Applying the mesolens to microbiology : visualising biofilm architecture and substructure

Biofilms pose a public health risk due to their ability to protect bacteria from mechanical, environmental and chemical factors. Thereby they can confer resistance to their constituent bacteria and serve as a vehicle for spread of antimicrobial resistance [1]. Understanding the structure of bacterial communities is critical to developing novel methods of biofilm eradication. Current techniques for imaging live biofilms are limited by sacrificing the size of the imaging volume or spatial resolution. Common approaches to imaging biofilm architecture include electron microscopy techniques [2], single or multi-photon confocal microscopy [3] or wide field epi-fluorescence microscopy using low-magnification, low-numerical aperture lenses [4]. Here we use the Mesolens, an optical microscope with a unique combination of a low magnification (x4) and a high numerical aperture (0.47) which can image specimens up to 6x6x3 mm in volume with a lateral resolution of 700 nm and an axial resolution of 7 μm [5]. Using the Mesolens, it is possible to image whole live colony biofilms with cellular resolution in a single dataset. We report the finding of intra-colony channels (measuring ca.15 μm in diameter) which form when Escherichia coli colonies are grown on a solid surface as an inherent property of biofilm formation. By tracking the movement of 200 nm fluorescent microspheres, we observe translocation of the microspheres from the base of the biofilm into the colony with specific localisation to the channel systems. The uptake of microspheres by the colony, infers that these features are inherent to biofilm formation and provide a role in structural support. The biofilms in this work were grown on a nutrient-rich solid medium, and by expanding from the observations of our bead uptake assay we can deduce that the channels may also play a role in nutrient uptake and dissemination throughout the colony. These findings serve as evidence of a fundamental principle of structural biology and bacterial organisation

Planetary Lake Lander - A Robotic Sentinel to Monitor a Remote Lake

The Planetary Lake Lander Project is studying the impact of rapid deglaciation at a high altitude alpine lake in the Andes, where disrupted environmental, physical, chemical, and biological cycles result in newly emerging natural patterns. The solar powered Lake Lander robot is designed to monitor the lake system and characterize both baseline characteristics and impacts of disturbance events such as storms and landslides. Lake Lander must use an onboard adaptive science-on-the-fly approach to return relevant data about these events to mission control without exceeding limited energy and bandwidth resources. Lake Lander carries weather sensors, cameras and a sonde that is winched up and down the water column to monitor temperature, dissolved oxygen, turbidity and other water quality parameters. Data from Lake Lander is returned via satellite and distributed to an international team of scientists via web-based ground data systems. Here, we describe the Lake Lander Project scientific goals, hardware design, ground data systems, and preliminary data from 2011. The adaptive science-on-the-fly system will be described in future papers

Disorder prediction methods, their applicability to different protein targets and their usefulness for guiding experimental studies

The role and function of a given protein is dependent on its structure. In recent years, however, numerous studies have highlighted the importance of unstructured, or disordered regions in governing a protein’s function. Disordered proteins have been found to play important roles in pivotal cellular functions, such as DNA binding and signalling cascades. Studying proteins with extended disordered regions is often problematic as they can be challenging to express, purify and crystallise. This means that interpretable experimental data on protein disorder is hard to generate. As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein. Currently, over 60 prediction servers exist, utilizing different methods for classifying disorder and different training sets. Here we review several good performing, publicly available prediction methods, comparing their application and discussing how disorder prediction servers can be used to aid the experimental solution of protein structure. The use of disorder prediction methods allows us to adopt a more targeted approach to experimental studies by accurately identifying the boundaries of ordered protein domains so that they may be investigated separately, thereby increasing the likelihood of their successful experimental solution

One-step immortalization of primary human airway epithelial cells capable of oncogenic transformation

BACKGROUND: The ability to transform normal human cells into cancer cells with the introduction of defined genetic alterations is a valuable method for understanding the mechanisms of oncogenesis. Easy establishment of immortalized but non-transformed human cells from various tissues would facilitate these genetic analyses. RESULTS: We report here a simple, one-step immortalization method that involves retroviral vector mediated co-expression of the human telomerase protein and a shRNA targeting the CDKN2A gene locus. We demonstrate that this method could successfully immortalize human small airway epithelial cells while maintaining their chromosomal stability. We further showed that these cells retain p53 activity and can be transformed by the KRAS oncogene. CONCLUSIONS: Our method simplifies the immortalization process and is broadly applicable for establishing immortalized epithelial cell lines from primary human tissues for cancer research

Is threat in the way they move? Influences of static and gait information on threat judgments of unknown people

Recognising intraspecies threat is essential for survival. However, this needs to be balanced against the undue avoidance of unknown others who may be useful to us. Research has shown that judgments of ‘aggression’ and ‘threat’ posed by an unknown person can accurately reflect that person’s general aggressive tendencies. To date, there has not been a within-sample comparison of the informativeness of static and walking stimuli for threat judgments. In this study, 193 participants rated the threat posed by 23 target people presented as both simplified gait presentations (point-light walkers) and still images. We analysed how threat judgments made by participants were predicted by the target’s self-reported aggression (accuracy), the sex of the targets and the medium of target presentation (point-light vs. still image). Our results showed that participants’ threat judgments accurately predicted targets’ aggression. Male targets received higher threat ratings than female targets and point-light displays were rated as more threatening than still images. There were no effects of target sex and presentation medium on accuracy of threat perception and no sex by medium interactions on judgments themselves. Overall, this study provides further evidence of the accuracy of threat judgments at detecting trait aggression. However, further research is needed to explain what features of the target people are enabling the accurate judgments of aggression