The evolution of barriers to exploitation: Sometimes the Red Queen can take a break.

We propose a general barrier theory as an evolutionary framework for understanding coevolutionary effects of conflicts of interest in natural and human systems. It is generalized from the barrier theory of cancer, which describes how cancer develops through the evasion of mechanisms, that block unregulated cellular reproduction and survival. Barriers are naturally evolved or artificially implemented mechanisms for blocking exploitation; restraints are mechanisms that impede but do not block exploitation. When conflicts of interest arise, selection will favor exploiters that are capable of overcoming barriers and restraints. When barriers are in place, they halt, at least temporarily, coevolutionary arms races (the Red Queen can stop running). Barriers occur in a broad spectrum of interactions characterized by conflicts of interest: barriers to cellular survival (apoptosis) and reproduction (cell cycle arrest) may block a virus from replicating its genome through reproduction of its host cell. Vaccines may completely protect against targeted pathogens. A plant may escape herbivory by evolving defensive chemicals that block herbivory. Obligate mutualisms may evolve when barriers to horizontal transmission favor symbionts that increasingly lose mechanisms that contribute to horizontal transmission. Here, we show how the barrier theory applies across a spectrum of natural and social systems

Effects of resource depression on use of inexpensive and escalated aggressive behavior: experimental tests using Anna hummingbirds

To test whether alterations in aggressive behavior are responses to short-term resource depression, use of inexpensive and escalated territorial defense by Anna hummingbirds was analyzed as a function of the degree to which food could be depressed by foraging activities of territory owners and intruders. On depressible territories use of gorget display (a low cost defense) decreased and durations of chases increased as time since the previous feeding by owners increased. On non-depressible territories neither variable was significantly correlated with time since feeding. The percentage of intruders chased by owners was positively correlated with time since feeding on both depressible and nondepressible territories, but the magnitude of this trend decreased as food production increased. Departures from the territory tended to occur shortly after feeding on both types of territories, but this tendency was stronger on depressible territories.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46868/1/265_2004_Article_BF00343199.pd

Ювілеї та пам’ятні дати

Native mass spectrometry is emerging as a powerful tool for the characterization of intact antibodies and antibody-based therapeutics. Here, we demonstrate new possibilities provided by the implementation of a high mass quadrupole mass selector on the recently introduced Orbitrap Exactive EMR mass spectrometer. This configuration allows precursor ion selection, and thus tandem mass spectrometry experiments, even on analytes with masses in the hundreds of kilodaltons. We apply tandem mass spectrometry to localize the drug molecules in the therapeutic antibody-drug conjugate brentuximab vedotin, which displays a heterogeneous drug load. Our tandem MS data reveal that drug conjugation takes place nonhomogeneously to cysteine residues both on the light and heavy chains. Next, we analyzed how many antigens bind to IgG hexamers, based on a recently described antibody mutant IgG1-RGY that forms hexamers and activates complement in solution. The fully saturated IgG1-RGY-antigen complexes displayed a stoichiometry of IgG:CD38 of 6:12, possessing a molecular weight of about 1.26 MDa and demonstrating that IgG assembly does not hamper antigen binding. Through tandem MS experiments, we retrieve information about the spatial arrangement and stoichiometry of the subunits within this complex. These examples underscore the potential of this further modified Orbitrap-EMR instrument especially for the in-depth characterization by native tandem mass spectrometry of antibodies and antibody-based constructs

Territory quality and territorial behavior in two sympatric species of hummingbirds

Changes in territorial behavior of blackchinned hummingbirds ( Archilochus alexandri ) in response to experimental changes in territory quality were investigated using artificial feeders and simultaneous, pair-wise observations of owners. Some of the responses of A. alexandri were similar to those documented by a previous study of the Anna's hummingbird ( Calypte anna): A. alexandri defending rich territories spent more time on their territories, encountered a greater percentage of intruders, and chased more intruders than did A. alexandri defending poor territories. In contrast to C. anna, A. alexandri supplemented chases with energetically inexpensive threat vocalizations more extensively when territory quality was increased. This difference may be related to A. alexandri's more tenuous control of rich territories. When both species were observed on very poor territories, A. alexandri chased a greater percentage of intruders, consumed a greater proportion of available food, and obtained a greater net energy gain from their territories. When observed simultaneously on territories with ad lib food, both species defended highly exclusive territories but A. alexandri suffered higher intrusion pressure and spent more time and energy in defense. These interspecific differences in territorial behavior may facilitate sympatric coexistence of the two species through aggressive partitioning of flower patches according to productivity: the greater payoff received by C. anna on rich territories and A. alexandri on poor territories should favor a corresponding monopolization of rich areas by C. anna and poor areas by A. alexandri .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46878/1/265_2004_Article_BF00292181.pd

Mass spectrometry-based metabolomics:a guide for annotation, quantification and best reporting practices

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography– and gas chromatography–mass spectrometry-based metabolomics-derived data.</p

Age, coloration and dominance in nonbreeding hummingbirds: A test of the asymmetry hypothesis

During the nonbreeding season, adult Anna and black-chinned hummingbirds ( Calypte anna and Archilochus alexandri ) have lower defense costs and more exclusive territories than juveniles. Adult C. anna are victorious over juveniles in aggressive encounters, and tend to monopolize the most temporally predictable resources.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46906/1/265_2004_Article_BF00300667.pd

The Myeloid Receptor PILRβ Mediates the Balance of Inflammatory Responses through Regulation of IL-27 Production

Paired immunoglobulin-like receptors beta, PILRβ, and alpha, PILRα, are related to the Siglec family of receptors and are expressed primarily on cells of the myeloid lineage. PILRβ is a DAP12 binding partner expressed on both human and mouse myeloid cells. The potential ligand, CD99, is found on many cell types, such as epithelial cells where it plays a role in migration of immune cells to sites of inflammation. Pilrb deficient mice were challenged with the parasite Toxoplasma gondii in two different models of infection induced inflammation; one involving the establishment of chronic encephalitis and a second mimicking inflammatory bowel disease in order to understand the potential role of this receptor in persistent inflammatory responses. It was found that in the absence of activating signals from PILRβ, antigen-presenting cells (APCs) produced increased amounts of IL-27, p28 and promoted IL-10 production in effector T cells. The sustained production of IL-27 led ultimately to enhanced survival after challenge due to dampened immune pathology in the gut. Similar protection was also observed in the CNS during chronic T. gondii infection after i.p. challenge again providing evidence that PILRβ is important for regulating aberrant inflammatory responses

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses

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