bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening for inborn errors of metabolism using untargeted metabolomics and out-of-batch controls
Authors: Bongaerts Michiel , Bonte Ramon , Demirdas Serwet , Jacobs Ed H. , Oussoren E. , van der Ploeg Ans T. , Wagenmakers Margreet A.E.M. , Hofstra Robert M.W. , Blom Henk J. , Reinders Marcel J.T. , Ruijter George J. G.
Published: April 2020

Motivation

Untargeted metabolomics is an emerging technology in the laboratory diagnosis of inborn errors of metabolism (IEM). In order to judge if metabolite levels are abnormal, analysis of a large number of reference samples is crucial to correct for variations in metabolite concentrations resulting from factors such as diet, age and gender. However, a large number of controls requires the use of out-of-batch controls, which is hampered by the semi-quantitative nature of untargeted metabolomics data, i.e. technical variations between batches. Methods to merge and accurately normalize data from multiple batches are urgently needed.

Methods & results

Based on six metrics, we compared existing normalization methods on their ability to reduce batch effects from eight independently processed batches. Many of those showed marginal performances, which motivated us to developMetchalizer, a normalization method which uses 17 stable isotope-labeled internal standards and a mixed effect model. In addition, we propose a regression model with age- and sex as covariates fitted on control samples obtained from all eight batches.Metchalizerapplied on log-transformed data showed the most promising performance on batch effect removal as well as in the detection of 178 known biomarkers across 45 IEM patient samples and performed at least similar to an approach using 15 within-batch controls. Furthermore, our regression model indicates that 10-24% of the considered features showed significant age-dependent variations.

Conclusions

Our comprehensive comparison of normalization methods showed that ourLog-Metchalizerapproach enables the use out-of-batch controls to establish clinically-relevant reference values for metabolite concentrations. These findings opens possibilities to use large scale out-of-batch control samples in a clinical setting, increasing throughput and detection accuracy.

Availability

Metchalizeris available athttps://github.com/mbongaerts/Metchalizer/
Double-targeted knockdown of miR-21 and CXCR4 inhibits malignant glioma progression by suppression of the PI3K/AKT and Raf/MEK/ERK pathways
Authors: Liu Feijiao , Yang Bo
Published: April 2020

Background

Currently, miR-21 and CXCR4 are being extensively investigated as two unrelated key regulators in glioma malignancy. In this study, we investigated the combined effect of these two factors on glioma progression.

Methods

We confirmed the expression of miR-21 and CXCR4 in malignant glioma tissue and glioma cells with qRT-PCR and western blotting. Single-targeted knockdown of miR-21 and CXCR4, as well as double-targeted knockdown of miR-21 and CXCR4 lentiviral vectors were constructed and they were transfected to U87 and U251 cells. Cell proliferation, apoptosis, invasion, and migration from different treatment groups were assessed by MTT assay, Flow Cytometry analysis, Transwell analysis, and Scratch assay, respectively. U87 xenograft mice were constructed to detect roles and potential mechanisms of miR-21 and CXCR4 in malignant glioma tumor growth.

Results

The expression of miR-21 and CXCR4 was increased in tumor tissues and cell lines. Inhibition of miR-21, CXCR4, and miR-21 and CXCR4 together all reduced the migration, invasiveness, proliferation and enhanced apoptosis in glioma cells, as well as reduced tumor volume and mass in xenograft model. The inhibition effect was strongest in double-targeted knockdown of miR-21 and CXCR4 group, whose downstream pathways involved in AKT axis and ERK axis activation.

Conclusions

Our findings reported that double-targeted knockdown of miR-21 and CXCR4 could more effectively inhibit the proliferation, migration, invasion and growth of transplanted tumor and promote cell apoptosis, which were involved in the PI3K/AKT and Raf/MEK/ERK signaling pathways.
A pan-cancer landscape of somatic substitutions in non-unique regions of the human genome
Authors: Tarabichi Maxime , Demeulemeester Jonas , Verfaillie Annelien , Flanagan Adrienne M. , Loo Peter Van , Konopka Tomasz
Published: April 2020

Around 13% of the human genome displays high sequence similarity with at least one other chromosomal position and thereby poses challenges for computational analyses such as detection of somatic events in cancer. We here extract features of sequencing data from across non-unique regions and employ a machine learning pipeline to describe a landscape of somatic substitutions in 2,658 cancers from the PCAWG cohort. We show mutations in non-unique regions are consistent with mutations in unique regions in terms of mutation load and substitution profiles, and can be validated with linked-read sequencing. This uncovers hidden mutations in ~1,700 coding sequences and thousands of regulatory elements, including known cancer genes, immunoglobulins, and highly mutated gene families.
In vivoidentification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning
Authors: Kranich Jan , Chlis Nikolaos-Kosmas , Rausch Lisa , Latha Ashretha , Schifferer Martina , Kurz Tilman , Kia Agnieszka Foltyn-Arfa , Simons Mikael , Theis Fabian J. , Brocker Thomas
Published: April 2020

Thein vivodetection of dead cells remains a major challenge due to technical hurdles. Here we present a novel method, where injection of fluorescent Milk fat globule-EGF factor 8 protein (MFG-E8)in vivocombined with imaging flow cytometry and deep learning allows the identification of dead cells based on their surface exposure of phosphatidylserine (PS) and other image parameters. A convolutional autoencoder (CAE) was trained on defined pictures and successfully used to identify apoptotic cellsin vivo. However, unexpectedly, these analyses also revealed that the great majority of PS+cells were not apoptotic, but rather live cells associated with PS+extracellular vesicles (EVs). During acute viral infection apoptotic cells increased slightly, while up to 30% of lymphocytes were decorated with PS+EVs of Dendritic cell exosomal origin. The combination of recombinant fluorescent MFG-E8 and the CAE-method will greatly facilitate analyses of cell death and EVsin vivo.
A widely distributed hydrogenase oxidises atmospheric H2during bacterial growth
Authors: Islam Zahra F. , Welsh Caitlin , Bayly Katherine , Grinter Rhys , Southam Gordon , Gagen Emma J. , Greening Chris
Published: April 2020

Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches:Acidithiobacillus ferrooxidans(phylum Proteobacteria),Chloroflexus aggregans(phylum Chloroflexota), andGemmatimonas aurantiaca(phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H2to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H2supported mixotrophic growth of the carbon-fixing strainsC. aggregansandA. ferrooxidans.Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H2oxidation and extends this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.
Optimization of cryopreservation andin vitrofertilization techniques for the African turquoise killifishNothobranchius furzeri
Authors: Dolfi Luca , Suen Tsz Kin , Ripa Roberto , Antebi Adam
Published: April 2020

Over the last decade, the African turquoise killifish,Nothobranchius furzeri, has emerged as an important model system for the study of vertebrate biology and ageing. However, rearing this fish in captivity can pose challenges, due to the short window of fertility, inbreeding problems, and the continuous maintenance of different strains and transgenic lines. To date, the main means of long term strain maintenance is to arrest embryos in diapause, a poorly understood and unreliable method. To solve these problems, we developed a robust protocol to cryopreserve sperm and to revive them forin vitrofertilization (IVF), as a better option for long term storage ofN. furzerilines. We tested a variety of extender and activator buffers for spermin vitrofertilization, as well as cryoprotectants to achieve maximal long term storage and fertilization conditions tailored to this species. Our optimized protocol was able to preserve sperm in a cryogenic condition for months and to revive an average of 40% upon thawing. Thawed sperm were able to fertilize nearly the same number of eggs as natural fertilization, with an average of ~25% and peaks of ~55% fertilization. This technical advance will greatly facilitate the use ofN. furzerias a model organism.
Simulating flow induced migration in vascular remodelling
Authors: Tabibian Ashkan , Ghaffari Siavash , Vargas Diego A. , Van Oosterwyck Hans , Jones Elizabeth A.V.
Published: April 2020

Shear stress induces directed endothelial cell (EC) migration in blood vessels leading to vessel diameter increase and induction of vascular maturation. Other factors, such as EC elongation and interaction between ECs and non-vascular areas are also important. Computational models have previously been used to study collective cell migration. These models can be used to predict EC migration and its effect on vascular remodelling during embryogenesis. We combined live time-lapse imaging of the remodelling vasculature of the quail embryo yolk sac with flow quantification using a combination of micro-Particle Image Velocimetry and computational fluid dynamics. We then used the flow and remodelling data to inform a model of EC migration during remodelling. To obtain the relation between shear stress and velocityin vitrofor EC cells, we developed a flow chamber to assess how confluent sheets of ECs migrate in response to shear stress. Using these data as an input, we developed a multiphase, self-propelled particles (SPP) model where individual agents are driven to migrate based on the level of shear stress while maintaining appropriate spatial relationship to nearby agents. These agents elongate, interact with each other, and with avascular agents at each time-step of the model. We compared predicted vascular shape to real vascular shape after 4 hours from our time-lapse movies and performed sensitivity analysis on the various model parameters. Our model shows that shear stress has the largest effect on the remodelling process. Importantly, however, elongation played an especially important part in remodelling. This model provides a powerful tool to study the input of different biological processes on remodelling.

Author summary

Shear stress is known to play a leading role in endothelial cell (EC) migration and hence, vascular remodelling. Vascular remodelling is, however, more complicated than only EC migration. To achieve a better understanding of this process, we developed a computational model in which, shear stress mediated EC migration has the leading role and other factors, such as avascular regions and EC elongation, are also accounted for. We have tested this model for different vessel shapes during remodelling and could study the role that each of these factors play in remodelling. This model gives us the possibility of addition of other factors such as biochemical signals and angiogenesis which will help us in the study of vascular remodelling in both development and disease.
Does the Antisecretory Peptide AF-16 modulate fluid balance and inflammation in experimental peritonitis induced sepsis?
Authors: Barrueta Tenhunen Annelie , van der Heijden Jaap , Blokhin Ivan , Massaro Fabrizia , Arne Hansson Hans , Feinstein Ricardo , Larsson Anders , Tenhunen Jyrki
Published: April 2020

Sepsis is a life-threatening condition due to a dysregulated immunological response to infection. Apart from source control and broad-spectrum antibiotics, management is based on fluid resuscitation and vasoactive drugs. Fluid resuscitation implicates the risk of volume overload, which in turn is associated with longer stay in intensive care, prolonged use of mechanical ventilation and increased mortality.

Antisecretory factor (AF), an endogenous protein, is detectable in most tissues and in plasma. The biologically active site of the protein is located in an 8-peptide sequence, contained in a synthetic 16-peptide fragment, named AF-16. The protein as well as the peptide AF-16 has multiple modulatory effects on abnormal fluid transport and edema formation/resolution as well as in a variety of inflammatory conditions. Apart from its’ anti-secretory and anti-inflammatory characteristics, AF is an inhibitor of capillary leakage in intestine. It is not known whether the protein AF or the peptide AF-16 can ameliorate symptoms in sepsis. We hypothesized that AF-16 decreases the degree of hemodynamic instability, the need of fluid resuscitation, vasopressor dose and tissue edema in fecal peritonitis.

To test the hypothesis, we induced peritonitis and sepsis by injecting autologous fecal solution into abdominal cavity of anesthetized pigs, and randomized (in a blind manner) the animals to intervention (AF-16, n=8) or control (saline, n=8) group. After onset of hemodynamic instability (defined as mean arterial pressure < 60 mmHg maintained for > 5 minutes), resuscitation was initiated by an infusion of AF-16 or saline. We recorded respiratory and hemodynamic parameters hourly for twenty hours and collected post mortem tissue samples at the end of the experiment.

No differences between the groups were observed regarding hemodynamics, fluid balance, lung mechanics, gas exchange or histology. This experimental study suggests that AF-16 does not modulate sepsis symptoms in peritonitis induced sepsis.
Assessment of whether published non-Cochrane systematic reviews of nursing follow the review protocols registered in the International Prospective Register of Systematic Reviews (PROSPERO): A comparative study
Authors: Hu Kaiyan , Mei Fan , Gao Qianqian , Zhao Li , Chen Fei , Liu Qinghua , Suo Lingling , Ma Yuxia , Zhang Ting , Zhang Weiyi , Zhao Bing , Ma Bin
Published: April 2020

Purpose

We compare published non-Cochrane reviews of nursing with their pre-registered protocols on PROSPERO to quantify the prevalence of differences and the extent to which the differences were explained.

Methods

We searched for protocols and their corresponding reviews in PROSPERO’s nursing group that were “completed and published” from inception to September 8th, 2019. Two authors independently identified differences and classified the difference as none, partial, or complete, and determined if the existed differences had been explained. Frequency (n), percentage (%), median, and inter-quartile ranges were used to analyze the extent of differences and explanations.

Results

We identified 22 pre-registered protocols and their reviews. All 22 pairs (100%) exhibited differences. Eighteen pairs (82%) showed differences in at least six methodological sections, while 21 pairs (95%) involved completed difference in at least one section. The median number of differences per review was 8.00 (upper quartile = 6.00, lower quartile = 9.75). The differences involved all 13 compared methodology-related sections. Only 5 (3%) of all differences were explained in the systematic reviews.

Conclusions

We observed widespread differences between non-Cochrane reviews of nursing and their protocols recorded in PROSPERO, with relatively few explanations for the changes. Measures including establishing a new item in the reporting guideline of systematic reviews to guide reporting and explaining the reasons for differences between protocols and systematic reviews or even requiring authors to do so at the Journal’s author guideline are recommended to improve transparency.
Allergen specific Treg upregulated by lung-stage schistosome infection alleviates allergic airway inflammation via inhibiting IgE secretion
Authors: Li Zhi dan , Zhang Wei , Luo fang , Li jian , Yang Wen bin , Zhu Bing kuan , Wu Qun feng , Wang Xiao ling , Sun Cheng song , Xie Yu xiang , Xu Bin , Wang Zhao jun , Qian Feng , Wan Yan min , Li Qing
Published: April 2020

Schistosome infection showed protective effects against allergic airway inflammation (AAI). However,controversial findings exist especially regarding the timing of helminth infection and the underlying mechanisms. Moreover, most previous studies focused on understanding the preventive effect of schistosome infection on asthma (infection before allergen sensitization), while its therapeutic effects (infection after allergen sensitization) were rarely investigated. In this study, we investigated the therapeutic effects of schistosome infection on AAI using a mouse model of OVA induced asthma. To explore how the timing of schistosome infection influences its therapeutic effect, the mice were percutaneously infected with cercaria of Schistosoma japonicum at either 1 day before OVA induced asthma attack (infection at lung-stage during AAI) or 14 days before OVA induced asthma attack (infection at post lung-stage during AAI). We found that lung-stage schistosome infection significantly ameliorated OVA-induced AAI, whereas post lung-stage infection showed no therapeutic effect. Mechanistically, the lung-stage schistosome infection significantly upregulated the frequency of Treg, especially OVA specific Treg, in lung tissue, which negatively correlated with the level of OVA specific IgE. Depletion of Treg in vivo counteracted the therapeutic effect. Furthermore, transcriptomic analysis of lung tissue showed that lung-stage schistosome infection during AAI shaped the microenvironment to favor Treg induction. In conclusion, our data showed that lung-stage schistosome infection could relieve OVA induced asthma in a mouse model. The therapeutic effect was mediated by the upregulated OVA specific Treg which suppressed IgE production and Th2 cytokine secretion. Our results may facilitate the discovery of a new therapy for AAI.
Specificities of and functional coordination between the two Cas6 maturation endonucleases inAnabaenasp. PCC 7120 assign orphan CRISPR arrays to three groups
Authors: Reimann Viktoria , Ziemann Marcus , Li Hui , Zhu Tao , Behler Juliane , Lu Xuefeng , Hess Wolfgang R.
Published: April 2020

The majority of bacteria and archaea possess an RNA-guided adaptive and inheritable immune system against viruses and other foreign genetic elements that consists of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. In most CRISPR-Cas systems, the maturation of CRISPR-derived small RNAs (crRNAs) is essential for functionality. In some bacteria, multiple instances ofcasgene-free (orphan) repeat-spacer arrays exist, while additional instances of arrays that are linked tocasgene cassettes are present elsewhere in the genome.

In the cyanobacteriumAnabaenasp. PCC 7120, ten CRISPR-Cas repeat-spacer arrays are present, but only twocasgene cassettes plus a Tn7-associated eleventh array are observed. In this study, we deleted the twocas6genesalr1482(Type III-D) oralr1566(Type I-D) and tested the specificities of the two corresponding enzymes in the resulting mutant strains, as recombinant proteins and in a cell-free transcription-translation system. The results assign the direct repeats (DRs) to three different groups. While Alr1566 is specific for one group, Alr1482 has a higher preference for the DRs of the second group but can also cleave those of the first group. We found that this cross-recognition limits crRNA accumulation for the Type I-D systemin vivo.

We also show that the DR of thecasgene-free CRISPR array of cyanophage N-1 is processed by these enzymes, suggesting that it is fully competent in association with host-encoded Cas proteins. The data support a strong tendency for array fragmentation in multicellular cyanobacteria and disfavor other possibilities, such as the nonfunctionality of these orphan repeat-spacer arrays. Our data demonstrate the functional coordination of Cas6 endonucleases with both neighboring and remote repeat-spacer arrays in the CRISPR-Cas system of cyanobacteria.
Syngap1 Dynamically Regulates the Fine-Scale Reorganization of Cortical Circuits in Response to Sensory Experience
Authors: Llamosas Nerea , Vaissiere Thomas , Rojas Camilo , Michaelson Sheldon , Miller Courtney A. , Rumbaugh Gavin
Published: April 2020

Experience induces complex, neuron-specific changes in population activity within sensory cortex circuits. However, the mechanisms that enable neuron-specific changes within cortical populations remain unclear. To explore the idea that synapse strengthening is involved, we studied fine-scale cortical plasticity inSyngap1mice, a neurodevelopmental disorder model useful for linking synapse biology to circuit functions. Repeated functional imaging of the same L2/3 somatosensory cortex neurons during single whisker experience revealed thatSyngap1selectively regulated the plasticity of a low-active, or “silent”, neuronal subpopulation.Syngap1also regulated spike-timing-dependent synaptic potentiation and experience-mediatedin vivosynapse bouton formation, but not synaptic depression or bouton elimination in L2/3. Adult re-expression ofSyngap1restored plasticity of “silent” neurons, demonstrating that this gene controls dynamic cellular processes required for population-specific changes to cortical circuits during experience. These findings suggest that abnormal experience-dependent redistribution of cortical population activity may contribute to the etiology of neurodevelopmental disorders.
A spatiotemporal translatome of mouse tissue development
Authors: Wang Hongwei , Wang Yan , Yang Jiaqi , Tang Nan , Li Huihui , Xie Mingzhe , Xie Zhi
Published: April 2020

The precise regulation of gene expression in mammalian tissues during development results in their functional specification. Although previous transcriptomic and proteomic analyses have provided great biological insights into tissue-specific gene expression and the physiological relevance of these tissues in development, our understanding of translational regulation in developing tissues is lacking. In this study, we performed a spatiotemporally resolved translatome analysis of six mouse tissues at the embryonic and adult stages to quantify the effects of translational regulation and identify new translational components. We quantified the spatial and temporal divergences of gene expression and detected specific changes in gene expression and pathways underlying these divergences. We further showed that dynamic translational control can be achieved by modulating the translational efficiency, which resulted in the enhancement of tissue specificity during development. We also discovered thousands of actively translated upstream open reading frames (ORFs) that exhibited spatiotemporal patterns and demonstrated their regulatory roles in translational regulation. Furthermore, we identified known and novel micropeptides encoded by small ORFs from long noncoding RNAs that are functionally relevant to tissue development. Our data and analyses facilitate a better understanding of the complexity of translational regulation across tissue and developmental spectra and serve as a useful resource of the mouse translatome.
Acetylcholine is released in the basolateral amygdala in response to predictors of reward and enhances learning of cue-reward contingency
Authors: Crouse Richard B. , Kim Kristen , Batchelor Hannah M. , Kamaletdinova Rufina , Chan Justin , Rajebhosale Prithviraj , Pittenger Steven T. , Role Lorna W. , Talmage David A. , Jing Miao , Li Yulong , Gao Xiao-Bing , Mineur Yann S. , Picciotto Marina R.
Published: April 2020

The basolateral amygdala (BLA) is critical for associating initially neutral cues with appetitive and aversive stimuli and receives dense neuromodulatory acetylcholine (ACh) projections. We measured BLA ACh signaling and principal neuron activity in mice during cue-reward learning using a fluorescent ACh sensor and calcium indicators. We found that ACh levels and activity of nucleus basalis of Meynert (NBM) cholinergic terminals in the BLA (NBM-BLA) increased sharply in response to reward-related events and shifted as mice learned the tone-reward contingency. BLA principal neuron activity followed reward retrieval and moved to the reward-predictive tone after task acquisition. Optical stimulation of cholinergic NBM-BLA terminal fibers during cue-reward learning led to more rapid learning of the cue-reward contingency. These results indicate that BLA ACh signaling carries important information about salient events in cue-reward learning and provides a framework for understanding how ACh signaling contributes to shaping BLA responses to emotional stimuli.
High-level stimulus template modulates neuronal response at the earlier processing stages
Authors: Maksimenko Vladimir , Kuc Alexander , Frolov Nikita , Kurkin Semen , Hramov Alexander
Published: April 2020

There is ample evidence that the brain matches sensory information with internal templates, but the details of this mechanism remain unknown. Here we consider the processing of repeatedly presented ambiguous stimuli with high ambiguity (HA) and low ambiguity (LA) and analyze how the processing depends on the ambiguity of the previous stimulus. On the behavioral level, we report a faster response to the HA stimulus after HA stimuli and a faster response to the LA stimulus after LA stimuli. The EEG analysis reveals that when HA stimulus follows LA stimuli, the neuronal activity in the sensory areas attenuates at the early processing stage but enhances during the latter stages. It evidences the hierarchical processing organization where low levels process the stimulus details, and high levels represent its interpretation. It also confirms that on low levels, HA and LA stimuli processing is similar due to their similar morphology. Therefore, the brain uses the LA stimulus template on the low levels to reduce the demands when processing the HA stimulus details. When LA stimulus follows HA stimuli, the attenuated response in the sensory regions accompanies high response in the frontal cortex. Namely, we observe highθpower in the medial frontal cortex and highβpower in the right inferior frontal cortex. It shows activation of the top-down cognitive control functions detecting the mismatch between the LA stimulus and the HA stimulus template and transfer this template to the low processing levels.

Significance statement

The brain attenuates its response to repeatedly presented similar stimuli. When an ambiguous visual stimulus follows unambiguous stimuli with the same morphology, the neuronal response in sensory areas decreases at the early processing stage but enhances during the latter stages. It evidences hierarchical processing organization where low levels process the details, and high levels represent the interpretation. It also confirms that the brain uses templates on different levels to reduce the processing demands. When an unambiguous stimulus follows ambiguous stimuli, a low response in the sensory regions accompanies high response in the frontal cortex. It manifests activation of the top-down mechanisms to detect the mismatch between an unambiguous stimulus and an ambiguous template and transfer this template to low levels.
An aptamer-based magnetic flow cytometer using matched filtering
Authors: Huang Chih-Cheng , Ray Partha , Chan Matthew , Zhou Xiahan , Hall Drew A.
Published: April 2020

Facing unprecedented population-ageing, the management of noncommunicable diseases (NCDs) urgently needs a point-of-care (PoC) testing infrastructure. Magnetic flow cytometers are one such solution for rapid cancer cellular detection in a PoC setting. In this work, we report a giant magnetoresistive spin-valve (GMR SV) biosensor array with a multi-stripe sensor geometry and matched filtering to improve detection accuracy without compromising throughput. The carefully designed sensor geometry generates a characteristic signature when cells labeled with magnetic nanoparticles (MNPs) pass by thus enabling multi-parametric measurement like optical flow cytometers (FCMs). Enumeration and multi-parametric information were successfully measured across two decades of throughput. 10-µm polymer microspheres were used as a biomimetic model where MNPs and MNP-decorated polymer conjugates were flown over the GMR SV sensor array and detected with a signal-to-noise ratio (SNR) as low as 2.5 dB due to the processing gain afforded by the matched filtering. The performance was compared against optical observation, exhibiting a 92% detection efficiency. The system achieved a 95% counting accuracy for biomimetic models and 98% for aptamer-based pancreatic cancer cell detection. This system demonstrates the ability to perform reliable PoC diagnostics towards the benefit for NCD control plans.
The FDA- approved gold drug Auranofin inhibits novel coronavirus (SARS-COV-2) replication and attenuates inflammation in human cells
Authors: Rothan Hussin A. , Stone Shannon , Natekar Janhavi , Kumari Pratima , Arora Komal , Kumar Mukesh
Published: April 2020

SARS-COV-2 has recently emerged as a new public health threat. Herein, we report that the FDA-approved gold drug, auranofin, inhibits SARS-COV-2 replication in human cells at low micro molar concentration. Treatment of cells with auranofin resulted in a 95% reduction in the viral RNA at 48 hours after infection. Auranofin treatment dramatically reduced the expression of SARS-COV-2-induced cytokines in human cells. These data indicate that auranofin could be a useful drug to limit SARS-CoV-2 infection and associated lung injury due to its anti-viral, anti-inflammatory and anti-ROS properties. Auranofin has a well-known toxicity profile and is considered safe for human use.
Multivariate Analysis Of Potato Genotypes For Genetic Diversity
Authors: Khan Arifa , Erum Shazia , Riaz Naveeda , Shinwari Muhammad Ibrar , Ibrar Shinwari Maryum
Published: April 2020

Sustainable production of food crops relies on germplasm improvement and genetic diversity that helps to identify appropriate parents, which is very important step in breeding of genotypes having high yield potential for future use. This study was conducted to investigate the extent of genetic diversity using multivariate technique on the basis of qualitative and quantitative traits. An experiment was comprised of 74 exotic genotypes and started at National Agriculture Research Center Islamabad, Pakistan during autumn 2017-2018 and 2018-2019. Data was recorded on qualitative and quantitative traits by following standard procedures and Biplot analysis was used to calculate the significance among the studied quantitative traits to exhibit the strength of relationship between traits. Results showed significant diversity in qualitative traits and quantitative traits. Red, yellowish, brown, light yellow, light brown color tubers were produced. Alike, genotypes produced yellow, cream and white flesh color tubers. Genotypes had oval, round, oblong, elliptic and reform with medium, small and large size tubers. Alike, brown, light brown, dark red and yellow eyes color was noted. In case of quantitative traits, genotypes had high variance regarding plant height, leaf area and number of tubers per lane. Genotypes had very high genetic variance for weight of tuber per plant and weight of tuber per lane while low variance was recorded for germination, number of stem per plant and number of eyes per tuber. Significant positive correlation was observed between number of tubers per plant (TPP) with number of eyes on tubers (r = 0.241) and number of tubers per lane (TPL) (r = 0.349). But negative correlation was noted between number of tubers per plant (TPP) with plant height (r = -246), leaf area (-0.529) and germination (r = -0.283). Plant height was found significantly positive correlated with leaf area (r= 0.456), germination percentage (r = 0.255) and weight of tubers per plant (r = 0.307). Leaf area (LA) showed positive significant correlation with number of tubers per plant (r = 0.466) and weight of tubers per plant (r = 0.263)., yield and harvest index (r = 0.798, 0.755, 0.255). Weight of tubers per lane (WTL) showed positive correlation with weight of tubers per plant (r = 0.387). Regarding the interrelation between the traits and genotypes, the first two principal component axes (PC1, 24.83% and PC2, 23.46%) accounted for about 48.29% of the total variability reflecting the complexity of the variation between the plotted traits of genotypes.
Forkhead box O1-mediated ubiquitination suppresses RIG-I-mediated antiviral immune responses via its DNA binding domain
Authors: Liu Wei , Yue Yanlei , Zhang Wenwen , Ma Zhenling , Yao Wen , Li Tao , Xu Jun , Li Wenqing , Sun Lei , Liu Wenjun , Yang Guoqing
Published: April 2020

Statement

The authors have withdrawn our manuscript whilst we perform additional experiments to test some of our conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Spatio-temporal mapping of mechanical force generated by macrophages during FcγR-dependent phagocytosis reveals adaptation to target stiffness
Authors: Rougerie Pablo , Cox Dianne
Published: April 2020

Macrophage phagocytosis is a strikingly flexible process central to pathogen clearance and is an attractive target for the development of anti-cancer immunotherapies. To harness the adaptability of phagocytosis, we must understand how macrophages can successfully deform their plasma membrane. While the signaling pathways and the molecular motors responsible for this deformation have been studied for many years, we only have limited insight into the mechanics that drive the formation of the phagocytic cup. Using Traction Force Microscopy (TFM), we have been able to characterize the spatio-temporal dynamics of mechanical forces generated in the course of FcγR-dependent frustrated phagocytosis and we determined whether this was affected by the stiffness of the potential phagocytic targets. We observed that frustrated phagocytosis is an atypical form of spreading where the cell deformation rate is unaffected by the substrate stiffness. Interestingly, the cell initially extends without forces being recorded then switches to a mode of pseudopod extension involving spatially organized force transmission. Importantly we demonstrate that macrophages adapt to the substrate stiffness primarily through a modulation of the magnitude of mechanical stress exerted, and not through modification of the mechanical stress kinetics or distribution. Altogether, we suggest that macrophage phagocytosis exhibits a clear resilience to variations of the phagocytic target stiffness and this is favored by an adaptation of their mechanical response.
Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers
Authors: Petrany Michael J , Swoboda Casey O , Sun Chengyi , Chetal Kashish , Chen Xiaoting , Weirauch Matthew T. , Salomonis Nathan , Millay Douglas P
Published: April 2020

While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology.
Extracellular adenosine signaling reverses the age-driven decline in the ability of neutrophils to killS. pneumoniae
Authors: Bhalla Manmeet , Simmons Shaunna R. , Abamonte Alexsandra , Herring Sydney E. , Roggensack Sara E. , Bou Ghanem Elsa N.
Published: April 2020

The elderly are susceptible to serious infections byStreptococcus pneumoniae(pneumococcus), which calls for a better understanding of the pathways driving the decline in host defense in aging. We previously found that extracellular adenosine (EAD) shaped polymorphonuclear cell (PMN) responses, which are crucial for controlling infection. EAD is produced by CD39 and CD73, and signals via A1, A2A, A2B and A3 receptors. The objective of this study was to explore the age-driven changes in the EAD pathway and its impact on PMN function. We found in comparison to young mice, PMNs from old mice expressed significantly less CD73, but similar levels of CD39 and adenosine receptors. PMNs from old mice failed to efficiently kill pneumococciex vivo; however, supplementation with adenosine rescued this defect. Importantly, transfer of PMNs expressing CD73 from young mice reversed the susceptibility of old mice to pneumococcal infection. To identify which adenosine receptor(s) is involved, we used specific agonists and inhibitors. We found that A1 receptor signaling was crucial for PMN function as inhibition or genetic ablation of A1 impaired the ability of PMNs from young mice to kill pneumococci. Importantly, activation of A1 receptors rescued the age-associated defect in PMN function. In exploring mechanisms, we found that PMNs from old mice failed to efficiently kill engulfed pneumococci and that A1 receptor controlled intracellular killing. In summary, targeting the EAD pathway reverses the age-driven decline in PMN antimicrobial function, which has serious implications in combating infections.
Oleic acid Induces Tissue Resident FoxP3 Regulatory T cell Lineage Stability and Suppressive Functions
Authors: Pompura Saige L. , Wagner Allon , Kitz Alexandra , LaPerche Jacob , Yosef Nir , Dominguez-Villar Margarita , Hafler David A.
Published: April 2020

FoxP3 positive regulatory T cells (Tregs) rely on fatty acid β-oxidation (FAO)-driven OXPHOS for differentiation and function. Recent data have demonstrated a role for Tregsin the maintenance of tissue homeostasis with tissue-resident Tregspossessing tissue-specific transcriptomes. However, specific signals that establish these tissue-resident Tregsprograms are largely unknown. As Tregsmetabolically rely on FAO, and considering the lipid-rich environments of tissues, we hypothesized that environmental lipids drive Treghomeostasis. Using human adipose tissue as a model for tissue residency, we identify oleic acid as the most prevalent free fatty acid in human adipose tissue. Mechanistically, oleic acid amplifies TregFAO-driven OXPHOS metabolism, creating a positive feedback mechanism that induces the expression of Foxp3 and enhances phosphorylation of STAT5, which acts to stabilize the Treglineage and increase suppressive function. Comparing the transcriptomic program induced by oleic acid to that of the pro-inflammatory arachidonic acid, we find that Tregssorted from peripheral blood and adipose of healthy donors transcriptomically resemble the oleic acidin vitrotreated Tregs, whereas Tregsobtained from the adipose tissue of relapsing-remitting MS patients more closely resemble an arachidonic acid profile. Finally, we find that oleic acid concentrations are reduced in the fat tissue of MS patients, and exposure of dysfunctional MS Tregsto oleic acid restores defects in their suppressive function. These data demonstrate the importance of fatty acids in regulating tissue inflammatory signals.
Expanding the space of protein geometries by computational design ofde novofold families
Authors: Pan Xingjie , Thompson Michael , Zhang Yang , Liu Lin , Fraser James S. , Kelly Mark J. S. , Kortemme Tanja
Published: April 2020

Naturally occurring proteins use a limited set of fold topologies, but vary the precise geometries of structural elements to create distinct shapes optimal for function. Here we present a computational design method termed LUCS that mimics nature’s ability to create families of proteins with the same overall fold but precisely tunable geometries. Through near-exhaustive sampling of loop-helix-loop elements, LUCS generates highly diverse geometries encompassing those found in nature but also surpassing known structure space. Biophysical characterization shows that 17 (38%) out of 45 tested LUCS designs were well folded, including 16 with designed non-native geometries. Four experimentally solved structures closely match the designs. LUCS greatly expands the designable structure space and provides a new paradigm for designing proteins with tunable geometries customizable for novel functions.

One Sentence Summary

A computational method to systematically sample loop-helix-loop geometries expands the structure space of designer proteins.
Constructing an ethanol utilization pathway inEscherichia colito produce acetyl-CoA derived compounds
Authors: Liang Hong , Ma Xiaoqiang , Ning Wenbo , Liu Yurou , Sinskey Anthony J. , Stephanopoulos Gregory , Zhou Kang
Published: April 2020

Engineering microbes to utilize non-conventional substrates could create short and efficient pathways to convert substrate into product. In this study, we designed and constructed a two-step heterologous ethanol utilization pathway (EUP) inEscherichia coliby using acetaldehyde dehydrogenase (encoded byada) fromDickeya zeaeand alcohol dehydrogenase (encoded byadh2) fromSaccharomyces cerevisiae. This EUP can convert ethanol into acetyl-CoA without ATP consumption, and generate two molecules of NADH per molecule of ethanol. We optimized the expression of these two genes and found that ethanol consumption could be improved by expressing them in a specific order (ada-adh2) with a constitutive promoter (PgyrA). The engineeredE. colistrain with EUP consumed approximately 8 g/L of ethanol in 96 hours when it was used as sole carbon source. Subsequently, we combined EUP with the biosynthesis of polyhydroxybutyrate (PHB), a biodegradable polymer derived from acetyl-CoA. The engineeredE. colistrain carrying EUP and PHB biosynthetic pathway produced 1.1 g/L of PHB from 10 g/L of ethanol and 1 g/L of aspartate family amino acids in 96 hours. We also engineeredE. colistrain to produced 24 mg/L of prenol from 10 g/L of ethanol in 48 hours, supporting the feasibility of converting ethanol into different classes of acetyl-CoA derived compounds.

Highlights

EngineeredEscherichia colistrains to grow on ethanol as sole carbon source

Demonstrated that ethanol was converted into acetyl-CoA (AcCoA) through two pathways (acetaldehyde-acetate-AcCoA and acetaldehyde-AcCoA)

Converted ethanol into two acetyl-CoA derived products with low structural similarity (polyhydroxybutyrate and prenol)

Discovered that supplementation of the aspartate family amino acids can substantially improve cell growth on ethanol
Butyrate producing Clostridiales utilize distinct human milk oligosaccharides correlating to early colonization and prevalence in the human gut
Authors: Pichler Michael Jakob , Yamada Chihaya , Shuoker Bashar , Alvarez-Silva Maria Camila , Gotoh Aina , Leth Maria Louise , Schoof Erwin , Katoh Toshihiko , Sakanaka Mikiyasu , Katayama Takane , Jin Chunsheng , Karlsson Niclas G. , Arumugam Manimozhiyan , Fushinobu Shinya , Hachem Maher Abou
Published: April 2020

The early life human gut microbiota exerts life-long health effects on the host, but the mechanisms underpinning its assembly remain elusive. Particularly, the early colonization of Clostridiales from theRoseburia-Eubacteriumgroup, associated with protection from colorectal cancer, immune- and metabolic disorders is enigmatic. Here we unveil the growth ofRoseburiaandEubacteriummembers on human milk oligosaccharides (HMOs) using an unprecedented catabolic apparatus. The described HMO pathways and additional glycan utilization loci confer co-growth withAkkermansia muciniphiliavia cross-feeding and access to mucinO-glycans. Strikingly, both, HMO and xylooligosaccharide pathways, were active simultaneously attesting an adaptation to a mixed HMO-solid food diet. Analyses of 4599Roseburiagenomes underscored the preponderance of HMO pathways and highlighted different HMO utilization phylotypes. Our revelations provide a possible rationale for the early establishment and resilience of butyrate producing Clostridiales and expand the role of specific HMOs in the assembly of the early life microbiota.
Full strain tensor measurements with X-ray diffraction and strain field mapping: a simulation study
Authors: Tang M. X. , Huang J. W. , E J. C. , Zhang Y. Y. , Luo S. N.
Published: April 2020

Strain tensor measurements are important for understanding elastic and plastic deformation, but full bulk strain tensor measurement techniques are still lacking, in particular for dynamic loading. Here, such a methodology is reported, combining imaging-based strain field mapping and simultaneous X-ray diffraction for four typical loading modes: one-dimensional strain/stress compression/tension. Strain field mapping resolves two in-plane principal strains, and X-ray diffraction analysis yields volumetric strain, and thus the out-of-plane principal strain. This methodology is validated against direct molecular dynamics simulations on nanocrystalline tantalum. This methodology can be implemented with simultaneous X-ray diffraction and digital image correlation in synchrotron radiation or free-electron laser experiments.
Measurement of the horizontal beam emittance of undulator radiation by tandem-double-slit optical system
Authors: Kagoshima Yasushi , Akada Tatsuki , Ikeda Takumi , Kawashima Motoki , Aoi Yuki , Takayama Yuki
Published: April 2020

A tandem-double-slit optical system was constructed to evaluate the practical beam emittance of undulator radiation. The optical system was a combination of an upstream slit (S1) and downstream slit (S2) aligned on the optical axis with an appropriate separation. The intensity distribution after the double slits, I(x
1, x
2), was measured by scanning S1 and S2 in the horizontal direction. Coordinates having 1/\sqrt e intensity were extracted from I(x
1, x
2), whose contour provided the standard deviation ellipse in the x
1–x
2 space. I(x
1, x
2) was converted to the corresponding distribution in the phase space, I(x
1, x
1′). The horizontal beam emittance was evaluated to be 3.1 nm rad, which was larger than the value of 2.4 nm rad estimated by using ray-tracing. It was found that the increase was mainly due to an increase in beam divergence rather than size.