118 research outputs found
SLU Aquas kunskapsförsörjning och rÄdgivning som stöd till en ekosystembaserad fiskförvaltning
The environment drives microbial trait variability in aquatic habitats
A prerequisite to improve the predictability of microbial community dynamics is to understand the mechanisms of microbial assembly. To study factors that contribute to microbial community assembly, we examined the temporal dynamics of genes in five aquatic metagenome time-series, originating from marine offshore or coastal sites and one lake. With this trait-based approach we expected to find gene-specific patterns of temporal allele variability that depended on the seasonal metacommunity size of carrier-taxa and the variability of the milieu and the substrates to which the resulting proteins were exposed. In more detail, we hypothesized that a larger seasonal metacommunity size would result in increased temporal variability of functional units (i.e., gene alleles), as shown previously for taxonomic units. We further hypothesized that multicopy genes would feature higher temporal variability than single-copy genes, as gene multiplication can result from high variability in substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins that are less exposed to environmental fluctuations. The first two hypotheses were confirmed in all data sets, while significant effects of the subcellular location of gene products was only seen in three of the five time-series. The gene with the highest allele variability throughout all data sets was an iron transporter, also representing a target for phage infection. Previous work has emphasized the role of phage-prokaryote interactions as a major driver of microbial diversity. Our finding therefore points to a potentially important role of iron transporter-mediated phage infections for the assembly and maintenance of diversity in aquatic prokaryotes
Effect of large magnetotactic bacteria with polyphosphate inclusions on the phosphate profile of the suboxic zone in the Black Sea
The Black Sea is the worldâs largest anoxic basin and a model system for studying processes across redox gradients. In
between the oxic surface and the deeper sulfidic waters there is an unusually broad layer of 10â40 m, where neither oxygen
nor sulfide are detectable. In this suboxic zone, dissolved phosphate profiles display a pronounced minimum at the upper and
a maximum at the lower boundary, with a peak of particulate phosphorus in between, which was suggested to be caused by
the sorption of phosphate on sinking particles of metal oxides. Here we show that bacterial polyphosphate inclusions within
large magnetotactic bacteria related to the genus Magnetococcus contribute substantially to the observed phosphorus peak,
as they contain 26â34% phosphorus compared to only 1â5% in metal-rich particles. Furthermore, we found increased gene
expression for polyphosphate kinases by several groups of bacteria including Magnetococcaceae at the phosphate
maximum, indicating active bacterial polyphosphate degradation. We propose that large magnetotactic bacteria shuttle up
and down within the suboxic zone, scavenging phosphate at the upper and releasing it at the lower boundary. In contrast to a
passive transport via metal oxides, this bacterial transport can quantitatively explain the observed phosphate profiles.We are grateful for the competent technical
assistance of Ronny Baaske, Christian Burmeister, Christin Laudan
and Christian Meeske. We are greatly indebted to Cindy Lee and Bo
Barker JĂžrgensen for providing extremely helpful comments on an
earlier version of the manuscript. Horst D. Schulz and René Friedland
are acknowledged for stimulating discussions on the modeling
approach. We thank the captain and the crew of the R/V âMaria S.
Merianâ for the excellent support on board and the DFG (MSM33) and
BMBF (01DK12043) for financing the cruise. The particle analysis
was funded by the BMBF (03F0663A). S.B. was funded by a BONUS
BLUEPRINT project (03F0679A awarded to KJ; http://blueprint-
project.org), supported by BONUS (Art 185), funded jointly by the EU
and the German Federal Ministry of Education and Research (BMBF).
T. S. was funded by the German research foundation (DFG) (awarded
to K.J., JU 367/16-1). Metagenome sequencing was done at the
Swedish National Genomics Infrastructure (NGI) at SciLifeLab
(Sweden).We are grateful for the competent technical
assistance of Ronny Baaske, Christian Burmeister, Christin Laudan
and Christian Meeske. We are greatly indebted to Cindy Lee and Bo
Barker JĂžrgensen for providing extremely helpful comments on an
earlier version of the manuscript. Horst D. Schulz and René Friedland
are acknowledged for stimulating discussions on the modeling
approach. We thank the captain and the crew of the R/V âMaria S.
Merianâ for the excellent support on board and the DFG (MSM33) and
BMBF (01DK12043) for financing the cruise. The particle analysis
was funded by the BMBF (03F0663A). S.B. was funded by a BONUS
BLUEPRINT project (03F0679A awarded to KJ; http://blueprint-
project.org), supported by BONUS (Art 185), funded jointly by the EU
and the German Federal Ministry of Education and Research (BMBF).
T. S. was funded by the German research foundation (DFG) (awarded
to K.J., JU 367/16-1). Metagenome sequencing was done at the
Swedish National Genomics Infrastructure (NGI) at SciLifeLab
(Sweden)
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Fog2 is required for normal diaphragm and lung development in mice and humans
Congenital diaphragmatic hernia and other congenital diaphragmatic defects are associated with significant mortality and morbidity in neonates; however, the molecular basis of these developmental anomalies is unknown. In an analysis of E18.5 embryos derived from mice treated with N-ethyl-N-nitrosourea, we identified a mutation that causes pulmonary hypoplasia and abnormal diaphragmatic development. Fog2 (Zfpm2) maps within the recombinant interval carrying the N-ethyl-N-nitrosourea-induced mutation, and DNA sequencing of Fog2 identified a mutation in a splice donor site that generates an abnormal transcript encoding a truncated protein. Human autopsy cases with diaphragmatic defect and pulmonary hypoplasia were evaluated for mutations in FOG2. Sequence analysis revealed a de novo mutation resulting in a premature stop codon in a child who died on the first day of life secondary to severe bilateral pulmonary hypoplasia and an abnormally muscularized diaphragm. Using a phenotype-driven approach, we have established that Fog2 is required for normal diaphragm and lung development, a role that has not been previously appreciated. FOG2 is the first gene implicated in the pathogenesis of nonsyndromic human congenital diaphragmatic defects, and its necessity for pulmonary development validates the hypothesis that neonates with congenital diaphragmatic hernia may also have primary pulmonary developmental abnormalities
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
The Baltic Sea is one of the worldâs largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset
Few multiyear precipitation-reduction experiments find a shift in the productivity-precipitation relationship
Well-defined productivityâprecipitation relationships of ecosystems are needed as benchmarks for the validation of land models used for future projections. The productivityâprecipitation relationship may be studied in two ways: the spatial approach relates differences in productivity to those in precipitation among sites along a precipitation gradient (the spatial fit, with a steeper slope); the temporal approach relates interannual productivity changes to variation in precipitation within sites (the temporal fits, with flatter slopes). Precipitationâreduction experiments in natural ecosystems represent a complement to the fits, because they can reduce precipitation below the natural range and are thus well suited to study potential effects of climate drying. Here, we analyse the effects of dry treatments in eleven multiyear precipitationâmanipulation experiments, focusing on changes in the temporal fit. We expected that structural changes in the dry treatments would occur in some experiments, thereby reducing the intercept of the temporal fit and displacing the productivityâprecipitation relationship downward the spatial fit. The majority of experiments (72%) showed that dry treatments did not alter the temporal fit. This implies that current temporal fits are to be preferred over the spatial fit to benchmark land-model projections of productivity under future climate within the precipitation ranges covered by the experiments. Moreover, in two experiments, the intercept of the temporal fit unexpectedly increased due to mechanisms that reduced either water loss or nutrient loss. The expected decrease of the intercept was observed in only one experiment, and only when distinguishing between the late and the early phases of the experiment. This implies that we currently do not know at which precipitationâreduction level or at which experimental duration structural changes will start to alter ecosystem productivity. Our study highlights the need for experiments with multiple, including more extreme, dry treatments, to identify the precipitation boundaries within which the current temporal fits remain valid
Spotlights on Contemporary Family Life
Spotlights on Contemporary Family Life covers four issues of
cross-cutting importance to families
Structures and forms of families: issues relating to a diversification of families
away from the âtraditional nuclear family formâ are relatively uncontroversial
from an academic perspective, but much more so for policy makers and family
associations. Chapter 1 provides a thorough overview of the state of contemporary
European families.
Solidarities in families: too often the issue of an âageing societyâ is simply
reduced to the problem of over-burdening social care systems, but longevity
also represents opportunities for new kinds of solidarities inside families and
family networks, and new relations between family members â not to mention
the satisfaction felt by people who can continue to live fulfilling and rewarding
lives long after theyâre considered âelderlyâ. Chapter 2 gives voice to authors who
identify these new opportunities and challenges.
Demographic change: women are having fewer children and having them
later in life. Having children is now a conscious decision and fertility rates have
declined below the level required to sustain our current populations. At the
same time we witness the âgreyingâ of Europe, which brings with it a whole host
of opportunities and challenges. Chapter 3 raises important issues for policy
makers today.
Volunteering: inspired by family associations who could not survive without
the support of volunteers, this chapter gives an overview of whatâs known -
and what isnât - about volunteering. Coinciding with the European Year of
Volunteering 2011, this chapter takes a timely look at the efforts that families
put into volunteering across Europe and the important benefits that Europe gains
from all of this combined voluntary effort.
Linden Farrer and William Lay work for the Confederation of Family Organisations
in the European Union (COFACE). This publication was produced by FAMILYPLATFORM,
a project funded by the European Commission
Sequential and Coordinated Actions of c-Myc and N-Myc Control Appendicular Skeletal Development
BACKGROUND: During limb development, chondrocytes and osteoblasts emerge from condensations of limb bud mesenchyme. These cells then proliferate and differentiate in separate but adjacent compartments and function cooperatively to promote bone growth through the process of endochondral ossification. While many aspects of limb skeletal formation are understood, little is known about the mechanisms that link the development of undifferentiated limb bud mesenchyme with formation of the precartilaginous condensation and subsequent proliferative expansion of chondrocyte and osteoblast lineages. The aim of this study was to gain insight into these processes by examining the roles of c-Myc and N-Myc in morphogenesis of the limb skeleton. METHODOLOGY/PRINCIPAL FINDINGS: To investigate c-Myc function in skeletal development, we characterized mice in which floxed c-Myc alleles were deleted in undifferentiated limb bud mesenchyme with Prx1-Cre, in chondro-osteoprogenitors with Sox9-Cre and in osteoblasts with Osx1-Cre. We show that c-Myc promotes the proliferative expansion of both chondrocytes and osteoblasts and as a consequence controls the process of endochondral growth and ossification and determines bone size. The control of proliferation by c-Myc was related to its effects on global gene transcription, as phosphorylation of the C-Terminal Domain (pCTD) of RNA Polymerase II, a marker of general transcription initiation, was tightly coupled to cell proliferation of growth plate chondrocytes where c-Myc is expressed and severely downregulated in the absence of c-Myc. Finally, we show that combined deletion of N-Myc and c-Myc in early limb bud mesenchyme gives rise to a severely hypoplastic limb skeleton that exhibits features characteristic of individual c-Myc and N-Myc mutants. CONCLUSIONS/SIGNIFICANCE: Our results show that N-Myc and c-Myc act sequentially during limb development to coordinate the expansion of key progenitor populations responsible for forming the limb skeleton
Regulation of human CD4+ T cell differentiation
Naive CD4+ T cells differentiate into specific effector subsetsâTh1, Th2, Th17, and T follicular helper (Tfh)âthat provide immunity against pathogen infection. The signaling pathways involved in generating these effector cells are partially known. However, the effects of mutations underlying human primary immunodeficiencies on these processes, and how they compromise specific immune responses, remain unresolved. By studying individuals with mutations in key signaling pathways, we identified nonredundant pathways regulating human CD4+ T cell differentiation in vitro. IL12RÎČ1/TYK2 and IFN-ÎłR/STAT1 function in a feed-forward loop to induce Th1 cells, whereas IL-21/IL-21R/STAT3 signaling is required for Th17, Tfh, and IL-10âsecreting cells. IL12RÎČ1/TYK2 and NEMO are also required for Th17 induction. Strikingly, gain-of-function STAT1 mutations recapitulated the impact of dominant-negative STAT3 mutations on Tfh and Th17 cells, revealing a putative inhibitory effect of hypermorphic STAT1 over STAT3. These findings provide mechanistic insight into the requirements for human T cell effector function, and explain clinical manifestations of these immunodeficient conditions. Furthermore, they identify molecules that could be targeted to modulate CD4+ T cell effector function in the settings of infection, vaccination, or immune dysregulation
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