S. mansoni Bolsters Anti-Viral Immunity in the Murine Respiratory Tract

The human intestinal parasite Schistosoma mansoni causes a chronic disease, schistosomiasis or bilharzia. According to the current literature, the parasite induces vigorous immune responses that are controlled by Th2 helper cells at the expense of Th1 helper cells. The latter cell type is, however, indispensable for anti-viral immune responses. Remarkably, there is no reliable literature among 230 million patients worldwide describing defective anti-viral immune responses in the upper respiratory tract, for instance against influenza A virus or against respiratory syncitial virus (RSV). We therefore re-examined the immune response to a human isolate of S. mansoni and challenged mice in the chronic phase of schistosomiasis with influenza A virus, or with pneumonia virus of mice (PVM), a mouse virus to model RSV infections. We found that mice with chronic schistosomiasis had significant, systemic immune responses induced by Th1, Th2, and Th17 helper cells. High serum levels of TNF-α, IFN-γ, IL-5, IL-13, IL-2, IL-17, and GM-CSF were found after mating and oviposition. The lungs of diseased mice showed low-grade inflammation, with goblet cell hyperplasia and excessive mucus secretion, which was alleviated by treatment with an anti-TNF-α agent (Etanercept). Mice with chronic schistosomiasis were to a relative, but significant extent protected from a secondary viral respiratory challenge. The protection correlated with the onset of oviposition and TNF-α-mediated goblet cell hyperplasia and mucus secretion, suggesting that these mechanisms are involved in enhanced immune protection to respiratory viruses during chronic murine schistosomiasis. Indeed, also in a model of allergic airway inflammation mice were protected from a viral respiratory challenge with PVM.     

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Background

Although it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.

Results

In total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.

Conclusions

Together, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.     

The human neonatal small intestine has the potential for arginine synthesis; developmental changes in the expression of arginine-synthesizing and -catabolizing enzymes

Background  

Milk contains too little arginine for normal growth, but its precursors proline and glutamine are abundant; the small intestine of rodents and piglets produces arginine from proline during the suckling period; and parenterally fed premature human neonates frequently suffer from hypoargininemia. These findings raise the question whether the neonatal human small intestine also expresses the enzymes that enable the synthesis of arginine from proline and/or glutamine. Carbamoylphosphate synthetase (CPS), ornithine aminotransferase (OAT), argininosuccinate synthetase (ASS), arginase-1 (ARG1), arginase-2 (ARG2), and nitric-oxide synthase (NOS) were visualized by semiquantitative immunohistochemistry in 89 small-intestinal specimens.     

The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase

Background

Soluble guanylate cyclases generate cyclic GMP when bound to nitric oxide, thereby linking nitric oxide levels to the control of processes such as vascular homeostasis and neurotransmission. The guanylate cyclase catalytic module, for which no structure has been determined at present, is a class III nucleotide cyclase domain that is also found in mammalian membrane-bound guanylate and adenylate cyclases.

Results

We have determined the crystal structure of the catalytic domain of a soluble guanylate cyclase from the green algae Chlamydomonas reinhardtii at 2.55 Å resolution, and show that it is a dimeric molecule.

Conclusion

Comparison of the structure of the guanylate cyclase domain with the known structures of adenylate cyclases confirms the close similarity in architecture between these two enzymes, as expected from their sequence similarity. The comparison also suggests that the crystallized guanylate cyclase is in an inactive conformation, and the structure provides indications as to how activation might occur. We demonstrate that the two active sites in the dimer exhibit positive cooperativity, with a Hill coefficient of ~1.5. Positive cooperativity has also been observed in the homodimeric mammalian membrane-bound guanylate cyclases. The structure described here provides a reliable model for functional analysis of mammalian guanylate cyclases, which are closely related in sequence.     

The rate of false positive sequence matches of peptides profiled by MALDI MS and identified by MS/MS

In most MALDI peptide profiling cases, sequencing is required to identify peptides of interest, preferentially by using different mass spectrometry techniques. Using identical samples, we determined the number of false positive matches in sequence of peptide identification using different mass spectrometers. This paper demonstrates that the reliability of the identification phase greatly benefits from concerted MS-technologies and determines the influence of mass accuracy, signal-to-noise and statistical score on peptide identification.     

Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks

The HIV-1 genome is highly heterogeneous. This variation affords the virus a wide range of molecular properties, including the ability to infect cell types, such as macrophages and lymphocytes, expressing different chemokine receptors on the cell surface. In particular, R5 HIV-1 viruses use CCR5 as co-receptor for viral entry, X4 viruses use CXCR4, whereas some viral strains, known as R5X4 or D-tropic, have the ability to utilize both co-receptors. X4 and R5X4 viruses are associated with rapid disease progression to AIDS. R5X4 viruses differ in that they have yet to be characterized by the examination of the genetic sequence of HIV-1 alone. In this study, a series of experiments was performed to evaluate different strategies of feature selection and neural network optimization. We demonstrate the use of artificial neural networks trained via evolutionary computation to predict viral co-receptor usage. The results indicate identification of R5X4 viruses with predictive accuracy of 75.5%.     

Decreasing the Abundance of Juncus effusus on Former Agricultural Lands with Noncalcareous Sandy Soils: Possible Effects of Liming and Soil Removal

More and more agricultural land in the Netherlands is becoming available for ecological restoration projects. However, nutrient levels in the top layer of the soils are high because the agricultural lands have been heavily fertilized for decades. As drainage ditches are no longer maintained when agricultural use ends, the agricultural lands usually become much wetter. As a result, former agricultural soils tend to develop extensive monotonous stands of Juncus effusus , which have little value from an ecological point of view. In this article, we present the results of field measurements/observations and experiments to examine the relationship between nutrient availability and J. effusus growth. In addition, we present and discuss results of experiments to study the potential beneficial effects of liming. Our findings show that the growth of J. effusus on moist or wet soils seems to be strongly determined by the Olsen-P concentration in the soil. The restoration of diverse, species-rich vegetation types on former agricultural lands with a noncalcareous sandy soil will in most cases not be possible within a reasonable time span without topsoil removal. Liming might be a valuable additional measure to enhance the quality of the soil after topsoil removal, and to prevent mobilization of P to groundwater or surface water. If removal of the topsoil is considered to create P limitation, it is important to study P concentrations at various depths to establish the amount of soil that has to be removed.     

Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene

The effect of solR inactivation on the metabolism of Clostridium acetobutylicum was examined using fermentation characterization and metabolic flux analysis. The solR-inactivated strain (SolRH) of this study had a higher rate of glucose utilization and produced higher solvent concentrations (by 25%, 14%, and 81%, respectively, for butanol, acetone, and ethanol) compared to the wild type. Strain SolRH(pTAAD), carrying a plasmid-encoded copy of the bifunctional alcohol/aldehyde dehydrogenase gene (aad) used in butanol production, produced even higher concentrations of solvents (by 21%, 45%, and 62%, respectively, for butanol, acetone, and ethanol) than strain SolRH. Clarithromycin used for strain SolRH maintenance during SolRH(pTAAD) fermentations did not alter product formation; however, tetracycline used for pTAAD maintenance resulted in 90% lower solvent production. Journal of Industrial Microbiology & Biotechnology (2001) 27, 322–328. Received 12 September 2000/ Accepted in revised form 21 July 2001     

Restoration of cut‐over bogs by floating raft formation: An experimental feasibility study

Abstract. Stimulation of floating peat by the introduction of poorly humified peat from four cut‐over bogs in The Netherlands was studied in a one‐year outdoor experiment. The pH of the various peat substrates was increased by adding different amounts of lime: 0–2 to 4–8 g‐CaCO₃.kg^‐1 fresh peat. Both peat type and lime addition were found to affect the buoyancy of the peat substrates. Low nutrient concentrations in the peat, together with a high bulk density, proved to be unfavourable for creating floating peat. Three of the peat types proved to be too acidic (pH < 4.5) to produce sufficient methane (ca. 400–600 μmol.L^‐1), and buoyancy was only achieved if lime was mixed in with the peat. The smallest amount of lime added (2 g.kg^‐1 fresh peat) was sufficient to maintain buoyancy for at least one year. Lime addition did not stimulate nutrient mobilization by mineralization, although P, N and K concentrations in the peat water were relatively high. It is concluded that floating peat can be initiated by the introduction of poorly humified peat. If the peat substrates are too acidic, lime can be added to stimulate buoyancy of the peat. Results are discussed in relation to restoration prospects.