bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perfluorononanoic acid impedes mouse oocyte maturation by inducing mitochondrial dysfunction and oxidative stress
Authors: Jiao Xiaofei , Liu Ning , Xu Yiding , Qiao Huanyu 
Published: July 2021

AbstractPerfluorononanoic acid (PFNA), a member of PFAS, is frequently detected in human blood and tissues, even in follicular fluid of women. The exposure of PFNA, but not PFOA and PFOS, is positively correlated with miscarriage and increased time to pregnancy. Toxicological studies indicated that PFNA exposure is associated with immunotoxicity, hepatotoxicity, developmental toxicity, and reproductive toxicity in animals. However, there is little information regarding the toxic effects of PFNA on oocyte maturation. In this study, we investigated the toxic effects of PFNA exposure on mouse oocyte maturation in vitro. Our results showed that 600 μM PFNA significantly inhibited germinal vesicle breakdown (GVBD) and polar body extrusion (PBE) in mouse oocytes. Our further study revealed that PFNA induced abnormal metaphase I (MI) spindle assembly, evidenced by malformed spindles and mislocalization of p-ERK1/2 in PFNA-treated oocytes. We also found that PFNA induced abnormal mitochondrial distribution and increased mitochondrial membrane potential. Consequently, PFNA increased reactive oxygen species (ROS) levels, leading to oxidative stress, DNA damage, and eventually early-stage apoptosis in oocytes. In addition, after 14 h culture, PFNA disrupted the formation of metaphase II (MII) spindle in most PFNA-treated oocytes with polar bodies. Collectively, our results indicate that PFNA interferes with oocyte maturation in vitro via disrupting spindle assembly, damaging mitochondrial functions, and inducing oxidative stress, DNA damage, and early-stage apoptosis.
β-Adrenergic Stimulation Synchronizes a Broad Spectrum of Action Potential Firing Rates of Cardiac Pacemaker Cells towards a Higher Population Average
Authors: Kim Mary S. , Monfredi Oliver , Maltseva Larissa A. , Lakatta Edward G. , Maltsev Victor A. 
Published: July 2021

AbstractThe heartbeat is initiated by pacemaker cells residing in the sinoatrial node (SAN). SAN cells generate spontaneous action potentials (APs), i.e. normal automaticity. The sympathetic nervous system increases heart rate commensurate with cardiac output demand via stimulation of SAN β-adrenergic receptors (βAR). While SAN cells reportedly represent a highly heterogeneous cell population, the current dogma is that in response to βAR stimulation all cells increase their spontaneous AP firing rate in a similar fashion. The aim of the present study was to investigate cell-to-cell variability in the responses of a large population of SAN cells. We measured βAR responses among 166 single SAN cells isolated from 33 guinea pig hearts. In contrast to the current dogma, the SAN cell responses to βAR stimulation substantially varied. In each cell, changes in AP cycle length highly correlated (R2=0.97) with the AP cycle length before βAR stimulation. While, as expected, on average the cells increased their pacemaker rate, greater responses were observed in cells with slower basal rates, and vice versa, cells with higher basal rates showed smaller responses, no responses, or even decreased their rate. Thus, βAR stimulation synchronizes the operation of the SAN cell population towards a higher average rate, rather than uniformly shifting the rate in each cell, creating a new paradigm of βAR-driven fight-or-flight response among individual pacemaker cells.
Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immuno-staining
Authors: Paramasivam Prasath , Stöter Martin , Corradi Eloina , Costa Irene Dalla , Höijer Andreas , Bartesaghi Stefano , Sabirsh Alan , Lindfors Lennart , Arteta Marianna Yanez , Nordberg Peter , Andersson Shalini , Baudet Marie-Laure , Bickle Marc , Zerial Marino 
Published: July 2021

AbstractDetection of nucleic acids within sub-cellular compartments is key to understanding their function. Determining the intracellular distribution of nucleic acids requires quantitative retention and estimation of their association with different organelles by immunofluorescence microscopy. This is important also for the delivery of nucleic acid therapeutics which depends on endocytic uptake and endosomal escape. However, the current methods fail to preserve the majority of exogenously delivered nucleic acids in the cytoplasm. To solve this problem, by monitoring Cy5-labeled mRNA delivered to primary human adipocytes via lipid nanoparticles (LNP), we optimized cell fixation, permeabilization and immuno-staining of a number of organelle markers, achieving quantitative retention of mRNA and allowing visualization of levels which escape detection using conventional procedures. Additionally, we demonstrated the protocol to be effective on exogenously delivered siRNA, miRNA, as well as endogenous miRNA. Our protocol is compatible with RNA probes of single molecule fluorescence in-situ hybridization (smFISH) and molecular beacon, thus demonstrating that it is broadly applicable to study a variety of nucleic acids.
Hurricane-induced population decrease in a Critically Endangered long-lived reptile
Authors: van den Burg Matthijs P. , Madden Hannah , van Wagensveld Timothy P. , Boman Erik 
Published: July 2021

ABSTRACTCatastrophic events, like hurricanes, bring lethal conditions that can have population-altering effects. The threatened Caribbean dry forest occurs in a region known for its high-intensity hurricane seasons and high species endemism, highlighting the necessity to better understand hurricane impacts as fragmentation and clearing of natural habitat continues. However, such studies remain rare, and for reptiles are mostly restricted toAnolis. Here we used single-season occupancy modeling to infer the impact of the intense 2017 Atlantic hurricane season on the critically endangered Lesser Antillean Iguana,Iguana delicatissima. We surveyed 30 transects across eight habitats on St. Eustatius during 2017-2019, which resulted in 344 individual surveys and 98 iguana observations. Analyses of abundance and site occupancy indicated both measures for 2018 and 2019 were strongly reduced compared to the pre-hurricane 2017 state. Iguanas at higher elevations were affected more profoundly, likely due to higher wind speeds, tree damage and extensive defoliation. Overall, our results indicate a decrease in population estimates (23.3-26.5%) and abundance (22-23.8%) for 2018 and 2019, and a 75% reduction in the number of opportunistic sightings of tagged iguanas between 2017-2018. As only small and isolatedI.delicatissimapopulations remain, our study further demonstrates their vulnerability to stochastic events. Considering the frequency and intensity of hurricanes are projected to increase, our results stress the urgent need for population-increasing conservation actions in order to secure the long-term survival ofI.delicatissimathroughout its range.
Molecular adaptation to folivory and the conservation implications for Madagascar’s lemurs
Authors: Guevara Elaine E. , Greene Lydia K. , Blanco Marina B. , Farmer Casey , Ranaivonasy Jeannin , Ratsirarson Joelisoa , Mahefarisoa Karine L. , Rajaonarivelo Tsiky , Rakotondrainibe Hajanirina H. , Junge Randall E. , Williams Cathy V. , Rambeloson Elodi , Rasoanaivo Hoby A. , Rahalinarivo Vololonirina , Andrianandrianina Laza H. , Clayton Jonathan B. , Rothman Ryan S. , Lawler Richard R. , Bradley Brenda J. , Yoder Anne D. 
Published: July 2021

AbstractFolivory evolved independently at least three times over the last 40 million years among Madagascar’s lemurs. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases of adaptation to folivory across species and lineages can provide insights into their differential physiology and potential to resist habitat change. We recently reported accelerated genetic change inRNASE1, a gene encoding an enzyme (RNase 1) involved in molecular adaptation in mammalian folivores, including various monkeys and sifakas (genusPropithecus; family Indriidae). Here, we sought to assess whether other lemurs, including phylogenetically and ecologically diverse folivores, might show parallel adaptive change inRNASE1that could underlie a capacity for efficient folivory. We characterizedRNASE1in 21 lemur species representing all five families and members of the three extant folivorous lineages: 1) bamboo lemurs (family Lemuridae), 2) sportive lemurs (family Lepilemuridae), and 3) indriids (family Indriidae). We found pervasive sequence change inRNASE1across all indriids, a dN/dSvalue > 3 in this clade, and evidence for shared change in isoelectric point, indicating altered enzymatic function. Sportive and bamboo lemurs, in contrast, showed more modest sequence change. The greater change in indriids may reflect a shared strategy emphasizing complex gut morphology and microbiota to facilitate folivory. This case study illustrates how genetic analysis may reveal differences in functional traits that could influence species’ ecology and, in turn, their resilience to habitat change. Moreover, our results support the contention that not all primate folivores are built the same and highlight the need to avoid generalizations about dietary guild in considering conservation outlook, particularly in lemurs where such diversity in folivory has probably led to extensive specialization via niche partitioning.
PECAn, a pipeline for image processing and statistical analysis of complex mosaic 3D tissues
Authors: Baumgartner Michael E. , Langton Paul F. , Mastrogiannopoulos Alex , Logeay Remi , Piddini Eugenia 
Published: July 2021

AbstractInvestigating organ biology requires sophisticated methodologies to induce genetically distinct clones within a tissue. Microscopic analysis of such samples produces information-rich 3D images. However, the 3D nature and spatial anisotropy of clones makes sample analysis challenging and slow and limits the amount of information that can be extracted manually. Here we have developed a pipeline for image processing and statistical data analysis which automatically extracts sophisticated parameters from complex multi-genotype 3D images. The pipeline includes data handling, machine-learning-enabled segmentation, multivariant statistical analysis, and graph generation. This enables researchers to run rigorous analyses on images and videos at scale and in a fraction of the time, without requiring programming skills. We demonstrate the power of this pipeline by applying it to the study of Minute cell competition. We find an unappreciated sexual dimorphism in Minute competition and identify, by statistical regression analysis, tissue parameters that model and predict competitive death.
Galleria mellonella as a novel eco-friendly in vivo approach for the assessment of the toxicity of medicinal plants
Authors: Arsene Mbarga Manga Joseph , Viktorovna Podoprigora Irina , Davares Anyutoulou Kitio Linda 
Published: July 2021

AbstractThe evaluation of medicinal plants’ toxicity is a prerequisite prior their usage. The vertebrate models used for this purpose are often the object of ethical consideration. Though invertebrate models including Galleria mellonella have shown their ability to be used to assess various products’ toxicity, to our knowledge, G. mellonella has never been exploited to determine the toxicity of medicinal plants. In this study, the toxicity of hydroalcoholic and aqueous extracts of seven (7) Cameroonian medicinal plants namely leaves of Cymbopogon citratus (DC.) Stapf, Moringa oleifera Lam and Vernonia amygdalina Delile; barks of Cinchona officinalis and Enantia chloranta Oliv; barks and seeds of Garcinia lucida Vesque and leaves and seeds of Azadirachta indica (Neem) were evaluated using the larval form of the Greater Wax Moth (Galleria mellonella). The median lethal doses (LD50), 90% lethal doses (LD90) and 100% lethal doses were successfully determined using the spline cubic survival curves and equations from the data obtained on the survival rate of G. mellonella 24h after the injection with the extracts. The LD50 values varied from 3.90 g/kg bw to >166.67 g/kg bw and the pattern of toxicity observed was in accordance with previous investigations on the plant materials concerned. The results obtained in this study suggest that G. mellonella can be used as a sensitive, reliable, and robust eco-friendly model to gauge the toxicity of medicinal plants. Thus, avoid the sacrifice of vertebrate models often used for this purpose to limit ethical concerns.
mDrop-seq: Massively parallel single-cell RNA-seq of Saccharomyces cerevisiae and Candida albicans
Authors: Dohn Ryan , Xie Bingqing , Back Rebecca , Selewa Alan , Eckart Heather , Rao Reeta Prusty , Basu A. 
Published: July 2021

AbstractAdvances in high-throughput single-cell mRNA sequencing (scRNA-seq) have been limited till date by technical challenges like tough cell walls and low RNA quantity that prevented transcriptomic profiling of microbial species at throughput. We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is used on two yeast species, Saccharomyces cerevisiae, a popular model organism and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA levels between them. As a proof of concept, we quantified expression differences in heat-shocked S. cerevisiae using mDrop-seq. We detected differential activation of stress response genes within a seemingly homogenous population of S. cerevisiae under heat-shock. We also applied mDrop-seq to C. albicans cells, a polymorphic and clinically relevant yeast species with thicker cell wall compared to S. cerevisiae. Single cell transcriptomes in 39,705 C. albicans cells was characterized using mDrop-seq under different conditions, including exposure to fluconazole, a common anti-fungal drug. We noted differential regulation in stress response and drug target pathways between C. albicans cells, changes in cell cycle patterns and marked increases in histone activity. These experiments are among the first high throughput single cell RNA-seq on different yeast species and demonstrate mDrop-seq as an affordable, easily implementable, and scalable technique that can quantify the variability in gene expression in different yeast species. We hope that mDrop-seq will lead to better understanding of genetic variation in yeasts in response to stimuli and find immediate applications in investigating drug resistance and infection outcome.
Human airway lineages derived from pluripotent stem cells reveal the epithelial responses to SARS-CoV-2 infection
Authors: Wang Ruobing , Hume Adam J. , Beermann Mary Lou , Simone-Roach Chantelle , Lindstrom-Vautrin Jonathan , Suer Jake Le , Huang Jessie , Olejnik Judith , Villacorta-Martin Carlos , Bullitt Esther , Hinds Anne , Ghaedi Mahboobe , Werder Rhiannon B. , Abo Kristine M. , Wilson Andrew A. , Mühlberger Elke , Kotton Darrell N. , Hawkins Finn J. 
Published: July 2021

SummaryThere is an urgent need to understand how SARS-CoV-2 infects the airway epithelium and in a subset of individuals leads to severe illness or death. Induced pluripotent stem cells (iPSCs) provide a near limitless supply of human cells that can be differentiated into cell types of interest, including airway epithelium, for disease modeling. We present a human iPSC-derived airway epithelial platform, composed of the major airway epithelial cell types, that is permissive to SARS-CoV-2 infection. Subsets of iPSC-airway cells express the SARS-CoV-2 entry factorsACE2andTMPRSS2.Multiciliated cells are the primary initial target of SARS-CoV-2 infection. Upon infection with SARS-CoV-2, iPSC-airway cells generate robust interferon and inflammatory responses and treatment with remdesivir or camostat methylate causes a decrease in viral propagation and entry, respectively. In conclusion, iPSC-derived airway cells provide a physiologically relevantin vitromodel system to interrogate the pathogenesis of, and develop treatment strategies for, COVID-19 pneumonia.Highlights and eTOC blurbSubsets of human iPSC-airway epithelial cells express SARS-Co-V entry factorsACE2andTMPRSS2.iPSC-airway cells are permissive to SARS-CoV-2 infection via multiciliated cells.SARS-CoV-2 infection of iPSC-airway leads to a robust interferon and inflammatory response.iPSC-airway is a physiologically relevant model to study SARS-CoV-2 infection.
Micronutrient supplements with iron promote disruptive protozoan and fungal communities in the developing infant gut
Authors: Popovic Ana , Bourdon Celine , Wang Pauline W. , Guttman David S. , Soofi Sajid , Bhutta Zulfiqar A. , Bandsma Robert H. J. , Parkinson John , Pell Lisa G. 
Published: July 2021

AbstractSupplementation with micronutrients, including vitamins, iron and zinc, is a key strategy to alleviate child malnutrition. However, adverse events resulting in gastrointestinal disorders, largely associated with iron, has resulted in ongoing debate over their administration. To better understand their impact on gut microbiota, we analysed the bacterial, protozoal, fungal and helminth communities of stool samples collected from children that had previously been recruited to a cluster randomized controlled trial of micronutrient supplementation in Pakistan. We show that while bacterial diversity was reduced in supplemented children, vitamins and iron may promote colonization with distinct protozoa and mucormycetes, whereas the addition of zinc ameliorates this effect. In addition to supplements, residence in a rural versus urban setting is an important determinant of eukaryotic composition. We suggest that the risks and benefits of such interventions may be mediated in part through eukaryotic communities, in a manner dependent on setting.
Zeb2 DNA-binding sites in neuroprogenitor cells reveal autoregulation and affirm neurodevelopmental defects, including in Mowat-Wilson Syndrome
Authors: Birkhoff Judith C. , Korporaal Anne L. , Brouwer Rutger W.W. , Nowosad Karol , Milazzo Claudia , Mouratidou Lidia , van den Hout Mirjam C.G.N. , van IJcken Wilfred F.J. , Huylebroeck Danny , Conidi Andrea 
Published: July 2021

AbstractPerturbation and mechanistic studies have shown that the DNA-binding transcription factor Zeb2 controls cell fate decision and differentiation and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs) Zeb2’s strong upregulation is necessary for the exit from primed pluripotency and for entering general and neural differentiation. We edited mouse ESCs to produce epitope-tagged Zeb2 from one of its two endogenous alleles. Using ChIP-sequencing, we mapped 2,432 DNA-binding sites of Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major site maps promoter-proximal to Zeb2 itself, and its homozygous removal demonstrates that Zeb2 autoregulation is necessary to elicit proper Zeb2-dependent effects in NPC differentiation. We then cross-referenced all Zeb2 DNA-binding sites with transcriptome data from Zeb2 perturbations in ESCs, ventral forebrain in mouse embryos, and adult neurogenesis from the mouse forebrain V-SVZ. While the characteristics of these neurodevelopmental systems differ, we still find interesting overlaps. This contributes to explaining neurodevelopmental disorders caused by ZEB2 deficiency, including Mowat-Wilson Syndrome.
CatSper mediates the chemotactic behavior and motility of the ascidian sperm
Authors: Kijima Taiga , Kurokawa Daisuke , Sasakura Yasunori , Ogasawara Michio , Aratake Satoe , Yoshida Kaoru , Yoshida Manabu 
Published: July 2021

AbstractSperm motility, including chemotactic behavior, is regulated by changes in the intracellular Ca2+ concentration. The cation channel of sperm (CatSper), plays an important role in the regulation of intracellular Ca2+ concentration. In mammals, CatSper is the only Ca2+ channel that functions in the sperm, and the mice that lack the genes for the subunits of CatSper, which make up the pore region of the Ca2+ channel, are infertile due to the inhibition of hyperactivation of the sperm. CatSper is also thought to be involved in chemotaxis in sea urchins. In contrast, in the ascidian, Ciona intestinalis, the sperm-activating and -attracting factor (SAAF) interacts with Ca2+/ATPase, which is a Ca2+-pump. Although the existence of CatSper genes has been reported, it is not clear whether CatSper is the specific Ca2+ channel that functions in the ascidian sperm. Therefore, in this study, we generated Catsper3 knockout (KO) animals that found that they were significantly less motile, with few motile sperms not exhibiting any chemotactic behavior. These results suggest that CatSper plays important roles in the spermatogenesis and basic motility mechanisms of sperms in both ascidians and mammals.