bluuebunny/crossref_metadata_2025 huggingface dataset:
Isotopic labelling reveals the efficient adaptation of wheat root TCA cycle flux modes to match carbon demand under ammonium nutrition
Authors: Vega-Mas Izargi , Cukier Caroline , Coleto Inmaculada , González-Murua Carmen , Limami Anis M. , González-Moro M Begoña , Marino Daniel
Published: June 2019

Proper carbon (C) supply is essential for nitrogen (N) assimilation especially when plants are grown under ammonium (NH4+) nutrition. However, how C and N metabolic fluxes adapt to achieve so remains uncertain. In this work, roots of wheat (Triticum aestivum L.) plants grown under exclusive NH4+ or nitrate (NO3−) supply were incubated with isotope-labelled substrates (15NH4+, 15NO3−, or [13C]Pyruvate) to follow the incorporation of 15N or 13C into amino acids and organic acids. Roots of plants adapted to ammonium nutrition presented higher capacity to incorporate both 15NH4+ and 15NO3− into amino acids, thanks to the previous induction of the NH4+ assimilative machinery. The 15N label was firstly incorporated into [15N]Gln vía glutamine synthetase; ultimately leading to [15N]Asn accumulation as an optimal NH4+ storage. The provision of [13C]Pyruvate led to [13C]Citrate and [13C]Malate accumulation and to rapid [13C]2-OG consumption for amino acid synthesis and highlighted the importance of the anaplerotic routes associated to tricarboxylic acid (TCA) cycle. Taken together, our results indicate that root adaptation to ammonium nutrition allowed efficient assimilation of N thanks to the promotion of TCA cycle open flux modes in order to sustain C skeleton availability for effective NH4+ detoxification into amino acids.
Proton Gradient-Dependent Transport of p-Glucocoumaryl Alcohol in Differentiating Xylem of Woody Plants
Authors: Tsuyama Taku , Matsushita Yasuyuki , Fukushima Kazuhiko , Takabe Keiji , Yazaki Kazufumi , Kamei Ichiro
Published: June 2019

Lignin is a cell wall component of vascular plants crucial for survival in terrestrial environments. While p-hydroxyphenyl lignin is minor, it is considered to be localised in the outermost part of the cell wall providing strong adhesion between cells, which determines cell shape. Transport of the lignin precursor from the cytosol to the cell wall is critical to regulate temporal and spatial lignin deposition; however, little information on the transport step is available. Here, we report transport activity of p-glucocoumaryl alcohol, a precursor of p-hydroxyphenyl lignin, in a broad-leaved tree (hybrid poplar, Populus sieboldii × P. grandidentata) and a coniferous tree (Japanese cypress, Chamaecyparis obtusa). Membrane vesicles of both trees were prepared from differentiating xylem with vigorous lignification and used for transport assays. Several inhibition assays indicated that not ABC transporters but the proton gradient and V-ATPase are involved in p-glucocoumaryl alcohol transport depending on ATP. These results support the hypothesis that p-glucocoumaryl alcohol is loaded into the secretory vesicles and delivered to the cell wall by exocytosis. Furthermore, this transport mechanism was common in both poplar and Japanese cypress, strongly suggesting that p-glucocoumaryl alcohol transport in the differentiating xylem is conserved within woody plants.
Food-provisioning negatively affects calf survival and female reproductive success in bottlenose dolphins
Authors: Senigaglia V. , Christiansen F. , Sprogis K. R. , Symons J. , Bejder L.
Published: June 2019

Food-provisioning of wildlife can facilitate reliable up-close encounters desirable by tourists and, consequently, tour operators. Food-provisioning can alter the natural behavior of an animal, encouraging adverse behavior (e.g. begging for food handouts), and affect the reproductive success and the viability of a population. Studies linking food-provisioning to reproductive success are limited due to the lack of long-term datasets available, especially for long-lived species such as marine mammals. In Bunbury, Western Australia, a state-licensed food-provisioning program offers fish handouts to a limited number of free-ranging bottlenose dolphins (Tursiops aduncus). Coupled with long-term historical data, this small (<200 individuals), resident dolphin population has been extensively studied for over ten years, offering an opportunity to examine the effect of food-provisioning on the reproductive success of females (ntotal = 63;nprovisioned females = 8). Female reproductive success was estimated as the number of weaned calves produced per reproductive years and calf survival at year one and three years old was investigated. The mean reproductive success of provisioned and non-provisioned females was compared using Bayes factor. We also used generalized linear models (GLMs) to examine female reproductive success in relation to the occurrence of food-provisioning, begging behavior and location (within the study area). Furthermore, we examined the influence of these variables and birth order and climatic fluctuations (e.g. El Niño Southern Oscillation) on calf survival. Bayes factor analyses (Bayes factor = 6.12) and results from the best fitting GLMs showed that female reproductive success and calf survival were negatively influenced by food-provisioning. The negative effects of food-provisioning, although only affecting a small proportion of the adult females’ population (13.2%), are of concern, especially given previous work showing that this population is declining.
Palladium/palladium oxide coated electrospun fibers for wearable sweat pH-sensors
Authors: Diculescu Victor C. , Beregoi Mihaela , Evanghelidis Alexandru , Negrea Raluca F. , Apostol Nicoleta G. , Enculescu Ionut
Published: June 2019

The work describes the development of a flexible, hydrogel embedded pH-sensor that can be integrated in inexpensive wearable and non-invasive devices at epidermal level for electrochemical quantification of H+ ions in sweat. Such a device can be useful for swift, real time diagnosis and for monitoring specific conditions. The sensors’ working electrodes are flexible poly(methyl methacrylate) electrospun fibers coated with a thin gold layer and electrochemically functionalized with nanostructured palladium/palladium oxide. The response to H+ ions is investigated by cyclic voltammetry and electrochemical impedance spectroscopy while open circuit potential measurements show a sensitivity of aprox. −59 mV per pH unit. The modification of the sensing interface upon basic and acid treatment is characterized by scanning and transmission electron microscopy and the chemical composition by X-ray photoelectron spectroscopy. In order to demonstrate the functionality of the pH-sensor at epidermal level, as a wearable device, the palladium/palladium oxide working electrode and silver/silver chloride reference electrode are embedded within a pad of polyacrylamide hydrogel and measurements in artificial sweat over a broad pH range were performed. Sensitivity up to −28 mV/pH unit, response time below 30 s, temperature dependence of approx. 1 mV/°C as well as the minimum volume to which the sensor responses of 250 nanoliters were obtained for this device. The proposed configuration represents a viable alternative making use of low-cost and fast fabrication processes and materials.
PolyBall: A new adsorbent for the efficient removal of endotoxin from biopharmaceuticals
Authors: Razdan Sidharth , Wang Jee-Ching , Barua Sutapa
Published: June 2019

The presence of endotoxin, also known as lipopolysaccharides (LPS), as a side product appears to be a major drawback for the production of certain biomolecules that are essential for research, pharmaceutical, and industrial applications. In the biotechnology industry, gram-negative bacteria (e.g., Escherichia coli) are widely used to produce recombinant products such as proteins, plasmid DNAs and vaccines. These products are contaminated with LPS, which may cause side effects when administered to animals or humans. Purification of LPS often suffers from product loss. For this reason, special attention must be paid when purifying proteins aiming a product as free as possible of LPS with high product recovery. Although there are a number of methods for removing LPS, the question about how LPS removal can be carried out in an efficient and economical way is still one of the most intriguing issues and has no satisfactory solution yet. In this work, polymeric poly-ε-caprolactone (PCL) nanoparticles (NPs) (dP = 780 ± 285 nm) were synthesized at a relatively low cost and demonstrated to possess sufficient binding sites for LPS adsorption and removal with ~100% protein recovery. The PCL NPs removed greater than 90% LPS from protein solutions suspended in water using only one milligram (mg) of NPs, which was equivalent to ~1.5 × 106 endotoxin units (EU) per mg of particle. The LPS removal efficacy increased to a higher level (~100%) when phosphate buffered saline (PBS containing 137 mM NaCl) was used as a protein suspending medium in place of water, reflecting positive effects of increasing ionic strength on LPS binding interactions and adsorption. The results further showed that the PCL NPs not only achieved 100% LPS removal but also ~100% protein recovery for a wide concentration range from 20–1000 μg/ml of protein solutions. The NPs were highly effective in different buffers and pHs. To scale up the process further, PCL NPs were incorporated into a supporting cellulose membrane which promoted LPS adsorption further up to ~100% just by running the LPS-containing water through the membrane under gravity. Its adsorption capacity was 2.8 × 106 mg of PCL NPs, approximately 2 -fold higher than that of NPs alone. This is the first demonstration of endotoxin separation with high protein recovery using polymer NPs and the NP-based portable filters, which provide strong adsorptive interactions for LPS removal from protein solutions. Additional features of these NPs and membranes are biocompatible (environment friendly) recyclable after repeated elution and adsorption with no significant changes in LPS removal efficiencies. The results indicate that PCL NPs are an effective LPS adsorbent in powder and membrane forms, which have great potential to be employed in large-scale applications.
Engineering a 3D functional human peripheral nerve in vitro using the Nerve-on-a-Chip platform
Authors: Sharma Anup D. , McCoy Laurie , Jacobs Elizabeth , Willey Hannah , Behn Jordan Q. , Nguyen Hieu , Bolon Brad , Curley J. Lowry , Moore Michael J.
Published: June 2019

Development of “organ-on-a-chip” systems for neuroscience applications are lagging due in part to the structural complexity of the nervous system and limited access of human neuronal & glial cells. In addition, rates for animal models in translating to human success are significantly lower for neurodegenerative diseases. Thus, a preclinical in vitro human cell-based model capable of providing critical clinical metrics such as nerve conduction velocity and histomorphometry are necessary to improve prediction and translation of in vitro data to successful clinical trials. To answer this challenge, we present an in vitro biomimetic model of all-human peripheral nerve tissue capable of showing robust neurite outgrowth (~5 mm), myelination of hNs by primary human Schwann cells (~5%), and evaluation of nerve conduction velocity (0.13–0.28 m/sec), previously unrealized for any human cell-based in vitro system. To the best of our knowledge, this Human Nerve-on-a-chip (HNoaC) system is the first biomimetic microphysiological system of myelinated human peripheral nerve which can be used for evaluating electrophysiological and histological metrics, the gold-standard assessment techniques previously only possible with in vivo studies.
Deep-learning-based imaging-classification identified cingulate island sign in dementia with Lewy bodies
Authors: Iizuka Tomomichi , Fukasawa Makoto , Kameyama Masashi
Published: June 2019

The differentiation of dementia with Lewy bodies (DLB) from Alzheimer’s disease (AD) using brain perfusion single photon emission tomography is important but is challenging because these conditions exhibit typical features. The cingulate island sign (CIS) is the most recently identified specific feature of DLB for a differential diagnosis. The current study aimed to examine the usefulness of deep-learning-based imaging classification for the diagnoses of DLB and AD. Furthermore, we investigated whether CIS was emphasized by a deep convolutional neural network (CNN) during differentiation. Brain perfusion single photon emission tomography images from 80 patients, each with DLB and AD, and 80 individuals with normal cognition (NL) were used for training and 20 each for final testing. The CNN was trained on brain surface perfusion images. Gradient-weighted class activation mapping (Grad-CAM) was applied to the CNN to visualize the features that was emphasized by the trained CNN. The binary classifications between DLB and NL, DLB and AD, and AD and NL were 93.1%, 89.3%, and 92.4% accurate, respectively. The CIS ratios closely correlated with the output scores before softmax for DLB–AD discrimination (DLB/AD scores). The Grad-CAM highlighted CIS in the DLB discrimination. Visualization of learning process by guided Grad-CAM revealed that CIS became more focused by the CNN as the training progressed. The DLB/AD score was significantly associated with the three core features of DLB. Deep-learning-based imaging classification was useful for an objective and accurate differentiation of DLB from AD and for predicting clinical features of DLB. The CIS was identified as a specific feature during DLB classification. The visualization of specific features and learning processes could be critical in deep learning to discover new imaging features.
Self-assembly of plant protein fibrils interacting with superparamagnetic iron oxide nanoparticles
Authors: Li Jing , Pylypchuk Ievgen , Johansson Daniel P. , Kessler Vadim G. , Seisenbaeva Gulaim A. , Langton Maud
Published: June 2019

In situ fibrillation of plant proteins in presence of the superparamagnetic iron oxide nanoparticles (NP) promoted formation of a hybrid nanocomposite. The morphology of NP-fibril composite was revealed using ex-situ atomic force microscopy (AFM) in air. The NP-fibrils were associated into extended multi-fibril structures, indicating that the addition of NPs promoted protein association via β-sheet assembly. Real-time movement of NPs attached to fibrils under an external magnetic field was visualized using in-situ AFM in liquid, revealing that composite structures were stable at low pH, and displaying dipolar property of the NPs in the composite at high pH. Changes in magnetic properties of NPs when interacting with protein fibrils were quantitatively mapped using magnetic force microscopy (MFM). The magnetic moment of the NPs in composite was increased by co-existing with protein at low pH, while their dipolar nature was maintained at high pH. Self-assembly of the protein into fibrils is accelerated with increasing NP concentration within an optimal range, which is attributed to a fibrillation-competent conformation of the peptides. The latter was explained by the formation of favorable hydrogen bonds, electrostatic interactions, and efficient surface energy transfer between NPs and proteins.
Computational analysis of single-cell transcriptomics data elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo
Authors: Gerovska Daniela , Araúzo-Bravo Marcos J.
Published: June 2019

Our computational analysis focuses on the 32- to 64-cell mouse embryo transition, Embryonic day (E3.25), whose study in literature is concentrated mainly on the search for an early onset of the second cell-fate decision, the specification of the inner cell mass (ICM) to primitive endoderm (PE) and epiblast (EPI). We analysed single-cell (sc) microarray transcriptomics data from E3.25 using Hierarchical Optimal k-Means (HOkM) clustering, and identified two groups of ICM cells: a group of cells from embryos with less than 34 cells (E3.25-LNCs), and another group of cells from embryos with more than 33 cells (E3.25-HNCs), corresponding to two developmental stages. Although we found massive underlying heterogeneity in the ICM cells at E3.25-HNC with over 3,800 genes with transcriptomics bifurcation, many of which are PE and EPI markers, we showed that the E3.25-HNCs are neither PE nor EPI. Importantly, analysing the differently expressed genes between the E3.25-LNCs and E3.25-HNCs, we uncovered a non-autonomous mechanism, based on a minimal number of four inner-cell contacts in the ICM, which activates Oct4 in the preimplantation embryo. Oct4 is highly expressed but unstable at E3.25-LNC, and stabilizes at high level at E3.25-HNC, with Bsg highly expressed, and the chromatin remodelling program initialised to establish an early naïve pluripotent state. Our results indicate that the pluripotent state we found to exist in the ICM at E3.25-HNC is the in vivo counterpart of a new, very early pluripotent state. We compared the transcriptomics profile of this in vivo E3.25-HNC pluripotent state, together with the profiles of E3.25-LNC, E3.5 EPI and E4.5 EPI cells, with the profiles of all embryonic stem cells (ESCs) available in the GEO database from the same platform (over 600 microarrays). The shortest distance between the set of inner cells (E3.25, E3.5 and E4.5) and the ESCs is between the E3.25-HNC cells and 2i + LIF ESCs; thus, the developmental transition from 33 to 34 cells decreases dramatically the distance with the naïve ground state of the 2i + LIF ESCs. We validated the E3.25 events through analysis of scRNA-seq data from early and late 32-cell ICM cells.
Intestinal translocation of enterococci requires a threshold level of enterococcal overgrowth in the lumen
Authors: Archambaud Cristel , Derré-Bobillot Aurélie , Lapaque Nicolas , Rigottier-Gois Lionel , Serror Pascale
Published: June 2019

Enterococci are subdominant members of the human gastrointestinal microbiota. Enterococcus faecalis is generally harmless for healthy individuals, but it can cause a diverse range of infections in immunodeficient or elderly patients with severe underlying diseases. In this study, we analysed the levels of intestinal translocation of indigenous enterococci in C57BL/6, CF-1 and CX3CR1−/− mice upon clindamycin antibiotic-induced dysbiosis. We found that C57BL/6 was the most permissive model for enterococcal translocation and that initiation of E. faecalis translocation coincided with a threshold of enterococcal colonisation in the gut lumen, which once reached, triggered E. faecalis dissemination to deeper organs. We showed that the extent to which E. faecalis clinical strain VE14821 competed with indigenous enterococci differed between the C57BL/6 and CX3CR1−/− models. Finally, using a simplified gnotobiotic model, we observed E. faecalis crossing an intact intestinal tract using intestinal epithelial cells as one route to reach the lamina propria. Our study opens new perspectives for assessing the effect of various immunodeficiencies and for investigating mechanisms underlying enterococcal translocation.
Localization of RalB signaling at endomembrane compartments and its modulation by autophagy
Authors: Singh Manish Kumar , Martin Alexandre P. J. , Joffre Carine , Zago Giulia , Camonis Jacques , Coppey Mathieu , Parrini Maria Carla
Published: June 2019

The monomeric GTPase RalB controls crucial physiological processes, including autophagy and invasion, but it still remains unclear how this multi-functionality is achieved. Previously, we reported that the RalGEF (Guanine nucleotide Exchange Factor) RGL2 binds and activates RalB to promote invasion. Here we show that RGL2, a major activator of RalB, is also required for autophagy. Using a novel automated image analysis method, Endomapper, we quantified the endogenous localization of the RGL2 activator and its substrate RalB at different endomembrane compartments, in an isogenic normal and Ras-transformed cell model. In both normal and Ras-transformed cells, we observed that RGL2 and RalB substantially localize at early and recycling endosomes, and to lesser extent at autophagosomes, but not at trans-Golgi. Interestingly the use of a FRET-based RalB biosensor indicated that RalB signaling is active at these endomembrane compartments at basal level in rich medium. Furthermore, induction of autophagy by nutrient starvation led to a considerable reduction of early and recycling endosomes, in contrast to the expected increase of autophagosomes, in both normal and Ras-transformed cells. However, autophagy mildly affected relative abundances of both RGL2 and RalB at early and recycling endosomes, and at autophagosomes. Interestingly, RalB activity increased at autophagosomes upon starvation in normal cells. These results suggest that the contribution of endosome membranes (carrying RGL2 and RalB molecules) increases total pool of RGL2-RalB at autophagosome forming compartments and might contribute to amplify RalB signaling to support autophagy.
Evolutionary analysis of human parechovirus type 3 and clinical outcomes of infection during the 2017–18 Australian epidemic
Authors: Chamings Anthony , Druce Julian , Caly Leon , Yoga Yano , Britton Philip N. , Macartney Kristine K. , Alexandersen Soren
Published: June 2019

Human parechovirus type 3 (HPeV3) can cause severe sepsis-like illness in young infants and may be associated with long term neurodevelopmental delay later in childhood. We investigated the molecular epidemiology of HPeV infection in thirty three infants requiring hospitalization before, during and after the peak of the 2017/18 HPeV epidemic wave in Australia. During the peak of the epidemic, all cases were infected with an HPeV3, while before and after the peak, HPeV1 was the predominant type detected. The predominant HPeV3 was the recombinant HPeV3 also detected in the 2013/14 and 2015/16 Australian epidemics. Sepsis-like or meningitis-like symptoms were only reported in cases infected with the recombinant HPeV3. Phylogenetic analysis of the recombinant HPeV3 revealed that the virus continued to evolve, also between the Australian outbreaks, thus indicating continued circulation, despite not being detected and reported in Australia or elsewhere in between epidemic waves. The recombinant HPeV3 continued to show a remarkable stability in its capsid amino acid sequence, further strengthening our previous argument for development of a vaccine or immunotherapeutics to reduce the severity of HPeV3 outbreaks due to this virus.
In-depth analysis of swim bladder-associated microbiota in rainbow trout (Oncorhynchus mykiss)
Authors: Villasante Alejandro , Ramírez Carolina , Rodríguez Héctor , Catalán Natalia , Díaz Osmán , Rojas Rodrigo , Opazo Rafael , Romero Jaime
Published: June 2019

Our knowledge regarding microbiota associated with the swim bladder of physostomous, fish with the swim bladder connected to the esophagus via the pneumatic duct, remains largely unknown. The goal of this study was to conduct the first in-depth characterization of the swim bladder-associated microbiota using high-throughput sequencing of the V4 region of the 16 S rRNA gene in rainbow trout (Oncorhynchus mykiss). We observed major differences in bacterial communities composition between swim bladder-associated microbiota and distal intestine digesta microbiota in fish. Whilst bacteria genera, such as Cohnella, Lactococcus and Mycoplasma were more abundant in swim bladder-associated microbiota, Citrobacter, Rhodobacter and Clavibacter were more abundant in distal intestine digesta microbiota. The presumptive metabolic function analysis (PICRUSt) revealed several metabolic pathways to be more abundant in the swim bladder-associated microbiota, including metabolism of carbohydrates, nucleotides and lipoic acid as well as oxidative phosphorylation, cell growth, translation, replication and repair. Distal intestine digesta microbiota showed greater abundance of nitrogen metabolism, amino acid metabolism, biosynthesis of unsaturated fatty acids and bacterial secretion system. We demonstrated swim bladder harbors a unique microbiota, which composition and metabolic function differ from microbiota associated with the gut in fish.
Bitter tastants and artificial sweeteners activate a subset of epithelial cells in acute tissue slices of the rat trachea
Authors: Lasconi Chiara , Pifferi Simone , Hernandez-Clavijo Andres , Merigo Flavia , Cecchini Maria Paola , Gonzalez-Velandia Kevin Y. , Agostinelli Emilio , Sbarbati Andrea , Menini Anna
Published: June 2019

Bitter and sweet receptors (T2Rs and T1Rs) are expressed in many extra-oral tissues including upper and lower airways. To investigate if bitter tastants and artificial sweeteners could activate physiological responses in tracheal epithelial cells we performed confocal Ca2+ imaging recordings on acute tracheal slices. We stimulated the cells with denatonium benzoate, a T2R agonist, and with the artificial sweeteners sucralose, saccharin and acesulfame-K. To test cell viability we measured responses to ATP. We found that 39% of the epithelial cells responding to ATP also responded to bitter stimulation with denatonium benzoate. Moreover, artificial sweeteners activated different percentages of the cells, ranging from 5% for sucralose to 26% for saccharin, and 27% for acesulfame-K. By using carbenoxolone, a gap junction blocker, we excluded that responses were mainly mediated by Ca2+ waves through cell-to-cell junctions. Pharmacological experiments showed that both denatonium and artificial sweeteners induced a PLC-mediated release of Ca2+ from internal stores. In addition, bitter tastants and artificial sweeteners activated a partially overlapping subpopulation of tracheal epithelial cells. Our results provide new evidence that a subset of ATP-responsive tracheal epithelial cells from rat are activated by both bitter tastants and artificial sweeteners.
Proteomic profiling of extracellular vesicles reveals additional diagnostic biomarkers for myocardial infarction compared to plasma alone
Authors: Gidlöf Olof , Evander Mikael , Rezeli Melinda , Marko-Varga György , Laurell Thomas , Erlinge David
Published: June 2019

Extracellular vesicles (EVs) are submicron, membrane-enclosed particles that are released from cells in various pathophysiological states. The molecular cargo of these vesicles is considered to reflect the composition of the cell of origin, and the EV proteome is therefore a potential source of biomarkers for various diseases. Our aim was to determine whether EVs isolated from plasma provide additional diagnostic value or improved pathophysiological understanding compared to plasma alone in the context of myocardial infarction (MI). A panel of proximity extension assays (n = 92) was employed to analyze EV lysates and plasma from patients with MI (n = 60) and healthy controls (n = 22). After adjustment for multiple comparisons, a total of 11 dysregulated proteins were identified in EVs of MI patients compared to the controls (q < 0.01). Three of these proteins: chymotrypsin C (CTRC), proto-oncogene tyrosine-protein kinase SRC (SRC) and C-C motif chemokine ligand 17 (CCL17) were unaltered in the corresponding plasma samples. As biomarkers for MI, rudimentary to no evidence exists for these proteins. In a separate group of patients with varying degrees of coronary artery disease, the decrease in EV-associated (but not plasma-related) SRC levels was confirmed by ELISA. Confirmation of the presence of SRC on EVs of different sizes and cellular origins was performed with ELISA, flow cytometry and nanoparticle tracking analysis. In conclusion, the data revealed that despite a similarity in the EV and plasma proteomes, analysis of isolated EVs does indeed provide additional diagnostic information that cannot be obtained from plasma alone.
The future of coffee and cocoa agroforestry in a warmer Mesoamerica
Authors: de Sousa Kauê , van Zonneveld Maarten , Holmgren Milena , Kindt Roeland , Ordoñez Jenny C.
Published: June 2019

Climate change threatens coffee production and the livelihoods of thousands of families in Mesoamerica that depend on it. Replacing coffee with cocoa and integrating trees in combined agroforestry systems to ameliorate abiotic stress are among the proposed alternatives to overcome this challenge. These two alternatives do not consider the vulnerability of cocoa and tree species commonly used in agroforestry plantations to future climate conditions. We assessed the suitability of these alternatives by identifying the potential changes in the distribution of coffee, cocoa and the 100 most common agroforestry trees found in Mesoamerica. Here we show that cocoa could potentially become an alternative in most of coffee vulnerable areas. Agroforestry with currently preferred tree species is highly vulnerable to future climate change. Transforming agroforestry systems by changing tree species composition may be the best approach to adapt most of the coffee and cocoa production areas. Our results stress the urgency for land use planning considering climate change effects and to assess new combinations of agroforestry species in coffee and cocoa plantations in Mesoamerica.
Adiponectin improves long-term potentiation in the 5XFAD mouse brain
Authors: Wang Ming , Jo Jihoon , Song Juhyun
Published: June 2019

Adiponectin is an adipokine that regulates apoptosis, glucose and lipid metabolism, and insulin sensitivity in metabolic diseases. As recent studies have associated changes in adipokines and other metabolites in the central nervous system with a risk for Alzheimer’s disease (AD), we investigated the effects of adiponectin treatment on hippocampal cells in the 5XFAD mouse model of AD and neuronal SH-SY5Y cells under amyloid beta toxicity. Adiponectin treatment reduced levels of cleaved caspase 3 and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) apoptosis signalling and decreased glycogen synthase kinase 3 beta (GSK3β) activation. Moreover, adiponectin treatment triggered long-term potentiation in the hippocampi of 5XFAD mice, which was associated with reduced expression of N-methyl-d-aspartate and its receptor as well as surface expression of the α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor. These findings suggest that adiponectin inhibits neuronal apoptosis and inflammatory mechanisms and promotes hippocampal long-term potentiation. Thus, adiponectin exhibits beneficial effect on hippocampal synaptic plasticity in Alzheimer’s disease mouse model.
Generation of fully functional hepatocyte-like organoids from human induced pluripotent stem cells mixed with Endothelial Cells
Authors: Pettinato Giuseppe , Lehoux Sylvain , Ramanathan Rajesh , Salem Mohamed M. , He Li-Xia , Muse Oluwatoyosi , Flaumenhaft Robert , Thompson Melissa T. , Rouse Emily A. , Cummings Richard D. , Wen Xuejun , Fisher Robert A.
Published: June 2019

Despite advances in stem cell research, cell transplantation therapy for liver failure is impeded by a shortage of human primary hepatocytes (HPH), along with current differentiation protocol limitations. Several studies have examined the concept of co-culture of human induced pluripotent cells (hiPSCs) with various types of supporting non-parenchymal cells to attain a higher differentiation yield and to improve hepatocyte-like cell functions both in vitro and in vivo. Co-culturing hiPSCs with human endothelial cells (hECs) is a relatively new technique that requires more detailed studies. Using our 3D human embryoid bodies (hEBs) formation technology, we interlaced Human Adipose Microvascular Endothelial Cells (HAMEC) with hiPSCs, leading to a higher differentiation yield and notable improvements across a wide range of hepatic functions. We conducted a comprehensive gene and protein secretion analysis of our HLCs coagulation factors profile, showing promising results in comparison with HPH. Furthermore, a stage-specific glycomic analysis revealed that the differentiated hepatocyte-like clusters (HLCs) resemble the glycan features of a mature tissue rather than cells in culture. We tested our HLCs in animal models, where the presence of HAMEC in the clusters showed a consistently better performance compared to the hiPSCs only group in regard to persistent albumin secretion post-transplantation.
Experimental Observation of Linear and Rotational Doppler Shifts from Several Designer Surfaces
Authors: Liu Baiyang , Chu Hongchen , Giddens Henry , Li Ronglin , Hao Yang
Published: June 2019

An orbital angular momentum (OAM) carrying beam has the ability to detect a spinning surface from its rotational Doppler effect. However, a mixture of linear and rotational Doppler effects can occur when an OAM beam is illuminated to a target, with not only spins but also vibrations. In this paper, we experimentally observe using OAM carrying beams, both linear and rotational Doppler effects from several designer surfaces. Specifically, a spinning polarization-independent metasurface, helicoidal reflector and propeller are applied respectively in this study. We demonstrate by the use of two microwave beams with opposite OAM to separate rotational Doppler shift from micro-Doppler shift. The proposed method can also be applied to measure the spinning speed of rotational objects, which have wider applications in intelligent sensing, radar and quantum optics.
Cardiovascular alterations in rats with Parkinsonism induced by 6-OHDA and treated with Domperidone
Authors: Rodrigues Laís D. , Oliveira Leandro F. , Shinoda Lucas , Scorza Carla A. , Faber Jean , Ferraz Henrique B. , Britto Luiz R. G. , Scorza Fulvio A.
Published: June 2019

After Alzheimer, Parkinson disease (PD) is the most frequently occurring progressive, degenerative neurological disease. It affects both sympathetic and parasympathetic nervous systems in a variable fashion. Cardiovascular symptoms are present in almost all stages of PD and narrower heart rate variability is the earliest sign. Administration of Levodopa to PD patients has proven to provide some degree of neurological protection. This drug, however, causes side effects including nausea and vomiting, lessened by the administration of domperidone. Autopsies in PD patients led some researchers to suggest the involvement of the ventricular arrhythmia induced by domperidone. The aim of the present study was to determine the impact of the adjusted human maximal dose of domperidone, on cardiological features of Wistar rats. domperidone was administered to both 6-hydroxydopamine Parkinsonism models and regular Wistar rats. Quantitative analysis of ranges of heart beat variation showed significant abnormal distribution in both groups receiving domperidone as compared with respective sham counterparts. However, qualitative analysis of Poincaré plots showed that 6-hydroxydopamine Parkinsonism models receiving domperidone had the narrowest full range of heart beat and the worst distribution heart beat ranges as compared with all study groups corroborating with previous suggestion that domperidone administration to PD patients is likely to play a role in sudden unexpected death in this group of patients.
Screening DNA-targeted anticancer drug in vitro based on cancer cells DNA-templated silver nanoclusters
Authors: Zhang Feng , Sheng Hao , Wang Shuang , Ma Yu , Cai Changqun
Published: June 2019

A reliable and sensitive cancer cells DNA-templated silver nanoclusters probe has been proposed for screening DNA-targeted anticancer drugs in vitro. In this paper, the DNA-templated silver nanoclusters was used to investigate the binding between anthracycline antibiotics and DNA. The template of DNA-templated silver nanoclusters was extracted from human liver carcinoma cells directly, which can express the drug activities against cancer cells more direct than the normal cells DNA. The anti-tumor activities of the four drugs were validated by MTT and apoptotic assay as Mitoxantrone > Epirubicin > Daunorubicin > Adriamycin.
Sleep-like slow oscillations improve visual classification through synaptic homeostasis and memory association in a thalamo-cortical model
Authors: Capone Cristiano , Pastorelli Elena , Golosio Bruno , Paolucci Pier Stanislao
Published: June 2019

The occurrence of sleep passed through the evolutionary sieve and is widespread in animal species. Sleep is known to be beneficial to cognitive and mnemonic tasks, while chronic sleep deprivation is detrimental. Despite the importance of the phenomenon, a complete understanding of its functions and underlying mechanisms is still lacking. In this paper, we show interesting effects of deep-sleep-like slow oscillation activity on a simplified thalamo-cortical model which is trained to encode, retrieve and classify images of handwritten digits. During slow oscillations, spike-timing-dependent-plasticity (STDP) produces a differential homeostatic process. It is characterized by both a specific unsupervised enhancement of connections among groups of neurons associated to instances of the same class (digit) and a simultaneous down-regulation of stronger synapses created by the training. This hierarchical organization of post-sleep internal representations favours higher performances in retrieval and classification tasks. The mechanism is based on the interaction between top-down cortico-thalamic predictions and bottom-up thalamo-cortical projections during deep-sleep-like slow oscillations. Indeed, when learned patterns are replayed during sleep, cortico-thalamo-cortical connections favour the activation of other neurons coding for similar thalamic inputs, promoting their association. Such mechanism hints at possible applications to artificial learning systems.
Energy absorption in the laser-QED regime
Authors: Savin Alex F. , Ross Aimee J. , Aboushelbaya Ramy , Mayr Marko W. , Spiers Ben , Wang Robin H.-W. , Norreys Peter A.
Published: June 2019

A theoretical and numerical investigation of non-ponderomotive absorption at laser intensities relevant to quantum electrodynamics is presented. It is predicted that there is a regime change in the dependence of fast electron energy on incident laser energy that coincides with the onset of pair production via the Breit-Wheeler process. This prediction is numerically verified via an extensive campaign of QED-inclusive particle-in-cell simulations. The dramatic nature of the power law shift leads to the conclusion that this process is a candidate for an unambiguous signature that future experiments on multi-petawatt laser facilities have truly entered the QED regime.
Delayed development of the protective IL-17A response following a Giardia muris infection in neonatal mice
Authors: Paerewijck Oonagh , Maertens Brecht , Gagnaire Aurélie , De Bosscher Karolien , Geldhof Peter
Published: June 2019

Giardia is an intestinal protozoan parasite that has the ability to infect a wide range of hosts, which can result in the clinical condition ‘giardiasis’. Over the years, experimental research has shown the crucial involvement of IL-17A to steer the protective immune response against Giardia. The development of the protective response, as reflected by a significant drop in cyst secretion, typically takes around 3 to 4 weeks. However, early-life infections often have a more chronic character lasting for several weeks or months. Therefore, the aim of the current study was to investigate the dynamics of a Giardia muris infection and the subsequent host immune response in neonatal mice infected 4 days after birth. The outcome of the study showed that a G. muris infection in pre-weaned mice failed to trigger a protective IL-17A response, which could explain the prolonged course of infection in comparison to older mice. Only after weaning, a protective intestinal immune response started to develop, characterized by an upregulation of IL-17A and Mbl2 and the secretion of parasite-specific IgA.
Improving the electrochemical performances using a V-doped Ni-rich NCM cathode
Authors: Sim Seoung-Ju , Lee Seung-Hwan , Jin Bong-Soo , Kim Hyun-Soo
Published: June 2019

Ni-rich layered LiNi0.84Co0.10Mn0.06O2 cathode material was modified by doping with vanadium to enhance the electrochemical performances. The XRD, FESEM and XPS analyses were indicated that the vanadium is successfully doped in the crystal lattice of LiNi0.84Co0.10Mn0.06O2 with high crystallinity. 0.05 mol% vanadium doped LiNi0.84Co0.10Mn0.06O2 exhibits superior initial discharge capacity of 204.4 mAh g−1, cycling retention of 88.1% after 80 cycles and rate capability of 86.2% at 2 C compared to those of pristine sample. It can be inferred that the vanadium doping can stabilize the crystal structure and improve the lithium-ion kinetics of the layered cathode materials.
Comparison of the Clinical Sensitivity of the Idylla Platform and the OncoBEAM RAS CRC Assay for KRAS Mutation Detection in Liquid Biopsy Samples
Authors: Vivancos Ana , Aranda Enrique , Benavides Manuel , Élez Elena , Gómez-España Maria Auxiliadora , Toledano Marta , Alvarez Martina , Parrado Maria Rosario Chica , García-Barberán Vanesa , Diaz-Rubio Eduardo
Published: June 2019

KRAS mutations are common in colorectal cancer (CRC). In this setting, mutation status determination in circulating-free DNA from blood samples (liquid biopsy) has been shown to be a viable alternative to tissue testing. The objective of this study was to compare the sensitivity of two liquid biopsy methods for detecting KRAS mutations in plasma samples from metastatic CRC patients. Samples with a positive (KRAS-MUT+) result and a mutant allelic fraction (MAF) < 5% according to the OncoBEAM RAS CRC assay were pairly analyzed by the Idylla ctKRAS Mutation Test (n = 116). In a cohort of 71 patients with at least 1 year of follow-up, the progression-free survival (PFS) was determined according to MAF values. Idylla detected KRAS mutations in 81/116 OncoBEAM KRAS-MUT+ samples with MAF < 5% and in 48/79 samples with MAF < 1%. Concordance between OncoBEAM and Idylla significantly improved at higher MAF values. PFS rates at 6 and 12 months tended to be lower in patients with MAF levels between 1% and 5% than in those with levels <1%. OncoBEAM demonstrated greater sensitivity for plasma detection of KRAS mutations than Idylla. Importantly, our data identified a “gray zone” below 1% MAF where Idylla showed reduced KRAS mutation detection, highlighting the importance of an accurate method to provide the mutational status of CRC patients.
Adopting machine learning to automatically identify candidate patients for corneal refractive surgery
Authors: Yoo Tae Keun , Ryu Ik Hee , Lee Geunyoung , Kim Youngnam , Kim Jin Kuk , Lee In Sik , Kim Jung Sub , Rim Tyler Hyungtaek
Published: June 2019

Recently, it has become more important to screen candidates that undergo corneal refractive surgery to prevent complications. Until now, there is still no definitive screening method to confront the possibility of a misdiagnosis. We evaluate the possibilities of machine learning as a clinical decision support to determine the suitability to corneal refractive surgery. A machine learning architecture was built with the aim of identifying candidates combining the large multi-instrument data from patients and clinical decisions of highly experienced experts. Five heterogeneous algorithms were used to predict candidates for surgery. Subsequently, an ensemble classifier was developed to improve the performance. Training (10,561 subjects) and internal validation (2640 subjects) were conducted using subjects who had visited between 2016 and 2017. External validation (5279 subjects) was performed using subjects who had visited in 2018. The best model, i.e., the ensemble classifier, had a high prediction performance with the area under the receiver operating characteristic curves of 0.983 (95% CI, 0.977–0.987) and 0.972 (95% CI, 0.967–0.976) when tested in the internal and external validation set, respectively. The machine learning models were statistically superior to classic methods including the percentage of tissue ablated and the Randleman ectatic score. Our model was able to correctly reclassify a patient with postoperative ectasia as an ectasia-risk group. Machine learning algorithms using a wide range of preoperative information achieved a comparable performance to screen candidates for corneal refractive surgery. An automated machine learning analysis of preoperative data can provide a safe and reliable clinical decision for refractive surgery.
ATP binds and inhibits the neurodegeneration-associated fibrillization of the FUS RRM domain
Authors: Kang Jian , Lim Liangzhong , Song Jianxing
Published: June 2019

Adenosine triphosphate (ATP) provides energy for cellular processes but has recently been found to act also as a hydrotrope to maintain protein homeostasis. ATP bivalently binds the disordered domain of FUS containing the RG/RGG sequence motif and thereby affects FUS liquid-liquid phase separation. Here, using NMR spectroscopy and molecular docking studies, we report that ATP specifically binds also to the well-folded RRM domain of FUS at physiologically relevant concentrations and with the binding interface overlapping with that of its physiological ssDNA ligand. Importantly, although ATP has little effect on the thermodynamic stability of the RRM domain or its binding to ssDNA, ATP kinetically inhibits the RRM fibrillization that is critical for the gain of cytotoxicity associated with ALS and FTD. Our study provides a previously unappreciated mechanism for ATP to inhibit fibrillization by specific binding, and suggests that ATP may bind additional proteins other than the classic ATP-dependent enzymes.
Membrane curvature induces cardiolipin sorting
Authors: Beltrán-Heredia Elena , Tsai Feng-Ching , Salinas-Almaguer Samuel , Cao Francisco J. , Bassereau Patricia , Monroy Francisco
Published: June 2019

Cardiolipin is a cone-shaped lipid predominantly localized in curved membrane sites of bacteria and in the mitochondrial cristae. This specific localization has been argued to be geometry-driven, since the CL’s conical shape relaxes curvature frustration. Although previous evidence suggests a coupling between CL concentration and membrane shape in vivo, no precise experimental data are available for curvature-based CL sorting in vitro. Here, we test this hypothesis in experiments that isolate the effects of membrane curvature in lipid-bilayer nanotubes. CL sorting is observed with increasing tube curvature, reaching a maximum at optimal CL concentrations, a fact compatible with self-associative clustering. Observations are compatible with a model of membrane elasticity including van der Waals entropy, from which a negative intrinsic curvature of −1.1 nm−1 is predicted for CL. The results contribute to understanding the physicochemical interplay between membrane curvature and composition, providing key insights into mitochondrial and bacterial membrane organization and dynamics.
Plastoquinone homoeostasis by Arabidopsis proton gradient regulation 6 is essential for photosynthetic efficiency
Authors: Pralon Thibaut , Shanmugabalaji Venkatasalam , Longoni Paolo , Glauser Gaetan , Ksas Brigitte , Collombat Joy , Desmeules Saskia , Havaux Michel , Finazzi Giovanni , Kessler Felix
Published: June 2019

Photosynthesis produces organic carbon via a light-driven electron flow from H2O to CO2 that passes through a pool of plastoquinone molecules. These molecules are either present in the photosynthetic thylakoid membranes, participating in photochemistry (photoactive pool), or stored (non-photoactive pool) in thylakoid-attached lipid droplets, the plastoglobules. The photoactive pool acts also as a signal of photosynthetic activity allowing the adaptation to changes in light condition. Here we show that, in Arabidopsis thaliana, proton gradient regulation 6 (PGR6), a predicted atypical kinase located at plastoglobules, is required for plastoquinone homoeostasis, i.e. to maintain the photoactive plastoquinone pool. In a pgr6 mutant, the photoactive pool is depleted and becomes limiting under high light, affecting short-term acclimation and photosynthetic efficiency. In the long term, pgr6 seedlings fail to adapt to high light and develop a conditional variegated leaf phenotype. Therefore, PGR6 activity, by regulating plastoquinone homoeostasis, is required to cope with high light.