bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractTargeted 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

ABSTRACTHigh 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.IMPORTANCEAmplification-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

ABSTRACTFungal 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.IMPORTANCEFungal 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

AbstractMechanical 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.
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

AbstractBackgroundNosocomial co-infections are a cause of morbidity and mortality in Intensive Care Units (ICU).ObjectivesOur aim was to describe bronchoscopy findings and analyse co-infection through bronchial aspirate (BA) samples in patients with COVID-19 pneumonia requiring ICU admission.MethodsWe conducted a retrospective observational study, analysing the BA samples collected from intubated patients with COVID-19 to diagnose nosocomial respiratory infection.ResultsOne-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.ConclusionNosocomial 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

AbstractAstrocytes 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

AbstractThe 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

AbstractChromosome 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

AbstractThe 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.ImportanceThe 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

AbstractNumerous 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

ABSTRACTTraditionally, 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

ABSTRACTThe 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.