bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterotrimeric G protein α subunit (GPA1) regulates the response to low-nitrogen stress in Arabidopsis by interacting with AtNRT1.4 and AtATG8a
Authors: Luo Mingzhao , Hu Liqin , Li Weiwei , Ge Linhao , Qin Yuhai , Zhou Yongbin , Tang Wensi , Wang Chunxiao , Xu Zhaoshi , Chen Jun , Delaplace Pierre , Ma Youzhi , Chen Ming 
Published: January 2022

ABSTRACTEfficient nitrogen absorption and utilization are important factors for higher plants to increase yield and reduce eutrophication (caused by excessive use of nitrogen fertilizers). Heterotrimeric G proteins, including three subunits of α, β, and γ, participate in the pathway regulating nitrogen absorption and utilization in plants. However, the regulatory mechanism remains largely obscured. In this study, our results revealed that the G protein α subunit (AtGPA1) mutant gpa1-4 was tolerant to low-nitrogen stress in Arabidopsis. AtGPA1 was shown to directly interact with a nitrate transporter (AtNRT1.4) and a key autophagy-related protein (AtATG8a) on the plasma membrane using the yeast hybrid system and pull-down assay (in vitro) and BiFC assay (in vivo). GUS staining and subcellular localization showed that AtGPA1 and AtNRT1.4 were co-expressed in roots and leaf veins and on the plasma membrane. Under low-nitrate conditions, the single mutant gpa1-4 and NRT1.4RNAi plants (AtNRT1.4RNA interference plants) and the double mutant NRT1.4RNAi/gpa1-4 plants (AtNRT1.4RNA interference plants on a gpa1-4 background) were healthier than the wild type plants. Moreover, the phenotype of the double mutant NRT1.4RNAi/gpa1-4 plants was closer to that of the NRT1.4RNAi plants compared to that of the gpa1-4 mutants. The results of the nitrate efflux rate assay in roots were consistent with the phenotypic changes under low-nitrogen conditions. These results indicated that AtGPA1 is an upstream factor that regulated the response to low-nitrogen stress through interaction with AtNRT1.4. In addition, we found that transgenic plants overexpressing AtATG8a were more tolerant to low-nitrogen stress, and their phenotype was similar to that of gpa1-4 mutants and double mutant ATG8aOX/gpa1-4 plants (AtATG8a overexpressing plants on a gpa1-4 mutant background). Further, autophagosome observations were consistent with the phenotypes in mutant plants, indicating that AtGPA1 regulated the response to low-nitrogen stress in Arabidopsis plants by affecting the autophagosome assembly. Our findings may provide a new model for improving nitrogen-use efficiency through genetical modification to boost crop yields.One sentence summaryAtGPA1 negative regulates low nitrogen stress response by interaction with a nitrate transporter, AtNRT1.4 and an autophagy-related protein, AtATG8a in Arabidopsis.
Building model prototypes from time-course data
Authors: Veliz-Cuba Alan , Voss Stephen Randal , Murrugarra David 
Published: January 2022

AbstractA primary challenge in building predictive models from temporal data is selecting the appropriate model topology and the regulatory functions that describe the data. Software packages are available for equation learning of continuous models, but not for discrete models. In this paper we introduce a method for building model prototypes. These model prototypes consist of a wiring diagram and a set of discrete functions that can explain the time course data. The method takes as input a collection of time course data or discretized measurements over time. After network inference, we use our toolbox to simulate the prototype model as a stochastic Boolean model. Our method provides a model that can qualitatively reproduce the patterns of the original data and can further be used for model analysis, making predictions, and designing interventions. We applied our method to a time-course, gene-expression data that were collected during salamander tail regeneration under control and intervention conditions. The inferred model captures important regulations that were previously validated in the research literature and gives novel interactions for future testing. The toolbox for inference and simulations is freely available at github.com/alanavc/prototype-model.
RTEL1 and MCM10 overcome topological stress during vertebrate replication termination
Authors: Campos Lillian V. , Greer Briana H. , Heintzman Darren R. , Kavlashvili Tamar , McDonald W. Hayes , Rose Kristie Lindsey , Eichman Brandt F. , Dewar James M. 
Published: January 2022

ABSTRACTTopological stress can cause replication forks to stall as they converge upon one another during termination of vertebrate DNA synthesis. However, replication forks ultimately overcome topological stress and complete DNA synthesis, suggesting that alternative mechanisms can overcome topological stress. We performed a proteomic analysis of converging replication forks that were stalled by topological stress in Xenopus egg extracts. We found that the helicase RTEL1 and the replisome protein MCM10 were highly enriched on DNA under these conditions. We show that RTEL1 normally plays a minor role during fork convergence while the role of MCM10 is normally negligible. However, RTEL1 and MCM10 both become crucially important for fork convergence under conditions of topological stress. RTEL1 and MCM10 exert non-additive effects on fork convergence and physically interact, suggesting that they function together. Furthermore, RTEL1 and MCM10 do not impact topoisomerase activity but do promote fork progression through a replication barrier. Thus, RTEL1 and MCM10 appear to play a general role in promoting progression of stalled forks, including when forks stall during termination. Overall, our data identify an alternate mechanism of termination involving RTEL1 and MCM10 that can be used to complete DNA synthesis under conditions of topological stress.
Puromycin is incorporated into regenerating flagella of Chlamydomonas reinhardtii as an indicator of nascent flagellar proteins
Authors: Kubo Tomohiro , Kanou Natsumi , Oda Toshiyuki 
Published: January 2022

AbstractThe unicellular alga Chlamydomonas reinhardtii assembles flagella after pH shock-induced deflagellation, in which process the cell vigorously synthesizes flagellar proteins. Previously, newly synthesized flagellar proteins were chased using radioisotopes. Here, we have developed an alternative, non-radioactive method using the surface sensing of translation (SUnSET) assay, an assay that takes advantage of the incorporation of the antibiotic puromycin into newly synthesized peptides. Just after deflagellation, puromycin-labeled proteins increased dramatically in the cytoplasm and newly assembled flagella. Axonemal incorporation of newly synthesized proteins occurred from the distal tip of the flagellum. Cycloheximide, a protein synthesis inhibitor, almost completely prevented the cellular and flagellar incorporation of puromycin, although, as reported previously, it allowed reassembly of half-length flagella from the cytoplasmic “flagellar precursor” proteins. In contrast to wild-type cells, a cycloheximide-resistant mutant act2 produced nearly full-length flagella containing puromycin-labeled proteins even in the presence of cycloheximide. These and other results demonstrate that the SUnSET method serves as a powerful tool for visualizing flagellar incorporation of nascent proteins in Chlamydomonas.
Assessment of AlphaFold2 residue conformations for human proteins
Authors: Bæk Kristoffer T. , Kepp Kasper P. 
Published: January 2022

AbstractMotivationAs only 35% of human proteins feature (often partial) PDB structures, the protein structure prediction tool AlphaFold2 (AF2) could have massive impact on human biology and medicine fields, making independent benchmarks of interest. We studied AF2’s ability to describe the backbone solvent exposure as an easily interpretable “natural coordinate” of protein conformation, using human proteins as test case.ResultsAfter screening for appropriate comparative sets, we matched 1818 human proteins predicted by AF2 against 7585 unique experimental PDBs, and after curation for sequence overlap, we assessed 1264 comparative pairs comprising 115 unique AF2-structures and 652 unique experimental structures. AF2 performed markedly worse for multimers, whereas ligands, cofactors and experimental resolution were interestingly not very important for performance. AF2 performed excellently for monomer proteins. Challenges relating to specific groups of residues and multimers were analyzed. We identify larger errors for lower-confidence scores (pLDDT) and exposed residues, and polar residues (Asp, Glu, Asn e.g.) being less accurately described than hydrophobic residues. Proline conformations were the hardest to predict, probably due to common location in dynamic solvent-accessible parts. In summary, using solvent exposure as a natural metric of local conformation, we quantify the performance of AF2 for human proteins and provide estimates of the expected error as a function of ligand presence, multimer/monomer status, resolution, local residue solvent exposure, pLDDT, and amino acid type. Overall performance was found to be excellent.Availability and ImplementationScripts used to perform benchmarking are available athttps://github.com/ktbaek/AlphaFold.
Fast and accurate joint inference of coancestry parameters for populations and/or individuals
Authors: Mary-Huard Tristan , Balding David 
Published: January 2022

AbstractWe introduce a fast, new algorithm for inferring jointly the FST parameters describing genetic distances among a set of populations and/or unrelated diploid individuals, and a tree representing their genetic structure, from allele count data. While the inferred tree typically reflects historical processes of splitting and divergence, its aim is to represent the actual genetic variance, with FST values specified by branch lengths. We generalise two major approaches to defining FST, via correlations and mismatch probabilities of sampled allele pairs, which measure shared and non-shared components of genetic variance. A diploid individual can be treated as a population of two gametes, which allows inference of coancestry coefficients for individuals as well as for populations, or a combination of the two. A simulation study illustrates that our fast method-of-moments estimation of FST values, simultaneously for multiple populations/individuals, gains statistical efficiency over pairwise approaches by pooling information about ancestral allele frequencies. We apply our approach to genome-wide genotypes from the 26 worldwide human populations of the 1000 Genomes Project. We first analyse at the population level, then a subset of individuals and in a final analysis we pool individuals from the more homogeneous populations. This flexible analysis approach gives many advantages over traditional approaches to population structure/coancestry, including visual and quantitative assessments of long-standing questions about the relative magnitudes of within- and between-population genetic differences.Author summaryWe propose new ways to measure, and visualise in a tree, the genetic distances among a set of populations using allele frequency data. The two genomes within a diploid individual can be treated as a small population, which allows a flexible framework for investigating genetic variation within and between populations. Genetic structure can be accurately and efficiently represented in a tree with nodes representing either homogeneous populations or genetically diverse individuals, for example due to admixture. We first generalise the long-established measure of genetic distance, FST, to tree-structured populations and individuals, finding that two measures are required for each pair of populations, corresponding to their shared and and non-shared genetic variation. We show using a simulation study that our novel tree-based estimators are more efficient than current pairwise estimators, and we illustrate the potential for novel ways to explore and visualise genetic variation within and between populations using a worldwide human genetic dataset.
Did Caenorhabditis nematodes recycle transposons to fight pathogens?
Authors: Li Zixin , Rödelsperger Christian 
Published: January 2022

AbstractAnimal genomes consist largely of sequences derived from transposons which were previously considered as junk DNA and active transposons can even be deleterious for organismal fitness. Nevertheless, the huge pool of transposon-derived sequences also forms the raw material for molecular innovations. Here, we follow up on the incidental finding of a transposon-derived DNA binding domain in a subset of F-box genes in Caenorhabditis elegans. Based on phylogenetic analysis, we show that a single gene fusion followed by individual losses explains most members of this novel gene family. Phylogenomic data of available Caenorhabditis genomes allowed us to trace this fusion event to the ancestor of the Elegans group. Additional homology searches suggest endogenous Mariner transposons as the likely source of the coopted sequence. Further bioinformatic characterization of different F-box families by Gene Ontology analysis, gene module comparisons, and literature research identified first evidence that some F-box genes might be involved in innate immunity, as it had been proposed previously based on adaptive signatures of molecular evolution. Specifically, the F-box gene fbxa-158 contains one of the transposon-derived domains and was shown to interact with the components of the intracellular pathogen response machinery targeting Microsporidia and viruses. Thus, cooption of transposon-derived sequences likely contributed to the adaptive evolution of the F-box superfamily in Caenorhabditis nematodes.Significance statementWhen considering transposons as genomic junk or selfish elements that are detrimental for organismal fitness, we often neglect the potential of transposon-derived sequences as a source of molecular innovation. Here, we characterize a case where a transposon-derived sequence has been coopted by one of the largest and fastest evolving gene superfamilies in Caenorhabditis nematodes which include the model organism C. elegans. The resulting chimeric gene family has been stably maintained for about 20 million years and bioinformatic analysis reveals first evidence for potential functions in innate immunity. Thus, strong evolutionary pressure might have forced Caenorhabditis nematodes to recycle transposons in order to fight pathogens.
Effective generation of tumor-infiltrating lymphocyte products from metastatic non-small-cell lung cancer (NSCLC) lesions irrespective of location and previous treatments
Authors: Castenmiller Suzanne M. , de Groot Rosa , Guislain Aurélie , Monkhorst Kim , Hartemink Koen J. , Veenhof Alexander A.F.A. , Smit Egbert F. , Haanen John B.A.G. , Wolkers Monika C. 
Published: January 2022

AbstractNon-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide. Because current treatment regimens show limited success rates, alternative therapeutic approaches are needed. We recently showed that treatment-naive, stage I/II primary NSCLC tumors contain a high percentage of tumor-reactive T cells, and that these tumor-reactive T cells can be effectively expanded and used for the generation of autologous TIL therapy. Whether these promising findings also hold true for metastatic lesions is unknown yet critical for the translation into the clinic. We here studied the lymphocytic composition and the feasibility to generate tumor-responsive TIL products from metastatic NSCLC lesions that were derived from different locations and from patients who had previously received different treatment regimens, or who were treatment naïve. The overall numbers and composition of lymphocyte infiltrates from this various metastatic lesions was by and large comparable to that of early-stage primary NSCLC tumors. With the clinically approved TIL expansion protocol, we effectively expanded TILs from metastatic NSCLC lesions to numbers that were compatible with TIL transfusion, irrespective of the location of the metastasis and of the previous treatment. Importantly, 16 of 21 (76%) tested TIL products displayed anti-tumoral activity, as determined by their production of the key pro-inflammatory cytokines IFN-γ, TNF, IL-2 and of CD137 expression upon incubation with autologous tumor digests by CD8+ and CD4+ T cells. In summary, metastatic NSCLC lesions constitute a viable source for the generation of tumor-reactive TIL products for therapeutic purposes irrespective of their location and the pretreatment regimens.
RNase L-mediated RNA decay alters 3’ end formation and splicing of host mRNAs
Authors: Burke James M. , Ripin Nina , Ferretti Max B. , St Clair Laura A. , Worden-Sapper Emma R. , Sawyer Sara L. , Perera Rushika , Lynch Kristen W. , Parker Roy 
Published: January 2022

ABSTRACTThe antiviral endoribonuclease, RNase L, is a vital component of the mammalian innate immune response that destroys host and viral RNA to reduce viral gene expression. Herein, we show that a consequence of RNase L-mediated decay of cytoplasmic host RNAs is the widespread re-localization of RNA-binding proteins (RBPs) from the cytoplasm to the nucleus, due to the presence of nuclear RNA. Concurrently, we observe global alterations to host RNA processing in the nucleus, including alterations of splicing and 3’ end formation, with the latter leading to downstream of gene (DoG) transcripts. While affecting many host mRNAs, these alterations are pronounced in mRNAs encoding type I and type III interferons and coincide with the retention of their mRNAs in the nucleus. Similar RNA processing defects also occur during infection with either dengue virus or SARS-CoV-2 when RNase L is activated. These findings reveal that the distribution of RBPs between the nucleus and cytosol is fundamentally dictated by the availability of RNA in each compartment and thus viral infections that trigger cytoplasmic RNA degradation alter RNA processing due to the nuclear influx of RNA binding proteins.
Elucidating Heterogeneous Iron Biomineralization Patterns in a Denitrifying As(III)-Oxidizing Bacterium: Implications for Arsenic Immobilization
Authors: Lopez-Adams Rebeca , Fairclough Simon M. , Lyon Ian C. , Haigh Sarah J. , Zhang Jun , Zhao Fang-Jie , Moore Katie L. , Lloyd Jonathan R. 
Published: January 2022

AbstractAnaerobic nitrate-dependent iron(II) oxidation is a process common to many bacterial species, which promotes the formation of Fe(III) minerals that can influence the fate of soil and groundwater pollutants, such as arsenic. Herein, we investigated simultaneous nitrate-dependent Fe(II) and As(III) oxidation byAcidovoraxsp. strain ST3 with the aim of studying the Fe biominerals formed, their As immobilization capabilities and the metabolic effect on cells. X-ray powder diffraction (XRD) and scanning transmission electron microscopy (STEM) nanodiffraction were applied for biomineral characterization in bulk and at the nanoscale, respectively. NanoSIMS (nanoscale secondary ion mass spectrometry) was used to map the intra and extracellular As and Fe distribution at the single-cell level and to trace metabolically active cells, by incorporation of a13C-labeled substrate (acetate). Metabolic heterogeneity among bacterial cells was detected, with periplasmic Fe mineral encrustation deleterious to cell metabolism. Interestingly, Fe and As were not co-localized in all cells, indicating delocalized sites of As(III) and Fe(II) oxidation. The Fe(III) minerals lepidocrocite and goethite were identified in XRD, although only lepidocrocite was identified via STEM nanodiffraction. Extracellular amorphous nanoparticles were formed earlier and retained more As(III/V) than crystalline “flakes” of lepidocrocite, indicating that longer incubation periods promote the formation of more crystalline minerals with lower As retention capabilities. Thus, the addition of nitrate promotes Fe(II) oxidation and formation of Fe(III) biominerals by ST3 cells which retain As(III/V), and although this process was metabolically detrimental to some cells, it warrants further examination as a viable mechanism for As removal in anoxic environments by biostimulation with nitrate.
Quality evaluation of gluten-free flat bread prepared by using rice and millet flour
Authors: Omran Azza A. , Mahgoub Saad A. 
Published: January 2022

PurposeDue to the need and interest of gluten-free products for celiac disease (CD) patients, the study aims to estimate the effect of the substitution of rice flour with millet flour in the presence of sweet lupin and sweet potato powder in gluten-free blends and the impact of the produced blends on gluten-free flat bread quality.Design/methodology/approachSeven gluten-free blends (B1, B2, B3, B4, B5, B6 and B7) were prepared with different percentages of rice flour (50–80%) and millet flour (5–35%), 10% sweet lupin and 5% sweet potato powder. Physicochemical analysis and particle size of gluten-free blends were evaluated. The resulted gluten-free bread samples were analyzed for chemical composition, color parameters and staling as well as sensory evaluation.FindingsResults indicated that substitution of rice flour with millet flour increased protein, fat, ash, crude fiber, calcium, zinc and iron contents of flour blends, while total carbohydrates content, water holding capacity (WHC) and oil holding capacity (OHC), bulk density, L*, a* and b* values were decreased with increasing millet flour substitution. In addition, substitution with millet flour significantly increased (p < 0.05) protein, fat, ash and crude fiber contents and affected color parameters and staling of produced bread.Research limitations/implicationsAs a researchers, the authors need more statistical data about type, needs, age and numbers of CD patients in worldwide and in Egypt to create a specific products for each of them. Besides, the collaboration between researchers, breeders, nutritionist and food manufactures are very vital to add new gluten-free crops.Practical implicationsNew gluten-free products will be launched in markets with affordable price.Social implicationsThe children with CD, especially Egyptians suffer from a shortage of varied, inexpensive and suitable gluten-free bread to achieve their needs. So the current work may help them to be satisfied.Originality/valueRice flour could be substituted up to 10% with millet flour without adverse effect on the sensory attributes of gluten-free bread and this may assist CD patients to discover a diversity of gluten-free blends.