Lactic acid bacterium and yeast microbiotas of 19 sourdoughs used for traditional/typical italian breads: interactions between ingredients and microbial species diversity

The study of the microbiotas of 19 Italian sourdoughs used for the manufacture of traditional/typical breads allowed the identification, through a culture-dependent approach, of 20 and 4 species of lactic acid bacteria (LAB) and yeasts, respectively. Numerically, the most frequent LAB isolates were Lactobacillus sanfranciscensis (ca. 28% of the total LAB isolates), Lactobacillus plantarum (ca. 16%), and Lactobacillus paralimentarius (ca. 14%). Saccharomyces cerevisiae was identified in 16 sourdoughs. Candida humilis, Kazachstania barnettii, and Kazachstania exigua were also identified. As shown by principal component analysis (PCA), a correlation was found between the ingredients, especially the type of flour, the microbial community, and the biochemical features of sourdoughs. Triticum durum flours were characterized by the high level of maltose, glucose, fructose, and free amino acids (FAA) correlated with the sole or main presence of obligately heterofermentative LAB, the lowest number of facultatively heterofermentative strains, and the low cell density of yeasts in the mature sourdoughs. This study highlighted, through a comprehensive and comparative approach, the dominant microbiotas of 19 Italian sourdoughs, which determined some of the peculiarities of the resulting traditional/typical Italian breads.     

Zoonotic transmission of tuberculosis between pastoralists and their livestock in South-East Ethiopia

Despite huge global efforts in tuberculosis (TB) control, pastoral areas remain under-investigated. During two years sputum and fine needle aspirate (FNA) specimens were collected from 260 Ethiopian pastoralists of Oromia and Somali Regional States with suspected pulmonary TB and from 32 cases with suspected TB lymphadenitis. In parallel, 207 suspected tuberculous lesions were collected from cattle, camels and goats at abattoirs. All specimens were processed and cultured for mycobacteria; samples with acid-fast stained bacilli (AFB) were further characterized by molecular methods including genus and deletion typing as well as spoligotyping. Non-tuberculous mycobacteria (NTM) were sequenced at the 16S rDNA locus. Culturing of AFB from human sputum and FNA samples gave a yield of 174 (67%) and 9 (28%) isolates, respectively. Molecular typing was performed on 173 of these isolates and 160 were confirmed as Mycobacterium tuberculosis, three as M. bovis, and the remaining 10 were typed as NTMs. Similarly, 48 AFB isolates (23%) yielded from tuberculous lesions of livestock, of which 39 were molecular typed, including 24 M. bovis and 4 NTMs from cattle, 1 M. tuberculosis and 1 NTM from camels and 9 NTMs from goats. Isolation of M. bovis from humans and M. tuberculosis from livestock suggests transmission between livestock and humans in the pastoral areas of South-East Ethiopia.     

On the ATP-Dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-CoA Dehydratase

Members of the 2-hydroxyacyl-CoA dehydratase enzyme family catalyze the β,α-dehydration of various CoA-esters in the fermentation of amino acids by clostridia. Abstraction of the nonacidic β-proton of the 2-hydroxyacyl-CoA compounds is achieved by the reductive generation of ketyl radicals on the substrate, which is initiated by the transfer of an electron at low redox potentials. The highly energetic electron needed on the dehydratase is donated by a [4Fe-4S] cluster containing ATPase, termed activator. We investigated the activator of the 2-hydroxyisocaproyl-CoA dehydratase from Clostridium difficile. The activator is a homodimeric protein structurally related to acetate and sugar kinases, Hsc70 and actin, and has a [4Fe-4S] cluster bound in the dimer interface. The crystal structures of the Mg-ADP, Mg-ADPNP, and nucleotide-free states of the reduced activator have been solved at 1.6-3.0 ? resolution, allowing us to define the position of Mg(2+) and water molecules in the vicinity of the nucleotides and the [4Fe-4S] cluster. The structures reveal redox- and nucleotide dependent changes agreeing with the modulation of the reduction potential of the [4Fe-4S] cluster by conformational changes. We also investigated the propensity of the activator to form a complex with its cognate dehydratase in the presence of Mg-ADP and Mg-ADPNP and together with the structural data present a refined mechanistic scheme for the ATP-dependent electron transfer between activator and dehydratase.     

Interleukin-6 induction by Helicobacter pylori in human macrophages is dependent on phagocytosis

BACKGROUND: The colonization of the gastric mucosa with Helicobacter pylori is accompanied by elevated levels of proinflammatory cytokines, such as interleukin-1 (IL-1), IL-6, and IL-8. The aim of our study was to determine the mechanisms of IL-6 stimulation in phagocytes upon H. pylori infection. MATERIALS AND METHODS: We investigated the secretion of IL-6 by different professional phagocytes from murine and human origin, including granulocyte- and monocyte-like cells and macrophages derived from human peripheral blood monocytes (PBMCs). The influence of viability, phagocytosis, and the impact of different subcellular fractions of H. pylori bacteria were evaluated. RESULTS: IL-6 levels induced by H. pylori were low in cell lines derived from murine and human monocytes and in human granulocyte-like cells. By contrast, macrophages derived from human PBMCs were highly responsive to both H. pylori and Escherichia coli. IL-6 induction was blocked by inhibition of actin-dependent processes prior to infection with H. pylori, but not with E. coli or E. coli lipopolysaccharide (LPS). Using cell fractionation, the most activity was found in the H. pylori membrane. H. pylori LPS exhibited a 10(3)- to 10(4)-fold lower biologic activity than E. coli LPS, suggesting a minor role for toll-like receptor 4 (TLR4)-mediated signalling from the exterior. CONCLUSIONS: From these data, we conclude that macrophages may be a major source of IL-6 in the gastric mucosa upon H. pylori infection. The IL-6 induction by H. pylori in these cells is a multifactorial process, which requires the uptake and presumably degradation of H. pylori bacteria.     

Colonization of barley (Hordeum vulgare) with Salmonella enterica and Listeria spp

Colonization of barley plants by the food-borne pathogens Salmonella enterica serovar typhimurium and three Listeria spp. (L. monocytogenes, L. ivanovii, L. innocua) was investigated in a monoxenic system. Herbaspirillum sp. N3 was used as a positive control and Escherichia coli HB101 as a negative control for endophytic root colonization. Colonization of the plants was tested 1-4 weeks after inoculation by determination of CFU, specific PCR assays and fluorescence in situ hybridization (FISH) with fluorescently labelled oligonucleotide probes in combination with confocal laser scanning microscopy (CLSM). Both S. enterica strains were found as endophytic colonizers of barley roots and reached up to 2.3 x 10(6) CFU per g root fresh weight after surface sterilization. The three Listeria strains had 10-fold fewer cell numbers after surface sterilization on the roots and therefore were similar to the results of nonendophytic colonizers, such as E. coli HB101. The FISH/CSLM approach demonstrated not only high-density colonization of the root hairs and the root surface by S. enterica but also a spreading to subjacent rhizodermis layers and the inner root cortex. By contrast, the inoculated Listeria spp. colonized the root hair zone but did not colonize other parts of the root surface. Endophytic colonization of Listeria spp. was not observed. Finally, a systemic spreading of S. enterica to the plant shoot (stems and leaves) was demonstrated using a specific PCR analysis and plate count technique.     

Reactive oxygen species impair Slo1 BK channel function by altering cysteine-mediated calcium sensing

Vascular dysfunction is a hallmark of many diseases, including coronary heart disease, stroke and diabetes. The underlying mechanisms of these disorders, which are intimately associated with inflammation and oxidative stress caused by excess reactive oxygen species (ROS), have remained elusive. Here we report that ROS are powerful inhibitors of vascular smooth muscle calcium-dependent Slo1 BK or Maxi-K potassium channels, an important physiological determinant of vascular tone. By targeting a cysteine residue near the Ca(2+) bowl of the BK alpha subunit, H(2)O(2) virtually eliminates physiological activation of the channel, with an inhibitory potency comparable to a knockout of the auxiliary subunit BK beta 1. These results reveal a molecular structural basis for the vascular dysfunction involving oxidative stress and provide a solid rationale for a potential use of BK openers in the prevention and treatment of cardiovascular disorders.     

Role of Hexose Transport in Control of Glycolytic Flux in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose concentrations and in the presence of oxygen, as in a glucose-limited chemostat, no ethanol is produced. The importance of the external glucose concentration suggests a central role for the affinity and maximal transport rates of yeast's glucose transporters in the control of ethanol production. Here we present a series of strains producing functional chimeras between the hexose transporters Hxt1 and Hxt7, each of which has distinct glucose transport characteristics. The strains display a range of decreasing glycolytic rates resulting in a proportional decrease in ethanol production. Using these strains, we show for the first time that at high glucose levels, the glucose uptake capacity of wild-type S. cerevisiae does not control glycolytic flux during exponential batch growth. In contrast, our chimeric Hxt transporters control the rate of glycolysis to a high degree. Strains whose glucose uptake is mediated by these chimeric transporters will undoubtedly provide a powerful tool with which to examine in detail the mechanism underlying the switch between fermentation and respiration in S. cerevisiae and will provide new tools for the control of industrial fermentations.     

Synovial fluid level of aggrecan ARGS fragments is a more sensitive marker of joint disease than glycosaminoglycan or aggrecan levels: a cross-sectional study

Introduction

The gene MICA encodes the protein major histocompatibility complex class I polypeptide-related sequence A. It is expressed in synovium of patients with rheumatoid arthritis (RA) and its implication in autoimmunity is discussed. We analyzed the association of genetic variants of MICA with susceptibility to RA.

Methods

Initially, 300 French Caucasian individuals belonging to 100 RA trio families were studied. An additional 100 independent RA trio families and a German Caucasian case-control cohort (90/182 individuals) were available for replication. As MICA is situated in proximity to known risk alleles of the HLA-DRB1 locus, our analysis accounted for linkage disequilibrium either by analyzing the subgroup consisting of parents not carrying HLA-DRB1 risk alleles with transmission disequilibrium test (TDT) or by implementing a regression model including all available data. Analysis included a microsatellite polymorphism (GCT)n and single-nucleotide polymorphisms (SNPs) rs3763288 and rs1051794.

Results

In contrast to the other investigated polymorphisms, the non-synonymously coding SNP MICA-250 (rs1051794, Lys196Glu) was strongly associated in the first family cohort (TDT: P = 0.014; regression model: odds ratio [OR] 0.46, 95% confidence interval [CI] 0.25 to 0.82, P = 0.007). Although the replication family sample showed only a trend, combined family data remained consistent with the hypothesis of MICA-250 association independent from shared epitope (SE) alleles (TDT: P = 0.027; regression model: OR 0.56, 95% CI 0.38 to 0.83, P = 0.003). We also replicated the protective association of MICA-250A within a German Caucasian cohort (OR 0.31, 95% CI 0.1 to 0.7, P = 0.005; regression model: OR 0.6, 95% CI 0.37 to 0.96, P = 0.032). We showed complete linkage disequilibrium of MICA-250 (D' = 1, r ² = 1) with the functional MICA variant rs1051792 (D' = 1, r ² = 1). As rs1051792 confers differential allelic affinity of MICA to the receptor NKG2D, this provides a possible functional explanation for the observed association.

Conclusions

We present evidence for linkage and association of MICA-250 (rs1051794) with RA independent of known HLA-DRB1 risk alleles, suggesting MICA as an RA susceptibility gene. However, more studies within other populations are necessary to prove the general relevance of this polymorphism for RA.     

The N Terminus of Phosphodiesterase TbrPDEB1 of Trypanosoma brucei Contains the Signal for Integration into the Flagellar Skeleton

The precise subcellular localization of the components of the cyclic AMP (cAMP) signaling pathways is a crucial aspect of eukaryotic intracellular signaling. In the human pathogen Trypanosoma brucei, the strict control of cAMP levels by cAMP-specific phosphodiesterases is essential for parasite survival, both in cell culture and in the infected host. Among the five cyclic nucleotide phosphodiesterases identified in this organism, two closely related isoenzymes, T. brucei PDEB1 (TbrPDEB1) (PDEB1) and TbrPDEB2 (PDEB2) are predominantly responsible for the maintenance of cAMP levels. Despite their close sequence similarity, they are distinctly localized in the cell. PDEB1 is mostly located in the flagellum, where it forms an integral part of the flagellar skeleton. PDEB2 is mainly located in the cell body, and only a minor part of the protein localizes to the flagellum. The current study, using transfection of procyclic trypanosomes with green fluorescent protein (GFP) reporters, demonstrates that the N termini of the two enzymes are essential for determining their final subcellular localization. The first 70 amino acids of PDEB1 are sufficient to specifically direct a GFP reporter to the flagellum and to lead to its detergent-resistant integration into the flagellar skeleton. In contrast, the analogous region of PDEB2 causes the GFP reporter to reside predominantly in the cell body. Mutagenesis of selected residues in the N-terminal region of PDEB2 demonstrated that single amino acid changes are sufficient to redirect the reporter from a cell body location to stable integration into the flagellar skeleton.In eukaryotes, the ubiquitous second messenger cyclic AMP (cAMP) is generated from ATP by membrane-integral or by cytoplasmic, CO₂-regulated cyclases (35, 44). The cAMP signal is processed by a small group of receiver proteins, including the regulatory subunit of protein kinase A (28), cAMP-gated ion channels (4), and the guanine-nucleotide-exchange proteins EPAC1 and EPAC2 (39). The cAMP signal is terminated by the action of a family of cyclic nucleotide-specific phosphodiesterases (PDEs) (9). This paradigm is rather straightforward, involves a limited number of players, and is generally well understood, at least in mammalian cells. However, much less is known about how individual cAMP signals are temporally and spatially controlled. Since most eukaryotic adenylyl cyclases are integral membrane proteins, often restricted to specific membrane subdomains (10), cAMP signaling is usually initiated at the cell membrane (40). However, diffusion of cAMP away from its site of generation is rapid, with diffusion coefficients being about 400 μm²/s (8, 15, 29), translating into diffusion velocities of 30 to 40 μm/s. As a consequence, the signal would reach the center of the cell with a diameter of 3 μm within less than 50 ms and would rapidly saturate the entire cell. While regulation through fluctuating cellular levels of cAMP represents a valid paradigm of cAMP signaling, it has become clear that other, more localized modes of cAMP signaling must also exist. Several groups have shown that the cAMP response of a given cell can differ depending on what set of receptors activates the cyclase response (14, 30, 41, 42). Similarly, the cAMP response of endothelial cells depends on the subcellular site where the cAMP is produced. They tighten their barrier function when cAMP is produced by membrane-bound adenylyl cyclases but become more permeable when cAMP is produced in the cytoplasm (17, 45). The distinct subcellular localization of cAMP signals was experimentally demonstrated using an array of techniques (29, 40, 55, 56).Physically tethered PDEs might serve to confine newly synthesized cAMP to defined microdomains. Only cAMP-binding proteins that are localized within or extend into such microdomains would be able to receive the cAMP signal (17, 49). cAMP concentrations within such domains might rise and fall rapidly, reaching peak concentrations much more rapidly and locally far beyond the steady-state cAMP levels measured in whole-cell extracts. Such spatially organized, tethered PDEs can generate local sinks into which cAMP disappears (1, 23). This paradigm would allow the simultaneous presence of numerous local cAMP concentration gradients within a single cell, allowing great flexibility in signal generation and intracellular signal transmission. This concept is based on the distinct subcellular localization and physical association of PDEs with subcellular structures and on the existence of localized subcellular cAMP pools, for which there is extensive experimental support (3, 5, 13, 50, 52). Interestingly, PDEs localized in different subcellular regions may still be able to compensate for each other. Ablation of the cilium-specific PDE1C from the olfactory neurons in the mouse did not prolong response termination, as long as the cytoplasmic PDE4 in the cell body was still present (11).The unicellular eukaryote Trypanosoma brucei is the causative agent of human sleeping sickness in sub-Saharan Africa. It belongs to the large order of the kinetoplastida, which includes many medically and economically important pathogens of humans, their livestock, and their crops worldwide (27). Trypanosomes are very small cells (about 15 by 3 μm in diameter) that carry a single flagellum (10 by 0.5 μm). The volume of a procyclic trypanosome of strain 427 is (9.6 ± 0.8) × 10⁻¹⁴ liter (Markus Engstler, personal communication), with the flagellum representing about 15% of this. A signaling threshold concentration of 1 μM cAMP corresponds to just about 30,000 molecules of cAMP per cell. Given a diffusion coefficient of 400 μm²/s (29), unrestricted diffusion of cAMP would swamp the cell within 50 ms. Obviously, temporal and spatial control of cAMP signaling is crucial for T. brucei. Strategically located, physically tethered PDEs might thus play an important role in the architecture of the cAMP signaling pathways in T. brucei.The genomes of T. brucei and of other kinetoplastids, such as T. vivax, T. cruzi, Leishmania major, L. infantum, and L. braziliensis, all code for the same set of five cyclic nucleotide-specific PDEs (25, 53). In T. brucei, the genes for T. brucei PDEB1 (TbrPDEB1; subsequently termed PDEB1) and TbrPDEB2 (PDEB2) are tandemly arranged on chromosome 9 and code for two very similar cAMP-specific PDEs, each with two GAF (mammalian cyclic GMP-dependent PDEs, Anabaena adenylyl cyclases, Escherichia coli FhlA) domains (21) in their N-terminal regions (38, 57). These two PDEs were also studied experimentally in T. cruzi (12) and L. major (24, 52), and orthologues are present in all kinetoplastid genomes available so far. Despite their high overall sequence similarity, PDEB1 and PDEB2 exhibit distinct subcellular localizations (31). PDEB1 is predominantly found in the flagellum, where it is stably associated with cytoskeletal components that are resistant to detergent extraction. In contrast, PDEB2 is mostly localized in the cell body, from where it is fully extractable by nonionic detergents. However, a minor fraction of PDEB2 also associates with the flagellar skeleton in a Triton-resistant manner, most likely through interaction with PDEB1. Earlier work has shown that both PDEB1and PDEB2 are essential enzymes in bloodstream-form T. brucei (31), while TbPDEA, TbPDEC, and TbPDED play minor roles (20; S. Kunz, unpublished data).     

Alien Invasive Slider Turtle in Unpredicted Habitat: A Matter of Niche Shift or of Predictors Studied?

Background

Species Distribution Models (SDMs) aim on the characterization of a species'' ecological niche and project it into geographic space. The result is a map of the species'' potential distribution, which is, for instance, helpful to predict the capability of alien invasive species. With regard to alien invasive species, recently several authors observed a mismatch between potential distributions of native and invasive ranges derived from SDMs and, as an explanation, ecological niche shift during biological invasion has been suggested. We studied the physiologically well known Slider turtle from North America which today is widely distributed over the globe and address the issue of ecological niche shift versus choice of ecological predictors used for model building, i.e., by deriving SDMs using multiple sets of climatic predictor.

Principal Findings

In one SDM, predictors were used aiming to mirror the physiological limits of the Slider turtle. It was compared to numerous other models based on various sets of ecological predictors or predictors aiming at comprehensiveness. The SDM focusing on the study species'' physiological limits depicts the target species'' worldwide potential distribution better than any of the other approaches.

Conclusion

These results suggest that a natural history-driven understanding is crucial in developing statistical models of ecological niches (as SDMs) while “comprehensive” or “standard” sets of ecological predictors may be of limited use.