Yes, one can obtain better quality structures from routine X-ray data collection

Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ < 0.75 Å−1). The TAAM approach is a very good option to obtain more adequate results even using data collected to the lower 2θmax angles. Also the results of translation–libration–screw (TLS) analysis and vibrational entropy values are more reliable for 2θmax > 65°

Improved culture enrichment broth for isolation of Arcobacter-like species from the marine environment

Arcobacter-like species are found associated with many matrices, including shellfish in marine environments. The culture media and conditions play a major role in the recovery of new Arcobacter-like species. This study was aimed to develop a culture media for isolation and enhanced growth of Arcobacter-like spp. from marine and shellfish matrices. For this purpose, 14 different Arcobacter-like spp. mostly isolated from shellfish, were grown in 24 different formulations of enrichment broths. The enrichment broths consisted of five main groups based on the organic contents (fresh oyster homogenate, lyophilized oyster either alone or in combination with other standard media), combined with artificial seawater (ASW) or 2.5% NaCl. Optical density (OD420nm) measurements after every 24 h were compared with the growth in control media (Arcobacter broth) in parallel. The mean and standard deviation were calculated for each species in each broth and statistical differences (p < 0.05) among broths were calculated by ANOVA. The results indicated that shellfish-associated Arcobacter-like species growth was significantly higher in Arcobacter broth + 50% ASW and the same media supplemented with lyophilized oysters. This is the first study to have used fresh or lyophilized oyster flesh in the enrichment broth for isolation of shellfish-associated Arcobacter-like spp.info:eu-repo/semantics/publishedVersio

Environmental metabolism of educational services : case study of nursery schools in the city of Barcelona

The environmental analysis of public nursery schools is of great interest since they are crucial in the early education of children and are expected to show high environmental standards. This paper aims to analyse the environmental profile (energy, water and transport flows) of this sector. A sample of 12 public nursery schools belonging to the Scholar Agenda 21 (SA21) of the city of Barcelona were selected given their data quality (eight centres applied to all analysis) to determine their energy and water consumption, as well as the greenhouse gas emissions resulting from energy consumption and transport use. For each centre, energy and water consumption were obtained from bills and surveys were conducted to get data regarding the transport associated with the centre. Results show that, on average, a child consumes 966 kWh of energy (electricity and gas) and 12.9 m3 of potable water every year. Nursery schools with more energy-efficient devices hold lower energy consumption, a trend which could not be found in the case of water and water-efficient devices. Regarding transport, car usage was the flow with highest impact, since it accounts for 69 % of CO2eq emissions, although only 19 % of the children commute by car

Mapping the knowledge of the main diseases affecting sea bass and sea bream in Mediterranean

Good knowledge on the disease situation and its impact on production is a base mechanism for designing health surveillance, risk analysis and biosecurity systems. Mediterranean marine fish farming, as any aquaculture production, is affected by various infectious diseases. However, seabass and seabream, the main produced species, are not listed as susceptible host species for the notifiable pathogens listed in the current EU legislation, which generates a lack of systematic reporting. The results presented in this study come from a survey directly to fish farms (50 hatchery and ongrowing units from 10 Mediterranean countries), with data from 2015‐2017, conducted by the H2020 project MedAID. Seabass showed a higher survival rate (85%) through a production cycle than seabream (80%) in spite of equal mortality due to pathogen infections (10%). The differences in survival may be explained by mortality “of other causes”. Seabream and seabass have different disease profiles, and the profile is slightly different between geographical regions. Among the most important diseases, tenacibaculosis and vibriosis were identified in seabass and Sparicotyle chrysophrii (a gill fluke) and nodavirus in seabream. Correlating mortality data to management variables showed that increasing density, buying fingerlings from external sources, and treatments due to disease are factors that negatively influence mortality rate. Most of the surveyed farms did not keep sufficient quality data to implement good health status reports and perform detailed impact studies, which shows the necessity of updating the current legislative framework to provide the basis for better reporting of relevant pathogens in the Mediterranean basin.info:eu-repo/semantics/publishedVersio

Environmental effects of using different construction codes applied to reinforced concrete beam designs based on Model Code 2010 and Spanish Standard EHE-08

Assuming specific behavior models, the variety of design codes currently used for the design of concrete beams inevitably results in different solutions, ensuring service during the expected lifetime with a maximum functional quality and safety. However, from a sustainable design perspective, such differences may have remarkable environmental impacts. This paper analyses if the approach of the newest design code, i.e., the Model Code, leads to a reduction in resource consumption and greenhouse gas emissions (GHG) over the life cycle of concrete beams. To do so, a comparative analysis of the environmental impact of concrete beams was carried out depending on the reference code used for their design (i.e., EHE-08 or Model Code). The results show that reducing the amount of reinforcing steel is essential to minimize the life cycle environmental impacts of concrete beams. Every country may have its own design codes and, thus, the reinforcing steel use can vary for structures subjected to the same loads and with equivalent structural reliability. Hence, regulations play a key role in the sustainability of construction assets. Conclusions depend on the beam’s length (L), height (h) and characteristic compressive strength (fck). For short beams (4 m), the greater the h, the greater the reinforcement difference between the two codes. With regard to beams with L = 8 m, these differences can lead to varying steel and GHG savings, e.g., up to 5.0 % with MC-2010 (h = 0.6 m and fck = 35 MPa), almost 40 % with EHE – 08 (h = 0.6 m and 35 MPa < fck = 50 MPa) and more than 30 % with MC-2010 (h = 1.0 m).. For long beams (L = 12.0 m), steel consumption is 0.3 % to 19 % lower when the beam is designed with EHE-08, and this difference decreases as fck increases.Peer ReviewedPostprint (author's final draft

Identifying eco-efficient year-round crop combinations for rooftop greenhouse agriculture

Unidad de excelencia María de Maeztu CEX2019-000940-MPurpose: Rooftop greenhouses (RTGs) are agricultural systems that can improve the food supply chain by producing vegetables in unused urban spaces. However, to date, environmental assessments of RTGs have only focused on specific crops, without considering the impacts resulting from seasonality, combinations of crops and nonoperational time. We analyze vegetable production in an RTG over 4 years to determine the crop combinations that minimize yearly environmental impacts while diversifying food supply. Methods: The system under study consists of an integrated RTG (i-RTG) with a hydroponic system in Barcelona, in the Mediterranean region. By using life cycle assessment (LCA), we evaluate the environmental performance of 25 different crop cycles and 7 species cultivated during the period 2015-2018. Three functional units are used: 1 kg of edible fresh production, 1 unit of economic value (€) in the wholesale market and 1 kcal of nutritional value. The system boundaries consider two subsystems: infrastructure (greenhouse structure, rainwater harvesting system and auxiliary equipment) and operation (fertilizers and their emissions into water and substrate). In addition, we perform an eco-efficiency analysis, considering the carbon footprint of the crop cycles and their value at the wholesale market during their harvesting periods. Results and discussion: Spring tomato cycles exert the lowest impacts in all categories, considering all three functional units, due to the high yields obtained. In contrast, spinach and arugula have the highest impacts. Regarding relative impact, the greenhouse structure presented a large impact, while fertilizer production had notable relative contributions in tomato cycles. Moreover, nitrogen and phosphorus emissions from fertigation are the main causes of freshwater and marine eutrophication. By combining the most eco-efficient cycles, we can see that growing two consecutive tomato cycles is the best alternative with the functional unit of yield (0.49 kg CO2 eq./kg), whereas a long spring tomato cycle combined with bean and lettuce cycles in the autumn/winter is the best scenario when using market (0.70 kg CO2 eq./€) and nutritional value (3.18·10−3 kg CO2/ kcal). Conclusions: This study shows that increasing the diversity of the system leads to better environmental performance of greenhouse urban agriculture if suitable crops are selected for the autumn/winter season. The functional unit involving the economic value and the eco-efficiency analysis are useful to demonstrate the capability of the growing system to produce added-value vegetables under harsher conditions while categorizing and classifying the crops to select the most suitable combinations based on economic and environmental parameters

Comparing Targeted vs. Untargeted MS2 Data-Dependent Acquisition for Peak Annotation in LC-MS Metabolomics

One of the most widely used strategies for metabolite annotation in untargeted LCMS is based on the analysis of MSn spectra acquired using data-dependent acquisition (DDA), where precursor ions are sequentially selected from MS scans based on user-selected criteria. However, the number of MSn spectra that can be acquired during a chromatogram is limited and a trade-off between analytical speed, sensitivity and coverage must be ensured. In this research, we compare four different strategies for automated MS2 DDA, which can be easily implemented in the frame of standard QA/QC workflows for untargeted LC-MS. These strategies consist of (i) DDA in the MS working range; (ii) iterated DDA split into several m/z intervals; (iii) dynamic iterated DDA of (pre)selected potentially informative features; and (iv) dynamic iterated DDA of (pre)annotated metabolic features using a reference database. Their performance was assessed using the analysis of human milk samples as model example by comparing the percentage of LC-MS features selected as the precursor ion for MS2, the number, and class of annotated features, the speed and confidence of feature annotation, and the number of LC runs required

Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue

Background: DNA methylation is involved in the regulation of gene expression and phenotypic variation, but the inter-relationship between genetic variation, DNA methylation and gene expression remains poorly understood. Here we combine the analysis of genetic variants related to methylation markers (methylation quantitative trait loci: mQTLs) and gene expression (expression quantitative trait loci: eQTLs) with methylation markers related to gene expression (expression quantitative trait methylation: eQTMs), to provide novel insights into the genetic/epigenetic architecture of colocalizing molecular markers. Results: Normal mucosa from 100 patients with colon cancer and 50 healthy donors included in the Colonomics project have been analyzed. Linear models have been used to find mQTLs and eQTMs within 1 Mb of the target gene. From 32,446 eQTLs previously detected, we found a total of 6850 SNPs, 114 CpGs and 52 genes interrelated, generating 13,987 significant combinations of co-occurring associations (meQTLs) after Bonferromi correction. Non-redundant meQTLs were 54, enriched in genes involved in metabolism of glucose and xenobiotics and immune system. SNPs in meQTLs were enriched in regulatory elements (enhancers and promoters) compared to random SNPs within 1 Mb of genes. Three colorectal cancer GWAS SNPs were related to methylation changes, and four SNPs were related to chemerin levels. Bayesian networks have been used to identify putative causal relationships among associated SNPs, CpG and gene expression triads. We identified that most of these combinations showed the canonical pathway of methylation markers causes gene expression variation (60.1%) or non-causal relationship between methylation and gene expression (33.9%); however, in up to 6% of these combinations, gene expression was causing variation in methylation markers. Conclusions: In this study we provided a characterization of the regulation between genetic variants and inter-dependent methylation markers and gene expression in a set of 150 healthy colon tissue samples. This is an important finding for the understanding of molecular susceptibility on colon-related complex diseases

Identification of a Twelve-microRNA Signature with Prognostic Value in Stage II Microsatellite Stable Colon Cancer

Simple Summary Colorectal cancer (CRC) is one of the most prevalent cancers, and approximately a quarter of patients diagnosed at stage II exhibit a significant risk of recurrence. In this study, we successfully identified a microRNA (miRNA) signature allowing the recognition of patients at high recurrence risk. The validity of these findings has been confirmed through an entirely separate group of patients diagnosed with stage II microsatellite stability (MSS) colon adenocarcinoma (COAD). Most of the miRNAs present in the signature have demonstrated prognostic relevance in various other cancer types. Upon examining their gene targets, we discovered that some of these miRNAs are intricately involved in pivotal pathways of cancer progression. We aimed to identify and validate a set of miRNAs that could serve as a prognostic signature useful to determine the recurrence risk for patients with COAD. Small RNAs from tumors of 100 stage II, untreated, MSS colon cancer patients were sequenced for the discovery step. For this purpose, we built an miRNA score using an elastic net Cox regression model based on the disease-free survival status. Patients were grouped into high or low recurrence risk categories based on the median value of the score. We then validated these results in an independent sample of stage II microsatellite stable tumor tissues, with a hazard ratio of 3.24, (CI95% = 1.05-10.0) and a 10-year area under the receiver operating characteristic curve of 0.67. Functional analysis of the miRNAs present in the signature identified key pathways in cancer progression. In conclusion, the proposed signature of 12 miRNAs can contribute to improving the prediction of disease relapse in patients with stage II MSS colorectal cancer, and might be useful in deciding which patients may benefit from adjuvant chemotherapy

Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR

Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5 &amp; PRIME;-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors