Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

It was hypothesized that seasonality and resource availability altered through tree girdling were major determinants of the phylogenetic composition of the archaeal and bacterial community in a temperate beech forest soil. During a 2-year field experiment, involving girdling of beech trees to intercept the transfer of easily available carbon (C) from the canopy to roots, members of the dominant phylogenetic microbial phyla residing in top soils under girdled versus untreated control trees were monitored at bimonthly intervals through 16S rRNA gene-based terminal restriction fragment length polymorphism profiling and quantitative PCR analysis. Effects on nitrifying and denitrifying groups were assessed by measuring the abundances of nirS and nosZ genes as well as bacterial and archaeal amoA genes. Seasonal dynamics displayed by key phylogenetic and nitrogen (N) cycling functional groups were found to be tightly coupled with seasonal alterations in labile C and N pools as well as with variation in soil temperature and soil moisture. In particular, archaea and acidobacteria were highly responsive to soil nutritional and soil climatic changes associated with seasonality, indicating their high metabolic versatility and capability to adapt to environmental changes. For these phyla, significant interrelations with soil chemical and microbial process data were found suggesting their potential, but poorly described contribution to nitrification or denitrification in temperate forest soils. In conclusion, our extensive approach allowed us to get novel insights into effects of seasonality and resource availability on the microbial community, in particular on hitherto poorly studied bacterial phyla and functional groups.     

A Fast Air-dry Dropping Chromosome Preparation Method Suitable for FISH in Plants

Preparation of chromosome spreads is a prerequisite for the successful performance of fluorescence in situ hybridization (FISH). Preparation of high quality plant chromosome spreads is challenging due to the rigid cell wall. One of the approved methods for the preparation of plant chromosomes is a so-called drop preparation, also known as drop-spreading or air-drying technique. Here, we present a protocol for the fast preparation of mitotic chromosome spreads suitable for the FISH detection of single and high copy DNA probes. This method is an improved variant of the air-dry drop method performed under a relative humidity of 50%-55%. This protocol comprises a reduced number of washing steps making its application easy, efficient and reproducible. Obvious benefits of this approach are well-spread, undamaged and numerous metaphase chromosomes serving as a perfect prerequisite for successful FISH analysis. Using this protocol we obtained high-quality chromosome spreads and reproducible FISH results for Hordeum vulgare, H. bulbosum, H. marinum, H. murinum, H. pubiflorum and Secale cereale.     

Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency in Chlamydomonas reinhardtii

The basic question addressed in this study is how energy metabolism is adjusted to cope with iron deficiency in Chlamydomonas reinhardtii. To investigate the impact of iron deficiency on bioenergetic pathways, comparative proteomics was combined with spectroscopic as well as voltametric oxygen measurements to assess protein dynamics linked to functional properties of respiratory and photosynthetic machineries. Although photosynthetic electron transfer is largely compromised under iron deficiency, our quantitative and spectroscopic data revealed that the functional antenna size of photosystem II (PSII) significantly increased. Concomitantly, stress-related chloroplast polypeptides, like 2-cys peroxiredoxin and a stress-inducible light-harvesting protein, LhcSR3, as well as a novel light-harvesting protein and several proteins of unknown function were induced under iron-deprivation. Respiratory oxygen consumption did not decrease and accordingly, polypeptides of respiratory complexes, harboring numerous iron-sulfur clusters, were only slightly diminished or even increased under low iron. Consequently, iron-deprivation induces a transition from photoheterotrophic to primarily heterotrophic metabolism, indicating that a hierarchy for iron allocations within organelles of a single cell exists that is closely linked with the metabolic state of the cell.     

A novel approach to sequence validating protein expression clones with automated decision making

Background  

Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an arduous and time consuming process. The ultimate goal of validation is to determine if a given plasmid clone matches its reference sequence sufficiently to be "acceptable" for use in protein expression experiments. Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation.     

Characterization of MHC class-I restricted TCRαβ<Superscript>+</Superscript> CD4<Superscript>−</Superscript> CD8<Superscript>−</Superscript> double negative T cells recognizing the gp100 antigen from a melanoma patient after gp100 vaccination

The immune attack against malignant tumors require the concerted action of CD8⁺ cytotoxic T lymphocytes (CTL) as well as CD4⁺ T helper cells. The contribution of T cell receptor (TCR) αβ⁺ CD4⁻ CD8⁻ double-negative (DN) T cells to anti-tumor immune responses is widely unknown. In previous studies, we have demonstrated that DN T cells with a broad TCR repertoire are present in humans in the peripheral blood and the lymph nodes of healthy individuals. Here, we characterize a human DN T cell clone (T4H2) recognizing an HLA-A2-restricted melanoma-associated antigenic gp100-peptide isolated from the peripheral blood of a melanoma patient. Antigen recognition by the T4H2 DN clone resulted in specific secretion of IFN-γ and TNF. Although lacking the CD8 molecule the gp100-specifc DN T cell clone was able to confer antigen-specific cytotoxicity against gp100-loaded target cells as well as HLA-A2⁺ gp100 expressing melanoma cells. The cytotoxic capacity was found to be perforin/granzymeB-dependent. Together, these data indicate that functionally active antigen-specific DN T cells recognizing MHC class I-restricted tumor-associated antigen (TAA) may contribute to anti-tumor immunity in vivo. A. Mackensen and K. Fischer contributed equally to this work and should be considered joint senior authors. This work was supported by the Deutsche Forschungsgemeinschaft (MA 1351/5-1, KFO 146) and NIH grants CA90873, CA102280, 104947 (MIN). Companion paper: “Relationship between CD8-dependent antigen recognition, T cell functional avidity, and tumor cell recognition” by Tamson V. Moore et al. doi: .     

Synthesis and derivatization of halflanthanidocene aryl(alk)oxide complexes

The reaction of halflanthanidocene aryloxides Cp^R′Ln(OAr^tBu,R)₂ (Ln = Y, La, Lu; Cp^R′ = C₅Me₅, C₄Me₄H; R = H, Me) and halflanthanidocene alkoxides [(C₅Me₅)Ln(OCH₂CMe₃)₂]₂ (Ln = Y, Lu) with trimethylaluminum (TMA) was investigated. Monomeric Cp^R′Ln(OAr^tBu,R)₂, derived from the ortho-tBu-substituted OC₆H₂tBu₂-2,6-R-4 (R = H, Me) ligands, form mono(tetramethylaluminate) complexes Cp^R′Ln(OAr^tBu,R)(AlMe₄) for the smaller lanthanide metal centers yttrium and lutetium. Such an [aryloxide] → [aluminate] ligand exchange was not observed at the larger lanthanum metal center. The mobility of the tetramethylaluminate ligands of complexes Cp^R′Ln(OAr^tBu,R)(AlMe₄) (Ln = Y, Lu) was examined by variable-temperature (VT) ¹H NMR spectroscopy, revealing two signals for bridging and terminal methyl groups at lower temperatures. The treatment of complexes Cp^R′Ln(OAr^tBu,R)(AlMe₄) with donor solvent d₈-THF gave Cp^R′Ln(OAr^tBu,R)(Me)(d₈-THF)₂ (Ln = Y, Lu) with terminal methyl groups, according to a donor-induced aluminate cleavage reaction. Dimeric [(C₅Me₅)Ln(OCH₂CMe₃)₂]₂ (Ln = Y, Lu) was synthesized from (C₅Me₅)Ln(NiPr₂)₂(THF) and reacted with two equivalents of TMA per Ln center to yield monomeric bis(TMA) adduct complexes (C₅Me₅)Ln(OCH₂CMe₃)₂(AlMe₃)₂(Ln = Y, Lu). VT NMR spectroscopic studies confirmed a high mobility of the Ln(μ-OCH₂CMe₃)(μ-Me)AlMe₂ moieties at an ambient temperature. Both bis(TMA) adduct complexes were characterized by X-ray structure analysis.     

Provenance- and life-history stage-specific responses of the dwarf shrub Calluna vulgaris to elevated vapour pressure deficit

Climate change may alter microscale-effective ecosystem properties such as atmospheric water vapour pressure, but consequences for plant growth are insufficiently understood. Within a northwest German heathland an open-top chamber experiment was established to analyse the effects of elevated vapour pressure deficit (eVPD) on growth responses of Calluna vulgaris considering both plant origin (Atlantic (AP), sub-Atlantic (SAP), sub-Continental (SCP)) and life-history stage (1-year vs. 10-year old plants). We hypothesised that the plants’ sensitivity to eVPD decreases (i) from AP to SCP and (ii) with progressing life-history stage. Elevated VPD caused a provenance-specific decrease of shoot increment whilst aboveground biomass productivity remained unaffected. AP and SAP responded with increasing belowground biomass δ¹³C signatures to eVPD, whereas δ¹³C values decreased for SCP. Moreover, eVPD increased and decreased belowground biomass δ¹³C signatures of 1- and 10-year old plants, respectively. These responses to eVPD were related to differences in morphological-chemical traits and the plants’ trait plasticity in response to eVPD. SCP showed the highest aboveground tissue mass density and significantly increased tissue C:N ratios under eVPD. One-year old plants had a tenfold higher shoot:root ratio than 10-year old plants, making young plants more sensitive to eVPD. Our findings demonstrate that the atmospheric water status affects the morphology and physiology of Calluna independent of the soil water status. The results have implications for the conservation of heathlands under climate change: (i) SCP may constitute an appropriate ecotype for assisted migration-approaches, and (ii) management needs to weigh different options for heathland rejuvenation.

     

Current Status of Human Papillomavirus-Related Head and Neck Cancer: From Viral Genome to Patient Care

Virologica Sinica - Human papillomavirus (HPV) infection identified as a definitive human carcinogen is increasingly being recognized for its role in carcinogenesis of human cancers. Up to...     

Laccase-catalyzed decolorization of the synthetic azo-dye diamond black PV 200 and of some structurally related derivatives

The kinetics of laccase-catalyzed transformation of the azo-dye Diamond Black PV 200 (CI Mordant Black 9) and various related synthesized derivatives were analyzed for dependence on pH and substrate structure. The reaction mixture of Diamond Black PV 200 was analyzed by HPLC/MS–MS and it was shown that upon laccase oxidation, reactive chinoid fragments of lower molecular weight were formed. These may further oligomerize as indicated by the appearance of a number of compounds with increased molecular weight. The pH optimum for the decolorization was pH 5 for Diamond Black PV 200 which did not change significantly when the substitution pattern of its basic structure was varied. Biodegradability, however, was strongly dependent on the structure of the dyes.