Nearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the ...perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due ...to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.
Avian eggs have a proteinaceous cuticle. The quantity of cuticle varies and the deposition of a good cuticle in the uterus (Shell-gland) prevents transmission of bacteria to the egg contents.
To ...understand cuticle deposition, uterus transcriptomes were compared between hens with i) naturally good and poor cuticle and, ii) where manipulation of the hypothalamo-pituitary-gonadal-oviduct axis produced eggs with or without cuticle. The highest expressed genes encoded eggshell matrix and cuticle proteins, e.g. MEPE (OC-116), BPIFB3 (OVX-36), RARRES1 (OVX-32), WAP (OVX-25), and genes for mitochondrial oxidative phosphorylation, active transport and energy metabolism. Expression of a number of these genes differed between hens laying eggs with or without cuticle. There was also a high expression of clock genes. PER2, CRY2, CRY1, CLOCK and BMAL1 were differentially expressed when cuticle deposition was prevented, and they also changed throughout the egg formation cycle. This suggests an endogenous clock in the uterus may be a component of cuticle deposition control. Cuticle proteins are glycosylated and glycosaminoglycan binding genes had a lower expression when cuticle proteins were deposited on the egg. The immediate early genes, JUN and FOS, were expressed less when the cuticle had not been deposited and changed over the egg formation cycle, suggesting they are important in oviposition and cuticle deposition. The uterus transcriptome of hens with good and poor cuticle deposition did not differ.
We have gained insights into the factors that can affect the production of the cuticle especially clock genes and immediate early genes. We have demonstrated that these genes change their expression over the period of eggshell formation supporting their importance. The lack of differences in expression between the uterus of hens laying eggs with the best and worse cuticle suggest the genetic basis of the trait may lie outside the oviduct.
Observational data of coastal change over much of the Arctic are limited largely due to its immensity, remoteness, harsh environment, and restricted periods of sunlight and ice-free conditions. ...Barter Island, Alaska, is one of the few locations where an extensive, observational dataset exists, which enables a detailed assessment of the trends and patterns of coastal change over decadal to annual time scales. Coastal bluff and shoreline positions were delineated from maps, aerial photographs, and satellite imagery acquired between 1947 and 2020, and at a nearly annual rate since 2004. Rates and patterns of shoreline and bluff change varied widely over the observational period. Shorelines showed a consistent trend of southerly erosion and westerly extension of the western termini of Barter Island and Bernard Spit, which has accelerated since at least 2000. The 3.2 km long stretch of ocean-exposed coastal permafrost bluffs retreated on average 114 m and at a maximum of 163 m at an average long-term rate (70 year) of 1.6 ± 0.1 m/yr. The long-term retreat rate was punctuated by individual years with retreat rates up to four times higher (6.6 ± 1.9 m/yr; 2012–2013) and both long-term (multidecadal) and short-term (annual to semiannual) rates showed a steady increase in retreat rates through time, with consistently high rates since 2015. A best-fit polynomial trend indicated acceleration in retreat rates that was independent of the large spatial and temporal variations observed on an annual basis. Rates and patterns of bluff retreat were correlated to incident wave energy and air and water temperatures. Wave energy was found to be the dominant driver of bluff retreat, followed by sea surface temperatures and warming air temperatures that are considered proxies for evaluating thermo-erosion and denudation. Normalized anomalies of cumulative wave energy, duration of open water, and air and sea temperature showed at least three distinct phases since 1979: a negative phase prior to 1987, a mixed phase between 1987 and the early to late 2000s, followed by a positive phase extending to 2020. The duration of the open-water season has tripled since 1979, increasing from approximately 40 to 140 days. Acceleration in retreat rates at Barter Island may be related to increases in both thermodenudation, associated with increasing air temperature, and the number of niche-forming and block-collapsing episodes associated with higher air and water temperature, more frequent storms, and longer ice-free conditions in the Beaufort Sea.
Conformational changes of linker units in metal‐organic frameworks (MOFs) are often responsible for gate‐opening phenomena in selective gas adsorption and stimuli‐responsive optical and electrical ...sensing behaviour. Herein, we show that pressure‐induced bathochromic shifts in both fluorescence emission and UV/Vis absorption spectra of a two‐fold interpenetrated Hf MOF, linked by 1,4‐phenylene‐bis(4‐ethynylbenzoate) ligands (Hf‐peb), are induced by rotation of the central phenyl ring of the linker, from a coplanar arrangement to a twisted, previously unseen conformer. Single‐crystal X‐ray diffraction, alongside in situ fluorescence and UV/Vis absorption spectroscopies, measured up to 2.1 GPa in a diamond anvil cell on single crystals, are in excellent agreement, correlating linker rotation with modulation of emission. Topologically isolating the 1,4‐phenylene‐bis(4‐ethynylbenzoate) units within a MOF facilitates concurrent structural and spectroscopic studies in the absence of intermolecular perturbation, allowing characterisation of the luminescence properties of a high‐energy, twisted conformation of the previously well‐studied chromophore. We expect the unique environment provided by network solids, and the capability of combining crystallographic and spectroscopic analysis, will greatly enhance understanding of luminescent molecules and lead to the development of novel sensors and adsorbents.
Pressure‐induced bathochromic shifts in both fluorescence emission and UV/Vis absorption spectra of a two‐fold interpenetrated Hf MOF are induced by rotation of the central phenyl ring of the linker. Single‐crystal X‐ray diffraction was measured up to 2.1 GPa, thus correlating linker rotation with modulation of emission.
Photophysical studies of chromophoric linkers in metal–organic frameworks (MOFs) are undertaken commonly in the context of sensing applications, in search of readily observable changes of optical ...properties in response to external stimuli. The advantages of the MOF construct as a platform for investigating fundamental photophysical behaviour have been somewhat overlooked. The linker framework offers a unique environment in which the chromophore is geometrically constrained and its structure can be determined crystallographically, but it exists in spatial isolation, unperturbed by inter‐chromophore interactions. Furthermore, high‐pressure studies enable the photophysical consequences of controlled, incremental changes in local environment or conformation to be observed and correlated with structural data. This approach is demonstrated in the present study of the trans‐azobenzene chromophore, constrained in the form of the 4,4’‐azobenzenedicarboxylate (abdc) linker, in a UiO topology framework. Previously unobserved effects of pressure‐induced solvation and conformational distortion on the lowest energy, nπ* transition are reported, and interpreted the light of crystallographic data. It was found that trans‐azobenzene remains non‐fluorescent (with a quantum yield less than 10−4) despite the prevention of trans‐cis isomerization by the constraining MOF structure. We propose that efficient non‐radiative decay is mediated by the local, pedal‐like twisting of the azo group that is evident as dynamic disorder in the crystal structure.
Putting the pressure on azobenzene photophysics: When locked in a UiO metal–organic framework, the azobenzene chromophore is geometrically constrained but exists in spatial isolation, unperturbed by inter‐chromophore interactions. This is a unique and advantageous environment in which to explore fundamental photophysical properties. Optical spectroscopy in a diamond anvil cell enables the photophysical consequences of pressure‐induced changes in solvation and conformation of the chromophore to be observed and correlated with crystallographic data.
We have prepared complexes of formula Eu(beta-diketonate)(3)(DPEPO) and shown quantitative excited-state energy transfer from the ligands combined with efficient Ln luminescence leading to ...exceptionally-high total photoluminescence quantum yield of up to 80% in solution and in PMMA.
The first molecular capsule based on an Ir(ppy)2+ unit (ppy = 2-phenylatopyridine) has been prepared. Following the development of a method to resolve rac-(Ir(ppy)2Cl)2 into its enantiopure forms, ...homochiral Ir6L4 octahedra where obtained with the tritopic 1,3,5-tricyanobenzene. Solution studies and X-ray diffraction show that these capsules encapsulate four of the six associated counteranions and that these can be exchanged for other anionic guests. Initial photophysical studies have shown that an ensemble of weakly coordinating ligands can lead to luminescence not present in comparable mononuclear systems.
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