Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing,benzene-degrading microbial consortium

Benzene is a major contaminant in various environments, but the mechanisms behind its biodegradation under strictly anoxic conditions are not yet entirely clear. Here we analyzed a benzene-degrading, sulfate-reducing enrichment culture originating from a benzene-contaminated aquifer by a metagenome-based functional metaproteomic approach, using protein-based stable isotope probing (protein-SIP). The time-resolved, quantitative analysis of carbon fluxes within the community supplied with either ¹³C-labeled benzene or ¹³C-labeled carbonate yielded different functional groups of organisms, with their peptides showing specific time dependencies of ¹³C relative isotope abundance indicating different carbon utilization. Through a detailed analysis of the mass spectrometric (MS) data, it was possible to quantify the utilization of the initial carbon source and the metabolic intermediates. The functional groups were affiliated to Clostridiales, Deltaproteobacteria and Bacteroidetes/Chlorobi. The Clostridiales-related organisms were involved in benzene degradation, putatively by fermentation, and additionally used significant amounts of carbonate as a carbon source. The other groups of organisms were found to perform diverse functions, with Deltaproteobacteria degrading fermentation products and Bacteroidetes/Chlorobi being putative scavengers feeding on dead cells. A functional classification of identified proteins supported this allocation and gave further insights into the metabolic pathways and the interactions between the community members. This example shows how protein-SIP can be applied to obtain temporal and phylogenetic information about functional interdependencies within microbial communities.     

Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing

A sulfate-reducing consortium maintained for several years in the laboratory with m-xylene as sole source of carbon and energy was characterized by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of PCR-amplified 16S rRNA genes and stable isotope probing of proteins (Protein-SIP). During growth upon m-xylene or methyl-labeled m-xylene (1,3-dimethyl-(13)C(2)-benzene), a phylotype affiliated to the family Desulfobacteriaceae became most abundant. A second dominant phylotype was affiliated to the phylum Epsilonproteobacteria. In cultures grown with methyl-labeled m-xylene, 331 proteins were identified by LC-MS/MS analysis. These proteins were either not (13)C-labeled (23%) or showed a (13)C-incorporation of 19-22 atom% (13)C (77%), the latter demonstrating that methyl groups of m-xylene were assimilated. (13)C-labeled proteins were involved in anaerobic m-xylene biodegradation, in sulfate reduction, in the Wood-Ljungdahl-pathway, and in general housekeeping functions. Thirty-eight percent of the labeled proteins were affiliated to Deltaproteobacteria. Probably due to a lack of sequence data from Epsilonproteobacteria, only 14 proteins were assigned to this phylum. Our data suggest that m-xylene is assimilated by the Desulfobacteriaceae phylotype, whereas the role of the Epsilonproteobacterium in the consortium remained unclear.     

Developing Neurons Form Transient Nanotubes Facilitating Electrical Coupling and Calcium Signaling with Distant Astrocytes

Despite the well-documented cooperation between neurons and astrocytes little is known as to how these interactions are initiated. We show here by differential interference contrast microscopy that immature hippocampal neurons generated short protrusions towards astrocytes resulting in tunneling nanotube (TNT) formation with an average lifetime of 15 minutes. Fluorescence microscopy revealed that all TNTs between the two cell types contained microtubules but 35% of them were F-actin negative. Immunolabeling against connexin 43 showed that this gap junction marker localized at the contact site of TNTs with astrocytes. Using optical membrane-potential measurements combined with mechanical stimulation, we observed that ∼35% of immature neurons were electrically coupled with distant astrocytes via TNTs up to 5 hours after co-culture but not after 24 hours. Connexin 43 was expressed by most neurons at 5 hours of co-culture but was not detected in neurons after 24 hours. We show that TNTs mediated the propagation of both depolarization and transient calcium signals from distant astrocytes to neurons. Our findings suggest that within a limited maturation period developing neurons establish electrical coupling and exchange of calcium signals with astrocytes via TNTs, which correlates with a high neuronal expression level of connexin 43. This novel cell-cell communication pathway between cells of the central nervous system provides new concepts in our understanding of neuronal migration and differentiation.     

Experimental investigation of nitrogen and oxygen isotope fractionation in nitrate and nitrite during denitrification

In batch experiments, we studied the isotope fractionation of nitrogen and oxygen during denitrification of two bacterial strains (Azoarcus sp. strain DSM 9056 and Pseudomonas pseudoalcaligenes strain F10). Denitrification experiments were conducted with succinate and toluene as electron donor in three waters with a distinct oxygen isotope composition. Nitrate consumption was observed in all batch experiments. Reaction rates for succinate experiments were more than six times higher than those for toluene experiments. Nitrogen and oxygen isotopes became progressively enriched in the remaining nitrate pool in the course of the experiments; the nitrogen and oxygen isotope fractionation varied between 8.6–16.2 and 4.0–7.3‰, respectively. Within this range, neither electron donors nor the oxygen isotope composition of the medium affected the isotope fractionation process. The experimental results provide evidence that the oxygen isotope fractionation during nitrate reduction is controlled by a kinetic isotope effect which can be quantified using the Rayleigh model. The isotopic examination of nitrite released upon denitrification revealed that nitrogen isotope fractionation largely follows the fractionation of the nitrate pool. However, the oxygen isotope values of nitrite are clearly influenced by a rapid isotope equilibration with the oxygen of the ambient water. Even though this equilibration may in part be due to storage, it shows that under certain natural conditions (re-oxidation of nitrite) the nitrate pool may also be indirectly affected by an isotope equilibration.     

Tunneling nanotube (TNT)-like structures facilitate a constitutive, actomyosin-dependent exchange of endocytic organelles between normal rat kidney cells

Tunneling nanotube (TNT)-like structures are intercellular membranous bridges that mediate the transfer of various cellular components including endocytic organelles. To gain further insight into the magnitude and mechanism of organelle transfer, we performed quantitative studies on the exchange of fluorescently labeled endocytic structures between normal rat kidney (NRK) cells. This revealed a linear increase in both the number of cells receiving organelles and the amount of transferred organelles per cell over time. The intercellular transfer of organelles was unidirectional, independent of extracellular diffusion, and sensitive to shearing force. In addition, during a block of endocytosis, a significant amount of transfer sustained. Fluorescence microscopy revealed TNT-like bridges between NRK cells containing F-actin but no microtubules. Depolymerization of F-actin led to the disappearance of TNT and a strong inhibition of organelle exchange. Partial ATP depletion did not affect the number of TNT but strongly reduced organelle transfer. Interestingly, the myosin II specific inhibitor S-(−)-blebbistatin strongly induced both organelle transfer and the number of TNT, while the general myosin inhibitor 2,3-butanedione monoxime induced the number of TNT but significantly inhibited transfer. Taken together, our data indicate a frequent and continuous exchange of endocytic organelles between cells via TNT by an actomyosin-dependent mechanism.     

Acoustic signals of a solitary subterranean rodent Ctenomys talarum (Rodentia: Ctenomyidae): physical characteristics and behavioural correlates

The purpose of this study was to analyse and describe vocalizations of a solitary subterranean rodent, Ctenomys talarum. In adult C. talarum five different sounds (four true vocalizations and one mechanical sound) were recorded during different behavioural contexts. Using data from the laboratory and literature, we classified these vocalizations as territorial, distress, and mating calls. We found that the vocalization range in C. talarum is shifted towards low frequencies, which transmit better in underground burrows and match well the hearing range described for other species of subterranean rodents. These low-frequency vocalizations, also found in other non-related subterranean rodents, may reflect an adaptation to the acoustic conditions of the habitat. Electronic Publication     

Parkinson Phenotype in Aged PINK1-Deficient Mice Is Accompanied by Progressive Mitochondrial Dysfunction in Absence of Neurodegeneration

Background

Parkinson''s disease (PD) is an adult-onset movement disorder of largely unknown etiology. We have previously shown that loss-of-function mutations of the mitochondrial protein kinase PINK1 (PTEN induced putative kinase 1) cause the recessive PARK6 variant of PD.

Methodology/Principal Findings

Now we generated a PINK1 deficient mouse and observed several novel phenotypes: A progressive reduction of weight and of locomotor activity selectively for spontaneous movements occurred at old age. As in PD, abnormal dopamine levels in the aged nigrostriatal projection accompanied the reduced movements. Possibly in line with the PARK6 syndrome but in contrast to sporadic PD, a reduced lifespan, dysfunction of brainstem and sympathetic nerves, visible aggregates of α-synuclein within Lewy bodies or nigrostriatal neurodegeneration were not present in aged PINK1-deficient mice. However, we demonstrate PINK1 mutant mice to exhibit a progressive reduction in mitochondrial preprotein import correlating with defects of core mitochondrial functions like ATP-generation and respiration. In contrast to the strong effect of PINK1 on mitochondrial dynamics in Drosophila melanogaster and in spite of reduced expression of fission factor Mtp18, we show reduced fission and increased aggregation of mitochondria only under stress in PINK1-deficient mouse neurons.

Conclusion

Thus, aging Pink1^−/− mice show increasing mitochondrial dysfunction resulting in impaired neural activity similar to PD, in absence of overt neuronal death.     

Creatine Fails to Augment the Benefits from Resistance Training in Patients with HIV Infection: A Randomized,Double-Blind,Placebo-Controlled Study

Background

Progressive resistance exercise training (PRT) improves physical functioning in patients with HIV infection. Creatine supplementation can augment the benefits derived from training in athletes and improve muscle function in patients with muscle wasting. The objective of this study was to determine whether creatine supplementation augments the effects of PRT on muscle strength, energetics, and body composition in HIV-infected patients.

Methodology/Principal Findings

This is a randomized, double blind, placebo-controlled, clinical research center-based, outpatient study in San Francisco. 40 HIV–positive men (20 creatine, 20 placebo) enrolled in a 14-week study. Subjects were randomly assigned to receive creatine monohydrate or placebo for 14 weeks. Treatment began with a loading dose of 20 g/day or an equivalent number of placebo capsules for 5 days, followed by maintenance dosing of 4.8 g/day or placebo. Beginning at week 2 and continuing to week 14, all subjects underwent thrice-weekly supervised resistance exercise while continuing on the assigned study medication (with repeated 6-week cycles of loading and maintenance). The main outcome measurements included muscle strength (one repetition maximum), energetics (³¹P magnetic resonance spectroscopy), composition and size (magnetic resonance imaging), as well as total body composition (dual-energy X-ray absorptiometry). Thirty-three subjects completed the study (17 creatine, 16 placebo). Strength increased in all 8 muscle groups studied following PRT, but this increase was not augmented by creatine supplementation (average increase 44 vs. 42%, difference 2%, 95% CI −9.5% to 13.9%) in creatine and placebo, respectively). There were no differences between groups in changes in muscle energetics. Thigh muscle cross-sectional area increased following resistance exercise, with no additive effect of creatine. Lean body mass (LBM) increased to a significantly greater extent with creatine.

Conclusions / Significance

Resistance exercise improved muscle size, strength and function in HIV-infected men. While creatine supplementation produced a greater increase in LBM, it did not augment the robust increase in strength derived from PRT.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00484627","term_id":"NCT00484627"}}NCT00484627     

The release of vaccinia virus from infected cells requires RhoA-mDia modulation of cortical actin

Prior to being released from the infected cell, intracellular enveloped vaccinia virus particles are transported from their perinuclear assembly site to the plasma membrane along microtubules by the motor kinesin-1. After fusion with the plasma membrane, stimulation of actin tails beneath extracellular virus particles acts to enhance cell-to-cell virus spread. However, we lack molecular understanding of events that occur at the cell periphery just before and during the liberation of virus particles. Using live cell imaging, we show that virus particles move in the cell cortex, independently of actin tail formation. These cortical movements and the subsequent release of virus particles, which are both actin dependent, require F11L-mediated inhibition of RhoA-mDia signaling. We suggest that the exit of vaccinia virus from infected cells has strong parallels to exocytosis, as it is dependent on the assembly and organization of actin in the cell cortex.     

Factors controlling the carbon isotope fractionation of tetra- and trichloroethene during reductive dechlorination by Sulfurospirillum ssp. and Desulfitobacterium sp. strain PCE-S

Carbon stable isotope fractionation of tetrachloroethene (PCE) and trichloroethene (TCE) was investigated during reductive dechlorination. Growing cells of Sulfurospirillum multivorans, Sulfurospirillum halorespirans, or Desulfitobacterium sp. strain PCE-S, the respective crude extracts and the abiotic reaction with cyanocobalamin (vitamin B(12)) were used. Fractionation of TCE (alphaC=1.0132-1.0187) by S. multivorans was more than one order of magnitude higher than values previously observed for tetrachloroethene (PCE) (alphaC=1.00042-1.0017). Similar differences in fractionation were observed during reductive dehalogenation by the close relative S. halorespirans with alphaC=1.0046-1.032 and alphaC=1.0187-1.0229 for PCE and TCE respectively. TCE carbon isotope fractionation (alphaC=1.0150) by the purified PCE-reductive dehalogenase from S. multivorans was more than one order of magnitude higher than fractionation of PCE (alphaC=1.0017). Carbon isotope fractionation of TCE by Desulfitobacterium sp. strain PCE-S (alphaC=1.0109-1.0122) as well as during the abiotic reaction with cyanocobalamin (alphaC=1.0154) was in a similar range to previously reported values for fractionation by mixed microbial cultures. In contrast with previous results with PCE, no effects due to rate limitations, uptake or transport of the substrate to the reactive site could be observed during TCE dechlorination. Our results show that prior to a mechanistic interpretation of stable isotope fractionation factors it has to be carefully verified how other factors such as uptake or transport affect the isotope fractionation during degradation experiments with microbial cultures.