bluuebunny/crossref_metadata_2025 huggingface dataset:
Model-based Evaluation of Continued COVID-19 Risk at Long Term Care Facilities
Authors: Fosdick Bailey K. , Bayham Jude , Dilliott Jake , Ebel Gregory D. , Ehrhart Nicole
Published: July 2021

The COVID-19 pandemic severely impacted long-term care facilities resulting in the death of approximately 8% of residents nationwide. As COVID-19 case rates decline and state and county restrictions are lifted, facility managers, local and state health agencies are challenged with defining their own policies moving forward to appropriately mitigate disease transmission. The continued emergence of variants of concern has highlighted the need for a readily available tool that can be employed at the facility-level to determine best practices for mitigation and ensure resident and staff safety. To assist leadership in determining the impact of various infection surveillance and response strategies, we developed an agent-based model and an online dashboard interface that simulates COVID-19 infection within congregate care settings under various mitigation measures. In this paper, we demonstrate how this dashboard can be used to quantify the continued risk for COVID-19 infections within a facility given a designated testing schedule and vaccine requirements. Our results highlight the critical nature of testing cadence, test sensitivity and specificity, and the impact of removing asymptomatic infected individuals from the workplace. We also show that monthly surveillance testing at long-term care facilities is unlikely to successfully mitigate SARS-CoV-2 outbreaks in congregate care settings.

Disclosures

This work was supported by Colorado State University’s Center for Healthy Aging, the Center for Vector-Bourne Infectious Disease, the Office of the Vice President for Research, the College of Health and Human Sciences, the Collage of Natural Sciences, the College of Veterinary Medicine and Biomedical Sciences, and the Walter Scott Jr College of Engineering.
Examining Medical Student Volunteering During The COVID-19 Pandemic As A Prosocial Behavior During An Emergency
Authors: Byrne Matthew H V , Ashcroft James , Wan Jonathan C M , Alexander Laith , Harvey Anna , Schindler Nicholas , Brown Megan E L , Brassett Cecilia
Published: July 2021

Introduction

COVID-19 has caused major disruptions to healthcare, with voluntary opportunities offered to medical students to provide clinical support. We used the conceptual framework of prosocial behavior during an emergency – behaviors whose primary focus is benefiting others – to examine volunteering during COVID-19.

Methods

We conducted an in-depth, mixed-methods cross-sectional survey, from 2nd May to 15th June 2020, of medical students studying at UK medical schools. Data analysis was informed by Latane and Darley’s theory of prosocial behavior during an emergency and aimed to understand students’ decision-making processes.

Results

A total of 1145 medical students from 36 medical schools completed the survey. While 947 (82.7%) of students were willing to volunteer, only 391 (34.3%) had volunteered. The majority (92.7%) of students understood that they may be asked to volunteer; however, we found that deciding one’s responsibility to volunteer was mitigated by a complex interaction between the interests of others and self-interest. Further, concerns revolving around professional role boundaries influenced students’ decisions over whether they had the required skills and knowledge to volunteer. Deciding to volunteer depended not only on possession of necessary skills, but also seniority and identification with the nature of volunteering roles offered.

Conclusions

We propose two additional domains to Latane and Darley’s theory of prosocial behavior during an emergency that students consider before making their final decision to volunteer. These are ‘logistics’ – whether it is logistically feasible to volunteer – and ‘safety’ – whether it is safe to volunteer. This study highlights a number of modifiable barriers to prosocial behavior that medical students encounter and provides suggestions regarding how Latane and Darley’s theory of prosocial behavior can be operationalized within educational strategies to address these barriers. Optimizing the process of volunteering can aid healthcare provision and may facilitate a safer volunteering process for all.
Life on leaves : uncovering temporal dynamics in Arabidopsis’ leaf microbiota
Authors: Almario Juliana , Mahmudi Maryam , Kroll Samuel , Agler Mathew , Placzek Aleksandra , Mari Alfredo , Kemen Eric
Published: July 2021

Leaves are primarily responsible for the plant’s photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plant’s lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota ofArabidopsis thaliana, integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grownArabidopsiswere used to follow leaf bacterial, fungal and oomycete communities, throughout the plant’s growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plant’s growing season. Despite a high turnover in these communities, we identified 19 ‘core’ taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network ‘hubs’ and ‘hubs’ alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.
Considerations for furbearer trapping regulations to prevent grizzly bear toe amputation and injury
Authors: Lamb Clayton , Smit Laura , Mclellan Bruce , Vander Vennen Lucas M. , Proctor Michael
Published: July 2021

Science and adaptive management form crucial components of the North American model of wildlife management. Under this model, wildlife managers are encouraged to update management approaches when new information arises whose implementation could improve the stewardship and viability of wildlife populations and the well-being of animals. Here we detail a troubling observation of several grizzly bears with amputated toes in southeast British Columbia and assemble evidence to inform management strategies to remedy the issue. During the capture of 59 grizzly bears, we noticed that four individuals (~7%) had amputated toes on one of their front feet. The wounds were all healed and linear in nature. Further opportunistic record collection revealed that similar examples of amputated toes occurred beyond our study area, and that furbearer traps were frequently responsible for toe loss. We found evidence that seasonal overlap between the active season for grizzly bears and the fall trapping seasons for small furbearers with body grip traps and for wolves with foothold traps may explain the issue. Multiple options to reduce or eliminate this issue exist, but have varying degrees of expected efficacy and require differing levels of monitoring. The most certain approach to greatly reduce the issue is to delay the start of the marten trapping season until December 1, when most bears have denned, instead of opening the season on or prior to November 1, when more than 50% of bears are still active. Additionally, innovative solutions, such as narrowing trap entrances to exclude bear feet while still allowing entrance of target furbearers, have the potential to minimize accidental capture of bears, but the effectiveness of these approaches is unknown. Experimental evidence suggested that better anchoring traps was not a viable solution. Solutions that do not involve season changes will require monitoring of efficacy and compliance to ensure success.
Reduction of nucleolar NOC1 accumulates pre-rRNAs and induces Xrp1 affecting growth and resulting in cell competition in Drosophila
Authors: Destefanis Francesca , Manara Valeria , Santarelli Stefania , Zola Sheri , Brambilla Marco , Viola Giacomo , Maragno Paola , Signoria Ilaria , Viero Gabriella , Pasini Maria Enrica , Penzo Marianna , Bellosta Paola
Published: July 2021

NOC1 is a nucleolar protein necessary in yeast for both transport and maturation of ribosomal subunits. Here we show that in Drosophila NOC1 is essential for the correct animal development, and that its ubiquitous downregulation results in small larvae with reduced polysome abundance and decreased protein synthesis. NOC1 expression in multiple organs, such as the prothoracic gland and the fat body, is necessary for proper organ functioning. Reduction of NOC1 in clones from the imaginal discs results in small clones with cells that die by apoptosis, an event that is partially rescued using a M/+ background, suggesting that reduction of NOC1 causes the cells to acquire a loser state. This event was supported also by an increase in the transcription of Xrp1 and by activation of the pro-apoptotic eiger-JNK pathway, resulting in the upregulation of DILP8 as an indication of cellular damage. Here, we show that Drosophila NOC1 is important in the control of pre-rRNAs maturation and essential step in the regulation of ribosome biogenesis and its downregulation results in defects in growth and in cell competition, highlighting its novel function in this field.

summary statement

NOC1 is a nucleolar protein necessary for protein synthesis and ribosomal assembling. Its modulation induces cell competition and affects animal growth.
Light-dependent synthesis of a nucleotide second messenger controls bacterial motility
Authors: Xu Jun , Koizumi Nobuo , Morimoto Yusuke V. , Ozuru Ryo , Masuzawa Toshiyuki , Nakamura Shuichi
Published: July 2021

Nucleotide second messengers are universally crucial factors for the signal transduction of various organisms. In prokaryotes, cyclic nucleotide messengers are involved in the bacterial life cycle and function, such as virulence, biofilm formation, and others mainly via gene regulation. Here we show that the swimming motility of a soil bacterium is rapidly modulated by cyclic adenosine monophosphate (cAMP) synthesized upon light exposure. Analysis of a loss-of-photoresponsivity mutant obtained by transposon random mutagenesis determined the novel sensory gene, and its expression in Escherichia coli through codon optimization revealed the light-dependent synthesis of cAMP. GFP labeling showed the localization of the photoresponsive enzyme at the cell poles where flagellar motors reside. The present findings highlight the new role of cAMP that rapidly controls the flagella-dependent bacterial motility and the global distribution of the discovered photoactivated cyclase among diverse microbial species.
MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
Authors: Dueholm Morten Simonsen , Nierychlo Marta , Andersen Kasper Skytte , Rudkjøbing Vibeke , Knutsson Simon ,   the MiDAS Global Consortium, Albertsen Mads , Nielsen Per Halkjær
Published: July 2021

Biological wastewater treatment and an increased focus on resource recovery is fundamental for environmental protection, human health, and sustainable development. Microbial communities are responsible for these processes, but our knowledge of their diversity and function is still poor, partly due to the lack of good reference databases and comprehensive global studies. Here, we sequenced more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and used the sequences to construct MiDAS 4, a full-length amplicon sequence variant resolved 16S rRNA gene reference database with a comprehensive taxonomy from the domain to species-level for all references. Using a study-independent amplicon dataset from the Global Water Microbiome Consortium project (269 WWTPs), we showed that the MiDAS 4 database provides much better coverage for bacteria in WWTPs worldwide compared to commonly applied universal references databases, and greatly improved the rate of genus and species-level classification. Hence, MiDAS 4 provides a unifying taxonomy for the majority of prokaryotic diversity in WWTPs globally, which can be used for linking microbial identities with their functions across studies. Taking advantage of MiDAS 4, we carried out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting the V1-V3 and V4 region of the 16S rRNA gene. We found that the V1-V3 primers were generally best suited for this ecosystem, and revealed how environmental conditions and biogeography shape the activated sludge microbiota. We also identified process-critical taxa (core and conditionally rare or abundant taxa), encompassing 966 genera and 1530 species. These represented approximately 80% and 50% of the accumulated read abundance, respectively, and represent targets for further investigations. Finally, we showed that for well-studied functional guilds, such as nitrifiers or polyphosphate accumulating organisms, the same genera were prevalent worldwide, with only a few abundant species in each genus.
Automatic decomposition of electrophysiological data into distinct non-sinusoidal oscillatory modes
Authors: Fabus Marco S. , Quinn Andrew J. , Warnaby Catherine E. , Woolrich Mark W.
Published: July 2021

Neurophysiological signals are often noisy, non-sinusoidal, and consist of transient bursts. Extraction and analysis of oscillatory features (such as waveform shape and cross-frequency coupling) in such datasets remains difficult. This limits our understanding of brain dynamics and its functional importance. Here, we develop Iterated Masking Empirical Mode Decomposition (itEMD), a method designed to decompose noisy and transient single channel data into relevant oscillatory modes in a flexible, fully data-driven way without the need for manual tuning. Based on Empirical Mode Decomposition (EMD), this technique can extract single-cycle waveform dynamics through phase-aligned instantaneous frequency. We test our method by extensive simulations across different noise, sparsity, and non-sinusoidality conditions. We find itEMD significantly improves the separation of data into distinct non-sinusoidal oscillatory components and robustly reproduces waveform shape across a wide range of relevant parameters. We further validate the technique on multi-modal, multi-species electrophysiological data. Our itEMD extracts known rat hippocampal theta waveform asymmetry and identifies subject-specific human occipital alpha without any prior assumptions about the frequencies contained in the signal. Notably, it does so with significantly less mode mixing compared to existing EMD-based methods. By reducing mode mixing and simplifying interpretation of EMD results, itEMD will enable new analyses into functional roles of neural signals in behaviour and disease.

New & Noteworthy

We introduce a novel, data-driven method to identify oscillations in neural recordings. This approach is based on Empirical Mode Decomposition and reduces mixing of components, one of its main problems. The technique is validated and compared with existing methods using simulations and real data. We show our method better extracts oscillations and their properties in highly noisy and non-sinusoidal datasets.

Running Head

Decomposition of data into non-sinusoidal oscillatory modes
MONI: A Pangenomics Index for Finding MEMs
Authors: Rossi Massimiliano , Oliva Marco , Langmead Ben , Gagie Travis , Boucher Christina
Published: July 2021

Recently, Gagie et al. proposed a version of the FM-index, called the r-index, that can store thousands of human genomes on a commodity computer. Then Kuhnle et al. showed how to build the r-index efficiently via a technique called prefix-free parsing (PFP) and demonstrated its effectiveness for exact pattern matching. Exact pattern matching can be leveraged to support approximate pattern matching but the r-index itself cannot support efficiently popular and important queries such as finding maximal exact matches (MEMs). To address this shortcoming, Bannai et al. introduced the concept of thresholds, and showed that storing them together with the r-index enables efficient MEM finding — but they did not say how to find those thresholds. We present a novel algorithm that applies PFP to build the r-index and find the thresholds simultaneously and in linear time and space with respect to the size of the prefix-free parse. Our implementation called MONI can rapidly find MEMs between reads and large sequence collections of highly repetitive sequences. Compared to other read aligners – PuffAligner, Bowtie2, BWA-MEM, and CHIC – MONI used 2–11 times less memory and was 2–32 times faster for index construction. Moreover, MONI was less than one thousandth the size of competing indexes for large collections of human chromosomes. Thus, MONI represents a major advance in our ability to perform MEM finding against very large collections of related references.

Availability

MONI is publicly available at https://github.com/maxrossi91/moni.
Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN, and the Neighbouring East Asian Countries: Features, Challenges, and Achievements
Authors: Cahyani Inswasti , Putro Eko W. , Ridwanuloh Asep M. , Wibowo Satrio H.B. , Hariyatun Hariyatun , Syahputra Gita , Akbariani Gilang , Utomo Ahmad R. , Ilyas Mohammad , Loose Matthew W. , Kusharyoto Wien ,   Indonesian SARS-CoV-2 Genomics Surveillance Network, Susanti Susanti
Published: July 2021

A year after the World Health Organisation (WHO) declared COVID-19 as a pandemic, much has been learned regarding SARS-CoV-2 epidemiology, vaccine production, and disease treatment. Whole-genome sequencing (WGS) has played a significant role in contributing to our understanding of the epidemiology and biology of this virus. In this paper, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asia and the impact of technological development, access to resources, and demography of individual countries on its uptake. Using Oxford Nanopore Technology (ONT), Nottingham-Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative has facilitated collaboration between the University of Nottingham and a team in Research Centre for Biotechnology, Indonesian Institute of Sciences (Lembaga Ilmu Pengetahuan Indonesia/LIPI) to carry out a small number of SARS-CoV-2 WGS in Indonesia. The ONT offers sequencing advantages that fit within the Indonesian context. Analyses of SARS-CoV-2 genomes deposited on GISAID from Southeast and East Asian countries reveal the importance of collecting clinical and demographic metadata and the importance of open access and data sharing. Lineage and phylogenetic analyses per 1 June 2021 found that: 1) B.1.466.2 variants were the most predominant in Indonesia, with mutations in the spike protein including D614G at 100%, N439K at 99.1%, and P681R at 69.7% frequency, 2) The variants of concern (VoCs) B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta) were first detected in Indonesia in January 2021, 3) B.1.470 was first detected in Indonesia and spread to the neighbouring regions, and 4) The highest rate of virus transmissions between Indonesia and the rest of the world appears to be through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia.
Downregulation of WT1 transcription factor gene expression is required to promote myocardial fate
Authors: Marques Ines J. , Ernst Alexander , Arora Prateek , Vianin Andrej , Hetke Tanja , Sanz-Morejón Andrés , Naumann Uta , Odriozola Adolfo , Langa Xavier , Andrés-Delgado Laura , Haberthür David , Zuber Benoît , Torroja Carlos , Hlushchuk Ruslan , Osterwalder Marco , Simões Filipa , Englert Christoph , Mercader Nadia
Published: July 2021

During cardiac development, cells from the precardiac mesoderm fuse to form the primordial heart tube, which then grows by addition of further progenitors to the venous and arterial poles. In the zebrafish, wilms tumor 1 transcription factor a (wt1a) and b (wt1b) are expressed in the pericardial mesoderm at the venous pole of the forming heart tube. The pericardial mesoderm forms a single layered mesothelial sheet that contributes to further the growth of the myocardium, and forms the proepicardium. Proepicardial cells are subsequently transferred to the myocardial surface and give rise to the epicardium, the outer layer covering the myocardium in the adult heart. wt1a/b expression is downregulated during the transition from pericardium to myocardium, but remains high in proepicardial cells. Here we show that sustained wt1 expression impaired cardiomyocyte maturation including sarcomere assembly, ultimately affecting heart morphology and cardiac function. ATAC-seq data analysis of cardiomyocytes overexpressing wt1 revealed that chromatin regions associated with myocardial differentiation genes remain closed upon wt1b overexpression in cardiomyocytes, suggesting that wt1 represses a myocardial differentiation program. Indeed, a subset of wt1a/b-expressing cardiomyocytes changed their cell adhesion properties, delaminated from the myocardial epithelium, and upregulated the expression of epicardial genes, as confirmed by in vivo imaging. Thus, we conclude that wt1 acts as a break for cardiomyocyte differentiation by repressing chromatin opening at specific genomic loci and that sustained ectopic expression of wt1 in cardiomyocytes can lead to their transformation into epicardial cells.
TAF8 regions important for TFIID lobe B assembly, or for TAF2 interactions, are required for embryonic stem cell survival
Authors: Scheer Elisabeth , Luo Jie , Ruffenach Frank , Garnier Jean-Marie , Kolb-Cheynel Isabelle , Gupta Kapil , Berger Imre , Ranish Jeff , Tora László
Published: July 2021

The human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. TFIID is composed of three lobes, named A, B and C. Structural studies showed that TAF8 forms a histone fold pair with TAF10 in lobe B and participates in connecting lobe B to lobe C. In the present study, we have investigated the requirement of the different regions of TAF8 for in vitro TFIID assembly, and the importance of certain TAF8 regions for mouse embryonic stem cell (ESC) viability. We have identified a TAF8 region, different from the histone fold domain of TAF8, important for assembling with the 5TAF core complex in lobe B, and four regions of TAF8 each individually required for interacting with TAF2 in lobe C. Moreover, we show that the 5TAF coreinteracting TAF8 domain, and the proline rich domain of TAF8 that interacts with TAF2, are both required for mouse embryonic stem cell survival. Thus, our study demonstrates that distinct TAF8 regions involved in connecting lobe B to lobe C are crucial for TFIID function and consequent ESC survival.
Constitutive gene expression differs in three brain regions important for cognition in neophobic and non-neophobic house sparrows (Passer domesticus)
Authors: Lattin Christine R. , Kelly Tosha R. , Kelly Morgan W. , Johnson Kevin M.
Published: July 2021

Neophobia (aversion to new objects, food, and environments) is a personality trait that affects the ability of wildlife to adapt to new challenges and opportunities. Despite the ubiquity and importance of this trait, the molecular mechanisms underlying repeatable individual differences in neophobia in wild animals are poorly understood. We evaluated wild-caught house sparrows (Passer domesticus) for neophobia in the lab using novel object tests. We then selected the most and least neophobic individuals (n=3 of each) and extracted RNA from four brain regions involved in learning, memory, threat perception, and executive function: striatum, dorsomedial hippocampus, medial ventral arcopallium, and caudolateral nidopallium (NCL). Our analysis of differentially expressed genes (DEGs) used 11,889 gene regions annotated in the house sparrow reference genome for which we had an average of 25.7 million mapped reads/sample. PERMANOVA identified significant effects of brain region, phenotype (neophobic vs. non-neophobic), and a brain region by phenotype interaction. Comparing neophobic and non-neophobic birds revealed constitutive differences in DEGs in three of the four brain regions examined: hippocampus (12% of the transcriptome significantly differentially expressed), striatum (4%) and NCL (3%). DEGs included important known neuroendocrine mediators of learning, memory, executive function, and anxiety behavior, including serotonin receptor 5A, dopamine receptors 1, 2 and 5 (downregulated in neophobic birds), and estrogen receptor beta (upregulated in neophobic birds). These results suggest that some of the behavioral differences between phenotypes may be due to underlying gene expression differences in the brain. The large number of DEGs in neophobic and non-neophobic birds also implies that there are major differences in neural function between the two phenotypes that could affect a wide variety of behavioral traits beyond neophobia.
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

Perfluorononanoic 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

The 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

Detection 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

Catastrophic 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

Folivory 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

Investigating 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

The 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

Advances 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

There 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 blurb

Subsets 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

Supplementation 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

Perturbation 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

Sperm 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.