bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time course metabolomics and13CO2mapping establish BBX31/miP1b mediated metabolic readjustments conferring UV-B tolerance in Arabidopsis
Authors: Lingwan Maneesh , Yadav Arpita , Datta Sourav , Masakapalli Shyam Kumar 
Published: April 2024

AbstractB-box proteins (BBXs) are transcription factors that act as signal transducers in light signaling pathways. The microprotein BBX31/miP1b is known to play a positive role in promoting photomorphogenesis and stress tolerance under UV-B. However, the BBX31-mediated metabolic reprogramming to confer UV-B tolerance in plants is not well characterised. Here, we integrate metabolomics with kinetic13CO2tracer-based metabolic mapping, morpho-physiological and biochemical analysis to determine the metabolic rewiring in the UV tolerant genotypes. Our results suggest that BBX31 modulates the levels of photosynthetic compounds, reduces TCA cycle intermediates and enhances GS/GOGAT metabolic intermediates and secondary metabolic pathways.13CO2tracing studies established BBX31 modulates phenylpropanoid and GS/GOGAT pathways to divert flux towards the accumulation of UV-B protective metabolites phenylalanine, oxoproline, glutamine, and others. Although metabolomics indicated a higher accumulation of branch chain amino acids (BCAAs) under UV-B, they had negligible 13C incorporation, indicating their biosynthesis from pre-existing intermediates or via protein degradation. Further, we demonstrate that the exogenous application of phenylalanine, identified as one of the marker metabolites, confers tolerance to plants under UV-B. This study sheds light on BBX31-mediated metabolic rewiring under UV-B, which can assist targeted enrichment of metabolites and metabolic engineering to promote UV-B tolerance in plants.HighlightBBX31/miP1b modulates the levels of photosynthetic compounds, reduces TCA cycle intermediates and enhances GS/GOGAT metabolic intermediates to confer UV-B tolerance.
Shewanellais a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthwormEisenia fetida
Authors: Wittlinger Jan-Philipp , Castejón Natalia , Hausmann Bela , Berry David , Schnorr Stephanie L. 
Published: April 2024

AbstractPolyunsaturated fatty acids (PUFAs) play a crucial role in aiding bacteria to adapt to extreme and stressful environments. While there is a well-established understanding of their production, accrual, and transfer within marine ecosystems, knowledge about terrestrial environments remains limited. Investigation of the intestinal microbiome of earthworms has illuminated the presence of PUFAs presumably of microbial origin, which contrasts with the surrounding soil.To comprehensively study this phenomenon, a multi-faceted approach was employed, combining fatty acid analysis with amplicon sequencing of the PfaA-KS domain of the anaerobic fatty acid synthase gene (pfa), as well as the 16S rRNA and 18S rRNA genes. This methodology was applied to scrutinize the gut microbiome ofEisenia fetida, its compost-based dietary source, and the resultant castings.This study unveiled a distinct gut soil ecosystem from input compost and output castings in fatty acid profile as well as type and abundance of organisms. 16S sequencing provided insights into the microbial composition, showing increased relative abundance of certain Pseudomonadota, includingShewanellaceae, and Planctomycetota, includingGemmataceaewithin the gut microbiome compared to input bulk soil compost, while Actinomycetota and Bacillota were relatively enriched compared to the casted feces. Sequencing of the PfaA-KS domain revealed ASVs belonging primarily toShewanella. Intriguingly, the 20C PUFAs were identified only in gut-soil samples, though PfaA-KS sequence abundance was highest in output castings, indicating a unique metabolism occurring only in the gut. Overall, the results indicate thatShewanellacan explain PUFA enrichment in the gut environment because ofpfagene presence detected via PfaA-KS sequence data.ImportancePrior research has demonstrated that earthworm microbiomes can potentially harbor PUFAs that are not found within their residing soil environment. Moreover, distinct indicator species have been pinpointed for various microbial genera in earthworm microbiomes. Nevertheless, none of these studies have integrated metataxonomic and fatty acid analysis to explore the origin of PUFA synthesis in any earthworm species, with the objective of identifying the specific organisms and locations responsible for this production. This study suggests that earthworms accumulate PUFAs produced from bacteria, especiallyShewanella,activated through the gut ecosystem.
An Evidenced-Based Prior for Estimating the Treatment Effect of Phase III Randomized Trials in Oncology
Authors: Sherry Alexander D. , Msaouel Pavlos , Kupferman Gabrielle S. , Lin Timothy A. , Abi Jaoude Joseph , Kouzy Ramez , McCaw Zachary R. , Ludmir Ethan B. , van Zwet Erik 
Published: April 2024

ABSTRACTPurposeThe primary results of phase III oncology trials may be challenging to interpret, given that such results are generally based on meetingP-value thresholds. The probability of whether a treatment is beneficial, although a more intuitive summary of the results, is not provided by most trials. In this study, we developed and released a user-friendly tool that calculates the probability that a treatment studied in a phase III oncology trial is beneficial using published summary statistics.MethodsWe curated the primary time-to-event outcomes of 415 phase III, superiority design, therapeutic randomized controlled trials of oncologic treatments enrolling 338,600 patients and published between 2004 and 2020. A phase III oncology-specific prior probability distribution for the treatment effect was developed based on an estimated three-component zero-mean mixture distribution of the observed z-scores. Using this prior, we computed the probability of any benefit (hazard ratio < 1) and the probability of clinically meaningful benefit (hazard ratio < 0.8) for each trial. The distribution of signal-to-noise ratios of phase III oncology trials was compared with that of 23,551 randomized trials from the Cochrane Database of Systematic Reviews.ResultsThe signal-to-noise ratios of phase III oncology trials tended to be much larger than randomized trials from the Cochrane database. Still, the median power of phase III oncology trials was only 49% (IQR, 14% to 95%), and the power was less than 80% in 65% of trials. Using the developed phase III, oncology-specific prior, only 53% of trials claiming superiority (114 of 216) had a ≥ 90% probability of providing clinically meaningful benefits. Conversely, the probability that the experimental arm was superior to the control arm (HR < 1) exceeded 90% in 17% of trials interpreted as having no benefit (34 of 199).ConclusionBy enabling computation of contextual probabilities for the treatment effect from summary statistics, our robust, highly practical tool, now posted on a user-friendly webpage, can aid the wider oncology community in the interpretation of phase III trials.
Optimal Timing of Organs-at-Risk-Sparing Adaptive Radiation Therapy for Head-and-Neck Cancer under Re-planning Resource Constraints
Authors: Nosrat Fatemeh , Dede Cem , McCullum Lucas B. , Garcia Raul , Mohamed Abdallah S. R. , Scott Jacob G. , Bates James E. , McDonald Brigid A. , Wahid Kareem A. , Naser Mohamed A. , He Renjie , Karagoz Aysenur , Moreno Amy C. , van Dijk Lisanne V. , Brock Kristy K. , Heukelom Jolien , Hosseinian Seyedmohammadhossein , Hemmati Mehdi , Schaefer Andrew J. , Fuller Clifton D. 
Published: April 2024

AbstractBackground and PurposePrior work on adaptive organ-at-risk (OAR)-sparing radiation therapy has typically reported outcomes based on fixed-number or fixed-interval re-planning, which represent one-size-fits-all approaches and do not account for the variable progression of individual patients’ toxicities. The purpose of this study was to determine the personalized optimal timing for re-planning in adaptive OAR-sparing radiation therapy, considering limited re-planning resources, for patients with head and neck cancer (HNC).Materials and MethodsA novel Markov decision process (MDP) model was developed to determine optimal timing of re-planning based on the patient’s expected toxicity, characterized by normal tissue complication probability (NTCP), for four toxicities. The MDP parameters were derived from a dataset comprising 52 HNC patients treated at the University of Texas MD Anderson Cancer Center between 2007 and 2013. Kernel density estimation was used to smooth the sample distributions. Optimal re-planning strategies were obtained when the permissible number of re-plans throughout the treatment was limited to 1, 2, and 3, respectively.ResultsThe MDP (optimal) solution recommended re-planning when the difference between planned and actual NTCPs (ΔNTCP) was greater than or equal to 1%, 2%, 2%, and 4% at treatment fractions 10, 15, 20, and 25, respectively, exhibiting a temporally increasing pattern. The ΔNTCP thresholds remained constant across the number of re-planning allowances (1, 2, and 3).ConclusionIn limited-resource settings that impeded high-frequency adaptations, ΔNTCP thresholds obtained from an MDP model could derive optimal timing of re-planning to minimize the likelihood of treatment toxicities.Graphical AbstractOverview of the analysis method. The sub-figures displaying Organs at risk and toxicities are adapted from [1] with permission. Abbreviation: NTCP = Normal tissue complications probability.
Long-read sequencing to detect full-length protein-protein interactions
Authors: Schaefer-Ramadan Stephanie , Guan Yue , Ahmed Ayeda A. , Aleksic Jovana , Elmagarmid Khadija A. , Syed Leena F. , Mohamoud Yasmin A. , Malek Joel A. 
Published: April 2024

ABSTRACTGiven the increased predictions on interactome size and demand for protein function information, methods for detecting protein-protein interactions remain a significant development area. The all-vs.-all sequencing (AVA-Seq) method utilizes a convergent fusion plasmid design to make two-hybrid technology amenable to next-generation sequencing. Here, we further innovate to take advantage of synthetic DNA technologies and Oxford Nanopore Technologies long-read sequencing improvements to allow us to determine full-length protein-protein interactions. Here, using this approach we recovered 159 protein-protein interactions from a set of 57 human proteins using multiple forms of validation. Further, when referencing a human gold standard set of interactions, eight full-length protein-protein interactions were recovered from an expected 28 interaction pairs (28.6%), a typical recovery rate for two-hybrid technologies. The AVA-Seq, in combination with the ease of synthetic DNA production and the MinION platform, offers a low-cost, high-throughput alternative for determining protein-protein interactions, which can be utilized in research labs at all stages.3Key PointsFirst application of long-read sequencing for full-length protein-protein interaction studies.The recovery rate of the AVA-Seq method using full-length proteins is on par with other leading methods.Advances in synthetic biology and sequencing technologies make full-length protein interactomes affordable and accessible.GRAPHICAL ABSTRACT
Developmental convergence and divergence in human stem cell models of autism spectrum disorder
Authors: Gordon Aaron , Yoon Se-Jin , Bicks Lucy K , Martin Jaqueline M , Pintacuda Greta , Arteaga Stephanie , Wamsley Brie , Guo Qiuyu , Elahi Lubayna , Dolmetsch Ricardo E. , Bernstein Jonathan A , O’Hara Ruth , Hallmayer Joachim F , Lage Kasper , Pasca Sergiu P , Geschwind Daniel H 
Published: April 2024

AbstractTwo decades of genetic studies in autism spectrum disorder (ASD) have identified over a hundred genes harboring rare risk mutations. Despite this substantial heterogeneity, transcriptomic and epigenetic analyses have identified convergent patterns of dysregulation across ASD post-mortem brain tissue. To identify shared and distinct mutational mechanisms, we assembled the largest hiPS cell patient cohort to date, consisting of 70 hiPS cell lines after stringent quality control representing 8 ASD-associated mutations, idiopathic ASD, and 20 lines from non-affected controls. We used these hiPS lines to generate human cortical organoids (hCO), profiling by RNAseq at four distinct timepoints up to 100 days ofin vitrodifferentiation. Early timepoints harbored the largest mutation-specific changes, but different genetic forms converged on shared transcriptional changes as development progressed. We identified a shared RNA and protein interaction network, which was enriched in ASD risk genes and predicted to drive the observed down-stream changes in gene expression. CRISPR-Cas9 screening of these candidate transcriptional regulators in induced human neural progenitors validated their downstream molecular convergent effects. These data illustrate how genetic risk can propagate via transcriptional regulation to impact convergently dysregulated pathways, providing new insight into the convergent impact of ASD genetic risk on human neurodevelopment.
Electric-field induced sleep promotion and lifespan extension in Gaucher’s disease model flies: Association with improving ER stress and autophagy
Authors: Nedachi Takaki , Kawasaki Haruhisa , Inoue Eiji , Suzuki Takahiro , Nakagawa-Yagi Yuzo , Ishida Norio 
Published: April 2024

AbstractGaucher’s disease (GD), one kind of genetic disease, is characterized by a mutation in metabolic enzyme, glucocerebrosidase (GBA), leading to accumulation of its substrate, glucosylceramide in tissues. We previously discovered that theminos-inserted mutation of theGBAgene in fruit flies,Drosophila melanogaster, reproduced human GD characteristics and can be used as a promising model for molecular mechanisms study. Recently, we reported that extremely low-frequency electric fields (ELF-EFs) promoted sleep and extended the lifespan of normal flies.In this study, GD model flies were exposed to ELF-EFs, and sleep parameters, gene expressions, and longevity were evaluated. The amount of sleep and lifespan increased after EF exposure. Simultaneously, the expression of the endoplasmic reticulum (ER) stress-related gene,PERKand the autophagy-related gene,p62was elevated. The data suggest that the healthy effects of EFs on GD flies are associated with improved adaptation to cellular stress.
Competing mechanisms for the buckling of an epithelial monolayer identified using multicellular simulation
Authors: Brown Phillip J. , Green J. Edward F. , Binder Benjamin J. , Osborne James M. 
Published: April 2024

AbstractA model using the rigid body multi–cellular framework (RBMCF) is implemented to investigate the mechanisms of buckling of an epithelial mono-layer. Specifically, the deformation of a monolayer of epithelial cells which are attached to a basement membrane and the surrounding stromal tissue. The epithelial monolayer, supporting basement membrane and stromal tissue are modelled using two separate vertex dynamics models (one for the epithelial monolayer layer and one for the basement membrane and stromal tissue combined) and interactions between the two are considered using the RBMCF to ensure biologically realistic interactions. Model simulations are used to investigate the effects of cell–stromal attachment and membrane rigidity on buckling behaviour. We demonstrate that there are two competing modes of buckling, stromal deformation and stromal separation.HighlightsA rigid body multi–cellular framework allows for the simulation of an epithelial monolayer which is connected to a basement membrane and surrounding tissue stroma.Interaction with basement membrane and tissue stroma allows epithelial cells to migrate forming a confluent monolayer.Buckling of monolayer can occur through separation from or deformation of the basement membrane.
Photophysics-informed two-photon voltage imaging using FRET-opsin voltage indicators
Authors: Brooks F. Phil , Davis Hunter C. , Park Pojeong , Qi Yitong , Cohen Adam E. 
Published: April 2024

AbstractMicrobial rhodopsin-derived genetically encoded voltage indicators (GEVIs) are powerful tools for mapping bioelectrical dynamics in cell culture and in live animals. Förster resonance energy transfer (FRET)-opsin GEVIs use voltage-dependent changes in opsin absorption to modulate the fluorescence of an atached fluorophore, achieving high brightness, speed, and voltage sensitivity. However, the voltage sensitivity of most FRET-opsin GEVIs has been reported to decrease or vanish under two-photon (2P) excitation. Here we investigated the photophysics of the FRET-opsin GEVIs Voltron1 and 2. We found that the voltage sensitivity came from a photocycle intermediate, not from the opsin ground state. The voltage sensitivities of both GEVIs were nonlinear functions of illumination intensity; for Voltron1, the sensitivity reversed sign under low-intensity illumination. Using photocycle-optimized 2P illumination protocols, we demonstrate 2P voltage imaging with Voltron2 in barrel cortex of a live mouse. These results open the door to high-speed 2P voltage imaging of FRET-opsin GEVIsin vivo.TeaserVoltage sensitivity in FRET-opsin indicators comes from a photocycle intermediate, reachable via optimized 2P excitation.
Decoding Missense Variants by Incorporating Phase Separation via Machine Learning
Authors: Feng Mofan , Wei Xiaoxi , Zheng Xi , Liu Liangjie , Lin Lin , Xia Manying , He Guang , Shi Yi , Lu Qing 
Published: April 2024

AbstractComputational models have made significant progress in predicting the effect of protein variants. However, deciphering numerous variants of unknown significance (VUS) located within intrinsically disordered regions (IDRs) remains challenging. To address this issue, we introduced phase separation (PS), which is tightly linked to IDRs, into the investigation of missense variants. Phase separation is vital for multiple physiological processes. By leveraging missense variants that alter phase separation propensity, we developed a machine learning approach named PSMutPred to predict the impact of missense mutations on phase separation. PSMutPred demonstrated robust performance in predicting missense variants that affect natural phase separation. In vitro experimental findings further underscore its validity. By applying PSMutPred on over 522,000 ClinVar missense variants, it significantly contributes to decoding the pathogenesis of disease variants, especially those in IDRs. Our work provides unique insights into the understanding of a vast number of VUSs in IDRs, thereby expediting clinical interpretation and diagnosis of disease variants.
Reanalysis of Orbitrap Astral DIA data demonstrates the capabilities of MS/MS-free proteomics to reveal new biological insights in disease-related samples
Authors: Ivanov Mark V. , Kopeykina Anna S. , Gorshkov Mikhail V. 
Published: April 2024

AbstractData-independent acquisition (DIA) became a method of choice for quantitative proteomics. With the advent of the combination of Orbitrap FTMS and asymmetric track lossless analyzer Astral these DIA capabilities were further extended with the recent demonstration of quantitative proteomic sample analyses at the speed of up to hundreds of samples per day. In particular, the dataset containing brain samples related to the multiple system atrophy was acquired using 7 and 28 min chromatography gradients and the Orbitrap Astral mass spectrometer (Guzman et al., Nat. Biotech.2024). In this work, we reanalysed the Orbitrap Astral DIA data using MS1 spectra without applying to fragmentation information using the recently introduced DirectMS1 approach. The results were compared with previous study of the same sample cohort by traditional long gradient DDA analysis. While the quantitation efficiency of DirectMS1 was comparable, we found additional five proteins of biological significance relevant to the analyzed tissue samples. Among the findings, DirectMS1 was able to detect decreased caspase activity for Vimentin protein in the multiple system atrophy samples which was barely observed from MS/MS-based methods. Our study suggests that DirectMS1 can be an efficient MS1-only addition to the analysis of DIA data in quantitative proteomic studies.
An effective and safe maize seed chipping protocol using clipping pliers with applications in small-scale genotyping and marker-assisted breeding
Authors: Zebosi Brian , Ssengo John , Geadelmann Lander F , Unger-Wallace Erica , Vollbrecht Erik 
Published: April 2024

AbstractIn applications such as marker-assisted breeding and positional cloning, tissue sampling and plant tracking are vital steps in the genotyping pipeline. They enable the identification of desirable seedlings, saving time and reducing the cost, space, and handling required for growing adult plants, especially for greenhouses and winter nurseries. Small-scale marker-assisted selection laboratories rely heavily on leaf-based genotyping, which involves over-planting large, segregating populations followed by leaf sampling, genotyping, and backtracking to identify desired individuals, which is costly and laborious. Thus, there is a need to adopt seed-based genotyping to reduce costs and save time. Therefore, we developed a safe and cheap seed-chipping protocol using clipping pliers to chip seeds to genotype before planting. To identify a cost-effective and high throughput DNA extraction method, we tested four extraction methods and assessed the quality of the seed DNA using PCR. For three of the methods, seed-based DNA was of comparable quality to DNA extracted from leaf punches. We also compared seed- and leaf-derived DNA from the same individuals in a segregating population to test for genotyping miscalls that could arise due to the presence of maternally derived pericarp in the seed samples and found zero miscalls of 43 potential instances. Germination rates of chipped and unchipped seeds were the same for the inbreds tested, B73 and Mo17. However, chipped seeds grew slower until ∼14 days after sowing. Overall, seed sampling using clipping pliers provides a simple, reliable, and high-throughput method to identify specific genotypes before planting.Key FeaturesProvides a quick, safe, and cheap sampling technique for maize kernels that may also be suitable for other plants with relatively large seeds.Includes procedures and materials to track and organize samples within and across batches involving hundreds to thousands of seeds.Seeds can be sampled and genotyped relatively quickly for planting; in one day 384 seeds can be sampled, processed for DNA, and genotyped by PCR.
Chemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases
Authors: Han Lin , Pendleton Augustus , Singh Adarsh , Xu Raymond , Scott Samantha A. , Palma Jaymee A. , Diebold Peter , Malarney Kien P. , Brito Ilana L. , Chang Pamela V. 
Published: April 2024

SummaryThe gut microbiome possesses numerous biochemical enzymes that biosynthesize metabolites that impact human health. Bile acids comprise a diverse collection of metabolites that have important roles in metabolism and immunity. The gut microbiota-associated enzyme that is responsible for the gateway reaction in bile acid metabolism is bile salt hydrolase (BSH), which controls the host’s overall bile acid pool. Despite the critical role of these enzymes, the ability to profile their activities and substrate preferences remains challenging due to the complexity of the gut microbiota, whose metaproteome includes an immense diversity of protein classes. Using a systems biochemistry approach employing activity-based probes, we have identified gut microbiota-associated BSHs that exhibit distinct substrate preferences, revealing that different microbes contribute to the diversity of the host bile acid pool. We envision that this chemoproteomic approach will reveal how secondary bile acid metabolism controlled by BSHs contributes to the etiology of various inflammatory diseases.