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Scientific Reports Nov 2016In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience,...
In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact of optogenetics has been limited by a lack of user-friendly, flexible, accessible hardware. Here, we engineer the Light Plate Apparatus (LPA), a device that can deliver two independent 310 to 1550 nm light signals to each well of a 24-well plate with intensity control over three orders of magnitude and millisecond resolution. Signals are programmed using an intuitive web tool named Iris. All components can be purchased for under $400 and the device can be assembled and calibrated by a non-expert in one day. We use the LPA to precisely control gene expression from blue, green, and red light responsive optogenetic tools in bacteria, yeast, and mammalian cells and simplify the entrainment of cyanobacterial circadian rhythm. The LPA dramatically reduces the entry barrier to optogenetics and photobiology experiments.
Topics: Calibration; Circadian Rhythm; Equipment Design; Gene Expression; Green Fluorescent Proteins; HeLa Cells; Humans; Light; Models, Theoretical; Optogenetics; Photobiology; Saccharomyces cerevisiae; Synechococcus; Tissue Engineering; Two-Hybrid System Techniques
PubMed: 27805047
DOI: 10.1038/srep35363 -
Frontiers in Microbiology 2014Coral reef ecosystems thrive in tropical oligotrophic oceans because of the relationship between corals and endosymbiotic dinoflagellate algae called Symbiodinium.... (Review)
Review
Coral reef ecosystems thrive in tropical oligotrophic oceans because of the relationship between corals and endosymbiotic dinoflagellate algae called Symbiodinium. Symbiodinium convert sunlight and carbon dioxide into organic carbon and oxygen to fuel coral growth and calcification, creating habitat for these diverse and productive ecosystems. Light is thus a key regulating factor shaping the productivity, physiology, and ecology of the coral holobiont. Similar to all oxygenic photoautotrophs, Symbiodinium must safely harvest sunlight for photosynthesis and dissipate excess energy to prevent oxidative stress. Oxidative stress is caused by environmental stressors such as those associated with global climate change, and ultimately leads to breakdown of the coral-algal symbiosis known as coral bleaching. Recently, large-scale coral bleaching events have become pervasive and frequent threatening and endangering coral reefs. Because the coral-algal symbiosis is the biological engine producing the reef, the future of coral reef ecosystems depends on the ecophysiology of the symbiosis. This review examines the photobiology of the coral-algal symbiosis with particular focus on the photophysiological responses and timescales of corals and Symbiodinium. Additionally, this review summarizes the light environment and its dynamics, the vulnerability of the symbiosis to oxidative stress, the abiotic and biotic factors influencing photosynthesis, the diversity of the coral-algal symbiosis, and recent advances in the field. Studies integrating physiology with the developing "omics" fields will provide new insights into the coral-algal symbiosis. Greater physiological and ecological understanding of the coral-algal symbiosis is needed for protection and conservation of coral reefs.
PubMed: 25202301
DOI: 10.3389/fmicb.2014.00422 -
The Journal of Investigative Dermatology Feb 1998
Topics: Humans; Lymphocyte Culture Test, Mixed; Photobiology; Sensitivity and Specificity; Skin; Sunscreening Agents
PubMed: 9457917
DOI: 10.1046/j.1523-1747.1998.00135.x -
Trends in Plant Science Feb 2020The discovery of visible fluorescence in the plant pigments betalains revealed the existence of fluorescent patterns in flowers of plants of the order Caryophyllales,... (Review)
Review
The discovery of visible fluorescence in the plant pigments betalains revealed the existence of fluorescent patterns in flowers of plants of the order Caryophyllales, where betalains substitute anthocyanins. The serendipitous initial discovery led to a systemized characterization of the role of different substructures on the photophysical phenomenon. Strong fluorescence is general to all members of the family of betaxanthins linked to the structural property that the betalamic acid moiety is connected to an amine group. This property has led to bioinspired tailor-made probes and to the development of novel biotechnological applications in screening techniques or microscopy labeling. Here, we comprehensively review the photophysics, photochemistry, and photobiology of betalain fluorescence and describe all current applications.
Topics: Anthocyanins; Betalains; Biotechnology; Flowers; Plants
PubMed: 31843371
DOI: 10.1016/j.tplants.2019.11.001 -
The International Journal of... 2005The timing of flower initiation is a highly plastic developmental process. To achieve reproductive success, plants must select the most favourable season to initiate... (Review)
Review
The timing of flower initiation is a highly plastic developmental process. To achieve reproductive success, plants must select the most favourable season to initiate reproductive development; this in turn requires continuous monitoring of environmental factors and a properly response. Environmental factors which change in a predictable fashion along the year, such as light and temperature, are the most relevant in terms of selection of the flowering season. In Arabidopsis and more recently in a few other species, molecular genetic analyses are providing a way to identify the genes involved in the regulation of flowering time. From gene sequences it is possible to develop hypotheses regarding molecular function and to infer some of the molecular mechanisms involved in the environmental regulation of flowering time. In this paper, we summarize recent discoveries concerning the mechanisms which plants use to perceive and respond to major environmental factors (light and temperature) and their different components. We focus mainly on annual plants and especially on Arabidopsis because most of the available molecular and functional data come from this species. However, additional information arising from other plant systems is also considered.
Topics: Arabidopsis; Environment; Flowers; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Genes, Plant; Models, Biological; Photobiology; Photoperiod; Photosynthetic Reaction Center Complex Proteins; Plant Development; Plants; Temperature
PubMed: 16096975
DOI: 10.1387/ijdb.052022ia -
Microbiology Spectrum May 2017The capacity for biological timekeeping arose at least three times through evolution, in prokaryotic cyanobacteria, in cells that evolved into higher plants, and within... (Review)
Review
The capacity for biological timekeeping arose at least three times through evolution, in prokaryotic cyanobacteria, in cells that evolved into higher plants, and within the group of organisms that eventually became the fungi and the animals. is a tractable model system for understanding the molecular bases of circadian rhythms in the last of these groups, and is perhaps the most intensively studied circadian cell type. Rhythmic processes described in fungi include growth rate, stress responses, developmental capacity, and sporulation, as well as much of metabolism; fungi use clocks to anticipate daily environmental changes. A negative feedback loop comprises the core of the circadian system in fungi and animals. In , the best studied fungal model, it is driven by two transcription factors, WC-1 and WC-2, that form the White Collar Complex (WCC). WCC elicits expression of the gene. FRQ complexes with other proteins, physically interacts with the WCC, and reduces its activity; the kinetics of these processes is strongly influenced by progressive phosphorylation of FRQ. When FRQ becomes sufficiently phosphorylated that it loses the ability to influence WCC activity, the circadian cycle starts again. Environmental cycles of light and temperature influence and FRQ expression and thereby reset the internal circadian clocks. The molecular basis of circadian output is also becoming understood. Taken together, molecular explanations are emerging for all the canonical circadian properties, providing a molecular and regulatory framework that may be extended to many members of the fungal and animal kingdoms, including humans.
Topics: Animals; Biological Clocks; Circadian Rhythm; DNA-Binding Proteins; Feedback, Physiological; Fungal Proteins; Fungi; Gene Expression Regulation, Fungal; Genes, Fungal; Humans; Light; Models, Biological; Neurospora; Photobiology; Temperature; Transcription Factors; Transcription, Genetic
PubMed: 28527179
DOI: 10.1128/microbiolspec.FUNK-0039-2016 -
Biochimica Et Biophysica Acta Sep 2015Photosystem I, an integral membrane and multi-subunit complex, catalyzes the oxidation of plastocyanin and the reduction of ferredoxin by absorbed light energy.... (Review)
Review
Photosystem I, an integral membrane and multi-subunit complex, catalyzes the oxidation of plastocyanin and the reduction of ferredoxin by absorbed light energy. Photosystem I participates in photosynthetic acclimation processes by being involved in cyclic electron transfer and state transitions for sustaining efficient photosynthesis. The photosystem I complex is highly conserved from cyanobacteria to higher plants and contains the light-harvesting complex and the reaction center complex. The assembly of the photosystem I complex is highly complicated and involves the concerted assembly of multiple subunits and hundreds of cofactors. A suite of regulatory factors for the assembly of photosystem I subunits and cofactors have been identified that constitute an integrative network regulating PSI accumulation. This review aims to discuss recent findings in the field relating to how the photosystem I complex is assembled in oxygenic organisms. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
Topics: Evolution, Molecular; Photosystem I Protein Complex; Protein Subunits
PubMed: 25582571
DOI: 10.1016/j.bbabio.2014.12.011 -
Photochemistry and Photobiology Mar 2022This article is a highlight of the paper by Ivanic and Schnermann et al. in this issue of Photochemistry and Photobiology (Daly et al. Photochem. Photobiol. 2022). The...
This article is a highlight of the paper by Ivanic and Schnermann et al. in this issue of Photochemistry and Photobiology (Daly et al. Photochem. Photobiol. 2022). The collaborative team utilized computational approaches to investigate the influence of electron-withdrawing groups at the 10' position of tetramethylrhodamine (TMR). Leveraging this information, the team was able to extend the emission of the TMR scaffold into the shortwave-infrared region (SWIR, 1000-2500 nm) by incorporation of a ketone functional group at the 10' position (Daly et al. Photochem. Photobiol. 2022). This work provides the first example of a TMR derivative with peak SWIR emission (λ : 862 nm, λ : 1058 nm). The authors utilize the ketone rhodamine scaffold to generate fluorogenic, pH-responsive reporters. This work demonstrates the potential of the classic xanthene scaffold for use as a SWIR reporter, an important step in the ultimate expansion of the repertoire of small-molecule organic fluorophore scaffolds available for deep-tissue imaging applications.
Topics: Fluorescent Dyes; Ionophores; Ketones; Xanthenes
PubMed: 34953073
DOI: 10.1111/php.13578 -
International Journal of Molecular... Feb 2023Light is an emerging treatment approach that is being used to treat many diseases and conditions such as pain, inflammation, and wound healing. The light used in dental... (Review)
Review
Light is an emerging treatment approach that is being used to treat many diseases and conditions such as pain, inflammation, and wound healing. The light used in dental therapy generally lies in visible and invisible spectral regions. Despite many positive results in the treatment of different conditions, this therapy still faces some skepticism, which has prevented its widespread adoption in clinics. The main reason for this skepticism is the lack of comprehensive information about the molecular, cellular, and tissular mechanisms of action, which underpin the positive effects of phototherapy. However, there is currently promising evidence in support of the use of light therapy across a spectrum of oral hard and soft tissues, as well as in a variety of important dental subspecialties, such as endodontics, periodontics, orthodontics, and maxillofacial surgery. The merging of diagnostic and therapeutic light procedures is also seen as a promising area for future expansion. In the next decade, several light technologies are foreseen as becoming integral parts of modern dentistry practice.
Topics: Photobiology; Orthodontics; Endodontics; Periodontics; Surgery, Oral
PubMed: 36835395
DOI: 10.3390/ijms24043985 -
Photochemistry and Photobiology 2016Although sunlight is essential for life on earth, the ultraviolet (UV) wavelengths in its spectrum constitute a major threat to life. Various cellular responses have... (Review)
Review
Although sunlight is essential for life on earth, the ultraviolet (UV) wavelengths in its spectrum constitute a major threat to life. Various cellular responses have evolved to deal with the damage inflicted in DNA by UV, and the study of these responses in model systems has spawned the burgeoning field of DNA repair. Although we now know of many types of deleterious alterations in DNA, the approaches for studying them and the early mechanistic insights have come in large part from pioneering research on the processing of UV-induced bipyrimidine photoproducts in bacteria. It is also notable that UV was one of the first DNA damaging agents for which exposure was directly linked to cancer; the sun-sensitive syndrome, xeroderma pigmentosum, was the first example of a cancer-prone hereditary disease involving a defect in DNA repair. We provide a short history of advances in the broad field of genomic maintenance as they have emerged from research in photochemistry and photobiology.
Topics: DNA Damage; DNA Repair; Genetic Predisposition to Disease; Genome, Human; Humans; Neoplasms, Radiation-Induced; Origin of Life; Ultraviolet Rays; Xeroderma Pigmentosum
PubMed: 26481112
DOI: 10.1111/php.12542