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71.
Hugo Schweke Qifang Xu Gerardo Tauriello Lorenzo Pantolini Torsten Schwede Frédéric Cazals Alix Lhéritier Juan Fernandez-Recio Luis Angel Rodríguez-Lumbreras Ora Schueler-Furman Julia K. Varga Brian Jiménez-García Manon F. Réau Alexandre M. J. J. Bonvin Castrense Savojardo Pier-Luigi Martelli Rita Casadio Jérôme Tubiana Haim J. Wolfson Romina Oliva Didier Barradas-Bautista Tiziana Ricciardelli Luigi Cavallo Česlovas Venclovas Kliment Olechnovič Raphael Guerois Jessica Andreani Juliette Martin Xiao Wang Genki Terashi Daipayan Sarkar Charles Christoffer Tunde Aderinwale Jacob Verburgt Daisuke Kihara Anthony Marchand Bruno E. Correia Rui Duan Liming Qiu Xianjin Xu Shuang Zhang Xiaoqin Zou Sucharita Dey Roland L. Dunbrack Emmanuel D. Levy Shoshana J. Wodak 《Proteomics》2023,23(17):2200323
Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy. 相似文献
72.
Divergence in cytochrome c oxidase 1 (COI), the genetic marker proposed for DNA barcoding, was investigated in marine bivalves from the genera Ennucula , Nucula , Yoldiella and Thyasira . No overlap in levels of intra- and interspecific variation was found. The levels of divergence found suggest that barcodes from COI will be useful in distinguishing between the species investigated in this study. The insufficiency of blast searches in GenBank to assign many of the obtained sequences to correct phylum was noted and clearly demonstrates the need for better search strategies specifically targeted at identification using DNA barcodes. 相似文献
73.
We studied two components of the mating system, copulation duration and early fecundity, in relation to body size in Drosophila melanogaster. Body size variation was created experimentally by varying the degree of crowding (starvation) among larvae from an inbred strain, keeping the genetics and temperature as constant as possible. Hence, in contrast to most previous studies, where genetic and environmental variation have been confounded, we aimed at investigating how much pure phenotypic variation could influence copulation duration and early fecundity. It is shown that copulation duration and fecundity both strongly dependent on female body size, but either not or much less so on male body size. Small females mate faster than medium or large females and small females have the lowest fecundity. Among males, medium-size males are more fecund than smaller or larger males, resulting in stabilising selection for intermediate male size. These results are in contrast with previous findings. 相似文献
74.
Christoffer Bugge Harder Thomas Læssøe Rasmus Kjøller Tobias G. Frøslev 《Mycological Progress》2010,9(3):395-405
The members of Mycena sect. Calodontes (Tricholomataceae s.l., Basidiomycota) are characterised by a collybioid aspect and more or less purplish to reddish colours
and a distinct raphanoid odour. In Europe, nine species have been recognised though some of these based on somewhat dubious
morphological differences. Historically, most were assigned to Mycena pura. However, since Mycena pura displays one of the most striking colour variabilities within European agarics, many attempts have been made to subdivide
it into independent entities, and several forms, varieties and species have been split from Mycena pura s.l. based largely on differences in colouration, gross macromorphology or other phenetic traits. We developed a large sample
of ITS sequences of all species of sect. Calodontes known from Europe for which vouchers exist. Furthermore, partial LSU data were developed and additional sequences downloaded
from GENBANK to assess the relationship of Calodontes with other Mycena spp. We show that most Calodontes form a monophyletic group including a few North and South American collections, but that this cannot be conclusively shown
when an additional North American sequence is added. For all other species than M. pura and M. diosma, we found morphological species recognition to be in agreement with the ITS data. Several significantly different clades
can be recognised within the M. pura morphospecies, none of which can be linked to the observed (and described by proxy) colour varieties/forms. Indications of
a possible environmental basis of the colour differentiation in the M. pura morphospecies are discussed. 相似文献
75.
Christoffer Nagel Christina Spiessl Joachim Pander Juergen Geist 《Zeitschrift fur angewandte Ichthyologie》2021,37(5):770-778
Scanning electron microscopy (SEM) has been widely used to describe interspecific differences in egg quality of teleost freshwater fish, but potential intraspecific differences are poorly studied. Eggs of many rheophilic cyprinids are covered with adhesive structures such as attaching villi facilitating egg attachment at substrates of spawning grounds with high currents. Recent findings indicate that the egg quality of the rheophilic cyprinid common nase (Chondrostoma nasus L.), a target species of conservation, differs in the adhesiveness between spawning populations, potentially explaining differences in recruitment success. In this study, a SEM image-based standardized protocol was established to assess egg surface quality of Chondrostoma nasus eggs. Multivariate statistics detected significant differences of egg surface properties among individual females and among three different populations. These differences were mainly attributed to length variability and merging of adhesive villi as well as to coating and filament-like connections of these structures. The findings of this study highlight the need for further investigations to better understand the relationship of egg surface properties, egg stickiness and hatching success to understand the recruitment ecology and performance of early life stages in freshwater fish. 相似文献
76.
The motion in the cytosol of microorganisms such as bacteria and yeast has been observed to undergo a dramatic slowing down upon cell energy depletion. These observations have been interpreted as the motion being “glassy,” but whether this notion is useful also for active, motor-protein-driven transport in eukaryotic cells is less clear. Here, we use fluorescence microscopy of beads in human (HeLa) cells to probe the motion of membrane-surrounded structures that are carried along the cytoskeleton by motor proteins. Evaluating several hallmarks of glassy dynamics, we show that at short length scales, the motion is heterogeneous, is nonergodic, is well described by a model for the displacement distribution in glassy systems, and exhibits a decoupling of the exchange and persistence times. Overall, these results suggest that the short length scale behavior of objects that can be transported actively by motor proteins in human cells shares features with the motion in glassy systems. 相似文献
77.
Thommie Karlsson B. Christoffer Lagerholm Elena Vikström Vesa M. Loitto Karl-Eric Magnusson 《Biochemical and biophysical research communications》2013,430(3):993-998
Cells move along surfaces both as single cells and multi-cellular units. Recent research points toward pivotal roles for water flux through aquaporins (AQPs) in single cell migration. Their expression is known to facilitate this process by promoting rapid shape changes. However, little is known about the impact on migrating epithelial sheets during wound healing and epithelial renewal. Here, we investigate and compare the effects of AQP9 on single cell and epithelial sheet migration. To achieve this, MDCK-1 cells stably expressing AQP9 were subjected to migration assessment. We found that AQP9 facilitated cell locomotion at both the single and multi-cellular level. Furthermore, we identified major differences in the monolayer integrity and cell size upon expression of AQP9 during epithelial sheet migration, indicating a rapid volume-regulatory mechanism. We suggest a novel mechanism for epithelial wound healing based on AQP-induced swelling and expansion of the monolayer. 相似文献
78.
Sine Godiksen Christoffer Soendergaard Stine Friis Jan K. Jensen Jette Bornholdt Katiuchia Uzzun Sales Mingdong Huang Thomas H. Bugge Lotte K. Vogel 《PloS one》2013,8(10)
Matriptase is a member of the family of type II transmembrane serine proteases that is essential for development and maintenance of several epithelial tissues. Matriptase is synthesized as a single-chain zymogen precursor that is processed into a two-chain disulfide-linked form dependent on its own catalytic activity leading to the hypothesis that matriptase functions at the pinnacle of several protease induced signal cascades. Matriptase is usually found in either its zymogen form or in a complex with its cognate inhibitor hepatocyte growth factor activator inhibitor 1 (HAI-1), whereas the active non-inhibited form has been difficult to detect. In this study, we have developed an assay to detect enzymatically active non-inhibitor-complexed matriptase by using a biotinylated peptide substrate-based chloromethyl ketone (CMK) inhibitor. Covalently CMK peptide-bound matriptase is detected by streptavidin pull-down and subsequent analysis by Western blotting. This study presents a novel assay for detection of enzymatically active matriptase in living human and murine cells. The assay can be applied to a variety of cell systems and species. 相似文献
79.
Eva C. Arnspang Jeremy Schwartzentruber Mathias P. Clausen Paul W. Wiseman B. Christoffer Lagerholm 《PloS one》2013,8(12)
The lateral dynamics of proteins and lipids in the mammalian plasma membrane are heterogeneous likely reflecting both a complex molecular organization and interactions with other macromolecules that reside outside the plane of the membrane. Several methods are commonly used for characterizing the lateral dynamics of lipids and proteins. These experimental and data analysis methods differ in equipment requirements, labeling complexities, and further oftentimes give different results. It would therefore be very convenient to have a single method that is flexible in the choice of fluorescent label and labeling densities from single molecules to ensemble measurements, that can be performed on a conventional wide-field microscope, and that is suitable for fast and accurate analysis. In this work we show that k-space image correlation spectroscopy (kICS) analysis, a technique which was originally developed for analyzing lateral dynamics in samples that are labeled at high densities, can also be used for fast and accurate analysis of single molecule density data of lipids and proteins labeled with quantum dots (QDs). We have further used kICS to investigate the effect of the label size and by comparing the results for a biotinylated lipid labeled at high densities with Atto647N-strepatvidin (sAv) or sparse densities with sAv-QDs. In this latter case, we see that the recovered diffusion rate is two-fold greater for the same lipid and in the same cell-type when labeled with Atto647N-sAv as compared to sAv-QDs. This data demonstrates that kICS can be used for analysis of single molecule data and furthermore can bridge between samples with a labeling densities ranging from single molecule to ensemble level measurements. 相似文献
80.
Detection and correction of blinking bias in image correlation transport measurements of quantum dot tagged macromolecules 下载免费PDF全文
Durisic N Bachir AI Kolin DL Hebert B Lagerholm BC Grutter P Wiseman PW 《Biophysical journal》2007,93(4):1338-1346
Semiconductor nanocrystals or quantum dots (QDs) are becoming widely used as fluorescent labels for biological applications. Here we demonstrate that fluorescence fluctuation analysis of their diffusional mobility using temporal image correlation spectroscopy is highly susceptible to systematic errors caused by fluorescence blinking of the nanoparticles. Temporal correlation analysis of fluorescence microscopy image time series of streptavidin-functionalized (CdSe)ZnS QDs freely diffusing in two dimensions shows that the correlation functions are fit well to a commonly used diffusion decay model, but the transport coefficients can have significant systematic errors in the measurements due to blinking. Image correlation measurements of the diffusing QD samples measured at different laser excitation powers and analysis of computer simulated image time series verified that the effect we observe is caused by fluorescence intermittency. We show that reciprocal space image correlation analysis can be used for mobility measurements in the presence of blinking emission because it separates the contributions of fluctuations due to photophysics from those due to transport. We also demonstrate application of the image correlation methods for measurement of the diffusion coefficient of glycosyl phosphatidylinositol-anchored proteins tagged with QDs as imaged on living fibroblasts. 相似文献