Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions.

Orthopoxviruses are among the largest and most complex of the animal viruses. In response to the recent emergence of monkeypox in Africa and the threat of smallpox bioterrorism, two orthopoxviruses with different pathogenic potentials, human monkeypox virus and vaccinia virus, were proteomically compared with the goal of identifying proteins required for pathogenesis. Orthopoxviruses were grown in HeLa cells to two different viral forms (intracellular mature virus and extracellular enveloped virus), purified by sucrose gradient ultracentrifugation, denatured using RapiGest surfactant, and digested with trypsin. Unfractionated samples and strong cation exchange HPLC fractions were analyzed by high-resolution reversed-phase nano-LC-MS/MS, and analyses of the MS/MS spectra using SEQUEST and X! Tandem resulted in the confident identification of hundreds of monkeypox, vaccinia, and copurified host-cell proteins. The unfractionated samples were additionally analyzed by LC-MS using an LTQ-Orbitrap, and the accurate mass and elution time tag approach was used to perform quantitative comparisons. Possible pathophysiological roles of differentially abundant Orthopoxvirus proteins are discussed. Data, processed results, and protocols are available at http://www.proteomicsresource.org/.     

Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

1. Download : Download high-res image (226KB)
2. Download : Download full-size image

     

The POLARIS peptide of Arabidopsis regulates auxin transport and root growth via effects on ethylene signaling

The rate and plane of cell division and anisotropic cell growth are critical for plant development and are regulated by diverse mechanisms involving several hormone signaling pathways. Little is known about peptide signaling in plant growth; however, Arabidopsis thaliana POLARIS (PLS), encoding a 36-amino acid peptide, is required for correct root growth and vascular development. Mutational analysis implicates a role for the peptide in hormone responses, but the basis of PLS action is obscure. Using the Arabidopsis root as a model to study PLS action in plant development, we discovered a link between PLS, ethylene signaling, auxin homeostasis, and microtubule cytoskeleton dynamics. Mutation of PLS results in an enhanced ethylene-response phenotype, defective auxin transport and homeostasis, and altered microtubule sensitivity to inhibitors. These defects, along with the short-root phenotype, are suppressed by genetic and pharmacological inhibition of ethylene action. PLS expression is repressed by ethylene and induced by auxin. Our results suggest a mechanism whereby PLS negatively regulates ethylene responses to modulate cell division and expansion via downstream effects on microtubule cytoskeleton dynamics and auxin signaling, thereby influencing root growth and lateral root development. This mechanism involves a regulatory loop of auxin-ethylene interactions.     

Characterization of the pollen growth transition in self-incompatible <Emphasis Type="Italic">Petunia inflata</Emphasis>

In Petunia inflata, as in other species that shed bicellular pollen, early pollen tube growth in the pistil is slow, then increases 2- to 5-fold depending on the genotype of the female parent. We refer to the time point at which pollen tubes enter the accelerated phase of growth as the pollen growth transition (PGT). Here, we present evidence that pre-PGT and post-PGT growth are quantitatively and qualitatively different, and that the PGT is triggered when pollen tubes reach the transition zone (TZ) below the stigma. The capacity of various pistil zones to precipitate the PGT was tested through 'stump' pollinations: varying lengths of the pistil apex were excised, the cut surface of the remaining pistil (the stump) coated with stigmatic exudates then dusted with compatible pollen. Pollen applied to TZ tissues entered the PGT earlier than pollen growing in intact control pistils; the PGT was delayed in stylar stumps, largely because of delayed germination and reduced pre-PGT growth. In immature pistils, the PGT was delayed by several hours relative to its onset in mature pistils. The PGT fails to occur in pollen cultured in vitro. Collectively, the data suggest that pollen tubes become competent to enter the PGT when they reach a critical size, but the physicochemical environment of the transmitting tissue is necessary for triggering the cellular changes that result in accelerated growth. An analysis of the distribution of pollen tube tips before and after the PGT suggests that pollen competition is most intense during the pre-PGT phase.     

Reducing the conservation reliance of the endangered Kirtland's warbler through adaptive management

Species are considered conservation-reliant when their continued existence is dependent on human assistance. Conservation reliance challenges the conservation community in terms of their ability to sustain the funding and public-private partnerships needed for indefinite management. Although increased funding for conservation is critical, reducing conservation reliance through adaptive management represents an attractive alternative. We used a large-scale ecological experiment as a case study in the use of adaptive management to reduce conservation reliance. For >40 years, the United States Fish and Wildlife Service has trapped and lethally removed an obligate brood parasite, the brown-headed cowbird (Molothrus ater), to protect the Kirtland's warbler (Setophaga kirtlandii) from the negative effects that brood parasitism has on its reproductive success. To determine if the conservation reliance of the Kirtland's warbler could be reduced through optimization of the cowbird control program, we used an adaptive management approach. In collaboration with stakeholders, we experimentally reduced cowbird trapping effort across nearly all of the Kirtland's warbler breeding range. We monitored the resulting cowbird abundance and rate of parasitism, and then adjusted the scale of trap reductions based on the previous year's results. Despite reducing (2015–2017) and eventually eliminating (2018) cowbird trapping, we detected only 20 cowbirds (2015–2017) and found that just 4 of 514 (<1%) nests were parasitized (2015–2018). Our results indicate that the cowbird control program can at least temporarily be suspended, thereby reducing conservation reliance in the Kirtland's warbler and freeing funds for other management. We urge the conservation community to consider the use of adaptive management to reduce conservation reliance in other threatened and endangered taxa. © 2019 The Wildlife Society.     

Stationary underwater prey missed by reef herons,Egretta gularis: head position and light refraction at the moment of strike

Summary This paper attempts to verify the importance of spatial positioning of the eyes of reef heronsEgretta gularis schistacea, when coping with light refraction at the air-water interface. The herons' striking of prey, while their approach angle was restricted, was observed. (a) The herons' capture success in the restricted situation was markedly lower than in the unrestricted situation. (b) The points of strike (STR) in unsuccessful strikes differed from those of successful strikes, and from those of the unrestricted situation. (c) The larger the difference between the observed and the predicted ratio of prey depth to apparent prey depth, the higher the probability of missing a prey. These results support predictions of a model presented elsewhere (Katzir and Intrator 1987) that a heron will attempt to reach spatial positions at which prey's real depth and apparent depth are linearly correlated.     

BCL::Fold - De Novo Prediction of Complex and Large Protein Topologies by Assembly of Secondary Structure Elements

Computational de novo protein structure prediction is limited to small proteins of simple topology. The present work explores an approach to extend beyond the current limitations through assembling protein topologies from idealized α-helices and β-strands. The algorithm performs a Monte Carlo Metropolis simulated annealing folding simulation. It optimizes a knowledge-based potential that analyzes radius of gyration, β-strand pairing, secondary structure element (SSE) packing, amino acid pair distance, amino acid environment, contact order, secondary structure prediction agreement and loop closure. Discontinuation of the protein chain favors sampling of non-local contacts and thereby creation of complex protein topologies. The folding simulation is accelerated through exclusion of flexible loop regions further reducing the size of the conformational search space. The algorithm is benchmarked on 66 proteins with lengths between 83 and 293 amino acids. For 61 out of these proteins, the best SSE-only models obtained have an RMSD100 below 8.0 Å and recover more than 20% of the native contacts. The algorithm assembles protein topologies with up to 215 residues and a relative contact order of 0.46. The method is tailored to be used in conjunction with low-resolution or sparse experimental data sets which often provide restraints for regions of defined secondary structure.     

Social effects on fruit fly courtship song

Courtship behavior in Drosophila has often been described as a classic innate behavioral repertoire, but more recently extensive plasticity has been described. In particular, prior exposure to acoustic signals of con‐ or heterspecific males can change courtship traits in both sexes that are liable to be important in reproductive isolation. However, it is unknown whether male courtship song itself is socially plastic. We examined courtship song plasticity of two species in the Drosophila melanogaster subgroup. Sexual isolation between the species is influenced by two male song traits, the interpulse interval (IPI) and sinesong frequency (SSF). Neither of these showed plasticity when males had prior experience of con‐ and heterospecific social partners. However, males of both species produced longer bursts of song during courtship when they were exposed to social partners (either con‐ or heterospecific) than when they were reared in isolation. D. melanogaster carrying mutations affecting short‐ or medium‐term memory showed a similar response to the social environment, not supporting a role for learning. Our results demonstrate that the amount of song a male produces during courtship is plastic depending on the social environment, which might reflect the advantage of being able to respond to variation in intrasexual competition, but that song structure itself is relatively inflexible, perhaps due to strong selection against hybridization.     

The evolution of photosystem I in light of phage-encoded reaction centres

Recent structural determinations and metagenomic studies shed light on the evolution of photosystem I (PSI) from the homodimeric reaction centre of primitive bacteria to plant PSI at the top of the evolutionary development. The evolutionary scenario of over 3.5 billion years reveals an increase in the complexity of PSI. This phenomenon of ever-increasing complexity is common to all evolutionary processes that in their advanced stages are highly dependent on fine-tuning of regulatory processes. On the other hand, the recently discovered virus-encoded PSI complexes contain a minimal number of subunits. This may reflect the unique selection scenarios associated with viral replication. It may be beneficial for future engineering of productive processes to utilize ‘primitive’ complexes that disregard the cellular regulatory processes and to avoid those regulatory constraints when our goal is to divert the process from its original route. In this article, we discuss the evolutionary forces that act on viral reaction centres and the role of the virus-carried photosynthetic genes in the evolution of photosynthesis.