Quantum transitions between states and cosmophysical fluctuations

An explanation of the appearance of the reproducible fine structure of the histograms corresponding to different processes from simple chemical reactions to radioactive decays is developed. Earlier this explanation was reduced to extremely strong influence of small changes between energy levels of a quantum system under study and its environment on the transition probability of the system (chemical reaction, radioactive decay, e.t.c.) from the system last quantum state to final result of the studied process. In the present paper it is supposed that the main factors determining this probability is the periodical or quasi-periodical low frequency changes of local gravitational field leading to corresponding changes of the system mass (the quantum transition probability depends exponentially on the latter). This approach seems to able to propose non-contradictory explanation of many manifestations of macroscopic fluctuation.     

On the periodicity in the fine structure of histograms during nuclear decay

A possible explanation for the occurrence of periodicity in the fine structure of histograms during nuclear decay is proposed. The hypothesis states that, even in the absence of polarization, when the spin distribution of decaying nuclei over directions is, on the average, isotropic, the fine structure of histograms should depend, due to fluctuations, on the angles at which the sample is observed. There fore, when the Earth after some period would make a full furn, the distribution of fluctuations would return to the initial one, and, correspondingly, the fine structure of the histograms would repeat.     

Periodicity in the fine structure of histograms during nuclear decay

A theoretical explanation is offered for the appearance of periodicity in the fine structure of histograms describing the processes of nuclear decay. This effect is observed in a sample containing nonpolarized radioactive nuclei, with largely isotropic spin distribution over directions. However, because of fluctuations occurring in any real sample, the number of nuclei having spin directed along some isolated axis would differ somewhat from the number of nuclei with spin directed along another axis. The same is immobile relating to the Earth but rotates in space together with it. At the same time, the nuclear spins, owing to quite weak interaction with the environment, keep their directions in space. Therefore, the spin ensemble rotates both relative to the sample itself and relative to the detector of α-particles directed onto the sample. Since fluctuations in the number of nuclei with spins directed at a certain angle relative to the detector direction affect the fine structure of histograms, the latter proves to depend, among other things, of the rotation of the Earth. Consequently, when the Earth makes a full revolution and the distribution of fluctuations in the number of nuclei with given spin direction returns to the initial one, the shape of the fine structure of histograms will be repeated, and repeated over the same definite time intervals.     

细根分解研究及其存在的问题

细根分解是陆地生态系统C和养分循环的重要环节。主要包括淋溶和破碎等物理过程和以生物作用为主的化学过程。这些过程受复杂的细根化学成分及外部土壤因子的综合控制,如细根本身养分含量、木质素和纤维素含量、土壤温度、水分、养分的有效性以及土壤动物、真菌和细菌等。但是,细根分解发生在不能直接观测的地下部分,人为改变细根分解的自然环境是研究过程中存在的主要问题。埋袋法虽然应用最为普遍,但是它严重地干扰了细根分解环境,导致低估分解速率。最近提出的原状土芯法(intact-core)克服了埋袋法的主要缺陷,是目前细根分解研究中最接近自然分解过程的研究方法,但也存在一些问题。因此,如何设计有效且能够真实的反映细根自然分解过程的试验方法是今后该领域研究最重要和最具挑战性的课题。     

Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots

Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (?31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin‐derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin‐derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin‐derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.     

Leaf litterfall, fine-root production, and decomposition in shrublands with different canopy structure induced by grazing in the Patagonian Monte, Argentina

Selective sheep grazing in the Patagonian Monte induces the reduction of total and perennial grass cover, species replacement within life forms, and the increase in dominance of long-lived evergreen woody plants with slow growth rates and high concentration of secondary compounds in leaves. We hypothesized that these changes in the canopy structure induced by sheep grazing will affect the mass, chemistry and decomposability of leaf litter and fine roots. We selected two sites in the Patagonian Monte, representative of ungrazed and grazed vegetation states. At each site, we assessed canopy structure (total cover and absolute and relative grass and shrub cover), monthly leaf litterfall, and fine-root biomass and production in the upper soil (15 cm). We also estimated the rates of mass, C, soluble phenolics, lignin and N decay in litterbags containing both leaf litter and fine roots of each site under field conditions during two consecutive years. The ungrazed site exhibited higher total plant cover, absolute and relative grass- and shrub-cover than the grazed one. Leaf litterfall was lower at the grazed site than at the ungrazed site. Fine-root production did not vary between sites. Leaf litter and fine root tissues had higher concentration of secondary compounds at the grazed than at the ungrazed site. However, fine roots showed lower mass and C decay than leaf litter, attributable to the predominant secondary compound (lignin and soluble phenolics, respectively). Leaf litter decomposed slower but released more N during decay at the ungrazed than at the grazed site, probably due to its low concentration of secondary compounds. We concluded that changes in canopy structure induced by grazing disturbance such as those explored in our study could reduce leaf litterfall mass and increase the concentration of secondary compounds of both leaf litter and fine roots leading to slow N release to soil during decay.     

Low-temperature photoreactions of halorhodopsin. 1. Detection of conformational substates of the chromoprotein

Absorption spectra of halorhodopsin (HR), a retinal protein in the halobacterial membrane, and its photostationary states were determined at 80 K. The absorption lines appear to narrow upon cooling, thereby revealing complex spectral fine structure of the main absorption band in the visible region, characteristic of conformational substates of HR. Illumination causes (1) the redistribution of these substrates and consequent changing of the fine structure ("hole-burning") and (2) the appearance of a hypsoproduct of undefined nature, in addition to the previously described bathoproduct HR600. Bacteriorhodopsin, a related retinal pigment, gives rise only to the bathointermediate (i.e., K590) under these conditions. After warming of illuminated HR to 110 K, and recooling to 80 K, relaxation of the illumination-induced change in spectral fine structure, and decay of the hypsoproduct but not the bathoproduct, was observed. The results are explained with a model in which one ensemble of HR conformational substates at 80 K is converted to another in a photoequilibrium via the excited state, which also produces the batho- and hypsoproducts. The original ensemble can be regained through thermal pathways at a somewhat higher temperature, and only the bathoproduct will decay thermally into the next intermediate of the HR photocycle.     

Distance decay in an old‐growth neotropical forest

Abstract. Questions: Does distance decay exist in an old‐growth neotropical forest? Is this distance decay stronger than expected due to environmental heterogeneity alone? At what spatial scales are distance decay manifested? Location: La Selva Biological Station, Costa Rica, Central America. Methods: An index of distance decay is applied appropriate for small quadrats (the probability of encountering a conspecific tree) to a grid of 1170 0.01‐ha plots. A null model is provided that accounts for environmental heterogeneity. Results: Significant, but weak, distance decay is found. After correcting for known patterns of environmental heterogeneity, the distance decay almost disappears, except for fine spatial scales. Conclusions: These results are inconsistent with models that predict distance decay at all spatial scales. However, biological processes leading to distance decay may be more relevant and detectable at scales broader than this study. Research utilizing objectively‐located samples over much broader scales is necessary to evaluate the generality and magnitude of distance decay.     

The fine structure of an absorptive epithelium in a viviparous teleost

Embryos of the viviparous teleost, “Characodon” eiseni, have unusual anal processes that function only during gestation and are lost shortly after birth. This study was undertaken to determine if the fine structure of the process epithelium supports the assumption that these cells have an absorptive function. The process epithelium is a single layer of columnar cells. At peak activity intercellular spaces become very large and isolate individual cells which simultaneously lose much of their cell mass. The cells are characterized by microvilli on their free surface, much pinocytic activity and by the formation of at least four different kinds of vesicles. There is much evidence that these vesicles fuse together. A distinctive characteristic of these cells is a system of tubules and flattened cisternae that somewhat resemble the endoplasmic reticulum yet they differ from it in several respects. It is suggested these profiles aid in fragmenting the cell at periods of peak absorptive activity, thereby increasing the cell surface. Possible mechanisms of food absorption are considered. The fine structure of these cells supports the contention that these embryonic processes serve as absorptive organs during gestation.     

Exciton dynamics in the chlorosomal antennae of the green bacteria Chloroflexus aurantiacus and Chlorobium tepidum

The energy transfer processes in isolated chlorosomes from green bacteria Chlorobium tepidum and Chloroflexus aurantiacus have been studied at low temperatures (1.27 K) by two-pulse photon echo and one-color transient absorption techniques with approximately 100 fs resolution. The decay of the coherence in both types of chlorosomes is characterized by four different dephasing times stretching from approximately 100 fs up to 300 ps. The fastest component reflects dephasing that is due to interaction of bacteriochlorophylls with the phonon bath, whereas the other components correspond to dephasing due to different energy transfer processes such as distribution of excitation along the rod-like aggregates, energy exchange between different rods in the chlorosome, and energy transfer to the base plate. As a basis for the interpretation of the excitation dephasing and energy transfer pathways, a superlattice-like structural model is proposed based on recent experimental data and computer modeling of the Bchl c aggregates (1994. Photosynth. Res. 41:225-233.) This model predicts a fine structure of the Q(y) absorption band that is fully supported by the present photon echo data.     

Distance decay of community dynamics in rocky intertidal sessile assemblages evaluated by transition matrix models

It is well known that the similarity in species composition between two communities decays with the geographic distance that separates them. It is thus likely that the similarity in the dynamics of two communities also decays with distance, because the distance–decay relationship is fundamental in nature. However, the distance–decay relationships of community dynamics have not yet been revealed. We used transition matrix models to evaluate distance–decay relationships of seasonal community dynamics (from spring to summer) in rocky intertidal sessile assemblages along the Pacific coast of Japan between 31°N and 43°N. We evaluated the distance–decay relationships of whole-community dynamics and of three dynamics-related components—recruitment, disturbance, and species interaction (competition and facilitation)—for communities separated by distances ranging from several meters to thousands of kilometers. The similarity of the recruitment dynamics among communities declined rapidly with distance within the fine spatial scale, but only moderately within larger scales. The similarity of the disturbance dynamics was independent of distance, and the similarity of species interaction declined slightly with increasing distance. The similarity of whole-community dynamics declined rapidly with distance at a fine spatial scale and moderately at larger scales. The fact that the distance–decay relationship of whole-community dynamics was similar to that of recruitment may suggest that recruitment processes are the most important determinant of spatial variability of community dynamics at our study sites during the study period.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

Relative influence of deterministic processes on structuring marsh plant communities varies across an abiotic gradient

Understanding the processes determining community structure is one of the major goals of ecological research. Both deterministic and stochastic processes may shape community structure. The challenge is to understand the relative influence of each type of process across different environmental conditions. We investigated the influence of deterministic and stochastic processes on plant community assembly in tidal marshes across a strong abiotic (salinity) gradient in three estuaries in Georgia, USA using probabilistic Raup–Crick community dissimilarity. Our results indicated that deterministic processes had an increasingly important influence on structuring plant communities in salt and brackish marshes, probably due to high heterogeneity of microhabitats produced by the interplay between abiotic stress and biotic interactions. In contrast, the influence of deterministic processes on plant community assembly decreased in tidal freshwater marshes, suggesting an increasingly important role of stochastic processes in plant community assembly in tidal freshwater marshes, probably due to the higher species richness, higher recruitment from seed, and lower levels of abiotic stress in these habitats. At the estuarine scale (across tidal freshwater, brackish and salt marshes in each estuary), our results suggested that deterministic processes also had a relatively important influence on shaping plant community structure. Our results illustrated that plant community structure in tidal marshes is influenced by both deterministic and stochastic processes, but that the relative influence of these two types of processes varies across estuarine landscapes.     

Rapid degradation of AU-rich element (ARE) mRNAs is activated by ribosome transit and blocked by secondary structure at any position 5' to the ARE.

The 3' noncoding region (NCR) AU-rich element (ARE) selectively confers rapid degradation on many mRNAs via a process requiring translation of the message. The role of cotranslation in destabilization of ARE mRNAs was examined by insertion of translation-blocking stable secondary structure at different sites in test mRNAs containing either the granulocyte-macrophage colony-stimulating factor (GM-CSF) ARE or a control sequence. A strong (-80 kcal/mol [1 kcal = 4.184 kJ]) but not a moderate (-30 kcal/mol) secondary structure prevented destabilization of mRNAs when inserted at any position upstream of the ARE, including in the 3' NCR. Surprisingly, a strong secondary structure did not block rapid mRNA decay when placed immediately downstream of the ARE. Studies are also presented showing that the turnover of mRNAs containing control or ARE sequences is not altered by insertion of long (1,000-nucleotide) intervening segments between the stop codon and the ARE or between the ARE and poly(A) tail. Characterization of ARE-containing mRNAs in polyadenylated and whole cytoplasmic RNA fractions failed to find evidence for decay intermediates degraded to the site of strong secondary structure from either the 5' or 3' end. From these and other data presented, this study demonstrates that complete translation of the coding region is essential for activation of rapid mRNA decay controlled by the GM-CSF ARE and that the structure of the 3' NCR can strongly influence activation. The results are consistent with activation of ARE-mediated decay by possible entry of translation-linked decay factors into the 3' NCR or translation-coupled changes in 3' NCR ribonucleoprotein structure or composition.     

Characterization of tryptophan phosphorescence of aspartate aminotransferase from Escherichia coli.

The Trp phosphorescence spectrum, intensity and decay kinetics of apo-aspartate aminotransferase, pyridoxamine-5P-aspartate-aminotransferase and pyridoxal-5P-aspartate aminotransferase were measured over a temperature range 160-273 K. The fine structure of the phosphorescence spectra in low-temperature glasses, with 0-0 vibrational bands centered at 408, 415 and 417 nm, for both apoenzyme and pyridoxamine-5P-enzyme reveals a marked heterogeneity of the chromophore environments. Only for the pyridoxal-5P form of the enzyme is the triplet emission strongly quenched and, in this case, the spectrum displays a unique 0-0 vibrational band centered at 415 nm. Concomitant to quenching, there is Trp-sensitized delayed fluorescence of the Schiff base, an indication that quenching of the excited triplet state is due, at least in part, to a process of triplet singlet energy transfer to the ketoenamine tautomer. All three forms of the enzyme are phosphorescent for temperatures up to 273 K. However, across the glass transition temperature the pyridoxal-5P enzyme shows a decrease in lifetime-normalized phosphorescence intensity, a thermal quenching that reduces even further the number of phosphorescing residues at ambient temperature. In fluid solution, the triplet decay is nonexponential and multiple lifetimes stress the heterogeneity in dynamical structure of the chromophores' sites. For the pyridoxal-5P enzyme, where only one or at most two residues are phosphorescent at 273 K, the nonexponential nature of the decay implies the presence of different conformers of the protein not interconverting in the millisecond time scale.     

The impact of mating systems and dispersal on fine‐scale genetic structure at maternally,paternally and biparentally inherited markers

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens—hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual‐level simulations to investigate the effects of dispersal and mating system on fine‐scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine‐scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex‐biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine‐scale genetic structure.     

Characterization of alkaline phosphatase inactivation by ascorbic acid

Ascorbic acid, isoascorbic acid and dehydroascorbic acid inhibit bovine kidney alkaline phosphatase activity. Ascorbic acid free radicals seem not to be involved. Dialysis does not make the inactivation reversible. A competitive mechanism can be inferred from experiments with phosphate and substrates, which block the activity decay. The influence of temperature, pH, other inhibitors and tertiary structure modifications on the inactivation process is also investigated.     

Photophysics of pyrene-labelled compounds of biophysical interest.

The effects of the chemical constitution and structure of the substituent on the excited state dynamics of several model fluorescent pyrene-labelled molecules of biophysical interest have been examined. Nine new 1-substituted pyrenyl compounds, Py-NH-CO-C2H5, Py-NH-CO-Leu-Boc, Py-CH2-NH-CO-C2H5, Py-CH2-NH-CO-Leu-Boc, Py-CO-NH-C3H7, Py-CO-NH-Leu-OMe, Py-CH2-CO-NH-C3H7, Py-CH2-CO-NH-Leu-OMe and Py-C3H6-CO-NH-Leu-OMe, have been synthesized and their electronic spectra, fluorescence quantum yields and excited state lifetimes measured. These data have been used to calculate the radiative, kr, and non-radiative decay constants of their S1 states and the values of these constants correlated with the structures of the tethers. Non-radiative S1 decay rates (mainly intersystem crossing to T1) vary in parallel with the radiative rates so that the excited state lifetimes and radiative rate constants change considerably with the structure of the substituent whereas the quantum yields of fluorescence do not. An excellent correlation between [epsilon]max of the S1-S0 transition and either kr or the excited state lifetime is observed as long as no additional intermolecular or intramolecular excited state decay process of significant rate competes with the 'normal' radiative and non-radiative (ISC) decay processes of the pyrenyl chromophore. This correlation may have predictive value. Rates of bimolecular quenching of the S1 states of these molecules by molecular oxygen have been measured. The quenching process is diffusion-controlled with a spin statistical factor of 1, indicating that the S1-T1 electronic energy spacings of all the derivatives exceed the O2(1Deltag-3Sigmag-) electronic excitation energy of ca. 1 eV.     

Fine root decay rates vary widely among lowland tropical tree species

Prolific fine root growth coupled with small accumulations of dead fine roots indicate rapid rates of fine root production, mortality and decay in young tree plantations in lowland Costa Rica. However, published studies indicate that fine roots decay relatively slowly in tropical forests. To resolve this discrepancy, we used the intact-core technique to quantify first-year decay rates of fine roots in four single-species plantations of native tree species. We tested three hypotheses: first, that fine roots from different tree species would decay at different rates; second, that species having rapid fine root growth rates would also have rapid rates of fine root decay; and third, that differences in fine root decay among species could be explained by fine root chemistry variables previously identified as influencing decay rates. Fine roots in Virola koschnyi plantations decayed very slowly (k = 0.29 ± 0.15 year⁻¹); those of Vochysia guatemalensis decayed seven times faster (k = 2.00 ± 0.13 year⁻¹). Decay rates of the remaining two species, Hieronyma alchorneoides and Pentaclethra macroloba, were 1.36 and 1.28 year⁻¹, respectively. We found a positive, marginally significant correlation between fine root decay rates and the relative growth rates of live fine roots (R = 0.93, n = 4, P = 0.072). There was a highly significant negative correlation between fine root decay and fine root lignin:N (R = 0.99, P = 0.01), which supports the use of lignin:N as a decay-controlling factor within terrestrial ecosystem models. The decay rates that we observed in this single study location encompassed the entire range of fine root decay rates previously observed in moist tropical forests, and thus suggest great potential for individual tree species to alter belowground organic matter and nutrient dynamics within a biotically rich rainforest environment. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.