The phagocytosis and toxicity of amorphous silica

Background

Inhalation of crystalline silica is known to cause an inflammatory reaction and chronic exposure leads to lung fibrosis and can progress into the disease, silicosis. Cultured macrophages bind crystalline silica particles, phagocytose them, and rapidly undergo apoptotic and necrotic death. The mechanism by which particles are bound and internalized and the reason particles are toxic is unclear. Amorphous silica has been considered to be a less toxic form, but this view is controversial. We compared the uptake and toxicity of amorphous silica to crystalline silica.

Methodology/Principal Findings

Amorphous silica particles are phagocytosed by macrophage cells and a single internalized particle is capable of killing a cell. Fluorescent dextran is released from endo-lysosomes within two hours after silica treatment and Caspase-3 activation occurs within 4 hours. Interestingly, toxicity is specific to macrophage cell lines. Other cell types are resistant to silica particle toxicity even though they internalize the particles.The large and uniform size of the spherical, amorphous silica particles allowed us to monitor them during the uptake process. In mCherry-actin transfected macrophages, actin rings began to form 1-3 minutes after silica binding and the actin coat disassembled rapidly following particle internalization. Pre-loading cells with fluorescent dextran allowed us to visualize the fusion of phagosomes with endosomes during internalization. These markers provided two new ways to visualize and quantify particle internalization. At 37°C the rate of amorphous silica internalization was very rapid regardless of particle coating. However, at room temperature, opsonized silica is internalized much faster than non-opsonized silica.

Conclusions/Significance

Our results indicate that amorphous and crystalline silica are both phagocytosed and both toxic to mouse alveolar macrophage (MH-S) cells. The pathway leading to apoptosis appears to be similar in both cases. However, the result suggests a mechanistic difference between FcγRIIA receptor-mediated and non-opsonized silica particle phagocytosis.     

The origins of bioinformatics

Bioinformatics is often described as being in its infancy, but computers emerged as important tools in molecular biology during the early 1960s. A decade before DNA sequencing became feasible, computational biologists focused on the rapidly accumulating data from protein biochemistry. Without the benefits of super computers or computer networks, these scientists laid important conceptual and technical foundations for bioinformatics today.     

The origins of plastids

A new theory of plastid origins is presented in which only two symbiotic events are needed to explain the origin of the six fundamentally different types of plastid, which all probably originated in anteriorly biciliated phagotrophic cells. Four of them can be derived directly from a single endosymbiotic cyanophyte by the independent loss of different cyanophyte characters and the evolution of new characters in the immediate descendants of this primary endosymbiosis. Retention of the phagosomal membrane as well as the prokaryotic plasma and outer membrane could produce the dinozoan and euglenid plastids with three envelope membranes, whereas the loss of the phagosomal membrane could produce the two-membraned envelopes characteristic of the Biliphyta and Verdiplantae*. The phycobilins were retained essentially unaltered in the Biliphyta, but are modified or lost in the other lines. In the ancestor of the Euglenozoa and Verdiplantae they were replaced by chlorophyll b. In the ancestor of algae possessing chlorophyll c they were modified to the cryptophyte type, concomitantly with the evolution of chlorophyll c₂: one line of descent from this ancestor produced the dinozoan plastid by the complete loss of phycobilins, while the other was incorporated by endosymbiosis into another phagotrophic bibiliate to produce the cryptophyte plastid. The latter evolved into the chromophyte plastid by the loss of phycobilins and the evolution of chlorophyll c₂. The conversion of the endosymbiont into a plastid depended on the evolution of a system to transport proteins into it. I argue that this occurred by the modification of the pre-existing mitochondrial transport system, and that the major modifications needed to adjust this to plastids with more than two envelope membranes led to evolution of a new tubular or disc-like morphology for the mitochondrial cristae of these groups. This new cristal morphology is maintained by stabilizing selection even in species that have secondarily lost plastids.     

The origins of molluscs

The interrelationships and evolutionary history of molluscs have seen great advances in the last decade. Recent phylogenetic studies have allowed alternative morphology‐based evolutionary scenarios to be tested and, most significantly, shown that the aplacophorans are sister group to polyplacophorans (chitons), corroborating palaeontological and embryological evolutionary scenarios in which aplacophorans are secondarily simplified from a chiton‐like ancestor. Aplacophoran morphology therefore does not represent the plesiomorphic condition for molluscs as a whole. The mollusc crown group radiated in the Early Cambrian, and rapidly thereafter, stem lineages to the major molluscan classes emerged: cephalopods, gastropods, bivalves (= pelecypods), monoplacophorans, rostroconchs (inferred stem scaphopods) and aculiferans. This attests to the fast, adaptive radiation of the crown group during the Cambrian explosion. Kimberella from the latest Ediacaran exhibits several molluscan traits, which justifies its position as a molluscan stem‐group member, rather than as a more basal Lophotrochozoan. The interrelationships among the conchiferan molluscs are still a matter of contention and require further palaeontological and molecular phylogenetic scrutiny.     

The origins of nations

Although the nation, as a named community of history and culture, possessing a common territory, economy, mass education system and common legal rights, is a relatively modern phenomenon, its origins can be traced back to pre‐modern ethnic communities. Such named ethnies with their myths of common descent, common memories, culture and solidarity, and associations with a homeland, are found in both the ancient and the medieval periods in many areas of the world. Two kinds of ethnie are important for the origins and routes of the formation of nations. Territorial, ‘civic’ nations tend to develop from aristocratic ‘lateral’ ethnies through a process of ‘bureaucratic incorporation’ of outlying regions and lower classes into the ethnic culture of the upper classes, as occurred in France, England and Spain. The more numerous ‘ethnic’ nations, on the other hand, have emerged from demotic ‘vertical’ ethnies through processes of cultural mobilization that turn an often religiously defined and passive community into an active, politicized nation. Here the intellectuals and professionals replace the state as agents of popular mobilization, creating new ‘maps’ and ‘moralities’ through the uses of landscape and golden ages of a rediscovered and reconstructed communal past, as in Ireland, Finland and Switzerland. It is from these often ancient ties and sentiments that modern nations draw much of their power and durability today.     

The throwing hypothesis and hominid origins

Fifer (1987) has provided a very useful hypothesis to explain the advent of bipedal gait and locomotion. Through re-focusing attention on a functional argument centred on throwing behaviour he has invigorated the debate surrounding the origins of thehominidae. The present article provides evidence of plastic and pathological osteological indicators of throwing that may aid in more precisely elucidating the timing of this adaptative event and its subsequent development.     

Human origins and the origins of humanity

As long asHomo sapiens was considered to be separated from the rest of the natural world by an unbridgeable if narrow gulf, there was no difficulty in defining, or at least in recognizing, what is «human» and what is not. But with the advent of evolutionary thought came the realization that the concept of humanity lacks any firm definition. While adminitting that any definition of humanness must be essentially intuitive and thus arbitrary, this article examines various innovations in the human fossil and archaeological records and discusses at what point humanness could be said to have been achieved. This task is complicated by the fact that there appears to be no correspondence whatever between biological and cultural innovation.     

Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery

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The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated.In this paper we review how the spliceosome has evolved and discuss its origin and subsequent evolution in light of different general hypotheses on the evolution of complexity. Comparative analyses have established that the catalytic core of this ribonucleoprotein (RNP) complex, as well as the spliceosomal introns, evolved from self-splicing group II introns. Most snRNAs evolved from intron fragments and the essential Prp8 protein originated from the protein that is encoded by group II introns. Proteins that functioned in other RNA processes were added to this core and extensive duplications of these proteins substantially increased the complexity of the spliceosome prior to the eukaryotic diversification. The splicing machinery became even more complex in animals and plants, yet was simplified in eukaryotes with streamlined genomes. Apparently, the spliceosome did not evolve its complexity gradually, but in rapid bursts, followed by stagnation or even simplification. We argue that although both adaptive and neutral evolution have been involved in the evolution of the spliceosome, especially the latter was responsible for the emergence of an enormously complex eukaryotic splicing machinery from simple self-splicing sequences.

Reviewers

This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Vivek Anantharaman.

     

The protistan origins of animals and fungi

Recent molecular studies suggest that Opisthokonta, the eukaryotic supergroup including animals and fungi, should be expanded to include a diverse collection of primitively single-celled eukaryotes previously classified as Protozoa. These taxa include corallochytreans, nucleariids, ministeriids, choanoflagellates, and ichthyosporeans. Assignment of many of these taxa to Opisthokonta remains uncorroborated as it is based solely on small subunit ribosomal RNA trees lacking resolution and significant bootstrap support for critical nodes. Therefore, important details of the phylogenetic relationships of these putative opisthokonts with each other and with animals and fungi remain unclear. We have sequenced elongation factor 1-alpha (EF-1alpha), actin, beta-tubulin, and HSP70, and/or alpha-tubulin from representatives of each of the proposed protistan opisthokont lineages, constituting the first protein-coding gene data for some of them. Our results show that members of all opisthokont protist groups encode a approximately 12-amino acid insertion in EF-1alpha, previously found exclusively in animals and fungi. Phylogenetic analyses of combined multigene data sets including a diverse set of opisthokont and nonopisthokont taxa place all of the proposed opisthokont protists unequivocally in an exclusive clade with animals and fungi. Within this clade, the nucleariid appears as the closest sister taxon to fungi, while the corallochytrean and ichthyosporean form a group which, together with the ministeriid and choanoflagellates, form two to three separate sister lineages to animals. These results further establish Opisthokonta as a bona fide taxonomic group and suggest that any further testing of the legitimacy of this taxon should, at the least, include data from opisthokont protists. Our results also underline the critical position of these "animal-fungal allies" with respect to the origin and early evolution of animals and fungi.     

The origins and evolution of ubiquitination sites

Protein ubiquitination is central to the regulation of various pathways in eukaryotes. The process of ubiquitination and its cellular outcome were investigated in hundreds of proteins to date. Despite this, the evolution of this regulatory mechanism has not yet been addressed comprehensively. Here, we quantify the rates of evolutionary changes of ubiquitination and SUMOylation (Small Ubiquitin-like MOdifier) sites. We estimate the time at which they first appeared, and compare them to acetylation and phosphorylation sites and to unmodified residues. We observe that the various modification sites studied exhibit similar rates. Mammalian ubiquitination sites are weakly more conserved than unmodified lysine residues, and a higher degree of relative conservation is observed when analyzing bona fide ubiquitination sites. Various reasons can be proposed for the limited level of excess conservation of ubiquitination, including shifts in locations of the sites, the presence of alternative sites, and changes in the regulatory pathways. We observe that disappearance of sites may be compensated by the presence of a lysine residue in close proximity, which is significant when compared to evolutionary patterns of unmodified lysine residues, especially in disordered regions. This emphasizes the importance of analyzing a window in the vicinity of functional residues, as well as the capability of the ubiquitination machinery to ubiquitinate residues in a certain region. Using prokaryotic orthologs of ubiquitinated proteins, we study how ubiquitination sites were formed, and observe that while sometimes sequence additions and rearrangements are involved, in many cases the ubiquitination machinery utilizes an already existing sequence without significantly changing it. Finally, we examine the evolution of ubiquitination, which is linked with other modifications, to infer how these complex regulatory modules have evolved. Our study gives initial insights into the formation of ubiquitination sites, their degree of conservation in various species, and their co-evolution with other posttranslational modifications.