Elevated level of the second messenger c-di-GMP in <Emphasis Type="Italic">Comamonas testosteroni</Emphasis> enhances biofilm formation and biofilm-based biodegradation of 3-chloroaniline

The bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous second messenger that determines bacterial lifestyle between the planktonic and biofilm modes of life. Although the role of c-di-GMP signaling in biofilm development and dispersal has been extensively studied, how c-di-GMP signaling influences environmental bioprocess activities such as biodegradation remains unexplored. To elucidate the impacts of elevating c-di-GMP level on environmental bioprocesses, we constructed a Comamonas testosteroni strain constitutively expressing a c-di-GMP synthase YedQ from Escherichia coli and examined its capability in biofilm formation and biodegradation of 3-chloroaniline (3-CA). The high c-di-GMP strain exhibited an increased binding to Congo red dye, a decreased motility, and an enhanced biofilm formation capability. In planktonic cultures, the strain with an elevated c-di-GMP concentration and the wild type could degrade 3-CA comparably well. However, under batch growth conditions with a high surface to volume ratio, an elevated c-di-GMP concentration in C. testosteroni significantly increased the contribution of biofilms in 3-CA biodegradation. In continuous submerged biofilm reactors, C. testosteroni with an elevated c-di-GMP level exhibited an enhanced 3-CA biodegradation and a decreased cell detachment rate. Taken together, this study provides a novel strategy to enhance biofilm-based biodegradation of toxic xenobiotic compounds through manipulating bacterial c-di-GMP signaling.     

Improved antimicrobial peptides based on acyl-lysine oligomers

We describe peptidomimetic oligomers that show rapid, nonhemolytic, broad-spectrum bactericidal properties in mice and do not induce the emergence of resistance. The oligomers contain acyl chains, which prevent the formation of stable secondary structure. This design appears advantageous over conventional antimicrobial peptides with respect to in vivo efficacy and safety, and may provide a convenient platform for the development of peptide antibiotics.     

Response variation following trauma: a translational neuroscience approach to understanding PTSD

Exposure to traumatic stress is a requirement for the development of posttraumatic stress disorder (PTSD). However, because the majority of trauma-exposed persons do not develop PTSD, examination of the typical effects of a stressor will not identify the critical components of PTSD risk or pathogenesis. Rather, PTSD represents a specific phenotype associated with a failure to recover from the normal effects of trauma. Thus, research must focus on identifying pre- and posttraumatic risk factors that explain the development of the disorder and the failure to reinstate physiological homeostasis. In this review, we summarize what is known about the clinical and biological characteristics of PTSD and articulate some of the gaps in knowledge that can be addressed by basic neuroscience research. We emphasize how knowledge about individual differences related to genetic and epigenetic factors in behavioral and brain responses to stress offers the hope of a deeper understanding of PTSD.     

Bile acids. LII. The synthesis of 24-nor-5α-cholic acid and its 3β-isomer

To aid in the identification of trihydroxy acidic metabolite(s) derived from β-sitosterol, 3α,7α,12α-trihydroxy-24-nor-5β-cholan-3oic acid was prepared and its methyl ester was treated with Raney nickel in boiling p-cymene to provide methyl 3-oxo-7α,12α-dihydroxy-24-nor-5α-cholanate, 3-oxo-7α,12α-dihydroxy-24-nor-5β-cholanate and 3-oxo-7α,12α-dihydroxy-24-norchol-4-enoate. The latter compound was synthesized from the 3-oxo-5β-derivative with SeO₂ to provide a product with identical properties. Catalytic reduction of either saturated 3-oxo-derivative provided the appropriate 3,7,12-triols isomeric at C-3. Results from gas liquid and partition chromatography, mass spectrometry, and other physical properties of the acids, their methyl esters and other derivatives are compatible with the assigned structures.     

Sustained release of cytokinins from natural polymers

The cytokinins 6-benzylaminopurine, 6-furfurylaminopurine and 6-(3-methyl-2-butenylamino) purine, were attached to starch and to cellulose by means of a carbamatic bond. The modified polysaccharides contained about one cytokinin molecule per 50 glucose units. The rate of release of the cytokinins was followed spectrophotometrically in aqueous solutions at different pHs. A good agreement with a first order model was found and the kinetic constants for the various systems were determined. The clear dependence on the pH of the medium supports a mechanism in which hydrolysis of the carbamatic bond is the rate determining step. The hormonal activity of the modified polymers was determined in the soybean callus bioassay and compared with the activities of non-bonded cytokinins. While high concentrations of free hormones cause inhibition of growth, such concentrations of bound hormone did not show inhibition.     

Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage

The handling and treatment of biological samples is critical when characterizing the composition of the intestinal microbiota between different ecological niches or diseases. Specifically, exposure of fecal samples to room temperature or long term storage in deep freezing conditions may alter the composition of the microbiota. Thus, we stored fecal samples at room temperature and monitored the stability of the microbiota over twenty four hours. We also investigated the stability of the microbiota in fecal samples during a six month storage period at −80°C. As the stability of the fecal microbiota may be affected by intestinal disease, we analyzed two healthy controls and two patients with irritable bowel syndrome (IBS). We used high-throughput pyrosequencing of the 16S rRNA gene to characterize the microbiota in fecal samples stored at room temperature or −80°C at six and seven time points, respectively. The composition of microbial communities in IBS patients and healthy controls were determined and compared using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline. The composition of the microbiota in fecal samples stored for different lengths of time at room temperature or −80°C clustered strongly based on the host each sample originated from. Our data demonstrates that fecal samples exposed to room or deep freezing temperatures for up to twenty four hours and six months, respectively, exhibit a microbial composition and diversity that shares more identity with its host of origin than any other sample.     

Testing in Microbiome-Profiling Studies with MiRKAT,the Microbiome Regression-Based Kernel Association Test

High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Distance-based analysis is a popular strategy for evaluating the overall association between microbiome diversity and outcome, wherein the phylogenetic distance between individuals’ microbiome profiles is computed and tested for association via permutation. Despite their practical popularity, distance-based approaches suffer from important challenges, especially in selecting the best distance and extending the methods to alternative outcomes, such as survival outcomes. We propose the microbiome regression-based kernel association test (MiRKAT), which directly regresses the outcome on the microbiome profiles via the semi-parametric kernel machine regression framework. MiRKAT allows for easy covariate adjustment and extension to alternative outcomes while non-parametrically modeling the microbiome through a kernel that incorporates phylogenetic distance. It uses a variance-component score statistic to test for the association with analytical p value calculation. The model also allows simultaneous examination of multiple distances, alleviating the problem of choosing the best distance. Our simulations demonstrated that MiRKAT provides correctly controlled type I error and adequate power in detecting overall association. “Optimal” MiRKAT, which considers multiple candidate distances, is robust in that it suffers from little power loss in comparison to when the best distance is used and can achieve tremendous power gain in comparison to when a poor distance is chosen. Finally, we applied MiRKAT to real microbiome datasets to show that microbial communities are associated with smoking and with fecal protease levels after confounders are controlled for.     

New tryptophanase inhibitors: Towards prevention of bacterial biofilm formation

Tryptophanase (tryptophan indole-lyase, Tnase, EC 4.1.99.1), a bacterial enzyme with no counterpart in eukaryotic cells, produces from L-tryptophan pyruvate, ammonia and indole. It was recently suggested that indole signaling plays an important role in the stable maintenance of multicopy plasmids. In addition, Tnase was shown to be capable of binding Rcd, a short RNA molecule involved in resolution of plasmid multimers. Binding of Rcd increases the affinity of Tnase for tryptophan, and it was proposed that indole is involved in bacteria multiplication and biofilm formation. Biofilm-associated bacteria may cause serious infections, and biofilm contamination of equipment and food, may result in expensive consequences. Thus, optimal and specific factors that interact with Tnase can be used as a tool to study the role of this multifunctional enzyme as well as antibacterial agents that may affect biofilm formation. Most known quasi-substrates inhibit Tnase at the mM range. In the present work, the mode of Tnase inhibition by the following compounds and the corresponding Ki values were: S-phenylbenzoquinone-L-tryptophan, uncompetitively, 101 μM; α-amino-2-(9,10-anthraquinone)-propanoic acid, noncompetitively, 174 μM; L-tryptophane-ethylester, competitively, 52 μM; N-acetyl-L-tryptophan, noncompetitively, 48 μM. S-phenylbenzoquinone-L-tryptophan and α-amino-2-(9,10-anthraquinone)-propanoic acid were newly synthesized.     

A distributed parameter model for an airlift fermentor. Effects of pressure

A previously presented model for an airlift fermentor is extended by considering the variations of pressure along the tubes. The fluid dynamics of the system is represented with the acid of correlations obtained from experiments. Only oxygen concentrations are considerations are considered. The influences of the various parameters affecting the system are analyzed. The model allows prediction of oxygen concentrations in the different points of an airlift fermentor and calculation of the best values of the gas flow rate.