bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pheromone receptor of the globally invasive quarantine pest of the palm tree, the red palm weevil (Rhynchophorus ferrugineus)
Authors: Antony Binu , Johny Jibin , Montagné Nicolas , Jacquin-Joly Emmanuelle , Capoduro Rémi , Cali Khasim , Persaud Krishna , Al-Saleh Mohammed Ali , Pain Arnab 
Published: August 2020

AbstractPalm trees are of immense economic, sociocultural, touristic and patrimonial significance all over the world, and date palm-related knowledge, traditions and practices are now included in UNESCO’s list of the Intangible Cultural Heritage of Humanity. Of all the pests that infest these trees, the red palm weevil (RPW),Rhynchophorus ferrugineus(Olivier) is its primary enemy. The RPW is a category-1 quarantine insect pest that causes enormous economic losses in the cultivation of palm trees worldwide. The RPW synchronizes mass gathering on the palm tree for feeding and mating, regulated by a male-produced pheromone composed of two methyl-branched compounds, (4RS,5RS)-4-methylnonan-5-ol (ferrugineol) and 4(RS)-methylnonan-5-one (ferrugineone). Despite the importance of odorant detection in long-range orientation towards palm trees, palm colonization and mating, nothing regarding the molecular mechanisms of pheromone detection in this species is known. In this study, we report the identification and characterization of the first RPW pheromone receptor,RferOR1. Using gene silencing and functional expression inDrosophilaolfactory receptor neurons, we demonstrate thatRferOR1is tuned to both ferrugineol and ferrugineone and binds five other structurally related molecules. We reveal the lifetime expression ofRferOR1, which correlates with adult mating success irrespective of age, a factor that could explain the wide distribution and spread of this pest. As palm weevils are challenging to control based on conventional methods, elucidation of the mechanisms of pheromone detection opens new routes for mating disruption and the early detection of this pestviathe development of pheromone receptor-based biosensors.
Top predators govern multitrophic diversity effects in tritrophic food webs
Authors: Ceulemans Ruben , Guill Christian , Gaedke Ursula 
Published: August 2020

AbstractIt is well known that functional diversity strongly affects ecosystem functioning. However, even in rather simple model communities consisting of only two or, at best, three trophic levels, the relationship between multitrophic functional diversity and ecosystem functioning appears difficult to generalize, due to its high contextuality. In this study, we considered several differently structured tritrophic food webs, in which the amount of functional diversity was varied independently on each trophic level. To achieve generalizable results, largely independent of parametrization, we examined the outcomes of 128, 000 parameter combinations sampled from ecologically plausible intervals, with each tested for 200 randomly sampled initial conditions. Analysis of our data was done by training a Random Forest model. This method enables the identification of complex patterns in the data through partial dependence graphs, and the comparison of the relative influence of model parameters, including the degree of diversity, on food web properties. We found that bottom-up and top-down effects cascade simultaneously throughout the food web, intimately linking the effects of functional diversity of any trophic level to the amount of diversity of other trophic levels, which may explain the difficulty in unifying results from previous studies. Strikingly, only with high diversity throughout the whole food web, different interactions synergize to ensure efficient exploitation of the available nutrients and efficient biomass transfer, ultimately leading to a high biomass and production on the top level. The temporal variation of biomass showed a more complex pattern with increasing multitrophic diversity: while the system initially became less variable, eventually the temporal variation rose again due to the increasingly complex dynamical patterns. Importantly, top predator diversity and food web parameters affecting the top trophic level were of highest importance to determine the biomass and temporal variability of any trophic level. Overall, our study reveals that the mechanisms by which diversity influences ecosystem functioning are affected by every part of the food web, hampering the extrapolation of insights from simple monotrophic or bitrophic systems to complex natural food webs.
RFPlasmid: Predicting plasmid sequences from short read assembly data using machine learning
Authors: van Bloois Linda van der Graaf , Wagenaar Jaap A. , Zomer Aldert L. 
Published: August 2020

AbstractAntimicrobial resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria. For molecular epidemiology purposes and risk assessment, it is important to know if the genes are located on highly transferable plasmids or in the more stable chromosomes. However, draft whole genome sequences are fragmented, making it difficult to discriminate plasmid and chromosomal contigs. Current methods that predict plasmid sequences from draft genome sequences rely on single features, like k-mer composition, circularity of the DNA molecule, copy number or sequence identity to plasmid replication genes, all of which have their drawbacks, especially when faced with large single copy plasmids, which often carry resistance genes. With our newly developed prediction tool RFPlasmid, we use a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict if the likely source of a contig is plasmid or chromosomal. The tool RFPlasmid supports models for 17 different bacterial species, includingCampylobacter,E. coli, andSalmonella, and has a species agnostic model for metagenomic assemblies or unsupported organisms. RFPlasmid is available both as standalone tool and via web interface.
Muscle Metabolic Energy Costs While Modifying Propulsive Force Generation During Walking
Authors: Pimentel Richard E. , Pieper Noah L. , Clark William H. , Franz Jason R. 
Published: August 2020

AbstractWe pose that an age-related increase in the metabolic cost of walking arises in part from a redistribution of joint power where muscles spanning the hip compensate for insufficient ankle push-off and smaller peak propulsive forces (FP). Young adults elicit a similar redistribution when walking with smaller FPvia biofeedback. We used targeted FPbiofeedback and musculoskeletal models to estimate the metabolic costs of operating lower limb muscles in young adults walking across a range of FP. Our simulations support the theory of distal-to-proximal redistribution of joint power as a determinant of increased metabolic cost in older adults during walking.
Purification of recombinant SARS-CoV-2 spike, its receptor binding domain, and CR3022 mAb for serological assay
Authors: Tee Kang Lan , Jackson Philip J. , Scarrott Joseph M. , Jaffe Stephen R. P. , Johnson Abayomi O. , Johari Yusuf , Pohle Thilo H. , Mozzanino Theo , Price Joseph , Grinham James , Brown Adam , Nicklin Martin J. , James David C. , Dickman Mark J. , Wong Tuck Seng 
Published: August 2020

ABSTRACTSerology testing for COVID-19 is highly attractive because of the relatively short diagnosis time and the ability to test for an active immune response against the SARS-CoV-2. In many types of serology tests, the sensitivity and the specificity are directly influenced by the quality of the antigens manufactured. Protein purification of these recombinantly expressed viral antigens [e.g., spike and its receptor binding domain (RBD)] is an important step in the manufacturing process. Simple and high-capacity protein purification schemes for spike, RBD, and CR3022 mAb, recombinantly expressed in CHO and HEK293 cells, are reported in this article. The schemes consist of an affinity chromatography step and a desalting step. Purified proteins were validated in ELISA-based serological tests. Interestingly, extracellular matrix proteins [most notably heparan sulfate proteoglycan (HSPG)] were co-purified from spike-expressing CHO culture with a long cultivation time. HSPG-spike interaction could play a functional role in the pathology and the pathogenesis of SARS-CoV-2 and other coronaviruses.
Characterisation ofMedicago truncatulaCLE34 and CLE35 in nodulation control
Authors: Mens Celine , Hastwell April H. , Su Huanan , Gresshoff Peter M. , Mathesius Ulrike , Ferguson Brett J. 
Published: August 2020

AbstractLegume plants form a symbiosis with N2-fixing soil rhizobia, resulting in new root organs called nodules that enable N2-fixation. Nodulation is a costly process that is tightly regulated by the host through Autoregulation of Nodulation (AON) and nitrate-dependent regulation of nodulation. Both pathways require legume-specific CLAVATA/ESR-related (CLE) peptides. Nitrogen-induced nodulation-suppressing CLE peptides have not previously been characterised inMedicago truncatula, with only rhizobia-induced MtCLE12 and MtCLE13 identified. Here, we report on novel peptides MtCLE34 and MtCLE35 in nodulation control pathways. The nodulation-suppressing CLE peptides of five legume species were classified into three clades based on sequence homology and phylogeny. This approached identified MtCLE34 and MtCLE35 and four new CLE peptide orthologues ofPisum sativum. Whereas MtCLE12 and MtCLE13 are induced by rhizobia, MtCLE34 and MtCLE35 respond to both rhizobia and nitrate. MtCLE34 was identified as a pseudogene lacking a functional CLE-domain. Overexpression ofMtCLE12, MtCLE13andMtCLE35inhibits nodulation. Together, our findings indicate that MtCLE12 and MtCLE13 have a distinct role in AON, while MtCLE35 regulates nodule numbers in a rhizobia- and nitrate-dependent manner. MtCLE34 likely had a similar role to MtCLE35 but its function was lost due to a nonsense mutation resulting in the loss of the mature peptide.
Single-cell cytometry via multiplexed fluorescence prediction by label-free reflectance microscopy
Authors: Cheng Shiyi , Fu Sipei , Kim Yumi Mun , Song Weiye , Li Yunzhe , Xue Yujia , Yi Ji , Tian Lei 
Published: August 2020

AbstractTraditional imaging cytometry uses fluorescence markers to identify specific structures, but is limited in throughput by the labeling process. Here we develop a label-free technique that alleviates the physical staining and provides highly multiplexed readouts via a deep learning-augmented digital labeling method. We leverage the rich structural information and superior sensitivity in reflectance microscopy and show that digital labeling predicts highly accurate subcellular features after training on immunofluorescence images. We demonstrate up to 3× improvement in the prediction accuracy over the state-of-the-art. Beyond fluorescence prediction, we demonstrate that single-cell level structural phenotypes of cell cycles are correctly reproduced by the digital multiplexed images, including Golgi twins, Golgi haze during mitosis and DNA synthesis. We further show that the multiplexed readouts enable accurate multi-parametric single-cell profiling across a large cell population. Our method can dramatically improve the throughput for imaging cytometry toward applications for phenotyping, pathology, and high-content screening.
A spark of 3D revisualization: new method for re-exploring segmented data
Authors: Hu Yuzhi , Limaye A. , Lu Jing 
Published: August 2020

Abstract3D scientific visualization is a popular non-destructive investigation tool, however current imaging processing and 3D visualization software has compatibility barriers which make replicability and reproducibility in research difficult. To solve this, we developed a new revisualization method and demonstrated four case studies using three mainstream image processing and 3D visualization software. Our method offers interchangeability amongst current image processing and 3D visualization software.
Subgenomic satellite particle generation in recombinant AAV vectors results from DNA lesion/breakage and non-homologous end joining
Authors: Zhang Junping , Guo Ping , Yu Xiangping , Pouchnik Derek , Firrman Jenni , Wei Hongying , Sang Nianli , Herzog Roland , Diao Yong , Xiao Weidong 
Published: August 2020

AbstractRecombinant AAV (rAAV) vectors have been developed for therapeutic treatment of genetic diseases. Nevertheless, current rAAV vectors administered to patients often contain non-vector related DNA contaminants. Here, we present a thorough molecular analysis of the configuration of non-standard AAV genomes generated during rAAV production. In addition to the sub-vector genomic size particles containing incomplete AAV genomes, our results found that rAAV preparations were contaminated with multiple categories of subgenomic particles with either snapback genomes or vector genomes with deletions in the mid regions. Through CRISPR and restriction enzyme-based in vivo and in vitro modeling, we identified that the main mechanism leading to the formation of non-canonical genome particles occurred through nonhomologous end joining of fragmented vector genomes caused by genome lesions or DNA breaks that were generated by the host cell/environment. The results of this study advance our understanding of AAV vectors and provide new clues on improving vector efficiency and safety profile for use in human gene therapy.
Oxidoreductases generate hydrogen peroxide that drives iron-dependent lipid peroxidation during ferroptosis
Authors: Yan Bo , Ai Youwei , Zhang Ze , Sun Qi , Ma Yan , Zhang Zhiyuan , Wang Xiaodong 
Published: August 2020

SUMMARYThe inhibition of antioxidant systems of glutathione peroxidase 4 (GPX4) or ferroptosis suppressor protein 1 (FSP1) causes iron-dependent peroxidation of polyunsaturated phospholipids that leads to cell death, a process known as ferroptosis. The mechanisms underlying iron-dependent lipid peroxidation are under active debate. Here, we report that two endoplasmic reticulum-residing oxidoreductases, NADPH-cytochrome P450 reductase (POR) and NADH-cytochrome b5 reductase (CYB5R1), are responsible for the iron-dependent peroxidation of polyunsaturated phospholipids and membrane disruption that executes ferroptosis. Genetic ablation of POR and CYB5R1 or mutations that eliminate POR’s electron transfer activity blocked ferroptosis.In vitroenzymatic assays established that POR and CYB5R1 catalyze hydrogen peroxide production by transferring electrons from NADPH/NADH to oxygen, which is then used to carry out iron-dependent lipid peroxidation via a Fenton reaction. The lipid peroxidation reaction catalyzed by POR and CYB5R1 additively disrupts polyunsaturated phospholipid-containing liposomes. Finally, POR knockdown confers significant protective effects during concanavalin A-induced, ferroptosis-associated acute liver injuryin vivo.Our study thus indicates that POR and CYB5R1 are the enzymes of the “oxidant” system that operates to contravene the antioxidant GPX4/FSP1 systems; the balance between these two systems determines cell commitment to ferroptosis.
Working and Reference Memory tasks trigger opposed long-term synaptic changes in the rat dentate gyrus
Authors: Missaire Mégane , Fraize Nicolas , Comte Jean-Christophe , Truchet Bruno , Parmentier Régis , Salin Paul-Antoine , Malleret Gaël 
Published: August 2020

AbstractLong-term storage of information into memory is supposed to rely on long-term synaptic plasticity processes. Detection of such synaptic changes after training in long-term or reference memory (RM) tasks has yet been scarce, variable and only studied on a short time scale. On the other hand, short-term or working memory (WM) is largely known to depend on persistent neuronal activity or short-term plasticity processes. However, processing information into WM could also involve long-term synaptic changes that could be responsible for the erasure/forgetting of items previously stored in WM playing the role of proactive interference. In order to study long-term synaptic changes associated with RM or WM, we trained chronically implanted rats in three different radial maze tasks: a classical RM task and two WM tasks involving different levels of proactive interference. Synaptic responses at the perforant path to dentate gyrus synapse were recorded on a long-time scale (24h) in freely-moving rats after training in one of these three tasks. We found that consolidation of long-term information leads to a delayed synaptic potentiation, occurring 9 hours after RM training and predicting good behavioral performance on the following day. In contrast, optimal information processing into WM triggers a synaptic depression immediately observed after training and lasting 3 hours, that could act as a mechanism for interference erasure/forgetting.
A sensory integration account for time perception
Authors: Toso Alessandro , Fassihi Arash , Paz Luciano , Pulecchi Francesca , Diamond Mathew E. 
Published: August 2020

ABSTRACTThe connection between stimulus perception and time perception remains unknown. The present study combines human and rat psychophysics with sensory cortical neuronal firing to construct a computational model for the percept of elapsed time embedded within sense of touch. When subjects judged the duration of a vibration applied to the fingertip (human) or whiskers (rat), increasing stimulus mean speed led to increasing perceived duration. Symmetrically, increasing vibration duration led to increasing perceived intensity. We modeled spike trains from vibrissal somatosensory cortex as input to dual leaky integrators – an intensity integrator with short time constant and a duration integrator with long time constant – generating neurometric functions that replicated the actual psychophysical functions of rats. Returning to human psychophysics, we then confirmed specific predictions of the dual leaky integrator model. This study offers a framework, based on sensory coding and subsequent accumulation of sensory drive, to account for how a feeling of the passage of time accompanies the tactile sensory experience.
A constitutively monomeric UVR8 photoreceptor allele confers enhanced UV-B photomorphogenesis
Authors: Podolec Roman , Lau Kelvin , Wagnon Timothée B. , Hothorn Michael , Ulm Roman 
Published: August 2020

AbstractThe plant UV-B photoreceptor UVR8 plays an important role in UV-B acclimation and survival. UV-B absorption by homodimeric UVR8 induces its monomerization and interaction with the E3 ubiquitin ligase COP1, leading ultimately to gene expression changes. UVR8 is inactivated through redimerization, facilitated by RUP1 and RUP2. Here, we describe a novel semi-dominant, hyperactive allele, namelyuvr8-17D, that harbors a glycine-101 to serine mutation. UVR8G101S-overexpression led to weak constitutive photomorphogenesis and extreme UV-B responsiveness. UVR8G101Swas observed to be predominantly monomericin vivoand, once activated by UV-B, was not efficiently inactivated. Analysis of a UVR8G101Scrystal structure revealed the distortion of a loop region normally involved in stabilization of the UVR8 homodimer. Plants expressing a UVR8 variant combining G101S with the previously described W285A mutation exhibited robust constitutive photomorphogenesis. This work provides further insight into UVR8 activation and inactivation mechanisms, and describes a genetic tool for the manipulation of photomorphogenic responses.
A Systemic and Molecular Study of Subcellular Localization of SARS-CoV-2 Proteins
Authors: Zhang Jing , Cruz-cosme Ruth , Zhuang Meng-Wei , Liu Dongxiao , Liu Yuan , Teng Shaolei , Wang Pei-Hui , Tang Qiyi 
Published: August 2020

AbstractCoronavirus possesses the largest RNA genome among all the RNA viruses. Its genome encodes about 29 proteins. Most of the viral proteins are non-structural proteins (NSP) except envelop (E), membrane (M), nucleocapsid (N) and Spike (S) proteins that constitute the viral nucleocapsid, envelop and surface. We have recently cloned all the 29 SARS-CoV-2 genes into vectors for their expressions in mammalian cells except NSP11 that has only 14 amino acids (aa). We are able to express all the 28 cloned SARS-CoV-2 genes in human cells to characterize their subcellular distributions. The proteins of SARS-CoV-2 are mostly cytoplasmic but some are both cytoplasmic and nuclear. Those punctate staining proteins were further investigated by immunofluorescent assay (IFA) using specific antibodies or by co-transfection with an organelle marker-expressing plasmid. As a result, we found that NSP15, ORF6, M and ORF7a are related to Golgi apparatus, and that ORF7b, ORF8 and ORF10 colocalize with endoplasmic reticulum (ER). Interestingly, ORF3a distributes in cell membrane, early endosome, endosome, late endosome and lysosome, which suggests that ORF3a might help the infected virus to usurp endosome and lysosome for viral use. Furthermore, we revealed that NSP13 colocalized with SC35, a protein standing for splicing compartments in the nucleus. Our studies for the first time visualized the subcellular locations of SARS-CoV-2 proteins and might provide novel insights into the viral proteins’ biological functions.
Detecting selection with a genetic cross
Authors: Fraser Hunter B. 
Published: August 2020

AbstractDistinguishing which traits have evolved under natural selection, as opposed to neutral evolution, is a major goal of evolutionary biology. Several tests have been proposed to accomplish this, but these either rely on false assumptions or suffer from low power. Here, I introduce a new approach to detecting lineage-specific selection that makes minimal assumptions and only requires phenotypic data from ∼10 individuals. The test compares the phenotypic difference between two populations to what would be expected by chance under neutral evolution, which can be estimated from the phenotypic distribution of an F2cross between those populations. Simulations show that the test is robust to parameters such as the number of loci affecting the trait, the distribution of locus effect sizes, heritability, dominance, and epistasis. Comparing its performance to the QTL sign test—an existing test of selection that requires both genotype and phenotype data—the new test achieves comparable power with 50- to 100-fold fewer individuals (and no genotype data). Applying the test to empirical data spanning over a century shows strong directional selection in many crops, as well as on naturally selected traits such as head shape in HawaiianDrosophilaand skin color in humans. Applied to gene expression data, the test reveals that the strength of stabilizing selection acting on mRNA levels in a species is strongly associated with that species’ effective population size. In sum, this test is applicable to phenotypic data from almost any genetic cross, allowing selection to be detected more easily and powerfully than previously possible.Significance StatementNatural selection is the force that underlies the spectacular adaptations of all organisms to their environments. However, not all traits are under selection; a key question is which traits have been shaped by selection, as opposed to the random drift of neutral traits. Here, I develop a test of selection on quantitative traits that can be applied to almost any genetic cross between divergent populations or species. The test is robust to a wide range of potential confounders, and has greater power to detect selection than existing tests. Applied to empirical data, the test reveals widespread selection in both domesticated and wild species, allowing selection to be detected more easily and powerfully than previously possible.