Comparative modelling of protein structure and its impact on microbial cell factories

Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems on protein production. For this reason, an introduction to comparative modeling is presented, with special emphasis on the basic concepts, opportunities and challenges of protein structure prediction. This review is intended to serve as a guide for the biologist who has no special expertise and who is not involved in the determination of protein structure. Selected applications of comparative modeling in microbial cell factories are outlined, and the role of microbial cell factories in the structural genomics initiative is discussed

Synthèse des impacts écologiques des feux et des coupes forestières sur les lacs de l'écozone boréale au Québec

Cet article présente une première synthèse comparative des impacts des feux et des coupes forestières sur la qualité des eaux et les communautés aquatiques des lacs de l'écozone boréale de l'est du Canada. La recherche a été réalisée de 1996 à 1998 dans le cadre d'un projet du Réseau de centre d'excellence sur la gestion durable des forêts (RCE-GDF) et porte sur 38 lacs du Bouclier Canadien du Québec. Les changements dans la qualité de l'eau ainsi que dans la diversité, la biomasse et la structure des communautés de plancton et de poissons ont été suivis pendant trois ans dans 20 lacs dont les bassins versants étaient non perturbés, dans 9 lacs qui avaient subit des coupes forestières et dans 9 lacs qui avaient subit des feux de forêt.Notre étude montre que les feux et les coupes ont des impacts significatifs qui diffèrent selon le type de perturbation. En général, les lacs affectés par les coupes et les feux ont des concentrations de phosphore 2 à 3 fois plus élevées que les lacs de référence. Toutefois, les lacs affectés par les feux montrent des concentrations en nitrates beaucoup plus élevées tandis que les lacs affectés par les coupes sont moins transparents et ont des eaux plus colorées, très riches en carbone organique dissous. Les feux et les coupes affectent aussi de façon différente la minéralisation des eaux et les concentrations des ions majeurs. Les feux et les coupes n'ont pas d'effet sur la biodiversité des communautés planctoniques, sauf dans les lacs ayant un grand bassin versant et plus de 40 % de perturbation. Aucune différence n'a été observée entre les lacs de référence et les lacs perturbés au niveau de l'occurrence, l'abondance et la croissance des espèces de poissons. En revanche, les feux et les coupes affectent la production et la structure des communautés aquatiques. Dans les lacs affectés par les feux, l'enrichissement en azote et phosphore provoque une hausse de la concentration en chlorophylle a, et de la biomasse du phytoplancton et du limnoplancton (seston > 53 µm), en particulier des diatomées, des rotifères et des gros crustacés, pendant deux à trois années après les feux. En revanche, dans les lacs affectés par les coupes, l'enrichissement en phosphore n'entraîne qu'une augmentation très faible et limitée à un an de la biomasse des algues et pas de changement dans les biomasses du limnoplancton, en raison de la forte couleur et de la transparence réduite des eaux, qui limite la production biologique. Les coupes ont un impact négatif sur les copépodes calanoïdes, un groupe de zooplancton caractéristique des lacs oligotrophes et transparents. Une diminution significative de la proportion des individus de petite taille a été observée chez les populations de perchaude et de meunier noir des lacs perturbés (lacs de coupe et de feux formant un seul groupe). Les impacts observés dans la qualité des eaux et la production du plancton augmentent avec l'importance relative des perturbations au niveau du bassin versant. Cependant, la variabilité dans les caractéristiques des bassins versants et des lacs, en particulier le rapport de drainage et le temps de résidence des eaux, a des effets confondants sur les réponses des écosystèmes lacustres aux perturbations par les feux et les coupes.This paper presents a comparative review on ecological impacts of wildfires and harvesting on water quality and aquatic community attributes of boreal lakes in eastern Canada. This project was carried out from 1996 to 1998, as part of the research program of the Sustainable Forest Management Network Centre of Excellence (NCE-SFM), on 38 lakes of the Boreal Canadian Shield (Québec, Canada). Changes in water quality, and in diversity, biomass and community structure of pelagic plankton and fish populations were monitored for 3 years in 20 reference lakes, 9 cut lakes and 9 burnt lakes.Our study shows that wildfires and logging have significant impacts on water quality as well as primary and secondary producers in boreal lakes. However, fire and logging does not have similar impacts. In general, cut and burnt lakes showed higher concentrations of total phosphorus (TP: 2-3 folds) than reference lakes. However nitrates concentrations (NO3-) were higher in burnt lakes than in reference and cut lakes, whereas dissolved organic carbon (DOC), light extinction coefficient (e PAR) and water colour were higher in cut lakes than in reference lakes, burnt lakes showing intermediate values. Wildfire and logging also affect ionic composition of lake water. Both burnt and cut lakes had higher concentrations of potassium (K+), chloride (Cl-) and calcium (Ca2+) than reference lakes, while sulphates (SO42-) and magnesium (Mg2+) increased only in burnt lakes. The observed increases in organic and mineral elements reflect their export from the watershed and were related to the drainage ratio. As mobile ions are rapidly flushed from the perturbed watersheds, ionic water composition returned to normal levels within three years after the perturbation. In contrast, some changes in water quality (P and N enrichment in perturbed lakes; DOC increase in cut lakes) seems to be on longer term and might have a more important effect on limnological features of lakes such as thermal stratification, mixed and euphotic depth, plankton biomass and bioaccumulation of mercury in zooplankton and fish.Wildfires and logging do not have significant impacts on species richness of planktonic communities, except for lakes with large drainage basins and those where the perturbation was higher than 40% of the watershed area. However, wildfires and logging affect biomass of plankton communities. In burnt lakes, the nutrient enrichment induced important increases in Chl. a concentration and phytoplankton biomass, and a small increase in limnoplankton biomass (seston > 53 µm). Diatoms, rotifers and large crustaceans showed significant increases. In burnt lakes, increases in phytoplankton were observed during the three years of the survey and were highest in the first 2 years after fires. Limnoplankton increases lasted only 2 years and were highest the second year after fires. In cut lakes, nutrient enrichment was not reflected in a proportional increase in plankton production due to increase in DOC concentrations and lake water colour that reduced water transparency. Phytoplankton slightly increased only the first year after logging and no increase was observed for limnoplankton and zooplankton. Logging negatively affect calanoids, a zooplankton group characteristic of clear and oligotrophic lakes. No significant differences were observed in the occurrence, abundance and growth of fish populations among reference and perturbed lakes. However, the proportion of small yellow perch and white sucker were significantly lower in populations of impacted lakes (burned and logged lakes pooled). In most cases, impacts on water quality and plankton communities were related to the intensity of fire or logging, when expressed as the percent area of watershed harvested or burnt divided by the lake surface or volume. Simple models may then be developed and help to predict the effect of harvesting practices on lake ecosystems. However, environmental variation in watershed and lakes characteristics, especially drainage ratio and lake water residence time, are important confounding factors in the responses of lakes to watershed perturbations by fire or logging. Lakes with drainage ratio > 4 and with more of 30% of their watershed perturbed are the most sensitive to fire and logging. These factors should be considered when developing lake management models in the boreal forest impacted by fire and logging

Correction: CO2 induced phase transitions in diamine-appended metal-organic frameworks.

[This corrects the article DOI: 10.1039/C5SC01828E.]

Peripheral venous blood gases and pulse-oximetry in acute cardiogenic pulmonary oedema

Background: The role of venous blood gases as an alternative to arterial blood gases in patients with severe acute heart failure has not been established. Objective: To assess the correlation between arterial and peripheral venous blood gases together with pulse-oximetry (SpO2), as well as to estimate arterial values from venous samples in the first hours upon admission of patients with acute cardiogenic pulmonary oedema. Methods: Simultaneous venous and arterial blood samples were extracted on admission and over the next 1, 2, 3, 4, and 10 hours. SpO2 was also registered at the same intervals. Results: A total of 178 pairs of samples were obtained from 34 consecutive patients with acute cardiogenic pulmonary oedema. Arterial and venous blood gases followed a parallel course in the first hours, showing high correlation rates at all time intervals. Venous samples underestimated pH (mean difference −0.028) and overestimated CO2 (+5.1 mmHg) and bicarbonate (+1 mEq/l). Conversely, SpO2 tended to underestimate SaO2 (mean±SD: 93.1±9.1 vs. 94.2±8.4). Applying simple mathematical formulae based on these differences, arterial values were empirically calculated from venous samples, showing acceptable agreement in the Bland−Altman test. Likewise, a venous pH 51.3 mmHg, and bicarbonate <22.8 mEq/l could fairly identify arterial acidosis, either respiratory or metabolic, with a test accuracy of 92, 68, and 91%, respectively. Conclusions: In patients with cardiogenic pulmonary oedema, arterial blood gas disturbances may be estimated from peripheral venous samples. By monitoring SpO2 simultaneously, arterial punctures could often be avoide

Transcriptomic characterization of the larval stage in gilthead seabream (Sparus aurata) by 454 pyrosequencing

Gilthead seabream (Sparus aurata) is a teleost belonging to the family Sparidae with a high economical relevance in the Mediterranean countries. Although genomic tools have been developed in this species in order to investigate its physiology at the molecular level and consequently its culture, genomic information on post-embryonic development is still scarce. In this study, we have investigated the transcriptome of a marine teleost during the larval stage (from hatching to 60 days after hatching) by the use of 454 pyrosequencing technology. We obtained a total of 68,289 assembled contigs, representing putative transcripts, belonging to 54,606 different clusters. Comparison against all S. aurata expressed sequenced tags (ESTs) from the NCBI database revealed that up to 34,722 contigs, belonging to about 61% of gene clusters, are sequences previously not described. Contigs were annotated through an iterative Blast pipeline by comparison against databases such as NCBI RefSeq from Danio rerio, SwissProt or NCBI teleost ESTs. Our results indicate that we have enriched the number of annotated sequences for this species by more than 50% compared with previously existing databases for the gilthead seabream. Gene Ontology analysis of these novel sequences revealed that there is a statistically significant number of transcripts with key roles in larval development, differentiation, morphology, and growth. Finally, all information has been made available online through user-friendly interfaces such as GBrowse and a Blast server with a graphical frontend

Correction: CO2 induced phase transitions in diamine-appended metal-organic frameworks (Chemical Science (2015) 6 (5177-5185) DOI: 10.1039/c5sc01828e)

The authors regret that there are some discrepancies reproducing the data in the original article due to the determined coordinates not being the fully optimised geometries. The authors have provided more information as follows. In the manuscript entitled \u27CO2 induced phase transitions in diamine-appended metal-organic frameworks\u27, minor errors with the attached coordinates and energies reported in the paper have recently been identified. In this communication, we correct these errors. Here, we present updated optimized geometries and binding energies. We also take this opportunity to include an extended computational details section to ensure reproducibility. In addition, we show that the overall conclusions of the paper are not affected by these changes. A detailed comparison with the results reported by Lee et al.1 revealed that the DFT optimization of the coordinates provided with the manuscript do not lead to the values reported in the manuscript, and they warrant correction. Corrected coordinates and updated tables (Tables 1-7) and figures (Fig. 1, 2, 4 and 5) are included here for calculations using the PBE functional. These structures have been repeated using a slightly tighter force threshold than in the original manuscript (details below). The M06-L calculations reported in the original manuscript are not revisited since they were performed to assess the role of dispersion. Since the publication of our work in 2015, a far more detailed study of this effect has been published by one of the authors rendering these M06-L calculations unnecessary and we refer readers interested in the role of dispersion on the carbamate formation to this more recent study by Lee et al.1 In addition to correcting our DFT calculations, we examine the effects of the revised DFT values on the lattice model in this work.We recompute the lattice model with the M06-L and PBE values fromthe original manuscript as well as the corrected PBE values reported below (Fig. 6-8 and Tables 8-10). In all three sets of isotherm plots the ordering is preserved but the inflection points are spaced differently with the new PBE numbers, leading to quantitative differences that are nonetheless qualitatively similar to previous work. Finally, we discuss different ways that CO2 can coordinate to the metal binding site, as shown in Fig. 3. We should have notedmore clearly in ourmanuscript that these were starting configurations and not necessarily the final converged structures since our goal was to try several starting geometries to determine which coordination environment around the metal site was lowest in energy. Take for example bidentate insertion. Chemical intuition suggests that this structure could rotate to one that has only one CO2 oxygen center closer to the metal than the other and we observe this in our optimized structure. The resulting geometries we obtained for the starting arrangements noted in the figure are higher in energy than the chain model as reported in our original paper.We wish to emphasize that at the time of our 2015 study, our objective was to understand whether or not CO2 was bound to the metal and if one-dimensional chain formation could lead to a step in the adsorption isotherm. It has since become clear that a far more thorough study of the arrangements of the amines is required to truly understand competing amine arrangements preset in experiment. This was outside the scope of our work. Once more, these calculations are perhaps now outdated given work in the field in recent years. We again refer interested readers to a more recent study by Lee et al.1 1. Extended computational details to ensure reproducibility In the course of rectifying the error in our calculations, we wanted to ensure that all revised calculations were converged using the exact same protocol; therefore, we repeated the PBE calculations for the pair and chain models using updated computational details given here to ensure reproducibility. The M2(dobpdc) MOF contains six unsaturated metal sites per unit cell. To calculate the binding energies of CO2 in its amine appended analogue mmen-M2(dobpdc), one mmen ligand per CO2 was added per unit cell. The smaller sized ethylenediamine (en) was used to saturate the remaining amines not involved in CO2 binding. In the case of the pair mode, two mmen-amines are included per unit cell only. All DFT calculations were performed with periodic boundary conditions carried out using the VASP 5.4.4 package (original calculations were performed with VASP 5.3.3). The PBE functional was employed to examine the energetics of CO2 adsorption.3 On-site Hubbard U corrections were employed for metal d electrons.4 The U values are determined to reproduce oxidation energies in the respective metal oxides and are given in the tables below. The electron-ion interactions in these calculations were described with the projector augmented wave (PAW) method developed by Blöchl with an energy cutoff of 550 eV.5 This combination of the PBE functional, PAW scheme, and energy cutoff was used for full geometry optimization of the various species investigated until the forces on all atoms were smaller than 0.02 eV Å-1 and the SCF convergence was set to 1 × 10-7 eV. Given the large size of the unit cell and the tests with other numbers of K-points from the original study, only results obtained from G-point calculations are reported here. Finally, heats of adsorption are now reported below along with E + ZPE values, while in the original manuscript only E + ZPE were reported. No changes were made to how the vibrational corrections were computed; however, we have included some additional details to ensure reproducibility.6 Harmonic vibrational modes (ωi) were computed for CO2 in the gas phase and its bound product state (amine-CO2-MOF complex). The framework itself was taken to be rigid and only the vibrational modes associated with the motion of the amine, the metal center, first coordination sphere (oxygen atoms bound to the metal in the MOF backbone), and (if present) the bound CO2 were computed. Since the harmonic approximation breaks down for low frequency modes, we replaced all modes less than 50 cm-1 with 50 cm-1 when computing the zero-point and thermal energies. The following standard harmonic expressions were used to compute the vibrational corrections: Zero-point vibrational energy (ZPE) is: [Equation presented here] While for the bound product, the rotational and translational degrees of freedom of CO2 have been converted to additional vibrational modes allowing one to compute the thermal correction simply as: [Equation presented here] 2. Values for the chain model The chain model used in our original study included 1 mmen- and 5 en-amines. The values from the original paper are reported in Table 1. When we repeat these calculations using the procedure described in Section 1, we obtain the values in Table 2. In addition to the chain model described above (1 mmen- and 5 en-amines per unit cell), during our original study we performed calculations with another model that was not included in the manuscript since its values yielded results further from experiment. This model includes only 1 mmen-amine per unit cell (no other amines) and was used to test the assumption that the five enamines are indeed spectators with respect to the metal dependence of the binding energy. We present the results from this model in Table 3. In the original paper we noted that the energy and bond length trends are correlated and are consistent with the Irving-Williams series. This is no longer true for all metals under investigation, with Zn being an outlier. The results for Zn can be explained by more recent work.1 3. Values for the pair model The model used to compute the pair adsorption mechanisms included 2 mmen-amines and 0 en-amines. The values in the original paper are presented in Table 5. 4. Lattice model plots The lattice models to generate adsorption isotherms for these systems were run at one temperature (∼25 °C) using four different input parameters. First the M06-L and PBE values from the original paper were used once more as it has been some time since we have run the lattice model. Then the model is repeated with the new set of values from PBE. If we compare Fig. 7 and 8, the order is preserved, but the infliction points are spaced a bit differently. This is due to the scaling factor being constant and is something we scaled for each of the different systems as well. The slope is also a bit different, but not more then we should expect for this simple lattice model. Furthermore, we only ever aimed to reproduce the step and the order of the metals. Any finer details cannot be expected to be obtained from this model. The exact values used to compute the isotherms are given in the tables below. The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers

Enzymatic production of defined chitosan oligomers with a specific pattern of acetylation using a combination of chitin oligosaccharide deacetylases

Chitin and chitosan oligomers have diverse biological activities with potentially valuable applications in fields like medicine, cosmetics, or agriculture. These properties may depend not only on the degrees of polymerization and acetylation, but also on a specific pattern of acetylation (PA) that cannot be controlled when the oligomers are produced by chemical hydrolysis. To determine the influence of the PA on the biological activities, defined chitosan oligomers in sufficient amounts are needed. Chitosan oligomers with specific PA can be produced by enzymatic deacetylation of chitin oligomers, but the diversity is limited by the low number of chitin deacetylases available. We have produced specific chitosan oligomers which are deacetylated at the first two units starting from the non-reducing end by the combined use of two different chitin deacetylases, namely NodB from Rhizobium sp. GRH2 that deacetylates the first unit and COD from Vibrio cholerae that deacetylates the second unit starting from the non-reducing end. Both chitin deacetylases accept the product of each other resulting in production of chitosan oligomers with a novel and defined PA. When extended to further chitin deacetylases, this approach has the potential to yield a large range of novel chitosan oligomers with a fully defined architecture

Prevalence and costs of multinutrution in hospitalized patients; the PREDyCES study

Justificación y objetivos: El estudio PREDyCES® tuvo dos objetivos principales. Primero, analizar la prevalencia de desnutrición hospitalaria (DH) en España tanto al ingreso como al alta, y segundo, estimar sus costes asociados. Métodos: Estudio nacional, transversal, observacional, multicéntrico, en condiciones de práctica clínica habitual que evaluó la presencia de desnutrición hospitalaria al ingreso y al alta mediante el NRS-2002®. Una extensión del estudio analizó la incidencia de complicaciones asociadas a la desnutrición, el exceso de estancia hospitalaria y los costes sanitarios asociados a la DH. Resultados: La prevalencia de desnutrición observada según el NRS-2002® fue del 23.7%. El análisis multivariante mostró que la edad, el género, la presencia de enfermedad oncológica, diabetes mellitus, disfagia y la polimedicación fueron los factores principales que se asociaron a la presencia de desnutrición. La DH se asoció a un incremento de la estancia hospitalaria, especialmente en aquellos pacientes que ingresaron sin desnutrición y que presentaron desnutrición al alta (15.2 vs 8.0 días; p < 0.001), con un coste adicional asociado de 5.829€ por paciente. Conclusiones: Uno de cada cuatro pacientes en los hospitales españoles se encuentra desnutrido. Esta condición se asocia a un exceso de estancia hospitalaria y costes asociados, especialmente en pacientes que se desnutren durante su hospitalización. Se debería generalizar el cribado nutricional sistemático con el objetivo de implementar intervenciones nutricionales de conocida eficacia.Background and aims: The main objective of the PREDyCES® study was twofold. First, to analyse the prevalence of hospital malnutrition in Spain, both at admission and at discharge, and second, to estimate the hospital costs associated with disease-related malnutrition. Methods: The study was a nationwide, cross-sectional, observational, multicentre study in routine clinical practice, which assessed the prevalence of hospital malnutrition both at patient admission and discharge using NRS- 2002®. A study extension analysed the incidence of complications associated with malnutrition, excess hospital stay and healthcare costs associated with hospital malnutrition. Results: Malnutrition was observed in 23.7% of patients according to NRS-2002®. Multivariate analysis revealed that age, gender, presence of malignant disease, diabetes mellitus, dysphagia and polymedication were the main factors associated with the presence of malnutrition. Malnutrition was associated with an increase in length of hospital stay, especially in patients admitted without malnutrition but who presented malnutrition at discharge (15.2 vs. 8.0 days, p < 0.001), with an associated additional cost of €5,829 per patient. Conclusion: In Spanish hospitals, almost one in four patients is malnourished. This condition is associated with increased length of hospital stay and associated costs, especially in patients developing malnutrition during hospitalization. Systematic screening for malnutrition should be generalised in order to implement nutritional interventions with well-known effectiveness

Lipidomics Reveals Reduced Inflammatory Lipid Species and Storage Lipids after Switching from EFV/FTC/TDF to RPV/FTC/TDF: A Randomized Open-Label Trial

HIV and antiretroviral therapy affect lipid metabolism. Lipidomics quantifies several individual species that are overlooked using conventional biochemical analyses, outperforming traditional risk equations. We aimed to compare the plasma lipidomic profile of HIV patients taking efavirenz (EFV) or rilpivirine (RPV). Patients >/= 18 years old on EFV co-formulated with emtricitabine and tenofovir disoproxil fumarate (FTC/TDF) with HIV-RNA /=6 months were randomized to continue EFV/FTC/TDF (n = 14) or switch to RPV/FTC/TDF (n =15). Lipidomic analyses conducted by mass spectrometry (MS) were performed at baseline and after 12 and 24 weeks. OWLiver((R)) Care and OWLiver((R)) tests were performed to estimate the presence of fatty liver disease (NAFLD). No significant differences (83% male, median age 44 years, 6 years receiving EFV/FTC/TDF, CD4(+) count 740 cells/mm(3), TC 207 [57 HDL-C/133 LDL-C] mg/dL, TG 117 mg/dL) were observed between the groups at baseline. Significant reductions in plasma lipids and lipoproteins but increased circulating bilirubin concentrations were observed in patients who switched to RPV/FTC/TDF. Patients on RPV/FTC/TDF showed a decrease in the global amount of storage lipids (-0.137 log2 [fold-change] EFV vs. 0.059 log2 [fold-change] RPV) but an increase in lysophosphatidylcholines (LPCs) and total steroids. Compared with EFV, RPV increased metabolites with anti-inflammatory properties and reduced the repository of specific lipotoxic lipids