bluuebunny/crossref_metadata_2025 huggingface dataset:
A curated knowledgebase enabling a network perspective on endocrine disrupting chemicals and their biological systems-level perturbations
Authors: Karthikeyan Bagavathy Shanmugam , Ravichandran Janani , Mohanraj Karthikeyan , Vivek-Ananth R.P. , Samal Areejit
Published: April 2019

Human well-being can be affected by exposure to several chemicals in the environment. One such group is endocrine disrupting chemicals (EDCs) that can perturb the hormonal homeostasis leading to adverse health effects. In this work, we have developed a detailed workflow to identify EDCs with supporting evidence of endocrine disruption in published experiments in humans or rodents. Thereafter, this workflow was used to manually evaluate more than 16000 published research articles and identify 686 potential EDCs with published evidence in humans or rodents. Importantly, we have compiled the observed adverse effects or endocrine-specific perturbations along with the dosage information for the potential EDCs from their supporting published experiments. Subsequently, the potential EDCs were classified based on the type of supporting evidence, their environmental source and their chemical properties. Additional compiled information for potential EDCs include their chemical structure, physicochemical properties, predicted ADMET properties and target genes. In order to enable future research based on this compiled information on potential EDCs, we have built an online knowledgebase, Database of Endocrine Disrupting Chemicals and their Toxicity profiles (DEDuCT), accessible at: https://cb.imsc.res.in/deduct/. After building this comprehensive resource, we employed a network biology approach to study the chemical space of EDCs and its potential link to the biological space of target genes of EDCs. Specifically, we have constructed two networks of EDCs using our resource based on similarity of chemical structures or target genes. Ensuing analysis of these two networks revealed that EDCs can differ both in their chemical structure and set of target genes. Though our detailed results highlight potential challenges in developing predictive models for EDCs, the compiled information in our resource will undoubtedly enable future research in the field, especially, those focussed towards mechanistic understanding of the systems-level perturbations caused by EDCs.
Slow life-history strategies are associated with negligible actuarial senescence in western Palearctic salamanders
Authors: Cayuela Hugo , Olgun Kurtuluş , Angelini Claudio , Üzüm Nazan , Peyronel Olivier , Miaud Claude , Avci Aziz , Lemaitre Jean-François , Schmidt Benedikt R.
Published: April 2019

Actuarial senescence (hereafter “senescence”) has been viewed for a long time as an inevitable and uniform process. However, the work on senescence has mainly focused on endotherms (especially mammals) with deterministic growth and low regeneration capacity at adult stages, leading to a strong taxonomic bias in the study of aging. Recent studies have highlighted that senescence could indeed display highly variable trajectory shape that correlates with species life history traits. Slow life histories and indeterminate growth seem to be associated with weak and late senescence. Furthermore, a few studies have suggested that high regenerative abilities could make senescence negligible in several ectotherms (e.g., hydra and salamanders). However, demographic data for species that would allow testing of these hypotheses are scarce and fragmented. Here, we investigated senescence patterns in a group of salamanders (i.e. “true salamanders”) from the Western Palearctic using capture-recapture data and Bayesian modeling. Our results showed that salamanders have slow life histories and that they experience negligible senescence. This pattern was consistent at both intra- and interspecific levels, suggesting that the absence of senescence may be a phylogenetically conserved trait. The regenerative capacities of true salamanders, and urodeles in general, likely explains why these small ectotherms have lifespans similar to that of large endotherms (e.g., ungulates, large birds) and undergo negligible senescence contrary to most amniotes including humans. Our study seriously challenges the idea that senescence is a ubiquitous phenomenon in the living world.
The scaling of genome size and cell size limits maximum rates of photosynthesis with implications for ecological strategies
Authors: Roddy Adam B. , Théroux-Rancourt Guillaume , Abbo Tito , Benedetti Joseph W. , Brodersen Craig R. , Castro Mariana , Castro Silvia , Gilbride Austin B. , Jensen Brook , Jiang Guo-Feng , Perkins John A. , Perkins Sally D. , Loureiro João , Syed Zuhah , Thompson R. Alexander , Kuebbing Sara E. , Simonin Kevin A.
Published: April 2019

A central challenge in plant ecology is to define the major axes of plant functional variation with direct consequences for fitness. Central to the three main components of plant fitness (growth, survival, and reproduction) is the rate of metabolic conversion of CO2into carbon that can be allocated to various structures and functions. Here we (1) argue that a primary constraint on the maximum rate of photosynthesis per unit leaf area is the size and packing density of cells and (2) show that variation in genome size is a strong predictor of cell sizes, packing densities, and the maximum rate of photosynthesis across terrestrial vascular plants. Regardless of the genic content associated with variation in genome size, the simple biophysical constraints of encapsulating the genome define the lower limit of cell size and the upper limit of cell packing densities, as well as the range of possible cell sizes and densities. Genome size, therefore, acts as a first-order constraint on carbon gain and is predicted to define the upper limits of allocation to growth, reproduction, and defense. The strong effects of genome size on metabolism, therefore, have broad implications for plant biogeography and for other theories of plant ecology, and suggest that selection on metabolism may have a role in genome size evolution.
Pupil-associated states modulate excitability but not stimulus selectivity in primary auditory cortex
Authors: Schwartz Zachary P. , Buran Brad N. , David Stephen V.
Published: April 2019

Recent research in mice indicates that luminance-independent fluctuations in pupil size predict variability in spontaneous and evoked activity of single neurons in auditory and visual cortex. These findings suggest that pupil is an indicator of large-scale changes in arousal state that affect sensory processing. However, it is not known whether pupil-related state also influences the selectivity of auditory neurons. We recorded pupil size and single-unit spiking activity in the primary auditory cortex (A1) of non-anesthetized male and female ferrets during presentation of natural vocalizations and tone stimuli that allow measurement of frequency and level tuning. Neurons showed a systematic increase in both spontaneous and sound-evoked activity when pupil was large, as well as desynchronization and a decrease in trial-to-trial variability. Relationships between pupil size and firing rate were non-monotonic in some cells. In most neurons, several measurements of tuning, including acoustic threshold, spectral bandwidth, and best frequency, remained stable across large changes in pupil size. Across the population, however, there was a small but significant decrease in acoustic threshold when pupil was dilated. In some recordings, we observed rapid, saccade-like eye movements during sustained pupil constriction, which may indicate sleep. Including the presence of this state as a separate variable in a regression model of neural variability accounted for some, but not all, of the variability and non-monotonicity associated with changes in pupil size.

New & Noteworthy

Cortical neurons vary in their response to repeated stimuli, and some portion of the variability is due to fluctuations in network state. By simultaneously recording pupil and single-neuron activity in auditory cortex of ferrets, we provide new evidence that network state affects the excitability of auditory neurons, but not sensory selectivity. In addition, we report the occurrence of possible sleep states, adding to evidence that pupil provides an index of both sleep and physiological arousal.
A genetic hazard score to personalize prostate cancer screening, applied to population data
Authors: Huynh-Le Minh-Phuong , Fan Chun Chieh , Karunamuni Roshan , Walsh Eleanor I. , Turner Emma L. , Lane J. Athene , Martin Richard M. , Neal David E. , Donovan Jenny L. , Hamdy Freddie C. , Parsons J. Kellogg , Eeles Rosalind A. , Easton Douglas F. , Kote-Jarai ZSofia , Olama Ali Amin Al , Garcia Sara Benlloch , Muir Kenneth , Gronberg Henrik , Wiklund Fredrik , Aly Markus , Schleutker Johanna , Sipeky Csilla , Tammela Teuvo LJ , Nordestgaard Børge G. , Key Tim J. , Travis Ruth C. , Pharoah Paul , Pashayan Nora , Khaw Kay-Tee , Thibodeau Stephen N. , McDonnell Shannon K. , Schaid Daniel J. , Maier Christiane , Vogel Walther , Luedeke Manuel , Herkommer Kathleen , Kibel Adam S. , Cybulski Cezary , Wokolorczyk Dominika , Kluzniak Wojciech , Cannon-Albright Lisa , Brenner Hermann , Schöttker Ben , Holleczek Bernd , Park Jong Y. , Sellers Thomas A. , Lin Hui-Yi , Slavov Chavdar , Kaneva Radka , Mitev Vanio , Batra Jyotsna , Clements Judith A. , Spurdle Amanda ,   Australian Prostate Cancer BioResource (APCB), Teixeira Manuel R. , Paulo Paula , Maia Sofia , Pandha Hardev , Michael Agnieszka , Kierzek Andrzej , Mills Ian G. , Andreassen Ole A. , Dale Anders M. , Seibert Tyler M. ,   The PRACTICAL Consortium
Published: April 2019

Background

Genetic risk stratification may inform decisions of whether—and when—a man should undergo prostate cancer (PCa) screening. We previously validated a polygenic hazard score (PHS), a weighted sum of 54 single-nucleotide polymorphism genotypes, for accurate prediction of age of onset of aggressive PCa and improved screening performance. We now assess the potential impact of PHS-informed screening.

Methods

United Kingdom population data were fit to a continuous model of age-specific PCa incidence. Using hazard ratios estimated from ProtecT trial data, age-specific incidence rates were calculated for percentiles of genetic risk. Incidence of higher-grade PCa (Gleason≥7) was estimated from age-specific data from the linked CAP trial. PHS and incidence data were combined to give a risk-equivalent age, when a man with a given PHS percentile will have risk of higher-grade PCa equivalent to that of a typical man at age 50 (50-years standard). Positive predictive value (PPV) of PSA testing was calculated using PHS-adjusted (PCa-risk-equivalent age) groups identified from ProtecT.

Results

Expected age of onset of higher-grade PCa is modulated by 19 years between the 1st and 99th PHS percentiles. A man with PHS in the 99th percentile reaches 50-years-standard risk at age 41; conversely, a man in the 1st percentile reaches this risk at age 60. PPV of PSA was higher for men with higher PHS-adjusted age.

Conclusions

PHS informs PCa screening strategies with individualized estimates of risk-equivalent age for higher-grade PCa. Screening initiation could be adjusted according to a man’s genetic hazard score, improving PPV of PSA screening.
Are the Matrix Metalloproteinases 2 and 9 beeing expressed in the mucosa of the rat small intestine during its intrauterine and postnatal life development ?
Authors: dos Reis Camila Audrey , Gomes José Rosa
Published: April 2019

MMP-2 and MMP-9 are proteins with well stablished roles on the remodeling of tissue during morphogenesis. This study aimed to evaluate the activity and expression of the MMP-2 and MMP-9 in the rat small intestine mucosa layer on 15thand 18thdays of intratuterine life (i.u.) and at 3rd, 10th, 17th, 25th, and 32thdays after birth (a.b.). Samples were submitted to zimography, immunohistochemistry methods and Masson trichrome staining. Results showed that MMP-2 and MMP-9 were not expressed in the small intestine epithelium during intrauterine life. MMP-9 was immunolocalized in the villi goblet cells and in the lamina propria in cells identified as being the mast cells (a.b.). We concluded that in the i.u. and a.b. life the MMP-2 and MMP-9 were not expressed in the small intestine epithelium. However, after birth, because MMP-9 was expressed in the mast cels present in the lamina propria it may be involved in the remodeling process of the innate immunity that occurs during the small intestine development.
Integrating patterns of thermal tolerance and phenotypic plasticity with population genetics to improve understanding of vulnerability to warming in a widespread copepod
Authors: Sasaki Matthew C. , Dam Hans G.
Published: April 2019

Differences in population vulnerability to warming are defined by spatial patterns in thermal adaptation. These patterns may be driven by natural selection over spatial environmental gradients, but can also be shaped by gene flow, especially in marine taxa with high dispersal potential. Understanding and predicting organismal responses to warming requires disentangling the opposing effects of selection and gene flow. We begin by documenting genetic divergence of thermal tolerance and developmental phenotypic plasticity. Ten populations of the widespread copepodAcartia tonsawere collected from sites across a large thermal gradient, ranging from the Florida Keys to Northern New Brunswick, Canada (spanning over 20 degrees latitude). Thermal performance curves from common garden experiments revealed local adaptation at the sampling range extremes, with thermal tolerance increasing at low latitudes and decreasing at high latitudes. The opposite pattern was observed in phenotypic plasticity, which was strongest at high latitudes. Over a large portion of the sampled range, however, we observed a remarkable lack of differentiation of thermal performance curves. To examine whether this lack of divergence is the result of selection for a generalist performance curve or constraint by gene flow, we analyzed cytochrome oxidase I mtDNA sequences, which revealed abundant genetic diversity and widely-distributed haplotypes. Strong divergence in thermal performance within genetic clades, however, suggests that the pace of thermal adaptation can be relatively rapid. The combined insight from the laboratory physiological experiments and genetic data indicate that gene flow constrains differentiation of thermal performance curves. This balance between gene flow and selection has implications for patterns of vulnerability to warming. Taking both genetic differentiation and phenotypic plasticity into account, our results suggest that local adaptation does not increase vulnerability to warming, and that low latitude populations in general may be more vulnerable to predicted temperature change over the next century.
Liquid-liquid phase separation and liquid-to-solid transition mediate α-synuclein amyloid fibril containing hydrogel formation
Authors: Ray Soumik , Singh Nitu , Pandey Satyaprakash , Kumar Rakesh , Gadhe Laxmikant , Datta Debalina , Patel Komal , Mahato Jaladhar , Navalkar Ambuja , Panigrahi Rajlaxmi , Chatterjee Debdeep , Maiti Siddhartha , Bhatia Sandhya , Mehra Surabhi , Singh Ajay , Gerez Juan , Chowdhury Arindam , Kumar Ashutosh , Padinhateeri Ranjith , Riek Roland , Krishnamoorthy G , Maji Samir K
Published: April 2019

α-Synuclein (α-Syn) aggregation and amyloid formation is directly linked with Parkinson’s disease (PD) pathogenesis. However, the early events involved in this process remain unclear. Here, using in vitro reconstitution and cellular model, we show that liquid-liquid phase separation (LLPS) of α-Syn precedes its aggregation. In particular, in vitro generated α-Syn liquid-like droplets eventually undergo a liquid-to-solid transition and form amyloid-hydrogel containing oligomers and fibrillar species. Factors known to aggravate α-Syn aggregation such as low pH, phosphomimic substitution, and familial PD mutation also promote α-Syn LLPS and its subsequent maturation. We further demonstrate α-Syn liquid droplet formation in cells, under oxidative stress. These cellular α-Syn droplets eventually transform into perinuclear aggresomes, the process regulated by microtubules. The present work provides detailed insights into the phase separation behavior of natively unstructured α-Syn and its conversion to a disease-associated aggregated state, which is highly relevant in PD pathogenesis.
Simultaneous ribosome profiling of human host cells infected with Toxoplasma gondii
Authors: Holmes Michael J. , Shah Premal , Wek Ronald C. , Sullivan William J.
Published: April 2019

Toxoplasma gondii is a ubiquitous obligate intracellular parasite that infects the nucleated cells of warm-blooded animals. From within the parasitophorous vacuole in which they reside, Toxoplasma tachyzoites secrete an arsenal of effector proteins that can reprogram host gene expression to facilitate parasite survival and replication. Gaining a better understanding of how host gene expression is altered upon infection is central for understanding parasite strategies for host invasion and for developing new parasite therapies. Here, we applied ribosome profiling coupled with mRNA measurements to concurrently study gene expression in the parasite and in host human foreskin fibroblasts. By examining the parasite transcriptome and translatome, we identified potential upstream open reading frames that may permit the stress-induced preferential translation of parasite mRNAs. We also determined that tachyzoites reduce host death-associated pathways and increase survival, proliferation, and motility in both quiescent and proliferative host cell models of infection. Additionally, proliferative cells alter their gene expression in ways consistent with massive transcriptional rewiring while quiescent cells were best characterized by re-entry into the cell cycle. We also identified a translational control regimen consistent with mTOR activation in quiescent cells, and to a lesser degree in proliferative cells. This study illustrates the utility of the method for dissection of gene expression programs simultaneously in parasite and host.

Importance

Toxoplasma gondii is a single-celled parasite that has infected up to one-third of the world’s population. Significant overhauls in gene expression in both the parasite and the host cell accompany parasite invasion, and a better understanding of these changes may lead to the development of new therapeutic agents. In this study, we employed ribosome profiling to determine the changes that occur at the levels of transcription and translation in both the parasite and the infected host cell at the same time. We discovered features of Toxoplasma mRNAs that suggest a means for controlling parasite gene expression under stressful conditions. We also show that differences in host gene expression occur depending on whether they are confluent or not. Our findings demonstrate the feasibility of using ribosomal profiling to interrogate the host-parasite dynamic under a variety of conditions.
Rotavirus NSP1 localizes in the nucleus to disrupt PML nuclear bodies during infection
Authors: Murphy Samantha K. , Arnold Michelle M.
Published: April 2019

The rotavirus nonstructural protein 1 (NSP1) antagonizes interferon (IFN) induction in infected host cells. The primary function of NSP1 is thought to be degradation of interferon regulatory factors (IRFs) and beta-transducin repeat-containing protein (β-TrCP) in the cytoplasm to inhibit IFN induction. Here, we report that NSP1 localizes to the cytoplasm and nucleus and disrupts promyelocytic (PML) nuclear bodies (NB) in the nucleus during infection. Nuclear localization of NSP1 did not require an intact C terminus, suggesting NSP1 has a novel function in the nucleus independent of degradation of IRFs or β-TrCP. NSP1 expression either led to a reduction in PML NB number or a change in PML NB morphology from sphere-shaped foci to oblong-shaped structures, depending on the virus strain. Additionally, infection was not affected when cells lack PML NB, suggesting that rotavirus does not require PML for replication in highly permissive cell types. PML was not essential for nuclear localization of NSP1, but PML was required for NSP1 nuclear focus formation. PML NBs play an important role in many cellular functions that include IFN induction and host stress responses. This is the first report that rotavirus, a cytoplasmically replicating virus, encodes a viral protein that localizes to the nucleus during infection, and may suggest a new function of NSP1 in the nucleus.

IMPORTANCE

Rotavirus causes severe gastroenteritis in young children and leads to over 200,000 deaths per year. Rotavirus is a cytoplasmically replicating virus, and must find ways to avoid or actively inhibit host antiviral responses to efficiently replicate. The nonstructural protein NSP1 is known to inhibit IFN induction by promoting degradation of host proteins in the cytoplasm of infected cells. Here, we demonstrate that NSP1 also localizes to the nucleus of infected cells, specifically to PML NB. NSP1 causes a disruption of PML NB, which may serve as an additional mechanism of IFN inhibition or interfere with other nuclear processes to promote viral replication. A detailed exploration of the manipulation of nuclear processes in cells infected with cytoplasmically replicating viruses will lead to new insights into viral evasion of host responses.
DNA methylation-based immune cell deconvolution in solid tumors
Authors: Liang Cong , Yu Xiaoqing , Li Bo , Chen Y. Ann , Conejo-Garcia Jose R. , Wang Xuefeng
Published: April 2019

Understanding of the tumor microenvironment (TME) structure is likely to have a profound and immediate impact on therapeutic interventions as well as the development of signatures for diagnostic and prognostic evaluations. DNA methylation arrays represent one of the most reproducible molecular assays across replicates and studies, but its value of profiling tumor-infiltrating immune lymphocytes (TILs) hasn’t been intensively investigated. Here we report a model-based evaluation of tumor TIL levels using DNA methylation profiles. By employing a hybrid method of stability selection and elastic net, we show that methylation array data in ten TCGA cancer types provide a strikingly accurate prediction of immune cell abundance, in particular the levels of T cells, B cells and cytotoxic cells in skin cutaneous melanoma (SKCM). The immune-informative CpG sites showed significant prognostic values, representing important candidates for further functional validation. Further, we present regression models each using only ten CpG sites to estimate the levels of infiltrated immune cell types in melanoma. To validate these models, we performed matched methylation EPIC array and RNA-seq on 30 new melanoma samples. We observed high concordance on methylation and gene expression predicted tumor immune infiltration levels in our new dataset. Our study demonstrated that DNA methylation data is a valuable resource in reliably evaluating tumor immune responses. The selected methylation panels provide candidate targets for future clinical researches. Our prediction models are easy to implement and will provide reference for future clinical practices.
Factors affecting the survival of tree seedlings following shifting cultivation in the Eastern Himalaya
Authors: Teegalapalli Karthik , Arthur Rohan , Quader Suhel , Datta Aparajita
Published: April 2019

The seedling stage is considered an important bottleneck determining forest community composition during succession. Seedling growth and survival are known to be affected by factors such as light availability, herbivory and competition with existing vegetation. A shifting cultivation landscape with a cycle of clearing and regeneration provides an experimental setup to understand secondary succession.

We introduced tree seedlings of three species with differing life history strategies in an uncut forest and in sites formed 2, 6, 12, 25, 50 and 100 years following shifting cultivation in a subtropical landscape in the Eastern Himalaya. Seedlings of a pioneer species Saurauia nepalensis, a mid-successional species Terminalia myriocarpa and a mature forest species Castanopsis indica were introduced in plots with a control and three treatments: shading (light manipulated), clearing of vegetation (reduced competition), and exclosures (mammal herbivory excluded) and monitored for 18, 22 and 23 months, respectively.

Saurauia survived relatively well in all sites, Terminalia seedlings survived relatively well in the 12 and 25 year sites, and Castanopsis seedlings survived well in the 100 year site and the uncut forest. In the early successional site, survival of Saurauia was higher within exclosures indicating negative effects of herbivory. In the same site, clearing vegetation improved the survival of Terminalia, implying competition with existing vegetation. Castanopsis had the highest survival in uncut forest and survival was almost nil in the early successional site.

Synthesis: Seedling survival in a successional landscape depended on species-as well as site-specific factors. The existing vegetation in an early successional site had a negative effect on the survival of the mid-successional species, while herbivory had a negative effect on the pioneer species. Survival of the mature forest species in the early successional site was negligible but was high in old successional and uncut forest sites, indicating that mature forest species can colonize sites and survive only after certain physical and biotic aspects of the environment have been met. Our experiments were useful to examine factors that affect survival of tree species with differing life history strategies in a shifting cultivation landscape.
DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning
Authors: Graving Jacob M. , Chae Daniel , Naik Hemal , Li Liang , Koger Benjamin , Costelloe Blair R. , Couzin Iain D.
Published: April 2019

Quantitative behavioral measurements are important for answering questions across scientific disciplines—from neuroscience to ecology. State-of-the-art deep-learning methods offer major advances in data quality and detail by allowing researchers to automatically estimate locations of an animal’s body parts directly from images or videos. However, currently-available animal pose estimation methods have limitations in speed and robustness. Here we introduce a new easy-to-use software toolkit,DeepPoseKit, that addresses these problems using an eZcient multi-scale deep-learning model, calledStacked DenseNet, and a fast GPU-based peak-detection algorithm for estimating keypoint locations with subpixel precision. These advances improve processing speed >2× with no loss in accuracy compared to currently-available methods. We demonstrate the versatility of our methods with multiple challenging animal pose estimation tasks in laboratory and field settings—including groups of interacting individuals. Our work reduces barriers to using advanced tools for measuring behavior and has broad applicability across the behavioral sciences.
DrosophilaSnazarus regulates a lipid droplet population at plasma membrane-droplet contacts in adipocytes
Authors: Ugrankar Rupali , Bowerman Jade , Hariri Hanaa , Chandra Mintu , Chen Kevin , Bossanyi Marie-France , Datta Sanchari , Rogers Sean , Eckert Kaitlyn M. , Vale Gonçalo , Victoria Alexia , Fresquez Joseph , McDonald Jeffrey G. , Jean Steve , Collins Brett M. , Henne W. Mike
Published: April 2019

Adipocytes store nutrients as lipid droplets (LDs), but how they organize their LD stores to balance lipid uptake, storage, and mobilization remains poorly understood. Here, usingDrosophilafat body (FB) adipocytes we characterize spatially distinct LD populations that are maintained by different lipid pools. We identify peripheral LDs (pLDs) that make close contact with the plasma membrane (PM) and are maintained by lipophorin-dependent lipid trafficking. pLDs are distinct from larger cytoplasmic medial LDs (mLDs) which are maintained by FASN1-dependentde novolipogenesis. We find that sorting nexin CG1514/Snazarus (Snz) associates with pLDs and regulates LD homeostasis at ER-PM contact sites. Loss ofSNZperturbs pLD organization whereas Snz over-expression drives LD expansion, triacylglyceride production, starvation resistance, and lifespan extension through a DESAT1-dependent pathway. We propose thatDrosophilaadipocytes maintain spatially distinct LD populations and identify Snz as a novel regulator of LD organization and inter-organelle crosstalk.
Human neutrophils produce antifungal extracellular vesicles againstAspergillus fumigatus
Authors: Shopova Iordana A. , Belyaev Ivan , Dasari Prasad , Jahreis Susanne , Stroe Maria C. , Cseresnyés Zoltán , Zimmermann Ann-Kathrin , Medyukhina Anna , Svensson Carl-Magnus , Krüger Thomas , Szeifert Viktòria , Nietzsche Sandor , Conrad Theresia , Blango Matthew G. , Kniemeyer Olaf , von Lilienfeld-Toal Marie , Zipfel Peter F. , Ligeti Erzsébet , Figge Marc Thilo , Brakhage Axel A.
Published: April 2019

Polymorphonuclear granulocytes (PMNs) are indispensable for controlling life-threatening fungal infections. In addition to various effector mechanisms, PMNs also produce extracellular vesicles (EVs). Their contribution to antifungal defense has remained unexplored. We reveal that the clinically important human pathogenic fungusAspergillus fumigatustriggers PMNs to release a distinct set of antifungal EVs (afEVs). Proteome analyses indicated that afEVs are enriched in antimicrobial proteins. The cargo and release kinetics of EVs are modulated by the fungal strain confronted. Tracking of afEVs indicated that they associated with fungal cells and even entered fungal hyphae, resulting in alterations in the morphology of the fungal cell wall and dose-dependent antifungal effects. Two human proteins enriched in afEVs, cathepsin G and azurocidin, were heterologously expressed in fungal hyphae, which led to reduced fungal growth relative to a control retinol binding protein 7 producing strain. In conclusion, the production of afEVs by PMNs offers an intriguing, previously overlooked mechanism of antifungal defense againstA. fumigatus.

Importance

Invasive fungal infections caused by the moldAspergillus fumigatusare a growing concern in the clinic due to the increasing use of immunosuppressive therapies and increasing antifungal drug resistance. These infections result in high mortality as treatment and diagnostic options remain limited. In healthy individuals, neutrophilic granulocytes are critical for elimination ofA. fumigatusfrom the host; however, the exact extracellular mechanism of neutrophil-mediated antifungal activity remains unresolved. Here, we present a mode of antifungal defense employed by human neutrophils againstA. fumigatusnot previously described. We find that extracellular vesicles produced by neutrophils in response toA. fumigatusinfection are able to associate with the fungus, limit growth, and elicit cell damage by delivering antifungal cargo. In the end, antifungal extracellular vesicle biology provides a significant step forward in our understanding ofA. fumigatushost pathogenesis and opens up novel diagnostic and therapeutic possibilities.
Impaired EAT-4 Vesicular Glutamate Transporter Leads to Defective Nocifensive Response of Caenorhabditis elegans to Noxious Heat
Authors: Leonelli Sophie , Nkambeu Bruno , Beaudry Francis
Published: April 2019

In mammals, glutamate is an important excitatory neurotransmitter. Glutamate and glutamate receptors are found in areas specifically involved in pain sensation, transmission and transduction such as peripheral nervous system, spinal cord and brain. In C. elegans, several studies have suggested glutamate pathways are associated with withdrawal responses to mechanical stimuli and to chemical repellents. However, few evidences demonstrate that glutamate pathways are important to mediate nocifensive response to noxious heat. The thermal avoidance behavior of C. elegans was studied and results illustrated that mutants of glutamate receptors (glr-1, glr-2, nmr-1, nmr-2) behaviors was not affected. However, results revealed that all strains of eat-4 mutants, C. elegans vesicular glutamate transporters, displayed defective thermal avoidance behaviors. Due to the interplay between the glutamate and the FLP-18/FLP-21/NPR-1 pathways, we analyzed the effectors FLP-18 and FLP-21 at the protein level, we did not observebiologically significant differences compared to N2 (WT) strain (fold-change < 2) except for the IK602 strain. The data presented in this manuscript reveals that glutamate signaling pathways are essential to elicit a nocifensive response to noxious heat in C. elegans.
Population-specific effect ofWolbachiaon the cost of fungal infection in spider mites
Authors: Zélé Flore , Altintaş Mustafa , Santos Inês , Cakmak Ibrahim , Magalhães Sara
Published: April 2019

Many studies have revealed the ability of the endosymbiotic bacteriaWolbachiato protect its arthropod hosts against diverse pathogens. However, asWolbachiamay also increase the susceptibility of its host to infection, predicting the outcome of a particularWolbachia-host-pathogen interaction remains elusive. Yet, understanding such interactions is crucial for disease and pest control strategies.Tetranychus urticaespider mites are herbivorous crop pests, causing severe damage on numerous economically important crops. Due to the rapid evolution of pesticide resistance, biological control strategies using generalist entomopathogenic are being developed. However, although spider mites are infected with variousWolbachiastrains worldwide, whether this endosymbiont protects them from fungi is as yet unknown. Here, we compared the survival of two populations, treated with antibiotics or harbouring differentWolbachiastrains, after exposure to the fungal biocontrol agentsMetarhizium brunneumandBeauveria bassiana. In one population,Wolbachiaaffected survival in absence of fungi but not in their presence, whereas in the other populationWolbachiaincreased the mortality induced byB. bassiana. To control for potential effects of the bacterial community of spider mites, we also compared the susceptibility of two populations naturally uninfected byWolbachia, treated with antibiotics or not. The antibiotic treatment increased the susceptibility of spider mites toM. brunneumin one naturallyWolbachia-uninfected population, but it had no effect in the other treatments. These results highlight the complexity of within-host pathogens interactions, and the importance of considering the whole bacterial community of arthropods when assessing the effect ofWolbachiain a particular system.
Association and impact of hypertension defined using the 2017 AHA/ACC guidelines on the risk of atrial fibrillation in the Atherosclerosis Risk in Communities Study
Authors: Rattani Anas , Claxton J’Neka S. , Ali Mohammed K. , Chen Lin Y. , Soliman Elsayed Z. , Alvaro Alonso
Published: April 2019

Hypertension is an established risk factor for the development of atrial fibrillation (AF). We evaluated the association and population impact of hypertension, defined using the new 2017 guidelines, on risk of AF. In this analysis, we included 9,207 participants in the Atherosclerosis Risk in Communities study without history of cardiovascular disease or diabetes. Participants underwent blood pressure measurements at baseline and their antihypertensive medication use was assessed. AF was ascertained from study electrocardiograms, hospital records and death certificates. Cox proportional models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) of AF among individuals with hypertension based on the JNC7 and 2017 ACC/AHA guidelines. Poisson models were used to obtain risk ratios and calculate population-attributable fractions (PAFs). We identified 1,573 cases of incident AF during 22.1 years of mean follow-up. Prevalence of hypertension was 29% and 43% under the JNC7 and 2017 ACC/AHA definitions, respectively. HRs (95%CI) of AF in hypertensives versus non-hypertensives were 1.54 (1.39, 1.72) and 1.45 (1.31, 1.61) after multivariable adjustment under the old and new guidelines, respectively. The corresponding PAF (95%CI) using the old and new guidelines were 12% (9%, 14%) and 14% (10%, 18%), respectively. Overall, our analysis shows that even though the prevalence of hypertension using the new criteria is 50% higher than with the old criteria, this does not translate into meaningful increases in AF attributable to hypertension. These results suggest that prevention or treatment of hypertension based on the new (versus old) guidelines may have limited impact on AF incidence.
Contributions of white matter connectivity and BOLD modulation to cognitive aging: A lifespan structure-function association study
Authors: Webb Christina E. , Rodrigue Karen M. , Hoagey David A. , Foster Chris M. , Kennedy Kristen M.
Published: April 2019

The ability to flexibly modulate brain activation to increasing cognitive challenge decreases with aging. This age-related decrease in dynamic range of function of regional gray matter may be, in part, due to age-related degradation of regional white matter tracts. Here, a lifespan sample of 171 healthy adults (aged 20-94) underwent MRI scanning including diffusion-weighted imaging (for tractography) and functional imaging (a digit n-back task). We utilized structural equation modeling to test the hypothesis that age-related decrements in white matter microstructure are associated with altered BOLD modulation, and both in turn, are associated with scanner-task accuracy and executive function performance. Specified structural equation model evidenced good fit, demonstrating that increased age negatively affects n-back task accuracy and executive function performance in part due to both degraded white matter tract microstructure and reduced task-difficulty related BOLD modulation. We further demonstrated that poorer white matter microstructure integrity was associated with weakened BOLD modulation, particularly in regions showing positive modulation effects, as opposed to negative modulation effects. This structure-function association study provides further evidence that structural connectivity influences functional activation, and the two mechanisms in tandem are predictive of cognitive performance, both during the task, and for cognition measured outside the scanner environment.
Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines
Authors: Tran Ngoc Hieu , Qiao Rui , Xin Lei , Chen Xin , Shan Baozhen , Li Ming
Published: April 2019

Tumor-specific neoantigens play the main role for developing personal vaccines in cancer immunotherapy. We propose, for the first time, a personalized de novo sequencing workflow to identify HLA-I and HLA-II neoantigens directly and solely from mass spectrometry data. Our workflow trains a personal deep learning model on the immunopeptidome of an individual patient and then uses it to predict mutated neoantigens of that patient. This personalized learning and mass spectrometry-based approach enables comprehensive and accurate identification of neoantigens. We applied the workflow to datasets of five melanoma patients and substantially improved the accuracy and identification rate of de novo HLA peptides by 14.3% and 38.9%, respectively. This subsequently led to the identification of 10,440 HLA-I and 1,585 HLA-II new peptides that were not presented in existing databases. Most importantly, our workflow successfully discovered 17 neoantigens of both HLA-I and HLA-II, including those with validated T cell responses and those novel neoantigens that had not been reported in previous studies.
Tendon response to matrix unloading is determined by the patho-physiological niche
Authors: Wunderli Stefania L. , Blache Ulrich , Piccoli Agnese Beretta , Niederöst Barbara , Holenstein Claude N. , Passini Fabian , Silván Unai , Bundgaard Louise , auf dem Keller Ulrich , Snedeker Jess G.
Published: April 2019

Aberrant matrix turnover with elevated matrix proteolysis is a hallmark of tendon pathology. While tendon disease mechanisms remain obscure, mechanical cues are central regulators. Unloading of tendon explants in standard culture conditions provokes rapid cell-mediated tissue breakdown. Here we show that biological response to tissue unloading depends on the mimicked physiological context. Our experiments reveal that explanted tendon tissues remain functionally stable in a simulated avascular niche of low temperature and oxygen, regardless of the presence of serum. This hyperthermic and hyperoxic niche-dependent catabolic switch was shown by whole transcriptome analysis (RNA-seq) to be a strong pathological driver of an immune-modulatory phenotype, with a stress response to reactive oxygen species (ROS) and associated activation of catabolic extracellular matrix proteolysis that involved lysosomal activation and transcription of a range of proteolytic enzymes. Secretomic and degradomic analysis through terminal amine isotopic labeling of substrates (TAILS) confirmed that proteolytic activity in unloaded tissues was strongly niche dependent. Through targeted pharmacological inhibition we isolated ROS mediated oxidative stress as a major checkpoint for matrix proteolysis. We conclude from these data that the tendon stromal compartment responds to traumatic mechanical unloading in a manner that is highly dependent on the extrinsic niche, with oxidative stress response gating the proteolytic breakdown of the functional collagen backbone.
Zebrafish use visual cues and geometric relationships to form a spatial memory
Authors: Yashina Ksenia , Tejero-Cantero Álvaro , Herz Andreas , Baier Herwig
Published: April 2019

Animals use salient cues to navigate in their environment, but their specific cognitive strategies are largely unknown. We developed a conditioned place avoidance paradigm to discover whether and how zebrafish form spatial memories in a Y-shaped maze. Juvenile zebrafish, older than three weeks, learned to avoid the arm of the maze that was cued with a mild electric shock. We found that the fish required distinct visual patterns to develop a conditioned response. Interestingly, individual fish solve this task in different ways: by staying in the safe center of the maze, by preference for one, or both, of the safe patterns, or by mixed strategies. In experiments in which the learned patterns were swapped, rotated or replaced, the animals could transfer the association of safety to a different arm or to a different pattern using either visual cues or location as the conditioned stimulus. These findings show that juvenile zebrafish exhibit several complementary spatial learning modes and pave the way for neurobiological studies of navigational mechanisms in this model species.
Museum epigenomics: characterizing cytosine methylation in historic museum specimens
Authors: Rubi Tricia L. , Knowles L. Lacey , Dantzer Ben
Published: April 2019

Museum genomics has transformed the field of collections-based research, opening up a range of new research directions for paleontological specimens as well as natural history specimens collected over the past few centuries. Recent work demonstrates that it is possible to characterize epigenetic markers such as DNA methylation in well-preserved ancient tissues. This approach has not yet been tested in traditionally-prepared natural history specimens such as dried bones and skins, the most common specimen types in vertebrate collections. In this study, we develop and test methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulfite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (Peromyscus spp.) collected in the same region in Michigan in 1940, 2003, and 2013-2016. We successfully estimated methylation in specimens of all age groups, though older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1-3 years old), which may reflectpost mortemhydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, such studies will need to accommodate the large variance in the quantity of data produced by older specimens.
Insect herbivory reshapes a native leaf microbiome
Authors: Humphrey Parris T , Whiteman Noah K
Published: April 2019

Insect herbivory is pervasive in plant communities, but its impact on microbial plant colonizers is not well-studied in natural systems. By calibrating sequencing-based bacterial detection to absolute bacterial load, we find that the within-host abundance of most leaf microbiome (phyllosphere) taxa colonizing a native forb is amplified within leaves impacted by insect herbivory. Herbivore-associated bacterial amplification reflects community-wide compositional shifts towards lower ecological diversity, but the extent and direction of such compositional shifts can be interpreted only by quantifying absolute abundance. Experimentally eliciting anti-herbivore defenses reshaped within-host fitness ranks among Pseudomonas spp. field isolates and amplified a subset of putative P. syringae phytopathogens in a manner causally consistent with observed field-scale patterns. Herbivore damage was inversely correlated with plant reproductive success and was highly clustered across plants, which predicts tight co-clustering with putative phytopathogens across hosts. Insect herbivory may thus drive the epidemiology of plant-infecting bacteria as well as the structure of a native plant microbiome by generating variation in within-host bacterial fitness at multiple phylogenetic and spatial scales. This study emphasizes that “non-focal” biotic interactions between hosts and other organisms in their ecological settings can be crucial drivers of the population and community dynamics of host-associated microbiomes.
Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs
Authors: Williams Rachel C. , Blanco Marina B. , Poelstra Jelmer W. , Hunnicutt Kelsie E. , Comeault Aaron A. , Yoder Anne D.
Published: April 2019

Madagascar’s biodiversity is notoriously threatened by deforestation and climate change. Many of these organisms are rare, cryptic, and severely threatened, making population-level sampling unrealistic. Such is the case with Madagascar’s dwarf lemurs (genusCheirogaleus), the only obligate hibernating primate. We here apply comparative genomic approaches to generate the first genome-wide estimates of genetic diversity within dwarf lemurs. We generate a reference genome for the fat-tailed dwarf lemur,Cheirogaleus medius, and use this resource to facilitate analyses of high-coverage (~30x) genome sequences for wild-caught individuals representing species:C. sp. cf. medius, C. major, C. crossleyiandC. sibreei. This study represents the largest contribution to date of novel genomic resources for Madagascar’s lemurs. We find concordant phylogenetic relationships among the four lineages ofCheirogaleusacross most of the genome, and yet detect a number of discordant genomic regions consistent with ancient admixture. We hypothesized that these regions could have resulted from adaptive introgression related to hibernation, indeed finding that genes associated with hibernation are present, though most significantly, that gene ontology categories relating to transcription are over-represented. We estimate levels of heterozygosity and find particularly low levels in an individual sampled from an isolated population ofC. mediusthat we refer to asC. sp. cf. medius. Results are consistent with a recent decline in effective population size, which is evident across species. Our study highlights the power of comparative genomic analysis for identifying species and populations of conservation concern, as well as for illuminating possible mechanisms of adaptive phenotypic evolution.