Protochlorophyllide forms in non-greening epicotyls of dark-grown pea (Pisum sativum)

Low-temperature fluorescence emission spectra of 6.5-day-old dark-grown epicotyls of pea ( Pisum sativum ) revealed the presence of protochlorophyll(ide). The upper part of the epicotyl contained 30% of the protochlorophyll(ide) content per fresh weight found in pea leaves, whereas the lower part contained 3%. Three discrete spectral forms of protochlorophyll(ide) were clearly distinguished after Gaussian deconvolution of fluorescence excitation and emission spectra. Adding the satellite bands of the Qy_(0-0) transitions (the emission vibrational (Emv) bands with correlated amplitudes, gave the following delineation: Ex439–Em629–Emv684, Ex447–Em636–Emv700 and Ex456–Em650–Emv728. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) followed by immunodetection of whole tissue extracts of the epicotyl indicated the presence of NADPH-protochlorophyllide oxidoreductase (EC 1.3.1.33). Electron micrographs showed prolamellar bodies in at most 11 % of the plastid profiles of the epicotyl cells. These prolamellar bodies were smaller, and many of them showed less regular structure than those of the leaves. Taken together, the results indicate that the protochlorophyll(ide) in epicotyls is arranged in a different way than in leaves.     

Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity.

Amino acid sequences of enzymes that catalyze hydrolysis or phosphorolysis of the N-glycosidic bond in nucleosides and nucleotides (nucleosidases and phosphoribosyltransferases) were explored using computer methods for database similarity search and multiple alignment. Two new families, each including bacterial and eukaryotic enzymes, were identified. Family I consists of Escherichia coli AMP hydrolase (Amn), uridine phosphorylase (Udp), purine phosphorylase (DeoD), uncharacterized proteins from E. coli and Bacteroides uniformis, and, unexpectedly, a group of plant stress-inducible proteins. It is hypothesized that these plant proteins have evolved from nucleosidases and may possess nucleosidase activity. The proteins in this new family contain 3 conserved motifs, one of which was found also in eukaryotic purine nucleosidases, where it corresponds to the nucleoside-binding site. Family II is comprised of bacterial and eukaryotic thymidine phosphorylases and anthranilate phosphoribosyltransferases, the relationship between which has not been suspected previously. Based on the known tertiary structure of E. coli thymidine phosphorylase, structural interpretation was given to the sequence conservation in this family. The highest conservation is observed in the N-terminal alpha-helical domain, whose exact function is not known. Parts of the conserved active site of thymidine phosphorylases and anthranilate phosphoribosyltransferases were delineated. A motif in the putative phosphate-binding site is conserved in family II and in other phosphoribosyltransferases. Our analysis suggests that certain enzymes of very similar specificity, e.g., uridine and thymidine phosphorylases, could have evolved independently. In contrast, enzymes catalyzing such different reactions as AMP hydrolysis and uridine phosphorolysis or thymidine phosphorolysis and phosphoribosyl anthranilate synthesis are likely to have evolved from common ancestors.     

The diversity and evolution of recruitment behaviour in ants,with a discussion of the usefulness of parsimony criteria in the reconstruction of evolutionary histories

Summary Three alternative hypotheses about the evolution of recruitment behaviour in ants, based on accounts in the literature, are compared by means of a cladistic analysis. The three hypotheses are the following:Hypothesis 1. Increasingly efficient recruitment behaviours exhibited by different ant species have been shaped by or are correlated with ant phylogeny.Hypothesis 2. Increasingly efficient recruitment behaviours represent necessary evolutionary steps independently followed during the evolution of different ant clades.Hypothesis 3. Differently efficient recruitment behaviours have been selected in a convergent way among different species by similar population/environmental constraints.In a first stage of the analysis, these hypotheses have been compared in terms of parsimony (i.e. in terms of tree length = TL) of alternative cladograms based on recruitment behaviour only. The analysis gave the following results: Hypothesis 1, TL = 4; Hypothesis 2, TL = 18; Hypothesis 3, TL = 11. At least in terms of parsimony, hence, Hypothesis 1 appears to be the best. This hypothesis, however, cannot be retained for its total lack of congruence with current views on ant phylogeny. Among the remaining two hypotheses, Hypothesis 3 is again much (ca. 40%) more parsimonious than Hypothesis 2, but the retention index for recruitment behaviour on the relative cladogram is 0.2 as compared with 0.7 for Hypothesis 2. Practically, this implies biologically very implausible behavioural evolution indicated by very improbable ancestors for the species included in the analysis. In the case of recruitment evolution the biological credibility of each hypothesis is inversely proportional to its parsimony.The three hypotheses on the evolution of recruitment behaviour are compared again taking into account the morphological and behavioural correlates of recruitment. The results confirm those obtained by simple cladistic analysis of behaviour alone, namely that an obligatory (i. e. neither reversible nor random) increase in recruitment efficiency has been repeatedly selected within different ant clades. Inclusion of the recruitment correlates allows, in addition, a more precise formulation of the implications of each hypothesis and a tentative test of two other alternatives deduced from the literature. Most papers dealing with recruitment assume this behaviour to be controlled by a single gland, while at least two experimental analyses show that more than one gland is likely to be involved as behavioural releaser. A cladistic approach allowed testing of the following two adaptational hypotheses: A) Synergic behavioural control by several glands, allowing shift of the dominant role from one gland to another. B) Single gland control, making improbable the replacement of one gland by another that performs the same function. The results of the analysis appear to favour alternative A slightly, though neither alternative results in implausible evolutionary paths.It is stressed that parsimony remains the sole decisional criterion when no other criteria are available but it can by no way be preferred to the slightest trace of biological common sense.     

The effect of temperature,light-spectrum,desiccation and salinity gradients on the photosynthetic performance of a subtidal brown alga,Sargassum macrocarpum,from Japan

The effect of temperature, light-spectrum, desiccation and salinity gradients on the photosynthesis of a Japanese subtidal brown alga, Sargassum macrocarpum (Fucales), was determined using a pulse amplitude modulation-chlorophyll fluorometer and dissolved oxygen sensors. Temperature responses of the maximum (F_v/F_m in darkness) and effective (ΔF/F_m′ at 50 μmol photons m⁻² s⁻¹; = Φ_PSII) quantum yields during 6-day culture (4–36°C) remained high at 12–28°C, but decreased at higher temperatures. Nevertheless, ΔF/F_m′ also dropped at temperatures below 8°C, suggesting light sensitivity under chilling temperatures because F_v/F_m remained high. Photosynthesis–irradiance responses at 24°C under red (660 nm), green (525 nm), blue (450 nm) and white light (metal halide lamp) showed that maximum net photosynthesis under blue and white light was greater than under red and green light, indicating the sensitivity and photosynthetic availability of blue light in the subtidal light environment. In the desiccation experiment, samples under aerial exposure of up to 8 h under dim-light at 24°C and 50% humidity showed that ΔF/F_m′ quickly declined after more than 45 min of emersion; furthermore, ΔF/F_m′ also failed to recover to initial levels even after 1 day of rehydration in seawater. Under the emersion state, the ΔF/F_m′ remained high when the relative water content (RWC) was greater than 50%; in contrast, it quickly dropped when the RWC was less than 50%. When the RWC was reduced below 50%, ΔF/F_m′ did not return to initial levels, regardless of subsequent re-hydration, suggesting a low capacity of photosynthesis to recover from desiccation. The stenohaline response of photosynthesis under 3-day culture is evident, given that ΔF/F_m′ declined when salinity was beyond 20–40 psu. Adaptation to subtidal environments in temperate waters of Japan can be linked to these traits.     

Low species turnover of upland Amazonian birds in the absence of physical barriers

Aim

One of the oldest and most powerful ways for ecologists to explain distinct biological communities is to invoke underlying environmental differences. But in hyper-diverse systems, which often display high species richness and low species abundance, these sorts of community comparisons are especially challenging. The classic view for Amazonian birds posits that riverine barriers and habitat specialization determine local and regional community composition. We test the tacit, complementary assumption that similar bird communities should therefore permeate uniform habitat between major rivers, regardless of distance.

Location

Upland (terra firme) rainforests of central Amazonia.

Methods

We conducted intensive whole-community surveys of birds in three pairs of 100-ha plots, separated by 40–60 km. We then used dissimilarity indices, cluster analysis, and ordination to characterize differences among the six avian communities.

Results

In all, we detected 244 forest-dependent birds, with an average of 190 species (78%) per plot. Species turnover was negligible, no unique indicator species were found among plot pairs, and all documented species were already known from a complete inventory at one of the three sites.

Main Conclusions

Our study corroborates the classic biogeographical pattern and suggests that turnover contributes little to regional avian diversity within upland forests. Using a grain size of 100 ha, this implies that upland birds perceive the environment as uniform, at least over distances of ~60 km. Therefore, to maximize both local species richness and population persistence, our findings support the conservation of very large tracts of upland rainforest. Our analyses also revealed that the avifauna at Reserva Ducke, encroached by urban sprawl from the city of Manaus, shows the hallmarks of a disturbed community, with fewer vulnerable insectivores. This defaunation signals that even an enormous preserve (10 × 10 km) in lowland Amazonia is not insulated from anthropogenic degradation within the surrounding landscape.     

Fire affects wood formation dynamics and ecophysiology of Pinus pinaster Aiton growing in a dry Mediterranean area

The increase in frequency and intensity of wildfires is seriously affecting forest ecosystems, especially in drought-prone areas. Trees’ recovery after fire is related to direct tree damage and is influenced by climate conditions, such as warm temperature and water shortage. In this study, we evaluate the post-fire effects on a Pinus pinaster Aiton forest growing in a hot and dry area of the Mediterranean region by comparing burned trees with severe crown reduction against unburned and not-defoliated trees. Inter-annual analyses of dendrochronology and stable isotopes in tree rings were combined with xylogenesis monitoring to investigate the effects of fire on tree growth, ecophysiological processes and wood formation. Tree-ring and isotope data showed a growth reduction and a decrease in photosynthetic activity in the burned trees, compared to control individuals, in the three years after fire. Further, the monitoring of cambial activity demonstrated a negative influence of warm and dry periods on wood formation, low xylem production, a delay in phenology and a reduction in xylem plasticity in burned trees. Our findings suggest that substantial photosynthetic limitations caused by crown defoliation and recurrent drought events could lead to severe growth decrease and reduction of trees ability to regain the pre-disturbance productivity rates.     

Nanodiamond-promoted white light emission in Eu,Dy, and Cu-containing phosphate glass: quantitative analysis and colorimetric study

A thorough analysis of glass containing Eu₂O₃ and Dy₂O₃, or Eu₂O₃, Dy₂O₃, and CuO melted together with nanodiamond powder was pursued based on measurements of optical absorption, photoluminescence (PL) emission and excitation spectra, and colorimetry. Nanodiamond facilitated the stabilization of Cu⁺ and Eu²⁺ ions with blue-emitting characteristics that, along with yellow-emitting Dy³⁺ and red-emitting Eu³⁺ led to the white light-emitting glass. Novel intensity notations implemented in intensity-based spectral ratios, and difference intensity correlation analysis were proposed for the assessment of PL properties. The chromaticity and correlated colour temperature of the emission were ultimately investigated as a two-parametric problem based on: (1) the different ionic components; and (2) the various excitation wavelengths employed. The optical analysis approach adds to the characterization methods to further fundamental understanding and provide helpful analytical tools for designing materials for tunable white light-emitting devices.     

Hatching plasticity in a Southeast Asian tree frog mitigates submergence-induced mortality

Environmentally cued hatching has been well-documented in amphibians in response to a wide range of abiotic and biotic factors. The hatching of terrestrial amphibian eggs in response to flooding may be basal within the group, but amphibian lineages in tropical Asia and sub-Saharan Africa have not received as much attention as their Neotropical counterparts. We investigated submergence-induced hatching in Feihyla hansenae, a Rhacophorid tree frog with terrestrial eggs. We quantified natural rates of clutch submergence at our study site in Thailand. Using submergence experiments, we found that embryos are capable of hatching early to escape flooding, and that failure to hatch results in mortality. Among the embryos that were able to hatch early, only the earliest, youngest hatchlings experienced a trade-off in body size that persisted for 6 days, while later, older hatchlings were not significantly smaller than spontaneous hatchlings under control conditions. By incorporating our natural and experimental data into Monte Carlo methods to simulate and compare survival probabilities with and without hatching plasticity, we found an overall 3.1% increase in submergence survival due to hatching plasticity. Our findings support the idea that flooding-induced hatching is widespread across amphibians with terrestrial eggs and highlight the importance of researching understudied tropical regions. As climate change is projected to affect rainfall patterns, the ability of embryos to escape abiotic egg-stage threats may be an indicator of species' ability to flexibly navigate a changing environment.     

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

Accurate retention time (RT) prediction is important for spectral library-based analysis in data-independent acquisition mass spectrometry-based proteomics. The deep learning approach has demonstrated superior performance over traditional machine learning methods for this purpose. The transformer architecture is a recent development in deep learning that delivers state-of-the-art performance in many fields such as natural language processing, computer vision, and biology. We assess the performance of the transformer architecture for RT prediction using datasets from five deep learning models Prosit, DeepDIA, AutoRT, DeepPhospho, and AlphaPeptDeep. The experimental results on holdout datasets and independent datasets exhibit state-of-the-art performance of the transformer architecture. The software and evaluation datasets are publicly available for future development in the field.