Understanding the trophic role of the Antarctic ctenophore,Callianira antarctica,using lipid biomarkers

To better understand the trophic role of ctenophores in Antarctica during austral fall and winter, a major species of cydippid ctenophore, Callianira antarctica, was collected during April/May (fall) and August/September (winter) 2002 in the vicinity of Marguerite Bay. Lipid content, lipid classes, fatty acids, fatty alcohols and sterols were analyzed in animals, together with lipid biomarkers in krill and copepod species representing potential ctenophore prey. Lipid content in ctenophores collected in winter was slightly higher than from animals in fall (4.8 and 3.5% of dry weight, respectively). Polar lipids were the dominant lipid class in ctenophores, accounting for over half of the lipid content, with significant amounts of free fatty alcohols (more than 10% of total lipid content) detected. Lipid-class composition, however, differed significantly between seasons, with significant amounts of neutral lipid (wax esters and triacylglycerols) only detected in animals from fall. Although the dominant lipid classes in ctenophores varied between fall and winter, individual lipids (i.e., fatty acids, alcohols and sterols) showed only minor changes between seasons. Specifically, long-chain polyunsaturated fatty acids [20:5(n-3) and 22:6(n-3)] found in high abundance in larval krill were also elevated in ctenophores collected in winter. Very high amounts of monounsaturated fatty alcohols, particularly 20:1(n-9) and 22:1(n-11), known to be important components of wax esters in calanoid copepods, were also observed. Multivariate analysis using the suite of lipids found indicated that copepods are an important diet item for ctenophores in the study area. Results further suggest that C. antarctica feed actively year-round, with larval krill providing a food resource during austral winter.     

Microbial processes in a high-latitude fjord (Kongsfjorden, Svalbard): II. Ciliates and dinoflagellates

The composition and ecological role of ciliates and dinoflagellates were investigated at one station in Kongsfjorden, Svalbard, during six consecutive field campaigns between March and December 2006. Total ciliate and dinoflagellate abundance mirrored the seasonal progression of phytoplankton, peaking with 5.8 × 10⁴ cells l⁻¹ in April at an average chlorophyll a concentration of 10 μg l⁻¹. Dinoflagellates were more abundant than ciliates, dominated by small athecates. Among ciliates, aloricate oligotrichs dominated the assemblage. A large fraction (>60%) of ciliates and dinoflagellates contained chloroplasts in spring and summer. The biomass of the purely heterotrophic fraction of the ciliate and dinoflagellate community (protozooplankton) was with 14 μg C l⁻¹ highest in conjunction with the phytoplankton spring bloom in April. Growth experiments revealed similar specific growth rates for heterotrophic ciliates and dinoflagellates (<0–0.8 d⁻¹). Food availability may have controlled the protozooplankton assemblage in winter, while copepods may have exerted a strong control during the post-bloom period. Calculations of the potential grazing rates of the protozooplankton indicated its ability to control or heavily impact the phytoplankton stocks at most times. The results show that ciliates and dinoflagellates were an important component of the pelagic food web in Kongsfjorden and need to be taken into account when discussing the fate of phytoplankton and biogeochemical cycling in Arctic marine ecosystems.     

Production and fate of faecal pellets during summer in an East Antarctic fjord

The abundance of small faecal pellets is high in marine waters. Little is known, however, about the processes governing their production and fate in the water column. We investigated faecal pellet production and flux in relation to the phytoplankton and copepod assemblages present in Ellis Fjord, Antarctica. Results show that the phytoplankton community shifted from a dominance of diatoms to that of a cryptomonad species during late January. This coincided with an increase in abundance of the small copepods Paralabidocera antarctica and Oithona similis, although Oncaea curvata was still the dominant species. The mean faecal pellet flux was 9943 pellets m^–2 d^–1. Only 37% of the faecal pellet flux at 5 m sedimented to 10 m depth, 15% to 20 m, and 12% to 40 m depth. Our results suggest that recycling of faecal pellets by copepods contributes to this decreased flux with increasing depth, which concurs with results from large scale oceanic studies. Additionally, we propose that the summer ice melt changes the physical characteristics of the water column and the phytoplankton species abundance and distribution; both of which potentially impact on the distribution and abundance of copepods, thereby regulating faecal pellet flux.     

Structure of bryozoan communities in an Antarctic glacial fjord (Admiralty Bay,South Shetlands)

Bryozoans are among the most important groups of the Southern Ocean benthic macrofauna, both in terms of species richness and abundance. However, there is a considerable lack of ecological research focused on their distribution patterns and species richness on smaller scale, especially in the soft bottom habitats of Antarctic glacial fjords. The aim of this study was to describe those patterns in the Admiralty Bay. Forty-nine Van Veen grab samples were collected at the depth range from 15 to 265 m, in the summer season of 1979/1980, at three sites distributed along the main axis of the fjord. Among 53 identified species of bryozoans, 32 were recorded in the Admiralty Bay for the first time. The most common and abundant species were Himantozoum antarcticum, Inversiula nutrix and Nematoflustra flagellata. Genera such as Arachnopusia, Cellarinella and Osthimosia were the most speciose taxa. It was demonstrated that depth was important for the distribution of the bryozoans. More than half of the recorded species were found only below 70 m. An influence of glacial disturbance was reflected in the dominance structure of colony growth-forms. The inner region of the fjord was dominated almost entirely by encrusting species, while the diversity of bryozoan growth-forms in less disturbed areas was much higher. In those sites the highest percentage of branched, tuft like species represented by buguliform and flustriform zoaria was observed.     

Fire, climate change and biodiversity in Amazonia: a Late-Holocene perspective

Fire is an important and arguably unnatural component of many wet Amazonian and Andean forest systems. Soil charcoal has been used to infer widespread human use of landscapes prior to European Conquest. An analysis of Amazonian soil carbon records reveals that the records have distinct spatial and temporal patterns, suggesting that either fires were only set in moderately seasonal areas of Amazonia or that strongly seasonal and aseasonal areas are undersampled. Synthesizing data from 300 charcoal records, an age–frequency diagram reveals peaks of fire apparently coinciding with some periods of very strong El Niño activity. However, the El Niño record does not always provide an accurate prediction of fire timing, and a better match is found in the record of insolation minima. After the time of European contact, fires became much scarcer within Amazonia. In both the Amazonia and the Andes, modern fire pattern is strongly allied to human activity. On the flank of the Andes, forests that have never burned are being eroded by fire spreading downslope from grasslands. Species of these same forests are being forced to migrate upslope due to warming and will encounter a firm artificial fire boundary of human activity.     

Reconstruction of a subalpine grass-dominated ecosystem,Lake Rutundu,Mount Kenya: a novel multi-proxy approach

Palaeoecological reconstructions based on a single proxy are limited, but by combining pollen, biogeochemistry and grass cuticle analysis, ecosystem structure and function can be better understood. Lake Rutundu is a small, subalpine lake on the northeast flank of Mt Kenya. During the last glacial, pollen evidence suggests a shrub grassland dominated by Afroalpine taxa and Poaceae, representing a dry, cold, open environment. The δ¹³C values of terrestrial biomarkers imply a high proportion of C₄ plants. Grass cuticle analysis allows resolution of the different C₄ subtypes and shows that the vegetation was dominated by tall C₄ panicoid grasses, prone to frequent fires. During the Holocene, Poaceae pollen declined while subalpine shrubs increased. The δ¹³C values of terrestrial biomarkers imply a C₃-dominated vegetation. Together with an expansion of rainforest at lower altitudes, this suggests wetter conditions more favourable to C₃ plants. Increased percentages of C₃ pooid grass cuticles confirm a reduction in moisture stress.     

Origin of mound-field landscapes: a multi-proxy approach combining contemporary vegetation, carbon stable isotopes and phytoliths

Background and aims

Seasonally flooded South American savannas harbor different kinds of mound-field landscapes of largely unknown origin. A recent study used soil carbon-isotope depth profiles and other proxies to infer vegetation history in murundu landscapes in Brazil. Results suggested that differential erosion, not building-up processes (e.g., termite mounds), produced mounds. We tested this approach to inferring mound origin in a mound-field landscape in French Guiana.

Methods

We examined carbon-isotope depth profiles of soil organic matter, phytolith profiles and contemporary vegetation composition in mounds and inter-mounds.

Results

Relative abundance of C3 and C4 plants across habitats was very different from that in murundu landscapes; C3 plants were better represented in inter-mounds than on mounds. Habitat differences in C3/C4 distribution were subtler than in murundu landscapes, limiting inference of vegetation history based on carbon isotopes. Still, carbon-isotope and phytolith depth profiles gave similar pictures of vegetation history, both favoring a building-up hypothesis, corroborating other evidence that these mounds are vestiges of ancient agricultural raised fields.

Conclusions

Carbon-isotope depth profiles are unlikely to be adequate for deciphering origin of mound-field landscapes from vegetation history in seasonally flooded savannas. Including data on current vegetation and phytoliths makes inferences more robust.     

Composition and succession of dinoflagellates and chrysophytes in the upper fast ice of Davis Station, East Antarctica

Little is known of the wider Antarctic distribution of the upper fast ice community now comprehensively described from McMurdo Sound. We determined the fast ice protist community at Davis Station, East Antarctica and compared it with that of McMurdo Sound. As at McMurdo Sound, Davis fast ice is characterised by extreme and transitory salinities (96–2.5 psu) and temperatures (−4.5 to −0.1°C) during the spring/summer transition. Both communities are dominated by Polarella glacialis (an autotrophic dinoflagellate), chrysophytes and their life cycle stages. Furthermore, the physical parameters of brine temperature and salinity at which these successions occurred approximated those of McMurdo Sound. The high degree of similarity between the communities from the geographically disparate locations indicates that this community type has a circum-Antarctic distribution. Confirming the areal extent and seasonality of this community type will assist in future predictions of sea ice productivity.     

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach

Background

The master transactivator CIITA is essential to the regulation of Major Histocompatibility Complex (MHC) class II genes and an effective immune response. CIITA is known to modulate a small number of non-MHC genes involved in antigen presentation such as CD74 and B2M but its broader genome-wide function and relationship with underlying genetic diversity has not been resolved.

Results

We report the first genome-wide ChIP-seq map for CIITA and complement this by mapping inter-individual variation in CIITA expression as a quantitative trait. We analyse CIITA recruitment for pathophysiologically relevant primary human B cells and monocytes, resting and treated with interferon-gamma, in the context of the epigenomic regulatory landscape and DNA-binding proteins associated with the CIITA enhanceosome including RFX, CREB1/ATF1 and NFY. We confirm recruitment to proximal promoter sequences in MHC class II genes and more distally involving the canonical CIITA enhanceosome. Overall, we map 843 CIITA binding intervals involving 442 genes and find 95% of intervals are located outside the MHC and 60% not associated with RFX5 binding. Binding intervals are enriched for genes involved in immune function and infectious disease with novel loci including major histone gene clusters. We resolve differentially expressed genes associated in trans with a CIITA intronic sequence variant, integrate with CIITA recruitment and show how this is mediated by allele-specific recruitment of NF-kB.

Conclusions

Our results indicate a broader role for CIITA beyond the MHC involving immune-related genes. We provide new insights into allele-specific regulation of CIITA informative for understanding gene function and disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0494-z) contains supplementary material, which is available to authorized users.     

A functional genomics approach using metabolomics and in silico pathway analysis

In the field of functional genomics increasing effort is being undertaken to analyze the function of orphan genes using metabolome data. Improved analytical equipment allows screening simultaneously for a high number of metabolites. Such metabolite profiles are analyzed using multivariate data analysis techniques and changes in the genotype will in many cases lead to different metabolite profiles. Here, a theoretical framework that may be applied to identify the function of orphan genes is presented. The approach is based on a combination of metabolome analysis combined with in silico pathway analysis. Pathway analysis may be carried out using convex analysis and a change in the active pathway structure of deletion mutants expressed in a different metabolite profile may disclose the function or the functional class of an orphan gene. The concept is illustrated using a simplified model for growth of Saccharomyces cerevisiae.     

Missing genes in metabolic pathways: a comparative genomics approach

The new techniques of genome context analysis--chromosomal gene clustering, protein fusions, occurrence profiles and shared regulatory sites--infer functional coupling between genes. In combination with metabolic reconstructions, these techniques can dramatically accelerate the pace of gene discovery.     

Effects of gastropod grazers on recruitment and succession of an estuarine assemblage: a multivariate and univariate approach

Grazers have been shown to affect assemblages of species in many habitats. Here we studied the effects of the gastropod grazers, Austrocochlea porcata and Bembicium auratum, on intertidal estuarine assemblages in a sheltered bay in New South Wales, Australia. We examined the effects of gastropods on individual species and on the assemblage as a whole. The multivariate response was compared with data on succession in these assemblages to estimate potential effects of grazers on succession. The experiment was repeated several times to determine the generality of grazer effects in the light of possible variation in the timing or intensity of recruitment. There were different responses of individual species to the presence of grazers. Grazers reduced the abundance of ephemeral algal species, bryozoans, copepods, insect larvae and Balanus spp. barnacles. They had a positive effect on oysters and spirorbids and no effect on the barnacles Elminius covertus and Hexaminius spp. These effects were consistent through time. Multivariate analyses confirmed that grazers caused significant changes to whole assemblages and that these effects were far-reaching and not only caused by changes to algal species. The removal of grazers appeared to neither speed up nor slow down succession, but rather caused a completely different assemblage to develop. Apparent important mechanisms affecting the composition of animal species when grazers were removed included accumulation of sediments and detritus and pre-emption of space by algae. Received: 13 May 1996 / Accepted: 1 September 1996     

Chemical genomics: a systematic approach in biological research and drug discovery

The knowledge of complete sequences of different organisms is dramatically changing the landscape of biological research and pharmaceutical development. We are experiencing a transition from a trial-and-error approach in traditional biological research and natural product drug discovery to a systematic operation in genomics and target-specific drug design and selection. Small, cell-permeable and target-specific chemical ligands are particularly useful in systematic genomic approaches to study biological questions. On the other hand, genomic sequence information, comparative and structural genomics, when combined with the cutting edge technologies in synthetic chemistry and ligand screening/identification, provide a powerful way to produce target-specific and/or function-specific chemical ligands and drugs. Chemical genomics or chemogenomics is a new term that describes the development of target-specific chemical ligands and the use of such chemical ligands to globally study gene and protein functions. We anticipate that chemical genomics plays a critical role in the genomic age of biological research and drug discovery.     

Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics

The crustacean marine isopod species Haploniscus bicuspis (Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using confocal laser scanning microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the GIF Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably instead refer to different male developmental stages.     

Controlled artificial upwelling in a fjord using a submerged fresh water discharge: computer and laboratory simulations

To enhance the conditions for producing shellfish in coastal waters, the possibility of employing artificial upwelling of nutrients is explored. The effectiveness of a submerged discharge of fresh water is studied by means of a numerical buoyant plume model, BJET, and laboratory simulations. An optimisation of the entrainment of deeper, nutrient-rich water to the proper intrusion depth is demonstrated. The studies show that a downward directed jet of fresh water below the euphotic zone can lift significant amounts of nutrients to the primary production near the surface. The outlet must be large enough to lift the deeper water through the pycnocline to the desired depth of primary production. The results are applied to a possible discharge arrangement in the Samnangerfjord, to the east of Bergen, Norway, using field data from 1999. With a discharge of up to 8 m³/s of fresh water at 35 m depth, the entrainment of deeper water into the buoyant plume, up to the 15 m depth, is 12 to 13 times as much. The chosen arrangement could give an expected vertical transport to the euphotic zone of 467 kg d^–1 N, 46 kg d^–1 P and 555 kg d^–1 Si during the summer growth period. This includes periods of coastal downwelling with greatly reduced values of nutrients, but not periods of strong, deep stratification with deeper intrusions. Further optimisation is possible using active controls of the discharge system.