bluuebunny/crossref_metadata_2025 huggingface dataset:
Basinwise Statistical Analysis of Factors Limiting Tropical Storm Formation From an Initial Tropical Circulation
Authors: Raavi Pavan Harika , Walsh K. J. E.
Published: April 2020

Tropical cyclones (TCs) form within a closed circulation region of large‐scale disturbances under certain dynamical and thermodynamical conditions. This study investigates differences in the large‐scale environmental conditions of a TC 48 hr before the declaration of tropical depression, comparing those that developed into tropical storms (TSs) with those depressions that did not develop. Here, we apply the Okubo‐Weiss Zeta Parameter detection and tracking scheme to ERA‐interim reanalysis from 1989–2018, across different ocean basins. The method detects storm‐system‐scale environmental conditions that favor TC formation. We construct spatial composites of thermodynamical and dynamical quantities for both developing and nondeveloping depressions, as well as storm‐relative streamlines. A statistical index (the Box Difference Index) is used to quantitatively estimate the dominant limiting factors of TS formation from the area‐averaged quantities of large‐scale variables. The relative contribution of large‐scale environmental variables impeding the development of an initial tropical depression to TS differs between ocean basins perhaps due to regional variations in the characteristics of large‐scale disturbances and the surrounding environmental conditions. A streamline analysis shows that the developing storms have a more pronounced cyclonic core and are protected from external influences by a stronger shear sheath layer surrounding the core extending from the lower to middle troposphere. This study, therefore, identifies the potential limiting variables and structural differences in an initial circulation that impede TS formation across different ocean basins.
Preorogenic Folds and Syn‐Orogenic Basement Tilts in an Inverted Hyperextended Margin: The Northern Pyrenees Case Study
Authors: Izquierdo‐Llavall Esther , Menant Armel , Aubourg Charles , Callot Jean‐Paul , Hoareau Guilhem , Camps Pierre , Péré Eve , Lahfid Abdeltif
Published: April 2020

The Chaînons Béarnais (CB, North Pyrenean Zone) resulted from the Cenozoic contractional reactivation of the salt tectonics‐bearing, hyperextended margin that initiated at the Europe‐Iberia transition during the Early Cretaceous. In this tectonic scenario, assessing the relative contribution of extension and contraction to the present‐day structure is crucial to reconstruct the hyperextended margin geometry and to quantify the subsequent shortening. This study undertakes this issue by defining the relationship between folding and two bedding‐independent references: peak temperature isotherms and paleomagnetic data. Isotherms were reconstructed from 76 new measurements of Raman spectroscopy on carbonaceous materials (RSCM) and indicate temperatures at the time of peak metamorphism in the CB (110–85 Ma, end of extension). They are shallowly to moderately northwards dipping and cut across most of the folds deforming the Mesozoic units. Paleomagnetic data from 29 sites evidence a widespread remagnetization carried by pyrrhotite that was probably blocked during the early Paleogene (before the onset of continental collision) and postdated folding in the CB. Abnormal inclinations in this remagnetization suggest syn‐collision tilts up to 60° to the north in the back limb of the Axial Zone. Based on the presented data set, we propose that the folding of the cover above the evaporitic décollement was almost fully completed by the end of the Cretaceous extension, with ~85–100% of the dip of fold limbs being acquired before the remagnetization time. Cenozoic contraction reactivated the extensional faults in the shallow basement as top‐to‐the‐S thrusts, leading to the passive transport and northwards tilting of the folded cover.
Hölder‐Conditioned Hypsometry: A Refinement to a Classical Approach for the Characterization of Topography
Authors: Keylock Christopher J. , Singh Arvind , Passalacqua Paola , Foufoula‐Georgiou Efi
Published: April 2020

The effective characterization of topographic surfaces is a central tenet of geomorphology. Differences in land surface properties reveal variations in structural controls and the nature and efficacy of Earth‐shaping processes. In this paper, we employ the Hölder exponents, α, characterizing the local scaling behavior of topography and commonly used in the study of the (multi)fractal properties of landscapes and show that the joint probability distribution of the area of the terrain with a given elevation and α contains a wealth of information on topographic structure. The conditional distributions of the hypsometric integrals as a function of α, that is, Ihyp|α, are shown to capture this structure. A multivariate analysis reveals three metrics that summarize these conditional distributions: Strahler's original hypsometric integral, the standard deviation of the Ihyp|α, and the nature of any trend of the Ihyp|α against α. An analysis of five digital elevation models (DEMs) from different regions of the United States shows that only one is truly described by the hypsometric integral (Mettman Ridge from central Oregon). In the other cases, the new metrics clearly discriminate between instances where topographic roughness is more clearly a function of elevation, as captured by the conditional variables. In a final example, we artificially sharpen the ridges and valleys of one DEM to show that while the hypsometric integral and standard deviation of Ihyp|α are invariant to the change, the trend of Ihyp|α against α captures the changes in topography.
Can the GPM IMERG Hourly Products Replicate the Variation in Precipitation During the Wet Season Over the Sichuan Basin, China?
Authors: Wang H. , Wang L. , He J. , Ge F. , Chen Q. , Tang S. , Yao S.
Published: April 2020

Two near‐real‐time and one post‐processing products from the Integrated Multi‐satellite Retrievals for Global Precipitation Measurement Mission (GPM IMERG) were evaluated during the period from 2016 to 2018 in the wet seasons (June–November) over the Sichuan Basin, China. Results indicated the following: (1) The three products could generally replicate strong precipitation well; however, significantly large biases were observed when detecting weak precipitation. (2) All three products replicated summer precipitation more accurately than autumn precipitation. The IMERG “early run” product (IMERG‐E) largely underestimated precipitation in the wet season, while the “latter run” (IMERG‐L) and “final run” products (IMERG‐F) could counteract this to a certain degree. (3) IMERG‐F captured weak, moderate, and strong precipitation well during the wet season, and IMERG‐E showed excellent potential in detecting different precipitation intensities. All the three products could replicate the diurnal cycle of the wet season precipitation. The findings of this study can facilitate the application of IMERG products in regions with complex topography and have also highlighted the potential of IMERG‐E for rapid early warning and forecast systems.
Meteorological Change and Impacts on Air Pollution: Results From North China
Authors: Xu Ziping , Chen Song Xi , Wu Xiaoqing
Published: April 2020

There have been speculations that the severe air pollution experienced in North China was the act of meteorological change in general and a decreasing northerly wind in particular. We conduct a retrospective analysis on 1979–2016 reanalysis data from ERA‐Interim of European Centre for Medium‐Range Weather Forecasts over a region in North China to detect meteorological changes over the 38 years. No significant reduction in the northerly wind within the mixing layer is detected. Statistically significant increases are detected in the surface temperature, boundary layer height and dissipation, and significant decreases in relative humidity in the region between the first and second 19‐year periods from 1979 to 2016. We build regression models of PM2.5on the meteorological variables using data in 2014, 2015, and 2016 to quantify effects of the meteorological changes between the two 19‐year periods on PM2.5under the emission scenarios of 2014–2016. It is found that despite the warming, dew point temperature had been largely kept under control as the region had gotten dryer. This made the effects of temperature warming largely favorable to PM2.5reduction as it enhances boundary layer height and dissipation. It is found that the meteorological changes would lead to 1.29% to 2.76% reduction in annual PM2.5averages with January, March, and December having more than 4% reduction in the 3 years. Thus, the meteorological change in North China had helped alleviate PM2.5to certain extent and should not be held responsible for the regional air pollution problem.
Spi-C positively regulates RANKL-mediated osteoclast differentiation and function
Authors: Go Eun Mi , Oh Ju Hee , Park Jin Hee , Lee Soo Young , Lee Na Kyung
Published: April 2020

Spi-C is an SPI-group erythroblast transformation-specific domain transcription factor expressed during B-cell development. Here, we report that Spi-C is a novel receptor activator of nuclear factor-κB ligand (RANKL)-inducible protein that positively regulates RANKL-mediated osteoclast differentiation and function. Knockdown of Spi-C decreased the expression of RANKL-induced nuclear factor of activated T-cells, cytoplasmic 1, receptor activator of nuclear factor-κB (RANK), and tartrate-resistant acid phosphatase (TRAP), resulting in a marked decrease in the number of TRAP-positive multinucleated cells. Spi-C-transduced bone marrow-derived monocytes/macrophages (BMMs) displayed a significant increase in osteoclast formation in the presence of RANKL. In addition, Spi-C-depleted cells failed to show actin ring formation or bone resorption owing to a marked reduction in the expression of RANKL-mediated dendritic cell-specific transmembrane protein and the d2 isoform of vacuolar (H+) ATPase V0 domain, which are known osteoclast fusion-related genes. Interestingly, RANKL stimulation induced the translocation of Spi-C from the cytoplasm into the nucleus during osteoclastogenesis, which was specifically blocked by inhibitors of p38 mitogen-activated protein kinase (MAPK) or PI3 kinase. Moreover, Spi-C depletion prevented RANKL-induced MAPK activation and the degradation of inhibitor of κB-α (IκBα) in BMMs. Collectively, these results suggest that Spi-C is a novel positive regulator that promotes both osteoclast differentiation and function.
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean
Authors: Han Qin , Ma Qun , Chen Yong , Tian Bing , Xu Lanxi , Bai Yang , Chen Wenfeng , Li Xia
Published: April 2020

Rhizobia–legume symbiosis is an important type of plant–microbe mutualism; however, the establishment of this association is complicated and can be affected by many factors. The soybean rhizosphere has a specific microbial community, yet whether these organisms affect rhizobial nodulation has not been well investigated. Here, we analyzed the compositions and relationships of soybean rhizocompartment microbiota in three types of soil. First, we found that the rhizosphere community composition of soybean varied significantly in different soils, and the association network between rhizobia and other rhizosphere bacteria was examined. Second, we found that some rhizosphere microbes were correlated with the composition of bradyrhizobia and sinorhizobia in nodules. We cultivated 278 candidate Bacillus isolates from alkaline soil. Finally, interaction and nodulation assays showed that the Bacillus cereus group specifically promotes and suppresses the growth of sinorhizobia and bradyrhizobia, respectively, and alleviates the effects of saline–alkali conditions on the nodulation of sinorhizobia as well as affecting its colonization in nodules. Our findings demonstrate a crucial role of the bacterial microbiota in shaping rhizobia–host interactions in soybean, and provide a framework for improving the symbiotic efficiency of this system of mutualism through the use of synthetic bacterial communities.
Island biogeography of soil bacteria and fungi: similar patterns, but different mechanisms
Authors: Li Shao-peng , Wang Pandeng , Chen Yongjian , Wilson Maxwell C , Yang Xian , Ma Chao , Lu Jianbo , Chen Xiao-yong , Wu Jianguo , Shu Wen-sheng , Jiang Lin
Published: April 2020

Microbes, similar to plants and animals, exhibit biogeographic patterns. However, in contrast with the considerable knowledge on the island biogeography of higher organisms, we know little about the distribution of microorganisms within and among islands. Here, we explored insular soil bacterial and fungal biogeography and underlying mechanisms, using soil microbiota from a group of land-bridge islands as a model system. Similar to island species-area relationships observed for many macroorganisms, both island-scale bacterial and fungal diversity increased with island area; neither diversity, however, was affected by island isolation. By contrast, bacterial and fungal communities exhibited strikingly different assembly patterns within islands. The loss of bacterial diversity on smaller islands was driven primarily by the systematic decline of diversity within samples, whereas the loss of fungal diversity on smaller islands was driven primarily by the homogenization of community composition among samples. Lower soil moisture limited within-sample bacterial diversity, whereas smaller spatial distances among samples restricted among-sample fungal diversity, on smaller islands. These results indicate that among-island differences in habitat quality generate the bacterial island species-area relationship, whereas within-island dispersal limitation generates the fungal island species-area relationship. Together, our study suggests that different mechanisms underlie similar island biogeography patterns of soil bacteria and fungi.
R-spondin2 signaling is required for oocyte-driven intercellular communication and follicular growth
Authors: De Cian Marie-Cécile , Gregoire Elodie P. , Le Rolle Morgane , Lachambre Simon , Mondin Magali , Bell Sheila , Guigon Céline J. , Chassot Anne-Amandine , Chaboissier Marie-Christine
Published: April 2020

R-spondin2 (RSPO2) is a member of the R-spondin family, which are secreted activators of the WNT/β-catenin (CTNNB1) signaling pathway. In the mouse postnatal ovary, WNT/CTNNB1 signaling is active in the oocyte and in the neighboring supporting cells, the granulosa cells. Although the role of Rspo2 has been previously studied using in vitro experiments, the results are conflicting and the in vivo ovarian function of Rspo2 remains unclear. In the present study, we found that RSPO2/Rspo2 expression is restricted to the oocyte of developing follicles in both human and mouse ovaries from the beginning of the follicular growth. In mice, genetic deletion of Rspo2 does not impair oocyte growth, but instead prevents cell cycle progression of neighboring granulosa cells, thus resulting in an arrest of follicular growth. We further show this cell cycle arrest to be independent of growth promoting GDF9 signaling, but rather associated with a downregulation of WNT/CTNNB1 signaling in granulosa cells. To confirm the contribution of WNT/CTNNB1 signaling in granulosa cell proliferation, we induced cell type specific deletion of Ctnnb1 postnatally. Strikingly, follicles lacking Ctnnb1 failed to develop beyond the primary stage. These results show that RSPO2 acts in a paracrine manner to sustain granulosa cell proliferation in early developing follicles. Taken together, our data demonstrate that the activation of WNT/CTNNB1 signaling by RSPO2 is essential for oocyte-granulosa cell interactions that drive maturation of the ovarian follicles and eventually female fertility.
The YY1/miR-548t-5p/CXCL11 signaling axis regulates cell proliferation and metastasis in human pancreatic cancer
Authors: Ge Wan-Li , Chen Qun , Meng Ling-Dong , Huang Xu-Min , Shi Guo-dong , Zong Qing-Qing , Shen Peng , Lu Yi-Chao , Zhang Yi-Han , Miao Yi , Zhang Jing-Jing , Jiang Kui-Rong
Published: April 2020

Pancreatic cancer (PC) is a malignant tumor with a poor prognosis and high mortality. However, the biological role of miR-548t-5p in PC has not been reported. In this study, we found that miR-548t-5p expression was significantly decreased in PC tissues compared with adjacent tissues, and that low miR-548t-5p expression was associated with malignant PC behavior. In addition, high miR-548t-5p expression inhibited the proliferation, migration, and invasion of PC cell lines. Regarding the molecular mechanism, the luciferase reporter gene, chromatin immunoprecipitation (ChIP), and functional recovery assays revealed that YY1 binds to the miR-548t-5p promoter and positively regulates the expression and function of miR-548t-5p. miR-548t-5p also directly regulates CXCL11 to inhibit its expression. A high level of CXCL11 was associated with worse Tumor Node Metastasis (TNM) staging in patients with PC, enhancing proliferation and metastasis in PC cells. Our study shows that the YY1/miR-548t-5p/CXCL11 axis plays an important role in PC and provides a new potential candidate for the treatment of PC.
The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming
Authors: Xie Wanhua , Miehe Michaela , Laufer Sandra , Johnsen Steven A.
Published: April 2020

Direct reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) requires a resetting of the epigenome in order to facilitate a cell fate transition. Previous studies have shown that epigenetic modifying enzymes play a central role in controlling induced pluripotency and the generation of iPSC. Here we show that RNF40, a histone H2B lysine 120 E3 ubiquitin-protein ligase, is specifically required for early reprogramming during induced pluripotency. Loss of RNF40-mediated H2B monoubiquitination (H2Bub1) impaired early gene activation in reprogramming. We further show that RNF40 contributes to tissue-specific gene suppression via indirect effects by controlling the expression of the polycomb repressive complex-2 histone methyltransferase component EZH2, as well as through more direct effects by promoting the resolution of H3K4me3/H3K27me3 bivalency on H2Bub1-occupied pluripotency genes. Thus, we identify RNF40 as a central epigenetic mediator of cell state transition with distinct functions in resetting somatic cell state to pluripotency.
Mesenchymal stem cell-derived exosomal miR-223 regulates neuronal cell apoptosis
Authors: Wei Hong , Xu Yuhao , Chen Qi , Chen Hui , Zhu Xiaolan , Li Yuefeng
Published: April 2020

Hypoxia limits the survival and function of neurons in the development of Alzheimer’s diseases. Exosome-dependent intercellular communication is an emerging signaling mechanism involved in tissue repair and regeneration; however, the effect and underlying mechanism of mesenchymal stem cell-derived exosomes in regulating neuronal cell apoptosis have not been determined. Here, we showed that the establishment of an AD cell model was accompanied by increased HIF-1α expression and cell apoptosis, impaired cell migration, and decreased miR-223. MSC-derived exosomes were internalized by the AD cell coculture model in a time-dependent manner, resulting in reduced cell apoptosis, enhanced cell migration and increased miR-223, and these effects were reversed by KC7F2, a hypoxic inhibitor. Furthermore, MSC-derived exosomal miR-223 inhibited the apoptosis of neurons in vitro by targeting PTEN, thus activating the PI3K/Akt pathway. In addition, exosomes isolated from the serum of AD patients promoted cell apoptosis. In short, our study showed that MSC-derived exosomal miR-223 protected neuronal cells from apoptosis through the PTEN-PI3K/Akt pathway and provided a potential therapeutic approach for AD.
Author Correction: “Dysfunctions” induced by Roux-en-Y gastric bypass surgery are concomitant with metabolic improvement independent of weight loss
Authors: Li Meiyi , Liu Zhiyuan , Qian Bangguo , Liu Weixin , Horimoto Katsuhisa , Xia Jie , Shi Meilong , Wang Bing , Zhou Huarong , Chen Luonan
Published: April 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Cytokines regulate the antigen-presenting characteristics of human circulating and tissue-resident intestinal ILCs
Authors: Rao Anna , Strauss Otto , Kokkinou Efthymia , Bruchard Mélanie , Tripathi Kumar P. , Schlums Heinrich , Carrasco Anna , Mazzurana Luca , Konya Viktoria , Villablanca Eduardo J. , Björkström Niklas K. , Lindforss Ulrik , Spits Hergen , Mjösberg Jenny
Published: April 2020

ILCs and T helper cells have been shown to exert bi-directional regulation in mice. However, how crosstalk between ILCs and CD4+ T cells influences immune function in humans is unknown. Here we show that human intestinal ILCs co-localize with T cells in healthy and colorectal cancer tissue and display elevated HLA-DR expression in tumor and tumor-adjacent areas. Although mostly lacking co-stimulatory molecules ex vivo, intestinal and peripheral blood (PB) ILCs acquire antigen-presenting characteristics triggered by inflammasome-associated cytokines IL-1β and IL-18. IL-1β drives the expression of HLA-DR and co-stimulatory molecules on PB ILCs in an NF-κB-dependent manner, priming them as efficient inducers of cytomegalovirus-specific memory CD4+ T-cell responses. This effect is strongly inhibited by the anti-inflammatory cytokine TGF-β. Our results suggest that circulating and tissue-resident ILCs have the intrinsic capacity to respond to the immediate cytokine milieu and regulate local CD4+ T-cell responses, with potential implications for anti-tumor immunity and inflammation.
Optoplasmonic characterisation of reversible disulfide interactions at single thiol sites in the attomolar regime
Authors: Vincent Serge , Subramanian Sivaraman , Vollmer Frank
Published: April 2020

Probing individual chemical reactions is key to mapping reaction pathways. Trace analysis of sub-kDa reactants and products is obfuscated by labels, however, as reaction kinetics are inevitably perturbed. The thiol-disulfide exchange reaction is of specific interest as it has many applications in nanotechnology and in nature. Redox cycling of single thiols and disulfides has been unresolvable due to a number of technological limitations, such as an inability to discriminate the leaving group. Here, we demonstrate detection of single-molecule thiol-disulfide exchange using a label-free optoplasmonic sensor. We quantify repeated reactions between sub-kDa thiolated species in real time and at concentrations down to 100’s of attomolar. A unique sensing modality is featured in our measurements, enabling the observation of single disulfide reaction kinetics and pathways on a plasmonic nanoparticle surface. Our technique paves the way towards characterising molecules in terms of their charge, oxidation state, and chirality via optoplasmonics.
Neutrophil swarming delays the growth of clusters of pathogenic fungi
Authors: Hopke Alex , Scherer Allison , Kreuzburg Samantha , Abers Michael S. , Zerbe Christa S. , Dinauer Mary C. , Mansour Michael K. , Irimia Daniel
Published: April 2020

Neutrophils employ several mechanisms to restrict fungi, including the action of enzymes such as myeloperoxidase (MPO) or NADPH oxidase, and the release of neutrophil extracellular traps (NETs). Moreover, they cooperate, forming “swarms” to attack fungi that are larger than individual neutrophils. Here, we designed an assay for studying how these mechanisms work together and contribute to neutrophil's ability to contain clusters of live Candida. We find that neutrophil swarming over Candida clusters delays germination through the action of MPO and NADPH oxidase, and restricts fungal growth through NET release within the swarm. In comparison with neutrophils from healthy subjects, those from patients with chronic granulomatous disease produce larger swarms against Candida, but their release of NETs is delayed, resulting in impaired control of fungal growth. We also show that granulocyte colony-stimulating factors (GCSF and GM-CSF) enhance swarming and neutrophil ability to restrict fungal growth, even during treatment with chemical inhibitors that disrupt neutrophil function.
Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C
Authors: Bilska Aleksandra , Kusio-Kobiałka Monika , Krawczyk Paweł S. , Gewartowska Olga , Tarkowski Bartosz , Kobyłecki Kamil , Nowis Dominika , Golab Jakub , Gruchota Jakub , Borsuk Ewa , Dziembowski Andrzej , Mroczek Seweryn
Published: April 2020

TENT5C is a non-canonical cytoplasmic poly(A) polymerase highly expressed by activated B cells to suppress their proliferation. Here we measure the global distribution of poly(A) tail lengths in responsive B cells using a Nanopore direct RNA-sequencing approach, showing that TENT5C polyadenylates immunoglobulin mRNAs regulating their half-life and consequently steady-state levels. TENT5C is upregulated in differentiating plasma cells by innate signaling. Compared with wild-type, Tent5c−/− mice produce fewer antibodies and have diminished T-cell-independent immune response despite having more CD138high plasma cells as a consequence of accelerated differentiation. B cells from Tent5c−/− mice also have impaired capacity of the secretory pathway, with reduced ER volume and unfolded protein response. Importantly, these functions of TENT5C are dependent on its enzymatic activity as catalytic mutation knock-in mice display the same defect as Tent5c−/−. These findings define the role of the TENT5C enzyme in the humoral immune response.
Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues
Authors: Susaki Etsuo A. , Shimizu Chika , Kuno Akihiro , Tainaka Kazuki , Li Xiang , Nishi Kengo , Morishima Ken , Ono Hiroaki , Ode Koji L. , Saeki Yuki , Miyamichi Kazunari , Isa Kaoru , Yokoyama Chihiro , Kitaura Hiroki , Ikemura Masako , Ushiku Tetsuo , Shimizu Yoshihiro , Saito Takashi , Saido Takaomi C. , Fukayama Masashi , Onoe Hirotaka , Touhara Kazushige , Isa Tadashi , Kakita Akiyoshi , Shibayama Mitsuhiro , Ueda Hiroki R.
Published: April 2020

Whole-organ/body three-dimensional (3D) staining and imaging have been enduring challenges in histology. By dissecting the complex physicochemical environment of the staining system, we developed a highly optimized 3D staining imaging pipeline based on CUBIC. Based on our precise characterization of biological tissues as an electrolyte gel, we experimentally evaluated broad 3D staining conditions by using an artificial tissue-mimicking material. The combination of optimized conditions allows a bottom-up design of a superior 3D staining protocol that can uniformly label whole adult mouse brains, an adult marmoset brain hemisphere, an ~1 cm3 tissue block of a postmortem adult human cerebellum, and an entire infant marmoset body with dozens of antibodies and cell-impermeant nuclear stains. The whole-organ 3D images collected by light-sheet microscopy are used for computational analyses and whole-organ comparison analysis between species. This pipeline, named CUBIC-HistoVIsion, thus offers advanced opportunities for organ- and organism-scale histological analysis of multicellular systems.
Influence of oil, dispersant, and pressure on microbial communities from the Gulf of Mexico
Authors: Noirungsee Nuttapol , Hackbusch Steffen , Viamonte Juan , Bubenheim Paul , Liese Andreas , Müller Rudolf
Published: April 2020

TheDeepwater Horizonincident in the Gulf of Mexico in 2010 released an unprecedented amount of petroleum hydrocarbons 1500 meters below the sea surface. Few studies have considered the influence of hydrostatic pressure on bacterial community development and activity during such spills. The goal of this study was to investigate the response of indigenous sediment microbial communities to the combination of increased pressure, hydrocarbons and dispersant. Deep-sea sediment samples collected from the northern Gulf of Mexico were incubated at atmospheric pressure (0.1 MPa) and at elevated pressure (10 MPa), with and without the addition of crude oil and dispersant. After incubations at 4 °C for 7 days,ColwelliaandPsychrobiumwere highly abundant in all samples. Pressure differentially impacted members of the Alteromonadales. The influences of pressure on the composition of bacterial communities were most pronounced when dispersant was added to the incubations.MoritellaandThalassotaleawere greatly stimulated by the addition of dispersant, suggesting their roles in dispersant biodegradation. However,Moritellawas negatively impacted by increasing pressure. The presence of dispersant was shown to decrease the relative abundance of a known hydrocarbon degrader,Cycloclasticus, while increasing pressure increased its relative abundance. This study highlights the significant influence of pressure on the development of microbial communities in the presence of oil and dispersant during oil spills and related response strategies in the deep sea.
Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System
Authors: Ogden Aaron J. , Wietsma Thomas W. , Winkler Tanya , Farris Yuliya , Myers Gabriel L. , Ahkami Amir H.
Published: April 2020

Root systems are dynamic and adaptable organs that play critical roles in plant development. However, how roots grow and accumulate biomass during plant life cycle and in relation to shoot growth phenology remains understudied. A comprehensive time-dependent root morphological analysis integrated with molecular signatures is then required to advance our understanding of root growth and development. Here we studiedBrachypodium distachyonrooting process by monitoring root morphology, biomass production, and C/N ratios during developmental stages. To provide insight into gene regulation that accompanies root growth, we generated comprehensive transcript profiles of Brachypodium whole-root system at four developmental stages. Our data analysis revealed that multiple biological processes including trehalose metabolism and various families of transcription factors (TFs) were differentially expressed in root system during plant development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated as plant entered the booting/heading stage, while ARFs and GRFs were downregulated suggesting these TF families as important factors involved in specific phases of rooting, and possibly in regulation of transition to plant reproductive stages. We identified several Brachypodium candidate root biomass-promoting genes andcis-regulatory elements for further functional validations and root growth improvements in grasses.
Plasma Metabolic Signature of Atherosclerosis Progression and Colchicine Treatment in Rabbits
Authors: Izidoro Mario Augusto , Cecconi Alberto , Panadero María Isabel , Mateo Jesús , Godzien Joanna , Vilchez Jean Paul , López-Gonzálvez Ángeles , Ruiz-Cabello Jesús , Ibañez Borja , Barbas Coral , Rupérez Francisco J.
Published: April 2020

Balloon catheter endothelial denudation in New Zealand white rabbits fed high cholesterol diet is a validated atherosclerosis model. Well-characterized in terms of atherosclerosis induction and progression, the metabolic changes associated with the atherosclerosis progression remain indeterminate. Non-targeted metabolomics permits to develop such elucidation and allows to evaluate the metabolic consequences of colchicine treatment, an anti-inflammatory drug that could revert these changes. 16 rabbits underwent 18 weeks of atherosclerosis induction by diet and aortic denudation. Thereafter animals were randomly assigned to colchicine treatment or placebo for 18 weeks while on diet. Plasma samples were obtained before randomization and at 36 weeks. Multiplatform (GC/MS, CE/MS, RP-HPLC/MS) metabolomics was applied. Plasma fingerprints were pre-processed, and the resulting matrixes analyzed to unveil differentially expressed features. Different chemical annotation strategies were accomplished for those significant features. We found metabolites associated with either atherosclerosis progression, or colchicine treatment, or both. Atherosclerosis was profoundly associated with an increase in circulating bile acids. Most of the changes associated with sterol metabolism could not be reverted by colchicine treatment. However, the variations in lysine, tryptophan and cysteine metabolism among others, have shown new potential mechanisms of action of the drug, also related to atherosclerosis progression, but not previously described.
Kairomone-like activity of bile and bile components: A step towards revealing the chemical nature of fish kairomone
Authors: Pijanowska Joanna , Markowska Magdalena , Ruszczyńska Anna , Bulska Ewa , Dawidowicz Piotr , Ślusarczyk Mirosław , Biesaga Magdalena
Published: April 2020

Despite the efforts of a number of research groups worldwide, we still have a poor understanding of the chemical nature of the fish kairomones which induce defensive morphology, life history and behavior in their planktonic prey. Bile excreted by foraging fish play a crucial role in their signaling systems. Using high-performance liquid chromatography (HPLC), we revealed the presence of primary and secondary bile acids and bile salts in fish-conditioned water, similar as in carp bile. Upon exposure to either fish bile or commercially acquired bile salts, Daphnia demonstrated similar changes in life history and behavior as when exposed to fish kairomones. The synergic effect of the injured Daphnia alarm substance with fish bile on Daphnia life history is similar to the adaptive effect of the same alarm substance combined with fish kairomones. This strongly supports the view that fish bile or selected bile acids/salts may be responsible for the biological activity of kairomones.
Effective microtissue RNA extraction coupled with Smart-seq2 for reproducible and robust spatial transcriptome analysis
Authors: Yamazaki Miki , Hosokawa Masahito , Arikawa Koji , Takahashi Kiyofumi , Sakanashi Chikako , Yoda Takuya , Matsunaga Hiroko , Takeyama Haruko
Published: April 2020

Spatial transcriptomics is useful for understanding the molecular organization of a tissue and providing insights into cellular function in a morphological context. In order to obtain reproducible results in spatial transcriptomics, we have to maintain tissue morphology and RNA molecule stability during the image acquisition and biomolecule collection processes. Here, we developed a tissue processing method for robust and reproducible RNA-seq from tissue microdissection samples. In this method, we suppressed RNA degradation in fresh-frozen tissue specimens by dehydration fixation and effectively collected a small amount of RNA molecules from microdissection samples by magnetic beads. We demonstrated the spatial transcriptome analysis of the mouse liver and brain in serial microdissection samples (100 μm in a diameter and 10 μm in thickness) produced by a microdissection punching system. Using our method, we could prevent RNA degradation at room temperature and effectively produce a sequencing library with Smart-seq2. This resulted in reproducible sequence read mapping in exon regions and the detection of more than 2000 genes compared to non-fixed samples in the RNA-seq analysis. Our method would be applied to various transcriptome analyses, providing the information for region specific gene expression in tissue specimens.
Greyhound racing ideal trajectory path generation for straight to bend based on jerk rate minimization
Authors: Hossain Md. Imam , Eager David , Walker Paul D.
Published: April 2020

This paper presents methods for modelling and designing an ideal path trajectory between straight and bend track path segments for racing greyhounds. To do this, we numerically generate clothoid and algebraic curve segments for racing quadrupeds using a sequential vector transformation method as well as using a helper equation for approaching ideal clothoid segments that would respect greyhound kinematic parameters and boundary conditions of the track. Further, we look into the limitations of using a clothoid curve for racing dog track path design and propose a smooth composite curve for track transition design which roughly maintains G3 curvature continuity for smooth jerk to overcome limitations of a clothoid transition. Finally, we show results from race data modelling and past injury data, which provide a strong indication of clothoid curve segments improving the dynamics and safety of racing greyhounds while reducing injuries.
Analysing the phenotype development of soybean plants using low-cost 3D reconstruction
Authors: Zhu Rongsheng , Sun Kai , Yan Zhuangzhuang , Yan Xuehui , Yu Jianglin , Shi Jia , Hu Zhenbang , Jiang Hongwei , Xin Dawei , Zhang Zhanguo , Li Yang , Qi Zhaoming , Liu Chunyan , Wu Xiaoxia , Chen Qingshan
Published: April 2020

With the development of digital agriculture, 3D reconstruction technology has been widely used to analyse crop phenotypes. To date, most research on 3D reconstruction of field crops has been limited to analysis of population characteristics. Therefore, in this study, we propose a method based on low-cost 3D reconstruction technology to analyse the phenotype development during the whole growth period. Based on the phenotypic parameters extracted from the 3D reconstruction model, we identified the “phenotypic fingerprint” of the relevant phenotypes throughout the whole growth period of soybean plants and completed analysis of the plant growth patterns using a logistic growth model. The phenotypic fingerprint showed that, before the R3 period, the growth of the five varieties was similar. After the R5 period, the differences among the five cultivars gradually increased. This result indicates that the phenotypic fingerprint can accurately reveal the patterns of phenotypic changes. The logistic growth model of soybean plants revealed the time points of maximum growth rate of the five soybean varieties, and this information can provide a basis for developing guidelines for water and fertiliser application to crops. These findings will provide effective guidance for breeding and field management of soybean and other crops.
High prevalence of albuminuria amongst people who inject drugs: A cross-sectional study
Authors: McGowan C. R. , Wright T. , Nitsch D. , Lewer D. , Brathwaite R. , Scott J. , Hope V. , Ciccarone D. , Dunn J. , Gillmore J. , Story A. , Harris M.
Published: April 2020

Albuminuria is a key biomarker for cardiovascular disease and chronic kidney disease. Our study aimed to describe the prevalence of albuminuria amongst people who inject drugs in London and to test any potential associations with demographic characteristics, past diagnoses, and drug preparation and administration practices. We carried out a cross-sectional survey amongst people who use drugs in London. The main outcome measure was any albuminuria including both microalbuminuria and macroalbuminuria. Three-hundred and sixteen samples were tested by local laboratory services. Our study initially employed point-of-care testing methods but this resulted in a high number of false positives. Our findings suggest the prevalence of albuminuria amongst PWID is twice that of the general population at 19% (95%CI 15.3–24.0%). Risk factors associated with albuminuria were HIV (aOR 4.11 [95% CI 1.37–12.38]); followed by overuse of acidifier for dissolving brown heroin prior to injection (aOR 2.10 [95% CI 1.04–4.22]). Albuminuria is high amongst people who inject drugs compared to the general population suggesting the presence of increased cardiovascular and renal pathologies. This is the first study to demonstrate an association with acidifier overuse. Dehydration may be common amongst this population and may affect the diagnostic accuracy of point-of-care testing for albuminuria.
Clinical outcome of breast cancer in carriers of BRCA1 and BRCA2 mutations according to molecular subtypes
Authors: De Talhouet Solene , Peron Julien , Vuilleumier Aurelie , Friedlaender Alex , Viassolo Valeria , Ayme Aurélie , Bodmer Alexandre , Treilleux Isabelle , Lang Noemie , Tille Jean- Christophe , Chappuis Pierre O. , Buisson Adrien , Giraud Sophie , Lasset Christine , Bonadona Valerie , Trédan Olivier , Labidi-Galy S.Intidhar
Published: April 2020

BRCA1/BRCA2 genes play a central role in DNA repair and their mutations increase sensitivity to DNA-damaging agents. There are conflicting data regarding the prognostic value of BRCA germline mutations in breast cancer (BC) patients. We collected clinical, pathological and genetic data of a cohort 925 BC patients preselected for genetic screening and treated with neoadjuvant or adjuvant chemotherapy, of whom 266 were BRCA carriers. Overall, 171 women carried a BRCA1 mutation, 95 carried a BRCA2 mutation, and 659 were non-carriers. In the entire cohort, there was a prolonged disease-free survival (DFS) for BRCA carriers (hazard ratio (HR) = 0.63; 95% confidence interval (CI), 0.44–0.90 for BRCA1; HR = 0.72; 95%CI, 0.47–1.1 for BRCA2; p = 0.020) and a trend toward prolonged disease-specific survival (DSS; HR = 0.65; 95%CI, 0.40–1.1 for BRCA1; HR = 0.78; 95%CI, 0.44–1.38 for BRCA2; p = 0.19) though not statistically significant. In the TNBC group, BRCA carriers had prolonged DFS (adjusted HR = 0.50; 95%CI, 0.28–0.89 for BRCA1; adjusted HR = 0.37; 95%CI, 0.11–1.25, for BRCA2; p = 0.034) and DSS (adjusted HR = 0.42; 95%CI, 0.21–0.82 for BRCA1; adjusted HR = 0.45; 95%CI, 0.11–1.9 for BRCA2; p = 0.023). In the non-TNBC group, the BRCA1 or BRCA2 mutations did not have any impact on survival. These results suggest that BRCA1/BRCA2 germline mutations are associated with prolonged survival only if women were diagnosed with TNBC.
Occurrence and genetic diversity of CRESS DNA viruses in wild birds: a Hungarian study
Authors: Kaszab Eszter , Lengyel György , Marton Szilvia , Dán Ádám , Bányai Krisztián , Fehér Enikő
Published: April 2020

Circoviruses, cycloviruses and other circular, replication-associated protein-encoding single stranded (CRESS) DNA viruses have been detected in a variety of animal taxa. In this study, cloacal swab samples (n = 90) were examined for CRESS DNA viruses from 31 wild bird species living at various aquatic sites in Hungary to identify possible reservoirs of viruses pathogenic to domestic poultry. A total of 30 (33.3%) specimens tested positive with pan-CRESS DNA virus specific PCR. Goose circovirus (GoCV), Duck associated cyclovirus 1 (DuACyV-1) and Garrulus glandarius associated circular virus 1 (GgaCV-1) were detected in nine, three and two different bird species, respectively. Selected specimens were subjected to whole genome sequencing. The obtained sequence data revealed conserved gene structure within the identified virus species and detected homologous (within GoCV) and possible heterologous recombination (within DuACyV-1) events. Results presented here provide new information on the genomic diversity and evolution of selected CRESS DNA viruses.
Effects of anti-PD-1 immunotherapy on tumor regression: insights from a patient-derived xenograft model
Authors: Martín-Ruiz Asunción , Fiuza-Luces Carmen , Martínez-Martínez Esther , Arias Clemente F. , Gutiérrez Lourdes , Ramírez Manuel , Martín-Acosta Paloma , Coronado Maria José , Lucia Alejandro , Provencio Mariano
Published: April 2020

Immunotherapies, such as checkpoint blockade of programmed cell death protein-1 (PD-1), have resulted in unprecedented improvements in survival for patients with lung cancer. Nonetheless, not all patients benefit equally and many issues remain unresolved, including the mechanisms of action and the possible effector function of immune cells from non-lymphoid lineages. The purpose of this study was to investigate whether anti-PD-1 immunotherapy acts on malignant tumor cells through mechanisms beyond those related to T lymphocyte involvement. We used a murine patient-derived xenograft (PDX) model of early-stage non–small cell lung carcinoma (NSCLC) devoid of host lymphoid cells, and studied the tumor and immune non-lymphoid responses to immunotherapy with anti-PD-1 alone or in combination with standard chemotherapy (cisplatin). An antitumor effect was observed in animals that received anti-PD-1 treatment, alone or in combination with cisplatin, likely due to a mechanism independent of T lymphocytes. Indeed, anti-PD-1 treatment induced myeloid cell mobilization to the tumor concomitant with the production of exudates compatible with an acute inflammatory reaction mediated by murine polymorphonuclear leukocytes, specifically neutrophils. Thus, while keeping in mind that more research is needed to corroborate our findings, we report preliminary evidence for a previously undescribed immunotherapy mechanism in this model, suggesting a potential cytotoxic action of neutrophils as PD-1 inhibitor effector cells responsible for tumor regression by necrotic extension.
A cognitively demanding working-memory intervention enhances extinction
Authors: de Voogd Lycia D. , Phelps Elizabeth A.
Published: April 2020

Improving extinction learning has the potential to optimize psychotherapy for persistent anxiety-related disorders. Recent findings show that extinction learning can be improved with a cognitively demanding eye-movement intervention. It is, however, unclear whether [1] any cognitively-demanding task can enhance extinction, or whether it is limited to eye movements, and [2] the effectiveness of such an intervention can be enhanced by increasing cognitive load. Participants (n = 102, n = 75 included in the final sample) completed a Pavlovian threat conditioning paradigm across two days. One group underwent standard extinction (Control), a second group underwent extinction paired with a 1-back working memory task (Low-Load), and a third group underwent extinction paired with a 2-back working memory task (High-Load). We found that the conditioned response during extinction was reduced for both the Low-Load and the High-Load groups compared to the Control group. This reduction persisted during recovery the following day when no working memory task was executed. Finally, we found that within the High-Load group, participants with lower accuracy scores on the 2-back task (i.e., for who the task was more difficult) had a stronger reduction in the conditioned response. We did not observe this relationship within the Low-Load group. Our findings suggest that cognitive load induced by a working memory intervention embedded during extinction reduces persistent threat responses.
Expected spatial patterns of alien woody plants in South Africa’s protected areas under current scenario of climate change
Authors: Bezeng Bezeng S. , Yessoufou Kowiyou , Taylor Peter J. , Tesfamichael Solomon G.
Published: April 2020

Although protected areas (PAs) are declared to provide sanctuaries for biodiversity, they are increasingly threatened by the synergistic effects of anthropic factors, invasive alien species and climate change. Consequently, interventions are required to minimize the impacts of these threats on PAs’ integrity. To inform these interventions in the South African context and under the current climate change scenario, we tested for geographic patterns of alien woody species across the network of 1,453 PAs using three alien invasion indices – alien species abundance, invaded area ratio and alien species richness. Our analysis shows that, under current climate change scenario, none of the PAs would be effective in shielding against alien plants and PAs that are geographically close tend to share similar invasion patterns. In addition, PAs that are hotspots of alien species are also geographically clustered but these findings are biome-dependent. Our outlier analysis reveals not only an island of disproportionately rich PAs in alien species, but also identifies some alien-poor PAs. We suggest that PAs that are hotspots of alien species as well as outliers of disproportionately rich PAs in alien species should be priority in monitoring and invasion control programmes in the context of the ongoing climate change.