bluuebunny/crossref_metadata_2025 huggingface dataset:
ITGB2 (Integrin β2) Immunomodulatory Gene Variants in Premature Infants With Necrotizing Enterocolitis
Authors: George Lovya , Menden Heather , Xia Sheng , Yu Wei , Holmes Anne , Johnston Jeffrey , Reid Kimberly J. , Josephson Cassandra D. , Patel Ravi M. , Ahmed Atif , Mulrooney Neil , Miller Neil A. , Farrow Emily , Sampath Venkatesh
Published: September 2020

Aberrant toll‐like receptor (TLR) activation is central to necrotizing enterocolitis (NEC) pathogenesis. β2 integrins regulate TLR signaling, and integrin β2 (ITGB2) deficiency causes TLR hyperresponsiveness. To test the hypothesis that ITGB2 genetic variants modulate NEC susceptibility, we sequenced the exonic ITGB2 locus to compare the prevalence of deleterious variants among 221 preterm infants with and without NEC. ITGB2 variants were not associated with NEC in our entire cohort (NEC [9/56] versus controls [16/165], P = 0.19) or in extremely low birthweight infants (ELBW, controls [7.9%] versus NEC [18.2%]; P = 0.11) but were increased compared to the populace (4.5%, gnomad.broadinstitute.org). Combined annotation‐dependent depletion ‐predicted deleterious ITGB2 variants increased proportionately with increasing NEC severity in ELBW infants (controls [6.7%] versus medical NEC [16.7%] versus surgical NEC [19%] (P = 0.03). Although ITGB2 variants were not associated with NEC in our preterm cohort, subgroup analysis showed a trend towards enrichment with NEC severity in ELBW infants.
Age, Disease Symptoms, and Depression are Associated With Body Image Dissatisfaction in Newly Diagnosed Pediatric Inflammatory Bowel Disease
Authors: Cushman Grace , Stolz Mary Gray , Shih Sharon , Listernick Zoe , Talmadge Clair , Gold Benjamin D. , Reed Bonney
Published: September 2020

Objectives:

Body image refers to the subjective, mental representation one makes regarding their physical appearance. Children and adolescents with inflammatory bowel disease (IBD) may be prone to experiencing negative self‐evaluations regarding their body image given disease‐related symptoms and treatment side‐effects. In this study, we aimed to examine demographic, medical, and psychosocial variables related to body image dissatisfaction (BID) in pediatric patients diagnosed with IBD and to determine which variables are most predictive of higher dissatisfaction.

Methods:

A total of 52 youth newly diagnosed with IBD (Crohn's disease, ulcerative colitis, indeterminate colitis) ages 8 to 17 years completed questionnaires regarding their psychosocial functioning (ie, depression, anxiety, health‐related quality of life, stress), disease symptoms, and BID. BID was assessed using the modified Adapted Satisfaction with Appearance questionnaire, yielding a total score and subscale scores assessing Perceived Social Impact and Subjective Dissatisfaction. Physician global assessment of disease activity and demographic and medical characteristics were abstracted from electronic chart review.

Results:

Youth endorsed low overall BID concerns but noted the highest dissatisfaction with their abdomen, chest, and arms. Older child age, greater patient‐reported disease symptoms, and worse depression symptoms were most strongly associated with overall body dissatisfaction when evaluated in a hierarchical regression model.

Conclusions:

Demographic, disease‐related, and psychosocial factors are associated with BID in youth newly diagnosed with IBD. Given associations between BID and adverse health outcomes in healthy youth, these findings highlight a unique opportunity to improve screening and interventions for BID in patients with IBD.
Level of Exercise Influences the Severity of Fatigue, Energy Levels, and Sleep Disturbance in Oncology Outpatients Receiving Chemotherapy
Authors: Moy Sally , Kober Kord M. , Viele Carol , Paul Steven M. , Hammer Marilyn , Melisko Michelle , Wright Fay , Conley Yvette P. , Levine Jon D. , Miaskowski Christine
Published: September 2020

Background

Fatigue and sleep disturbance are common co-occurring symptoms in patients receiving chemotherapy. While the results from meta-analyses support the use of exercise to decrease the severity of these symptoms, information is needed on patients’ “real world experiences” with the use of exercise.

Objective

The aims of this study were to determine distribution of patients who did and did not exercise on a regular basis and evaluate for differences in demographic and clinical characteristics, as well as the severity of fatigue, decrements in energy, and sleep disturbance among the exercise groups.

Methods

Patients (n = 1033) completed self-report questionnaires prior to their second or third cycle of chemotherapy. Patients were categorized into 3 exercise (Ex) groups (ie, NoEx, <150 min/wk [LessEx]; ≥150 min/wk [RecEx]). Differences among the groups were evaluated using parametric and nonparametric tests.

Results

Only 19.1% of the patients were in the RecEx group. Patients in the NoEx group (37.2%) had fewer years of education, were more likely to be non-White and unemployed, had a higher body mass index, and a worse comorbidity profile. Patients in the NoEx group had higher levels of morning fatigue, lower levels of morning and evening energy, and higher levels of sleep disturbance.

Conclusions

Findings from this real-world study suggest that lack of physical activity is associated with higher levels of fatigue and sleep disturbance.

Implications for Practice

Given that the most frequently used intervention in this study was walking, clinicians can recommend this inexpensive intervention to patients to manage fatigue and sleep disturbance.
Carbon acquisition in a Baltic pico-phytoplankton species - Where does the carbon for growth come from?
Authors: Listmann Luisa , Kerl Franziska , Martens Nele , Schaum C-Elisa
Published: September 2020

- Pico-phytoplankton have ample scope to react to environmental change. But we know little about the underlying physiological mechanisms that govern how evolutionary history may affect short-term responses to environmental change.

- We investigated growth rates and carbon uptake related traits (i.e. fitness proxies) in different temperatures and at different times during the microbial growth curve of eight novel strains of Ostreococcus sp. (ca. 1-2µm). The strains were isolated from two distinct regions of the Baltic Sea differing in salinity and temperature from North-East (Bornholm Basin) to South-West (Kiel area).

- Strains from the warmer, more variable Kiel area had higher growth rates in general and showed more variable growth rates compared to strains from the colder and less variable Bornholm Basin.

- In addition, growth was maintained in early stages of the growth curve by organic carbon acquisition and the increase in growth over time and with temperature was associated with an increase in inorganic carbon acquisition (net primary productivity).

- Based on the differences between net primary productivity and potential growth on organic carbon, we postulate a shift in carbon acquisition between inorganic and organic sources in Ostreococcus sp. with potential implications on ecological dynamics within microbial communities.
AA_stat: intelligent profiling ofin vivoandin vitromodifications from open search results
Authors: Levitsky Lev I. , Bubis Julia A. , Gorshkov Mikhail V. , Tarasova Irina A.
Published: September 2020

Characterization of post-translational modifications is among the most challenging tasks in tandem mass spectrometry-based proteomics which has yet to find an efficient solution. The ultra-tolerant (open) database search attempts to meet this challenge. However, interpretation of the mass shifts observed in open search still requires an effective and automated solution. We have previously introduced the AA_stat tool for analysis of amino acid frequencies at different mass shifts and generation of hypotheses on unaccountedin vitromodifications. Here, we report on the new version of AA_stat, which now complements amino acid frequency statistics with a number of new features: (1) MS/MS-based localization of mass shifts and localization scoring, including shifts which are the sum of modifications; (2) inferring fixed modifications to increase method sensitivity; (3) inferring monoisotopic peak assignment errors and variable modifications based on abundant mass shift localizations to increase the yield of closed search; (4) new mass calibration algorithm to account for partial systematic shifts; (5) interactive integration of all results and a rated list of possible mass shift interpretations. With these options, we improve interpretation of open search results and demonstrate the utility of AA_stat for profiling of abundant and rare amino acid modifications. AA_stat is implemented in Python as an open-source command-line tool available athttps://github.com/SimpleNumber/aa_stat.
Genome sequencing of turmeric provides evolutionary insights into its medicinal properties
Authors: Chakraborty Abhisek , Mahajan Shruti , Jaiswal Shubham K. , Sharma Vineet K.
Published: September 2020

Curcuma longa, or turmeric, is traditionally known for its immense medicinal properties and has diverse therapeutic applications. However, the absence of a reference genome sequence is a limiting factor in understanding the genomic basis of the origin of its medicinal properties. In this study, we present the draft genome sequence ofCurcuma longa, the first species sequenced from Zingiberaceae plant family, constructed using 10x Genomics linked reads. For comprehensive gene set prediction and for insights into its gene expression, the transcriptome sequencing of leaf tissue was also performed. The draft genome assembly had a size of 1.24 Gbp with ~74% repetitive sequences, and contained 56,036 coding gene sequences. The phylogenetic position ofCurcuma longawas resolved through a comprehensive genome-wide phylogenetic analysis with 16 other plant species. Using 5,294 orthogroups, the comparative evolutionary analysis performed across 17 species includingCurcuma longarevealed evolution in genes associated with secondary metabolism, plant phytohormones signaling, and various biotic and abiotic stress tolerance responses. These mechanisms are crucial for perennial and rhizomatous plants such asCurcuma longafor defense and environmental stress tolerance via production of secondary metabolites, which are associated with the wide range of medicinal properties inCurcuma longa.
Joint Microbial and Metabolomic Network Estimation with the Censored Gaussian Graphical Model
Authors: Ma Jing
Published: September 2020

Joint analysis of microbiome and metabolomic data represents an imperative objective as the field moves beyond basic microbiome association studies and turns towards mechanistic and translational investigations. We present a censored Gaussian graphical model framework, where the metabolomic data are treated as continuous and the microbiome data as censored at zero, to identify direct interactions (defined as conditional dependence relationships) between microbial species and metabolites. Simulated examples show that our method metaMint performs favorably compared to existing ones. metaMint also provides interpretable microbe-metabolite interactions when applied to a bacterial vaginosis data set. R implementation of metaMint is available on GitHub.
Computational pharmacogenomics screen identifies synergistic statin-compound combinations as anti-breast cancer therapies
Authors: van Leeuwen Jenna , Ba-Alawi Wail , Branchard Emily , Longo Joseph , Silvester Jennifer , Cescon David W. , Haibe-Kains Benjamin , Penn Linda Z. , Gendoo Deena M.A.
Published: September 2020

Statins are a family of FDA-approved cholesterol-lowering drugs that inhibit the rate-limiting enzyme of the metabolic mevalonate pathway, which have been shown to have anti-cancer activity. As therapeutic efficacy is increased when drugs are used in combination, we sought to identify agents, like dipyridamole, that potentiate statin-induced tumor cell death. As an antiplatelet agent dipyridamole will not be suitable for all cancer patients. Thus, we developed an integrative pharmacogenomics pipeline to identify agents that were similar to dipyridamole at the level of drug structure, in vitro sensitivity and molecular perturbation. To enrich for compounds expected to target the mevalonate pathway, we took a pathway-centric approach towards computational selection, which we called mevalonate drug network fusion (MVA-DNF). We validated two of the top ranked compounds, nelfinavir and honokiol and demonstrated that, like dipyridamole, they synergize with fluvastatin to potentiate tumor cell death by blocking the restorative feedback loop. This is achieved by inhibiting activation of the key transcription factor that induces mevalonate pathway gene transcription, sterol regulatory element-binding protein 2 (SREBP2). Mechanistically, the synergistic response of fluvastatin+nelfinavir and fluvastatin+honokiol was associated with similar transcriptomic and proteomic pathways, indicating a similar mechanism of action between nelfinavir and honokiol when combined with fluvastatin. Further analysis identified the canonical epithelial-mesenchymal transition (EMT) gene, E-cadherin as a biomarker of these synergistic responses across a large panel of breast cancer cell lines. Thus, our computational pharmacogenomic approach can identify novel compounds that phenocopy a compound of interest in a pathway-specific manner.

Significance Statement

We provide a rapid and cost-effective strategy to expand a class of drugs with a similar phenotype. Our parent compound, dipyridamole, potentiated statin-induced tumor cell death by blocking the statin-triggered restorative feedback response that dampens statins pro-apoptotic activity. To identify compounds with this activity we performed a pharmacogenomic analysis to distinguish agents similar to dipyridamole in terms of structure, cell sensitivity and molecular perturbations. As dipyridamole has many reported activities, we focused our molecular perturbation analysis on the pathway inhibited by statins, the metabolic mevalonate pathway. Our strategy was successful as we validated nelfinavir and honokiol as dipyridamole-like drugs at both the phenotypic and molecular levels. Our pathway-specific pharmacogenomics approach will have broad applicability.
Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2
Authors: Holcomb David , Alexaki Aikaterini , Hernandez Nancy , Laurie Kyle , Kames Jacob , Hamasaki-Katagiri Nobuko , Komar Anton A. , DiCuccio Michael , Kimchi-Sarfaty Chava
Published: September 2020

Thrombosis has been one of the complications of the Coronavirus disease of 2019 (COVID-19), often associated with poor prognosis. There is a well-recognized link between coagulation and inflammation, however, the extent of thrombotic events associated with COVID-19 warrants further investigation. Poly(A) Binding Protein Cytoplasmic 4 (PABPC4), Serine/Cysteine Proteinase Inhibitor Clade G Member 1 (SERPING1) and Vitamin K epOxide Reductase Complex subunit 1 (VKORC1), which are all proteins linked to coagulation, have been shown to interact with SARS proteins. We computationally examined the interaction of these with SARS-CoV-2 proteins and, in the case of VKORC1, we describe its binding to ORF7a in detail. We examined the occurrence of variants of each of these proteins across populations and interrogated their potential contribution to COVID-19 severity. Potential mechanisms by which some of these variants may contribute to disease are proposed. Some of these variants are prevalent in minority groups that are disproportionally affected by severe COVID-19. Therefore, we are proposing that further investigation around these variants may lead to better understanding of disease pathogenesis in minority groups and more informed therapeutic approaches.

Author summary

Increased blood clotting, especially in the lungs, is a common complication of COVID-19. Infectious diseases cause inflammation which in turn can contribute to increased blood clotting. However, the extent of clot formation that is seen in the lungs of COVID-19 patients suggests that there may be a more direct link. We identified three human proteins that are involved indirectly in the blood clotting cascade and have been shown to interact with proteins of SARS virus, which is closely related to the novel coronavirus. We examined computationally the interaction of these human proteins with the viral proteins. We looked for genetic variants of these proteins and examined how these variants are distributed across populations. We investigated whether variants of these genes could impact severity of COVID-19. Further investigation around these variants may provide clues for the pathogenesis of COVID-19 particularly in minority groups.
DatingAlphaproteobacteriaevolution with eukaryotic fossils
Authors: Wang Sishuo , Luo Haiwei
Published: September 2020

Elucidating the timescale of evolution of bacteria is key to testing hypotheses on their co-evolution with eukaryotic hosts, which, however, is largely limited by the scarcity of bacterial fossils. Here, we incorporate eukaryotic fossils to date the divergence times ofAlphaproteobacteria, based on the endosymbiosis theory that mitochondria evolved from an alphaproteobacterial lineage. We estimate thatAlphaproteobacteriaarose ~1900 million years (Ma) ago, followed by rapid divergence of their major clades. We show that the origin ofRickettsiales, an order of obligate intracellular bacteria whose hosts are mostly animals, predates the emergence of animals for ~700 Ma but coincides with that of eukaryotes. This, together with reconstruction of ancestral hosts, strongly suggests that earlyRickettsialeslineages had established previously underappreciated interactions with unicellular eukaryotes. Our mitochondria-based approach displays higher precision and robustness to uncertainties compared with the traditional strategy using cyanobacterial fossils, and suggests that previous applications using divergence times of the modern hosts of symbiotic bacteria to date the bacterial tree of life may need to be revisited.
Cell culture-based shark karyotyping as a resource for chromosome-scale genome analysis
Authors: Uno Yoshinobu , Nozu Ryo , Kiyatake Itsuki , Higashiguchi Nobuyuki , Sodeyama Shuji , Murakumo Kiyomi , Sato Keiichi , Kuraku Shigehiro
Published: September 2020

Karyotyping is indispensable for validating genome assemblies whose sequence lengths can be scaled up to chromosome sizes using modern methods and is traditionally performed using cytogenetic techniques. Karyotype reports of chondrichthyans are scarce, mainly because of their unique osmoregulatory mechanism, which hinders cell culture. Here, we focused on carpet shark species and the culture conditions for fibroblasts and lymphocytes. Using this method, we performed high-fidelity characterization of their karyotypes, namely 2n = 102 for the whale shark (Rhincodon typus) and zebra shark (Stegostoma fasciatum), and 2n = 106 for the brownbanded bamboo shark (Chiloscyllium punctatum) and whitespotted bamboo shark (C. plagiosum). We identified heteromorphic XX/XY sex chromosomes for the two latter species and demonstrated the first-ever fluorescencein situhybridization of shark chromosomes prepared from cultured cells. Our technical solution is applicable to diverse chondrichthyan species and will deepen the understanding of early vertebrate evolution at the molecular level.
Rapid, high-yield production of full-length SARS-CoV-2 spike ectodomain by transient gene expression in CHO cells
Authors: Stuible Matthew , Gervais Christian , Lord-Dufour Simon , Perret Sylvie , L’Abbe Denis , Schrag Joseph , St-Laurent Gilles , Durocher Yves
Published: September 2020

Recombinant forms of the spike protein of SARS-CoV-2 and related viruses have proven difficult to produce with good yields in mammalian cells. Given the panoply of potential COVID-19 diagnostic tools and therapeutic candidates that require purified spike protein and its importance for ongoing SARS-CoV-2 research, we have explored new approaches for spike production and purification. Three transient gene expression methods based on PEI-mediated transfection of CHO or HEK293 cells in suspension culture in chemically-defined media were compared for rapid production of full-length SARS-CoV-2 ectodomain. A high-cell-density protocol using DXB11-derived CHOBRI/rcTAcells gave substantially better yields than the other methods. Different forms of the spike were expressed, including the wild-type SARS-CoV-2 sequence and a mutated/stabilized form (to favor expression of the full-length spike in prefusion conformation), with and without fusion to putative trimerization domains. An efficient two-step affinity purification method was also developed. Ultimately, we have been able to produce highly homogenous preparations of full-length spike, both monomeric and trimeric, with yields of 100-150 mg/L. The speed and productivity of this method support further development of CHO-based approaches for recombinant spike protein manufacturing.
Exploring genetic resistance to Infectious Salmon Anaemia Virus in Atlantic salmon by genome-wide association and RNA sequencing
Authors: Gervais O. , Barria A. , Papadopoulou A. , Gratacap R. , Hillestad B. , Tinch A.E. , Martin S.A.M. , Robledo D , Houston R.D.
Published: September 2020

Infectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon breeders and producers worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV in commercial strains of Atlantic salmon is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing. A total of 2,833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1,353 animals were genotyped using a 55K SNP array, and the estimate of heritability for the trait of binary survival was 0.33 (±0.04). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome 13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4,927 and 2,437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated, while several metabolic pathways were up-regulated in infected fish compared to controls. The interferon pathway was mildly activated at 7 days and showed no sign of up-regulation at 14 days post infection, implying a crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance (4 high resistance and 4 low resistance animals per time point) highlighted TRIM25 as being up-regulated in resistant fish, suggesting it may be a key antiviral gene involved in the functional genetic basis of resistance to ISAV.
Chromatin accessibility analysis uncovers regulatory element landscape in prostate cancer progression
Authors: Uusi-Mäkelä Joonas , Afyounian Ebrahim , Tabaro Francesco , Häkkinen Tomi , Lussana Alessandro , Shcherban Anastasia , Annala Matti , Nurminen Riikka , Kivinummi Kati , Tammela Teuvo L.J. , Urbanucci Alfonso , Latonen Leena , Kesseli Juha , Granberg Kirsi J. , Visakorpi Tapio , Nykter Matti
Published: September 2020

Aberrant oncogene functions and structural variation alter the chromatin structure in cancer cells. While gene regulation by chromatin states has been studied extensively, chromatin accessibility and its relevance in aberrant gene expression during prostate cancer progression is not well understood. Here, we report a genome-wide chromatin accessibility analysis of clinical tissue samples of benign prostatic hyperplasia (BPH), untreated primary prostate cancer (PC) and castration-resistant prostate cancer (CRPC) and integrative analysis with transcriptome, methylome, and proteome profiles of the same samples to uncover disease-relevant regulatory elements and their association to altered gene expression during prostate cancer progression. While promoter accessibility is consistent during disease initiation and progression, at distal sites chromatin accessibility is variable enabling transcription factors (TFs) binding patterns that are differently activated in different patients and disease stages. We identify consistent progression-related chromatin alterations during the progression to CRPC. By studying the TF binding patterns, we demonstrate the activation and suppression of androgen receptor-driven regulatory programs during PC progression and identify complementary TF regulatory modules characterized by e.g. MYC and glucocorticoid receptor. By correlation analysis we assign at least one putative regulatory region for 62% of genes and 85% of proteins differentially expressed during prostate cancer progression. Taken together, our analysis of the chromatin landscape in PC identifies putative regulatory elements for the majority of cancer-associated genes and characterizes their impact on the cancer phenotype.
Global drivers of eukaryotic plankton biogeography in the sunlit ocean
Authors: Guilhem Sommeria-Klein , Romain Watteaux , Daniele Iudicone , Chris Bowler , Hélène Morlon
Published: September 2020

Eukaryotic plankton are a core component of marine ecosystems with exceptional taxonomic and ecological diversity. Yet how their ecology interacts with the environment to drive global distribution patterns is poorly understood. Here, we useTaraOceans metabarcoding data covering all the major ocean basins combined with a probabilistic model of taxon co-occurrence to compare the biogeography of 70 major groups of eukaryotic plankton. We uncover two main axes of biogeographic variation. First, more diverse groups display stronger biogeographic structure. Second, large-bodied consumers are structured by oceanic basins, mostly via the main currents, while small-bodied phototrophs are structured by latitude, with a comparatively stronger influence of environmental conditions. Our study highlights striking differences in biogeographies across plankton groups and investigates their determinants at the global scale.

One-sentence summary

Eukaryotic plankton biogeography and its determinants at global scale reflect differences in ecology and body size.
Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
Authors: Schmidt Tobias , Samaras Patroklos , Dorfer Viktoria , Panse Christian , Kockmann Tobias , Bichmann Leon , van Puyvelde Bart , Perez-Riverol Yasset , Deutsch Eric W. , Kuster Bernhard , Wilhelm Mathias
Published: September 2020

Here we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/). Mass spectra under investigation can either be provided manually by the user (table format), or automatically retrieved from online repositories supporting access to spectral data via the universal spectrum identifier (USI), or requested from other resources and services implementing a newly designed REST interface. As a proof of principle, we implemented such an interface in ProteomicsDB thereby allowing the retrieval of spectra acquired within the ProteomeTools project or real-time prediction of tandem mass spectra from the deep learning framework Prosit. Annotated mirror spectrum plots can be exported from the USE as editable scalable high quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and integration into other websites (https://github.com/kusterlab/universal_spectrum_explorer).
Phenology and flowering overlap drive specialization in pollinator networks
Authors: Glaum Paul , Wood Thomas J. , Morris Jonathan R. , Valdovinos Fernanda S.
Published: September 2020

Variation in diet breadth and specialization stems from fundamental interactions species have with their environment1-3. Consequently, understanding the drivers of this variation is key to understanding ecological and evolutionary processes, and will facilitate the development of predictive tools as ecological networks respond to environmental change4,5. Diet breadth in wild bees has been an area of focus due to both their close mutualistic dependence on plants, and because both groups are under threat from global biodiversity loss6. Though many of the principles governing specialization for pollinators have been identified7,8, they remain largely unvalidated. Using mechanistic models of adaptive foraging in pollinators9,10, we show that while temporal resource overlap has little impact on specialization in pollinators with extended flight periods, reduced overlap increases specialization as pollinator flight periods decrease. These results are corroborated empirically using pollen load data taken from bees with shorter (genusAndrena) and longer (genusLasioglossum) flight periods across environments with both high and low temporal resource overlap. This approach reveals how interacting phenologies structure plant-pollinator networks and drive pollinator diet breadth via the temporal overlap of floral resources.
The Benefits of Mycorrhizae are Frequency-Dependent: A Case Study With a Non-Mycorrhizal Mutant of Pisum Sativum
Authors: McNickle Gordon G. , Guinel Frédérique C. , Sniderhan Anastasia E. , Wallace Cory A. , McManus Allison S. , Fafard Melissa M. , Baltzer Jennifer L
Published: September 2020

Mutualisms are remarkably common in the plant kingdom. The mycorrhizal association which involves plant roots and soil fungi is particularly common, and found among members of the majority of plant families. This association is a resource-resource mutualism, where plants trade carbon-based compounds for nutrients, such as phosphorus and nitrogen, mined by the fungi.

Evolutionary models usually assume that a mutation grants a small number of individual plants the ability to associate with mycorrhizal fungi, and that this subsequently spreads through the population resulting in the evolution of mutualism. This frequency-dependent hypothesis has been difficult to test, because it is rare to have members of the same species that are capable and incapable of forming the mutualism.

Here we describe the results of an experiment that took advantage of a mutant pea (Pisum sativum L. R25) that is incapable of forming mycorrhizal (or rhizobial) associations, and differs from the wildtype (P. sativum cv. Sparkle) by a single recessive Mendelian allele (Pssym8). We grew each genotype either alone or in every combination of pairwise mixed- or same-genotype. We also present an evolutionary matrix game, which we parameterize from the experimental 15N results, that allows us to estimate the costs and benefits of the mutualism.

We find that there was no difference between R25 and WT when grown with a competitor of the same genotype, but when R25 and WT compete, WT has a significant fitness advantage. From the model, we estimate that the benefit in units of fitness (g pod mass) obtained from direct plant nitrogen uptake is 22.2 g, and mycorrhizae increase this by only 0.6 g. The costs of plant nitrogen uptake are 9.4 g, while the cost of trade with mycorrhizae is 0.1g.

From the model and experiment, we conclude that this relatively small cost-benefit ratio of the mycorrhizal association is enough to drive the evolution of mutualism in frequency-dependent selection. However, without the mutant R25 genotype we would not have been able to draw this conclusion. This validation of frequency-dependent evolutionary models is important for continued theoretical development.
Antagonism between killer yeast strains as an experimental model for biological nucleation dynamics
Authors: Giometto Andrea , Nelson David R , Murray Andrew W
Published: September 2020

Antagonistic interactions are widespread in the microbial world and affect microbial evolutionary dynamics. Natural microbial communities often display spatial structure, which affects biological interactions, but much of what we know about microbial warfare comes from laboratory studies of well-mixed communities. To overcome this limitation, we manipulated two killer strains of the budding yeastSaccharomyces cerevisiae,expressing different toxins, to independently control the rate at which they released their toxins. We developed mathematical models that predict the experimental dynamics of competition between toxin-producing strains in both well-mixed and spatially structured populations. In both situations, we experimentally verified theory’s prediction that a stronger antagonist can invade a weaker one only if the initial invading population exceeds a critical frequency or size. Finally, we found that toxin-resistant cells and weaker killers arose in spatially structured competitions between toxin-producing strains, suggesting that adaptive evolution can affect the outcome of microbial antagonism in spatial settings.
Open source 3D phenotyping of chickpea plant architecture across plant development
Authors: Salter William T. , Shrestha Arjina , Barbour Margaret M
Published: September 2020

In this work, we developed a low-cost 3D scanner and used an open source data processing pipeline to phenotype the 3D structure of individual chickpea plants. Being able to accurately assess the 3D architecture of plant canopies can allow us to better estimate plant productivity and improve our understanding of underlying plant processes. This is especially true if we can monitor these traits across plant development. Photogrammetry techniques, such as structure from motion, have been shown to provide accurate 3D reconstructions of monocot crop species such as wheat and rice, yet there has been little success reconstructing crop species with smaller leaves and more complex branching architectures, such as chickpea. The imaging system we developed consists of a user programmable turntable and three cameras that automatically captures 120 images of each plant and offloads these to a computer for processing. The capture process takes 5-10 minutes for each plant and the majority of the reconstruction process on a Windows PC is automated. Plant height and total plant surface area were validated against “ground truth” measurements, producing R2> 0.99 and a mean absolute percentage error < 10%. We demonstrate the ability to assess several important architectural traits, including canopy volume and projected area, and estimate relative growth rate in commercial chickpea cultivars and lines from local and international breeding collections. Detailed analysis of individual reconstructions also allowed us to investigate partitioning of plant surface area, and by proxy plant biomass.
A Customizable Low-Cost System for Massively Parallel Zebrafish Behavior Phenotyping
Authors: Joo William , Vivian Michael D. , Graham Brett J. , Soucy Edward R. , Thyme Summer B.
Published: September 2020

High-throughput behavioral phenotyping is critical to genetic or chemical screening approaches. Zebrafish larvae are amenable to high-throughput behavioral screening because of their rapid development, small size, and conserved vertebrate brain architecture. Existing commercial behavior phenotyping systems are expensive and not easily modified for new assays. Here, we describe a modular, highly adaptable, and low-cost behavior system. Along with detailed assembly and operation instructions, we provide data acquisition software and a robust, parallel analysis pipeline. We validate our approach by analyzing stimulus response profiles in larval zebrafish, confirming prepulse inhibition phenotypes of two previously isolated mutants, and highlighting best practices for growing larvae prior to behavioral testing. Our new design thus allows rapid construction and streamlined operation of many large-scale behavioral setups with minimal resources and fabrication expertise, with broad applications to other aquatic organisms.
Suberoyl bis-hydroxamic acid reactivates Kaposi’s sarcoma-associated herpesvirus through histone acetylation and induces apoptosis in lymphoma cells
Authors: Iida Shun , Mine Sohtaro , Ueda Keiji , Suzuki Tadaki , Hasegawa Hideki , Katano Harutaka
Published: September 2020

Kaposi’s sarcoma-associated herpesvirus (KSHV) is an etiologic agent of Kaposi’s sarcoma as well as primary effusion lymphoma (PEL), an aggressive B-cell neoplasm which mostly arises in immunocompromised individuals. At present, there is no specific treatment available for PEL and its prognosis is poor. Lytic replication of KSHV is also associated with a subset of multicentric Castleman diseases. In this study, we found that the histone deacetylase inhibitor suberoyl bis-hydroxamic acid (SBHA) induced KSHV reactivation in PEL cells in a dose-dependent manner. Next-generation sequencing analysis showed that more than 40% of all transcripts expressed in SBHA-treated PEL cells originated from the KSHV genome compared with less than 1% in untreated cells. Chromatin immunoprecipitation assays demonstrated that SBHA induced histone acetylation targeting the promoter region of the KSHV replication and transcription activator gene. However, there was no significant change in methylation status of the promoter region of this gene. In addition to its effect of KSHV reactivation, this study revealed that SBHA induces apoptosis in PEL cells in a dose-dependent manner, inducing cleavage of caspases and expression of proapoptotic factors, including Bim and Bax. These findings suggest that SBHA reactivates KSHV from latency and induces apoptosis through the mitochondrial pathway in PEL cells. Therefore, SBHA can be considered a new tool for induction of KSHV reactivation, and could provide a novel therapeutic strategy against PEL.

Importance

Kaposi’s sarcoma and primary effusion lymphoma cells are latently infected with Kaposi’s sarcoma-associated herpesvirus (KSHV), whereas KSHV replication is frequently observed in multicentric Castleman disease. Although KSHV replication can be induced by some chemical reagents (e.g. 12-O-tetradecanoylphorbol-13-acetate), the mechanism of KSHV replication is not fully understood. We found that the histone deacetylase inhibitor suberoyl bis-hydroxamic acid (SBHA) induced KSHV reactivation with high efficiency, through histone acetylation in the promoter of the replication and transcription activator gene, compared with 12-O-tetradecanoylphorbol-13-acetate. SBHA also induced apoptosis through the mitochondrial pathway in KSHV-infected cells, with a lower EC50than measured for viral reactivation. SBHA could be used in a highly efficient replication system for KSHVin vitro,and as a tool to reveal the mechanism of replication and pathogenesis of KSHV. The ability of SBHA to induce apoptosis at lower levels than needed to stimulate KSHV reactivation, indicates its therapeutic potential.
Influenza A virus-induced thymus atrophy differentially affects dynamics of conventional and regulatory T cell development
Authors: Elfaki Yassin , Robert Philippe A. , Binz Christoph , Falk Christine S. , Bruder Dunja , Prinz Immo , Floess Stefan , Meyer-Hermann Michael , Huehn Jochen
Published: September 2020

Foxp3+regulatory T (Treg) cells, which are crucial for maintenance of self-tolerance, mainly develop within the thymus, where they arise from CD25+Foxp3-or CD25-Foxp3+Treg cell precursors. Although it is known that infections can cause transient thymic involution, the impact of infection-induced thymus atrophy on thymic Treg (tTreg) cell development is unknown. Here, we infected mice with influenza A virus (IAV) and studied thymocyte population dynamics post infection. IAV infection caused a massive, but transient thymic involution, dominated by a loss of CD4+CD8+double-positive (DP) thymocytes, which was accompanied by a significant increase in the frequency of CD25+Foxp3+tTreg cells. Differential apoptosis susceptibility could be experimentally excluded as a reason for the relative tTreg cell increase, and mathematical modeling suggested that enhanced tTreg cell generation cannot explain the increased frequency of tTreg cells. Yet, an increased death of DP thymocytes and augmented exit of single-positive (SP) thymocytes was suggested to be causative. Interestingly, IAV-induced thymus atrophy resulted in a significantly reduced T cell receptor (TCR) repertoire diversity of newly produced tTreg cells. Taken together, IAV-induced thymus atrophy is substantially altering the dynamics of major thymocyte populations, finally resulting in a relative increase of tTreg cells with an altered TCR repertoire.
Interaction network of SARS-CoV-2 with host receptome through spike protein
Authors: Gu Yunqing , Cao Jun , Zhang Xinyu , Gao Hai , Wang Yuyan , Wang Jia , Zhang Jinlan , Shen Guanghui , Jiang Xiaoyi , Yang Jie , Zheng Xichen , Xu Jianqing , Zhang Cheng Cheng , Lan Fei , Qu Di , Zhao Yun , Xu Guoliang , Xie Youhua , Luo Min , Lu Zhigang
Published: September 2020

Host cellular receptors are key determinants of virus tropism and pathogenesis. Virus utilizes multiple receptors for attachment, entry, or specific host responses. However, other than ACE2, little is known about SARS-CoV-2 receptors. Furthermore, ACE2 cannot easily interpret the multi-organ tropisms of SARS-CoV-2 nor the clinical differences between SARS-CoV-2 and SARS-CoV. To identify host cell receptors involved in SARS-CoV-2 interactions, we performed genomic receptor profiling to screen almost all human membrane proteins, with SARS-CoV-2 capsid spike (S) protein as the target. Twelve receptors were identified, including ACE2. Most receptors bind at least two domains on S protein, the receptor-binding-domain (RBD) and the N-terminal-domain (NTD), suggesting both are critical for virus-host interaction. Ectopic expression of ASGR1 or KREMEN1 is sufficient to enable entry of SARS-CoV-2, but not SARS-CoV and MERS-CoV. Analyzing single-cell transcriptome profiles from COVID-19 patients revealed that virus susceptibility in airway epithelial ciliated and secretory cells and immune macrophages highly correlates with expression of ACE2, KREMEN1 and ASGR1 respectively, andACE2/ASGR1/KREMEN1 (ASK) together displayed a much better correlation than any individual receptor. Based on modeling of systemic SARS-CoV-2 host interactions through S receptors, we revealed ASK correlation with SARS-CoV-2 multi-organ tropism and provided potential explanations for various COVID-19 symptoms. Our study identified a panel of SARS-CoV-2 receptors with diverse binding properties, biological functions, and clinical correlations or implications, including ASGR1 and KREMEN1 as the alternative entry receptors, providing insights into critical interactions of SARS-CoV-2 with host, as well as a useful resource and potential drug targets for COVID-19 investigation.
Ecological niche adaptation of a bacterial pathogen associated with reduced zoonotic potential
Authors: Kirkwood Mark , Vohra Prerna , Bawn Matt , Thilliez Gaëtan , Pye Hannah , Tanner Jennifer , Chintoan-Uta Cosmin , Branchu Priscilla , Petrovska Liljana , Dallman Timothy , Hall Neil , Stevens Mark P. , Kingsley Robert A.
Published: September 2020

The emergence of new bacterial pathogens is a continuing challenge for agriculture and food safety.Salmonella entericaserovar Typhimurium (S. Typhimurium) is a major cause of foodborne illness worldwide, with pigs a major zoonotic reservoir. Two variants,S. Typhimurium phage type U288 and monophasicS. Typhimurium (S. 4,[5],12:i:-) ST34 emerged and have accounted for the majority of isolates from pigs in the UK in the past two decades, but have distinct host range and risk to food safety. ST34 accounts for over 50% of allS. Typhimurium infections in people while U288 less than 2%. U288 and ST34 form distinct phylogenetic clusters withinS. Typhimurium, defined by approximately 600 SNPs within their 5 Mbp genomes. Evolution of the U288 clade from an LT2-like ancestor was characterised by the acquisition of AMR genes, insertions and deletions in the virulence plasmid pU288-1, and the accumulation of polymorphisms, some of which resulted in truncation of coding sequences. U288 isolates exhibited lower growth rate and viability following desiccation compared to ST34 isolates, characteristics that could affect transmission through the food chain. U288 and ST34 isolates exhibited distinct outcomes of infection in the murine model of colitis, and colonised pigs in a manner that affected the disease symptoms and distribution in organs. U288 infection was more disseminated in the lymph nodes while ST34 were recovered in greater numbers in the intestinal contents. These data are consistent with the evolution ofS. Typhimurium U288 adaptation to pigs that may determine their reduced zoonotic potential.

Importance

Bacterial pathogens continually evolve to exploit new ecological niches as they emerge due to human activity including agricultural, medical or societal practice. The consequences of the emergence of new pathogens may affect outcome of infection and risk to human or animal health. Genome sequence can resolve the population structure, identify variants that are evolving as they enter a new niche, and pinpoint potential functional divergence. We report a variantS. Typhimurium that adapted to a unique niche distinct to that occupied by a secondS. Typhimurium variant circulating in the same pig populations. Adaptation was accompanied by phenotypic and genotypic changes consistent with a more invasive lifestyle and a decreased zoonotic potential observed in the epidemiological record. Our findings suggest that pathogen genotypic variation may be useful in estimating zoonotic potential and threat to livestock welfare.
Molecular-scale visualization of sarcomere contraction within native cardiomyocytes
Authors: Burbaum Laura , Schneider Jonathan , Scholze Sarah , Böttcher Ralph T , Baumeister Wolfgang , Schwille Petra , Plitzko Jürgen M , Jasnin Marion
Published: September 2020

Sarcomeres, the basic contractile units of striated muscle, produce the forces driving muscular contraction through cross-bridge interactions between actin-containing thin filaments and myosin II-based thick filaments. Until now, direct visualization of the molecular architecture underlying sarcomere contractility has remained elusive. Here, we usein situcryo-electron to-mography to unveil sarcomere contraction in frozen-hydrated neonatal rat cardiomyocytes. We show that the hexagonal lattice of the thick filaments is already established at the neonatal stage, with an excess of thin filaments outside the trigonal positions. Structural assessment of actin polarity by subtomogram averaging reveals that thin filaments in the fully activated state form overlapping arrays of opposite polarity in the center of the sarcomere. Our approach provides direct evidence for thin filament sliding during muscle contraction and may serve as a basis for structural understanding of thin filament activation and actomyosin interactions inside unperturbed cellular environments.