Diversity of reed (Phragmites australis) stem biofilm bacterial communities in two Hungarian soda lakes

From reed biofilm samples of Kelemen-szék (Kiskunság National Park, KNP) and Nagy-Vadas (Hortobágy National Park, HNP) altogether 260 bacterial isolates were gained after serial dilutions and plating onto different media. Following a primary selection 164 strains were investigated by "traditional" phenotypic tests and clustered by numerical analysis. Fifty-six representative strains were selected to ARDRA and 16S rDNA sequence analysis for identification. Strains were identified as members of genera Agrobacterium, Paracoccus, Halomonas, Pseudomonas, Bacillus, Planococcus and Nesterenkonia. The species diversity was also investigated by a cultivation independent method. A clone library was constructed using the community DNA isolated from the biofilm sample of Kelemen-szék. Screening of the 140 bacterial clones resulted in 45 different ARDRA groups. Sequence analysis of the representatives revealed a great phylogenetic diversity. A considerable majority of the clones was affiliated with uncultured bacterial clones (with sequence similarity between 93 and 99%) originating from diverse environmental samples (for example salt marshes, compost or wastewater treatment plants). The DNA sequences of other clones showed the presence of genera Flavobacterium, Sphingobacterium, Pseudomonas and Agrobacterium.     

Age-related changes in immunity: implications for vaccination in the elderly

Average life expectancy is continuously rising in all developed countries, leading to an ever-increasing elderly population. Of the many functions of the body affected by the complex process of ageing, the immune system in particular undergoes various changes, collectively termed immunosenescence. As a result, elderly people are more susceptible to infections and are frequently less protected by vaccines. This review summarises the effect of ageing on immunity, emphasising the age-associated changes within T and B cells at a molecular and cellular level. Furthermore, it discusses strategies, such as the addition of immunostimulatory adjuvants and the use of potent antigen-delivery systems, that may counteract age-related defects in immune responses to vaccination. A proper understanding of how immunological memory is affected by ageing, and the introduction of strategies to ameliorate vaccine efficacy in the elderly, might reduce the incidence and the severity of infectious disease within this fragile age group and have a strong impact on the quality of life of elderly individuals.     

Older adults have unstable gait kinematics during weight transfer

The present article investigates gait stability of healthy older persons during weight transfer. Ten healthy older persons and ten younger persons walked 10 min each on a treadmill at 3 different gait speeds. The intra-stride change in gait stability was defined by the local divergence exponent λ(t) estimated by a newly developed method. The intra-stride changes in λ(t) during weight transfer were identified by separating each stride into a single and double support phase. The intra-stride changes in λ(t) were also compared to changes in the variation of the gait kinematics, i.e., SD(t). The healthy older persons walked at the same preferred walking speed as the younger persons. However, they exhibited significantly larger λ(t) (p<0.001) during weight transfer in the double support phase. Local divergence was closely related to intra-stride changes in SD(t) of the feet in the anterior-posterior direction. Furthermore, a high correlation was found between local divergence and the variation in step length and step width for both older (R>0.67, p<0.05) and younger persons (R>0.67, p<0.05). The present results indicate that the gait kinematics of older adults are more dynamical unstable during the weight transfer compared to younger persons. Furthermore, a close relationship exists between intra-stride changes in dynamical stability and variation in step length and step width. Further work will validate the results of the present study using real-life perturbations of the gait kinematics of both younger and older adults.     

Acute diarrhea in west african children: diverse enteric viruses and a novel parvovirus genus

Parvoviruses cause a variety of mild to severe symptoms or asymptomatic infections in humans and animals. During a viral metagenomic analysis of feces from children with acute diarrhea in Burkina Faso, we identified in decreasing prevalence nucleic acids from anelloviruses, dependoviruses, sapoviruses, enteroviruses, bocaviruses, noroviruses, adenoviruses, parechoviruses, rotaviruses, cosavirus, astroviruses, and hepatitis B virus. Sequences from a highly divergent parvovirus, provisionally called bufavirus, were also detected whose NS1 and VP1 proteins showed <39% and <31% identities to those of previously known parvoviruses. Four percent of the fecal samples were PCR positive for this new parvovirus, including a related bufavirus species showing only 72% identity in VP1. The high degree of genetic divergence of these related genomes from those of other parvoviruses indicates the presence of a proposed new Parvoviridae genus containing at least two species. Studies of the tropism and pathogenicity of these novel parvoviruses will be facilitated by the availability of their genome sequences.     

Expression of type I interferon by splenic macrophages suppresses adaptive immunity during sepsis

Early during Gram-negative sepsis, excessive release of pro-inflammatory cytokines can cause septic shock that is often followed by a state of immune paralysis characterized by the failure to mount adaptive immunity towards secondary microbial infections. Especially, the early mechanisms responsible for such immune hypo-responsiveness are unclear. Here, we show that TLR4 is the key immune sensing receptor to initiate paralysis of T-cell immunity after bacterial sepsis. Downstream of TLR4, signalling through TRIF but not MyD88 impaired the development of specific T-cell immunity against secondary infections. We identified type I interferon (IFN) released from splenic macrophages as the critical factor causing T-cell immune paralysis. Early during sepsis, type I IFN acted selectively on dendritic cells (DCs) by impairing antigen presentation and secretion of pro-inflammatory cytokines. Our results reveal a novel immune regulatory role for type I IFN in the initiation of septic immune paralysis, which is distinct from its well-known immune stimulatory effects. Moreover, we identify potential molecular targets for therapeutic intervention to overcome impairment of T-cell immunity after sepsis.     

Homocysteine transport by human aortic endothelial cells: identification and properties of import systems

Hyperhomocysteinemia is an independent risk factor for cardiovascular disease. Transport of L-homocysteine into and out of the human vascular endothelium is poorly understood. We hypothesized that cultured human aortic endothelial cells (HAEC) would import L-homocysteine on one or more of the L-cysteine transport systems. Inhibitors of the transporters were used to characterize the uptake of [35S]L-homocysteine, [35S]L-homocystine, and [35S]L-cysteine. We found that L-homocysteine uptake is mediated by the sodium-dependent cysteine transport systems X(AG), ASC, and A, and the sodium-independent transport system L. Thus, HAEC utilize multiple cysteine transporters (X(AG) > or = L > ASC > A) to import L-homocysteine. Kinetic analysis supported the uptake results. Michaelis-Menten constants (Km) for the four systems yielded values of 19.0, 27.1, 112, and 1000 microM for systems L, X(AG), ASC, and A, respectively. The binding and uptake of [35S]L-homocystine, the disulfide homodimer of L-homocysteine, was mediated by systems X(AG), L, and ASC but not by system A. In contrast to [35S]L-homocysteine, system x(c) was active for [35S]L-homocystine uptake. A similar pattern was observed for [35S]L-cysteine. Thus, L-homocysteine and L-homocystine found in hyperhomocysteinemic subjects can gain entry into the vascular endothelium by way of multiple L-cysteine transporters.     

A novel principle for partial agonism of liver X receptor ligands. Competitive recruitment of activators and repressors

Partial, selective activation of nuclear receptors is a central issue in molecular endocrinology but only partly understood. Using LXRs as an example, we show here that purely agonistic ligands can be clearly and quantitatively differentiated from partial agonists by the cofactor interactions they induce. Although a pure agonist induces a conformation that is incompatible with the binding of repressors, partial agonists such as GW3965 induce a state where the interaction not only with coactivators, but also corepressors is clearly enhanced over the unliganded state. The activities of the natural ligand 22(R)-hydroxycholesterol and of a novel quinazolinone ligand, LN6500 can be further differentiated from GW3965 and T0901317 by their weaker induction of coactivator binding. Using biochemical and cell-based assays, we show that the natural ligand of LXR is a comparably weak partial agonist. As predicted, we find that a change in the coactivator to corepressor ratio in the cell will affect NCoR recruiting compounds more dramatically than NCoR-dissociating compounds. Our data show how competitive binding of coactivators and corepressors can explain the tissue-specific behavior of partial agonists and open up new routes to a rational design of partial agonists for LXRs.     

Shortest path analysis using partial correlations for classifying gene functions from gene expression data

MOTIVATION: Gaussian graphical models (GGMs) are a popular tool for representing gene association structures. We propose using estimated partial correlations from these models to attach lengths to the edges of the GGM, where the length of an edge is inversely related to the partial correlation between the gene pair. Graphical lasso is used to fit the GGMs and obtain partial correlations. The shortest paths between pairs of genes are found. Where terminal genes have the same biological function intermediate genes on the path are classified as having the same function. We validate the method using genes of known function using the Rosetta Compendium of yeast (Saccharomyces Cerevisiae) gene expression profiles. We also compare our results with those obtained using a graph constructed using correlations. RESULTS: Using a partial correlation graph, we are able to classify approximately twice as many genes to the same level of accuracy as when using a correlation graph. More importantly when both methods are tuned to classify a similar number of genes, the partial correlation approach can increase the accuracy of the classifications.     

Identification of evolutionarily conserved genetic regulators of cellular aging

To identify new genetic regulators of cellular aging and senescence, we performed genome-wide comparative RNA profiling with selected human cellular model systems, reflecting replicative senescence, stress-induced premature senescence, and distinct other forms of cellular aging. Gene expression profiles were measured, analyzed, and entered into a newly generated database referred to as the GiSAO database. Bioinformatic analysis revealed a set of new candidate genes, conserved across the majority of the cellular aging models, which were so far not associated with cellular aging, and highlighted several new pathways that potentially play a role in cellular aging. Several candidate genes obtained through this analysis have been confirmed by functional experiments, thereby validating the experimental approach. The effect of genetic deletion on chronological lifespan in yeast was assessed for 93 genes where (i) functional homologues were found in the yeast genome and (ii) the deletion strain was viable. We identified several genes whose deletion led to significant changes of chronological lifespan in yeast, featuring both lifespan shortening and lifespan extension. In conclusion, an unbiased screen across species uncovered several so far unrecognized molecular pathways for cellular aging that are conserved in evolution.