bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality-quantity tradeoffs drive functional trait evolution in a model microalgal “climate change winner”
Authors: Lindberg Rasmus T. , Collins Sinéad 
Published: October 2019

AbstractPhytoplankton are the unicellular photosynthetic microbes that form the base of aquatic ecosystems, and their responses to global change will impact everything from food web dynamics to global nutrient cycles. Some taxa respond to environmental change by increasing population growth rates in the short-term, and, based on this, are projected to increase in frequency over decades. To gain insight into how functional traits in these projected “climate change winners” change over different timescales, we evolved populations of microalgae in ameliorated environments for several hundred generations. While populations initially responded to environmental amelioration by increasing photosynthesis and population growth rates as expected, this response was not sustained. Instead, most populations evolved to allocate a smaller proportion of carbon to growth while increasing their ability to tolerate and metabolise reactive oxygen species (ROS). This diversion of fixed carbon from growth to catabolism underlies a quality-quantity tradeoff in daughter cell production which drives the evolution of population growth rates and of functional traits that underlie the ecological and biogeochemical roles of phytoplankton. There is intraspecific variation in the trait combinations that evolve, but all are consistent with mitigating ROS production and accumulation in ameliorated environments over hundreds of generations. This offers both an evolutionary and a metabolic framework for understanding how functional traits can change in primary producers projected to be “climate change winners”, and suggests that short-term population booms and associated trait shifts have the potential to be dampened or reversed if environmental amelioration persists.
Molecular Tuning of Styryl Dyes Leads to Versatile and Efficient Plasma Membrane Probes for Cell and Tissue Imaging
Authors: Collot Mayeul , Boutant Emmanuel , Fam Kyong Tkhe , Danglot Lydia , Klymchenko Andrey S. 
Published: October 2019

ABSTRACTThe plasma membrane (PM) plays a major role in many biological processes; therefore its proper fluorescence staining is required in bioimaging. Among the commercially available PM probes, styryl dye FM1-43 is one of the most widely used. In this work, we demonstrated that fine chemical modifications of FM1-43 can dramatically improve the PM staining. The newly developed probes, SP-468 and SQ-535 were found to display enhanced photophysical properties (reduced crosstalk, higher brightness, improved photostability) and unlike FM1-43, provided excellent and immediate PM staining in 5 different mammalian cell lines including neurons (primary culture and tissue imaging). Additionally, we showed that the new probes displayed differences in their internalization pathways compared to their parent FM1-43. Finally, we demonstrated that the modifications made to FM1-43 did not impair the ability of the new probes to stain the PM of plant cells. Overall, this work presents new useful probes for PM imaging in cells and tissues and provides insights on the molecular design of new PM targeting molecules.
Phylogeographic structure of the pygmy shrew: revisiting the roles of southern and northern refugia in Europe
Authors: Vega Rodrigo , McDevitt Allan D. , Stojak Joanna , Mishta Alina , Wójcik Jan M. , Kryštufek Boris , Searle Jeremy B. 
Published: October 2019

ABSTRACTSouthern and northern glacial refugia are considered paradigms that explain the complex phylogeographic patterns and processes of European biota. Although the Eurasian pygmy shrewSorex minutusLinnaeus, 1766 (Eulipotyphla, Soricidae) has been used a model species to study geographic isolation and genetic diversification in Mediterranean peninsulas in the Last Glacial Maximum (LGM), and post-glacial population expansion from cryptic northern glacial refugia in Western and Central Europe, there has been incomplete knowledge about the phylogeographic structure, genetic differentiation and demographic history within these regions. Here, we provide a revisited statistical phylogeographic study ofS. minutuswith greater sampling coverage in terms of numbers of individuals and geographic range, making it the most comprehensive investigation of this species to date. The results showed support for genetically distinct and diverse phylogeographic groups consistent with southern and northern glacial refugia, as expected from previous studies, but also identified geographical barriers concordant with glaciated mountain ranges during the LGM, early diversification events dated between the Upper Pleistocene and Lower Holocene for the main phylogeographic groups, and recent (post-LGM) patterns of demographic expansions. The results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential ofS. minutus.
Live-Cell Imaging and Quantification of PolyQ Aggregates by Stimulated Raman Scattering of Selective Deuterium Labeling
Authors: Miao Kun , Wei Lu 
Published: October 2019

AbstractHuntington’s disease, a major neurodegenerative disorder, involves deposition of aggregation-prone proteins with long polyglutamine (polyQ) expansions. The ability to non-perturbatively visualize the formation of aggregates could offer new molecular insight for their pathologic roles. Here, we propose stimulated Raman scattering imaging of deuterium-labeled glutamine to investigate native polyQ aggregates in live cells with subcellular resolution. Through the enrichment of deuterated glutamine in the polyQ sequence of mutant Huntingtin (mHtt) proteins, we first achieved sensitive and specific SRS imaging of carbon-deuterium bonds (C-D) from aggregates without GFP labeling. These aggregates become 1.8-fold denser compared to those with GFP. Second, we performed ratiometric quantification, which revealed a dependence of protein compositions on aggregation sizes. Moreover, we calculated the absolute concentrations for sequestered mHtt and non-mHtt proteins within the same aggregates. Our method may readily reveal new features of polyQ aggregates and could be suited forin vivoinvestigations on multicellular organisms.
HPV-positive head and neck cancer derived exosomal miR-9 induces M1 macrophage polarization and increases tumor radiosensitivity
Authors: Tong Fangjia , Zhang Siwei , Xie Huanhuan , Yan Bingqing , Song Lianhao , Wei Lanlan 
Published: October 2019

AbstractHuman papillomavirus (HPV) is an etiological risk factor for a subset of head and neck squamous cell carcinoma (HNSCC). HPV+ HNSCC is significant more radiosensitive than HPV-HNSCC, but the underlying mechanism is still unknown. Tumor microenvironment can affect tumor response to radiation therapy. Cancer secreted exosomes are emerging as crosstalk mediators between tumor cells and the tumor microenvironment. The main objectives of this study were to determine the role of HPV+ HNSCC-derived exosomes in increased radiation sensitivity. Here, we found that exosomes derived from HPV+ HNSCC cells activate macrophages into the M1 phenotype, which then increases the radiosensitivity of HNSCC cells. miR-9 was enriched in exosomes released from HPV+ HNSCC cells and it could be transported to macrophages, leading to altered cellular functions. Overexpression of miR-9 in macrophages induced polarization into the M1 phenotype via downregulation of PPARδ. Increased radiosensitivity was observed for HNSCC cells co-cultured with macrophages in which miR-9 was upregulated or treated with M1 macrophages. These observations suggest that HPV+ HNSCC cells secrete miR-9-rich exosomes, which then polarize macrophages into M1 phenotype and lead to increased radiosensitivity of HNSCC cells. Hence, miR-9 may be a potential treatment strategy for HNSCC.Statement of significanceHPV+ HNSCC through the release of miR-9-rich exosomes polarize macrophages into M1 phenotype and lead to increased radiosensitivity of HNSCC.
12-oxophytodienoic acid reductase 3 (OPR3) functions as NADPH-dependent α,β-ketoalkene reductase in detoxification and monodehydroascorbate reductase in redox homeostasis
Authors: Maynard Daniel , Kumar Vijay , Sproß Jens , Dietz Karl-Josef 
Published: October 2019

AbstractArabidopsis (Arabidopsis thaliana) 12-oxophytodienoic acid reductase isoform 3 (OPR3) is involved in the synthesis of jasmonic acid by reducing the α,β-unsaturated double bond of the cyclopentenone moiety in 12-oxo-phytodienoic acid. Recent research revealed that jasmonic acid synthesis is not strictly dependent on the peroxisomal OPR3. In addition, OPR3 is able to reduce trinitrotoluene suggesting that the old yellow enzyme homologue OPR3 has additional functions. Here we demonstrate that OPR3 catalyzes the reduction of a wide spectrum of electrophilic species that share a reactivity towards the major redox buffers glutathione (GSH) and ascorbate (ASC). Furthermore, we demonstrate that OPDA reacts with ascorbate to form an ASC-OPDA adduct, but in addition OPR3 has the ability to regenerate ASC from monodehydroascorbate (MDHA). The presented data characterize OPR3 as a bifunctional enzyme with NADPH-dependent α,β-ketoalkene double bond reductase and monodehydroascorbate reductase activities (MDHAR).opr3mutants exhibited a slightly less reduced ASC pool in leaves in line with the MDHAR activity of OPR3in vitro. These functions link redox homeostasis as mediated by ASC and GSH with OPR3 activity and metabolism of reactive electrophilic species (RES).
De novo indol-3-ylmethyl glucosinolate biosynthesis, and not long-distance transport, contributes to defence of Arabidopsis against powdery mildew
Authors: Hunziker Pascal , Ghareeb Hassan , Wagenknecht Lena , Crocoll Christoph , Halkier Barbara Ann , Lipka Volker , Schulz Alexander 
Published: October 2019

AbstractPowdery mildew is a fungal disease that affects a wide range of plants and reduces crop yield worldwide. As obligate biotrophs, powdery mildew fungi manipulate living host cells to suppress defence responses and to obtain nutrients. Members of the plant order Brassicales produce indole glucosinolates that effectively protect them from attack by non-adapted fungi. Indol-3-ylmethyl glucosinolates are constitutively produced in the phloem and transported to epidermal cells for storage. Upon attack, indol-3-ylmethyl glucosinolates are activated by CYP81F2 to provide broad-spectrum defence against fungi. How de novo biosynthesis and transport contribute to defence of powdery mildew-attacked epidermal cells is unknown. Bioassays and glucosinolate analysis indicate that GTR glucosinolate transporters are not involved in antifungal defence. Using quantitative live-cell imaging of fluorophore-tagged markers, we show that accumulation of the glucosinolate biosynthetic enzymes CYP83B1 and SUR1 is induced in epidermal cells attacked by the non-adapted barley powdery mildew Blumeria graminis f.sp. hordei. By contrast, glucosinolate biosynthesis is attenuated during interaction with the virulent powdery mildew Golovinomyces orontii. Interestingly, SUR1 induction is delayed during the Golovinomyces orontii interaction. We conclude that epidermal de novo synthesis of indol-3-ylmethyl glucosinolate contributes to CYP81F2-mediated broad-spectrum antifungal resistance and that adapted powdery mildews may target this process.
Generalizing RNA velocity to transient cell states through dynamical modeling
Authors: Bergen Volker , Lange Marius , Peidli Stefan , Wolf F. Alexander , Theis Fabian J. 
Published: October 2019

AbstractThe introduction of RNA velocity in single cells has opened up new ways of studying cellular differentiation. The originally proposed framework obtains velocities as the deviation of the observed ratio of spliced and unspliced mRNA from an inferred steady state. Errors in velocity estimates arise if the central assumptions of a common splicing rate and the observation of the full splicing dynamics with steady-state mRNA levels are violated. With scVelo (https://scvelo.org), we address these restrictions by solving the full transcriptional dynamics of splicing kinetics using a likelihood-based dynamical model. This generalizes RNA velocity to a wide variety of systems comprising transient cell states, which are common in development and in response to perturbations. We infer gene-specific rates of transcription, splicing and degradation, and recover the latent time of the underlying cellular processes. This latent time represents the cell’s internal clock and is based only on its transcriptional dynamics. Moreover, scVelo allows us to identify regimes of regulatory changes such as stages of cell fate commitment and, therein, systematically detects putative driver genes. We demonstrate that scVelo enables disentangling heterogeneous subpopulation kinetics with unprecedented resolution in hippocampal dentate gyrus neurogenesis and pancreatic endocrinogenesis. We anticipate that scVelo will greatly facilitate the study of lineage decisions, gene regulation, and pathway activity identification.
Effects of physiological parameter evolution on the dynamics of tonic-clonic seizures
Authors: Deeba Farah , Sanz-Leon Paula , Robinson P. A. 
Published: October 2019

AbstractThe temporal and spectral characteristics of tonic-clonic seizures are investigated using a neural field model of the corticothalamic system in the presence of a temporally varying connection strength between the cerebral cortex and thalamus. Increasing connection strength drives the system into ∼ 10 Hz seizure oscillations once a threshold is passed and a subcritical Hopf bifurcation occurs. In this study, the spectral and temporal characteristics of tonic-clonic seizures are explored as functions of the relevant properties of physiological connection strengths, such as maximum strength, time above threshold, and the ramp rate at which the strength increases or decreases. Analysis shows that the seizure onset time decreases with the maximum connection strength and time above threshold, but increases with the ramp rate. Seizure duration and offset time increase with maximum connection strength, time above threshold, and rate of change. Spectral analysis reveals that the power of nonlinear harmonics and the duration of the oscillations increase as the maximum connection strength and the time above threshold increase. A secondary limit cycle at ∼ 18 Hz, termed a saddle-cycle, is also seen during seizure onset and becomes more prominent and robust with increasing ramp rate. If the time above the threshold is too small, the system does not reach the 10 Hz limit cycle, and only exhibits 18 Hz saddle-cycle oscillations. It is also seen that the times to reach the saturated large amplitude limit-cycle seizure oscillation from both the instability threshold and from the end of the saddle-cycle oscillations are inversely proportional to the square root of the ramp rate.Author SummaryEpilepsy, which is characterized by recurrent seizures, affects around 1% of the world population at some point in their lives. Tonic-clonic seizures are the most commonly encountered primary generalized seizures and it is widely considered that they can be induced by an increase in the connection strength between the cerebral cortex and the thalamus. In this paper, we analyze the detailed dynamics of tonic-clonic seizures along with their dependence on the parameters of the changing connection strength. We study the relationship of the seizure onset, offset, oscillation strength, and oscillation frequency to the duration, amplitude, and rate of change of the connection strength. A detailed understanding of the dynamics and their dependence on the physiological parameters of the brain may explain the variability of seizure dynamics among patients. It may also help to constitute successful seizure prediction.
The histone methyltransferase DOT1L is essential for humoral immune responses
Authors: Kealy Liam , Di Pietro Andrea , Hailes Lauren , Scheer Sebastian , Dalit Lennard , Groom Joanna R , Zaph Colby , Good-Jacobson Kim L 
Published: October 2019

SUMMARYHistone modifiers are essential molecular regulators that underpin the ability of immune cells to reprogram their gene expression during differentiation. The recruitment of the histone methyltransferase DOT1L induces oncogenic gene expression in a subset of B cell leukemia. Despite its importance, little is known about its role in the humoral immune system. Herein, we demonstrate that DOT1L is a critical regulator of B cell biology. Dot1lf/fMb1Cre/+ mice had a block in B cell development, culminating in a significant reduction of mature B cells in the periphery. Upon immunization or influenza infection of Dot1lf/fCd23Cre/+ mice, germinal centers failed to form and class-switched antibody-secreting cells were significantly attenuated. Consequently, immunized mice revealed that DOT1L was essential for the formation of B cell memory populations. Transcriptome, pathway and histological analysis identified a key role for DOT1L in reprogramming gene expression for migration and localization during the initial stages of a humoral response. Together, these results demonstrate an essential role for DOT1L in antigen-dependent B cell differentiation and hence, in generating an effective and lasting humoral immune response.
Testing the basic tenet of the molecular clock and neutral theory by using ancient proteomes
Authors: Liu Tiantian , Huang Shi 
Published: October 2019

AbstractEarly research on orthologous protein sequence comparisons by Margoliash in 1963 discovered the astonishing phenomenon of genetic equidistance, which has inspired thead hocinterpretation known as the molecular clock. Kimura then developed the neutral theory and claimed the molecular clock as its best evidence. However, subsequent studies over the years have largely invalidated the universal molecular clock. Yet, a watered down version of the molecular clock and the neutral theory still reigns as the default model for phylogenetic inferences. The seemingly obvious tenet of the molecular clock on evolutionary time scales remains to be established by using ancient sequences: the longer the time of evolutionary divergence, the larger the genetic distance. We here analyzed the recently published Early Pleistocene enamel proteome from Dmanisi and found that ancient proteins were not closer to an outgroup than their orthologs from the extant sister species were. Together with a previous study, the combined results showed that most ancient proteins were in fact more distant to the outgroup. The results are unexpected from the molecular clock but fully predicted by the notion that genetic distances or diversities are largely at optimum saturation levels as described by the maximum genetic diversity (MGD) theory.
Recruiting RyRs to open in a Ca2+release unit: Single-RyR gating properties make RyR group dynamics
Authors: Gillespie D. 
Published: October 2019

ABSTRACTIn cardiac myocytes, clusters of type-2 ryanodine receptors (RyR2s) release Ca2+from the sarcoplasmic reticulum (SR) via a positive feedback mechanism where fluxed Ca2+activates nearby RyRs. While the general principles of this are understood, less is known about how single-RyR gating properties define the RyR group dynamics in an array of many channels. Here, we examine this using simulations with three models of RyR gating that have identical open probabilities. The commonly-used two-state Markov gating model produces frequent, large, and long Ca2+release events because the single exponential that defines its open time (OT) and closed time (CT) distributions reproduces the experimental data poorly. In contrast, simulations that utilize complete single-channel OT and CT distributions fit with multiple exponentials produce infrequent Ca2+release events with far fewer open RyRs. Moreover, when experimentally-measured correlations between single-channel OTs and CTs are included, Ca2+release events become even smaller. This occurs because the correlations produce a small but consistent bias against recruiting more RyRs to open during the middle of a Ca2+release event, between the initiation and termination phases (which are unaltered compared to the uncorrelated simulations). Beyond the effects of full OT and CT distributions and OT/CT correlations on SR Ca2+release, we also show that Ca2+release events can terminate spontaneously without any reduction in SR [Ca2+] or physical coupling between RyRs when Ca2+flux is below a threshold value. This both supports and extends the pernicious attrition/induction decay hypothesis that SR Ca2+release events terminate below a threshold Ca2+flux.STATEMENT OF SIGNIFICANCEThis work provides insights into RyR2-mediated Ca2+release by a cluster of RyRs interacting only via their fluxed Ca2+. It is shown that: 1) common proxies like the single-RyR open probability versus cytosolic [Ca2+] curve and mean open or closed times are poor predictors of SR Ca2+release dynamics; 2) Ca2+release events can self-terminate below a flux threshold without any physical coupling between channels; 3) commonly-used two-state Markov gating models can produce qualitatively different Ca2+release events (larger and longer) compared to simulations where complete single-channel open and closed time distributions are used; 4) correlations between a RyR’s open times and previous closed duration (and vice versa) significantly limit Ca2+release by tamping down the number of open RyRs.