SuperLigands – a database of ligand structures derived from the Protein Data Bank

Background  

Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function.     

Microbial–meiofaunal interrelationships in coastal sediments of the Red Sea

Population density and biomass of bacteria and meiofauna were investigated seasonally in the sediments of the north-western bank of Red Sea. Samples of sediments were collected seasonally from three different stations to determine microphytobenthic biomass (chlorophyll a), protein, lipid, carbohydrate, and total organic matter concentrations. These investigations revealed that microbial components tended to increase their dominancy, whereas sensitive meiofauna were extremely reduced during the entire study period. Thus a very low density of the total meiofauna (with an annual average of 109 ± 26 ind./10 cm²) was recorded whilst the benthic microbial population densities exhibited higher values (ranging from 0.31 ± 0.02 × 10⁸ to 43.67 ± 18.62 × 10⁸/g dry sediment). These changes in the relative importance analysis of benthic microbial components versus meiofaunal ones seem to be based on the impact of organic matter accumulation on the function and structure of these benthic communities. Proteins, lipids and carbohydrates showed very low concentration values, and the organic matter mostly consisted of carbohydrates, reflecting lower nutritional values for benthic fauna in general and meiofauna in particular. The distribution of microbial and meiofaunal communities seems to be dependent on the quality of the organic matter rather than on its quantity. Total organic matter concentrations varied between 5.8 and 7.6 mg/g, with organic carbon accounting for only 32% of the total organic matter. Chlorophyll a attained very low values, fluctuating between 0.11 and 0.56 μg/g, indicating the oligotrophy of the studied area. The very low concentration of chlorophyll a in the Red Sea sediment suggests that the sedimentary organic matter, heterotrophic bacteria and/or protozoa constitute an alternative resource that is consumed by meiofauna when algae are less abundant. Protozoa, therefore, represent the “missing link in bacteria–meiofauna interaction in the Red Sea marine sediment ecosystem.     

Macroecology in the age of Big Data – Where to go from here?

Recent years have seen an exponential increase in the amount of data available in all sciences and application domains. Macroecology is part of this “Big Data” trend, with a strong rise in the volume of data that we are using for our research. Here, we summarize the most recent developments in macroecology in the age of Big Data that were presented at the 2018 annual meeting of the Specialist Group Macroecology of the Ecological Society of Germany, Austria and Switzerland (GfÖ). Supported by computational advances, macroecology has been a rapidly developing field over recent years. Our meeting highlighted important avenues for further progress in terms of standardized data collection, data integration, method development and process integration. In particular, we focus on (a) important data gaps and new initiatives to close them, for example through space- and airborne sensors, (b) how various data sources and types can be integrated, (c) how uncertainty can be assessed in data-driven analyses and (d) how Big Data and machine learning approaches have opened new ways of investigating processes rather than simply describing patterns. We discuss how Big Data opens up new opportunities, but also poses new challenges to macroecological research. In the future, it will be essential to carefully assess data quality, the reproducibility of data compilation and analytical methods, and the communication of uncertainties. Major progress in the field will depend on the definition of data standards and workflows for macroecology, such that scientific quality and integrity are guaranteed, and collaboration in research projects is made easier.     

New record of Ptarmus gallus Kossmann & Räuber, 1877 from the northern Red Sea (Teleostei: Aploactinidae), with a redescription of the species

The aploactinid fish Ptarmus gallus is redescribed and recorded from the Gulf of Suez (Egypt) for the first time. The species is apparently endemic to the Red Sea. Identification keys to the genera of aploactinid fishes, and to species of the genus Ptarmus are presented.     

Distribution of Recombination Hotspots in the Human Genome – A Comparison of Computer Simulations with Real Data

Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar.     

Do clades of symbiotic dinoflagellates in scleractinian corals of the Gulf of Eilat (Red Sea) differ from those of other coral reefs?

The symbiotic association between corals and zooxanthellae has been a major contributing factor in the success of reef-building corals. Most of these endocellular microalgal symbionts belong to the dinoflagellate genus Symbiodinium. However, considerable genetic diversity was revealed within this taxon, as is evident in the several clades of Symbiodinium found in association with hermatypic corals all over the world. The coral reefs of Eilat (Aqaba), where winter temperature minima of 21 °C are close to threshold values that prevent reef development, are among the northernmost reefs in the world. Furthermore, due to the circulation patterns of the Gulf, the extremely high evaporation, and lack of any riverine inputs, the Gulf's waters are highly saline (40.5‰). In spite of the extreme location, a high diversity of coral species has been reported in this area. In this study, using PCR, we specifically amplified zooxanthellae 18S ribosomal DNA from symbionts of 11 coral species, and analyzed it with respect to RFLP and DNA sequence.Of the several clades described from the same coral hosts in other localities, only A and C were found in the present study. Symbiodinium populations in the host examined from Eilat were different relative to other parts of the world. This distribution is discussed in relation to reproduction strategy: broadcasting versus brooding. Based on our results, we suggest that clade A is transferred through a closed system. As mass bleaching in the Gulf has never been observed, we suggest that the adaptive mechanisms presumably favoring clade diversity were not yet significant in our relatively cool area.     

Enhanced biodegradation of transformer oil in soils with cyclodextrin – from the laboratory to the field

The use cyclodextrins for the intensification of bioremediation by improving the mobility and bioavailability of contaminants has recently been studied. In this work, the role of randomly methylated -cyclodextrin in the bioremediation of soils contaminated with transformer oil was studied both in bench scale bioreactors and through field experiments. The aims of this research were to (a) establish the scientific background of a cyclodextrin-based soil bioremediation technology, (b) demonstrate its feasibility and effectiveness in the field, and (c) develop an integrated methodology, consisting of a combination of physical, chemical, biological and ecotoxicological analytical methods, for efficiently monitoring the technology performances. The stepwise increasing scale of the experiments and the application of the integrated analytical methodology supported the development of a scientifically established new technology and the identification of the advantages and the limitations of its application in the field. At each phase of the study, randomly methylated -cyclodextrin was found to significantly enhance the bioremediation and detoxification of the transformer oil-contaminated soils employed by increasing the bioavailability of the pollutants and the activity of indigenous microorganisms.     

Structural and Functional Characterization of the Redβ Recombinase from Bacteriophage λ

The Red system of bacteriophage λ is responsible for the genetic rearrangements that contribute to its rapid evolution and has been successfully harnessed as a research tool for genome manipulation. The key recombination component is Redβ, a ring-shaped protein that facilitates annealing of complementary DNA strands. Redβ shares functional similarities with the human Rad52 single-stranded DNA (ssDNA) annealing protein although their evolutionary relatedness is not well established. Alignment of Rad52 and Redβ sequences shows an overall low level of homology, with 15% identity in the N-terminal core domains as well as important similarities with the Rad52 homolog Sak from phage ul36. Key conserved residues were chosen for mutagenesis and their impact on oligomer formation, ssDNA binding and annealing was probed. Two conserved regions were identified as sites important for binding ssDNA; a surface basic cluster and an intersubunit hydrophobic patch, consistent with findings for Rad52. Surprisingly, mutation of Redβ residues in the basic cluster that in Rad52 are involved in ssDNA binding disrupted both oligomer formation and ssDNA binding. Mutations in the equivalent of the intersubunit hydrophobic patch in Rad52 did not affect Redβ oligomerization but did impair DNA binding and annealing. We also identified a single amino acid substitution which had little effect on oligomerization and DNA binding but which inhibited DNA annealing, indicating that these two functions of Redβ can be separated. Taken together, the results provide fresh insights into the structural basis for Redβ function and the important role of quaternary structure.     

Seasonal monitoring of coral–algae interactions in fringing reefs of the Gulf of Aqaba, Northern Red Sea

This paper presents seasonal in situ monitoring data on benthic coverage and coral–algae interactions in high-latitude fringing reefs of the Northern Red Sea over a period of 19 months. More than 30% of all hermatypic corals were involved in interaction with benthic reef algae during winter compared to 17% during summer, but significant correlation between the occurrence of coral–algae interactions and monitored environmental factors such as temperature and inorganic nutrient availability was not detected. Between 5 and 10-m water depth, the macroalgae Caulerpa serrulata, Peyssonnelia capensis and filamentous turf algae represented almost 100% of the benthic algae involved in interaction with corals. Turf algae were most frequently (between 77 and 90% of all interactions) involved in interactions with hermatypic corals and caused most tissue damage to them. Maximum coral tissue loss of 0.75% day⁻¹ was observed for Acropora-turf algae interaction during fall, while an equilibrium between both groups of organisms appeared during summer. Slow-growing massive corals were more resistant against negative algal influence than fast-growing branching corals. Branching corals of the genus Acropora partly exhibited a newly observed phenotypic plasticity mechanism, by development of a bulge towards the competing organism, when in interaction with algae. These findings may contribute to understand the dynamics of phase shifts in coral reefs by providing seasonally resolved in situ monitoring data on the abundance and the competitive dynamic of coral–algae interactions.     

Data envelopment analysis of cities – Investigation of the ecological and economic efficiency of cities using a benchmarking concept from production management

To better understand the economic performance of cities and the accompanying social and environmental implications, one focus of research has been on ways to quantify performance advantages of growth and size while considering the impact of economies of scale. An important aspect of the current discussion is the introduction of the merely environmental driven concept of resource efficiency, defined as minimizing resource consumption while enhancing the quality of life. However, as yet there is no commonly agreed method on how best to measure efficiency. In order to contribute to this debate, an approach is described here of applying Data Envelopment Analysis (DEA) to study the resource efficiency of cities. Originating in the field of economics, DEA is a non-parametric, deterministic method to measure the efficiency of economic production, specifically the relative efficiency of Decision Making Units (DMUs).Here we test the usefulness of DEA to analyze urban efficiency by applying it to an investigation of 116 cities throughout Germany. This entailed the development of two separate economic and ecological models in order to allow more precise identification of the relevance of individual parameters during the evaluation process. The results allow a ranking of cities as well as an estimation of the ratios of economic and ecological efficiencies of the investigated cities, realized with the aid of a nine-field matrix (portfolio).DEA is at the same time a promising heuristic tool to help draw the basic outlines of a resource efficient city and to shed light on the underlying factors that boost or reduce efficiency. We recommend a three-step approach. First, two separate models should be defined (ecological, economic) and used to feed the DEA computation. Second, the results are spread in a portfolio to give an overview of the ecological and economic efficiency scores. This provides a basic overview of the DEA results for the selected cities following a basic and abstract model without determination of causal relationships between these values. Third, the field-dependent commonalities between the cities are considered. Additional indicators that also characterize the selected cities (but which were not selected as inputs to the algorithm) can now be examined. In this way, it is possible to understand the common factors that determine the level of efficiency as well as to learn about the qualitative difference and specific features of cities in the particular matrix quadrants.     

Trade-offs between plant species richness and carbon storage in the context of afforestation – Examples from afforestation scenarios in the Mulde Basin,Germany

The German Federal State of Saxony aims to increase forest cover, supported by the implementation of afforestation programs. To analyze consequences of an increase in forest cover, this study investigates possible trade-offs between carbon storage and plant biodiversity caused by afforestation. Six afforestation scenarios with total forest cover ranging from 27.7% to 46% were generated in the Mulde river basin in Saxony with regard to different forest types. Carbon storage was calculated by the process-based Dynamic Vegetation Model LPJ-GUESS while random forest models were used to predict changes in plant species richness. We used eight different plant groups as responses: total number of plant species, endangered species, as well as species grouped by native status (three groups) and pollination traits (three groups). Afforestation led to an increase in carbon storage that was slightly stronger in coniferous forests as compared to deciduous forests. The relationship between plant species richness and afforestation was context dependent. Species richness showed a non-linear relationship with forest cover share. The relationship was influenced by shares of land use types, climatic conditions and land use configuration expressed by the number of land use patches. The effect of forest type on plant species richness was marginal. On average the relationship between carbon storage and plant species richness was synergistic for most plant groups. However, the relationship between change in species richness and change in carbon storage varied across space. This changing relationship was used to identify priority areas for afforestation. The different plant groups responded differently to an increase in forest cover. The change in species richness for Red List species was relatively distinct from the other species groups. Neophytes and archeophytes (i.e. alien plant species introduced after and before the discovery of the Americas) showed a similar response to the afforestation scenarios. While afforestation had overall positive effects both on plant species richness and carbon storage, a number of locations were identified for which afforestation would lead to a decrease in plant species richness. Spatial planning should therefore avoid afforestation at these locations.     

Risky Business: Factor Analysis of Survey Data – Assessing the Probability of Incorrect Dimensionalisation

This paper undertakes a systematic assessment of the extent to which factor analysis the correct number of latent dimensions (factors) when applied to ordered-categorical survey items (so-called Likert items). We simulate 2400 data sets of uni-dimensional Likert items that vary systematically over a range of conditions such as the underlying population distribution, the number of items, the level of random error, and characteristics of items and item-sets. Each of these datasets is factor analysed in a variety of ways that are frequently used in the extant literature, or that are recommended in current methodological texts. These include exploratory factor retention heuristics such as Kaiser’s criterion, Parallel Analysis and a non-graphical scree test, and (for exploratory and confirmatory analyses) evaluations of model fit. These analyses are conducted on the basis of Pearson and polychoric correlations. We find that, irrespective of the particular mode of analysis, factor analysis applied to ordered-categorical survey data very often leads to over-dimensionalisation. The magnitude of this risk depends on the specific way in which factor analysis is conducted, the number of items, the properties of the set of items, and the underlying population distribution. The paper concludes with a discussion of the consequences of over-dimensionalisation, and a brief mention of alternative modes of analysis that are much less prone to such problems.     

Assessment of the Efficacy of Solutes from Extremophiles on Protein Aggregation in Cell Models of Huntington’s and Parkinson’s Diseases

Protein misfolding and deposition in the brain are implicated in the etiology of numerous neurodegenerative disorders. Here, organic solutes characteristic of microorganisms adapted to hot environments, were tested on experimental cell models of Huntington’s and Parkinson’s diseases. Diglycerol phosphate, di-myo-inositol phosphate, mannosylglycerate, and mannosylglyceramide were not toxic to the cells, at 10 mM concentration, but caused a decrease in cell density, which suggested an effect on proliferation. In contrast, mannosyl-lactate, an artificial analogue of mannosylglycerate, had a negative impact on cell viability. Concerning protein aggregation, inclusions of mutant huntingtin were reduced in the presence of diglycerol phosphate and di-myo-inositol phosphate, increased with mannosylglycerate, while mannosyl-lactate and mannosylglyceramide had no significant effect. α-Synuclein aggregation was not affected by the solutes tested, except for di-myo-inositol phosphate that led to a slight increased percentage of cells displaying visible aggregates. These solutes might be useful in the development of therapies for protein misfolding diseases.     

Mining of Egypt’s Red Sea invertebrates for potential bioactive producers

Objective

The objective of this work was to isolate bacteria from Red Sea invertebrates, determine their antimicrobial activity, and screen for the biosynthetic gene clusters [polyketides (PKs) and nonribosomal peptides (NRPs)] which could be involved in the production of bioactive secondary metabolites.

Result

Eleven different samples of marine invertebrates’ were collected from Egypt’s Red Sea (El-Tor-Sharm El-Sheikh and Hurghada) by scuba diving, and a total 80 isolates of the associated microorganisms were obtained from the cultivation on six different cultural medium. Seven isolates of them showed an antimicrobial activity against five pathogenic reference strains, while the most active antimicrobial agent was isolate number HFF-8 which was 99% identical to Bacillus amyloliquefaciens. HFF-8’s extract showed positive results against Gram negative bacteria, Gram positive bacteria and yeast. Moreover, the isolates gave positive bands when screened for the presence of PK synthase (PKS) I and II and NRP synthetase (NRPS) I and II biosynthetic genes, those biosynthetic fragments when cloned and sequenced were primitively predicted as biosynthetic fragments for kirromycin and leinamycin production by NaPDoS program with 56 and 55%, respectively.

Conclusion

The Red Sea can provide a sustainable solution to combat bacterial resistance. The contribution of this work is that B. amyloliquefaciens was isolated from Heteroxenia fuscescens, Red Sea, Egypt. Moreover, the bacterial extract showed a broad spectrum with a potent antimicrobial activity.

     

Connectivity across the Caribbean Sea: DNA Barcoding and Morphology Unite an Enigmatic Fish Larva from the Florida Straits with a New Species of Sea Bass from Deep Reefs off Cura?ao

Integrative taxonomy, in which multiple disciplines are combined to address questions related to biological species diversity, is a valuable tool for identifying pelagic marine fish larvae and recognizing the existence of new fish species. Here we combine data from DNA barcoding, comparative morphology, and analysis of color patterns to identify an unusual fish larva from the Florida Straits and demonstrate that it is the pelagic larval phase of a previously undescribed species of Liopropoma sea bass from deep reefs off Curaçao, southern Caribbean. The larva is unique among larvae of the teleost family Serranidae, Tribe Liopropomini, in having seven elongate dorsal-fin spines. Adults of the new species are similar to the golden bass, Liopropoma aberrans, with which they have been confused, but they are distinct genetically and morphologically. The new species differs from all other western Atlantic liopropomins in having IX, 11 dorsal-fin rays and in having a unique color pattern–most notably the predominance of yellow pigment on the dorsal portion of the trunk, a pale to white body ventrally, and yellow spots scattered across both the dorsal and ventral portions of the trunk. Exploration of deep reefs to 300 m using a manned submersible off Curaçao is resulting in the discovery of numerous new fish species, improving our genetic databases, and greatly enhancing our understanding of deep-reef fish diversity in the southern Caribbean. Oh the mother and child reunion is only a moment away. Paul Simon.