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

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

UGA: a dual signal for ``stop'' and for recoding in protein synthesis

UGA remains an enigma as a signal in protein synthesis. Long recognized as a stop signal that is prone to failure when under competition from near cognate events, there was growing belief that there might be functional significance in the production of small amounts of extended proteins. This view has been reinforced with the discovery that UGA is found at some recoding sites where frameshifting occurs as a regulatory mechanism for controlling the gene expression of specific proteins, and it also serves as the code for selenocysteine (Sec), the 21st amino acid. Why does UGA among the stop signals play this role specifically, and how does it escape being used to stop protein synthesis efficiently at recoding sites involving Sec incorporation or shifts to a new translational frame? These issues concerning the UGA stop signals are discussed in this review

Efficiency of compaction and compositional convection during mafic crystal mush solidification: the Sept Iles layered intrusion, Canada

Adcumulate formation in mafic layered intrusions is attributed either to gravity-driven compaction, which expels the intercumulus melt out of the crystal matrix, or to compositional convection, which maintains the intercumulus liquid at a constant composition through liquid exchange with the main magma body. These processes are length-scale and time-scale dependent, and application of experimentally derived theoretical formulations to magma chambers is not straightforward. New data from the Sept Iles layered intrusion are presented and constrain the relative efficiency of these processes during solidification of the mafic crystal mush. Troctolites with meso- to ortho-cumulate texture are stratigraphically followed by Fe–Ti oxide-bearing gabbros with adcumulate texture. Calculations of intercumulus liquid fractions based on whole-rock P, Zr, V and Cr contents and detailed plagioclase compositional profiles show that both compaction and compositional convection operate, but their efficiency changes with liquid differentiation. Before saturation of Fe–Ti oxides in the intercumulus liquid, convection is not active due to the stable liquid density distribution within the crystal mush. At this stage, compaction and minor intercumulus liquid crystallization reduce the porosity to 30%. The velocity of liquid expulsion is then too slow compared with the rate of crystal accumulation. Compositional convection starts at Fe–Ti oxide-saturation in the pore melt due to its decreasing density. This process occurs together with crystallization of the intercumulus melt until the residual porosity is less than 10%. Compositional convection is evidenced by external plagioclase rims buffered at An 61 owing to continuous exchange between the intercumulus melt and the main liquid body. The change from a channel flow regime that dominates in troctolites to a porous flow regime in gabbros results from the increasing efficiency of compaction with differentiation due to higher density contrast between the cumulus crystal matrix and the equilibrium melts and to the bottom-up decreasing rate of crystal accumulation in the magma chamber