Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

BACKGROUND: Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA. RESULTS: A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology. CONCLUSIONS: This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA

Increasing picocyanobacteria success in shelf waters contributes to long-term food web degradation

Continental margins are disproportionally important for global primary production, fisheries and CO2 uptake. However, across the Northeast Atlantic shelves, there has been an ongoing summertime decline of key biota—large diatoms, dinoflagellates and copepods—that traditionally fuel higher tropic levels such as fish, sea birds and marine mammals. Here, we combine multiple time series with in situ process studies to link these declines to summer nutrient stress and increasing proportions of picophytoplankton that can comprise up to 90% of the combined pico- and nanophytoplankton biomass in coastal areas. Among the pico-fraction, it is the cyanobacterium Synechococcus that flourishes when iron and nitrogen resupply to surface waters are diminished. Our field data show how traits beyond small size give Synechococcus a competitive edge over pico- and nanoeukaryotes. Key is their ability to grow at low irradiances near the nutricline, which is aided by their superior light-harvesting system and high affinity to iron. However, minute size and lack of essential biomolecules (e.g. omega-3 polyunsaturated fatty acids and sterols) render Synechococcus poor primary producers to sustain shelf sea food webs efficiently. The combination of earlier spring blooms and lower summer food quantity and quality creates an increasing period of suboptimal feeding conditions for zooplankton at a time of year when their metabolic demand is highest. We suggest that this nutrition-related mismatch has contributed to the widespread, ~50% decline in summer copepod abundance we observe over the last 60 years. With Synechococcus clades being prominent from the tropics to the Arctic and their abundances increasing worldwide, our study informs projections of future food web dynamics in coastal and shelf areas where droughts and stratification lead to increasing nutrient starvation of surface waters

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable

Physical and biogeochemical controls on seasonal iron, manganese, and cobalt distributions in Northeast Atlantic shelf seas

Dissolved (<0.2 μm) trace metals (dTMs) including iron (Fe), manganese (Mn), and cobalt (Co) are micronutrients that (co-) limit phytoplankton growth in many ocean regions. Here, we present the spatial and seasonal distributions of dFe, dMn, and dCo on the Northeast Atlantic continental margin (Celtic Sea), along a transect across the shelf and two off-shelf transects along a canyon and a spur. Waters on the continental shelf showed much higher dTM concentrations (dFe 0.07–6.50 nmol L−1, average 1.41 ± 0.96 nmol L−1, n = 138; dMn 0.868–14.8 nmol L−1, 2.75 ± 2.37 nmol L−1, n = 148; dCo 54.8–217 pmol L−1, 109 ± 32 pmol L−1, n = 144) than on the slope (dFe 0.03–1.90 nmol L−1, 0.65 ± 0.43 nmol L−1, n = 454; dMn 0.223–1.14 nmol L−1, 0.58 ± 0.20 nmol L−1, n = 458; dCo 27.3–122 pmol L−1, 71.7 ± 11.7 pmol L−1, n = 441), attributed to strong dTM contributions from a low-salinity endmember, i.e., riverine discharge. Benthic sedimentary input via reductive dissolution (especially for dFe and dMn), delineated by short-lived radium (Ra) isotopic activities (223Raxs and 224Raxs), was only prominent at a station (Site A) characterized by fine sediments. On the continental slope, dMn levels at depth were mainly determined by the formation of insoluble Mn oxides and the intrusion of Mediterranean Outflow Waters. In contrast, dFe and dCo concentrations at depth were balanced by the regeneration from remineralization of sinking organic particles and scavenging removal. In addition, bottom and intermediate nepheloid layers along the slope illustrated both elevated dTM concentrations and Ra isotopic activities. The presence of nepheloid layers is especially significant along the canyon transect relative to the spur transect, demonstrating the importance of slope topography on the off-shelf transport of dTMs into the Northeast Atlantic Ocean. As a seasonal stratified shelf sea, dTMs and nutrients showed synchronized seasonal variations on the shelf, indicating the influence of biological processes in addition to source effects. Surface dFe and dCo were depleted in summer due to enhanced biological uptake, while sub-surface dFe and dCo were elevated in summer and autumn ascribed to the remineralization of sinking organic particles. In contrast, surface dMn levels were predominantly controlled by the seasonal variations in photoreduction, while sub-surface dMn concentrations were relatively constant throughout the year. The combined effects of fluvial and benthic sources, topographical controls, and biological processes shape the seasonal variations of dTM distributions. Such seasonal variations in dTMs and biological activities can affect the biological carbon pump on the Northeast Atlantic continental margin, and may further influence the carbon cycle in the Atlantic Ocean via the dynamic dTM exchange between continental margins and the open ocean

Equilibrium calculations of iron speciation and apparent iron solubility in the Celtic Sea at ambient seawater pH using the NICA-Donnan model

We used a combined ion pairing - organic matter speciation model (NICA-Donnan) to predict the organic complexation of iron (Fe) at ambient pH and temperature in the Celtic Sea. We optimized our model by direct comparison with Fe speciation determined by Adsorptive Cathodic Stripping Voltammetry using the added Fe-binding ligand 1-nitroso-2-naphthol (HNN) in the presence and absence of natural organic matter. We compared determined Fe speciation with simulated titrations obtained via application of the NICA-Donnan model with four different NICA parameter sets representing a range of binding site strengths and heterogeneities. We tested the assumption that binding sites scale to dissolved organic carbon (DOC) concentrations in marine waters. We found that a constant low DOC concentration resulted in an improved fit of our titration data to the simulated titrations, suggesting that inputs of autochthonous marine DOM may not increase the heterogeneity or concentrations of Fe binding sites. Using the optimal parameter set, we calculated pFe(III)´ (−log(∑Fe(OH)i3−i)) and apparent Fe(III) solubility (SFe(III)app) at ambient pH and temperature in the water column of the Celtic Sea. SFe(III)app was defined as the sum of aqueous inorganic Fe(III) species and Fe(III) bound to DOM formed at a free Fe (Fe3+) concentration equal to the limiting solubility of Fe hydroxide (Fe(OH)3(s)). SFe(III)app was within range of the determined dissolved Fe concentrations observed after winter mixing on the shelf and in waters >1500 m depth at our most offshore stations. Our study supports the hypothesis that the ocean dissolved Fe inventory is controlled by the interplay between Fe solubility and Fe binding by organic matter, although the overall number of metal binding sites in the marine environment may not be directly scalable to DOC concentrations

Ocean circulation and biological processes drive seasonal variations of dissolved Al, Cd, Ni, Cu, and Zn on the Northeast Atlantic continental margin

Nutrients and nutrient-like dissolved trace metals (dTMs) are essential for the functioning of marine organisms and therefore form an important part of ocean biogeochemical cycles. Here, we report on the seasonal distributions of dissolved zinc (dZn), nickel (dNi), copper (dCu), cadmium (dCd), aluminum (dAl), and nutrients on the Northeast Atlantic continental margin (Celtic Sea), which is representative for temperate shelf seas globally. Variations in surface water dTM and nutrient concentrations were mainly regulated by seasonal changes in biological processes. The stoichiometry of dTMs (especially for dCu and dZn) and nutrients on the continental shelf was additionally affected by fluvial inputs. Nutrients and dTMs at depth on the continental slope were determined by water mass mixing driven by ocean circulation, without an important role for local remineralization processes. The Mediterranean Outflow Waters are especially important for delivering Mediterranean-sourced dTMs to the Northeast Atlantic Ocean and drive dTM:nutrient kinks at a depth of ~1000 m. These results highlight the importance of riverine inputs, seasonality of primary production and ocean circulation on the distributions of nutrients and nutrient-like dTMs in temperate continental margin seas. Future climate related changes in the forcing factors may impact the availability of nutrients and dTMs to marine organisms in highly productive continental shelf regions and consequently the regional carbon cycle