Immune activation of type I IFNs by Listeria monocytogenes occurs independently of TLR4, TLR2, and receptor interacting protein 2 but involves TNFR-associated NF kappa B kinase-binding kinase 1

Type I IFNs are well established antiviral cytokines that have also been shown to be induced by bacteria. However, the signaling mechanisms regulating the activation of these cytokines during bacterial infections remain poorly defined. We show that although Gram-negative bacteria can activate the type I IFN pathway through TLR4, the intracellular Gram-positive bacterium Listeria monocytogenes (LM) can do so independently of TLR4 and TLR2. Furthermore, experiments using genetic mutants and chemical inhibitors suggest that LM-induced type I IFN activation occurs by an intracellular pathway involving the serine-threonine kinase TNFR-associated NF-kappaB kinase (TANK)-binding kinase 1 (TBK1). Interestingly, receptor-interacting protein 2, a component of the recently discovered nucleotide-binding oligomerization domain-dependent intracellular detection pathway, was not involved. Taken together, our data describe a novel signal transduction pathway involving TBK1 that is used by LM to activate type I IFNs. Additionally, we provide evidence that both the LM- and TLR-dependent pathways converge at TBK1 to activate type I IFNs, highlighting the central role of this molecule in modulating type I IFNs in host defense and disease.     

Histology of vitamin A induced ectopic limbs and normal hind limbs in tadpoles of Polypedates maculatus

Marked histological similarities were observed between normal and vitamin A induced ectopic limb buds of P. maculatus. However, close association of nephric tubule and lateral plate mesoderm, as seen in normal hind limb bud does not seem to be essential for ectopic limb development. The ectopic limbs tend to develop in pairs.     

Dynamic influences on a high-affinity, high-specificity interaction involving the C-terminal SH3 domain of p67phox

An analysis of the backbone dynamics of the C-terminal Src homology 3 (SH3) domain of p67(phox), p67(phox)SH3(C), in complex with a 32-residue high-affinity (K(d) = 24 nM) peptide, Pf, from the C-terminal region of p47(phox) is presented. This paper represents the first detailed analysis of the backbone dynamics and the ligand-induced changes therein of a high-affinity, high-specificity interaction involving an SH3 domain. The dynamic features are compared with those in the high-affinity, highly specific interaction between the SH3 domain of C-terminal Src kinase (Csk-SH3) and a proline-rich peptide from proline-enriched phosphatase (PEP). Both systems share common dynamic features especially in the canonical PxxP motif recognition surface where slow micro- to millisecond time scale dynamics persist on complex formation especially in several residues that are implicated in ligand recognition and in stabilizing the SH3 fold. These residues are highly conserved in SH3 domains. Ile505, which lies outside the PxxP recognition motif on p67(phox)SH3(C) and is key in conferring high specificity to the p67(phox)SH3(C)/Pf interaction, becomes more disordered upon complex formation. This behavior is similar to that seen in the residues that constitute the specificity surface in Csk-SH3.     

Can contact potentials reliably predict stability of proteins?

The simplest approximation of interaction potential between amino acid residues in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation. Finding a contact potential capable of predicting free energies of protein states across a variety of protein families will aid protein folding and engineering in silico on a computationally tractable time-scale. We test the ability of contact potentials to accurately and transferably (across various protein families) predict stability changes of proteins upon mutations. We develop a new methodology to determine the contact potentials in proteins from experimental measurements of changes in protein's thermodynamic stabilities (DeltaDeltaG) upon mutations. We apply our methodology to derive sets of contact interaction parameters for a hierarchy of interaction models including solvation and multi-body contact parameters. We test how well our models reproduce experimental measurements by statistical tests. We evaluate the maximum accuracy of predictions obtained by using contact potentials and the correlation between parameters derived from different data-sets of experimental (DeltaDeltaG) values. We argue that it is impossible to reach experimental accuracy and derive fully transferable contact parameters using the contact models of potentials. However, contact parameters may yield reliable predictions of DeltaDeltaG for datasets of mutations confined to the same amino acid positions in the sequence of a single protein.     

Sterilizing filtration of plasmid DNA: effects of plasmid concentration, molecular weight, and conformation

Plasmid DNA purification development has been driven by the increased need for large quantities of highly purified, sterile plasmid DNA for clinical studies. Detailed characterization and development of the terminal sterile filtration process step is often limited due to time constraints and the scarcity of sufficient quantities of purified plasmid. However, the large size of the plasmid molecule and variations in conformation can lead to significant yield losses if this process step is not optimized. In this work, the gradual pore-plugging model of flow decay was found to be valid for plasmid DNA by using an ultra scaledown apparatus (1-4 cm(2) filter area). Filtration capacity was found to be insensitive to pressure. Multiple filter types were screened and both source and composition of materials were found to affect filter capacity dramatically. The filter capacity for plasmid was improved by increasing plasmid concentrations as well as by modifying buffer conditions to reduce the apparent size of the plasmid. Filtration capacities varied over a greater than 2 log range when plasmids with sizes ranging from 5.5 to 11 kb and supercoiled plasmid content of 55-95% were explored. Larger plasmids and feeds with lower supercoiled contents led to reduced capacities. These results can be used to define conditions for scale-up of plasmid sterile filtration, as evidenced by processing a 30 g lot using a filtration area of 1,000 cm(2), with a 96% yield, based on filtration capacity data from 4 cm(2) test filters.     

In-cell NMR for protein-protein interactions (STINT-NMR)

We describe an in-cell NMR-based method for mapping the structural interactions (STINT-NMR) that underlie protein-protein complex formation. This method entails sequentially expressing two (or more) proteins within a single bacterial cell in a time-controlled manner and monitoring their interactions using in-cell NMR spectroscopy. The resulting NMR data provide a complete titration of the interaction and define structural details of the interacting surfaces at atomic resolution. Unlike the case where interacting proteins are simultaneously overexpressed in the labeled medium, in STINT-NMR the spectral complexity is minimized because only the target protein is labeled with NMR-active nuclei, which leaves the interactor protein(s) cryptic. This method can be combined with genetic and molecular screens to provide a structural foundation for proteomic studies. The protocol takes 4 d from the initial transformation of the bacterial cells to the acquisition of the NMR spectra.     

Superoxide formation and interaction with nitric oxide modulate systemic arterial pressure and renal function in salt-depleted dogs

To determine the role of superoxide (O(2)(-)) formation in the kidney during alterations in the renin-angiotensin system, we evaluated responses to the intra-arterial infusion of an O(2)(-) - scavenging agent, tempol, in the denervated kidney of anesthetized salt-depleted (SD, n=6) dogs and salt-replete (SR, n=6) dogs. As expected, basal plasma renin activity was higher in SD than in SR dogs (8.4 +/- 1.0 vs. 2.3 +/- 0.6 ng angiotensin 1/ml/hr). Interestingly, the basal level of urinary F(2)-isoprostanes excretion (marker for endogenous O(2)(-) activity) relative to creatinine (Cr) excretion was also significantly higher in SD compared to SR dogs (9.1 +/- 2.8 vs. 1.6 +/- 0.4 ng F(2)-isoprostanes/mg of Cr). There was a significant increase in renal blood flow (4.3 +/- 0.5 to 4.9 +/- 0.6 ml/min/g) and decreases in renal vascular resistance (38.2 +/- 5.8 to 33.2 +/- 4.7 mm Hg/ml/min/g) and mean systemic arterial pressure (148 +/- 6 to 112 +/- 10 mm Hg) in SD dogs but not in SR dogs during infusion of tempol at 1 mg/kg/min for 30 mins. Glomerular filtration rate and urinary sodium excretion (U(Na)V) did not change significantly during tempol infusion in both groups of dogs. Administration of the nitric oxide synthase inhibitor nitro-L-arginine (50 mug/kg/min) during tempol infusion caused a reduction in U(Na)V in SR dogs (47% +/- 12%) but did not cause a decrease in SD dogs. These data show that low salt intake enhances O(2)(-) activity that influences renal and systemic hemodynamics and thus may contribute to the regulation of arterial pressure in the salt-restricted state.     

Degradation of phenanthrene via meta-cleavage of 2-hydroxy-1-naphthoic acid by Ochrobactrum sp. strain PWTJD

The present study describes the assimilation of phenanthrene by an aerobic bacterium, Ochrobactrum sp. strain PWTJD, isolated from municipal waste-contaminated soil sample utilizing phenanthrene as a sole source of carbon and energy. The isolate was identified as Ochrobactrum sp. based on the morphological, nutritional and biochemical characteristics as well as 16S rRNA gene sequence analysis. A combination of chromatographic analyses, oxygen uptake assay and enzymatic studies confirmed the degradation of phenanthrene by the strain PWTJD via 2-hydroxy-1-naphthoic acid, salicylic acid and catechol. The strain PWTJD could also utilize 2-hydroxy-1-naphthoic acid and salicylic acid, while the former was metabolized by a ferric-dependent meta-cleavage dioxygenase. In the lower pathway, salicylic acid was metabolized to catechol and was further degraded by catechol 2,3-dioxygenase to 2-hydroxymuconoaldehyde acid, ultimately leading to tricarboxylic acid cycle intermediates. This is the first report of the complete degradation of a polycyclic aromatic hydrocarbon molecule by Gram-negative Ochrobactrum sp. describing the involvement of the meta-cleavage pathway of 2-hydroxy-1-naphthoic acid in phenanthrene assimilation.     

Exposure to indoor fungi in different working environments: A comparative study

In this study an attempt was made to evaluate the qualitative and quantitative fungal burden (load) in five different working environments of South Assam (India) and the possible risks of indoor fungi to employees and stored products. Fungal concentrations in different working environments were studied using a Burkard personal petriplate sampler. The survey was done in five different working environments for one year. A total of 76 fungal types were recorded in the indoor air of South Assam during the survey period. The maximum fungal concentration (5,437.6 ± 145.3 CFU m⁻³ air) was recorded in the indoor air of medical wards, followed by the paper-processing industry (3,871.7 ± 93.4 CFU m⁻³ air). However the lowest concentration was observed in the indoor air of a bakery (1,796.8 ± 54.4 CFU m⁻³ air). The most dominant fungal genera were Aspergillus (34.2%) followed by Penicillium (17.8%), Geotrichum (7.0%) and the most dominant fungal species were Aspergillus fumigatus (2,650.4 CFU m⁻³ air) followed by Aspergillus flavus (1,388.2 CFU m⁻³ air), Geotrichum candidum (1,280.3 CFU m⁻³ air), Aspergillus niger (783.3 CFU m⁻³ air), and Penicillium aurantiovirens (774.0 CFU m⁻³ air). The fungal species viz., Aspergillus fumigatus, Penicillium aurantiovirens, Aspergillus flavus, Aspergillus niger, Geotrichum candidum, and Penicillium thomii, which were recorded well above threshold levels, may lead to adverse health hazards to indoor workers. Setting occupational exposure limits for indoor fungal spores as reference values is obligatory for prevention and control of adverse effects of indoor fungal exposure.