(light sense) articles in PubMed
- Making sense of the yeast sphingolipid pathway. [Review]
- J Mol Biol 2016 Sep 21JM
- Sphingolipids (SL) and their metabolites play key roles both as structural components of membranes and as signalling molecules. Many of the key enzymes and regulators of SL metabolism were discovered...
Sphingolipids (SL) and their metabolites play key roles both as structural components of membranes and as signalling molecules. Many of the key enzymes and regulators of SL metabolism were discovered using the yeast Saccharomyces cerevisiae, and based on the high degree of conservation, a number of mammalian homologs were identified. Although yeast continues to be an important tool for SL research, the complexity of SL structure and nomenclature often hampers the ability of new researchers to grasp the subtleties of yeast SL biology and to discover modulators of this intricate pathway. Moreover, the emergence of lipidomics by mass spectrometry has enabled rapid identification of SL species in yeast and rendered analysis of SL composition under various physiological and pathophysiological conditions readily amenable. However, the complex nomenclature of the identified species renders much of the data inaccessible to non-specialists. In this review, we focus on parsing both the classical SL nomenclature and the nomenclature normally used during mass spectrometry analysis, which should facilitate understanding yeast SL data and might shed light on biological processes in which SLs are involved. Finally, we discuss a number of putative roles of various yeast SL species.
- Evolution of Cilia. [Journal Article]
- Cold Spring Harb Perspect Biol 2016 Sep 23CS
- Anton van Leeuwenhoek's startling microscopic observations in the 1600s first stimulated fascination with the way that cells use cilia to generate currents and to swim in a fluid environment. Researc...
Anton van Leeuwenhoek's startling microscopic observations in the 1600s first stimulated fascination with the way that cells use cilia to generate currents and to swim in a fluid environment. Research in recent decades has yielded deep knowledge about the mechanical and biochemical nature of these organelles but only opened a greater fascination about how such beautifully intricate and multifunctional structures arose during evolution. Answers to this evolutionary puzzle are not only sought to satisfy basic curiosity, but also, as stated so eloquently by Dobzhansky (Am Zool 4: 443 ), because "nothing in biology makes sense except in the light of evolution." Here I attempt to summarize current knowledge of what ciliary organelles of the last eukaryotic common ancestor (LECA) were like, explore the ways in which cilia have evolved since that time, and speculate on the selective processes that might have generated these organelles during early eukaryotic evolution.
- Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in GFP. [Journal Article]
- J Am Chem Soc 2016 Sep 23JA
- The green fluorescent protein and its designed variants fluoresce efficiently. Because the isolated chromophore is not fluorescent in the practical sense, it is apparent that the protein environment ...
The green fluorescent protein and its designed variants fluoresce efficiently. Because the isolated chromophore is not fluorescent in the practical sense, it is apparent that the protein environment plays a crucial role toward the efficiency. Due to various obstacles in studying excited state dynamics of complex systems, however, the detailed mechanism of this efficiency enhancement is not yet clearly elucidated. Here, by adopting excited state non-adiabatic molecular dynamics simulations together with an interpolated quantum chemical potential model of the chromophore, we find that the strong electric field from the protein matrix contributes dominantly to the motional restriction of the chromophore. The delay in twisting motion subsequently obstructs the non-radiative decay that competes with fluorescence, leading naturally to an enhancement in light emitting efficiency. Surprisingly, steric constraints make only a minor contribution to these aspects. Through residue specific analyses, we identify a group of key residues that control the excited state behavior. Testing with a series of mutant GFPs with different brightness also supports the view regarding the importance of protein electrostatics. Our findings may provide a useful guide toward designing new fluorescent chemical systems in the future.
- Photoreception and vision in the ultraviolet. [Review]
- J Exp Biol 2016 Sep 15; 219(Pt 18):2790-2801JE
- Ultraviolet (UV) light occupies the spectral range of wavelengths slightly shorter than those visible to humans. Because of its shorter wavelength, it is more energetic (and potentially more photodam...
Ultraviolet (UV) light occupies the spectral range of wavelengths slightly shorter than those visible to humans. Because of its shorter wavelength, it is more energetic (and potentially more photodamaging) than 'visible light', and it is scattered more efficiently in air and water. Until 1990, only a few animals were recognized as being sensitive to UV light, but we now know that a great diversity, possibly even the majority, of animal species can visually detect and respond to it. Here, we discuss the history of research on biological UV photosensitivity and review current major research trends in this field. Some animals use their UV photoreceptors to control simple, innate behaviors, but most incorporate their UV receptors into their general sense of vision. They not only detect UV light but recognize it as a separate color in light fields, on natural objects or living organisms, or in signals displayed by conspecifics. UV visual pigments are based on opsins, the same family of proteins that are used to detect light in conventional photoreceptors. Despite some interesting exceptions, most animal species have a single photoreceptor class devoted to the UV. The roles of UV in vision are manifold, from guiding navigation and orientation behavior, to detecting food and potential predators, to supporting high-level tasks such as mate assessment and intraspecific communication. Our current understanding of UV vision is restricted almost entirely to two phyla: arthropods and chordates (specifically, vertebrates), so there is much comparative work to be done.
- The elementary representation of spatial and color vision in the human retina. [Journal Article]
- Sci Adv 2016; 2(9):e1600797SA
- The retina is the most accessible element of the central nervous system for linking behavior to the activity of isolated neurons. We unraveled behavior at the elementary level of single input units-t...
The retina is the most accessible element of the central nervous system for linking behavior to the activity of isolated neurons. We unraveled behavior at the elementary level of single input units-the visual sensation generated by stimulating individual long (L), middle (M), and short (S) wavelength-sensitive cones with light. Spectrally identified cones near the fovea of human observers were targeted with small spots of light, and the type, proportion, and repeatability of the elicited sensations were recorded. Two distinct populations of cones were observed: a smaller group predominantly associated with signaling chromatic sensations and a second, more numerous population linked to achromatic percepts. Red and green sensations were mainly driven by L- and M-cones, respectively, although both cone types elicited achromatic percepts. Sensations generated by cones were rarely stochastic; rather, they were consistent over many months and were dominated by one specific perceptual category. Cones lying in the midst of a pure spectrally opponent neighborhood, an arrangement purported to be most efficient in producing chromatic signals in downstream neurons, were no more likely to signal chromatic percepts. Overall, the results are consistent with the idea that the nervous system encodes high-resolution achromatic information and lower-resolution color signals in separate pathways that emerge as early as the first synapse. The lower proportion of cones eliciting color sensations may reflect a lack of evolutionary pressure for the chromatic system to be as fine-grained as the high-acuity achromatic system.
- A multichannel smartphone optical biosensor for high-throughput point-of-care diagnostics. [Journal Article]
- Biosens Bioelectron 2016 Sep 9; 87:686-692BB
- Current reported smartphone spectrometers are only used to monitor or measure one sample at a time. For the first time, we demonstrate a multichannel smartphone spectrometer (MSS) as an optical biose...
Current reported smartphone spectrometers are only used to monitor or measure one sample at a time. For the first time, we demonstrate a multichannel smartphone spectrometer (MSS) as an optical biosensor that can simultaneously optical sense multiple samples. In this work, we developed a novel method to achieve the multichannel optical spectral sensing with nanometer resolution on a smartphone. A 3D printed cradle held the smartphone integrated with optical components. This optical sensor performed accurate and reliable spectral measurements by optical intensity changes at specific wavelength or optical spectral shifts. A custom smartphone multi-view App was developed to control the optical sensing parameters and to align each sample to the corresponding channel. The captured images were converted to the transmission spectra in the visible wavelength range from 400nm to 700nm with the high resolution of 0.2521nm per pixel. We validated the performance of this MSS via measuring the concentrations of protein and immunoassaying a type of human cancer biomarker. Compared to the standard laboratory instrument, the results sufficiently showed that this MSS can achieve the comparative analysis detection limits, accuracy and sensitivity. We envision that this multichannel smartphone optical biosensor will be useful in high-throughput point-of-care diagnostics with its minimizing size, light weight, low cost and data transmission function.
- Toluene biodegradation in an algal-bacterial airlift photobioreactor: Influence of the biomass concentration and of the presence of an organic phase. [Journal Article]
- J Environ Manage 2016 Sep 9JE
- The potential of algal-bacterial symbiosis for off-gas abatement was investigated for the first time by comparatively evaluating the performance of a bacterial (CB) and an algal-bacterial (PB) airlif...
The potential of algal-bacterial symbiosis for off-gas abatement was investigated for the first time by comparatively evaluating the performance of a bacterial (CB) and an algal-bacterial (PB) airlift bioreactors during the treatment of a 6 g m(-3) toluene laden air emission. The influence of biomass concentration and of the addition of a non-aqueous phase was also investigated. A poor and fluctuating performance was recorded during the initial stages of the experiment, which was attributed to the low biomass concentration present in both reactors and to the accumulation of toxic metabolites. In this sense, an increase in the dilution rate from 0.23 to 0.45 d(-1) and in biomass concentration from ∼1 to ∼5 g L(-1) resulted in elimination capacities (ECs) of 300 g m(-3) h(-1) (corresponding to removal efficiencies ∼ 90%). Microalgae activity allowed for a reduction in the emitted CO2 and an increase in dissolved O2 concentration in the PB. However, excess biomass growth over 11 g L(-1) hindered light penetration and severely decreased photosynthetic activity. The addition of silicone oil at 20% (on a volume basis) stabilized system performance, leading to dissolved O2 concentrations of 7 mg L(-1) and steady ECs of 320 g m(-3) h(-1) in the PB. The ECs here recorded were considerably higher than those previously reported in toluene-degrading bioreactors. Finally, microbial population analysis by DGGE-sequencing demonstrated the differential specialization of the microbial community in both reactors, likely resulting in different toluene degradation pathways and metabolites production.
- Rumours about wildlife pest introductions: European rabbits in Spain. [Journal Article]
- Ambio 2016 Sep 9A
- Rumours associated with wildlife are frequent, although they have received little attention in the scientific literature. Studying rumours is important because of their relevance not only in a broad ...
Rumours associated with wildlife are frequent, although they have received little attention in the scientific literature. Studying rumours is important because of their relevance not only in a broad theoretical sense but also in environmental management. The goal of this study is to explore the complexity of the relationships between humans and wildlife through a thematic analysis of rumours associated with allegedly introduced European rabbits (Oryctolagus cuniculus) that cause crop damage in Spain. For this purpose, potential rumours were identified using the Google search engine. Data analysis consisted of reading and re-reading Web-based texts to identify main themes, ideas and topics with the assistance of NVivo 10 software. The analysis identified three main themes: (1) the reviewed websites referred to allegedly introduced rabbits which differed from native rabbits; (2) differences were based on alleged observations of unnatural behaviour, physiology or physical appearance of introduced rabbits; (3) rumours were frequently used in the context of the rabbit management conflict; e.g. farmers accused hunters of releasing harmful rabbits. This study suggests that the analysis of wildlife-release rumours sheds light on the position of parties involved in conflicts associated with the (alleged) introduction of wildlife species. It stresses the importance of rumours in conservation and environmental management, and opens the door to future research.
- Crown-of-thorns starfish have true image forming vision. [Journal Article]
- Front Zool 2016; 13(1):41FZ
- CONCLUSIONS: For crown-of-thorns starfish, visual cues are essential for close range orientation towards objects, such as coral boulders, in the wild. These visually guided behaviours can be replicated in aquarium conditions. Our observation that crown-of-thorns starfish respond to black-and-white shapes on a mid-intensity grey background is the first direct proof of true spatial vision in starfish and in the phylum Echinodermata.
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- Continuous de novo generation of spatially segregated hepatitis C virus replication organelles revealed by pulse-chase imaging. [Journal Article]
- J Hepatol 2016 Sep 3JH
- CONCLUSIONS: Thus, our results reveal that HCV replication organelles are not static structures, but instead are continuously generated and dynamically change in composition and possibly also in function.