Tuscia University

About: Tuscia University is a education organization based out in Viterbo, Italy. It is known for research contribution in the topics: Population & Climate change. The organization has 1497 authors who have published 3163 publications receiving 97711 citations. The organization is also known as: Università degli Studi della Tuscia & Universita degli Studi della Tuscia.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

FLUXNET: A New Tool to Study the Temporal and Spatial Variability of Ecosystem-Scale Carbon Dioxide, Water Vapor, and Energy Flux Densities

Abstract: FLUXNET is a global network of micrometeorological flux measurement sites that measure the exchanges of carbon dioxide, water vapor, and energy between the biosphere and atmosphere. At present over 140 sites are operating on a long-term and continuous basis. Vegetation under study includes temperate conifer and broadleaved (deciduous and evergreen) forests, tropical and boreal forests, crops, grasslands, chaparral, wetlands, and tundra. Sites exist on five continents and their latitudinal distribution ranges from 70°N to 30°S. FLUXNET has several primary functions. First, it provides infrastructure for compiling, archiving, and distributing carbon, water, and energy flux measurement, and meteorological, plant, and soil data to the science community. (Data and site information are available online at the FLUXNET Web site, http://www-eosdis.ornl.gov/FLUXNET/.) Second, the project supports calibration and flux intercomparison activities. This activity ensures that data from the regional networks are intercomparable. And third, FLUXNET supports the synthesis, discussion, and communication of ideas and data by supporting project scientists, workshops, and visiting scientists. The overarching goal is to provide information for validating computations of net primary productivity, evaporation, and energy absorption that are being generated by sensors mounted on the NASA Terra satellite. Data being compiled by FLUXNET are being used to quantify and compare magnitudes and dynamics of annual ecosystem carbon and water balances, to quantify the response of stand-scale carbon dioxide and water vapor flux densities to controlling biotic and abiotic factors, and to validate a hierarchy of soil–plant–atmosphere trace gas exchange models. Findings so far include 1) net CO 2 exchange of temperate broadleaved forests increases by about 5.7 g C m −2 day −1 for each additional day that the growing season is extended; 2) the sensitivity of net ecosystem CO 2 exchange to sunlight doubles if the sky is cloudy rather than clear; 3) the spectrum of CO 2 flux density exhibits peaks at timescales of days, weeks, and years, and a spectral gap exists at the month timescale; 4) the optimal temperature of net CO 2 exchange varies with mean summer temperature; and 5) stand age affects carbon dioxide and water vapor flux densities.

Climate extremes and the carbon cycle

Abstract: The terrestrial biosphere is a key component of the global carbon cycle and its carbon balance is strongly influenced by climate. Continuing environmental changes are thought to increase global terrestrial carbon uptake. But evidence is mounting that climate extremes such as droughts or storms can lead to a decrease in regional ecosystem carbon stocks and therefore have the potential to negate an expected increase in terrestrial carbon uptake. Here we explore the mechanisms and impacts of climate extremes on the terrestrial carbon cycle, and propose a pathway to improve our understanding of present and future impacts of climate extremes on the terrestrial carbon budget.

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.