bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ant fungus garden acts as an external digestive system
Authors: Caraballo-Rodríguez Andrés Mauricio , Puckett Sara P. , Kyle Kathleen E. , Petras Daniel , da Silva Ricardo , Nothias Louis-Félix , Ernst Madeleine , van der Hooft Justin J.J. , Tripathi Anupriya , Wang Mingxun , Balunas Marcy J. , Klassen Jonathan L. , Dorrestein Pieter C. 
Published: November 2020

AbstractMost animals digest their food within their own bodies, but some do not. Many species of ants grow fungus gardens that pre-digest food as an essential step of the ants’ nutrient uptake. To better understand this digestion process, we generated a 3D molecular map of anAtta texanafungus garden, revealing chemical modifications mediated by the fungus garden as plant material passes through.
Dynamic tracing using ultra-bright labelling and multi-photon microscopy identifies endothelial uptake of poloxamer 188 coated poly(lactic-co-glycolic acid) nano-carriersin vivo
Authors: Khalin Igor , Severi Caterina , Heimburger Doriane , Wehn Antonia , Hellal Farida , Reisch Andreas , Klymchenko Andrey S. , Plesnila Nikolaus 
Published: November 2020

AbstractPoly(lactic-co-glycolic acid) (PLGA)-based drug formulations are approved for the use in humans, however, the potential of PLGA to design nanoparticles (NPs) and target the central nervous system remains to be exploited.The aim of the current study was design PLGA NPs, loading them with bulky fluorophores thereby increasing single particle fluorescence to a level visible byin vivomicroscopy, and investigate their brain biodistribution. We developed, highly fluorescent 70 nm PLGA NPs significantly brighter then quantum dots enabling their visualization by intravital real-time 2-photon microscopy. We found that PLGA NPs coated with pluronic F-68 (PF-68) had a substantially longer plasma half-life than uncoated NPs and were taken up by cerebro-vascular endothelial cells. High resolution confocal microscopy revealed that coated PLGA NPs were present in late endothelial endosomes of cerebral vessels within 1 hour after systemic injection and were more readily taken up by endothelial cells in peripheral organs.The current data suggest that PF-68 coated PLGA NPs are taken up by mouse cerebral and peripheral endothelial cellsin vivo. The combination of ultra-bright NPs andin vivoimaging may thus represent a promising approach to reduce the gap between development and clinical application of nanoparticle-based drug carriers.
Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation
Authors: Haase Robert , Jain Akanksha , Rigaud Stéphane , Vorkel Daniela , Rajasekhar Pradeep , Suckert Theresa , Lambert Talley J. , Nunez-Iglesias Juan , Poole Daniel P. , Tomancak Pavel , Myers Eugene W. 
Published: November 2020

AbstractModern life science relies heavily on fluorescent microscopy and subsequent quantitative bio-image analysis. The current rise of graphics processing units (GPUs) in the context of image processing enables batch processing large amounts of image data at unprecedented speed. In order to facilitate adoption of this technology in daily practice, we present an expert system based on the GPU-accelerated image processing library CLIJ: The CLIJ-assistant keeps track of which operations formed an image and suggests subsequent operations. It enables new ways of interaction with image data and image processing operations because its underlying GPU-accelerated image data flow graphs (IDFGs) allow changes to parameters of early processing steps and instantaneous visualization of their final results. Operations, their parameters and connections in the IDFG are stored at any point in time enabling the CLIJ-assistant to offer an undo-function for virtually unlimited rewinding parameter changes. Furthermore, to improve reproducibility of image data analysis workflows and interoperability with established image analysis platforms, the CLIJ-assistant can generate code from IDFGs in programming languages such as ImageJ Macro, Java, Jython, JavaScipt, Groovy, Python and C++ for later use in ImageJ, Fiji, Icy, Matlab, QuPath, Jupyter Notebooks and Napari. We demonstrate the CLIJ-assistant for processing image data in multiple scenarios to highlight its general applicability. The CLIJ-assistant is open source and available online:https://clij.github.io/assistant/
Human hepatocyte PNPLA3 148M exacerbates rapid non-alcoholic steatohepatitis development in chimeric mice
Authors: Kabbani Mohammad , Michailidis Eleftherios , Steensels Sandra , Fulmer Clifton G. , Luna Joseph M. , Le Pen Jérémie , Tardelli Matteo , Razooky Brandon , Ricardo-Lax Inna , Zou Chenhui , Zeck Briana , Stenzel Ansgar F. , Quirk Corrine , Foquet Lander , Ashbrook Alison W. , Schneider William M. , Belkaya Serkan , Lalazar Gadi , Liang Yupu , Pittman Meredith , Devisscher Lindsey , Suemizu Hiroshi , Theise Neil D. , Chiriboga Luis , Cohen David E. , Copenhaver Robert , Grompe Markus , Meuleman Philip , Ersoy Baran A. , Rice Charles M. , de Jong Ype P. 
Published: November 2020

ABSTRACTAdvanced non-alcoholic fatty liver disease (NAFLD) is a rapidly emerging global health problem associated with pre-disposing genetic polymorphisms, most strikingly an isoleucine to methionine substitution in patatin-like phospholipase domain-containing protein 3 (PNPLA3-I148M). Here, we study how human hepatocytes with PNPLA3 148I and 148M variants engrafted in the livers of chimeric mice respond to a hypercaloric Western-style diet. As early as 4 weeks, mice developed dyslipidemia, impaired glucose tolerance, and steatohepatitis selectively in the human graft, followed by pericellular fibrosis after 8 weeks of hypercaloric feeding. The PNPLA3 148M variant, either from a homozygous 148M human donor or overexpressed in a homozygous 148I donor background, caused widespread microvesicular steatosis and even more severe steatohepatitis. We conclude that PNPLA3 148M in human hepatocytes exacerbates NAFLD. These models will facilitate mechanistic studies into human genetic variants associated with advanced fatty liver diseases.
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Authors: Beghini Francesco , McIver Lauren J. , Blanco-Míguez Aitor , Dubois Leonard , Asnicar Francesco , Maharjan Sagun , Mailyan Ana , Thomas Andrew Maltez , Manghi Paolo , Valles-Colomer Mireia , Weingart George , Zhang Yancong , Zolfo Moreno , Huttenhower Curtis , Franzosa Eric A. , Segata Nicola 
Published: November 2020

AbstractCulture-independent analyses of microbial communities have advanced dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1,262 metagenomes) and IBD (1,635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4,077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbeRuminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.
Biological autoluminescence for assessing oxidative processes in yeast cell cultures
Authors: Vahalová Petra , Červinková Kateřina , Cifra Michal 
Published: November 2020

ABSTRACTNowadays, modern medicine is looking for new, more gentle, and more efficient diagnostic methods. A pathological state of an organism is often closely connected with increased amount of reactive oxygen species. They can react with biomolecules and subsequent reactions can lead to very low endogenous light emission (biological autoluminescence -BAL). This phenomenon can be potentially used as a non-invasive and low-operation-cost tool for monitoring oxidative stress during diseases. To contribute to the understanding of the parameters affecting BAL, we analyzed the BAL from yeastSaccharomyces cerevisiaeas a representative eukaryotic organism. The relationship between the BAL intensity and the amount of reactive oxygen species that originates as a result of the Fenton reaction as well as correlation between spontaneous BAL and selected physical and chemical parameters (pH, oxygen partial pressure, and cell concentration) during cell growth were established. Our results contribute to real-time non-invasive methodologies for monitoring oxidative processes in biomedicine and biotechnology.
ATP triggers macropinocytosis that internalizes and is regulated by PANX1
Authors: Boyce Andrew K.J. , van der Slagt Emma , Sanchez-Arias Juan C. , Swayne Leigh Anne 
Published: November 2020

ABSTRACTMacropinocytosis is an endocytic process that allows cells to respond to changes in their environment by internalizing nutrients and cell surface proteins, as well as modulating cell size. Here, we identify that adenosine triphosphate (ATP) triggers macropinocytosis in murine neuroblastoma cells, thereby internalizing the ATP release channel pannexin 1 (PANX1) while concurrently increasing cross-sectional cellular area. Amiloride, a potent inhibitor of macropinocytosis-associated GTPases, abolished ATP-induced PANX1 internalization and cell area expansion. Transient expression of the GTP-hydrolysis resistant GTPase ARF6 Q67L led to increased PANX1 internalization and increased cell area equivalent to levels seen with ATP stimulation. Mutation of an extracellular tryptophan (W74) in PANX1 abolished ATP-evoked cell area enlargement suggesting that PANX1 regulates this form of macropinocytosis. This novel role of PANX1 in macropinocytosis could be particularly important for disease states implicating PANX1, such as cancer, where ATP can act as a purinergic regulator of cell growth/metastasis and as a supplementary energy source following internalization.
Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains
Authors: Hung Po-Hsiang , Liao Chia-Wei , Ko Fu-Hsuan , Tsai Huai-Kuang , Leu Jun-Yi 
Published: November 2020

AbstractEnhanced phenotypic diversity increases the likelihood of a population surviving catastrophic conditions. It has been suggested that Hsp90, an essential molecular chaperone in eukaryotes, can suppress (i.e., buffer) or enhance (i.e., potentiate) the effects of genetic variation, enabling organisms to adjust their levels of phenotypic diversity in response to environmental cues. Many Hsp90-interacting proteins are involved in signaling transduction pathways and transcriptional regulation. However, it remains unclear if Hsp90-dependent differential gene expression is common in natural populations. By examining the gene expression profiles of five diverse yeast strains, we identified many genes exhibiting Hsp90-dependent strain-specific differential expression. We employed an analysis pipeline to identify transcription factors (TFs) potentially contributing to variable expression. We found that upon Hsp90 inhibition or heat stress, activities or abundances of Hsp90-dependent TFs varied among strains, resulting in differential strain-specific expression of their target genes, which consequently led to phenotypic diversity. We provide evidence that individual populations can readily display specific Hsp90-dependent gene expression, suggesting that the evolutionary impacts of Hsp90 are widespread in nature.HighlightsHsp90-dependent gene expression varies among different yeast strains.Hsp90 differentially influences transcriptional activity or protein abundances of transcription factors among yeast strains.Differential strain-specific gene expression is correlated with phenotypic variations upon Hsp90 inhibition.Hsp90-mediated strain-specific regulation manifests under environmental stress.
Anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) potency of Mefloquine as an entry inhibitor in vitro
Authors: Shionoya Kaho , Yamasaki Masako , Iwanami Shoya , Ito Yusuke , Fukushi Shuetsu , Ohashi Hirofumi , Saso Wakana , Tanaka Tomohiro , Aoki Shin , Kuramochi Kouji , Iwami Shingo , Takahashi Yoshimasa , Suzuki Tadaki , Muramatsu Masamichi , Takeda Makoto , Wakita Takaji , Watashi Koichi 
Published: November 2020

AbstractCoronavirus disease 2019 (COVID-19) has caused serious public health, social, and economic damage worldwide and effective drugs that prevent or cure COVID-19 are urgently needed. Approved drugs including Hydroxychloroquine, Remdesivir or Interferon were reported to inhibit the infection or propagation of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), however, their clinical efficacies have not yet been well demonstrated. To identify drugs with higher antiviral potency, we screened approved anti-parasitic/anti-protozoal drugs and identified an anti-malarial drug, Mefloquine, which showed the highest anti-SARS-CoV-2 activity among the tested compounds. Mefloquine showed higher anti-SARS-CoV-2 activity than Hydroxychloroquine in VeroE6/TMPRSS2 and Calu-3 cells, with IC50= 1.28 μM, IC90= 2.31 μM, and IC99= 4.39 μM in VeroE6/TMPRSS2 cells. Mefloquine inhibited viral entry after viral attachment to the target cell. Combined treatment with Mefloquine and Nelfinavir, a replication inhibitor, showed synergistic antiviral activity. Our mathematical modeling based on the drug concentration in the lung predicted that Mefloquine administration at a standard treatment dosage could decline viral dynamics in patients, reduce cumulative viral load to 7% and shorten the time until virus elimination by 6.1 days. These data cumulatively underscore Mefloquine as an anti-SARS-CoV-2 entry inhibitor.
Detecting flying insects using mega-nets and meta-barcoding
Authors: Svenningsen Cecilie S. , Frøslev Tobias Guldberg , Bladt Jesper , Pedersen Lene Bruhn , Larsen Jonas Colling , Ejrnæs Rasmus , Fløjgaard Camilla , Hansen Anders Johannes , Heilmann-Clausen Jacob , Dunn Robert R. , Tøttrup Anders P. 
Published: November 2020

AbstractInsect diversity and abundance are increasingly reported as being under pressure. However, monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect diversity across a large spatial scale within a limited time period.During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples were processed with a DNA metabarcoding protocol to estimate taxonomic composition, and the results were compared to known flying insect diversity and occurrence data.We detected 15 out of 19 flying insect orders present in Denmark. Diptera. Psocoptera and Thysanoptera were overrepresented, while Hymenoptera, Coleoptera, Lepidoptera, Trichoptera, Odonata, Neuroptera and Plecoptera were underrepresented, compared to Danish estimates. We detected 319 species not known for Denmark. Our results indicate that this method can assess the flying insect fauna to a wide extent, but may be, like other methods, biased towards certain insect orders. Furthermore, car net sampling and DNA metabarcoding can update species records for Denmark while preserving specimens for natural history collections.
A Unique Renal Architecture inTribolium castaneumInforms the Evolutionary Origins of Systemic Osmoregulation in Beetles
Authors: Koyama Takashi , Naseem Muhammad Tayyib , Kolosov Dennis , Vo Camilla Trang , Mahon Duncan , Jakobsen Amanda Sofie Seger , Jensen Rasmus Lycke , Denholm Barry , O’Donnell Michael , Halberg Kenneth Agerlin 
Published: November 2020

AbstractMaintaining internal salt and water balance in response to fluctuating external conditions is essential for animal survival. This is particularly true for insects as their high surface-to-volume ratio makes them highly susceptible to osmotic stress. However, the cellular and hormonal mechanisms that mediate the systemic control of osmotic homeostasis in beetles (Coleoptera), the largest group of insects, remain largely unidentified. Here, we demonstrate that eight neurons in the brain of the red flour beetleTribolium castaneumrespond to internal changes in osmolality by releasing diuretic hormone (DH) 37 and DH47 – homologues of vertebrate corticotropinreleasing factor (CRF) hormones – to control systemic water balance. Knockdown of the gene encoding the two hormones (Urinate, Urn8) reduces renal secretion and restricts organismal fluid loss, whereas injection of DH37 or DH47 reverses these phenotypes. We further identify a novel CRF-like receptor, Urinate Receptor (Urn8R), which is exclusively expressed in a unique secondary cell (SC) in the beetle renal organs, as underlying this response. Activation of Urn8R increases K+secretion specifically through SCs, creating a lumen-positive transepithelial potential that drives fluid secretion. Together, these data show that beetle renal organs operate by fundamentally different mechanism than those of other insects. Finally, we adopt a fluorescent labelling strategy to identify the evolutionary origin of this unusual renal architecture within the large Order of Coleoptera. Our work thus uncovers an important homeostatic program that is key to maintaining osmotic control in beetles, which evolved in parallel to the radiation of the higher beetle families.Significance StatementBeetles are the most diverse animal group on the planet. Their evolutionary success suggests unique physiological adaptations in overcoming water stress, yet the mechanisms underlying this ability are unknown. Here we use molecular genetic, electrophysiology and behavioral studies to show that a group of brain neurons responds to osmotic disturbances by releasing diuretic hormones that regulate salt and water balance. These hormones bind to their receptor exclusively localized to a unique secondary cell in the renal organs to modulate fluid secretion and organismal water loss. This renal architecture, common to all higher beetle families, is novel within the insects, and provides an important clue to the evolutionary success of the beetles in colonizing an astounding range of habitats on Earth.
Deciphering the genetic basis of wheat seminal root anatomy uncovers ancestral axial conductance alleles
Authors: Hendel Elisha , Bacher Harel , Oksenberg Adi , Walia Harkamal , Schwartz Nimrod , Peleg Zvi 
Published: November 2020

ABSTRACTRoot axial conductance which describes the ability of water to pass throw the xylem, contributes to the rate of water uptake from the soil throughout the whole plant lifecycle. In a rainfed wheat agro-system, grain-filling is typically occurring during declining water availability (i.e. terminal drought). Therefore, preserving soil water moisture during grain filling could serve as a key adaptive trait. We hypothesized that lower wheat root axial conductance can promote higher yields under terminal drought. A segregating population derived from a cross between durum wheat and its direct progenitor wild emmer wheat was used to underpin the genetic basis of seminal root architectural and functional traits. We detected 75 QTL associated with seminal roots morphological, anatomical, and physiological traits, with several hotspots harboring co-localized QTL. We further validated the axial conductance and central metaxylem QTL using wild introgression lines. Field-based characterization of genotypes with contrasting axial conductance suggested the contribution of low axial conductance as a mechanism for water conservation during grain filling and consequent increase in grain size and yield. Our findings underscore the potential of introducing wild alleles to reshape the wheat root system architecture for greater adaptability under changing climate.
LncRNA H19X is required for placenta development and angiogenesis through regulating a noncoding RNA regulatory network
Authors: Tongtong Li , Cao Yacong , Zou Yanting , Yang Ye , Ke Wang , Gelin Huang , Xiaoliang Li , Rui Zheng , Li Tang , Jiao Lv , Ming Yang , Jiabei He , Xiaohu Zhang , Shujun Bai , Qintong Li , Lang Qin , Miao Zhao Xiao , Wenming Xu 
Published: November 2020

AbstractH19X is a lncRNA specifically expressed in the placenta, whose expression is induced by hypoxia. H19X overexpression promoted trophoblast proliferation and invasion, while its knockdown or knockout inhibited trophoblast proliferation and invasion. Mechanistically, we demonstrated that reciprocal regulation exists with miR-424/miR-503 in the control of genes related to placental development and angiogenesis, including VEGF and VEGFR2. H19X inhibited ubiquitination of PIWIL1, thereby maintaining its stability and homeostatic expression of piRNAs. PIWIL1 overexpression rescued the defects of cell behavior caused by H19X KO. H19X deletion led to compromised HIF-1A/HIF-2A expression, which was correlated with the dysregulation of downstream genes under hypoxic conditions. CRISPR/Cas-9 knockout of H19X in animals led to defective placenta differentiation and compromised embryo development under hypoxic conditions. Western blotting showed reduced expression levels of PIWIL1 as well as angiogenesis marker genes, including VEGF and VEGFR2, in H19X KO mice. Thus, this study provides evidence of an unexpected link among lncRNA, miRNA, PIWIL1-related piRNA, and angiogenesis in placentation, the dysregulation of which leads to poor placental development and embryo loss under hypoxic conditions.
TRPV channel OCR-2 is distributed alongC. eleganschemosensory cilia by diffusion in a local interplay with intraflagellar transport
Authors: van Krugten Jaap , Danné Noémie , Peterman Erwin J.G. 
Published: November 2020

AbstractSensing and reacting to the environment is essential for survival and procreation of most organisms.Caenorhabditis eleganssenses soluble chemicals with transmembrane proteins (TPs) in the cilia of its chemosensory neurons. Development, maintenance and function of these cilia relies on intraflagellar transport (IFT), in which motor proteins transport cargo, including sensory TPs, back and forth along the ciliary axoneme. Here we use live fluorescence imaging to show that IFT machinery and the sensory TP OCR-2 reversibly redistribute along the cilium after exposure to repellant chemicals. To elucidate the underlying mechanisms, we performed single-molecule tracking experiments and found that OCR-2 distribution depends on an intricate interplay between IFT-driven transport, normal diffusion and subdiffusion that depends on the specific location in the cilium. These insights in the role of IFT on the dynamics of cellular signal transduction contribute to a deeper understanding of the regulation of sensory TPs and chemosensing.