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The subject of the study was investigation of influence of substituent type on the properties of starch derivates in diluted solutions. Three samples were prepared: two anionic (carboxymethyl starch, CMS) and one cationic starch (KS). Starch derivates were synthesized in two steps. The first step was preparation of alkali starch by the addition of sodium-hydroxide to the starch dispersed in ethanol or water. In the second step, the required amount of sodium monocloracetate or 3-chloro-2-hydroxypropyl-threemethylamonium chloride was added to the obtained alkali starch in order to prepare CMS or KS, respectively. The degree of substitution of carboxymethyl starch was determined by back titration method, and the degree of substitution of cationic starch was determined by potentiometric titration. The degrees of substitution of prepared samples were: 0.50 (assigned as CMS-0.50) and 0.70 (assigned as CMS-0.70) for carboxymethyl starch and 0.30 (assigned as KS-0.30) for cationic starch. The properties of starch derivatives in dilute solutions were investigated by the methods of static and dynamic light scattering. Aqueous solutions of sodium chloride of different concentrations were used as solvent. The values of the mass average molar mass, MW, radius of gyration, Rg, and second virial coefficient, A2, were determined for all samples together with hydrodynamic radius, Rh. Molar masses of the samples were: 5.06×106, 15.4×106 and 19.2×106 g/mol for CMS-0.50, CMS-0.70 and KS-0.30, respectively. The samples, CMS-0.70 and KS-0.30 had similar molar mass and hydrodynamic radius, but radius of gyration of KS-0.30 was smaller then radius of gyration of CMS-0.70 at all sodium chloride concentrations. Consequently, ρ value for KS-0.30 was smaller then for CMS-0.70, as a result of more compact architecture of KS-0.30 then of CMS-0.70. Kratky graph confirmed this result. For all samples, radius of gyration and hydrodynamic radius decreased with increasing of sodium chloride concentration, but decrease of the radius was greater for CMS-0.50 then for other two samples due to its significantly lower molar mass. On the other hand, change of both radius of gyration and hydrodynamic radius of CMS-0.70 and of KS-0.30 with increasing sodium chloride concentration were similar. It can be concluded that the decrease of both Rg and Rh with increasing sodium chloride concentration in water depends far more on molar mass than on degree of substitution.

In this paper, properties of the commercially available Boltorn® hydroxy-functional aliphatic hyperbranched polyesters of the second, third and fourth pseudo generation, were investigated. Beside that, samples of the third and fourth pseudo generation were fractionated using the precipitation fractionation method to obtain three fractions of each sample, which were also investigated in this paper. According to the results obtained by GPC analysis, molar mass and polydispersity of the investigated Boltorn® hyperbranched polyesters increased with increase of the pseudo generation number. Value of the limiting viscosity number of the investigated samples, determined using the viscosity measurements of dilute solutions of these polymers in N-methyl-2-pyrrolidone, increased with increase of the pseudo generation number. On the other side, value of the limiting viscosity number of the fractions decreased from the first up to the third fraction. The same trend was also observed for the values of the hydrodynamic diameter of parent samples and their fractions, determined by dynamic light scattering using N-methyl-2-pyrrolidone as solvent. The thermal properties of the investigated Boltorn® hyperbranched polyesters were determined by thermogravimetry in nitrogen atmosphere and it has been shown that thermal stability of these samples increased with increase of the pseudo generation number. End hydroxyl groups of the second and third pseudo generation samples were modified with β-alanine to obtain hyperbranched samples soluble in water. That was fully accomplished only for the Boltorn® hyperbranched polyester of the second pseudo generation. On the other side, modified sample of the third pseudo generation was possible to dissolve in water only after adding small amount of the NaOH.

The results of an investigation of the influence of the synthesis procedure, number of pseudo generations and degree of branching of hydroxy-functional aliphatic hyperbranched polyesters (AHBP) on the values of limiting viscosity number, [η], hydrodynamic radius, Rη, molar mass and polydispersity index, Q, are presented in this paper. Two series of AHBP, synthesized from 2,2-bis(hydroxymethyl) propionic acid and di-trimethylolpropane using a pseudo-one-step and a one-step procedure were investigated. The obtained results show that the values of [η] and Rη for all examined samples are the highest in a 0.7 mass % solution of LiCl in N,N-dimethylacetamide (LiCl/DMAc), which indicates that this solvent is the best from the investigated ones. The values of [η] in N-methyl-2-pyrrolidinone (NMP) increased up to the sixth pseudo generation, after which a slight decrease occurred as the consequence of the presence of side-reaction products, formed during the synthesis. The appearance of these side-reaction products was also confirmed from the characteristic GPC chromatograms. For the samples of AHBP synthesized using the pseudo- one-step procedure, a good linear dependence between log [η] and log Mw was obtained up to the fifth pseudo generation, when LiCl/DMAc, NMP and DMAc were used as solvents. The values of the "shrinking" factor, g’, were calculated for all investigated AHBPs.

In this work, MALDI-TOF mass spectrometry was used for the characterization of aliphatic hyperbranched polyesters (AHBP), synthesized from 2,2-bis(hydroxymethyl)propionic acid (bis-MPA) and di-trimethylolpropane. From the obtained results it was concluded that it was not possible to take complete advantages of MALDI-TOF MS in this particular case, since the AHBP used in this work were polydisperse. The intensity of the signals from the high mass tail of these samples (pseudo generation higher than four) was underestimated and insufficient to distinguish it from the baseline and to use it for the analysis of the spectra. As a consequence of that, lower values of the Mn were obtained. At the same time, Mw were also underestimated, which led to very low values of the polydispersity index. On the other hand, it was possible to obtain molar masses of individual molecules from the MALDI-TOF mass spectra of AHBP and to qualitatively determine the extent of cyclization (side reactions) at each degree of polymerization. Using the adequate set of equations and results obtained from MALDI-TOF mass spectra of AHBP, every signal from the spectra was identified. The obtained results show that formation of poly(bis-MPA), intramolecular esterification and intramolecular etherification occurred as side reactions during the synthesis of these polyesters. The relative amount of the cycles increases with the number of pseudo generation (from the second up to the fifth pseudo generation). It was also observed that the relative proportion of the signals which represent cyclic structures increases with the increasing degree of polymerization. In this work the basic principles of MALDI-TOF MS are also presented, as well as, a review of adequate published articles.

Nanoparticles are used in large quantities for very different applications. A precise determination of the diameter and the particle size distribution which is responsible for the application properties is therefore essential. Reliable methods for measuring the above mentioned quantities are photometric measurements and analytical ultracentrifugation with an UV optics detector. Both methods are ruled by the Mie effect, that is scattering and absorption of the particles as function of the diameter, the wavelength, and the shape of the particles. The extinction coefficients ε=τ/c for spheres, rods, and core shell particles have been calculated and plotted over a wide range of the size parameter πd/λ. Two examples for multimodal latex particles and core shell particles have been given and demonstrate the applicability of the method.

The influence of the molar mass (generation), number and type of end groups on the thermal stability of aliphatic hyperbranched polyesters are presented in this study. Different end groups were obtained by modification of the samples with chlorides of propionic acid and stearic acid. The thermal stability of the hyperbranched polyesters was determined by thermogravimetry using a NET-ZSCH TG 209 instrument in nitrogen atmosphere at a heating rate of 10°C/min. A comparison of the temperatures obtained for mass losses of 5 20 and 40 wt% for unmodified samples showed that the thermal stability increased up to the fourth generation and then remained practically constant. An increase in the thermal stability of modified samples of the second, third and fourth generation was observed.

Sheet-bulk metal forming allows the manufacturing of sheet metal parts with integrated functional elements. The investigated process combines deep drawing and upsetting. The occurring 2D and 3D stress and strain states lead to challenges regarding material flow control due to different geometries of functional elements. The numerical analysis shows the transferability for the results of the different functional elements for their combination and the interaction between those functional elements regarding the material flow. The results are validated by experimental tests.

Due to the good mechanical properties of forged parts, the forging process plays a decisive role in the manufacturing of seamless stainless steel pipes for oil country tubular goods (OCTG) lines. Tough competition between manufacturers gives them plenty of incentive to make their processes in raw material and energy usage more and more efficient. In this context the expansion process is one of the critical production steps in the manufacturing of seamless stainless steel pipes. This work presents a sensitivity analysis of a finite element method (FEM) for the simulation of the expansion of the alloy UNS N08028. The input parameters ram speed, tool angle, initial ID and final ID of the billet as well as temperature were used to describe responses like tool wear and material loss. With the aim to minimize the tool wear and to reduce the material waste, a study of influence of the input parameters on the mentioned responses were performed. This development is supported by experimental work in order to validate the simulation model. The sector demand for new materials with specific properties and the cost-intensive experimental trials justifies the use of such simulation tools and opens great opportunities for the industry.

Using sheet-bulk metal forming processes the application of bulk forming operations on sheet metals enables the manufacturing of functional components with local wall thickness variations. As these processes come along with a two- and three-dimensional material flow, the control of the material flow is crucial for ensuring a proper filling of functional elements and thus ensuring the components quality. Controlling the material flow can be achieved by different solutions: the local adaption of tribological conditions and the application of process adapted semi-finished parts. In this paper, both solutions as well as their general qualification in two sheet-bulk metal forming processes are presented.

Abstract BMC Research Notes recently published a research article regarding the use of ligated DNA extracted from formalin-fixed paraffin embedded (FFPE) tissue on the Illumina Infinium methylation platform - “Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue” Jasmine et al. BMC Research Notes 2012, 5:117. This article repeatedly refers to our previous work and concludes that methylation data obtained from ligated FFPE extracted DNA should be used with great caution. In this Discussion we review the data analysis performed in Jasmine et al’s paper and suggest limitations which subsequently lead the authors to draw what we believe are incorrect conclusions. Moreover, we continue to analyse genome-wide methylation data from DNA extracted from FFPE tissue successfully on both the HumMeth27 and 450 K arrays.

Abstract Background Tumor immune tolerance can derive from the recruitment of suppressor cell populations, including myeloid-derived suppressor cells (MDSC). In cancer patients, MDSC accumulation correlates with increased tumor burden, but the mechanisms of MDSC induction remain poorly understood. Methods This study examined the ability of human tumor cell lines to induce MDSC from healthy donor PBMC using in vitro co-culture methods. These human MDSC were then characterized for morphology, phenotype, gene expression, and function. Results Of over 100 tumor cell lines examined, 45 generated canonical CD33+HLA-DRlowLineage- MDSC, with high frequency of induction by cervical, ovarian, colorectal, renal cell, and head and neck carcinoma cell lines. CD33+ MDSC could be induced by cancer cell lines from all tumor types with the notable exception of those derived from breast cancer (0/9, regardless of hormone and HER2 status). Upon further examination, these and others with infrequent CD33+ MDSC generation were found to induce a second subset characterized as CD11b+CD33lowHLA-DRlowLineage-. Gene and protein expression, antibody neutralization, and cytokine-induction studies determined that the induction of CD33+ MDSC depended upon over-expression of IL-1β, IL-6, TNFα, VEGF, and GM-CSF, while CD11b+ MDSC induction correlated with over-expression of FLT3L and TGFβ. Morphologically, both CD33+ and CD11b+ MDSC subsets appeared as immature myeloid cells and had significantly up-regulated expression of iNOS, NADPH oxidase, and arginase-1 genes. Furthermore, increased expression of transcription factors HIF1α, STAT3, and C/EBPβ distinguished MDSC from normal counterparts. Conclusions These studies demonstrate the universal nature of MDSC induction by human solid tumors and characterize two distinct MDSC subsets: CD33+HLA-DRlowHIF1α+/STAT3+ and CD11b+HLA-DRlowC/EBPβ+, which should enable the development of novel diagnostic and therapeutic reagents for cancer immunotherapy.

Abstract Background Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. Results The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Conclusions Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.

Abstract Background Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B. petrii from the other sequenced Bordetellae is the presence of a large number of mobile genetic elements including several large genomic regions with typical characteristics of genomic islands collectively known as integrative and conjugative elements (ICEs). These elements mainly encode accessory metabolic factors enabling this bacterium to grow on a large repertoire of aromatic compounds. Results During in vitro culture of Bordetella petrii colony variants appear frequently. We show that this variability can be attributed to the presence of a large number of metastable mobile genetic elements on its chromosome. In fact, the genome sequence of B. petrii revealed the presence of at least seven large genomic islands mostly encoding accessory metabolic functions involved in the degradation of aromatic compounds and detoxification of heavy metals. Four of these islands (termed GI1 to GI3 and GI6) are highly related to ICEclc of Pseudomonas knackmussii sp. strain B13. Here we present first data about the molecular characterization of these islands. We defined the exact borders of each island and we show that during standard culture of the bacteria these islands get excised from the chromosome. For all but one of these islands (GI5) we could detect circular intermediates. For the clc-like elements GI1 to GI3 of B. petrii we provide evidence that tandem insertion of these islands which all encode highly related integrases and attachment sites may also lead to incorporation of genomic DNA which originally was not part of the island and to the formation of huge composite islands. By integration of a tetracycline resistance cassette into GI3 we found this island to be rather unstable and to be lost from the bacterial population within about 100 consecutive generations. Furthermore, we show that GI3 is self transmissible and by conjugation can be transferred to B. bronchiseptica thus proving it to be an active integrative and conjugative element Conclusion The results show that phenotypic variation of B. petrii is correlated with the presence of genomic islands. Tandem integration of related islands may contribute to island evolution by the acquisition of genes originally belonging to the bacterial core genome. In conclusion, B. petrii appears to be the first member of the genus in which horizontal gene transfer events have massively shaped its genome structure.

Abstract Background Rhesus macaques infected with lymphocytic choriomeningitis virus (LCMV) provide a model for human Lassa fever. Disease begins with flu-like symptoms and progresses rapidly with fatal consequences. Previously, we profiled the blood transcriptome of LCMV-infected monkeys (M. Djavani et al J. Virol. 2007) showing distinct pre-viremic and viremic stages that discriminated virulent from benign infections. In the present study, changes in liver gene expression from macaques infected with virulent LCMV-WE were compared to gene expression in uninfected monkeys as well as to monkeys that were infected but not diseased. Results Based on a functional pathway analysis of differentially expressed genes, virulent LCMV-WE had a broader effect on liver cell function than did infection with non-virulent LCMV-Armstrong. During the first few days after infection, LCMV altered expression of genes associated with energy production, including fatty acid and glucose metabolism. The transcriptome profile resembled that of an organism in starvation: mRNA for acetyl-CoA carboxylase, a key enzyme of fatty acid synthesis was reduced while genes for enzymes in gluconeogenesis were up-regulated. Expression was also altered for genes associated with complement and coagulation cascades, and with signaling pathways involving STAT1 and TGF-β. Conclusion Most of the 4500 differentially expressed transcripts represented a general response to both virulent and mild infections. However, approximately 250 of these transcripts had significantly different expression in virulent infections as compared to mild infections, with approximately 30 of these being differentially regulated during the pre-viremic stage of infection. The genes that are expressed early and differently in mild and virulent disease are potential biomarkers for prognosis and triage of acute viral disease.

Abstract Background Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. Results In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. Conclusion The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches.