Microbial Response to Experimentally Controlled Redox Transitions at the Sediment Water Interface

The sediment–water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment–water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NO_x. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment–water interface.     

Diffusion Tensor Magnetic Resonance Imaging of the Brain in APP Transgenic Mice: A Cohort Study

Introduction

Fast in-vivo high resolution diffusion tensor imaging (DTI) of the mouse brain has recently been shown to enable cohort studies by the combination of appropriate pulse sequences and cryogenically cooled resonators (CCR). The objective of this study was to apply this DTI approach at the group level to β-amyloid precursor protein (APP) transgenic mice.

Methods

Twelve mice (5 wild type, 7 APP transgenic tg2576) underwent DTI examination at 156²×250 µm³ spatial resolution with a CCR at ultrahigh field (11.7 T). Diffusion images were acquired along 30 gradient directions plus 5 references without diffusion encoding with a total acquisition time of 35 minutes. Fractional anisotropy (FA) maps were statistically compared by whole brain-based spatial statistics (WBSS) at the group level vs. wild type controls.

Results

FA-map comparison showed characteristic regional patterns of differences between the groups with localizations associated with Alzheimer’s disease in humans, such as the hippocampus, the entorhinal cortex, and the caudoputamen.

Conclusion

In this proof-of-principle study, regions associated with amyloid-β deposition could be identified by WBSS of FA maps in APP transgenic mice vs. wild type mice. Thus, DTI in the mouse brain acquired at 11.7 T by use of a CCR was demonstrated to be feasible for cohort studies.     

Geodermatophilus africanus sp. nov., a halotolerant actinomycete isolated from Saharan desert sand

A novel Gram-strain positive, aerobic, actinobacterial strain, designated CF11/1^T, was isolated from a sand sample obtained in the Sahara Desert, Chad. The black-pigmented isolate was aerobic and exhibited optimal growth from 25 to 35 °C at pH 6.0–8.0 and with 0–8 % (w/v) NaCl, indicating that it is a halotolerant mesophile. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The G+C content in the genome was 74.4 mol%. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diaminoacid. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and a minor fraction of phosphatidylglycerol; MK-9(H₄) was the dominant menaquinone, and galactose was detected as a diagnostic sugar. The major cellular fatty acid was branched-chain saturated acid iso-C_16:0. Analysis of 16S rRNA gene sequences showed 95.3–98.6 % pairwise sequence identity with the members of the genus Geodermatophilus. Based on phenotypic and chemotaxonomic properties, as well as phylogenetic distinctiveness, the isolate represents a novel species, Geodermatophilus africanus, with the type strain CF11/1^T (DSM 45422 = CCUG 62969 = MTCC 11556).     

B lymphocyte-typing for prediction of clinical response to rituximab

Introduction

The prediction of therapeutic response to rituximab in rheumatoid arthritis is desirable. We evaluated whether analysis of B lymphocyte subsets by flow cytometry would be useful to identify non-responders to rituximab ahead of time.

Methods

Fifty-two patients with active rheumatoid arthritis despite therapy with TNF-inhibitors were included in the national rituximab registry. DAS28 was determined before and 24 weeks after rituximab application. B cell subsets were analyzed by high-sensitive flow cytometry before and 2 weeks after rituximab administration. Complete depletion of B cells was defined as CD19-values below 0.0001 x10⁹ cells/liter.

Results

At 6 months 19 patients had a good (37%), 23 a moderate (44%) and 10 (19%) had no EULAR-response. The extent of B lymphocyte depletion in peripheral blood did not predict the success of rituximab therapy. Incomplete depletion was found at almost the same frequency in EULAR responders and non-responders. In comparison to healthy controls, non-responders had elevated baseline CD95⁺ pre-switch B cells, whereas responders had a lower frequency of plasmablasts.

Conclusions

The baseline enumeration of B lymphocyte subsets is still of limited clinical value for the prediction of response to anti-CD20 therapy. However, differences at the level of CD95+ pre switch B cells or plasmablasts were noticed with regard to treatment response. The criterion of complete depletion of peripheral B cells after rituximab administration did not predict the success of this therapy in rheumatoid arthritis.     

Lectin histochemistry of human bone marrow: investigation of trephine biopsy specimens in normal and reactive states and neoplastic disorders

Summary The lectin binding pattern of bone marrow cells in normal and reactive states and in various neoplastic disorders was investigated using trephine biopsy specimens taken from the iliac crest. The tissue samples were routinely processed (fixed in formalin and embedded in paraffin wax) and subjected to mild decalcification with EDTA. The following results were obtained. (1) More than half of the 23 fluoresceinated lectins used reacted with normal blood cells and/or their neoplastic derivatives. Inhibition tests with the appropriate sugars confirmed the specificity of binding for the majority, but not all, of the lectins. (2) WGA, Con A, PSA, STA and RCA₆₀ and RCA₁₂₀ produced a particularly intense reaction with normal, reactive and neoplastic myeloid cells. Erythroblasts exhibited weak staining in a few cases by a few lectins (WGA producing the strongest staining), while megakaryocytes nearly always remained unstained. Neoplastic lymphoid cells in various lymphoproliferative disorders and plasmacytoma cells generally reacted with the same lectins as the myeloid cells. (3) Since neoplastic myeloid cells in various myelodysplastic and myeloproliferative disorders exhibited a lectin binding pattern similar to that of myeloid cells in normal and reactive bone marrow, it is unlikely that lectin histochemistry of the bone marrow will prove of great value in the diagnosis of myelodysplastic—myeloproliferative disorders.     

Respiratory chain supercomplexes in the plant mitochondrial membrane

The intricate, heavily folded inner membrane of mitochondria houses the respiratory chain complexes. These complexes, together with the ATP synthase complex, are responsible for energy production, which is stored as ATP. The structure of the individual membrane-bound protein components has been well characterized. In particular, the use of Blue-native polyacrylamide gel electrophoresis has been instrumental in recent years in providing evidence that these components are organized into supercomplexes. Single particle electron microscopy studies have enabled a structural characterization of some of the mitochondrial supercomplexes. This has provided the opportunity to define a functional role for these supercomplexes for the first time, in particular for the dimeric ATP synthase complex, which appears to be responsible for the folding of the inner mitochondrial membrane.     

Rhodoferax-related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes

The presence of aerobic anoxygenic phototrophs (AAPs) has been repeatedly reported from various marine environments, but their distribution in freshwater lakes was neglected until recently. We investigated the phylogenetic composition of AAP communities in 10 lakes in Northeastern Germany with different trophic status including oligotrophic Lake Stechlin and humic matter rich Lake Grosse Fuchskuhle. The AAP community was composed by members of Alpha- and Betaproteobacteria, but their contribution varied largely among the studied lakes. Our results show that AAP community composition in the studied lakes was affected mostly by pH and humic matter content. While alkaline lakes were mostly composed of Betaproteobacteria, the acidic and humic matter rich south-west (SW) basin of Lake Grosse Fuchskule was dominated (87%) by Alphaproteobacteria. The most frequent group within Betaproteobacteria was a cluster of pufM genes which was phylogenetically related to Rhodoferax representing 38.5% of all retrieved sequences. Alphaproteobacteria-related sequences had a broader phylogenetic diversity including six different taxa dominated by Sphingomonas- and Rhodobacter-like bacteria in lakes with alkaline to neutral pH. In the acidic and humic matter-rich SW basin of Lake Grosse Fuchskuhle, however, Methylobacterium-related sequences dominated the AAP community. We suggest that the variable AAP community structure might reflect the potential of these bacteria to cope with the contrasting conditions in freshwater environments.     

Kinetics and Yields of Pesticide Biodegradation at Low Substrate Concentrations and under Conditions Restricting Assimilable Organic Carbon

The fundamentals of growth-linked biodegradation occurring at low substrate concentrations are poorly understood. Substrate utilization kinetics and microbial growth yields are two critically important process parameters that can be influenced by low substrate concentrations. Standard biodegradation tests aimed at measuring these parameters generally ignore the ubiquitous occurrence of assimilable organic carbon (AOC) in experimental systems which can be present at concentrations exceeding the concentration of the target substrate. The occurrence of AOC effectively makes biodegradation assays conducted at low substrate concentrations mixed-substrate assays, which can have profound effects on observed substrate utilization kinetics and microbial growth yields. In this work, we introduce a novel methodology for investigating biodegradation at low concentrations by restricting AOC in our experiments. We modified an existing method designed to measure trace concentrations of AOC in water samples and applied it to systems in which pure bacterial strains were growing on pesticide substrates between 0.01 and 50 mg liter⁻¹. We simultaneously measured substrate concentrations by means of high-performance liquid chromatography with UV detection (HPLC-UV) or mass spectrometry (MS) and cell densities by means of flow cytometry. Our data demonstrate that substrate utilization kinetic parameters estimated from high-concentration experiments can be used to predict substrate utilization at low concentrations under AOC-restricted conditions. Further, restricting AOC in our experiments enabled accurate and direct measurement of microbial growth yields at environmentally relevant concentrations for the first time. These are critical measurements for evaluating the degradation potential of natural or engineered remediation systems. Our work provides novel insights into the kinetics of biodegradation processes and growth yields at low substrate concentrations.     

Low-SDS Blue native PAGE

SDS normally is strictly avoided during Blue native (BN) PAGE because it leads to disassembly of protein complexes and unfolding of proteins. Here, we report a modified BN-PAGE procedure, which is based on low-SDS treatment of biological samples prior to native gel electrophoresis. Using mitochondrial OXPHOS complexes from Arabidopsis as a model system, low SDS concentrations are shown to partially dissect protein complexes in a very defined and reproducible way. If combined with 2-D BN/SDS-PAGE, generated subcomplexes and their subunits can be systematically investigated, allowing insights into the internal architecture of protein complexes. Furthermore, a 3-D BN/low-SDS BN/SDS-PAGE system is introduced to facilitate structural analysis of individual protein complexes without their previous purification.     

Codivergence of mycoviruses with their hosts

Background

The associations between pathogens and their hosts are complex and can result from any combination of evolutionary events such as codivergence, switching, and duplication of the pathogen. Mycoviruses are RNA viruses which infect fungi and for which natural vectors are so far unknown. Thus, lateral transfer might be improbable and codivergence their dominant mode of evolution. Accordingly, mycoviruses are a suitable target for statistical tests of virus-host codivergence, but inference of mycovirus phylogenies might be difficult because of low sequence similarity even within families.

Methodology

We analyzed here the evolutionary dynamics of all mycovirus families by comparing virus and host phylogenies. Additionally, we assessed the sensitivity of the co-phylogenetic tests to the settings for inferring virus trees from their genome sequences and approximate, taxonomy-based host trees.

Conclusions

While sequence alignment filtering modes affected branch support, the overall results of the co-phylogenetic tests were significantly influenced only by the number of viruses sampled per family. The trees of the two largest families, Partitiviridae and Totiviridae, were significantly more similar to those of their hosts than expected by chance, and most individual host-virus links had a significant positive impact on the global fit, indicating that codivergence is the dominant mode of virus diversification. However, in this regard mycoviruses did not differ from closely related viruses sampled from non-fungus hosts. The remaining virus families were either dominated by other evolutionary modes or lacked an apparent overall pattern. As this negative result might be caused by insufficient taxon sampling, the most parsimonious hypothesis still is that host-parasite evolution is basically the same in all mycovirus families. This is the first study of mycovirus-host codivergence, and the results shed light not only on how mycovirus biology affects their co-phylogenetic relationships, but also on their presumable host range itself.