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.     

rDNA analysis of the Red Sea seagrass,Halophila, reveals vicariant evolutionary diversification

The effects of opening the Suez Canal as a connection between the Red Sea and the Mediterranean Sea were reported for a number of marine species. However, the evolutionary origin of the seagrasses in the Red Sea and the linking population genetics of seagrasses between the Arabian Sea, the Gulf of Aden, the Red Sea and the Mediterranean Sea have not yet been investigated in detail. The invasion of Halophila stipulacea Asch. from the Red Sea into the Mediterranean Sea after the opening of the Suez Canal was already recorded. We hypothesize that Halophila ovalis populations in the Red Sea developed through long-term historical processes such as vicariant evolutionary diversification. Seagrass samples were collected along the Egyptian coastline of the Red Sea and analysed by the molecular marker ITS. The sequences were compared with published ITS sequences from seagrasses collected in the whole area of interest. In this study, we reveal the linking population genetics, phylogeography and phylogenetics of two dominant seagrass species, Halophila stipulacea and Halophila ovalis, among species collected in the Red Sea and worldwide. The results indicate that the Red Sea Halophila ovalis populations do not group to Halophila ovalis worldwide, and Halophila major, Halophila ovalis collected worldwide and Halophila ovalis collected at the Red Sea are sister clades. Hence, vicariant evolutionary diversification for Halophila ovalis may occur in the Red Sea.     

Introgressive hybridization of Senecio hercynicus and S. ovatus (Compositae,Senecioneae) along an altitudinal gradient in Harz National Park (Germany)

Introgressive hybridization of Senecio hercynicus and S. ovatus (Compositae, Senecioneae) was studied in a hybrid zone on the southern slopes of Mt Brocken (Harz Mountains, Germany). A total of 415 plants representing 10 stands along an altitudinal gradient were investigated using multivariate statistical analyses of morphological characters and molecular markers (random amplified polymorphic DNA[RAPD]). Both types of traits detected pure S. hercynicus stands on the summit plateau, pure S. ovatus stands at the lowest elevations, and hybrid swarms at intermediate elevations. While morphological and molecular patterns coincided, some individuals in hybrid stands combined morphological patterns typical of S. ovatus with RAPD patterns typical of S. hercynicus, and vice versa. In general, introgression was symmetrical within stands, though one stand combined S. ovatus characters with the glandular hair typical for S. hercynicus, and two stands combined a S. hercynicus typical RAPD genotype with morphological characters shifted towards S. ovatus. Because pure stands of S. hercynicus occurred only on the summit plateau of Mt Brocken, and markers typical for S. ovatus were detectable in stands up to 1040 m a.s.l., future fusion or assimilation of the rare form, S. hercynicus, by the more widespread S. ovatus appears possible at Mt Brocken.     

Negative Effects of Conspecific Floral Density on Fruit Set of Two Neotropical Understory Plants

Plant reproductive success is usually positively related to conspecific floral density, but neutral or negative effects of floral density on reproduction have also been reported. Differences in the relationship between reproduction and floral density largely originate from a trade‐off between increasing attractiveness versus increasing competition for pollinators at high floral densities. Although floral densities strongly vary in the understory of tropical forests, for instance, due to variation in light availability, little is known about the density dependence of reproduction in tropical understory plants. We used path analyses to disentangle direct and indirect effects of canopy openness and floral density on fruit set and analyzed the relationship between pollen load and floral density for two Neotropical understory plants, Heliconia metallica and Besleria melancholica. In both species, fruit set was not directly related to canopy openness, but decreased with increasing floral density. In H. metallica, canopy openness had an indirect negative effect on reproduction mediated by its effects on floral density. Effects of floral density on pollen loads were species‐specific. In B. melancholica, pollen loads linearly decreased with increasing floral density, indicating competition for pollinators at high densities. In H. metallica, pollen loads were reduced at both low and high densities, indicating an interplay of facilitative and competitive effects of floral density on pollen deposition. In contrast to other studies, we found negative density dependence of reproduction in both understory species. Negative effects of floral density on reproduction appear to be related to pollinator‐mediated effects on reproduction rather than to variation in abiotic conditions.     

Old‐male paternity advantage is a function of accumulating sperm and last‐male precedence in a butterfly

Old‐male mating advantage has been convincingly demonstrated in Bicyclus anynana butterflies. This intriguing pattern may be explained by two alternative hypotheses: (i) an increased aggressiveness and persistence of older males during courtship, being caused by the older males' low residual reproductive value; and (ii) an active preference of females towards older males what reflects a good genes hypothesis. Against this background, we here investigate postcopulatory sexual selection by double‐mating Bicyclus anynana females to older and younger males, thus allowing for sperm competition and cryptic mate choice, and by genotyping the resulting offspring. Virgin females were mated with a younger virgin (2–3 days old) and afterwards an older virgin male (12–13 days old) or vice versa. Older males had a higher paternity success than younger ones, but only when being the second (=last) mating partner, while paternity success was equal among older and younger males when older males were the first mating partner. Older males produced larger spermatophores with much higher numbers of fertile sperm than younger males. Thus, we found no evidence for cryptic female mate choice. Rather, the findings reported here seem to result from a combination of last‐male precedence and the number of sperm transferred upon mating, both increasing paternity success.     

The reproductive biology of two understory plants in the Atlantic rain forest, Brazil

Outcrossing and sexual reproduction of most flowering plants depends on pollinators. Plant traits likely to be involved in pollinator attraction include flower color, shape, and size. Furthermore, plant or flower density and the temporal flowering pattern may have an effect on reproduction. In this study, we examine the pollination ecology, breeding system, female reproductive output, and germination of two tropical understory species, Stenostephanus lobeliiformis (Acanthaceae) and Besleria melancholica (Gesneriaceae), which differ in these traits. Pollinator observations revealed that the dense flowering S. lobeliiformis with pinkish flowers received a higher diversity of pollinators, but visitor frequency measured as visits per flower per hour was much less (0.1 h^?1) than that to B. melancholica, which has a smaller floral display of dull-colored flowers (1.5 h^?1). Pollination experiments revealed that S. lobeliiformis but not B. melancholica is pollen-limited. In addition, both species are partially self-incompatible and depend on pollinators for outcrossing. Natural fruit set of open-pollinated unmanipulated flowers (control treatment) in both species is 22–26 %. Germination studies indicated inbreeding depression in S. lobeliiformis. We conclude that the pollination ecology of these species is influenced by a broad set of traits and that very different combinations of these traits can be successful in terms of reproduction.     

N2-fixation,ammonium release and N-transfer to the microbial and classical food web within a plankton community

We investigated the role of N₂-fixation by the colony-forming cyanobacterium, Aphanizomenon spp., for the plankton community and N-budget of the N-limited Baltic Sea during summer by using stable isotope tracers combined with novel secondary ion mass spectrometry, conventional mass spectrometry and nutrient analysis. When incubated with ¹⁵N₂, Aphanizomenon spp. showed a strong ¹⁵N-enrichment implying substantial ¹⁵N₂-fixation. Intriguingly, Aphanizomenon did not assimilate tracers of ¹⁵NH₄⁺ from the surrounding water. These findings are in line with model calculations that confirmed a negligible N-source by diffusion-limited NH₄⁺ fluxes to Aphanizomenon colonies at low bulk concentrations (<250 nm) as compared with N₂-fixation within colonies. No N₂-fixation was detected in autotrophic microorganisms <5 μm, which relied on NH₄⁺ uptake from the surrounding water. Aphanizomenon released about 50% of its newly fixed N₂ as NH₄⁺. However, NH₄⁺ did not accumulate in the water but was transferred to heterotrophic and autotrophic microorganisms as well as to diatoms (Chaetoceros sp.) and copepods with a turnover time of ~5 h. We provide direct quantitative evidence that colony-forming Aphanizomenon releases about half of its recently fixed N₂ as NH₄⁺, which is transferred to the prokaryotic and eukaryotic plankton forming the basis of the food web in the plankton community. Transfer of newly fixed nitrogen to diatoms and copepods furthermore implies a fast export to shallow sediments via fast-sinking fecal pellets and aggregates. Hence, N₂-fixing colony-forming cyanobacteria can have profound impact on ecosystem productivity and biogeochemical processes at shorter time scales (hours to days) than previously thought.     

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 ).     

A human novel gene DERPC on 16q22.1 inhibits prostate tumor cell growth and its expression is decreased in prostate and renal tumors

BACKGROUND: Deletion of chromosome 16q is frequently associated with diverse tumors. Numerous studies strongly suggest the presence of one or more tumor suppressor genes on chromosome 16q22 to 16qter including the widely studied cadherin gene family. However, the specific tumor suppressor genes residing in this region need better definition and characterization. MATERIAL AND METHODS: Standard molecular biology approaches have been used to clone and characterize the DERPC cDNA and its protein product on chromosome 16q22.1. Northern blotting was used to define the expression pattern in a multiple human tissue blots. DERPC expression was examined in multi-tumor array (Clontech, CA, USA) dot blot as well as in laser capture microdissection (LCM) derived prostate cancer (CaP) specimens by quantitative RT-PCR. Western blot analysis and a fluorescent microscopy were used to characterize the molecular size and the cellular location of green fluorescent protein (GFP)-tagged DERPC fusion proteins. A colony formation assay was conducted to determine the effects of DERPC expression on tumor cell growth. RESULTS: A novel gene DERPC (Decreased Expression in Renal and Prostate Cancer) was identified and characterized. DERPC encoded a strong basic, proline- and glycine-rich nuclear protein. DERPC was ubiquitously expressed, with abundant expression in kidney, skeletal muscle, testis, liver, ovary, and heart and moderate expression in prostate. DERPC expression was reduced in renal (67%) and prostate tumors (33%). Expression of DERPC has inhibitory potential on CaP cell growth. Further, overexpression of DERPC in LNCaP cells caused alterations of nuclear morphology. CONCLUSION: This study suggests that decreased expression of DERPC may be implicated in tumorigenesis of renal and CaPs.     

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.