Kappa-chain constant-region gene sequences in genus Rattus: coding regions are diverging more rapidly than noncoding regions

We have determined the nucleotide sequence of a 1,200-base pair (bp) genomic fragment that includes the kappa-chain constant-region gene (C kappa) from two species of native Australian rodents, Rattus leucopus cooktownensis and Rattus colletti. Comparison of these sequences with each other and with other rodent C kappa genes shows three surprising features. First, the coding regions are diverging at a rate severalfold higher than that of the nearby noncoding regions. Second, replacement changes within the coding region are accumulating at a rate at least as great as that of silent changes. Third, most of the amino acid replacements are localized in one region of the C kappa domain--namely, the carboxy-terminal "bends" in the alpha-carbon backbone. These three features have previously been described from comparisons of the two allelic forms of C kappa genes in R. norvegicus. These data imply the existence of considerable evolutionary constraints on the noncoding regions (based on as yet undetermined functions) or powerful positive selection to diversify a portion of the constant-region domain (whose physiological significance is not known). These surprising features of C kappa evolution appear to be characteristic only of closely related C kappa genes, since comparison of rodent with human sequences shows the expected greater conservation of coding regions, as well as a predominance of silent nucleotide substitutions within the coding regions.      

Feeding studies on gynoparae, males and apterous virginoparae of Myzus persicae on potato by electrical penetration graph

Abstract:  Feeding behaviour of parthenogenetic apterae, post-teneral gynoparae and males of a holocyclic parthenogenetic lineage of Myzus persicae (Sulzer) (Hem., Aphididae) was studied on potato plants, Solanum tuberosum L. (Solanaceae) by DC-electrical penetration graph recording. Differences were observed between morphs during the 7-h recordings, specifically in the first phase of subcuticular probing and in xylem and phloem-related activities. The time required for the first penetration and first cell puncture of the non-vascular tissues was shorter in apterae than in gynoparae and males. Apterae more often showed phloem activities and sustained sap ingestion (100%) than winged morphs ( ca. 25%). In addition, phloem ingestion was much longer in apterae than in winged morphs, 3458 s and 25–70 s respectively. In contrast, winged morphs spent 14–21% of the available time ingesting sap from xylem while in apterae xylem sap uptake was only for 2% of the time. Furthermore, the data showed that males perform in general all the feeding behaviours that other conspecific morphs exhibit. The differences in feeding behaviour among morphs of M. persicae are discussed in relation to host specialization and to their possible involvement in non-persistent transmission of viruses.     

Pirfenidone improves survival in IPF: results from a real-life study

Background

Pirfenidone is an antifibrotic compound approved for the treatment of idiopathic pulmonary fibrosis (IPF). We present our real-world experience in terms of Pirfenidone’s effect on mortality and adverse events profile outside the restrictions of a clinical trial.

Methods

This is a retrospective observational intention to treat study of 82 consecutive IPF patients (UHH cohort).

Results

We observed a high 3-years survival rate of 73% without excluding patients who discontinued treatment for different reasons. The survival was compared to the survival of an IPF cohort from a tertiary referral center (RBH cohort). After exclusion of severe cases (DLco<?30%), in unadjusted analysis, the survival in the UHH cohort was better than in the RBH cohort (HR:0.32, 95% CI: 0.19–0.53, p?<?0.0001). After adjustment for age, gender and FVC, the survival remained higher in the UHH cohort (HR:0.28, 95% CI: 0.16–0.48, p?<?0.0001). We observed a similar safety profile compared to previously published data and a lower rate of drug discontinuation due to photosensitivity reactions. Conclusion: Pirfenidone provides a survival benefit in a real-life IPF cohort compared to previously used medications. Counselling patients and proactively managing possible adverse effects can reduce the necessity to discontinue pirfenidone.

     

Growth of a Molecular Base for Feeding: The Mind Body Dualism

It is often difficult to identify the ‘who, when, and where’ of advances in medicine and surgery because it's a rare advance indeed (such as the use of digitalis by William Withering) that can be clearly related to the astuteness of one person at one time and place.     

A Hidden Markov Model approach to variation among sites in rate of evolution

The method of Hidden Markov Models is used to allow for unequal and unknown evolutionary rates at different sites in molecular sequences. Rates of evolution at different sites are assumed to be drawn from a set of possible rates, with a finite number of possibilities. The overall likelihood of phylogeny is calculated as a sum of terms, each term being the probability of the data given a particular assignment of rates to sites, times the prior probability of that particular combination of rates. The probabilities of different rate combinations are specified by a stationary Markov chain that assigns rate categories to sites. While there will be a very large number of possible ways of assigning rates to sites, a simple recursive algorithm allows the contributions to the likelihood from all possible combinations of rates to be summed, in a time proportional to the number of different rates at a single site. Thus with three rates, the effort involved is no greater than three times that for a single rate. This "Hidden Markov Model" method allows for rates to differ between sites and for correlations between the rates of neighboring sites. By summing over all possibilities it does not require us to know the rates at individual sites. However, it does not allow for correlation of rates at nonadjacent sites, nor does it allow for a continuous distribution of rates over sites. It is shown how to use the Newton-Raphson method to estimate branch lengths of a phylogeny and to infer from a phylogeny what assignment of rates to sites has the largest posterior probability. An example is given using beta-hemoglobin DNA sequences in eight mammal species; the regions of high and low evolutionary rates are inferred and also the average length of patches of similar rates.      

Transmission of Zucchini yellow mosaic virus by Colonizing and Non-colonizing Aphids in Greece and New Aphid Species Vectors of the Virus

Nineteen aphid species were tested for their ability to transmit Zucchini yellow mosaic virus (ZYMV) from and to zucchini under laboratory conditions. Sixteen species were found to be new vectors of ZYMV (i.e. Aphis craccae, Aphis fabae, Aphis nerii, Aulacorthum solani, Brachycaudus cardui, Brevicoryne brassicae, Hyalopterus pruni complex, Hyperomyzus lactucae, Macrosiphoniella sanborni, Macrosiphum rosae, Metopolophium dirhodum, Myzus cerasi, Rhopalosiphum maidis, R. padi, Semiaphis dauci and Sipha maydis). Their transmission efficiency by a single aphid was low (0.1–4.2%). Myzus persicae was used as a control and was the most efficient vector (41.1%, one aphid per plant). Hayhurstia atriplicis, Myzus ascalonicus and Sitobion avenae did not transmit the virus. In four out of six new vectors assayed in arena tests for propensity estimation, propensity was higher than efficiency. Data from an experimental zucchini field in northern Greece revealed a high correlation between ZYMV spread and alatae of the vector species. The most abundant aphid vectors during 2 years experimentation were M. persicae, Aphis gossypii and Aphis spiraecola. The possible role of the 16 new and the previously known aphid vectors in the epidemiology of ZYMV was investigated using data of transmission efficiency combined with the captures of their alatae in the Greek net of a Rothamsted type suction trap.     

Comparing the genetic structure of codling moth Cydia pomonella (L.) from Greece and France: long distance gene-flow in a sedentary pest species

Codling moth Cydia pomonella L. (Lepidoptera: Tortricidae) is the most important insect pest of apple production in Europe. Despite the economic importance of this pest, there is not information about the genetic structure of its population in Greece and the patterns of gene-flow which might affect the success of control programs. In this study, we analysed nine samples from apple, pear and walnut from various regions of mainland Greece using 11 microsatellite loci. Six samples from the aforementioned hosts from southern France were also examined for comparison. Bayesian clustering and genetic distance analyses separated the codling moth samples in two genetic clusters. The first cluster consisted mainly of the individuals from Greece, and the second of those from France, although admixture and miss-classified individuals were also observed. The low genetic differentiation among samples within each country was also revealed by F(ST) statistics (0.009 among Greek samples and 0.0150 among French samples compared to 0.050 global value among all samples and 0.032 the mean of the pair-wise values between the two countries). These F(ST) values suggest little structuring at large geographical scales in agreement with previous published studies. The host species and local factors (climatic conditions, topography, pest control programs) did not affect the genetic structure of codling moth populations within each country. The results are discussed in relation to human-made activities that promote gene-flow even at large geographic distances. Possible factors for the genetic differentiation between the two genetic clusters are also discussed.     

The invasion route for an insect pest species: the tobacco aphid in the New World

Biological invasions are rapid evolutionary events in which populations are usually subject to a founder event during introduction followed by rapid adaptation to the new environment. Molecular tools and Bayesian approaches have shown their utility in exploring different evolutionary scenarios regarding the invasion routes of introduced species. We examined the situation for the tobacco aphid, Myzus persicae nicotianae, a recently introduced aphid species in Chile. Using seven microsatellite loci and approximate Bayesian computation, we studied populations of the tobacco aphid sampled from several American and European countries, identifying the most likely source populations and tracking the route of introduction to Chile. Our population genetic data are consistent with available historical information, pointing to an introduction route of the tobacco aphid from Europe and/or from other putative populations (e.g. Asia) with subsequent introduction through North America to South America. Evidence of multiple introductions to North America from different genetic pools, with successive loss of genetic diversity from Europe towards North America and a strong bottleneck during the southward introduction to South America, was also found. Additionally, we examined the special case of a widespread multilocus genotype that was found in all American countries examined. This case provides further evidence for the existence of highly successful genotypes or 'superclones' in asexually reproducing organisms.     

Organic farming-compatible insecticides against the aphid Myzus persicae (Sulzer) in peach orchards

Abstract:  Three products allowed in organic farming (kaolin, mineral oil and insecticidal soap) as alternatives to chemical insecticides, were evaluated for the control of Myzus persicae (Sulzer) in a peach orchard. Their efficacy was compared with the neonicotinoid imidacloprid and an untreated control. The experiment was replicated for 2 years (2003 and 2004). The products were applied once in May every year and aphid infestation was recorded three to four times post-treatment. In 2004, the effect of the products on the predatory coccinellid species was also recorded. In 2003, all four products showed good control with average Abbott's efficiency ranging from 80% to 88%. In the next year, however, the products were less effective and only imidacloprid and kaolin reduced aphid population significantly compared with the untreated control, with an average Abbott's efficiency of 62% and 31%, respectively. This reduced efficiency was attributed to high rainfall occurring post-treatment. Regarding the effects on beneficial coccinellids, only imidacloprid and mineral oil reduced their numbers after application. The results showed that the three alternative products and especially kaolin are promising for aphid control in peach orchards. Kaolin has also low side-effects on beneficials and it could be used in organic peach orchards.