bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA Binding Induces acistotransSwitch in Cre Recombinase to Enable Intasome Assembly
Authors: Unnikrishnan Aparna , Amero Carlos D. , Yadav Deepak Kumar , Stachowski Kye , Potter Devante , Foster Mark P.
Published: May 2020

Mechanistic understanding of DNA recombination in the Cre-loxPsystem has largely been guided by crystallographic structures of tetrameric synaptic complexes. Those studies have suggested a role for protein conformational dynamics that has not been well characterized at the atomic level. We used solution NMR to discover the link between intrinsic flexibility and function in Cre recombinase. TROSY-NMR spectra show the N-terminal and C-terminal catalytic domains (CreNTD, CreCat) to be structurally independent. Amide15N relaxation measurements of the CreCatdomain reveal fast time scale dynamics in most regions that exhibit conformational differences inactiveandinactiveCre protomers in crystallographic tetramers. However, the C-terminal helix αN, implicated in assembly of synaptic complexes and regulation of DNA cleavage activity viatransprotein-protein interactions, is unexpectedly rigid in free Cre. Chemical shift perturbations and intra- and inter-molecular paramagnetic relaxation enhancement (PRE) NMR data reveal an alternative auto-inhibitory conformation for the αN region of free Cre, wherein it packsin cisover the protein DNA binding surface and active site. Moreover, binding toloxPDNA induces a conformational change that dislodge the C-terminus, resulting in acistotransswitch that is likely to enable protein-protein interactions required for assembly of recombinogenic Cre intasomes. These findings necessitate a re-examination of the mechanisms by which this widely-utilized gene editing tool selects target sites, avoids spurious DNA cleavage activity, and controls DNA recombination efficiency.

SIGNIFICANCE STATEMENT

The Cre-loxPsystem is a widely used gene editing tool that has enabled transformative advances in immunology, neuroscience and cardiovascular research. Still, off-target activities confound research results and present obstacles to biomedical applications. Overcoming those limitations requires understanding the steps leading to assembly of recombination complexes,intasomes. We measured the magnetic properties of nitrogen nuclei in the backbone of the enzyme to correlate its intrinsic dynamics with its function in DNA recognition and cleavage. Remarkably, we found that in the absence of DNA the C-terminus of Cre appears to block the DNA binding surface and active site of the enzyme. Binding toloxPDNA induces a conformational switch that would enable the intermolecular protein-protein interactions required for assembly of recombinogenic Cre intasomes.
Evidence for the agricultural origin of antimicrobial resistance in a fungal pathogen of humans
Authors: Kang S. Earl , Sumabat Leilani G. , Melie Tina , Mangum Brandon , Momany Michelle , Brewer Marin T.
Published: May 2020

Resistance to clinical antimicrobials is an urgent problem, reducing our ability to combat deadly pathogens of humans. Azole antimicrobials target ergosterol synthesis and are highly effective against fungal pathogens of both humans and plants leading to their widespread use in clinical and agricultural settings1,2. The fungusAspergillus fumigatuscauses 300,000 life-threatening infections in susceptible human hosts annually and azoles are the most effective treatment3. Resistance to clinical azole antifungals has become a major problem in Europe and India over the last decade, where identical mutations incyp51A, an ergosterol biosynthetic gene, have been found in strains from both clinical and agricultural settings4. Sharedcyp51Agenotypes suggest that clinical azole resistance might have had an agricultural origin; however, until now, independent origins of clinical and agricultural mutations could not be ruled out. Here we show that azole-resistant isolates ofA. fumigatusfrom clinical and agricultural settings also carry mutations conferring resistance to quinone outside inhibitor (QoI) fungicides, which are used exclusively in agricultural settings. This is the first report of a clear marker for the agricultural origin of resistance to a clinical antifungal. We anticipate that our work will increase the understanding of interactions between pathogens of plants and pathogens of humans.
Deep Metric Learning Network using Proxies for Chromosome Classification and Retrieval in Karyotyping Test
Authors: Jung Hwejin , Park Bogyu , Lee Sangmun , Hyun Seungwoo , Lee Jinah , Seo Junseok , Koo Sunyoung , Lee Mina
Published: May 2020

In karyotyping, the classification of chromosomes is a tedious, complicated, and time-consuming process. It requires extremely careful analysis of chromosomes by well-trained cytogeneticists. To assist cytogeneticists in karyotyping, we introduce Proxy-ResNeXt-CBAM which is a metric learning based network using proxies with a convolutional block attention module (CBAM) designed for chromosome classification. RexNeXt-50 is used as a backbone network. To apply metric learning, the fully connected linear layer of the backbone network (ResNeXt-50) is removed and is replaced with CBAM. The similarity between embeddings, which are the outputs of the metric learning network, and proxies are measured for network training.

Proxy-ResNeXt-CBAM is validated on a public chromosome image dataset, and it achieves an accuracy of 95.86%, a precision of 95.87%, a recall of 95.9%, and an F-1 score of 95.79%. Proxy-ResNeXt-CBAM which is the metric learning network using proxies outperforms the baseline networks. In addition, the results of our embedding analysis demonstrate the effectiveness of using proxies in metric learning for optimizing deep convolutional neural networks. As the embedding analysis results show, Proxy-ResNeXt-CBAM obtains a 94.78% Recall@1 in image retrieval, and the embeddings of each chromosome are well clustered according to their similarity.
Targeted CRISPR screening identifies PRMT5 as synthetic lethality combinatorial target with gemcitabine in pancreatic cancer cells
Authors: Wei Xiaolong , Yang Jiekun , Adair Sara J. , Kuscu Cem , Lee Kyung Yong , Kane William , O’hara Patrick , Liu Denis , Demirlenk Yusuf Mert , Habieb Alaa Hamdi , Yilmaz Ebru , Dutta Anindya , Bauer Todd W. , Adli Mazhar
Published: May 2020

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most challenging cancer to treat. Due to the asymptomatic nature of the disease and ineffective drug treatment modalities, the survival rate of PDAC patients remains one of the lowest. The recurrent genetic alterations in PDAC are yet to be targeted; therefore, identifying effective therapeutic combinations is desperately needed. Here, we performed anin vivoCRISPR screening in a clinically relevant patient-derived xenograft (PDX) model system to identify synergistic drug combinations for PDAC treatment. Our approach revealed protein arginine methyltransferase gene 5 (PRMT5) as a promising druggable candidate whose inhibition creates synergistic vulnerability of PDAC cells to gemcitabine. Genetic and pharmacological inhibition results indicate that of PRMT5 depletion results in synergistic cytotoxicity with Gem due to depleted replication protein A (RPA) levels and an impaired non-homology end joining (NHEJ) DNA repair. Thus, the novel combination creates conditional lethality through the accumulation of excessive DNA damage and cell death, bothin vitroandin vivo. The findings demonstrate that unbiased genetic screenings combined with a clinically relevant model system is an effective approach in identifying synthetic lethal drug combinations for cancer treatment.

STATEMENT of SIGNIFICANCE

Identify synergistic drug combinations for PDAC is a significant unmet need. Through CRISPR screening, we discovered and validated that PRMT5 depletion creates synergistic vulnerability of PDAC cells to gemcitabine. Mechanistically, the combination impairs DNA repair, synergistic accumulation of DNA damage and cell deathin vitroandin vivo.
Combined Selective Plane Illumination Microscopy and FRAP maps intranuclear diffusion of NLS-GFP
Authors: Hobson Chad M. , O’Brien E. Timothy , Falvo Michael R. , Superfine Richard
Published: May 2020

Since its initial development in 1976, fluorescence recovery after photobleaching (FRAP) has been one of the most popular tools for studying diffusion and protein dynamics in living cells. Its popularity is derived from the widespread availability of confocal microscopes and the relative ease of the experiment and analysis. FRAP, however, is limited in its ability to resolve spatial heterogeneity. Here, we combine selective plane illumination microscopy (SPIM) and FRAP to create SPIM-FRAP, wherein we use a sheet of light to bleach a 2D plane and subsequently image the recovery of the same image plane. This provides simultaneous quantification of diffusion or protein recovery for every pixel in a given 2D slice, thus moving FRAP measurements beyond these previous limitations. We demonstrate this technique by mapping intranuclear diffusion of NLS-GFP in live MDA-MB-231 cells; SPIM-FRAP proves to be an order of magnitude faster than fluorescence correlation spectroscopy (FCS) based techniques for such measurements. We observe large length-scale (> ~500 nm) heterogeneity in the recovery times of NLS-GFP, which is validated against simulated data sets. 2D maps of recovery times were correlated with fluorescence images of H2B to address conflicting literature on the role of chromatin in diffusion of small molecules. We observed no correlation between histone density and diffusion. We developed a diffusion simulation for our SPIM-FRAP experiments to compare across techniques; our measured diffusion coefficients are on the order of previously reported results, thus validating the quantitative accuracy of SPIM-FRAP relative to well-established methods. With the recent rise of accessibility of SPIM systems, SPIM-FRAP is set to provide a simple and quick means of quantifying the spatial distribution of protein recovery or diffusion in living cells.

Statement of Significance

We developed selective plane illumination microscopy combined with fluorescence recovery after photobleaching (SPIM-FRAP) to perform simultaneous FRAP measurements for each pixel in a 2D slice. This technique has the potential to be implemented on almost any light sheet microscope with minimal software development. FRAP studies were previously unable to resolve spatial heterogeneity and FCS techniques require minute-long acquisition times; SPIM-FRAP remedies both of these issues by generating FRAP-based diffusion maps in 4 seconds. This technique can easily be expanded to 3D by photobleaching a single plane and performing light sheet volumetric imaging, which has the benefits of minimal photobleaching and phototoxicity for studying long-term protein turnover. Furthermore, SPIM-FRAP of slowly-recovering structures enables characterization of spatial distortions to measure intracellular stresses.
Visual gene expression reveals a cone to rod developmental progression in deep-sea fishes
Authors: Lupše Nik , Cortesi Fabio , Freese Marko , Marohn Lasse , Pohlman Jan-Dag , Wysujack Klaus , Hanel Reinhold , Musilova Zuzana
Published: May 2020

Vertebrates use cone cells in the retina for colour vision and rod cells to see in dim light. Many deep-sea fishes have adapted to their environment to have only rod cells in the retina, while both rod and cone genes are still preserved in their genomes. As deep-sea fish larvae start their lives in the shallow, and only later submerge to the depth, they have to cope with diverse environmental conditions during ontogeny. Using a comparative transcriptomic approach in 20 deep-sea fish species from eight teleost orders, we report on a developmental cone-to-rod switch. While adults mostly rely on rod opsin (RH1) for vision in dim light, larvae almost exclusively express middle-wavelength-sensitive (“green”) cone opsins (RH2) in their retinas. The phototransduction cascade genes follow a similar ontogenetic pattern of cone-followed by rod-specific gene expression in most species, except for the pearleye and sabretooth (Aulopiformes), in which the cone cascade remains dominant throughout development. By inspecting the whole genomes of five deep-sea species (four of them sequenced within this study:Idiacanthus fasciola, Chauliodus sloani; Stomiiformes;Coccorella atlantica,andScopelarchus michaelsarsi; Aulopiformes), we found that deep-sea fish possess one or two copies of the rodRH1opsin gene, and up to seven copies of the coneRH2opsin genes in their genomes, while other cone opsin classes have been mostly lost. Our findings hence provide molecular evidence for a limited opsin gene repertoire and a conserved vertebrate pattern whereby cone photoreceptors develop first and rod photoreceptors are added only at later developmental stages.
Neuronal timescales are functionally dynamic and shaped by cortical microarchitecture
Authors: Gao Richard , van den Brink Ruud L. , Pfeffer Thomas , Voytek Bradley
Published: May 2020

Complex cognitive functions such as working memory and decision-making require information maintenance over many timescales, from transient sensory stimuli to long-term contextual cues. While theoretical accounts predict the emergence of a corresponding hierarchy of neuronal timescales, direct electrophysiological evidence across the human cortex is lacking. Here, we infer neuronal timescales from invasive intracranial recordings. Timescales increase along the principal sensorimotor-to-association axis across the entire human cortex, and scale with single-unit timescales within macaques. Cortex-wide transcriptomic analysis shows direct alignment between timescales and expression of excitation- and inhibition-related genes, as well as genes specific to voltage-gated transmembrane ion transporters. Finally, neuronal timescales are functionally dynamic: prefrontal cortex timescales expand during working memory maintenance and predict individual performance, while cortex-wide timescales compress with aging. Thus, neuronal timescales follow cytoarchitectonic gradients across the human cortex, and are relevant for cognition in both short- and long-terms, bridging microcircuit physiology with macroscale dynamics and behavior.
Basis of Specificity for a Conserved and Promiscuous Chromatin Remodeling Protein
Authors: Donovan Drake A. , Crandall Johnathan G. , Truong Vi N. , Vaaler Abigail L. , Bailey Thomas B. , Dinwiddie Devin , McKnight Laura E. , McKnight Jeffrey N.
Published: May 2020

Eukaryotic genomes are organized dynamically through the repositioning of nucleosomes. Isw2 is an enzyme that has been previously defined as a genome-wide, non-specific nucleosome spacing factor. Here, we show that Isw2 instead acts as an obligately targeted nucleosome remodelerin vivothrough physical interactions with sequence-specific factors. We demonstrate that Isw2-recruiting factors use small and previously uncharacterized epitopes, which direct Isw2 activity through highly conserved acidic residues in the Isw2 accessory protein Itc1. This interaction orients Isw2 on target nucleosomes, allowing for precise nucleosome positioning at targeted loci. Finally, we show that these critical acidic residues have been lost in theDrosophilalineage, potentially explaining the inconsistently characterized function of Isw2-like proteins. Altogether, these data suggest an “interacting barrier model” where Isw2 interacts with a sequence-specific factor to accurately and reproducibly position a single, targeted nucleosome to define the precise border of phased chromatin arrays.
Alveolar early progenitors in the aged human lung have increased expression of ACE2 accompanied with genes involved in beta-amyloid clearance: Indication of SARS-CoV-2 also using soluble ACE2 in aged-lungs to enter ACE2-negative cells
Authors: Chaudhri Virendra K.
Published: May 2020

COVID-19 is the current pandemic caused by severe acute respiratory syndrome virus 2 (SARS-CoV-2) that uses ACE2 protein on the cell surface. By analyzing publicly available datasets, I uncovered that alveolar early progenitors (AEP), a subset of the type-2 pneumocytes, showed increased ACE2 expression in the older lungs. AEPs co-express TMPRSS2, CTSL. Aged AEP-gene expression signature suggested an active response to beta-amyloid-induced ACE2 shedding, to limit the intercellular beta-amyloid accumulation in otherwise healthy human lungs. Susceptibility of AEP to SARS-CoV2 and ACE2 secretory capacity of these cells makes aged human lung sensitive for rapid-infection, by a possible in-solution ACE2 binding and entry into ACE2-negative cells, thereby increasing the target cell diversity and numbers. Single-cell analysis of COVID19 patients with moderate and severe infections, clearly showed that severe infections showed SARS-CoV-2 transcript in ACE2-negative TMPRSS-negative but CTSL-positive cell types in their bronchoalveolar lavage fluid, validating in-solution ACE2-binding enabling infection.
The fate of SARS-CoV-2 in WWTPs points out the sludge line as a suitable spot for monitoring
Authors: Balboa Sabela , Mauricio-Iglesias Miguel , Rodriguez Santiago , Martínez-Lamas Lucía , Vasallo Francisco J. , Regueiro Benito , Lema Juan M.
Published: May 2020

Abstract

SARS-CoV-2 genetic material is detectable in the faeces of a considerable part of COVID-19 cases and hence, in the urban wastewater. This fact was confirmed early during the spread of the COVID-19 pandemic and prompted several studies that proposed monitoring its incidence by wastewater. This paper studies the fate of SARS-CoV-2 genetic material in wastewater treatment plants using RT-qPCR with a two-fold goal: i) to check the safety of the water effluent and also of the sludge produced and ii) based on the understanding of the virus particles fate, to identify the most suitable spots for detecting the incidence of COVID-19 and monitor its evolution. On the grounds of the affinity of enveloped virus towards biosolids, we hypothesized that the sludge line acts as a concentrator of SARS-CoV-2 genetic material. Sampling several spots in primary, secondary and sludge treatment at the Ourense (Spain) WWTP showed that, in effect, most of SARS-CoV-2 particles cannot be detected in the water effluent as they are retained by the sludge line. We identified the sludge thickener as a suitable spot for detecting SARS-CoV-2 particles thanks to its higher solids concentration (more virus particles) and longer residence time (less sensitive to dilution caused by precipitation). Although more studies will be needed for confirmation, these results contribute to clarify the role of WWTPs in COVID-19 mitigation.
Somatostatin interneurons activated by 5-HT2Areceptor suppress slow oscillations in medial entorhinal cortex
Authors: De Filippo Roberto , Rost Benjamin R. , Stumpf Alexander , Cooper Claire , Tukker John J. , Harms Christoph , Beed Prateep , Schmitz Dietmar
Published: May 2020

Serotonin (5-HT) is one of the major neuromodulators present in the mammalian brain and has been shown to play a role in multiple physiological processes. The mechanisms by which 5-HT modulates cortical network activity, however, are not yet fully understood. We investigated the effects of 5-HT on slow oscillations (SOs), a synchronized cortical network activity universally present across species. SOs are observed during anesthesia and are considered to be the default cortical activity pattern. We discovered that (±)3,4-methylenedioxymethamphetamine (MDMA) and fenfluramine, two potent 5-HT releasers, inhibit SOs within the entorhinal cortex (EC) in anesthetized mice. Combining opto- and pharmacogenetic manipulations within vitroelectrophysiological recordings, we uncovered that somatostatin-expressing (Sst) interneurons activated by the 5-HT2Areceptor (5-HT2AR) play an important role in the suppression of SOs. Since 5-HT2AR signaling is involved in the etiology of different psychiatric disorders and mediates the psychological effects of many psychoactive serotonergic drugs, we propose that the newly discovered link between Sst interneurons and 5-HT will contribute to our understanding of these complex topics.
Investigating the spectral features of the brain meso-scale structure at rest
Authors: Iandolo Riccardo , Semprini Marianna , Sona Diego , Mantini Dante , Avanzino Laura , Chiappalone Michela
Published: May 2020

Recent studies provide novel insights into the meso-scale organization of the brain, highlighting the co-occurrence of different structures: classic assortative (modular), disassortative and core-periphery. However, the spectral properties of the brain meso-scale remain mostly unexplored. To fill this knowledge gap, we investigated how the meso-scale structure is organized across the frequency domain. We analyzed the resting state activity of healthy participants with source-localized high-density electroencephalography signals. Then, we inferred the community structure using weighted stochastic block-modelling to capture the landscape of meso-scale structures across the frequency domain. We found that meso-scale modalities were mixed over the frequency spectrum, with a core-periphery structure predominance. Nevertheless, we also highlighted a selective increase of disassortativity in the delta and theta bands, and of assortativity in the low gamma band (30-50 Hz). We further described other features of the meso-scale organization by identifying those brain regions which, at the same time, i) exhibited the highest degree of assortativity, disassortativity and core-peripheriness (i.e. participation), ii) were consistently assigned to the same community, irrespective from the granularity imposed by WSBM (i.e. granularity-invariance). We defined those brain areas as Participation and Granularity Invariant. In conclusion, we observed that the brain spontaneous activity shows frequency-specific meso-scale organization which may support spatially distributed and local information processing.
The impact of daily caffeine intake on nighttime sleep: signs of overnight withdrawal?
Authors: Weibel Janine , Lin Yu-Shiuan , Landolt Hans-Peter , Kistler Joshua , Rehm Sophia , Rentsch Katharina M. , Slawik Helen , Borgwardt Stefan , Cajochen Christian , Reichert Carolin F.
Published: May 2020

Acute caffeine intake can delay sleep initiation and reduce sleep intensity, particularly when consumed in the evening. However, it is not clear whether these sleep disturbances disappear when caffeine is continuously consumed during daytime, which is common for most coffee drinkers. To address this question, we investigated the sleep of twenty male young habitual caffeine consumers during a double-blind, randomized, crossover study including three 10-day conditions: caffeine (3 x 150 mg caffeine daily), withdrawal (3 x 150 mg caffeine for eight days, then switch to placebo), and placebo (3 x placebo daily). After nine days of continuous treatment, electroencephalographically (EEG)-derived sleep structure and intensity were recorded during a scheduled 8-h nighttime sleep episode starting 8 (caffeine condition) and 15 h (withdrawal condition) after the last caffeine intake. Upon scheduled wake up time, subjective sleep quality and caffeine withdrawal symptoms were assessed. Unexpectedly, neither polysomnography-derived total sleep time, sleep latency, sleep architecture, nor subjective sleep quality differed among placebo, caffeine, and withdrawal conditions. Nevertheless, EEG power density in the sigma frequencies (12-16 Hz) during non-rapid eye movement (NREM) sleep was reduced in both caffeine and withdrawal conditions when compared to placebo. These results indicate that daily caffeine intake in the morning and afternoon hours does not strongly impair nighttime sleep structure or subjective sleep quality in healthy good sleepers who regularly consume caffeine. The reduced EEG power density in the sigma range might represent early signs of overnight withdrawal from the continuous presence of the stimulant during the day.

Statement of Significance

Caffeine consumption is highly prevalent worldwide and has been repeatedly shown to acutely disrupt sleep, particularly when consumed after several days of abstinence or close to bedtime. However, commonly, caffeine is consumed daily and during daytime. Our well-controlled laboratory study revealed that this common pattern of intake affects nighttime sleep differently: While slow-wave sleep duration or slow-wave activity were rather similar compared to placebo, caffeine intake surprisingly reduced EEG power density in the sigma frequencies. In the light of earlier studies, this might present early signs of caffeine withdrawal which occurs due to overnight caffeine abstinence. The present findings provide novel insights into the impact of daily presence and nightly abstinence of caffeine on nighttime sleep in regular consumers.
Epidemiological study on foot-and-mouth disease in small ruminants: sero-prevalence and risk factor assessment in Kenya
Authors: Chepkwony Eunice C. , Gitao George C. , Muchemi Gerald M. , Sangula Abraham K. , Kairu-Wanyoike Salome W.
Published: May 2020

Foot-and-mouth disease (FMD) is endemic in Kenya affecting cloven-hoofed ruminants. The epidemiology of the disease in small ruminants (SR) is not documented. We carried out a cross-sectional study, the first in Kenya, to estimate the sero-prevalence of FMD in SR and the associated risk factors nationally. Selection of animals to be sampled used a multistage cluster sampling approach. Serum samples totaling 7564 were screened for FMD antibodies of Non-Structural-Proteins using ID Screen®NSP Competition ELISA kit. Data were analysed using Statistical Package for Social Studies Version 20. To identify the risk factors, chi-square and logistic regression analyses were used. The country animal level sero-prevalence was 23.3% (95% CI: 22.3-24.3%) while herd level sero-prevalence was 77.6% (95% CI: 73.9-80.9%). Sero-positivity was significantly higher in the pastoral zone (31.5%) than in the sedentary zone at 14.5% (χ2 =303.2, p<0.05). In the most parsimonious backward fitting logistic multivariable regression, the only risk factors that were significantly positively associated with FMD sero-positivity in SR were multipurpose (OR=1.150; p=0.034) and dairy production types (OR=2.029; p=0.003). Those that were significantly negatively associated with FMD sero-positivity were male sex (OR=0.856; p=0.026), young age (OR=0.601; p=0.037), sedentary production zone (OR=0.471; p<0.001), bringing in of SR (OR=0.838; p=0.004), purchase of SR from market/middlemen (OR=0.877; p=0.049), no interaction with wildlife (OR=0.657; p<0.001), mixed production type (OR=0.701; p=0.016), enclosure of SR day and night (OR=0.515; p=0.001), migratory grazing system (OR=0.807; p=0.047), on-farm watering system (OR=0.724; p=0.002), male-from-another-farm (OR=0.723; p=0.030) and artificial insemination (OR=0.357; p=0.008) breeding methods.

This study showed that there is widespread undetected virus circulation in SR indicated by ubiquitous spatial distribution of significant FMD sero-positivity in the country. The risk factors were mainly husbandry related. Strengthening of risk-based FMD surveillance in carrier SR which pose potential risk of virus transmission to other susceptible species is recommended. Adjustment of husbandry practices to control FMD in SR and in-contact species is suggested. Cross-transmission and more risk factors need to be researched.
Coleoborers (Curculionidae: Scolytinae) in native and homogeneous systems of Brazil nut (Bertholletia excelsabonpl.) in the Southern Amazon, Brazil
Authors: Martins e Silva Marcus Henrique , Garlet Juliana , Luis Silva Fernando , da Silva Paula Carla
Published: May 2020

Brazil nut is one of the most important species of the Amazon due to its socioeconomic importance. Especially in homogeneous production systems, it may be susceptible to damage by wood-boring insects, as by the subfamily Scolytinae (Coleoptera: Curculionidae); thus, inadequate management conditions can cause economic damage. Therefore, the objective of the present work is to evaluate the occurrence of wood-boring insects (Curculionidae: Scolytinae) in native and homogeneous systems of Brazil nut in the Meridional Amazonian, Brazil. The study was conducted in three environments: Conserved Native Planting nut, Anthropized Native Planting nut and Homogeneous Planting nut. Twelve ethanol traps were installed in each environment during four sampling periods. The data were submitted to entomofaunistic analysis, Pearson’s correlation analysis and cluster analysis. A total of 2,243 individuals from 31 species were sampled, of which 23 were from the Anthropized Native Planting nut, 24 from the Homogeneous Planting nut and 26 from the Conserved Native Planting nut. In the faunistic analysis, we highlight the speciesXyleborus affinis(Eichhoff, 1868), which was the most representative one in the three environments and a super-dominant species in all four sampling periods. There was a greater similarity between the Anthropized Native Planting nut and the Conserved Native Planting nut; these two environments showed dissimilarity with the Homogeneous Planting nut. Monitoring coleoborers in Brazil nut agroecosystems is fundamental for the establishment of integrated pest management strategies.
N-Aryl Pyrido Cyanine derivatives: nuclear and organelle DNA markers for two-photon and super-resolution imaging
Authors: Uno Kakishi , Sugimoto Nagisa , Sato Yoshikatsu
Published: May 2020

Live cell imaging using DNA-binding fluorescent probes is an essential molecular tool in various biological and biomedical fields. The major challenges in currently used DNA probes are to avoid UV light photo-excitation with high DNA selectivity and cell-permeability and are the availability of the cutting-edge imaging techniques such as a super-resolution microscopy. Herein we report new orange to red fluorogenic DNA probes having N-aryl pyrido cyanine (PC) moiety as a basic skeleton. Their DNA selectivity and cell-permeabilities are so high that organelle DNA as well as nuclear DNA can be clearly stained in various cell types and plant tissues with wash-free manner. PC dyes are also compatible with a stimulated emission depletion fluorescent lifetime imaging microscopy (STED-FLIM) for super-resolution imaging as well as two-photon microscopy for deep tissue imaging, should release the utilization limitation of synthetic DNA probes.
A selective autophagy pathway for phase separated endocytic protein deposits
Authors: Wilfling Florian , Lee Chia-Wei , Erdmann Philipp , Zheng Yumei , Jentsch Stefan , Pfander Boris , Schulman Brenda A. , Baumeister Wolfgang
Published: May 2020

Autophagy eliminates cytoplasmic content selected by autophagy receptors, which link cargoes to the membrane bound autophagosomal ubiquitin-like protein Atg8/LC3. Here, we discover a selective autophagy pathway for protein condensates formed by endocytic proteins. In this pathway, the endocytic yeast protein Ede1 functions as a selective autophagy receptor. Distinct domains within Ede1 bind Atg8 and mediate phase separation into condensates. Both properties are necessary for an Ede1-dependent autophagy pathway for endocytic proteins, which differs from regular endocytosis, does not involve other known selective autophagy receptors, but requires the core autophagy machinery. Cryo-electron tomography of Ede1-containing condensates – at the plasma membrane and in autophagic bodies – shows a phase-separated compartment at the beginning and end of the Ede1-mediated selective autophagy pathway. Our data suggest a model for autophagic degradation of membraneless compartments by the action of intrinsic autophagy receptors.

Highlights

Ede1 is a selective autophagy receptor for aberrant CME protein assemblies

Aberrant CME assemblies form by liquid-liquid phase separation

Core autophagy machinery and Ede1 are important for degradation of CME condensates

Ultrastrucural view of a LLPS compartment at the PM and within autophagic bodies
Meltwater runoff from the Greenland Ice Sheet reveals microbial consortia from contrasting subglacial drainage systems
Authors: Lamarche-Gagnon Guillaume , Anesio Alexandre M. , Wadham Jemma L. , Zarsky Jakub D. , Kohler Tyler J. , Bagshaw Elizabeth A. , Telling Jon , Hawkings Jon R. , Stibal Marek
Published: May 2020

Ice sheets overlay active and putatively widespread microbial ecosystems. An active subglacial biota has the potential to impact strongly on the (bio)geochemistry of local as well as downstream environments. Such impacts partly depend on the distribution of microbial populations, the types of habitats present beneath the ice, and their connectivity. In the ablation zone of the Greenland Ice Sheet (GrIS), supraglacial meltwaters are routed to the ice-sheet bed during the melt season, flushing out subglacial waters, sediments, and cells to proglacial environments via runoff. Here, we report on the diversity, composition, and niche differentiation of microbial assemblages exported in bulk runoff from a large (~600 km2) GrIS catchment. Proglacial river samples were collected over a period of subglacial drainage evolution in order to capture potential shifts in exported microbial community alongside hydrochemical transitions. We use high-resolution hydrochemical and hydrological information from the proglacial river to guide microbial (16S rRNA gene) interpretations. Core populations closely matched sequences previously isolated from other (pro)glacial environments, and phylogenetic characterisation of main OTUs alluded to a central role for subglacial iron, sulphur, and methane cycling. Whilst results indicate that bulk populations exported are likely true members of sub ice-sheet communities, we also find evidence of a supraglacial signature influencing composition of exported assemblages. Changes in assemblage structure accompanied those of major hydrological periods, with enhanced subglacial flushing coinciding with distinct shifts in microbial composition. Timing of sampling therefore matters when attempting to infer more nuanced changes in exported communities, or reveal the biogeochemical processes likely occurring in regions of the bed less influenced by surface melt. This is likely especially true when studying larger glacial systems, which experience complex hydrological changes throughout the melt-season, and that periods of extensive subglacial flushing offer opportunities to assess diversity from more isolated regions of the bed. Still, an apparent strong buffering signal from marginal zones appear to mask some of the diversity intrinsic to more remote, likely anoxic, subglacial niches, which may ultimately only be sampled via direct access to the subsurface.
Assessing the Utility and Accuracy of ICD10-CM Nontraumatic Subarachnoid Hemorrhage Codes for Intracranial Aneurysm Research
Authors: Roark Christopher , Wilson Melissa P. , Kubes Sheila , Mayer David , Wiley Laura K.
Published: May 2020

Background

The 10th revision of International Classification of Disease, Clinical Modification (ICD10-CM) increased the number of codes to identify nontraumatic subarachnoid hemorrhage from one to twenty-two. ICD10-CM codes are able to specify the location of aneurysms causing subarachnoid hemorrhage (aSAH), however it is not clear how frequently or accurately these codes are being used in practice.

Objective

To systematically evaluate the usage and accuracy of location-specific ICD10-CM codes for aSAH.

Methods

We extracted all uses of ICD10-CM codes for nontraumatic subarachnoid hemorrhage (I60.x) during the first three years following the implementation of ICD10-CM from the billing module of the EHR for UCHealth. For those codes that specified aSAH location (I60.0-I60.6), EHR documentation was reviewed to determine whether there was an active aSAH, any patient history of aSAH, or unruptured intracranial aneurysm/s and the locations of those outcomes.

Results

Between October 1, 2015 – September 30, 2018, there were 3,119 instances of nontraumatic subarachnoid hemorrhage ICD10-CM codes (I60.00-I60.9), of which 297 (9.5%) code instances identified aSAH location (I60.0-I60.6). These codes accurately identified current aSAH (64%), any patient history of aSAH (84%), and any patient history of intracranial aneurysm (87%). The accuracy of identified outcome location was 53% in current aSAH, 72% for any history of aSAH, and 76% for any history of an intracranial artery.

Conclusions

Researchers should use ICD10-CM codes with caution when attempting to detect active aSAH and/or aneurysm location.
Aerosol blocking assessment by different types of fabrics for homemade respiratory masks: spectroscopy and imaging study
Authors: Foschini Mauricio , MONTE ADAMO FG , Mendes Ana CM , Scarabucci Renata J , Maletta Alexandre , Giuliani Carla D , Duarte Bruna AR , Del-Claro Kleber
Published: May 2020

During the COVID-19 pandemic, there is no agreement, until the current date, about the recommendations of homemade face mask use for the general population, and one of the reasons is a lack of information about their real protective rule on spreading aerosols and viruses. This is a comparative study regarding the relative efficiencies of commercial respiratory masks (medical masks) and homemade fabric masks, which may guide authorities across the globe, following the 'Advice on the use of masks in the context of COVID-19', by the World Health Organization. We described two optical methodologies for charactering respiratory masks. It happens that the aerosol scattering coefficient is linear as a function of its concentration inside the mask chamber. Quantitative optical properties of scattering for a large batch fabrication of masks were demonstrated, making the mask N95 suitable for use as a reference standard.
Efficacy and harms of remdesivir for the treatment of COVID-19: a systematic review and meta-analysis
Authors: Piscoya Alejandro , Ng-Sueng Luis Fernando , Riego Angela Parra del , Cerna-Viacava Renato , Pasupuleti Vinay , Roman Yuani M. , Thota Priyaleela , White C. Michael , Hernandez Adrian V.
Published: May 2020

Background

We evaluated the efficacy and safety of remdesivir for the treatment of COVID-19.

Methods

Systematic review in five engines, pre-print webpages and RCT registries until May 22, 2020 for randomized controlled trials (RCTs) and observational studies evaluating remdesivir on confirmed, COVID-19 adults with pneumonia and/or respiratory insufficiency. Primary outcomes were all-cause mortality, clinical improvement or recovery, need for invasive ventilation, and serious adverse events (SAE). Secondary outcomes included length of hospital stay, progression of pneumonia, and adverse events (AE). Inverse variance random effects meta-analyses were performed.

Results

Two placebo-controlled RCTs (n=1300) and two case series (n=88) were included. All studies used remdesivir 200mg IV the first day and 100mg IV for 9 more days, and followed up until 28 days. Wang et al. RCT was stopped early due to AEs; ACTT-1 was preliminary reported at 15-day follow up. Time to clinical improvement was not decreased in Wang et al. RCT, but median time to recovery was decreased by 4 days in ACTT-1. Remdesivir did not decrease all-cause mortality (RR 0.71, 95%CI 0.39 to 1.28) and need for invasive ventilation at 14 days (RR 0.57, 95%CI 0.23 to 1.42), but had fewer SAEs (RR 0.77, 95%CI 0.63 to 0.94). AEs were similar between remdesivir and placebo arms. Risk of bias ranged from some concerns to high risk in RCTs.

Interpretation

There is paucity of adequately powered and fully reported RCTs evaluating effects of remdesivir in adult, hospitalized COVID-19 patients. Remdesivir should not be recommended for the treatment of severe COVID-19.
Saliva as a Candidate for COVID-19 Diagnostic Testing: A Meta-Analysis
Authors: Czumbel László Márk , Kiss Szabolcs , Farkas Nelli , Mandel Iván , Hegyi Anita , Nagy Ákos , Lohinai Zsolt , Szakács Zsolt , Hegyi Péter , Steward Martin C. , Varga Gábor
Published: May 2020

Objectives

Our aim was to conduct a meta-analysis on the reliability and consistency of SARS-CoV-2 viral RNA detection in saliva specimens.

Methods

We reported our meta-analysis according to the Cochrane Handbook. We searched the Cochrane Library, Embase, Pubmed, Scopus, Web of Science and clinical trial registries for eligible studies published between 1 January and 25 April 2020. The number of positive tests and total number of conducted tests were collected as raw data. The proportion of positive tests in the pooled data were calculated by score confidence interval estimation with the Freeman-Tukey transformation. Heterogeneity was assessed using the I2 measure and the χ2 test.

Results

The systematic search revealed 96 records after removal of duplicates. 26 records were included for qualitative analysis and 5 records for quantitative synthesis. We found 91% (95%CI = 80%-99%) sensitivity for saliva tests and 98% (95%CI 89%-100%) sensitivity for nasopharyngeal swab (NPS) tests in previously confirmed COVID-19 infected patients, with moderate heterogeneity among studies. Additionally, we identified 18 registered, ongoing clinical trials on saliva-based tests for detection of the virus.

Conclusion

Saliva tests offer a promising alternative to NPS for COVID-19 diagnosis. However, further diagnostic accuracy studies are needed to improve their specificity and sensitivity.
Seek COVER: Development and validation of a personalized risk calculator for COVID-19 outcomes in an international network
Authors: Williams Ross D. , Markus Aniek F. , Yang Cynthia , Salles Talita Duarte , DuVall Scott L. , Falconer Thomas , Jonnagaddala Jitendra , Kim Chungsoo , Rho Yeunsook , Williams Andrew , Alberga Amanda , An Min Ho , Aragón María , Areia Carlos , Burn Edward , Choi Young Hwa , Drakos Iannis , Fernandes Abrahão Maria Tereza , Fernández-Bertolín Sergio , Hripcsak George , Kaas-Hansen Benjamin Skov , Kandukuri Prasanna L , Kors Jan A. , Kostka Kristin , Liaw Siaw-Teng , Lynch Kristine E. , Machnicki Gerardo , Matheny Michael E. , Morales Daniel , Nyberg Fredrik , Park Rae Woong , Prats-Uribe Albert , Pratt Nicole , Rao Gowtham , Reich Christian G. , Rivera Marcela , Seinen Tom , Shoaibi Azza , Spotnitz Matthew E , Steyerberg Ewout W. , Suchard Marc A. , You Seng Chan , Zhang Lin , Zhou Lili , Ryan Patrick B. , Prieto-Alhambra Daniel , Reps Jenna M. , Rijnbeek Peter R.
Published: May 2020

Objective

To develop and externally validate COVID-19 Estimated Risk (COVER) scores that quantify a patient’s risk of hospital admission (COVER-H), requiring intensive services (COVER-I), or fatality (COVER-F) in the 30-days following COVID-19 diagnosis.

Methods

We analyzed a federated network of electronic medical records and administrative claims data from 14 data sources and 6 countries. We developed and validated 3 scores using 6,869,127 patients with a general practice, emergency room, or outpatient visit with diagnosed influenza or flu-like symptoms any time prior to 2020. The scores were validated on patients with confirmed or suspected COVID-19 diagnosis across five databases from South Korea, Spain and the United States. Outcomes included i) hospitalization with pneumonia, ii) hospitalization with pneumonia requiring intensive services or death iii) death in the 30 days after index date.

Results

Overall, 44,507 COVID-19 patients were included for model validation. We identified 7 predictors (history of cancer, chronic obstructive pulmonary disease, diabetes, heart disease, hypertension, hyperlipidemia, kidney disease) which combined with age and sex discriminated which patients would experience any of our three outcomes. The models achieved high performance in influenza. When transported to COVID-19 cohorts, the AUC ranges were, COVER-H: 0.69-0.81, COVER-I: 0.73-0.91, and COVER-F: 0.72-0.90. Calibration was overall acceptable.

Conclusions

A 9-predictor model performs well for COVID-19 patients for predicting hospitalization, intensive services and fatality. The models could aid in providing reassurance for low risk patients and shield high risk patients from COVID-19 during de-confinement to reduce the virus’ impact on morbidity and mortality.
Deteriorated Covid19 control due to delayed lockdown resulting from strategic interactions between Governments and oppositions
Authors: Carrozzo-Magli Alessio , d’Onofrio Alberto , Manfredi Piero
Published: May 2020

Background

In many European countries and the US, the burden of Covid-19 epidemic could be much lower if Governments had been able to learn from the China and Lombardy stories and to declare full lockdown without delays.

Methods

We use a simple game-theoretic framework for the strategic interaction between the Government, political oppositions and lobbies, combined with a Covid-19 transmission model, to analyse the role of political factors delaying the lockdown declaration, depending on the degrees of “responsibility” of political actors.

Results

The lockdown can always be declared immediately (i.e., without delay) as sustained transmission arises, only if the government feels fully “responsible” towards all citizens. If this is not the case, epidemic growth will eventually dominate the agents’ payoffs, so that sooner or later the lockdown will always be declared i.e., both the government and the opposition will be forced by the epidemic to switch towards a higher degree of responsibility, but with a delay. There is a further nontrivial situation where the lockdown can be declared without delay, occurring when the political opposition is at least as responsible as the Government. This however requires the solution of a coordination issue, which cannot be taken for granted. Eventually, a vicious circle emerges, where the delayed lockdown requires a much longer lockdown period to achieve adequate control results, thereby causing the explosion of economic losses and so calling for unlocking long before it should.

Conclusions

Lockdown delays have dramatically worsened the impact of the current Covid-19 wave in a number of countries. Citizens should be made cogently aware of this to claim maximal responsibility from political actors and economic lobbies to avoid that such stories repeat in the future when further threats, due to Covid-19 itself or other pathogens, will re-appear.