Seasonal and annual variability in the phytoplankton community of the Raunefjord,west coast of Norway from 2001–2006

Changes in phytoplankton community composition potentially affect the entire marine food web. Because of seasonal cycles and inter-annual variations in species composition, long-term monitoring, covering many sequential years, is required to establish a baseline study and to reveal long-term trends. The current study describes the phytoplankton biomass variations and species composition in relation to hydrographic and meteorological conditions in the Raunefjord, western Norway, over a 6-year period from 2001 to 2006. The extent of inflow or upwelling in the fjord varied from year to year and resulted in pronounced differences in water column stability. The annual phytoplankton community succession showed some repeated seasonal patterns, but also high variability between years. Two to four diatom blooms were observed per year, and the spring blooms occurring before water column stratification in March were dominated by Skeletonema marinoi and Chaetoceros socialis, and other Chaetoceros and Thalassiosira spp. Blooms of the haptophytes Phaeocystis pouchetii and Emiliania huxleyi were irregular and in some years totally absent. Although E. huxleyi was present all year round it appeared in bloom concentrations only in 2003, when the summer was warm and the water column characterized by high surface temperatures and pronounced stratification. The annual average abundance of both diatoms and flagellates increased during the six years. Despite the high variation from year to year, our investigation provides valuable knowledge about annual phytoplankton community patterns in the region, and can be used as a reference to detect possible future changes.     

A practical guide to interpreting and generating bottom-up proteomics data visualizations

Mass-spectrometry based bottom-up proteomics is the main method to analyze proteomes comprehensively and the rapid evolution of instrumentation and data analysis has made the technology widely available. Data visualization is an integral part of the analysis process and it is crucial for the communication of results. This is a major challenge due to the immense complexity of MS data. In this review, we provide an overview of commonly used visualizations, starting with raw data of traditional and novel MS technologies, then basic peptide and protein level analyses, and finally visualization of highly complex datasets and networks. We specifically provide guidance on how to critically interpret and discuss the multitude of different proteomics data visualizations. Furthermore, we highlight Python-based libraries and other open science tools that can be applied for independent and transparent generation of customized visualizations. To further encourage programmatic data visualization, we provide the Python code used to generate all data figures in this review on GitHub ( https://github.com/MannLabs/ProteomicsVisualization ).     

Performance and responses to competition in two congeneric annual species: does seed heteromorphism matter?

Variations in seed characteristics observed in heteromorphic species may affect various stages of their life cycles, e.g. seed dormancy, germination characteristics or even adult plant performance. Highly specialised seed morphs – described as colonisers and maintainers – exhibit a trade‐off between colonisation capacity and competitive traits. The performance of distinct seed morph progeny under competitive conditions, and especially in multi‐species arrangements, had previously not been given much attention. In this study, we compared performance and response to competition among distinct seed morph progenies in two congeneric, co‐occurring species: the invasive Bidens frondosa and the non‐invasive Bidens tripartita. We hypothesised that maintainer seed morphs of both species would perform better under increased plant densities and within inter‐morphic mixtures, while coloniser morphs would show stronger responses to increased densities and perform relatively poorly in inter‐morphic mixtures. We conducted a growth trial and a greenhouse experiment, which revealed that seed morph progeny differed significantly in plant height when grown without competition, while under competitive conditions such differences became less apparent. The observed pattern was more strongly pronounced in B. frondosa, which showed a general predominance in stature and biomass over its non‐invasive congener. Although seed morphs performed equally well under competitive conditions, increased plant height and more rapid germination can favour the maintainer seed morph on sites where vegetation is already present.     

Whole Cell Formaldehyde Cross-Linking Simplifies Purification of Mitochondrial Nucleoids and Associated Proteins Involved in Mitochondrial Gene Expression

Mitochondrial DNA/protein complexes (nucleoids) appear as discrete entities inside the mitochondrial network when observed by live-cell imaging and immunofluorescence. This somewhat trivial observation in recent years has spurred research towards isolation of these complexes and the identification of nucleoid-associated proteins. Here we show that whole cell formaldehyde crosslinking combined with affinity purification and tandem mass-spectrometry provides a simple and reproducible method to identify potential nucleoid associated proteins. The method avoids spurious mitochondrial isolation and subsequent multifarious nucleoid enrichment protocols and can be implemented to allow for label-free quantification (LFQ) by mass-spectrometry. Using expression of a Flag-tagged Twinkle helicase and appropriate controls we show that this method identifies many previously identified nucleoid associated proteins. Using LFQ to compare HEK293 cells with and without mtDNA, but both expressing Twinkle-FLAG, identifies many proteins that are reduced or absent in the absence of mtDNA. This set not only includes established mtDNA maintenance proteins but also many proteins involved in mitochondrial RNA metabolism and translation and therefore represents what can be considered an mtDNA gene expression proteome. Our data provides a very valuable resource for both basic mitochondrial researchers as well as clinical geneticists working to identify novel disease genes on the basis of exome sequence data.     

The Impact of Implementing a Test,Treat and Retain HIV Prevention Strategy in Atlanta among Black Men Who Have Sex with Men with a History of Incarceration: A Mathematical Model

Background

Annually, 10 million adults transition through prisons or jails in the United States (US) and the prevalence of HIV among entrants is three times higher than that for the country as a whole. We assessed the potential impact of increasing HIV Testing/Treatment/Retention (HIV-TTR) in the community and within the criminal justice system (CJS) facilities, coupled with sexual risk behavior change, focusing on black men-who-have-sex-with-men, 15–54 years, in Atlanta, USA.

Methods

We modeled the effect of a HIV-TTR strategy on the estimated cumulative number of new (acquired) infections and mortality, and on the HIV prevalence at the end of ten years. We additionally assessed the effect of increasing condom use in all settings.

Results

In the Status Quo scenario, at the end of 10 years, the cumulative number of new infections in the community, jail and prison was, respectively, 9246, 77 and 154 cases; HIV prevalence was 10815, 69 and 152 cases, respectively; and the cumulative number of deaths was 2585, 18 and 34 cases, respectively. By increasing HIV-TTR coverage, the cumulative number of new infections could decrease by 15% in the community, 19% in jail, and 8% in prison; HIV prevalence could decrease by 8%, 9% and 7%, respectively; mortality could decrease by 20%, 39% and 18%, respectively. Based on the model results, we have shown that limited use and access to condoms have contributed to the HIV incidence and prevalence in all settings.

Conclusions

Aggressive implementation of a CJS-focused HIV-TTR strategy has the potential to interrupt HIV transmission and reduce mortality, with benefit to the community at large. To maximize the impact of these interventions, retention in treatment, including during the period after jail and prison release, and increased condom use was vital for decreasing the burden of the HIV epidemic in all settings.     

Clonal Diversity and Fine‐scale Genetic Structure in a High Andean Treeline Population

Clonal propagation becomes more abundant with increasing altitudes as environmental conditions worsen. To date, little attention has been paid to the way in which clonal propagation affects genetic diversity and the fine‐scale spatial genetic structure (FSGS) of clonal alpine trees. An AFLP study was undertaken to quantify the clonal and genetic diversity and FSGS of the vulnerable treeline species Polylepis reticulata in Ecuador. We successfully genotyped 32 and 75 ramets within 4 m × 100 m (coarse scale) and 4 m × 4 m (fine scale) transects of one population, respectively. Higher genotypic diversity was detected at the coarse scale than at the fine scale, while lower genetic diversity was detected for P. reticulata than other Polylepis spp. at both scales. Significantly stronger FSGS was detected at the ramet level than the genet level for P. reticulata within a spatial distance of 3 m. The studied P. reticulata population showed pronounced FSGS (Sp = 0.012 at the genet level, a statistic reflecting declining pairwise kinship with distance) revealed restricted gene dispersal, which implies restricted seed dispersal for this population, assuming pollen flow is as extensive as that described for other wind‐pollinated tree species. Our results revealed that clonal diversity is a function of both sample size and the spatial scale of the sampling area. The findings highlights that clonal propagation has affected FSGS within a spatial distance of 3 m for this species.     

Mating system,outcrossing distance effects and pollen availability in the wind-pollinated treeline species Polylepis australis BITT. (Rosaceae)

Fragmentation may negatively affect plant fitness through pollen limitation and increased levels of inbreeding. Effects of fragmentation may vary with regard to life form and breeding system, and few studies exist for wind-pollinated trees. We examined the effects of hand-selfing, varying outcrossing distances and pollen addition on seed mass and germination rate of Polylepis australis BITT. (Rosaceae), a wind-pollinated treeline species endemic to Argentina. We also investigated pollen germination on the stigma and pollen tube growth to determine compatibility resulting from selfing and outcrossing. Selfing reduced seed germination rates with significant differences between open pollination and outcrosses at 30 km. In addition, we found a tendency for pollen germination and pollen tube growth to decrease following selfing. Between-fragment crosses resulted in a trend of higher reproductive output than within-fragment crosses, whereas values were similar between open pollination and between-fragment crosses. Pollen addition did not increase reproductive success neither in small nor in larger fragments. Our results suggest that highly isolated P. australis forests have a potential for inbreeding depression through selfing and within-fragment crosses. However, the results also indicate that pollen flow between P. australis forest fragments is still effective at the current fragmentation level, counteracting negative effects on seed quality resulting from reproductive isolation.     

Adaptation of neuronal cells to chronic oxidative stress is associated with altered cholesterol and sphingolipid homeostasis and lysosomal function

Chronic oxidative stress has been causally linked to several neurodegenerative disorders. As sensitivity for oxidative stress greatly differs between brain regions and neuronal cell types, specific cellular mechanisms of adaptation to chronic oxidative stress should exist. Our objective was to identify molecular mechanisms of adaptation of neuronal cells after applying chronic sublethal oxidative stress. We demonstrate that cells resistant to oxidative stress exhibit altered cholesterol and sphingomyelin metabolisms. Stress-resistant cells showed reduced levels of molecules involved in cholesterol trafficking and intracellular accumulation of cholesterol, cholesterol precursors, and metabolites. Moreover, stress-resistant cells exhibited reduced SMase activity. The altered lipid metabolism was associated with enhanced autophagy. Treatment of stress-resistant cells with neutral SMase reversed the stress-resistant phenotype, whereas it could be mimicked by treatment of neuronal cells with a specific inhibitor of neutral SMase. Analysis of hippocampal and cerebellar tissue of mouse brains revealed that the obtained cell culture data reflect the in vivo situation. Stress-resistant cells in vitro showed similar features as the less vulnerable cerebellum in mice, whereas stress-sensitive cells resembled the highly sensitive hippocampal area. These findings suggest an important role of the cell type-specific lipid profile for differential vulnerabilities of different brain areas toward chronic oxidative stress.     

Do we need livestock grazing to promote <Emphasis Type="Italic">Polylepis australis</Emphasis> tree recruitment in the Central Argentinean Mountains?

South American Polylepis mountain forests are endangered due to centuries of logging, fire clearance, and intensive livestock grazing. Polylepis australis (Rosaceae) dominates the tree canopy in the Central Argentinean Mountains, where livestock have been excluded or reduced to very low densities over wide areas. Lowered plant and bird diversity in these abandoned grazing areas suggest that some livestock grazing may be beneficial for conservation purposes. Our study aimed to determine whether this may also be true for forest regeneration. In 300 plots of 1 m² distributed in sub-regions of high to moderate grazing pressure as well as grazing exclusion, we recorded the presence of P. australis seedlings and grazing indicators. Topographical parameters as well as vegetation and soil characteristics were also assessed. Seedling frequencies were highest in the region with moderate grazing, intermediate with grazing exclusion, and the lowest with high grazing pressures. Logistic regression models revealed that seedling occurrence was highest close to seeder trees, with intermediate litter coverage and at intermediate altitudes above sea level. Since grazing ultimately affects seeder tree occurrence through browsing and reduces litter cover and predominates in higher areas, we conclude that grazing is an important driving factor for P. australis regeneration. We confirm previous studies determining high grazing pressure to be detrimental for P. australis regeneration, but also provide data suggesting that its complete exclusion may not be recommendable either. Management should aim to alternate between a moderate grazing intensity to promote seedling recruitment, with subsequent exclusion to accelerate the growth of the established seedlings.     

Genetic differentiation between alpine and lowland populations of a butterfly is related to PGI enzyme genotype

Understanding the ecological process of population differentiation and identifying the molecular changes that contribute to adaptation is a central aspect of evolutionary biology. In this study we analyzed the geographic variation in allozyme allele frequencies (based on 15 enzyme systems representing 18 loci) across 18 populations of the butterfly Lycaena tityrus from different altitudes. Population genetic analyses showed that within population genetic diversity (e.g. mean number of alleles per loci: 1.8; expected heterozygosity: 12%) was within the typical value range for the Lepidoptera. The populations of L. tityrus investigated showed a remarkable genetic differentiation (F_ST: 0.065), being clearly divided into an alpine (high-altitude) and a non-alpine (low-altitude) cluster. This differentiation was almost entirely caused by variation at a single enzyme locus, PGI. Although the involvement of historical events cannot be ruled out, several lines of evidence suggest that the specific pattern of allozyme (and in this case particularly PGI) variation found is caused by thermal selection. For example, genetic variation was highly locus-specific rather than relatively uniform, as should be expected for effects of natural selection. Further, the PGI 2–2 genotype dominating in alpine (in contrast to low-altitude) populations is known to exhibit increased cold stress resistance and relatively long development times typical of alpine populations. Thus, PGI (or possibly a closely linked gene) is an obvious target for thermal selection in L. tityrus . This study exemplifies how allozyme analyses can be used to detect candidate loci likely to be under selection.