Real-time quantification of Pseudomonas fluorescens cell removal from glass surfaces due to bacteriophage varphiS1 application

Aims:  To study the efficacy of the lytic phage φS1 in eliminating Pseudomonas fluorescens in the early stage of biofilm formation, using an in situ and real time methodology for cell quantification.
Methods and Results:  Cell adhesion and phage infection studies were carried out in a parallel plate flow chamber under laminar conditions. Cells were allowed to adhere until reaching 1·7–1·8 × 10⁶ cells cm⁻² and phage infection was performed with two different phage concentrations (2 × 10⁹ PFU ml⁻¹ and 1 × 10¹⁰ PFU ml⁻¹). Phage concentration clearly affects the speed of infection. The less concentrated phage solution promoted a three times slower rate of cell removal but did not affect the overall percentage of cell removal. In fact, after a longer infection period the less concentrated phage solution reached the same 93% cell removal value.
Conclusions:  Phages are efficient in the eradication of bacterial cells at the early stage of biofilm formation and their presence at the surface did not allow bacterial recolonization of the surface.
Significance and Impact of the Study:  To date, no published studies have been made concerning in situ and real time quantification of cell removal from surfaces due to phage action.     

Effects of inoculation strategy and cultivation approach on the performance of microbial fuel cell using marine sediment as bio-matrix

Aims: To investigate the effects of inoculation strategy and cultivation approach on the performance of microbial fuel cell (MFC). Methods and Results: A dual‐chamber sediment fuel cell was set up fed with glucose under batch condition. At day 30, the supernatant consortium was partly transferred and used as inoculum for the evaluation of cultivation approach. Power output gradually increased to 9·9 mW m^?2 over 180 days, corresponding to coulombic efficiency (CE) of 29·6%. Separated biofilms attached anode enabled power output and CE dramatically up to 100·9 mW m^?2 and over 50%, respectively, whereas the residual sediment catalysed MFC gave a poor performance. MFC catalysed by in situ supernatant consortium demonstrated more than twice higher power than MFC catalysed by the supernatant consortium after Fe(OH)₃ cultivation. However, the re‐generation of biofilms from the latter largely enhanced the cell performance. Conclusions: MFC exhibited a more efficient inducement of electroactive consortium than Fe(OH)₃ cultivation. MFC performance varied depending on different inoculation strategies. Significance and Impact of the Study: This is the first time to study cultivation approach affecting electricity generation. In addition, anodic limitations of mass and electron transfer were discussed through MFC catalysed by sediment‐based bio‐matrix.     

A combined computational-experimental analyses of selected metabolic enzymes in Pseudomonas species

Comparative genomic analysis has revolutionized our ability to predict the metabolic subsystems that occur in newly sequenced genomes, and to explore the functional roles of the set of genes within each subsystem. These computational predictions can considerably reduce the volume of experimental studies required to assess basic metabolic properties of multiple bacterial species. However, experimental validations are still required to resolve the apparent inconsistencies in the predictions by multiple resources. Here, we present combined computational-experimental analyses on eight completely sequenced Pseudomonas species. Comparative pathway analyses reveal that several pathways within the Pseudomonas species show high plasticity and versatility. Potential bypasses in 11 metabolic pathways were identified. We further confirmed the presence of the enzyme O-acetyl homoserine (thiol) lyase (EC: 2.5.1.49) in P. syringae pv. tomato that revealed inconsistent annotations in KEGG and in the recently published SYSTOMONAS database. These analyses connect and integrate systematic data generation, computational data interpretation, and experimental validation and represent a synergistic and powerful means for conducting biological research.     

Probability of detecting disease-associated single nucleotide polymorphisms in case-control genome-wide association studies

Some case-control genome-wide association studies (CCGWASs) select promising single nucleotide polymorphisms (SNPs) by ranking corresponding p-values, rather than by applying the same p-value threshold to each SNP. For such a study, we define the detection probability (DP) for a specific disease-associated SNP as the probability that the SNP will be "T-selected," namely have one of the top T largest chi-square values (or smallest p-values) for trend tests of association. The corresponding proportion positive (PP) is the fraction of selected SNPs that are true disease-associated SNPs. We study DP and PP analytically and via simulations, both for fixed and for random effects models of genetic risk, that allow for heterogeneity in genetic risk. DP increases with genetic effect size and case-control sample size and decreases with the number of nondisease-associated SNPs, mainly through the ratio of T to N, the total number of SNPs. We show that DP increases very slowly with T, and the increment in DP per unit increase in T declines rapidly with T. DP is also diminished if the number of true disease SNPs exceeds T. For a genetic odds ratio per minor disease allele of 1.2 or less, even a CCGWAS with 1000 cases and 1000 controls requires T to be impractically large to achieve an acceptable DP, leading to PP values so low as to make the study futile and misleading. We further calculate the sample size of the initial CCGWAS that is required to minimize the total cost of a research program that also includes follow-up studies to examine the T-selected SNPs. A large initial CCGWAS is desirable if genetic effects are small or if the cost of a follow-up study is large.     

Effects of water gradients on soil enzyme activity and active organic carbon composition under Carex lasiocarpa marsh

The responses of soil enzyme activity of freshwater marsh, microbial biomass carbon (MBC), dissolved organic carbon (DOC) and aboveground biomass to water gradients were studied with Carex lasiocarpa pot culture experiment. The relationships between soil enzyme activity and MBC, DOC and aboveground biomass were discussed. The water gradients were W1, 15 cm; W2, ?5 cm; W3, ?5–5 cm; W4, submerged. The results indicated that acid phosphatase, invertase and urease activities were decreased with the increase of water level, while catalase activity was increased with moisture content increasing. Drying-wetting alternation (W3) increased soil enzyme activities if compared with W1. MBC content followed the order of W3 > W1 > W2 > W4, and the activities of invertase, urease and catalase were significantly positively correlated with MBC (p < 0.05). DOC content presented the order of W4 > W1 > W3 > W2, and the activities of urease and acid phosphatase were most significantly negatively correlated with DOC (p < 0.01). In addition, drying-wetting alternation promoted the growth of Carex lasiocarpa. When water submerged plants, the growth of Carex lasiocarpa was significantly inhibited. The aboveground biomass was positively related to soil enzyme activities. There were close relationships between the activities of invertase, urease and catalase and the growth situation of Carex lasiocarpa.     

Contribution of dipole-dipole interactions to the stability of the collagen triple helix

Unveiling sequence-stability and structure-stability relationships is a major goal of protein chemistry and structural biology. Despite the enormous efforts devoted, answers to these issues remain elusive. In principle, collagen represents an ideal system for such investigations due to its simplified sequence and regular structure. However, the definition of the molecular basis of collagen triple helix stability has hitherto proved to be a difficult task. Particularly puzzling is the decoding of the mechanism of triple helix stabilization/destabilization induced by imino acids. Although the propensity-based model, which correlates the propensities of the individual imino acids with the structural requirements of the triple helix, is able to explicate most of the experimental data, it is unable to predict the rather high stability of peptides embedding Gly-Hyp-Hyp triplets. Starting from the available X-ray structures of this polypeptide, we carried out an extensive quantum chemistry analysis of the mutual interactions established by hydroxyproline residues located at the X and Y positions of the Gly-X-Y motif. Our data clearly indicate that the opposing rings of these residues establish significant van der Waals and dipole-dipole interactions that play an important role in triple helix stabilization. These findings suggest that triple helix stabilization can be achieved by distinct structural mechanisms. The interplay of these subtle but recurrent effects dictates the overall stability of this widespread structural motif.     

Growth with high planktonic biomass in Shewanella oneidensis fuel cells

Shewanella oneidensis MR-1 grew for over 50 days in microbial fuel cells, incompletely oxidizing lactate to acetate with high recovery of the electrons derived from this reaction as electricity. Electricity was produced with lactate or hydrogen and current was comparable to that of electricigens which completely oxidize organic substrates. However, unlike fuel cells with previously described electricigens, in which cells are primarily attached to the anode, at least as many of the S. oneidensis cells were planktonic as were attached to the anode. These results demonstrate that S. oneidensis may conserve energy for growth with an electrode serving as an electron acceptor and suggest that multiple strategies for electron transfer to fuel cell anodes exist.     

Yeast N(alpha)-terminal acetyltransferases are associated with ribosomes

N-terminal acetylation is one of the most common modifications, occurring on the vast majority of eukaryotic proteins. Saccharomyces cerevisiae contains three major NATs, designated NatA, NatB, and NatC, with each having catalytic subunits Ard1p, Nat3p, and Mak3p, respectively. Gautschi et al. (Gautschi et al. [2003] Mol Cell Biol 23: 7403) previously demonstrated with peptide crosslinking experiments that NatA is bound to ribosomes. In our studies, biochemical fractionation in linear sucrose density gradients revealed that all of the NATs are associated with mono- and polyribosome fractions. However only a minor portion of Nat3p colocalized with the polyribosomes. Disruption of the polyribosomes did not cause dissociation of the NATs from ribosomal subparticles. The NAT auxiliary subunits, Nat1p and Mdm20p, apparently are required for efficient binding of the corresponding catalytic subunits to the ribosomes. Deletions of the genes corresponding to auxiliary subunits significantly diminish the protein levels of the catalytic subunits, especially Nat3p, while deletions of the catalytic subunits produced less effect on the stability of Nat1p and Mdm20p. Also two ribosomal proteins, Rpl25p and Rpl35p, were identified in a TAP-affinity purified NatA sample. Moreover, Ard1p copurifies with Rpl35p-TAP. We suggest that these two ribosomal proteins, which are in close proximity to the ribosomal exit tunnel, may play a role in NatA attachment to the ribosome.     

Protein-protein docking by simulating the process of association subject to biochemical constraints

We present a computational procedure for modeling protein-protein association and predicting the structures of protein-protein complexes. The initial sampling stage is based on an efficient Brownian dynamics algorithm that mimics the physical process of diffusional association. Relevant biochemical data can be directly incorporated as distance constraints at this stage. The docked configurations are then grouped with a hierarchical clustering algorithm into ensembles that represent potential protein-protein encounter complexes. Flexible refinement of selected representative structures is done by molecular dynamics simulation. The protein-protein docking procedure was thoroughly tested on 10 structurally and functionally diverse protein-protein complexes. Starting from X-ray crystal structures of the unbound proteins, in 9 out of 10 cases it yields structures of protein-protein complexes close to those determined experimentally with the percentage of correct contacts >30% and interface backbone RMSD <4 A. Detailed examination of all the docking cases gives insights into important determinants of the performance of the computational approach in modeling protein-protein association and predicting of protein-protein complex structures.     

The role of testosterone in aggressive and non-aggressive risk-taking in adolescent boys

While there exists increasing evidence of a relationship between testosterone (T) and risk-taking (RT), many issues remain unsolved. This paper tries to address two main-questions: (i) does T influence aggressive risk-taking (ART) and/or non-aggressive risk-taking (NART) behavior and (ii) is this relationship stable throughout age and pubertal development and how is the relationship affected by affiliations with peers that are highly involved in RT, referred to as differential association (DA)? For a sample of 301 third-grade adolescent boys (mean age 14.4 years), we assessed the relationship between serum levels of T and estradiol (E2), DA and ART/NART. Significant effects of SHBG (Beta=-0.15; p<0.029) and free testosterone (FT) (Beta=0.23; p<0.003) on NART were shown. No significant effects were found with respect to ART. Further analyses showed that the FT-NART and the FT-ART relations differed as to age but not as to pubertal development (PD) and that the relationship between FT and RT is mediated by DA as such that individuals with higher levels of FT have friends that are more involved in RT and their influence contributes to increased levels of RT. Our results indicate that hormone-related interests and predispositions may influence the development of affiliations with risk-taking peers, a factor which is crucial in understanding adolescent RT.