Simbiotics is a spatially explicit multiscale modeling platform for the design, simulation and analysis of bacterial populations. Systems ranging from planktonic cells and colonies, to biofilm formation and development may be modeled. Representation of biological systems in Simbiotics is flexible, and user-defined processes may be in a variety of forms depending on desired model abstraction. Simbiotics provides a library of modules such as cell geometries, physical force dynamics, genetic circuits, metabolic pathways, chemical diffusion and cell interactions. Model defined processes are integrated and scheduled for parallel multithread and multi-CPU execution. A virtual lab provides the modeler with analysis modules and some simulated lab equipment, enabling automation of sample interaction and data collection. An extendable and modular framework allows for the platform to be updated as novel models of bacteria are developed, coupled with an intuitive user interface to allow for model definitions with minimal programming experience. Simbiotics can integrate existing standards such as SBML, and process microscopy images to initialize the 3D spatial configuration of bacteria consortia. Two case studies, used to illustrate the platform flexibility, focus on the physical properties of the biosystems modeled. These pilot case studies demonstrate Simbiotics versatility in modeling and analysis of natural systems and as a CAD tool for synthetic biology.
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http://dx.doi.org/10.1021/acssynbio.6b00315 | DOI Listing |
We describe an outbreak of invasive meningococcal disease (IMD) caused by Neisseria meningitidis serogroup C in Fiji. We created surveillance case definitions and collected data by using standard investigation forms. Bacterial identification, antimicrobial susceptibility testing, and PCR were performed in Fiji.
View Article and Find Full Text PDFEscherichia coli producing OXA-48-like carbapenemases (OXA-EC) is considered a high-risk pathogen spread primarily in the community in low- and middle-income countries and nosocomially in high-income countries. We investigated the emergence and spread of OXA-EC in Israel, a high-income country with strong carbapenemase-directed infection control in healthcare institutions, by conducting a population-based study using data and isolates from the national surveillance system. A total of 3,510 incident cases of OXA-EC occurred during 2007-2023.
View Article and Find Full Text PDFISME J
December 2024
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
Most of the microbes in nature infrequently receive nutrients and are thus in slow- or non-growing states. How quickly they can resume their growth upon an influx of new resources is crucial to occupy environmental niches. Isogenic microbial populations are known to harbor only a fraction of cells with rapid growth resumption, yet little is known about the physiological characteristics of those cells and their emergence in the population.
View Article and Find Full Text PDFJ Virol
December 2024
Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.
Bacteriophages are viruses infecting bacteria. The vast majority of them bear a tail, allowing host recognition, cell wall perforation, and DNA injection into the host cytoplasm. Using electron cryo-microscopy (cryo-EM) and single particle analysis, we determined the organization of the tail proximal extremity of siphophage T5 that possesses a long flexible tail and solved the structure of its tail terminator protein p142 (TrP).
View Article and Find Full Text PDFJ Virol
December 2024
Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, USA.
Unlabelled: transmits Liberibacter asiaticus (CLas) between citrus plants which causes the expression of huanglongbing disease in citrus. flavi-like virus (DcFLV) co-occurs intracellularly with CLas in populations in the field. However, the impact(s) of DcFLV presence on the insect vector and its interaction with the CLas phytopathogen remain unclear.
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