Chain-Extendable Crosslinked Hydrogels Using Branching RAFT Modification.

Functional crosslinked hydrogels were prepared from 2-hydroxyethyl methacrylate (HEMA) and acrylic acid (AA). The acid monomer was incorporated both via copolymerization and chain extension of a branching, reversible addition-fragmentation chain-transfer agent incorporated into the crosslinked polymer gel. The hydrogels were intolerant to high levels of acidic copolymerization as the acrylic acid weakened the ethylene glycol dimethacrylate (EGDMA) crosslinked network. Hydrogels made from HEMA, EGDMA and a branching RAFT agent provide the network with loose-chain end functionality that can be retained for subsequent chain extension. Traditional methods of surface functionalization have the downside of potentially creating a high volume of homopolymerization in the solution. Branching RAFT comonomers act as versatile anchor sites by which additional polymerization chain extension reactions can be carried out. Acrylic acid grafted onto HEMA-EGDMA hydrogels showed higher mechanical strength than the equivalent statistical copolymer networks and was shown to have functionality as an electrostatic binder of cationic flocculants.

Principles and analytical performance of Papilloplex® HR-HPV, a new commercial CE-IVD molecular diagnostic test for the detection of high-risk HPV genotypes.

The accurate detection and genotyping of high-risk human papillomavirus (HR-HPV) are critical for cervical cancer screening and epidemiological investigations. GeneFirst Papilloplex® HR-HPV is a new CE-IVD-marked real-time PCR test based on patented multiplex probe amplification technology. Papilloplex® HR-HPV provides the simultaneous detection and differentiation of 14 HR-HPV genotypes (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68a/b) in a single closed-tube reaction ensuring rapid, cost-effective, and contamination-free results. In this study, the analytical performance characteristics in terms of the assay's sensitivity, specificity, range, reproducibility, and cross-reactivity were evaluated. Papilloplex® HR-HPV provided sensitive detection and differentiation of 14 HR-HPV types with highly reproducible results. The differential HR-HPV specificity and sensitivity were further confirmed through the participation in the WHO HPV Laboratory Network Proficiency Study (2014). Overall, GeneFirst Papilloplex® HR-HPV assay demonstrated a robust analytical performance with reproducible and reliable results in the detection of HR-HPV genotypes.

Patient, Family, and Community Advisory Councils in Health Care and Research: a Systematic Review.

BACKGROUND: Patient-centeredness is a characteristic of high-quality medical care and requires engaging community members in health systems' decision-making. One key patient engagement strategy is patient, family, and community advisory boards/councils (PFACs), yet the evidence to guide PFACs is lacking. Systematic reviews on patient engagement may benefit from patient input, but feasibility is unclear. METHODS: A team of physicians, researchers, and a PFAC member conducted a systematic review to examine the impact of PFACs on health systems and describe optimal strategies for PFAC conduct. We searched MEDLINE, Embase, PsycINFO, CINAHL, Scopus, and Social Science Citation Index from inception through September 2016, as well as pre-identified websites. Two reviewers independently screened and abstracted data from studies, then assessed randomized studies for risk of bias and observational studies for quality using standardized measures. We performed a realist synthesis-which asks what works, for whom, under what circumstances-of abstracted data via 12 monthly meetings between investigators and two feedback sessions with a hospital-based PFAC. RESULTS: Eighteen articles describing 16 studies met study criteria. Randomized studies demonstrated moderate to high risk of bias and observational studies demonstrated poor to fair quality. Studies engaged patients at multiple levels of the health care system and suggested that in-person deliberation with health system leadership was most effective. Studies involving patient engagement in research focused on increasing study participation. PFAC recruitment was by nomination (n = 11) or not described (n = 5). No common measure of patient, family, or community engagement was identified. Realist synthesis was enriched by feedback from PFAC members. DISCUSSION: PFACs engage communities through individual projects but evidence of their impact on outcomes is lacking. A paucity of randomized controlled trials or high-quality observational studies guide strategies for engagement through PFACs. Standardized measurement tools for engagement are needed. Strategies for PFAC recruitment should be investigated and reported. PFAC members can feasibly contribute to systematic reviews. REGISTRATION AND FUNDING SOURCE: A protocol for record eligibility was developed a priori and was registered in the PROSPERO database of systematic reviews (registration number CRD42016052817). The Department of Veterans Affairs' Office of Academic Affiliations, through the National Clinician Scholars Program, funded this study.

Different sized somatic NF1 locus rearrangements in neurofibromatosis 1-associated malignant peripheral nerve sheath tumors.

Neurofibromatosis type 1 (NF1) patients are at increased risk of developing both benign (neurofibromas) and malignant (malignant peripheral nerve sheath tumors, MPNST) tumors. Molecular data on tumor progression are scarce, and few studies have compared the NF1 locus copy number in these two tumor types. To further explore the role of such NF1 locus rearrangements in NF1 tumorigenesis, and the likely disruption to the associated genes, the NF1 gene region was analyzed in NF1-associated tumors. DNA from three MPNSTs and one neurofibroma, excised from three unrelated NF1 patients, were analyzed using an NF1 region customized array-based comparative genomic hybridization. The somatic NF1 inactivation mutational mechanisms associated with MPNSTs appear to be different from those in benign neurofibromas. Interestingly, the MPNST-associated deletion breakpoints did not involve the paralogous repetitive sequences that are involved in most germline NF1 deletions. The somatic smallest common region of deletion overlap, however, was restricted to approximately the same ~2.2-Mb interval that encompassed most of the genes deleted in NF1 recurrent constitutional deletions. A number of genes in addition to NF1 on 17q (centromere to 17q24.2) may be involved in MPNST development. A larger study is warranted to confirm these findings. As NF1 patients with such germline NF1 deletions do exhibit increased risk of developing MPNST, these present findings emphasize the likely role of at least some of these NF1 flanking genes in MPNST pathobiology.

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization.

BACKGROUND: Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density (one probe per gene) PCR-based spotted arrays. Here we use new experimentally optimised 104,000 × 60-mer probe arrays to characterize in detail the genomic differences between wild-type S. lividans 66, a derivative industrial strain, TK24, and S. coelicolor M145. RESULTS: The high coverage and specificity (detection of three nucleotide differences) of the new microarrays used has highlighted the macroscopic genomic differences between two S. lividans strains and S. coelicolor. In a series of case studies we have validated the microarray and have identified subtle changes in genomic structure which occur in the Asp-activating adenylation domains of CDA non-ribosomal peptide synthetase genes which provides evidence of gene shuffling between these domains. We also identify single nucleotide sequence inter-species differences which exist in the actinorhodin biosynthetic gene cluster. As the glyoxylate bypass is non-functional in both S. lividans strains due to the absence of the gene encoding isocitrate lyase it is likely that the ethylmalonyl-CoA pathway functions as the alternative mechanism for the assimilation of C2 compounds. CONCLUSIONS: This study provides evidence for widespread genetic recombination, rather than it being focussed at 'hotspots', suggesting that the previously proposed 'archipelago model' of genomic differences between S. coelicolor and S. lividans is unduly simplistic. The two S. lividans strains investigated differ considerably in genetic complement, with TK24 lacking 175 more genes than its wild-type parent when compared to S. coelicolor. Additionally, we confirm the presence of bldB in S. lividans and deduce that S. lividans 66 and TK24, both deficient in the glyoxylate bypass, possess an alternative metabolic mechanism for the assimilation of C2 compounds. Given that streptomycetes generally display high genetic instability it is envisaged that these high-density arrays will find application for rapid assessment of genome content (particularly amplifications/deletions) in mutational studies of S. coelicolor and related species.

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).

BACKGROUND: In recent years there has been an increasing problem with Staphylococcus aureus strains that are resistant to treatment with existing antibiotics. An important starting point for the development of new antimicrobial drugs is the identification of "essential" genes that are important for bacterial survival and growth. RESULTS: We have developed a robust microarray and PCR-based method, Transposon-Mediated Differential Hybridisation (TMDH), that uses novel bioinformatics to identify transposon inserts in genome-wide libraries. Following a microarray-based screen, genes lacking transposon inserts are re-tested using a PCR and sequencing-based approach. We carried out a TMDH analysis of the S. aureus genome using a large random mariner transposon library of around a million mutants, and identified a total of 351 S. aureus genes important for survival and growth in culture. A comparison with the essential gene list experimentally derived for Bacillus subtilis highlighted interesting differences in both pathways and individual genes. CONCLUSION: We have determined the first comprehensive list of S. aureus essential genes. This should act as a useful starting point for the identification of potential targets for novel antimicrobial compounds. The TMDH methodology we have developed is generic and could be applied to identify essential genes in other bacterial pathogens.

Metabolite and transcriptome analysis of Campylobacter jejuni in vitro growth reveals a stationary-phase physiological switch.

Campylobacter jejuni is a prevalent cause of food-borne diarrhoeal illness in humans. Understanding of the physiological and metabolic capabilities of the organism is limited. We report a detailed analysis of the C. jejuni growth cycle in batch culture. Combined transcriptomic, phenotypic and metabolic analysis demonstrates a highly dynamic 'stationary phase', characterized by a peak in motility, numerous gene expression changes and substrate switching, despite transcript changes that indicate a metabolic downshift upon the onset of stationary phase. Video tracking of bacterial motility identifies peak activity during stationary phase. Amino acid analysis of culture supernatants shows a preferential order of amino acid utilization. Proton NMR (1H-NMR) highlights an acetate switch mechanism whereby bacteria change from acetate excretion to acetate uptake, most probably in response to depletion of other substrates. Acetate production requires pta (Cj0688) and ackA (Cj0689), although the acs homologue (Cj1537c) is not required. Insertion mutants in Cj0688 and Cj0689 maintain viability less well during the stationary and decline phases of the growth cycle than wild-type C. jejuni, suggesting that these genes, and the acetate pathway, are important for survival.

Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon.

BACKGROUND: DNA microarrays are a key resource for global analysis of genome content, gene expression and the distribution of transcription factor binding sites. We describe the development and application of versatile high density ink-jet in situ-synthesized DNA arrays for the G+C rich bacterium Streptomyces coelicolor. High G+C content DNA probes often perform poorly on arrays, yielding either weak hybridization or non-specific signals. Thus, more than one million 60-mer oligonucleotide probes were experimentally tested for sensitivity and specificity to enable selection of optimal probe sets for the genome microarrays. The heat-shock HspR regulatory system of S. coelicolor, a well-characterized repressor with a small number of known targets, was exploited to test and validate the arrays for use in global chromatin immunoprecipitation-on-chip (ChIP-chip) and gene expression analysis. RESULTS: In addition to confirming dnaK, clpB and lon as in vivo targets of HspR, it was revealed, using a novel ChIP-chip data clustering method, that HspR also apparently interacts with ribosomal RNA (rrnD operon) and specific transfer RNA genes (the tRNAGln/tRNAGlu cluster). It is suggested that enhanced synthesis of Glu-tRNAGlu may reflect increased demand for tetrapyrrole biosynthesis following heat-shock. Moreover, it was found that heat-shock-induced genes are significantly enriched for Gln/Glu codons relative to the whole genome, a finding that would be consistent with HspR-mediated control of the tRNA species. CONCLUSIONS: This study suggests that HspR fulfils a broader, unprecedented role in adaptation to stresses than previously recognized -- influencing expression of key components of the translational apparatus in addition to molecular chaperone and protease-encoding genes. It is envisaged that these experimentally optimized arrays will provide a key resource for systems level studies of Streptomyces biology.

H-NS mediates the silencing of laterally acquired genes in bacteria.

Histone-like nucleoid structuring protein (H-NS) is a modular protein that is associated with the bacterial nucleoid. We used chromatin immunoprecipitation to determine the binding sites of H-NS and RNA polymerase on the Salmonella enterica serovar Typhimurium chromosome. We found that H-NS does not bind to actively transcribed genes and does not co-localize with RNA polymerase. This shows that H-NS principally silences gene expression by restricting the access of RNA polymerase to the DNA. H-NS had previously been shown to preferentially bind to curved DNA in vitro. In fact, at the genomic level we discovered that the level of H-NS binding correlates better with the AT-content of DNA. This is likely to have evolutionary consequences because we show that H-NS binds to many Salmonella genes acquired by lateral gene transfer, and functions as a gene silencer. The removal of H-NS from the cell causes un-controlled expression of several Salmonella pathogenicity islands, and we demonstrate that this has deleterious consequences for bacterial fitness. Our discovery of this novel role for H-NS may have implications for the acquisition of foreign genes by enteric bacteria.

Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome.

Chromatin immunoprecipitation and high-density microarrays have been used to monitor the distribution of the global transcription regulator Escherichia coli cAMP-receptor protein (CRP) and RNA polymerase along the E. coli chromosome. Our results identify targets occupied by CRP and genes transcribed by RNA polymerase in vivo. Many of the loci of CRP binding are at known CRP regulated promoters. However, our results show that CRP also interacts with thousands of weaker sites across the whole chromosome and that this "background" binding can be used as a probe for organization within the E. coli folded chromosome. In rapidly growing cells, we show that the major sites of RNA polymerase binding are approximately 90 transcription units that include genes needed for protein synthesis. Upon the addition of rifampicin, RNA polymerase is distributed among >500 functional promoters. We show that the chromatin immunoprecipitation and high-density-microarrays methodology can be used to study the redistribution of RNA polymerase induced by environmental stress, revealing previously uncharacterized aspects of RNA polymerase behavior and providing an alternative to the "transcriptomics" approach for studying global transcription patterns.