bluuebunny/crossref_metadata_2025_split huggingface dataset:
The making of cauliflowers: the story of unsuccessful flowers
Authors: Azpeitia Eugenio , Tichtinsky Gabrielle , Le Masson Marie , Serrano-Mislata Antonio , Gregis Veronica , Gimenez Carlos , Prunet Nathanaёl , Lucas Jérémy , Farcot Etienne , Kater Martin M. , Bradley Desmond , Madueño Francisco , Godin Christophe , Parcy Francois 
Published: February 2021

AbstractThe arrangement of plant organs, called phyllotaxis, produce remarkable spiral or whorled patterns. Cauliflowers present a unique phyllotaxis with a multitude of spirals over a wide range of scales. How such a self-similar fractal organization emerges from developmental mechanisms has remained elusive. Combining experimental assays with modeling, we found that cauliflowers arise due to the hysteresis of the bistable floral network that generates inflorescences imprinted by a transient floral state. We further show how additional mutations affecting meristem growth dynamics can induce the production of conical phyllotactic structures reminiscent of the conspicuous fractal Romanesco shape. This study reveals how the spectacular morphological modification of the inflorescences in cauliflower and Romanesco shape arises from the hysteresis of the genetic programs controlling inflorescence development.One Sentence SummaryThe molecular making of cauliflowers
The Evolution of Chunks in Sequence Learning
Authors: Tosatto Laure , Fagot Joël , Nemeth Dezso , Rey Arnaud 
Published: February 2021

AbstractChunking mechanisms are central to several cognitive processes and notably to the acquisition of visuo-motor sequences. Individuals segment sequences into chunks of items to perform visuo-motor tasks more fluidly, rapidly, and accurately. However, the exact dynamics of chunking processes in the case of extended practice remain unclear. Using an operant conditioning device, eighteen Guinea baboons (Papio papio) produced a fixed sequence of nine movements during 1,000 trials by pointing to a moving target on a touch screen. Response times analyses revealed a specific chunking pattern of the sequence for each baboon. More importantly, we found that these patterns evolved during the course of the experiment, with chunks becoming progressively fewer and longer. We identified two chunk reorganization mechanisms: therecombinationof preexisting chunks and theconcatenationof two distinct chunks into a single one. These results provide new evidence on chunking mechanisms in sequence learning and challenge current models of associative and statistical learning.
Dynamics of primary productivity in relation to submerged vegetation of a shallow, eutrophic lagoon: a field and mesocosm study
Authors: Berthold Maximilian , Paar Martin 
Published: February 2021

AbstractAquatic ecosystems nowadays are under constant pressure, either from recent or historical events. In most systems with increased nutrient supply, submerged macrophytes got replaced by another stable state, dominated by phytoplankton as main primary producer. Yet, reducing the nutrient supply did not yield the aimed goal of restored habitats for submerged macrophytes in systems worldwide. The question arises, why submerged macrophytes do not re-colonize, and if they are actually competitive. Therefore, primary production assays were conducted inex-situbentho-pelagic mesocosms and compared to the actual ecosystem, a turbid brackish lagoon of the southern Baltic Sea. Mesocosm were either manipulated to be colonized by macrophytes, or stayed phytoplankton dominated. Oxygen evolution was monitored over a period of five months in 5 min (mesocosms) to 10 min (ecosystem) intervals. Surface and depth-integrated production was calculated to analyse seasonal and areal resolved production patterns. It was found that macrophyte mesocosms were more stable, when considering only surface O2production. However, calculating depth-integrated production resulted in net-heterotrophy in both shallow mesocosms approaches and the actual ecosystem. This heterotrophy is likely mediated by sediment respiration and POC accumulation in mesocosms, and a low share of productive to respiring water column in the actual ecosystem. Therefore, it seems unlikely that macrophytes will re-settle, as constant net-heterotrophy may allow for high-nutrient turnover at sediment-water interfaces and within the water column, favouring phytoplankton. Changes within the ecosystem cannot be expected without further restoration measures within and in the systems proximity.
KCTD19 associates with ZFP541 and HDAC1 and is required for meiotic exit in male mice
Authors: Oura Seiya , Koyano Takayuki , Kodera Chisato , Horisawa-Takada Yuki , Matsuyama Makoto , Ishiguro Kei-ichiro , Ikawa Masahito 
Published: February 2021

AbstractMeiosis is a cell division process with complex chromosome events where various molecules must work in tandem. To find meiosis-related genes, we screened evolutionarily conserved and reproductive tract-enriched genes using the CRISPR/Cas9 system and identified potassium channel tetramerization domain containing 19 (Kctd19) as an essential factor for meiosis. In prophase I,Kctd19deficiency did not affect synapsis or the DNA damage response, and chiasma structures were also observed in metaphase I spermatocytes ofKctd19KO mice. However, spermatocytes underwent apoptotic elimination during the metaphase-anaphase transition. We were able to rescue theKctd19KO phenotype with an epitope-taggedKctd19transgene. Immunoprecipitation-mass spectrometry identified zinc finger protein 541 (ZFP541) and histone deacetylase 1 (HDAC1) as binding partners of KCTD19, indicating that KCTD19 is involved in chromatin modification. Phenotyping ofZfp541KO spermatocytes demonstrated XY chromosome asynapsis and recurrent DNA damage in the late pachytene stage, leading to apoptosis. In summary, our study reveals that KCTD19 associates with ZFP541 and HDAC1, and that both KCTD19 and ZFP541 were essential for meiotic exit in male mice.Author summaryMeiosis is a fundamental process that consisting of one round of genomic DNA replication and two rounds of chromosome segregation producing four haploid cells. To properly distribute their genetic material, cells need to undergo complex chromosome events such as a physical linkage of homologous chromosomes (termed synapsis) and meiotic recombination. The molecules involved in these events have not been fully characterized yet, especially in mammals. Using a CRISPR/Cas9-screening system, we identified the potassium channel tetramerization domain containing 19 (Kctd19) as an essential factor for meiosis in male mice. Further, we identified zinc finger protein 541 (ZFP541) and histone deacetylase 1 (HDAC1) as binding partners of KCTD19. By observing meiosis ofZfp541knockout germ cells, we found thatZfp541was also essential for meiotic completion. These results show that the KCTD19/ZFP541 complex plays a critical role and is indispensable for male meiosis and fertility.
Integration of electric, calcium, reactive oxygen species and hydraulic signals during rapid systemic signaling in plants
Authors: Fichman Yosef , Mittler Ron 
Published: February 2021

AbstractThe sensing of abiotic stress, mechanical injury, or pathogen attack by a single plant tissue results in the activation of systemic signals that travel from the affected tissue to the entire plant, alerting it of an impending stress or pathogen attack. This process is essential for plant survival during stress and is termed systemic signaling. Among the different signals triggered during this process are calcium, electric, reactive oxygen species (ROS) and hydraulic signals. These are thought to propagate at rapid rates through the plant vascular bundles and to regulate many of the systemic processes essential for plant survival. Although the different signals activated during systemic signaling are thought to be interlinked, their coordination and hierarchy remain to be determined. Here, using a combination of advanced whole-plant imaging and hydraulic pressure measurements, we studied the activation of all four systemic signals in wild type and differentArabidopsis thalianamutants subjected to a local high light (HL) stress or wounding. Our findings reveal that in response to wounding systemic changes in membrane potential, calcium, ROS, and hydraulic pressure are coordinated by glutamate receptor-like (GLR) proteins 3.3 and 3.6, while in response to HL the respiratory burst oxidase homolog D-driven systemic ROS signal could be separated from systemic changes in membrane potential and calcium levels. We further determine that plasmodesmata functions are required for systemic changes in membrane potential, calcium, and ROS during systemic signaling. Our findings shed new light on the different mechanisms that integrate different systemic signals in plants during stress.Significance statementThe ability of plants to transmit a signal from a stressed or wounded tissue to the entire plant, termed systemic signaling, is key to plant survival during conditions of environmental stress. At least four different systemic signals are thought to be involved in this process: electric, calcium, reactive oxygen and hydraulic. However, how are they coordinated and whether they can be stress-specific is mostly unknown. Here we report that different types of stimuli can induce different types of systemic signals that may or may not be linked with each other. We further reveal that hydraulic waves can be actively regulated in plants in response to wounding, and that proteins that regulate plasmodesmata pores play a key role in systemic signaling.
Photoperiod shapes aluminium tolerance in plants
Authors: Siqueira João Antonio , Wakin Thiago , Batista-Silva Willian , Silva José Cleydson F. , Vicente Matheus H. , Silva Jéssica C. , Clarindo Wellington R. , Zsögön Agustin , Peres Lazaro E. P. , De Veylder Lieven , Fernie Alisdair R. , Nunes-Nesi Adriano , Araújo Wagner L. 
Published: February 2021

AbstractAluminium is a limiting factor for crop productivity in acidic soils (pH ≤ 5.5). Since acid soil distribution on Earth cannot adequately explain the differential Al tolerance across the plant kingdom, we investigated photoperiod effects on plant Al tolerance. We observed that with increasing distance from the equator, Al tolerance disappears, suggesting a relationship with the photoperiod. Long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. DNA-checkpoint-related genes are under positive selection inArabidopsisaccessions from regions with shorter days, suggesting photoperiod acts as a selective barrier for Al tolerance. Our findings revealed that diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance.One-Sentence SummaryAluminum is a major constraint for crop yield worldwide. We reveal that photoperiod acts as a barrier for Al tolerance in plants.
Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2
Authors: Ehling Roy A. , Weber Cédric R. , Mason Derek M. , Friedensohn Simon , Wagner Bastian , Bieberich Florian , Kapetanovic Edo , Vazquez-Lombardi Rodrigo , Di Roberto Raphaël B. , Hong Kai-Lin , Wagner Camille , Sheward Daniel J. , Murrell Ben , Yermanos Alexander , Cuny Andreas P. , Savic Miodrag , Rudolf Fabian , Reddy Sai T. 
Published: February 2021

ABSTRACTIsolation and characterization of antibodies in COVID-19 patients has largely focused on memory B cells, however it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in controlling and resolving SARS-CoV-2 infection. To date there is little known about the specificity of plasma cells in COVID-19 patients. This is largely because plasma cells lack surface antibody expression, which complicates their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and high-throughput mammalian display screening to interrogate the specificity of plasma cells from 16 convalescent COVID-19 patients. Single-cell sequencing allows us to profile antibody repertoire features in these patients and identify highly expanded clonal lineages. Mammalian display screening is employed to reveal that 37 antibodies (out of 132 candidates) derived from expanded plasma cell clonal lineages are specific for SARS-CoV-2 antigens, including antibodies that target the receptor binding domain (RBD) with high affinity and exhibit potent neutralization of SARS-CoV-2.One Sentence SummarySingle-cell antibody repertoire sequencing and high-throughput screening identifies highly expanded plasma cells from convalescent COVID-19 patients that produce SARS-CoV-2-specific antibodies capable of potent neutralization.
GRK2/3/5/6 knockout: The impact of individual GRKs on arrestin-binding and GPCR regulation
Authors: Drube J. , Haider R.S. , Matthees E.S.F. , Reichel M. , Zeiner J. , Fritzwanker S. , Ziegler C. , Barz S. , Klement L. , Kliewer A. , Miess E. , Kostenis E. , Schulz S. , Hoffmann C. 
Published: February 2021

AbstractG protein-coupled receptors (GPCRs) comprise the largest family of transmembrane receptors and represent major drug targets. Upon ligand stimulation, GPCRs activate G proteins and undergo a complex regulation by interaction with GPCR kinases (GRKs) and formation of receptor–arrestin complexes. For many GPCRs, this mechanism triggers receptor desensitisation, internalisation, and possibly a second intracellular signalling wave. Here we created eleven different HEK293 knockout cell clones for GRK2, 3, 5, and 6 individually and in combination. These include four single, two double, four triple, and the quadruple GRK knockout. The statistical evaluation of β-arrestin1/2 interactions for twelve different receptors grouped the tested GPCRs into two main subsets: those for which β-arrestin interaction was mediated by either GRK2, 3, 5, or 6 and those that are mediated by GRK2 or 3 only. Interestingly, the overexpression of specific GRKs was found to induce a robust, ligand-independent β-arrestin interaction with the V2R and AT1R. Finally, using GRK knockout cells, PKC inhibitors, and β-arrestin mutants, we present evidence for differential AT1R–β-arrestin2 complex configurations mediated by selective engagement of PKC, GRK2, or GRK6. We anticipate our novel GRK-knockout platform to facilitate the elucidation of previously unappreciated details of GRK-specific GPCR regulation and β-arrestin complex formation.
The role of auxin and sugar signaling in dominance inhibition of inflorescence growth by fruit load
Authors: Goetz Marc , Rabinovich Maia , Smith Harley M. 
Published: February 2021

ABSTRACTDominance inhibition of shoot growth by fruit load is a major factor that regulates shoot architecture and limits yield in agriculture and horticulture crops. In annual plants, the inhibition of inflorescence growth by fruit load occurs at a late stage of inflorescence development termed the end of flowering transition. Physiological studies show that this transition is mediated by production and export of auxin from developing fruits in close proximity to the inflorescence apex. In the meristem, cessation of inflorescence growth is controlled in part by the age dependent pathway, which regulates the timing of arrest. Here, results show that the end of flowering transition is a two-step process in which the first stage is characterized by a cessation of inflorescence growth, while immature fruit continue to develop. At this stage, dominance inhibition of inflorescence growth by fruit load correlates with a selective dampening of auxin transport in the apical region of the stem. Subsequently, an increase in auxin response in the vascular tissues of the apical stem where developing fruits are attached marks the second stage for the end of flowering transition. Similar to the vegetative and floral transition, the end of flowering transition correlates with a change in sugar signaling and metabolism in the inflorescence apex. Taken together, our results suggest that during the end of flowering transition, dominance inhibition of inflorescence shoot growth by fruit load is mediated by auxin and sugar signaling.One-sentence summaryDominance inhibition of inflorescence shoot growth by fruit load is involves auxin and sugar signaling during the end of flowering transition.
Non-invasive sex genotyping of paicheArapaima gigasby qPCR: An applied bioinformatic approach to identify sex differences
Authors: López-Landavery Edgar A. , Corona-Herrera Guillermo A. , Santos-Rojas Luis E. , Herrera-Castillo Nadhia M. , Delgadin Tomás H. , Tapia-Morales Sandra , González-Martinez Sophia , Reyes-Flores Lorenzo E. , Marín Alan , Yzásiga-Barrera Carmen G. , Fernandino Juan I. , Zelada-Mázmela Eliana 
Published: February 2021

AbstractArapaima gigas, one of the largest freshwater fish in the world, is suffering from high fishing pressure and habitat loss, which threaten the conservation status of its natural populations. Of great cultural importance to Amazonian people, the paiche or pirarucuA. gigasis in high demand for its meat, ornamental uses and other byproducts such as scales. Aquaculture is a feasible solution to this dilemma. However, the fact thatA. gigaspresents no sexual dimorphism until it is 5 years old and its long period to sexual maturity are major obstacles for brood-stock management and fingerling production. Thus, the aim of this study was to develop a molecular tool for non-invasive genotypic sexing of paiche throughout its life cycle. We collected samples from gonads, fins and gill mucus of juvenile specimens from local facilities for histological and molecular analysis. Based on the recently available genome sequence of the paiche and making use of current NGS method, we implemented a novel approach, called Genome Differences by Unmapped Reads, to identify DNA sex markers. We found a Male-Specific Region (MSR), identified as MSR_3728, to be present only in males. Next, we designed two specific sets of primers on this region to identify genotypic sex by qPCR assays. Both primer sets, MSR_107 and MSR_129, detected males with 100% accuracy. Then we developed a duplex qPCR reaction for each primer set along a reference gene, analyzed the melting curves and detected males by observing two distinct peaks, one for MSR_107 or MSR_129 and one for the reference, while females only presented the reference peak. The same results were obtained for gonads, fins and interestingly, a non-invasive source from gill mucus samples. Finally, the gonads were evaluated histologically in a double-blind test, showing 100% accuracy with qPCR assay for identifying males and females. Data clearly demonstrated a novel pipeline approach for identifying DNA sex markers, followed by a quick, non-invasive, cost-effective duplex qPCR method for sexing A.gigas. These results may be valuable to efficient paiche aquaculture and conservation studies, helping to reduce the fishing pressure on its natural populations.Highlights of the manuscript–Implementation of a novel approach, called Genome Differences by Unmapped Reads, to identify DNA sex markers.–Finding of a Male-Specific Region (MSR), present only in males.–Development of a duplex qPCR to identify genotypic sex through non-invasive sampling.
SalmonellaTyphimurium outer membrane protein A (OmpA) renders protection against nitrosative stress by promoting SCV stability in murine macrophages
Authors: Roy Chowdhury Atish , Sah Shivjee , Varshney Umesh , Chakravortty Dipshikha 
Published: February 2021

AbstractPorins are highly conserved bacterial outer membrane proteins involved in the selective transport of charged molecules across the membrane. Despite their significant contributions to the pathogenesis of Gram-negative bacteria, their precise role in salmonellosis remains elusive. In this study, we investigated the role of porins (OmpA, OmpC, OmpD, and OmpF) inSalmonellaTyphimurium (STM) pathogenesis. OmpA played a multifaceted role in STM pathogenesis, and a strain deleted forompA(STMΔompA) showed enhanced proneness to phagocytosis and compromised proliferation in macrophages. However, in the epithelial cells, despite being invasion deficient, it was hyper-proliferative. The poor colocalization of STMΔompAwith LAMP-1 confirmed impaired stability of SCV membrane around the intracellular bacteria, resulting in its (STMΔompA) release into the cytosol of macrophages where it is assaulted with reactive nitrogen intermediates (RNI). The cytosolic localization of STMΔompAwas responsible for the downregulation of SPI-2 encoded virulence factor SpiC, which is required to suppress the activity of iNOS. The reduced recruitment of nitrotyrosine on STM in the macrophage cytosol upon ectopically expressing Listeriolysin O (LLO) explicitly supported the pro-bacterial role of OmpA against the host nitrosative stress. Further, we show that the generation of time-dependent redox burst could be responsible for the enhanced sensitivity of STMΔompAtowards nitrosative stress. The absence of OmpA in STMΔompAresulted in the loss of integrity and enhanced porosity of the bacterial outer membrane, which was attributed to the upregulated expression ofompC,ompD,andompF. We showed the involvement of OmpF in the entry of excess nitrite in STMΔompA,thus increasing the susceptibility of the bacteria towardsin vitroandin vivonitrosative stress. In conclusion, we illustrated a mechanism of strategic utilization of OmpA compared to other porins by wildtypeSalmonellafor combating the nitrosative stress in macrophages.
Benchmarking Association Analyses of Continuous Exposures with RNA-seq in Observational Studies
Authors: Sofer Tamar , Kurniansyah Nuzulul , Aguet François , Ardlie Kristin , Durda Peter , Nickerson Deborah A. , Smith Joshua D. , Liu Yongmei , Gharib Sina A. , Redline Susan , Rich Stephen S. , Rotter Jerome I. , Taylor Kent D. 
Published: February 2021

AbstractLarge datasets of hundreds to thousands of individuals measuring RNA-seq in observational studies are becoming available. Many popular software packages for analysis of RNA-seq data were constructed to study differences in expression signatures in an experimental design with well-defined conditions (exposures). In contrast, observational studies may have varying levels of confounding of the transcript-exposure associations; further, exposure measures may vary from discrete (exposed, yes/no) to continuous (levels of exposure), with non-normal distributions of exposure. We compare popular software for gene expression -DESeq2, edgeR, andlimma- as well as linear regression-based analyses for studying the association of continuous exposures with RNA-seq. We developed a computation pipeline that includes transformation, filtering, and generation of empirical null distribution of association p-values, and we apply the pipeline to compute empirical p-values with multiple testing correction. We employ a resampling approach that allows for assessment of false positive detection across methods, power comparison, and the computation of quantile empirical p-values. The results suggest that linear regression methods are substantially faster with better control of false detections than other methods, even with the resampling method to compute empirical p-values. We provide the proposed pipeline with fast algorithms in R.