Signatures of arithmetic simplicity in metabolic network architecture

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life's origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictable accumulation of multiple historical accidents? Here we search for such principles by applying to an artificial chemical universe some of the methodologies developed for the study of genome scale models of cellular metabolism. In particular, we use metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions. Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbon atom reaction backbone, we find that several of the properties predicted by the artificial chemistry model hold for real metabolic networks. These findings suggest that optimality principles and arithmetic simplicity might lie beneath some aspects of biochemical complexity

Identification and regulation of genes involved in carbon dioxide fixation in Rhodobacter sphaeroides

A region of DNA from the genome of the photoheterotrophic bacterium, Rhodobacter sphaeroides, was shown to contain several genes involved in CO\sb2 fixation, namely fructose 1,6-bisphosphatase (fbpA), phosphoribulokinase (prkA), a 37-kDa polypeptide (designed CFX A) with a putative regulatory role (cfxA), and Form I ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL,S).The prkA gene was localized and identified by expression of the prkA gene product in vivo and in vitro. The PRK activity expressed in Escherichia coli was characterized, the product of the reaction identified chemically, and the prkA gene product expressed was identical to the gene product produced in Rb. sphaeroides.The fbpA and rbcL,S genes were identified and localized by comparing the amino acid sequences deduced from the DNA sequence analysis with the amino acid sequence of known Fbp and RbcL proteins. These genes are all transcribed in the same direction and are tandomly arranged.A second region of the genome contained a non-identical but similar duplicate set of these genes, namely, fbpB, prkB, cfxB and rbcR but had 3 kb of DNA between the 3\sp\prime end of prkB and the 5\sp\prime end of cfxB, a portion of which codes for glyceraldehyde 3-phosphate dehydrogenase (gapB).Strains were constructed which contained null mutations in cfxA and/or cfxB. Each mutation eliminated downstream rbc expression. Studies utilizing these strains demonstrated that each form of ribulose 1,5-bisphosphate carboxylase/oxygenase plays an essential role in maintaining the cellular redox balance during photoheterotrophic growth at differing CO\sb2 concentrations.Strains were also constructed which contained null mutations in prkA and/or prkB. Studies utilizing these strains demonstrated that CO\sb2 fixation was critical for photoheterotrophic growth but could be replaced by the alternative reduction of dimethylsulfoxide. Thus, CO\sb2 fixation was identified as an essential mediator in maintaining cellular redox balance critical for photoheterotrophic growth. The product of phosphoribulokinase, ribulose 1,5-bisphosphate, is suggested to be one factor involved in the control of expression of ribulose 1,5-bisphosphate carboxylase/oxygenase. Each form of phosphoribulokinase and ribulose 1,5-bisphosphate carboxylase/oxygenase were shown to have distinct roles in CO\sb2 fixation, and the existence and location of a region encoding a repressor of prkA expression and an activator of rbcR expression (cfxR) was postulated.U of I OnlyETDs are only available to UIUC Users without author permissio

TEM8 in Oncogenesis: Protein Biology, Pre-Clinical Agents, and Clinical Rationale

The TEM8 protein represents an emerging biomarker in many solid tumor histologies. Given the various roles it plays in oncogenesis, including but not limited to angiogenesis, epithelial-to-mesenchymal transition, and cell migration, TEM8 has recently served and will continue to serve as the target of novel oncologic therapies. We review herein the role of TEM8 in oncogenesis. We review its normal function, highlight the additional roles it plays in the tumor microenvironment, and synthesize pre-clinical and clinical data currently available. We underline the protein’s prognostic and predictive abilities in various solid tumors by (1) highlighting its association with more aggressive disease biology and poor clinical outcomes and (2) assessing its associated clinical trial landscape. Finally, we offer future directions for clinical studies involving TEM8, including incorporating pre-clinical agents into clinical trials and combining previously tested oncologic therapies with currently available treatments, such as immunotherapy

Crystallization and preliminary X-ray diffraction studies of Seneca Valley Virus-001, a new member of the Picornaviridae family

Seneca Valley Virus-001 of the Picornavirdae family was crystallized in the space group R3 and X-ray diffraction data was collected to a resolution of 2.3 Å. Rotation-function studies suggested the presence of two distict sets of 20 protomers that belong to two different virus particles in the crystallographic asymmetric unit

Systemic Gene-Directed Enzyme Prodrug Therapy of Hepatocellular Carcinoma Using a Targeted Adenovirus Armed with Carboxypeptidase G2

Systemic gene-directed enzyme prodrug therapy of hepatocellular carcinoma using a targeted adenovirus armed with carboxypeptidase G2 Hepatocellular carcinoma is the fifth most common cancer worldwide, and there is no effective therapy for unresectable disease. We have developed a targeted systemic therapy for hepatocellular carcinoma. The gene for a foreign enzyme is selectively expressed in the tumor cells and a nontoxic prodrug is then given, which is activated to a potent cytotoxic drug by the tumor-localized enzyme. This approach is termed gene- directed enzyme prodrug therapy (GDEPT). Adenoviruses have been used to target cancer cells, have an intrinsic tropism for liver, and are efficient gene vectors. Oncolytic adenoviruses produce clinical benefits, particularly in combination with conventional anticancer agents and are well tolerated. We rationalized that such adenoviruses, if their expression were restricted to telomerase-positive cancer cells, would make excellent gene vectors for GDEPT therapy of hepatocellular carcinoma. Here we use an oncolytic adenovirus to deliver the prodrug-activating enzyme carboxypeptidase G2 (CPG2) to tumors in a single systemic administration. The adenovirus replicated and produced high levels of CPG2 in two different hepatocellular carcinoma xenografts (Hep3B and HepG2) but not other tissues. GDEPT enhanced the adenovirus-alone therapy to elicit tumor regressions in the hepatocellular carcinoma models. This is the first time that CPG2 has been targeted and expressed intracellularly to effect significant therapy, showing that the combined approach holds enormous potential as a tumor-selective therapy for the systemic treatment of hepatocellular carcinoma