Virogenomics: the virus-host interaction revisited

Genomics tools allow us to assess gene expression 'genome wide' providing an unprecedented view on the host-side of the virus-host interaction. The success of the application of these tools crucially depends on our ability to reduce the total information load while increasing the information density of the data collected. In addition to the advanced data analysis algorithms, gene annotation-pathway databases, and theoretical models, specifically designed sets of complementary experiments are crucial in translating the collected genomics data into palatable knowledge. A better understanding of the molecular basis of virus-host interactions will support the rational design of improved and novel intervention strategies for viral infections.     

Pangloss revisited: a critique of the dilution effect and the biodiversity-buffers-disease paradigm

The twin concepts of zooprophylaxis and the dilution effect originated with vector-borne diseases (malaria), were driven forward by studies on Lyme borreliosis and have now developed into the mantra "biodiversity protects against disease". The basic idea is that by diluting the assemblage of transmission-competent hosts with non-competent hosts, the probability of vectors feeding on transmission-competent hosts is reduced and so the abundance of infected vectors is lowered. The same principle has recently been applied to other infectious disease systems--tick-borne, insect-borne, indirectly transmitted via intermediate hosts, directly transmitted. It is claimed that the presence of extra species of various sorts, acting through a variety of distinct mechanisms, causes the prevalence of infectious agents to decrease. Examination of the theoretical and empirical evidence for this hypothesis reveals that it applies only in certain circumstances even amongst tick-borne diseases, and even less often if considering the correct metric--abundance rather than prevalence of infected vectors. Whether dilution or amplification occurs depends more on specific community composition than on biodiversity per se. We warn against raising a straw man, an untenable argument easily dismantled and dismissed. The intrinsic value of protecting biodiversity and ecosystem function outweighs this questionable utilitarian justification.     

Scatter factor and the c-met receptor: a paradigm for mesenchymal/epithelial interaction

Epithelia and mesenchyme interact during various physiologic and pathologic processes. Scatter factor is a mesenchyme-derived cytokine that stimulates motility, proliferation, and morphogenesis of epithelia. Recent studies suggest that scatter factor and its receptor (c-met) mediate mesenchyme/epithelia signalling and even interconversion. In this mini-review, we will discuss how scatter factor and c-met may mediate interactions between mesenchyme and epithelia during embryogenesis, organ repair, and neoplasia.     

Cutting edge: paradigm revisited: antibody provides resistance to Listeria infection.

Listeriolysin O (LLO) is a secreted pore-forming toxin of the facultative intracellular bacterium Listeria monocytogenes. We assessed the ability of a murine anti-LLO mAb to affect the course of infection in mice challenged with Listeria. This mAb was previously shown to be capable of neutralizing LLO-mediated pore formation in vitro, and here we show that the passive administration of this Ab to mice before infection provides increased resistance. Mice treated with the mAb were protected from a lethal challenge with virulent Listeria and showed a significant reduction in Listeria burden during the first hours to days postinfection. These effects of the Ab were independent of host B or T cells, since treatment with the mAb provided enhanced resistance to SCID mice. The titer of anti-LLO Abs during the regular infection of mice with Listeria was found to be low to negative.     

Trichogin: a paradigm for lipopeptaibols.

Lipopeptaibols are members of a novel family of naturally occurring, short peptides with antimicrobial activity, characterized by a lipophilic acyl chain at the N-terminus, a high content of turn/helix inducing alpha-aminoisobutyric acid and a 1,2-amino alcohol at the C-terminus. Using solution methods, the prototypical lipopeptaibol trichogin GA IV and a large series of appropriately designed analogues were synthesized, which allow: (i) determination of the minimal lipid chain and peptide main-chain lengths for the onset of membrane activity, and (ii) exploitation of a number of physico-chemical techniques aimed at assessing the trichogin preferred conformation under a variety of conditions and at investigating its mechanism of interaction with the phospholipid membranes.     

Systemic inflammation in chronic obstructive pulmonary disease: a population-based study

Background

Investigations on pulmonary macrophages (MΦ) mostly focus on alveolar MΦ (AM) as a well-defined cell population. Characteristics of MΦ in the interstitium, referred to as lung interstitial MΦ (IM), are rather ill-defined. In this study we therefore aimed to elucidate differences between AM and IM obtained from human lung tissue.

Methods

Human AM and IM were isolated from human non-tumor lung tissue from patients undergoing lung resection. Cell morphology was visualized using either light, electron or confocal microscopy. Phagocytic activity was analyzed by flow cytometry as well as confocal microscopy. Surface marker expression was measured by flow cytometry. Toll-like receptor (TLR) expression patterns as well as cytokine expression upon TLR4 or TLR9 stimulation were assessed by real time RT-PCR and cytokine protein production was measured using a fluorescent bead-based immunoassay.

Results

IM were found to be smaller and morphologically more heterogeneous than AM, whereas phagocytic activity was similar in both cell types. HLA-DR expression was markedly higher in IM compared to AM. Although analysis of TLR expression profiles revealed no differences between the two cell populations, AM and IM clearly varied in cell reaction upon activation. Both MΦ populations were markedly activated by LPS as well as DNA isolated from attenuated mycobacterial strains (M. bovis H37Ra and BCG). Whereas AM expressed higher amounts of inflammatory cytokines upon activation, IM were more efficient in producing immunoregulatory cytokines, such as IL10, IL1ra, and IL6.

Conclusion

AM appear to be more effective as a non-specific first line of defence against inhaled pathogens, whereas IM show a more pronounced regulatory function. These dissimilarities should be taken into consideration in future studies on the role of human lung MΦ in the inflammatory response.     

Simulating mechanical consequences of voluntary movement upon whole-body equilibrium: the arm-raising paradigm revisited

Voluntary arm-raising movement performed during the upright human stance position imposes a perturbation to an already unstable bipedal posture characterised by a high body centre of mass (CoM). Inertial forces due to arm acceleration and displacement of the CoM of the arm which alters the CoM position of the whole body represent the two sources of disequilibrium. A current model of postural control explains equilibrium maintenance through the action of anticipatory postural adjustments (APAs) that would offset any destabilising effect of the voluntary movement. The purpose of this paper was to quantify, using computer simulation, the postural perturbation due to arm raising movement. The model incorporated four links, with shoulder, hip, knee and ankle joints constrained by linear viscoelastic elements. The input of the model was a torque applied at the shoulder joint. The simulation described mechanical consequences of the arm-raising movement for different initial conditions. The variables tested were arm inertia, the presence or not of gravity field, the initial standing position and arm movement direction. Simulations showed that the mechanical effect of arm-raising movement was mainly local, that is to say at the level of trunk and lower limbs and produced a slight forward displacement of the CoM (1.5 mm). Backward arm-raising movement had the same effect on the CoM displacement as the forward arm-raising movement. When the mass of the arm was increased, trunk rotation increased producing a CoM displacement in the opposite direction when compared to arm movement performed without load. Postural disturbance was minimised for an initial standing posture with the CoM vertical projection corresponding to the ankle joint axis of rotation. When the model was reduced to two degrees of freedom (ankle and shoulder joints only) the postural perturbation due to arm-raising movement increased compared to the four-joints model. On the basis of these results the classical assumption that APAs stabilise the CoM is challenged.     

Reproductive failure: a new paradigm for extinction

Extinction was recognized as a scientific fact 200 years ago, although no adequate paradigm has emerged to explain the process. Prevailing theory has focused on ‘cause(s)’ of extinction but has neglected ‘effect’ and ‘mechanism’. These omissions preclude the formulation of a functional paradigm necessary for remedial action in response to the impending anthropogenic mediated, worldwide extinction crisis. The new paradigm is defined as the multi‐generational, attritional loss of reproductive fitness. Stabilizing selection continuously adapts species to specific ecosystems, which often results in highly evolved species prone to extinction when environments shift. Some species survive by tracking the declining palaeoclimates in which they presumably evolved, often becoming relicts prior to extinction. Compelling new evidence shows that even mass extinctions are largely a result of environmental change leading to widespread, attritional reproductive decline, rather than a result of instantaneous global catastrophes.     

Flagellin perception: a paradigm for innate immunity

There are surprising similarities between how animals and plants perceive pathogens. In animals, innate immunity is based on the recognition of pathogen-associated molecular patterns. This is mediated by the Toll-like receptor (TLR) family, which rapidly induce the innate immunity response, a first line of defence against infectious disease. Plants have highly sensitive perception systems for general elicitors and they respond to these stimuli with a defence response. One of these general elicitors is flagellin, the main component of the bacterial flagellum. Genetic analysis in Arabidopsis has shown that FLS2, which encodes a receptor-like kinase, is essential for flagellin perception. FLS2 shares homology with the TLR family, and TLR5 is responsible for flagellin perception in mammals.     

Quantum computing: a new paradigm for ecology

A global technology arms race is underway to build evermore powerful and precise quantum computers. Quantum computers have the potential to tackle certain quantitative problems quicker than classical computers. The current focus of quantum computing is on pushing the boundaries of fundamental quantum information and commercial applications in industrial sectors, financial services, and other profit-led sectors, particularly where improvements in optimisation and sampling can improve increased economic return. We believe that ecologists could exploit the computational power of quantum computers because the statistical approaches commonly used in ecology already have proven pathways on quantum computers. Moreover, quantum computing could ultimately leapfrog our understanding of complex ecological systems, if the hardware, opportunity, and creativity of quantitative ecologists all align.