The mathematical model of concentration polarization coefficient in membrane transport and volume flows

In this paper, the authors investigate the membrane transport of aqueous non-electrolyte solutions in a single-membrane system with the membrane mounted horizontally. The purpose of the research is to analyze the influence of volume flows on the process of forming concentration boundary layers (CBLs). A mathematical model is provided to calculate dependences of a concentration polarization coefficient (ζ _s ) on a volume flux (J _vm ), an osmotic force (Δπ) and a hydrostatic force (ΔP) of different values. Property ζ _s ?=?f(J _vm ) for J _vm ?>?0 and for J _vm ?≈?0 and property ζ _s ?=?f(ΔC ₁) are calculated. Moreover, results of a simultaneous influence of ΔP and Δπ on a value of coefficient ζ _s when J _vm ?=?0 and J _vm ?≠?0 are investigated and a graphical representation of the dependences obtained in the research is provided. Also, mathematical relationships between the coefficient ζ _s and a concentration Rayleigh number (R _C ) were studied providing a relevant graphical representation. In an experimental test, aqueous solutions of glucose and ethanol were used.     

Capsular Polysaccharides of <Emphasis Type="Italic">Lactobacillus</Emphasis> spp.: Theoretical and Practical Aspects of Simple Visualization Methods

Lactobacillus strains can synthesize capsular polysaccharides (CPS), which are important substances in the dairy industry—they exhibit many important technological as well as health-promoting properties. Technological advancements have made it possible to detect bacterial capsules using costly and labor-intensive methods, such as serological reactions, molecular genetic techniques, and electron microscopy. Light microscopy, which is the method of interest in this paper, is one of the most widely accessible and cheapest techniques. CPS may be observed under a light microscope after staining bacterial cells and the background with a basic die and an acidic die, respectively (negative–positive staining), with the capsules remaining transparent. The literature offers many polysaccharide staining methods, but due to the considerable structural diversity of CPS and possible dye-capsule interactions, a suitable staining technique should be carefully selected for each strain. The current study showed that not all methods adequately reveal Lactobacillus CPS, with the most effective ones being those proposed by Hiss and Maneval.     

A segmental maximum a posteriori approach to genome-wide copy number profiling

MOTIVATION: Copy number profiling methods aim at assigning DNA copy numbers to chromosomal regions using measurements from microarray-based comparative genomic hybridizations. Among the proposed methods to this end, Hidden Markov Model (HMM)-based approaches seem promising since DNA copy number transitions are naturally captured in the model. Current discrete-index HMM-based approaches do not, however, take into account heterogeneous information regarding the genomic overlap between clones. Moreover, the majority of existing methods are restricted to chromosome-wise analysis. RESULTS: We introduce a novel Segmental Maximum A Posteriori approach, SMAP, for DNA copy number profiling. Our method is based on discrete-index Hidden Markov Modeling and incorporates genomic distance and overlap between clones. We exploit a priori information through user-controllable parameterization that enables the identification of copy number deviations of various lengths and amplitudes. The model parameters may be inferred at a genome-wide scale to avoid overfitting of model parameters often resulting from chromosome-wise model inference. We report superior performances of SMAP on synthetic data when compared with two recent methods. When applied on our new experimental data, SMAP readily recognizes already known genetic aberrations including both large-scale regions with aberrant DNA copy number and changes affecting only single features on the array. We highlight the differences between the prediction of SMAP and the compared methods and show that SMAP accurately determines copy number changes and benefits from overlap consideration.     

Isolated nodal failure after chemo-radiotherapy in limited disease small cell lung cancer (LD-SCLC)

BackgroundThe irradiation volume for treatment of limited disease small cell lung cancer (LD-SCLC), are still controversial. One of the aspects of radiation volume is the use of elective nodal irradiation (ENI), which has never been subjected to randomized study in SCLC patients.AimTo review retrospectively patterns of failure in relation to the radiation field after chemoradiotherapy (CHT-RT) in patients with limited disease small cell lung cancer (LD-SCLC).Material and MethodsBetween 1997 and 2006, 117 consecutive patients with LD-SCLC received chemotherapy with sequential radiotherapy (70%) and concurrent or alternating CHT-RT (30%). All but one case had predefined elective nodal irradiation (ENI) without inclusion of supraclavicular regions. Prophylactic cranial irradiation (PCI) was administered to 39% of patients.ResultsThe median follow-up for the 20 living patients was 33 months. The overall survival at 2 years was 36% (median survival: 18 months). In-field locoregional progression was observed in 42 patients (36%). Distant metastases occurred in 71 patients (61%). Five patients (4%) developed isolated nodal failure (INF) without local progression in the supraclavicular region. Patients with INF had N3 disease more often than those without INF (60% vs 21%, p = 0.04). There was 5% RTOG grade 3 or higher early radiation toxicity.ConclusionsINF failures are rare; however, the need for extension of ENI to supraclavicular areas may be reconsidered in N3 patients.     

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. Linearized λ DNA is modified to have a biotin on the end of one strand, and a digoxigenin moiety on the other end of the same strand. The biotinylated end is attached to a functionalized glass coverslip and the digoxigeninated end to a small bead. The assembly of these DNA-bead tethers on the surface of a flow cell allows a laminar flow to be applied to exert a drag force on the bead. As a result, the DNA is stretched close to and parallel to the surface of the coverslip at a force that is determined by the flow rate (Figure 1). The length of the DNA is measured by monitoring the position of the bead. Length differences between single- and double-stranded DNA are utilized to obtain real-time information on the activity of the replication proteins at the fork. Measuring the position of the bead allows precise determination of the rates and processivities of DNA unwinding and polymerization (Figure 2).Open in a separate windowClick here to view.^{(103M, flv)}     

Trinucleotide repeat sequence-based PCR as a potential approach for genotyping Mycobacterium gordonae strains

Diseases that are caused by non-tuberculous mycobacteria (NTM) continue to pose difficult clinical problems, and the epidemiological aspect of NTM-caused diseases is of great importance. In the case of Mycobacterium gordonae there is no adequate genotyping scheme. Here we present a potential rapid and reproducible genetic assay that uses trinucleotide repeat sequence-based PCR (TRS-PCR) for genotyping M. gordonae. The proposed method constitutes a useful single-primer PCR screen for genotyping this species. Among 10 TRS-containing primers, after applying (CAC)₄-based PCR to 36 strains of M. gordonae, we found a discriminatory index of 0.975. The accuracy of this analysis was supported by a reasonable reproducibility of 92%. These results were compared with the Enterobacterial Repetitive Intergenic Consensus Sequences (ERIC)-PCR typing scheme which had lower discriminatory index of 0.93 and its reproducibility was only 86.3%.     

You cannot oxidize what you cannot reach: Oxidative susceptibility of buried methionine residues

Oxidation of protein methionines to methionine sulfoxides can result in protein structural alterations with a wide variety of biological implications. Factors that determine susceptibility to oxidation are not well understood. The recent JBC Editors Pick by Walker et al. applied proteomic methodologies to show that the oxidative susceptibility of buried methionine residues is strongly correlated with folding stability of the contextual peptide. Proteome-wide analysis of oxidation-susceptible methionines promises to answer open questions about the biological functions of reversible methionine oxidation.     

Ureter Regeneration–The Proper Scaffold Has to Be Defined

The aim of this study was to compare two different acellular scaffolds: natural and synthetic, for urinary conduit construction and ureter segment reconstruction. Acellular aortic arch (AAM) and poly(L-lactide-co-caprolactone) (PLCL) were used in 24 rats for ureter reconstruction in both tested groups. Follow-up period was 4 weeks. Intravenous pyelography, histological and immunohistochemical analysis were performed. All animals survived surgical procedures. Patent uretero-conduit junction was observed only in one case using PLCL. In case of ureter segment reconstruction ureters were patent in one case using AAM and in four cases using PLCL scaffolds. Regeneration of urothelium layer and focal regeneration of smooth muscle layer was observed on both tested scaffolds. Obtained results indicates that synthetic acellular PLCL scaffolds showed better properties for ureter reconstruction than naturally derived acellular aortic arch.