bluuebunny/crossref_metadata_2025 huggingface dataset:
Bone marrow adipocytes drive the development of tissue invasive Ly6Chighmonocytes during obesity
Authors: Boroumand Parastoo , Prescott David , Mukherjee Tapas , Bilan Philip J. , Wong Michael , Shen Jeff , Tattoli Ivan , Zhou Yuhuan , Li Angela , Sivasubramaniyam Tharini , Shi Nancy , Zhu Lucie Y , Liu Zhi , Robbins Clinton , Philpott Dana J. , Girardin Stephen E. , Klip Amira
Published: December 2020

During obesity and high fat-diet (HFD) feeding in mice, sustained low-grade inflammation includes not only increased pro-inflammatory macrophages in the expanding adipose tissue, but also bone marrow (BM) production of invasive Ly6Chighmonocytes. As BM adiposity also accrues with HFD, we explored the relationship between the gains in BM white adipocytes and invasive Ly6Chighmonocytesin vivoand throughex vivoparadigms. We find a temporal and causal link between BM adipocyte whitening and the Ly6Chighmonocyte surge, preceding the adipose tissue macrophage rise during HFD. Phenocopying this,ex vivotreatment of BM cells with conditioned media from BM adipocytes or frombona fidewhite adipocytes favoured Ly6Chighmonocyte preponderance. Notably, the switch towards the Ly6Chighsubset was preceded by monocyte metabolic reprogramming towards glycolysis, reduced oxidative potential and increased mitochondrial fission. In sum, short-term HFD changes BM cellularity, resulting in local adipocyte whitening driving a gradual increase and activation of invasive Ly6Chighmonocytes.
Communicating Regulatory High Throughput Sequencing Data Using BioCompute Objects
Authors: King Charles Hadley S. , Keeney Jonathon , Guimera Nuria , Das Souvik , Fochtman Brian , Walderhaug Mark O , Talwar Sneh , Patel Janisha , Mazumder Raja , Donaldson Eric
Published: December 2020

For regulatory submissions of next generation sequencing (NGS) data it is vital for the analysis workflow to be robust, reproducible, and understandable. This project demonstrates that the use of the IEEE 2791-2020 Standard, (BioCompute objects [BCO]) enables complete and concise communication of NGS data analysis results. One arm of a clinical trial was replicated using synthetically generated data made to resemble real biological data. Two separate, independent analyses were then carried out using BCOs as the tool for communication of analysis: one to simulate a pharmaceutical regulatory submission to the FDA, and another to simulate the FDA review. The two results were compared and tabulated for concordance analysis: of the 118 simulated patient samples generated, the final results of 117 (99.15%) were in agreement. This high concordance rate demonstrates the ability of a BCO, when a verification kit is included, to effectively capture and clearly communicate NGS analyses within regulatory submissions. BCO promotes transparency and induces reproducibility, thereby reinforcing trust in the regulatory submission process.
Pervasive low-frequency vocal modulation during territorial contests in Eurasian Scops Owls (Otus scops)
Authors: Grieco Fabrizio
Published: December 2020

In several animal species, including birds, individuals are known to produce low-frequency vocalizations during aggressive interactions with conspecifics. In this study, I investigated territorial interactions between male Eurasian Scops Owls that occupy territories in a densely-packed area. The single-note hoot of the Scops Owl is generally assumed to be highly repeatable, however extensive recording of male-male interactions identified previously unrecognized variation in the hoots’ structure. Male Scops Owls gave hoots at a frequency lower than usual when engaging in short-distance contests with neighbouring males. Within-subject analysis revealed that the caller’s average hoot frequency was positively correlated with the distance from its rival. During contests, males gradually reduced their hoot frequency as they approached one another, perhaps reflecting changes in the degree of escalation. Male Scops Owls reduced their hoot frequency immediately after the rival initiated countersinging, and returned to their usual frequency range at the end of the contest. These findings demonstrate that vocal modulation is pervasive in social contexts in the Scops Owl, and suggests that individuals have full voluntary control of the structure of their vocalizations. This study confirms in part the findings of other authors’ experimental work, where male owls adjusted their vocal frequency when challenged by an opponent. However, that study suggested that vocal frequency would encode information about the caller’s body weight. In contrast, the present study revealed context-dependent fluctuations in hoot frequency, which may suggest that the hoot of the Scops Owl dynamically reflects the current motivational state of the caller during the contest.
Misalignment of selection, plasticity, and among-individual variation: A test of theoretical predictions withPeromyscus maniculatus
Authors: Berdal Monica Anderson , Dochtermann Ned A.
Published: December 2020

Genetic variation and phenotypic plasticity are predicted to align with selection surfaces, a prediction that has rarely been empirically tested. Understanding the relationship between sources of phenotypic variation, i.e. genetic variation and plasticity, with selection surfaces improves our ability to predict a population’s ability to adapt to a changing environment and our understanding of how selection has shaped phenotypes. Here, we estimated the (co)variances among three different behaviors (activity, aggression, and anti-predator response) in a natural population of deer mice (Peromyscus maniculatus). Using multi-response generalized mixed effects models, we divided the phenotypic covariance matrix into among- and within-individual matrices. The among-individual covariances includes genetic and permanent environmental covariances (e.g. developmental plasticity) and is predicted to align with selection. Simultaneously, we estimated the within-individual (co)variances, which include reversible phenotypic plasticity. To determine whether genetic variation, plasticity and selection align in multivariate space we calculated the dimensions containing the greatest among-individual variation and the dimension in which most plasticity was expressed (i.e. the dominant eigenvector for the among- and within-individual covariance matrices respectively). We estimated selection coefficients based on survival estimates from a mark-recapture model. Alignment between the dominant eigenvectors of behavioural variation and the selection gradient was estimated by calculating the angle between them, with an angle of 0 indicating perfect alignment. The angle between vectors ranged from 68° to 89°, indicating that genetic variation, phenotypic plasticity, and selection are misaligned in this population. This misalignment could be due to the behaviors being close to their fitness optima, which is supported by low evolvabilities, or because of low selection pressure on these behaviors.
Injectable prevascularized mature adipose tissues (iPAT) to achieve long-term survival in soft tissues regeneration
Authors: Louis Fiona , Sowa Yoshihiro , Irie Shinji , Kitano Shiro , Mazda Osam , Matsusaki Michiya
Published: December 2020

Soft tissue regeneration remains a challenge in reconstructive surgery. Current autologous fat implantations lead to high fat absorption ratios, while artificial implants can be associated with lymphoma occurrence. To overcome these limitations, our aim was to reproduce adipose tissue vasculature structure before implantation. Here, we developed injectable prevascularized adipose tissues (iPAT), using physiological collagen microfibers (CMF) mixed with human mature adipocytes, adipose-derived stem cells (ADSC) and human umbilical vein endothelial cells (HUVEC). Following murine subcutaneous implantation, higher cell survival (84±6% viability) and volume maintenance were shown after 3 months for the iPAT (up to twice heavier than the non-prevascularized balls). This higher survival can be explained by the greater amount of blood vessels (up to 1.6 folds increase), with balanced host anastomosis (51±1% of human/mouse lumens), also involving infiltration by the lymphatic and neural vasculature networks. These iPAT tissues allowed non-invasive soft tissue reconstruction for long-term outcomes, and the ability to cryopreserve them with maintained viability and functionality also enables a later reinjection usually required before reaching the final patient desired graft volume.
Universal Spectrum Identifier for mass spectra
Authors: Deutsch Eric W. , Perez-Riverol Yasset , Carver Jeremy , Kawano Shin , Mendoza Luis , Van Den Bossche Tim , Gabriels Ralf , Binz Pierre-Alain , Pullman Benjamin , Sun Zhi , Shofstahl Jim , Bittremieux Wout , Mak Tytus D. , Klein Joshua , Zhu Yunping , Lam Henry , Vizcaíno Juan Antonio , Bandeira Nuno
Published: December 2020

Mass spectra provide the ultimate evidence for supporting the findings of mass spectrometry (MS) proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USIs enable greater transparency for providing spectral evidence in support of key findings in publications, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.
Investigating pleiotropy between depression and autoimmune diseases using the UK Biobank
Authors: Glanville Kylie P , Coleman Jonathan R I , O’Reilly Paul F , Galloway James , Lewis Cathryn M
Published: December 2020

Background

Epidemiological studies have shown increased comorbidity between depression and autoimmune diseases. The mechanisms driving the comorbidity are poorly understood, and a highly powered investigation is needed to understand the relative importance of shared genetic influences. We investigated the evidence for pleiotropy from shared genetic risk alleles between these traits in the UK Biobank (UKB).

Methods

We defined autoimmune and depression cases using information from hospital episode statistics, self-reported conditions and medications, and mental health questionnaires. Pairwise comparisons of depression prevalence between autoimmune cases and controls, and vice-versa, were performed. Cross-trait polygenic risk score (PRS) analyses were performed to test for pleiotropy, i.e. testing whether PRS for depression could predict autoimmune disease status, and vice-versa.

Results

We identified 28k cases of autoimmune diseases (pooling across 14 traits) and 324k autoimmune controls, and 65k cases of depression and 232k depression controls. The prevalence of depression was significantly higher in autoimmune cases compared to controls, and vice-versa. PRS for myasthenia gravis and psoriasis were significantly higher in depression cases compared to controls (p < 5.2×10−5, R2 <= 0.04%). PRS for depression were significantly higher in inflammatory bowel disease, psoriasis, psoriatic arthritis, rheumatoid arthritis and type 1 diabetes cases compared to controls (p < 5.8×10−5, R2 range 0.06% to 0.27%), and lower in coeliac disease cases compared to controls (p < 5.4×10−7, R2 range 0.11% to 0.15%).

Conclusions

Consistent with the literature, depression was more common in individuals with autoimmune diseases compared to controls, and vice-versa, in the UKB. PRS showed some evidence for involvement of shared genetic factors, but the modest R2 values suggest that shared genetic architecture accounts for only a small proportion of the increased risk across traits.
Reproducible Correlations Of Corpus Callosum And Cingulum Generalized Fractional Anisotropy With Anxiety Ratings In Healthy Participants
Authors: Kartashov Sergey , Tetereva Alina , Martynova Olga
Published: December 2020

Diffusion tensor imaging revealed that trait anxiety predicts the microstructural properties of fiber tracts between the anterior cingulate cortex, prefrontal cortex, and amygdala. However, the whole-brain structural connectivity has been rarely reported in the non-clinical populations with marginal deviations in trait anxiety and substantial changes in state anxiety. This work is aimed to assess the correlation of state and trait anxiety inventory (STAI) scores and their one-day deviation with white matter connectivity at the whole-brain scale. 64-direction diffusion-weighted images were collected in 25 participants without prior complaints of excess anxiety and/or clinical history of anxiety disorders. The self-reported ranking of STAI was collected twice with 24-hour interval: one day before and several minutes before the MRI scanning. A correlation analysis between the generalized fractional anisotropy (GFA) and the STAI ratings was performed for all regions of the brain. According to the diffusion connectometry, the most reproducible positive correlation of GFA and anxiety scores was observed for corpus callosum. For both days of psychological assessment, the left cingulum GFA correlated negatively with State anxiety ratings, while the right cingulum GFA was strongly associated with Trait anxiety. Our results suggest that the density of the corpus callosum and bilateral cingulum tracts are associated with the individual level of anxiety.
A Machine Learning Model of Microscopic Agglutination Test for Diagnosis of Leptospirosis
Authors: Oyamada Yuji , Ozuru Ryo , Masuzawa Toshiyuki , Miyahara Satoshi , Nikaido Yasuhiko , Obata Fumiko , Saito Mitsumasa , Villanueva Sharon Yvette Angelina M. , Fujii Jun
Published: December 2020

Leptospirosis is a zoonosis caused by the pathogenic bacteriumLeptospira. The Microscopic Agglutination Test (MAT) is widely used as the gold standard for diagnosis of leptospirosis. In this method, diluted patient serum is mixed with serotype-determined Leptospiras, and the presence or absence of aggregation is determined under a dark-field microscope to calculate the antibody titer. Problems of the current MAT method are 1) a requirement of examining many specimens per sample, and 2) a need of distinguishing contaminants from true aggregates to accurately identify positivity. Therefore, increasing efficiency and accuracy are the key to refine MAT. It is possible to achieve efficiency and standardize accuracy at the same time by automating the decision making process. In this study, we built an automatic identification algorithm of MAT using a machine learning method to determine aggregation within microscopic images. The machine learned the features from 316 positive and 230 negative MAT images created with sera of Leptospira- infected (positive) and non-infected (negative) hamsters, respectively. In addition to the acquired original images, wavelet-transformed images were also considered as features. We utilized a support vector machine (SVM) as a proposed decision method. We validated the trained SVMs with 210 positive and 154 negative images. When the features were obtained from original or wavelet-transformed images, all negative images were misjudged as positive, and the classification performance was very low with sensitivity of 1 and specificity of 0. In contrast, when the histograms of wavelet coefficients were used as features, the performance was greatly improved with sensitivity of 0.99 and specificity of 0.99. We confirmed that the current algorithm judges the positive or negative of agglutinations in MAT images and gives the further possibility of automatizing MAT procedure.
A connectome of theDrosophilacentral complex reveals network motifs suitable for flexible navigation and context-dependent action selection
Authors: Hulse Brad K. , Haberkern Hannah , Franconville Romain , Turner-Evans Daniel B. , Takemura Shinya , Wolff Tanya , Noorman Marcella , Dreher Marisa , Dan Chuntao , Parekh Ruchi , Hermundstad Ann M. , Rubin Gerald M. , Jayaraman Vivek
Published: December 2020

Flexible behaviors over long timescales are thought to engage recurrent neural networks in deep brain regions, which are experimentally challenging to study. In insects, recurrent circuit dynamics in a brain region called the central complex (CX) enable directed locomotion, sleep, and context- and experience-dependent spatial navigation. We describe the first complete electron-microscopy-based connectome of theDrosophilaCX, including all its neurons and circuits at synaptic resolution. We identified new CX neuron types, novel sensory and motor pathways, and network motifs that likely enable the CX to extract the fly’s head-direction, maintain it with attractor dynamics, and combine it with other sensorimotor information to perform vector-based navigational computations. We also identified numerous pathways that may facilitate the selection of CX-driven behavioral patterns by context and internal state. The CX connectome provides a comprehensive blueprint necessary for a detailed understanding of network dynamics underlying sleep, flexible navigation, and state-dependent action selection.
Workflow for Protein N-terminal Acetylation and C-terminal Amidation Application using CcpNmr Analysis v2.4 Platform and Aria2.3 Structure Calculation Software
Authors: de Paula Oliveira Santos Bruno , Silva Bruno Marques , de Magalhães Mariana Torquato Quezado
Published: December 2020

Structural biology is a field that enables a better understanding of proteins from scratch. From the available techniques, solution NMR is one well established that provides structure, dynamics and protein-molecules interaction. In a NMR lab routine, from data acquisition until protein/mechanisms elucidation comes a process that can undergo months. During the past decades, different tools were developed for NMR data processing, peaks assignment, structure elucidation and data submission. Since many of these programs demand great computational skills, a few groups have tried to combine those programs and make them more friendly and useful, what can possibilite a faster process. Here we highlight CCPNMR2.4 analysis and ARIA2.3, responsible for peak assignment and structure calculation, respectively, and can work associated. Although being academic free and the possibility of working with a GUI interface, the common N-terminal acetylation and C-terminal amidation modifications are not implemented in a way that possibilities to work with them in combination, what results in a dilemma. This work brings visual data that evidences the low usability of CCPN and ARIA with N-terminal acetylated and C-terminal amidated proteins and propose a workflow to overcome this problem, which may improve the usage of both software in the mentioned versions and facilitate the lab users already used to these programs. As a proof of concept, we have chosen a N-terminal amidated peptide, L-Phenylseptin, whose structure has already been solved with other programs. Statistical data shows that no significant difference was found with the structure obtained with the new protocol. In conclusion, we exhibit a new protocol that can be used in combination with CCPNMR2.4 and ARIA2.3 for protein with the mentioned modifications and it successfully works and manipulates these molecules.
Highly multiplexed quantitative phosphosite assay for biology and preclinical studies
Authors: Keshishian Hasmik , McDonald E. Robert , Melanson Randy , Porter Dale A. , Mundt Filip , Krug Karsten , Wallace Luke , Forestier Dominique , Rabasha Bokang , Marlow Sara E , Jane-Valbuena Judit , Todres Ellen , Specht Harrison , Golji Javad , Kuhn Eric , Burgess Michael , MacMullan Melanie , Satpathy Shankha , Mani D.R. , Gillette Michael , Clauser Karl , Rejtar Tomas , Wang Karen , Garraway Levi A. , Sellers William R. , Carr Steven A.
Published: December 2020

Reliable methods to quantify dynamic signaling changes across diverse pathways are needed to better understand the effects of disease and drug-treatment in cells and tissues but are presently lacking. Here we present SigPath, a targeted mass spectrometry (MS) assay that measures 284 phosphosites in 200 phosphoproteins of biological interest. SigPath probes a broad swath of signaling biology with high throughput and quantitative precision. We applied the assay to investigate changes in phospho-signaling in drug-treated cancer cell lines, breast cancer preclinical models and human medulloblastoma tumors. In addition to validating previous findings, SigPath detected and quantified a large number of differentially regulated phosphosites newly associated with disease models and human tumors at baseline or with drug perturbation. Our results highlight the potential of SigPath to monitor phosphoproteomic signaling events and to nominate mechanistic hypotheses regarding oncogenesis, response and resistance to therapy.
A protease-initiated model of wound detection
Authors: O’Connor James T. , Stevens Aaron C. , Shannon Erica K. , Akbar Fabiha Bushra , LaFever Kimberly S. , Narayanan Neil , Hutson M. Shane , Page-McCaw Andrea
Published: December 2020

Wounds trigger surrounding cells to initiate repair, but it is unclear how cells detect wounds. The first known wound response of epithelial cells is a dramatic increase in cytosolic calcium, which occurs within seconds, but it is not known what initiates this calcium response. Specifically, is there an instructive signal detected by cells surrounding wounds? Here we identify a signal transduction pathway in epithelial cells initiated by the G-protein coupled receptor Methuselah-like 10 (Mthl10) activated around wounds by its cytokine ligands, Growth-blocking peptides (Gbps). Gbps are present in unwounded tissue in latent form, requiring proteolytic activation for signaling. Multiple protease families can activate Gbps, suggesting it acts as a detector to signal the presence of several proteases. We present experimental and computational evidence that proteases released during cell lysis serve as the instructive signal from wounds, liberating Gbp ligands to diffuse to the Mthl10 receptors on epithelial cells and activate downstream release of calcium. Thus, the presence of a nearby wound is signaled by the activation of a Gbp protease detector, sensitive to multiple proteases released after cellular damage.
Does arsenic contamination affect DNA methylation patterns in a wild bird population? An experimental approach
Authors: Laine Veronika N. , Verschuuren Mark , van Oers Kees , Espín Silvia , Sánchez-Virosta Pablo , Eeva Tapio , Ruuskanen Suvi
Published: December 2020

Pollutants, such as toxic metals, negatively influence organismal health and performance, even leading to population collapses. Studies in model organisms have shown that epigenetic marks, such as DNA methylation, can be modulated by various environmental factors, including pollutants, influencing gene expression and various organismal traits. Yet experimental data on the effects of pollution on DNA methylation from wild animal populations is largely lacking. We here experimentally investigated for the first time the effects of early-life exposure to environmentally relevant levels of a key pollutant, arsenic (As), on genome-wide DNA methylation in a wild bird population. We experimentally exposed nestlings of great tits (Parus major) to arsenic during their post-natal developmental period (3 to 14 days post-hatching) and compared their erythrocyte DNA methylation levels to those of respective controls. In contrast to predictions, we found no overall hypomethylation in the arsenic group. We found evidence for loci to be differentially methylated between the treatment groups, but for five CpG sites only. Three of the sites were located in gene bodies of zinc finger and BTB domain containing 47 (ZBTB47), HIVEP zinc finger 3 (HIVEP3) and insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1). Further studies are needed to evaluate whether epigenetic dysregulation is a commonly observed phenomena in polluted populations, and what the consequences are for organism functioning and for population dynamics.
Cactaceae: uses and knowledge of rural communities in the semi-arid zones of Cucaita, Ráquira and Villa de Leyva (Boyacá, Colombia)
Authors: Porras–Flórez Daniela , Albesiano Sofía , Hernández–Herrera Kendry , Gómez–Velázco Nubia , Arrieta–Violet Leopoldo
Published: December 2020

Taxa of the family Cactaceae presents morphological and reproductive characteristics, which are used by rural communities in arid and semi-arid areas, for food, medicinal and ornamental purposes. The objectives were to identify the most used species and to relate the socioeconomic factors of the informants with their knowledge of the species. To this end, 262 semi-structured interviews were applied, with questions such as name, age, gender, educational level, source of employment, among others; eight categories of use were established: agro-ecological, agricultural, commercial, environmental service, food, medicinal, ornamental and technological; three indexes were calculated, relative importance, the value of use for each of the species and wealth of knowledge of the interviewees. Nine species are reported, from which eight are used as food and ornamental, standing outOpuntia ficus-indicafor its diversity of uses, whileCylindropuntia tunicatadoes not report any utility. Variables such as age and residence time showed a significant relationship with the number of plants used by the interviewees. It is expected to contribute to the preservation of cacti, local knowledge and encourage large-scale cultivation since species such asMammillaria columbiana, Melocactus andinus, andMelocactus curvispinusare being used in an unsustainable way, which could cause their local extinction.
Condensins are essential forPseudomonas aeruginosacorneal virulence through their control of phenotypic programs
Authors: Zhao Hang , Clevenger April L. , Coburn Phillip S. , Callegan Michelle C. , Rybenkov Valentin
Published: December 2020

Pseudomonas aeruginosais a significant opportunistic pathogen responsible for a variety of human infections. Its high pathogenicity resides in a diverse array of virulence factors and an ability to adapt to hostile environments. We report that these factors are tied to the activity of condensins, SMC and MksBEF, which primarily function in structural chromosome maintenance. This study revealed that both proteins are required forP. aeruginosavirulence during corneal infection. The reduction in virulence was traced to broad changes in gene expression. Transcriptional signatures ofsmcandmksBmutants were largely dissimilar and non-additive, with the double mutant displaying a distinct gene expression profile. Affected regulons included those responsible for lifestyle control, primary metabolism, surface adhesion and biofilm growth, iron and sulfur assimilation, and denitrification. Additionally, numerous virulence factors were affected, including type 3 and type 6 secretion systems, hemagglutinin, pyocin and macroglobulin production, and a host of virulence regulators.in vitroproperties of condensin mutants mirrored their transcriptional profiles. MksB-deficient cells were impaired in pyocyanin, c-di-GMP production, and sessile growth whereassmcmutants mildly upregulated c-di-GMP, secreted fewer proteases and were growth deficient under nutrient-limiting conditions. Moreover, condensin mutants displayed an abnormal regulation upon transition to stationary phase. These data reveal that condensins are integrated into the control of multiple genetic programs related to epigenetic and virulent behavior, establishing condensins as an essential factor inP. aeruginosaocular infections.

Author Summary

Bacterial pathogenicity is a complex phenomenon dependent on the ability of a bacterium to thrive in a hostile environment while combating the host using an array of virulence factors. This study reports that pathogenicity is also tied to structural chromosome maintenance through condensins, proteins that are responsible for the global organization of the chromosome. We show that the twoPseudomonas aeruginosacondensins, SMC and MksB, act as global regulators of gene expression. The inactivation of SMC and MksB induces opposite regulatory programs in the cell that resemble those observed during the acute and chronic phases of infection. A substantial portion of this regulation is mediated by the intracellular signaling network ofP. aeruginosa. Accordingly, virulence regulation is altered in condensin mutants. The results were validated by genetic, phenotypic and virulence studies of condensin mutants. Overall, these data establish condensins as an essential factor during ocularP. aeruginosainfections revealing their involvement in the regulatory virulence network and the control of the bacterial lifestyle.
Balancing the influenza neuraminidase and hemagglutinin responses by exchanging the vaccine virus backbone
Authors: Gao Jin , Wan Hongquan , Li Xing , Martinez Mira Rakic , Gao Yamei , Ye Zhiping , Daniels Robert
Published: December 2020

Virions are a common antigen source for many viral vaccines. One limitation to using virions is that the antigen abundance is determined by the content of each protein in the virus. This caveat especially applies to viral-based influenza vaccines where the low abundance of the neuraminidase (NA) surface antigen remains a bottleneck for improving the NA antibody response. Here, we used the WHO recommended H1N1 antigens (2019-2020 season) in a systematic analysis to demonstrate that the NA to hemagglutinin (HA) ratio in virions can be improved by exchanging the viral backbone internal genes, thereby preserving the antigens. The purified inactivated virions with higher NA content show a more spherical morphology, a different balance between the HA receptor binding and NA receptor release functions, and induce a better NA inhibitory antibody response in mice. These results indicate that influenza viruses support a range of ratios for a given NA and HA pair that can be utilized to produce viral-based influenza vaccines with increased NA content which can elicit more balanced inhibitory antibody responses to NA and HA.
Mouse retinal specializations reflect knowledge of natural environment statistics
Authors: Qiu Yongrong , Zhao Zhijian , Klindt David , Kautzky Magdalena , Szatko Klaudia P. , Schaeffel Frank , Rifai Katharina , Franke Katrin , Busse Laura , Euler Thomas
Published: December 2020

Pressures for survival drive sensory circuit adaption to a species’ habitat, making it essential to statistically characterise natural scenes. Mice, a prominent visual system model, are dichromatic with enhanced sensitivity to green and UV. Their visual environment, however, is rarely considered. Here, we built a UV-green camera to record footage from mouse habitats. We found chromatic contrast to greatly diverge in the upper but not the lower visual field, an environmental difference that may underlie the species’ superior colour discrimination in the upper visual field. Moreover, training an autoencoder on upper but not lower visual field scenes was sufficient for the emergence of colour-opponent filters. Furthermore, the upper visual field was biased towards dark UV contrasts, paralleled by more light-offset-sensitive cells in the ventral retina. Finally, footage recorded at twilight suggests that UV promotes aerial predator detection. Our findings support that natural scene statistics shaped early visual processing in evolution.

Lead contact

Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Thomas Euler (thomas.euler@cin.uni-tuebingen.de)
A Quantitative Measurement to Describe the Relative Proximity of Fluorescent Biomarkers
Authors: Dyer Joshua D. , Brown Alan R. , Owen Alex , Metz Jeremy
Published: December 2020

Determining the relationship between biomarkers via fluorescence microscopy is a key step in the characterisation of cellular phenotypes. We define a simple distance-based measurement termed a perimeter distance mean (PDmean) which quantifies the relative proximity of objects in one fluorescent channel to objects in a second fluorescent channel in 2D or 3D microscopy datasets. PDmeanmeasurements were able to accurately identify known changes in colocalisation in computer-generated and real-world microscopy datasets. We argue that this approach provides substantial advantages over currently used distance-based colocalisation analysis methods. We also introduce PyBioProx, an extensible open-source Python module and graphical user interface that produces PDmeanmeasurements.
Data-informed discovery of hydrolytic nanozymes
Authors: Li Sirong , Zhou Zijun , Tie Zuoxiu , Wang Bing , Ye Meng , Du Lei , Cui Ran , Liu Wei , Wan Cuihong , Liu Quanyi , Zhao Sheng , Wang Quan , Zhang Yihong , Zhang Shuo , Zhang Huigang , Du Yan , Wei Hui
Published: December 2020

Nanozyme is a collection of nanomaterials with enzyme-like activity but exhibits higher environmental tolerance and long-term stability than their natural counterparts. Improving the catalytic activity and expanding the category of nanozymes are prerequisites to complement or even supersede natural enzymes. Specifically, a powerful hydrolytic nanozyme is demanded to degrade the unsustainable substance which natural enzymes hardly achieve. However, the development of hydrolytic nanozymes is still hindered by diverse hydrolytic substrates and following complicated mechanisms. Here, we apply two strategies which are informed by data to screen and predict catalytic active sites of MOF (metal–organic framework) based hydrolytic nanozymes. One is to increase the intrinsic activity by finely tuned Lewis acidity of the metal clusters. The other is to adjust the volume density of the active sites by shortening the length of ligands. Finally, we construct a Ce-FMA-MOF-based hydrolytic nanozyme with robust cleavage ability towards phosphate bonds, amide bonds, glycosidic bonds whose energy ascend in order; and even their mixture, biofilms. This work provides a rational methodology to design hydrolytic nanozyme, enriches the diversity of nanozymes, and potentially sheds a light on the evolution of enzyme engineering in the future.
Epithelial-to-mesenchymal transition activates Bcat1 expression to promote recurrent tumor growth
Authors: Fox Douglas B. , Alvarez James V.
Published: December 2020

Branched-chain amino acid metabolism has emerged as a crucial regulator of tumor proliferation. In particular, the branched-chain amino acid transaminase 1 (BCAT1), which catalyzes the conversion of branched-chain amino acids to α-keto acids in the cytoplasm, has been identified as a promising therapeutic target for several different cancer types, including gliomas and leukemias. BCAT1 expression has also been associated with resistance to anti-estrogen therapy in breast cancer, suggesting a role in therapeutic resistance and tumor progression. Yet a functional role for BCAT1 in promoting breast cancer recurrence has not been described. Further, BCAT1 expression is restricted to just a few specialized tissues, such as the testes and central nervous system, and the mechanism by which it becomes transcriptionally activated in tumors that arise from tissues that do not typically express BCAT1 is unclear. Here, we report that Bcat1 is upregulated in recurrent breast tumors to promote recurrent tumor growth. We find that Bcat1 is upregulated by the epithelial-to-mesenchymal transition (EMT) in mammary epithelial cells and breast cancer cells. Finally, we analyze human tumor datasets to show that BCAT1 expression is strongly correlated with epithelial-to-mesenchymal gene signatures, suggesting that EMT is the predominant regulator of BCAT1 expression in cancer. Because EMT is associated with therapy resistance, metastasis, and tumor recurrence, these findings suggest a broad clinical potential for BCAT1 inhibition.
Unusual Features of the Membrane Kinome ofTrypanosoma brucei
Authors: Jensen Bryan C. , Vaney Pashmi , Flaspohler John , Coppens Isabelle , Parsons Marilyn
Published: December 2020

In many eukaryotes, multiple protein kinases are situated in the plasma membrane where they respond to extracellular ligands. Ligand binding elicits a signal that is transmitted across the membrane, leading to activation of the cytosolic kinase domain. Humans have over 100 receptor protein kinases. In contrast, our search of theTrypanosoma bruceikinome showed that there were only ten protein kinases with predicted transmembrane domains, and unlike other eukaryotic transmembrane kinases, seven are predicted to bear multiple transmembrane domains. Most of the ten kinases, including their transmembrane domains, are conserved in bothTrypanosoma cruziandLeishmaniaspecies. Several possess accessory domains, such as Kelch, nucleotide cyclase, and forkhead-associated domains. Surprisingly, two contain multiple regions with predicted structural similarity to domains in bacterial signaling proteins. A few of the protein kinases have previously been localized to subcellular structures such as endosomes or lipid bodies. We examine here the localization of epitope-tagged versions of seven of the predicted transmembrane kinases inT. bruceibloodstream forms and show that five localized to the endoplasmic reticulum. The last two kinases are integral membrane proteins associated with the flagellum, flagellar pocket, or adjacent structures, as shown by both fluorescence and immunoelectron microscopy. Thus, these kinases are positioned in structures suggesting participation in signal transduction from the external environment.
Persistent Cellular Immunity to SARS-CoV-2 Infection
Authors: Breton Gaëlle , Mendoza Pilar , Hagglof Thomas , Oliveira Thiago Y. , Schaefer-Babajew Dennis , Gaebler Christian , Turroja Martina , Hurley Arlene , Caskey Marina , Nussenzweig Michel C.
Published: December 2020

SARS-CoV-2 is responsible for an ongoing pandemic that affected millions of individuals around the globe. To gain further understanding of the immune response in recovered individuals we measured T cell responses in paired samples obtained an average of 1.3 and 6.1 months after infection from 41 individuals. The data indicate that recovered individuals show persistent polyfunctional SARS-CoV-2 antigen specific memory that could contribute to rapid recall responses. In addition, recovered individuals show enduring immune alterations in relative numbers of CD4+and CD8+T cells, expression of activation/exhaustion markers, and cell division.

We show that SARS-CoV-2 infection elicits broadly reactive and highly functional memory T cell responses that persist 6 months after infection. In addition, recovered individuals show enduring immune alterations in CD4+and CD8+T cells compartments.
A sinusoidal transform of the visual field in cortical area V2
Authors: Sedigh-Sarvestani Madineh , Lee Kuo-Sheng , Satterfield Rachel , Shultz Nicole , Fitzpatrick David
Published: December 2020

The retinotopic maps of many visual cortical areas are thought to follow the fundamental principles that have been described for primary visual cortex (V1) where nearby points on the retina map to nearby points on the surface of V1, and orthogonal axes of the retinal surface are represented along orthogonal axes of the cortical surface. Here we demonstrate a striking departure from this conventional mapping in the secondary visual area (V2) of the tree shrew. Although local retinotopy is preserved, orthogonal axes of the retina are represented along the same axis of the cortical surface, an unexpected geometry explained by an orderly sinusoidal transform of the retinal surface. This sinusoidal topography is ideally suited for achieving uniform coverage in an elongated area like V2, is predicted by mathematical models designed to achieve wiring minimization, and provides a novel explanation for stripe-like patterns of intra-cortical connections and stimulus response properties in V2. Our findings suggest that cortical circuits flexibly implement solutions to sensory surface representation, with dramatic consequences for the large-scale layout of topographic maps.
The effects of multi-echo fMRI combination and rapidT2*-mapping on offline and real-time BOLD sensitivity
Authors: Heunis Stephan , Breeuwer Marcel , Caballero-Gaudes César , Hellrung Lydia , Huijbers Willem , Jansen Jacobus FA , Lamerichs Rolf , Zinger Svitlana , Aldenkamp Albert P
Published: December 2020

A variety of strategies are used to combine multi-echo functional magnetic resonance imaging (fMRI) data, yet recent literature lacks a systematic comparison of the available options. Here we compare six different approaches derived from multi-echo data and evaluate their influences on BOLD sensitivity for offline and in particular real-time use cases: a single-echo time series (based on Echo 2), the real-timeT2*-mapped time series (T2*FIT) and four combined time series (T2*-weighted, tSNR-weighted, TE-weighted, and a new combination scheme termedT2*FIT-weighted). We compare the influences of these six multi-echo derived time series on BOLD sensitivity using a healthy participant dataset (N=28) with four task-based fMRI runs and two resting state runs. We show that theT2*FIT-weighted combination yields the largest increase in temporal signal-to-noise ratio across task and resting state runs. We demonstrate additionally for all tasks that theT2*FITtime series consistently yields the largest offline effect size measures and real-time region-of-interest based functional contrasts. These improvements show the possible utility of multi-echo fMRI for studies employing real-time paradigms, while caution is still advised due to decreased tSNR of theT2*FITtime series. We recommend the use and continued exploration ofT2*FITfor offline task-based and real-time fMRI analysis. Supporting information includes: a data repository (https://dataverse.nl/dataverse/rt-me-fmri), an interactive web-based application to explore the data (https://rt-me-fmri.herokuapp.com/), and further materials and code for reproducibility (https://github.com/jsheunis/rt-me-fMRI).
Single dose immunization with a COVID-19 DNA vaccine encoding a chimeric homodimeric protein targeting receptor binding domain (RBD) to antigen-presenting cells induces rapid, strong and long-lasting neutralizing IgG, Th1 dominated CD4+T cells and strong CD8+T cell responses in mice
Authors: Norheim Gunnstein , Stubsrud Elisabeth , Skullerud Lise Madelene , Stankovic Branislava , Chellappa Stalin , Bjerkan Louise , Kuczkowska Katarzyna , Müller Elisabeth , Sekelja Monika , Fredriksen Agnete B.
Published: December 2020

The pandemic caused by the SARS-CoV-2 virus in 2020 has led to a global public health emergency, and non-pharmaceutical interventions required to limit the viral spread are severely affecting health and economies across the world. A vaccine providing rapid and persistent protection across populations is urgently needed to prevent disease and transmission. We here describe the development of novel COVID-19 DNA plasmid vaccines encoding homodimers consisting of a targeting unit that binds chemokine receptors on antigen-presenting cells (human MIP-1α /LD78β), a dimerization unit (derived from the hinge and CH3 exons of human IgG3), and an antigenic unit (Spike or the receptor-binding domain (RBD) from SARS-CoV-2). The candidate encoding the longest RBD variant (VB2060) demonstrated high secretion of a functional protein and induced rapid and dose-dependent RBD IgG antibody responses that persisted up to at least 3 months after a single dose of the vaccine in mice. Neutralizing antibody (nAb) titers against the live virus were detected from day 7 after one dose. All tested dose regimens reached titers that were higher or comparable to those seen in sera from human convalescent COVID-19 patients from day 28. T cell responses were detected already at day 7, and were subsequently characterized to be multifunctional CD8+and Th1 dominated CD4+T cells. Responses remained at sustained high levels until at least 3 months after a single vaccination, being further strongly boosted by a second vaccination at day 89. These findings, together with the simplicity and scalability of plasmid DNA manufacturing, safety data on the vaccine platform in clinical trials, low cost of goods, data indicating potential long term storage at +2° to 8°C and simple administration, suggests the VB2060 candidate is a promising second generation candidate to prevent COVID-19.
Adaptation of a fluoroquinolone-sensitiveShigella sonneito norfloxacin exposure
Authors: Wong Bao Chi , Law Soffi Kei Kei , Md Zoqratt Muhammad Zarul Hanifah , Ayub Qasim , Tan Hock Siew
Published: December 2020

1.

Shigellacauses shigellosis that requires antibiotic treatment in severe cases. Sub-lethal antibiotic concentrations can promote resistance, but their effect on antibiotic-sensitive bacteria before resistance development is unknown. This study investigated the effects of sublethal norfloxacin (NOR) challenges on a norfloxacin-sensitive strain,Shigella sonneiUKMCC1015. Firstly, the whole genome ofS. sonneiUKMCC1015 was assembled, and 45 antimicrobial resistance (AMR) genes were identified. However, transcriptomic analysis showed that low NOR levels do not change the expression of AMR genes and norfloxacin targets. Instead, multiple ribosomal protein genes were downregulated, which could be attributed to decreased ribosomal protein promoter activity, modulated by elevated ppGpp levels. This alarmone is involved in the bacterial stringent response during environmental stress, and it is mainly produced from the ppGpp synthetase (relA). However, high levels of ppGpp (due torelAoverexpression) are detrimental to the continued survival ofS. sonneiduring prolonged exposure to NOR. This study revealed that a norfloxacin-sensitive strain responds differently to sub-lethal NOR than commonly reported in resistant strains. Overexpression ofrelA(high ppGpp levels) may reduce the mutability ofS. sonneiUKMCC1015 in response to NOR exposure and affect NOR tolerance.
Quantitative 3D Imaging of the Cranial Microvascular Environment at Single-Cell Resolution
Authors: Rindone Alexandra N. , Liu Xiaonan , Farhat Stephanie , Perdomo-Pantoja Alexander , Witham Timothy F. , Coutu Daniel L. , Wan Mei , Grayson Warren L.
Published: December 2020

Vascularization is critical for skull development, maintenance, and healing. Yet, there remains a significant knowledge gap in the relationship of blood vessels to cranial skeletal progenitors during these processes. Here, we introduce a quantitative 3D imaging platform to enable visualization and analysis of high-resolution datasets (>100 GB) throughout the entire murine calvarium. Using this technique, we provide single-cell resolution 3D maps of vessel phenotypes and skeletal progenitors in the frontoparietal cranial bones. Through these high-resolution datasets, we demonstrate that CD31hiEmcnhivessels are spatially correlated with both Osterix+ and Gli1+ skeletal progenitors during postnatal growth, healing, and stimulated remodeling, and are concentrated at transcortical canals and osteogenic fronts. Interestingly, this relationship was weakened in mice with a conditional knockout of PDGF-BB in TRAP+ osteoclasts, suggesting a potential role for osteoclasts in maintaining the native cranial microvascular environment. Our findings provide a foundational framework for understanding how blood vessels and skeletal progenitors spatially interact in cranial bone, and will enable more targeted studies into the mechanisms of skull disease pathologies and treatments. Additionally, our technique can be readily adapted to study numerous cell types and investigate other elusive phenomena in cranial bone biology.