COMMD proteins: COMMing to the scene.
Ontology highlight
ABSTRACT:
SUBMITTER: Maine GN
PROVIDER: S-EPMC2938186 | biostudies-literature | 2007 Aug
REPOSITORIES: biostudies-literature
Publications
COMMD proteins: COMMing to the scene.
Cellular and molecular life sciences : CMLS 20070801 15
COMM Domain-containing or COMMD proteins are a recently discovered group of factors defined by the presence of a unique motif in their extreme carboxy termini (Copper metabolism MURR1, or COMM domain). This protein family is comprised of ten members which are widely conserved throughout evolution and share certain functional properties. At the present time, a number of seemingly discrete functions have been ascribed to these factors. These include the regulation of such events as the activity of ...[more]
Similar Datasets
Project description:The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos. How these complexes are formed however is completely unknown. Here, we have systematically characterised the interactions between human COMMD proteins, and determined structures of COMMD proteins using X-ray crystallography and X-ray scattering to provide insights into the underlying mechanisms of homo- and heteromeric assembly. All COMMD proteins possess an α-helical N-terminal domain, and a highly conserved C-terminal domain that forms a tightly interlocked dimeric structure responsible for COMMD-COMMD interactions. The COMM domains also bind directly to components of CCC and mediate non-specific membrane association. Overall these studies show that COMMD proteins function as obligatory dimers with conserved domain architectures.
| S-EPMC6089597 | biostudies-literature
Project description:Copper is an essential transition metal for all eukaryotes. In mammals, intestinal copper absorption is mediated by the ATP7A copper transporter, whereas copper excretion occurs predominantly through the biliary route and is mediated by the paralog ATP7B. Both transporters have been shown to be recycled actively between the endosomal network and the plasma membrane by a molecular machinery known as the COMMD/CCDC22/CCDC93 or CCC complex. In fact, mutations in COMMD1 can lead to impaired biliary copper excretion and liver pathology in dogs and in mice with liver-specific Commd1 deficiency, recapitulating aspects of this phenotype. Nonetheless, the role of the CCC complex in intestinal copper absorption in vivo has not been studied, and the potential redundancy of various COMMD family members has not been tested. In this study, we examined copper homeostasis in enterocyte-specific and hepatocyte-specific COMMD gene-deficient mice. We found that, in contrast to effects in cell lines in culture, COMMD protein deficiency induced minimal changes in ATP7A in enterocytes and did not lead to altered copper levels under low- or high-copper diets, suggesting that regulation of ATP7A in enterocytes is not of physiological consequence. By contrast, deficiency of any of three COMMD genes (Commd1, Commd6 or Commd9) resulted in hepatic copper accumulation under high-copper diets. We found that each of these deficiencies caused destabilization of the entire CCC complex and suggest that this might explain their shared phenotype. Overall, we conclude that the CCC complex plays an important role in ATP7B endosomal recycling and function.
| S-EPMC7803461 | biostudies-literature
Project description:Fixation durations provide insights into processing demands. We investigated factors controlling fixation durations during scene viewing in two experiments. In Experiment 1, we tested the degree to which fixation durations adapt to global scene processing difficulty by manipulating the contrast (from original contrast to isoluminant) and saturation (original vs. grayscale) of the entire scene. We observed longer fixation durations for lower levels of contrast, and longer fixation durations for grayscale than for color scenes. Thus fixation durations were globally slowed as visual information became more and more degraded, making scene processing increasingly more difficult. In Experiment 2, we investigated two possible sources for this slow-down. We used "checkerboard" stimuli in which unmodified patches alternated with patches from which luminance information had been removed (isoluminant patches). Fixation durations showed an inverted immediacy effect (longer, rather than shorter, fixation durations on unmodified patches) along with a parafoveal-on-foveal effect (shorter fixation durations, when an unmodified patch was fixated next). This effect was stronger when the currently fixated patch was isoluminant as opposed to unmodified. Our results suggest that peripheral scene information substantially affects fixation durations and are consistent with the notion of competition among the current and potential future fixation locations.
| S-EPMC7405803 | biostudies-literature
Project description:We internally represent the structure of our surroundings even when there is little layout information available in the visual image, such as when walking through fog or darkness. One way in which we disambiguate such scenes is through object cues; for example, seeing a boat supports the inference that the foggy scene is a lake. Recent studies have investigated the neural mechanisms by which object and scene processing interact to support object perception. The current study examines the reverse interaction by which objects facilitate the neural representation of scene layout. Photographs of indoor (closed) and outdoor (open) real-world scenes were blurred such that they were difficult to categorize on their own but easily disambiguated by the inclusion of an object. fMRI decoding was used to measure scene representations in scene-selective parahippocampal place area (PPA) and occipital place area (OPA). Classifiers were trained to distinguish response patterns to fully visible indoor and outdoor scenes, presented in an independent experiment. Testing these classifiers on blurred scenes revealed a strong improvement in classification in left PPA and OPA when objects were present, despite the reduced low-level visual feature overlap with the training set in this condition. These findings were specific to left PPA/OPA, with no evidence for object-driven facilitation in right PPA/OPA, object-selective areas, and early visual cortex. These findings demonstrate separate roles for left and right scene-selective cortex in scene representation, whereby left PPA/OPA represents inferred scene layout, influenced by contextual object cues, and right PPA/OPA represents a scene's visual features.
| S-EPMC6033316 | biostudies-literature
Project description:Presenting consistent objects in scenes facilitates object recognition as compared to inconsistent objects. Yet the mechanisms by which scenes influence object recognition are still not understood. According to one theory, consistent scenes facilitate visual search for objects at expected places. Here, we investigated two predictions following from this theory: If visual search is responsible for consistency effects, consistency effects could be weaker (1) with better-primed than less-primed object locations, and (2) with less-primed than better-primed scenes. In Experiments 1 and 2, locations of objects were varied within a scene to a different degree (one, two, or four possible locations). In addition, object-scene consistency was studied as a function of progressive numbers of repetitions of the backgrounds. Because repeating locations and backgrounds could facilitate visual search for objects, these repetitions might alter the object-scene consistency effect by lowering of location uncertainty. Although we find evidence for a significant consistency effect, we find no clear support for impacts of scene priming or location priming on the size of the consistency effect. Additionally, we find evidence that the consistency effect is dependent on the eccentricity of the target objects. These results point to only small influences of priming to object-scene consistency effects but all-in-all the findings can be reconciled with a visual-search explanation of the consistency effect.
| S-EPMC4039012 | biostudies-literature
Project description:Recent research has demonstrated that the parahippocampal place area represents both the shape and texture features of scenes, with the importance of each feature varying according to perceived scene category. Namely, shape features are predominately more diagnostic to the processing of artificial human-made scenes, while shape and texture are equally diagnostic in natural scene processing. However, to date little is known regarding the degree of interactivity or independence observed in the processing of these scene features. Furthermore, manipulating the scope of visual attention (i.e., globally vs. locally) when processing ensembles of multiple objects-stimuli that share a functional neuroanatomical link with scenes-has been shown to affect their cognitive visual representation. It remains unknown whether manipulating the scope of attention impacts scene processing in a similar manner. Using the well-established Garner speeded-classification behavioral paradigm, we investigated the influence of both feature diagnosticity and the scope of visual attention on potential interactivity or independence in the shape and texture processing of artificial human-made scenes. The results revealed asymmetric interference between scene shape and texture processing, with the more diagnostic feature (i.e., shape) interfering with the less diagnostic feature (i.e., texture), but not vice versa. Furthermore, this interference was attenuated and enhanced with more local and global visual processing strategies, respectively. These findings suggest that the scene shape and texture processing are mediated by shared cognitive mechanisms and that, although these representations are governed primarily via feature diagnosticity, they can nevertheless be influenced by the scope of visual attention.
| S-EPMC8297417 | biostudies-literature
Project description:COMMD [copper metabolism gene MURR1 (mouse U2af1-rs1 region 1) domain] proteins constitute a recently identified family of NF-kappaB (nuclear factor kappaB)-inhibiting proteins, characterized by the presence of the COMM domain. In the present paper, we report detailed investigation of the role of this protein family, and specifically the role of the COMM domain, in NF-kappaB signalling through characterization of protein-protein interactions involving COMMD proteins. The small ubiquitously expressed COMMD6 consists primarily of the COMM domain. Therefore COMMD1 and COMMD6 were analysed further as prototype members of the COMMD protein family. Using specific antisera, interaction between endogenous COMMD1 and COMMD6 is described. This interaction was verified by independent techniques, appeared to be direct and could be detected throughout the whole cell, including the nucleus. Both proteins inhibit TNF (tumour necrosis factor)-induced NF-kappaB activation in a non-synergistic manner. Mutation of the amino acid residues Trp24 and Pro41 in the COMM domain of COMMD6 completely abolished the inhibitory effect of COMMD6 on TNF-induced NF-kappaB activation, but this was not accompanied by loss of interaction with COMMD1, COMMD6 or the NF-kappaB subunit RelA. In contrast with COMMD1, COMMD6 does not bind to IkappaBalpha (inhibitory kappaBalpha), indicating that both proteins inhibit NF-kappaB in an overlapping, but not completely similar, manner. Taken together, these data support the significance of COMMD protein-protein interactions and provide new mechanistic insight into the function of this protein family in NF-kappaB signalling.
| S-EPMC1525016 | biostudies-other
Project description:During natural vision, humans categorize the scenes they encounter: an office, the beach, and so on. These categories are informed by knowledge of the way that objects co-occur in natural scenes. How does the human brain aggregate information about objects to represent scene categories? To explore this issue, we used statistical learning methods to learn categories that objectively capture the co-occurrence statistics of objects in a large collection of natural scenes. Using the learned categories, we modeled fMRI brain signals evoked in human subjects when viewing images of scenes. We find that evoked activity across much of anterior visual cortex is explained by the learned categories. Furthermore, a decoder based on these scene categories accurately predicts the categories and objects comprising novel scenes from brain activity evoked by those scenes. These results suggest that the human brain represents scene categories that capture the co-occurrence statistics of objects in the world.
| S-EPMC5464350 | biostudies-literature
Project description:Computer vision-based research has shown that scene semantics (e.g., presence of meaningful objects in a scene) can predict memorability of scene images. Here, we investigated whether and to what extent overt attentional correlates, such as fixation map consistency (also called inter-observer congruency of fixation maps) and fixation counts, mediate the relationship between scene semantics and scene memorability. First, we confirmed that the higher the fixation map consistency of a scene, the higher its memorability. Moreover, both fixation map consistency and its correlation to scene memorability were the highest in the first 2 seconds of viewing, suggesting that meaningful scene features that contribute to producing more consistent fixation maps early in viewing, such as faces and humans, may also be important for scene encoding. Second, we found that the relationship between scene semantics and scene memorability was partially (but not fully) mediated by fixation map consistency and fixation counts, separately as well as together. Third, we found that fixation map consistency, fixation counts, and scene semantics significantly and additively contributed to scene memorability. Together, these results suggest that eye-tracking measurements can complement computer vision-based algorithms and improve overall scene memorability prediction.
| S-EPMC7476653 | biostudies-literature
Project description:In complex real-world scenes, image content is conveyed by a large collection of intertwined visual features. The visual system disentangles these features in order to extract information about image content. Here, we investigate the role of one integral component: the content of spatial frequencies in an image. Specifically, we measure the amount of image content carried by low versus high spatial frequencies for the representation of real-world scenes in scene-selective regions of human visual cortex. To this end, we attempted to decode scene categories from the brain activity patterns of participants viewing scene images that contained the full spatial frequency spectrum, only low spatial frequencies, or only high spatial frequencies, all carefully controlled for contrast and luminance. Contrary to the findings from numerous behavioral studies and computational models that have highlighted how low spatial frequencies preferentially encode image content, decoding of scene categories from the scene-selective brain regions, including the parahippocampal place area (PPA), was significantly more accurate for high than low spatial frequency images. In fact, decoding accuracy was just as high for high spatial frequency images as for images containing the full spatial frequency spectrum in scene-selective areas PPA, RSC, OPA and object selective area LOC. We also found an interesting dissociation between the posterior and anterior subdivisions of PPA: categories were decodable from both high and low spatial frequency scenes in posterior PPA but only from high spatial frequency scenes in anterior PPA; and spatial frequency was explicitly decodable from posterior but not anterior PPA. Our results are consistent with recent findings that line drawings, which consist almost entirely of high spatial frequencies, elicit a neural representation of scene categories that is equivalent to that of full-spectrum color photographs. Collectively, these findings demonstrate the importance of high spatial frequencies for conveying the content of complex real-world scenes.
| S-EPMC5741213 | biostudies-literature