The occurrence and structural heterogeneity of arabinoxylan in commercial pilsner beers and their non-alcoholic counterparts.

The impact of arabinoxylan (AX) on the brewing process and beer characteristics depends on its content and structure and is often overlooked in research and industry. This paper reports on the occurrence and structural heterogeneity of AX in a set of commercial pilsner beers and their non-alcoholic counterparts. Fractionation by graded ethanol precipitation allowed us to isolate AX-rich fractions from beer with a number-average degree of polymerisation of 4 to 308 and an average degree of substitution in the range of 0.43 to 0.88. Pilsner beers had a higher content of high-molecular-weight AX than their non-alcoholic counterparts. The structural heterogeneity among the various commercial beers differed. By comparing the chemical composition of the beers, differences in beer production methods and ingredient selection were deduced and used to tentatively explain the differences in AX content and structural heterogeneity.

Starch hydrolysis during mashing: A study of the activity and thermal inactivation kinetics of barley malt α-amylase and ß-amylase.

Hydrolysis of starch is key in several industrial processes, including brewing. Here, the activity and inactivation kinetics of amylases throughout barley malt mashing are investigated, as a prerequisite for rational optimisation of this process. Varietal differences were observed in the activity of α- and ß-amylases as a function of temperature for six barley and malt varieties. These differences were not reflected in the resulting wort composition after mashing, using three isothermal phases of 30 min at 45 °C, 62 °C and 72 °C with intermediate heating by 1 °C/min. Thermal inactivation kinetics parameters determined for α- and ß-amylases of an industrially relevant malt variety in a diluted system showed that enzymes were inactivated at lower temperatures than expected. The obtained kinetic parameters could predict α-amylase, but not ß-amylase inactivation in real mashing conditions, suggesting that ß-amylase stability is enhanced during mashing by components present or formed in the mash.

Accurate quantification of small and large starch granules in barley and malt.

The proportion of small and large starch granules in barley and malt is often neglected, leading to underestimation of their importance in processes in which they are used. This study aimed to accurately determine the volume and number based percentages of small and large starch granules for three barley varieties, their micro-malted malts and three commercial malts. Quantitative starch isolation was performed and starch granule proportions were estimated using microscopic and image analysis, taking the non-sphericity of the large starch granules into account. Results show that barley starch consists of 32-39 volume% of small starch granules. Upon malting, this percentage is reduced to 17-27 volume%, showing that small granules are hydrolyzed faster than large granules during this process. The analyzed commercial malt samples have a small starch granule content of 22-25 volume%. Malt hence still contains a substantial amount of small starch granules, which can be expected to impact processing.

NMR metabolomics profiling of blood plasma mimics shows that medium- and long-chain fatty acids differently release metabolites from human serum albumin.

Metabolite profiling by NMR of body fluids is increasingly used to successfully differentiate patients from healthy individuals. Metabolites and their concentrations are direct reporters of body biochemistry. However, in blood plasma the NMR-detected free-metabolite concentrations are also strongly affected by interactions with the abundant plasma proteins, which have as of yet not been considered much in metabolic profiling. We previously reported that many of the common NMR-detected metabolites in blood plasma bind to human serum albumin (HSA) and many are released by fatty acids present in fatted HSA. HSA is the most abundant plasma protein and main transporter of endogenous and exogenous metabolites. Here, we show by NMR how the two most common fatty acids (FAs) in blood plasma - the long-chain FA, stearate (C18:0) and medium-chain FA, myristate (C14:0) - affect metabolite-HSA interaction. Of the set of 18 common NMR-detected metabolites, many are released by stearate and/or myristate, lactate appearing the most strongly affected. Myristate, but not stearate, reduces HSA-binding of phenylalanine and pyruvate. Citrate signals were NMR invisible in the presence of HSA. Only at high myristate-HSA mole ratios 11:1, is citrate sufficiently released to be detected. Finally, we find that limited dilution of blood-plasma mimics releases HSA-bound metabolites, a finding confirmed in real blood plasma samples. Based on these findings, we provide recommendations for NMR experiments for quantitative metabolite profiling.

(1)H NMR signal at 2.10 ppm in the spectrum of KMnO(4)-bleached heparin sodium: identification of the chemical origin using an NMR-only approach.

The recently revised European Pharmacopeia and US Pharmacopeia heparin sodium monographs include nuclear magnetic resonance (NMR) tests on both identity and purity. In KMnO(4)-bleached heparin, an unidentified NMR signal is present at 2.10 ppm at a level of 15-20% of the mean of signal height of the major glucosamine (GlcNAc/GlcNS,6S) anomeric proton signal at 5.42 ppm and of the major iduronic acid (IdoA2S) anomeric proton signal at 5.21 ppm. According to the new monographs, no unidentified signals greater than 4% should be detected at that position. Thus, the material did not meet the acceptance criterion. The signal at 2.10 ppm has been present at the same level in all released MSD KMnO(4)-bleached heparin sodium batches analyzed over the past 10 years. The signal is a result of the KMnO(4) bleaching. No (oversulfated) chondroitin sulfate or dermatan sulfate was detected in this material. A comprehensive NMR study using long-range heteronuclear 2D techniques identifies this signal at 2.10 ppm as originating from the acetyl methyl group of (6-sulfated) 2-N-acetyl-2-deoxy-glucono-1,5-lactone. This modified monosaccharide is formed by the KMnO(4) oxidation of the reducing end of a terminal N-acetylglucosamine.

Initial staging of malignant melanoma by positron emission tomography and sentinel node biopsy.

UNLABELLED: By a retrospective study and literature review we aimed to evaluate the accuracy of Sentinel Node Biopsy (SNB) and F-18-fluorodeoxyglucose positron emission tomography (PET) for early detection of lymph node metastases. MATERIAL AND METHODS: Every patient presenting with a malignant melanoma without clinical lymph node involvement and a Breslow index over 1 mm or a recurrence was subjected to a preoperative PET scan and a sentinel node biopsy. Over a period of 10 months, 5 patients were included. They were submitted to conventional staging techniques, PET and SNB. RESULTS: In none of the patients the PET scan showed signs of lymph node involvement or distant metastases. However, two patients, both with a Breslow index of 1.4, had micrometastases in the sentinel node. CONCLUSION: Already in this small group of patients, PET scanning missed two metastases (40%). This is confirmed by several recent publications, stating that the resolution of positron emission tomography is about 5 mm and thus insufficient to detect micrometastases. Several larger series showed a sensitivity of PET to detect lymph node involvement of 15-50%. Therefore we conclude that PET is of limited use in these patients without palpable lymph nodes. Sentinel node biopsy however proves to be a useful tool and should be considered in the initial staging of malignant melanoma without palpable lymph node or distant metastases.

Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting.

RNA pseudoknots play important roles in many biological processes. In the simian retrovirus type-1 (SRV-1) a pseudoknot together with a heptanucleotide slippery sequence are responsible for programmed ribosomal frameshifting, a translational recoding mechanism used to control expression of the Gag-Pol polyprotein from overlapping gag and pol open reading frames. Here we present the three-dimensional structure of the SRV-1 pseudoknot determined by NMR. The structure has a classical H-type fold and forms a triple helix by interactions between loop 2 and the minor groove of stem 1 involving base-base and base-sugar interactions and a ribose zipper motif, not identified in pseudoknots so far. Further stabilization is provided by a stack of five adenine bases and a uracil in loop 2, enforcing a cytidine to bulge. The two stems of the pseudoknot stack upon each other, demonstrating that a pseudoknot without an intercalated base at the junction can induce efficient frameshifting. Results of mutagenesis data are explained in context with the present three-dimensional structure. The two base-pairs at the junction of stem 1 and 2 have a helical twist of approximately 49 degrees, allowing proper alignment and close approach of the three different strands at the junction. In addition to the overwound junction the structure is somewhat kinked between stem 1 and 2, assisting the single adenosine in spanning the major groove of stem 2. Geometrical models are presented that reveal the importance of the magnitude of the helical twist at the junction in determining the overall architecture of classical pseudoknots, in particular related to the opening of the minor groove of stem 1 and the orientation of stem 2, which determines the number of loop 1 nucleotides that span its major groove.

Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site.

The cleavage site of the Neurospora VS RNA ribozyme is located in a separate hairpin domain containing a hexanucleotide internal loop with an A-C mismatch and two adjacent G-A mismatches. The solution structure of the internal loop and helix la of the ribozyme substrate hairpin has been determined by nuclear magnetic resonance (NMR) spectroscopy. The 2 nt in the internal loop, flanking the cleavage site, a guanine and adenine, are involved in two sheared G.A base pairs similar to the magnesium ion-binding site of the hammerhead ribozyme. Adjacent to the tandem G.A base pairs, the adenine and cytidine, which are important for cleavage, form a noncanonical wobble A+-C base pair. The dynamic properties of the internal loop and details of the high-resolution structure support the view that the hairpin structure represents a ground state, which has to undergo a conformational change prior to cleavage. Results of chemical modification and mutagenesis data of the Neurospora VS RNA ribozyme can be explained in context with the present three-dimensional structure.

New developments in structure determination of pseudoknots.

Recently, several high-resolution structures of-RNA pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type pseudoknot family. The most complicated pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double pseudoknot. In particular, the structure-function relationships of the H-type pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs.

A conformational change in the catalytic core of the hammerhead ribozyme upon cleavage of an RNA substrate.

Heteronuclear multidimensional NMR structural studies have been performed on a hammerhead ribozyme complexed with a cleaved and an uncleaved substrate. The NMR data demonstrate that the three helices surrounding the conserved catalytic core hammerhead are stably formed in both complexes. Evidence is also presented that indicates that the sheared G-A base pairs in the conserved core are formed in the absence of Mg2+. The NMR structural data demonstrate that there is a significant structural change of the conserved core of the hammerhead ribozyme-substrate complex upon cleavage of the substrate. Molecular dynamics calculations were performed to generate models of the ribozyme-cleaved substrate complex, and these results are used to help understand the mechanism of the hammerhead cleavage reaction.

Protonatable hairpins are conserved in the 5'-untranslated region of tymovirus RNAs.

The secondary structures of the 5'-untranslated region (5'-UTR) of five different tymoviruses have been determined by structure probing, computer prediction and sequence comparison. Despite large sequence differences, there are remarkable similarities in the secondary structure. In all viruses two or four hairpins are found, most of which contain a symmetrical internal loop consisting of adjacent C-C or C-A mismatches. Since it is known that such mismatches can be protonated and protonated cytosines play an important role in RNA-protein interactions in tymoviral virions, the influence of pH on the conformation of the internal loop was studied. UV melting experiments and 1-dimensional proton NMR at varying pH values and salt concentrations confirm that the hairpins can be protonated under relatively mild conditions. The hairpin found in the 5'-UTR of erysimum latent virus, which has an asymmetrical internal loop consisting of cytosines and uridines, shows comparable behaviour. It is concluded that all tymoviral RNAs contain protonatable hairpins in the 5'-UTR. Binding experiments with empty viral capsids, however, do not yet establish a role in capsid protein binding.