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

Driving factors behind litter decomposition and nutrient release at temperate forest edges

Forest edges have become important features in landscapes worldwide. Edges are exposed to a different microclimate and higher atmospheric nitrogen (N) deposition compared to forest interiors. It is, however, unclear how microclimate and elevated N deposition affect nutrient cycling at forest edges. We studied litter decomposition and release of N, phosphorus (P), total cations (TC) and C/N ratios during 18 months via the litterbag technique along edge-to-interior transects in two oak (Quercus robur L.) and two pine (Pinus nigra ssp. laricio Maire and ssp. nigra Arnold) stands in Belgium. Furthermore, the roles of edge conditions (microclimate, atmospheric deposition, soil fauna and soil physicochemical conditions), litter quality and edge decomposer community were investigated as underlying driving factors for litter decomposition. Litter of edge and interior was interchanged (focusing on the influence of edge conditions and litter quality) and placed in open-top chamber (OTC), which create an edge (warmer) microclimate. As the decomposer macrofauna was more abundant at the edge than in the interior, the OTCs were used to isolate the effects of warming versus soil fauna. Oak litter at the edge lost 87 and 37% more mass than litter in the interior. We demonstrated an edge effect on litter decomposition and nutrient release, caused by an interplay of edge conditions (atmospheric deposition of N and TC, soil pH and C/N ratio), litter quality and soil fauna. Consequently, edge effects must be accounted for when quantifying ecosystem processes, such as litter decomposition and nutrient cycling in fragmented landscapes

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.Peer reviewe