bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short heat shock factor A2 confers heat sensitivity inArabidopsis: Insights into heat resistance and growth balance
Authors: Chen Wanxia , Zhao Jiaqi , Tao Zhanxia , Zhang Shan , Bei Xiujuan , Lu Wen , Qi Xiaoting 
Published: June 2024

AbstractCells prevent heat damage through a highly conserved canonical heat stress response (HSR) in which heat shock factors (HSFs) bind heat shock elements (HSEs) to activate heat shock proteins (HSPs). Plants generate short HSFs that originate from HSF splicing variants, but little is known about S-HSFs. Although an enhanced canonical HSR confers thermotolerance, its hyperactivation inhibits plant growth. How this process is prevented to ensure proper plant growth has not been determined. Here, we report thatArabidopsisS-HsfA2, S-HsfA4c, and S-HsfB1 confer extreme heat (45°C) sensitivity and represent new kinds of HSF with a unique truncated DNA-binding domain (tDBD) that binds a new heat-regulated element (HRE). The HRE conferred a minimal promoter response to heat and exhibited heat stress sensing and transmission patterns. We used S-HsfA2 to investigate whether and how S-HSFs prevent hyperactivation of the canonical HSR.HSP17.6B,a direct target gene of HsfA2, conferred thermotolerance, but its overexpression caused HSR hyperactivation. We revealed that S-HsfA2 alleviated this hyperactivation in two different ways. 1) S-HsfA2 negatively regulatesHSP17.6B viathe HRE-HRE-like element, thus constructing a noncanonical HSR (S-HsfA2-HRE-HSP17.6B) to antagonistically repress HsfA2-activatedHSP17.6Bexpression. 2) S-HsfA2 binds to the DBD of HsfA2 to prevent HsfA2 from binding to HSEs, eventually attenuating HsfA2-activatedHSP17.6Bpromoter activity. Overall, our findings underscore the biological importance of S-HSFs, namely, preventing plant heat tolerance hyperactivation to maintain proper growth.Graphical Abstract
Functional carbohydrate-active enzymes acquired by horizontal gene transfer from plants in the whiteflyBemisia tabaci
Authors: Colinet D , Haon M , Drula E , Boyer M , Grisel S , Belliardo C , Koutsovoulos GD , Berrin JG , Danchin EGJ 
Published: June 2024

AbstractCarbohydrate-active enzymes (CAZymes) involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of CAZymes acquired by horizontal gene transfer (HGT) from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whiteflyBemisia tabaciis a major agricultural pest, knowledge of HGT-acquired CAZymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of HGT candidates inB. tabaciand identified 136 HGT events, 14 of which corresponding to CAZymes. TheB. tabaciHGT-acquired CAZymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 (GH17) and 152 (GH152) acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two CAZymes are the first characterized GH17 and GH152 glucanases in an animal. We identified a lower number of HGT events in the related AleyrodinaeTrialeurodes vaporariorum, with only three HGT-acquired CAZymes, including a GH152 glucanase, with phylogenetic analysis suggesting a unique HGT event in the ancestor of the Aleyrodinae. Another GH152 CAZyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired CAZymes in the biology of piercing-sucking insects.Significance statementCarbohydrate-active enzymes (CAZymes) are crucial for sugar metabolism. Those involved in plant cell wall degradation are usually absent from animal genomes. In this study, we explored CAZyme repertoires in the genomes of several insects: the phloem-feeding whiteflyBemisia tabaci, a major agricultural pest, and the related greenhouse whiteflyTrialeurodes vaporariorum, as well as two Thysanoptera species that feed on plant cell contents. We identified several cases of CAZymes acquired from plant via horizontal gene transfer in the genome of these insects. Notably, we showed that twoB. tabaciCAZymes of plant origin function as glucanases with distinct substrate specificities, potentially helping the insect to overcome plant defenses. Overall, these findings enhance our understanding of how the ability to feed on plants evolved in insects.
Piximi - An Images to Discovery web tool for bioimages and beyond
Authors: Moser Levin M , Gogoberidze Nodar , Papaleo Andréa , Lucas Alice , Dao David , Friedrich Christoph A , Paavolainen Lassi , Molnar Csaba , Stirling David R , Hung Jane , Wang Rex , Tromans-Coia Callum , Li Bin , Evans Edward L , Eliceiri Kevin W , Horvath Peter , Carpenter Anne E , Cimini Beth A 
Published: June 2024

AbstractDeep learning has greatly accelerated research in biological image analysis yet it often requires programming skills and specialized tool installation. Here we present Piximi, a modern, no-programming image analysis tool leveraging deep learning. Implemented as a web application at Piximi.app, Piximi requires no installation and can be accessed by any modern web browser. Its client-only architecture preserves the security of researcher data by running all computation locally. Piximi offers four core modules: a deep learning classifier, an image annotator, measurement modules, and pre-trained deep learning segmentation modules. Piximi is interoperable with existing tools and workflows by supporting import and export of common data and model formats. The intuitive researcher interface and easy access to Piximi allows biological researchers to obtain insights into images within just a few minutes. Piximi aims to bring deep learning-powered image analysis to a broader community by eliminating barriers to entry.
The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation
Authors: Longan Emery R. , Fay Justin C. 
Published: June 2024

AbstractDomesticated strains ofSaccharomyces cerevisiaehave adapted to resist copper and sulfite, two chemical stressors commonly used in winemaking.S. paradoxus, has not adapted to these chemicals despite being consistently present in sympatry withS. cerevisiaein vineyards. This contrast represents a case of apparent evolutionary constraints favoring greater adaptive capacity inS. cerevisiae. In this study, we used a comparative mutagenesis approach to test whetherS. paradoxusis mutationally constrained with respect to acquiring greater copper and sulfite resistance. For both species, we assayed the rate, effect size, and pleiotropic costs of resistance mutations and sequenced a subset of 150 mutants isolated from our screen. We found that the distributions of mutational effects displayed by the two species were very similar and poorly explained the natural pattern. We also found that chromosome VIII aneuploidy and loss of function mutations inPMA1confer copper resistance in both species, whereas loss of function mutations inREG1were only a viable route to copper resistance inS. cerevisiae. We also observed a singlede novoduplication of theCUP1gene inS. paradoxusbut none inS. cerevisiae. For sulfite, loss of function mutations inRTS1andKSP1confer resistance in both species, but mutations inRTS1have larger average effects inS. paradoxus. Our results show that even when the distributions of mutational effects are largely similar, species can differ in the adaptive paths available to them. They also demonstrate that assays of the distribution of mutational effects may lack predictive insight concerning adaptive outcomes.
Degradation Bottlenecks and Resource Competition in Transiently and Stably Engineered Mammalian Cells
Authors: Gabrielli Jacopo , Di Blasi Roberto , Kontoravdi Cleo , Ceroni Francesca 
Published: June 2024

AbstractDegradation tags, otherwise known as degrons, are portable sequences that can be used to alter protein stability. Here, we report that degron-tagged proteins compete for cellular degradation resources in engineered mammalian cells leading to coupling of the degradation rates of otherwise independently expressed proteins when constitutively targeted human degrons are adopted. By adopting inducible bacterial and plant degrons we also highlight how orthogonality and uncoupling of synthetic construct degradation from the native machinery can be achieved. We show the effect of this competition to be dependent on the context of the degrons where C-terminal degradation appears to impact competition the most across our tested settings. We then build a genomically integrated capacity monitor tagged with different degrons and confirm resource competition between genomic and transiently expressed DNA constructs. This work expands the characterisation of resource competition in engineered mammalian cells to degradation also including integrated systems, providing a framework for the optimisation of heterologous expression systems to advance applications in fundamental and applied biological research.
A transformer model forde novosequencing of data-independent acquisition mass spectrometry data
Authors: Sanders Justin , Wen Bo , Rudnick Paul , Johnson Rich , Wu Christine C. , Oh Sewoong , MacCoss Michael J. , Noble William Stafford 
Published: June 2024

AbstractA core computational challenge in the analysis of mass spectrometry data is thede novosequencing problem, in which the generating amino acid sequence is inferred directly from an observed fragmentation spectrum without the use of a sequence database. Recently, deep learning models have made significant advances inde novosequencing by learning from massive datasets of high-confidence labeled mass spectra. However, these methods are primarily designed for data-dependent acquisition (DDA) experiments. Over the past decade, the field of mass spectrometry has been moving toward using data-independent acquisition (DIA) protocols for the analysis of complex proteomic samples due to their superior specificity and reproducibility. Hence, we present a newde novosequencing model called Cascadia, which uses a transformer architecture to handle the more complex data generated by DIA protocols. In comparisons with existing approaches forde novosequencing of DIA data, Cascadia achieves state-of-the-art performance across a range of instruments and experimental protocols. Additionally, we demonstrate Cascadia’s ability to accurately discoverde novocoding variants and peptides from the variable region of antibodies.
Ultrahigh yields of giant vesicles obtained through mesophase evolution and breakup
Authors: Cooper Alexis , Subramaniam Anand Bala 
Published: June 2024

AbstractSelf-assembly odry amphiphilic lipid films on surfaces upon hydration is a crucial step in the formation of cell-like giant unilamellar vesicles (GUVs). GUVs are useful as model biophysical systems, as chassis for synthetic biology, and in biomedical applications. Here via combined quantitative measurements of the molar yield and distributions of sizes and high-resolution imaging of the evolution of lipid films on surfaces, we report the discovery of a previously unknown pathway for the assembly of GUVs which can lead to ultrahigh yields of > 50 %. This yield is about 60 % higher than any GUV yield reported to date. The “shear-induced fragmentation” pathway occurs in membranes containing 3 mol % of the poly(ethylene glycol) modified lipid PEG2000-DSPE (1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000]), when a lipid-dense foam-like mesophase forms upon hydration. The membranes in the mesophase fragment and close to form GUVs upon application of fluid shear. Experiments with varying mol % of PEG2000-DSPE and with lipids with partial molecular similarity to PEG2000-DSPE show that ultrahigh yields are only achievable under conditions where the lipid-dense mesophase forms. The increased yield of GUVs compared to mixtures without PEG2000-DSPE was general to other flat supporting surfaces such as stainless steel sheets and to various lipid mixtures. Since FDA-approved liposomal and lipid nanoparticle formulations use PEG2000-DSPE, these results provide a useful route to obtaining ultrahigh yields of GUVs that are suitable for biomedical applications.
Evidence of Activity-Silent Working Memory in Prefrontal Cortex
Authors: Tao Weicheng , Libedinsky Camilo 
Published: June 2024

AbstractThe lateral prefrontal cortex encodes working memory and motor preparation information, but the underlying neural mechanisms are debated. Recurrent neural network models relying on persistent neural activity have been challenged by the observation of periods of absent activity and information during memory maintenance, implying the existence of activity-silent mechanisms. To assess whether activity-silent mechanisms are needed for working memory maintenance, we recorded neural activity in macaque prefrontal cortex during a delayed-saccade task. We replicated the observation of periods of absent activity and decreased information between bursts of gamma power, but we show that these results are consistent with models that rely exclusively on persistent activity. However, an assessment of the length of periods with absent selective activity across the population revealed that activity-silent mechanisms are indeed needed to maintain memory information, although this is only evidenced in a small fraction of trials.
Differences in Methanotrophic Community Structure in Two Methane-Rich Habitats: Oil Natural Gas Field & Paddy Field
Authors: Verma Akanksha , Maitra S.S. 
Published: June 2024

AbstractMethanotrophic bacterial isolates were identified in this study using the molecular detection method, isolated using microbiological techniques, and studied their cellular shape using atomic force microscopy. Two methanotrophic bacterial species belonging to theMethylocaldumandMethylomonasgenera were provisionally designated as Isolate 1 and Isolate 5, thus isolated from the Oil-Natural Gas Field and Paddy Field, respectively. The Oil-Natural Gas Field Isolate 1 showed 91.82-97.25% sequence homology to the reference Methanotrophic species, whereas Paddy Field Isolate 5 showed 79.72-84.99% sequence homology to the referenceMethylomonasspecies in the NCBI database. As per the phylogenetic analysis, Oil-Natural Gas Field Isolate 1 and Paddy Field Isolate 5 are possibly new species ofMethylocaldumandMethylomonasgenus, respectively. In addition, the microscopic study also supported the molecular identification and phylogenetic analysis of isolated species by showing the cocci and rod shapes for the Oil-Natural Gas Field Isolate 1 and Paddy Field Isolate 5, respectively.
Mild traumatic brain injury is associated with increased thalamic subregion volume in the subacute period following injury
Authors: Baird Maggie E , Beare Richard , Seal Marc L , Yang Joseph Yuan-Mou , Anderson Jacqueline F. I. 
Published: June 2024

ABSTRACTStructural vulnerability of the thalamus remains under investigated in mild traumatic brain injury (mTBI), and few studies have addressed its constituent nuclei using robust segmentation methods. This study aimed to investigate thalamic subnuclei volume in the subacute period following mTBI. Trauma control (TC) and mTBI patients aged 18 – 60 years old completed an MRI neuroimaging protocol including both high resolution structural (T1w) and diffusion weighted sequences at 6 – 11 weeks following injury (mean: 57 days; sd 11). Each thalamus was segmented into its constituent subnuclei, which were grouped into eight lateralised subregions. Volumes of the subregions were calculated. Neurite Orientation Dispersion and Density (NODDI) maps with parameters optimised for grey matter were computed for the same subregions. Group differences in subregion volumes and NODDI parameters were investigated using Bayesian linear modelling, with age, sex, and intracranial volume included as covariates. Comparisons of mTBI (n = 39) and TC (n = 28) groups revealed evidence of relatively increased grey matter volume in the mTBI group for the bilateral medial and right intralaminar subregions (BF10> 3). Of the subregions which showed volume differences, there was no evidence for differences in NODDI metrics between groups. This study demonstrates that in the subacute period following mTBI, there is evidence of increased volume in specific thalamic subregions. Putative mechanisms underpinning the increased volume observed here are disordered remyelination, or myelin debris yet to be cleared.Significance statementDespite the prevalence of continued cognitive, somatic, and vestibular symptoms in the subacute period (6 – 12 weeks) following an mTBI, a clear neuropathophysiological profile is yet to be determined. One key vulnerable structure in mTBI could be the thalamus, a subcortical grey matter structure which comprises numerous subregions. The present study investigated whether changes in thalamic subregion volume are evident in the subacute period. For the first time, we show that at approximately 8 weeks following injury, mTBI is associated with increased volume in specific thalamus subregions. This provides an important avenue for continued investigation into the clinical significance of these findings.
Single-cell multi-omics and spatial multi-omics data integration via dual-path graph attention auto-encoder
Authors: Lv Tongxuan , Zhang Yong , Liu Junlin , Kang Qiang , Liu Lin 
Published: June 2024

AbstractSingle-cell multi-omics data integration enables joint analysis of the resolution at single-cell level to provide comprehensive and accurate understanding of complex biological systems, while spatial multi-omics data integration is benefit to the exploration of cell spatial heterogeneity to facilitate more diversified downstream analyses. Existing methods are mainly designed for single-cell multi-omics data with little consideration on spatial information, and still have the room for performance improvement. A reliable multi-omics data integration method that can be applied to both single-cell and spatially resolved data is necessary and significant. We propose a single-cell multi-omics and spatial multi-omics data integration method based on dual-path graph attention auto-encoder (SSGATE). It can construct neighborhood graphs based on single-cell expression data and spatial information respectively, and perform self-supervised learning for data integration through the graph attention auto-encoders from two paths. SSGATE is applied to data integration of transcriptomics and proteomics, including single-cell and spatially resolved data of various tissues from different sequencing technologies. SSGATE shows better performance and stronger robustness than competitive methods and facilitates downstream analysis.
Long-range neuropeptide relay as a central-peripheral communication mechanism for the context-dependent modulation of interval timing behaviors
Authors: Zhang Tianmu , Wu Zekun , Song Yutong , Li Wenjing , Sun Yanying , Zhang Xiaoli , Wong Kyle , Schweizer Justine , Nguyen Khoi-Nguyen Ha , Kwan Alex , Kim Woo Jae 
Published: June 2024

ABSTRACTNeuropeptides play crucial roles in regulating context-dependent behaviors, but the underlying mechanisms remain elusive. We investigate the role of the neuropeptide SIFa and its receptor SIFaR in regulating two distinct mating duration behaviors in maleDrosophila: Longer-Mating-Duration (LMD) and Shorter-Mating-Duration (SMD). We found that SIFaR expression in specific neurons is required for both LMD and SMD behaviors. Social context and sexual experience lead to synaptic reorganization between SIFa and SIFaR neurons, altering internal states of brain. We revealed that the SIFa-SIFaR/Crz-CrzR neuropeptide relay pathway is essential for generating distinct interval timing behaviors, with Crz neurons being responsive to the activity of SIFa neurons. Additionally, CrzR expression in non-neuronal cells is critical for regulating LMD and SMD behaviors. Our study provides insights into how neuropeptides and their receptors modulate context-dependent behaviors through synaptic plasticity and calcium signaling, with implications for understanding the neural circuitry underlying interval timing and neuropeptidergic system modulation of behavioral adaptations.
Incoherent tune measurement of an ion storage ring using single ions
Authors: Liao T. , Guo C. , Yan X. L. , Zhou X. , Xing Y. M. , Wang M. , Yuan Y. J. , Zhang Y. H. , Zhou X. H. , Zhang M. , Ge W. W. , Jiao H. Y. , Jiang Y. L. , Mao L. J. , Chen R. J. , Fu C. Y. , Mao R. S. , Yang J. C. , Litvinov S. A. , Litvinov Yu. A. 
Published: June 2024

The measurement of betatron tunes is important in the studies of beam dynamics in circular accelerators. Here, we report a new method to extract the fractional tune values using revolution times of single ions stored for a few hundred turns in a heavy-ion storage ring utilizing a single time-of-flight detector. The experiment was done at the experimental Cooler Storage Ring (CSRe) in Lanzhou. The unbunched cocktail secondary beam was injected into the ring and allowed to coast without further excitation. Since the average number of simultaneously stored ions inside the 128.8 m-circumference ring was merely ∼20, the obtained tune values are considered to be incoherent. Given that the revolution time of an individual ion is related to its momentum, the chromaticity of the ring could be addressed. Moreover, the data indicate a possible beam mismatch in vertical direction y^ at the injection into CSRe. The new method is developed for ultralow beam intensities and is thus a sensitive approach to tune measurements. Thanks to its simplicity, the method can straightforwardly be employed at other circular accelerators by applying the same detection approach.

Published by the American Physical Society
2024
Ultrasound-assisted synthesis of a Eu3+-functionalized ZnII coordination polymer as a fluorescent dual detection probe for highly sensitive recognition of HgII and L-Cys
Authors: Farahmand Kateshali Arash , Soleimannejad Janet , Janczak Jan 
Published: June 2024

A new ZnII coordination polymer (CP) based on 2,3-pyrazine dicarboxylic acid (H2pzdc) and 4,4′-bipyridine (bpy) (ZCP) was synthesized using a facile slow evaporation method. Single-crystal X-ray diffraction revealed that ZCP is a two-dimensional porous CP, [Zn2(pzdc)2(bpy)(H2O)2]
n
, with van der Waals forces as the dominant interaction within its layers forming a 63 network. Employing energetic ultrasound irradiation, nanoscale ZCP (nZCP) was successfully synthesized and Eu3+ ions were incorporated within its host lattice (Eu@nZCP). The resulting platform exhibits superior fluorescence characteristics and demonstrates notable optical durability. Therefore, it was used as a dual detection fluorescent sensing platform for the detection of mercury and L-cysteine (L-Cys) in aqueous media through a turn-off/on strategy. In the turn-off process, the fluorescence emission of Eu@nZCP progressively quenches by the addition of HgII
via a photo-induced electron transfer (PET) mechanism. The fluorescence of Eu@nZCP is quenched to establish a low fluorescence background through the incorporation of HgII. This devised turn-on fluorescent system is suitable for the recognition of L-Cys (based on the strong affinity of L-Cys to the HgII ion) through a quencher detachment mechanism. This method attained a relatively wide linear range, spanning from 0.001 to 25 µM, with the low detection limit of 5 nM for the sensing of HgII. Also, the corresponding limit of detection (LOD) for L-Cys is 8 nM in a relatively wide linear range, spanning from 0.001 to 40 µM.