Homology and phylogeny and their automated inference

The analysis of the ever-increasing amount of biological and biomedical data can be pushed forward by comparing the data within and among species. For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts. Here, I review the foundations and advantages of this "historical" approach and evaluate recent attempts at automating such analyses. Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene. If the family has relatives in other species, we can assume that the ancestral gene was present in the ancestral species from which all the other species evolved. In particular, describing the relationships among the duplicated biological sequences found in the various species is often possible by a phylogeny, which is more informative than homology statements. Detecting and elaborating on common origins may answer how certain biological sequences developed, and predict what sequences are in a particular species and what their function is. Such knowledge transfer from sequences in one species to the homologous sequences of the other is based on the principle of 'my closest relative looks and behaves like I do', often referred to as 'guilt by association'. To enable knowledge transfer on a large scale, several automated 'phylogenomics pipelines' have been developed in recent years, and seven of these will be described and compared. Overall, the examples in this review demonstrate that homology and phylogeny analyses, done on a large (and automated) scale, can give insights into function in biology and biomedicine.     

Influence of ship emissions on air quality and input of contaminants in southern Alaska National Parks and Wilderness Areas during the 2006 tourist season

The impact of ship emissions on air quality in Alaska National Parks and Wilderness Areas was investigated using the Weather Research and Forecasting model inline coupled with chemistry (WRF/Chem). The visibility and deposition of atmospheric contaminants was analyzed for the length of the 2006 tourist season. WRF/Chem reproduced the meteorological situation well. It seems to have captured the temporal behavior of aerosol concentrations when compared with the few data available. Air quality follows certain predetermined patterns associated with local meteorological conditions and ship emissions. Ship emissions have maximum impacts in Prince William Sound where topography and decaying lows trap pollutants. Along sea-lanes and adjacent coastal areas, NO_x, SO₂, O₃, PAN, HNO₃, and PM_2.5 increase up to 650 pptv, 325 pptv, 900 pptv, 18 pptv, 10 pptv, and 100 ng m^?3. Some of these increases are significant (95% confidence). Enhanced particulate matter concentrations from ship emissions reduce visibility up to 30% in Prince William Sound and 5–25% along sea-lanes.     

Crimson-breasted Shrike females with extra pair offspring contributed more to duets

Many socially monogamous bird species follow a genetically promiscuous reproductive strategy. Duetting birds may be an exception, as they appear to exhibit very low levels of extra pair paternity—which is thought to be connected to duetting. Duets are predicted to function either in paternity guarding or as signals of commitment to the pair bond, reciprocally reducing extra pair mating in both sexes. In this study, we used four microsatellites to document paternity loss in the Crimson-breasted Shrike (Laniarius atrococcineus), a socially monogamous subtropical duetting species. Extra pair paternity was surprisingly high, with extra pair males siring 20 % of young in 30 % of broods. Furthermore, we compared the levels of extra pair paternity of each pair to certain characteristics of their duets to test the paternity guard and the commitment hypotheses. Our results offered no support that duets function in paternity guarding, although the fact that males which had been cuckolded answered more of their female’s calls could represent an adaptation to avoid future cuckoldry. We also found no evidence for duets functioning as signal of commitment. Female vocal behaviour was in fact the reverse of that predicted: Levels of infidelity amongst social females were positively related to female answer rate of their mates’ songs. These results indicate that females may use increased answer rates as a form of manipulation, in an attempt to avoid potential costs associated with their extra pair matings.     

Mercury in compact fluorescent lamps (CFLs): European legislation introduces an avoidable analytical bias

European legislation has set a limit of 5 mg Hg per compact fluorescent lamp (CFL). Compliance with this regulation is tested with a method given in a European law from 2002 (“EU method”). According to the EU method, the arc tube has to be placed inside a fume cupboard and cut into segments. These pieces are collected and washed with HNO₃, which is finally analyzed for Hg. In this study, we investigated the losses of Hg via the gas phase, which are ignored by the EU method, using a semiquantitative radiochemical neutron activation analysis (RNAA) technique developed at the TRIGA Mark II reactor in Vienna (Austria). Depending on the product, the losses range as high as approximately 2 % at 20 °C. At higher ambient temperatures (hot summer days), the losses may increase by a factor of 4. Quality products generally suffer lower emission via the gas phase than cheap products, which is probably due to amalgam or other techniques that retain the Hg from broken CFLs. In any case, the EU method introduces a small but avoidable systematic error into the analysis and, in contrast to recommended practices, underestimates the Hg content of the CFL in question. Having technical alternatives at hand, we urge European lawmakers to adjust the law accordingly.     

PCDD/F and dioxin-like PCB in human blood and milk from German mothers

Blood samples of pregnant women aged between 19 and 42 years at the time they gave birth and milk samples from the same women following delivery were collected between September 2000 and January 2003 from 169 participants living in an industrialized area of Germany (Duisburg birth cohort study). All samples were analyzed for their content of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/F) as well as dioxin-like and indicator polychlorinated biphenyls (PCB). Levels of WHO-TEq were in the range of 4.34-97.3 pg/g(lipid base) (median: 26.37, arithmetic mean: 28.36) for blood, or 3.01-78.7 pg/g(lipid base) (median: 26.40, arithmetic mean: 27.27) for milk, respectively. The four congeners 12378-PeCDD, 23478-PeCDF, 33'44'5-PeCB (# 126) and 233'44'5-HxCB (# 156) contribute the main share to total WHO-TEq. The contribution of PCDD/F in relation to PCB to total WHO-TEq was 60:40% in blood and 52:48% in milk. Good correlations of the contaminant levels in lipid base between both matrices were found. The distribution between blood and milk depends on the molecular weight of the substances. Higher chlorinated PCDD/F- and PCB-congeners were found in 2-4-fold higher concentrations in blood in relation to milk and the concentrations of lower chlorinated PCB-congeners were up to 2-fold higher in milk in relation to blood. The body burden of PCDD/F and PCB increases with age and decreases over the total nursing period. Women who had lived outside highly industrialized countries showed lower concentrations of PCDD/F and PCB. In some cases, elevated levels of PCB were observed when the women had previously lived in Eastern Europe for a long time. In comparison with recent data, the decline in human PCDD/F and PCB levels observed during the nineties seems to have stopped. The individual exposures of the infants due to breastfeeding within the first 18 months were calculated to be from 4.4 to 318 ng WHO-TEq (median: 106, arithmetic mean: 118). The actual mean daily exposure of a breastfed infant can be estimated to 131 pg WHO-TEq/kg(body weight).     

Defining Chlorophyll-a Reference Conditions in European Lakes

The concept of “reference conditions” describes the benchmark against which current conditions are compared when assessing the status of water bodies. In this paper we focus on the establishment of reference conditions for European lakes according to a phytoplankton biomass indicator—the concentration of chlorophyll-a. A mostly spatial approach (selection of existing lakes with no or minor human impact) was used to set the reference conditions for chlorophyll-a values, supplemented by historical data, paleolimnological investigations and modelling. The work resulted in definition of reference conditions and the boundary between “high” and “good” status for 15 main lake types and five ecoregions of Europe: Alpine, Atlantic, Central/Baltic, Mediterranean, and Northern. Additionally, empirical models were developed for estimating site-specific reference chlorophyll-a concentrations from a set of potential predictor variables. The results were recently formulated into the EU legislation, marking the first attempt in international water policy to move from chemical quality standards to ecological quality targets.     

Provenancing of archeological pumice finds from North Sinai

Seven pumice samples from excavations in North Sinai have been investigated with respect to their geochemical composition. This type of volcanic rock has been used as an abrasive and thus has been an object of trade since antiquity. With the help of Instrumental Neutron Activation Analysis, six of these Bronze Age samples could be correlated to their volcanic sources on the islands of Santorini, Nisyros and Giali (Greece) using the typical element concentrations (“chemical fingerprint”). The source of one pumice sample remains unidentified excluding, however, the Santorini eruption as a possible source. The concluding section of this article discusses the possible contribution, however indirect, of the pumice from Sinai and elsewhere in the Eastern Mediterranean to the controversial issue of the accurate date of the “Minoan” eruption of Santorini.     

Umbilical cord haematoma as a complication of intrauterine intravascular blood transfusion

Between October 1985 and February 1989, 49 ultrasound-guided intravascular fetal blood transfusions were performed in 16 patients (14 with rhesus (Rh) isoimmunization, 2 with non-immunologic hydrops fetalis (NIHF)). As an intra-operative complication, perivascular haematoma of the cord occurred in three patients (7 per cent). In two cases, fetal bradycardia necessitated delivery by Caesarean section at 30 and 32 weeks' gestation, respectively. In the third case, fetal bradycardia developed during transfusion, at 31 weeks' gestation, but normalized within 3 min. The baby was delivered as planned at 36 weeks of gestation, after another transfusion at 34 weeks. Dislodgement of the needle tip into perivascular tissue, caused by sudden fetal or maternal movements, is the reason for this complication. The haematoma develops as a result of delayed recognition and continuous transfusion into Wharton' s jelly. Cord haematoma may be diagnosed in time by continuous ultrasound imaging, as illustrated in case 3. To minimize the risk of needle dislodgement during transfusion, sedation of the mother and complete immobilization of the fetus by injecting a short-acting muscle relaxant into the umbilical vessel are recommended.     

The Chemical and Meteorological Conditions Associated with High and Low Ozone Concentrations in Southeastern Michigan and Nearby Areas of Ontario

This analysis represents the first characterization of the photochemistry and transport of ozone in the Detroit metropolitan area and provides a basis for comparing data for Detroit to that for other cities. The characterization is based on a comprehensive set of meteorological and chemical measurements obtained at a site in the urban core of Detroit during the summer of 1981, together with measurements of O₃, nitrogen oxides (NO _X ), and nonmethane organic compounds (NMOC) from rural, suburban, and urban areas in southeastern Michigan and adjacent areas of Ontario.

For the quartile (23 days) with highest ozone maxima (97-180 ppb), the maxima occurred 10-70 km north-northeast of the city on days that were warm and hazy with light southsouthwest winds. On such days there was a marked accumulation of ozone precursors (NMOC and NO_X) in the early morning, as well as a rapid chemical removal of NO _X (NO _X half-life of ～5 h) from morning to midday. The timing of the daily ozone increase across the study region suggests that local photochemical generation in a moving plume was responsible for more than half of the ozone measured downwind. However, there was also evidence that ozone transported into Detroit as part of the regional background was a significant part of the O₃ maxima on high ozone days. The average contributions of photochemistry and transport for the 23 days with the highest ozone maxima were estimated to be 57 ppb and 47 ppb, respectively.