Effects of temperature, salinity and fish in structuring the macroinvertebrate community in shallow lakes: implications for effects of climate change

Climate warming may lead to changes in the trophic structure and diversity of shallow lakes as a combined effect of increased temperature and salinity and likely increased strength of trophic interactions. We investigated the potential effects of temperature, salinity and fish on the plant-associated macroinvertebrate community by introducing artificial plants in eight comparable shallow brackish lakes located in two climatic regions of contrasting temperature: cold-temperate and Mediterranean. In both regions, lakes covered a salinity gradient from freshwater to oligohaline waters. We undertook day and night-time sampling of macroinvertebrates associated with the artificial plants and fish and free-swimming macroinvertebrate predators within artificial plants and in pelagic areas. Our results showed marked differences in the trophic structure between cold and warm shallow lakes. Plant-associated macroinvertebrates and free-swimming macroinvertebrate predators were more abundant and the communities richer in species in the cold compared to the warm climate, most probably as a result of differences in fish predation pressure. Submerged plants in warm brackish lakes did not seem to counteract the effect of fish predation on macroinvertebrates to the same extent as in temperate freshwater lakes, since small fish were abundant and tended to aggregate within the macrophytes. The richness and abundance of most plant-associated macroinvertebrate taxa decreased with salinity. Despite the lower densities of plant-associated macroinvertebrates in the Mediterranean lakes, periphyton biomass was lower than in cold temperate systems, a fact that was mainly attributed to grazing and disturbance by fish. Our results suggest that, if the current process of warming entails higher chances of shallow lakes becoming warmer and more saline, climatic change may result in a decrease in macroinvertebrate species richness and abundance in shallow lakes.     

Life cycle inventory modeling of phosphorus substitution,losses and crop uptake after land application of organic waste products

Purpose

Life cycle assessments (LCAs) that attempt to provide advice on treatment options for phosphorus (P) containing organic waste products encounter problems related to the quantification of mineral P fertilizer substitution, P loss and crop P uptake after land application. The purpose of this study was to develop a relatively easy to use life cycle inventory model, known as PLCI, that could be used to estimate these values.

Methods

A life cycle inventory model for P was developed, which estimates the effect of an application of organic waste followed by ordinary fertilizer management in the modeling period. This was compared with a simulation without the initial waste application. The difference in mineral P fertilizer application (substitution), P loss and crop P uptake was then calculated and expressed as a proportion of the amount of waste applied. As an example, the effect of an initial application of mineral fertilizer, sewage sludge and ash on two farm types was simulated. These results were applied in an LCA case study of different sewage sludge treatment options.

Results and discussion

Farm type influenced the P fertilizer substitution, loss and crop uptake factors. The application on an arable farm showed a substitution of 28 to 31%, relatively low P loss and a large spread in crop P uptake for the different P sources, compared with the pig farm. Application on a pig farm showed no mineral P substitution. For substitution, mineral fertilizer outperformed waste product fertilizer with a short modeling period, due to higher immediate P availability, which was not the case with a long period. The LCA case study showed that the P substitution factor had an influence on the environmental impact categories climate change and depletion of reserve-based abiotic resources while the P loss factor influenced freshwater eutrophication. Application of the P loss and substitution factors generated from the PLCI model resulted in higher environmental burdens and lower savings than using conventional factors.

Conclusions

The soil P status mainly affected P substitution and loss, with the fertilizer type only having a small influence when soils had a low P status. The PLCI model can facilitate more coherent and rigorous estimates of P substitution and loss to be used in LCA studies involving application of waste products on agricultural land. This is important since P substitution and loss can have an important influence on impact categories, such as freshwater eutrophication and resource depletion.

     

Enzymic basis for leakiness of auxotrophs for phenylalanine in Pseudomonas aeruginosa

The dual enzymic routes for phenylalanine biosynthesis that exist in Pseudomonas aeruginosa complicate the isolation of phenylalanine auxotrophs. Mutants blocked in each of the various phenylalanine-pathway steps are essential for full appreciation of the physiological nature and gene-enzyme relationships of this biochemical system. A leaky phenylalanine-requiring mutant of P. aeruginosa (PAT1051) was found to lack the bifunctional P-protein (chorismate mutase-prephenate dehydratase), but retained the monofunctional isozyme species of chorismate mutase (chorismate mutase-F) as well as cyclohexadienyl dehydratase (components of the arogenate 'overflow' route to phenylalanine). This is the first mutant of P. aeruginosa shown to be deficient in any enzyme specific for phenylalanine synthesis. It is concluded that although the arogenate pathway has the demonstrated potential to overproduce phenylalanine, the substrate levels normally available to the arogenate pathway in the wild-type are inadequate to satisfy the full metabolic demand for phenylalanine.     

Molecular analysis of a beta-lactam resistance gene encoded within the cephamycin gene cluster of Streptomyces clavuligerus.

A Streptomyces clavuligerus gene (designated pcbR) which is located immediately downstream from the gene encoding isopenicillin N synthase in the cephamycin gene cluster was characterized. Nucleotide sequence analysis and database searching of PcbR identified a significant similarity between PcbR and proteins belonging to the family of high-molecular-weight group B penicillin-binding proteins (PBPs). Eight of nine boxes (motifs) conserved within this family of proteins are present in the PcbR protein sequence in the same order and with approximately the same spacing between them. When a mutant disrupted in pcbR was constructed by gene replacement, the resulting pcbR mutant exhibited a significant decrease in its resistance to benzylpenicillin and cephalosporins, indicating that pcbR is involved in beta-lactam resistance in this organism. Western blot (immunoblot) analysis of S. clavuligerus cell membranes using PcbR-specific antibodies suggested that PcbR is a membrane protein. PcbR was also present in cell membranes when expressed in Escherichia coli and was able to bind radioactive penicillin in a PBP assay, suggesting that PcbR is a PBP. When genomic DNAs from several actinomycetes were probed with pcbR, hybridization was observed to some but not all beta-lactam-producing actinomycetes.     

Body mass growth in common marmosets: Toward a model of pediatric obesity

While much is known about adult obesity in nonhuman primates, very little is known regarding development of childhood adiposity. As small monkeys that are easy to handle and have a relatively fast life history, common marmoset monkeys (Callithrix jacchus) offer interesting opportunities to examine the question of fat versus lean mass growth in a nonhuman primate. This article provides an overview of our understanding of early life growth in mass in marmoset monkeys, based primarily upon our past 20 years of research, culminating in our recent findings on early life obesity in this species. Common marmosets display variance in early life growth patterns that is related to both pre‐ and postnatal factors and the marmoset uterine environment is exquisitely designed to reflect resources available for the gestation of multiple offspring, making them an interesting model of developmental programming. We have demonstrated that obesity can be generated in very early life in captive marmosets, with excess adiposity evident by one month of age, making this species a potentially valuable model in which to study pediatric obesity and its sequelae. Birth weight is associated with adiposity in animals vulnerable to obesity. Early life exposure to higher fat diets enhances the chances of postweaning obesity development. However, overall higher food consumption is also associated with obesity development at later ages. One unexpected finding in our studies has been the relatively high body fat percentage of neonatal (12–18%) marmosets suggesting that hypotheses regarding the uniqueness of high human neonatal adiposity merit further examination. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.     

Domestication‐related variation in social preferences in chickens is affected by genotype on a growth QTL

A growth‐related QTL on chicken chromosome 1 has previously been shown to influence domestication behaviour in chickens. In this study, we used Red Junglefowl (RJF) and White Leghorn (WL) as well as the intercross between them to investigate whether stress affects the way birds allocate their time between familiar and unfamiliar conspecifics in a social preference test (‘social support seeking’), and how this is related to genotype at specific loci within the growth QTL. Red Junglefowl males spent more time with unfamiliar chickens before the stressful event compared to the other birds, whereas all birds except WL males tended to spend less time with unfamiliar ones after stress. A significant QTL locus was found to influence both social preference under undisturbed circumstances and social support seeking. The WL allele at this QTL was associated not only with a preference for unfamiliar individuals but also with a shift towards familiar ones in response to stress (social support seeking). A second, suggestive QTL also affected social support seeking, but in the opposite direction; the WL allele was associated with increased time spent with unfamiliar individuals. The region contains several possible candidate genes, and gene expression analysis of a number of them showed differential expression between RJF and WL of AVPR2 (receptor for vasotocin), and possibly AVPR1a (another vasotocin receptor) and NRCAM (involved in neural development) in the lower frontal lobes of the brains of RJF and WL animals. These three genes continue to be interesting candidates for the observed behavioural effects .     

Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains

BackgroundCirculating cell-free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the maternal and fetal DNA. Testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA; however, this depends on knowledge of the methylomes of circulating cell-free DNA and its cellular contributors.ResultsWe perform whole genome bisulfite sequencing on a set of unmatched samples including circulating cell-free DNA from non-pregnant and pregnant female donors and genomic DNA from maternal buffy coat and placenta samples. We find CpG cytosines within longer fragments are more likely to be methylated. Comparison of the methylomes of placenta and non-pregnant circulating cell-free DNA reveal many of the 51,259 identified differentially methylated regions are located in domains exhibiting consistent placenta hypomethylation across millions of consecutive bases. We find these placenta hypomethylated domains are consistently located within regions exhibiting low CpG and gene density. Differentially methylated regions identified when comparing placenta to non-pregnant circulating cell-free DNA are recapitulated in pregnant circulating cell-free DNA, confirming the ability to detect differential methylation in circulating cell-free DNA mixtures.ConclusionsWe generate methylome maps for four sample types at single-base resolution, identify a link between DNA methylation and fragment length in circulating cell-free DNA, identify differentially methylated regions between sample groups, and uncover the presence of megabase-size placenta hypomethylated domains.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0645-x) contains supplementary material, which is available to authorized users.     

Environmental,geographical and time-related impacts on avian malaria infections in native and introduced populations of house sparrows (Passer domesticus), a globally invasive species

Aim

The increasing spread of vector-borne diseases has resulted in severe health concerns for humans, domestic animals and wildlife, with changes in land use and the introduction of invasive species being among the main possible causes for this increase. We explored several ecological drivers potentially affecting the local prevalence and richness of avian malaria parasite lineages in native and introduced house sparrows (Passer domesticus) populations.

Location

Global.

Time period

2002–2019.

Major taxa studied

Avian Plasmodium parasites in house sparrows.

Methods

We analysed data from 2,220 samples from 69 localities across all continents, except Antarctica. The influence of environment (urbanization index and human density), geography (altitude, latitude, hemisphere) and time (bird breeding season and years since introduction) were analysed using generalized additive mixed models (GAMMs) and random forests.

Results

Overall, 670 sparrows (30.2%) were infected with 22 Plasmodium lineages. In native populations, parasite prevalence was positively related to urbanization index, with the highest prevalence values in areas with intermediate urbanization levels. Likewise, in introduced populations, prevalence was positively associated with urbanization index; however, higher infection occurred in areas with either extreme high or low levels of urbanization. In introduced populations, the number of parasite lineages increased with altitude and with the years elapsed since the establishment of sparrows in a new locality. Here, after a decline in the number of parasite lineages in the first 30 years, an increase from 40 years onwards was detected.

Main conclusions

Urbanization was related to parasite prevalence in both native and introduced bird populations. In invaded areas, altitude and time since bird introduction were related to the number of Plasmodium lineages found to be infecting sparrows.     

The interstitial cells in the renal medulla of rat,rabbit, and gerbil in different states of diuresis

Summary The inner zone of the renal medulla of rats, gerbils, and rabbits was investigated to determine whether or not there are any characteristic ultrastructural differences between the interstitial cells of these species. The effects on the interstitial cells of water deprivation and water loading were also investigated.In all three species, the Type 1 interstitial cells, the lipid containing cells, were abundant and their distribution and topographical relations as well as their general ultrastructure were similar. The previously reported significantly higher frequency in desert rats could not be confirmed. Although the lipid droplets of the interstitial cells were smaller in gerbils and rabbits when compared to rats, their fine structure was similar. Their electron dense outer zone was sometimes associated with a granular material and/or a lamellar material with a periodicity of about 40 Å resembling phospholipid myelin figures.Water-loaded rats showed a considerable increase in the number of lipid droplets when compared to dehydrated or untreated animals. In contrast, the interstitial cells of waterloaded gerbils and rabbits were depleted of lipid droplets.We are indebted to Professor A.B. Maunsbach for valuable discussions and criticism and to Mrss. Hanne Weiling and Birthe Overgaard for competent technical assistance. The gerbils used in this study were a gift from Leo AB, Helsingborg, Sweden. This study was supported by the Danish Medical Research Council (J. nos. 512-1067, 512-1545, 512-3633)     

Characterization of the viral O-glycopeptidome: a novel tool of relevance for vaccine design and serodiagnosis

Viral envelope proteins mediate interactions with host cells, leading to internalization and intracellular propagation. Envelope proteins are glycosylated and are known to serve important functions in masking host immunity to viral glycoproteins. However, the viral infectious cycle in cells may also lead to aberrant glycosylation that may elicit immunity. Our knowledge of immunity to aberrant viral glycans and glycoproteins is limited, potentially due to technical limitations in identifying immunogenic glycans and glycopeptide epitopes. This work describes three different complementary methods for high-throughput screening and identification of potential immunodominant O-glycopeptide epitopes on viral envelope glycoproteins: (i) on-chip enzymatic glycosylation of scan peptides, (ii) chemical glycopeptide microarray synthesis, and (iii) a one-bead-one-compound random glycopeptide library. We used herpes simplex virus type 2 (HSV-2) as a model system and identified a simple O-glycopeptide pan-epitope, (501)PPA(GalNAc)TAPG(507), on the mature gG-2 glycoprotein that was broadly recognized by IgG antibodies in HSV-2-infected individuals but not in HSV-1-infected or noninfected individuals. Serum reactivity to the extended sialyl-T glycoform was tolerated, suggesting that self glycans can participate in immune responses. The methods presented provide new insight into viral immunity and new targets for immunodiagnostic and therapeutic measures.