The 11th edition of Harrison's Principles of Internal Medicine welcomes Anthony Fauci to its editorial staff, in addition to more than 85 new contributors. While the organization of the book is similar to previous editions, major emphasis has been placed on disorders that affect multiple organ systems. Important advances in genetics, immunology, and oncology are emphasized. Many chapters of the book have been rewritten and describe major advances in internal medicine. Subjects that received only a paragraph or two of attention in previous editions are now covered in entire chapters. Among the chapters that have been extensively revised are the chapters on infections in the compromised host, on skin rashes in infections, on many of the viral infections, including cytomegalovirus and Epstein-Barr virus, on sexually transmitted diseases, on diabetes mellitus, on disorders of bone and mineral metabolism, and on lymphadenopathy and splenomegaly. The major revisions in these chapters and many

Harrison's Principles of Internal Medicine

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.

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

Bid, a Bcl2 Interacting Protein, Mediates Cytochrome c Release from Mitochondria in Response to Activation of Cell Surface Death Receptors

A variety of physiological death signals, as well as pathological cellular insults, trigger the genetically programmed pathway of apoptosis (Vaux and Korsmeyer 1999). Apoptosis manifests in two major execution programs downstream of the death signal: the caspase pathway and organelle dysfunction, of which mitochondrial dysfunction is the best characterized (for reviews, see Green and Reed 1998; Thornberry and Lazebnik 1998). As the BCL-2 family members reside upstream of irreversible cellular damage and focus much of their efforts at the level of mitochondria, they play a pivotal role in deciding whether a cell will live or die (Fig. 1). The founder of this family, the BCL-2 proto-oncogene, was discovered at the chromosomal breakpoint of t(14;18) bearing human B-cell lymphomas. The BCL-2 family of proteins has expanded significantly and includes both proas well as anti-apoptotic molecules. Indeed, the ratio between these two subsets helps determine, in part, the susceptibility of cells to a death signal (Oltvai et al. 1993) (Fig. 1). An additional characteristic of the members of this family is their frequent ability to form homoas well as heterodimers, suggesting neutralizing competition between these proteins. A further characteristic of probable functional significance is their ability to become integral membrane proteins. BCL-2 family members possess up to four conserved BCL-2 homology (BH) domains designated BH1, BH2, BH3, and BH4, which correspond to a-helical segments (Adams and Cory 1998; Kelekar and Thompson 1998; Reed 1998) (Fig. 2). Many of the anti-apoptotic members display sequence conservation in all four domains. The pro-apoptotic molecules frequently display less sequence conservation of the first a-helical segment, BH4. Deletion and mutagenesis studies argue that the amphipathic a-helical BH3 domain serves as a critical death domain in the pro-apoptotic members. This concept is supported by an emerging subset of “BH3-domain-only” members who display sequence homology only within the BH3 domain and to date are all pro-apoptotic. However, the three-dimensional structure of at least one BH3-domainonly molecule, BID, demonstrates a very similar overall a-helical content to the anti-apoptotic molecule BCL-XL (Chou et al. 1999; McDonnell et al. 1999). Many BCL-2 family members also contain a carboxy-terminal hydrophobic domain, which in the case of BCL-2 is essential for its targeting to membranes such as the mitochondrial outer membrane (Nguyen et al. 1993).

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BCL-2 family members and the mitochondria in apoptosis

Irrespective of the morphological features of end-stage cell death (that may be apoptotic, necrotic, autophagic, or mitotic), mitochondrial membrane permeabilization (MMP) is frequently the decisive event that delimits the frontier between survival and death. Thus mitochondrial membranes constitute the battleground on which opposing signals combat to seal the cell's fate. Local players that determine the propensity to MMP include the pro- and antiapoptotic members of the Bcl-2 family, proteins from the mitochondrialpermeability transition pore complex, as well as a plethora of interacting partners including mitochondrial lipids. Intermediate metabolites, redox processes, sphingolipids, ion gradients, transcription factors, as well as kinases and phosphatases link lethal and vital signals emanating from distinct subcellular compartments to mitochondria. Thus mitochondria integrate a variety of proapoptotic signals. Once MMP has been induced, it causes the release of catabolic hydrolases and activators of such enzymes (including those of caspases) from mitochondria. These catabolic enzymes as well as the cessation of the bioenergetic and redox functions of mitochondria finally lead to cell death, meaning that mitochondria coordinate the late stage of cellular demise. Pathological cell death induced by ischemia/reperfusion, intoxication with xenobiotics, neurodegenerative diseases, or viral infection also relies on MMP as a critical event. The inhibition of MMP constitutes an important strategy for the pharmaceutical prevention of unwarranted cell death. Conversely, induction of MMP in tumor cells constitutes the goal of anticancer chemotherapy.

Mitochondrial Membrane Permeabilization in Cell Death

Amyloidoses are heterogeneous diseases that result from the deposition of toxic insoluble β-sheet fibrillar protein aggregates in different tissues. The cascade of molecular events leading to amyloidoses and to the related clinical manifestations is not completely understood. Nevertheless, it is known that tissue damage associated to this disease involves alteration of tissue architecture, interaction with cell surface receptors, inflammation elicited by the amyloid protein deposition, oxidative stress, and apoptosis. However, another important aspect to consider is that systemic protein massive deposition not only subverts tissue architecture but also determines a progressive cellular hypertrophy and dilation of the extracellular space enlarging the volume of the organ. Such an alteration increases the distance between cells and vessels with a drop in pO2 that, in turn, causes both necrotic cell death and activation of the hypoxia transcription factor HIF-1α. Herewith, we propose the hypothesis that both cell death and hypoxia represent two important events for the pathogenesis of damage and progression of amyloidoses. In fact, molecules released by necrotic cells activate inflammatory cells from one side while binding to HIF-1α-dependent membrane receptors expressed on hypoxic parenchymal cells on the other side. This latter event generates a signaling cascade triggering NFκB activation and chronic inflammation. Finally, we also suggest that this scenario, once proved and detailed, might suggest important targets for new therapeutic interventions.

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Hypoxia and Inflammation as a Consequence of β -Fibril Accumulation: A Perspective View for New Potential Therapeutic Targets.

Assembled IgG molecules are exported from the endoplasmic reticulum in myeloma cells despite the retention signal SEKDEL.

Modulation of sirtuins during acute inflammatory pain: the role of ROS

Molecular Nutrient Targeting with Mediterranean Diets

Author details Department of Experimental Medicine and Biochemical Sciences, University of Rome \"Tor Vergata\" Via Montpellier 1, 00133, Rome, Italy. Department of Cellular and Molecular Pathology, IRCCS San Raffaele Pisana, Via dei Bonacolsi snc, 00163, Rome, Italy. Human Nutrition Unit, University of Rome \"Tor Vergata\" Via Montpellier 1, 00133, Rome, Italy. Department of Experimental Medicine, La Sapienza University, Viale Regina Elena 324, 00161, Rome, Italy. School of Sport and Exercise Sciences, University of Rome Tor Vergata\" Via Columbia s.n.c., 00133, Rome, Italy.

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Erratum:: The effect of marathon on mRNA expression of anti-apoptotic and pro-apoptotic proteins and sirtuins family in male recreational long-distance runners (BMC Physiology (2010) 10(7))

Marco Tafani

Papers

Hypoxia and Inflammation as a Consequence of β -Fibril Accumulation: A Perspective View for New Potential Therapeutic Targets.

Assembled IgG molecules are exported from the endoplasmic reticulum in myeloma cells despite the retention signal SEKDEL.

Modulation of sirtuins during acute inflammatory pain: the role of ROS

Molecular Nutrient Targeting with Mediterranean Diets

Erratum:: The effect of marathon on mRNA expression of anti-apoptotic and pro-apoptotic proteins and sirtuins family in male recreational long-distance runners (BMC Physiology (2010) 10(7))