bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving the dynamics of photosynthetically produced ROS by high-resolution monitoring of chloroplastic EGSHinArabidopsis
Authors: Haber Zachary , Rosenwasser Shilo 
Published: March 2020

AbstractPlants are naturally subjected to fluctuations in light intensity, causing unbalanced photosynthetic electron fluxes and overproduction of reactive oxygen species (ROS). While high rates of ROS production are harmful, moderate levels play a signaling role, coordinating photosynthetic activity and downstream metabolism. Here, we explore the dynamics of light-dependent oxidant production by high-temporal-resolution monitoring of chloroplastic glutathione redox potential (chl-EGSH) using chloroplast-targeted-roGFP2-expressingArabidopsislines, over several days, under dynamic environmental conditions and in correlation with PSII operating efficiency. Peaks in chl-EGSHoxidation during light-darkness transitions, when light harvesting is not balanced with downstream metabolism, were observed. Increasing light intensities triggered a binary oxidation response, with a threshold around the light saturating point, pointing for two regulated oxidative states of the chl-EGSH. These patterns were not affected innpq1plants which are impaired in non-photochemical quenching. Frequency-dependent oscillations between the two oxidation states were observed under fluctuating light in WT andnpq1plants, but not inpgr5plants, suggesting a role for PSI photoinhibition in regulation of oxidant production. Remarkably,pgr5plants showed an increase in chl-EGSHoxidation during the nights following light stresses, linking between day photoinhibition and night redox metabolism. This work provides a comprehensive view on the balance between photosynthesis-dependent ROS production and antioxidant activity during light acclimation.
Expanding the Coverage of the Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches
Authors: Li Xuetong , Zhou Hongxia , Xiao Ning , Wu Xueting , Shan Yuanhong , Chen Longxian , Wang Cuiting , Wang Zixuan , Huang Jirong , Li Aihong , Li Xuan 
Published: March 2020

AbstractGenome-scale metabolomics analysis is increasingly used for pathway and function discovery in post-genomics era. The great potential offered by developed mass spectrometry (MS)-based technology has been hindered by the obstacle that only a small portion of detected metabolites were identifiable so far. To address the critical issue of low identification coverage in metabolomics, we adopted a deep metabolomics analysis strategy by integrating advanced algorithms and expanded reference databases. The experimental reference spectra, andin silicoreference spectra were adopted to facilitate the structural annotation. To further characterize the structure of metabolites, two approaches, structural motif search combined with neutral loss scanning, and metabolite association network were incorporated into our strategy. An untargeted metabolomics analysis was performed on 150 rice cultivars using Ultra Performance Liquid Chromatography (UPLC)-Quadrupole (Q)-Orbitrap mass spectrometer. 1939 of 4491 metabolite features in MS/MS spectral tag (MS2T) library were annotated, representing an extension of annotation coverage by an order of magnitude on rice. The differential accumulation patterns of flavonoids betweenindicaandjaponicacultivars were revealed, especially O-sulfated flavonoids. A series of closely-related flavonolignans were characterized, adding further evidence for the crucial role of tricin-oligolignols in lignification. Our study provides a great template in the exploration of phytochemical diversity for more plant species.
A Computational Design of a Programmable Biological Processor
Authors: Moškon Miha , Pušnik Žiga , Magdevska Lidija , Zimic Nikolaj , Mraz Miha 
Published: March 2020

AbstractBasic synthetic information processing structures, such as logic gates, oscillators and flip-flops, have already been implemented in living organisms. Current implementations of these structures are, however, hardly scalable and are yet to be extended to more complex processing structures that would constitute a biological computer.Herein, we make a step forward towards the construction of a biological computer. We describe a model-based computational design of a biological processor, composed of an instruction memory containing a biological program, a program counter that is used to address this memory and a biological oscillator that triggers the execution of the next instruction in the memory. The described processor uses transcription and translation resources of the host cell to perform its operations and is able to sequentially execute a set of instructions written within the so-called instruction memory implemented with non-volatile DNA sequences. The addressing of the instruction memory is achieved with a biological implementation of the Johnson counter, which increases its state after an instruction is executed. We additionally describe the implementation of a biological compiler that compiles a sequence of human-readable instructions into ordinary differential equations-based models. These models can be used to simulate the dynamics of the proposed processor.The proposed implementation presents the first programmable biological processor that exploits cellular resources to execute the specified instructions. We demonstrate the application of the proposed processor on a set of simple yet scalable biological programs. Biological descriptions of these programs can be written manually or can be generated automatically with the employment of the provided compiler.
Co-occurrence, habitat use and activity pattern of carnivore species in a coastal area of Argentina
Authors: Caruso N.C. , Luengos Vidal E.M. , Manfredi M.C. , Araujo M.S. , Lucherini M. , Casanave E.B. 
Published: March 2020

AbstractLand-sea interface is an ecotone where the intersection of marine and terrestrial ecosystems create unique ecological conditions for terrestrial mobile species and freshwater-adapted organisms to exploit marine-derived food resources. Mammalian carnivores play an important role in almost any ecosystem where they live due to their top-down (or trophic cascade) effects on prey species and primary producers, thus structuring ecosystems along varied food-web pathways. We use camera trapping to study the patterns of coexistence, habitat use and activity pattern of carnivores species in a coastal area in southern Buenos Aires province, Argentina. We were able to detect five of the seven species of Mammalian carnivores being the Pampas foxLycalopex gymnocercusand Geoffroy’s catLeopardus geoffroyithe two most common. Geoffroy’s cat seems to use more intensively those areas close to the shoreline, while we found little support of it for Pampas fox; which seems to use more inland areas. Congruently, we found evidence of a lack of spatial and, to a lower extent, temporal avoidance between the two most common carnivore species of our study area. Our findings support those previous studies indicating that the coastal dunes have an important role in the conservation of the biodiversity of Buenos Aires province. Wildlife conservation is compatible with carefully-designed ecotourism and limited infrastructure development and this may be a unique chance for the areas of Buenos Aires coast that have not been affected yet by poorly planned, conservation-unfriendly urbanization.
mrMLM v4.0: An R Platform for Multi-locus Genome-wide Association Studies
Authors: Zhang Ya-Wen , Tamba Cox Lwaka , Wen Yang-Jun , Li Pei , Ren Wen-Long , Ni Yuan-Li , Gao Jun , Zhang Yuan-Ming 
Published: March 2020

AbstractPrevious studies reported that some important loci are missed in single-locus genome-wide association studies (GWAS), especially because of the large phenotypic error in field experiments. To solve this issue, multi-locus GWAS methods have been recommended. However, only a few software packages are available. Therefore, an R software mrMLM, which includes our six multi-locus methods, was developed. mrMLM includes three components: dataset input, parameter setting and result output. The fread function in data.table is used to quickly read datasets, especially big datasets, and the doParallel package is used to conduct parallel computation using multiple CPUs. In addition, the graphical user interface software mrMLM.GUI v4.0, built upon Shiny, is also available. To confirm the correctness of the above programs, the same simulation datasets as used in previous studies, along with three real datasets, were re-analyzed by all the methods in mrMLM v4.0 and three widely-used methods. The results confirmed the advantages of our multi-locus methods over the current methods. The conclusion is also consistent with those in a Research Topic in Frontiers in Plant Science. Although a less stringent significance threshold is adopted, the false positive rates are effectively controlled. mrMLM is publicly available athttps://cran.r-project.org/web/packages/mrMLM/index.htmlorhttps://bigd.big.ac.cn/biocode/tools/BT007077as an open-source software.
Open Science Datasets from PREVENT-AD, a Longitudinal Cohort of Pre-symptomatic Alzheimer’s Disease
Authors: Tremblay-Mercier Jennifer , Madjar Cécile , Das Samir , Binette Alexa Pichet , Dyke Stephanie O.M. , Étienne Pierre , Lafaille-Magnan Marie-Elyse , Remz Jordana , Bellec Pierre , Collins D. Louis , Rajah M. Natasha , Bohbot Veronique , Leoutsakos Jeannie-Marie , Iturria-Medina Yasser , Kat Justin , Hoge Richard D. , Gauthier Serge , Tardif Christine L. , Chakravarty M. Mallar , Poline Jean-Baptiste , Rosa-Neto Pedro , Evans Alan C. , Villeneuve Sylvia , Poirier Judes , Breitner John C. S. ,   the PREVENT-AD Research Group
Published: March 2020

ABSTRACTTo move Alzheimer Disease (AD) research forward it is essential to collect data from large cohorts, but also make such data available to the global research community. We describe the creation of an open science dataset from the PREVENT-AD (PResymptomatic EValuation of Experimental or Novel Treatments for AD) cohort, composed of cognitively unimpaired older individuals with a parental or multiple-sibling history of AD. From 2011 to 2017, 386 participants were enrolled (mean age 63 years old ± 5) for sustained investigation among whom 349 have retrospectively agreed to share their data openly. Repositories are findable through the unified interface of the Canadian Open Neuroscience Platform (https://portal.conp.ca/) and contain up to five years of longitudinal imaging data, cerebral fluid biochemistry, neurosensory capacities, cognitive, genetic, and medical information. Imaging data can be accessed openly athttps://openpreventad.loris.cawhile most of the other information, sensitive by nature, is accessible by qualified researchers athttps://registeredpreventad.loris.ca. In addition to being a living resource for continued data acquisition, PREVENT-AD offers opportunities to facilitate understanding of AD pathogenesis.
Thalamic activity patterns unfolding over multiple time scales predict seizure onset in absence epilepsy
Authors: Sorokin Jordan Michael , Williams Alex , Ganguli Surya , Huguenard John 
Published: March 2020

AbstractThe brain has a remarkable, yet poorly understood, capacity to perform rapid dynamic switching between different cognitive states. Absence epilepsy, characterized by sudden transitions to and from highly synchronous thalamocortical oscillations, provides a unique window to investigate rapid state switching. Here we explored the transition into seizures in detail using simultaneous extracellular unit recordings from the thalamocortical circuit in the Scn8a mouse, a validated murine model of absence epilepsy. We find that trial-averaged neural firing in the thalamus, but not cortex, was transiently elevated several seconds prior to seizure onset. However, we observed large single-trial variability in pre-ictal dynamics both within and across subjects, suggesting possible heterogeneous transition dynamics into absence seizures. To quantify the single-trial amplitude and temporal variability, we developed a statistical model, which revealed that individual seizures are preceded by low dimensional neural dynamics that vary in amplitude and time across seizures. Interestingly, the single-trial pre-seizure amplitude modulation uncovered by the model showed strong periodicity over trials, suggesting that pre-ictal dynamics may co-modulate with arousal state. To our knowledge, our results are the first characterization of single-unit pre-ictal firing dynamics across the thalamocortical circuit in absence epilepsy. Our results argue that seizure-monitoring devices may be able to capitalize on seizure-by-seizure changes in pre-ictal activity to better predict seizure onset, and that the thalamus may be a source of clinically useful pre-ictal signatures.
Asymmetric second-generation genomic incompatibility in interspecific crosses betweenCiona robustaandCiona intestinalis
Authors: Ohta Naoyuki , Kaplan Nicole , Ng James Tyler , Gravez Basile Jules , Christiaen Lionel 
Published: March 2020

AbstractReproductive isolation is central to speciation, but interspecific crosses between two closely related species can produce viable and fertile hybrids. Two different species in the tunicate genusCiona,Ciona robustaandCiona intestinaliscan produce hybrids. However, wild sympatric populations display limited gene flow, suggesting the existence of obstacles to interspecific reproduction that remain unknown. Here, we took advantage of a closed inland culture system to crossC. robustawithC. intestinalisand established F1 and F2 hybrids. We monitored post-embryonic development, survival, and sexual maturation to further probe the physiological mechanisms underlying reproductive isolation. Partial viability of first and second generation hybrids indicated that both pre- and postzygotic mechanisms contributed to genomic incompatibilities in hybrids. Asymmetrical second generation inviability and infertility suggested that interspecific genomic incompatibilities involved interactions between the maternal, zygotic and mitochondrial genomes during development. This study paves the way to quantitative genetic approaches to study the mechanisms underlying genomic incompatibilities and other complex traits in the genome-enabledCionamodel.
Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments
Authors: Pálinkás Hajnalka L. , Békési Angéla , Róna Gergely , Pongor Lőrinc , Tihanyi Gergely , Holub Eszter , Póti Ádám , Gemma Carolina , Ali Simak , Morten Michael J. , Rothenberg Eli , Pagano Michele , Szüts Dávid , Győrffy Balázs , Vértessy Beáta G. 
Published: March 2020

ABSTRACTNumerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug-treatment in human cancer cell-line HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined within situsuper-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards more active/functional segments. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can also be applied to study the dynamicspatio-temporalnature of genomic uracil.
Addition of new neurons and the emergence of a local neural circuit for precise timing
Authors: Tupikov Yevhen , Jin Dezhe Z. 
Published: March 2020

AbstractDuring development, neurons arrive at local brain areas in extended period of time, but how they form local neural circuits is unknown. Here we computationally model the emergence of a network for precise timing in the premotor nucleus HVC in songbird. We show that new motor projection neurons, mostly added to HVC before and during song learning, are recruited to the end of a growing feedforward network. High spontaneous activity of new neurons makes them the prime targets for recruitment in a self-organized process via synaptic plasticity. Once recruited, the new neurons fire readily at precise times, and they become mature. Neurons that are not recruited become silent and replaced by new immature neurons. Our model incorporates realistic HVC features such as interneurons, spatial distributions of neurons, and distributed axonal delays. The model predicts that the birth order of the projection neurons correlates with their burst timing during the song.Significance StatementFunctions of local neural circuits depend on their specific network structures, but how the networks are wired is unknown. We show that such structures can emerge during development through a self-organized process, during which the network is wired by neuron-by-neuron recruitment. This growth is facilitated by steady supply of immature neurons, which are highly excitable and plastic. We suggest that neuron maturation dynamics is an integral part of constructing local neural circuits.
Lysine63-linked ubiquitin chains earmark GPCRs for BBSome-mediated removal from cilia
Authors: Shinde Swapnil Rohidas , Nager Andrew R. , Nachury Maxence V. 
Published: March 2020

ABSTRACTRegulated trafficking of G-protein coupled receptors (GPCRs) controls cilium-based signaling pathways. β-arrestin, a molecular sensor of activated GPCRs, and the BBSome, a complex of Bardet-Biedl Syndrome (BBS) proteins, are required for the signal-dependent exit of ciliary GPCRs but the functional interplay between β-arrestin and the BBSome remains elusive. Here we find that, upon activation, ciliary GPCRs become tagged with K63-linked ubiquitin (K63Ub) chains in a β-arrestin-dependent manner prior to BBSome-mediated exit. Removal of ubiquitin acceptor residues from the somatostatin receptor 3 (SSTR3) and from the orphan GPCR GPR161 demonstrates that ubiquitination of ciliary GPCRs is required for their regulated exit from cilia. Furthermore, targeting a K63Ub-specific deubiquitinase to cilia blocks the exit of GPR161, SSTR3 and Smoothened (SMO) from cilia. Finally, ubiquitinated proteins accumulate in cilia of mammalian photoreceptors andChlamydomonascells when BBSome function is compromised. We conclude that K63Ub chains mark GPCRs and other unwanted ciliary proteins for recognition by the ciliary exit machinery.
Histidine-Triad Hydrolases Provide Resistance to Peptide-Nucleotide Antibiotics
Authors: Yagmurov Eldar , Tsibulskaya Darya , Livenskyi Alexey , Serebryakova Marina , Wolf Yury I. , Borukhov Sergei , Severinov Konstantin , Dubiley Svetlana 
Published: March 2020

ABSTRACTTheEscherichia colimicrocin C (McC) and related compounds are potent Trojan-horse peptide-nucleotide antibiotics. The peptide part facilitates transport into sensitive cells. Inside the cell, the peptide part is degraded by non-specific peptidases releasing an aspartamide-adenylate containing a phosphoramide bond. This non-hydrolyzable compound inhibits aspartyl-tRNA synthetase. In addition to the efficient export of McC outside of the producing cells, special mechanisms evolved to avoid self-toxicity caused by the degradation of the peptide part inside the producers. Here, we report that histidine triad (HIT) hydrolases encoded in biosynthetic clusters of some McC homologs or by stand-alone genes confer resistance to McC–like compounds by hydrolyzing the phosphoramide bond in toxic aspartamide-adenosine, rendering them inactive.IMPORTANCEUncovering the mechanisms of resistance is a required step for countering the looming antibiotic resistance crisis. In this communication, we show how universally conserved histidine triad hydrolases provide resistance to microcin C – a potent inhibitor of bacterial protein synthesis.
Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information
Authors: Nguyen Thanh Minh , Jeevan Jacob John , Xu Nuo , Chen Jake 
Published: March 2020

AbstractIn this work, we design the Polar Gini Curve (PGC) technique, which combines the gene expression and the 2D embedded visual information to detect biomarkers from single-cell data. Theoretically, a Polar Gini Curve characterizes the shape and ‘evenness’ of cell-point distribution of cell-point set. To quantify whether a gene could be a marker in a cell cluster, we can combine two Polar Gini Curves: one drawn upon the cell-points expressing the gene, and the other drawn upon all cell-points in the cluster. We hypothesize that the closers these two curves are, the more likely the gene would be cluster markers. We demonstrate the framework in several simulation case-studies. Applying our framework in analyzing neonatal mouse heart single-cell data, the detected biomarkers may characterize novel subtypes of cardiac muscle cells. The source code and data for PGC could be found athttps://figshare.com/projects/Polar_Gini_Curve/76749.
Solanaceae specialized metabolism in a non-model plant: trichome acylinositol biosynthesis
Authors: Leong Bryan J. , Hurney Steven M. , Fiesel Paul D. , Moghe Gaurav D. , Jones A. Daniel , Last Robert L. 
Published: March 2020

AbstractPlants make hundreds of thousands of biologically active specialized metabolites varying widely in structure, biosynthesis and the processes that they influence. An increasing number of these compounds are documented to protect plants from harmful insects, pathogens, or herbivores, or mediate interactions with beneficial organisms including pollinators and nitrogen fixing microbes. Acylsugars – one class of protective compounds – are made in glandular trichomes of plants across the Solanaceae family. While most described acylsugars are acylsucroses, published examples also include acylsugars with hexose cores. The South American fruit cropSolanum quitoense(Naranjilla) produces acylsugars that contain amyo-inositol core. We identified an enzyme that acetylates triacylinositols, a function homologous to the last step in theSolanum lycopersicumacylsucrose biosynthetic pathway. Our analysis reveals parallels betweenS. lycopersicumacylsucrose andS. quitoenseacylinositol biosynthesis, suggesting a common evolutionary origin.Material availabilityThe author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Robert L. Last (lastr@msu.edu).One sentence summaryEvidence that the final step inSolanum quitoenseacylinositol biosynthesis evolved from an acylsucrose acetyltransferase enzyme.