bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying rhythmicity in perceptual reports
Authors: Tosato Tommaso , Rohenkohl Gustavo , Dowdall Jarrod Robert , Fries Pascal 
Published: May 2022

AbstractSeveral recent studies investigated the rhythmic nature of cognitive processes that lead to perception and behavioral report. These studies used different methods, and there has not yet been an agreement on a general standard. Here, we present a way to test and quantitatively compare these methods. We simulated behavioral data from a typical experiment and analyzed these data with several methods. We applied the main methods found in the literature, namely sine-wave fitting, the Discrete Fourier Transform (DFT) and the Least Square Spectrum (LSS). DFT and LSS can be applied both on the averaged accuracy time course and on single trials. LSS is mathematically equivalent to DFT in the case of regular, but not irregular sampling - which is more common. LSS additionally offers the possibility to take into account a weighting factor which affects the strength of the rhythm, such as arousal. Statistical inferences were done either on the investigated sample (fixed-effect) or on the population (random-effect) of simulated participants. Multiple comparisons across frequencies were corrected using False-Discovery-Rate, Bonferroni, or the Max-Based approach. To perform a quantitative comparison, we calculated Sensitivity, Specificity and D-prime of the investigated analysis methods and statistical approaches. Within the investigated parameter range, single-trial methods had higher sensitivity and D-prime than the methods based on the averaged-accuracy-time-course. This effect was further increased for a simulated rhythm of higher frequency. If an additional (observable) factor influenced detection performance, adding this factor as weight in the LSS further improved Sensitivity and D-prime. For multiple comparison correction, the Max-Based approach provided the highest Specificity and D-prime, closely followed by the Bonferroni approach. Given a fixed total amount of trials, the random-effect approach had higher D-prime when trials were distributed over a larger number of participants, even though this gave less trials per participant. Finally, we present the idea of using a dampened sinusoidal oscillator instead of a simple sinusoidal function, to further improve the fit to behavioral rhythmicity observed after a reset event.
Single molecule analyses of Salmonella translocated effector proteins reveal targeting to and dynamics in host cell endomembranes
Authors: Göser Vera , Schulte Marc , Scharte Felix , Franzkoch Rico , Liss Viktoria , Psathaki Olympia E. , Hensel Michael 
Published: May 2022

AbstractBacterial pathogens deliver proteins in temporal and spatial coordinated manner to manipulate mammalian host cells. The facultative intracellular pathogen Salmonella enterica remodels the host endosomal system for survival and proliferation inside host cells. The pathogen resides in a membrane-bound compartment termed Salmonella-containing vacuole (SCV). By Salmonella- induced fusions of host endomembranes, the SCV is connected with extensive tubular structures termed Salmonella-induced filaments (SIF). The intracellular lifestyle of Salmonella critically depends on effector molecules translocated by the SPI2-encoded type III secretion system (SPI2-T3SS) into host cells. A subset of these effectors is associated with, or integral in SCV and SIF membranes. It remained to be determined how SPI2-T3SS effectors reach their subcellular destination, and how these effectors interact with endomembranes remodeled by Salmonella. We deployed self-labeling enzyme (SLE) tags as novel approach to label translocated effector proteins in living host cells, and analyzed their dynamics on single molecule level. We found that SPI2-T3SS effector proteins diffuse in membranes of SIF with mobility comparable to membrane-integral host proteins in endomembranes. Dynamics differed between various effector proteins investigated and was dependent on membrane architecture of SIF. In the early infection, we observed host endosomal vesicles associated with Salmonella effector proteins. Effector-positive vesicles continuously fused with SCV and SIF membranes, providing a route of effector delivery by SPI2-T3SS translocation, interaction with endosomal vesicles, and ultimately fusion with the continuum of SCV/SIF membranes. This novel mechanism controls membrane deformation and vesicular fusion to generate the specific intracellular niche for bacterial survival and proliferation.
Does sexual conflict contribute to the evolution of novel warning patterns?
Authors: Hausmann Alexander E. , Freire Marília , Alfthan Sara A. , Kuo Chi-Yun , Linares Mauricio , McMillan Owen , Pardo-Diaz Carolina , Salazar Camilo , Merrill Richard M. 
Published: May 2022

AbstractWhy warning patterns are so diverse is an enduring evolutionary puzzle. Because predators associate particular patterns with unpleasant experiences, an individual’s predation risk should decrease as the local density of its warning pattern increases, promoting pattern monomorphism. DistastefulHeliconiusbutterflies are known for their diversity of warning patterns. Here, we explore whether interlocus sexual conflict can contribute to their diversification. MaleHeliconiususe warning patterns as mating cues, but mated females may suffer costs if this leads to harassment, favoring novel patterns. Using simulations, we show that drift alone is unlikely to cause pattern diversification, but that sexual conflict can assist such process. We also find that genetic architecture influences the evolution of male preferences, which track changes in warning pattern due to sexual selection. When male attraction imposes costs on females, this affects the speed at which novel pattern alleles increase. In two experiments, females laid fewer eggs with males present. However, although males in one experiment showed less interest in females with manipulated patterns, we found no evidence that female coloration mitigates sex-specific costs. Overall, male attraction to conspecific warning patterns may impose an unrecognized cost onHeliconiusfemales, but further work is required to determine this experimentally.
Knockouts of positive and negative elements of the circadian clock disrupt photoperiodic diapause induction in the silkworm,Bombyx mori
Authors: Tobita Hisashi , Kiuchi Takashi 
Published: May 2022

AbstractDiapause is one of the most important traits that have sustained insects to thrive. Insects can prospectively arrest their development and increase environmental stress-resistance by entering diapause. The photoperiod is the signal that indicates insects the proper timing to enter diapause. Circadian clock genes are shown to be involved in photoperiodic diapause induction in various insect species. The silkworm,Bombyx mori, enters diapause at the embryonic stage. In bivoltine strains, diapause determination is affected by embryonic temperature and photoperiodic conditions during embryonic and larval stages. Two independent studies showed that knocking out the core clock gene,period, perturb photoperiodic diapause induction. However, whether the circadian clock as whole or individual clock genes are responsible for the photoperiodic diapause induction remains unknown. In this study, using CRISPR/Cas9 we knocked out negative (periodandtimeless) and positive elements (Clockandcycle) in p50T, a bivoltine strain which exhibits photoperiodic diapause induction during both embryonic and larval stages. The temporal expression patterns of clock genes changed in each core clock gene knockout strain, suggesting disruption of normal feedback loops produced by circadian clock genes. Furthermore, photoperiodic diapause induction during both embryonic and larval stages was lost in all knockout strains. Our results indicate the involvement of circadian clock in photoperiodic diapause induction inB. mori.HighlightsWe established knockoutBombyx moristrains of four core clock genesThe temporal expression patterns of clock genes changed in knockout strainsPhotoperiodic diapause induction was not observed in any knockout strainsGraphical abstract
Recalibrating the cerebellum DNA methylation clock: implications for ageing rates comparison
Authors: Wang Yucheng , Grant Olivia A. , Zhai Xiaojun , McDonald-Maier Klaus D. , Schalkwyk Leonard C. 
Published: May 2022

BackgroundDNA methylation (DNAm) based age clocks have been studied extensively as a biomarker of human ageing and risk factor for age-related diseases. Despite different tissues having vastly different rates of proliferation, it is still largely unknown whether they age at different rates. It was previously reported that the cerebellum ages slowly, however, this claim was drawn from a single clock using a small sample size and so warrants further investigation.ResultsWe collected the largest cerebellum DNAm dataset (N=752). We found the respective epigenetic ages are all severely underestimated by six representative DNAm age clocks, with the underestimation effects more pronounced in the four clocks whose training datasets do not include brain-related tissues. We identified 613 age-associated CpGs in the cerebellum, which accounts for only 14.5% of the number found in the middle temporal gyrus from the same population (N=404), of which only 201 CpGs are both age-associated in the two tissue types. We built a highly accurate age prediction model for the cerebellum named CerebellumClockspecific(Pearson correlation=0.941, MAD=3.18 years). Furthermore, based on the 201 age-associated CpGs, we built two other clocks CerebellumClockcommonand CortexClockcommonfor the cerebellum and non-cerebellar brain cortex tissues separately, they both support that the cerebellum has a relative lower DNAm ageing rate.ConclusionsThe large underestimation for the cerebellum by previous clocks mainly reflects the improper usage of the age clocks. There exist strong and consistent ageing effects on the cerebellar methylome despite the cerebellum having unique age-dependent methylome changes. The DNAm clock based ageing rates comparisons are valid only upon models constructed on a small group of CpGs, therefore, more evidence is required to support the idea that different DNAm ageing rates represent different biological ageing rates.
Evaluating trait-based sets for taxonomic enrichment analysis applied to human microbiome data sets
Authors: Nguyen Quang P. , Hoen Anne G. , Frost H. Robert 
Published: May 2022

AbstractBackgroundSet-based pathway analysis is a powerful tool that allows researchers to summarize complex genomic variables in the form of biologically interpretable sets. Since the microbiome is characterized by a high degree of inter-individual variability in taxonomic compositions, applying enrichment methods using functionally driven taxon sets can increase both the reproducibility and interpretability of microbiome association studies. However, there is still an open question of which knowledge base to utilize for set construction. Here, we evaluate microbial trait databases, which aggregate experimentally determined microbial phenotypes, as a potential avenue for meaningful construction of taxon sets.MethodUsing publicly available microbiome sequencing data sets (both 16S rRNA gene metabarcoding and whole-genome metagenomics), we assessed these trait-based sets on two criteria: first, do they cover the diversity of microbes obtained from a typical data set, and second, do they confer additional predictive power on disease prediction tasks when assessed against measured pathway abundances and PICRUSt2 prediction.ResultsTrait annotations are well annotated to a small number but most abundant taxa within the community, concordant with the concept of the core-peripheral microbiome. This pattern is consistent across all categories of traits and body-sites for whole genome sequencing data, but much more heterogenous and inconsistent in 16S rRNA metabarcoding data due to difficulties in assigning species-level traits to genus. However, trait-set features are well predictive of disease outcomes compared against predicted and measured pathway abundances. Most important trait-set features are more interpreable and reveal interesting insights on the relationship between microbiome, its function, and health outcomes.
Differential Evasion of Delta and Omicron Immunity and Enhanced Fusogenicity of SARS-CoV-2 Omicron BA.4/5 and BA.2.12.1 Subvariants
Authors: Qu Panke , Faraone Julia N. , Evans John P. , Zou Xue , Zheng Yi-Min , Carlin Claire , Bednash Joseph S. , Lozanski Gerard , Mallampalli Rama K. , Saif Linda J. , Oltz Eugene M. , Mohler Peter J. , Gumina Richard J. , Liu Shan-Lu 
Published: May 2022

SummaryThe rising case numbers of the SARS-CoV-2 Omicron BA.4, BA.5, and BA.2.12.1 subvariants has generated serious concern about the course of the pandemic. Here we examine the neutralization resistance, infectivity, processing, and fusogenicity of spike from the BA.4/5 and BA.2.12.1 SARS-CoV-2 variants compared with other Omicron subvariants and Delta. Critically, we found that the new Omicron subvariants BA.4/5 and BA.2.12.1 were more resistant to neutralization by mRNA-vaccinated and boosted health care worker sera and Omicron-BA.1-wave patient sera than were the BA.1 and BA.2 variants. Interestingly, Delta-wave patient sera neutralized more efficiently against not only Delta but also BA.4/5 and BA.2.12.1 variants that also contain substitutions at position L452, similar to Delta. The BA.4/5 and BA.2.12.1 variants also exhibited higher fusogenicity, and increased spike processing, dependent on the L452 substitution. These results highlight the key role of the L452R and L452Q mutations in BA.4/5 and BA.2.12.1 subvariants.
A study of a diauxic growth experiment using an expanded dynamic flux balance framework
Authors: Karlsen Emil , Gylseth Marianne , Schulz Christian , Almaas Eivind 
Published: May 2022

AbstractFlux balance analysis (FBA) remains one of the most used methods for modeling the entirety of cellular metabolism, and a range of applications and extensions based on the FBA framework have been generated. Dynamic flux balance analysis (dFBA), the expansion of FBA into the time domain, still has issues regarding accessibility limiting its widespread adoption and application, such as a lack of a consistently rigid formalism and tools that can be applied without expert knowledge. Recent work has combined dFBA with enzyme-constrained flux balance analysis (decFBA), which has been shown to greatly improve accuracy in the comparison of computational simulations and experimental data, but such approaches generally do not take into account the fact that altering the enzyme composition of a cell is not an instantaneous process.Here, we have developed a decFBA method that explicitly takes enzyme change constraints (ecc) into account, decFBAecc. The resulting software is a simple yet flexible framework for using genome-scale metabolic modeling for simulations in the time domain that has full interoperability with COBRA toolbox 3.0. To assess the quality of the computational predictions of decFBAecc, we conducted a diauxic growth fermentation experiment with Escherichia coli BW2523 in glucose minimal M9 medium. The comparison of experimental data with dFBA, decFBA and decFBAecc predictions demonstrates how systematic analyses within a fixed constraint-based framework can aid the study of model parameters.Finally, in explaining experimentally observed phenotypes, our computational analysis also demonstrates the importance of non-linear dependence of exchange fluxes on medium metabolite concentrations and the non-instantaneous change in enzyme composition, effects of which have not previously been accounted for in constraint-based analysis.
COR27/28 Regulate the Evening Transcriptional Activity of the RVE8-LNK1/2 Circadian Complex
Authors: Sorkin Maria L. , Tzeng Shin-Cheng , Romanowski Andrés , Kahle Nikolai , Bindbeutel Rebecca , Hiltbrunner Andreas , Yanovsky Marcelo J. , Evans Bradley S. , Nusinow Dmitri A. 
Published: May 2022

AbstractThe timing of many molecular and physiological processes in plants occurs at a specific time of day. These daily rhythms are driven by the circadian clock, a master timekeeper that uses daylength and temperature to maintain rhythms of approximately 24 hours in various clock-regulated phenotypes. The circadian MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its transcriptional coactivators NIGHT LIGHT INDUCIBLE AND CLOCK REGULATED 1 (LNK1) and LNK2 to promote the expression of evening-phased clock genes and cold tolerance factors. While genetic approaches have commonly been used to discover new connections within the clock and between other pathways, here we use affinity purification coupled with mass spectrometry to discover time-of-day-specific protein interactors of the RVE8-LNK1/2 complex. Among the interactors of RVE8/LNK1/LNK2 were COLD REGULATED GENE 27 (COR27) and COR28, which were coprecipitated in an evening-specific manner. In addition to COR27/28, we found an enrichment of temperature-related interactors that led us to establish a novel role for LNK1/2 in temperature entrainment of the clock. We established that RVE8, LNK1, and either COR27 or COR28 form a tripartite complex in yeast and that the effect of this interaction in planta serves to antagonize transcriptional activation of RVE8 target genes through mediating RVE8 protein degradation in the evening. Together, these results illustrate how a proteomic approach identified time-of-day-specific protein interactions and a novel RVE8-LNK-COR protein complex that implicates a new regulatory mechanism for circadian and temperature signaling pathways.
A plastidial DEAD box RNA helicase plays a critical role in high light acclimation by modulating ribosome biogenesis inChlamydomonas reinhardtii
Authors: Djouani-Tahri El Batoul , Nellaepalli Sreedhar , Auroy Pascaline , Billon Emmanuelle , Burlacot Adrien , Chaux-Jukic Frédéric , Cuiné Stéphan , Epting Virginie , Huleux Marie , Ghysels Bart , Schulz-Raffelt Miriam , Te Isabelle , Brugière Sabine , Couté Yohann , Takahashi Yuichiro , Li-Beisson Yonghua , Peltier Gilles 
Published: May 2022

ABSTRACTPhotosynthetic organisms have developed sophisticated strategies to fine-tune light energy conversion to meet the metabolic demand, thereby optimizing growth in fluctuating light environments. Although mechanisms such as energy dissipation, photosynthetic control, or the photosystem II (PSII) damage and repair have been widely studied, little is known about the regulation of protein synthesis capacity during light acclimation. By screening aChlamydomonas reinhardtiiinsertional mutant library using chlorophyll fluorescence imaging, we isolated a high chlorophyll fluorescence mutant (hf0) defected in a gene encoding a putative plastid targeted DEAD-box RNA helicase called CreRH22. CreRH22 is rapidly induced upon illumination and belongs to the GreenCut, a set of proteins specific to photosynthetic organisms. While photosynthesis is slightly affected in the mutant under low light (LL), exposure to high light (HL) induces a marked decrease in both PSII and PSI, and a strong alteration of the light-induced gene expression pattern. These effects are explained by the inability ofhf0to increase plastid ribosome amounts under HL. We conclude that CreRH22, by promoting ribosomal RNA precursor maturation in a light-dependent manner, enables the assembly of extra-ribosomes required to synthesize photosystem subunits at a higher rate, a critical step in the acclimation of algae to HL.
Carbon footprint of South Dakota dairy production system and assessment of mitigation options
Authors: Naranjo Anna M. , Sieverding Heidi , Clay David , Kebreab Ermias 
Published: May 2022

AbstractLivestock production contributes to greenhouse gas (GHG) emissions. However, there is a considerable variability in the carbon footprint associated with livestock production. Site specific estimates of GHG emissions are needed to accurately focus GHG emission reduction efforts. A holistic approach must be taken to assess the full environmental impact of livestock production using appropriate geographical scale. The objective of this study was to determine baseline GHG emissions from dairy production in South Dakota using a life cycle assessment (LCA) approach. A cradle-to-farm gate LCA was used to estimate the GHG emissions to produce 1 kg of energy-and-protein corrected milk (ECM) in South Dakota. The system boundary was divided into feed production, farm management, enteric methane emissions, and manure management as these activities are the main contributors to the overall GHG emissions. The production of 1 kg ECM in South Dakota dairies was estimated to emit 1.21 kg CO2 equivalents. The major contributors were enteric methane emissions (46.3%) and manure management (32.6%). Feed production and farm management made up 13.9 and 7.2 %, respectively. The estimate was similar to the national average but slightly higher than the California dairy system. The source of corn used in the dairies influences the footprint. For example, South Dakota corn had fewer GHG emissions than grain produced in Iowa. Therefore, locally and more sustainably sourced feed input will contribute to further reducing the environmental impacts. Improvements in efficiency of milk production through better genetics, nutrition animal welfare and feed production are expected to further reduce the carbon footprint of South Dakota dairies. Furthermore, use of feed additives and anaerobic digesters will reduce emissions from enteric and manure sources, respectively.
Second-generation transfer mediates efficient propagation of ICEBs1 in biofilms
Authors: Bourassa Jean-Sébastien , Jeannotte Gabriel , Lebel-Beaucage Sandrine , Beauregard Pascale B. 
Published: May 2022

AbstractHorizontal gene transfer (HGT) by integrative and conjugative elements (ICEs) is an important mechanism in the spread of antibiotic resistance genes. However, little is known about the spatiotemporal dynamic of ICEs propagation in bacterial biofilms, which are multicellular structures ubiquitous in the natural and clinical environment. Using a fluorescently marked ICEBs1, we report here that its propagation in biofilms is favored in recipient cells expressing the biofilm matrix. Also, conjugation appears restricted to clusters of bacteria in a close neighborhood in which a high level of ICEBs1 transfer occurs. These conjugative clusters are heterogenously distributed in the biofilm, forming close to the air-biofilm interface. Importantly, we established that transconjugant cells are the main contributors to ICEBs1 propagation in biofilms. Our findings provide a novel spatiotemporal understanding of ICEs propagation in biofilms, which should have an important role in our understanding of horizontal gene transfer in relevant settings.ImportanceThe transfer of mobile genetic elements between bacteria is the main cause of the spread of antibiotic resistance genes. While biofilms are the predominant bacterial lifestyle both in the environment and in clinical settings, their impact on the propagation of mobile genetic elements is still poorly understood. In this study, we examined the spatiotemporal propagation of the well-characterized integrative and conjugative element (ICE) ICEBs1. Using the Gram-positive B. subtilis, we observed that the main actors of ICEBs1 propagation in biofilms are the newly formed transconjugants that allow rapid transfer of ICEBs1 to new recipients. Our study provides a better understanding of the spatiotemporal dynamic of conjugative transfer in biofilms.