bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat fragmentation and food security in crop pollination systems
Authors: Montoya Daniel , Haegeman Bart , Gaba Sabrina , De Mazancourt Claire , Loreau Michel 
Published: May 2020

AbstractEnsuring stable food supplies is recognized as a major challenge for the 21stcentury, and one of the UN Sustainable Development Goals. Biodiversity-based approaches to food security are increasingly being supported based on the fact that biodiversity can increase and stabilize crop yields. But agricultural systems are often highly fragmented and it is unclear how such fragmentation affects biodiversity and food production, limiting our capacity to manage agricultural landscapes for food security. Here, we develop a model of crop yield dynamics to investigate how fragmentation of natural habitats for agricultural conversion impacts food production, with a focus on crop pollination. Our results show that fragmentation produces spatial and biodiversity-mediated effects that affect the mean and stability of pollination-dependent crops, with strong consequences for food security. The net effects of fragmentation depend on the strength of the spillover of pollinators to crop land and the degree to which crops depend on animal pollination. Our study sheds new light in the food security debate by showing that high and stable yields depend on biodiversity and the spatial structure of agricultural landscapes, and by revealing the ecological mechanisms of food security in crop pollination systems.
Minimum conductance in leaves—cuticle, leaky stomata, or water vapor saturation?
Authors: Tominaga Jun , Stinziano Joseph R. , Hanson David T. 
Published: May 2020

SummaryMinimum conductance (gw,min) in leaves is important for water relations in land plants. Yet, its regulation is unclear due to measurement constraints.Cuticle conductance to water vapor (gcw) was estimated from the difference between calculated and direct measurement of CO2concentration in the leaf airspace (Ci) of amphi-stomatous tobacco and sunflower. We estimatedgcwin a series of light and dark experiments, and partitionedgw,mininto cuticle and stomatal components. Some leaves were detached to simulate severe drought through desiccation conditions wheregw,minis generally determined.Between light and dark experiments eachgcwwas in close agreement, and successfully corrected the discrepancies of calculations from direct measurements. In the dark, either stomatal or cuticle conductance dominated thegw,min, suggesting either of them can control the minimum water loss. In the detached leaves,gcwcould not be estimated likely due to unsaturation in the leaf airspace, andgw,minwas progressively underestimated.Besides cuticle, leaf water status is a potential pitfall of the standard gas exchange model. Our technique is useful to study the minimal gas exchange as well as to refine the model.
Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus: the experimental and theory studies
Authors: He Zhesheng , Zhao Wencong , Niu Wenchao , Gao Xuejiao , Gao Xingfa , Gong Yong , Gao Xueyun 
Published: May 2020

SummarySARS-CoV-2 has emerged as a world public health threat. Herein, we report that the clinical approved auranofin could perfectly inhibit the activity of 3-chymotrypsin-like cysteine protease (Mpro or 3CLpro) of SARS-CoV-2. Gold cluster could significantly inhibit 3CLpro of SARS-COV-2. Phenyl isothiocyanate and Vitamin K3 could well suppress the activity of 3CLpro. For Mpro inhibition, IC50 of auranofin, Vitamin K3, phenyl isothiocyanate, gold cluster are about 0.51μM, 7.96μM, 10.13μM, 1.61μM, respectively. These compounds may be with potentials for treatment SARS-CoV-2 virus replication. Especially for FDA approved auranofin, it is an anti-inflammation drug in clinic, thus it may with strong potential to inhibit virus replication and suppress the inflammation damage in COVID-19 patients. Gold cluster is with better safety index and well anti-inflammation in vitro/vivo, therefore it is with potential to inhibit virus replication and suppress the inflammation damage caused by COVID-19 virus. As Au(I) ion is active metabolism specie derived from gold compounds or gold clusters in vivo, further computational studies revealed Au ion could tightly bind thiol group of Cys145 residue of 3CLpro thus inhibit enzyme activity. Also, phenyl isothiocyanate and Vitamin K3 may interact with thiol group of Cys145 via Michael addition reaction, molecular dynamic (MD) theory studied are applied to confirmed these small molecules are stable in the pocket and inhibit Mpro activity.
Tumor-free elongation of mammalian nephrogenesis by excess fetal GDNF
Authors: Li Hao , Kupari Jussi , Gui Yujuan , Siefker Edward , Lu Benson , Mätlik Kärt , Olfat Soophie , Montaño-Rodríguez Ana R , Huh Sung-Ho , Costantini Franklin , Andressoo Jaan-Olle , Kuure Satu 
Published: May 2020

ABSTRACTDue to poor regenerative capacity of adult kidneys, nephron endowment defined by the nephrogenic program during the fetal period dictates renal and related cardiovascular health throughout life. We show that the neurotropic factor GDNF, which is in clinical trials for Parkinson’s disease, is capable of prolonging the nephrogenic program beyond its normal cessation without increasing the risk of kidney tumors. Our data demonstrates that excess GDNF expands the nephrogenic program by maintaining nephron progenitors and nephrogenesis in postnatal mouse kidneys. GDNF, through its transcriptional targets excreted from the adjacent epithelium, has a major effect on nephron progenitor self-renewal and maintenance; abnormally high GDNF inhibits nephron progenitor proliferation, but lowering its level normalizes the nephrogenic program to that permissive for nephron progenitor self-renewal and differentiation. Based on our results, we propose that the lifespan of nephron progenitors is determined by mechanisms related to perception of GDNF and other signaling levels.
Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats
Authors: Bosco-Lauth Angela M. , Hartwig Airn E. , Porter Stephanie M. , Gordy Paul W. , Nehring Mary , Byas Alex D. , VandeWoude Sue , Ragan Izabela K. , Maison Rachel M. , Bowen Richard A. 
Published: May 2020

AbstractThe pandemic caused by SARS-CoV-2 has reached nearly every country in the world with extraordinary person-to-person transmission. The most likely original source of the virus was spillover from an animal reservoir and subsequent adaptation to humans sometime during the winter of 2019 in Wuhan Province, China. Because of its genetic similarity to SARS-CoV-1, it is likely that this novel virus has a similar host range and receptor specificity. Due to concern for human-pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naïve cats. We report that cats are highly susceptible to subclinical infection, with a prolonged period of oral and nasal viral shedding that is not accompanied by clinical signs, and are capable of direct contact transmission to other cats. These studies confirm that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease. Further, we document that cats develop a robust neutralizing antibody response that prevented re-infection to a second viral challenge. Conversely, we found that dogs do not shed virus following infection, but do mount an anti-viral neutralizing antibody response. There is currently no evidence that cats or dogs play a significant role in human exposure; however, reverse zoonosis is possible if infected owners expose their domestic pets during acute infection. Resistance to re-exposure holds promise that a vaccine strategy may protect cats, and by extension humans, to disease susceptibility.
The evolution of non-motif selectivity determinants inMonosiga brevicollisPDZ domains
Authors: Gao Melody , Mackley Iain G. P. , Mesbahi-Vasey Samaneh , Bamonte Haley A. , Struyvenberg Sarah A. , Landolt Louisa , Pederson Nick J. , Williams Lucy I. , Bahl Christopher D. , Brooks Lionel , Amacher Jeanine F. 
Published: May 2020

AbstractThe evolution of signaling pathways is complex and well-studied. In particular, the emergence of animal multicellularity had a major impact on protein-protein interactions and signaling systems in eukaryotic cells. However, choanoflagellates, our closest non-metazoan ancestor, contain a number of closely related signaling and trafficking proteins and domains. In addition, because choanoflagellates can adopt a rosette-/multicellular-like state, a lot can be gained by comparing proteins involved in choanoflagellate and human signaling pathways. Here, we look at how selectivity determinants evolved in the PDZ domain. There are over 250 PDZ domains in the human proteome, which are involved in critical protein-protein interactions that result in large multimolecular complexes, e.g., in the postsynaptic density of neuronal synapses. Binding of C-terminal sequences by PDZ domains is often transient and recognition typically involves 6 residues or less, with only 2 residues specifying the binding motif. We solved high resolution crystal structures ofMonosiga brevicollisPDZ domains homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains to investigate if the non-motif preferences are conserved, despite hundreds of millions of years of evolution. We also calculated binding affinities for GIPC, SHANK1, and SNX27 PDZ domains fromM. brevicollis. Overall, we found that peptide selectivity is conserved between these two disparate organisms, with one exception, mbDLG-3. In addition, we identify 178 PDZ domains in theM. brevicollisproteome, including 11 new sequences, which we verified using Rosetta and homology modeling. Overall, our results provide novel insight into signaling pathways in the choanoflagellate organism.
On the complexity of resting state spiking activity in monkey motor cortex
Authors: Dąbrowska Paulina Anna , Voges Nicole , von Papen Michael , Ito Junji , Dahmen David , Riehle Alexa , Brochier Thomas , Grün Sonja 
Published: May 2020

AbstractResting state has been established as a classical paradigm of brain activity studies, mostly based on large scale measurements such as fMRI or M/EEG. This term typically refers to a behavioral state characterized by the absence of any task or stimuli. The corresponding neuronal activity is often called idle or ongoing. Numerous modeling studies on spiking neural networks claim to mimic such idle states, but compare their results to task- or stimulus-driven experiments, which might lead to misleading conclusions. To provide a proper basis for comparing physiological and simulated network dynamics, we characterize simultaneously recorded single neurons’ spiking activity in monkey motor cortex and show the differences from spontaneous and task-induced movement conditions. The resting state shows a higher dimensionality, reduced firing rates and less balance between population level excitation and inhibition than behavior-related states. Additionally, our results stress the importance of distinguishing between rest with eyes open and closed.
Serial cryoFIB/SEM reveals profound cytoarchitectural disruptions caused by a pathogenic mutation in Leigh syndrome patient cells
Authors: Zhu Yanan , Sun Dapeng , Schertel Andreas , Ning Jiying , Fu Xiaofeng , Gwo Pam Pam , Watson Alan M. , Freyberg Zachary , Zhang Peijun 
Published: May 2020

AbstractThe advancement of serial cryo-FIB/SEM offers a new opportunity to study large volumes of near-native, fully hydrated frozen cells and tissues at voxel sizes of 10 nm and below. We explored this capability for pathologic characterization of vitrified human patient cells. We demonstrate profound disruption of subcellular architecture in primary fibroblasts from a Leigh syndrome patient harboring a disease-causing mutation in USMG5 protein responsible for impaired mitochondrial energy production.
Posttranslational modification of the RHO of plants protein RACB by phosphorylation and cross-kingdom conserved ubiquitination
Authors: Weiß Lukas , Gaelings Lana , Reiner Tina , Mergner Julia , Kuster Bernhard , Fehér Attila , Hensel Götz , Gahrtz Manfred , Kumlehn Jochen , Engelhardt Stefan , Hückelhoven Ralph 
Published: May 2020

AbstractSmall RHO-type G-proteins act as signaling hubs and master regulators of polarity in eukaryotic cells. Their activity is tightly controlled, as defective RHO signaling leads to aberrant growth and developmental defects. Two major processes regulate G-protein activity: canonical shuttling between different nucleotide bound states and posttranslational modification (PTM), of which the latter can support or suppress RHO signaling, depending on the individual PTM. In plants, regulation of Rho of plants (ROPs) signaling activity has been shown to act through nucleotide exchange and GTP hydrolysis, as well as through lipid modification, but there is little data available on phosphorylation or ubiquitination of ROPs. Hence, we applied proteomic analyses to identify PTMs of the barley ROP RACB. We observedin vitrophosphorylation by barley ROP binding kinase 1 andin vivoubiquitination of RACB. Comparative analyses of the newly identified RACB phosphosites and human RHO protein phosphosites revealed conservation of modified amino acid residues, but no overlap of actual phosphorylation patterns. However, the identified RACB ubiquitination site is conserved in all ROPs fromHordeum vulgare,Arabidopsis thalianaandOryza sativaand in mammalian Rac1 and Rac3. Point mutation of this ubiquitination site leads to stabilization of RACB. Hence, this highly conserved lysine residue may regulate protein stability across different kingdoms.
Integrative Molecular Characterization of Sarcomatoid and Rhabdoid Renal Cell Carcinoma Reveals Determinants of Poor Prognosis and Response to Immune Checkpoint Inhibitors
Authors: Bakouny Ziad , Braun David A. , Shukla Sachet A. , Pan Wenting , Gao Xin , Hou Yue , Flaifel Abdallah , Tang Stephen , Bosma-Moody Alice , He Meng Xiao , Vokes Natalie , Nyman Jackson , Xie Wanling , Nassar Amin H. , Alaiwi Sarah Abou , Flippot Ronan , Bouchard Gabrielle , Steinharter John A. , Nuzzo Pier Vitale , Ficial Miriam , Sant’Angelo Miriam , Forman Juliet , Berchuck Jacob E. , Dudani Shaan , Bi Kevin , Park Jihye , Camp Sabrina , Sticco-Ivins Maura , Hirsch Laure , Wind-Rotolo Megan , Ross-Macdonald Petra , Sun Maxine , Lee Gwo-Shu Mary , Chang Steven L. , Wei Xiao X. , McGregor Bradley A. , Harshman Lauren C. , Genovese Giannicola , Ellis Leigh , Pomerantz Mark , Hirsch Michelle S. , Freedman Matthew L. , Atkins Michael B. , Wu Catherine J. , Ho Thai H. , Linehan W. Marston , McDermott David F. , Heng Daniel Y.C. , Viswanathan Srinivas R. , Signoretti Sabina , Van Allen Eliezer M. , Choueiri Toni K. 
Published: May 2020

AbstractSarcomatoid and rhabdoid (S/R) renal cell carcinoma (RCC) are highly aggressive tumors with limited molecular and clinical characterization. Emerging evidence suggests immune checkpoint inhibitors (ICI) are particularly effective for these tumors1–3, although the biological basis for this property is largely unknown. Here, we evaluate multiple clinical trial and real-world cohorts of S/R RCC to characterize their molecular features, clinical outcomes, and immunologic characteristics. We find that S/R RCC tumors harbor distinctive molecular features that may account for their aggressive behavior, includingBAP1mutations,CDKN2Adeletions, and increased expression ofMYCtranscriptional programs. We show that these tumors are highly responsive to ICI and that they exhibit an immune-inflamed phenotype characterized by immune activation, increased cytotoxic immune infiltration, upregulation of antigen presentation machinery genes, and PD-L1 expression. Our findings shed light on the molecular drivers of aggressivity and responsiveness to immune checkpoint inhibitors of S/R RCC tumors.
The apple palmitoyltransferase MdPAT16 regulates sugar content via an MdCBL1-MdCIPK13-MdSUT2.2 pathway
Authors: Jiang Han , Ma Qi-Jun , Zhong Ming-Shuang , Gao Huai-Na , Li Yuan-Yuan , Hao Yu-Jin 
Published: May 2020

ABSTRACTProtein palmitoylation, a post-translational protein modification, plays an important role in the regulation of substrate protein stability, protein interactions, and protein localization. It is generally believed that there are two mechanisms of palmitoylation: one by acyl-CoA and the other by protein acyltransferase (PAT). In this study, an MdPAT family member, MdPAT16, was identified and shown to have palmitoyltransferase activity. We found that this gene responded to salt stress and that its expression improved plant salt resistance. MdPAT16 was shown to interact with MdCBL1 and stabilize MdCBL1 protein levels through palmitoylation. MdPAT16 further regulated apple sugar content by stabilizing the MdCIPK13-MdSUT2.2 protein complex. We found that the N-terminal sequence of MdCBL1 contains a palmitoylation site and that the N-terminal deletion of MdCBL1 leads to changes in protein stability and subcellular localization. Finally, exogenous salt stress increased the interaction of MdPAT16 with MdCBL1 and the sugar content in apple. These findings suggest that MdPAT16 functions as a stable means for the palmitoylation of downstream protein. It may be a missing link in the plant salt stress response pathway and have an important impact on fruit quality.
2’-O-methylation alters the RNA secondary structural ensemble
Authors: Assi Hala Abou , Shi Honglue , Liu Bei , Clay Mary C. , Erharter Kevin , Kreutz Christopher , Holley Christopher L. , Al-Hashimi Hashim M. 
Published: May 2020

ABSTRACT2’-O-methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3’-endoconformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of non-canonical RNA motifs. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of a low-populated short-lived excited state by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi (Φ) value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.
ACE2 expression in human dorsal root ganglion sensory neurons: implications for SARS-CoV-2 virus-induced neurological effects
Authors: Shiers Stephanie , Ray Pradipta R. , Wangzhou Andi , Tatsui Claudio Esteves , Rhines Larry , Li Yan , Uhelski Megan L , Dougherty Patrick M. , Price Theodore J 
Published: May 2020

AbstractSARS-CoV-2 has created a global crisis. COVID-19, the disease caused by the virus, is characterized by pneumonia, respiratory distress and hypercoagulation and is often fatal1. An early sign of infection is loss of smell, taste and chemesthesis - loss of chemical sensation2. Other neurological effects of the disease have been described, but not explained3,4. We show that human dorsal root ganglion (DRG) neurons express the SARS-CoV-2 receptor5,6, ACE2. ACE2 mRNA is expressed by a subset of nociceptors that express MRGPRD mRNA suggesting that SARS-CoV-2 may gain access to the nervous system through entry into neurons that form free-nerve endings at the outer-most layers of skin and luminal organs. Therefore, sensory neurons are a potential target for SARS-CoV-2 invasion of the nervous system.
SPIAT: An R package for the Spatial Image Analysis of Cells in Tissues
Authors: Yang Tianpei , Ozcoban Volkan , Pasam Anu , Kocovski Nikolce , Pizzolla Angela , Huang Yu-Kuan , Bass Greg , Keam Simon P. , Neeson Paul J. , Sandhu Shahneen K. , Goode David L. , Trigos Anna S. 
Published: May 2020

AbstractSpatial technologies that query the location of cells in tissues at single-cell resolution are gaining popularity and are likely to become commonplace. The resulting data includes the X, Y coordinates of millions of cells, cell phenotypes and marker or gene expression levels. However, to date, the tools for the analysis of this data are largely underdeveloped, making us severely underpowered in our ability to extract quantifiable information. We have developed SPIAT (SpatialImageAnalysis ofTissues), an R package with a suite of data processing, quality control, visualization, data handling and data analysis tools. SPIAT includes our novel algorithms for the identification of cell clusters, cell margins and cell gradients, the calculation of neighbourhood proportions, and algorithms for the prediction of cell phenotypes. SPIAT also includes speedy implementations of the calculation of cell distances and detection of cell communities. This version of SPIAT is directly compatible with Opal multiplex immunohistochemistry images analysed through the HALO and InForm analysis software, but its intuitive implementation allows use with a diversity of platforms. We expect SPIAT to become a user-friendly and speedy go-to package for the spatial analysis of cells in tissues.SPIAT is available on Github:https://github.com/cancer-evolution/SPIAT
Transfer of orientation memories in untethered wood ants (Formica rufa) from walking in an arena to walking on a motion compensation treadmill
Authors: Goulard Roman , Buehlmann Cornelia , Niven Jeremy E. , Graham Paul , Webb Barbara 
Published: May 2020

AbstractThe scale of natural insect navigation during foraging makes it challenging to study, in a controlled way, the navigation processes that an insect brain can support. Virtual Reality and trackball setups have offered experimental control over visual environments while studying tethered insects, but potential limitations and confounds introduced by tethering motivates the development of alternative untethered solutions. In this paper we validate the use of a motion compensator (or ‘treadmill’) to study visually-driven behaviour of freely moving wood ants (Formica rufa). We show how this setup allows naturalistic walking behaviour and motivation over long timeframes. Furthermore, we show that ants are able to transfer associative and navigational memories from classical maze and arena contexts to our treadmill. Thus, we demonstrate the possibility to study navigational behaviour over ecologically relevant durations (and virtual distances) in precisely controlled environments, bridging the gap between natural and highly controlled laboratory experiments.1Summary statementWe have developed and validated a motion compensating treadmill for wood ants which opens new perspectives to study insect navigation behaviour in a fully controlled manner over ecologically relevant durations.