Evolutionary distances in the twilight zone--a rational kernel approach

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.     

Anaesthetic considerations of adults with Morquio's syndrome - a case report

Background

Base deficit (BD) is commonly used in the operating room (OR) as an endpoint of resuscitation. BD is used as a surrogate marker for the accumulation of lactic acid(Lac). However, the BD can be affected by large amounts of saline.

Methods

We conducted a survey of anesthesiologists regarding the use of BD. We also studied the reliability of BD to determine the presence of hyperlactatemia (HL). Patients undergoing general anesthesia were eligible for enrollment if they were receiving an arterial line as part of their routine care. If an arterial blood gas was drawn by the operative team as part of the routine care, the remainder of the unused blood was also used to measure Lac.

Results

Survey: 73 staff anesthesiologists were surveyed. Over 70% of respondents used BD as an endpoint of resuscitation. Base Deficit Study: 35 patients were enrolled resulting in 88 arterial blood gases with corresponding Lac. Mean age was 61.4 ± 14.3 years, 43% were male. Mean pH was 7.39 ± 0.05, the mean bicarbonate was 23.0 ± 2.3 meq/L, the mean BD 1.34 ± 2.3, and the mean Lac was 1.58 ± 0.71 mmol/L. Mean ASA risk score was 3.16 ± 0.71. ROC area under the curve for base deficit to detect HL was 0.58.

Conclusion

BD can often mislead the clinician as to the actual Lac. Lac can now be measured in the OR in real time. Therefore, if clinicians in the operative setting want to know the Lac, it should be measured directly.     

Escherichia coli and enterococci are sensitive and reliable indicators for human,livestock and wildlife faecal pollution in alpine mountainous water resources

Aims: This study evaluated the applicability of standard faecal indicator bacteria (SFIB) for alpine mountainous water resources monitoring. Methods and Results: Escherichia coli, enterococci (ENTC) and Clostridium perfringens were investigated by standard or frequently applied phenotypic and genotypic methods in a broad range of animal and human faecal sources in a large alpine mountainous area. Clostridium perfringens occurred only in human, livestock and carnivorous source groups in relevant average concentrations (log 4·7–7·0 CFU g^?1) but not in herbivorous wildlife sources. Escherichia coli proved to be distributed in all faecal source groups with remarkably balanced average concentrations (log 7·0–8·4 CFU g^?1). Except for single faecal samples from the cattle source group, prevalence rates for ENTC source groups were generally >87% with average concentrations of log 5·3–7·7 CFU g^?1. To test the faecal indication capacity in the environment, faecal prevalence data were comparatively analysed with results from the concurrently performed multi‐parametric microbial source tracking effort on karst spring water quality from the investigated alpine mountainous catchment ( Reischer et al. 2008 ; Environ Microbiol 10:2598–2608). Conclusion: Escherichia coli and enterococci are reliable faecal indicators for alpine mountainous water resources monitoring, although E. coli is the more sensitive one. Clostridium perfringens did not prove to be an indicator of general faecal pollution but is suggested a conservative microbial source tracking marker for anthropogenic faecal influence. Significance and Impact of the Study: Applicability of SFIB is currently hotly debated. This is the first study providing comprehensive information on the applicability of SFIB at alpine mountainous habitats.     

Are environmental factors responsible for geographic variation in the sex ratio of the Greenlandic seed‐bug Nysius groenlandicus?

Until recently nothing indicated an unequal sex ratio in the widespread Greenland seed‐bug Nysius groenlandicus (Zetterstedt) (Heteroptera: Lygaeidae). However, recently populations more or less devoid of males were discovered in high arctic Northeast Greenland. This initiated an inspection of the entire material of the species collected in Greenland and now preserved at the Zoological Museum, University of Copenhagen. It was found that the sex ratio varied significantly among different locations. In most cases females were most abundant, but males were either scarce or absent only in samples from Northeast Greenland, indicating that here the species reproduces asexually. This paper demonstrates that the differing sex distributions can be explained by climatic factors (temperature, precipitation) and that the degree of continentality (distance from the open sea) promotes female‐biased sex ratios.     

Methyl 2-methoxy-7-(4-methylbenzoyl)-4-oxo-6-p-tolyl-4H-furo[3,2-c]pyran-3-carboxylate:A combined experimental and theoretical investigation

The title compound, methyl 2-methoxy-7-(4-methylbenzoyl)-4-oxo-6-p-tolyl-4H-furo[3,2-c]pyran-3-carboxylate (C₂₅H₂₀O₇), was prepared and characterized by IR and single-crystal X-ray diffraction (XRD). The compound crystallizes in the triclinic space group P ?1 with a?=?8.9554(9) Å, b?=?10.0018(10) Å, c?=?12.7454(13) Å, α?=?67.678(7)°, β?=?89.359(8)° and γ?=?88.961(8)°. In addition to the molecular geometry from X-ray experiment, the molecular geometry and vibrational frequencies of the title compound in the ground state have been calculated using semiempirical AM1 and PM3 methods, as well as Hartree-Fock (HF) and density functional (B3LYP) levels of theory with 6–31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Besides, frontier molecular orbitals (FMO) analysis and thermodynamic properties of the title compound were performed by the B3LYP/6–31G(d) method.     

Species-specific distribution of two sympatric Maculinea butterflies across different meadow edges

An important consequence of habitat fragmentation is the increase of edge habitats. Environmental factors in the edges are different from those in the interiors, which causes changes in the distribution of plant and animal species. We aimed to study how edges affect the distribution of two butterfly species within meadow fragments. We therefore investigated the effect of distance from edge and edge type (road edge versus tree edge) on two sympatric large blue species (Maculinea teleius and M. nausithous). Our results showed that edge type had contrasting effects on the two species. M. teleius favoured both interiors and road edges, while M. nausithous preferred the tree edges. In the case of the latter species a strong positive edge effect was also found. This kind of within-habitat niche segregation is probably related to the different microenvironmental conditions at the edges. Foodplant density did not seem to limit the distribution of these species. Our results suggest that interiors of meadows are important for M. teleius, while tree edges maintain the habitats of the regionally rarer butterfly, M. nausithous.     

Allogrooming in cattle: Relationships between social preferences,feeding displacements and social dominance

The aim of this study was to describe the allogrooming behaviour of group-housed lactating cows (Bos taurus) as it relates to social dominance, friendship, parity and level of feeding competition. We measured the socio-negative (displacements at the feeder and in the lying stalls) and socio-positive interactions (allogrooming and preferential spatial associations) in six groups of eight dairy cows. This experimental model has been shown to be useful in investigating the effects of high social pressure in groups of cattle. The level of social competition was manipulated by halving the access to the feeder. Allogrooming was observed mostly at the feeder after fresh feed delivery and during the night between 12 and 2 a.m. Dominance rank had no effect on the expression of allogrooming. When competition between animals increased, allogrooming declined, especially in low-ranking, primiparous animals. In addition to its role in coat hygiene and potential role in reducing tension between animals competing for feed, we conclude that allogrooming may be a behaviour reflecting friendship in cows, because it is correlated to preferential associations between partners at the feeder. We suggest that primiparous cows are more susceptible to suffer from a lack of hygiene or socio-positive relationships when submitted to high competitive pressure, especially when they are mixed with more experienced animals that could have better coping strategies in a high competition situation.     

Iodine concentration of milk in a dose–response study with dairy cows and implications for consumer iodine intake

Most feed is poor in iodine and iodine supplementation of cow's diets must guarantee milk iodine concentrations for humans that contribute to prevention of the deficiency and minimize the risk of exceeding an upper limit of iodine intake. Five Holstein cows were fed four iodine doses (via Ca(ΙO₃)₂·6H₂O). In four sequential 14-d periods, doses of 0.2 (basal diet), 1.3, 5.1, and 10.1 mg iodine kg^?1 diet dry matter (DM) were administered. Samples of milk were collected during each period; blood was also sampled from each cow for each iodine dosage. In an 18-d depletion period, a non-supplemented diet was provided. Iodine was determined by inductively coupled plasma-mass spectrometry. The iodine content of milk and serum reflected the iodine dosages in feed significantly. The levels for the four doses tested in milk were 101±32, 343±109, 1215±222, and 2762±852 μg iodine kg^?1. The total amount of iodine in milk per day was 30–40% of ingested supplemental iodine. Omitting additional iodine resulted in a short-term reduction of serum and milk iodine following an exponential decay function. The iodine supplementation of 0.5–1.5 mg kg^?1 diet DM represents the requirement of the cow, resulting in 100–300 μg iodine L^?1 milk, which optimally contributes to human supply. The maximum dietary levels of former and present EU legislations (10 and 5 mg iodine kg^?1 cow feed) increase the risk of iodine excess in humans.