scholarly journals Differential Affinities of a Pocillopora damicornis Galectin to Five Genera of Symbiodiniaceae at Different Temperatures

2021 ◽  
Vol 8 ◽  
Author(s):  
Xingjuan Wang ◽  
Zhongjie Wu ◽  
Yibo Wu ◽  
Mingxun An ◽  
Zhi Zhou ◽  
...  
Keyword(s):  
Pattern Recognition ◽  
Cell Surface ◽  
Binding Affinity ◽  
Molecular Basis ◽  
Binding Affinities ◽  
Pocillopora Damicornis ◽  
Coral Reef Ecosystem ◽  
Symbiodinium Microadriaticum ◽  
Different Temperatures ◽  
Reef Ecosystem

The symbiosis of coral-Symbiodiniaceae is the quintessential basis of the coral reef ecosystem, and its breakdown results in coral bleaching, one of the most severe ecological catastrophes in the ocean. Critical to the establishment of the symbiosis is the host’s specific recognition of the symbionts through the binding of the coral host’s pattern recognition receptors (PRRs) to the symbiont cell surface’s glycoconjugates. However, the molecular basis for this recognition process is poorly understood. The present study investigated the binding affinities of the coral galectin PdGLT-1 to different symbiodiniacean species under different temperatures. At 25°C, the PdGLT-1 recombinant protein (rPdGLT-1) exhibited different binding affinities to different symbiodiniacean species from five genera, with a significantly higher binding affinity (p < 0.05) to Fugacium kawagutii (2.6-fold) and Cladocopium goreaui (1.9-fold) than Symbiodinium microadriaticum. The binding topology of rPdGLT-1 differed among the five symbiodiniacean species; for S. microadriaticum, Breviolum minutum, and Durusdinium trenchii, the binding was on some specific sites on the cell surface, whereas for C. goreaui and F. kawagutii, the binding signals were detected over the whole cell surface. Interestingly, PdGLT-1 binding induced agglutination of F. kawagutii cells but not of C. goreaui, explaining why C. goreaui was the most dominant symbiodiniacean symbionts in corals. Moreover, the affinity of rPdGLT-1 to Symbiodiniaceae was affected by temperature, and the highest binding affinities were observed at 30, 20, 30, 35, and 30°C for S. microadriaticum, B. minutum, C. goreaui, D. trenchii, and F. kawagutii, respectively. The optimal binding temperatures were consistent with the current understanding that D. trenchii was the most thermal resistant among these species. These results suggest that the binding affinity of the PRR PdGLT-1 may determine the specificity of host-symbiont pairing and explain why Cladocopium is the dominant symbionts of coral P. damicornis at normal temperature, and corals with Durusdinium symbionts may survive better at high temperature.

THE COMPOSITION AND DISTRIBUTION OF BENTHIC FORAMINIFERA AT CORAL REEF ECOSYSTEM IN THOUSANDS ISLAND

2013 ◽  
Vol 5 (1) ◽  
Author(s):  
Lumban Nauli Lumban Toruan ◽  
Dedi Soedharma ◽  
Kresna Tri Dewi
Keyword(s):  
Coral Reef ◽  
Human Activities ◽  
Close Association ◽  
Mesh Size ◽  
Coral Reef Ecosystem ◽  
Composition Distribution ◽  
Benthic Foraminifers ◽  
High Nutrient ◽  
Binocular Microscope ◽  
Reef Ecosystem

Composition and distribution of foraminifers are affected by human activities and have close association with coral reef ecosystem. The aims of this research were to investigate the benthic foraminifers’ composition and distribution in sediment of coral reef ecosystem. Eleven stations of Karang Bongkok, Pramuka, and Onrust Island were observed in this study. The sediments were taken from surface substrate up to 2 cm under the substrate. Samples were washed on sieve with mesh size 0,063 mm, and then dried in oven with 50°C of temperature  for two hours. After separating from the sediment, the foraminifers were laid on foraminiferal slide and indentified using binocular microscope. The highest composition of symbiont-bearing foraminiferal assemblages which associated with reef ecosystem was in East Pramuka (78.17%) and the lowest was in South Onrust (21,83%). The opportunistic type had the highest composition in South Onrust (38.67%) and the lowest was in South Karang Bongkok. In west Pramuka had the highest composition of heterotrophic type (57.17%) and the lowest was in North Onrust (11.33%). Onrust Island was dominated by opportunistic type, indicating high nutrient. The highest amount of foraminifers’ taxa was found in Karang Bongkok with good coral reef coverage, while the lowest in Onrust facing with Jakarta Bay. Keywords: composition, distribution, benthic foraminifers, coral reef.

Measurement of the trophic level of fish in a coral reef ecosystem using stable isotopes

2013 ◽  
Vol 19 (1) ◽  
pp. 105-115 ◽  
Author(s):  
Guohuan YANG ◽  
Xingli SUN ◽  
Xiuqiong HOU ◽  
Chunliang CHEN
Keyword(s):  
Stable Isotopes ◽  
Coral Reef ◽  
Trophic Level ◽  
Coral Reef Ecosystem ◽  
Reef Ecosystem

scholarly journals SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Surendra Kumar ◽  
Mi-hyun Kim
Keyword(s):  
Ligand Binding ◽  
Binding Affinity ◽  
Scoring Functions ◽  
Binding Affinities ◽  
Ligand Interaction ◽  
Fingerprint Pattern ◽  
Comparable Performance ◽  
Direct Interpretation ◽  
Benchmark Datasets ◽  
Complex Features

AbstractIn drug discovery, rapid and accurate prediction of protein–ligand binding affinities is a pivotal task for lead optimization with acceptable on-target potency as well as pharmacological efficacy. Furthermore, researchers hope for a high correlation between docking score and pose with key interactive residues, although scoring functions as free energy surrogates of protein–ligand complexes have failed to provide collinearity. Recently, various machine learning or deep learning methods have been proposed to overcome the drawbacks of scoring functions. Despite being highly accurate, their featurization process is complex and the meaning of the embedded features cannot directly be interpreted by human recognition without an additional feature analysis. Here, we propose SMPLIP-Score (Substructural Molecular and Protein–Ligand Interaction Pattern Score), a direct interpretable predictor of absolute binding affinity. Our simple featurization embeds the interaction fingerprint pattern on the ligand-binding site environment and molecular fragments of ligands into an input vectorized matrix for learning layers (random forest or deep neural network). Despite their less complex features than other state-of-the-art models, SMPLIP-Score achieved comparable performance, a Pearson’s correlation coefficient up to 0.80, and a root mean square error up to 1.18 in pK units with several benchmark datasets (PDBbind v.2015, Astex Diverse Set, CSAR NRC HiQ, FEP, PDBbind NMR, and CASF-2016). For this model, generality, predictive power, ranking power, and robustness were examined using direct interpretation of feature matrices for specific targets.

scholarly journals A Single-Pass Type I Membrane Protein from the Apicomplexan Parasite Cryptosporidium parvum with Nanomolar Binding Affinity to Host Cell Surface

2021 ◽  
Vol 9 (5) ◽  
pp. 1015
Author(s):  
Tianyu Zhang ◽  
Xin Gao ◽  
Dongqiang Wang ◽  
Jixue Zhao ◽  
Nan Zhang ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Cell Surface ◽  
Host Cell ◽  
Binding Affinity ◽  
Cryptosporidium Parvum ◽  
Host Cells ◽  
Watery Diarrhea ◽  
Type I ◽  
Single Pass ◽  
Host Cell Surface

Cryptosporidium parvum is a globally recognized zoonotic parasite of medical and veterinary importance. This parasite mainly infects intestinal epithelial cells and causes mild to severe watery diarrhea that could be deadly in patients with weakened or defect immunity. However, its molecular interactions with hosts and pathogenesis, an important part in adaptation of parasitic lifestyle, remain poorly understood. Here we report the identification and characterization of a C. parvum T-cell immunomodulatory protein homolog (CpTIPH). CpTIPH is a 901-aa single-pass type I membrane protein encoded by cgd5_830 gene that also contains a short Vibrio, Colwellia, Bradyrhizobium and Shewanella (VCBS) repeat and relatively long integrin alpha (ITGA) N-terminus domain. Immunofluorescence assay confirmed the location of CpTIPH on the cell surface of C. parvum sporozoites. In congruence with the presence of VCBS repeat and ITGA domain, CpTIPH displayed high, nanomolar binding affinity to host cell surface (i.e., Kd(App) at 16.2 to 44.7 nM on fixed HCT-8 and CHO-K1 cells, respectively). The involvement of CpTIPH in the parasite invasion is partly supported by experiments showing that an anti-CpTIPH antibody could partially block the invasion of C. parvum sporozoites into host cells. These observations provide a strong basis for further investigation of the roles of CpTIPH in parasite-host cell interactions.

Marine reserves, fisheries ban, and 20 years of positive change in a coral reef ecosystem

2021 ◽  
Author(s):  
Peter J. Mumby ◽  
Robert S. Steneck ◽  
George Roff ◽  
Valerie J. Paul
Keyword(s):  
Coral Reef ◽  
Marine Reserves ◽  
Positive Change ◽  
Coral Reef Ecosystem ◽  
Reef Ecosystem

scholarly journals Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics

2021 ◽  
Author(s):  
Tomio Iwasaki ◽  
Masashi Maruyama ◽  
Tatsuya Niwa ◽  
Toshiki Sawada ◽  
Takeshi Serizawa
Keyword(s):  
Methyl Methacrylate ◽  
Binding Affinity ◽  
Molecular Simulation ◽  
Dynamics Simulation ◽  
Binding Affinities ◽  
Materials Informatics ◽  
Poly Methyl Methacrylate ◽  
Strong Binding ◽  
Experimental Values ◽  
Pmma Resin

AbstractPeptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on molecular dynamics simulation for the purpose of covering the resin surface with adhesive peptides, which were expected to result in eco-friendly and biocompatible biomaterials. From the results of binding affinity obtained with this molecular simulation, it was confirmed that experimental values could be predicted with errors <10%. By analyzing the simulation data with the response-surface method, we found that three peptides (RWWRPWW, EWWRPWR, and RWWRPWR), which consist of arginine (R), tryptophan (W), and proline (P), have strong binding affinity to the PMMA resin. These amino acids were effective because arginine and tryptophan have strong binding affinities for methoxycarbonyl groups and methyl groups, which are the main constituents of the PMMA resin, and proline stabilizes the flat zigzag structures of the peptides in water. The strong binding affinities of the three peptides were confirmed by experiments (surface plasmon resonance methods).

scholarly journals Natural Cytotoxicity Receptors: Pattern Recognition and Involvement of Carbohydrates

2005 ◽  
Vol 5 ◽  
pp. 151-154 ◽  
Author(s):  
Angel Porgador
Keyword(s):  
Pattern Recognition ◽  
Cell Membrane ◽  
Cell Surface ◽  
Innate Immune ◽  
Target Cells ◽  
Natural Cytotoxicity ◽  
Tumor Cell Membrane ◽  
Infected Cells ◽  
Natural Cytotoxicity Receptors ◽  
New Evidence

Natural cytotoxicity receptors (NCRs), expressed by natural killer (NK) cells, trigger NK lysis of tumor and virus-infected cells on interaction with cell-surface ligands of these target cells. We have determined that viral hemagglutinins expressed on the surface of virus-infected cells are involved in the recognition by the NCRs, NKp44 and NKp46. Recognition of tumor cells by the NCRs NKp30 and NKp46 involves heparan sulfate epitopes expressed on the tumor cell membrane. Our studies provide new evidence for the identity of the ligands for NCRs and indicate that a broader definition should be applied to pathological patterns recognized by innate immune receptors. Since nonmicrobial endogenous carbohydrate structures contribute significantly to this recognition, there is an imperative need to develop appropriate tools for the facile sequencing of carbohydrate moieties.

Integrity evaluation and dynamic simulation of Xisha coral reef ecosystem

2021 ◽  
Vol 41 (10) ◽  
Author(s):  
王耕，董瑞，周腾禹，徐惠民，丁德文 WANG Geng
Keyword(s):  
Coral Reef ◽  
Dynamic Simulation ◽  
Coral Reef Ecosystem ◽  
Reef Ecosystem
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