Sulfated glycosaminoglycan-like polymers are present in an acidophilic biofilm from a sulfidic cave.

Sulfated glycosaminoglycans (sGAG) are negatively charged extracellular polymeric substances that occur in biofilms from various environments. Yet, it remains unclear whether these polymers are acquired from the external environment or produced by microbes in the biofilm. To resolve this, we analyzed the presence of sGAGs in samples of an acidophilic biofilm collected from Sulfur Cave in Puturosu Mountain (Romania), an environment that is largely inaccessible to contamination. A maximum of 55.16 ± 2.06 µg sGAG-like polymers were recovered per mg of EPS. Enzymatic treatment with chondroitinase ABC resulted in a decrease of the mass of these polymers, suggesting the structure of the recovered sGAG is similar to chondroitin. Subsequent FT-IR analysis of these polymers revealed absorbance bands at 1230 cm-1, 1167 cm-1 and 900 cm-1, indicating a possible presence of polysaccharides and sulfate. Analysis of genomic sequences closely related to those predominant in the acidophilic biofilm, contained genes coding for sulfotransferase (an enzyme needed for the production of sGAG), which supports the hypothesis of microbial synthesis of sGAGs within the biofilm.

International point prevalence study of Intensive Care Unit transfusion practices-Pilot study in the Netherlands.

BACKGROUND: Anaemia and coagulopathy are common issues in critically ill patients. Transfusion can be lifesaving, however, is associated with potential life threatening adverse events. As an international transfusion guideline for this specific patient population is lacking, we hypothesize that a high heterogeneity in transfusion practices exists. In this pilot-study we assessed transfusion practice in a university hospital in the Netherlands and tested the feasibility of this protocol for an international multi-centre study. METHODS: A prospective single centre cohort study was conducted. For seven days all consecutive non-readmitted patients to the adult Intensive Care Unit (ICU) were included and followed for 28 days. Patients were prospectively followed until ICU discharge or up to day 28. Patient outcome data was collected at day 28. Workload for this study protocol was scored in hours and missing data. RESULTS: In total, 48 patients were included, needed in total three hours patient to include and collect all data, with 1.6% missing data showing the feasibility of the data acquisition. Six (12.5%) patients received red blood cells (RBCs), three patients (6.3%) received platelet concentrates, and two (4.2%) patients received plasma units. In total eight (16.7%) patients were transfused with one or more blood products. Median pre- and post-transfusion haemoglobin (Hb) levels were 7.6 (6.7-7.7) g/dL and 8.1 (7.6-8.7) g/dL, respectively. CONCLUSION: In this pilot-study we proved the feasibility of our protocol and observed in this small population a restrictive transfusion practice for all blood products.

[Cost variation in care groups?] / Verschillen zorgkosten tussen zorggroepen?

OBJECTIVE: Is the simple mean of the costs per diabetes patient a suitable tool with which to compare care groups? Do the total costs of care per diabetes patient really give the best insight into care group performance? DESIGN: Cross-sectional, multi-level study. METHOD: The 2009 insurance claims of 104,544 diabetes patients managed by care groups in the Netherlands were analysed. The data were obtained from Vektis care information centre. For each care group we determined the mean costs per patient of all the curative care and diabetes-specific hospital care using the simple mean method, then repeated it using the 'generalized linear mixed model'. We also calculated for which proportion the differences found could be attributed to the care groups themselves. RESULTS: The mean costs of the total curative care per patient were €3,092 - €6,546; there were no significant differences between care groups. The mixed model method resulted in less variation (€2,884 - €3,511), and there were a few significant differences. We found a similar result for diabetes-specific hospital care and the ranking position of the care groups proved to be dependent on the method used. The care group effect was limited, although it was greater in the diabetes-specific hospital costs than in the total costs of curative care (6.7% vs. 0.4%). CONCLUSION: The method used to benchmark care groups carries considerable weight. Simply stated, determining the mean costs of care (still often done) leads to an overestimation of the differences between care groups. The generalized linear mixed model is more accurate and yields better comparisons. However, the fact remains that 'total costs of care' is a faulty indicator since care groups have little impact on them. A more informative indicator is 'costs of diabetes-specific hospital care' as these costs are more influenced by care groups.

Genetic analysis of short children with apparent growth hormone insensitivity.

BACKGROUND/AIMS: In short children, a low IGF-I and normal GH secretion may be associated with various monogenic causes, but their prevalence is unknown. We aimed at testing GH1, GHR, STAT5B, IGF1, and IGFALS in children with GH insensitivity. SUBJECTS AND METHODS: Patients were divided into three groups: group 1 (height SDS <-2.5, IGF-I <-2 SDS, n = 9), group 2 (height SDS -2.5 to -1.9, IGF-I <-2 SDS, n = 6) and group 3 (height SDS <-1.9, IGF-I -2 to 0 SDS, n = 21). An IGF-I generation test was performed in 11 patients. Genomic DNA was used for direct sequencing, multiplex ligation-dependent probe amplification and whole-genome SNP array analysis. RESULTS: Three patients in group 1 had two novel heterozygous STAT5B mutations, in two combined with novel IGFALS variants. In groups 2 and 3 the association between genetic variants and short stature was uncertain. The IGF-I generation test was not predictive for the growth response to GH treatment. CONCLUSION: In severely short children with IGF-I deficiency, genetic assessment is advised. Heterozygous STAT5B mutations, with or without heterozygous IGFALS defects, may be associated with GH insensitivity. In children with less severe short stature or IGF-I deficiency, functional variants are rare.

Day care at green care farms: a novel way to stimulate dietary intake of community-dwelling older people with dementia?

OBJECTIVE: This study aimed to compare dietary intake of older people with dementia receiving day care at regular day care facilities (RDCFs) or at so-called green care farms (GCFs). DESIGN AND SETTINGS: A comparative cross-sectional study was performed at 10 GCFs and 10 RDCFs in the Netherlands. PARTICIPANTS: 30 subjects from GCFs and 23 subjects from RDCFs, aged 65 years or over, were included in the study. Subjects from GCFs were mostly married males who were aged younger than the subjects from RDCFs who were mostly widowed females. MEASUREMENTS: Dietary intake of the subjects was observed and/or recorded both at home and during their time at the day care facility. RESULTS: In the GCF group, average total energy intake was significantly higher than in the RDCF group (8.8 MJ/d vs. 7.2 MJ/d). Also total carbohydrates and protein intakes were higher in the GCF group than in the RDCF group (with 257 g/d vs. 204 g/d, and 76 g/d vs. 65 g/d respectively). In addition, average total fluid intake was significantly higher in the GCF group than in the RDCF group (2577 g/d vs. 1973 g/d). Multiple linear regression analyses revealed that after taking possible confounders into account, day care type was still significantly related to the intake of energy, carbohydrates and fluids. CONCLUSION: This study suggests beneficial effects of this new type of day care on dietary intake by community-dwelling older people with dementia.

Induction of HSV-gD2 specific CD4(+) cells in Peyer's patches and mucosal antibody responses in mice following DNA immunization by both parenteral and mucosal administration.

A DNA vaccine encoding glycoprotein D (gD) of herpes simplex virus type 2 (pHSV-gD2) was injected via parenteral and mucosal routes to determine the optimal route of delivery for immune stimulation. Generation of distal mucosal immunity following parenteral vaccination was also evaluated. While all routes of DNA vaccine administration resulted in systemic cellular and humoral responses, the intra-muscular (i.m.) and intra-dermal (i.d.) routes of delivery produced the highest responses. Furthermore, i.m. and i.d. routes produced mucosal humoral responses that were comparable to those obtained via mucosal routes. Specific pHSV-gD2 PCR signals were detected in the Peyer's patches (PP) within hours following vaccination and antigen specific IgA was detected in secretions and supernatants from gut fragment cultures. Furthermore, antigen specific CD4(+) cells were found in PP. Collectively these results suggest that the DNA vaccine stimulated a response in the PP, a major inductive site for mucosal responses.

IL-12 gene as a DNA vaccine adjuvant in a herpes mouse model: IL-12 enhances Th1-type CD4+ T cell-mediated protective immunity against herpes simplex virus-2 challenge.

IL-12 has been shown to enhance cellular immunity in vitro and in vivo. Recent reports have suggested that combining DNA vaccine approach with immune stimulatory molecules delivered as genes may significantly enhance Ag-specific immune responses in vivo. In particular, IL-12 molecules could constitute an important addition to a herpes vaccine by amplifying specific immune responses. Here we investigate the utility of IL-12 cDNA as an adjuvant for a herpes simplex virus-2 (HSV-2) DNA vaccine in a mouse challenge model. Direct i.m. injection of IL-12 cDNA induced activation of resting immune cells in vivo. Furthermore, coinjection with IL-12 cDNA and gD DNA vaccine inhibited both systemic gD-specific Ab and local Ab levels compared with gD plasmid vaccination alone. In contrast, Th cell proliferative responses and secretion of cytokines (IL-2 and IFN-gamma) and chemokines (RANTES and macrophage inflammatory protein-1alpha) were significantly increased by IL-12 coinjection. However, the production of cytokines (IL-4 and IL-10) and chemokine (MCP-1) was inhibited by IL-12 coinjection. IL-12 coinjection with a gD DNA vaccine showed significantly better protection from lethal HSV-2 challenge compared with gD DNA vaccination alone in both inbred and outbred mice. This enhanced protection appears to be mediated by CD4+ T cells, as determined by in vivo CD4+ T cell deletion. Thus, IL-12 cDNA as a DNA vaccine adjuvant drives Ag-specific Th1 type CD4+ T cell responses that result in reduced HSV-2-derived morbidity as well as mortality.

Hairpin formation in synthetic oligonucleotides.

The structure and dynamics of the homologous series of the (partly) self-complementary DNA fragments, d(ATCCTATnTAGGAT) n = 0-7, were investigated in a combined NMR, T-jump, and optical melting study. It is shown that all compounds in the series may adopt hairpin like conformations, even for n less than 3, although for these smaller n values this only occurs in significant amounts at relatively low concentrations (approximately 10 microM). The enthalpy change accompanying the hairpin-coil melting transition turns out to depend on the number of intervening thymidines, n. It is shown that this does not mean that the enthalpy of loop closure is significantly different from zero, but that loop formation stabilizes the base pair closing the loop. The results indicate that for DNA the optimal loop consists of four or five residues. The observation that hairpins are formed for n less than 3 and that the stability of DNA hairpins is at its maximum for loop lengths of four to five residues is at variance with earlier findings for RNA. In the latter case the optimal loop size consists of six to seven residues, whereas for less than three intervening residues only, dimer, and no hairpin formation, was observed [17, 20]. A direct comparison with RNA behaviour was made by studying r(AUCCUAUT4UAGGAU), T = ribothymidine. In contrast to its DNA analogue, d(ATCCTAT4TAGGAT), the ribo-fragment forms a dimer as well as a hairpin at low (10 microM) concentrations. With the thermodynamic melting parameters deduced from the present experiments the differences between DNA and RNA melting behaviour can be explained.

The effect of single base-pair mismatches on the duplex stability of d(T-A-T-T-A-A-T-A-T-C-A-A-G-T-T-G) . d(C-A-A-C-T-T-G-A-T-A-T-T-A-A-T-A).

The stabilitye and dynamics of the duplex d(T-A-T-T-A-A--T-A-T-C-A-A-G-T-T-G) . d(C-A-A-C-T-T-G-A-T-A-T-T-A-A-T-A) has been studied by means of ultraviolet-melting, temperature-jump relaxation kinetics, stopped-flow and NMR spectroscopy. In addition, the influence of the mismatches A . A, G . T, A .C and T . C,-incorporated in this double helix through the introduction of non-complementary bases in the second strand, on these parameters has been investigated. The thermodynamic parameters characterizing the melting of the duplexes have been determined. Interestingly, a substantial decrease was observed for the values of the melting enthalpy when proceeding from 0.015 M to 0.1 M NaCl solutions. All duplexes that contain mismatches have melting temperatures below that of the totally complementary double helix. On the basis of NMR experiments and differences in the free enthalpy values between the totally complementary double helix and the duplexes with mismatches, it could be concluded that some degree of stacking of the two mispaired bases between the neighbouring base pairs is maintained. At 1 M NaCl the enthalpy and entropy of the helix-to-coil transition of the totally complementary double helix are in good agreement with values calculated on the basis of the thermodynamic data of Borer et al. [Borer, Ph. N., Dengler, B. & Tinoco, I. (1974) J. Mol. Biol. 86, 843--853] which were derived for RNA. The kinetics of the complementary duplex and duplexes with G . T and A . C mismatches were studied by means of stopped-flow and temperature-jump techniques. The rate constants of formation are the same for the three double helices. The decrease in stability of the duplexes with mismatches is therefore entirely due to an increase of the dissociation constant. In temperature-jump experiments very often a fast relaxation process is observed in addition to the relaxation characterizing the disruption of the double helix. This fast relaxation process is customarily attributed to base destacking in the single helix. By combining temperature-jump relaxation kinetics with NMR melting experiments, it is shown that at the low temperature side of the melting transition this fast relaxation process is caused by rapid changes in the double-helical structure.

High-resolution proton magnetic resonance studies of the 3'-terminal colicin fragment of 16 S ribosomal RNA from Escherichia coli. Assignment of iminoproton resonances by nuclear Overhauser effect experiments and the influence of adenine dimethylation on the hairpin conformation.

The "colicin" fragments comprising the 49 3'-terminal nucleotides of 16 S ribosomal RNA have been isolated from wild-type Escherichia coli and from a kasugamycin-resistant mutant that lacks methylation of two geminal adenine residues. Proton nuclear magnetic resonance (n.m.r.) spectra (500 MHz) were recorded at various temperatures. The low-field resonances arising from the hydrogen-bonded iminoprotons of paired bases were assigned using the nuclear Overhauser effect (n.o.e.). Crucial to the interpretation of the spectra are the resonances that originate from the two hydrogen-bonded iminoprotons of a U X G basepair. Combined with temperature-jump relaxation kinetics experiments the n.o.e.s lead to the conclusion that a conserved A X U/U X G junction in the hairpin is a thermolabile dislocation in the helix. The n.m.r. spectra of the wild-type and mutant fragment are only different with respect to the iminoproton resonances of the two base-pairs adjoining the hairpin loop. The spectra recorded at various temperatures tend to indicate that dimethylation of the adenosines labilizes these base-pairs, but no definitive conclusions are drawn. The results confirm our previous views that dimethylation of the adenosine residues affects the conformation of the hairpin loop.

Structure, kinetics and thermodynamics of DNA hairpin fragments in solution.

The hairpin-to-coil equilibrium of the hexadecadeoxynucleotide d(ATCCTATTTTTAGGAT) was extensively studied by means of NMR, T-jump and UV. The thermodynamic and kinetic parameters for this equilibrium were determined, yielding a consistent picture of the dynamical behavior of this hairpin structure, which is shown to be a clear example of a situation in which the linebroadening of the imino proton resonances is not determined by the lifetime of the double helix. A comparative study of the homologous hairpins in which the size of the loop was elongated from 4 to 7 thymidine residues shows a monotonous decrease in Tm for the hairpin-to-coil transitions. This finding is in contrast with the view that the stability of hairpins reaches a maximum with a loop size of 6-7 residues. The NMR results indicate that the accessibility of the thymine bases in the loop towards solvent molecules or complementary nucleotides greatly depends on the size of the loop.

500-MHz 1H-NMR studies of ribosomal proteins isolated from 70-S ribosomes of Escherichia coli.

A method for the large-scale isolation of ribosomal proteins is described avoiding pre-separation of 30-S and 50-S subunits. Five proteins isolated in this way were studied with high-resolution 1H NMR at 500 MHz. These are S21, L18, L25, L30 and L33. The results show that L18, L25 and L30 exhibit tertiary structure in solution and indications for secondary structure in S21 are found. Protein L33 appears to be a random coil. Several resonances in the 1H NMR spectra are assigned to particular protons of amino acid residues, e.g. the aromatic ring protons of tyrosines and histidines, and epsilon-protons of lysines.

Destabilization of secondary structure in 16S ribosomal RNA by dimethylation of two adjacent adenosines.

Fragments comprising the 49 nucleotides from the 3'-end have been purified from 16S ribosomal RNA of wild-type Escherichia coli and from a kasugamycin-resistant mutant that specifically lacks dimethylation of two adjacent adenines near the 3'-terminus. These fragments, obtained after treatment of ribosomes in vitro with the bacteriocin cloacin DF13, were used to study the effect of the methyl groups on the temperature dependent unfolding of double-stranded regions. Both fragments contain at least 3 independent melting transitions, of which the one with the highest Tm corresponds with the unfolding of a nine-basepair long central hairpin. Dimethylation of the adenines in the loop of this hairpin lowers the melting temperature (Tm) by approximately 2 degrees C at 0.2 M NaCl and by about 5 degrees C at 0.15 M NaCl. It is suggested that m6(2)Am6(2)A is more antagonistic to loop formation that ApA and that the function of the methyl groups is to help to destabilize the 3'-terminal hairpin in 16S rRNA in order to facilitate intermolecular interactions.

31P NMR study of the kinetics of binding of myo-inositol hexakisphosphate to human hemoglobin. Observation of fast-exchange kinetics in high-affinity systems.

The association and dissociation kinetics of the complexes of myo-inositol hexakisphosphate (P6-inositol) with deoxyhemoglobin (Hb) and carboxyhemoglobin (HbCO) have been investigated by 31P NMR between pH 6.8 and pH 5.5. These complexes represent high-affinity systems with binding constants varying between 10(5) M-1 and 2 X 10(9) M-1. 31P NMR spectra of P6-inositol were recorded in the presence of hemoglobin as a function of the P6-inositol/hemoglobin molar ratio. It appeared that the exchange of the polyphosphate molecule between the solution and the central cavity binding site is fast on the NMR time scale. This observation cannot be reconciled with a single-step binding mechanism of P6-inositol to hemoglobin. Analysis of the spectra revealed the occurrence of additional binding of P6-inositol to both Hb and HbCO. This binding was also observed in pH-state experiments performed at low ionic strength. 31P NMR experiments carried out with hemoglobin of which the alpha-chain N termini were carbamylated, strongly suggest that these termini constitute the additional binding site for P6-inositol. A model is proposed which accounts for the enhancement of exchange kinetics in these high-affinity systems. In this model a rapid migration is assumed for P6-inositol between the central cavity binding site and an entry/leaving site on the hemoglobin molecule. Based on this model 31P NMR linewidths and chemical shift patterns for this three-site exchange problem were calculated.

Equilibrium aspects of the binding of myo-inositol hexakisphosphate to human hemoglobin as studied by 31P NMR and pH-stat techniques.

The interaction of myo-inositol hexakisphosphate (P6-inositol) with human hemoglobin has been studied as a function of pH using pH-stat techniques and 31P NMR. With the pH-stat method the following data were obtained: the association constants for the P6-inositol/deoxyhemoglobin and P6-inositol/carboxyhemoglobin complexes at alkaline and acid pH respectively and the proton absorption curves associated with the protein/phosphate interaction for both complexes from pH 5.5 to pH 9. From these data affinities of P6-inositol towards deoxyhemoglobin (Hb) and carboxyhemoglobin (HbCO) have been calculated as a function of pH. The shape of the proton absorption curves was found to be strongly dependent on the ligation state of the hemoglobin molecule. The pH dependence of the 31P NMR spectra of P6-inositol bound to Hb or HbCO provides a monitor for the proton-binding behaviour of the phosphate groups of P6-inositol when present in the central cavity of the protein. It appears that this behaviour is only slightly dependent on the ligation state of the hemoglobin molecule. The NMR spectral data were interpreted in terms of a model which takes into account the electrostatic interaction between the phosphate groups within the P6-inositol molecule as well as the electrostatic interaction between the phosphate groups and positively charged groups on the protein. To account for the discrepancy between the pH-stat and 31P NMR results, i.e. a strong dependence of the proton-absorption curves and a weak dependence of the proton-binding behaviour of P6-inositol on the ligation state of the protein respectively, it is proposed that a conformational change takes place in HbCO upon P6-inositol binding.

Identification of the residues involved in the oxygen-linked chloride-ion binding sites in human deoxyhemoglobin and oxyhemoglobin.

The number of Bohr protons released upon oxygenation of human hemoglobin was measured at 25 degrees C and 37 degrees C as a function of the concentration of chloride ions. From the results obtained association constants could be evaluated for the binding of chloride ions to both deoxy and oxyhemoglobin at these two temperatures. Furthermore, pK values could be determined for those protonic groups involved in chloride ion binding to deoxy and oxyhemoglobin. From these data it was inferred that in oxyhemoglobin only imidazole groups are participating in chloride binding, whereas in deoxyhemoglobin the chloride binding site contained the alpha NH2 group of valine-1 alpha. The same conclusions were reached by measuring the pK values of the aminogroups of valine 1 alpha and valine-1 beta at different temperatures and ionic strengths. The pK values were measured by following the rate of reaction of 1-fluoro-2,4-dinitrobenzene with the alpha-NH2 group by spectrophotometric means. We further showed that binding of Cl-, Br- and I- to oxyhemoglobin follows the lyotropic or Hofmeister series, while this effect is much less for deoxyhemoglobin. This result indicates that for the binding of anions to oxyhemoglobin interactions with non-polar groups contribute to the free-energy change of binding.

The pH dependence of the binding of D-glycerate 2,3-bisphosphate to deoxyhemoglobin and oxyhemoglobin. Determination of the number of binding sites in oxyhemoglobin.

The number of Bohr protons released upon oxygenation has been measured over a large range of human hemoglobin concentrations (0.02 to 4.5 mM) in the presence of equimolar amounts of D-glycerate 2,3-bisphosphate. From these data the association constants for the binding of this organic phosphate to deoxyhemoglobin and oxyhemoglobin were calculated at different pH values. The maximum number of protons absorbed upon binding to oxyhemoglobin was determined as well. The maximum number of protons bound to deoxyhemoglobin upon binding of D-glycerate 2,3-bisphosphate was measured independently. From the pH dependence of the association constants and the maximum number of protons absorbed it could be concluded that only one D-glycerate 2,3-bisphosphate can be bound to both deoxyhemoglobin and oxyhemoglobin.

The binding of chloride ions to ligated and unligated human hemoglobin and its influence on the Bohr effect.

The contribution of the interaction of chloride ions with deoxy and oxyhemoglobin to the Bohr effect can be described by a simple binding model. Applying this model to experiment data reveals that at physiological pH and ionic strength about half of the release of Bohr protons is due to a difference in chloride ion binding to deoxy- and oxyhemoglobin. The chloride-independent part of the Bohr effect corresponds with the shift in pK which His-146 beta shows upon oxygenation. The proton absorptioon by hemoglobin observed upon oxygenation below pH 6 is apparently due to a chloride-ion-induced proton uptake, which is larger for oxyhemoglobin than for deoxyhemoglobin. The analysis of the experimental data indicates the existence of only two oxygen-linked chloride ion binding sites in both deoxy and oxyhemoglobin. In deoxyhemoglobin the binding sites most likely consist of Val-1 alpha of one chain and Arg-141 alpha of the partner chain. The sites in oxyhemoglobin consist of groups with a pK value in the neutral pH range; they do not contain lysyl or arginyl residues.