From remotely-sensed solar-induced chlorophyll fluorescence to ecosystem structure,function, and service: Part II—Harnessing data

Although our observing capabilities of solar-induced chlorophyll fluorescence (SIF) have been growing rapidly, the quality and consistency of SIF datasets are still in an active stage of research and development. As a result, there are considerable inconsistencies among diverse SIF datasets at all scales and the widespread applications of them have led to contradictory findings. The present review is the second of the two companion reviews, and data oriented. It aims to (1) synthesize the variety, scale, and uncertainty of existing SIF datasets, (2) synthesize the diverse applications in the sector of ecology, agriculture, hydrology, climate, and socioeconomics, and (3) clarify how such data inconsistency superimposed with the theoretical complexities laid out in (Sun et al., 2023) may impact process interpretation of various applications and contribute to inconsistent findings. We emphasize that accurate interpretation of the functional relationships between SIF and other ecological indicators is contingent upon complete understanding of SIF data quality and uncertainty. Biases and uncertainties in SIF observations can significantly confound interpretation of their relationships and how such relationships respond to environmental variations. Built upon our syntheses, we summarize existing gaps and uncertainties in current SIF observations. Further, we offer our perspectives on innovations needed to help improve informing ecosystem structure, function, and service under climate change, including enhancing in-situ SIF observing capability especially in “data desert” regions, improving cross-instrument data standardization and network coordination, and advancing applications by fully harnessing theory and data.     

Microproteins—Discovery,structure, and function

Advances in proteogenomic technologies have revealed hundreds to thousands of translated small open reading frames (sORFs) that encode microproteins in genomes across evolutionary space. While many microproteins have now been shown to play critical roles in biology and human disease, a majority of recently identified microproteins have little or no experimental evidence regarding their functionality. Computational tools have some limitations for analysis of short, poorly conserved microprotein sequences, so additional approaches are needed to determine the role of each member of this recently discovered polypeptide class. A currently underexplored avenue in the study of microproteins is structure prediction and determination, which delivers a depth of functional information. In this review, we provide a brief overview of microprotein discovery methods, then examine examples of microprotein structures (and, conversely, intrinsic disorder) that have been experimentally determined using crystallography, cryo-electron microscopy, and NMR, which provide insight into their molecular functions and mechanisms. Additionally, we discuss examples of predicted microprotein structures that have provided insight or context regarding their function. Analysis of microprotein structure at the angstrom level, and confirmation of predicted structures, therefore, has potential to identify translated microproteins that are of biological importance and to provide molecular mechanism for their in vivo roles.     

Habitat structure, trophic structure and ecosystem function: interactive effects in a bromeliad–insect community

Although previous studies have shown that ecosystem functions are affected by either trophic structure or habitat structure, there has been little consideration of their combined effects. Such interactions may be particularly important in systems where habitat and trophic structure covary. I use the aquatic insects in bromeliads to examine the combined effects of trophic structure and habitat structure on a key ecosystem function: detrital processing. In Costa Rican bromeliads, trophic structure naturally covaries with both habitat complexity and habitat size, precluding any observational analysis of interactions between factors. I therefore designed mesocosms that allowed each factor to be manipulated separately. Increases in mesocosm complexity reduced predator (damselfly larva) efficiency, resulting in high detritivore abundances, indirectly increasing detrital processing rates. However, increased complexity also directly reduced the per capita foraging efficiency of the detritivores. Over short time periods, these trends effectively cancelled each other out in terms of detrital processing. Over longer time periods, more complex patterns emerged. Increases in mesocosm size also reduced both predator efficiency and detritivore efficiency, leading to no net effect on detrital processing. In many systems, ecosystem functions may be impacted by strong interactions between trophic structure and habitat structure, cautioning against examining either effect in isolation.     

Are changes in remotely sensed canopy cover associated to changes in vegetation structure,diversity, and composition in recovered tropical shrublands?

The recovery of vegetation cover is a process that has important implications for the conservation of biodiversity and ecosystem services. Generally, the recovery of vegetation cover is documented over large areas using remote sensing, and it is often assumed that ecosystem properties and processes recover along with remotely sensed canopy cover. Here we analyze and compare the structure, composition, and diversity of trees and shrubs among plots established in a stratified random sampling design over four remotely sensed canopy cover change (CCC) categories defined according to a gradient in the percent of canopy cover. Plots were located in the Lake Cuitzeo basin (Mexico), where canopy recovery associated with agricultural abandonment has occurred in recent decades (1975–2000). We found that diversity measures, basal area, tree and shrub density, ground-truthed canopy cover, and mean plant height increased with increasing CCC category. However, Shannon index (H′) was lower in the CCC category with the most closed canopy cover category than in plots apparently not affected by agriculture. Furthermore, ordination analyses showed that composition of dominant species were not associated with CCC categories. Our results suggest that canopy closure in our study area is not associated with the recovery of species diversity, and does not result in similar species dominance as in sites not affected by agriculture.     

Plant dehydrins — Tissue location, structure and function

Dehydrins (DHNs) are part of a large group of highly hydrophilic proteins known as LEA (Late Embryogenesis Abundant). They were originally identified as group II of the LEA proteins. The distinctive feature of all DHNs is a conserved, lysine-rich 15-amino acid domain, EKKGIMDKIKEKLPG, named the K-segment. It is usually present near the C-terminus. Other typical dehydrin features are: a track of Ser residues (the S-segment); a consensus motif, T/VDEYGNP (the Y-segment), located near the N-terminus; and less conserved regions, usually rich in polar amino acids (the Φ-segments). They do not display a well-defined secondary structure. The number and order of the Y-, S-and K-segments define different DHN sub-classes: Y_nSK_n, Y_nKn, SK_n, K_n and K_nS. Dehydrins are distributed in a wide range of organisms including the higher plants, algae, yeast and cyanobacteria. They accumulate late in embryogenesis, and in nearly all the vegetative tissues during normal growth conditions and in response to stress leading to cellular dehydration (e.g. drought, low temperature and salinity). DHNs are localized in different cell compartments, such as the cytosol, nucleus, mitochondria, vacuole, and the vicinity of the plasma membrane; however, they are primarily localized to the cytoplasm and nucleus. The precise function of dehydrins has not been established yet, but in vitro experiments revealed that some DHNs (YSK_n-type) bind to lipid vesicles that contain acidic phospholipids, and others (K_nS) were shown to bind metals and have the ability to scavenge hydroxyl radicals [Asghar, R. et al. Protoplasma 177 (1994) 87–94], protect lipid membranes against peroxidation or display cryoprotective activity towards freezing-sensitive enzymes. The SK_n-and K-type seem to be directly involved in cold acclimation processes. The main question arising from the in vitro findings is whether each DHN structural type could possess a specific function and tissue distribution. Much recent in vitro data clearly indicates that dehydrins belonging to different subclasses exhibit distinct functions. An erratum to this article is available at .     

Satellite Ecology (SATECO)—linking ecology,remote sensing and micrometeorology,from plot to regional scale,for the study of ecosystem structure and function

There is a growing requirement for ecosystem science to help inform a deeper understanding of the effects of global climate change and land use change on terrestrial ecosystem structure and function, from small area (plot) to landscape, regional and global scales. To meet these requirements, ecologists have investigated plant growth and carbon cycling processes at plot scale, using biometric methods to measure plant carbon accumulation, and gas exchange (chamber) methods to measure soil respiration. Also at the plot scale, micrometeorologists have attempted to measure canopy- or ecosystem-scale CO₂ flux by the eddy covariance technique, which reveals diurnal, seasonal and annual cycles. Mathematical models play an important role in integrating ecological and micrometeorological processes into ecosystem scales, which are further useful in interpreting time-accumulated information derived from biometric methods by comparing with CO₂ flux measurements. For a spatial scaling of such plot-level understanding, remote sensing via satellite is used to measure land use/vegetation type distribution and temporal changes in ecosystem structures such as leaf area index. However, to better utilise such data, there is still a need for investigations that consider the structure and function of ecosystems and their processes, especially in mountainous areas characterized by complex terrain and a mosaic distribution of vegetation. For this purpose, we have established a new interdisciplinary approach named ‘Satellite Ecology’, which aims to link ecology, remote sensing and micrometeorology to facilitate the study of ecosystem function, at the plot, landscape, and regional scale. This article was contributed at the invitation of the Editorial Committee.     

Sperm PLCζ: From structure to Ca oscillations,egg activation and therapeutic potential

Significant evidence now supports the assertion that cytosolic calcium oscillations during fertilization in mammalian eggs are mediated by a testis-specific phospholipase C (PLC), termed PLC-zeta (PLCζ) that is released into the egg following gamete fusion. Herein, we describe the current paradigm of PLCζ in this fundamental biological process, summarizing recent important advances in our knowledge of the biochemical and physiological properties of this enzyme. We describe the data suggesting that PLCζ has distinct features amongst PLCs enabling the hydrolysis of its substrate, phosphatidylinositol 4,5-bisphosphate (PIP₂) at low Ca²⁺ levels. PLCζ appears to be unique in its ability to target PIP₂ that is present on intracellular vesicles. We also discuss evidence that PLCζ may be a significant factor in human fertility with potential therapeutic capacity.     

Medicine in Society—Part I: Change and Challenge

The Committee to Study the Role of Medicine of the California Medical Education and Research Foundation (CMERF) is grateful to Dr. Watts for the following paper which served as the philosophical basis for the Committee''s study and discussions. The Committee is also grateful to CMERF and to its president, James C. Doyle, for the encouragement and cooperation it has received in the course of its intensive study of a problem which is of great interest and concern to the medical profession of California.Dr. Watts'' background paper has served as a potent stimulus in directing the Committee''s attention to the continuing dialogue between medicine and society, and in focussing on problems and issues which will be the subject of the Committee''s Second Progress Report, excerpts from which are scheduled for publication in the next issue of California Medicine.     

Phytosociological synrelevés and plant landscape mapping: From theory to practice

Abstract

A mapping methodology is presented here that allows the practical implementation of synphytosociological and geosynphytosociological surveys. The proposed methodology consists in carrying out synrelevés from vegetation maps produced through the use of geographic information system (GIS). Such mapping has the great advantage of allowing the overlaying of the study area map with many thematic maps that are particularly useful in the definition of the areas of potential vegetation. In the present case, the use of solar radiation maps is proposed, as these are more representative than aspect maps (exposure) of the actual conditions of the mapped areas. Indeed, the main ecological factors that delimit the ecological niche of plant communities, the vegetation series and the geosigmeta are defined qualitatively and quantitatively. The methodology is here applied to an area of the Italian Adriatic coast that has a great diversity of environmental conditions. The conclusions confirm that the proposed methodology allows predictive models of the plant landscape units (geosigmeta) to be obtained with great precision; they can be mapped and quantified in concrete terms insofar as they are defined through multidimensional correlations.     

Current developments in groundwater ecology — from biodiversity to ecosystem function and services

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Human Nicotinic Acetylcholine Receptors: Part I—Structure,Function, and Role in Neuromuscular Transmission and CNS Functioning

Russian Journal of Bioorganic Chemistry - Nicotinic acetylcholine receptors (nAChRs) are the ligand-gated ion channels important for intercellular signaling. These receptors are abundant in...     

Chloroplast movements in leaves: Influence on chlorophyll fluorescence and measurements of light-induced absorbance changes related to ΔpH and zeaxanthin formation

Light-induced chloroplast movements were found to cause changes in chlorophyll fluorescence emission, closely matching those in leaf absorptance, both in terms of the kinetics and the maximum extent of the changes observed in different species. The results demonstrate that chloroplast movements can have a significant effect on the efficiency of light utilization in photosynthesis. They further show that chloroplast movements need to be taken into account in measurements of fluorescence quenching and especially in measurements of light-induced optical changes used to monitor zeaxanthin formation and pH associated light scattering in leaves. Means of minimizing and of adjusting for the influences of chloroplast movements in such measurements are discussed.Abbreviations F fluorescence emission - PFD photon flux density - R reflectance - T transmittance - absorptance C.I.W.-D.P.B. Publication No. 1116.