A structured overview of simultaneous component based data integration

Background  

Data integration is currently one of the main challenges in the biomedical sciences. Often different pieces of information are gathered on the same set of entities (e.g., tissues, culture samples, biomolecules) with the different pieces stemming, for example, from different measurement techniques. This implies that more and more data appear that consist of two or more data arrays that have a shared mode. An integrative analysis of such coupled data should be based on a simultaneous analysis of all data arrays. In this respect, the family of simultaneous component methods (e.g., SUM-PCA, unrestricted PCovR, MFA, STATIS, and SCA-P) is a natural choice. Yet, different simultaneous component methods may lead to quite different results.     

BMP2 signals loss of epithelial character in epicardial cells but requires the Type III TGFβ receptor to promote invasion

Coronary vessel development depends on a subpopulation of epicardial cells that undergo epithelial to mesenchymal transformation (EMT) and invade the subepicardial space and myocardium. These cells form the smooth muscle of the vessels and fibroblasts, but the mechanisms that regulate these processes are poorly understood. Mice lacking the Type III Transforming Growth Factor β Receptor (TGFβR3) die by E14.5 due to failed coronary vessel development accompanied by reduced epicardial cell invasion. BMP2 signals via TGFβR3 emphasizing the importance of determining the relative contributions of the canonical BMP signaling pathway and TGFβR3-dependent signaling to BMP2 responsiveness. Here we examined the role of TGFβR3 in BMP2 signaling in epicardial cells. Whereas TGFβ induced loss of epithelial character and smooth muscle differentiation, BMP2 induced an ALK3-dependent loss of epithelial character and modestly inhibited TGFβ-stimulated differentiation. Tgfbr3(-/-) cells respond to BMP2 indicating that TGFβR3 is not required. However, Tgfbr3(-/-) cells show decreased invasion in response to BMP2 and overexpression of TGFβR3 in Tgfbr3(-/-) cells rescued invasion. Invasion was dependent on ALK5, ALK2, ALK3, and Smad4. Expression of TGFβR3 lacking the 3 C-terminal amino acids required to interact with the scaffolding protein GIPC (GAIP-interacting protein, C terminus) did not rescue. Knockdown of GIPC in Tgfbr3(+/+) or Tgfbr3(-/-) cells rescued with TGFβR3 decreased BMP2-stimulated invasion confirming a requirement for TGFβR3/GIPC interaction. Our results reveal the relative roles of TGFβR3-dependent and TGFβR3-independent signaling in the actions of BMP2 on epicardial cell behavior and demonstrate the critical role of TGFβR3 in mediating BMP2-stimulated invasion.     

The Diversity of Flower Flies (Diptera: Syrphidae) in Colombia and Their Neotropical Distribution

In Colombia, like most Neotropical countries, faunistic studies on flower flies have been occasional and most of them have been primarily focused on taxonomy. Colombia is the second-most species-rich country in flower fly diversity in the Neotropics after Brazil, and has one of the highest numbers of species per unit area (2.49 per 10,000?km²), based on a review of literature and national collections. Including new data presented here, a total of 47 genera and 300 species are recorded in Colombia. The genera Scaeva Fabricius and Lycastrirhyncha Bigot, as well as 101 species are recorded here for the first time. The altitudinal range and the distribution of the flower fly genera in Colombia are presented. A preliminary comparison of the fauna of Colombia with that of other Neotropical countries is given. A historical perspective is also provided in order to illustrate how Colombian Syrphidae knowledge has progressed over the last 168?years. Information presented here will be useful for ongoing and future biodiversity research as well as conservation projects on Syrphidae in the Neotropical region.     

Morphology and Phylogeny of Two New Pleurostomatid Ciliates,Epiphyllum shenzhenense n. sp. and Loxophyllum spirellum n. sp. (Protozoa,Ciliophora) from A Mangrove Wetland,South China

ABSTRACT. The morphology, infraciliature, and small subunit (SSU) rRNA gene sequences of two new pleurostomatid ciliates, Epiphyllum shenzhenense n. sp. and Loxophyllum spirellum n. sp., isolated from a mangrove wetland near Shenzhen, South China, were investigated. Epiphyllum shenzhenense n. sp. is morphologically characterized by leaf‐shaped cell about 150 × 35 μm in vivo, usually with four contractile vacuoles, 20–29 right kineties and 10–26 left kineties, ca. four macronuclear nodules, and two types of extrusomes (i.e. short spindle‐shaped and long bar‐shaped). As a new species, L. spirellum n. sp. is distinguished from its congeners by its posterior dorsal margin twisted onto the left side, the distribution of extrusomes (evenly arranged along the oral slit, the posterior end, and clustered to 7–13 warts on dorsal margin), the subterminally positioned contractile vacuole, the number of kineties (8–10 on right side, 4–5 on left side), and its genetic distance from congeners. Phylogenetic trees based on the SSU rRNA gene sequence for both organisms were constructed, which indicate that Epiphyllum is a distinct genus and occupies a basal position in the Pleurostomatida clade; L. spirellum n. sp. falls well into the Loxophyllum clade, which has a close relationship with Litonotus and Spiroloxophyllum.     

Dermatoglyphic variation in Spanish Basque populations

The present study involves the evaluation of digital dermatoglyphic traits of 2185 unrelated individuals (1152 females and 1033 males) from 17 natural valleys of the four Basque provinces (Vizcaya, Guipúzcoa, Navarra, and Alava) in the Spanish Basque Country. Univariate intervalley and between-sex comparisons were carried out by means of chi-square contingency analysis for pattern types and by means of one-way analysis of variance for ridge counts. Multivariate intervalley comparison was carried out by means of correspondence analysis for pattern types and by principal component analysis for ridge counts. The results of this study are notable for the following findings: (1) in general, all variables are significantly heterogeneous among valley populations; (2) there was a greater differentiation among the valley populations than between sexes in one valley population; (3) affinities among the intervalley populations depend on the variables considered; (4) the valley populations from Vizcaya resemble those from the Pyrenees; (5) based on interprovince comparisons, the Vizcaya and Navarra samples are the closest: (6) in general, the valley samples from Alava are the worst clustered; (7) the universality of dermatoglyphic component structure fits better in males.     

Interspecific variability in sensitivity to UV radiation and subsequent recovery in selected isolates of marine bacteria

The interspecific variability in the sensitivity of marine bacterial isolates to UV-B (295- to 320-nm) radiation and their ability to recover from previous UV-B stress were examined. Isolates originating from different microenvironments of the northern Adriatic Sea were transferred to aged seawater and exposed to artificial UV-B radiation for 4 h and subsequently to different radiation regimens excluding UV-B to determine the recovery from UV-B stress. Bacterial activity was assessed by thymidine and leucine incorporation measurements prior to and immediately after the exposure to UV-B and after the subsequent exposure to the different radiation regimens. Large interspecific differences among the 11 bacterial isolates were found in the sensitivity to UV-B, ranging from 21 to 92% inhibition of leucine incorporation compared to the bacterial activity measured in dark controls and from 14 to 84% for thymidine incorporation. Interspecific differences in the recovery from the UV stress were also large. An inverse relation was detectable between the ability to recover under dark conditions and the recovery under photosynthetic active radiation (400 to 700 nm). The observed large interspecific differences in the sensitivity to UV-B radiation and even more so in the subsequent recovery from UV-B stress are not related to the prevailing radiation conditions of the microhabitats from which the bacterial isolates originate. Based on our investigations on the 11 marine isolates, we conclude that there are large interspecific differences in the sensitivity to UV-B radiation and even larger differences in the mechanisms of recovery from previous UV stress. This might lead to UV-mediated shifts in the bacterioplankton community composition in marine surface waters.     

Structural analysis and optimised production of fructo- oligosaccharides by levansucrase from Acetobacter diazotrophicus SRT4

Major fructo-oligosaccharides (FOS) produced by levansucrase (EC 2.4.1.10) from Acetobacter diazotrophicus SRT4 were characterised as 1-kestose and nystose by acid hydrolysis and 13C-NMR spectroscopy. The highest yields of 1-kestose (481 mM; 241 g/l) and nystose (81 mM; 54 g/l) were achieved at initial sucrose concentration of 1754 mM (600 g/l), pH 5.5 and 40°C. The synthesized FOS reached 50% (w/w) of total sugars in the reaction mixture, with a conversion efficiency over 70% (w/w) based on the amount of sucrose converted to 1-kestose.     

Fatal pulmonary acariasis in an aged indoor rhesus macaque (Macaca mulatta)

Pulmonary acariasis is a sporadic, incidental finding in colony‐raised rhesus macaques (Macaca mulatta). Prophylactic treatment in indoor‐raised and indoor‐housed macaques is not routine due to low prevalence, lack of clinical significance, and potential risk of toxicosis. This case is an unusually severe infestation of Pneumonyssus simicola in an indoor‐housed rhesus macaque, which ultimately resulted in this animal's death.