bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring correlates of SARS-CoV-2 infection in cell culture using two-photon microscopy and a novel fluorescent calcium-sensitive dye
Authors: Máthé Domokos , Szalay Gergely , Cseri Levente , Kis Zoltán , Pályi Bernadett , Földes Gábor , Kovács Noémi , Fülöp Anna , Szepesi Áron , Hajdrik Polett , Csomos Attila , Zsembery Ákos , Kádár Kristóf , Katona Gergely , Mucsi Zoltán , Rózsa Balázs József , Kovács Ervin 
Published: September 2022

AbstractThe organism-wide effects of viral infection SARS-CoV-2 are well studied, but little is known about the dynamics of how the infection spreads in time among or within cells due to the scarcity of suitable high-resolution experimental systems. Two-photon (2P) imaging combined with a proper subcellular staining technique has been an effective tool for studying mechanisms at such resolutions and organelle levels. Herein, we report the development of a novel calcium sensor molecule along with a 2P-technique for identifying imaging patterns associated with cellular correlates of infection damage within the cells. The method works as a cell viability assay and also provides valuable information on how the calcium level and intracellular distribution are perturbed by the virus. Moreover, it allows the quantitative analysis of infection dynamics. This novel approach facilitates the study of the infection progression and the quantification of the effects caused by viral variants and viral load.
CimpleG: Finding simple CpG methylation signatures
Authors: Maié Tiago , Schmidt Marco , Erz Myriam , Wagner Wolfgang , Costa Ivan G. 
Published: September 2022

AbstractDNA methylation (DNAm) at specific CG dinucleotides (CpG sites) in the genome provides powerful biomarkers for a wide range of applications, such as epigenetic clocks, cell type deconvolution, and stratification of cancer patients. Such epigenetic signatures are usually based on multivariate approaches that require hundreds of DNAm sites for predictions. In contrast, targeted assays for only a few selected CpGs may facilitate faster turnover, better standardisation, and reduced costs. Here, we propose a computational framework named CimpleG for the detection of small CpG methylation signatures, exemplarily used for cell type classification. We evaluate the performance of CimpleG and competing methods on two distinct datasets in regard to the cell-type classification of blood cells and of other somatic cells. Furthermore, we evaluate how well these classifiers perform cellular deconvolution of blood cell mixtures. We show that CimpleG is both time efficient and performs as well as Elastic Net, while basing its prediction on a single DNAm site per cell type. Altogether, CimpleG provides a complete computational framework for the delineation of DNAm signatures and cellular deconvolution.
Far-red light increases maize volatile emissions in response to volatile cues from neighboring plants
Authors: Escobar-Bravo Rocío , Schimmel Bernardus C.J. , Zhang Yaqin , Wang Lei , Robert Christelle A.M. , Glauser Gaétan , Ballaré Carlos L. , Erb Matthias 
Published: September 2022

AbstractPlants perceive the presence and defense status of their neighbors through light and volatile cues, but how plants integrate both stimuli is poorly understood. We investigated if and how low Red to Far red light (R:FR) ratios, indicative of shading or canopy closure, affect maize (Zea mays) responses to herbivore-induced plant volatiles (HIPVs), including the green leaf volatile (Z)-3-hexenyl acetate. We modulated light signaling and perception by using FR supplementation and aphyB1phyB2mutant, and we determined volatile release as a response readout. To gain mechanistic insights, we examined expression of volatile biosynthesis genes, hormone accumulation, and photosynthesis. Exposure to a full blend of HIPVs or (Z)-3-hexenyl acetate induced maize volatile release. Short-term FR supplementation increased this response. In contrast, prolonged FR supplementation or constitutive phytochrome B inactivation inphyB1phyB2plants showed the opposite response. Short-term FR supplementation enhanced photosynthesis and stomatal conductance and (Z)-3-hexenyl acetate-induced JA-Ile levels. We conclude that a FR-enriched light environment can prompt maize plants to respond more strongly to HIPVs emitted by neighbors, which might be explained by changes in photosynthetic processes and phytochrome B signaling. Our findings reveal interactive responses to light and volatile cues with potentially important consequences for plant-plant and plant-herbivore interactions.
Mapping the Constrained Coding Regions in the human genome to their corresponding proteins
Authors: Hasenahuer Marcia A. , Sanchis-Juan Alba , Laskowski Roman A. , Baker James A. , Stephenson James D. , Orengo Christine A. , Raymond F. Lucy , Thornton Janet M. 
Published: September 2022

ABSTRACTConstrained Coding Regions (CCRs) in the human genome have been derived from DNA sequencing data of large cohorts of healthy control populations, available in the Genome Aggregation Database (gnomAD) [1]. They identify regions depleted of protein-changing variants and thus identify segments of the genome that have been constrained during human evolution. By mapping these DNA-defined regions from genomic coordinates onto the corresponding protein positions and combining this information with protein annotations, we have explored the distribution of CCRs and compared their co-occurrence with different protein functional features, previously annotated at the amino acid level in public databases. As expected, our results reveal that functional amino acids involved in interactions with DNA/RNA, protein-protein contacts and catalytic sites are the protein features most likely to be highly constrained for variation in the control population. More surprisingly, we also found that linear motifs, linear interacting peptides (LIPs), disorder-order transitions upon binding with other protein partners and liquid-liquid phase separating (LLPS) regions are also strongly associated with high constraint for variability. We also compared intra-species constraints in the human CCRs with inter-species conservation and functional residues to explore how such CCRs may contribute to the analysis of protein variants. As has been previously observed, CCRs are only weakly correlated with conservation, suggesting that intraspecies constraints complement interspecies conservation and can provide more information to interpret variant effects.
A protocol for rapid generation cycling (speed breeding) of hemp (Cannabis sativa) for research and agriculture
Authors: Schilling Susanne , Melzer Rainer , Dowling Caroline A. , Shi Jiaqi , Muldoon Shaun , McCabe Paul F. 
Published: September 2022

AbstractHemp (Cannabis sativa) is a highly versatile multi-purpose crop with a multitude of applications, from textiles, biofuel and building material to high-value food products for consumer markets. Furthermore, non-hallucinogenic cannabinoids like cannabidiol (CBD), which can be extracted from female hemp flowers, are potentially valuable pharmacological compounds. In addition, hemp has high carbon sequestration potential due to its rapid growth rate. Therefore, the hemp industry is gaining more traction and breeding hemp cultivars adapted to local climate conditions or bred for specific applications is becoming increasingly important.Here, we present a method for rapid generation cycling (speed breeding) for hemp. The speed breeding protocol makes use of the photoperiod sensitivity of Cannabis. It encompasses vegetative growth of the plants for two weeks under continuous light, followed by flower induction, pollination and seed development for four weeks under short-day conditions and a seed ripening phase under continuous light and water stress. With the protocol introduced here, a generation time of under nine weeks (61 days) from seed to seed can be achieved. Our method furthermore synchronises flowering time of different hemp cultivars, thus facilitating crosses between cultivars. The extremely short generation time will enable hemp researchers and breeders to perform crosses in a time-efficient way and generate new hemp cultivars with defined genetic characteristics in a shorter amount of time.
Evolutionary metabolomics of specialized metabolism diversification in the genusNicotianahighlights allopolyploidy-mediated innovations inN-acylnornicotine metabolism
Authors: Elser David , Pflieger David , Villette Claire , Moegle Baptiste , Miesch Laurence , Gaquerel Emmanuel 
Published: September 2022

AbstractSpecialized metabolite (SM) diversification is a core process to plants’ adaptation to diverse ecological niches. Here we implemented a computational mass spectrometry (MS)-based metabolomics approach to explore SM diversification in tissues of 20 species coveringNicotianaphylogenetics sections. To drastically increase metabolite annotation, we created a largein silicofragmentation database, comprising more than 1 million structures, and scripts for connecting class prediction to consensus substructures. Altogether, the approach provides an unprecedented cartography of SM diversity and section-specific innovations in this genus. As a case-study, and in combination with NMR and MS imaging, we explored the distribution ofN-acyl nornicotines, alkaloids predicted to be specific toRepandaeallopolyploids, and revealed their prevalence in the genus, albeit at much lower magnitude, as well as a greater structural diversity than previously thought. Altogether, the novel data integration approaches provided here should act as a resource for future research in plant SM evolution.TeaserComputational metabolomics delineates main trends in the diversification of specialized metabolism in the genusNicotiana
Measuring Capillary Flow Dynamics using Interlaced Two-Photon Volumetric Scanning
Authors: Giblin John T , Park Seong-Wook , Jiang John , Kılıç Kıvılcım , Kura Sreekanth , Boas David A. , Chen Ichun A. 
Published: September 2022

AbstractTwo photon microscopy and optical coherence tomography (OCT) are two standard methods for measuring flow speeds of red blood cells in microvessels, particularly in animal models. However, traditional two photon microscopy lacks the depth of field to adequately capture the full volumetric complexity of the cerebral microvasculature and OCT lacks the specificity offered by fluorescent labeling. In addition, the traditional raster scanning technique utilized in both modalities requires a balance of image frame rate and field of view, which severely limits the study of RBC velocities in the microvascular network. Here, we overcome this by using a custom two photon system with an axicon based Bessel beam to obtain volumetric images of the microvascular network with fluorescent specificity. We combine this with a novel scan pattern that generates pairs of frames with short time delay sufficient for tracking red blood cell flow in capillaries. We track flow speed in 10 or more capillaries simultaneously at 1 Hz in a 237 μm x 237μm x 120 μm volume and quantify both spatial and temporal variability in speed. We also demonstrate the ability to track flow speed changes around stalls in capillary flow.
Genozip 14 - advances in compression of BAM and CRAM files
Authors: Lan Divon , Llamas Bastien 
Published: September 2022

AbstractSummaryGenozip performs compression of a wide range of genomic data, including widely used FASTQ, BAM and VCF file formats. Here, we introduce the latest advancement in Genozip technology, focused on compression of BAM and CRAM files. We demonstrate Genozip’s ability to compress data generated by a variety of study types (e.g., whole genome sequencing, DNA methylation, RNASeq), sequencing technologies and aligners, up to 2.7 times better than the current state of the art compressor, CRAM version 3.1.Availability and implementationGenozip is freely available for academic research use and has been tested for Linux, Mac and Windows. Installation instructions are available at https://genozip.com/installing.html. A user manual is available at https://genozip.com/manual.html.Supplementary informationSupplementary data are available.
The Ecosystem Pressure-Volume Curve
Authors: Binks Oliver , Meir Patrick , Mencuccini Maurizio 
Published: September 2022

AbstractThe ecosystem pressure-volume curve (EPV) is the relationship between vegetation water content and a representative value of water potential applied on a ground-area basis. The EPV attempts to reconcile our detailed and physically rigorous understanding of small-scale field-measureable processes to the spatial scale applicable to ecosystem and climate science. Successfully bridging that gap in scale potentially allows us to use field measurements to interpret remote sensing data, and then remote sensing data to inform our understanding of vegetation-climate interactions. Here we clearly define the idea of the EPV, evaluate the limitations of applying values of water content and water potential to ecosystems on a ground area basis, and discuss practical ways to construct the EPV with existing data. We also present the first EPVs based on data from nine different plots, including tropical rainforest, savanna, temperate forest, and a long-term drought experiment in Amazonian rainforest (Caxiuanã, State of Pará, Brazil). The initial findings suggest high levels of consistency among sites. In particular, the ratio of water to biomass across ecosystems appears to be constrained to around 1:3. Seven of nine sites had closely converging ‘relative maximum water storage’ (the proportion of total stored water than can be lost before an ecosystem succumbs to physiological damage) at 9.1% +/-1.8 standard deviation. Relative ecosystem capacitance may increase with site biomass (P = 0.091), but varied little across sites with a mean of 0.068 MPa−1 +/-0.029 standard deviation. These first estimates suggest that the EPV idea may reveal useful trends across ecosystems, potentially paving the way to increasing the ecophysiological significance of remote sensing data, and enabling an alternative method for modelling long-term ecosystem-climate feedbacks based on equilibrium thermodynamics.
MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization
Authors: Zhang Yuwen , Cao Xuan , Gao Zehua , Ma Xuying , Wang Qianfeng , Cai Xiumei , Zhang Yan , Zhang Zhao , Wei Gang , Wen Bo 
Published: September 2022

AbstractLong interspersed nuclear elements (LINEs) play essential role in shaping chromatin state, while the factors that cooperate with LINEs and their roles in higher-order chromatin organization remain poorly understood. Here we show that MATR3, a nuclear matrix protein, interplays with antisense LINE1 (AS L1) RNAs to form into a gel-like meshwork via phase-separation, providing a partially dynamic platform for chromatin spatial organization. Either depletion of MATR3 or AS L1 RNAs changes nuclear distribution of each other and leads to chromatin reorganization in the nucleus. After MATR3 depletion, topologically associating domains (TADs) that highly transcribed MATR3-associated AS L1 RNAs showed a decrease on local chromatin interactions. Furthermore, amyotrophic lateral sclerosis (ALS)-associated MATR3 mutants alter biophysical features of the MATR3-AS L1 RNA meshwork and cause chromatin reorganization. Collectively, we revealed an essential role of meshwork formed by nuclear matrix and retrotransposon-derived RNAs in gathering chromatin in the nucleus.
Vowel and formant representation in human auditory speech cortex
Authors: Oganian Yulia , Bhaya-Grossman Ilina , Johnson Keith , Chang Edward F. 
Published: September 2022

SummaryVowel sounds are a fundamental component of human speech across all languages. Vowels are cued acoustically by formants, the resonance frequencies determined by the shape of the vocal tract during speaking. An outstanding question in neurolinguistics is how the human brain processes vowel formants during speech perception. We used high-density intracranial recordings from the human speech cortex on the superior temporal gyrus (STG) while participants listened to natural continuous speech to address this question. We derived two-dimensional receptive fields based on the first and second formants to characterize tuning to vowel sounds. We found that neural activity at single STG sites was highly selective for particular zones in the formant space. Furthermore, this formant tuning shifted dynamically to adjust for speaker-specific spectral context. Despite this formant selectivity, local cortical responses were not sufficient to reliably discriminate between vowel categories. Instead, vowel category representations could be accurately decoded when using the entire population of formant encoding electrodes. Together, our results reveal that vowels are locally encoded in STG with complex acoustic tuning in two-dimensional formant space. As a population code this gives rise to phonological vowel perception.
ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development
Authors: Graham-Paquin Adda-Lee , Saini Deepak , Sirois Jacinthe , Hossain Ishtiaque , Katz Megan S. , Zhuang Qinwei Kim-Wee , Kwon Sin Young , Yamanaka Yojiro , Bourque Guillaume , Bouchard Maxime , Pastor William A. 
Published: September 2022

ABSTRACTZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found thatZmym2-/-mice show embryonic lethality by E10.5. Molecular characterization ofZmym2-/-embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice.Zmym2-/-embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. Interaction and colocalization data indicate that ZMYM2 homes to germline genes via binding to the non-canonical polycomb complex PRC1.6 and to transposons via the TRIM28 complex. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation.ZMYM2-/-human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.
Steric-free bioorthogonal profiling of cellular acetylation and glycosylation via a fluorine-selenol displacement reaction (FSeDR)
Authors: Zhao Yue , Zhao Mi , Lyu Zhigang , Gorman Nicole , Lewis Todd R. , Goldman Aaron R. , Tang Hsin-Yao , Wang Rongsheng E. 
Published: September 2022

AbstractGlobal detection and identification of protein post-translational modification (PTM) is a major bottleneck due to its dynamic property and rather low abundance. Tremendous efforts have been since made to develop antibody-based immunoaffinity enrichment or bioorthogonal chemistry-based chemical reporter approach but both suffer from inherent limitations. Following our previously reported steric-free tagging strategy, we hereby report the invention of selenol as a new generation of fluorine-displacement probe. The fluorine-selenol based displacement reaction enabled us to efficiently label and image acetylation and glycosylation at cellular level. We further pursued FSeDR in tandem with SILAC based quantitative proteomics to globally profile acetylation substrate proteins in a representative prostate cancer cell line PC3. Our results unraveled the fluorine-based toolbox for powerful chemical biology probing and allow for the future study of PTMs in a systemic manner.
Real-time TIRF imaging of single adiponectin vesicle exocytosis in 3T3-L1 adipocytes stably expressing mCherry fused to human adiponectin
Authors: Shrestha Man Mohan , Barg Sebastian , Olofsson Charlotta S. 
Published: September 2022

AbstractAdiponectin is a peptide hormone abundantly released from adipocytes, and reduced circulating levels are associated with obesity-related diseases, such as type 2 diabetes, insulin resistance and cardiovascular disease. Adiponectin is released by regulated exocytosis of secretory vesicles, but traditional molecular biology and imaging techniques lack the specificity and time resolution to adequately quantify exocytosis and trafficking of adiponectin-containing vesicles. Here we generated 3T3-L1 adipocytes that stably express mCherry-tagged human adiponectin, resulting in robust labelling of small adiponectin vesicles with a diameter of 200-300 nm, in live cells. Total internal reflection fluorescence (TIRF) microscopy was used to visualise and quantify exocytosis and adiponectin release in real-time, observed as rapid disappearance of the fluorescence of individual vesicles. Bulk adiponectin secretion measurements confirmed that the labelled adiponectin was secreted to the surrounding solution under these conditions, and expressed in the same vesicle population as endogenous adiponectin. In contrast to previous electrophysiological results, elevation of cytosolic Ca2+alone was sufficient to induce exocytosis, although at a lower rate compared to elevated cytosolic cAMP. We conclude that the adiponectin-mCherry-labelled cells are useful for studying adiponectin exocytosis at the single vesicle level, and that an intracellular elevation of either cAMP or Ca2+can trigger adiponectin vesicle release.
A flexible and efficient microfluidics platform for the characterization and isolation of novel bacteriophages
Authors: Mabrouk Adam Sidi , Ongenae Véronique , Claessen Dennis , Brenzinger Susanne , Briegel Ariane 
Published: September 2022

ABSTRACTBacteriophages are viruses that infect bacteria. This property makes them highly suitable for varied uses in industry or in the development of the treatment of bacterial infections. However, the conventional methods that are used to isolate and analyze these bacteriophages from the environment are generally cumbersome and time-consuming. Here, we adapted a high-throughput microfluidic setup for long-term analysis of bacteriophage-bacteria interaction and demonstrate isolation of phages from environmental samples.
CTNND2 regulation by the SRGAP2 protein family links human evolution to synaptic neoteny
Authors: Assendorp Nora , Fossati Matteo , Libé-Philippot Baptiste , Christopoulou Eirini , Depp Marine , Rapone Roberta , Dingli Florent , Loew Damarys , Vanderhaeghen Pierre , Charrier Cécile 
Published: September 2022

SUMMARYHuman-specific genes are potential drivers of brain evolution. Among them, SRGAP2C has contributed to the emergence of features characterizing human cortical synapses, including their extended period of maturation. SRGAP2C inhibits its ancestral copy, the postsynaptic protein SRGAP2A; yet the synaptic molecular pathways differentially regulated in humans by SRGAP2 proteins remain largely unknown. Here, we identify CTNND2, a protein implicated in severe intellectual disability (ID) in the Cri-du-Chat syndrome, as an SRGAP2 effector. We demonstrate that CTNND2 slows down synaptic maturation and promotes neuronal homeostasis. During postnatal development, CTNND2 moderates neuronal excitation and excitability. In adults, it supports synapse maintenance. While CTNND2 deficiency is deleterious and results in the synaptic loss of SYNGAP1, another major ID-associated protein, the human-specific protein SRGAP2C enhances CTNND2 synaptic accumulation in human neurons. Our findings reveal that CTNND2 regulation by SRGAP2C contributes to synaptic neoteny in humans, and link human-specific and ID genes at the synapse.