bluuebunny/crossref_metadata_2025 huggingface dataset:
Intralaboratory evaluation of luminescence based high-throughput Serum Bactericidal Assay (L-SBA) to determine bactericidal activity of human sera againstShigella
Authors: Rossi O. , Molesti E. , Saul A. , Giannelli C. , Micoli F. , Necchi F.
Published: April 2020

Despite the huge decrease in deaths caused byShigellaworldwide in the last decades, shigellosis is still causing over 200,000 deaths every year. No vaccine is currently available, and the morbidity of disease coupled with the rise of antimicrobial resistance renders the introduction of an effective vaccine extremely urgent. Although a clear immune correlate of protection against shigellosis has not been established yet, the demonstration of bactericidal activity of antibodies induced upon vaccination may provide one means of functionality of antibodies induced on protecting againstShigella.The method of choice to evaluate the complement-mediated functional activity of vaccine-induced antibodies is the Serum Bactericidal Assay (SBA).

Here we present the development and intra-laboratory characterisation of a high-throughput luminescence-based SBA (L-SBA) method, based on the detection of ATP as a proxy of surviving bacteria, to evaluate the complement-mediated killing of human sera. We demonstrated the high specificity of the assay against homologous strain without any heterologous aspecificity detected against species-related and not species-related strains. We assessed linearity, repeatability and reproducibility of L-SBA on human sera.

This work will guide the bactericidal activity assessment of clinical sera raised againstS. sonnei.The method has the potential of being applicable with similar performances to determine bactericidal activity of any non-clinical and clinical sera that rely on complement mediated killing.

IMPORTANCE

Shigellais an important cause of diarrhoea worldwide and antimicrobial resistance is on rise, thus efforts by several groups are ongoing to produce a safe and effective vaccine against shigellosis. Although a clear immune correlate of protection has not been established, demonstration of bactericidal capacity of sera from patients immunised withShigellavaccines may provide one means of protecting against shigellosis. We have developed and fully characterised a novel high-throughput L-SBA method for evaluation of functionality of antibodies raised againstS. sonneiin human sera. This work will allow the clinical testing of human sera raised against GMMA-based and potentially all vaccines producing antibodies than can workviacomplement mediated manner.
ACE2gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population
Authors: Elisa Benetti , Rossella Tita , Ottavia Spiga , Andrea Ciolfi , Giovanni Birolo , Alessandro Bruselles , Gabriella Doddato , Annarita Giliberti , Caterina Marconi , Francesco Musacchia , Tommaso Pippucci , Annalaura Torella , Alfonso Trezza , Floriana Valentino , Margherita Baldassarri , Alfredo Brusco , Rosanna Asselta , Mirella Bruttini , Simone Furini , Marco Seri , Vincenzo Nigro , Giuseppe Matullo , Marco Tartaglia , Francesca Mari , Alessandra Renieri , Maria Pinto Anna
Published: April 2020

In December 2019, an initial cluster of interstitial bilateral pneumonia emerged in Wuhan, China. A human-to-human transmission was assumed and a previously unrecognized entity, termed coronavirus-disease-19 (COVID-19) due to a novel coronavirus (SARS-CoV-2) was described. The infection has rapidly spread out all over the world and Italy has been the first European country experiencing the endemic wave with unexpected clinical severity in comparison with Asian countries.

It has been shown that SARS-CoV-2 utilizes angiotensin converting enzyme 2 (ACE2) as host receptor and host proteases for cell surface binding and internalization. Thus, a predisposing genetic background can give reason for inter-individual disease susceptibility and/or severity. Taking advantage of the Network of Italian Genomes (NIG), here we mined whole-exome-sequencing data of 6930 Italian control individuals from five different centers looking forACE2variants. A number of variants with a potential impact on protein stability were identified. Among these, three more common missense changes, p.(Asn720Asp), p.(Lys26Arg), p.(Gly211Arg) were predicted to interfere with protein structure and stabilization. Rare variants likely interfering with the internalization process, namely p.(Leu351Val) and p.(Pro389His), predicted to interfere with SARS-CoV-2 spike protein binding, were also observed. Comparison ofACE2WES data between a cohort of 131 patients and 258 controls allowed identifying a statistically significant (P value <0,029) higher allelic variability in controls compared to patients. These findings suggest that a predisposing genetic background may contribute to the observed inter-individual clinical variability associated with COVID-19, allowing an evidence-based risk assessment leading to personalized preventive measures and therapeutic options.
Classification of Coronavirus Images using Shrunken Features
Authors: Ozturk Saban , Ozkaya Umut , Barstugan Mucahid
Published: April 2020

Necessary screenings must be performed to control the spread of the Corona Virus (COVID-19) in daily life and to make a preliminary diagnosis of suspicious cases. The long duration of pathological laboratory tests and the wrong test results led the researchers to focus on different fields. Fast and accurate diagnoses are essential for effective interventions with COVID-19. The information obtained by using X-ray and Computed Tomography (CT) images is vital in making clinical diagnoses. Therefore it was aimed to develop a machine learning method for the detection of viral epidemics by analyzing X-ray images. In this study, images belonging to 6 situations, including coronavirus images, are classified. Since the number of images in the dataset is deficient and unbalanced, it is more convenient to analyze these images with hand-crafted feature extraction methods. For this purpose, firstly, all the images in the dataset are extracted with the help of four feature extraction algorithms. These extracted features are combined in raw form. The unbalanced data problem is eliminated by producing feature vectors with the SMOTE algorithm. Finally, the feature vector is reduced in size by using a stacked auto-encoder and principal component analysis to remove interconnected features in the feature vector. According to the obtained results, it is seen that the proposed method has leveraging performance, especially in order to make the diagnosis of COVID-19 in a short time and effectively.
Monitoring Italian COVID-19 spread by an adaptive SEIRD model
Authors: Piccolomini Elena Loli , Zama Fabiana
Published: April 2020

Due to the recent diffusion of COVID-19 outbreak, the scientific community is making efforts in analysing models for understanding the present situation and predicting future scenarios. In this paper, we propose a Susceptible-Infected-Exposed-Recovered-Dead (SEIRD) differential model [Weitz J. S. and Dushoff J., Scientific reports, 2015] for the analysis and forecast of the COVID-19 spread in Italian regions, using the data from the Italian Protezione Civile from February 24th 2020. In this study, we investigate an adaptation of SEIRD that takes into account the actual policies of the Italian government, consisting of modelling the infection rate as a time-dependent function (SEIRD(rm)). Preliminary results on Lombardia and Emilia-Romagna regions confirm that SEIRD(rm) fits the data more accurately than the original SEIRD model with constant rate infection parameter. Moreover, the increased flexibility in the choice of the infection rate function makes it possible to better control the predictions due to the lockdown policy.
What does simple power law kinetics tell about our response to coronavirus pandemic?
Authors: Jha Prateek K.
Published: April 2020

Coronavirus pandemic of 2019-2020 has already affected over a million people and caused over 50,000 deaths worldwide (as on April 3, 2020). Roughly half of the world population has been asked to work from home and practice social distancing as the search for a vaccine continues. Though government interventions such as lockdown and social distancing are theoretically useful, its debatable whether such interventions are effective in flattening the curve, which is ceasing or reducing the growth of infection in control populations. In this article, I present a simple power law model that enables a comparison of countries in time windows of 14 days since first coronavirus related death is reported in that country. It therefore provides means to access the efficacy of above interventions.
Clinical meanings of rapid serological assay in patients tested for SARS-Co2 RT-PCR
Authors: VirgilioParadiso Angelo , De Summa Simona , Loconsole Daniela , Procacci Vito , Sallustio Anna , Centrone Francesca , Silvestris Nicola , Cafagna Vito , De Palma Giuseppe , Tufaro Antonio , Garrisi Vito , Chironna Maria
Published: April 2020

Background

RT-PCR test for identification of viral nucleic acid is the current standard diagnostic method for the diagnosis of COVID-19 disease but technical reasons limit the utilization of this assay onlarge scalescreenings.

Method

We verified in a consecutive series of 191 symptomatic patients the clinical information that new rapid serological colorimetric test qualitatively analyzing IgM/IgG expression can provide with respect to standard assay and with respect to clinical outcome of patients.

Results

Rapid serological test showed a sensitivity of 30% and a specificity of 89% with respect to the standard assay but, interestingly, these performances improve after 8 days of symptoms appearance. After 10 days of symptoms the predictive value of rapid serological test is higher than that of standardassay. When the behaviour of the two immunoglobulins was evaluated with respect to time length of symptoms appaerance, no significant difference in immunoglobulins behaviour was shown.

Conclusions

The rapid serological test analyzed in the present study is candidate to provide information on immunoreaction of the subject to COVID-19 exposure.
Computational Recipe for Designing Antibodies against the Ebola Virus
Authors: Farimani Amir Barati , Aluru Narayana R. , Tajkhorshid Emad , Jakobsson Eric
Published: April 2020

A conceptual basis for antiviral therapy is to deliver a synthetic antibody that binds to a viral surface protein, and thus prevents the virus from deploying its cell-entry mechanism. The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. In this paper, we devised a computational recipe to predict both the viral escape mutations and the possible inhibitory synthetic antibodies. We combined bioinformatics, structural biology, and molecular dynamics (MD) simulations to explore the most likely viral mutations and the candidate antibodies that can inhibit those escape mutations. Specifically, using the crystal structures of the Sudan and Zaire Ebola viral GPs in complex to their respective antibodies (ABs), we have performed an extensive set of MD simulations, both on the wild-type structures and on a large array of additional complexes designed and generated through combinatorial mutations. We discovered that our methods enabled the successful redesign of antibody sequences to essentially all likely glycoprotein mutations. Our findings and the computational methodology developed here for general antibody design can facilitate therapy of current and possibly next generations of viruses.

Significance of the Manuscript

This manuscript has high significance both methodologically and in potential biomedical application. In methodology, the manuscript combines molecular dynamics, Monte Carlo calculations, and bioinformatics in a novel way to simulate the evolutionary arms race between an evolving viral coat protein and a counter-evolving antibody against the virus. This simulation is shown to provide a method for designing a synthetic antibody against the newly emerging viral strains. This work is done in the context of ongoing work in other laboratories in which cells can be induced to produce synthetic antibodies and those synthetic antibodies can be edited (via, for example, CRISPR) to have an arbitrary sequence in the region that binds the viral coat protein. Putting those experimental methods together with the computational methods we present in this paper has the potential to provide a important approach to produce antibodies-on-demand against evolving viruses.
Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines
Authors: Mei Wenwen , Jiang Zhiwen , Chen Yang , Chen Li , Sancar Aziz , Jiang Yuchao
Published: April 2020

Circadian rhythms are oscillations of behavior, physiology, and metabolism in many organisms. Recent advancements in omics technology make it possible for genome-wide profiling of circadian rhythms. Here, we conducted a comprehensive analysis of seven existing algorithms commonly used for circadian rhythm detection. Using gold-standard circadian and non-circadian genes, we systematically evaluated the accuracy and reproducibility of the algorithms on empirical datasets generated from various omics platforms under different experimental designs. We also carried out extensive simulation studies to test each algorithm’s robustness to key variables, including sampling patterns, replicates, waveforms, signal-to-noise ratios, uneven samplings, and missing values. Furthermore, we examined the distributions of the nominal p-values under the null and raised issues with multiple testing corrections using traditional approaches. With our assessment, we provide method selection guidelines for circadian rhythm detection, which are applicable to different types of high-throughput omics data.

Key points

Various methods have been developed for circadian rhythm detection on a genome-wide scale using omics technologies, yet there has not been a comprehensive summary and evaluation of all existing methods to date.

Using gold-standard circadian and non-circadian genes, we systematically evaluated the accuracy and reproducibility of seven existing algorithms for circadian rhythm detection on empirical datasets generated from various omics platforms.

We carried out extensive simulation studies to test each algorithm’s robustness to key variables, including sampling patterns, replicates, waveforms, signal-to-noise ratios, uneven samplings, and missing values.

We examined the distributions of the nominal p-values under the null and raised issues with multiple testing corrections using the Benjamini-Hochberg procedure due to gene-gene correlation and testing being overly conservative.

We provide method selection guidelines for circadian rhythm detection, which are applicable to different types of high-throughput omics data.
Post-synaptic morphology of mouse neuromuscular junctions is linked to muscle fibre type
Authors: Mech Aleksandra M. , Brown Anna-Leigh , Schiavo Giampietro , Sleigh James N.
Published: April 2020

The neuromuscular junction (NMJ) is the highly specialised peripheral synapse formed between lower motor neuron terminals and muscle fibres. Post-synaptic acetylcholine receptors (AChRs), which are found in high density in the muscle membrane, bind to acetylcholine released into the synaptic cleft of the NMJ, ultimately facilitating the conversion of motor action potentials to muscle contractions. NMJs have been studied for many years as a general model for synapse formation, development and function, and are known to be early sites of pathological changes in many neuromuscular diseases. However, information is limited on the diversity of NMJs in different muscles, whether muscle fibre type impacts NMJ morphology and growth, and the relevance of these parameters to neuropathology. Here, this crucial gap was addressed using a robust and standardised semi-automated workflow called NMJ-morph to quantify features of pre- and post-synaptic NMJ architecture in an unbiased manner. Five wholemount muscles from wild-type mice were dissected and compared at immature (post-natal day, P7) and early adult (P31-32) timepoints. Post-synaptic AChR morphology was found to be more variable between muscles than that of the motor neuron terminal and there were greater differences in the developing NMJ than at the mature synapse. Post-synaptic architecture, but not neuronal morphology or post-natal synapse growth, correlates with fibre type and is largely independent of muscle fibre diameter. Counter to previous observations, this study indicates that smaller NMJs tend to innervate muscles with higher proportions of fast twitch fibres and that NMJ growth rate is not conserved across all muscles. Furthermore, healthy pre- and post-synaptic NMJ morphological parameters were collected for five anatomically and functionally distinct mouse muscles, generating reference data that will be useful for the future assessment of neuromuscular disease models.

Graphical Abstract
Structure of intact human MCU supercomplex with the auxiliary MICU subunits
Authors: Zhuo Wei , Zhou Heng , Guo Runyu , Yi Jingbo , Yu Lei , Sui Yinqiang , Zhang Laixing , Zeng Wenwen , Wang Peiyi , Yang Maojun
Published: April 2020

The mitochondrial Ca2+uniporter (MCU) supercomplex is essential for mitochondrial Ca2+uptake. Here, we present high-resolution cryo-EM structures of human MCU-EMRE supercomplex (MES, 3.41 Å) and MCU-EMRE-MICU1-MICU2 supercomplex (MEMMS, 3.64 Å). MES adopts a V-shaped dimer architecture comprising two hetero-octamers, and a pair of MICU1-MICU2 hetero-dimers form a bridge across the two halves of MES to constitute an O-shaped architecture of MEMMS. The MES and MEMMS pore profiles are almost identical, with Ca2+in the selectivity filters and no obstructions, indicating both channels are conductive. Contrary to the current model in which MICUs block the MCU pore, MICU1-MICU2 dimers are located on the periphery of the MCU pores and do not occlude them. However, MICU1-MICU2 dimers may modulate MCU gating by affecting the matrix gate through the EMRE lever.
EngineeringYarrowia lipolyticaas a chassis forde novosynthesis of five aromatic-derived natural products and chemicals
Authors: Gu Yang , Ma Jingbo , Zhu Yonglian , Ding Xinyu , Xu Peng
Published: April 2020

Abstracts

Yarrowia lipolyticais a novel microbial chassis to upgrade renewable low-cost carbon feedstocks to high-value commodity chemicals and natural products. In this work, we systematically characterized and removed the rate-limiting steps of the shikimate pathway and achievedde novosynthesis of five aromatic chemicals inY. lipolytica. We determined that eliminating amino acids formation and engineering feedback-insensitive DAHP synthases are critical steps to mitigate precursor competition and relieve the feedback regulation of shikimate pathway. Further overexpression of heterologous phosphoketolase and deletion of pyruvate kinase provided a sustained metabolic driving force that channels E4P (erythrose 4-phosphate) and PEP (phosphoenolpyruvate) precursors through the shikimate pathway. Precursor competing pathways and byproduct formation pathways were also blocked by inactivating chromosomal genes. To demonstrate the utility of our engineered chassis strain, three natural products, 2-phenylethanol (2-PE),p-coumaric acid and violacein, which were derived from phenylalanine, tyrosine and tryptophan, respectively, were chosen to test the chassis performance. We obtained 2426.22 ± 48.33 mg/L of 2-PE, 593.53 ± 28.75 mg/L ofp-coumaric acid, 12.67 ± 2.23 mg/L of resveratrol, 366.30 ± 28.99 mg/L of violacein and 55.12 ± 2.81 mg/L of deoxyviolacein from glucose in shake flask. The 2-PE production represents a 286-fold increase over the initial strain (8.48 ± 0.50 mg/L). Specifically, we obtained the highest 2-PE, violacein and deoxyviolacein titer ever reported from thede novoshikimate pathway in yeast. These results set up a new stage of engineeringY. lipolyticaas a sustainable biorefinery chassis strain forde novosynthesis of aromatic compounds with economic values.
Action-based organization and function of cerebellar cortical microcircuits
Authors: Cerminara Nadia L , Garwicz Martin , Darch Henry , Houghton Conor , Marple-Horvat Dilwyn E , Apps Richard
Published: April 2020

The cerebellum is the largest sensorimotor structure in the brain, but its mode of operation is not well understood. However, a fundamental organizational feature of the cerebellar cortex is division into elongated zones, defined by their inputs from specific parts of the inferior olive and Purkinje cell output to cerebellar and vestibular nuclei. Little is known about how the pattern of neuronal activity in zones, and their functional microcircuit subdivisions, microzones, is related to behaviour in awake animals. Here, we studied the organization of microzones within the C3 zone and their activity during a skilled forelimb reaching task in cats. Neurons in different parts of the C3 zone, functionally determined by receptive field characteristics, differed in their patterns of activity during movement. Our results suggest that the cerebellar C3 zone is organized and operates within an action-based frame of reference, with different microcircuits within the zone controlling specific muscle synergies.
Monocyte recruitment to the inflamed central nervous system: migration pathways and distinct functional polarization
Authors: Ivan Daniela C. , Walthert Sabrina , Locatelli Giuseppe
Published: April 2020

The central nervous system (CNS) parenchyma is enclosed by anatomical interfaces including multilayered meninges, the blood-brain barrier (BBB), the choroid plexuses within ventricles and the glia limitans. These border areas hold distinct functional specializations which control the trafficking of monocyte-derived cells toward the CNS parenchyma, altogether maintaining CNS homeostasis. By crossing activated endothelial, epithelial and glial borders, circulating leukocytes gain however access to the CNS parenchyma in several inflammatory diseases including multiple sclerosis.

Studies in animal models of neuroinflammation have helped describing the phenotypic specifications of these invading monocyte-derived cells, able to exert detrimental or beneficial functions depending on the local environment. In this context,in vivovisualization of iNOS+pro-inflammatory and arginase-1+anti-inflammatory macrophages has recently revealed that these distinct cell phenotypes are highly compartmentalized by CNS borders. While arginase-1+macrophages densely populate the leptomeninges, iNOS+macrophages rather accumulate in perivascular spaces and at the pia mater-CNS parenchymal interface.

How and where these macrophages acquire their functional commitment, and whether differentially-activated monocyte-derived cells infiltrate the CNS through distinct gateways, remains however unclear.

In this study, we have investigated the interaction of monocyte-derived macrophages with endothelial (BBB) and epithelial (choroid plexus) barriers of the CNS, bothin vitroandin vivo. By using primary mouse brain microvascular endothelial cells asin vitromodel of the BBB, we observed that, compared to unpolarized primary macrophages, adhesion of functionally-committed macrophages to endothelial cells was drastically reduced, literally abrogating their diapedesis across the BBB. Conversely, when interacting with an activated choroid plexus epithelium, both pro- and anti-inflammatory macrophages displayed substantial adhesive and migratory properties. Accordingly,in vivoanalysis of choroid plexuses revealed increased macrophage trafficking and a scattered presence of polarized cells upon induction of anti-CNS inflammation.

Altogether, we show that acquisition of distinct macrophage polarizations significantly alters the adhesive and migratory properties of these cells in a barrier-specific fashion. While monocytes trafficking at the level of the BBB seem to acquire their signature phenotype only following diapedesis, other anatomical interfaces can be the entry site for functionally activated monocyte-derived cells. Our study highlights the choroid plexus as a key access gateway for macrophages during neuroinflammation, and its stroma as a potential priming site for their functional polarization.
Reward impacts visual statistical learning
Authors: Park Su Hyoun , Rogers Leeland L. , Johnson Matthew R. , Vickery Timothy J.
Published: April 2020

Humans automatically detect and remember regularities in the visual environment—a type of learning termed visual statistical learning (VSL). Many aspects of learning from reward resemble statistical learning in respects, yet whether and how reward learning impacts VSL is largely unexamined. In two studies, we found that reward contingencies affect VSL, with high-value associated with stronger behavioral and neural signatures of such learning than low-value images. In Experiment 1, participants learned values (high or low) of images through a trial-and-error risky choice task. Unbeknownst to them, images were paired as four types—High-High, High-Low, Low-High, and Low-Low. In subsequent recognition and reward memory tests, participants chose the more familiar of two pairs (a target and a foil) and recalled the value of images. We found better recognition when the first images of pairs have high-values, with High-High pairs showing the highest recognition rate. In Experiment 2, we provided evidence that brain responses were affected by both value and statistical contingencies. When we compared responses between the high-value first image and the low-value first image, greater activation in regions that included inferior frontal gyrus, anterior cingulate gyrus, hippocampus, among other regions were found. These findings were driven by the interaction between statistically structured information and reward—the same value contrast yielded no regions for second-image contrasts and for singletons. Our results suggested that the powerful allocation of attention in response to the high-value first image potentially enables better memory for statistically learned pairs and reward information than low-value first image.
Mental geometry of perceiving 3D size in pictures
Authors: Maruya Akihito , Zaidi Qasim
Published: April 2020

We show that the classical problem of 3D size perception in obliquely viewed pictures can be understood by comparing human performance to the optimal geometric solution. A photograph seen from the camera position, forms the same retinal projection as the physical 3D scene, but retinal projections of sizes and shapes are distorted in oblique viewing. For real scenes, we previously showed that size and shape inconstancy result despite observers using the correct geometric back-transform, because some retinal images evoke misestimates of viewing elevation. Now, we examine how observers estimate 3D sizes in oblique views of pictures of objects in different poses on the ground. Compared to the camera position estimates, sizes in oblique views were seriously underestimated for objects at fronto-parallel poses, but there was almost no change for objects perceived as pointing towards the viewer. The inverse of the function relating projected length to pose, camera elevation and viewing azimuth, gives the optimal correction factor for inferring correct 3D lengths if the elevation and azimuth are estimated accurately. Empirical correction functions had similar shapes to optimal, but lower amplitude. Measurements revealed that observers systematically underestimated viewing azimuth, similar to the fronto-parallel bias for object pose perception. A model that adds underestimation of viewing azimuth to the geometrical back-transform, provided good fits to estimated 3D lengths from oblique views. These results add to accumulating evidence that observers use internalized projective geometry to perceive sizes, shapes and poses in 3D scenes and their pictures.
Incorporating selfing to purge deleterious alleles in a cassava genomic selection program
Authors: Somo Mohamed , Jannink Jean-Luc
Published: April 2020

Cassava has been found to carry high levels of recessive deleterious mutations and it is known to suffer from inbreeding depression. Breeders therefore consider specific approaches to decrease cassava’s genetic load. Using self fertilization to unmask deleterious recessive alleles and therefore accelerate their purging is one possibility. Before implementation of this approach we sought to understand better its consequences through simulation. Founder populations with high directional dominance were simulated using a natural selection forward simulator. The founder population was then subjected to five generations of genomic selection in schemes that did or did not include a generation of phenotypic selection on selfed progeny. We found that genomic selection was less effective under the directional dominance model than under the additive models that have commonly been used in simulations. While selection did increase favorable allele frequencies, increased inbreeding during selection caused decreased gain in genotypic values under the directional dominance. While purging selection on selfed individuals was effective in the first breeding cycle, it was not effective in later cycles, an effect we attributed to the fact that the generation of selfing decreased the relatedness of the genomic prediction training population from selection candidates. That decreased relatedness caused genomic prediction accuracy to be lower in schemes incorporating selfing. We found that selection on individuals partially inbred by one generation of selfing did increase mean genetic value of the partially inbred population, but that this gain was accompanied by a relatively small increase in favorable allele frequencies such that improvement in the outbred population was lower than might have been intuited.
Characterization of exosporium layer variability ofClostridioides difficilespores in the epidemically relevant strain R20291
Authors: Pizarro-Guajardo Marjorie , Calderón Paulina , Romero-Rodriguez Alba , Paredes-Sabja Daniel
Published: April 2020

Clostridioides difficileis a Gram-positive anaerobic intestinal pathogenic bacterium and the causative agent of antibiotic-associated diarrhea and spores are the transmission vehicle of the disease. InC. difficilespores, the outermost exosporium layer is the first barrier of interaction with the host and should carry spore ligands involved in spore-host interactions.C. difficileforms two types of spores (i.e., thin and thick exosporium layers). In this communication, we contribute to understand several biological aspects of these two exosporium morphotypes. By transmission electron microscopy, we demonstrate that both exosporium morphotypes appear simultaneously during sporulation and that the laminations of the spore-coat are formed under anaerobic conditions. Nycodenz density-gradient allows enrichment of spores with a thick-exosporium layer morphotype and presence of polar appendage. Using translational fluorescent fusions with exosporium proteins BclA3, CdeA, CdeC and CdeM as well as with several spore coat proteins, we observed that expression intensity and distribution of SNAP-translational fusions in R20291 strain is highly heterogeneous. Electron micrographs demonstrate that multicopy expression of CdeC, but not CdeM, SNAP translational fusion, increases the abundance of the thick exosporium morphotype. Collectively, these results raise further questions on how these distinctive exosporium morphotypes are made during spore formation.
Citrus vascular proteomics highlights the role of peroxidases and serine proteases during Huanglongbing disease progression
Authors: Franco Jessica Y. , Thapa Shree P. , Pang Zhiqian , Gurung Fatta B. , Liebrand Thomas W.H. , Stevens Danielle M , Ancona Veronica , Wang Nian , Coaker Gitta
Published: April 2020

Huanglongbing (HLB) is the most devastating and widespread citrus disease. All commercial citrus varieties are susceptible to the HLB-associated bacterium,CandidatusLiberibacter asiaticus (CLas), which resides in the phloem. The phloem is part of the plant vascular system and is involved in sugar transport. To investigate the plant response toCLas, we enriched for proteins surrounding the phloem in an HLB susceptible sweet orange variety, Washington navel (Citrus sinensis(L) Osbeck). Quantitative proteomics revealed global changes in the citrus proteome afterCLas inoculation. Plant metabolism and translation were suppressed, while defense-related proteins such as peroxidases, proteases and protease inhibitors were induced in the vasculature. Transcript accumulation and enzymatic activity of plant peroxidases in CLas infected sweet orange varieties under greenhouse and field conditions were assessed. While peroxidase transcript accumulation was induced inCLas infected sweet orange varieties, peroxidase enzymatic activity varied. Specific serine proteases were upregulated in Washington navel in the presence ofCLas based on quantitative proteomics. Subsequent activity-based protein profiling revealed increased activity of two serine proteases, and reduced activity of one protease in twoC. sinensissweet orange varieties under greenhouse and field conditions. The observations in the current study highlight global reprogramming of the citrus vascular proteome and differential regulation of enzyme classes in response toCLas infection. These results open an avenue for further investigation of diverse responses to HLB across different environmental conditions and citrus genotypes.
Learning to see the Ebbinghaus illusion in the periphery reveals a top-down stabilization of size perception across the visual field
Authors: Eymond Cécile , Malkinson Tal Seidel , Naccache Lionel
Published: April 2020

Our conscious visual perception relies on predictive signals, notably in the periphery where sensory uncertainty is high. We investigated how such signals could support perceptual stability of objects’ size across the visual field. When attended carefully, the same object appears slightly smaller in the periphery compared to the fovea. Could this perceptual difference be encoded as a strong prior to predict the peripheral perceived size relative to the fovea? Recent studies emphasized the role of foveal information in defining peripheral size percepts. However, they could not disentangle bottom-up from top-down mechanisms. Here, we revealed a pure top-down contribution to the perceptual size difference between periphery and fovea. First, we discovered a novel Ebbinghaus illusion effect, inducing a typical reduction of foveal perceived size, but a reversed increase effect in the periphery. The size percept was similar at both retinal locations and deviated from the classic perceptual difference. Then through an updating process of successive peripheral-foveal viewing, the unusual peripheral perceived size decreased. The classic perceptual eccentricity difference was restored and the peripheral illusion effect changed into a fovea-like reduction. Therefore, we report the existence of a prior that actively shapes peripheral size perception and stabilizes it relative to the fovea.
Urine proteome changes in an α-synuclein transgenic mouse model of Parkinson’s disease
Authors: Li Lujun , Pan Xuanzhen , Wang Ting , Hua Yuanrui , Gao Youhe
Published: April 2020

Urine accommodates more changes than other fluids, and it is a good source in the search for early sensitive biomarkers. The present study collected urine samples from 2-, 4-, 6-, 8- and 10-month-old α-synuclein transgenic mice. Based on data-independent acquisition (DIA) technology, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for quantitative analysis. Seventeen human homologous differential proteins were screened and compared with those in the urine of 2-month-old mice, and 9 proteins were related to Parkinson’s disease (PD). Formin-2, Splicing factor 3A subunit 1, and Isopentenyl-diphosphate Delta-isomerase 1 changed continuously in months 6, 8 and 10. These experiments and analyses demonstrated that the urine proteome reflected the development of α-synuclein transgenic mice and provided clues for the early clinical diagnosis of PD.
“Amantadine disrupts lysosomal gene expression; potential therapy for COVID19”
Authors: Smieszek Sandra P. , Przychodzen Bart P , Polymeropoulos Mihael H
Published: April 2020

SARS-coronavirus 2 is the causal agent of the COVID-19 outbreak. SARS-Cov-2 entry into a cell is dependent upon binding of the viral spike (S) protein to cellular receptor and on cleavage of the spike protein by the host cell proteases such as Cathepsin L and Cathepsin B. CTSL/B are crucial elements of lysosomal pathway and both enzymes are almost exclusively located in the lysosomes.CTSL disruption offers potential for CoVID-19 therapies. The mechanisms of disruption include: decreasing expression of CTSL, direct inhibition of CTSL activity and affecting the conditions of CTSL environment (increase pH in lysosomes).

We have conducted a high throughput drug screen gene expression analysis to identify compounds that would downregulate the expression of CTSL/CTSB. One of the top significant results shown to downregulate the expression of the CTSL gene is Amantadine. Amantadine was approved by the US Food and Drug Administration in 1968 as a prophylactic agent for influenza and later for Parkinson’s disease. It is available as a generic drug..

Amantadine in addition to downregulating CTSL appears to further disrupt lysosomal pathway, hence interfering with the capacity of the virus to replicate. It acts as a lysosomotropic agent altering the CTSL functional environment. We hypothesize that Amantadine could decrease the viral load in SARS-CoV-2 positive patients and as such it may serve as a potent therapeutic decreasing the replication and infectivity of the virus likely leading to better clinical outcomes. Clinical studies will be needed to examine the therapeutic utility of amantadine in COVID-19 infection.
Zα2 domain of ZBP1 is a molecular switch regulating Influenza-induced PANoptosis and perinatal lethality during development
Authors: Kesavardhana Sannula , Subbarao Malireddi R. K. , Burton Amanda R. , Porter Shaina N. , Vogel Peter , Pruett-Miller Shondra M. , Kanneganti Thirumala-Devi
Published: April 2020

Z-DNA-binding protein 1 (ZBP1) is an innate nucleic acid sensor which regulates host defense responses and development. ZBP1 activation triggers inflammation and pyroptosis, necroptosis, and apoptosis (PANoptosis) by activating RIPK3, caspase-8, and the NLRP3 inflammasome. ZBP1 is unique among innate sensors because of its N-terminal Zα1 and Zα2 domains, which bind to nucleic acids in the Z-conformation. However, the specific role of these Zα domains in orchestrating ZBP1 activation and subsequent inflammation and cell death is not clear. Here we have generatedZbp1ΔZα2/ΔZα2mice that lack the Zα2 domain of ZBP1 and demonstrate that this domain is critical for influenza A virus (IAV)-induced PANoptosis and perinatal lethality in RIPK1-RHIM mutated (Ripk1RHIM/RHIM) mice. Deletion of the Zα2 domain in ZBP1 abolished IAV-induced PANoptosis and NLRP3 inflammasome activation. Furthermore, deletion of the Zα2 domain of ZBP1 was sufficient to rescueRipk1RHIM/RHIMmice from the perinatal lethality which is caused by ZBP1-driven cell death and inflammation. Our findings identify the essential role of the Zα2 domain of ZBP1 in physiological functions and establish a link between sensing of Z-RNAs via the Zα2 domain and the promotion of influenza-induced PANoptosis and perinatal lethality.
Pavlov’s pea plants? Not so fast. An attempted replication of Gaglianoet al. (December 2016)
Authors: Markel Kasey
Published: April 2020

Gaglianoet al. (Learning by association in plants, 2016) reported associative learning in pea plants. Associative learning has long been considered a behavior performed only by animals, making this claim particularly newsworthy and interesting. In the experiment, plants were trained in Y-shaped mazes for three days with fans and lights attached at the top of the maze. Training consisted of wind consistently preceding light from either the same or the opposite arm of the maze. When plant growth forced a decision between the two arms of the maze, fans alone were able to influence growth direction, whereas the growth direction of untrained plants was not affected by fans. Importantly, some plants were trained to grow towards the fan and others to grow away, demonstrating the flexibility of associative learning. However, a replication of their protocol failed to demonstrate the same result, calling for further verification and study before mainstream acceptance of this paradigm-shifting phenomenon. This replication attempt used a larger sample size and fully blinded analysis.
Exploring ligand binding pathways on proteins using hypersound–accelerated molecular dynamics
Authors: Araki Mitsugu , Matsumoto Shigeyuki , Bekker Gert-Jan , Isaka Yuta , Sagae Yukari , Kamiya Narutoshi , Okuno Yasushi
Published: April 2020

Capturing the dynamic processes of biomolecular systems in atomistic detail remains difficult despite recent experimental advances. Although molecular dynamics (MD) techniques enable atomic-level observations, simulations of “slow” biomolecular processes (with timescales longer than submilliseconds) are challenging, due to current computer speed limitations. Therefore, we developed a new method to accelerate MD simulations by high-frequency ultrasound perturbation. The binding events between the protein CDK2 and its small-molecule inhibitors were nearly undetectable in 100-ns conventional MD, but the new method successfully accelerated their slow binding rates by up to 10–20 times. The accelerated MD simulations revealed a variety of microscopic kinetic features of the inhibitors on the protein surface, such as the existence of different binding pathways to the active site. Moreover, the simulations allowed estimating the corresponding kinetic parameters and exploring other druggable pockets. This method can thus provide deeper insight into the microscopic interactions controlling biomolecular processes.
Unbundling subjective career success: a sequential mediation analysis
Authors: Rossenkhan Zubeida , Au Wee Chan , Ahmed Pervaiz Khalid
Published: April 2020

Purpose

This study aims to contribute to subjective career success (SCS) literature using sequential mediation modeling to interrogate the inter-relationships between dimensions of SCS, including interpersonal success, financial success, job success and hierarchical success. In doing so, the research provides a nuanced understanding of career behavior among young adults using the perspective of a non-western developing context.

Design/methodology/approach

The study is operationalized using 342 survey questionnaires from Malaysian young working adults (18-34 years). Partial least square structural equation modeling is used as the main analytic tool.

Findings

The results of the study revealed that dimensions of SCS were related in a sequential mediating manner. Specifically, an individual’s interpersonal success is the foundation for one to accomplish job tasks (job success), which then leads to increased prospects for promotion (hierarchical success) and subsequently financial success.

Practical implications

These findings highlight the importance of interpersonal success as a foundation of career success and provide evidence for the study recommendation to support young working adults in building interpersonal relationships, which will help realize other forms of career success. However, the establishment of a sequential mediation pathway suggests that developing relationships alone are not sufficient. Study roles and tasks must also be designed to align with individuals’ personal goals for advancement and success.

Originality/value

The research contributes to knowledge on understanding career behavior specifically relating to the dynamics and complexities of SCS. The study sheds light on the potential limitation of operationalizing SCS as a multi-dimensional aggregate construct and provides empirical support for the proposed sequential mediation model of SCS.
An elderly assistive device substitutes for traditional online library catalogs
Authors: Chiang Cheng-Wei , Liu Yi-Hui , Wang Chien-Po
Published: April 2020

Purpose

This paper aims to present an augmented reality (AR) application to aid the elderly in library reference search. The application supports the elderly in searching books and videos in a large library when librarians have insufficient time to meet their needs. The elderly searching in a large library could be difficult for them due to the vast area, complicated online library catalogs and their physical deterioration, such as failing eyesight, tendinitis and memory problems. Our system, SearchAR, fully supports the 3D images of object content based on books and videos in Ling Tung University (LTU) library catalogs. Using the latest AR technology, users can use mobile phone to scan the quick response (QR) code in front of the LTU library, and then the elderly can experience LTU library map labeled by different colors in real-time and understand the locations of the video areas and book shelves areas. Later, they can use SearchAR to scan the QR codes on bookshelves, books or videos to view the 3D graphics without reading complicated catalogs and content. The results show that among the images, the elderly recognition of the “3 D images” was the highest, and the experimental group using AR technology as a searching aid shows a higher searching effectiveness than the control group; 60 per cent of the elderly felt they saved more time for searching books and videos with the help of SearchAR, and it was easy to arouse their association; the elderly indicated that combined image of the library map and the labels with different colors are clear and simple; the content of books and videos are easy associated with the 3D images; the elderly mentioned that using SearchAR is a great experience without any reading complicated online catalogs. Finally, this study concludes that AR technology does enhance the elderly searching ability in LTU large library.

Design/methodology/approach

The SearchAR application was an integrating library catalog, which provides AR and 3D graphics. The elderly can also use SearchAR to see a library map and every library element via 3D graphics before they start searching in a wide area.

Findings

This makes it easier for elderly to navigate a library without using complicated online catalogs, and it reduces time spent on reading and searching.

Originality/value

AR has been used for a variety of guiding and educational purposes. However, AR has been rarely applied to supplement traditional library services for elderly.