bluuebunny/crossref_metadata_2025_split huggingface dataset:
EGCG modulates nuclear formaldehyde-induced Tau phosphorylation in Neuronal cells
Authors: Sonawane Shweta Kishor , Raina Anshu , Majumdar Amitabha , Chinnathambi Subashchandrabose 
Published: October 2020

AbstractTau hyperphosphorylation is one of the major causes of Alzheimer’s disease pathology. The abnormal phosphorylation curtails the physiological function of Tau of microtubule stabilization and renders it more prone to aggregation. Apart from its function in the cytoplasm, Tau is attributed to play a role in the nucleus. Nuclear function of Tau is dependent on its residue-specific phosphorylation. We studied the effect of a green tea polyphenol, EGCG, on the formaldehyde-induced Tau phosphorylation and Tau kinase CDK5. Interestingly, we observed unique localization of phospho-Tau (AT 8 and AT 100) in the nucleus in various EGCG treatments. EGCG was also found to lower the levels of CDK5 in the formaldehyde-treated cells. Further, the role of EGCG was testedin vivoin drosophila eye model of hyperphosphorylated Tau (Tau E14). The results suggest that EGCG can modulate nuclear Tau phosphorylation and lower the levels of Tau kinase CDK5.
A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity
Authors: Bebber Daniel P. , Richards Victoria R. 
Published: October 2020

ABSTRACTOrganic agriculture, employing manures or composts, has been proposed as a way of mitigating undesirable impacts of mineral fertilizer use. Of particular interest is the effect of fertilizer regime on soil microbes, which are key to nutrient cycling, plant health and soil structure. However, the effect of fertilizers on soil microbial diversity remains poorly understood. Since biological diversity is an important determinant of ecosystem function and a fundamental metric in community ecology, the effects of fertilizer regimes on soil microbial diversity are of theoretical and applied interest. Here, we conduct a meta-analysis of 37 studies reporting microbial diversity metrics in mineral fertilized (NPK), organically fertilized (ORG) and unfertilized control (CON) soils. Of these studies, 32 reported taxonomic diversity derived from sequencing, gradient gel electrophoresis, or RFLP. Functional diversity, derived from Biolog Ecoplate™ measures of carbon substrate metabolism, was reported in 8 studies, with 3 studies reporting both diversity metrics. Bacterial and archaeal diversity was reported in 28 taxonomic studies, and fungal diversity in 8 taxonomic studies. We found that functional diversity was 2.8 % greater in NPK compared with CON, 7.0 % greater in ORG vs CON, and 3.8 % greater in ORG vs NPK. Bacterial and archaeal taxonomic diversity was not significantly different between NPK and CON, but on average 2.9% greater in ORG vs CON, and 2.4 % greater in ORG vs. NPK. Fungal taxonomic diversity was not significantly different between any treatment pairs. There was very high residual heterogeneity in all meta-analyses of soil diversity, suggesting that a large amount of further research is required to fully understand the influence of fertilizer regimes on microbial diversity and ecosystem function.
Environmental flexibility does not explain metabolic robustness
Authors: Libiseller-Egger Julian , Coltman Ben , Gerstl Matthias P. , Zanghellini Jürgen 
Published: October 2020

Cells show remarkable resilience against genetic and environmental perturbations. However, its evolutionary origin remains obscure. In order to leverage methods of systems biology for examining cellular robustness, a computationally accessible way of quantification is needed. Here, we present an unbiased metric of structural robustness in genome-scale metabolic models based on concepts prevalent in reliability engineering and fault analysis.The probability of failure (PoF) is defined as the (weighted) portion of all possible combinations of loss-of-function mutations that disable network functionality. It can be exactly determined, if all essential reactions, synthetic lethal pairs of reactions, synthetic lethal triplets of reactions etc., are known. In theory, these minimal cut sets (MCSs) can be calculated for any network, but for large models the problem remains computationally intractable. Herein, we demonstrate that even at the genome scale only the lowest-cardinality MCSs are required to efficiently approximate the PoF with reasonable accuracy.We analysed the robustness of 489E. coli, Shigella, Salmonella, and fungal genome-scale metabolic models (GSMMs). In contrast to the popular “congruence theory”, which explains the origin of genetic robustness as a byproduct of selection for environmental flexibility, we found no correlation between network robustness and the diversity of growth-supporting environments. On the contrary, our analysis indicates that amino acid synthesis rather than carbon metabolism dominates metabolic robustness.
Approach trajectory and solar position affect host plant attractiveness to the small white butterfly
Authors: Blake Adam J. , Couture Samuel , Go Matthew C. , Gries Gerhard 
Published: October 2020

AbstractWhile it is well documented that insects exploit polarized sky light for navigation, their use of reflected polarized light for object detection has been less well studied. Recently, we have shown that the small white butterfly,Pieris rapae, distinguishes between host and non-host plants based on the degree of linear polarization (DoLP) of light reflected from their leaves. To determine how polarized light cues affect host plant foraging by femaleP. rapaeacross their entire visual range including the ultraviolet (300-650 nm), we applied photo polarimetry demonstrating large differences in theDoLPof leaf-reflected light among plant species generally and between host and non-host plants specifically. As polarized light cues are directionally dependent, we also tested, and modelled, the effect of approach trajectory on the polarization of plant-reflected light and the resulting attractiveness toP. rapae. Using photo polarimetry measurements of plants under a range of light source and observer positions, we reveal several distinct effects when polarized reflections are examined on a whole-plant basis rather than at the scale of pixels or of entire plant canopies. Most notably from our modeling, certain approach trajectories are optimal for foraging butterflies, or insects generally, to discriminate between plant species on the basis of theDoLPof leaf-reflected light.
CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer
Authors: Li Ruidong , Qu Han , Wang Shibo , Chater John M. , Wang Xuesong , Cui Yanru , Yu Lei , Zhou Rui , Jia Qiong , Traband Ryan , Wang Meiyue , Xie Weibo , Yuan Dongbo , Zhu Jianguo , Zhong Wei-De , Jia Zhenyu 
Published: October 2020

ABSTRACTMicroRNAs (miRNAs), which play critical roles in gene regulatory networks, have emerged as promising diagnostic and prognostic biomarkers for human cancer. In particular, circulating miRNAs that are secreted into circulation exist in remarkably stable forms, and have enormous potential to be leveraged as non-invasive biomarkers for early cancer detection. Novel and user-friendly tools are desperately needed to facilitate data mining of the vast amount of miRNA expression data from The Cancer Genome Atlas (TCGA) and large-scale circulating miRNA profiling studies. To fill this void, we developed CancerMIRNome, a comprehensive database for the interactive analysis and visualization of miRNA expression profiles based on 10,998 samples from 33 TCGA projects and 21,993 samples from 40 public circulating miRNome datasets. A series of cutting-edge bioinformatics tools and machine learning algorithms have been packaged in CancerMIRNome, allowing for the pan-cancer analysis of a miRNA of interest across multiple cancer types and the comprehensive analysis of miRNome profiles to identify dysregulated miRNAs and develop diagnostic or prognostic signatures. The data analysis and visualization modules will greatly facilitate the exploit of the valuable resources and promote translational application of miRNA biomarkers in cancer. The CancerMIRNome database is publicly available athttp://bioinfo.jialab-ucr.org/CancerMIRNome.
β-Amyloid peptides tailor switching behaviors of Donor-Acceptor Stenhouse Adducts
Authors: Zheng Chao , Yu Yue , Shi Kuang , Zhu Biyue , Zhou Heng , Zhang Shao-Qing , Yang Jing , Shi Liang , Ran Chongzhao 
Published: October 2020

AbstractMolecular switching plays a critical role in biological and displaying systems. Here we demonstrate the first use of peptides to operate molecular switches of donor-acceptor Stenhouse adducts (DASAs), a series of negative photochromes that are highly promising for applications ranging from smart material to biological systems. Fluorescence imaging proved Aβ40 species could make SHA-2 more stable in the linear configuration than without peptide and decrease the rate of molecular switching. According to molecular dynamics simulation, SHA-2 bound to protein resulted in substantial changes in the tertiary structure of Aβ40 monomer with the region of Glu22-Ala30 partially unfolded and being more exposed to water. This structural change is likely to impede the aggregation of Aβ40, as evidenced by fluorescence and ProteoStat®aggresome detection experiments. SHA-2 is able to inhibit the aggregation of Aβ40 by producing the off-pathway structures. These results open ample opportunities for optically addressable potential widely apply DASAs in the biological system based on this peptides-tailor process.
A brief glimpse at a haptic target is sufficient for multisensory integration in reaching movements
Authors: Camponogara Ivan , Volcic Robert 
Published: October 2020

AbstractGoal-directed aiming movements toward visuo-haptic targets (i.e., seen and handheld targets) are generally more precise than those toward visual only or haptic only targets. This multisensory advantage stems from a continuous inflow of haptic and visual target information during the movement planning and execution phases. However, in everyday life, multisensory movements often occur without the support of continuous visual information. Here we investigated whether and to what extent limiting visual information to the initial stage of the action still leads to a multisensory advantage. Participants were asked to reach a handheld target while vision was briefly provided during the movement planning phase (50 ms, 100 ms, 200 ms of vision before movement onset), or during the planning and early execution phases (400 ms of vision), or during the entire movement. Additional conditions were performed in which only haptic target information was provided, or, only vision was provided either briefly (50 ms, 100 ms, 200 ms, 400 ms) or throughout the entire movement. Results showed that 50 ms of vision before movement onset were sufficient to trigger a direction-specific visuo-haptic integration process that increased endpoint precision. We conclude that, when a continuous support of vision is not available, endpoint precision is determined by the less recent, but most reliable multisensory information rather than by the latest unisensory (haptic) inputs.
Prevalence of SARS-CoV-2 in human post-mortem ocular tissues
Authors: Sawant Onkar B. , Singh Sneha , Wright Robert Emery , Jones Kayla M. , Titus Michael S. , Dennis Eugene , Hicks Eric , Majmudar Parag A. , Kumar Ashok , Mian Shahzad I. 
Published: October 2020

AbstractBackgroundSARS-CoV-2 is found in conjunctival swabs and tears of COVID-19 patients. However, the presence of SARS-CoV-2 has not been detected in the human eye to date. We undertook this study to analyze the prevalence of SARS-CoV-2 in human post-mortem ocular tissues.MethodsThe expression of SARS-CoV-2 RNA was assessed by RT-PCR in corneal and scleral tissues from 33 surgical-intended donors who were eliminated from a surgical use per Eye Bank Association of America (EBAA) donor screening guidelines or medical director review or positive COVID-19 test. Ocular levels of SARS-CoV-2 RNA (RT-PCR), Envelope and Spike proteins (immunohistochemistry) and anti-SARS-CoV-2 IgG and IgM antibodies (ELISA) in blood were evaluated in 10 COVID-19 donors.FindingsOf 132 ocular tissues from 33 surgical-intended donors, the positivity rate for SARS-CoV-2 RNA was ∼13% (17/132). Of 10 COVID-19 donors, six had PCR positive post-mortem nasopharyngeal swabs whereas eight exhibited positive post-mortem anti-SARS-CoV-2 IgG levels. Among 20 eyes recovered from 10 COVID-19 donors: three conjunctival, one anterior corneal, five posterior corneal, and three vitreous swabs tested positive for SARS-CoV-2 RNA. SARS-CoV-2 spike and envelope proteins were detected in epithelial layer of the corneas that were procured without Povidone-Iodine (PVP-I) disinfection.InterpretationsOur study showed a small but noteworthy prevalence of SARS-CoV-2 in ocular tissues from COVID-19 donors. These findings underscore the criticality of donor screening guidelines, post-mortem nasopharyngeal PCR testing and PVP-I disinfection protocol to eliminate any tissue harboring SARS-CoV-2 being used for corneal transplantation.FundingResearch grant from EBAA and National Institutes of Health.
A Numerical Study of the Current COVID-19 Spread Patterns in India, the USA and the World
Authors: Baruah Hemanta K. 
Published: October 2020

AbstractIn this article, we are going to study the current COVID-19 spread patterns in India and the United States. We are interested to show how the daily increase in the total number of cases in these two countries is affecting the COVID-19 spread pattern in the World. For the study, we have considered the cumulative total numbers of cases in India, the United States and the World. We have found that the situation in the United States is already on the threshold of a change towards retardation. In the World as a whole also we have observed that a similar conclusion can be made. In India, the situation can be expected to move towards betterment soon, and once that happens the situation in the World as a whole would start improving. We shall demonstrate that as long as the rate of change of the logarithm of the cumulative total number of cases with respect to time in a pandemic continues to reduce, the pattern of growth would continue to remain nearly exponential, and as soon as it is seen that the rate of change starts to become nearly constant the growth can be expected to start to change towards a nearly logarithmic pattern.
Hepatic FGF21 mediates tissue tolerance during bacterial inflammation by preserving cardiac function
Authors: Huen Sarah C. , Wang Andrew , Feola Kyle , Desrouleaux Reina , Luan Harding H. , Hogg Richard , Zhang Cuiling , Zhang Qing-Jun , Liu Zhi-Ping , Medzhitov Ruslan 
Published: October 2020

AbstractSickness behaviors, including anorexia, are evolutionarily conserved responses to acute infections. Inflammation-induced anorexia causes dramatic metabolic changes, of which components critical to survival are unique depending on the type of inflammation. Glucose supplementation during the anorectic period induced by bacterial inflammation suppresses adaptive fasting metabolic pathways, including fibroblast growth factor-21 (FGF21), and decreases survival. Consistent with this observation, FGF21 deficient mice are more susceptible to mortality from endotoxemia and poly-bacterial peritonitis, but not viral infection. Here we report that increased circulating FGF21 during bacterial inflammation is hepatic-derived, promotes cardiac function, and is required for survival. FGF21 signaling downstream of its obligate co-receptor beta-Klotho (KLB) is required. However, mice with central nervous system or adipose-specific deletion ofKlbdo not demonstrate any difference in response to bacterial inflammation, suggesting that multiple tissues and/or a novel FGF21 target tissue are required for the full protective effect of FGF21. These data suggest that hepatic FGF21 is a novel cardioprotective factor in bacterial sepsis.eTOC SummaryIn response to bacterial inflammation, hepatic fibroblast growth factor 21 (FGF21), an endocrine hormone that mediates adaptive responses to metabolic stresses such as starvation, promotes survival by supporting heart function.
Opportunities and limits of combining microbiome and genome data for complex trait prediction
Authors: Pérez-Enciso Miguel , Zingaretti Laura M. , Ramayo-Caldas Yuliaxis , de los Campos Gustavo 
Published: October 2020

AbstractThe analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: How useful can the microbiome be for complex trait prediction? Are microbiability estimates reliable? Can the underlying biological links between the host’s genome, microbiome, and the phenome be recovered? Here, we address these issues by (i) developing a novel simulation strategy that uses real microbiome and genotype data as input, and (ii) proposing a variance-component approach which, in the spirit of mediation analyses, quantifies the proportion of phenotypic variance explained by genome and microbiome, and dissects it into direct and indirect effects. The proposed simulation approach can mimic a genetic link between the microbiome and SNP data via a permutation procedure that retains the distributional properties of the data. Results suggest that microbiome data could significantly improve phenotype prediction accuracy, irrespective of whether some abundances are under direct genetic control by the host or not. Overall, random-effects linear methods appear robust for variance components estimation, despite the highly leptokurtic distribution of microbiota abundances. Nevertheless, we observed that accuracy depends in part on the number of microorganisms’ taxa influencing the trait of interest. While we conclude that overall genome-microbiome-links can be characterized via variance components, we are less optimistic about the possibility of identifying the causative effects, i.e., individual SNPs affecting abundances; power at this level would require much larger sample sizes than the ones typically available for genome-microbiome-phenome data.Author summaryThe microbiome consists of the microorganisms that live in a particular environment, including those in our organism. There is consistent evidence that these communities play an important role in numerous traits of relevance, including disease susceptibility or feed efficiency. Moreover, it has been shown that the microbiome can be relatively stable throughout an individual’s life and that is affected by the host genome. These reasons have prompted numerous studies to determine whether and how the microbiome can be used for prediction of complex phenotypes, either using microbiome alone or in combination with host’s genome data. However, numerous questions remain to be answered such as the reliability of parameter estimates, or which is the underlying relationship between microbiome, genome, and phenotype. The few available empirical studies do not provide a clear answer to these problems. Here we address these issues by developing a novel simulation strategy and we show that, although the microbiome can significantly help in prediction, it will be difficult to retrieve the actual biological basis of interactions between the microbiome and the trait.
Chromosomes distribute randomly to, but not within, human neutrophil nuclear lobes
Authors: Keenan Christine R , Mlodzianoski Michael J , Coughlan Hannah D , Bediaga Naiara G , Naselli Gaetano , Lucas Erin C , Wang Qike , de Graaf Carolyn A , Hilton Douglas J , Harrison Leonard C , Smyth Gordon K , Rogers Kelly L , Boudier Thomas , Allan Rhys S , Johanson Timothy M 
Published: October 2020

AbstractThe proximity pattern and radial distribution of chromosome territories within spherical nuclei are well understood to be random and non-random, respectively. Whether this distribution pattern is conserved in the partitioned or lobed nuclei of polymorphonuclear cells is unclear. Here we use chromosome paint technology and a novel high-throughput imaging analysis pipeline to examine the chromosome territories of all 46 chromosomes in hundreds of single human neutrophils – an abundant and famously polymorphonuclear immune cell.By comparing the distribution of chromosomes to randomly shuffled controls, and validating with orthogonal chromosome conformation capture technology, we show for the first time that all human chromosomes randomly distribute to neutrophil nuclear lobes, while maintaining a non-random radial distribution within these lobes. Furthermore, by leveraging the power of this vast dataset, we are able to reveal characteristics of chromosome territories not detected previously. For example, we demonstrate that chromosome length correlates with three-dimensional volume not only in neutrophils but other human immune cells.This work demonstrates that chromosomes are largely passive passengers during the neutrophil lobing process, but are able to maintain their macro-level organisation within lobes. Furthermore, the random distribution of chromosomes to the naturally partitioned nuclear lobes suggests that specific transchromosomal interactions are unimportant in mature neutrophils.
An experimental-mathematical approach to predict tumor cell growth as a function of glucose availability in breast cancer cell lines
Authors: Yang Jianchen , Virostko Jack , Hormuth David A. , Liu Junyan , Brock Amy , Kowalski Jeanne , Yankeelov Thomas E. 
Published: October 2020

AbstractWe present the development and validation of a mathematical model that predicts how glucose dynamics influence metabolism and therefore tumor cell growth. Glucose, the starting material for glycolysis, has a fundamental influence on tumor cell growth. We employed time-resolved microscopy to track the temporal change of the number of live and dead tumor cells under different initial glucose concentrations and seeding densities. We then constructed a family of mathematical models (where cell death was accounted for differently in each member of the family) to describe overall tumor cell growth in response to the initial glucose and confluence conditions. The Akaikie Information Criteria was then employed to identify the most parsimonious model. The selected model was then trained on 75% of the data to calibrate the system and identify trends in model parameters as a function of initial glucose concentration and confluence. The calibrated parameters were applied to the remaining 25% of the data to predict the temporal dynamics given the known initial glucose concentration and confluence, and tested against the corresponding experimental measurements. With the selected model, we achieved an accuracy (defined as the fraction of measured data that fell within the 95% confidence intervals of the predicted growth curves) of 77.2 ± 6.3% and 87.2 ± 5.1% for live BT-474 and MDA-MB-231 cells, respectively.
Correlative fluorescence microscopy, transmission electron microscopy and secondary ion mass spectrometry (CLEM-SIMS) for cellular imaging
Authors: Lange Felix , Agüi-Gonzalez Paola , Riedel Dietmar , Phan Nhu T.N. , Jakobs Stefan , Rizzoli Silvio O. 
Published: October 2020

AbstractElectron microscopy (EM) has been employed for decades to analyze cell structure. To also analyze the positions and functions of specific proteins, one typically relies on immuno-EM or on a correlation with fluorescence microscopy, in the form of correlated light and electron microscopy (CLEM). Nevertheless, neither of these procedures is able to also address the isotopic composition of cells. To solve this, a correlation with secondary ion mass spectrometry (SIMS) would be necessary. SIMS has been correlated in the past to EM or to fluorescence microscopy in biological samples, but not to CLEM. We achieved this here, using a protocol based on transmission EM, conventional epifluorescence microscopy and nanoSIMS. The protocol is easily applied, and enables the use of all three technologies at high performance parameters. We suggest that CLEM-SIMS will provide substantial information that is currently beyond the scope of conventional correlative approaches.