Performance of ZDOCK and IRAD in CAPRI rounds 39-45.

We report docking performance on the six targets of Critical Assessment of PRedicted Interactions (CAPRI) rounds 39-45 that involved heteromeric protein-protein interactions and had the solved structures released since the rounds were held. Our general strategy involved protein-protein docking using ZDOCK, reranking using IRAD, and structural refinement using Rosetta. In addition, we made extensive use of experimental data to guide our docking runs.

The effects of expanding outpatient and inpatient evaluation and management services in a pediatric interventional radiology practice.

Background: Despite a continuing emphasis on evaluation and management clinical services in adult interventional radiology (IR) practice, the peer-reviewed literature addressing these services - and their potential economic benefits - is lacking in pediatric IR practice.

Objective: To measure the effects of expanding evaluation and management (E&M) services through the establishment of a dedicated pediatric interventional radiology outpatient clinic and inpatient E&M reporting system.

Materials And Methods: We collected and analyzed E&M current procedural terminology (CPT) codes from all patients seen in a pediatric interventional radiology outpatient clinic between November 2014 and August 2015.

Random close packing in protein cores.

Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ ≈ 0.75, a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model.

Kinetic profile of amyloid formation in the presence of an aromatic inhibitor by nuclear magnetic resonance.

The self-assembly of amyloid proteins into β-sheet rich assemblies is associated with human amyloidoses including Alzheimer's disease, Parkinson's disease, and type 2 diabetes. An attractive therapeutic strategy therefore is to develop small molecules that would inhibit protein self-assembly. Natural polyphenols are potential inhibitors of β-sheet formation.

Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308.

Hfq is an RNA-binding protein that functions in post-transcriptional gene regulation by mediating interactions between mRNAs and small regulatory RNAs (sRNAs). Two proteins encoded by BAB1_1794 and BAB2_0612 are highly over-produced in a Brucella abortus hfq mutant compared with the parental strain, and recently, expression of orthologues of these proteins in Agrobacterium tumefaciens was shown to be regulated by two sRNAs, called AbcR1 and AbcR2. Orthologous sRNAs (likewise designated AbcR1 and AbcR2) have been identified in B.

The RNA chaperone Hfq independently coordinates expression of the VirB type IV secretion system and the LuxR-type regulator BabR in Brucella abortus 2308.

The type IV secretion system encoded by the virB operon is required for full virulence of Brucella sp., and the present study links the RNA chaperone Hfq to wild-type expression of virB in Brucella abortus 2308. Studies employing virB-lacZ fusions, quantitative reverse transcription-PCR, and immunoblot analysis showed that both transcription and translation of virB are decreased in an isogenic hfq mutant compared to those in the parental strain.

The iron-responsive regulator irr is required for wild-type expression of the gene encoding the heme transporter BhuA in Brucella abortus 2308.

Irr and RirA, rather than Fur, serve as the major iron-responsive regulators in the alphaproteobacteria. With only a few exceptions, however, the relative contributions of these transcriptional regulators to the differential expression of specific iron metabolism genes in Brucella strains are unclear. The gene encoding the outer membrane heme transporter BhuA exhibits maximum expression in Brucella abortus 2308 during growth under iron-deprived conditions, and mutational studies indicate that this pattern of bhuA expression is mediated by the iron-responsive regulator Irr.

Subversion of innate immune responses by Brucella through the targeted degradation of the TLR signaling adapter, MAL.

Gram-negative bacteria belonging to the Brucella species cause chronic infections that can result in undulant fever, arthritis, and osteomyelitis in humans. Remarkably, Brucella sp. genomes encode a protein, named TcpB, that bears significant homology with mammalian Toll/IL-1 receptor domains and whose expression causes degradation of the phosphorylated, signal competent form of the adapter MyD88-adapter-like (MAL).

Survival of the fittest: how Brucella strains adapt to their intracellular niche in the host.

Brucella strains produce abortion and infertility in their natural hosts and a zoonotic disease in humans known as undulant fever. These bacteria do not produce classical virulence factors, and their capacity to successfully survive and replicate within a variety of host cells underlies their pathogenicity. Extensive replication of the brucellae in placental trophoblasts is associated with reproductive tract pathology in natural hosts, and prolonged persistence in macrophages leads to the chronic infections that are a hallmark of brucellosis in both natural hosts and humans.

The manganese transporter MntH is a critical virulence determinant for Brucella abortus 2308 in experimentally infected mice.

The gene designated BAB1_1460 in the Brucella abortus 2308 genome sequence is predicted to encode the manganese transporter MntH. Phenotypic analysis of an isogenic mntH mutant indicates that MntH is the sole high-affinity manganese transporter in this bacterium but that MntH does not play a detectable role in the transport of Fe(2+), Zn(2+), Co(2+), or Ni(2+). Consistent with the apparent selectivity of the corresponding gene product, the expression of the mntH gene in B.

Broad-host-range expression vectors with tightly regulated promoters and their use to examine the influence of TraR and TraM expression on Ti plasmid quorum sensing.

Experiments requiring strong repression and precise control of cloned genes can be difficult to conduct because of the relatively high basal level of expression of currently employed promoters. We report the construction of a family of vectors that contain a reengineered lacI(q)-lac promoter-operator complex in which cloned genes are strongly repressed in the absence of inducer. The vectors, all based on the broad-host-range plasmid pBBR1, are mobilizable and stably replicate at moderate copy number in representatives of the alpha- and gammaproteobacteria.

Regulation of the Pseudomonas aeruginosa toxA, regA and ptxR genes by the iron-starvation sigma factor PvdS under reduced levels of oxygen.

The level of environmental oxygen (EO) within various Pseudomonas aeruginosa infection sites is low (microaerobic), and this can affect the production of different virulence factors. Expression of the toxA gene, encoding exotoxin A (ETA), is regulated by regA, ptxR and pvdS. Moreover, the iron-starvation sigma factor PvdS directs the transcription of pyoverdine siderophore genes (e.

Transcriptional analysis of the Pseudomonas aeruginosa toxA regulatory gene ptxR.

The expression of the exotoxin A gene (toxA) in Pseudomonas aeruginosa is a complicated process that involves several regulators, including ptxR, which enhances toxA expression by 4- to 5-fold. Available evidence suggests that ptxR is expressed from two separate promoters, P1 and P2. Previous evidence indicated the presence, within the ptxR upstream region, of binding sites for several regulatory proteins, including PtxS, which negatively regulates ptxR expression.

Effect of static growth and different levels of environmental oxygen on toxA and ptxR expression in the Pseudomonas aeruginosa strain PAO1.

Within certain infection sites, such as the lung of cystic fibrosis patients, Pseudomonas aeruginosa grows statically under either decreased oxygen tension or anaerobic conditions, a situation that is likely to influence the production of virulence factors. The goal of this study was to determine the effect of static growth under microaerobic (decreased oxygen) and anaerobic conditions on the expression of the P. aeruginosa exotoxin A (ETA) gene toxA and its positive regulator ptxR.