Endotoxin recognition: in fish or not in fish?

The interaction between pathogens and their multicellular hosts is initiated by activation of pathogen recognition receptors (PRRs). These receptors, that include most notably members of the toll-like receptor (TLR) family, recognize specific pathogen-associated molecular patterns (PAMPs). TLR4 is a central part of the receptor complex that is involved in the activation of the immune system by lipopolysaccharide (LPS) through the specific recognition of its endotoxic moiety (Lipid A). This is a critical event that is essential for the immune response to Gram-negative bacteria as well as the etiology of endotoxic shock. Interestingly, compared to mammals, fish are resistant to endotoxic shock. This in vivo resistance concurs with in vitro studies demonstrating significantly lowered sensitivity of fish leukocytes to LPS activation. Further, our in vitro analyses demonstrate that in trout mononuclear phagocytes, LPS fails to induce antiviral genes, an event that occurs downstream of TLR4 and is required for the development of endotoxic shock. Finally, an in silico approach that includes mining of different piscine genomic and EST databases, reveals the presence in fish of all of the major TLR signaling elements except for the molecules specifically involved in TLR4-mediated endotoxin recognition and signaling in mammals. Collectively, our analysis questions the existence of TLR4-mediated cellular responses to LPS in fish. We further speculate that other receptors, in particular beta-2 integrins, may play a primary role in the activation of piscine leukocytes by LPS.     

Oxidative stress in acute pancreatitis: lost in translation?

Abstract

Oxidative stress has been implicated in the pathogenesis of acute pancreatitis, a severe and debilitating inflammation of the pancreas that carries a significant mortality, and which imposes a considerable financial burden on the health system due to patient care. Although extensive efforts have been directed towards the elucidation of critical underlying mechanisms and the identification of novel therapeutic targets, the disease remains without a specific therapy. In experimental animal models of acute pancreatitis, increased oxidative stress and decreased antioxidant defences have been observed, changes also detected in patients clinically. However, despite the promise of studies evaluating the effects of antioxidants in these model systems, translation to the clinic has thus far been disappointing. This may reflect many factors involved in the design of both preclinical and clinical evaluations of antioxidant therapy, not least the fact that most experimental studies have focussed on pre-treatment rather than post-injury assessment. This review has examined evidence relating to the involvement of oxidative stress in the pathophysiology of acute pancreatitis, focussing on experimental models and the clinical experience, including the experimental techniques employed and potential of antioxidant therapy.     

Biotechnology in Japan: A lesson in logistics? Part II: The research policy

Research in the natural sciences in Japan is not bound by tradition to the same extent as it is in Europe and the USA. The great economic upsurge of the Japanese bio-industry has only occurred during the last 40 years. Its expansion is largely due to Japan's capabilities for rapid adaptation and commercial exploitation of new knowledge and skills. However, the creativity behind this speedy development did not emanate exclusively from the country's own resources. In this article, an attempt is made to trace the origins of high technology in the Japanese bio-industry and to illustrate the research policy facilitating its development.     

Biotechnology in Japan: A lesson in logistics? Part I: The political substrate

Japan, like Europe and the USA, has accepted the challenge of biotechnology, which opens up the way towards new fundamental knowledge and capabilities. Government and industry have joined forces to exploit biotechnology as a means of restructuring whole sectors of the country's economy, to ensure their continued viability in the coming decades. The strategy the Japanese have adopted in their bid for world leadership in this area differs from those of the Western countries. The extraordinarily complex infrastructure created for this purpose and its functional efficiency are unparalleled and evince the innate force and ingenuity of Japanese competition.     

Plasmodium vivax in Africa: hidden in plain sight?

People who live in tropical Africa, south of the Sahara, are predominantly negative for the Duffy blood-group antigen, which mediates invasion of reticulocytes by Plasmodium vivax. Recent reports of a parasite that was molecularly diagnosed as P. vivax from populations who are suspected, or known, to be Duffy negative confound a large body of evidence that states that invasion of P. vivax requires the Duffy antigen. If confirmed, one of several possible explanations is that P. vivax, which originated in Asia, is now evolving to exploit alternate invasion receptors in Africa.     

Epsins: adaptors in endocytosis?

Endocytic adaptor proteins select specific cargo for internalization by endocytosis through clathrin-coated pits or vesicles. Recent studies indicate that epsins might also be classified as adaptors.     

CNB: requiescat in pace?

Despite its failure to predict variation in secondary chemistry for many metabolites and taxa, the Carbon/Nutrient Balance (CNB) hypothesis continues to be invoked with regularity. According to Lerdau and Coley (2002) , the value of the hypothesis is that it explains phytochemical phenotypic plasticity outside of an evolutionary context. We contend that the CNB hypothesis impedes a more comprehensive understanding of plant biology and that an approach divorcing plant chemistry from function is inherently limited in its ability to predict responses of plants to the environmental conditions in which they have evolved. Although it is possible for a mechanistically flawed hypothesis to predict phenomena, such hypotheses almost always suffer a lack of generality. Lerdau and Coley argue that the limitations of the CNB model are its strengths, not its weaknesses, and set forth refinements that, in essence, further limit its applicability. We address these refinements and explore alternative adaptive explanations for adjustments of secondary metabolism in relation to resource availability and environmental variation. In view of its flawed nature and the existence of alternative approaches, CNB no longer warrants consideration as a viable hypothesis.     

Methylation: lost in hydroxylation?

Methylation of histone tails is a key determinant in forming active and silent states of chromatin. Histone methylation was regarded as irreversible until the recent identification of a lysine-specific histone demethylase (LSD1), which acts specifically on mono- and dimethylated histone H3 lysine 4. Here, we propose that the fission yeast protein Epe1 is a putative histone demethylase that could act by oxidative demethylation. Epe1 modulates the stability of silent chromatin and contains a JmjC domain. The Epe1 protein can be modelled onto the structure of the 2-oxoglutarate-Fe(II)-dependent dioxygenase, factor inhibiting hypoxia inducible factor (FIH), which is a protein hydroxylase that also contains a JmjC domain. Thus, Epe1 and certain other chromatin-associated JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification. Another intriguing possibility is that, by hydroxylating the methyl groups, Epe1 and certain other JmjC-domain proteins may be able to demethylate mono-, di- or trimethylated histones.     

The cytoskeleton in plasmodesmata: a role in intercellular transport?

Actin and myosin are components of the plant cell cytoskeleton that extend from cell to cell through plasmodesmata (PD), but it is unclear how they are organized within the cytoplasmic sleeve or how they might behave as regulatory elements. Early work used antibodies to locate actin and myosin to PD, at the electron microscope level, or to pitfields (aggregations of PD in the cell wall), using immunofluorescence techniques. More recently, a green fluorescent protein (GFP)-tagged plant myosin VIII was located specifically at PD-rich pitfields in cell walls. Application of actin or myosin disrupters may modify the conformation of PD and alter rates of cell-cell transport, providing evidence for a role in regulating PD permeability. Intriguingly, there is now evidence of differentiation between types of PD, some of which open in response to both actin and myosin disrupters, and others which are unaffected by actin disrupters or which close in response to myosin inhibitors. Viruses also interact with elements of the cytoskeleton for both intracellular and intercellular transport. The precise function of the cytoskeleton in PD may change during cell development, and may not be identical in all tissue types, or even in all PD within a single cell. Nevertheless, it is likely that actin- and myosin-associated proteins play a key role in regulating cell-cell transport, by interacting with cargo and loading it into PD, and may underlie the capacity for one-way transport across particular cell and tissue boundaries.     

Wing pigmentation in Calopteryx damselflies: a role in thermoregulation?

Body melanization may show adaptive variation related to thermoregulation ability, and it is to be expected that the degree of melanization will change among populations or closely related species across environmental gradients of solar radiation and/or environmental temperature. Some melanized secondary sexual traits may also play a role in sexual selection, leading to interpopulation variation, which would not be predicted by thermoregulation pressures alone. We studied the relationships between the interpopulation variation in wing pigmentation level (i.e. melanized secondary sexual trait) of two closely related species of Calopteryx damselfly, and both solar radiation and maximum environmental temperature estimates. Wing pigmentation differs between these species, is gender specific and is used in species' discrimination. Only Calopteryx virgo meridionalis males showed a significant negative partial correlation between wing pigmentation degree and temperature. However, C. virgo meridionalis females showed a positive significant partial correlation between wing pigmentation degree and solar radiation. Wing pigmentation in Calopteryx xanthostoma males was not related to solar radiation or temperature. Thus, thermoregulation pressures poorly explained the observed variations in wing pigmentation between populations, although they might have an adaptive significance at the species' level. As wing pigmentation showed important latitudinal variation, several other selection pressures which might act on melanized traits are briefly discussed. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 36–44.     

TGFβ signaling in Tribolium: vertebrate-like components in a beetle

The cytokines of the TGFβ superfamily are highly conserved in evolution and elicit a diverse range of cellular responses in all metazoa. In Drosophila, the signaling pathways of the two TGFβ subfamilies, Activins and Bone Morphogenetic Proteins (BMPs), have been well studied. To address the question of whether the findings from Drosophila are representative of insects in general, we analyzed the components of TGFβ-signaling present in the genome of the beetle Tribolium castaneum. We were able to identify orthologs of the BMPs Decapentaplegic and Glass bottom boat, of the Activins Activinβ and Dawdle, as well as orthologs of the less well-known ligands Myoglianin and Maverick, together with orthologs of all TGFβ receptors and cytoplasmic signal transducers present in Drosophila. This indicates that the diversity of TGFβ signaling components is generally well conserved between Drosophila and Tribolium. However, the genome of the beetle—and of the bee Apis mellifera—lacks an ortholog of the Drosophila BMP Screw but does contain a vertebrate-like BMP10 homolog which is not found in Drosophila. Concerning BMP inhibitors, Tribolium displays an even more vertebrate-like ensemble of components. We found two orthologs of the vertebrate DAN family, Dan and Gremlin, and show embryonic expression of a vertebrate-like BAMBI ortholog, all of which are absent in Drosophila. This suggests that Tribolium might have retained a more ancestral composition of TGFβ signaling components and that TGFβ signaling underwent considerable change in the Drosophila lineage. Tribolium is an excellent model to study the function of these ancestral signaling components in insects. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Kleptoplasty in an Antarctic dinoflagellate: caught in evolutionary transition?

Photosynthetic dinoflagellates contain a diverse collection of plastid types, a situation believed to have arisen from multiple endosymbiotic events. In addition, a number of heterotrophic (phagotrophic) dinoflagellates possess the ability to acquire chloroplasts temporarily by engulfing algae and retaining their chloroplasts in a functional state. These latter relationships typically last from a few days to weeks, at which point the chloroplasts lose function, are digested and replaced with newly acquired plastids. A novel and abundant dinoflagellate related to the icthyotoxic genera Karenia and Karlodinium was recently discovered by us in the Ross Sea, Antarctica. Sequencing of its plastid small subunit ribosomal gene indicated that it did not share evolutionary history with the plastids of Karenia or Karlodinium, but was closely related to the free-living haptophyte Phaeocystis antarctica, a species that often dominates phytoplankton blooms in the Ross Sea. Chloroplast uptake was observed to occur rapidly (within 2 days), with retention in cultures being long-lived (several months) but not permanent. The dinoflagellate was also incapable of growing indefinitely in continuous darkness with algae as prey. Our findings may indicate an emerging endosymbiotic event yielding a dinoflagellate that is presently neither purely phototrophic nor purely heterotrophic, but occupies a niche juxtaposed between these contrasting nutritional modes.     

π–π Interactions in Structural Stability: Role in RNA Binding Proteins

RNA binding proteins play significant roles in many bio-macromolecular systems. Aromatic amino acid residues are vital for several biological functions. In the present work, the influences of π–π interactions in RNA binding proteins are analyzed. There are a total of 3,396 π-residues in RNA binding proteins out of which 1,547, 1,241, and 608 are phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), respectively. Among these 945, 634, and 356 Phe, Tyr, and Trp residues, respectively, are involved in π–π interactions. The observations indicate that majority of the aromatic residues in RNA binding proteins are involved in π–π interactions. Side chain–side chain π–π interactions are the predominant type of interactions in RNA binding proteins. These π–π interactions stabilize the core regions within RNA binding proteins. π–π interacting residues are evolutionary conserved. Residue-wise analysis indicates that π–π interacting residues have higher long-range contacts and hence they are important in the global conformational stability of these proteins.     

Holliday junctions in the eukaryotic nucleus: resolution in sight?

The Holliday junction is a key recombination intermediate whose resolution generates crossovers. Interplay between recombination, repair and replication has moved the Holliday junction to the center stage of nuclear DNA metabolism. Holliday junction resolvases in the eukaryotic nucleus have long eluded identification. The endonucleases Mus81/Mms4-Eme1 and XPF-MEI-9/MUS312 are structurally related to the archaeal resolvase Hjc and were found to be involved in crossover formation in budding yeast and flies, respectively. Although these endonucleases might represent one class of eukaryotic resolvases, their substrate preference opens up the possibility that junctions other than classical Holliday junctions might contribute to crossovers. Holliday junction resolution to non-crossover products can also be achieved topologically, for example, by the action of RecQ-like DNA helicases combined with topoisomerase III.     

Gas vesicles in actinomycetes: old buoys in novel habitats?

Gas vesicles are gas-filled prokaryotic organelles that function as flotation devices. This enables planktonic cyanobacteria and halophilic archaea to position themselves within the water column to make optimal use of light and nutrients. Few terrestrial microbes are known to contain gas vesicles. Genome sequences that have become available recently for many bacteria from non-planktonic habitats reveal gas vesicle gene clusters in members of the actinomycete genera Streptomyces, Frankia and Rhodococcus, which typically live in soils and sediments. Remarkably, there is an additional level of complexity in cluster number and gene content. Here, we discuss whether putative gas vesicle proteins in these actinomycetes might actually be involved in flotation or whether they might fulfil other cellular functions.     

Mitochondrial Trafficking in Neurons: A Key Variable in Neurodegeneration?

Mitochondria are the proximate target of a number of different neurotoxins. Typically, impairing of the key bioenergetic function of mitochondria by toxins is considered as the main mechanism of action. However, the effective maintenance of energy generation in neurons depends on the biogenesis, trafficking, and degradation of mitochondria in addition to the traditional bioenergetic functions. We have recently demonstrated that glutamate alters both the trafficking and morphology of mitochondria in primary neurons. In addition, several other potential neurotoxins, including nitric oxide and zinc, inhibit mitochondrial movement and, in some cases, alter morphology too. This suggests that some part of the action of neurotoxins might include the impairment of mitochondrial trafficking in neurons, with the resultant failure of local ATP delivery.