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1) Photosynthesis: The ultimate source of biofuel, how does it work?

This lecture will cover basic concepts in energy transduction associated with photosynthesis, and relate those reactions to productivity.

2) Photosynthesis: Sugar metabolism, key products of photosynthesis and plant productivity. This lecture outlines the pathways leading to sugar synthesis from atmospheric CO2 and emphasize the link between energy transduction and assimilation of CO2.

3) Assimilate partitioning: Getting the building blocks for growth and cell wall biosynthesis from leaf tissue to actively growing tissues. This lecture will describe how plants use an elaborate vascular system to move assimilate carbohydrate from sites of primarily assimilation to growing centers of the plant. The function and regulation of this step has a direct impact on plant productivity as a feedstock for biofuel.


1) Photosynthesis and carbohydrate metabolism in sugarcane. In this class, it is expected that the students will be able to understand the connections among photosynthesis and metabolism and growth so that new biotechnological routes could be designed for the production of bioethanol from lignocellulosic materials.

2) Structure and architecture of the plant cell wall. In this class, we will discuss the enormous challenge that is to understand how the complex composite containing interacting polysaccharides (i.e. the cell wall) is assembled in plants and how they are degraded by enzymes. It is intended that the students will be able to discuss and propose ideas about how this knowledge impacts biofuel technologies and could be used to design possible routes that could be used towards the development of the technologies related to the production cellulosic ethanol.


 1) Oil biosynthetic pathways. Triacylglycerols (TAGs) are abundant, sustainable and energy-rich reduced forms of carbon that contain three fatty acyl chains. These fatty acyl chains are usually 16-18 carbon long and are esterified to a glycerol backbone. These fatty acyl groups are chemically and functionally similar to hydrocarbons present in petroleum fuel. Gaining full knowledge of oil biochemical pathways can improve our ability to partially replace fossil oil by biobased fuels.

2) Biochemical and genetic switches in glucose utilization for starch synthesis and re-direction of the reduced carbon to oil biosynthesis in-planta.

3) Genetic and genomic approaches directed at enhanced production of plant oil.


1) Lignin biosynthesis: Role and importance of the phenylpropanoid biosynthetic pathway, monolignol biosynthesis, export and polymerization. The objective is to understand to what extent plant lignin content and composition can be modified in useful ways without deleterious consequences to plant growth and development. Since lignin cannot be removed, a better control of lignin deposition and cross-linking within the cell wall may increase sugar recovery from the cell wall polysaccharides.

2) Using synthetic biology in plants to overcome lignin recalcitrance. Couple strategies are currently developed to modify lignin composition by introducing weaker bonds that are easier  to break down by pretreatment.

3) Lignocellulosic biofuels: This will address cell wall recalcitrance, sugar yield, pretreatment (ionic liquid and saccharification), biomass inhibitors and sugar conversion to biofuels. Basically, it will summarize the activities run in our research center and address bottlenecks and sustainability issues.


1) The structure and biosynthesis of the cell walls of grasses – The cell walls of grasses and commelinoid monocots are compositionally different from all dicots and other monocots. I will outline these chemical differences and discuss special features of synthesis and dynamics particular to grass walls.

2) How plants make cellulose and other (1,4)-beta-D-glycans– Cellulose, xylans, and chitin are the most abundant biopolymers in Nature, and consequently, they share the most abundant linkage. We still have only a hazy understanding of the biochemical mechanisms of synthesis. All living organisms that make this linkage have solved a perplexing steric problem of inverting one sugar almost 180° with respect to each neighbor yet processively adding sugars to the non-reducing end of the growing chain. I will present a hypothesis that explains how the steric problem was solved and some evidence we have accumulated in support of it.

3) Capturing the genetic diversity of maize for improvement of energy grasses– With recently completed genomes and numerous genetic resources, maize and sorghum are excellent genetic models for the improvement of all C4 energy grasses. We have launched a gene discovery program for variants in quantity and quality of lignocellulosic biomass in recombinant inbred lines for rapid identification of QTL for beneficial traits. Tropical maize and sweet sorghum are also promising high producing energy crops with remarkably low input requirements, and we are extending gene discovery to traits such as sugar and biomass accumulation in these inbreds and landraces.


1) Biosynthesis of pectic polysaccharides – Pectic polysaccharides constitute one of the three major classes of polysaccharides present in the walls of all plants, and are distinguished by their high galacturonic acid (GalA) content. Recent molecular genetic and biochemical advances will be summarized and their implications for the synthesis of wall polysaccharides in general will be discussed.

2) Immunological approaches for studies of plant cell walls and biomass. I. The complexity and diversity of polysaccharides present in plant cell walls requires new tools that allow studies of plant cell walls at diverse levels of resolution, ranging from tissue-level down to sub-cellular studies. An overview of the current toolkit of monoclonal antibodies against plant glycans will be provided, including how the antibodies were generated and how they have been characterized.

3) Immunological approaches II. Immunolocalization of cell wall polysaccharide structures (epitopes) provides information about where and when cell wall polysaccharides are made and/or modified in plant cells. Glycome profiling provides complementary information about composition and overall structure of plant cell walls, and lends itself to high through-put studies. Contributions from these experimental approaches will be discussed.


1) Synthetic biology for fuel biologists -This lecture will review metabolic pathways for biosynthesis of various fuel molecules, and challenges in engineering them. The basic biochemical pathways, genes, and variations will be discussed, with emphasis on higher alcohols, isoprenoids and fatty acids.

2) Tutorial: Metabolic pathway design and theoretical yield calculation.

The purpose of this lecture is to introduce methods for yield calculation so that biologists can gain understand the basis behind the matrix. Students are encouraged to bring laptop computers with Excel installed in order to work with spreadsheets.

3) Optimization of microbial metabolism for fuel production. This lecture will discuss examples of strain design and optimization for biofuel production. Both rational design and evolutionary approaches will be discussed, with examples from production of 1-butanol, isobutanol and pentanol.


1) Synthetic genomics: DNA synthesis and assembly. This tutorial will review how to synthesize DNA from oligonucleotides as well as natural and synthetic segments of DNA. I will review both the history of this essential set of techniques needed by synthetic biologists as well as technical details on best current approaches to design and build large DNA constructs.

2) Creation of a synthetic bacterial cell. This will be a presentation about the recent work published by my group at the J. Craig Venter Institute.

3) Societal and ethical Issues for the practice of synthetic biology. Synthetic biology has great potential for the solution of important problems, but must be carefully applied and fully understand.


© 2017 Advanced School on Biochemistry of Biofuels