Structure aided design of chimeric antibiotics

The rise of antibiotic resistance is of great clinical concern. One approach to reducing the development of resistance is to co-administer two or more antibiotics with different modes of action. However, it can be difficult to control the distribution and pharmacokinetics of two drugs to ensure both concentrations remain within the range of therapeutic efficacy whilst avoiding adverse effects. Hybrid drugs, where two drugs are linked together with a flexible linker, have been explored, but the resultant large, flexible molecules can have poor bioavailability. We have developed a chimeric approach using click chemistry where the pharmacophores of two drugs are overlapped into a single smaller, more drug-like molecule. Design and selection of compounds were assisted by in silico structural docking. We prepared a series of compounds that include candidates showing activity against the targets of both trimethoprim; dihydrofolate reductase, and ciprofloxacin; DNA gyrase and topoisomerase IV. The resultant triazole containing molecules show modest, but broad spectrum activities against drug sensitive and resistant Gram-negative and Gram-positive bacteria, with no observable cytotoxicity.     

Contingency in ecosystem but not plant community response to multiple global change factors

Community and ecosystem responses to global environmental change are contingent on the magnitude of change and interacting global change factors. To reveal whether responses are also contingent on the magnitude of each interacting factor, multifactor, multilevel experiments are required, but are rarely conducted. We exposed model grassland ecosystems to six levels of atmospheric CO(2) and six levels of nitrogen enrichment, applying the latter both chronically (simulating deposition) and acutely (simulating fertilization). The 66 treatments were maintained for 6?months under controlled growing conditions, with biomass harvested every 28?d and sorted to species. Aboveground plant productivity responses to CO(2) were contingent on nitrogen amount, and the responses to nitrogen amount were dependent on whether applications were chronic or acute. Specifically, productivity responses to increasing CO(2) concentrations were accentuated with higher nitrogen enrichments, and productivity was greater when higher nitrogen enrichments were applied acutely. Plant community composition was influenced only by nitrogen enrichment, where the co-dominant grass species with the greatest leaf trait plasticity increasingly dominated with higher nitrogen amounts. Community processes are considered to be unpredictable, but our data suggest that the prediction of the impacts of simultaneous global changes is more complex for ecosystem processes, given that their responses are contingent on the levels of interacting factors.     

The interaction between propagule pressure,habitat suitability and density‐dependent reproduction in species invasion

Seedling recruitment limitations create a demographic bottleneck that largely determines the viability and structure of plant populations and communities, and pose a core restriction on the colonization of novel habitat. We use a shade‐tolerant, invasive grass, Microstegium vimineum, to examine the interplay between seed and establishment limitations – phenomena that together determine recruitment success but usually are investigated individually. We add increasing amounts of seed to microhabitats containing variable levels of leaf litter thickness – with reduced leaf litter simulating disturbance – to investigate whether reduced seed limitation overcomes the establishment limitation posed by litter cover. We do this across gradients in understory light, moisture and temperature, and quantify germination, survival, and then per capita adult biomass and reproduction in order to understand the implications for invasion across the landscape. We find that the combined effects of seed and establishment limitation influence recruitment; however, propagule pressure overwhelms the inhibitory effects of leaf litter thickness. Leaf litter reduces germination by 22–57% and seedling survival by 13–15% from that observed on bare soil. However, density‐dependent reproduction compensates as 1–3 plants can produce far more seeds (approx. 525) than are required for persistence. As such, just a few plants may establish in understory forest habitat and subsequently overwhelm establishment barriers with copious propagule production. These results, for a widespread, invasive plant, are consistent with the emerging perspective for native plants that seed and establishment limitation jointly influence recruitment. The ability for an exotic plant species to compensate for low population densities with high per capita seed production, that then overrides establishment limitations, makes its invasive potential daunting. Further work is required to test if this is a common mechanism underlying plant invasions.     

Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers

We used a lectin chromatography/MS-based approach to screen conditioned medium from a panel of luminal (less aggressive) and triple negative (more aggressive) breast cancer cell lines (n=5/subtype). The samples were fractionated using the lectins Aleuria aurantia (AAL) and Sambucus nigra agglutinin (SNA), which recognize fucose and sialic acid, respectively. The bound fractions were enzymatically N-deglycosylated and analyzed by LC-MS/MS. In total, we identified 533 glycoproteins, ～90% of which were components of the cell surface or extracellular matrix. We observed 1011 glycosites, 100 of which were solely detected in ≥3 triple negative lines. Statistical analyses suggested that a number of these glycosites were triple negative-specific and thus potential biomarkers for this tumor subtype. An analysis of RNaseq data revealed that approximately half of the mRNAs encoding the protein scaffolds that carried potential biomarker glycosites were up-regulated in triple negative vs luminal cell lines, and that a number of genes encoding fucosyl- or sialyltransferases were differentially expressed between the two subtypes, suggesting that alterations in glycosylation may also drive candidate identification. Notably, the glycoproteins from which these putative biomarker candidates were derived are involved in cancer-related processes. Thus, they may represent novel therapeutic targets for this aggressive tumor subtype.     

Grass Invasions Across a Regional Gradient are Associated with Declines in Belowground Carbon Pools

The composition of plant communities everywhere now likely comprises alien as well as native species, and those aliens that become invasive have wide-ranging impacts on the structure and function of recipient ecosystems. These impacts include perturbations to soil carbon (C) cycling, but the direction and magnitude of impacts are species and climate dependent, making it difficult to generalize whether a specific invader will promote losses or gains in soil C stocks. Generalizations of a specific invader??s impacts are necessary; however, because the range of an invader can encompass thousands of square kilometers, meaning their effects can have broad, regional consequences. To quantify broad-scale and context-dependent impacts of a specific invader, multi-site investigations that capture and measure local and regional environmental heterogeneity are necessary. Using this approach, we show that a widespread grass invader of forest understories is associated with declines in soil C during infilling (spreading within the invaded range). Across the 36 study sites, total soil C stocks declined (P?=?0.113) by approximately 12% (estimated mean?±?SD, uninvaded: 2,429?±?512.9 vs. invaded: 2,140?±?520.7?g?C?m^?2). The decline in total soil C is driven by a significant (P?=?0.047) reduction in the native-derived, mineral-associated soil C fraction. This fraction, whose mass and slow turnover makes it an important C store, is approximately 15% lower in invaded (estimated mean?±?SD: 1,560?±?400.4?g?C?m^?2) than uninvaded plots (1,826?±?398.1?g?C?m^?2). Notably, declines in this C fraction are only apparent at 21 of the sites, reflecting how environmental heterogeneity in other variables (specifically pH, soil moisture, and clay content) are important to quantify to determine invader impacts across a region. The 26% decline in microbial biomass with invasion (P?=?0.011; estimated mean?±?SD, uninvaded: 10.05?±?1.79 vs. invaded: 7.40?±?1.80?g?C?m^?2) is also dependent on site characteristics (pH), and reductions are greater where the invader occurs at higher densities. Reductions in microbial biomass and soil C with invasion suggest that grass invasion will alter soil C cycling and decrease forest-C stores across the study region, although invader effects at a specific-site will be dependent on environmental context.     

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.     

Pneumococci in the African Meningitis Belt: Meningitis Incidence and Carriage Prevalence in Children and Adults

Background

The development of optimal vaccination strategies for pneumococcal conjugate vaccines requires serotype-specific data on disease incidence and carriage prevalence. This information is lacking for the African meningitis belt.

Methods

We conducted hospital-based surveillance of acute bacterial meningitis in an urban and rural population of Burkina Faso during 2007–09. Cerebrospinal fluid was evaluated by polymerase chain reaction for species and serotype. In 2008, nasopharyngeal swabs were obtained from a representative population sample (1 month to 39 years; N = 519) and additional oropharyngeal swabs from 145 participants. Swabs were evaluated by culture.

Results

Annual pneumococcal meningitis incidence rates were highest among <6-month-old (58/100,000) and 15- to 19-year-old persons (15/100,000). Annual serotype 1 incidence was around 5/100,000 in all age groups. Pneumococcal carriage prevalence in nasopharyngeal swabs was 63% among <5-year-old children and 22% among ≥5-year-old persons, but adding oropharyngeal to nasopharyngeal swabs increased the estimated carriage prevalence by 60%. Serotype 1 showed high propensity for invasive disease, particularly among persons aged ≥5 years.

Conclusions

Serotype 1 causes the majority of cases with a relatively constant age-specific incidence. Pneumococcal carriage is common in all age groups including adults. Vaccination programs in this region may need to include older target age groups for optimal impact on disease burden.     

Passive immunization reduces murine cytomegalovirus-induced brain pathology in newborn mice

Human cytomegalovirus (HCMV) is the most frequent cause of congenital viral infections in humans and frequently leads to long-term central nervous system (CNS) abnormalities that include learning disabilities, microcephaly, and hearing loss. The pathogenesis of the CNS infection has not been fully elucidated and may arise as a result of direct damage of CMV-infected neurons or indirectly secondary to inflammatory response to infection. We used a recently established model of mouse CMV (MCMV) infection in newborn mice to analyze the contribution of humoral immunity to virus clearance from the brain. In brains of MCMV-infected newborn mice treated with immune serum, the titer of infectious virus was reduced below detection limit, whereas in the brains of mice receiving control (nonimmune) serum significant amounts of virus were recovered. Moreover, histopathological and immunohistological analyses revealed significantly less CNS inflammation in mice treated with immune serum. Treatment with MCMV-specific monoclonal antibodies also resulted in the reduction of virus titer in the brain. Recipients of control serum or irrelevant antibodies had more viral foci, marked mononuclear cell infiltrates, and prominent glial nodules in their brains than mice treated with immune serum or MCMV-specific antibodies. In conclusion, our data indicate that virus-specific antibodies have a protective role in the development of CNS pathology in MCMV-infected newborn mice, suggesting that antiviral antibodies may be an important component of protective immunological responses during CMV infection of the developing CNS.     

The implications of stochastic synthesis for the conjugation of functional groups to nanoparticles

Stochastic synthesis of a ligand coupled to a nanoparticle results in a distribution of populations with different numbers of ligands per nanoparticle. This distribution was resolved and quantified using HPLC and is in excellent agreement with the ligand/nanoparticle average measured by 1H NMR, gel permeation chromatography (GPC), and potentiometric titration, and yet significantly more disperse than commonly held perceptions of monodispersity. Two statistical models were employed to confirm that the observed heterogeneity is consistent with theoretical expectations.