Differential responses of stream water and bed sediment microbial communities to watershed degradation.

The importance of microbial communities in the function of lotic ecosystems is unequivocal. However, traditional watershed studies on biodiversity have mostly focused on benthic macroinvertebrates, macroalgae and fish assemblages. Here, we investigated the diversity and interaction patterns of microbial communities in water and bed sediment of streams impacted by intensive watershed activities versus streams with relatively pristine conditions via next-generation sequencing of 16S rRNA amplicons using Illumina HiSeq platform.

Deriving metabolic engineering strategies from genome-scale modeling with flux ratio constraints.

Optimized production of bio-based fuels and chemicals from microbial cell factories is a central goal of systems metabolic engineering. To achieve this goal, a new computational method of using flux balance analysis with flux ratios (FBrAtio) was further developed in this research and applied to five case studies to evaluate and design metabolic engineering strategies. The approach was implemented using publicly available genome-scale metabolic flux models.

Minimum requirements of flagellation and motility for infection of Agrobacterium sp. strain H13-3 by flagellotropic bacteriophage 7-7-1.

The flagellotropic phage 7-7-1 specifically adsorbs to Agrobacterium sp. strain H13-3 (formerly Rhizobium lupini H13-3) flagella for efficient host infection. The Agrobacterium sp.

Are we ready for genome-scale modeling in plants?

As it is becoming easier and faster to generate various types of high-throughput data, one would expect that by now we should have a comprehensive systems-level understanding of biology, biochemistry, and physiology at least in major prokaryotic and eukaryotic model systems. Despite the wealth of available data, we only get a glimpse of what is going on at the molecular level from the global perspective. The major reason is the high level of cellular complexity and our limited ability to identify all (or at least important) components and their interactions in virtually infinite number of internal and external conditions.

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico.

Background: Genome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential metabolic engineering strategies in silico.

Results: A new method called "flux balance analysis with flux ratios (FBrAtio)" was developed in this research and applied to a new genome-scale model of Clostridium acetobutylicum ATCC 824 (iCAC490) that contains 707 metabolites and 794 reactions.