Alessio Papini

Bio: Alessio Papini is an academic researcher from University of Florence. The author has contributed to research in topics: Medicine & Phytochemical. The author has an hindex of 25, co-authored 97 publications receiving 6657 citations.

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.

Tracking the invasion of the alien fruit pest Drosophila suzukii in Europe

Abstract: Biological invasions are a leading threat to native wildlife, human health and food production worldwide. Understanding the invasion history helps identifying introduction pathways and organizing integrated management strategies especially aimed at avoiding multiple reintroductions. We coupled a recently developed spatial analysis (Geographic profiling) with trade flows quantification to identify the most likely spreading centre of a recent invader of Europe, the spotted wing drosophila, Drosophila suzukii. This polyphagous vinegar fly recently colonized western countries, where it is heavily threatening fruit production causing severe economic losses. Characterized by a rapid spread and a huge impact, the invasion of this pest has a few precedents and it is becoming a model in invasion biology and pest management. Thanks to our spatial approach based on data presence of D. suzukii in European countries in the very first years of it spread, we update the current knowledge of a first spread in Spain and Italy, suggesting on the contrary that the South of France may be the most likely spreading centre of D. suzukii in Europe. Estimates of propagule pressure (fresh host fruits importation) support this finding as imports from contaminated South East Asian countries are higher in France than in Spain or Italy. Our study provides a first step in the comprehension of invasion history of this pest species and emphasizes geographic profiling as an efficient technique to track down invaders colonization patterns.

Programmed-cell-death events during tapetum development of angiosperms

Abstract: Programmed-cell-death events in the tapetum of two angiosperms (Lobivia rauschii Zecher andTillandsia albida Mez et Purpus) are described by ultrastructural methods. Tapetum degradation appears to be a type of programmed cell death, with the cellular remnants necessary for pollen development, acting as products of holocrine secretion. Diagnostic features of apoptosis during tapetum development are: general shrinkage of the whole cell and the nuclei; condensation of the chromatin at the periphery of the internal nuclear membrane; the enlargement of the endoplasmicreticulum cisternae to circumscribe portions of the cytoplasm; the persistence of mitochondria together with microfilament bundles until the last stages of tapetal degeneration.

Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification

Abstract: The cyanobacteria are the most important prokaryotic primary producers on Earth, inhabiting a great diversity of aquatic and terrestrial environments exposed to light. However, the evolutionary forces leading to their divergence and speciation remain largely enigmatic compared to macroorganisms due to their prokaryotic nature, including vast population sizes, and largely asexual reproduction. The advent of modern molecular techniques has facilitated an understanding of the important factors shaping cyanobacterial evolution, including horizontal gene transfer and homologous recombination. We review the forces shaping the evolution of cyanobacteria and discuss the role of cohesive forces on speciation. Further, while myriad species concepts and definitions are currently used, only a limited subset might be applied to cyanobacteria due to their asexual reproduction. Additionally, concepts based solely on phenotypes provide insufficient resolution. A monophyletic species concept which is universal may be ideal for cyanobacteria. Actual identification of the cyanobacteria is difficult due to cryptic diversity, lack of morphological variability, and frequent convergent evolutionary events. Thus, applied molecular techniques such as DNA barcoding will be useful for identifications of environmental samples. Lastly, we show that the real biodiversity of the cyanobacteria is widely underestimated, due in part to low sampling efforts, sensitivity to the molecular markers employed, and the species definitions employed by researchers. In conclusion, we anticipate a rapid increase in cyanobacterial taxa described and large revisions of the system in the future as scientists adopt a common approach to cyanobacterial systematics.

Ultrastructure of autophagy in plant cells: A review

Abstract: Just as with yeasts and animal cells, plant cells show several types of autophagy. Microautophagy is the uptake of cellular constituents by the vacuolar membrane. Although microautophagy seems frequent in plants it is not yet fully proven to occur. Macroautophagy occurs farther away from the vacuole. In plants it is performed by autolysosomes, which are considerably different from the autophagosomes found in yeasts and animal cells, as in plants these organelles contain hydrolases from the onset of their formation. Another type of autophagy in plant cells (called mega-autophagy or mega-autolysis) is the massive degradation of the cell at the end of one type of programmed cell death (PCD). Furthermore, evidence has been found for autophagy during degradation of specific proteins, and during the internal degeneration of chloroplasts. This paper gives a brief overview of the present knowledge on the ultrastructure of autophagic processes in plants.

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.

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Abstract: Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field.

Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012

Abstract: In 2009, the Nomenclature Committee on Cell Death (NCCD) proposed a set of recommendations for the definition of distinct cell death morphologies and for the appropriate use of cell death-related terminology, including 'apoptosis', 'necrosis' and 'mitotic catastrophe'. In view of the substantial progress in the biochemical and genetic exploration of cell death, time has come to switch from morphological to molecular definitions of cell death modalities. Here we propose a functional classification of cell death subroutines that applies to both in vitro and in vivo settings and includes extrinsic apoptosis, caspase-dependent or -independent intrinsic apoptosis, regulated necrosis, autophagic cell death and mitotic catastrophe. Moreover, we discuss the utility of expressions indicating additional cell death modalities. On the basis of the new, revised NCCD classification, cell death subroutines are defined by a series of precise, measurable biochemical features.

Targeting autophagy in cancer

Abstract: Autophagy is a mechanism by which cellular material is delivered to lysosomes for degradation, leading to the basal turnover of cell components and providing energy and macromolecular precursors. Autophagy has opposing, context-dependent roles in cancer, and interventions to both stimulate and inhibit autophagy have been proposed as cancer therapies. This has led to the therapeutic targeting of autophagy in cancer to be sometimes viewed as controversial. In this Review, we suggest a way forwards for the effective targeting of autophagy by understanding the context-dependent roles of autophagy and by capitalizing on modern approaches to clinical trial design.

Anatomy of Seed Plants

Abstract: INTRODUCTION. Internal Organization of the Plant Body. Summary of Types of Cells and Tissues. General References. DEVELOPMENT OF THE SEED PLANT. The Embryo. From embryo to the Adult Plant. Apical Meristems and Their Derivatives. Differentiation, Specialization, and Morphogenesis. References. THE CELL. Cytoplasm. Nucleus. Plastids. Mitochondria. Microbodies. Vacuoles. Paramural Bodies. Ribosomes. Dictyosomes. Endoplasmic Reticulum. Lipid Globules. Microtubules. Ergastic Substances. References. CELL WALL. Macromolecular Components and Their Organization in the Wall. Cell Wall Layers. Intercellular Spaces. Pits, Primary Pit--Fields, and Plasmodesmata. Origin of Cell Wall During Cell Division. Growth of Cell Wall. References. PARENCHYMA AND COLLENCHYMA. Parenchyma. Collenchyma. References. SCLERENCHYMA. Sclereids. Fibers. Development of Sclereids and Fibers. References. EPIDERMIS. Composition. Developmental Aspects. Cell Wall. Stomata. Trichomes. References. XYLEM: GENERAL STRUCTURE AND CELL TYPES. Gross Structure of Secondary Xylem. Cell Types in the Secondary Xylem. Primary Xylem. Differentiation of Tracheary Elements. References. XYLEM: VARIATION IN WOOD STRUCTURE. Conifer Wood. Dicotyledon Wood. Some Factors in Development of Secondary Xylem. Identification of Wood. References. VASCULAR CAMBIUM. Organization of Cambium. Developmental Changes in the Initial Layer. Patterns and Causal Relations in Cambial Activity. References. PHLOEM. Cell Types. Primary Phloem. Secondary Phloem. References. PERIDERM. Structure of Periderm and Related Tissues. Development of Periderm. Outer Aspect of Bark in Relation to Structure. Lenticels. References. SECRETORY STRUCTURES. External Secretory Structures. Internal Secretory Structures. References. THE ROOT: PRIMARY STATE OF GROWTH. Types of Roots. Primary Structure. Development. References. THE ROOT: SECONDARY STATE OF GROWTH AND ADVENTITIOUS ROOTS. Common Types of Secondary Growth. Variations in Secondary Growths. Physiologic Aspects of Secondary Growth in Roots. Adventitious Roots. References. THE STEM: PRIMARY STATE OF GROWTH. External Morphology. Primary Structure. Development. References. THE STEM: SECONDARY GROWTH AND STRUCTURAL TYPES. Secondary Growth. Types of Stems. References. THE LEAF: BASIC STRUCTURE AND DEVELOPMENT. Morphology. Histology of Angiosperm Leaf. Development. Abscission. References. THE LEAF: VARIATIONS IN STRUCTURE. Leaf Structure and Environment. Dicotyledon Leaves. Monocotyledon Leaves. Gymnosperm Leaves. References. THE FLOWER: STRUCTURE AND DEVELOPMENT. Concept. Structure. Development. References. THE FLOWER: REPRODUCTIVE CYCLE. Microsporogenesis. Pollen. Male Gametophyte. Megasporogenesis. Female Gametophyte. Fertilization. References. THE FRUIT. Concept and Classification. The Fruit Wall. Fruit Types. Fruit Growths. Fruit Abscission. References. THE SEED. Concept and Morphology. Seed Development. Seed Coat. Nutrient Storage Tissues. References. EMBRYO AND SEEDLING. Mature Embryo. Development of Embryo. Classification of Embryos. Seedling. References. Glossary. Index.