THE PONTIA DAPLIDICE-ED USA HYBRID ZONE IN NORTHWESTERN ITALY

The pierid butterflies Pontia daplidice and P. edusa, parapatrically distributed in southern Europe, have very similar morphologies and life histories, but show fixed differences at four allozyme markers. We sampled these allozymes in a 28-population transect north of Genoa in Italy, through the hybrid zone where these taxa meet. We used the numerical techniques developed for hybrid zone analysis to study the patterns of genetic differentiation and their underlying evolutionary causes. The hybrid zone is characterized by a very short and steep central region, flanked by broad tails of introgression extended up to 100 km in either direction. From mean two-locus disequilibium of D = 0.148 (maximum-likelihood two-unit support limits 0.139-0.153), and after accounting for minor differences in the center locations of the single-locus clines, which act to bias the dispersal estimate, we estimated a dispersal rate of σ = 4.4 (3.7-5.5) km/gen^1/2. The effective selection needed to maintain the steep central portion is strong, 0.47 < s? < 0.64, when combined over potential intrinsic (genetic background) and extrinsic (ecological) sources of selection. The clines in allozyme loci showed variation that was significantly different between the most divergent shapes, and the differences are attributable to different degrees of introgression on the edusa side of the zone. The average selection acting on individual allozyme loci was high at s_???e  1.5%, but because of the narrowness of the central region of the cline, we suspect that this estimate is somewhat biased by selection on loci closely linked to the allozyme markers. A common question for taxa that show fixed allozyme differences in parapatry is whether or not they are genetically isolated. A fairly general measure of genetic isolation across hybrid zones is the time, T, that it takes a neutral allele to cross the hybrid zone and recombine into the opposite genetic background, given by T = (β/σ)², where β is the barrier strength of the hybrid zone. Genetic isolation in the Pontia zone is weak, with T  25 generations for most allozyme markers. By this measure, populations of daplidice and edusa on opposite sides of the hybrid zone share more identical-by-descent alleles than do populations of phenotypically pure daplidice in, say, France and Morocco. Accordingly, we think it best for systematists to consider edusa as a well-marked subspecies of P. daplidice.     

Isolation of a human serum protein that inhibits the growth of Cryptococcus neoformans

Human serum at 5 to 10% (v/v) in tissue culture medium RPMI-1640, inhibits the growth of Cryptococcus neoformans by 80 to 93%. Serum fractionated on molecular sieve columns (Sephadex G-200) yielded an active protein fraction. This fraction at 100 μg protein/ml inhibited the growth of C. neoformans by 54%. When an active G-200 fraction was applied to a dye affinity column (Affi-Gel Blue) the fraction with inhibitory activity was bound by the column and was eluted with 1.4 M NaCl in 0.1 M phosphate buffer (pH 7.4). The bound fraction at 62.5 μg protein/ml inhibited C. neoformans growth by 82%. On native polyacrylamide gel electrophoresis (Nu-PAGE) the bound fraction migrated as a major and a minor band. Under the reducing conditions of sodium dodecyl sulfate (SDS)-PAGE the bound fraction yielded 4 prominent bands with MW ranging from 175 kDa to 45 kDa. Purification of the active Sephadex G-200 peak was achieved using an anion exchange column (DEAE-Sephacel). Protein eluted with 0.1 M NaCl had strong anticryptococcal activity (12.5 μg/ml, 79% inhibition), which in SDS-PAGE migrated as a single band with an approximate MW of 85 kDA. This protein appears important in natural host resistance to C. neoformans and polymorphisms or deficiencies may have epidemiologic and diagnostic relevance. This revised version was published online in August 2006 with corrections to the Cover Date.     

Comparing concentration‐based (AOT40) and stomatal uptake (PODY) metrics for ozone risk assessment to European forests

Tropospheric ozone (O₃) produces harmful effects to forests and crops, leading to a reduction of land carbon assimilation that, consequently, influences the land sink and the crop yield production. To assess the potential negative O₃ impacts to vegetation, the European Union uses the Accumulated Ozone over Threshold of 40 ppb (AOT40). This index has been chosen for its simplicity and flexibility in handling different ecosystems as well as for its linear relationships with yield or biomass loss. However, AOT40 does not give any information on the physiological O₃ uptake into the leaves since it does not include any environmental constraints to O₃ uptake through stomata. Therefore, an index based on stomatal O₃ uptake (i.e. PODY), which describes the amount of O₃ entering into the leaves, would be more appropriate. Specifically, the PODY metric considers the effects of multiple climatic factors, vegetation characteristics and local and phenological inputs rather than the only atmospheric O₃ concentration. For this reason, the use of PODY in the O₃ risk assessment for vegetation is becoming recommended. We compare different potential O₃ risk assessments based on two methodologies (i.e. AOT40 and stomatal O₃ uptake) using a framework of mesoscale models that produces hourly meteorological and O₃ data at high spatial resolution (12 km) over Europe for the time period 2000–2005. Results indicate a remarkable spatial and temporal inconsistency between the two indices, suggesting that a new definition of European legislative standard is needed in the near future. Besides, our risk assessment based on AOT40 shows a good consistency compared to both in‐situ data and other model‐based datasets. Conversely, risk assessment based on stomatal O₃ uptake shows different spatial patterns compared to other model‐based datasets. This strong inconsistency can be likely related to a different vegetation cover and its associated parameterizations.     

Complexity and algorithms for copy-number evolution problems

Background

Cancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations is copy number aberrations, which alter the number of copies of genomic regions. The number of copies of each position along a chromosome constitutes the chromosome’s copy-number profile. Understanding how such profiles evolve in cancer can assist in both diagnosis and prognosis.

Results

We model the evolution of a tumor by segmental deletions and amplifications, and gauge distance from profile \(\mathbf {a}\) to \(\mathbf {b}\) by the minimum number of events needed to transform \(\mathbf {a}\) into \(\mathbf {b}\). Given two profiles, our first problem aims to find a parental profile that minimizes the sum of distances to its children. Given k profiles, the second, more general problem, seeks a phylogenetic tree, whose k leaves are labeled by the k given profiles and whose internal vertices are labeled by ancestral profiles such that the sum of edge distances is minimum.

Conclusions

For the former problem we give a pseudo-polynomial dynamic programming algorithm that is linear in the profile length, and an integer linear program formulation. For the latter problem we show it is NP-hard and give an integer linear program formulation that scales to practical problem instance sizes. We assess the efficiency and quality of our algorithms on simulated instances.

Availability

https://github.com/raphael-group/CNT-ILP

     

Further studies on the pharmacological features of the nociceptin/orphanin FQ receptor ligand ZP120

ZP120 is a nociceptin/orphanin FQ (N/OFQ) peptide receptor (NOP) ligand. In previous studies, the effects of ZP120 were found to be sensitive to J-113397 in mouse tissues while resistant to UFP-101 in rat tissues. The aim of this study was to further investigate the ZP120 pharmacological profile using mouse and rat preparations, J-113397 and UFP-101, as well as NOP receptor knockout (NOP(-/-)) mice. Electrically stimulated mouse and rat vas deferens were used to characterize the pharmacology of ZP120 in vitro. For in vivo studies the tail-withdrawal assay was performed in wild type (NOP(+/+)) and NOP knockout (NOP(-/-)) mice. In the mouse and rat vas deferens ZP120 mimicked the effects of N/OFQ showing higher potency but lower maximal effects. In both preparations, J-113397 antagonized N/OFQ and ZP120 effects showing similar pK(B) values ( approximately 7.8). UFP-101 antagonized the actions of N/OFQ (pK(B) values approximately 7.3) but did not modify the effects of ZP120. The inhibitory effects of N/OFQ and ZP120 were no longer evident in vas deferens tissues taken from NOP(-/-) mice. In NOP(+/+) mice subjected to the tail-withdrawal assay, ZP120 (1 nmol) mimicked the pronociceptive action of N/OFQ (10 nmol), producing longer lasting effects. The effects of both peptides were absent in NOP(-/-) animals. The NOP receptor ligand ZP120 is a high potency NOP selective partial agonist able to evoke long-lasting effects; its diverse antagonist sensitivity in comparison with N/OFQ may derive from different modality of binding to the NOP receptor.     

Effect of ambient air pollution on the incidence of appendicitis

Background

The pathogenesis of appendicitis is unclear. We evaluated whether exposure to air pollution was associated with an increased incidence of appendicitis.

Methods

We identified 5191 adults who had been admitted to hospital with appendicitis between Apr. 1, 1999, and Dec. 31, 2006. The air pollutants studied were ozone, nitrogen dioxide, sulfur dioxide, carbon monoxide, and suspended particulate matter of less than 10 μ and less than 2.5 μ in diameter. We estimated the odds of appendicitis relative to short-term increases in concentrations of selected pollutants, alone and in combination, after controlling for temperature and relative humidity as well as the effects of age, sex and season.

Results

An increase in the interquartile range of the 5-day average of ozone was associated with appendicitis (odds ratio [OR] 1.14, 95% confidence interval [CI] 1.03–1.25). In summer (July–August), the effects were most pronounced for ozone (OR 1.32, 95% CI 1.10–1.57), sulfur dioxide (OR 1.30, 95% CI 1.03–1.63), nitrogen dioxide (OR 1.76, 95% CI 1.20–2.58), carbon monoxide (OR 1.35, 95% CI 1.01–1.80) and particulate matter less than 10 μ in diameter (OR 1.20, 95% CI 1.05–1.38). We observed a significant effect of the air pollutants in the summer months among men but not among women (e.g., OR for increase in the 5-day average of nitrogen dioxide 2.05, 95% CI 1.21–3.47, among men and 1.48, 95% CI 0.85–2.59, among women). The double-pollutant model of exposure to ozone and nitrogen dioxide in the summer months was associated with attenuation of the effects of ozone (OR 1.22, 95% CI 1.01–1.48) and nitrogen dioxide (OR 1.48, 95% CI 0.97–2.24).

Interpretation

Our findings suggest that some cases of appendicitis may be triggered by short-term exposure to air pollution. If these findings are confirmed, measures to improve air quality may help to decrease rates of appendicitis.Appendicitis was introduced into the medical vernacular in 1886.¹ Since then, the prevailing theory of its pathogenesis implicated an obstruction of the appendiceal orifice by a fecalith or lymphoid hyperplasia.² However, this notion does not completely account for variations in incidence observed by age,^3,4 sex,^3,4 ethnic background,^3,4 family history,⁵ temporal–spatial clustering⁶ and seasonality,^3,4 nor does it completely explain the trends in incidence of appendicitis in developed and developing nations.^3,7,8The incidence of appendicitis increased dramatically in industrialized nations in the 19th century and in the early part of the 20th century.¹ Without explanation, it decreased in the middle and latter part of the 20th century.³ The decrease coincided with legislation to improve air quality. For example, after the United States Clean Air Act was passed in 1970,⁹ the incidence of appendicitis decreased by 14.6% from 1970 to 1984.³ Likewise, a 36% drop in incidence was reported in the United Kingdom between 1975 and 1994¹⁰ after legislation was passed in 1956 and 1968 to improve air quality and in the 1970s to control industrial sources of air pollution. Furthermore, appendicitis is less common in developing nations; however, as these countries become more industrialized, the incidence of appendicitis has been increasing.⁷Air pollution is known to be a risk factor for multiple conditions, to exacerbate disease states and to increase all-cause mortality.¹¹ It has a direct effect on pulmonary diseases such as asthma¹¹ and on nonpulmonary diseases including myocardial infarction, stroke and cancer.^11–13 Inflammation induced by exposure to air pollution contributes to some adverse health effects.^14–17 Similar to the effects of air pollution, a proinflammatory response has been associated with appendicitis.^18–20We conducted a case–crossover study involving a population-based cohort of patients admitted to hospital with appendicitis to determine whether short-term increases in concentrations of selected air pollutants were associated with hospital admission because of appendicitis.     

In Situ Investigation of Leaf Water Status by Portable Unilateral Nuclear Magnetic Resonance

A portable unilateral nuclear magnetic resonance (NMR) instrument was used to detect in field conditions the water status of leaves of herbaceous crops (Zea mays, Phaseolus vulgaris), mesophyllous trees (Populus nigra), and natural Mediterranean vegetation characterized by water-spending shrubs (Cistus incanus) and water-saving sclerophyllous trees (Quercus ilex). A good relationship was observed between NMR signal, leaf relative water content, and leaf transpiration in herbaceous leaves undergoing fast dehydration or slowly developing a drought stress. A relationship was also observed between NMR signal and water potential of Populus leaves during the development of a water stress and when leaves recovered from the stress. In the natural vegetation, the relationship between NMR signal and water status was found in Cistus, the species characterized by high transpiration rates, when measured during a drought stress period and after a rainfall. In the case of the sclerophyllous Quercus, the NMR signal, the relative water content, and the transpiration rate did not change at different leaf water status, possibly because a large amount of water is compartmentalized in cellular structures and macromolecules. The good association between NMR signal and relative water content was lost in leaves exposed for 24 h to dehydration or to an osmotic stress caused by polyethylene glycol feeding. At this time, the transverse relaxation time became longer than in leaves maintained under optimal water conditions, and two indicators of membrane damage, the ion leakage and the emission of products of membrane lipoxygenation [(Z)-3-hexenal, (Z)-3-hexenol, and (E)-2-hexenol], increased. These results taken all together give information on the physiological state of a leaf under a developing stress and show the usefulness of the NMR instrumentation for screening vegetation health and fitness in natural and cultivated conditions. It is concluded that the portable unilateral NMR instrument may be usefully employed in field conditions to monitor nondestructively the water status of plants and to assist agricultural practices, such as irrigation scheduling, to minimize stomatal closure and the consequent limitation to plant production.     

Role of CCL3/MIP-1α and CCL5/RANTES during acute Trypanosoma cruzi infection in rats

Chagas’ disease is caused by Trypanosoma cruzi infection and is characterized by chronic fibrogenic inflammation and heart dysfunction. Chemokines are produced during infection and drive tissue inflammation. In rats, acute infection is characterized by intense myocarditis and regression of inflammation after control of parasitism. We investigated the role of CCL3 and CCL5 during infection by using DNA vaccination encoding for each chemokine separately or simultaneously. MetRANTES treatment was used to evaluate the role of CCR1 and CCR5, the receptors for CCL3 and CCL5. Vaccination with CCL3 or CCL5 increased heart parasitism and decreased local IFN-γ production, but did not influence intensity of inflammation. Simultaneous treatment with both plasmids or treatment with MetRANTES enhanced cardiac inflammation, fibrosis and parasitism. In conclusion, chemokines CCL3 and CCL5 are relevant, but not essential, for control of T. cruzi infection in rats. On the other hand, combined blockade of these chemokines or their receptors enhanced tissue inflammation and fibrosis, clearly contrasting with available data in murine models of T. cruzi infection. These data reinforce the important role of chemokines during T. cruzi infection but suggest that caution must be taken when expanding the therapeutic modulation of the chemokine system in mice to the human infection.     

New approaches to high-throughput structure characterization of SH3 complexes: the example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae

SH3 domains are small protein modules that are involved in protein-protein interactions in several essential metabolic pathways. The availability of the complete genome and the limited number of clearly identifiable SH3 domains make the yeast Saccharomyces cerevisae an ideal proteomic-based model system to investigate the structural rules dictating the SH3-mediated protein interactions and to develop new tools to assist these studies. In the present work, we have determined the solution structure of the SH3 domain from Myo3 and modeled by homology that of the highly homologous Myo5, two myosins implicated in actin polymerization. We have then implemented an integrated approach that makes use of experimental and computational methods to characterize their binding properties. While accommodating their targets in the classical groove, the two domains have selectivity in both orientation and sequence specificity of the target peptides. From our study, we propose a consensus sequence that may provide a useful guideline to identify new natural partners and suggest a strategy of more general applicability that may be of use in other structural proteomic studies.