Dynamic Analysis of Soil Fertility Improvement: A Bioeconomic Model for Senegal

Land Economics/Use, Downloads July 2008 - June 2009: 8,

Promoting Farm Investment for Sustainable Intensification of African Agriculture

Farm Management, Downloads July 2008-July 2009: 9,

AXJ1749+684: a narrow emission-line galaxy with a flat X-ray spectrum

We report the serendipitous detection of an X-ray source, AXJ1749+684, with the ASCA Gas Imaging Spectrometer. AXJ1749+684 is identified with a LINER/starburst-type spiral galaxy KUG 1750+683A at a redshift z = 0.05. It has a hard X-ray spectrum, consistent with that of the X-ray background (XRB) in the 1-10 keV band. Despite the optical classification, the X-ray luminosity cannot be explained by starburst activity. Combined with spatial variations in the optical emission line ratios, this suggests the presence of an obscured Seyfert nucleus embedded within a starforming galaxy. Similar behaviour could explain the ambiguous properties of the faint narrow-line X-ray galaxies (NLXGs) emerging from deep X-ray surveys.Comment: MNRAS Letters in press, 6 pages, 7 figures in MNRAS LaTex styl

X-ray emission from the field of the hyperluminous IRAS galaxy IRASF15307+3252

We report on a 20-ks observation of the z = 0.93 hyperluminous galaxy IRAS F15307+3252 with the ROSAT HRI. No X-ray source is detected at the position of F15307+3252 at an upper limit of ∼4 × 10⁴³ erg s⁻¹. This is less than 2 × 10⁻⁴ of the bolometric luminosity of the object, and indicates either that the nucleus emits an unusually small fraction of its total power in X-rays, or that little of the nuclear X-ray flux is scattered into our line of sight by electrons. The lack of an X-ray detection around F15307+3252 also rules out it being at the centre of a cluster, such as is observed for IRAS P09104+4109. A weak, possibly extended, X-ray source is detected 13 arcsec south of the galaxy, spatially coincident with a clump of faint objects visible in a Keck K_s-band image of the field. This may be the core of a cluster near the line of sight to F15307+3252

The optical variability of the narrow line Seyfert 1 galaxy IRAS 13224-3809

We report on a short optical monitoring programme of the narrow-line Seyfert 1 Galaxy IRAS 13224-3809. Previous X-ray observations of this object have shown persistent giant variability. The degree of variability at other wavelengths may then be used to constrain the conditions and emission processes within the nucleus. Optical variability is expected if the electron population responsible for the soft X-ray emission is changing rapidly and Compton-upscattering infrared photons in the nucleus, or if the mechanism responsible for X-ray emission causes all the emission processes to vary together. We find that there is no significant optical variability with a firm upper limit of 2 per cent and conclude that the primary soft X-ray emission region produces little of the observed optical emission. The X-ray and optical emission regions must be physically distinct and any reprocessing of X-rays into the optical waveband occurs some distance from the nucleus. The lack of optical variability indicates that the energy density of infrared radiation in the nucleus is at most equal to that of the ultraviolet radiation since little is upscattered into the optical waveband. The extremely large X-ray variability of IRAS 13224-3809 may be explained by relativistic boosting of more modest variations. Although such boosting enhances X-ray variability over optical variability, this only partially explains the lack of optical variability.Comment: 5 pages with 8 postscript figures. Accepted for publication in MNRA

Birth/birth-death processes and their computable transition probabilities with biological applications

Birth-death processes track the size of a univariate population, but many biological systems involve interaction between populations, necessitating models for two or more populations simultaneously. A lack of efficient methods for evaluating finite-time transition probabilities of bivariate processes, however, has restricted statistical inference in these models. Researchers rely on computationally expensive methods such as matrix exponentiation or Monte Carlo approximation, restricting likelihood-based inference to small systems, or indirect methods such as approximate Bayesian computation. In this paper, we introduce the birth(death)/birth-death process, a tractable bivariate extension of the birth-death process. We develop an efficient and robust algorithm to calculate the transition probabilities of birth(death)/birth-death processes using a continued fraction representation of their Laplace transforms. Next, we identify several exemplary models arising in molecular epidemiology, macro-parasite evolution, and infectious disease modeling that fall within this class, and demonstrate advantages of our proposed method over existing approaches to inference in these models. Notably, the ubiquitous stochastic susceptible-infectious-removed (SIR) model falls within this class, and we emphasize that computable transition probabilities newly enable direct inference of parameters in the SIR model. We also propose a very fast method for approximating the transition probabilities under the SIR model via a novel branching process simplification, and compare it to the continued fraction representation method with application to the 17th century plague in Eyam. Although the two methods produce similar maximum a posteriori estimates, the branching process approximation fails to capture the correlation structure in the joint posterior distribution

Cash Crop and Foodgrain Productivity in Senegal: Historical View, New Survey Evidence, and Policy Implications

Crop Production/Industries, Productivity Analysis, Downloads July 2008 - June 2009: 10,

Loss of very-long O-antigen chains optimizes capsule-mediated immune evasion by Salmonella enterica serovar Typhi.

UnlabelledExpression of capsular polysaccharides is a variable trait often associated with more-virulent forms of a bacterial species. For example, typhoid fever is caused by the capsulated Salmonella enterica serovar Typhi, while nontyphoidal Salmonella serovars associated with gastroenteritis are noncapsulated. Here we show that optimization of the immune evasive properties conferred by the virulence-associated (Vi) capsular polysaccharide involved an additional alteration to the cell envelope of S. Typhi, namely inactivation of the fepE gene, encoding the regulator of very-long O-antigen chains. Introduction of the capsule-encoding viaB locus into the nontyphoidal S. enterica serovar Typhimurium reduced complement deposition in vitro and intestinal inflammation in a mouse colitis model. However, both phenotypes were markedly enhanced when the viaB locus was introduced into an S. Typhimurium fepE mutant, which lacks very-long O-antigen chains. Collectively, these data suggest that during the evolution of the S. Typhi lineage, loss of very-long O-antigen chains by pseudogene formation was an adaptation to maximize the anti-inflammatory properties of the Vi capsular polysaccharide.ImportanceGenomic comparison illustrates that acquisition of virulence factors by horizontal gene transfer is an important contributor to the evolution of enteric pathogens. Acquisition of complex virulence traits commonly involves horizontal transfer of a large gene cluster, and integration of the gene cluster into the host genome results in the formation of a pathogenicity island. Acquisition of the virulence-associated (Vi) capsular polysaccharide encoded by SPI7 (Salmonella pathogenicity island 7) was accompanied in the human-adapted Salmonella enterica serovar Typhi by inactivation of the fepE gene, encoding the regulator of very-long O-antigen chains. We show that the resulting loss of very-long O-antigen chains was an important mechanism for maximizing immune evasion mediated by the Vi capsular polysaccharide. These data suggest that successful incorporation of a capsular polysaccharide requires changes in the cell envelope of the hosting pathogen

Cystatins as calpain inhibitors: Engineered chicken cystatin- and stefin B-kininogen domain 2 hybrids support a cystatin-like mode of interaction with the catalytic subunit of μ-calpain

Within the cystatin superfamily, only kininogen domain 2 (KD2) is able to inhibit μ- and m-calpain. In an attempt to elucidate the structural requirements of cystatins for calpain inhibition, we constructed recombinant hybrids of human stefin B (an intracellular family 1 cystatin) with KD2 and Delta L110 deletion mutants of chicken cystatin-KD2 hybrids. Substitution of the N-terminal contact region of stefin B by the corresponding KD2 sequence resulted in a calpain inhibitor of K-i = 188 nM. Deletion of L110, which forms a beta -bulge in family 1 and 2 cystatins but is lacking in KD2, improved inhibition of mu -calpain 4- to 8-fold. All engineered cystatins were temporary inhibitors of calpain due to slow substrate-like cleavage of a single peptide bond corresponding to Gly9-Ala10 in chicken cystatin. Biomolecular interaction analysis revealed that, unlike calpastatin, the cystatin-type inhibitors do not bind to the calmodulin-like domain of the small subunit of calpain, and their interaction with the mu -calpain heterodimer is completely prevented by a synthetic peptide comprising subdomain B of calpastatin domain 1. Based on these results we propose that (i) cystatin-type calpain inhibitors interact with the active site of the catalytic domain of calpain in a similar cystatin-like mode as with papain and (ii) the potential for calpain inhibition is due to specific subsites within the papain-binding regions of the general cystatin fold