The influence of solvent on conformational properties of peptides with Aib residue—a DFT study

The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe₂ (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N–H?O hydrogen bonds, i.e., C₅ and C₇ conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/?60°, +/?40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data.

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Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue

     

Environmental drivers of α-diversity patterns in monsoonal tropical stream fish assemblages: a case study from tributaries of Narmada basin,India

Environmental factors, such as local physico-chemical water parameters, habitat-structural conditions, geography and human disturbances can have a profound impact on the structure and composition of biotic communities. This study investigates the relationship of these factors with fish diversity in medium to small streams in Central India and identifies the key determinants of species richness and diversity in habitats increasingly facing impacts of urban development. Data on fish diversity on eighteen sites, representative of undisturbed and disturbed aquatic habitats, located in the Narmada river basin were collected across different seasons over two years. Seasonal patterns of alpha diversity for this region were analysed and the effect of environmental drivers on seasonal patterns of alpha diversity were assessed. Analyses of species data revealed significant differences in diversity patterns across seasons for both species richness and Shannon diversity. Results of generalized linear mixed models showed that along with disturbance, altitude and substrate heterogeneity, dissolved oxygen, pH and stream width proved to be important environmental variables that predict species richness. Further, variations in pH, dissolved oxygen, temperature, stream width, stream depth and stream width heterogeneity were found to also predict Shannon diversity index. Our study revealed that seasonal changes across the year play a crucial role in shaping diversity patterns. This study is relevant as an important step in identifying roles of various ecological factors driving fish diversity in the region and towards developing long term management plans for critical catchment areas of major rivers in tropical systems.     

The influence of storage on the “chemical age” of red wines

Storage conditions and duration have a considerable influence on wine quality. Optimum temperature and humidity conditions may improve wine quality through ageing, while incorrect or excessively long storage leads to negative results. In order to evaluate the global effects of storage on red wine composition, 20 Sangiovese wines were stored in two different conditions (cellar or house) for a period of 2 years and analysed every 6 months. Untargeted LC–MS analysis showed various putative markers for the type and length of conservation (i.e. pigments, flavanols, pantothenic acid etc.), while targeted LC–MS confirmed and expanded these results within specific metabolic groups. The results of multivariate analysis showed that wines stored in the cellar changed little even after 2 years of storage, while wines stored in typical domestic conditions (house) developed approximately four times faster, reaching a composition similar to wines stored in the cellar for 2 years after just 6 months. The formation of several monosulfonated flavanols during domestic ageing provided the first evidence in wine of a reaction between wine tannins—both catechins and proanthocyanidins—and the exogenous antioxidant bisulfite. Moreover, ageing in domestic conditions appeared to induce an accelerated decrease in wine pigments, while specifically promoting the formation of pinotin A-like pigments and the hydrolysis of flavonol glycosides.     

The aftermath of coral bleaching on a Maldivian reef—a quantitative study

Since the bleaching event of 1998, the development of the reef flat and upper reef slope on a Maldivian reef (the Komandoo house reef; Komandoo Island, Lhaviyani atoll or Fadiffolu atoll) is under detailed observation. We quantitatively recorded specific losses, re-colonisation by coral larvae on transects on the reef flat and on dead Acropora tables at the reef slope and regeneration of partly damaged large Porites and Diploastrea—colonies over the period from 1999 to 2004. The detrimental effects on the reef structure by bioerosion and hydrodynamics, as well as the overall status of the reef community were qualitatively assessed. Recruitment soon after the bleaching was more pronounced than in the following years, Pavona varians being a main constituent. The temporal re-colonisation pattern points at an emergency spawning of local Scleractinia just prior to the bleaching, whereas a sharp decrease of young settlers in 2001 and 2002 confirms a reduction of fertile colonies. The dominant species in the coral community shifted from acroporids and pocilloporids to agariciids. The skeletal deposition of recovering Diploastrea heliopora was equivalent to that before the bleaching, but much less than that of neighbouring Porites lobata colonies. The slow and scattered formation of new reef substance, which would structurally strengthen the reef, is however outweighed by the collapse of dead protruding and spacious colonies (e.g., Acropora tables). Six years after the bleaching, the formerly three-dimensional structure of the reef flat and upper reef slope presents as a levelled field of rubble, only partly consolidated by incrusting corals. Considering the recurrence of bleaching events (1987, 1998) and the results of the present study, one may assume a cascading deterioration of the status of the reef for the future.     

The influence of changes to river hydrology on freshwater fish in regulated rivers of the Murray–Darling basin

Freshwater fish are often used as an indicator of the response of the ecosystem to the restoration of river flows or the provision of environmental flows. The ability to model the biological response of fish depends on the capacity to establish clear relationships between changes in river hydrology and the fish assemblages in a river. The fish assemblage structure and the abundances of individual fish species were examined in relation to a hydrological index that described hydrological change in six regulated rivers in the Murray–Darling Basin. The hydrological index explained only a small amount of variation in fish assemblage structure. In addition, the abundances of individual fish species were only weakly correlated with the index of flow deviation. It is suggested that these results make the modelling of responses of fish assemblages to environmental water allocations unfeasible at a large scale and that future studies should concentrate on potentially more simple responses, such as the relationships of fish spawning and recruitment to specific aspects of river hydrology.     

The influence of external factors on bacteriophages—review

The ability of bacteriophages to survive under unfavorable conditions is highly diversified. We summarize the influence of different external physical and chemical factors, such as temperature, acidity, and ions, on phage persistence. The relationships between a phage’s morphology and its survival abilities suggested by some authors are also discussed. A better understanding of the complex problem of phage sensitivity to external factors may be useful not only for those interested in pharmaceutical and agricultural applications of bacteriophages, but also for others working with phages.     

The effect of hay blowing instead of hay raking on plant biodiversity – a case study of a dry meadow in a Swiss mountain region

Low-input dry meadows are habitats of high nature value. More and more, less time-consuming harvesting techniques replace different steps of the traditional hay making process. The use of leaf blowers instead of rakes for hay making became popular in the last ten years in Switzerland. Thus, we set up a case study to test effects on the conservation value. The studied dry meadow of high nature value is located in the municipality of Stans (Switzerland). After five years no significant differences between blown and raked plots in species richness, richness of target an indicator species, medium plant-indicator values, i.e. nutrients, humidity, light or in the species assemblages were observed. From 2010 until 2014 the moss cover increased in all plots. The differences between raked and blown plots were not significant. In 2015, however, the difference between the two treatments increased to 13%. While the moss cover of the blown plots remained at 20%, the moss cover of the raked plots dropped to 7%. These results from only one case study and only a short observation period of five years do not allow a generalization, but they give a first impression of the short-term effects. We recommend managers of dry meadows with high nature values to keep an eye on the change of moss cover and potential changes of conservation values when leaf blowers instead of rakes are used for hay harvesting.     

The influence of social deprivation on bone donation: a 10 year retrospective study

An audit identifying all surgical bone donors over a 10 year period was conducted. Postcodes were used to link data from the index of multiple deprivation (IMD) 2007 to give each donor a deprivation score. An audit from 2000 to 2010 of primary total hip replacement (THR) patients was also conducted, and similarly a deprivation score was identified for each patient. IMD scores are split into quintiles. A high IMD score indicates a high degree of social deprivation. Conversely low IMD scores indicate a more affluent community. The mean IMD 2007 score was 13.36 (95 % CI 13.12–13.60). The national mean IMD score is 21.7 (CI 21.52–21.88). The difference is significant (p < 0.0001). The mean IMD 2007 score of primary THR patients identified in the arthroplasty database was 19.19 (CI 19.00–19.38). The difference between the mean arthroplasty score and the mean score of donors is significant (p < 0.0001). The donation rate increases as social deprivation decreases from quintile to quintile in both: the older patients (CI 1.08–1.14; p < 0.0001) and the general population (CI 1.20–1.25; p < 0.0001). Bone donors are substantially less deprived than their donor pool of THR patients. Donor rates are consistently lower in quintiles which are more deprived.     

Is there a core set of organisms that structure macroinvertebrate assemblages in freshwater wetlands?

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The effect of riverine networks on fish β-diversity patterns in a Neotropical system

Hydrobiologia - We investigated how the riverine network influences taxonomic and functional beta diversity patterns of fish assemblages in the mainstem/headwater (lateral) and upstream/downstream...     

The effect of using a case study on the academic achievement of students in learning about the topic of ‘Vitamins’

This study investigates the impact of the Case-Based Learning (CBL) method for the topic of ‘B6, B9 and B12 Vitamins’ on students’ academic achievement in a biochemistry course for an associate degree level in health. To this end, a case study with the title ‘The Reasons for Depression: Do We Know What They Are?’ was developed and implemented. The study had a one-group pre-test and post-test research design. The ‘Vitamins’ Achievement Test’ (VAT) and a Structured Interview Form were used as data collection tools. First-year students of Medical Laboratory Techniques at the Ahmet Erdogan Vocational School of Health Services at Bulent Ecevit University (N = 34) who were aged between18 and 20 made up the study group. The VAT and the Structured Interview Form were analysed using content analysis and the paired-samples t-test was used for the VAT. The results indicated that the frequency of students’ responses in the ‘clear understanding’ category improved in the VAT post-test and it was concluded that there was a significant positive difference in the post-test scores of students. The results of the structured interview indicated that most of the students had positive opinions about the method, material and case study.     

What's in a name? The case of cyanobacteria

A redefinition of the cyanobacterial lineage has been proposed based on phylogenomic analysis of distantly related nonphototrophic lineages. We define Cyanobacteria here as “Organisms in the domain bacteria able to carry out oxygenic photosynthesis with water as an electron donor and to reduce carbon dioxide as a source of carbon, or those secondarily evolved from such organisms.”     

The phagophore in four dimensions—a study in wood

One of the key features of macroautophagy/autophagy is the dynamic nature of the membrane rearrangements that take place during expansion of the phagophore, the sequestering compartment that matures into an autophagosome. There are various ways to depict this process, but in most cases the method ultimately relies on a two-dimensional medium. Most people working in the field of autophagy realize that the typical ‘C’-shaped drawing of a phagophore is meant to represent a cup- or bowl-like structure that exists in the cell in 3 dimensions. However, explaining this concept to a lay person often leads to confusion and misinterpretation. Accordingly, we decided to generate a four-dimensional version of the expanding phagophore as a wood sculpture, that depicts this transient compartment in 3 dimensions over time.

Abbreviations: ER: endoplasmic reticulum     

The influence of landscape structure on ants and dung beetles diversity in a Mediterranean savanna—Forest ecosystem

Ants and dung beetles are focal indicators of change in several ecological processes and successional vegetation stages in Mediterranean landscapes. Despite relatively good knowledge of local species distributions, there are few data on their distributions at different scales. In the present study, the influence of multiscale landscape structure was examined using both ants and dung beetles to identify species that can serve as indicators and detectors of changes in vegetation structure. Multiscale analysis is necessary to explore the different roles of indicator and detector species for use as tools in studies focused on monitoring ecological changes. The study area was the Cabañeros National Park, in the center of the Iberian Peninsula. This site was selected because it is a good setting to evaluate the effects of typical vegetation mosaics on Mediterranean species at different scales. In this study, dung beetles and ants were trapped for one year. A multiscale analysis was designed using three different vegetation habitats (forest, scrubland and grassland) and landscape matrices (woodland, scrubland and grassland). Among dung beetles, 23 indicator species (IndVal values higher than 70%) were found at different scales of analysis. In addition, 20 dung beetle species were characterized as detector species (IndVal values between 45 and 70%) for the three different levels analyzed. Similar to the dung beetles, the ants had different species assemblages at various habitats and landscape levels; however, no indicator ant species were found in this study. All species with significant IndVal values (n = 8) were identified as detector species. Thus, ant and dung beetle assemblages were influenced in different ways by vegetation structure. Both groups showed strong individual species responses to different Mediterranean landscape conditions and vegetation types. Further, both insect groups showed a great number of detector species, which can be useful in ecosystem management because they have varying degrees of preference and sensitivity for different ecological states (such as successional vegetation stages). The diverse indicator and detector species identified in this work could be useful tools for the detection of landscape structure changes at both levels habitat patches and landscape matrix. However, a generalisation of the results at landscape scale should be taken with precaution, but they encourage to study more regions and similar landscapes. The use of more than one indicator group in the analysis confirms the importance of selecting groups with different sensitivities at varying spatial scales as well as different ecosystem functions. This strategy allows the establishment of a clear baseline with which to analyze future direct and indirect impacts of management in Mediterranean protected areas.     

Quantifying drivers of variability in life cycle greenhouse gas emissions of consumer products—a case study on laundry washing in Europe

Purpose

Variability in consumer behaviour can significantly influence the environmental performance of products and their associated impacts and this is typically not quantified in life cycle assessments. The goal of this paper is to demonstrate how consumer behaviour data can be used to understand and quantify the variability in the greenhouse gas emissions from domestic laundry washing across Europe.

Methods

Data from a pan-European consumer survey of product usage and washing habits was combined with internal company data on product format greenhouse gas (GHG) footprints and in-home measurement of energy consumption of laundry washing as well as literature data to determine the GHG footprint of laundry washing. The variability associated with four laundry detergent product formats and four wash temperature settings in washing machines were quantified on a per wash cycle basis across 23 European countries. The variability in GHG emissions associated with country electricity grid mixes was also taken into account. Monte Carlo methods were used to convert the variability in the input parameters into variability of the life cycle GHG emissions. Rank correlation analysis was used to quantify the importance of the different sources of variability.

Results and discussion

Both inter-country differences in background electricity mix as well as intra-country variation in consumer behaviour are important for determining the variability in life cycle GHG emissions of laundry detergents. The average GHG emissions related to the laundry washing process in the 23 European countries in 2014 was estimated to be 5?×?10² g CO_2?eq/wash cycle, but varied by a factor of 6.5 between countries. Intra-country variability is between a factor of 3.5 and 5.0 (90% interval). For countries with a mainly fossil-based electricity system, the dominant source of variability in GHG emissions results from consumer choices in the use of washing machines. For countries with a relatively low-carbon electricity mix, variability in life cycle GHG emissions is mainly determined by laundry product-related parameters.

Conclusions

The combination of rich data sources enabled the quantification of the variability in the life cycle GHG emissions of laundry washing which is driven by a variety of consumer choices, manufacturer choices and infrastructural differences of countries. The improved understanding of the variability needs to be balanced against the cost and challenges of assessing of consumer habits.

     

Fast bioassessment of wastewater and surface water quality using freshwater flagellate Euglena gracilis—a case study from Pakistan

Wastewater is a big source of water pollution in the world. Selected wastewater samples from Dera Ismail Khan (D.I. Khan), a city in Pakistan, were analyzed for physicochemical and ecotoxicological properties. Samples from the Indus River before and after the municipal wastewater is discharged into it were tested to determine the effects of municipal wastewaters from D.I. Khan on the river Indus. Different parameters of the freshwater flagellate Euglena gracilis such as motility, swimming velocity, gravitactic orientation, cell shape, and photosynthetic efficiency were used as end points. Gravitactic orientation and cell shape were found to be significantly impaired by the wastewater samples. Swimming velocity and relative electron transport rate of cells were positively affected by all water samples. Quantum yield of photosystem II (F _v/F _m) was not affected, except by ghee (oil) industry effluent where it was significantly increased. Comparison of upstream and downstream samples from the Indus River showed that waste effluents from D.I. Khan affect the physicochemical and ecological properties of the river Indus.     

Does climate influence assemblages of anurans and lizards in a coastal area of north-eastern Brazil?

Environmental factors influence diverse assemblage features such as species abundances, richness, and nestedness. Amphibians and reptiles play important roles in terrestrial ecosystems, but there is still a lack of information about the assemblages of these animals in many regions. In this study, we aimed to understand how environmental factors influence the anurans and lizards assemblages from São Gonçalo do Amarante, Ceará, Brazil. Herpetofauna samplings were performed monthly in São Gonçalo do Amarante from January 2008 to May 2009, excluding April 2008. We sampled animals (anurans and lizards) using pitfall traps and active searches. The abundance and richness of lizards were positively related to temperature and negatively related to precipitation. Anuran assemblage was not influenced by precipitation, but its abundance was negatively influenced by temperature. Temperature generated a nested pattern in the lizard assemblage, but precipitation did not produce this pattern in anurans. Finally, our results reinforce the importance of environmental factors, mainly temperature, in structuring assemblages of anurans and lizards.     

In search of expression bottlenecks in recombinant CHO cell lines—a case study

The efficient production of recombinant proteins such as antibodies typically involves the screening of an extravagant number of clones in order to finally select a stable and high-producing cell line. Thereby, the underlying principles of a powerful protein machinery, but also potential expression limitations, often remain poorly understood. To shed more light on this topic, we applied several different techniques to investigate a previously generated cell line (4B3-IgA), which expressed recombinant immunoglobulin A (IgA) with an unusually low specific productivity. Results were compared to the host cell line and to another recombinant CHO cell line (3D6-IgA) expressing another IgA that binds to an overlapping epitope. The low specific productivity of clone 4B3-IgA could not be explained by GCN or mRNA levels, but insufficiencies in protein maturation and/or secretion were determined. Despite the presence of free light chain polypeptides, they occasionally failed to associate with their heavy chain partners. Consequently, heavy chains were misassembled and accumulated to form intracellular aggregates, so-called Russell bodies. These protein deposits evoked the expression of increased amounts of ER-resident chaperones to combat the induced stress. Despite bottlenecks in protein processing, the cells’ quality checkpoints remained intact, and predominantly correctly processed IgA was exported into the culture medium. The results of our study demonstrated that recombinant protein expression was impaired by heavy chain aggregation despite the presence of a disposable light chain and revealed elevated chaperone formation in combination with limited antibody assembly. Our studies suggest that the primary amino acid sequence and consequently the resulting structure of an expressed protein need to be considered as a factor influencing a cell’s productivity.