What is an immunological synapse?

Immunological synapses (IS) are emerging as highly organized 3D structures -formed by surface and cytoplasmic signalling and cytoskeletal molecules – that assemble at the zone of contact between a T cell and an antigen presenting cell (APC). The IS control functions that allow APC and T cells modulate the immune response.     

What is an individual organism? A multilevel selection perspective

Most biologists implicitly define an individual organism as "one genome in one body." This definition is based on physiological and genetic criteria, but it is problematic for colonial organisms. We propose a definition based instead on the evolutionary criteria of alignment of fitness, export of fitness by germ-soma specialization, and adaptive functional organization. We consider how these concepts apply to various putative individual organisms. We conclude that complex multicellular organisms and colonies of eusocial insects satisfy these three criteria, but that, in most cases (with at least one notable exception), colonies of modular organisms and genetic chimeras do not. While species do not meet these criteria, they may meet the criteria for a broader concept--that of an evolutionary individual--and sexual reproduction may be a species-level exaptation for enhancing evolvability. We also review the costs and benefits of internal genetic heterogeneity within putative individuals, demonstrating that high relatedness is neither a necessary nor a sufficient condition for individuality, and that, in some cases, genetic variability may have adaptive benefits at the level of the whole.     

What is an autotroph?

The concept of autotrophy depends on the growth media for pure cultures supplying a single one carbon source for anabolism. Secondary carbon compounds added to the medium as chelators and/or vitamins confuse the meaning. This note suggests a clarification of definition suitable for contemporary biochemical studies of true autotrophs.     

What is an endocrine disruptor?

Endocrine disrupting chemicals (EDCs) and potential EDCs are mostly man-made found in various materials. By interfering with the body's endocrine system, endocrine disruptors produce adverse developmental, reproductive, neurological, and immune effects in humans, abnormal growth patterns and neurodevelopmental delays in children. Thus, diethylstilbestrol (DES) a non-steroidal estrogen, which is regarded as a proof of concept, induces clear cell carcinoma among young women. EDCS may be found in plastic bottles and metal food cans (BPA), medical devices (phthalates), detergents, flame retardants (polybrominated diphenyl ethers), food (BPA), toys (phthalates), cosmetics and drugs (parabens), and pesticides (alkyl phenols such as nonylphenol). The deleterious effects of endocrine disruptors constitute a real public health issue. However concerning the mechanisms of action of EDCs, many questions remain unanswered and need further investigations.     

What is an auditory object?

Objects are the building blocks of experience, but what do we mean by an object? Increasingly, neuroscientists refer to 'auditory objects', yet it is not clear what properties these should possess, how they might be represented in the brain, or how they might relate to the more familiar objects of vision. The concept of an auditory object challenges our understanding of object perception. Here, we offer a critical perspective on the concept and its basis in the brain.     

What is an apex predator?

Large ‘apex’ predators influence ecosystems in profound ways, by limiting the density of their prey and controlling smaller ‘mesopredators’. The loss of apex predators from much of their range has lead to a global outbreak of mesopredators, a process known as ‘mesopredator release’ that increases predation pressure and diminishes biodiversity. While the classifications apex‐ and meso‐predator are fundamental to current ecological thinking, their definition has remained ambiguous. Trophic cascades theory has shown the importance of predation as a limit to population size for a variety of taxa (top–down control). The largest of predators however are unlikely to be limited in this fashion, and their densities are commonly assumed to be determined by the availability of their prey (bottom–up control). However, bottom–up regulation of apex predators is contradicted by many studies, particularly of non‐hunted populations. We offer an alternative view that apex predators are distinguishable by a capacity to limit their own population densities (self‐regulation). We tested this idea using a set of life‐history traits that could contribute to self‐regulation in the Carnivora, and found that an upper limit body mass of 34 kg (corresponding with an average mass of 13–16 kg) marks a transition between extrinsically‐ and self‐regulated carnivores. Small carnivores share fast reproductive rates and development and higher densities. Large carnivores share slow reproductive rates and development, extended parental care, sparsely populated territories, and a propensity towards infanticide, reproductive suppression, alloparental care and cooperative hunting. We discuss how the expression of traits that contribute to self‐regulation (e.g. reproductive suppression) depends on social stability, and highlight the importance of studying predator–prey dynamics in the absence of predator persecution. Self‐regulation in large carnivores may ensure that the largest and the fiercest do not overexploit their resources.     

The phenoptosis problem: What is causing the death of an organism? Lessons from acute kidney injury

Programmed execution of various cells and intracellular structures is hypothesized to be not the only example of elimination of biological systems — the general mechanism can also involve programmed execution of organs and organisms. Modern rating of programmed cell death mechanisms includes 13 mechanistic types. As for some types, the mechanism of actuation and manifestation of cell execution has been basically elucidated, while the causes and intermediate steps of the process of fatal failure of organs and organisms remain unknown. The analysis of deaths resulting from a sudden heart arrest or multiple organ failure and other acute and chronic pathologies leads to the conclusion of a special role of mitochondria and oxidative stress activating the immune system. Possible mechanisms of mitochondria-mediated induction of the signaling cascades involved in organ failure and death of the organism are discussed. These mechanisms include generation of reactive oxygen species and damage-associated molecular patterns in mitochondria. Some examples of renal failure-induced deaths are presented with mechanisms and settings determined by some hypothetical super system rather than by the kidneys themselves. This system plays the key role in the process of physiological senescence and termination of an organism. The facts presented suggest that it is the immune system involved in mitochondrial signaling that can act as the system responsible for the organism’s death.