RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits

Background  

Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. However, the branching order of the individual phlya is not well-resolved in 16S rRNA-based trees. In search of an improvement, new phylogenetic methods have been developed alongside with the growing availability of complete genome sequences. Unfortunately, only a few genes in prokaryotic genomes qualify as universal phylogenetic markers and almost all of them have a lower information content than the 16S rRNA gene. Therefore, emphasis has been placed on methods that are based on multiple genes or even entire genomes. The concatenation of ribosomal protein sequences is one method which has been ascribed an improved resolution. Since there is neither a comprehensive database for ribosomal protein sequences nor a tool that assists in sequence retrieval and generation of respective input files for phylogenetic reconstruction programs, RibAlign has been developed to fill this gap.     

Taxonomy of the glycerol fermenting clostridia and description of Clostridium diolis sp. nov

Six Clostridium strains which ferment glycerol to 1,3-propanediol were tested for their taxonomic and phylogenetic relatedness. All but one were known as C butyricum. By physiological tests, 16S rDNA sequences and fatty acid composition two groups were distinguished. The first comprised the strains VPI 3266, DSM 2478 and DSM 523 (C. "kainantoi") and was consistent with the type strain of C. butyricum in almost all characters. The second group comprising the strains DSM 5430, DSM 5431 and E5 was related to C. beijerinckii. The 16S rDNAs of these strains were almost identical with that of the type strain of C. beijerinckii, DSM 791. The DNA-DNA hybridization value of DSM 5431 and ES with C. beijerinckii DSM 791 was markedly but not decisively lower (67 and 72%, respectively). However, there were significant physiological differences to C. beijerinckii which suggested to describe the strains as a separate species, Clostridium diolis with strain SH1 (= DSM 5431) as the type strain. The new species is distinguished from C. beijerinckii, which requires complex nutrients, by its ability to grow in glucose mineral medium with biotin as the only growth factor and by differences in substrate utilization. "C. kainantoi" Takeda and Matsui was recognized as a later synonym of C. butyricum.     

Putting biogeography’s cart back behind taxonomy’s horse: a response to Triantis et al.

In a recent paper, two of us discussed diversity patterns and diversification processes in the Azores flora. Triantis et al. (2012, Journal of Biogeography, 39, 1179–1184) challenged our hypothesis that palaeoclimatic differences had an effect on diversification rates and suggested that area, island age and isolation explain diversity patterns. They did not, however, fully address the results from our subsequent paper, in which we showed that diversity patterns evident from phylogeographic studies differ markedly from those suggested by checklists. Checklists are working hypotheses and we suggest that the discrepancies evident between molecular data and checklists may be indicative of deficiencies in our taxonomic understanding of the Azores flora. Patterns of molecular and morphological diversity need to be better understood, and the discrepancies between checklists and molecular data accounted for, before we can establish the relative importance of factors such as palaeoclimate, area, island age or isolation in generating endemic diversity patterns in the Azores flora.     

Selected coccal green algae are not affected by the humic substance Huminfeed<Superscript>®</Superscript> in term of growth or photosynthetic performance

Humic substances (HSs) have been shown to influence growth, photophysiology, and redox homeostasis in phototrophs. However, many ecological studies deliver controversial results indicating inhibitory or stimulating effects depending on the kind of phototrophic organism or type of HSs applied. Here we analyzed the effect of Huminfeed^® (HF), a preparation from leonardite associated with lignite deposits, on growth and photosynthetic performance of three different coccal green algae. Concentrations of HF in the range of 2–20 mg l^?1 dissolved organic carbon (DOC) did neither affect the growth rate nor the light-adapted photosynthetic electron transport. Even photoinhibitory light intensities of 1,600 μmol photons m^?2 s^?1, representing the tenfold of growth light intensity, did not result in a decline of the maximal photosynthetic rate in HF-treated algae. In HF-grown algae, a very subtle decrease by about 10% could be observed in thermoluminescent light emission, a sensitive method to detect changes in photosystem II (PSII) chemistry. However, thermoluminescence (TL) represents only 3% of the light-induced charge separated states in PSII. Hence, rather small changes will not have significant effects on overall photosynthetic performance and growth. Therefore, the physiological effect of HSs on freshwater phototrophs has to be revisited.     

Familial longevity is marked by lower diurnal salivary cortisol levels: the Leiden Longevity Study

Background

Reported findings are inconsistent whether hypothalamic-pituitary-adrenal (HPA) signaling becomes hyperactive with increasing age, resulting in increasing levels of cortisol. Our previous research strongly suggests that offspring from long-lived families are biologically younger. In this study we assessed whether these offspring have a lower HPA axis activity, as measured by lower levels of cortisol and higher cortisol feedback sensitivity.

Methods

Salivary cortisol levels were measured at four time points within the first hour upon awakening and at two time points in the evening in a cohort comprising 149 offspring and 154 partners from the Leiden Longevity Study. A dexamethasone suppression test was performed as a measure of cortisol feedback sensitivity. Age, gender and body mass index, smoking and disease history (type 2 diabetes and hypertension) were considered as possible confounding factors.

Results

Salivary cortisol secretion was lower in offspring compared to partners in the morning (Area Under the Curve = 15.6 versus 17.1 nmol/L, respectively; p = 0.048) and in the evening (Area Under the Curve = 3.32 versus 3.82 nmol/L, respectively; p = 0.024). Salivary cortisol levels were not different after dexamethasone (0.5 mg) suppression between offspring and partners (4.82 versus 5.26 nmol/L, respectively; p = 0.28).

Conclusion

Offspring of nonagenarian siblings are marked by a lower HPA axis activity (reflected by lower diurnal salivary cortisol levels), but not by a difference in cortisol feedback sensitivity. Further in-depth studies aimed at characterizing the HPA axis in offspring and partners are needed.     

Prolactin secretion in healthy adults is determined by gender, age and body mass index

Background

Prolactin (PRL) secretion is quantifiable as mean, peak and nadir PRL concentrations, degree of irregularity (ApEn, approximate entropy) and spikiness (brief staccato-like fluctuations).

Hypothesis

Distinct PRL dynamics reflect relatively distinct (combinations of) subject variables, such as gender, age, and BMI.

Location

Clinical Research Unit.

Subjects

Seventy-four healthy adults aged 22–77 yr (41 women and 33 men), with BMI 18.3–39.4 kg/m².

Measures

Immunofluorometric PRL assay of 10-min samples collected for 24 hours.

Results

Mean 24-h PRL concentration correlated jointly with gender (P<0.0001) and BMI (P = 0.01), but not with age (overall R² = 0.308, P<0.0001). Nadir PRL concentration correlated with gender only (P = 0.017) and peak PRL with gender (P<0.001) and negatively with age (P<0.003), overall R² = 0.325, P<0.0001. Forward-selection multivariate regression of PRL deconvolution results demonstrated that basal (nonpulsatile) PRL secretion tended to be associated with BMI (R² = 0.058, P = 0.03), pulsatile secretion with gender (R² = 0.152, P = 0.003), and total secretion with gender and BMI (R² = 0.204, P<0.0001). Pulse mass was associated with gender (P = 0.001) and with a negative tendency to age (P = 0.038). In male subjects older than 50 yr (but not in women) approximate entropy was increased (0.942±0.301 vs. 1.258±0.267, P = 0.007) compared with younger men, as well as spikiness (0.363±0.122 vs. 0463±2.12, P = 0.031). Cosinor analysis disclosed higher mesor and amplitude in females than in men, but the acrophase was gender-independent. The acrophase was determined by age and BMI (R² = 0.186, P = 0.001).

Conclusion

In healthy adults, selective combinations of gender, age, and BMI specify distinct PRL dynamics, thus requiring balanced representation of these variables in comparative PRL studies.     

Inhalation of endothelin receptor blockers in pulmonary hypertension

Endothelin 1 (ET-1) is a potent pulmonary vasoconstrictor and mediator of lung diseases. Antagonism of the ET-1-mediated effects has become an important therapeutic approach. ET-1 (A and B) receptors are differentially distributed in the lung vasculature. Whereas the ET(A) receptors mainly mediate vasoconstriction, the endothelial ET(B) receptor seems to have vasodilative properties. We sought to determine if antagonism of ET receptors can be achieved by inhalation of specific blockers in a model of ET-1-mediated pulmonary hypertension.     

Proteomic approaches to the analysis of multiprotein signaling complexes

Signal transduction is one of the most active fields in modern biomedical research. Increasing evidence has shown that signaling proteins associate with each other in characteristic ways to form large signaling complexes. These diverse structures operate to boost signaling efficiency, ensure specificity and increase sensitivity of the biochemical circuitry. Traditional methods of protein analysis are inadequate to fully characterize and understand these structures, which are intricate, contain many components and are highly dynamic. Instead, proteomics technologies are currently being applied to investigate the nature and composition of multimeric signaling complexes. This review presents commonly used and potential proteomic methods of analyzing diverse protein complexes along with a discussion and a brief evaluation of alternative approaches. Challenges associated with proteomic analysis of signaling complexes are also discussed.     

Self-Organized Shape and Frontal Density of Fish Schools

Models of swarming (based on avoidance, alignment and attraction) produce patterns of behaviour also seen in schools of fish. However, the significance of such similarities has been questioned, because some model assumptions are unrealistic [e.g. speed in most models is constant with random error, the perception is global and the size of the schools that have been studied is small (up to 128 individuals)]. This criticism also applies to our former model, in which we demonstrated the emergence of two patterns of spatial organization, i.e. oblong school form and high frontal density, which are supposed to function as protection against predators. In our new model we respond to this criticism by making the following improvements: individuals have a preferred ‘cruise speed’ from which they can deviate in order to avoid others or to catch up with them. Their range of perception is inversely related to density, with which we take into account that high density limits the perception of others that are further away. Swarm sizes range from 10 to 2000 individuals. The model is three‐dimensional. Further, we show that the two spatial patterns (oblong shape and high frontal density) emerge by self‐organization as a side‐effect of coordination at two speeds (of two or four body lengths per second) for schools of sizes above 20. Our analysis of the model leads to the development of a new set of hypotheses. If empirical data confirm these hypotheses, then in a school of real fish these patterns may arise as a side‐effect of their coordination in the same way as in the model.