bluuebunny/crossref_metadata_2025 huggingface dataset:
Accurate wisdom of the crowd from unsupervised dimension reduction
Authors: Wang Lingfei , Michoel Tom
Published: July 2019

Wisdom of the crowd, the collective intelligence from responses of multiple human or machine individuals to the same questions, can be more accurate than each individual and improve social decision-making and prediction accuracy. Crowd wisdom estimates each individual’s error level and minimizes the overall error in the crowd consensus. However, with problem-specific models mostly concerning binary (yes/no) predictions, crowd wisdom remains overlooked in biomedical disciplines. Here we show, in real-world examples of transcription factor target prediction and skin cancer diagnosis, and with simulated data, that the crowd wisdom problem is analogous to one-dimensional unsupervised dimension reduction in machine learning. This provides a natural class of generalized, accurate and mature crowd wisdom solutions, such as PCA and Isomap, that can handle binary and also continuous responses, like confidence levels. They even outperform supervised-learning-based collective intelligence that is calibrated on historical performance of individuals, e.g. random forest. This study unifies crowd wisdom and unsupervised dimension reduction, and extends its applications to continuous data. As the scales of data acquisition and processing rapidly increase, especially in high-throughput sequencing and imaging, crowd wisdom can provide accurate predictions by combining multiple datasets and/or analytical methods.
Catalytic self-folding of 2D structures through cascading magnet reactions
Authors: Southern Emily J. , Besnard Valentin , Lahaye Bastien , Tyrrell Andy M. , Miyashita Shuhei
Published: July 2019

While thousands of proteins involved in development of the human body are capable of self-assembling in a distributed manner from merely 20 types of amino acid, macroscopic products that can be assembled spontaneously from ‘alive’ components remains an aspiration in engineering. To attain such a mechanism, a major challenge lies in understanding which attributes from the bio-molecular realm must be leveraged at the macro-scale. Inspired by protein folding, we present a centimetre-size 1D tile chain whose self-folding processes are directed by structure-embedded magnetic interactions, which can theoretically self-assemble into convex 2D structures of any size or shape without the aid of a global ‘controller’. Each tile holds two magnets contained in paths designed to control their interactions. Once initiated by a magnetic unit (termed Catalyst), the chain self-reconfigures by consuming magnetic potential energy stored between magnet pairs, until the final 2D structure is reached at an energetic minimum. Both simulation and experimental results are presented to illustrate the method’s efficacy on chains of arbitrary length. Results demonstrate the promise of a physically implemented, bottom-up, and scalable self-assembly method for novel 2D structure manufacturing, bridging the bio-molecular and mechanical realms.
Palaeoepidemiology in extinct vertebrate populations: factors influencing skeletal health in Jurassic marine reptiles
Authors: Pardo-Pérez Judith M. , Kear Benjamin , Maxwell Erin E.
Published: July 2019

Palaeoepidemiological studies related to palaeoecology are rare, but have the potential to provide information regarding ecosystem-level characteristics by measuring individual health. In order to assess factors underlying the prevalence of pathologies in large marine vertebrates, we surveyed ichthyosaurs (Mesozoic marine reptiles) from the Posidonienschiefer Formation (Early Jurassic: Toarcian) of southwestern Germany. This Formation provides a relatively large sample from a geologically and geographically restricted interval, making it ideal for generating baseline data for a palaeoepidemiological survey. We examined the influence of taxon, anatomical region, body size, ontogeny and environmental change, as represented by the early Toarcian Oceanic Anoxic Event, on the prevalence of pathologies, based ona prioriideas of factors influencing population skeletal health. Our results show that the incidence of pathologies is dependent on taxon, with the small-bodied genusStenopterygiusexhibiting fewer skeletal pathologies than other genera. WithinStenopterygius, we detected more pathologies in large adults than in smaller size classes. Stratigraphic horizon, a proxy for palaeoenvironmental change, did not influence the incidence of pathologies inStenopterygius. The quantification of the occurrence of pathologies within taxa and across guilds is critical to constructing more detailed hypotheses regarding changes in the prevalence of skeletal injury and disease through Earth history.
Interdisciplinary optimism? Sentiment analysis of Twitter data
Authors: Weber Charlotte Teresa , Syed Shaheen
Published: July 2019

Interdisciplinary research has faced many challenges, including institutional, cultural and practical ones, while it has also been reported as a ‘career risk’ and even ‘career suicide’ for researchers pursuing such an education and approach. Yet, the propagation of challenges and risks can easily lead to a feeling of anxiety and disempowerment in researchers, which we think is counterproductive to improving interdisciplinarity in practice. Therefore, in the search of ‘bright spots’, which are examples of cases in which people have had positive experiences with interdisciplinarity, this study assesses the perceptions of researchers on interdisciplinarity on the social media platform Twitter. The results of this study show researchers’ many positive experiences and successes of interdisciplinarity, and, as such, document examples of bright spots. These bright spots can give reason for optimistic thinking, which can potentially have many benefits for researchers’ well-being, creativity and innovation, and may also inspire and empower researchers to strive for and pursue interdisciplinarity in the future.
Characterization of β-glucan extracts and purified extracts from medicinal mushrooms and their biological activities
Authors: Kim Ha-Na , Kim Joo-Young , Kim Young-Chan , Kim Chang-Seob , Jung Young Hoon , Chung Shin-Kyo
Published: July 2019

Phellinus baumii and Ganoderma lucidum are the representative medicinal mushrooms in Korea. The β-glucan extract was prepared from these mushrooms, and their physicochemical characteristics, antioxidant contents, antioxidant activities, cell viability, and inhibition activities of cancer cell migration were investigated. The optimum β-glucan extraction condition was 6% (v/w) concentration of enzyme (Viscozyme L), 50:50 (w/w) mushroom ratio, and 8 hours of reaction time, respectively. The β-glucan purity of PGBEP (Phellinus baumii and Ganoderma lucidum β-glucan extract with purification) was higher than of PGBE (Phellinus baumii and Ganoderma lucidum β-glucan extract). In contrast, the extraction yield and β-glucan contents of PGBEP were lower than of PGBE (p<0.05). The FT-IR spectrum of PGBE and PGBEP showed that α-glycosidic and β-glycosidic linkage formation was determined by the appearance of the peaks at 890-822 cm-1 range. The antioxidant contents and antioxidant activities of PGBE were higher than of PGBEP. The cell viability by MTT assay of PGBE and PGBEP was higher than 80%. The inhibition activity of cancer cell migration by wound healing assay of PGBEP was significantly higher than of PGBE and positive control.
Effects of Cynanchi Wilfordii Radix and Polygoni Multiflori Radix liquors on lipid peroxidation and antioxidant activity in rat serum amd brain tissue
Authors: Kong Hyeun-Ju , Yang Kyung-Mi
Published: July 2019

This study was conducted to identify the effects of Cynanchi Wilfordii Radix and Polygoni Multiflori Radix liquors on lipid peroxidation and antioxidant activity in rats. Male Sprague-Dawley rats were placed on a liquid diet for six weeks. The rats were assigned to one of four experimental groups according to the following liquid diet types: a normal liquid diet (C), the soju liquid diet (A), a Cynanchi Wilfordii Radix liquor diet (WA) and a Polygoni Multiflori Radix liquor diet (RA). Except group C, alcohol contributed 12% of the total calories consumed by the rats. The results of MDA level and antioxidant activity of serum and brain tissue of rats were as follows. The serum and brain MDA levels of WA and RA groups could be lowered to the group C level. The nitric oxide (NO) level of the brain tissue of the RA group was lowest in all the groups. Serum superoxide dismutase (SOD) activity in the A and WA groups were significantly elevated. Serum catalase activity was significantly higher in the WA group than it was in groups C and A. Glutathione peroxidase (GSH-Px) activity in brain tissue was significantly elevated in the WA and RA groups relative to group A. Among all the experimental groups, the total serum antioxidant capacity in group A was lowest. This indicated the soju liquid diet led to oxidative damage in these rats. In contrast, the Cynanchi Wilfordii Radix and Polygoni Multiflori Radix liquor diets effectively inhibited lipid peroxidation and NO production.
Analysis of quality characteristics for food ingredients using fine powder of Jeju citrus
Authors: Choi Hee-Jeong , Ra Jeong-Sic , Chung Shin-Kyo , Lee Sang-Han
Published: July 2019

In order to assess whether the fine powder of Jeju citrus can be used for better quality characteristics in food processing, we first prepared ultra-fine powder C20 (20 mesh of citrus), C40 (40 mesh of citrus), and C100 (100 mesh of citrus). The mean particle size of C20, C40, and C100 were 662.6±176.9, 344.6±126.8, and 91.7±54.9 μm, respectively. The antioxidant activity measured by the 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) radical scavenging assay and ferric Reducing Antioxidant Power (FRAP) assay was the highest in C100. Moreover, increasing mesh of citrus increased the L* and b* values of citrus, but not the a* value of citrus. Using a prototype developed from the powder, we performed sensory tests for taste, color, texture, flavor and overall preference. C100 showed the highest score compared to C20 and C40 in the sensory evaluation. Particularly, C100 had excellent flavor among all the powders. Our results collectively indicate that the Jeju citrus supplementation has better quality characteristics during food processing; this may aid in the development of food ingredients for functional food materials. Furthermore, a high mesh of citrus provides better quality in citrus-based food processing.
Towards Improved Molecular Identification Tools in Fine Fescue (FestucaL., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing
Authors: Qiu Yinjie , Hirsch Cory D. , Yang Ya , Watkins Eric
Published: July 2019

Fine fescues (FestucaL., Poaceae) are turfgrass species that perform well in low-input environments. Based on morphological characteristics, the most commonly-utilized fine fescues are divided into five taxa: three are subspecies withinF. rubraL. and the remaining two are treated as species within theF. ovinaL. complex. Morphologically, these five taxa are very similar, both identification and classification of fine fescues remain challenging. In an effort to develop identification methods for fescues, we used flow cytometry to estimate genome size, ploidy level, and sequenced the chloroplast genome of all five taxa. Fine fescue chloroplast genome sizes ranged from 133,331 to 133,841 bp and contained 113 to 114 genes. Phylogenetic relationship reconstruction using whole chloroplast genome sequences agreed with previous work based on morphology. Comparative genomics suggested unique repeat signatures for each fine fescue taxon that could potentially be used for marker development for taxon identification.
HD-tDCS over mIPS causally modulates online reach correction
Authors: Goettker Alexander , Caie Brandon , Jeyachandra Jerrold , Xu Sisi , Gallivan Jason , Dmochowski Jacek , Fiehler Katja , Blohm Gunnar
Published: July 2019

Brain lesion and stimulation studies have suggested posterior parietal cortex and the medial intraparietal sulcus in particular as a crucial hub for online movement error corrections. However, causal evidence for this is still sparse. Indeed, lesion studies are potentially confounded by compensatory reorganization mechanisms while brain stimulation studies have produced heterogeneous results when employing transcranial magnetic stimulation. Here we designed a new complementary paradigm using fMRI-guided high-definition transcranial direct current stimulation (HD-tDCS) of the left medial intraparietal sulcus (mIPS) together with regression-based mediation analysis to re-examine the causal role of mIPS in online reach corrections to jumping targets. We obtained two independent measures of stimulation-induced changes in brain activity by modeling current flow in the brain and through EEG recordings before and after HD-tDCS stimulation. Third, to quantify behavioral effects of HD-tDCS we computed movement curvature as a measure of online correction. We demonstrate that both of our measurements of brain activity were consistent with a polarity-specific modulation of the online correction for targets jumping to the contralateral side of the stimulation. Importantly, using a mediation analysis of the relationship between stimulation current and movement curvature suggests that the induced current modifies brain activity, which then leads to the observed behavioral changes. This unique combination of methods and analysis thus provides complementary evidence for the crucial role of the posterior parietal cortex in online error correction, while at the same time setting a new methodological standard with respect to the causal influence of transcranial direct current stimulation.

New & Noteworthy

Transcranial direct current stimulation (tDCS) is an interesting and potentially useful tool for asking causal scientific questions and design clinical treatments. With our unique combination of highly accurate fMRI guided stimulation, current forward modeling, EEG recordings before and after the stimulation and behavioral changes we could unravel the causal structure of tDCS. Our approach naturally deals with the variability of tDCS results, increasing its potential usefulness as a tool for research and clinical applications.
Effects of size and elasticity on the relation between flow velocity and wall shear stress in side-wall aneurysms: A lattice Boltzmann-based computer simulation study
Authors: Wang Haifeng , Krüger Timm , Varnik Fathollah
Published: July 2019

Blood flow in an artery is a fluid-structure interaction problem. It is widely accepted that aneurysm formation, enlargement and failure are associated with wall shear stress (WSS) which is exerted by flowing blood on the aneurysmal wall. To date, the combined effect of aneurysm size and wall elasticity on intra-aneurysm (IA) flow characteristics, particularly in the case of side-wall aneurysms, is poorly understood. Here we propose a model of three-dimensional viscous flow in a compliant artery containing an aneurysm by employing the immersed boundary-lattice Boltzmann-finite element method. This model allows to adequately account for the elastic deformation of both the blood vessel and aneurysm walls. Using this model, we perform a detailed investigation of the flow through aneurysm under different conditions with a focus on the parameters which may influence the wall shear stress. Most importantly, it is shown in this work that the use of flow velocity as a proxy for wall shear stress is well justified only in those sections of the vessel which are close to the ideal cylindrical geometry. Within the aneurysm domain, however, the correlation between wall shear stress and flow velocity is largely lost due to the complexity of the geometry and the resulting flow pattern. Moreover, the correlations weaken further with the phase shift between flow velocity and transmural pressure. These findings have important implications for medical applications since wall shear stress is believed to play a crucial role in aneurysm rupture.
On the early-life origins of vulnerability to opioid addiction
Authors: Levis Sophia C , Bentzley Brandon S , Molet Jenny , Bolton Jessica L , Perrone Christina R , Baram Tallie Z , Mahler Stephen V
Published: July 2019

The origins and neural bases of the current opioid addiction epidemic are unclear. Genetics plays a major role in addiction vulnerability, but cannot account for the recent exponential rise in opioid abuse, so environmental factors must contribute. Individuals with history of early-life adversity (ELA) are disproportionately prone to opioid addiction, yet whether ELA interacts with factors such as increased access to opioids to directly influence brain development and function and cause opioid addiction vulnerability is unknown. We simulated ELA in female rats and this led to a striking opioid addiction-like phenotype. This was characterized by resistance to extinction, increased relapse-like behavior, and, as in addicted humans, major increases in opioid economic demand. By contrast, seeking of a less salient natural reward was unaffected by ELA, whereas demand for highly palatable treats was augmented. These discoveries provide novel insights into the origins and nature of reward circuit malfunction that may set the stage for addiction.
The case for using Mapped Exonic Non-Duplicate (MEND) read counts in RNA-Seq experiments: examples from pediatric cancer datasets
Authors: Beale Holly C. , Roger Jacquelyn M. , Cattle Matthew A. , McKay Liam T. , Thomson Drew K. A. , Learned Katrina , Lyle A. Geoffrey , Kephart Ellen T. , Currie Rob , Lam Du Linh , Sanders Lauren , Pfeil Jacob , Vivian John , Bjork Isabel , Salama Sofie R. , Haussler David , Vaske Olena M.
Published: July 2019

Background

The accuracy of gene expression as measured by RNA sequencing (RNA-Seq) is dependent on the amount of sequencing performed. However, some types of reads are not informative for determining this accuracy. Unmapped and non-exonic reads do not contribute to gene expression quantification. Duplicate reads can be the product of high gene expression or technical errors.

Findings

We surveyed bulk RNA-Seq datasets from 2179 tumors in 48 cohorts to determine the fractions of uninformative reads. Total sequence depth was 0.2-668 million reads (median (med.) 61 million; interquartile range (IQR) 53 million). Unmapped reads constitute 1-77% of all reads (med. 3%; IQR 3%); duplicate reads constitute 3-100% of mapped reads (med. 27%; IQR 30%); and non-exonic reads constitute 4-97% of mapped, non-duplicate reads (med. 25%; IQR 21%). Informative reads--Mapped, Exonic, Non-duplicate (MEND) reads--constitute 0-79% of total reads (med. 50%; IQR 31%). Further, we find that MEND read counts have a 0.22 Pearson correlation to the number of genes expressed above 1 Transcript Per Million, while total reads have a correlation of −0.05.

Conclusions

Since the fraction of uninformative reads vary, we propose using only definitively informative reads, MEND reads, for the purposes of asserting the accuracy of gene expression measured in a bulk RNA-Seq experiment. We provide a Docker image containing 1) the existing required tools (RSeQC, sambamba and samblaster) and 2) a custom script. We recommend that all results, sensitivity studies and depth recommendations use MEND units.
Viral gene drive in herpesviruses
Authors: Walter Marius , Verdin Eric
Published: July 2019

Herpesviruses are ubiquitous pathogens in need of novel therapeutic solutions. Current engineered gene drive strategies rely on sexual reproduction, and are thought to be restricted to sexual organisms. Here, we report on the design of a novel gene drive system that allows the spread of an engineered trait in populations of DNA viruses and, in particular, herpesviruses. We describe the successful transmission of a gene drive sequence between distinct strains of human cytomegalovirus (human herpesvirus 5) and show that gene drive viruses can efficiently target and replace wildtype populations in cell culture experiments. Our results indicate that viral gene drives can be used to suppress a viral infection and may represent a novel therapeutic strategy against herpesviruses.
The Implications of Over-Estimating Gene Tree Discordance on a Rapid-Radiation Species Tree (Blattodea: Blaberidae)
Authors: Evangelista Dominic A. , Gilchrist Michael A. , Legendre Frédéric , O’Meara Brian
Published: July 2019

Patterns of discordance between gene trees and the species trees they reside in are crucial to the debate over the superiority of coalescent or concatenation approaches to tree inference. However, errors in estimating gene tree topologies obfuscate the issue by making gene trees appear erroneously discordant with the species tree. We thus test the prevalence of discordance between gene trees and their species tree using an empirical dataset for a clade with a rapid radiation (Blaberidae). We find that one model of codon evolution (FMutSel0) prefers gene trees that are less discordant, while another (SelAC) shows no such preference. We compare the species trees resulting from the selected sets of gene trees on the basis of internal consistency, predictive ability, and congruence with independent data. The species tree resulting from gene trees those chosen by FMutSel0, a set with low discordance, is the most robust and biologically plausible. Thus, we conclude that the results from FMutSel0 are better supported: simple models (i.e., GTR and ECM) infer trees with erroneously high levels of gene tree discordance. Furthermore, the amount of discordance in the set of gene trees has a large effect on the downstream phylogeny. Thus, decreasing gene tree error by lessening erroneous discordance can result in higher quality species trees. These results allow us to support relationships among blaberid cockroaches that were previously in flux as they now demonstrate molecular and morphological congruence.
Mendelian Randomization analyses reveal a causal effect of thyroid function on stroke via atrial fibrillation
Authors: Marouli Eirini , Kus Aleksander , Del Greco M. Fabiola , Chaker Layal , Peeters Robin , Teumer Alexander , Deloukas Panos , Medici Marco
Published: July 2019

Background

Several observational studies suggest that variations in thyroid function, even within the normal range, are a risk factor for cardiovascular diseases, but it remains to be determined if these associations are causal or not. This study investigates whether the relationship between variation in normal range thyroid function, as well as hypothyroidism and hyperthyroidism, and the risk of stroke and Coronary Artery Disease (CAD) are causal and via which pathways these relations are mediated.

Methods and Findings

We performed Mendelian Randomization (MR) analyses for stroke and CAD using genetic instruments associated with TSH and FT4 levels respectively within either the normal range, hypothyroidism or hyperthyroidism. In detected associations, the potential mediatory role of known stroke and CAD risk factors was also examined. A one standard deviation increase in TSH was associated with a 5% decrease in the risk of stroke (OR=0.95, 95% CI= 0.91 to 0.99). Multivariable MR analyses indicated that this effect is mediated through atrial fibrillation (AF). Hashimoto’s Disease (HD) was associated with a 7% increased risk of CAD (OR=1.07, 95% CI= 1.01 to 1.13). The effect of Hashimoto’s Disease (HD) on CAD risk appears to be mediated via body mass index (BMI).

Conclusions

These results provide important new insights into the causal relationships and mediating pathways between thyroid function, stroke and CAD. Specifically, we identify normal range TSH levels and HD as potential modifiable risk factors for stroke and CAD, respectively.
Age and ketogenic diet have dissociable effects on synapse-related gene expression between hippocampal subregions
Authors: Hernandez Abbi R. , Hernandez Caesar M. , Truckenbrod Leah M. , Campos Keila T. , McQuail Joseph A. , Bizon Jennifer L. , Burke Sara N.
Published: July 2019

As the number of individuals living beyond the age of 65 is rapidly increasing, so is the need to develop strategies to combat the age-related cognitive decline that may threaten independent living. Although the link between altered neuronal signaling and age-related cognitive impairments is not completely understood, it is evident that declining cognitive abilities are at least partially due to synaptic dysfunction. Aging is accompanied by well-documented changes in both excitatory and inhibitory synaptic signaling across species. Age-related synaptic alterations are not uniform across the brain, however, with different regions showing unique patterns of vulnerability in advanced age. In the hippocampus, increased activity within the CA3 subregion has been observed across species, and this can be reversed with anti-epileptic medication (Bakker et al., 2012). In contrast to CA3, the dentate gyrus shows reduced activity with age and declining metabolic activity. Ketogenic diets have been shown to decrease seizure incidence and severity in epilepsy, improve metabolic function in diabetes type II, and improve cognitive function in aged rats. This link between neuronal activity and metabolism suggests that metabolic interventions may be able to ameliorate synaptic signaling deficits accompanying advanced age. We therefore investigated the ability of a dietary regimen capable of inducing nutritional ketosis and improving cognition to alter synapse-related gene expression across the dentate gyrus, CA3 and CA1 subregions of the hippocampus. Following 12 weeks of a ketogenic or calorie-matched standard diet, RTq-PCR was used to quantify expression levels of excitatory and inhibitory synaptic signaling genes within CA1, CA3 and dentate gyrus. While there were no age or diet-related changes in CA1 gene expression, expression levels were significantly altered within CA3 by age and within the dentate gyrus by diet for several genes involved in presynaptic glutamate regulation and postsynaptic excitation and plasticity. These data demonstrate subregion-specific alterations in synaptic signaling with age and the potential for a ketogenic diet to alter these processes in dissociable ways across different brain structures that are uniquely vulnerable in older animals.
Carotid intima-media thickness in UK Biobank: Identification of novel genome-wide loci, sex-specific effects and genetic correlations with obesity and glucometabolic traits
Authors: Strawbridge Rona J. , Ward Joey , Bailey Mark E.S. , Cullen Breda , Ferguson Amy , Graham Nicholas , Johnston Keira J.A. , Lyall Laura M. , Pearsall Robert , Pell Jill , Shaw Richard J , Tank Rachana , Lyall Donald M. , Smith Daniel J.
Published: July 2019

Objectives

Atherosclerosis is the underlying cause of most cardiovascular disease, but mechanisms underlying atherosclerosis are incompletely understood. Ultra-sound measurement of the carotid artery intima-media thickness (cIMT) can be used to measure vascular remodelling, which is indicative of atherosclerosis. Genome-wide association studies have identified a number of genetic loci associated with cIMT, but heterogeneity of measurements collected by many small cohorts have been a major limitation in these efforts. Here we conducted genome-wide association analyses in UK Biobank (N=22,179), the largest single study with consistent cIMT measurements.

Approach and results

We used BOLT-LMM to run linear regression of cIMT in UK Biobank, adjusted for age, sex, genotyping platform and population structure. In white British participants, we identified 4 novel loci associated with cIMT and replicated most previously reported loci. In the first sex-specific analyses of cIMT, we identified a female-specific locus on Chromosome 5, associated with cIMT in women only and highlightVCANas a good candidate gene at this locus. Genetic correlations with body-mass index and glucometabolic traits were also observed.

Conclusion

These findings replicate previously reported associations, highlight novel biology and provide new directions for investigating the sex differences observed in cardiovascular disease presentation and progression.
ERK activation in CAR T cells is amplified by CD28-mediated increase in CD3ζ phosphorylation
Authors: Rohrs Jennifer A. , Siegler Elizabeth L. , Wang Pin , Finley Stacey D.
Published: July 2019

Chimeric antigen receptors (CARs) are engineered receptors that mediate T cell activation. CARs are comprised of activating and costimulatory intracellular signaling domains derived from endogenous T cells that initiate signaling required for T cell activation, including ERK activation through the MAPK pathway. Understanding the mechanisms by which co-stimulatory domains influence signaling can help guide the design of next-generation CARs. Therefore, we constructed an experimentally-validated computational model of anti-CD19 CARs in T cells bearing the CD3ζ domain alone or in combination with CD28. We used ensemble modeling to explore different mechanisms of CD28 co-stimulation on the ERK response time. Model simulations show that CD28 primarily influences ERK activation by enhancing the phosphorylation kinetics of CD3ζ, predictions that are validated by experimental measurements. Overall, we present a mechanistic mathematical modeling framework that can be used to gain insights into the mechanism of CAR T cell activation and produce new testable hypotheses.
Characterizing the Emergence of Liver and Gallbladder from the Embryonic Endoderm through Single-Cell RNA-Seq
Authors: Mu Tianhao , Xu Liqin , Zhong Yu , Liu Xinyu , Zhao Zhikun , Huang Chaoben , Lan Xiaofeng , Lufei Chengchen , Zhou Yi , Su Yixun , Xu Luang , Jiang Miaomiao , Zhou Hongpo , Lin Xinxin , Wu Liang , Peng Siqi , Liu Shiping , Brix Susanne , Dean Michael , Dunn Norris R. , Zaret Kenneth S. , Fu Xin-Yuan , Hou Yong
Published: July 2019

The liver and gallbladder are among the most important internal organs derived from the endoderm. Several inductive signals regulate liver development, yet the pure nascent hepatic and gallbladder cells are unable to be isolated due to limited cell markers and cell numbers. The transcriptome networks of the hepatic lineage in the endoderm, and how the gallbladder differentiates from the adjacent endoderm population, are not fully understood. Using a transgenic Foxa2eGFPreporter mouse line, we performed deep single-cell RNA sequencing on 1,966 individual cells, including nascent hepatic and gallbladder cells, isolated from the endoderm and hepatic regions from ten embryonic stages, ranging from day E7.5 to E15.5. We identified the embryonic liver developmental trajectory from primitive streak to hepatoblasts and characterized the transcriptome of the hepatic lineage. During pre-hepatogenesis (5-6 somite stage), we have identified two groups of foregut endoderm cells, one derived from visceral endoderm and the second derived from primitive streak via a mesenchymal-epithelial transition (MET). During the liver specification stages, liver primordium was identified to share both foregut and liver features. We also documented dynamic gene expression during the epithelial-hepatic transition (EHT). Six gene groups were found to switch on or off at different stages during liver specification. Importantly, we found that RXR complex signaling and newly identified transcription factors associated with liver specification. Moreover, we revealed the gallbladder primordium cells at E9.5 and found genes that transcriptionally distinguish them from the liver primordium. The present data provides a high-resolution resource and critical insights for understanding the emergence of the endoderm, liver and gallbladder development.
DDIT3 (CHOP) contributes to retinal ganglion cell somal loss but not axonal degeneration in DBA/2J mice
Authors: Marola Olivia J. , Syc-Mazurek Stephanie B. , Libby Richard T.
Published: July 2019

Glaucoma is an age-related neurodegenerative disease characterized by the progressive loss of retinal ganglion cells (RGCs). Chronic ocular hypertension, an important risk factor for glaucoma, leads to RGC axonal injury at the optic nerve head. This insult triggers molecularly distinct cascades governing RGC somal apoptosis and axonal degeneration. The molecular mechanisms activated by ocular hypertensive insult that drive both RGC somal apoptosis and axonal degeneration are incompletely understood. The cellular response to endoplasmic reticulum stress and induction of pro-apoptotic DNA damage inducible transcript 3 (DDIT3, also known as CHOP) has been implicated as a driver of neurodegeneration in many disease models, including glaucoma. RGCs express DDIT3 upon glaucoma-relevant insults, and importantly, DDIT3 has been shown to contribute to both RGC somal apoptosis and axonal degeneration after acute induction of ocular hypertension. However, the role of DDIT3 in RGC somal and axonal degeneration has not been critically tested in a model of age-related chronic ocular hypertension. Here, we investigated the role of DDIT3 in glaucomatous RGC death using an age-related, naturally occurring ocular hypertensive mouse model of glaucoma, DBA/2J mice (D2). To accomplish this, a null allele of Ddit3 was backcrossed onto the D2 background. Homozygous Ddit3 deletion did not alter gross retinal or optic nerve head morphology, nor did it change the ocular hypertensive profile of D2 mice. In D2 mice, Ddit3 deletion conferred mild protection to RGC somas but did not significantly prevent RGC axonal degeneration. Together, these data suggest that DDIT3 plays a minor role in perpetuating RGC somal apoptosis caused by chronic ocular hypertension-induced axonal injury, but does not significantly contribute to distal axonal degeneration.
17α-ethynylestradiol (EE2) limits the impact of ibuprofen upon respiration by streambed biofilms in a sub-urban stream
Authors: McClean Peter , Hunter William Ross
Published: July 2019

Pharmaceutical compounds such as the non-steroidal anti-inflammatory drug ibuprofen and the artificial estrogen 17α-ethynylestradiol (EE2) are contaminants of emerging concern in freshwater systems. Globally, human pharmaceutical use is growing by around ∼3 % per year, yet we know little about how interactions between different pharmaceuticals may affect aquatic ecosystems. Here we test how interactions between ibuprofen and EE2 affect the growth and respiration of streambed biofilms. We used contaminant exposure experiments to quantify how these compounds affected biofilm growth (biomass), respiration, net primary production (NPP) and gross primary production (GPP), both individually and in combination. We found no effects of either ibuprofen or EE2 on biofilm biomass (using ash free dry mass as a proxy) or gross primary production. Ibuprofen significantly reduced biofilm respiration and altered NPP. Concomitant exposure to EE2, however, counteracted the inhibitory effects of ibuprofen upon biofilm respiration. Our study, thus, demonstrates that interactions between pharmaceuticals in the environment may have complex effects upon microbial contributions to aquatic ecosystem functioning.
Calibrated feedback illumination for precise conventional fluorescence and PALM imaging applications
Authors: Mancebo A. , DeMars L. , Ertsgaard C. T. , Puchner E. M.
Published: July 2019

Spatial light modulation using cost efficient digital mirror arrays (DMA) is finding broad applications in fluorescence microscopy due to the reduction of phototoxicity and bleaching and the ability to manipulate proteins in optogenetic experiments. However, the precise calibration of DMAs and their application to single-molecule localization microscopy (SMLM) remained a challenge because of non-linear distortions between the DMA and camera coordinate system caused by optical components. Here we develop a fast and easy to implement calibration procedure that determines these distortions by means of an optical feedback and matches the DMA and camera coordinate system with ~50 nm precision. As a result, a region from a fluorescence image can be selected with a higher precision for illumination compared to manual alignment of the DMA. We first demonstrate the application of our precisely calibrated light modulation by performing a proof-of concept fluorescence recovery after photobleaching experiment with the endoplasmic reticulum-localized protein IRE1 fused to GFP. Next, we develop a spatial feedback photoactivation approach for SMLM in which only regions of the cell are selected for photoactivation that contain photoactivatable fluorescent proteins. The reduced exposure of the cells to 405 nm light increases the possible imaging time by 44% until phototoxic effects cause a dominant fluorescence background and a change in the cell’s morphology. As a result, the mean number of reliable single molecule localizations is also significantly increased by 28%. Since the localization precision and the ability for single molecule tracking is not altered compared to traditional photoactivation of the entire field of view, spatial feedback photoactivation significantly improves the quality of SMLM images and the precision of single molecule tracking. Our calibration method therefore lays the foundation for improved SMLM with active feedback photoactivation far beyond the applications in this work.

Statement of significance

Actively patterned illumination in fluorescence microscopy can reduce bleaching and phototoxicity as well as actively manipulate proteins in optogenetic applications. Matching the coordinate system of the camera and the light patterning device such as digital mirror arrays (DMA) remains a challenge. We developed a fast and easy calibration procedure that determines and corrects for the transformation between the camera and DMA coordinate system with ~50 nm precision. Using this approach, we develop spatial feedback photoactivation for Single Molecule Localization Microscopy (SMLM) to photoswitch only intracellular regions containing photoswitchable fluorophores. Our results show a 44% improvement in the possible data acquisition time before phototoxic effects become detectable and a 28% increase in detected localizations. Spatial feedback photoactivation thus significantly improves SMLM experiments.
Increased presynaptic excitability in a migraine with aura mutation
Authors: Suryavanshi Pratyush , Sawant-Pokam Punam , Clair Sarah , Brennan KC
Published: July 2019

Migraine is a common and disabling neurological disorder. The headache and sensory amplifications that characterize migraine are attributed to hyperexcitable sensory circuits, but a detailed understanding remains elusive. This is partly due to the paucity of genetic animal models associated with the common, less severe form of the disease. A mutation in casein kinase 1 delta (CK1δ) was identified in familial migraine with aura and advanced sleep phase syndrome. Spreading depolarization (SD), the phenomenon that underlies migraine aura, is facilitated in mice carrying one of the mutations (CK1δT44A). However, the mechanism of this susceptibility is not known. We used a combination of whole-cell electrophysiology and imaging,in vivoand inex vivobrain slices, to understand the cellular and synaptic underpinnings of this apparent circuit excitability. We found that despite normal synaptic activity and hyperpolarized neuronal membrane potentials at rest, CK1δT44Aneurons were more excitable upon repetitive stimulation compared to wild-type (WT) controls. This was due to reduced presynaptic adaptation to high-frequency stimuli at excitatory, but not inhibitory synapses. Reduced adaptation at glutamatergic CK1δT44Asynapses was mediated by a calcium-dependent enhancement of the size of the readily releasable pool of synaptic vesicles. This caused an increase in the cumulative amplitude of excitatory currents, and a higher excitation-to-inhibition ratio during sustained activity, bothin vivoand in brain slices. Fluorescence imaging revealed increased glutamate release in CK1δT44Acompared to WT brain slices, corroborating the presynaptic gain of function observed with electrophysiology. Action potential bursts elicited in individual CK1δT44Aneurons enhanced glutamatergic feedback excitation within local microcircuits, further amplifying firing frequencies. At a network levelin vivo, CK1δT44Amice showed increased duration of up state activity, which is dependent on recurrent excitation. Finally, we demonstrated that SD susceptibility of CK1δT44Abrain slices could be returned to WT levels with the same reductions in extracellular calcium that normalized presynaptic adaptation. Taken together, these findings show a stimulus-dependent presynaptic gain of function at glutamatergic synapses in a genetic model of migraine, that accounts for the increased SD susceptibility and may also explain the sensory amplifications that are associated with the disease.
Global profiling of myristoylation inToxoplasma gondiireveals key roles for lipidation in CDPK1 and MIC7 function
Authors: Broncel Malgorzata , Dominicus Caia , Hunt Alexander , Wallbank Bethan , Federico Stefania , Young Joanna , Treeck Moritz
Published: July 2019

N-myristoylation is a ubiquitous class of protein lipidation across eukaryotes andN-myristoyl transferase has been proposed as an attractive drug target in several pathogens. Functionally the myristate often primes for subsequent palmitoylation and stable membrane attachment, however, growing evidence also suggests additional regulatory roles for myristoylation on proteins. Here we describe the first global chemoproteomic screening of protein myristoylation inToxoplasma gondii. Through quantitative mass spectrometry coupled with validated chemoproteomic tools, we identify 65 myristoylated proteins. We report functionally important myristoylation on the key signalling protein CDPK1 and, surprisingly, myristoylation of the microneme protein 7 (MIC7), a predicted type-I-transmembrane protein. We demonstrate that myristoylation of MIC7 is not important for the trafficking to micronemes, but appears to play a role in host cell invasion. This dataset represents a large fraction of the parasite’s myristoylated proteome and a prerequisite to investigate this modification inToxoplasma.
Comparison of Mortality and Viral Load in Rainbow Trout (Oncorhynchus mykiss) infected with Infectious Pancreatic Necrosis Virus (IPNV) Genogroups 1 and 5
Authors: Tapia David , Barría Agustín , Yáñez José M.
Published: July 2019

Infectious Pancreatic Necrosis Virus (IPNV) is the etiological agent of a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into eight genogroups, of which two are present in Chile, genogroups 1 and 5. Here we compare the mortality rate caused by isolates from both genogroups in rainbow trout (Oncorhynchus mykiss) fry to determine if there is an association between host susceptibility and phylogenetic characterization of IPNV. Fish were challenged by immersion with one of four isolates (two of each genogroup) and mortality curves were assessed after 30 days. Viral load was measured in all mortalities and in live fish sampled at 1, 7 and 20 days post-infection. Although mortality was low throughout the challenge, differences were found between fish infected with different isolates. Both isolates from genogroup 1, caused greater cumulative mortalities than either of the isolates from Genogroup 5. When combined, the overall mortality rate of fish challenged with genogroup 1 isolates was significantly higher than those infected with genogroup 5. However, viral load was lower on trout infected with genogroup 1 isolates. These results suggest that rainbow trout are more susceptible to IPNV isolates from genogroup 1 than genogroup 5.
Chromosome-level genome assembly of a butterflyfish,Chelmon rostratus
Authors: Huang Xiaoyun , Song Yue , Zhang Suyu , Yunga A , Zhang Mengqi , Chang Yue , Zhang He , Li Chang , Zhao Yong , Liu Meiru , Seim Inge , Fan Guangyi , Liu Xin , Liu Shanshan
Published: July 2019

Chelmon rostratus(Teleostei, Perciformes, Chaetodontidae) is a copperband butterflyfish. As an ornamental fish, the genome information for this species might help understanding the genome evolution of Chaetodontidae and adaptation/evolution of coral reef fish.

In this study, using the stLFR co-Barcode reads data, we assembled a genome of 638.70 Mb in size with contig and scaffold N50 sizes of 294.41 kb and 2.61 Mb, respectively. 94.40% of scaffold sequences were assigned to 24 chromosomes using Hi-C data and BUSCO analysis showed that 97.3% (2,579) of core genes were found in our assembly. Up to 21.47 % of the genome was found to be repetitive sequences and 21,375 protein-coding genes were annotated. Among these annotated protein-coding genes, 20,163 (94.33%) proteins were assigned with possible functions.

As the first genome for Chaetodontidae family, the information of these data helpfully to improve the essential to the further understanding and exploration of marine ecological environment symbiosis with coral and the genomic innovations and molecular mechanisms contributing to its unique morphology and physiological features.
Altered phosphorylation of the proteasome subunit Rpt6 has minimal impact on synaptic plasticity and learning
Authors: Scudder Samantha L. , Gonzales Frankie R. , Howell Kristin K. , Stein Ivar S. , Dozier Lara E. , Anagnostaras Stephan G. , Zito Karen , Patrick Gentry N.
Published: July 2019

Dynamic control of protein degradation via the ubiquitin proteasome system is thought to play a crucial role in neuronal function and synaptic plasticity. The proteasome subunit Rpt6, an AAA ATPase subunit of the 19S regulatory particle, has emerged as an important site for regulation of 26S proteasome function in neurons. Phosphorylation of Rpt6 on serine 120 (S120) can stimulate the catalytic rate of substrate degradation by the 26S proteasome and this site is targeted by the plasticity-related kinase calcium/calmodulin-dependent kinase II (CaMKII), making it an attractive candidate for regulation of proteasome function in neurons. Several in vitro studies have shown that altered Rpt6 S120 phosphorylation can affect the structure and function of synapses. To evaluate the importance of Rpt6 S120 phosphorylation in vivo, we created two mouse models which feature mutations at S120 that block or mimic phosphorylation at this site. We find that peptidase and ATPase activities are upregulated in the phospho-mimetic mutant and downregulated in the phospho-dead mutant (S120 mutated to aspartic acid (S120D) or alanine (S120A), respectively). Surprisingly, these mutations had no effect on basal synaptic transmission, long-term potentiation, and dendritic spine dynamics and density in the hippocampus. Furthermore, these mutants displayed no deficits in cued and contextual fear memory. Thus, in a mouse model that blocks or mimics phosphorylation at this site, either compensatory mechanisms negate these effects, or small variations in proteasome activity are not enough to induce significant changes in synaptic structure, plasticity, or behavior.