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Abstract Background Escherichia coli C forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Results Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43, waaSBOJYZUL for lipopolysaccharide (LPS) synthesis, and cpsB for curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the − 35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of the csgD gene. And finally, E. coli C encodes an additional sigma70 subunit driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions provided insights into understanding this regulatory pathway in E. coli. Conclusions Biofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains of E. coli grown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain of E. coli C produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence of this classic strain, which provides for a base level of characterization and makes it useful for many biofilm-based applications.

Streptococcus pneumoniae (Spn) is a leading respiratory tract pathogen that colonizes the nasopharynx (NP) through adhesion to epithelial cells and immune evasion. Spn actively interacts with other microbiota in NP but the nature of these interactions are incompletely understood. Using 16S rRNA gene sequencing, we analyzed the microbiota composition in the NP of children with or without Spn colonization. 96 children were included in the study cohort. 74 NP samples were analyzed when children were 6 months old and 85 NP samples were analyzed when children were 12 months old. We found several genera that correlated negatively or positively with Spn colonization, and some of these correlations appeared to be influenced by daycare attendance or other confounding factors such as upper respiratory infection (URI) or Moraxella colonization. Among these genera, Corynebacterium showed a consistent inverse relationship with Spn colonization with little influence by daycare attendance or other factors. We isolated Corynebacterium propinquum and C. pseudodiphtheriticum and found that both inhibited the growth of Spn serotype 22F strain in vitro.

Urban agriculture is practiced in spatially fragmented landscapes with unique characteristics that can impact species occurrence in time and space. As a result, biological control services, an ecosystem service from naturally occurring arthropod natural enemies, can be negatively impacted. Many urban farms forgo pesticides and utilize agroecological pest-management strategies that rely on natural enemies to help regulate pest populations. Understanding how these enemies are affected by landscape composition and on-farm management practices is critical to understanding agroecological pest management in UA and furthering our understanding of landscape-mediated population dynamics. Over two growing seasons, we sampled brassica crops in urban agriculture sites occurring on a spectrum of surrounding landscape imperviousness, spatial composition, size, and management practices to better understand parasitic Hymenoptera abundance, richness, and parasitism rates on the common cabbage aphid (Brevicoryne brassicae). We found that on-farm agroecological pest-management practices such as mulch coverage, floral richness, and overall crop-plant richness impacted parasitic Hymenoptera abundance. Larger proportions of on-farm noncrop area increased parasitoid abundance on urban farms. Aphid parasitism increased in relation to on-farm management practices, including increased crop-plant richness. These findings add to a growing understanding of urban agroecosystem function and support the enemies hypothesis in urban agroecosystems.

As a result of antiretroviral therapeutic strategies, human immunodeficiency virus type 1 (HIV-1) infection has become a long-term clinically manageable chronic disease for many infected individuals. However, despite this progress in therapeutic control, including undetectable viral loads and CD4+ T-cell counts in the normal range, viral mutations continue to accumulate in the peripheral blood compartment over time, indicating either low level reactivation and/or replication. Using patients from the Drexel Medicine CNS AIDS Research and Eradication Study (CARES) Cohort, whom have been sampled longitudinally for more than 7 years, genetic change was modeled against to the dominant integrated proviral quasispecies with respect to selection pressures such as therapeutic interventions, AIDS defining illnesses, and other factors. Phylogenetic methods based on the sequences of the LTR and tat exon 1 of the HIV-1 proviral DNA quasispecies were used to obtain an estimate of an average mutation rate of 5.3 nucleotides (nt)/kilobasepair (kb)/year (yr) prior to initiation of antiretroviral therapy (ART). Following ART the baseline mutation rate was reduced to an average of 1.02 nt/kb/yr. The post-ART baseline rate of genetic change, however, appears to be unique for each patient. These studies represent our initial steps in quantifying rates of genetic change among HIV-1 quasispecies using longitudinally sampled sequences from patients at different stages of disease both before and after initiation of combination ART. Notably, while long-term ART reduced the estimated mutation rates in the vast majority of patients studied, there was still measurable HIV-1 mutation even in patients with no detectable virus by standard quantitative assays. Determining the factors that affect HIV-1 mutation rates in the peripheral blood may lead to elucidation of the mechanisms associated with changes in HIV-1 disease severity.

Many philosophers claim that intuitions are evidential. Yet it is hard to see how introspecting one's mental states could provide evidence for such synthetic truths as those concerning, for example, the abstract and the counterfactual. Such considerations have sometimes been taken to lead to mentalism---the view that philosophy must concern itself only with matters of concept application or other mind-dependent topics suited to a contemplative approach---but this provides us with a poor account of what it is that philosophers take themselves to be doing, for many of them are concerned with the extra-mental facts about the universe. Evidentialism therefore gestates a disaster for philosophy, for it ultimately demands an epistemology for the investigation into such matter as the abstract and the modal that simply will not be forthcoming. We make a different suggestion: That intuitions are inclinations to believe. Hence, according to us, a philosophical argument does well, as a socio-rhetorical matter of fact, when it is founded on premises philosophers are generally inclined to believe, whether or not those inclinations to believe connect appropriately to the extra-mental facts. Accordingly, the role of intuitions (inclinations to believe) in philosophical methodology is non-evidential, and the question of how they could be used as evidence falls away.