatham-Jensen Mary , McKay Daniel J. 
Published: May 2022

AbstractSteroid hormones perform diverse biological functions in developing and adult animals. However, the mechanistic basis for their tissue specificity remains unclear. InDrosophila, the ecdysone steroid hormone is essential for coordinating developmental timing across physically separated tissues. Ecdysone directly impacts genome function through its nuclear receptor, a heterodimer of the EcR and Usp proteins. Ligand binding to EcR triggers a transcriptional cascade, including activation of a set of primary response transcription factors. The hierarchical organization of this pathway has left the direct role of EcR in mediating ecdysone responses obscured. Here, we investigate the role of EcR in controlling tissue-specific ecdysone responses, focusing on two tissues that diverge in their response to rising ecdysone titers: the larval salivary gland, which undergoes programmed destruction, and the wing imaginal disc, which initiates metamorphosis. We find that EcR functions bimodally, with both gene repressive and activating functions, even at the same developmental stage. EcR DNA binding profiles are highly tissue-specific, and transgenic reporter analyses demonstrate that EcR plays a direct role in controlling enhancer activity. Finally, despite a strong correlation between tissue-specific EcR binding and tissue-specific open chromatin, we find that EcR does not control chromatin accessibility at genomic targets. We conclude that EcR contributes extensively to tissue-specific ecdysone responses. However, control over access to its binding sites is subordinated to other transcription factors.SignificanceHormones affect an incredible array of biological processes in both normal development and in disease. In insects, the steroid hormone ecdysone controls processes ranging from neuronal diversification to morphogenesis. Despite its importance, the mechanisms through which ecdysone generates wide-ranging yet tissue-specific responses remain incompletely understood. Like many hormones, ecdysone triggers a cascade of gene expression. At the top of this hierarchy is a nuclear receptor, EcR, which functions both as a hormone receptor and as a transcription factor. However, EcR is not the only transcription factor that functions in the ecdysone cascade; multiple other transcription factors are induced by ecdysone. As a result, the extent to which EcR plays a direct role in regulating tissue-specific responses to ecdysone remains unclear.
Gammaherpesvirus ncRNAs share conserved features of binding and virulence despite lack of sequence conservation
Authors: Knox Ashley N. , Medina Eva M. , Oldenburg Darby G. , Clambey Eric T. , van Dyk Linda F. 
Published: May 2022

ABSTRACTGammaherpesvirus (γHV) non-coding RNAs (ncRNAs) are integral modulators of viral infection. The γHVs engage RNA polymerase III (pol III)-dependent transcription of both host and viral ncRNAs, which contribute to viral establishment, gene expression, and pathogenesis. Viral ncRNAs, such as the EBV-encoded RNAs (EBERs), reportedly interact with multiple host RNA-binding proteins (RBPs) and contribute to inflammatory responses implicated in the development of malignancies. Here, we examined RBP interactions of the pol III-transcribed tRNA-miRNA encoded non-coding RNAs (TMERs) of murine γHV68, and the potential contributions of these and the related EBERs to in vivo pathogenesis. Using sequential enzymatic treatments, we found that several TMER1 forms retain a 5’-triphosphate, lending the possibility of recognition by the innate immune sensor RIG-I. We further examined the interactions of TMERs and EBERs with host RBPs, and found that multiple TMERs and EBERs interact with the La protein, though minimal interaction was detected with RIG-I during primary virus infection. Finally, we investigated the contributions of the TMERs and EBERs to disease in an immune-compromised mouse model with a series of viral recombinants. We found that expression of multiple single TMERs, or the EBERs expressed in place of the TMERs, was capable of restoring virulence to a viral recombinant lacking expression of all TMERs. Ultimately, these studies demonstrate that divergent pol III-transcribed γHV ncRNAs share interaction characteristics with two host RBPs and conserved contributions to disease, despite little to no significant sequence conservation. These findings support a model of convergent functions of the sequence-variable pol III-transcribed γHV ncRNAs.IMPORTANCEViruses manipulate the infected cell and host inflammatory responses through expression of coding and non-coding RNAs. The gammaherpesviruses are a subfamily of herpesviruses associated with chronic inflammatory diseases and malignancies, especially in immune-compromised individuals. Among these, the human Epstein-Barr virus and murine gammaherpesvirus 68 (γHV68) express highly abundant, RNA polymerase III-dependent, short non-coding RNAs. Whether these sequence-divergent ncRNAs have conserved functional properties is unknown. By using viral recombinants to allow direct comparison of these ncRNAs during primary infection, we find that the sequence-divergent ncRNAs of γHV68 and EBV share a conserved property to bind to the host RNA binding protein, La, and function interchangeably to facilitate in vivo pathogenesis. These studies demonstrate that abundant, RNA polymerase III-dependent viral ncRNAs can potently function to alter the host cell landscape and promote disease in a sequence-independent manner.