High Species Richness and Extremely Low Abundance of Cumacean Communities Along the Shelf and Slope of the Gulf of Guinea (West Africa)

The Gulf of Guinea belongs to the most scarcely sampled marine basins in the oceans of the world. We have analyzed diversity and distribution patterns of cumacean communities on the shelf and slope, along the coast of Ghana. The material was collected in October and November of 2012 using a van Veen grab (0.1 m2) on nine transects. Six stations were located at each transect (25, 50, 100, 250, 500, and 1,000 m). Sixty-three species of Cumacea were recorded with Leucon and Eocuma as the most speciose genera, with 12 and eight species, respectively. Comparisons of species richness with literature data pointed that the Ghanaian coast hosts very diverse communities. About 95% of species were new to science, and the number of cumacean species known from the West Africa increased by over 100%. Nevertheless, most of the species had extremely low abundance, 13 singletons and 15 doubletons were found. Mean density of cumaceans was estimated at only 1.5 ind./0.1 m2. Species accumulation curve did not reach the asymptotic level, suggesting undersampling, despite the fact that sampling effort was high (250 samples). The highest species richness was recorded in the inner shelf (25–50 m) and on the slope (1,000 m). Cluster analysis separated shallow water communities from deeper regions on the shelf and upper slope. The most unique species composition was found at 1,000 m. Principal component analysis showed the importance of oxygen, sediments, and human-related disturbance for distribution of cumacean communities. In the shallows, oxygen content and presence of gravel were the most important factors structuring communities. In the deeper bottom areas (250–1,000 m), cumacean fauna was affected by local pollution, mainly by higher concentration of barium, other heavy metals, and THC.publishedVersio

Enhancing the Steroid Sulfatase Activity of the Arylsulfatase from Pseudomonas aeruginosa

Steroidal sulfate esters play a central role in many physiological processes. They serve as the reservoir for endogenous sex hormones and form a significant fraction of the steroid metabolite pool. The analysis of steroid sulfates is thus essential in fields such as medical science and sports drug testing. Although the direct detection of steroid sulfates can be readily achieved using liquid chromatography-mass spectrometry, many analytical approaches, including gas chromatography-mass spectrometry, are hampered due to the lack of suitable enzymatic or chemical methods for sulfate ester hydrolysis prior to analysis. Enhanced methods of steroid sulfate hydrolysis would expand analytical possibilities for the study of these widely occurring metabolites. The arylsulfatase from Pseudomonas aeruginosa (PaS) is a purified enzyme capable of hydrolysing steroid sulfates. However, this enzyme requires improvement to hydrolytic activity and substrate scope in order to be useful in analytical applications. These improvements were sought by applying semi-rational design to mutate amino acid residues neighbouring the enzyme active site. Mutagenesis was implemented on both single and multiple residue sites. Screening by UPLC-MS was performed to test the steroid sulfate hydrolysis activity of these mutant libraries against testosterone sulfate. This approach revealed the steroid sulfate binding pocket and resulted in three mutants that showed an improvement in catalytic efficiency (Vmax/KM) of more than 150 times that of wild-type PaS. The substrate scope of PaS was expanded and a modest increase in thermostability was observed. Finally, molecular dynamics simulations of enzyme-substrate complexes were used to provide qualitative insight into the structural origin of the observed effects.The authors thank the World Anti-Doping Agency’s Science Research Grants (13A13MM and 16A06MM), the Swedish Research Council (VR, Grant 2015-04928), as well as the Knut and Alice Wallenberg and Wenner-Gren foundations for financial support as well as fellowships to SCLK and AP respectively. All computational work in this paper was supported by computational resources provided by the Swedish National Infrastructure for Computing (SNIC, grants 2016-34-27 and 2017-12-11)

Amphipod family distributions around Iceland

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The significant impact of age on the clinical outcomes of laparoscopic appendectomy : results from the Polish Laparoscopic Appendectomy multicenter large cohort study

Acute appendicitis (AA) is the most common surgical emergency and can occur at any age. Nearly all of the studies comparing outcomes of appendectomy between younger and older patients set cut-off point at 65 years. In this multicenter observational study, we aimed to compare laparoscopic appendectomy for AA in various groups of patients with particular interest in the elderly and very elderly in comparison to younger adults. Our multicenter observational study of 18 surgical units assessed the outcomes of 4618 laparoscopic appendectomies for AA. Patients were divided in 4 groups according to their age: Group 1- 8 days. Logistic regression models comparing perioperative results of each of the 3 oldest groups compared with the youngest one showed significant differences in odds ratios of symptoms lasting >48hours, presence of complicated appendicitis, perioperative morbidity, conversion rate, prolonged LOS (>8 days). The findings of this study confirm that the outcomes of laparoscopic approach to AA in different age groups are not the same regarding outcomes and the clinical picture. Older patients are at high risk both in the preoperative, intraoperative, and postoperative period. The differences are visible already at the age of 40 years old. Since delayed diagnosis and postponed surgery result in the development of complicated appendicitis, more effort should be placed in improving treatment patterns for the elderly and their clinical outcome

Risk factors for serious morbidity, prolonged length of stay and hospital readmission after laparoscopic appendectomy : results from Pol-LA (Polish Laparoscopic Appendectomy) multicenter large cohort study

Laparoscopic appendectomy (LA) for treatment of acute appendicitis has gained acceptance with its considerable benefits over open appendectomy. LA, however, can involve some adverse outcomes: morbidity, prolonged length of hospital stay (LOS) and hospital readmission. Identification of predictive factors may help to identify and tailor treatment for patients with higher risk of these adverse events. Our aim was to identify risk factors for serious morbidity, prolonged LOS and hospital readmission after LA. A database compiled information of patients admitted for acute appendicitis from eighteen Polish and German surgical centers. It included factors related to the patient characteristics, peri- and postoperative period. Univariate and multivariate logistic regression models were used to identify risk factors for serious perioperative complications, prolonged LOS, and hospital readmissions in acute appendicitis cases. 4618 laparoscopic appendectomy patients were included. First, although several risk factors for serious perioperative complications (C-D III-V) were found in the univariate analysis, in the multivariate model only the presence of intraoperative adverse events (OR 4.09, 95% CI 1.32-12.65, p = 0.014) and complicated appendicitis (OR 3.63, 95% CI 1.74-7.61, p = 0.001) was statistically significant. Second, prolonged LOS was associated with the presence of complicated appendicitis (OR 2.8, 95%CI: 1.53-5.12, p = 0.001), postoperative morbidity (OR 5.01, 95% CI: 2.33-10.75, p < 0.001), conversions (OR 6.48, 95% CI: 3.48-12.08, p < 0.001) and reinterventions after primary procedure (OR 8.79, 95% CI: 3.2-24.14, p < 0.001) in the multivariate model. Third, although several risk factors for hospital readmissions were found in univariate analysis, in the multivariate model only the presence of postoperative complications (OR 10.33, 95% CI: 4.27-25.00), reintervention after primary procedure (OR 5.62, 95% CI: 2.17-14.54), and LA performed by resident (OR 1.96, 95%CI: 1.03-3.70) remained significant. Laparoscopic appendectomy is a safe procedure associated with low rates of complications, prolonged LOS, and readmissions. Risk factors for these adverse events include complicated appendicitis, postoperative morbidity, conversion, and re-intervention after the primary procedure. Any occurrence of these factors during treatment should alert the healthcare team to identify the patients that require more customized treatment to minimize the risk for adverse outcomes

Cooperativity and flexibility in enzyme evolution

Enzymes are flexible catalysts, and there has been substantial discussion about the extent to which this flexibility contributes to their catalytic efficiency. What has been significantly less discussed is the extent to which this flexibility contributes to their evolvability. Despite this, recent years have seen an increasing number of both experimental and computational studies that demonstrate that cooperativity and flexibility play significant roles in enzyme innovation. This review covers key developments in the field that emphasize the importance of enzyme dynamics not just to the evolution of new enzyme function(s), but also as a property that can be harnessed in the design of new artificial enzymes.The European Research Council has provided financial support under the European Community’s Seventh Framework Program (FP7/2007-2013)/ERC Grant Agreement No. 306474. This work was also funded by the Feder Funds, Grants from the Spanish Ministry of Economy and Competitiveness (BIO2015-66426-R and CSD2009-00088) and the Human Frontier Science Program (RGP0041/2017). A.P. is a Wenner-Gren Foundations Postdoctoral Fellow and S. C. L. K. is a Wallenberg Academy Fellow

Representative MD structures and setup files

The data package contains: 1. PDB files with representative structures of top clusters, with clustering performed using RMSD as a similarity measure between the structures in simulated trajectories. 2. Topologies, input structures and files containing additional parameters and settings used in the simulations for each simulated system. 3. Sample inputs for a single MD run. Detailed description of the contents of the data package can be found in the README file

A theoretical study of carbon–carbon bond formation by a Michael-type addition

A theoretical study of the Michael-type addition of 1,3-dicarbonyl compounds to α,β-unsaturated carbonyl compounds has been performed in the gas phase by means of the AM1 semiempirical method and by density functional theory (DFT) calculations within the B3LYP and M06-2X hybrid functionals. A molecular model has been selected to mimic the role of a base, which is traditionally used as a catalyst in Michael reactions, an acetate moiety to modulate its basicity, and point charges to imitate the stabilization of the negative charge developed in the substrate during the reaction when taking place in enzymatic environments. Results of the study of six different reactions obtained at the three different levels of calculations show that the reaction takes place in three steps: in the first step the α proton of the acetylacetone is abstracted by the base, then the nucleophilic attack on the β-carbon of the α,β-unsaturated carbonyl compound takes place generating the negatively charged enolate intermediate, and finally the product is formed through a proton transfer back from the protonated base. According to the energy profiles, the rate limiting step corresponds to the abstraction of the proton or the carbon-carbon bond formation step, depending on substituents of the substrates and method of calculation. The effect of the substituents on the acidity of the α proton of the acetylacetone and the steric hindrance can be analyzed by comparing these two separated steps. Moreover, the result of adding a positive charge close to the center that develops a negative charge during the reaction confirms the catalytic role of the oxyanion hole proposed in enzyme catalysed Michael-type additions. Stabilization of the intermediate implies, in agreement with the Hammond postulate, a reduction of the barrier of the carbon-carbon bond formation step. Our results can be used to predict the features that a new designed biocatalyst must present to efficiently accelerate this fundamental reaction in organic synthesis.We thank the Spanish Ministerio de Ciencia e Inovación for project CTQ2009-14541-C2, Universitat Jaume I – BANCAIXA Foundation for project P1·1B2011-23, Generalitat Valenciana for Prometeo/2009/053 project. The authors also acknowledge the Servei d’Informatica, Universitat Jaume I, Academic Computer Centre CYFRONET, AGH, Krakow, grant MNiSW/SGI3700/ PLodzka/088/2009, for generous allotment of computer time. V. Moliner would like to thank the Spanish Ministry Ministerio de Educación for traveling financial support, project PR2009-0539

Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily

Catalytic promiscuity, that is, the ability of single enzymes to facilitate the turnover of multiple, chemically distinct substrates, is a widespread phenomenon that plays an important role in the evolution of enzyme function. Additionally, such pre-existing multifunctionality can be harnessed in artificial enzyme design. The members of the alkaline phosphatase superfamily have served extensively as both experimental and computational model systems for enhancing our understanding of catalytic promiscuity. In this Opinion, we present key recent computational studies into the catalytic activity of these highly promiscuous enzymes, highlighting the valuable insight they have provided into both the molecular basis for catalytic promiscuity in general, and its implications for the evolution of phosphatase activity

Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer

The enzymes that facilitate phosphate and sulfate hydrolysis are among the most proficient natural catalysts known to date. Interestingly, a large number of these enzymes are promiscuous catalysts that exhibit both phosphatase and sulfatase activities in the same active site and, on top of that, have also been demonstrated to efficiently catalyze the hydrolysis of other additional substrates with varying degrees of efficiency. Understanding the factors that underlie such multifunctionality is crucial both for understanding functional evolution in enzyme superfamilies and for the development of artificial enzymes. In this Current Topic, we have primarily focused on the structural and mechanistic basis for catalytic promiscuity among enzymes that facilitate both phosphoryl and sulfuryl transfer in the same active site, while comparing this to how catalytic promiscuity manifests in other promiscuous phosphatases. We have also drawn on the large number of experimental and computational studies of selected model systems in the literature to explore the different features driving the catalytic promiscuity of such enzymes. Finally, on the basis of this comparative analysis, we probe the plausible origins and determinants of catalytic promiscuity in enzymes that catalyze phosphoryl and sulfuryl transfer