bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light exposure decreases infectivity of theDaphniaparasitePasteuria ramosa
Authors: Overholt Erin P. , Duffy Meghan A. , Meeks Matthew P. , Leach Taylor H. , Williamson Craig E. 
Published: October 2019

ABSTRACTClimate change is altering light regimes in lakes, which should impact disease outbreaks, since sunlight can harm aquatic pathogens. However, some bacterial endospores are resistant to damage from light, even surviving exposure to UV-C. We examined the sensitivity ofPasteuria ramosaendospores, an aquatic parasite infectingDaphniazooplankton, to biologically relevant wavelengths of light. Laboratory exposure to increasing intensities of UV-B, UV-A, and visible light significantly decreasedP. ramosainfectivity, though there was no effect of spore exposure on parasitic castration of the host.P. ramosais more sensitive than itsDaphniahost to damage by longer wavelength UV-A and visible light; this may enableDaphniato seek an optimal light environment in the water column where both UV-B damage and parasitism are minimal. Studies of pathogen light sensitivity help us uncover factors controlling epidemics in lakes, which is especially important given that water transparency is decreasing in many lakes.
Phenylethynylbenzyl-Modified Biguanides Inhibit Pancreatic Cancer Tumor Growth
Authors: Hébert Audrey , Parisotto Maxime , Rowell Marie-Camille , Doré Alexandra , Fernandez Ana , Lefrancois Guillaume , Kalegari Paloma , Ferbeyre Gerardo , Schmitzer Andreea R. 
Published: October 2019

AbstractWe present the design and synthesis of a small library of substituted biguanidium salts and their capacity to inhibit the growth/viability of pancreatic cancer cells. We first present their in vitro and membrane activity, before we address their mechanism of action in living cells and in vivo activity. We show that phenylethynyl biguanidium salts possess higher ability to cross hydrophobic barriers, improved mitochondrial accumulation and anticancer activity. Mechanistically, the most active compound 1b, like metformin, decreases the NAD+/NADH ratio and mitochondrial respiration, but at 800-fold lower concentration. In vivo studies with, the most active, compound 1b show a significant growth inhibition of pancreatic cancer xenografts in mice, while biguanides currently in clinical trials had no activity.
The norepinephrine transporter regulates dopamine-dependent synaptic plasticity in the mouse dorsal hippocampus
Authors: Sonneborn Alex , Greene Robert W. 
Published: October 2019

AbstractThe rodent dorsal hippocampus is essential for episodic memory consolidation, a process dependent on dopamine D1-like receptor activation. It was previously thought that the ventral tegmental area provided the only supply of dopamine to dorsal hippocampus, but several recent studies have established the locus coeruleus (LC) as a second major source. However, the mechanism for LC-dependent dopamine release has never been explored. Our data identify norepinephrine transporter reversal as one plausible mechanism by demonstrating that transporter blockade can reduce dopamine-dependent long-term potentiation in hippocampal slices. We also suggest that presynaptic NMDA receptors on LC terminals may initiate this norepinephrine transporter reversal. Furthermore, as dopamine and norepinephrine should be co-released from the LC, we show that they act together to enhance synaptic strength. Since LC activity is highly correlated with attentional processes and memory, these experiments provide insight into how selective attention influences memory formation at the synaptic and circuit levels.
Evaluating the performance of malaria genomics for inferring changes in transmission intensity using transmission modelling
Authors: Watson Oliver J. , Okell Lucy C. , Hellewell Joel , Slater Hannah C. , Unwin H. Juliette T. , Omedo Irene , Bejon Philip , Snow Robert W. , Noor Abdisalan M. , Rockett Kirk , Hubbart Christina , Nankabirwa Joaniter I. , Greenhouse Bryan , Chang Hsiao-Han , Ghani Azra C. , Verity Robert 
Published: October 2019

AbstractAdvances in genetic sequencing and accompanying methodological approaches have resulted in pathogen genetics being used in the control of infectious diseases. To utilise these methodologies for malaria we first need to extend the methods to capture the complex interactions between parasites, human and vector hosts, and environment. Here we develop an individual-based transmission model to simulate malaria parasite genetics parameterised using estimated relationships between complexity of infection and age from 5 regions in Uganda and Kenya. We predict that cotransmission and superinfection contribute equally to within-host parasite genetic diversity at 11.5% PCR prevalence, above which superinfections dominate. Finally, we characterise the predictive power of six metrics of parasite genetics for detecting changes in transmission intensity, before grouping them in an ensemble statistical model. The best performing model successfully predicted malaria prevalence with mean absolute error of 0.055, suggesting genetic tools could be used for monitoring the impact of malaria interventions.
Chimpanzees use advanced spatial cognition to plan least-cost routes
Authors: Green Samantha J. , Boruff Bryan J. , Grueter Cyril C. 
Published: October 2019

SummaryWhile the ability of naturally ranging animals to recall the location of food resources and use straight-line routes between them has been demonstrated in several studies, it is not known whether animals can use knowledge of their physical landscape to plan least-cost routes. This ability is likely to be particularly important for animals living in highly variable energy landscapes, where movement costs are exacerbated. Here, we used least-cost modelling to investigate whether chimpanzees (Pan troglodytes) living in a rugged, montane environment use advanced cognitive skills to plan energy efficient routes. We used a subset of chimpanzee movement segments together with the available laboratory measurements of chimpanzee energy expenditure to assign movement ‘costs’ which were incorporated in an anisotropic least-cost model and straight-line null model. The least-cost model performed better than the straight-line model across all parameters, and linear mixed modelling showed a strong relationship between the cost of observed chimpanzee travel and predicted least-cost routes. To our knowledge, our study provides the first example of spatial memory for landscape and the ability to plan least-cost routes in non-human animals. These cognitive abilities may be a key trait that have enabled chimpanzees to maintain their energy balance in a low-resource environment. Our findings provide a further example of how the advanced cognitive complexity of hominids have facilitated their adaptation to a variety of environmental conditions and lead us to hypothesise that landscape complexity may play a role in shaping cognition.
Human gut mobileome during antibiotic therapy. A trajectory-based approach to analysis of the metagenomic time-series datasets
Authors: Górska Anna , Schlaberg Robert , Willmann Matthias , Liese Jan , Monjaras Feria Julia Victoria , Wagner Samuel , Autenrieth Ingo , Huson Daniel H. , Peter Silke 
Published: October 2019

AbstractMotivationAntibiotic resistance is widely recognized as a severe threat to current medical practice. Each antibiotic therapy drives the emergence and subsequent retention of antibiotics resistance genes within the human gut microbiome. However, the details on how the resistance spreads between bacteria within the human gut remain unknown, as does the role of horizontal gene transfer in this process, too.ResultsWe present a novel approach to the analysis of time-series whole-genome metagenomic sequencing data. This involves partitioning the scaffolds from the metagenomic assembly into groups corresponding to bacterial chromosomes, plasmids and those with prophages and transposons. Using specialized sequencing of the bacteriophages we were able to track the flow of ciprofloxacin resistance genes from bacterial chromosomes, through the plasmids, to prophages and phages.Contactanna.gorska@univr.it.
UAV Based Imaging Platform for Monitoring Maize Growth Throughout Development
Authors: Tirado Sara B. , Hirsch Candice N. , Springer Nathan M. 
Published: October 2019

ABSTRACTPlant height (PH) data collected at high temporal resolutions can give insight into important growth parameters useful for identifying elite material in plant breeding programs and developing management guidelines in production settings. However, in order to increase the temporal resolution of PH data collection, more robust, rapid and low-cost methods are needed to evaluate field plots than those currently available. Due to their low cost and high functionality, unmanned aerial vehicles (UAVs) can be an efficient means for collecting height at various stages throughout development. We have developed a procedure for utilizing structure from motion algorithms to collect PH from RGB drone imagery and have used this platform to characterize a yield trial consisting of 24 maize hybrids planted in replicate under two dates and three planting densities in St Paul, MN in the summer of 2018. The field was imaged weekly after planting using a DJI Phantom 4 Advanced drone to extract PH and hand measurements were collected following aerial imaging of the field. In this work, we test the error in UAV PH measurements and compare it to the error obtained within manually acquired PH measurements. We also propose a method for improving the correspondence of manual and UAV measured height and evaluate the utility of using UAV obtained PH data for assessing growth of maize genotypes and for estimating end-season height.
CodAn: predictive models for the characterization of mRNA transcripts in Eukaryotes
Authors: Nachtigall Pedro G , Kashiwabara Andre Y , Durham Alan M 
Published: October 2019

AbstractCharacterization of the coding sequences (CDSs) is an essential step on transcriptome annotation. Incorrect characterization of CDSs can lead to the prediction of non-existent proteins that can eventually compromise knowledge if databases are populated with similar incorrect predictions made in different genomes. Even though some recent methods have succeeded in correctly prediction of the stop codon position in strand-specific sequences, prediction of the complete CDS is still far from a gold standard. More importantly, prediction in strand-blind sequences and in partial sequences is deficient, presenting very low accuracy. Here, we present CodAn, a new computational approach to predict CDS and UTR, that significantly pushes the boundaries of CDS prediction in strand-blind and in partial sequences, increases strand-specific full-CDS predictions and matches or surpasses gold-standard results in strand-specific stop codon predictions. CodAn is freely available for download at https://github.com/pedronachtigall/CodAn.
Regional differences in gene regulation may underlie patterns of sensitivity to novel insecticides in Colorado potato beetle
Authors: Dively Galen P. , Crossley Michael S. , Schoville Sean D. , Steinhauer Nathalie , Hawthorne David J. 
Published: October 2019

AbstractAgricultural insect pests frequently exhibit geographic variation in levels of insecticide resistance, which are often presumed to be due to the intensity of insecticide use for pest management. However, regional differences in the evolution of resistance to novel insecticides suggests that other factors are influencing rates of adaptation. We examined LC50 bioassay data spanning 15 years and six insecticides (abamectin, imidacloprid, spinosad, cyantraniliprole, chlorantraniliprole, and metaflumizone) for evidence of regional differences in Colorado potato beetle (CPB) baseline sensitivity to insecticides as they became commercially available. We consistently found that CPB populations from the Western USA had the highest baseline sensitivity to novel insecticides, while populations from the Eastern USA had the lowest. Comparisons of gene expression between populations from these regions revealed constitutively elevated expression of an array of detoxification genes in the East, but no evidence of additional induction when exposed to imidacloprid. Our results suggest a mechanism for geographic variation in rates of adaptation to insecticides whereby baseline levels of gene expression determine a population’s response to novel insecticides. These findings have implications for the regional development of insecticide resistance management strategies and for the fundamental question of what determines the rate of adaptation to insecticides.
Diversity and seasonality of horse flies (Diptera: Tabanidae) in Uruguay
Authors: Lucas Martín , Krolow Tiago K. , Riet-Correa Franklin , Barros Antonio Thadeu M. , Krüger Rodrigo F. , Saravia Anderson , Miraballes Cecilia 
Published: October 2019

AbstractHorse flies (Diptera: Tabanidae) are hematophagous insects that cause direct and indirect losses in livestock production and are important vectors of pathogens. The aim of this study was to determine the diversity and seasonality of horse fly species at an experimental farm in Tacuarembó and the diversity of species in different departments of Uruguay. For 20 months, systematic collections were performed using Nzi and Malaise traps in two different environments at the experimental farm. Temperature, humidity and rainfall were recorded using a local climatological station. In addition, nonsystematic collections were made at farms located in the departments of Paysandú, Tacuarembó and Colonia. A total of 3,666 horse flies were collected, allowing the identification of 16 species. Three species were recorded for the first time in Uruguay:Dasybasis ornatissima(Brèthes),Dasybasis missionum(Macquart), andTabanus aff. platensisBrèthes. A species that had not been previously taxonomically described was identified (Tabanussp.1). In the systematic captures, the most abundant species wereTabanus campestrisBrèthes,T. aff. platensisandD. missionum, representing 77.6% of the collected specimens. The environment was an important factor related to the abundance of horse flies, as well as the mean temperature. The horse fly season in Tacuarembó started in September and ended in May, with three evident peaks, the most important one during summer. No horse flies were caught during winter. Variations in the prevalence of species in the different departments were observed, indicating the need to carry out new sampling efforts in different areas.
Similar network compositions, but distinct neural dynamics underlying belief updating in environments with and without explicit outcomes
Authors: Fiore Vincenzo G. , Gu Xiaosi 
Published: October 2019

AbstractClassic decision theories, such as reinforcement learning, typically require the presence of explicit outcomes for learning and belief updating. However, ecological environments are often opaque and explicit feedback, such as those based on values, might not be immediately accessible. It remains unclear whether the neural dynamics underlying belief updating in absence of outcomes differ from those responsible for decision-making based on accessible outcomes. Here, we investigated this question in healthy humans (n=28) using Bayesian modeling and two multi-option fMRI tasks, one with and one without immediate outcome. Model-based fMRI analysis revealed two opposing networks encoding belief updating regardless of the presence of immediate outcomes. A “confidence-building” network including the hippocampus, amygdala, and medial prefrontal cortex (mPFC) became more active as beliefs about action-outcome probabilities were confirmed by newly acquired information. Meanwhile, an “uncertainty-building” network including the anterior insular (AIC), dorsal anterior cingulate (dACC), and dorsolateral prefrontal (dlPFC) cortices became more active as new evidence conflicted with action-outcome estimates. Interestingly, dynamic causal modeling revealed that the confidence network was driven either by the hippocampus when outcomes were not available, or by the mPFC and amygdala when value-based outcomes were immediately accessible. Convsersely, the AIC always drove the activities of dACC and dlPFC, under the modulation of increasing uncertainty, independent of outcome availability. These findings reveal similar network compositions but distinct neural dynamics underlying belief updating in changing environments with and without explicit outcomes, highlighting an asymmetric relationship between decision confidence and uncertainty computation across levels of analysis.HighlightsWe investigated belief updating in two tasks, with and without explicit feedback.Model-based fMRI analysis revealed similar neural responses across tasks.The anterior insula drove an uncertainty-encoding network, across tasks.The anterior hippocampus drove a confidence-encoding network, w/o feedbacks.The medial PFC and amygdala drove a confidence-encoding network, with feedbacks.
Amitosis confers benefits of sex in the absence of sex to Tetrahymena
Authors: Zhang Hao , West Joe A. , Zufall Rebecca A. , Azevedo Ricardo B. R. 
Published: October 2019

AbstractSex appears to be the most successful reproductive strategy in eukaryotes despite its many costs. While a complete explanation for sex’s success remains elusive, several evolutionary benefits of sex have been identified. It is predicted that, by forgoing these benefits, asexual lineages are evolutionary dead-ends. Consistent with this prediction, many asexual lineages show signs of accelerated accumulation of deleterious mutations compared to their sexual relatives. Despite these low expectations, some asexual eukaryotic lineages appear to be successful, including the ciliate Tetrahymena. Here, we show that the mechanism of somatic nuclear division in Tetrahymena, known as amitosis, provides benefits similar to sex, allowing for the long-term success of asexual lineages. We found that, when compared to mitosis, amitosis with chromosome copy number control reduces mutation load deterministically, slows the accumulation of deleterious mutations under genetic drift, and accelerates adaptation. These benefits arise because, like sex, amitosis can generate substantial genetic variation in fitness among (asexual) progeny. Our results indicate that the ability of Tetrahymena to persist in the absence of sex may depend on non-sexual genetic mechanisms conferring benefits typically provided by sex, as has been found in other asexual lineages.
Intragenic Recombination Influences Rotavirus Diversity and Evolution
Authors: Hoxie Irene , Dennehy John J. 
Published: October 2019

AbstractBecause of their replication mode and segmented dsRNA genome, homologous recombination is assumed to be rare in the rotaviruses. We analyzed 23,627 complete rotavirus genome sequences available in the NCBI Virus Variation database, and found 109 instances of homologous recombination, at least 11 of which prevailed across multiple sequenced isolates. In one case, recombination may have generated a novel rotavirus VP1 lineage. We also found strong evidence for intergenotypic recombination in which more than one sequence strongly supported the same event, particularly between different genotypes of segment 9, which encodes the serotype protein, VP7. The recombined regions of many putative recombinants showed amino acid substitutions differentiating them from their major and minor parents. This finding suggests that these recombination events were not overly deleterious, since presumably these recombinants proliferated long enough to acquire adaptive mutations in their recombined regions. Protein structural predictions indicated that, despite the sometimes substantial amino acid replacements resulting from recombination, the overall protein structures remained relatively unaffected. Notably, recombination junctions appear to occur non-randomly with hot spots corresponding to secondary RNA structures, a pattern seen consistently across segments. In total, we found strong evidence for recombination in nine of eleven rotavirus A segments. Only segment 7 (NSP3) and segment 11 (NSP5) did not show strong evidence of recombination. Collectively, the results of our computational analyses suggest that, contrary to the prevailing sentiment, recombination may be a significant driver of rotavirus evolution and may influence circulating strain diversity.
A plant host enables the heterologous production and combinatorial study of fungal lignin-degrading enzymes
Authors: Khlystov Nikita A. , Yoshikuni Yasuo , Deutsch Samuel , Sattely Elizabeth S. 
Published: October 2019

AbstractLignin has significant potential as an abundant and renewable source for commodity chemicals yet remains vastly underutilized. Efforts towards engineering a biochemical route to the valorization of lignin are currently limited by the lack of a suitable heterologous host for the production of lignin-degrading enzymes. Here, we show that expression of fungal genes inNicotiana benthamianaenables production of members from seven major classes of enzymes associated with lignin degradation (23 of 35 tested) in soluble form for direct use in lignin activity assays. We combinatorially characterized a subset of these enzymes in the context of model lignin dimer oxidation, revealing that fine-tuned coupling of peroxide-generators to peroxidases results in more extensive C-C bond cleavage compared to direct addition of peroxide. Comparison of peroxidase isoform activity revealed that the extent of C-C bond cleavage depends on peroxidase identity, suggesting that peroxidases are individually specialized in the context of lignin oxidation. We anticipate the use ofN. benthamianaas a platform to rapidly produce a diverse array of fungal lignin-degrading enzymes will facilitate a better understanding of their concerted role in nature and unlock their potential for lignin valorization, including within the plant host itself.