Truncation of type IV pilin induces mucoidy in Pseudomonas aeruginosa strain PAO579

Pseudomonas aeruginosa is a Gram negative, opportunistic pathogen that uses the overproduction of alginate, a surface polysaccharide, to form biofilms in vivo. Overproduction of alginate, also known as mucoidy, affords the bacterium protection from the host\u27s defenses and facilitates the establishment of chronic lung infections in individuals with cystic fibrosis. Expression of the alginate biosynthetic operon is primarily controlled by the alternative sigma factor AlgU (AlgT/σ22). In a nonmucoid strain, AlgU is sequestered by the transmembrane antisigma factor MucA to the cytoplasmic membrane. AlgU can be released from MucA via regulated intramembrane proteolysis by proteases AlgW and MucP causing the conversion to mucoidy. Pseudomonas aeruginosastrain PAO579, a derivative of the nonmucoid strain PAO1, is mucoid due to an unidentified mutation (muc-23). Using whole genome sequencing, we identified 16 nonsynonymous and 15 synonymous single nucleotide polymorphisms (SNP). We then identified three tandem single point mutations in the pilA gene (PA4525), as the cause of mucoidy in PAO579. These tandem mutations generate a premature stop codon resulting in a truncated version of PilA (PilA108), with a C-terminal motif of phenylalanine-threonine-phenylalanine (FTF). Inactivation of pilA108 confirmed it was required for mucoidy. Additionally, algW and algU were also required for mucoidy of PAO579. Western blot analysis indicated that MucA was less stable in PAO579 than nonmucoid PAO1 or PAO381. The mucoid phenotype and high PalgU and PalgD promoter activities of PAO579 require pilA108, algW, algU, and rpoN encoding the alternative sigma factor σ54. We also observed that RpoN regulates expression of algW and pilA in PAO579. Together, these results suggest that truncation in type IV pilin in P. aeruginosa strain PAO579 can induce mucoidy through an AlgW/AlgU-dependent pathway

A Non-Oxidative Approach toward Chemically and Electrochemically Functionalizing Si(111)

A general method for the non-oxidative functionalization of single-crystal silicon(111) surfaces is described. The silicon surface is fully acetylenylated using two-step chlorination/alkylation chemistry. A benzoquinone-masked primary amine is attached to this surface via Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition (“click” chemistry). The benzoquinone is electrochemically reduced, resulting in quantitative cleavage of the molecule and exposing the amine terminus. Molecules presenting a carboxylic acid have been immobilized to the exposed amine sites. X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), cyclic voltammetry (CV), and contact angle goniometry were utilized to characterize and quantitate each step in the functionalization process. This work represents a strategy for providing a general platform that can incorporate organic and biological molecules on Si(111) with minimal oxidation of the silicon surface

Benefits of Turbid River Plume Habitat for Lake Erie Yellow Perch (Perca flavescens) Recruitment Determined by Juvenile to Larval Genotype Assignment

Nutrient-rich, turbid river plumes that are common to large lakes and coastal marine ecosystems have been hypothesized to benefit survival of fish during early life stages by increasing food availability and (or) reducing vulnerability to visual predators. However, evidence that river plumes truly benefit the recruitment process remains meager for both freshwater and marine fishes. Here, we use genotype assignment between juvenile and larval yellow perch (Perca flavescens) from western Lake Erie to estimate and compare recruitment to the age-0 juvenile stage for larvae residing inside the highly turbid, south-shore Maumee River plume versus those occupying the less turbid, more northerly Detroit River plume. Bayesian genotype assignment of a mixed assemblage of juvenile (age-0) yellow perch to putative larval source populations established that recruitment of larvae was higher from the turbid Maumee River plume than for the less turbid Detroit River plume during 2006 and 2007, but not in 2008. Our findings add to the growing evidence that turbid river plumes can indeed enhance survival of fish larvae to recruited life stages, and also demonstrate how novel population genetic analyses of early life stages can contribute to determining critical early life stage processes in the fish recruitment process

Iterative in Situ Click Chemistry Assembles a Branched Capture Agent and Allosteric Inhibitor for Akt1

We describe the use of iterative in situ click chemistry to design an Akt-specific branched peptide triligand that is a drop-in replacement for monoclonal antibodies in multiple biochemical assays. Each peptide module in the branched structure makes unique contributions to affinity and/or specificity resulting in a 200 nM affinity ligand that efficiently immunoprecipitates Akt from cancer cell lysates and labels Akt in fixed cells. Our use of a small molecule to preinhibit Akt prior to screening resulted in low micromolar inhibitory potency and an allosteric mode of inhibition, which is evidenced through a series of competitive enzyme kinetic assays. To demonstrate the efficiency and selectivity of the protein-templated in situ click reaction, we developed a novel QPCR-based methodology that enabled a quantitative assessment of its yield. These results point to the potential for iterative in situ click chemistry to generate potent, synthetically accessible antibody replacements with novel inhibitory properties

Extracurricular Activities and Disadvantaged Youth: A Complicated - But Promising - Story

Increased political and research interest in extracurricular activities stems, in part, from the claim that these programs especially benefit disadvantaged youth. However, little literature has synthesized studies across types of disadvantage to assess this claim. This article reviews research on disadvantaged youth in extracurricular programs, including differences by gender, socioeconomic status, race/ethnicity, and immigrant status. Our review reveals a promising, if complicated, picture. Although disadvantaged youth are less likely to participate in extracurricular activities, they often experience greater benefits, depending on the risk status and activity type. Evidence clearly supports expanding access to extracurricular programs for disadvantaged youth

TSC22 in mammary gland development and breast cancer

Mammary gland involution is characterised by a high degree of apoptosis. By identifying genes that are upregulated at this developmental stage, we aimed to discover key factors that are involved in the induction of mammary epithelial cell death and therefore present potential tumour suppressors for breast cancer. Among 96 genes recently identified as specifically upregulated early during involution were the transforming growth factor beta (TGFβ)-stimulated clone 22 homologue (TSC-22/TGFβ1-induced transcript 4) and TGFβ3 [1]. TGFβ3 has recently been shown to be necessary for induction of apoptosis during mammary gland involution, while TSC-22 overexpression can lead to cell death. We have therefore tested whether TSC-22 mRNA expression can be induced by TGFβ3 and whether it is involved in or necessary for TGFβ-induced apoptosis. We further show that TSC-22 can enhance TGFβ3-induced Smad response and epithelial cell death. In addition, overexpression of TSC-22 alone can induce a Smad response and apoptosis in mammary epithelial cell cultures, which is independent of p53. Further, we have performed tests to study the necessity for Smad proteins during TSC-22-induced apoptosis, and to establish the intracellular localisation of TSC-22. A pilot study on a small cohort of archival breast cancer cases, representing all stages of malignant progression, shows that TSC-22 protein was reduced or undetectable in 60% of breast carcinomas when compared with adjacent normal breast tissue, suggesting that TSC-22 could indeed be a potential novel tumour suppressor gene. We shall present data showing that methylation of the TSC-22 promoter is not involved in the reduction of TSC-22 protein in breast cancer

Inferential models: A framework for prior-free posterior probabilistic inference

Posterior probabilistic statistical inference without priors is an important but so far elusive goal. Fisher's fiducial inference, Dempster-Shafer theory of belief functions, and Bayesian inference with default priors are attempts to achieve this goal but, to date, none has given a completely satisfactory picture. This paper presents a new framework for probabilistic inference, based on inferential models (IMs), which not only provides data-dependent probabilistic measures of uncertainty about the unknown parameter, but does so with an automatic long-run frequency calibration property. The key to this new approach is the identification of an unobservable auxiliary variable associated with observable data and unknown parameter, and the prediction of this auxiliary variable with a random set before conditioning on data. Here we present a three-step IM construction, and prove a frequency-calibration property of the IM's belief function under mild conditions. A corresponding optimality theory is developed, which helps to resolve the non-uniqueness issue. Several examples are presented to illustrate this new approach.Comment: 29 pages with 3 figures. Main text is the same as the published version. Appendix B is an addition, not in the published version, that contains some corrections and extensions of two of the main theorem

Illinois Waterfowl Surveys and Investigations W-43-R-64 Annual Progress Report FY2017 Period: 1 July 2016 – 30 June 2017

Objectives 1) Inventory abundance and distribution of waterfowl, shorebirds, and other waterbirds (a minimum of 10 species and guilds) during autumn migration at a minimum of 30 sites along and nearby the Illinois and central Mississippi rivers, 2) Estimate waterfowl and other waterbird population sizes (a minimum of 10 species and guilds) during autumn migration using an aerial quadrat survey in the central Illinois River Valley for comparison with aerial inventories (Objective 1), 3) Investigate movement and population ecology of lesser scaup, canvasback, and other diving ducks by trapping and leg-banding a minimum of 1,000 individuals during spring migration along the Illinois and Mississippi rivers, 4) Investigate the ecology of American green-winged teal and gadwall by radio-marking a minimum of 40 individuals of each species during spring migration in and nearby the central Illinois River Valley, 5) Investigate movements and home range size of a minimum of 10 Canada geese during winter in and near the Greater Chicago Metropolitan Area (GCMA) of Illinois, 6) Determine habitat quality of a minimum of 50 wetland and deepwater polygons during spring, summer, and early autumn for migrating dabbling ducks, breeding wetland birds, and migrating shorebirds in Illinois, and 7) Distribute results and findings to site managers and biologists of the Illinois Department of Natural Resources (IDNR) and other state agencies, the Mississippi Flyway Technical Section, the Upper Mississippi River and Great Lakes Region (UMRGLR) Joint Venture, the U.S. Fish and Wildlife Service, other scientists and collaborators as requested, and the general public through oral presentations, popular articles, technical reports, and peer reviewed publications; make recommendations for future wetland management practices and research needs based on results and related research; contribute to regional conservation planning efforts during the project period as appropriate and requested.Illinois Department of Natural Resources, Division of Wildlife & U.S. Fish and Wildlife Service Contract Number: RC09-13FWUIUCunpublishednot peer reviewedOpe

The SAMI pilot survey: The kinematic morphology-density relation in Abell 85, Abell 168 and Abell 2399

We examine the kinematic morphology of early-type galaxies (ETGs) in three galaxy clusters Abell 85, 168 and 2399. Using data from the Sydney-AAOMulti-object Integral field spectrograph we measure spatially resolved kinematics for 79 ETGs in these clusters. We calculate λR, a proxy for the projected specific stellar angular momentum, for each galaxy and classify the 79 ETGs in our samples as fast or slow rotators. We calculate the fraction of slow rotators in the ETG populations (fSR) of the clusters to be 0.21 ± 0.08, 0.08 ± 0.08 and 0.12 ± 0.06 for Abell 85, 168 and 2399, respectively, with an overall fraction of 0.15 ± 0.04. These numbers are broadly consistent with the values found in the literature, confirming recent work asserting that the fraction of slow rotators in the ETG population is constant across many orders of magnitude in global environment. We examine the distribution of kinematic classes in each cluster as a function of environment using the projected density of galaxies: the kinematic morphology-density relation.We find that in Abell 85 fSR increases in higher density regions but in Abell 168 and 2399 this trend is not seen. We examine the differences between the individual clusters to explain this. In addition, we find slow rotators on the outskirts of two of the clusters studied, Abell 85 and 2399. These galaxies reside in intermediate to low density regions and have clearly not formed at the centre of a cluster environment. We hypothesize that they formed at the centres of groups and are falling into the clusters for the first time

Occurrence, function and evolutionary origins of ‘2A-like’ sequences in virus genomes

2A is an oligopeptide sequence mediating a ribosome ‘skipping’ effect, producing an apparent ‘cleavage’ of polyproteins. First identified and characterized in picornaviruses, ‘2A-like’ sequences are found in other mammalian viruses and a wide range of insect viruses. Databases were analysed using a motif conserved amongst 2A/2A-like sequences. The newly identified 2A-like sequences (30 aa) were inserted into a reporter polyprotein to determine their cleavage activity. Our analyses showed that these sequences fall into two categories. The majority mediated very high (complete) cleavage to separate proteins and a few sequences mediated cleavage with lower efficiency, generating appreciable levels of the uncleaved form. Phylogenetic analyses of 2A-like sequences and RNA-dependent RNA polymerases (RdRps) indicated multiple, independent, acquisitions of these sequences at different stages during virus evolution. Within a virus family, 2A sequences are (probably) homologous, but diverge due to other evolutionary pressures. Amongst different families, however, 2A/2A-like sequences appear to be homoplasic