bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of petal transpiration in floral humidity generation
Authors: Harrap Michael J. M. , Rands Sean A. 
Published: April 2021

ABSTRACTFloral humidity, an area of elevated humidity in the headspace of flowers, has been detected across angiosperms and may function as a pollinator cue for insect pollinators. It is believed floral humidity is produced predominantly through a combination of evaporation of both liquid nectar and transpirational water loss from the flower. However, the role of transpiration in floral humidity generation has not been tested and is largely inferred by continued humidity production when nectar is removed from flowers. Understanding the extent that transpiration contributes to floral humidity has important implications for understanding the function of floral humidity. We test whether transpiration contributes to the floral humidity generation of two species previously identified to produce elevated floral humidity,Calystegia silvaticaandEschscholzia californica. Floral humidity production of flowers that underwent an antitranspirant treatment, petrolatum gel which blocks transpiration from treated tissues, is compared to flowers that did not receive such treatments. Gel treatments reduced floral humidity production to approximately a third of that produced by untreated flowers inC. silvatica, and half of that inE. californica. This confirms, the previously untested, inferences that transpiration has a large contribution to floral humidity generation and that this contribution may vary between species.HIGHLIGHTWe confirm, the previously untested, inferences that transpiration has a large contribution to floral humidity generation and show that this contribution may vary between species.
Highly parallel genomic selection response in replicatedDrosophila melanogasterpopulations with reduced genetic variation
Authors: Claire Burny , Viola Nolte , Marlies Dolezal , Christian Schlötterer 
Published: April 2021

ABSTRACTMany adaptive traits are polygenic and frequently more loci contributing to the phenotype than needed are segregating in populations to express a phenotypic optimum. Experimental evolution provides a powerful approach to study polygenic adaptation using replicated populations adapting to a new controlled environment. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequencing (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbredDrosophila melanogasterstrains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.
Bonsai: An efficient method for inferring large human pedigrees from genotype data
Authors: Jewett Ethan M. , McManus Kimberly F. , Freyman William A. ,   the 23andMe Research Team, Auton Adam 
Published: April 2021

1.AbstractPedigree inference from genotype data is a challenging problem, particularly when pedigrees are sparsely sampled and individuals may be distantly related to their closest genotyped relatives. We present a new method that infers small pedigrees of close relatives and then assembles them into larger pedigrees. To assemble large pedigrees, we introduce several new formulas and tools including a new likelihood for the degree separating two small pedigrees, a method for detecting individuals who share background identity-by-descent (IBD) that does not reflect recent common ancestry, and a method for identifying the ancestral branches through which distant relatives are connected. Our method also takes several new approaches that help to improve the accuracy and efficiency of pedigree inference. In particular, we incorporate age information directly into the likelihood rather than using ages only for consistency checks and we employ a heuristic branch-and-bound-like approach to more efficiently explore the space of possible pedigrees. Together, these approaches make it possible to construct large pedigrees that are challenging or intractable for current inference methods. The new method, Bonsai, is available athttps://github.com/23andMe/bonsaitree.
Chemogenetically decreasing activity of the dorsal cochlear nucleus can ameliorate noise-induced tinnitus in mice
Authors: Malfatti Thawann , Ciralli Barbara , Hilscher Markus M. , Leao Richardson N. , Leao Katarina E. 
Published: April 2021

AbstractThe dorsal cochlear nucleus (DCN) is a region known to integrate somatosensory and auditory inputs and is identified as a potential key structure in the generation of phantom sound perception, especially noise-induced tinnitus. Yet, how altered homeostatic plasticity of the DCN induces and maintains the sensation of tinnitus is not clear. Here, we chemogenetically decrease activity of a subgroup of DCN neurons, Ca2+/Calmodulin kinase 2α(CaMKIIα) positive DCN neurons, using Gi-coupled human M4 Designer Receptors Exclusively Activated by Designer Drugs (hM4Di DREADDs), to investigate their role in noise-induced tinnitus. Mice were exposed to loud noise (9-11kHz, 90dBSPL, 1h, followed by 2h of silence) and auditory brainstem responses (ABRs) and gap prepulse inhibition of acoustic startle (GPIAS) were recorded two days before and two weeks after noise exposure to identify animals with a significantly decreased inhibition of startle, indicating tinnitus but without permanent hearing loss. Neuronal activity of CaMKIIα+ neurons expressing hM4Di in the DCN was lowered by administration of clozapine-N-oxide (CNO). We found that acutely decreasing firing rate of CaMKIIα+ DCN units decrease tinnitus-like responses (p = 0.038, n = 11 mice), compared to the control group that showed no improvement in GPIAS (control virus; CaMKIIα-YFP + CNO, p = 0.696, n = 7 mice). Extracellular recordings confirmed CNO to decrease unit firing frequency of CaMKIIα-hM4Di+ mice and alter best frequency and tuning width of response to sound. However, these effects were not seen if CNO had been previously administered during the noise exposure (n = 6 experimental and 6 control mice). Our results suggest that CaMKIIα-hM4Di positive cells in the DCN are not crucial for tinnitus induction but play a significant role in maintaining tinnitus perception in mice.
Using Hierarchical Similarity To Examine The Genetics of Behçet’s Disease
Authors: Shenoi Samuel J , Baker Erich J 
Published: April 2021

AbstractBehçet’s disease (BD) is a multisystem inflammatory disease that affects patients along the historic silk road. Thus far, the pathogenesis of the disease has proved elusive due to the complex genetic interactions and unknown environmental or viral triggering factors of the disease. In this paper, we seek to clarify the genetic factors of the disease while also uncovering other diseases of interest that present with a similar genotype as BD. To do this, we employ a convergent functional genomics approach by leveraging the hierarchical similarity tool available in Geneweaver. Through our analysis, we were able to ascertain 7 BD consensus genes and 16 autoimmune diseases with genetic overlap with BD. The results of our study will inform further research into the pathogenesis of Behçet’s Disease.
Bacterioplankton diversity and pollution levels in the estuarine regions of Chaliyar and Anjarakkandi rivers, Kerala, India
Authors: Nikhitha D. , Narayanankutty Arunaksharan , Jacob Jisha 
Published: April 2021

AbstractRivers and the estuarine regions play crucial roles in the environment by controlling the nutrient cycling, waste disposal, and also in supporting biodiversity. However, the estuarine regions of rivers are highly susceptible to disruptive changes by anthropogenic pollutants and eutrophication. Bacterioplankton diversity is the best indicators of the pollution level and eutrophication status of the rivers. The present study evaluated the eutrophication status and bacterioplankton diversity of the estuarine regions of Chaliyar and the Anjarakkandi originated from the Western Ghats. The present study observed the presence of increased incidence of bacterioplankton comprising of proteobacteria, actinobacteria and cyanobacteria in the estuarine regions of Anjarakkandi river compared to that of Chaliyar river. Further, the percentage incidence of faecal bacteria including Bacillus subtilis and E. coli, were also found to be in high in the Anjarakkandi river; in corroborating with this, the diversity of nitrogen metabolizing bacteria was also higher in the estuarine samples of Anjarakkandi river. Corroborating with this, the levels of water nutrients including nirates, nitrites and phosphates were high in the Anjarakkandi compared to the Chaliyar river. Together, it is possible that there might be increased faecal contamination and subsequent increased eutrophication in the estuarine regions of Anjarakkandi river. Altogether, the study concludes that the Anjarakkandi river may be more polluted and which is partly contributed by faecal contaminants and also responsible for the change in the bacterioplankton community of the estuaries.
Systematic review of the entomological impact of insecticide-treated nets evaluated using experimental hut trials in Africa
Authors: Nash Rebecca K , Lambert Ben , N’Guessan Raphael , Ngufor Corine , Rowland Mark , Oxborough Richard , Moore Sarah , Tungu Patrick , Sherrard-Smith Ellie , Churcher Thomas S 
Published: April 2021

AbstractBackgroundResistance of anopheline mosquitoes to pyrethroid insecticides is spreading rapidly across sub-Saharan Africa, diminishing the efficacy of insecticide-treated nets (ITNs) — the primary tool for preventing malaria. The entomological efficacy of indoor vector control interventions can be measured in experimental hut trials (EHTs), which are specially designed to quantify the protection provided under controlled conditions. Experimental hut structures resemble local housing but allow collection of surviving exiting mosquitoes as well as dead or dying mosquitoes. There is a need to understand how the spread of resistance changes ITN efficacy and to elucidate factors influencing EHT results, including differences in experimental hut construction and design features, to support the development of novel vector control tools.MethodsA comprehensive database of EHTs was compiled and summarised following a systematic review to identify all known trials investigating ITNs or indoor residual spraying (IRS) across sub-Saharan Africa. This analysis focuses on EHTs investigating ITNs and uses Bayesian statistical models to characterise the complex interaction between ITNs and mosquitoes, the variability between studies, and the impact of pyrethroid resistance.ResultsAs resistance rises, the entomological efficacy of ITNs declines. They induce less mortality and are less likely to deter mosquitoes from entering huts. Despite this, ITNs continue to offer considerable personal protection by reducing mosquito feeding until resistance reaches high levels. There are clear associations between the different entomological impacts of ITNs, though there is still substantial variability between studies, some of which can be accounted for by hut design. The relationship between EHT outcomes and the level of resistance (as measured by discriminating dose bioassays) is highly uncertain.ConclusionsThe meta-analyses show that EHTs are an important reproducible assay for capturing the complex entomological efficacy of ITNs on blood-feeding mosquitoes. The impact of pyrethroid resistance on these measures appears broadly consistent across a wide geographical area once hut design is accounted for, suggesting results can be extrapolated beyond the sites where the trials were conducted. Further work is needed to understand factors influencing EHT outcomes and how the relationship between outcomes and resistance varies when different methods are used to assess the level of resistance in wild mosquito populations. This will allow more precise estimates of the efficacy of these important vector control tools.
The immunomodulatory dCache chemoreceptor TlpA ofHelicobacter pyloribinds multiple attractant and antagonistic ligands via distinct sites
Authors: Johnson Kevin S. , Elgamoudi Bassam , Jen Freda E.-C. , Day Christopher , Sweeney Emily Goers , Pryce Megan L. , Guillemin Karen , Haselhorst Thomas , Korolik Victoria , Ottemann Karen M. 
Published: April 2021

AbstractTheHelicobacter pylorichemoreceptor TlpA plays a role in dampening host inflammation during chronic stomach colonization. TlpA has a periplasmic dCache_1 domain, a structure that is capable of sensing many ligands; however, the only characterized TlpA signals are arginine, bicarbonate, and acid. To increase our understanding of TlpA’s sensing profile, we screened for diverse TlpA ligands using ligand binding arrays. TlpA bound seven ligands with affinities in the low to middle micromolar ranges. Three of these ligands, arginine, fumarate, and cysteine, were TlpA-dependent chemoattractants, while the others elicited no response. Molecular docking experiments, site-directed point mutants, and competition surface plasmon resonance binding assays suggested that TlpA binds ligands via both the membrane-distal and -proximal dCache_1 binding pockets. Surprisingly, one of the non-active ligands, glucosamine, acted as a chemotaxis antagonist, preventing the chemotaxis response to chemoattractant ligands and acted to block binding of ligands irrespective of whether they bound the membrane-distal or -proximal dCache_1 subdomains. In total, these results suggest TlpA senses multiple attractant ligands as well as antagonist ones, an emerging theme in chemotaxis systems.ImportanceNumerous chemotactic bacterial pathogens depend on the ability to sense a diverse array of signals through chemoreceptors to achieve successful colonization and virulence within their host. The signals sensed by chemoreceptors, however, are not always fully understood. This is the case for TlpA, a dCache_1 chemoreceptor ofH. pylorithat enables the bacteria to induce less inflammation during chronic infections.H. pyloricauses a significant global disease burden, which is driven by the development of gastric inflammation. Accordingly, it is essential to understand the processes by whichH. pylorimodulates host inflammation. This work uncovers the signals that TlpA can sense and highlights the underappreciated ability for regulating chemotactic responses by antagonistic chemoreceptor ligands, which is an emerging theme among other chemotactic systems.
Engineering paralog-specific PSD-95 synthetic binders as potent and minimally invasive imaging probes
Authors: Rimbault Charlotte , Breillat Christelle , Compans Benjamin , Toulmé Estelle , Vicente Filipe Nunes , Fernandez-Monreal Monica , Mascalchi Patrice , Genuer Camille , Puente-Muñoz Virginia , Gauthereau Isabel , Hosy Eric , Giannone Gregory , Chamma Ingrid , Mackereth Cameron D. , Poujol Christel , Choquet Daniel , Sainlos Matthieu 
Published: April 2021

ABSTRACTDespite the constant advances in fluorescence imaging techniques, monitoring endogenous proteins still constitutes a major challenge in particular when considering dynamics studies or super-resolution imaging. We have recently evolved specific protein-based binders for PSD-95, the main postsynaptic scaffold proteins at excitatory synapses. Since the synthetic binders recognize epitopes not directly involved in the target protein activity, we consider them here as tools to develop endogenous PSD-95 imaging probes. After confirming their lack of impact on PSD-95 function, we validated their use as intrabody fluorescent probes. We further engineered the probes and demonstrated their usefulness in different super-resolution imaging modalities (STED, PALM and DNA-PAINT) in both live and fixed neurons. Finally, we exploited the binders to enrich at the synapse genetically encoded calcium reporters. Overall, we demonstrate that these evolved binders constitute a robust and efficient platform to selectively target and monitor endogenous PSD-95 using various fluorescence imaging techniques.
Thermal stress induces positive phenotypic and molecular feedback loops in zebrafish embryos
Authors: Feugere Lauric , Scott Victoria F. , Rodriguez-Barucg Quentin , Beltran-Alvarez Pedro , Wollenberg Valero Katharina C. 
Published: April 2021

AbstractAquatic organisms must cope with both rising and rapidly changing temperatures. These environmental changes can affect numerous traits, from molecular to ecological scales. Biotic stressors can induce the release of chemical cues which trigger behavioural responses in other individuals. In this study, we infer whether abiotic stressors, such as fluctuating temperature, may similarly propagate stress responses between individuals in fish not directly exposed to the stressor. To test this hypothesis, zebrafish (Danio rerio) embryos were exposed for 24 hours to fluctuating thermal stress, to medium in which another embryo was thermally stressed before (“stress medium”), and to a combination of these. Growth, behaviour, and expression of a panel of genes were used to characterise the thermal stress response and its propagation between embryos. Both high temperatures and stress medium significantly accelerated development and altered embryonic behaviour. Thermal stress significantly decreased the expression of the antioxidant gene SOD1, eight hours after the end of exposure. Of note, we found that the expression of sulfide:quinone oxidoreductase (SQOR), likewise a part of the antioxidant metabolism relevant in vertebrate stress response, and of interleukin-1β (IL-1β), involved in the immune response, were significantly altered by stress medium. This study illustrates the existence of positive thermal stress feedback loops in zebrafish embryos that induce stress in conspecifics. This evidence that thermal stress due to fluctuating, high temperatures can be propagated may be relevant for species found in high densities, either in aquaculture or in the natural environment, in a context of global change.
The human GID complex engages two independent modules for substrate recruitment
Authors: Mohamed Weaam I. , Park Sophia L. , Rabl Julius , Leitner Alexander , Boehringer Daniel , Peter Matthias 
Published: April 2021

AbstractThe human GID (hGID) complex is an evolutionary conserved E3 ubiquitin ligase regulating diverse biological processes including glucose metabolism and cell cycle progression. However, the biochemical function and substrate recognition of the multi-subunit complex remains poorly understood. While the yeast GID complex recognizes Pro/N-end rule substrates via yeast Gid4, the human GID complex requires a WDR26/Gid7-dependent module to trigger proteasomal degradation of mammalian HBP1. Here, using biochemical assays, crosslinking-mass spectrometry and cryo-electron microscopy, we show that hGID unexpectedly engages two distinct modules for substrate recruitment, dependent on either WDR26 or GID4. WDR26 together with RanBP9 cooperate to ubiquitinate HBP1in vitro, while GID4 is dispensable for this reaction. In contrast, GID4 functions as an adaptor for the substrate ZMYND19, which surprisingly lacks a Pro/N-end rule degron. GID4 substrate binding and ligase activity is regulated by ARMC8α, while the shorter ARMC8β isoform assembles into a stable hGID complex that is unable to recruit GID4. Cryo-EM reconstructions of these hGID complexes reveal the localization of WDR26 within a ring-like, tetrameric architecture and suggest that GID4 and WDR26/Gid7 utilize different, non-overlapping binding sites. Together, these data advance our mechanistic understanding of how the hGID complex recruits cognate substrates and provide insights into the regulation of its ligase activity.
On the Non-uniqueness Problem in Integrated Information Theory
Authors: Hanson Jake R. , Walker Sara I. 
Published: April 2021

AbstractIntegrated Information Theory is currently the leading mathematical theory of consciousness. The core of the theory relies on the calculation of a scalar mathematical measure of consciousness, Φ, which is deduced from the phenomenological axioms of the theory. Here, we show that despite its widespread use, Φ is not a well-defined mathematical concept in the sense that the value it specifies is neither unique nor specific. This problem, occasionally referred to as “undetermined qualia”, is the result of degeneracies in the optimization routine used to calculate Φ, which leads to ambiguities in determining the consciousness of systems under study. As demonstration, we first apply the mathematical definition of Φ to a simpleAND+ORlogic gate system and show 83 non-unique Φ values result, spanning a substantial portion of the range of possibilities. We then introduce a Python package calledPyPhi-Spectrumwhich, unlike currently available packages, delivers the entire spectrum of possible Φ values for a given system. We apply this to a variety of examples of recently published calculations of Φ and show how virtually all Φ values from the sampled literature are chosen arbitrarily from a set of non-unique possibilities, the full range of which often includes both conscious and unconscious predictions. Lastly, we review proposed solutions to this degeneracy problem, and find none to provide a satisfactory solution, either because they fail to specify a unique Φ value or yield Φ = 0 for systems that are clearly integrated. We conclude with a discussion of requirements moving forward for scientifically valid theories of consciousness that avoid these degeneracy issues.
Impact of ecotourism on abundance, diversity and activity pattern of medium-large terrestrial mammals at Brownsberg Nature Park, Suriname
Authors: Ouboter Dimitri A. , Kadosoe Vanessa S. , Ouboter Paul E. 
Published: April 2021

AbstractThe impacts of ecotourism on biodiversity are poorly understood and the outcome of research is often contradictory. On the one hand ecotourism could impact the occurrence, survival or behavior of species, on the other hand ecotourism is often mentioned as providing a “human shield” by deterring negative practices like gold mining, logging and hunting.Brownsberg Nature Park is easily the most visited protected area of Suriname, with a high number of ecotourists visiting from abroad. A four-year study on the impact of ecotourism on medium-large terrestrial mammals was carried out between 2013 and 2016 using 16 camera trapping stations. The area has a clear gradient of tourism pressure, with the pressure decreasing further away from the lodging facilities. Evidently, the impacts of human presence on the mammal communities were more significant in the busiest areas. Most species avoided areas with many hikers or switched to a more nocturnal activity pattern. In these areas the impact was not reflected in species numbers, however it was causing a significant lowering of the diversity of mammals. On the other hand, vehicles had little impact on species avoidance or diversity, but did increase nocturnality even more than hikers. A few species seemed to be “attracted” by hikers and/or traffic. Giant armadillos and spotted pacas used the pools in the road created by traffic. Ocelots, margays and red-rumped agoutis seemed to favor human disturbance probably because of predator release. Some of the most impacted species were the jaguar, puma and lowland tapir, all three species with significant contribution to ecosystem balance. Their avoidance or even disappearance from highly human frequented areas could easily result in ecosystem changes in these areas. Management measures should focus on lowering the number of hikers in popular places and limiting the number of vehicles in recreational or tourist areas.