bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Dynamic Programming Approach for the Alignment of Molecules
Authors: Williams Ryan A. , Liberles David A. 
Published: January 2024

I.AbstractThere is a need for computational approaches to compare molecules based upon chemical similarity or for evaluating biochemical transformations. Here, a new approach to molecular alignment in the Simplified Molecular Input Line Entry System (SMILES) format is introduced. Leveraging dynamic programming and scoring alignments to minimize differences in a measure of electronegativity, the study addresses the challenge of comprehending structural transformations in reaction pathways, notably transitions from linear to cyclical structures. The method is built from the Needleman-Wunsch algorithm for sequence alignment, but with a modified scoring function for different input data. Validation against a benchmarked dataset from the Krebs cycle based upon known chemical mechanisms of molecular transformations confirmed the efficacy of the approach. The transformations of the Pentose Phosphate Pathway were quantified using this algorithm and was compared with Glycolysis. The study introduces an algorithm that quantifies molecular transformations in metabolic pathways, highlighting a midpoint dissimilarity peak in cyclical pathways and a progressive decrease in molecular similarity in linear pathways. The software is available at:https://github.com/rwills5042/SMILES_Alignment.
Different fluorescent labels report distinct components of spHCN channel voltage sensor movement
Authors: Wojciechowski Magdalena N , McKenzie Chaseley E , Hung Andrew , Kuanyshbek Alibek , Soh Ming S , Reid Christopher A , Forster Ian C 
Published: January 2024

AbstractVoltage clamp fluorometry was used to probe the S4 helix movement in the voltage sensing domain of the sea urchin HCN channel expressed inXenopusoocytes. Markedly different fluorescence responses were obtained with either ALEXA-488 or MTS-TAMRA covalently linked to Cys332 at the N-terminal end of S4. With hyperpolarizing steps, ALEXA-488 fluorescence increased rapidly showing characteristics consistent with it reporting the initial inward movement of S4 in agreement with previous studies. In contrast, MTS-TAMRA fluorescence was slower and correlated with the early phase of channel opening. In addition, a slow fluorescence component was resolved with both labels that tracked the development of the mode shift or channel hysteresis. This was quantitated as an increased deactivation tail current delay with concomitantly longer activation periods and was found to depend strongly on the presence of K+ions in the pore. This indicated that the microenvironment of the fluorescent probes attached to Cys332 was strongly influenced by conformational changes in the pore domain. Collisional quenching experiments established that ALEXA-488 was more exposed to solvent than MTS-TAMRA. This was supported by structural predictions based on homology modelling of spHCN in the closed and open conformations with covalently linked fluorophores. This study demonstrates that components of S4 movement during channel activation can be kinetically resolved using different fluorescent probes to reveal three distinct biophysical properties: voltage-sensor movement, early channel opening and mode-shift. These data support the use of different labelling probes to interrogate distinct biophysical aspects of voltage-gated membrane proteins.SummaryVoltage clamp fluorometry was used to probe the S4 helix movement in the voltage sensing domain of the spHCN channel expressed inXenopusoocytes, labeled with either ALEXA-488 or MTS-TAMRA. Each fluorophore reported different components of S4 movement.
Explaining plant trait variation in response to soil water availability using an optimal height-growth model
Authors: Towers Isaac R. , O’Reilly-Nugent Andrew , Sabot Manon E.B. , Vesk Peter A. , Falster Daniel S. 
Published: January 2024

1AbstractClimate change is expected to bring about changes in precipitation and temperature regimes that, together with rising atmospheric CO2concentrations, will likely reorganise the functional trait composition of ecosystems. Predicting plant trait responses to emerging environmental conditions including, in particular, water availability, is a tremendous challenge, but is one that eco-evolutionary optimality theory (EEO) can help us undertake. However, most EEO approaches are based on the hypothesis that traits are selected to maximise carbon assimilation which omits the important role that size growth plays in determining fitness outcomes. Using a height-growth based EEO framework, we predict magnitude and directional shifts in four key traits: leaf mass per area, sapwood area to leaf area ratio (Huber value), wood density and sapwood-specific conductivity in response to variation in soil moisture availability, atmospheric aridity, CO2and light availability. Consistent with empirical patterns, we predict that trait optima shift from resource-acquisitive strategies characterised by low tissue constructions costs and high rates of tissue turnover and sapwood conductivity to resource-conservative strategies - characterised by low rates of tissue turnover and greater xylem embolism resistance - as conditions become increasingly dry. The EEO model that we use here highlights the important role that both carbon assimilation and tissue construction costs jointly play in predicting the response of trait optima to the environment, laying the groundwork for future height-growth based EEO models aiming to predict shifts in the functional composition of ecosystems in response to global change.
Can’t carve air, can’t weave names: Plant species used in Colombian artisan crafts are not equally assessed for vulnerability at the international and national level
Authors: Hernandez Katherine Victoria , Andrade-Rivas Federico , Zapata Felipe , Batista Natasha , Cárdenas-Navarrete Anaid , Dávila Arenas Armando , Herrera-R Guido A. , Langhans Kelley E. , Levey Dallas , Neill Andrew , Nguyen Oliver , Ocampo-Peñuela Natalia , Sánchez Lopez Sergio , Echeverri Alejandra 
Published: January 2024

AbstractHumanity has maintained cultural connections with our environments for time immemorial. Plants and artisan crafts are a prime example, as craft purpose, skill, design, and species used can vary greatly between communities and the loss of a critical plant species can result in a loss of access to cultural craft practices. To mitigate global biodiversity loss, conservationists are faced with the challenge of assessing species vulnerability to extinction and prioritizing species for conservation funding using information instruments, like the IUCN red list. This process does not necessarily consider a species’ cultural importance. In this paper we sought to address this gap for plant species used in artisan crafts in Colombia. We aim to answer the following: (1) how represented are endemic species in artisan crafts; (2) how threatened are artisan craft species according to (a) international and (b) national vulnerability status? We used the number of species-associated common names as a proxy for cultural awareness. We found that continentally regional species were far more represented in Colombian artisan crafts than national endemics. We also found a strong positive relationship between number of common names and national vulnerability assessment status, but no statistically significant relationship for international vulnerability status. Based on our results, well-known plants used in Colombian artisan crafts are more likely to be assessed nationally than internationally. While the IUCN is thorough in their recommendations, more can be done to prioritize the inclusion of conservation assessments for species based on their contributions to cultural diversity.Positionality statementWe are 14 scientists and practitioners who are deeply committed to the conservation of nature and culture in a changing world. We are trained in diverse fields including ecology, evolutionary biology, botany, music, anthropology, law, and public health. We all have postgraduate academic education (Masters or PhDs underway) but most of us are early career scholars. Six of us grew up in Colombia and we represent many places including Mexico, the United States, Ireland, Chile, Brazil, Germany, and Viet Nam. None of us self-identify as Indigenous.
The molecular core of transcriptome responses to abiotic stress in plants: a machine learning-driven meta-analysis
Authors: Sanchez-Munoz Raul , Depaepe Thomas , Samalova Marketa , Hejatko Jan , Zaplana Isiah , Van Der Straeten Dominique 
Published: January 2024

AbstractUnderstanding how plants adapt their physiology to overcome severe stress conditions is vital in light of the current climate crisis. This remains a challenge given the complex nature of the underlying molecular mechanisms. To provide a full picture of stress mitigation mechanisms, an exhaustive analysis of publicly available stress-related transcriptomic data was conducted. We combined a meta-analysis with an unsupervised machine learning algorithm to identify a core of stress-related genes. To ensure robustness and biological significance of the output, often lacking in meta-analyses, a three-layered biovalidation was incorporated. Our results present a ‘stress gene core’, a set of key genes involved in plant tolerance to a multitude of adverse environmental conditions rather than specific ones. In addition, we provide a biologically validated database to assist in design of multi-stress resilience. Taken together, our results pave the way towards future-proof sustainable agriculture.TeaserUsing a machine learning-driven meta-analysis, a plant ‘stress gene core’ was identified as a hub mediating multi-stress regulation
Plant response to intermittent heat stress involves modulation of mRNA translation efficiency
Authors: Dannfald Arnaud , Carpentier Marie-Christine , Merret Rémy , Favory Jean-Jacques , Deragon Jean-Marc 
Published: January 2024

AbstractAcquired thermotolerance (also known as priming) is the ability of cells or organisms to better survive an acute heat stress if it is preceded by a milder one. In plants, acquired thermotolerance has been studied mainly at the transcriptional level, including recent descriptions of sophisticated regulatory circuits that are essential for this learning capacity. In this work, we tested the involvement of polysome-related processes (translation and cotranslational mRNA decay (CTRD)) in plant thermotolerance using two heat stress regimes with and without a priming event. We found that priming is essential to restore the general translational potential of plants shortly after acute heat stress. We observed that mRNAs not involved in heat stress suffer from a reduction in translation efficiency at high temperature, whereas heat stress-related mRNAs are translated more efficiently under the same condition. We also show that the induction of the unfolded protein response (UPR) pathway in acute heat stress is favoured by a previous priming event and that, in the absence of priming, ER-translated mRNAs become preferential targets of CTRD. Finally, we present evidence that CTRD can specifically regulate more than a thousand genes during heat stress and should be considered as an independent gene regulatory mechanism.
RNA Secondary Structure Prediction Using a Genetic Algorithm with a Selection Method Based on Free Energy Value and Topological Index
Authors: Benedetti Giorgio 
Published: January 2024

AbstractThis paper presents a genetic algorithm designed to predict RNA secondary structures, which utilizes selection criteria based on free energy (fitness) and topological similarity. This approach represents structural information using a simple number, facilitating comparisons between foldings. The simplified graph representation identifies similarities between structures that have the same type of branches. The results demonstrate that the algorithm identifies the final secondary structure with the same level of precision as the commonly used dynamic programming, but with the advantage of producing more optimal structures with different topologies. This approach maintains high population diversity and allows for the exploration of many suboptimal structures in parallel, avoiding the possibility of getting stuck in a local minimum. This permits the investigation of not only the structure with the minimum free energy, but also of other low-energy structures with different topologies that are closer to the natural fold.
Predicting assembly/disassembly orders of protein complexes using coarse-grained simulations
Authors: Lu Yunxiao , Liu Xin , Zhang Zhiyong 
Published: January 2024

AbstractAssembly of a protein complex is very important to its biological function, which can be investigated by determining assembly/disassembly order of its protein subunits. Although static structures of many protein complexes are available in the protein data bank, their assembly/disassembly orders of subunits are largely unknown. In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex, computational methods can be used to predict the assembly/disassembly order. Since sampling is a nontrivial issue in simulating the assembly/disassembly process, coarse-grained simulations are more efficient than atomic simulations are. In this work, we developed computational protocols for predicting assembly/disassembly orders of protein complexes using coarse-grained simulations. The protocols were illustrated using two protein complexes, and the predicted assembly/disassembly orders are consistent with available experimental data.
Single-shot Echo Planar Time-resolved Imaging for multi-echo functional MRI and distortion-free diffusion imaging
Authors: Dong Zijing , Wald Lawrence L. , Polimeni Jonathan R. , Wang Fuyixue 
Published: January 2024

AbstractPurposeTo develop EPTI, a multi-shot distortion-free multi-echo imaging technique, into a single-shot acquisition to achieve improved robustness to motion and physiological noise, increased temporal resolution, and high SNR efficiency for dynamic imaging applications.MethodsA new spatiotemporal encoding was developed to achieve single-shot EPTI by enhancing spatiotemporal correlation ink-tspace. The proposed single-shot encoding improves reconstruction conditioning and sampling efficiency, with additional optimization under various accelerations to achieve optimized performance. To achieve high SNR efficiency, continuous readout with minimized deadtime was employed that begins immediately after excitation and extends for an SNR-optimized length. Moreover,k-tpartial Fourier and simultaneous multi-slice acquisition were integrated to further accelerate the acquisition and achieve high spatial and temporal resolution.ResultsWe demonstrated that ss-EPTI achieves higher tSNR efficiency than multi-shot EPTI, and provides distortion-free imaging with densely-sampled multi-echo images at resolutions ∼1.25–3 mm at 3T and 7T— with high SNR efficiency and withcomparabletemporal resolutions to ss-EPI. The ability of ss-EPTI to eliminate dynamic distortions common in EPI also further improves temporal stability. For fMRI, ss-EPTI also provides early-TE images (e.g., 2.9ms) to recover signal-intensity and functional-sensitivity dropout in challenging regions. The multi-echo images provide TE-dependent information about functional fluctuations, successfully distinguishing noise-components from BOLD signals and further improving tSNR. For diffusion MRI, ss-EPTI provides high-quality distortion-free diffusion images and multi-echo diffusion metrics.Conclusionss-EPTI provides distortion-free imaging with high image quality, rich multi-echo information, and enhanced efficiency within comparable temporal resolution to ss-EPI, offering a robust and efficient acquisition for dynamic imaging.
Developmental divergence in gene regulation among rapidly radiating cichlid species
Authors: Duenser Anna , Singh Pooja , Ahi Ehsan Pashay , Durdevic Marija , Schaeffer Sylvia , Gallaun Julian , Gessl Wolfgang , Seehausen Ole , Sturmbauer Christian 
Published: January 2024

AbstractDevelopmental shifts in gene regulation underlying key innovations remain largely uncharacterized over short evolutionary timescales. Here, we investigate the gene regulatory landscape of trophic innovations in the fastest vertebrate adaptive radiation: cichlid fishes from Lake Victoria. By analyzing the whole-transcriptomes of the oral and pharyngeal jaws from two life stages in five species adapted to divergent trophic niches, we find that both gene and isoform expression are developmentally dynamic. Expression signatures are most similar across jaws at the early stage and then diverge into species-specific developmental programs in adults. However, even at the early stage, expression in the oral jaws of species adapted to herbivory is distinct from those of carnivores, a pattern not observed for the pharyngeal jaws. We further show that differentially expressed and spliced genes between herbivorous and carnivorous species regulate different genes and pathways, particularly in adults. Interestingly, we find that splicing-mediated exonization of a craniofacial development gene, kaznb, may have contributed to the evolution of herbivory in Lake Victoria cichlids. Overall, our results contribute to our understanding of how ontogenetic shifts in gene regulation can facilitate rapid adaptive evolution.
Evolution, diversity, function, and marker-based elimination of the disease susceptibility geneSnn1in wheat
Authors: Seneviratne Sudeshi , Shi Gongjun , Szabo-Hever Agnes , Zhang Zengcui , Peters Haugrud Amanda R. , Running Katherine L. D. , Singh Gurminder , Nandety Raja Sekhar , Fiedler Jason D. , McClean Phillip E. , Xu Steven S. , Friesen Timothy L. , Faris Justin D. 
Published: January 2024

AbstractSeptoria nodorum blotch (SNB), caused byParastagonospora nodorum,is a disease of durum and common wheat initiated by the recognition of pathogen-produced necrotrophic effectors (NEs) by specific wheat genes. The wheat geneSnn1encodes a wall-associated kinase that directly interacts with the NE SnTox1 leading to the development of SNB. Here, sequence analysis ofSnn1from 114 accessions including diploid, tetraploid and hexaploid wheat species revealed that some wheat lines possess two copies ofSnn1(designatedSnn1-B1andSnn1-B2) approximately 120 kb apart.Snn1-B2evolved relatively recently as a paralog ofSnn1-B1, and both genes have undergone diversifying selection. Three point mutations associated with the formation of the first SnTox1-sensitiveSnn1-B1allele from a primitive wild wheat were identified. Four subsequent and independent SNPs, three inSnn1-B1and one inSnn1-B2, converted the sensitive alleles to insensitive forms. Protein modeling indicated these four mutations could abolishSnn1-SnTox1 compatibility either through destabilization of the Snn1 protein or direct disruption of the protein-protein interaction. High-throughput markers were developed for the causal mutations and evaluated on panels of durum and common wheat. The markers were able to correctly identify 96.9 % of SnTox1-sensitive durum wheat accessions, and a marker for the null allele was 100% accurate at predicting SnTox1-insensitive lines in both durum and spring wheat. Results of this study increase our understanding of the evolution, diversity, and function ofSnn1-B1andSnn1-B2genes and will be useful for marker-assisted elimination of these genes for better host resistance.
Bridge RNAs direct modular and programmable recombination of target and donor DNA
Authors: Durrant Matthew G. , Perry Nicholas T. , Pai James J. , Jangid Aditya R. , Athukoralage Januka S. , Hiraizumi Masahiro , McSpedon John P. , Pawluk April , Nishimasu Hiroshi , Konermann Silvana , Hsu Patrick D. 
Published: January 2024

ABSTRACTGenomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables DNA insertion into genomic target sites as well as programmable DNA excision and inversion. The IS110 bridge system expands the diversity of nucleic acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design.
WRKY1 confers resistance to powdery mildew by accelerating SAR and preventing over-immunity in apple
Authors: Lan Liming , Cao Lifang , Zhang Lulu , Fu Weihong , Qu Shenchun , Wang Sanhong 
Published: January 2024

AbstractPowdery mildew is one of the most serious diseases in apple production. SAR has a broad-spectrum immunity in plants against pathogen. Plants activate SAR against pathogen invasion and also prevent over-immunity. The relevant mechanism is still unknown in apple. In this study, we isolated and identified powdery mildew pathogen from the field and preserved them on the apple tissue culture seedlings. We performed DAP-seq of powdery mildew-inducible WRKY40. WRKY40 positively regulates NPR3like by directly binding to the W-box element of its promoter. NPR3like represses the expression of the PR1 gene in the presence of SA by competing with TGA2 for binding to NPR1. WRKY1 positively regulates WRKY40 by directly binding to the dual W-box element of its promoter, while WRKY1 positively regulates NPR3like by directly binding to the W-box element of its promoter. The expression trends of WRKY1, WRKY40, and NPR3like were basically the same as that of PR1 within 24 h after powdery mildew and SA treatments. Besides, WRKY1 increased SA content by positively regulating EPS1. After inoculation with powdery mildew, the up-regulation of PR1 in RNAi-silenced plants of WRKY1 was more slowly compared with the wild type, and the number of spores and mycelium increased significantly. In summary, we established a new model of NPR3like inhibition of NPR1 activity positively regulated by the WRKY1-WRKY40 module and found that the WRKY1-EPS1 module accelerated the up-regulation of PR1 by increasing the SA content. Finally, we elucidated WRKY1 confers resistance to powdery mildew by accelerating SAR and preventing over-immunity in apple.