The characterization of complex continuous norms of reaction

Recent focus on the array of phenotypes expressed under differing environmental conditions, or phenotypic plasticity, has led to increased understanding of its genetic basis as well as its adaptive significance. However, the quantification of plasticity has proven difficult, hampered by both the limited number of environments over which plasticity may typically be assessed and by the need to assume, a priori, the general form of reaction norms under study. Our understanding of the shapes of continuous norms of reaction and, consequently, the subtle differences that may exist in shapes among genotypes or populations is rudimentary. Here, we propose the use of the loess smoothing function to analyze complex norms of reaction and to quantify total plasticity over many environments. A thermogradient incubator offers an ideal means to provide many environments for a demonstration of the use of the loess method. We test seed germination in three populations of two monocarpic plant species for population differentiation in plasticity to temperature. First, we test for differentiation in norms of reaction to 30 temperature environments among three populations of the monocarpic perennial, Lobelia inflata . The second demonstration assesses plasticity to eight temperature environments of three populations of the arctic-alpine annual, Koenigia islandica . Our demonstration shows that the loess technique can detect significant genetic differentiation among populations in complex norms of reaction for both species studied, and suggests that the use of this procedure should be considered where the form of norms of reaction might be complex. The general applicability of the approach is discussed.     

A Gene Signature to Determine Metastatic Behavior in Thymomas

Purpose

Thymoma represents one of the rarest of all malignancies. Stage and completeness of resection have been used to ascertain postoperative therapeutic strategies albeit with limited prognostic accuracy. A molecular classifier would be useful to improve the assessment of metastatic behaviour and optimize patient management.

Methods

qRT-PCR assay for 23 genes (19 test and four reference genes) was performed on multi-institutional archival primary thymomas (n = 36). Gene expression levels were used to compute a signature, classifying tumors into classes 1 and 2, corresponding to low or high likelihood for metastases. The signature was validated in an independent multi-institutional cohort of patients (n = 75).

Results

A nine-gene signature that can predict metastatic behavior of thymomas was developed and validated. Using radial basis machine modeling in the training set, 5-year and 10-year metastasis-free survival rates were 77% and 26% for predicted low (class 1) and high (class 2) risk of metastasis (P = 0.0047, log-rank), respectively. For the validation set, 5-year metastasis-free survival rates were 97% and 30% for predicted low- and high-risk patients (P = 0.0004, log-rank), respectively. The 5-year metastasis-free survival rates for the validation set were 49% and 41% for Masaoka stages I/II and III/IV (P = 0.0537, log-rank), respectively. In univariate and multivariate Cox models evaluating common prognostic factors for thymoma metastasis, the nine-gene signature was the only independent indicator of metastases (P = 0.036).

Conclusion

A nine-gene signature was established and validated which predicts the likelihood of metastasis more accurately than traditional staging. This further underscores the biologic determinants of the clinical course of thymoma and may improve patient management.     

Mixed Convection Boundary Layer Flow over a Moving Vertical Flat Plate in an External Fluid Flow with Viscous Dissipation Effect

The steady boundary layer flow of a viscous and incompressible fluid over a moving vertical flat plate in an external moving fluid with viscous dissipation is theoretically investigated. Using appropriate similarity variables, the governing system of partial differential equations is transformed into a system of ordinary (similarity) differential equations, which is then solved numerically using a Maple software. Results for the skin friction or shear stress coefficient, local Nusselt number, velocity and temperature profiles are presented for different values of the governing parameters. It is found that the set of the similarity equations has unique solutions, dual solutions or no solutions, depending on the values of the mixed convection parameter, the velocity ratio parameter and the Eckert number. The Eckert number significantly affects the surface shear stress as well as the heat transfer rate at the surface.     

Encrusting micro-organisms and microbial structures in Upper Jurassic limestones from the Southern Carpathians (Romania)

Late Jurassic–Early Cretaceous ?tramberk-type reef limestones are known from some parts of the Southern Carpathians in Romania. The Upper Jurassic deposits mainly consist of massif reef limestones including a variety of microbialites associated with micro-encrusters. They played an important role in the formation and evolution of the reef frameworks and thus are of significant importance for deciphering the depositional environments. For our study, the most important encrusting organisms are Crescentiella morronensis, Koskinobullina socialis, Lithocodium aggregatum, Bacinella-type structures, Radiomura cautica, Perturbatacrusta leini, Coscinophragma sp., and crust-forming coralline sponges such as Calcistella. Based on microscopic observations, microbial contribution to reef construction is documented by the abundance of dense micrite, laminate structures, clotted, thrombolithic or peloidal microfabrics, constructive micritic cortices, biogenic encrustations and cement crusts, as well as by other types of microbial structures and crusts. Most of the investigated carbonate deposits can be classified as “coral-microbial-microencruster boundstones” which are characteristic for the Intra-Tethyan domain. Their paleogeographical significance is indicated by the presence of many features comparable with carbonate deposits of rimmed platform systems from the Northern Calcareous Alps or Central Apennines. Based on the distribution of the facies and facies associations within the carbonate sequences under study we can distinguish slope and external shelf margin environments. The microbial crusts, the encrusting micro-organisms, and in some cases the syndepositional cements have stabilized and bound the carbonates of the slope facies types. Subsequently, the stable substrate favored the installation of coral-microbial bioconstruction levels.     

Non-invasive label-free monitoring the cardiac differentiation of human embryonic stem cells in-vitro by Raman spectroscopy

Background

Online label-free monitoring of in-vitro differentiation of stem cells remains a major challenge in stem cell research. In this paper we report the use of Raman micro-spectroscopy (RMS) to measure time- and spatially-resolved molecular changes in intact embryoid bodies (EBs) during in-vitro cardiogenic differentiation.

Methods

EBs formed by aggregation of human embryonic stem cells (hESCs) were cultured in defined medium to induce differentiation towards cardiac phenotype and maintained in purpose-built micro-bioreactors on the Raman microscope for 5 days (between days 5 and 9 of differentiation) and spatially-resolved spectra were recorded at 24 h intervals.

Results

The Raman spectra showed that the onset of spontaneous beating of EBs at day 7 coincided with an increase in the intensity of the Raman bands at 1340 cm^− 1, 1083 cm^− 1, 937 cm^− 1, 858 cm^− 1, 577 cm^− 1 and 482 cm^− 1. The spectral maps corresponding to these bands had a high positive correlation with the expression of the cardiac-specific α-actinin obtained by immuno-fluorescence imaging of the same EBs. The spectral markers obtained here are also in agreement with previous studies performed on individual live hESC-derived CMs.

Conclusions

The intensity profile of these Raman bands can be used for label-free in-situ monitoring of EBs to estimate the efficacy of cardiogenic differentiation.

General significance

As the acquisition of the time-course Raman spectra did not affect the viability or the differentiation potential of the hESCs, this study demonstrates the feasibility of using RMS for on-line non-invasive continuous monitoring of such processes inside bioreactor culture systems.     

In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations

Most of the currently known light‐harvesting complexes 2 (LH2) rings are formed by 8 or 9 subunits. As of now, questions like “what factors govern the LH2 ring size?” and “are there other ring sizes possible?” remain largely unanswered. Here, we investigate by means of molecular dynamics (MD) simulations and stochastic modeling the possibility of predicting the size of an LH2 ring from the sole knowledge of the high resolution crystal structure of a single subunit. Starting with single subunits of two LH2 rings with known size, that is, an 8‐ring from Rs. moliscianum (MOLI) and a 9‐ring from Rps. acidophila (ACI), and one with unknown size (referred to as X), we build atomic models of subunit dimers corresponding to assumed 8‐, 9‐, and 10‐ring geometries. After inserting each of the dimers into a lipid‐water environment, we determine the preferred angle between the corresponding subunits by three methods: (1) energy minimization, (2) free MD simulations, and (3) potential of mean force calculations. We find that the results from all three methods are consistent with each other, and when taken together, it allows one to predict with reasonable level of confidence the sizes of the corresponding ring structures. One finds that X and ACI very likely form a 9‐ring, while MOLI is more likely to form an 8‐ring than a 9‐ring. Finally, we discuss both the merits and limitations of all three prediction methods. Proteins 2011; © 2011 Wiley‐Liss, Inc.     

Cellulose extraction from orange peel using sulfite digestion reagents

Orange peel (OP) was used as raw material for cellulose extraction. Two different pulping reagents were used, sodium sulfite and sodium metabisulfite. The effect of the main process parameters, sulfite agent dosage and reaction duration, on cellulose yield was investigated. A central composite rotatable design involving two variables at five levels and response surface methodology were used for the optimization of cellulose recovery. Other two invariable parameters were reaction temperature and hydromodulus. The optimum yields, referred to the weight of double extracted OP, were 40.4% and 45.2% for sodium sulfite and sodium metabisulfite digestions, respectively. The crude celluloses were bleached with hypochlorite and oxygen. The physicochemical characterization data of these cellulose materials indicate good levels of purity, low crystallinities, good whitenesses, good water retention and moderate molecular weights. According to these specific properties the recovered celluloses could be used as fillers, water absorbents, or as raw materials for cellulose derivatives.     

Kidney Shear Wave Speed Values in Subjects with and without Renal Pathology and Inter-Operator Reproducibility of Acoustic Radiation Force Impulse Elastography (ARFI) - Preliminary Results

Aim

to assess the inter-operator reproducibility of kidney shear wave speed, evaluated by means of Acoustic Radiation Force Impulse (ARFI) elastography, and the factors which influence it.

Methods

Our prospective pilot study included 107 subjects with or without kidney pathology in which kidney shear wave speed was evaluated by means of ARFI elastography. Intraclass correlation coefficient (ICC) was used to assess ARFI elastography reproducibility.

Results

A strong agreement was obtained between kidney shear wave speed measurements obtained by the two operators: ICC = 0.71 (right kidney) and 0.69 (left kidney). Smaller ICCs were obtained in “healthy subjects”, as compared to patients with kidney diseases (0.68 vs. 0.75), in women as compared with men (0.59 vs. 0.78), in subjects younger than 50 years as compared with those aged at least 50 years (0.63 vs. 0.71), in obese as compared with normal weight and overweight subjects (0.36 vs. 0.66 and 0.78) and in case of measurements depth <4 cm or >6 cm as compared with those performed at a depth of 4–6 cm from the skin (0.32 and 0.60 vs. 0.81).

Conclusion

ARFI elastography is a reproducible method for kidney shear wave speed assessment.     

Monalysin,a Novel ?-Pore-Forming Toxin from the Drosophila Pathogen Pseudomonas entomophila,Contributes to Host Intestinal Damage and Lethality

Pseudomonas entomophila is an entomopathogenic bacterium that infects and kills Drosophila. P. entomophila pathogenicity is linked to its ability to cause irreversible damages to the Drosophila gut, preventing epithelium renewal and repair. Here we report the identification of a novel pore-forming toxin (PFT), Monalysin, which contributes to the virulence of P. entomophila against Drosophila. Our data show that Monalysin requires N-terminal cleavage to become fully active, forms oligomers in vitro, and induces pore-formation in artificial lipid membranes. The prediction of the secondary structure of the membrane-spanning domain indicates that Monalysin is a PFT of the ß-type. The expression of Monalysin is regulated by both the GacS/GacA two-component system and the Pvf regulator, two signaling systems that control P. entomophila pathogenicity. In addition, AprA, a metallo-protease secreted by P. entomophila, can induce the rapid cleavage of pro-Monalysin into its active form. Reduced cell death is observed upon infection with a mutant deficient in Monalysin production showing that Monalysin plays a role in P. entomophila ability to induce intestinal cell damages, which is consistent with its activity as a PFT. Our study together with the well-established action of Bacillus thuringiensis Cry toxins suggests that production of PFTs is a common strategy of entomopathogens to disrupt insect gut homeostasis.