Lessons Learned as President of the Institute for Systems Biology(2000–2018)

正I stepped down as president of the Institute for Systems Biology(ISB)on Jan 1,2018.As I think about my 17-year term as President,I am astounded at how much I have learned,not only about science but also about,among other things,what it takes to build a unique world-class institution.The beginningsI came to the non-pro?t,independent ISB from 30 years in academia.For 22 years,I was a faculty member of Division of Biology at the California Institute of Technology(Caltech),     

Systems Biocatalysis: Development and engineering of cell-free “artificial metabolisms” for preparative multi-enzymatic synthesis

Systems Biocatalysis is an emerging concept of organizing enzymes in vitro to construct complex reaction cascades for an efficient, sustainable synthesis of valuable chemical products. The strategy merges the synthetic focus of chemistry with the modular design of biological systems, which is similar to metabolic engineering of cellular production systems but can be realized at a far lower level of complexity from a true reductionist approach. Such operations are free from material erosion by competing metabolic pathways, from kinetic restrictions by physical barriers and regulating circuits, and from toxicity problems with reactive foreign substrates, which are notorious problems in whole-cell systems. A particular advantage of cell-free concepts arises from the inherent opportunity to construct novel biocatalytic reaction systems for the efficient synthesis of non-natural products (“artificial metabolisms”) by using enzymes specifically chosen or engineered for non-natural substrate promiscuity. Examples illustrating the technology from our laboratory are discussed.     

Luminescence Spectroscopy – a Useful Tool in Real-Time Monitoring of Viscosity during In-Vitro Digestion

Luminescence spectroscopy coupled with molecular rotors was used in the TNO Intestinal Model-1 (TIM-1) to monitor in situ changes to luminal viscosity of three maize starch samples varying in the amylose-to-amylopectin ratio (AM: AP): normal, high amylose (AM) and high amylopectin (AP). The fluorescence intensity (FI) of Fast Green (FG), a proven micro (and bulk) viscosity probe, was monitored throughout digestion to track changes in the gastric viscosity. The FI of FG and the viscosity imparted by the starch followed a power-law relationship. The emission of the MR was unaffected by the composition of TIM-1 secretion fluids nor pH. Hence, direct measurements of digesta FI are sensitive to changing viscosity during the simulated digestion. The viscosity was highest for AP, followed by normal starch, and high AM had the lowest viscosity. In the TIM-1 gastric compartment, from highest to lowest FI, and thus viscosity was high AM > high AP > normal maize starches. We conclude the validity of the proposed method to facilitate the measurement of luminal viscosity, in vitro, when the microviscosity represents bulk viscosity (i.e., when the increase in bulk viscosity is a result of molecular crowding and the surrounding environment around the rotor is homogeneous). Careful consideration is required when foods are heterogeneous as molecular rotors report only on their local non-uniform environment.

     

16S rRNA Gene-Based Oligonucleotide Microarray for Environmental Monitoring of the Betaproteobacterial Order “Rhodocyclales”

For simultaneous identification of members of the betaproteobacterial order “Rhodocyclales” in environmental samples, a 16S rRNA gene-targeted oligonucleotide microarray (RHC-PhyloChip) consisting of 79 probes was developed. Probe design was based on phylogenetic analysis of available 16S rRNA sequences from all cultured and as yet uncultured members of the “Rhodocyclales.” The multiple nested probe set was evaluated for microarray hybridization with 16S rRNA gene PCR amplicons from 29 reference organisms. Subsequently, the RHC-PhyloChip was successfully used for cultivation-independent “Rhodocyclales” diversity analysis in activated sludge from an industrial wastewater treatment plant. The implementation of a newly designed “Rhodocyclales”-selective PCR amplification system prior to microarray hybridization greatly enhanced the sensitivity of the RHC-PhyloChip and thus enabled the detection of “Rhodocyclales” populations with relative abundances of less than 1% of all bacteria (as determined by fluorescence in situ hybridization) in the activated sludge. The presence of as yet uncultured Zoogloea-, Ferribacterium/Dechloromonas-, and Sterolibacterium-related bacteria in the industrial activated sludge, as indicated by the RHC-PhyloChip analysis, was confirmed by retrieval of their 16S rRNA gene sequences and subsequent phylogenetic analysis, demonstrating the suitability of the RHC-PhyloChip as a novel monitoring tool for environmental microbiology.     

Systems biology of epistasis: Shedding light on genetic interaction network “hubs”

Comment on: Szappanos B, et al. Nat Genet 2011; 43:656-62.     

Lipopolysaccharide-Binding Protein for Monitoring of Postoperative Sepsis: Complemental to C-Reactive Protein or Redundant?

Introduction

To prospectively evaluate the performance of Lipopolysaccharide-Binding Protein (LBP) in prediction of hospital mortality and its correlation to C-reactive Protein (CRP), we studied sixty consecutive, postoperative patients with sepsis admitted to the university hospital intensive care unit.

Measurements and Methods

Plasma LBP and CRP were serially measured from day(d)1 (onset of sepsis) to d14 in parallel with clinical data until d28. Predictive value and correlation of LBP and CRP were analyzed by Receiver Operating Characteristic (ROC) curve analysis and Pearson''s test, respectively.

Main Results

LBP and CRP showed the highest levels on d2 or d3 after the onset of sepsis with no significant difference between survivors and nonsurvivors. Only at d7, nonsurvivors had significantly (p = .03) higher levels of CRP than survivors. Accordingly, in ROC analysis, concentration of CRP and LBP on d7 poorly discriminated survivors from nonsurvivors (area under curve = .62 and .55, respectively) without significant difference between LBP- and CRP-ROC curves for paired comparison. LBP and CRP plasma levels allocated to quartiles correlated well with each other (r² = .95; p = .02). Likewise, changes in plasma concentrations of LBP and CRP from one observation to the next showed a marked concordance as both parameters concomitantly increased or decreased in 76% of all cases.

Conclusions

During the first 14 days of postoperative sepsis, LBP plasma concentrations showed a time course that was very similar to CRP with a high concordance in the pattern of day-to-day changes. Furthermore, like CRP, LBP does not provide a reliable clue for outcome in this setting.     

“Barcoding” and ISSR data illuminate a problematic infraspecific taxonomy for Chrysanthemoides monilifera (Calenduleae; Asteraceae): Lessons for biocontrol of a noxious weed

Chrysanthemoides monilifera Tourn. ex Medik is a noxious weed in Australia and New Zealand. It is a widespread species in southern Africa, where it shows considerable morphological variation that has resulted in a confusing infraspecific taxonomy. We use DNA sequence data from the nuclear Internal Transcribed Spacer (ITS) region from 78 samples of this species from its indigenous distribution range and 10 samples from Australia and New Zealand to determine the regions of origin of the invasive plants. These data are augmented by a smaller study using ISSR markers. Bayesian Inference analysis was somewhat resolved, with many weakly supported nodes. Clades with support tended to correspond to infraspecific taxonomic entities, and were geographically coherent. In contrast, a neighbour-net analysis was not as well resolved and indicated considerable reticulation. All analyses of ITS data retrieved two major clades corresponding to Western and Eastern distributions, with some overlap. Samples from New Zealand and Australia correspond to the taxon C. monilifera subsp. monilifera, and are resolved as most closely related to samples from the greater Cape Town area. Biological control agent populations for C. monilifera subsp. monilifera should be sourced from this region in order to avoid host plant incompatibility problems.     

Convincing the “Herd” of immunity: Lessons from smallpox vaccination in 19th century Germany

Although vaccination is a cost-effective way to control infectious diseases, it is often met with popular resistance. Studying smallpox in 19th century Germany, this paper explores how economic incentives contribute to this phenomenon. The paper adds to the literature by combining mathematical epidemiology and unpublished archival evidence from two German states - Baden and Wurttemberg. The two states are an intriguing case because their initial conditions and vaccination laws were similar. Despite this, Baden experienced lower smallpox prevalence and higher vaccination uptake than Wurttemberg. The epidemiological model predicts that incentives to vaccinate decline rapidly when immunization reduces prevalence. The archival evidence reveals that Baden offset this decline by creating a public vaccination system which reduced costs for vaccinees and vaccinators alike. This suggests that the high fixed costs of centralized immunization policies can be compensated by economies of scale and popular acceptance.