Investigation of the sugar content in wood hydrolysates with iodometric titration and UPLC-ELSD

ArticleAutohydrolysis of birch wood is a mild pretreatment process, which gives a notable yield of sugars – monosaccharides and oligosaccharides – in the aqueous hydrolysate, while a solid lignocellulose fraction can be further processed into other valuable products within a biorefinery concept. In this work two analytical methods – iodometric titration and ultra-high performance liquid chromatography with evaporative light scattering detection (UPLC-ELSD) – have been optimized and compared for the determination of the sugar content in series of birch wood hydrolysates. The results of both methods were consistent and showed that the highest yield of sugars, mostly xylose, was obtained by hydrolysis at 180 °C after 75 min

Impact of different fertilisers on elemental content in young hybrid aspen stem wood

The biomass production using fast-growing tree species such as hybrid aspen (Populus tremuloides Michx. x Populus tremula L.) has been recognized as an environmentally friendly and cost-effective approach. Growing these species can reduce the negative impact of earlier land mismanagement and at the same time provide additional biomass growth. The application of fertilisers may introduce not only the necessary macro elements (N, P, K) but also significant amounts of toxic heavy metals. Therefore, the knowledge about elemental flows from fertilised soil to the different parts of hybrid aspen trees is essential and especially meaningful for the evaluation of element content in specific environmental ecosystems. The impact of different fertilisers (sewage sludge, digestate and wood ash) on the concentrations of micro- and macro elements in the wood of six-year-old hybrid aspen stands grown on former agricultural land was studied. The determination of element concentrations in different tree rings of hybrid aspen trees was accomplished by inductively coupled plasma mass spectrometry (ICP–MS). Isotope ratio mass spectrometry (IRMS) was used to determine the nitrogen and carbon content and isotope ratios in different parts of hybrid aspen trees. Stem disc samples from hybrid aspen trees were obtained from agricultural land in the central part of Latvia. Samples were taken from six-yearold hybrid aspen trees that at the moment of planting were fertilised with sewage sludge, a residue of biogas production (digestate) and wood ash. The obtained results indicated that the chemical element accumulation in hybrid aspen was affected by the applied fertiliser type. In this study, the use of wood ash, as well as digestate, affected the elemental content in hybrid aspen to a greater extent than the use of sewage sludge, relative to unfertilised (control) subplot. The analysed elements varied in the analysed stem plane (across the tree rings). The most significant changes between the rings were observed for the content of K and Ca

Clinical features of double infection with tick-borne encephalitis and Lyme borreliosis transmitted by tick bite

Background: In Latvia and other endemic regions, a single tick bite has the potential to transmit both tick-borne encephalitis (TBE) and Lyme borreliosis. Objective: To analyse both the clinical features and differential diagnosis of combined tick-borne infection with TBE and Lyme borreliosis, in 51 patients with serological evidence, of whom 69% had tick bites. Results: Biphasic fever suggestive of TBE occurred in 55% of the patients. Meningitis occurred in 92%, with painful radicular symptoms in 39%. Muscle weakness occurred in 41%; in 29% the flaccid paralysis was compatible with TBE. Only two patients presented with the bulbar palsy typical of TBE. Typical Lyme borreliosis facial palsy occurred in three patients. Typical TBE oculomotor disturbances occurred in two. Other features typical of Lyme borreliosis detected in our patients were distal peripheral neuropathy (n = 4), arthralgia (n = 9), local erythema 1-12 days after tick bite (n = 7) and erythema chronicum migrans (n = 1). Echocardiogram abnormalities occurred in 15. Conclusions: Patients with double infection with TBE and Lyme borreliosis fell into three main clinical groups: febrile illness, 3 (6%); meningitis, 15 (30%); central or peripheral neurological deficit (meningoencephalitis, meningomyelitis, meningoradiculitis and polyradiculoneuritis), 33 (65%). Systemic features pointing to Lyme borreliosis were found in 25 patients (49%); immunoglobulin (Ig)M antibodies to borreliosis were present in 18 of them. The clinical occurrence of both Lyme borreliosis and TBE vary after exposure to tick bite, and the neurological manifestations of each disorder vary widely, with considerable overlap. This observational study provides no evidence that co-infection produces unusual manifestations due to unpredicted interaction between the two diseases. Patients with tick exposure presenting with acute neurological symptoms in areas endemic for both Lyme borreliosis and TBE should be investigated for both conditions. The threshold for simultaneous treatment of both conditions should be low, given the possibility of co-occurrence and the difficulty in ascribing individual neurological manifestations to one condition or the other.Peer reviewe

Sol-Gel Synthesis and Characterization of Cerium Substituted Calcium Hydroxyapatite

In this study, an aqueous sol-gel chemistry route based on phosphoric acid as the phosphorus precursor, calcium acetate monohydrate and cerium (III) nitrate hexahydrate as source of calcium and cerium ions, respectively, have been used to prepare cerium-substituted calcium hydroxyapatite (CHAp) powders. The tartaric acid was used as complexing agent in the sol-gel processing. The final products were obtained by calcination of the dry precursor gels for 5 h at 1000 °C. The phase transformations, composition, and structural changes in the polycrystalline samples were studied by infrared spectroscopy (IR), X-ray powder diffraction analysis (XRD), scanning electron microscopy (SEM), UV-visible reflection spectroscopy and luminescence measurements. It was demonstrated, however, that the high substitution of calcium by cerium does not proceed in the CHAp. The reflectance spectra of Ce substituted CHAp show nearly 100% reflection in the wavelength range of 450-800 nm. The luminescent properties of these samples were also investigated. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/3493

A comparative study of the properties of industrially produced humic substances

Humic substances (HSs) are produced industrially in large quantities from low rank coal, weathered coal, peat, also from soils, composts and other sources. Considering that the applications of industrially produced HSs also include food, pharmaceutical applications and environmental technologies, it is important to evaluate their composition and quality and to identify their sources. The aim of the present study is to compare the properties of industrially produced HS samples. HSs were characterised using spectroscopic and other methods. For the identification of origin of HSs, different methods can be used, such as elemental analysis and ratios of light stable isotopes. The results of the study indicate that many industrially produced HSs are of poor quality (low concentration of basic substance, admixture of undesirable substances, pollutants, no quality indications). In this situation, rigorous quality control should be implemented, providing detailed characteristics of the product. The composition of materials suggested for agricultural applications has not been analysed much. Most of the studied materials were designated as HAs, followed by fulvic acids (FAs) and HSs. However, an analysis of the humic matter types indicates that the majority of substances offered on the market are in fact mixtures of HAs and FAs; so, it would be more appropriate to designate them as HSs or their salts. This study identifies the main quality problems of industrially produced humic substances: 1) lack of strict quality indicators, 2) absence of indication of source materials/origins of HSs

An optimized TOPS+ comparison method for enhanced TOPS models

This article has been made available through the Brunel Open Access Publishing Fund.Background Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+. Results We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method. Conclusions Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy. Software Availability: The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/.This article is available through the Brunel Open Access Publishing Fun

Analytic Markovian Rates for Generalized Protein Structure Evolution

A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not appreciably reduce the fitness of the organism. Such constraints can have multiple origins, in this work we present a model for constrained evolutionary trajectories represented by a Markovian process throughout a set of protein-like structures artificially constructed to be topological intermediates between the structure of two natural occurring proteins. The number and type of intermediate steps defines how constrained the total evolutionary process is. By using a coarse-grained representation for the protein structures, we derive an analytic formulation of the transition rates between each of the intermediate structures. The results indicate that compact structures with a high number of hydrogen bonds are more probable and have a higher likelihood to arise during evolution. Knowledge of the transition rates allows for the study of complex evolutionary pathways represented by trajectories through a set of intermediate structures

TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model

<p>Abstract</p> <p>Background</p> <p>Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have managed to capture the intuitive understanding of protein structures developed in structural biology, especially in the context of rapid database searches. Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses.</p> <p>Results</p> <p>We developed a TOPS++FATCAT algorithm that uses an intuitive description of the proteins' structures as captured in the popular TOPS diagrams to limit the search space of the aligned fragment pairs (AFPs) in the flexible alignment of protein structures performed by the FATCAT algorithm. The TOPS++FATCAT algorithm is faster than FATCAT by more than an order of magnitude with a minimal cost in classification and alignment accuracy. For beta-rich proteins its accuracy is better than FATCAT, because the TOPS+ strings models contains important information of the parallel and anti-parallel hydrogen-bond patterns between the beta-strand SSEs (Secondary Structural Elements). We show that the TOPS++FATCAT errors, rare as they are, can be clearly linked to oversimplifications of the TOPS diagrams and can be corrected by the development of more precise secondary structure element definitions.</p> <p>Software Availability</p> <p>The benchmark analysis results and the compressed archive of the TOPS++FATCAT program for Linux platform can be downloaded from the following web site: <url>http://fatcat.burnham.org/TOPS/</url></p> <p>Conclusion</p> <p>TOPS++FATCAT provides FATCAT accuracy and insights into protein structural changes at a speed comparable to sequence alignments, opening up a possibility of interactive protein structure similarity searches.</p

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications. As a domain set, we have selected a consensus set of 2,890 domains decomposed very similarly in SCOP and CATH. As an alignment algorithm, we used a global version of MAMMOTH developed in our group, which is both rapid and accurate. As a similarity measure, we used the size-normalized contact overlap, and as a clustering algorithm, we used average linkage. The resulting automatic classification at the cross-over point was more consistent than expert ones with respect to the structure similarity measure, with 86% of the clusters corresponding to subsets of either SCOP or CATH superfamilies and fewer than 5% containing domains in distinct folds according to both SCOP and CATH. Almost 15% of SCOP superfamilies and 10% of CATH superfamilies were split, consistent with the notion of fold change in protein evolution. These results were qualitatively robust for all choices that we tested, although we did not try to use alignment algorithms developed by other groups. Folds defined in SCOP and CATH would be completely joined in the regime of large transitivity violations where clustering is more arbitrary. Consistently, the agreement between SCOP and CATH at fold level was lower than their agreement with the automatic classification obtained using as a clustering algorithm, respectively, average linkage (for SCOP) or single linkage (for CATH). The networks representing significant evolutionary and structural relationships between clusters beyond the cross-over point may allow us to perform evolutionary, structural, or functional analyses beyond the limits of classification schemes. These networks and the underlying clusters are available at http://ub.cbm.uam.es/research/ProtNet.ph

A Genome-Wide Metabolic QTL Analysis in Europeans Implicates Two Loci Shaped by Recent Positive Selection

We have performed a metabolite quantitative trait locus (mQTL) study of the 1H nuclear magnetic resonance spectroscopy (1H NMR) metabolome in humans, building on recent targeted knowledge of genetic drivers of metabolic regulation. Urine and plasma samples were collected from two cohorts of individuals of European descent, with one cohort comprised of female twins donating samples longitudinally. Sample metabolite concentrations were quantified by 1H NMR and tested for association with genome-wide single-nucleotide polymorphisms (SNPs). Four metabolites' concentrations exhibited significant, replicable association with SNP variation (8.6×10−11<p<2.8×10−23). Three of these—trimethylamine, 3-amino-isobutyrate, and an N-acetylated compound—were measured in urine. The other—dimethylamine—was measured in plasma. Trimethylamine and dimethylamine mapped to a single genetic region (hence we report a total of three implicated genomic regions). Two of the three hit regions lie within haplotype blocks (at 2p13.1 and 10q24.2) that carry the genetic signature of strong, recent, positive selection in European populations. Genes NAT8 and PYROXD2, both with relatively uncharacterized functional roles, are good candidates for mediating the corresponding mQTL associations. The study's longitudinal twin design allowed detailed variance-components analysis of the sources of population variation in metabolite levels. The mQTLs explained 40%–64% of biological population variation in the corresponding metabolites' concentrations. These effect sizes are stronger than those reported in a recent, targeted mQTL study of metabolites in serum using the targeted-metabolomics Biocrates platform. By re-analysing our plasma samples using the Biocrates platform, we replicated the mQTL findings of the previous study and discovered a previously uncharacterized yet substantial familial component of variation in metabolite levels in addition to the heritability contribution from the corresponding mQTL effects