bluuebunny/crossref_metadata_2025_split huggingface dataset:
Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics
Authors: Kumler William , Hazelton Bryna J. , Ingalls Anitra E. 
Published: July 2023

AbstractBackgroundChromatographic peakpicking continues to represent a significant bottleneck in automated LC-MS workflows. Uncontrolled false discovery rates and the lack of manually-calibrated quality metrics require researchers to visually evaluate individual peaks, requiring large amounts of time and breaking replicability. This problem is exacerbated in noisy environmental datasets and for novel separation methods such as hydrophilic interaction columns in metabolomics, creating a demand for a simple, intuitive, and robust metric of peak quality.ResultsHere, we manually labeled four HILIC oceanographic particulate metabolite datasets to assess the performance of individual peak quality metrics. We used these datasets to construct a predictive model calibrated to the likelihood that visual inspection by an MS expert would include a given mass feature in the downstream analysis. We implemented two novel peak quality metrics, a custom signal-to-noise metric and a test of similarity to a bell curve, both calculated from the raw data in the extracted ion chromatogram and found that these outperformed existing measurements of peak quality. A simple logistic regression model built on two metrics reduced the fraction of false positives in the analysis from 70-80% down to 1-5% and showed minimal overfitting when applied to novel datasets. We then explored the implications of this quality thresholding on the conclusions obtained by the downstream analysis and found that while only 10% of the variance in the dataset could be explained by depth in the default output from the peakpicker, approximately 40% of the variance was explained when restricted to high-quality peaks alone.ConclusionsWe conclude that the poor performance of peakpicking algorithms significantly reduces the power of both univariate and multivariate statistical analyses to detect environmental differences. We demonstrate that simple models built on intuitive metrics and derived from the raw data are more robust and can outperform more complex models when applied to new data. Finally, we show that in properly curated datasets, depth is a major driver of variability in the marine microbial metabolome and identify several interesting metabolite trends for future investigation.
Virus-derived circular RNAs populate hepatitis C virus-infected cells
Authors: Cao Qian , Boonchuen Pakpoom , Chen Tzu-Chun , Lei Shaohua , Somboonwiwat Kunlaya , Sarnow Peter 
Published: July 2023

SummaryIt is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a back- splicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into novel proteins that displayed pro-viral functions. Furthermore, a highly abundant, non-translated vcircRNA was shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus.Significance StatementProcessing of an RNA viral genome into hundreds of circular RNAs provides novel pro-viral functions and can promote translation of novel viral peptides.
Surface crosslinking of virus-like particles increases resistance to proteases, low pH, and mechanical stress for mucosal applications
Authors: Ali Ahmed , Ganguillet Suwannee , Turgay Yagmur , Keys Tim , Causa Erika , Fradique Ricardo , Lutz-Bueno Viviane , Chesnov Serge , Lin Chia-wei , Lentsch Verena , Kotar Jurij , Cicuta Pietro , Mezzenga Raffaele , Slack Emma , Radiom Milad 
Published: July 2023

AbstractVirus-like particles (VLPs) are emerging as nano-scaffolds in a variety of biomedical applications including the delivery of vaccine antigens to mucosal surfaces. These soft, colloidal, and proteinaceous structures (capsids) are nevertheless susceptible to mucosal environmental factors which limit their usefulness. We addressed this issue by crosslinking multiple capsid surface reactive residues using polyethylene glycol tethers. Surface crosslinking enhanced the colloidal stability and mechanical strength of VLPs against low pH, proteases, and mechanical agitation, while it did not interfere with function as vaccine. Chemical crosslinking thus offers a viable means to enhance the resilience of VLPs in mucosal applications.
AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein
Authors: Guo Hao-Bo , Huntington Baxter , Perminov Alexander , Smith Kenya , Hastings Nicholas , Dennis Patrick , Kelley-Loughnane Nancy , Berry Rajiv 
Published: July 2023

AbstractWe use AlphaFold2 (AF2) to model the monomer and dimer structures of an intrinsically disordered protein (IDP),Nvjp-1, assisted by molecular dynamics (MD) simulations. We observe relatively rigid dimeric structures ofNvjp-1when compared with the monomer structures. We suggest that protein conformations from multiple AF2 models and those from MD trajectories exhibit a coherent trend: the conformations of an IDP are deviated from each other and the conformations of a well-folded protein are consistent with each other. We use a residue-residue interaction network (RIN) derived from the contact map which show that the residue-residue interactions inNvjp-1are mainly transient; however, those in a well-folded protein are mainly persistent. Despite the variation in 3D shapes, we show that the AF2 models of both disordered and ordered proteins exhibit highly consistent profiles of the pLDDT (predicted local distance difference test) scores. These results indicate a potential protocol to justify the IDPs based on multiple AF2 models and MD simulations.The TOC figure:
Effect of a topically applied gel containing antibodies from bovine milk on the relative abundance of Staphylococci in the canine skin microbiome
Authors: Klaassens Eline S. , Auxilia Silvia , Baak Mirna L. , Bongoni Radhika , van Damme Catharina M.M. , Bijker Sannah , Dietz Nardy , Winter Esther , Broere Femke , Foerster Beatrix 
Published: July 2023

AbstractCanine pyoderma is characterised by a predominant colonisation of the skin withStaphylococcus pseudintermediusand inflammatory symptoms associated with it. Immunoglobulins isolated from cow’ ss milk are neutralizing virulence factors and toxins ofS. pseudintermedius. In a pilot study with four dogs with pyoderma we were able to show that the application of immunoglobulin gel leads to a decrease in the staphylococcal population and an increase in the diversity of the skin microbiome.Due to the limited number of animals, the measurable effect is not statistically significant. Therefore, we are planning a follow-up study that includes more animals.
Machine learning assisted health viability assay for mouse embryos with artificial confocal microscopy (ACM)
Authors: Goswami Neha , Winston Nicola , Choi Wonho , Lai Nastasia Z. E. , Arcanjo Rachel B. , Chen Xi , Sobh Nahil , Nowak Romana A. , Anastasio Mark A. , Popescu Gabriel 
Published: July 2023

AbstractThe combination of a good quality embryo and proper maternal health factors promise higher chances of a successful in vitro fertilization (IVF) procedure leading to clinical pregnancy and live birth. Of these two factors, selection of a good embryo is a controllable aspect. The current gold standard in clinical practice is visual assessment of an embryo based on its morphological appearance by trained embryologists. More recently, machine learning has been incorporated into embryo selection “packages”. Here, we report a machine-learning assisted embryo health assessment tool utilizing a quantitative phase imaging technique called artificial confocal microscopy (ACM). We present a label-free nucleus detection method with novel quantitative embryo health biomarkers. Two viability assessment models are presented for grading embryos into two classes: healthy/intermediate (H/I) or sick (S) class. The models achieve a weighted F1 score of 1.0 and 0.99 respectively on the in-distribution test set of 72 fixed embryos and a weighted F1 score of 0.9 and 0.95 respectively on the out-of-distribution test dataset of 19 time-instances from 8 live embryos.
Intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase dependent mechanism
Authors: Gilsbach Bernd K. , Ho Franz Y. , Riebenbauer Benjamin , Zhang Xiaojuan , Guaitoli Giambattista , Kortholt Arjan , Gloeckner Christian Johannes 
Published: August 2023

AbstractThe Parkinson’s Disease (PD)-linked protein Leucine Rich Repeat Kinase 2 (LRRK2) consists of seven domains, including a kinase and a Roc G domain. Despite the availability of several high-resolution structures, the dynamic regulation of its unique intramolecular domain stack is nevertheless still not well understood. By in-depth biochemical analysis, assessing the Michaelis-Menten kinetics of the Roc G domain, we have confirmed that LRRK2 has, similar to other Roco protein family members, a KMvalue of LRRK2 that lays within the range of the physiological GTP concentrations within the cell. Furthermore, the R1441G PD variant located within a mutational hotspot in the Roc domain showed an increased catalytic efficiency. In contrast, the most common PD variant G2019S, located in the kinase domain, showed an increased KMand reduced catalytic efficiency, suggesting a negative feedback mechanism from the kinase domain to the G domain. Autophosphorylation of the G1+2 residue (T1343) in the Roc P-loop motif is critical for this phosphoregulation of both the KMas well as the kcatvalues of the Roc-catalyzed GTP hydrolysis, most likely by changing the monomer-dimer equilibrium. The LRRK2 T1343A variant has a similar increased kinase activity in cells compared to G2019S and the double mutant T1343A/G2019S has no further increased activity suggesting that T1343 is crucial for the negative feedback in the LRRK2 signaling cascade. Together our data reveal a novel intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase dependent mechanism. Interestingly, PD mutants differently change the kinetics of the GTPase cycle, which might in part explain the difference in penetrance of these mutations in PD patients.
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
Authors: Meijer Jeroen , Skiadas Petros , Rainey Paul B. , Hogeweg Paulien , Dutilh Bas E. 
Published: August 2023

AbstractBacteriophages are important drivers of microbial ecosystems, but their influence and dynamics in terrestrial biomes remain poorly understood compared to aquatic and host-associated systems. To investigate this, we analyzed shotgun metagenomics datasets from ten compost-derived microbial communities propagated over 48 weeks. We found that the communities clustered into two distinct types consisting of hundreds of microbial genera, and in one community type identified Theomophage, a lytic bacteriophage representing a newSchitoviridaesubfamily, which accounted for up to 74.3% of the total community metagenome, indicating massive viral outbreaks. We tracked molecular evolution of Theomophage and found that isolated communities were dominated by a single strain that showed little molecular evolution during outbreaks. However, when experimental manipulation allowed phages to migrate between communities, we observed transient coexistence of strains followed by genomic recombination that underpinned replacement of the ancestral strains. Additionally, when Theomophage colonized mesocosms where it was originally absent, new mutations evolved that fixed and spread to other communities. Our study describes the largest bacteriophage outbreak reported to date and reveals the spatial and temporal scales at which terrestrial bacteriophage microdiversity evolves. It also demonstrates that mixing of viral communities, which may be frequent in natural systems, promotes rapid bacteriophage evolution.Significance StatementTerrestrial viral ecology and evolution is an active research area, but current knowledge on soil viruses still lags behind that of other biomes, and the terrestrial microbiome harbors untapped viral diversity. This study describes parallel, massive outbreaks of a novel bacteriophage in a 48- week evolution experiment with compost-derived microbial communities. The unprecedented abundance of this bacteriophage highlights the importance of accounting for viral sequences – which may be challenging to identify and annotate – when analyzing community sequence data. Moreover, we show how dispersal accelerates the dynamics of molecular evolution on a timescale of weeks. These results advance understanding of the spatiotemporal scales at which bacteriophage eco-evolutionary dynamics play out in terrestrial biomes.
Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP
Authors: Pulsford Sacha B. , Outram Megan A. , Förster Britta , Rhodes Timothy , Williams Simon J. , Badger Murray R. , Price G. Dean , Jackson Colin J. , Long Benedict M. 
Published: August 2023

ABSTRACTCyanobacterial CO2concentrating mechanisms (CCMs) sequester a globally significant proportion of carbon into the biosphere. Proteinaceous microcompartments, called carboxysomes, play a critical role in CCM function, housing two enzymes to enhance CO2fixation: carbonic anhydrase (CA) and Rubisco. Despite its importance, our current understanding of the carboxysomal CAs found in ɑ-cyanobacteria, CsoSCA, remains limited, particularly regarding the regulation of its activity. Here, we present the first structural and biochemical study of CsoSCA from the cyanobacteriumCyanobium PCC7001. Our results show that theCyanobiumCsoSCA is allosterically activated by the Rubisco substrate ribulose-1,5-bisphosphate (RuBP), and forms a hexameric trimer of dimers. Comprehensive phylogenetic and mutational analyses are consistent with this regulation appearing exclusively in cyanobacterial ɑ-carboxysome CAs. These findings clarify the biologically relevant oligomeric state of α-carboxysomal CAs and advance our understanding of the regulation of photosynthesis in this globally dominant lineage.One-Sentence SummaryThe carboxysomal carbonic anhydrase, CsoSCA, is allosterically activated by the Rubisco substrate RuBP, revealing a novel mechanism controlling key enzyme activity in cyanobacterial α-carboxysomes.
Wolbachiaeffects on thermal preference of naturalDrosophila melanogasterare influenced by host genetic background,Wolbachiatype and bacterial titer
Authors: Strunov Anton , Schoenherr Charlotte , Kapun Martin 
Published: August 2023

SummaryTemperature plays a fundamental role for the fitness of all organisms. In particular, it strongly affects metabolism and reproduction in ectotherms that have limited physiological capabilities to regulate their body temperature. Ectotherms thus have to maintain thermal homeostasis by behavioral adjustments. The influence of temperature variation on the physiology and behavior of ectotherms is well studied but we still know little about the influence of symbiotic interactions on thermal preference (Tp) of the host. TheWolbachia-Drosophilahost-symbiont system represents an ideal model for addressing these questions. A growing number of studies demonstrated that differentWolbachiatypes can influenceTpin differentDrosophilaspecies, but these results may be confounded by the use of long-termDrosophilalab-strains that may not be representative for natural fly populations. To account for this, we investigated the effect ofWolbachiaonTpin wild-typeD. melanogasterflies recently collected from nature. Consistent with previous data, we found reducedTpcompared to an uninfected control in one of two fly strains infected with the wMelCSWolbachiatype. Additionally, we, for the first time, found thatWolbachiatiter variation influences thermal preference of the host fly. These data indicate that the interaction ofWolbachiaandDrosophilaresulting in behavioral variation is complex and strongly influenced by the genetic background of host and symbiont. Our results further emphasize the necessity for more in-depth studies to better understand the evolutionary significance ofTpvariation influenced byWolbachiain naturalDrosophilapopulations.
Omics driven onboarding of the carotenoid producing red yeastXanthophyllomyces dendrorhousCBS 6938
Authors: Tobin Emma E. , Collins Joseph H. , Marsan Celeste B. , Nadeau Gillian T. , Mori Kim , Lipzen Anna , Mondo Stephen , Grigoriev Igor V. , Young Eric M. 
Published: August 2023

ABSTRACTTranscriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Genetic part discovery has never been more necessary, as advances in synthetic biology increase the number of tractable organisms that need tunable gene expression for genetic circuits and metabolic pathways. Therefore, approaches are needed to assess a tractable organism and obtain a convenient set of genetic parts to support future research. Here, we describe a genomic and transcriptomic approach to derive a modular integrative part library with constitutive and regulated promoters in the basidiomycete yeast Xanthophyllomyces dendrorhous CBS 6938. X. dendrorhous is currently the sole biotechnologically relevant organism in the Tremellomycete family - it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Particularly for this yeast, there are not large libraries of parts from related organisms that could be transferred. They must be derived. To do this, a contiguous genome was first obtained through combined short read and long read sequencing. Then, differential gene expression (DGE) analysis using transcriptomics was performed, comparing oxidative stress and exposure to different wavelengths of light. This revealed a set of putative light-responsive regulators that mediate a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was then used to derive 26 constitutive and regulated gene expression elements from the genome. The gene expression elements were designed to be compatible with a new modular cloning system for X. dendrorhous which includes integration sites, terminators, selection markers, and reporters. Each element was characterized by luciferase assay of an integrated gene expression cassette. Notably, a novel promoter from a hypothetical gene that has 9-fold activation upon UV exposure was characterized. This study defines an advanced modular genetic part collection for engineering the basidiomycete X. dendrorhous CBS 6938 while simultaneously discovering potential targets for increasing tetraterpenoid biosynthesis. Further, it demonstrates that -omics-to-parts workflows can simultaneously provide useful genomic data and advance genetic tools for nonconventional microbes, particularly those without a related model organism. This approach will be broadly useful in current efforts to engineer diverse microbes.KEY POINTSOmics-to-parts can be applied to non-model organisms for rapid “onboarding”.26 promoters native toX. dendrorhouswere identified.Omics revealed unique photobiology inX. dendrorhous.
Monitoring of drought stress and transpiration rate using proximal thermal and hyperspectral imaging in an indoor automated plant phenotyping platform
Authors: Mertens Stien , Verbraeken Lennart , Sprenger Heike , De Meyer Sam , Demuynck Kirin , Cannoot Bernard , Merchie Julie , De Block Jolien , Vogel Jonathan , Bruce Wesley , Nelissen Hilde , Maere Steven , Inzé Dirk , Wuyts Nathalie 
Published: August 2023

AbstractBackgroundThermography is a popular tool to assess plant water use behavior, as plant temperature is influenced by transpiration rate, and is commonly used in field experiments to detect drought stress. Its application in indoor automated phenotyping platforms is still limited and mainly focuses on differences in plant temperature between genotypes or treatments, instead of estimating stomatal conductance or transpiration rate. In this study, the transferability of commonly used thermography analysis protocols from the field to greenhouse phenotyping platforms was evaluated. In addition, the added value of combining thermal infrared (TIR) with hyperspectral imaging to monitor drought effects on plant transpiration rate (E) was evaluated.ResultsThe sensitivity of commonly used TIR indices to detect drought-induced and genotypic differences in water status was investigated in eight maize inbred lines in the automated phenotyping platform PHENOVISION. Indices that normalized plant temperature for vapor pressure deficit and/or air temperature at the time of imaging were most sensitive to drought and could detect genotypic difference in the plants’ water use behavior. However, these indices were not strongly correlated to stomatal conductance and E. The canopy temperature depression index, the crop water stress index and the simplified stomatal conductance index were more suitable to monitor these traits, and were consequently used to develop empirical E prediction models by combining them with hyperspectral indices and/or environmental variables. Different modeling strategies were evaluated including single index-based, machine learning and mechanistic models. Model comparison showed that combining multiple thermal infrared indices in a random forest model can improve E prediction accuracy, and that the contribution of the hyperspectral data is limited when multiple indices are used. However, the empirical models trained on one genotype were not transferable to all eight inbred lines.ConclusionOverall, this study demonstrates that existing TIR indices can be used to monitor drought stress and develop E prediction models in an indoor setup, as long as the indices normalize plant temperature for ambient air temperature or relative humidity.
Cell-Specific Disruptions in the Basolateral Amygdala-Accumbens Pathway of Fragile X mouse
Authors: Giua Gabriele , Lassalle Olivier , Chavis Pascale , Manzoni Olivier J. 
Published: August 2023

AbstractFragile X syndrome (FXS), a neurodevelopmental disorder caused by the inactivation of theFMR1gene, is one of the most common causes of autism spectrum disorder (ASD). People with FXS and ASD often have difficulty regulating their emotions and behaving in a socially appropriate way. The specific neuronal circuits and synaptic dysfunctions involved in social deficits in FXS are not yet fully understood. The basolateral amygdala (BLA) to accumbens core (NAcC) pathway is central to normal social behavior, and we investigated the functionality of this pathway in a novel mouse model of FXS (Fmr1−/y::Drd1a-tdTomato). We used optogenetics to distinguish synapses between BLA neurons and spiny projection neurons (SPNs) in the NAcC. We found that the BLA-NAcC connection in FXS mice displayed heightened synaptic strength along with specific alterations in synaptic plasticity. In FXS, enhanced AMPA and NMDA postsynaptic currents elevated BLA-D2 SPN synaptic strength, while BLA-D1 SPNs’ increased firing probability occurred without altered transmission. This results in an overall increase in postsynaptic integration in both D1 and D2 SPN BLA-NAcC pathways compared to WT littermates. Further, the absence of FMRP leads to a specific deficit in long-term depression for BLA-D1 SPNs connections. The neurobiological changes identified in this study may underlie the susceptibility to stressors, socio-communicative difficulties, and altered reward-related processes that are characteristic of FXS pathology.