ALBERT

Description: 〈p〉Publication date: Available online 5 July 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Biophysical Journal〈/p〉 〈p〉Author(s): Thomas M. Kennelly, Yiran Li, Yi Cao, Eva E. Qwarnstrom, Mark Geoghegan〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Dynamic single-molecule force spectroscopy was performed to monitor the unbinding of fibronectin with the proteoglycans syndecan-4 (SDC4) and decorin and to compare this with the unbinding characteristics of 〈em〉α〈/em〉〈sub〉5〈/sub〉〈em〉β〈/em〉〈sub〉1〈/sub〉-integrin. A single energy barrier was sufficient to describe the unbinding of both SDC4 and decorin from fibronectin, whereas two barriers were observed for the dissociation of 〈em〉α〈/em〉〈sub〉5〈/sub〉〈em〉β〈/em〉〈sub〉1〈/sub〉-integrin from fibronectin. The outer (high-affinity) barriers in the interactions of fibronectin with 〈em〉α〈/em〉〈sub〉5〈/sub〉〈em〉β〈/em〉〈sub〉1〈/sub〉-integrin and SDC4 are characterized by larger barrier heights and widths and slower dissociation rates than those of the inner (low-affinity) barriers in the interactions of fibronectin with 〈em〉α〈/em〉〈sub〉5〈/sub〉〈em〉β〈/em〉〈sub〉1〈/sub〉-integrin and decorin. These results indicate that SDC4 and (ultimately) 〈em〉α〈/em〉〈sub〉5〈/sub〉〈em〉β〈/em〉〈sub〉1〈/sub〉-integrin have the ability to withstand deformation in their interactions with fibronectin, whereas the decorin-fibronectin interaction is considerably more brittle.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 3 July 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Biophysical Journal〈/p〉 〈p〉Author(s): Sabine Oldemeyer, Maria Mittag, Tilman Kottke〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Cryptochromes function as flavin-binding photoreceptors in bacteria, fungi, algae, land plants, and insects. The discovery of an animal-like cryptochrome in the green alga 〈em〉Chlamydomonas reinhardtii〈/em〉 has expanded the spectral range of sensitivity of these receptors from ultraviolet A/blue light to almost the complete visible spectrum. The broadened light response has been explained by the presence of the flavin neutral radical as a chromophore in the dark. Concomitant with photoconversion of the flavin, an unusually long-lived tyrosyl radical with a red-shifted ultraviolet-visible spectrum is formed, which is essential for the function of the receptor. In this study, the microenvironment of this key residue, tyrosine 373, was scrutinized using time-resolved Fourier transform infrared spectroscopy on several variants of animal-like cryptochrome and density functional theory for band assignment. The reduced tyrosine takes on distinct hydrogen bond scenarios depending on the presence of the C-terminal extension and of a neighboring cysteine. Upon radical formation, all variants showed a signal at 1400 cm〈sup〉−1〈/sup〉, which we assigned to the 〈em〉ν〈/em〉7′a marker band of the CO stretching mode. The exceptionally strong downshift of this band cannot be attributed to a loss of hydrogen bonding only. Time-resolved ultraviolet-visible spectroscopy on W322F, a mutant of the neighboring tryptophan residue, revealed a decrease of the tyrosyl radical lifetime by almost two orders of magnitude, along with a shift of the absorbance maximum from 416 to 398 nm. These findings strongly support the concept of a 〈em〉π〈/em〉-〈em〉π〈/em〉 stacking as an apolar interaction between Y373 and W322 to be responsible for the characteristics of the tyrosyl radical. This concept of radical stabilization has been unknown to cryptochromes so far but might be highly relevant for other homologs with a tetrad of tryptophans and tyrosines as electron donors.〈/p〉〈/div〉

Description: 〈p〉Publication date: September 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Marine Pollution Bulletin, Volume 146〈/p〉 〈p〉Author(s): Ofrat Raveh, Dror L. Angel, Peleg Astrahan, Natalia Belkin, Edo Bar-Zeev, Eyal Rahav〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Human-induced eutrophication of coastal water may be a major threat to aquatic life. Here, we investigated the effects of N-rich well amelioration brines (WAB) on coastal phytoplankton population's habitat in the surface oligotrophic waters of the southeastern Mediterranean Sea (SEM). To this end, we added WAB (2 concentrations) to mesocosms (1-m〈sup〉3〈/sup〉 bags) to surface SEM water during summer and winter, where changes in phytoplankton biomass, activity and diversity was monitored daily for 8 days. Our results demonstrate that WAB addition triggered a phytoplankton bloom, resulting in elevated algal biomass (maximal +780%), increased primary production rates (maximal +675%) and a decrease in eukaryotic algal α-diversity (〈em〉ca〈/em〉. −20%). Among the species that bloomed following WAB amendments, we found the potentially toxic dinoflagellate 〈em〉Karlodinium venificum〈/em〉. This study adds valuable perspective to the effect of nutrients discharged into nutrient limited SEM coastal waters, and in particular of N-derived WAB.〈/p〉〈/div〉 〈/div〉 〈div xml:lang="en"〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0025326X19305132-ga1.jpg" width="301" alt="Unlabelled Image" title="Unlabelled Image"〉〈/figure〉〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Marine Pollution Bulletin, Volume 145〈/p〉 〈p〉Author(s): Jorge Valdés, Joseline S. Tapia〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉To assess environmental conditions along the coast of northern Chile, 457 sediment samples were collected between 22° S and 28° S in order to evaluate the Cu, Zn, Pb, Ni, V, Cd, As and Al content as well as its corresponding relationship to nearby anthropogenic activities. In general, the results of most metals showed that bays without industrial activity accumulate lower concentrations of contaminant elements in the sediments and thus mostly represent natural conditions. The highest Cu, Pb and V levels were measured in coastal zones were different industrial mining activities have been developed during the last decades.〈/p〉 〈p〉Results of different indices of environmental evaluation and ecological impact suggest that, metal content of sediments from pollution-free zones characterized by similar oceanographic and geological conditions to those under study, would be the most appropriate background level for assessing the anthropogenic impact on coastal areas of northern Chile.〈/p〉 〈/div〉 〈/div〉 〈div xml:lang="en"〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0025326X19304825-ga1.jpg" width="301" alt="Unlabelled Image" title="Unlabelled Image"〉〈/figure〉〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 29 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Biophysical Journal〈/p〉 〈p〉Author(s): Sebastian Hillringhaus, Anil K. Dasanna, Gerhard Gompper, Dmitry A. Fedosov〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Invasion of erythrocytes by merozoites is an essential step for the survival and progression of malaria parasites. In order to invade red blood cells (RBCs), apicomplexan parasites have to adhere with their apex to the RBC membrane. This necessary apex-membrane contact (or alignment) is not immediately established, because the orientation of a free merozoite with respect to RBC membrane is random when an adhesion contact first occurs. Therefore, it has been suggested that after the initial adhesion, merozoites facilitate their proper alignment by inducing considerable membrane deformations, frequently observed before the invasion process. This proposition is based on a positive correlation between RBC membrane deformation and successful invasion; however, the role of RBC mechanics and its deformation in the alignment process remains elusive. Using a mechanically realistic model of a deformable RBC, we investigate numerically the importance of RBC deformability for merozoite alignment. Adhesion between the parasite and RBC membrane is modeled by an attractive potential which might be inhomogeneous, mimicking possible adhesion gradients at the surface of a parasite. Our results show that RBC membrane deformations are crucial for successful merozoite alignment, and require interaction strengths comparable to adhesion forces measured experimentally. Adhesion gradients along the parasite body further improve its alignment. Finally, an increased membrane rigidity is found to result in poor merozoite alignment, which can be a possible reason for a reduction in the invasion efficiency of RBCs in several blood diseases associated with membrane stiffening.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 21 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Biophysical Journal〈/p〉 〈p〉Author(s): Orkide Ordu, Alexandra Lusser, Nynke H. Dekker〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Eukaryotic genomes are hierarchically organized into protein-DNA assemblies for compaction into the nucleus. Nucleosomes, with the (H3-H4)〈sub〉2〈/sub〉 tetrasome as a likely intermediate, are highly dynamic in nature by way of several different mechanisms. We have recently shown that tetrasomes spontaneously change the direction of their DNA wrapping between left- and right-handed conformations, which may prevent torque build-up in chromatin during active transcription or replication. DNA sequence has been shown to strongly affect nucleosome positioning throughout chromatin. It is not known, however, whether DNA sequence also impacts the dynamic properties of tetrasomes. To address this question, we examined tetrasomes assembled on a high-affinity DNA sequence using freely orbiting magnetic tweezers. In this context, we also studied the effects of mono- and divalent salts on the flipping dynamics. We found that neither DNA sequence nor altered buffer conditions affect overall tetrasome structure. In contrast, tetrasomes bound to high-affinity DNA sequences showed significantly altered flipping kinetics, predominantly via a reduction in the lifetime of the canonical state of left-handed wrapping. Increased mono- and divalent salt concentrations counteracted this behaviour. Thus, our study indicates that high-affinity DNA sequences impact not only the positioning of the nucleosome, but that they also endow the subnucleosomal tetrasome with enhanced conformational plasticity. This may provide a means to prevent histone loss upon exposure to torsional stress, thereby contributing to the integrity of chromatin at high-affinity sites.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 21 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Biophysical Journal〈/p〉 〈p〉Author(s): Heiko Heerklotz, Erwin London〈/p〉

Description: 〈p〉Publication date: Available online 22 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Biophysical Journal〈/p〉 〈p〉Author(s): J.F. Nagle〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Extraction from simulations of the area compressibility moduli of the monolayers in a bilayer is considered theoretically. A statistical mechanical derivation shows that the bilayer modulus is the sum of the two monolayer moduli, as is often supposed, but contrary to a recent study. Seemingly plausible assumptions regarding fluctuations are tested rigorously. Prospects for future research are discussed.〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Marine Pollution Bulletin, Volume 149〈/p〉 〈p〉Author(s): Chun Kit Ooi, Michael Ware, Trevor Lewis, Jeremy Lyle, Barbara F. Nowak〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Melanisation of muscle, observed as black pigmentation of the normally white flesh, has been reported in sand flathead from Tasmania and investigated in this study. There was a significant difference in the presence of melanised muscle in sand flathead from two sites within the Tamar Estuary (northern Tasmania), with higher proportion of sand flathead from Deceitful Cove with this condition. Presence of melanisation was not related to length or weight of the fish. No parasitic infections were detected in the muscles of the affected sand flathead. However, concentration of zinc in melanised regions of muscle in the affected fish was significantly higher, about 1.7 to 1.8 times, than non-melanised regions of muscle in the same fish. Furthermore, the concentration of zinc in melanised regions of affected fish was on average about 2.0 times higher when compared to muscle of unaffected fish that had no melanised spots.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: November 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Marine Pollution Bulletin, Volume 148〈/p〉 〈p〉Author(s): Laura Valisano, Marco Palma, Ubaldo Pantaleo, Barbara Calcinai, Carlo Cerrano〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Thanks to several European directives and conventions there is a general increase of awareness regarding the key ecological role of coralligenous habitats in the Mediterranean Sea, addressing several research projects to standardize protocols for the description of its integrity. Here we surveyed 13 stations along the Italian coasts of the Western Mediterranean Sea, using video-transects technique, comparing the biological structure of coralligenous assemblages and testing the importance of their three-dimensional complexity as a proxy to define their health conditions. We considered the diversity of taxa, fishing impacts and the entity of damage on gorgonian's choenenchyme due to thermal stress, to evidence a gradient in the coralligenous health conditions. Here we developed a method to evaluate coralligenous complexity, selecting categories of taxa particularly sensitive to multiple stressors, named Structural Descriptors to describe the three-dimensional structure of the bioconcretions and to assess a unique Index of 3D - Structural Complexity.〈/p〉〈/div〉