Can a plant physiologist be considered a naturalist?

Abstract not availabl

Heat tolerance in a wild Oryza species is attributed to maintenance of Rubisco activation by a thermally stable Rubisco activase ortholog

• The response of photosynthesis and plant growth to short periods of supra-optimal heat was tested in rice (Oryza sativa) and two wild Oryza species from the Australian savanna, O. meridionalis and O. australiensis. The mechanism of heat tolerance in the wild species was explored, particularly focusing on the heat-labile protein Rubisco activase (RCA). • We compared leaf elongation rates, net photosynthesis and Rubisco activation state at moderate (28°C) and high temperature (45°C). Sequence analysis followed by enzyme kinetics of RCA was used to identify structural differences and thermal stability. • Oryza australiensis was the most heat-tolerant species. Rubisco activation state was positively correlated with leaf elongation rates across all three species at four times following exposure to 45°C. Oryza australiensis had multiple polymorphisms in the RCA primary protein sequence, and the protein was thermally stable up to 42°C relative to RCA from O. sativa which became inhibited at 36°C. • We attribute the heat tolerance of growth and photosynthesis in these wild species to thermal stability of RCA, enabling Rubisco to remain active. Because thermal stability of RCA in O. australiensis co-occurs with reduced enzyme specific activity, an increased RCA to Rubisco ratio is required in vivo to maintain high Rubisco activation

Mesophyll diffusion conductance to CO 2: An unappreciated central player in photosynthesis

Mesophyll diffusion conductance to CO 2 is a key photosynthetic trait that has been studied intensively in the past years. The intention of the present review is to update knowledge of g m, and highlight the important unknown and controversial aspects that require future work. The photosynthetic limitation imposed by mesophyll conductance is large, and under certain conditions can be the most significant photosynthetic limitation. New evidence shows that anatomical traits, such as cell wall thickness and chloroplast distribution are amongst the stronger determinants of mesophyll conductance, although rapid variations in response to environmental changes might be regulated by other factors such as aquaporin conductance.Gaps in knowledge that should be research priorities for the near future include: how different is mesophyll conductance among phylogenetically distant groups and how has it evolved? Can mesophyll conductance be uncoupled from regulation of the water path? What are the main drivers of mesophyll conductance? The need for mechanistic and phenomenological models of mesophyll conductance and its incorporation in process-based photosynthesis models is also highlighted.The study was financially supported by the Estonian Ministry of Science and Education (grant SF1090065s07), the Spanish Ministry of Science and Innovation through projects BFU2008-01072 (MEFORE), AGL2009-11310/AGR, BFU2011-23294 (MECOME) and CGL2009-13079-C02-01 (PALEOISOTREE), and the European Commission through European Regional Fund (the Estonian Center of Excellence in Environmental Adaptation), and the Marie Curie project MC-ERG-246725 (FP7). J.P.F. is supported by the Ramón y Cajal program (RYC-2008-02050). A.G. had a Swiss National Science Fellowship (PA00P3_126259). M.M.B. and C.R.W are supported by Future Fellowships from the Australian Research Council (FT0992063 and FT100100024). C.D. was supported by a grant from the French government and by the cooperation project Tranzfor (Transferring Research between EU and Australia–New Zealand on Forestry and Climate Change, PIRSES-GA-2008-230793) funded by the European Union

Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers

BACKGROUND: To unravel molecular targets involved in glycopeptide resistance, three isogenic strains of Staphylococcus aureus with different susceptibility levels to vancomycin or teicoplanin were subjected to whole-genome microarray-based transcription and quantitative proteomic profiling. Quantitative proteomics performed on membrane extracts showed exquisite inter-experimental reproducibility permitting the identification and relative quantification of >30% of the predicted S. aureus proteome. RESULTS: In the absence of antibiotic selection pressure, comparison of stable resistant and susceptible strains revealed 94 differentially expressed genes and 178 proteins. As expected, only partial correlation was obtained between transcriptomic and proteomic results during stationary-phase. Application of massively parallel methods identified one third of the complete proteome, a majority of which was only predicted based on genome sequencing, but never identified to date. Several over-expressed genes represent previously reported targets, while series of genes and proteins possibly involved in the glycopeptide resistance mechanism were discovered here, including regulators, global regulator attenuator, hyper-mutability factor or hypothetical proteins. Gene expression of these markers was confirmed in a collection of genetically unrelated strains showing altered susceptibility to glycopeptides. CONCLUSION: Our proteome and transcriptome analyses have been performed during stationary-phase of growth on isogenic strains showing susceptibility or intermediate level of resistance against glycopeptides. Altered susceptibility had emerged spontaneously after infection with a sensitive parental strain, thus not selected in vitro. This combined analysis allows the identification of hundreds of proteins considered, so far as hypothetical protein. In addition, this study provides not only a global picture of transcription and expression adaptations during a complex antibiotic resistance mechanism but also unravels potential drug targets or markers that are constitutively expressed by resistant strains regardless of their genetic background, amenable to be used as diagnostic targets

BLOOM: A 176B-Parameter Open-Access Multilingual Language Model

Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License

Changes of photosynthetic traits in beech saplings (Fagus sylvatica) under severe drought stress and during recovery

In the context of an increased risk of extreme drought events across Europe during the next decades, the capacity of trees to recover and survive drought periods awaits further attention. In summer 2005, 4-year-old beech (Fagus sylvatica L.) saplings were watered regularly or were kept for 4 weeks without irrigation in the field and then re-watered again. Changes of plant water status, leaf gas exchange and Chl a fluorescence parameters, as well as alterations in leaf pigment composition were followed. During the drought period, stomatal conductance (g(s)) and net photosynthesis (P(n)) decreased in parallel with increased water deficit. After 14 days without irrigation, stomata remained closed and P(n) was almost completely inhibited. Reversible downregulation of PSII photochemistry [the maximum quantum efficiency of PSII (F(v)/F(m))], enhanced thermal dissipation of excess excitation energy and an increased ratio of xanthophyll cycle pigments to chlorophylls (because of a loss of chlorophylls) contributed to an enhanced photo-protection in severely stressed plants. Leaf water potential was restored immediately after re-watering, while g(s), P(n) and F(v)/F(m) recovered only partially during the initial phase, even when high external CO(2) concentrations were applied during the measurements, indicating lasting non-stomatal limitations. Thereafter, P(n) recovered completely within 4 weeks, meanwhile g(s) remained permanently lower in stressed than in control plants, leading to an increased 'intrinsic water use efficiency' (P(n)/g(s)). In conclusion, although severe drought stress adversely affected photosynthetic performance of F. sylvatica (a rather drought-sensitive species), P(n) was completely restored after re-watering, presumably because of physiological and morphological adjustments (e.g. stomatal occlusions)

Meta-analysis assessing potential of steady-state chlorophyll fluorescence for remote sensing detection of plant water, temperature and nitrogen stressplant

Many laboratory studies investigating chlorophyll fluorescence (F) of plants have provided sufficient evidence of the functional link between dynamic changes in photosynthetic activity and F emissions. Far fewer studies, however, have been devoted to detailed analysis of F emission under steady-state conditions, which may be amenable to measurement by passive spectroradiometers onboard airborne or satellite missions. Here, we provide a random-effects meta-analysis of studies using both passively (sun-induced) and actively (e.g. laser-induced) measured steady-state F for detecting stress reactions in terrestrial vegetation. Specifically, we review behaviour of F in red and far-red wavelengths, and also the red to far-red F ratio, for plants physiologically stressed by water deficit, temperature extremes, and nitrogen insufficiency. Results suggest that water stress is, in general, associated with a decline in red and far-red F signal intensity measured at both leaf and canopy levels, whereas the red to far-red F ratio displays an inconsistent behaviour. Chilling, for which only studies with active measurements at the leaf level are available, significantly increased red and far-red F, whereas heat stress produced a less convincing decrease in both F emissions, notably in canopies measured passively. The clearest indicator of temperature stress was the F ratio, which declined significantly and consistently. The F ratio was also the strongest indicator of nitrogen deficiency, revealing a nearly uniformly increasing pattern driven by predominantly declining far-red F. Although significant knowledge gaps were encountered for certain scales and F measurement techniques, the analyses indicate that future airborne or space-borne acquisitions of both red and far-red F signals would be beneficial for timely detection of plant stress events