Platelet membrane proteomics: a novel repository for functional research

Abstract Being central players in thrombosis and hemostasis, platelets react in manifold and complex ways to extracellular stimuli. Cell-matrix and cell-cell interactions are mandatory for initial adhesion as well as for final development of stable plugs. Primary interfaces for interactions are plasma membrane proteins, of which many have been identified over the past decades in individual studies. However, due to their enucleate structure, platelets are not accessible to large-scale genomic screens and thus a comprehensive inventory of membrane proteins is still missing. For this reason, we here present an advanced proteomic setup for the detailed analysis of enriched platelet plasma membranes and the so far most complete collection of platelet membrane proteins. In summary, 1282 proteins were identified, of which more than half are termed to be of membrane origin. This study provides a brief overview of gene ontology subcellular and functional classification, as well as interaction network analysis. In addition, the mass spectrometric data were used to assemble a first tentative relative quantification of large-scale data on the protein level. We therefore estimate the presented data to be of major interest to the platelet research field and to support rational design of functional studies.

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Interaction of platelet plasma membranes with thrombin-activated platelets

Blood ◽

10.1182/blood.v57.2.305.305 ◽

1981 ◽

Vol 57 (2) ◽

pp. 305-312 ◽

Cited By ~ 2

Author(s):

HR Prasanna ◽

HH Edwards ◽

DR Phillips

Keyword(s):

Human Erythrocyte ◽

Plasma Membranes ◽

Membrane Binding ◽

Human Platelets ◽

Platelet Membrane ◽

Erythrocyte Membranes ◽

Functional Sites ◽

Activated Platelets ◽

Platelet Membranes ◽

Human Erythrocyte Membranes

Abstract This study described the binding of platelet plasma membranes to either control or thrombin-activated platelets. Glycoproteins in plasma membranes isolated from human platelets were labeled by oxidation with periodate followed by reduction with [3H]NaBH4. Labeled membranes were incubated with either control or thrombin-activated platelets. The amount of membranes bound was measured by separating platelets with bound membranes from solution by rapid centrifugation through 27% sucrose and determining the amount of radioactivity associated with platelets. Five- to sevenfold more membranes bound to thrombin- activated platelets than to control platelets. This enhanced binding of labeled membranes was completely inhibited by an excess of unlabeled platelet membranes. Human erythrocyte membranes had little affinity for either washed or thrombin-activated platelets and therefore did not compete for platelet-membrane binding. Binding of platelet membranes to thrombin-treated platelets was inhibited by prior incubation of the platelets with PGI2 suggesting that the enhanced binding of membranes was to activated platelets. This study demonstrates that the purified platelet membranes have functional sites that can mediate membrane binding to platelets and that quantitation of membrane binding appears to reflect the increased aggregation capability of activated platelets.

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Extraction of short chain chitooligosaccharides from fungal biomass and their use as promoters of arbuscular mycorrhizal symbiosis

Scientific Reports ◽

10.1038/s41598-021-83299-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Andrea Crosino ◽

Elisa Moscato ◽

Marco Blangetti ◽

Gennaro Carotenuto ◽

Federica Spina ◽

...

Keyword(s):

Fungal Biomass ◽

Large Scale ◽

Low Cost ◽

Trichoderma Viride ◽

Arbuscular Mycorrhizal ◽

Am Fungi ◽

Production Costs ◽

Short Chain ◽

Mycorrhizal Symbiosis ◽

Major Interest

AbstractShort chain chitooligosaccharides (COs) are chitin derivative molecules involved in plant-fungus signaling during arbuscular mycorrhizal (AM) interactions. In host plants, COs activate a symbiotic signalling pathway that regulates AM-related gene expression. Furthermore, exogenous CO application was shown to promote AM establishment, with a major interest for agricultural applications of AM fungi as biofertilizers. Currently, the main source of commercial COs is from the shrimp processing industry, but purification costs and environmental concerns limit the convenience of this approach. In an attempt to find a low cost and low impact alternative, this work aimed to isolate, characterize and test the bioactivity of COs from selected strains of phylogenetically distant filamentous fungi: Pleurotus ostreatus, Cunninghamella bertholletiae and Trichoderma viride. Our optimized protocol successfully isolated short chain COs from lyophilized fungal biomass. Fungal COs were more acetylated and displayed a higher biological activity compared to shrimp-derived COs, a feature that—alongside low production costs—opens promising perspectives for the large scale use of COs in agriculture.

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Transformer Meets Convolution: A Bilateral Awareness Network for Semantic Segmentation of Very Fine Resolution Urban Scene Images

Remote Sensing ◽

10.3390/rs13163065 ◽

2021 ◽

Vol 13 (16) ◽

pp. 3065

Author(s):

Libo Wang ◽

Rui Li ◽

Dongzhi Wang ◽

Chenxi Duan ◽

Teng Wang ◽

...

Keyword(s):

Large Scale ◽

Texture Features ◽

Semantic Segmentation ◽

Autonomous Driving ◽

Research Field ◽

Learning Approaches ◽

Fine Grained ◽

Urban Scene ◽

Fine Resolution ◽

With Memory

Semantic segmentation from very fine resolution (VFR) urban scene images plays a significant role in several application scenarios including autonomous driving, land cover classification, urban planning, etc. However, the tremendous details contained in the VFR image, especially the considerable variations in scale and appearance of objects, severely limit the potential of the existing deep learning approaches. Addressing such issues represents a promising research field in the remote sensing community, which paves the way for scene-level landscape pattern analysis and decision making. In this paper, we propose a Bilateral Awareness Network which contains a dependency path and a texture path to fully capture the long-range relationships and fine-grained details in VFR images. Specifically, the dependency path is conducted based on the ResT, a novel Transformer backbone with memory-efficient multi-head self-attention, while the texture path is built on the stacked convolution operation. In addition, using the linear attention mechanism, a feature aggregation module is designed to effectively fuse the dependency features and texture features. Extensive experiments conducted on the three large-scale urban scene image segmentation datasets, i.e., ISPRS Vaihingen dataset, ISPRS Potsdam dataset, and UAVid dataset, demonstrate the effectiveness of our BANet. Specifically, a 64.6% mIoU is achieved on the UAVid dataset.

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Time-resolved PIV measurements of a deflected submerged jet interacting with liquid-gas and liquid-liquid interfaces

Experimental and Computational Multiphase Flow ◽

10.1007/s42757-020-0103-1 ◽

2021 ◽

Author(s):

Stefan Puttinger ◽

Mahdi Saeedipour

Keyword(s):

Liquid Layer ◽

Large Scale ◽

Free Surface Flow ◽

Industrial Applications ◽

Liquid Pool ◽

Surface Flow ◽

Two Phase ◽

Time Resolved ◽

Submerged Jet ◽

Major Interest

AbstractThis paper presents an experimental investigation on the interactions of a deflected submerged jet into a liquid pool with its above interface in the absence and presence of an additional lighter liquid. Whereas the former is a free surface flow, the latter mimics a situation of two stratified liquids where the liquid-liquid interface is disturbed by large-scale motions in the liquid pool. Such configurations are encountered in various industrial applications and, in most cases, it is of major interest to avoid the entrainment of droplets from the lighter liquid into the main flow. Therefore, it is important to understand the fluid dynamics in such configurations and to analyze the differences between the cases with and without the additional liquid layer. To study this problem, we applied time-resolved particle image velocimetry experiments with high spatial resolution. A detailed data analysis of a small layer beneath the interface shows that although the presence of an additional liquid layer stabilizes the oscillations of the submerged jet significantly, the amount of kinetic energy, enstrophy, and velocity fluctuations concentrated in the proximity of the interface is higher when the oil layer is present. In addition, we analyze the energy distribution across the eigenmodes of a proper orthogonal distribution and the distribution of strain and vortex dominated regions. As the main objective of this study, these high-resolution time-resolved experimental data provide a validation platform for the development of new models in the context of the volume of fluid-based large eddy simulation of turbulent two-phase flows.

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Skill assessment of post-processing methods for ECMWF SEAS5 seasonal forecasts over Europe

10.5194/egusphere-egu21-11019 ◽

2021 ◽

Author(s):

Alice Crespi ◽

Marcello Petitta ◽

Lucas Grigis ◽

Paola Marson ◽

Jean-Michel Soubeyroux ◽

...

Keyword(s):

Large Scale ◽

Production Management ◽

Spatial Scales ◽

Research Field ◽

Skill Assessment ◽

Post Processing ◽

Seasonal Forecasts ◽

Climate Services ◽

Local Climate ◽

Climate Conditions

Seasonal forecasts provide information on climate conditions several months ahead and therefore they could represent a valuable support for decision making, warning systems as well as for the optimization of industry and energy sectors. However, forecast systems can be affected by systematic biases and have horizontal resolutions which are typically coarser than the spatial scales of the practical applications. For this reason, the reliability of forecasts needs to be carefully assessed before applying and interpreting them for specific applications. In addition, the use of post-processing approaches is recommended in order to improve the representativeness of the large-scale predictions of regional and local climate conditions. The development and evaluation downscaling and bias-correction procedures aiming at improving the skills of the forecasts and the quality of derived climate services is currently an open research field. In this context, we evaluated the skills of ECMWF SEAS5 forecasts of monthly mean temperature, total precipitation and wind speed over Europe and we assessed the skill improvements of calibrated predictions.For the calibration, we combined a bilinear interpolation and a quantile mapping approach to obtain corrected monthly forecasts on a 0.25&#176;x0.25&#176; grid from the original 1&#176;x1&#176; values. The forecasts were corrected against the reference ERA5 reanalysis over the hindcast period 1993&#8211;2016. The processed forecasts were compared over the same domain and period with another calibrated set of ECMWF SEAS5 forecasts obtained by the ADAMONT statistical method.The skill assessment was performed by means of both deterministic and probabilistic verification metrics evaluated over seasonal forecasted aggregations for the first lead time. Greater skills of the forecast systems in Europe were generally observed in spring and summer, especially for temperature, with a spatial distribution varying with the seasons. The calibration was proved to effectively correct the model biases for all variables, however the metrics not accounting for bias did not show significant improvements in most cases, and in some areas and seasons even small degradations in skills were observed.The presented study supported the activities of the H2020 European project SECLI-FIRM on the improvement of the seasonal forecast applicability for energy production, management and assessment.

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Large-scale purification of presynaptic plasma membranes from Torpedo marmorata electric organ.

The Journal of Cell Biology ◽

10.1083/jcb.101.5.1757 ◽

1985 ◽

Vol 101 (5) ◽

pp. 1757-1762 ◽

Cited By ~ 29

Author(s):

N Morel ◽

J Marsal ◽

R Manaranche ◽

S Lazereg ◽

J C Mazie ◽

...

Keyword(s):

Plasma Membrane ◽

Large Scale ◽

Plasma Membranes ◽

Electric Organ ◽

Acetylcholinesterase Activity ◽

Cholinergic Nerve Terminals ◽

Membrane Bound ◽

Torpedo Electric Organ ◽

Presynaptic Plasma Membrane ◽

Glycera Convoluta

The presynaptic plasma membrane (PSPM) of cholinergic nerve terminals was purified from Torpedo electric organ using a large-scale procedure. Up to 500 g of frozen electric organ were fractioned in a single run, leading to the isolation of greater than 100 mg of PSPM proteins. The purity of the fraction is similar to that of the synaptosomal plasma membrane obtained after subfractionation of Torpedo synaptosomes as judged by its membrane-bound acetylcholinesterase activity, the number of Glycera convoluta neurotoxin binding sites, and the binding of two monoclonal antibodies directed against PSPM. The specificity of these antibodies for the PSPM is demonstrated by immunofluorescence microscopy.

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Large scale characterization of plant plasma membrane proteins

Biochimie ◽

10.1016/s0300-9084(99)80122-9 ◽

1999 ◽

Vol 81 (6) ◽

pp. 655-661 ◽

Cited By ~ 46

Author(s):

Véronique Santoni ◽

Patrick Doumas ◽

David Rouquié ◽

Monique Mansion ◽

Thierry Rabilloud ◽

...

Keyword(s):

Plasma Membrane ◽

Membrane Proteins ◽

Large Scale ◽

Plasma Membrane Proteins ◽

Scale Characterization ◽

Plant Plasma Membrane

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End-to-End Transition-Based Online Dialogue Disentanglement

Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence ◽

10.24963/ijcai.2020/535 ◽

2020 ◽

Author(s):

Hui Liu ◽

Zhan Shi ◽

Jia-Chen Gu ◽

Quan Liu ◽

Si Wei ◽

...

Keyword(s):

Large Scale ◽

Online Algorithm ◽

Research Field ◽

Semantic Coherence ◽

Large Scale Dataset ◽

End To End ◽

Sequential Information ◽

Almost All ◽

Classification And Clustering ◽

Sequential Semantics

Dialogue disentanglement aims to separate intermingled messages into detached sessions. The existing research focuses on two-step architectures, in which a model first retrieves the relationships between two messages and then divides the message stream into separate clusters. Almost all existing work puts significant efforts on selecting features for message-pair classification and clustering, while ignoring the semantic coherence within each session. In this paper, we introduce the first end-to- end transition-based model for online dialogue disentanglement. Our model captures the sequential information of each session as the online algorithm proceeds on processing a dialogue. The coherence in a session is hence modeled when messages are sequentially added into their best-matching sessions. Meanwhile, the research field still lacks data for studying end-to-end dialogue disentanglement, so we construct a large-scale dataset by extracting coherent dialogues from online movie scripts. We evaluate our model on both the dataset we developed and the publicly available Ubuntu IRC dataset [Kummerfeld et al., 2019]. The results show that our model significantly outperforms the existing algorithms. Further experiments demonstrate that our model better captures the sequential semantics and obtains more coherent disentangled sessions.

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The role of airborne volcanic ash for the surface ocean biogeochemical iron-cycle: a review

Biogeosciences Discussions ◽

10.5194/bgd-6-6441-2009 ◽

2009 ◽

Vol 6 (4) ◽

pp. 6441-6489 ◽

Cited By ~ 8

Author(s):

S. Duggen ◽

N. Olgun ◽

P. Croot ◽

L. Hoffmann ◽

H. Dietze ◽

...

Keyword(s):

Large Scale ◽

Volcanic Ash ◽

Volcanic Eruptions ◽

Research Field ◽

Ash Deposition ◽

Future Directions ◽

Iron Cycle ◽

Surface Ocean ◽

Wide Range

Abstract. Iron is a key micronutrient for phytoplankton growth in the surface ocean. Yet the significance of volcanism for the marine biogeochemical iron-cycle is poorly constrained. Recent studies, however, suggest that offshore deposition of airborne ash from volcanic eruptions is a way to inject significant amounts of bio-available iron into the surface ocean. Volcanic ash may be transported up to several tens of kilometres high into the atmosphere during large-scale eruptions and fine ash may encircle the globe for years, thereby reaching even the remotest and most iron-starved oceanic areas. Scientific ocean drilling demonstrates that volcanic ash layers and dispersed ash particles are frequently found in marine sediments and that therefore volcanic ash deposition and iron-injection into the oceans took place throughout much of the Earth's history. The data from geochemical and biological experiments, natural evidence and satellite techniques now available suggest that volcanic ash is a so far underestimated source for iron in the surface ocean, possibly of similar importance as aeolian dust. Here we summarise the development of and the knowledge in this fairly young research field. The paper covers a wide range of chemical and biological issues and we make recommendations for future directions in these areas. The review paper may thus be helpful to improve our understanding of the role of volcanic ash for the marine biogeochemical iron-cycle, marine primary productivity and the ocean-atmosphere exchange of CO2 and other gases relevant for climate throughout the Earth's history.

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Efficient Synthesis of Rare Disaccharides by Engineered β-Glucosidase Based on Hydropathy Index

10.26434/chemrxiv.11942016.v1 ◽

2020 ◽

Author(s):

Kangle Niu ◽

Zhengyao Liu ◽

Yuhui Feng ◽

Tianlong Gao ◽

Zhenzhen Wang ◽

...

Keyword(s):

Amino Acid ◽

Rational Design ◽

Large Scale ◽

Catalytic Site ◽

Scale Production ◽

Total Production ◽

Amino Acid Residues ◽

Hydropathy Index ◽

Reverse Hydrolysis ◽

Hydrolysis Activity

Oligosaccharides have important therapeutic applications. A useful route for oligosaccharides synthesis, especially rare disaccharides, is reverse hydrolysis by β-glucosidase. However, the low conversion efficiency of disaccharides from monosaccharides limits its large-scale production because the equilibrium is biased in the direction of hydrolysis. Based on the analysis of the docking results, we hypothesized that the hydropathy index of key amino acid residues in the catalytic site is closely related with disaccharide synthesis and more hydrophilic residues located in the catalytic site would enhance reverse hydrolysis activity. In this study, positive variants TrCel1bI177S, TrCel1bI177S/I174S, and TrCel1bI177S/I174S/W173H, and one negative variant TrCel1bN240I were designed according to the Hydropathy Index For Enzyme Activity (HIFEA) strategy. The reverse hydrolysis with TrCel1bI177S/I174S/W173H was accelerated and then the maximum total production (<a>195.8 mg/ml/mg enzyme</a>) of the synthesized disaccharides was increased 3.5-fold compared to that of wildtype. On the contrary, <a>TrCel1b</a>N240I lost reverse hydrolysis activity. The results demonstrate that<a> </a><a>the average hydropathy index</a> of <a>the key amino acid residues </a>in the catalytic site of TrCel1b is an important factor for the synthesis of laminaribiose, sophorose, and cellobiose. The HIFEA strategy provides a new perspective for the rational design of β-glucosidases used for the synthesis of oligosaccharides.

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