Drift dynamics in microbial communities and the effective community size

The structure and diversity of all open microbial communities are shaped by individual births, deaths, speciation and immigration events; the precise timings of these events are unknowable and unpredictable. This randomness is manifest as ecological drift in the population dynamics, the importance of which has been a source of debate for decades. There are theoretical reasons to suppose that drift would be imperceptible in large microbial communities, but this is at odds with circumstantial evidence that effects can be seen even in huge, complex communities. To resolve this dichotomy we need to observe dynamics in simple systems where key parameters, like migration, birth and death rates can be directly measured. We monitored the dynamics in the abundance of two genetically modified strains of Escherichia coli, with tuneable growth characteristics, that were mixed and continually fed into 10 identical chemostats. We demonstrated that the effects of demographic (non-environmental) stochasticity are very apparent in the dynamics. However, they do not conform to the most parsimonious and commonly applied mathematical models, where each stochastic event is independent. For these simple models to reproduce the observed dynamics we need to invoke an ‘effective community size’, which is smaller than the census community size.     

Oxidative Stress Alters the Morphology and Toxicity of Aortic Medial Amyloid

The aggregation and fibril deposition of amyloid proteins have been implicated in a range of neurodegenerative and vascular diseases, and yet the underlying molecular mechanisms are poorly understood. Here, we use a combination of cell-based assays, biophysical analysis, and atomic force microscopy to investigate the potential involvement of oxidative stress in aortic medial amyloid (AMA) pathogenesis and deposition. We show that medin, the main constituent of AMA, can induce an environment rich in oxidative species, increasing superoxide and reducing bioavailable nitric oxide in human cells. We investigate the role that this oxidative environment may play in altering the aggregation process of medin and identify potential posttranslational modification sites where site-specific modification and interaction can be unambiguously demonstrated. In an oxidizing environment, medin is nitrated at tyrosine and tryptophan residues, with resultant effects on morphology that lead to longer fibrils with increased toxicity. This provides further motivation to investigate the role of oxidative stress in AMA pathogenicity.     

The Fastest Western in Town: A Contemporary Twist on the Classic Western Blot Analysis

The Western blot techniques that were originally established in the late 1970s are still actively utilized today. However, this traditional method of Western blotting has several drawbacks that include low quality resolution, spurious bands, decreased sensitivity, and poor protein integrity. Recent advances have drastically improved numerous aspects of the standard Western blot protocol to produce higher qualitative and quantitative data. The Bis-Tris gel system, an alternative to the conventional Laemmli system, generates better protein separation and resolution, maintains protein integrity, and reduces electrophoresis to a 35 min run time. Moreover, the iBlot dry blotting system, dramatically improves the efficacy and speed of protein transfer to the membrane in 7 min, which is in contrast to the traditional protein transfer methods that are often more inefficient with lengthy transfer times. In combination with these highly innovative modifications, protein detection using infrared fluorescent imaging results in higher-quality, more accurate and consistent data compared to the standard Western blotting technique of chemiluminescence. This technology can simultaneously detect two different antigens on the same membrane by utilizing two-color near-infrared dyes that are visualized in different fluorescent channels. Furthermore, the linearity and broad dynamic range of fluorescent imaging allows for the precise quantification of both strong and weak protein bands. Thus, this protocol describes the key improvements to the classic Western blotting method, in which these advancements significantly increase the quality of data while greatly reducing the performance time of this experiment.     

Changes in growth and sleep across school nights,weekends and a winter holiday period in two Australian schools

Studies suggest that there may be an association between sleep and growth; however, the relationship is not well understood. Changes in biology and external factors such as school schedule heavily impact the sleep of adolescents, during a critical phase for growth. This study assessed the changes in sleep across school days, weekends and school holidays, while also measuring height and weight changes, and self-reported alterations in food intake and physical activity. The impact of morningness–eveningness (M-E) on height change and weight gain was also investigated. In a sample of 63 adolescents (mean age = 13.13, SD = 0.33, 31 males) from two independent schools in South Australia, height and weight were measured weekly for 4 weeks prior to the school holidays and 4 weeks after the school holidays. Participants also completed a Morningness/Eveningness Scale and 7-day sleep, diet and physical activity diaries prior to, during and after the school holidays. Participants at one school had earlier wake times during the weekends than participants attending the other school, leading to a significantly shorter sleep duration on weekends for those participants. Regardless of school, sleep was significantly later and longer during the holidays (p < 0.001) and those with a stronger morning preference fell asleep (F_18,36 = 3.4, p = 0.001) and woke (F_18,44 = 2.0, p = 0.027) earlier than evening types. Growth rate was lower during the holiday weeks. For those attending the school with limited sleep in opportunities, growth after the holidays was lower for those with greater evening preference, whereas for those at the other school, growth was greater for those with greater evening preference. The increase in average weight from pre- to post-holidays was greater for those attending the school with limited opportunities to sleep longer. Participants reported greater food intake during the holidays compared to school days and greater physical activity levels on weekends compared to school days, and school days compared to holidays. Results suggest that time of day preference may impact growth, with evening types who cannot sleep in growing at a slower rate than evening types who can or morning types. This may be related to sleep restriction. Despite sleep being both later and longer during the school holidays, participants’ growth slowed during the holiday period. It is possible that this may be a reflection of other behavioural changes in the holidays (increased food intake and reduced physical activity), as sleep timing during the school period was related to growth.     

Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities

Natural microbial communities are extremely diverse and contain uncharacterized but functionally important small molecules. By coupling a deuterium (D) labeling technique to high mass accuracy untargeted liquid chromatography-electrospray ionization-mass spectrometry (LC?CESI?CMS) metabolomic analysis, we found that natural acidophilic microbial biofilms dominated by bacteria of the genus Leptospirillum contained unusual lyso phosphatidylethanolamine (PE) lipids in high abundance (more than 10?nmol/mg of dry biomass). The unusual polar head group structure of these lipids is similar to lipids found in phylogenetically unrelated acidophilic chemoautolithotrophs and may be related to the affinity of these lipids for iron and calcium ions. Correlations of lyso phospholipid and proteome abundance patterns suggest a link between the lyso phospholipids and the UBA-type substrain of Leptospirillum group II. By combining untargeted metabolomics with D exchange we demonstrate the ability to identify cryptic but biologically functional small molecules in mixed microbial communities.