bluuebunny/crossref_metadata_2025_split huggingface dataset:
Common physiological processes control mercury reduction during photosynthesis and fermentation
Authors: Grégoire Daniel S. , Janssen Sarah E. , Lavoie Noémie C. , Tate Michael T. , Poulain Alexandre J. 
Published: October 2020

ABSTRACTMercury (Hg) is a global pollutant and potent neurotoxin that bioaccumulates in food webs as monomethylmercury (MeHg). The production of MeHg is driven by anaerobic and Hg redox cycling pathways such as Hg reduction, which control the availability of Hg to methylators. Anaerobes play an important role in Hg reduction in methylation hotspots, yet their contributions remain underappreciated due to how challenging these pathways are to study in the absence of dedicated genetic targets and low levels of Hg0in anoxic environments. In this study we used Hg stable isotope fractionation to explore Hg reduction during anoxygenic photosynthesis and fermentation in the model anaerobeHeliobacterium modesticaldumIce1. We show that cells preferentially reduce lighter Hg isotopes in both metabolisms leading to mass-dependent fractionation, but mass-independent fractionation commonly induced by UV-visible light is absent. We show that isotope fractionation is affected by the interplay between pathways controlling Hg recruitment, accessibility, and availability alongside metabolic redox reactions. The combined contributions of these processes lead to isotopic enrichment during anoxygenic photosynthesis that is in between the values reported for anaerobic respiratory microbial Hg reduction and abiotic photoreduction. Isotope enrichment during fermentation is closer to what has been observed in aerobic bacteria that reduce Hg through dedicated detoxification pathways. These results demonstrate that common controls exist at the atomic level for Hg reduction during photosynthesis and fermentation inH. modesticaldum. Our work suggests that similar controls likely underpin diverse microbe-mediated Hg transformations that affect Hg’s fate in oxic and anoxic habitats.IMPORTANCEAnaerobic and photosynthetic bacteria that reduce mercury affect mercury delivery to microbes in methylation sites that drive bioaccumulation in food webs. Anaerobic mercury reduction pathways remain underappreciated in the current view of the global mercury cycle because they are challenging to study, bearing no dedicated genetic targets to establish physiological mechanisms. In this study we used stable isotopes to show that common physiological processes control mercury reduction during photosynthesis and fermentation in the model anaerobeHeliobacterium modesticaldumIce1. The sensitivity of isotope analyses highlighted the subtle contribution of mercury uptake towards the isotope signature associated with anaerobic mercury reduction. When considered alongside the isotope signatures associated with microbial pathways for which genetic determinants have been identified, our findings underscore the narrow range of isotope enrichment that is characteristic of microbial mercury transformations. This suggests that there exist common atomic-level controls for biological mercury transformations across a broad range of geochemical conditions.
Expression of Castanea crenata Allene Oxide Synthase in Arabidopsis Improves the Defense to Phytophthora cinnamomi
Authors: Serrazina Susana , Machado Helena , Costa Rita , Duque Paula , Malhó Rui 
Published: October 2020

ABSTRACTAllene oxide synthase (AOS) is a key enzyme of the jasmonic acid (JA) signaling pathway. The AOS gene was previously found to be upregulated in an Asian chestnut species resistant to infection by the oomycete Phytophthora cinnamomi (Castanea crenata), while lower expression values were detected in the susceptible European chestnut (Castanea sativa). Here, we report a genetic and functional characterization of the C. crenata AOS (CcAOS) upon its heterologous gene expression in a susceptible ecotype of Arabidopsis thaliana, which contains a single AOS gene. It was found that Arabidopsis plants expressing CcAOS delay pathogen progression and exhibit more vigorous growth in its presence. They also show upregulation of jasmonic acid and salicylic acid-related genes. As in its native species, heterologous CcAOS localized to plastids, as revealed by confocal imaging of the CcAOS-eGFP fusion protein in transgenic Arabidopsis roots. This observation was confirmed upon transient expression in Nicotiana benthamiana leaf epidermal cells. To further confirm a specific role of CcAOS in the defense mechanism against the pathogen, we performed crosses between transgenic CcAOS plants and an infertile Arabidopsis AOS knockout mutant line. It was found that plants expressing CcAOS exhibit normal growth, remain infertile but are significantly more tolerant to the pathogen than wild type plants.Together, our results indicate that CcAOS is an important player in plant defense responses against oomycete infection and that its expression in susceptible varieties may be a valuable tool to mitigate biotic stress responses.One-sentence summaryHeterologous expression of the Castanea crenata allene oxide synthase gene in Arabidopsis thaliana improves the defense response to the pathogen Phytophthora cinnamomi.
Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for QTL mapping in maize
Authors: Xie Jiayang , Mayfield-Jones Dustin , Erice Gorka , Choi Min , Leakey Andrew D.B. 
Published: October 2020

AbstractStomata are adjustable pores on leaf surfaces that regulate the trade-off of CO2uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping epidermal cell traits have limited the use of quantitative, forward and reverse genetics to discover the genetic basis of stomatal patterning. A new high-throughput epidermal cell phenotyping pipeline is presented here and used for quantitative trait loci (QTL) mapping in field-grown maize. The locations and sizes of stomatal complexes and pavement cells on images acquired by an optical topometer from mature leaves were automatically determined. Computer estimated stomatal complex density (SCD; R2= 0.97) and stomatal complex area (SCA; R2= 0.71) were strongly correlated with human measurements. Leaf gas exchange traits correlated with the dimensions and proportion of stomatal complexes but, unexpectedly, did not correlate with SCD. Genetic variation in epidermal traits were consistent across two field seasons. Out of 143 QTLs in total, 36 QTLs were consistently identified for a given trait in both years. 24 hotspots of overlapping QTLs for multiple traits were identified. Orthologs of genes known to regulate stomatal patterning inArabidopsiswere located within some, but not all, of these regions. This study demonstrates how discovery of the genetic basis for stomatal patterning can be accelerated in maize, a model for C4species where these processes are poorly understood.One sentence summaryOptical topometry and machine learning tools were developed to assess epidermal cell patterning, and applied to analyze its genetic architecture alongside leaf photosynthetic gas exchange in maize.
Transmission of SARS-CoV-2 from Children and Adolescents
Authors: Chu Victoria T. , Yousaf Anna R. , Chang Karen , Schwartz Noah G. , McDaniel Clinton J. , Szablewski Christine M. , Brown Marie , Winglee Kathryn , Lee Scott H. , Cui Zhaohui , Adebayo Adebola , Aholou Tiffiany , Amin Minal M. , Aryee Peter , Castaneda Cindy , Chambers Trudy , Fleshman Amy C. , Goodman Christin , Holmes Tony , Ivey-Stephenson Asha , Kamitani Emiko , Katz Susan , Knapp Jennifer K. , Kolasa Maureen , Lumsden Maranda , Mayweather Erin , Mohammed Asfia , Moorman Anne , Patel-Larson Alpa , Perinet Lara , Pilgard Mark , Pratt Deirdre D. , Railey Shanica , Shah Jaina , Tuckey Dawn , Dirlikov Emilio , Rose Dale A. , Villanueva Julie , Fry Alicia M. , Hall Aron J. , Kirking Hannah L. , Tate Jacqueline E. , Drenzek Cherie L. , Lanzieri Tatiana M. , Stewart Rebekah J. 
Published: October 2020

AbstractA better understanding of SARS-CoV-2 transmission from children and adolescents is crucial for informing public health mitigation strategies. We conducted a retrospective cohort study among household contacts of primary cases defined as children and adolescents aged 7⍰19 years with laboratory evidence of SARS-CoV-2 infection acquired during an overnight camp outbreak. Among household contacts, we defined secondary cases using the Council of State and Territorial Epidemiologists definition. Among 526 household contacts of 224 primary cases, 48 secondary cases were identified, corresponding to a secondary attack rate of 9% (95% confidence interval [CI], 7%–12%). Our findings show that children and adolescents can transmit SARS-CoV-2 to adult contacts and other children in a household setting.
Identifying Optimal COVID-19 Testing Strategies for Schools and Businesses: Balancing Testing Frequency, Individual Test Technology, and Cost
Authors: Lyng Gregory D. , Sheils Natalie E. , Kennedy Caleb J. , Griffin Daniel , Berke Ethan M. 
Published: October 2020

ABSTRACTBackgroundCOVID-19 test sensitivity and specificity have been widely examined and discussed yet optimal use of these tests will depend on the goals of testing, the population or setting, and the anticipated underlying disease prevalence. We model various combinations of key variables to identify and compare a range of effective and practical surveillance strategies for schools and businesses.MethodsWe coupled a simulated data set incorporating actual community prevalence and test performance characteristics to a susceptible, infectious, removed (SIR) compartmental model, modeling the impact of base and tunable variables including test sensitivity, testing frequency, results lag, sample pooling, disease prevalence, externally-acquired infections, and test cost on outcomes case reduction.ResultsIncreasing testing frequency was associated with a non-linear positive effect on cases averted over 100 days. While precise reductions in cumulative number of infections depended on community disease prevalence, testing every 3 days versus every 14 days (even with a lower sensitivity test) reduces the disease burden substantially. Pooling provided cost savings and made a high-frequency approach practical; one high-performing strategy, testing every 3 days, yielded per person per day costs as low as $1.32.ConclusionsA range of practically viable testing strategies emerged for schools and businesses. Key characteristics of these strategies include high frequency testing with a moderate or high sensitivity test and minimal results delay. Sample pooling allowed for operational efficiency and cost savings with minimal loss of model performance.
Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach
Authors: Cantera Isabel , Decotte Jean-Baptiste , Dejean Tony , Murienne Jérôme , Vigouroux Régis , Valentini Alice , Brosse Sébastien 
Published: October 2020

AbstractEnvironmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA.Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species.eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with distance between sites. The distance decay of similarity derived from eDNA was similar, and even more pronounced, than that obtained with capture-based methods (gil-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species.Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provide a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture based methods, which describes fish fauna over a few hundred metres.
A single-cell atlas of Plasmodium falciparum transmission through the mosquito
Authors: Real Eliana , Howick Virginia M. , Dahalan Farah , Witmer Kathrin , Cudini Juliana , Andradi-Brown Clare , Blight Joshua , Davidson Mira S. , Dogga Sunil Kumar , Reid Adam J. , Baum Jake , Lawniczak Mara K. N. 
Published: October 2020

AbstractMalaria parasites have a complex life cycle featuring diverse developmental strategies, each uniquely adapted to navigate specific host environments. Here we use single-cell transcriptomics to illuminate gene usage across the transmission cycle of the most virulent agent of human malaria – Plasmodium falciparum. We reveal developmental trajectories associated with the colonisation of the mosquito midgut and salivary glands and elucidate the transcriptional signatures of each transmissible stage. Additionally, we identify both conserved and nonconserved gene usage between human and rodent parasites, which point to both essential mechanisms in malaria transmission and species-specific adaptations potentially linked to host tropism. Together, the data presented here, which are made freely available via an interactive website, establish the most complete atlas of the P. falciparum transcriptional journey to date.One sentence summarySingle-cell transcriptomics of P. falciparum transmission stages highlights developmental trajectories and gene usage.
BOLD response to multiple grip forces in MS: going beyond the main effect of movement in BA 4a and BA 4p
Authors: Alahmadi Adnan A.S. , Pardini Matteo , Samson Rebecca S , D’Angelo Egidio , Friston Karl J , Toosy Ahmed T , Gandini Wheeler-Kingshott Claudia A.M. 
Published: October 2020

AbstractThis study highlights the importance of looking beyond the main effect of movement to study alterations in functional response in the presence of central nervous system pathologies such as multiple sclerosis (MS). Data show that MS selectively affects regional BOLD (Blood Oxygenation Level Dependent) responses to variable grip forces (GF). It is known that the anterior and posterior BA 4 areas (BA 4a and BA 4p) are anatomically and functionally distinct. It has also been shown in Healthy volunteers that there are linear (1storder, typical of BA 4a) and non-linear (2nd-4thorder, typical of BA 4p) BOLD responses to different levels of GF applied during a dynamic motor paradigm. After modelling the BOLD response with a polynomial expansion of the applied GFs, the particular case of BA 4a and BA 4p were investigated in Healthy Volunteers (HV) and MS subjects. The main effect of movement (0th order) analysis showed that the BOLD signal is greater in MS compared to healthy volunteers within both BA 4 sub-regions. At higher order, BOLD-GF responses were similar in BA 4a but showed a marked alteration in BA 4p of MS subjects, with those with greatest disability showing the greatest deviations from the healthy response profile. Therefore, the different behaviour in HV and MS could only be uncovered through a polynomial analysis looking beyond the main effect of movement into the two BA 4 sub-regions. Future studies will investigate the source of this pathophysiology, combining the present fMRI paradigm with blood perfusion and non-linear neuronal response analysis.
Adaptive management plans rooted in quantitative ecological predictions of ecosystem processes: putting monitoring data to practical use
Authors: Damgaard Christian 
Published: October 2020

AbstractIt is demonstrated how a hierarchical structural equation model that is fitted to temporal ecological monitoring data from a number of sites may be used to generate local ecological predictions and how these local ecological predictions may form the basis of adaptive management plans. Local ecological predictions will be made for the cover of cross-leaved heath on Danish wet heathlands, which is one of the indicators that determine the conservation status of wet heathlands under different management scenarios. Based on a realistic example, the model predictions concludes that grazing by domestic herbivores on wet heathlands with a relatively low cover cross-leaved heath cannot be recommended as the only management practice. Generally, it is recommended to use ecological monitoring data to generate quantitative and credible local adaptive management plans where the uncertainty is taken into account.
Statistics used to infer inter-breeding between humans and Neanderthals are strongly predicted by flanking sequence heterozygosity
Authors: Amos William 
Published: October 2020

AbstractA large and rapidly expanding literature has grown out of the observation that humans carry a genetic legacy reflecting ancient inter-breeding with archaic hominins such as Neanderthals and Denisovans. However, a recent study suggests that a commonly used statistic used to assess legacy size, D, is driven mainly by heterozygous sites in Africa acting to increase divergence from our common ancestor rather than introgressed fragments outside Africa reducing divergence. To test this new model, I analysed how D is influenced by heterozygosity within a kilobase of each putative introgressed base. I find that flanking heterozygosity is a potent predictor of D, with introgression always being inferred as having occurred into the population with lower heterozygosity. This pattern cannot be driven by any introgressed fragments themselves, which simulations show create the exact converse pattern, but instead appears to be generated by heterozygosity acting to drive increased divergence from the ancestral sequence. This new model explains why introgression of haploid or semi-haploid regions is essentially lacking and why introgression is often inferred around immune genes and other regions under strong selection. More generally, these results raise the possibility that reported legacies are largely an artefact arising out of the false assumption that mutation rate is constant.
Dopamine neuron synaptic connectivity defines physiological striatal domains
Authors: Chuhma Nao , Oh Soo Jung , Rayport Stephen 
Published: October 2020

AbstractDopamine neurons projecting to the striatum control movement, cognition, and motivation. They do so via slower, dopamine volume transmission and also via faster synaptic dopamine, glutamate and GABA transmission. To define the scope of these synaptic actions, we recorded dopamine neuron synaptic currents in the four major classes of striatal neurons. This revealed that dopaminergic and GABAergic synaptic actions are widespread; glutamatergic synaptic actions are robust in the medial nucleus accumbens and the anterolateral dorsal striatum, mediating fast and slow excitation, respectively. Dopamine neuron synaptic actions in cholinergic interneurons are the strongest and most complex, involving all three transmitters, their multiple receptors, and are the most regionally heterogeneous. The caudal striatum forms a single domain with overall weak dopamine neuron synaptic actions. This synaptic mapping reveals that dopamine neuron synaptic actions extend across the entire striatum, are regionally heterogeneous and organized in physiological domains, determined mainly by their excitatory actions.
Motor resonance is modulated by an object’s weight distribution
Authors: Rens Guy , de Xivry Jean-Jacques Orban , Davare Marco , van Polanen Vonne 
Published: October 2020

AbstractTranscranial magnetic stimulation (TMS) studies showed that corticospinal excitability (CSE) is modulated during observation of object lifting, an effect termed ‘motor resonance’. Specifically, motor resonance is driven by movement features indicating object weight, such as object size or observed movement kinematics. We investigated in 16 humans (8 females) whether motor resonance is also modulated by an object’s weight distribution. Participants were asked to lift an inverted T-shaped manipulandum with interchangeable center of mass after first observing an actor lift the same manipulandum. Participants and actor were instructed to minimize object roll and rely on constrained digit positioning during lifting. Constrained positioning was either collinear (i.e., fingertips on the same height) or noncollinear (i.e., fingertip on the heavy side higher than the one on the light side). The center of mass changed unpredictably before the actor’s lifts and participants were explained that their weight distribution always matched the actor’s one. Last, TMS was applied during both lift observation and planning of lift actions. Our results showed that CSE was similarly modulated during lift observation and planning: when participants observed or planned lifts in which the weight distribution was asymmetrically right-sided, CSE recorded from the thumb muscles was significantly increased compared to when the weight distribution was left-sided. During both lift observation and planning, this increase seemed to be primarily driven by the weight distribution and not specifically by the (observed) digit positioning or muscle contraction. In conclusion, our results indicate that complex intrinsic object properties such as weight distributions can modulate activation of the motor system during both observation and planning of lifting actions.Highlights•Motor resonance is observation-induced activity in the observer’s motor system•We used a dyadic lifting task of objects with asymmetrical weight distribution•We investigated which movement features modulate motor resonance•Motor resonance is modulated by the object’s weight distribution•Motor resonance is driven by observed and planned digit positioning
A synthetic RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux
Authors: Ortega Alvaro D. , Takhaveev Vakil , Bonsing-Vedelaar Silke , Long Yi , Mestre-Farràs Neus , Incarnato Danny , Ersoy Franziska , Olsen Lars Folke , Mayer Günter , Heinemann Matthias 
Published: October 2020

ABSTRACTMetabolic heterogeneity, the occurrence of different metabolic phenotypes among cells, represents a key challenge in health and biotechnology. To unravel its molecular basis, tools probing metabolism of single cells are needed. While RNA devices harbor huge potential for the development of such tools, until today, it is challenging to createin vivo-functional sensors for any given metabolite. Here, we developed from scratch an RNA-based sensor for fructose-1,6-bisphosphate (FBP), a doubly phosphorylated intermediate of glycolysis. Starting fromin vitroselection of an RNA aptamer and its structural analyses, we developed libraries of RNA-based regulatory devices with this aptamer and the hammerhead ribozyme as an actuator. Through FACS-seq-based high-throughput screening in yeast, we identifiedin vivo-functional FBP-sensing devices that generate fluorescent readout dependent on intracellular FBP concentration. As FBP reports the flux through glycolysis, the developed RNA device can be used to sense the glycolytic rate in single cells, offering unprecedented possibilities to investigate the causes of metabolic heterogeneity.