bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterogeneity in the response of different subtypes ofDrosophila melanogasterenteroendocrine cells to viral infections
Authors: Silva João M. F. , Nagata Tatsuya , Melo Fernando L. , Elena Santiago F.
Published: July 2020

Single cell RNA sequencing (scRNA-seq) offers the possibility to monitor both host and pathogens transcriptomes at the cellular level. Here, public scRNA-seq data fromDrosophila melanogasterhave been used to compare the differences in replication strategy and cellular response between two viruses, Thika virus (TV) andD. melanogasterNora virus (DMelNV) in enteroendocrine cells (EEs). TV and DMelNV exhibited different patterns of replication and for TV, accumulation varied according to cell subtype. Cells infected with TV underwent down-regulation of genes that represent bottlenecks in the fruit fly interactome, while cells infected with DMelNV went through a down-expression of translation-related genes that represent both hubs and bottlenecks in the host interactome. In contrast, flies infected with DMelNV show only a systemic level down-regulation of bottleneck genes. Here, we use scRNA-seq to highlight the differences and commonalities between cellular response to TV and DMelNV and between cellular and systemic response to DMelNV.
Identification of differentially expressed genes in the longissimus dorsi muscle of Luchuan and Duroc pigs by transcriptome sequencing
Authors: Pan Pengcheng , Qin Zhaoxian , Xie Wan , Jiao Di , Chen Baojian , Guan Zhihui , Xie Bingkun
Published: July 2020

The Duroc pig originated in the United States and is a typical lean meat pig. The breed grows fast and the body size is large, but the meat quality is poor. The Luchuan pig is one of the eight local excellent breeds in China; it has tender meat but a small size. To study the factors that determine growth, we selected the longissimus dorsi muscle of Luchuan and Duroc pigs for transcriptome sequencing. The results of transcriptome showed that 3682 genes were differentially expressed (DEGs) in the longissimus dorsi muscle of Duroc and Luchuan pigs. We screened out forty genes related to muscle development and selected the Myosin light chain-2 (MYL2) gene to perform preliminary research. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most of the forty gene were mainly involved in the Akt/FoxO signaling pathway, Fatty acid metabolism, Arachidonic acid metabolism and Glycine, serine and threonine metabolism. Such pathways contributed to skeletal muscle growth, fatty acid metabolism and intramuscular fat deposition. These results provide insight into the mechanisms underlying the formation of skeletal muscle and provide candidate genes to improve growth traits and meat quality traits, as well as contribute to improving the growth and development traits of pigs through molecular breeding.
Association of the invasiveHaemaphysalis longicornistick with vertebrate hosts, other native tick vectors, and tick-borne pathogens in New York City
Authors: Tufts Danielle M. , Goodman Laura B. , Benedict Meghan C. , Davis April D. , VanAcker Meredith C. , Diuk-Wasser Maria
Published: July 2020

Haemaphysalis longicornis, the Asian longhorned tick, is an invasive ixodid tick that has rapidly spread across the northeastern and southeastern regions of the United States since first reported in 2017. The emergence ofH. longicornispresents a potential threat for livestock, wildlife, and human health as the host associations and vector potential of this invasive pest in the United States are poorly understood. Previous field data from the United States has shown thatH. longicorniswas not associated with natural populations of small mammals or birds, but they show a preference for medium sized mammals in laboratory experiments. Therefore, medium and large sized mammals were sampled on Staten Island, New York to determineH. longicornishost associations and vector potential for a range of human and veterinary pathogens. A total of 97 hosts were sampled and five species of tick (Amblyomma americanum, Dermacentor variabilis, H. longicornis, Ixodes scapularis, Ixodes cookei) were found feeding concurrently on these hosts.Haemaphysalis longicorniswas found in the highest proportions compared to other native tick species on raccoons (55.4%), Virginia opossums (28.9%), and white-tailed deer (11.5%). Tissue, blood, and engorged larvae were tested for 17 different pathogens using a nanoscale PCR platform. Infection with five pathogens (Borrelia burgdorferi, Anaplasma phagocytophilum, Rickettsiaspp.,Mycoplasma haemocanis, andBartonellaspp.) was detected in host samples, but no pathogens were found in any larval samples. These results suggest that although large and medium sized mammals feed large numbers ofH. longicornisticks in the environment there is presently a low potential forH. longicornisto acquire pathogens from these wildlife hosts.

Highlights

H. longicorniswere sampled from seven genera of large and medium-sized mammals

Raccoons, opossums, and white-tailed deer fed a large proportion ofH. longicornis

H. longicornisdid not acquire pathogens through co-feeding with native tick vectors

Host species were infected with a range of pathogens of human and veterinary concern

Host-derivedH. longicornisengorged larvae were not infected with any pathogens
DFG-1 residue controls inhibitor binding mode and affinity providing a basis for rational design of kinase inhibitor selectivity
Authors: Schröder Martin , Bullock Alex N. , Federov Oleg , Bracher Franz , Chaikuad Apirat , Knapp Stefan
Published: July 2020

Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, non-canonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK and CLK. Using the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a non-canonical binding mode in CLK1, providing a rational for selectivity over the closely-related CLK3 which harbors a smaller DFG-1 alanine. Our data suggests that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
Protein kinase A catalytic-α and catalytic-β proteins have non-redundant functions
Authors: Raghuram Viswanathan , Salhadar Karim , Limbutara Kavee , Park Euijung , Yang Chin-Rang , Knepper Mark A.
Published: July 2020

Vasopressin regulates osmotic water transport in the renal collecting duct by PKA-mediated control of the water channel aquaporin-2 (AQP2). Collecting duct principal cells express two seemingly redundant PKA catalytic subunits, PKA catalytic α (PKA-Cα) and PKA catalytic β (PKA-Cβ). To identify the roles of these two protein kinases, we carried out deep phosphoproteomic analysis in cultured mpkCCD cells in which either PKA-Cα or PKA-Cβ was deleted using CRISPR-Cas9-based genome editing. Controls were cells carried through the genome editing procedure, but without deletion of PKA. TMT mass tagging was used for protein mass spectrometric quantification. Of the 4635 phosphopeptides that were quantified 67 were significantly altered in abundance with PKA-Cα deletion, while 21 were significantly altered in abundance with PKA-Cβ deletion. However, only four sites were changed in both. The target proteins identified in PKA-Cα-null cells were largely associated with cell membranes and membrane vesicles, while target proteins in the PKA-Cβ-null cells were largely associated with the actin cytoskeleton and cell junctions. In contrast, in vitro incubation of mpkCCD proteins with recombinant PKA-Cα and PKA-Cβ resulted in virtually identical phosphorylation changes. In addition, analysis of total protein abundances in the in vivo samples showed that PKA-Cα deletion resulted in a near disappearance of AQP2 protein, while PKA-Cβ deletion did not decrease AQP2 abundance. We conclude that PKA-Cα and PKA-Cβ serve substantially different functions in renal collecting duct cells and that differences in phosphorylation targets may be due to differences in protein interactions, e.g. mediated by AKAP, C-KAP or PDZ binding.
Chronic activation of fear engrams induces extinction-like behavior in ethanol-exposed mice
Authors: Cincotta Christine , Murawski Nathen J. , Grella Stephanie L. , McKissick Olivia , Doucette Emily , Ramirez Steve
Published: July 2020

Alcohol withdrawal directly impacts the brain’s stress and memory systems, which may underlie individual susceptibility to persistent drug and alcohol-seeking behaviors. Numerous studies demonstrate that forced alcohol abstinence, which may lead to withdrawal, can impair fear-related memory processes in rodents such as extinction learning, however the underlying neural circuits mediating these impairments remain elusive. Here, we tested an optogenetic strategy aimed at mitigating fear extinction impairments in male c57BL/6 mice following exposure to alcohol (i.e., ethanol) and forced abstinence. In the first experiment, extensive behavioral extinction training in a fear-conditioned context was impaired in ethanol-exposed mice compared to controls. In the second experiment, neuronal ensembles processing a contextual fear memory in the dorsal hippocampus were tagged and optogenetically reactivated repeatedly in a distinct context in ethanol-exposed and control mice. Chronic activation of these cells resulted in a context-specific, extinction-like reduction in fear responses in both control and ethanol-exposed mice. These findings suggest that while ethanol can impair fear extinction learning, optogenetic manipulation of a fear engram is sufficient to induce an extinction-like reduction in fear responses.
Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria
Authors: Kapli Paschalia , Natsidis Paschalis , Leite Daniel J. , Fursman Maximilian , Jeffrie Nadia , Rahman Imran A. , Philippe Hervé , Copley Richard R. , Telford Maximilian J.
Published: July 2020

The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia and Deuterostomia. Protostomia contains the Ecdysozoa and the Lophotrochozoa; Deuterostomia contains the Chordata and the Xenambulacraria (Hemichordata, Echinodermata and Xenacoelomorpha). Their names refer to a supposed distinct origin of the mouth (stoma) in the two clades, but these groups have been differentiated by other embryological characters including embryonic cleavage patterns and different ways of forming their mesoderm and coeloms. Deuterostome monophyly is not consistently supported by recent studies. Here we compare support for Protostomia and Deuterostomia using five recently published, phylogenomic datasets. Protostomia is always strongly supported, especially by longer and higher quality genes. Support for Deuterostomia is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that can cause tree reconstruction errors - inadequate models, short internal branch, faster evolving genes, and unequal branch lengths - correlate with statistical support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. A survey of molecular characters supposedly diagnostic of deuterostomes shows many are not valid synapomorphies. The branch between bilaterian and deuterostome common ancestors, if real, is very short. This finding fits with growing evidence suggesting the common ancestor of all Bilateria had many deuterostome characteristics. This finding has important implications for our understanding of early animal evolution and for the interpretation of some enigmatic Cambrian fossils such as vetulicolians and banffiids.
Surface-Based Connectivity Integration
Authors: Cole Martin , Murray Kyle , St-Onge Etienne , Risk Benjamin , Zhong Jianhui , Schifitto Giovanni , Descoteaux Maxime , Zhang Zhengwu
Published: July 2020

There has been increasing interest in jointly studying structural connectivity (SC) and functional connectivity (FC) derived from diffusion and functional MRI. However, several fundamental problems are still not well considered when conducting such connectome integration analyses, e.g., “Which structure (e.g., gray matter, white matter, white surface or pial surface) should be used for defining SC and FC and exploring their relationships”, “Which brain parcellation should be used”, and “How do the SC and FC correlate with each other and how do such correlations vary in different locations of the brain?”. In this work, we develop a new framework calledsurface-based connectivity integration(SBCI) to facilitate the integrative analysis of SC and FC with a re-thinking of these problems. We propose to use the white surface (the interface of white matter and gray matter) to build both SC and FC since diffusion signals are in the white matter while functional signals are more present in the gray matter. SBCI also represents both SC and FC in a continuous manner at very high spatial resolution on the white surface, avoiding the need of pre-specified atlases which may bias the comparison of SC and FC. Using data from the Human Connectome Project, we show that SBCI can create reproducible, high quality SC and FC, in addition to three novel imaging biomarkers reflective of the similarity between SC and FC throughout the brain, called global, local, and discreteSC-FC coupling. Further, we demonstrate the usefulness of these biomarkers in finding group effects due to biological sex throughout the brain.
Species traits predict extinction risk across the Tree of Life
Authors: Chichorro Filipe , Urbano Fernando , Teixeira Dinarte , Väre Henry , Pinto Tiago , Brummitt Neil , He Xiaolan , Hochkirch Axel , Hyvönen Jaakko , Kaila Lauri , Juslén Aino , Cardoso Pedro
Published: July 2020

Biodiversity is eroding at unprecedented rates due to human activity1. Species’ trajectories towards extinction are shaped by multiple factors, including life-history traits2as well as human pressures3. Previous studies linking these factors to extinction risk have been narrow in their taxonomic and geographic scope4, thus limiting the ability for identifying global predictors. We studied the relation between 12 traits and the extinction risk of almost 900 species representing 15 groups across the tree of life (vertebrates, invertebrates and plants) at a global scale. We show that threatened species share narrow habitat breadth, poor dispersal ability, low fecundity, small altitudinal range, and are affected by a large human footprint. Other traits either show contrasting responses among groups (body size, offspring size, and change in human footprint), or relations were found for only a limited number of taxa (generation length, diet breadth, microhabitat). Our study suggests that in the absence of data on the precise distribution and population trends of species, traits can be used as predictors of extinction risk and thus help guide future research, monitoring and conservation efforts.
Smoothened Transduces Hedgehog Signals via Activity-Dependent Sequestration of PKA Catalytic Subunits
Authors: Arveseth Corvin D. , Happ John T. , Hedeen Danielle S. , Zhu Ju-Fen , Capener Jacob L. , Shaw Dana Klatt , Deshpande Ishan , Liang Jiahao , Xu Jiewei , Stubben Sara L. , Nelson Isaac B. , Walker Madison F. , Krogan Nevan J. , Grunwald David J. , Hüttenhain Ruth , Manglik Aashish , Myers Benjamin R.
Published: July 2020

The Hedgehog (Hh) pathway is essential for organ development, homeostasis, and regeneration. Dysfunction of this cascade drives several cancers. To control expression of pathway target genes, the G protein-coupled receptor (GPCR) Smoothened (SMO) activates glioma-associated (GLI) transcription factors via an unknown mechanism. Here we show that, rather than conforming to traditional GPCR signaling paradigms, SMO activates GLI by binding and sequestering protein kinase A (PKA) catalytic subunits at the membrane. This sequestration, triggered by GPCR kinase 2 (GRK2)-mediated phosphorylation of SMO intracellular domains, prevents PKA from phosphorylating soluble substrates, releasing GLI from PKA-mediated inhibition. Our work provides a mechanism directly linking Hh signal transduction at the membrane to GLI transcription in the nucleus. This process is more fundamentally similar between species than prevailing hypotheses suggest. The mechanism described here may apply broadly to other GPCR- and PKA-containing cascades in diverse areas of biology.
Development of a Synthetic Poxvirus-Based SARS-CoV-2 Vaccine
Authors: Chiuppesi Flavia , Salazar Marcela d’Alincourt , Contreras Heidi , Nguyen Vu H , Martinez Joy , Park Soojin , Nguyen Jenny , Kha Mindy , Iniguez Angelina , Zhou Qiao , Kaltcheva Teodora , Levytskyy Roman , Ebelt Nancy D , Kang Tae Hyuk , Wu Xiwei , Rogers Thomas , Manuel Edwin R , Shostak Yuriy , Diamond Don J , Wussow Felix
Published: July 2020

Modified Vaccinia Ankara (MVA) is a highly attenuated poxvirus vector that is widely used to develop vaccines for infectious diseases and cancer. We developed a novel vaccine platform based on a unique three-plasmid system to efficiently generate recombinant MVA vectors from chemically synthesized DNA. In response to the ongoing global pandemic caused by SARS coronavirus-2 (SARS-CoV-2), we used this novel vaccine platform to rapidly produce fully synthetic MVA (sMVA) vectors co-expressing SARS-CoV-2 spike and nucleocapsid antigens, two immunodominant antigens implicated in protective immunity. Mice immunized with these sMVA vectors developed robust SARS-CoV-2 antigen-specific humoral and cellular immune responses, including potent neutralizing antibodies. These results demonstrate the potential of a novel vaccine platform based on synthetic DNA to efficiently generate recombinant MVA vectors and to rapidly develop a multi-antigenic poxvirus-based SARS-CoV-2 vaccine candidate.
Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential
Authors: French Courtney E. , Wei Gang , Lloyd James P. B. , Hu Zhiqiang , Brooks Angela N. , Brenner Steven E.
Published: July 2020

To explore the regulatory potential of nonsense-mediated mRNA decay (NMD) coupled with alternative splicing, we globally surveyed the transcripts targeted by this pathway via RNA-Seq analysis of HeLa cells in which NMD had been inhibited. We identified putative NMD-targeted transcripts as those with a termination codon more than 50 nucleotides upstream of an exon-exon junction (premature termination as defined by the ‘50nt rule’) and that significantly increased in abundance upon NMD inhibition. We additionally controlled for potential transcriptional up-regulation by requiring the putative NMD targets to increase in abundance substantially more than the isoforms from the same gene that do not contain a premature termination codon. This resulted in a conservative set of 2,793 transcripts derived from 2,116 genes as physiological NMD targets (9.2% of expressed transcripts and >20% of alternatively spliced genes). Our analysis identified previously inferred unproductive isoforms and numerous heretofore-uncharacterized ones. NMD-targeted transcripts were derived from genes involved in many functional categories, and are particularly enriched for RNA splicing genes as well as for those harboring ultraconserved elements. By investigating the features of all transcripts impacted by NMD, we find that the 50nt rule is a strong predictor of NMD degradation while 3’ UTR length on its own generally has only a small effect in this human cell line. Additionally, thousands more transcripts without a premature termination codon in the main coding sequence contain a uORF and display significantly increased abundance upon NMD inhibition indicating potentially widespread regulation through decay coupled with uORF translation. Our results support that alternative splicing coupled with NMD is a prevalent post-transcriptional mechanism in human cells with broad potential for biological regulation.
mutyper: assigning and summarizing mutation types for analyzing germline mutation spectra
Authors: DeWitt William S.
Published: July 2020

Characterization of germline mutation spectrum variation from population genomics data has shed light on the biological complexity of the mutation process, and its evolution within and between species. This analysis augments available population SNP data with estimates of local ancestral genomic context to assign mutation types and aggregate summary statistics thereof, and is increasingly common. There is a need for standardized computational tools to extract mutation spectrum information from sequencing data. Here I describemutyper, a command-line utility and Python package that uses an ancestral genome estimate to assign mutation types to SNP data, compute mutation spectra for individuals, and compute sample frequency spectra resolved by mutation type for population genetic inference.

Availability and implementation

mutypercan be installed using the pip package manager and is compatible with Python 3.6+. Documentation is provided athttps://harrispopgen.github.io/mutyper; source code is available athttps://github.com/harrispopgen/mutyper.
All hands on deck: Large-scale (re)sculpting of cortical circuits in post-resection children
Authors: Maallo Anne Margarette S. , Granovetter Michael C. , Freud Erez , Kastner Sabine , Pinsk Mark A. , Patterson Christina , Behrmann Marlene
Published: July 2020

Despite the relative successes in the surgical treatment of pharmacoresistant epilepsy, there is rather little research on the neural (re)organization that potentially subserves behavioral compensation. Here, we examined the post-surgical functional connectivity (FC) in children and adolescents who have undergone unilateral cortical resection and, yet, display remarkably normal behavior. Conventionally, FC has been investigated in terms of the mean correlation of the BOLD time courses extracted from different brain regions. Here, we demonstrated the value of segregating the voxel-wise relationships into mutually exclusive populations that were either positively or negatively correlated. While, relative to controls, the positive correlations were largely normal, negative correlations among networks were increased. Together, our results point to reorganization in the contralesional hemisphere, possibly suggesting competition for cortical territory due to the demand for representation of function. Conceivably, the ubiquitous negative correlations enable the differentiation of function in the reduced cortical volume following a unilateral resection.
Reverse transcription quantitative PCR to detect low density malaria infections
Authors: Christensen Peter , Bozdech Zbynek , Watthanaworawit Wanitda , Renia Laurent , Malleret Benoit , Ling Clare , Nosten Francois
Published: July 2020

Targeted malaria elimination strategies require highly sensitive tests to detect low density malaria infections (LDMI). Commonly used methods for malaria diagnosis such as light microscopy and antigen-based rapid diagnostic tests (RDTs) are not sensitive enough for reliable identification of infections with parasitaemia below 200 parasites per milliliter of blood. While targeted malaria elimination efforts on the Thailand-Myanmar border have successfully used high sample volume ultrasensitive quantitative PCR (uPCR) to determine malaria prevalence, the necessity for venous collection and processing of large quantities of patient blood limits the widespread tractability of this method. Here we evaluated a real-time quantitative reverse transcription PCR (qRT-PCR) method that significantly reduces the required sample volume compared to uPCR. To do this, 304 samples collected from an active case detection program in Kayin state, Myanmar were compared using uPCR and qRT-PCR.Plasmodiumspp. qRT-PCR confirmed 18 of 21 uPCRPlasmodium falciparumpositives, whileP. falciparumspecific qRT-PCR confirmed 17 of the 21 uPCRP. falciparumpositives. Combining both qRT-PCR results increased the sensitivity to 100% and specificity was 95.1%. These results show that malaria detection in areas of low transmission and LDMI, can benefit from the increased sensitivity of qRT-PCR especially where sample volume is limited.
MetaFunPrimer: primer design for targeting genes observed in metagenomes
Authors: Liu Jia , Villanueva Paul , Choi Jinlyung , Gunturu Santosh , Ouyang Yang , Tiemann Lisa , Cole James R. , Lee Jaejin , Howe Adina
Published: July 2020

High throughput primer design is needed to simultaneously design primers for multiple genes of interest, such as a group of functional genes. We have developed MetaFunPrimer, a bioinformatic pipeline to design primer targets for genes of interests, with a prioritization based on ranking the presence of gene targets in references, such as metagenomes. MetaFunPrimer takes inputs of protein and nucleotide sequences for gene targets of interest accompanied by a set of reference metagenomes or genomes for determining genes of interest. Its output is a set of primers that may be used to amplify genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 HT-qPCR primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 soil metagenomes. We demonstrate that these primers can significantly improve targeting ofamoA-AOB genes in soil metagenomes compared to previously published primers.

IMPORTANCE

Amplification-based gene characterization allows for sensitive and specific quantification of functional genes. Often, there is a large diversity of genes represented for a function of interest, and multiple primers may be necessary to target associated genes. Current primer design tools are limited to designing primers for only a few genes of interest. MetaFunPrimer allows for high throughput primer design for functional genes of interest and also allows for ranking gene targets by their presence and abundance in environmental datasets. This tool enables high throughput qPCR approaches for characterizing functional genes.
Production of diverse beauveriolide analogs in closely related fungi: a rare case of fungal chemodiversity
Authors: Yin Ying , Chen Bo , Song Shuangxiu , Li Bing , Yang Xiuqing , Wang Chengshu
Published: July 2020

Fungal chemodiversity is well known in part due to the production of diverse analogous compounds by a single biosynthetic gene cluster (BGCs). Usually, similar metabolites are produced by closely related fungal species. Here we report a rare case of the production of the cyclodepsipeptide beauveriolides (BVDs) in three insect pathogenic fungi. We found that the more closely-related fungiBeauveria bassianaandB. brongniartiiproduce structurally distinct analogs of BVDs whereas the rather divergently evolved speciesB. brongniartiiandCordyceps militarisproduce structural analogs in a similar pattern. It was verified that a conserved BGC containing four genes is responsible for BVD biosynthesis in three fungi including a polyketide synthase (PKS) for the production of 3-hydroxy fatty acids (FAs) with chain length variations. In contrast to BVD production patterns, phylogenetic analysis of the BGC enzymes or enzyme domains largely resulted in the congruence relationship with fungal speciation. Feeding assays demonstrated that a FA with a chain length of eight carbon atoms was preferentially utilized whereas a FA with a chain longer than 10 carbon atoms could not be used as a substrate for BVD biosynthesis. We also found that addition ofD-type amino acids could not enableB. bassianato produce those analogs biosynthesized by other two fungi. Insect survival assays suggested that the contribution of BVD to fungal virulence might be associated with the susceptibility of insect species. The results of this study enrich the knowledge of fungal secondary metabolic diversity.

IMPORTANCE

Fungal chemotaxonomy is an approach to classify fungi based on fungal production of natural compounds especially the secondary metabolites. We found an atypical example that could question chemical classification of fungi in this study: the more closely-related entomopathogenic speciesBeauveria bassianaandB. brongniartiiproduce structurally different analogs of the cyclodepsipeptide beauveriolides whereas the rather divergent speciesB. brongniartiiandCordyceps militarisbiosynthesize similar analogs under the same growth condition. The conserved BGC containing four genes is present in each species and responsible for beauveriolide production. In contrast to the compound formation profiles, the phylogenies of biosynthetic enzymes or enzymatic domains show associations with fungal speciation relationship. Dependent on insect species, production of beauveriolides may contribute to fungal virulence against insect. The findings in this study augment the diversity of fungal secondary metabolisms.
Is it safe to use a single ventilator for two or more patients?
Authors: Ubiergo Sebastián Ugarte , Merino Felipe Castillo , Arellano-Pérez Óscar
Published: July 2020

Mechanical ventilation is essential in the SARS-CoV-2 pandemic context. Considering the limited availability of mechanical ventilators due to high costs increased by global demand, the use of a single ventilator for two or more patients has been encouraged. An experimental model that ventilates two test lungs with a single machine has been designed in order to measure possible asymmetries during parallel circuit ventilation under different lung compliance conditions. This paper reports a first assessment of the risks involved in ventilating two patients with a single machine. Since some volumetric differences are not monitored by the ventilator itself, the main risks involved are distension or alveolar collapse if used in actual patients that have different thoracopulmonary mechanics.
Numerical Analysis of Disastrous Effect of Reopening Too Soon in Georgia, USA
Authors: Basu Santanu
Published: July 2020

Social distancing restrictions were lifted in Georgia, USA before the daily new Covid-19 cases were significantly reduced below the peak. In this paper we show through numerical analysis the disastrous consequence of this action resulting in a second peak of daily cases which caused additional fatalities.
Bronchoscopy in critically ill COVID-19 Patients: microbiological profile and factors related to nosocomial respiratory infection
Authors: Serra Pere , Centeno Carmen , Garcia-Olivé Ignasi , Antuori Adrià , Casadellà Maria , Tazi Rachid , Armestar Fernando , Fernández Ester , Andreo Felipe , Rosell Antoni
Published: July 2020

Background

Nosocomial co-infections are a cause of morbidity and mortality in Intensive Care Units (ICU).

Objectives

Our aim was to describe bronchoscopy findings and analyse co-infection through bronchial aspirate (BA) samples in patients with COVID-19 pneumonia requiring ICU admission.

Methods

We conducted a retrospective observational study, analysing the BA samples collected from intubated patients with COVID-19 to diagnose nosocomial respiratory infection.

Results

One-hundred and fifty-five consecutive BA samples were collected from 75 patients. Of them, 90 (58%) were positive cultures for different microorganisms, 11 (7.1%) were polymicrobial, and 37 (23.7%) contained resistant microorganisms. There was a statistically significant association between increased days of orotracheal intubation (OTI) and positive BA (18.9 days versus 10.9 days, p<0.01), polymicrobial infection (22.11 versus 13.54, p<0.01) and isolation of resistant microorganisms (18.88 versus 10.94, p<0.01). In 88% of the cases a change in antibiotic treatment was made.

Conclusion

Nosocomial respiratory infection in intubated COVID-19 patients seems to be higher than in non-epidemic periods. The longer the intubation period, the greater the probability of co-infection, isolation of resistant microorganisms and polymicrobial infection. Microbiological sampling through BA is an essential tool to manage these patients appropriately.
The LRRK2 G2019S mutation alters astrocyte-to-neuron communication via extracellular vesicles and induces neuron atrophy in a human iPSC-derived model of Parkinson’s disease
Authors: de Rus Jacquet Aurelie , Tancredi Jenna L. , Lemire Andrew L. , DeSantis Michael C. , Li Wei-Ping , O’Shea Erin K.
Published: July 2020

Astrocytes are essential cells of the central nervous system, characterized by dynamic relationships with neurons that range from functional metabolic interactions and regulation of neuronal firing activities, to the release of neurotrophic and neuroprotective factors. In Parkinson’s disease (PD), dopaminergic neurons are progressively lost during the course of the disease, but the effects of PD on astrocytes and astrocyte-to-neuron communication remains largely unknown. This study focuses on the effects of the PD-related mutation LRRK2 G2019S in astrocytes generated from patient-derived induced pluripotent stem cells. We report the alteration of extracellular vesicle (EV) biogenesis in astrocytes, and we identify the abnormal accumulation of key PD-related proteins within multi vesicular bodies (MVBs). We found that dopaminergic neurons internalize astrocyte-secreted EVs and that LRRK2 G2019S EVs are abnormally enriched in neurites and fail to provide full neurotrophic support to dopaminergic neurons. Thus, dysfunctional astrocyte-to-neuron communication via altered EV biological properties may participate in the progression of PD.
Mobbing-like response to secondary predator cues informs group behaviour in wild meerkats
Authors: Driscoll Isabel , Manser Marta , Thornton Alex
Published: July 2020

The assessment of current risk is essential in informing defensive behaviours. Many animals use cues left behind by predators, known as secondary predator cues (SPCs), to assess risk and respond appropriately. However, meerkats, Suricata suricatta, exhibit seemingly unique mobbing-like responses to these cues. The benefit of this high-intensity recruitment response is unclear, as unlike genuine mobbing, it cannot help to drive the predator away. One potential explanation is that mobbing-like responses promote information gathering and collective decision-making by the whole group. To examine this, we investigated (i) how meerkats’ responses to SPCs differ from mobbing live animals and (ii) the subsequent behavioural changes following a SPC encounter. Using a dataset gathered over a 20-year period, we first compared the rate of SPC recruitment versus the rate of animal mobbing. We then investigated changes in behaviour (alarm calling, sentinel bouts, distance travelled and pup provisioning) in the hour before and after a SPC encounter. Abiotic factors did not affect recruitment rate to SPCs or live animals, or influence the change in behavioural responses following a SPC encounter. The presence of pups reduced response rate to SPCs, but had no effect on animal mobbing rate, supporting experimental findings that responses towards SPCs are unlikely to function as a form of teaching. Alarm calling rate increased and the distance travelled by the group decreased following a SPC encounter, and were unaffected by the presence of pups or abiotic conditions. The results indicate group-level behavioural changes following a SPC encounter, and a greater degree of plasticity in recruitment to SPCs than to live animals. This response plasticity may reflect a context-dependent need to gather information to make collective decisions for defensive behaviour according to the level of threat perceived.
Evolution of a sex megachromosome
Authors: Conte Matthew A. , Clark Frances E. , Roberts Reade B. , Xu Luohao , Tao Wenjing , Zhou Qi , Wang Deshou , Kocher Thomas D.
Published: July 2020

Chromosome size and morphology vary within and among species, but little is known about either the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual megachromosome that is ~3 times longer than any of the other chromosomes. This megachromosome functions as a sex chromosome in some of these species. We explore two hypotheses of how this sex megachromosome may have evolved. The first hypothesis proposes that it developed by the accumulation of repetitive elements as recombination was reduced around a dominant sex-determination locus, as suggested by traditional models of sex chromosome evolution. An alternative hypothesis is that the megachromosome originated via the fusion of an autosome with a highly-repetitive B chromosome, one of which had carried a sex-determination locus. Here we test these hypotheses using comparative analysis of several chromosome-scale cichlid and teleost genomes. We find the megachromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. A WZ sex-determination locus encompasses the last ~105Mbp of the 134Mbp megachromosome and the last 47Mbp of the megachromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal the megachromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long non-coding RNAs. Although the origin of this megachromosome remains ambiguous, it has clearly been a focal point of extensive evolutionary genomic conflicts. This megachromosome represents an interesting system for studying sex chromosome evolution and genomic conflicts.
Role of SpoIVA ATPase Motifs DuringClostridioides difficileSporulation
Authors: de la Puebla Hector Benito , Giacalone David , Cooper Alexei , Shen Aimee
Published: July 2020

The nosocomial pathogen,Clostridioides difficile, is a spore-forming obligate anaerobe that depends on its aerotolerant spore form to transmit infections. Functional spore formation depends on the assembly of a proteinaceous layer known as the coat around the developing spore. InC. difficile, coat assembly depends on the conserved coat protein, SpoIVA, and the clostridial-specific coat protein, SipL, which directly interact. Mutations that disrupt their interaction cause coat to mislocalize and decrease functional spore formation. InB. subtilis, SpoIVA is an ATPase that uses ATP hydrolysis to help drive its polymerization around the forespore. Loss of SpoIVA ATPase activity impairsB. subtilisSpoIVA encasement of the forespore and activates a quality control mechanism that eliminates these defective cells. Since this mechanism is lacking inC. difficile, we tested whether mutations inC. difficile’s SpoIVA ATPase motifs impair functional spore formation. DisruptingC. difficileSpoIVA ATPase motifs resulted in phenotypes that were typically >104less severe than the equivalent mutations inB. subtilis. Interestingly, mutation of ATPase motif residues predicted to abrogate SpoIVA binding to ATP decreased SpoIVA-SipL interaction, whereas mutation of ATPase motif residues predicted to disrupt ATP hydrolysis but retain binding to ATP enhanced SpoIVA-SipL interaction. When asipLmutation known to reduce binding to SpoIVA was combined with aspoIVAmutation predicted to prevent SpoIVA binding to ATP, spore formation was severely exacerbated. Since this phenotype is allele-specific, our data implies that SipL recognizes the ATP-bound form of SpoIVA and highlights the importance of this interaction for functionalC. difficilespore formation.

Importance

The aerotolerant spores formed by the major nosocomial pathogenClostridioides difficileare its primary infectious particle. However, the mechanism by which this critical cell type is assembled remains poorly characterized, especially with respect to its protective coat layer. We previously showed that binding between the spore morphogenetic proteins, SpoIVA and SipL, regulates coat assembly around the forespore. SpoIVA is widely conserved among spore-forming bacteria, and its ATPase activity is essential forBacillus subtilisto form functional spores. In this study, we determined that mutations inC. difficileSpoIVA’s ATPase motifs result in relatively minor defects in spore formation in contrast withB. subtilis. Nevertheless, our data suggest that SipL preferentially recognizes the ATP-bound form of SpoIVA and identify a specific residue in SipL’s C-terminal LysM domain that is critical for recognizing the ATP-bound form of SpoIVA. These findings advance our understanding of how SpoIVA-SipL interactions regulateC. difficilespore assembly.
Developmental, cellular, and biochemical basis of transparency in the glasswing butterflyGreta oto
Authors: Pomerantz Aaron F. , Siddique Radwanul H. , Cash Elizabeth I. , Kishi Yuriko , Pinna Charline , Hammar Kasia , Gomez Doris , Elias Marianne , Patel Nipam H.
Published: July 2020

Numerous species of Lepidoptera have transparent wings, which often possess scales of altered morphology and reduced size, and the presence of membrane surface nanostructures that dramatically reduce reflection. Optical properties and anti-reflective nanostructures have been characterized for several ‘clearwing’ Lepidoptera, but the developmental basis of wing transparency is unknown. We apply confocal and electron microscopy to create a developmental time-series in the glasswing butterfly,Greta oto, comparing transparent and non-transparent wing regions. We find that scale precursor cell density is reduced in transparent regions, and cytoskeletal organization differs between flat scales in opaque regions, and thin, bristle-like scales in transparent regions. We also reveal that sub-wavelength nanopillars on the wing membrane are wax-based, derive from wing epithelial cells and their associated microvillar projections, and demonstrate their role in enhancing-anti-reflective properties. These findings provide insight into morphogenesis of naturally organized micro- and nanostructures and may provide bioinspiration for new anti-reflective materials.
Large genomic variants reveal unexplored intraspecific diversity inBrassica rapagenomes
Authors: Boutte Julien , Maillet Loeiz , Chaussepied Thomas , Letort Sébastien , Aury Jean-Marc , Belser Caroline , Boideau Franz , Brunet Anael , Coriton Olivier , Deniot Gwenaëlle , Falentin Cyril , Huteau Virginie , Lodé Maryse , Morice Jérôme , Trotoux Gwenn , Chèvre Anne-Marie , Rousseau-Gueutin Mathieu , de Carvalho Julie Ferreira
Published: July 2020

Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Using twoBrassica rapagenomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection.

We explored the structural consequences of the presence of large repeated sequences inB. rapa‘Z1’ genome versus theB. rapa‘Chiifu’ genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09 and A10 are due to large insertions and inversions when comparingB. rapa‘Z1’ andB. rapa‘Chiifu’ at the origin of important length differences in some chromosomes. For instance, lengths of ‘Z1’ and ‘Chiifu’ A06 chromosomes were estimatedin silicoto be 55Mb and 29Mb, respectively. To validate these observations, we compared using fluorescentin-situhybridization (FISH) the two A06 chromosomes present in a F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of ‘Z1’ compared to ‘Chiifu’. Alternatively, using a Copy Number Variation approach, we were able to quantify the presence of a higher number of rDNA and Gypsy elements in ‘Z1’ genome compared to ‘Chiifu’ on different chromosomes including A06. Using flow cytometry, the total genome size of 12Brassicaaccessions corresponding to aB. rapaavailable core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions.

This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups ofB. rapaand highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.
The renal hepcidin/ferroportin axis controls iron reabsorption and determines renal and hepatic susceptibility to iron overload
Authors: Mohammad Goran , Matakidou Athena , Robbins Peter A , Lakhal-Littleton Samira
Published: July 2020

The hepcidin/ferroportin axis controls systemic iron homeostasis by regulating iron acquisition from the duodenum and the reticuloendothelial system, respective sites of iron absorption and recycling. Ferroportin is also abundant in the kidney, where it has been implicated in iron reabsorption. However, it remains unknown whether hepcidin regulates ferroportin-mediated iron reabsorption and whether such regulation is important for systemic iron homeostasis. To address these questions, we generated a novel mouse model with an inducible renal-tubule specific knock-in offpnC326Y, which encodes a hepcidin-resistant FPNC326Y. Under iron-replete conditions, female mice harbouring this allele had lower renal iron content and higher serum and liver iron levels than controls. Under conditions of excess iron availability, male and female mice harbouring this allele had greater liver iron overload, but lower renal iron overload relative to controls. In addition, hemochromatosis mice harbouring a ubiquitous knock-in offpnC326Ydid not develop renal iron overload otherwise seen in the setting of excess iron availability. These findings are the first formal demonstration that hepcidin regulates ferroportin-mediated iron reabsorption. They also show that loss of this regulation contributes to liver iron overload while protecting the kidney in the setting of hemochromatosis. Our findings have important implications. First, they indicate that targeting the hepcidin/ferroportin axis for treating iron overload disorders will inhibit iron reabsorption and increase renal iron content. Second, they suggest that inhibition of iron reabsorption by raised hepcidin in chronic inflammatory conditions contributes to iron deficiency and that parenteral iron supplementation in this setting may cause renal iron overload.
Alpha-1 antitrypsin inhibits SARS-CoV-2 infection
Authors: Wettstein Lukas , Conzelmann Carina , Müller Janis A. , Weil Tatjana , Groß Rüdiger , Hirschenberger Maximilian , Seidel Alina , Klute Susanne , Zech Fabian , Bozzo Caterina Prelli , Preising Nico , Fois Giorgio , Lochbaum Robin , Knaff Philip , Mailänder Volker , Ständker Ludger , Thal Dietmar Rudolf , Schumann Christian , Stenger Steffen , Kleger Alexander , Lochnit Günter , Sparrer Konstantin , Kirchhoff Frank , Frick Manfred , Münch Jan
Published: July 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). To identify factors of the respiratory tract that suppress SARS-CoV-2, we screened a peptide/protein library derived from bronchoalveolar lavage, and identified α1-antitrypsin (α1-AT) as specific inhibitor of SARS-CoV-2. α1-AT targets the viral spike protein and blocks SARS-CoV-2 infection of human airway epithelium at physiological concentrations. Our findings show that endogenous α1-AT restricts SARS-CoV-2 and repurposes α1-AT-based drugs for COVID-19 therapy.