Molecular Biology Review

“The Antimicrobial Defense of Drosophila: A Paradigm for Innate Immunity” by Dr. Jules Hoffman

Dr. Hoffman gives an elaborate review of the mechanism of the antimicrobial defense of drosophila. Drosophila is a widely studied model organism, and the research can be applied to higher organisms, such as mammals. Using drosophila, Hoffman has demonstrated the manner in which the adaptive immune system is activated by the innate immune system. Drosophila insects are prone to many types of infections from bacteria, protozoa, and fungi. Dr. Hoffman’s study is based on the systemic defense mechanism of drosophila. After microbial infection, drosophila releases various antimicrobial peptides, which are a part of its defense mechanism. These comprise of drosomycin, metchnikowin, defensin, cecropin, drosocin, attacin, and diptericin. Dr. Hoffman has studied the controlled expression of antimicrobial peptides. Kappa B genes, especially kappa B response elements, play a crucial role in the expression of antimicrobial peptides, especially NF-Kb proteins. Successful mutation of these genes was shown to compromise the expression of antimicrobial peptides via the toll and immune deficiency (Imd) pathway. Imd mutants of drosophila were found sensitive to both fungal and bacterial infections. The toll pathway was found integral in the expression of drosomycin but was not found to play any role in diptericin expression.

Most important, Dr. Hoffman has demonstrated the manner in which the adaptive immunity is activated by innate immunity. The microbial ligands/antigens via a hypothetical receptor bind to antigen cells and activate the kappa B proteins (NF-κB). This activation causes the upregulated expression of major histocompatibility complex II (MHC II), thereby, leading to the stimulation of naïve T cells. Dr. Hoffman has demonstrated the role of Peptidoglycan recognition proteins-PGRP in the activation of adaptive immunity, as well as NF-Kb activation by toll and IL-1 and TLR family members. The activation of adaptive immunity by the innate immune system in drosophila can be utilized to study inflammation. The role of antimicrobial peptides in inflammation has already been established. Reduced activation of the innate immune system can be executed via inhibition of kappa B genes and kappa B response elements. There is also the need to carry out studies on receptors that bind these microbial ligands. Mutation of these receptors will also inhibit the activation of the innate immune response, thereby, reducing the activation of the adaptive immune response.

“Molecular Chaperones in Protein Folding and Neurodegeneration” by Dr. Arthur Horwich

The aggregation of aberrant proteins is the most prominent feature of neurodegenerative disease. This has been shown in Alzheimer disease, which is characterized by the formation of amyloid plaques and neurofibrillary tangles. Dr. Norwich observed the formation of amyloid plaques in the grey and white matter brain areas of a mouse. Neurodegenerative disease is a condition of aberrant protein conformation that is also characterized by the aggregation of misfolded proteins. Misfolded proteins usually overload the body’s proteolytic machinery, and it leads to the cytotoxic accumulation of protein aggregates. These protein aggregates also stimulate the sequestration of normal proteins, causing impairments in cellular functioning. Normally aberrant and waste proteins are destroyed via the autophagy-lysosome pathway (ALP) and the ubiquitin-proteasome system (UPS).

Molecular chaperones comprise of highly conserved proteins that direct the proper folding of nascent proteins. The bind and stabilize nascent proteins in the proper conformation prevent protein misfolding. Molecular chaperones also assist in the identification and targeted destruction of aberrant proteins via autophagy and proteasomal degradation. Neurons have a long life span as compared to other cells, and chaperones play a crucial role in stress response and cellular maintenance. Dr. Horwich, in his lifelong work, has helped in the conceptualization of molecular chaperones. Initially, they were identified as heat shock proteins that played a key role in protein folding. In addition, they facilitated the maturation of proteins in the yeast mitochondrial matrix to the native protein state. The heat shock proteins (HSPs) conferred thermo-tolerance to folding proteins, and they prevented the kinetic trapping of proteins. The knowledge of protein misfolding explains the formation of amyloid plaques in neurodegenerative disease. A therapeutic intervention lies in the prevention of amyloid plaques. This is provided via enhanced expression of molecular chaperones that direct the autophagy of amyloid plaques. Chaperones can prevent the conformation change of proteins to beta-sheet structures and the aggregation of such aberrant proteins. They are fundamental in preventing the misfolding of proteins. Heat shock proteins have been found to prevent the formation of amyloid fibrils in neurodegenerative conditions, such as Parkinson’s disease and Alzheimer’s disease. Therapeutic interventions based on chaperones hold great potential in relieving neurodegenerative diseases, such as Gaucher’s disease, cystic fibrosis, Huntington’s disease, Alzheimer’s disease, Creutzfeldt-Jakob disease, and Parkinson’s diseases. Molecular chaperones should be administered to reduce the severity and progression of neurodegenerative disease. The production of molecular chaperones for therapeutic purposes can be realized via biotechnology.

“Biofuels & Photosynthesis” by Dr. Himadri Pakrasi

Dr. Pakrasi makes reference to the global photosynthesis as an important process. Plants combine carbon dioxide and water in the presence of light energy to form simple carbohydrates. Carbon dioxide is captured, and oxygen is liberated. Photosynthesis maintains an important gaseous equilibrium of oxygen and carbon dioxide in the atmosphere. Owing to the increasing interest of biofuel, Dr. Pakrasi refers to this alternative source of energy as the green dream. Plant carbohydrates, such as cellulose and lignocelluloses, are important sources of energy. Most interesting, photosynthesis and biofuel are entwined as a biofuel is a product of photosynthesis. Simply put, sunlight has been harnessed to form gasoline. Algae are cited as sustainable sources of biofuel and biomaterial. Using biotechnology, algae can produce natural oils that can be converted to gasoline. The Science of biofuel production from algae is simple. Algae require carbon dioxide, sunlight, and water for proliferation. Through genetic modification, the production of oil can be enhanced. This oil is harvested and converted to biodiesel. The cellulose component of algae is fermented to yield ethanol. Both ethanol and biodiesel are alternative clean fuels as compared to petroleum-based fuels.

NASA has also recognized the potential of algae as a source of energy. A feedstock of algae can produce 10k to 20k gallon/acre/year of bio-derived oil. It is estimated that algae can produce 150-300 more times oil than a crop of soybeans. Algae are a promising potential source of energy for aircraft in the future. Unlike fossils which are depleted, algae can be continuously regenerated.

The world is shaking from the adverse effects of high fuel prices. The high cost of fuel increases the cost of production, and this affects directly the consumer who has to buy commodities at a high price. Algae are a viable and cheap alternative to energy. Unlike food crops, arable land does not need to be set aside for the purpose of growing algae. In addition, the use of food crops to produce energy is not viable as it is tantamount to food insecurity. The process of oil production can be scaled up in bio-reactors. Biofuel produced from algae can be utilized to drive industrial processes, as well as the transport sector.

“Novel Insights into the Enzymatic Conversion of Recalcitrant Polysaccharides” by Vincent Eijsink

In his keynote address, Vincent stresses on the role of efficient (enzymatic) methods in biomass saccharification as essential processes in the future of bio-economy. Indeed, the degradation of recalcitrant polysaccharides is of great economic importance. Chitin is abundant in nature, and it would be helpful to have efficient enzymatic processes that convert chitin to useful fermentable products, as well as biofuel. He has extensively studied enzymatic processes that can be applied in the degradation of recalcitrant polysaccharides, such as chitin and cellulose. Chitinases (Chi A and Chi B) exhibit high processivity in the degradation of chitosan. Processivity refers to the enzymatic stepwise degradation of chitin. Enzymes act on the chitin crystalline surface, and chain breaks are introduced, and oxidized chain ends are formed in the process. The formation of chain ends promotes the activity of chitinases. Mutation of the tryptophan residue in Chi B was found to abolish its processivity. This mutation reduces mutation towards chitin but increases efficiency towards chitosan. This demonstrates that processivity enhances the degradation of the insoluble substrate but slows down the enzyme activity. In chitinase A processivity mutants, reduced processivity is accompanied by decreased activity towards chitin and increased activity towards chitosan.

Substrate disrupting proteins can aid in the degradation of recalcitrant proteins. CBP21 is used as the model example of a substrate disrupting a protein. Most noteworthy, chitinases have been found to work synergistically with substrate disrupting proteins. In addition, CBP 21 improves substrate accessibility for non-chitanase, such as desaturases. Chitin is abundant, and it is necessary to understand the efficient enzymatic methods that will lead to its degradation. Processivity contributes to the degradation of recalcitrant polysaccharides as detached polypeptide chains do not re-associate with the solid substrate. However, there is a need for caution in the use of processive enzymes, since their activity is slow. Substrate disrupting proteins, which aid in substrate accessibility, should be utilized to enhance the degradation of recalcitrant polysaccharides, such as chitin.