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This disclosure provides a genetically-modified bacterium from the genus Megasphaera that comprises an exogenous nucleic acid encoding a bifunctional aldehyde/alcohol dehydrogenase that produces butanol as the final product. The disclosure further provides methods for producing butanol using such genetically-modified bacterium.
The present invention relates to genetically modified bacteria and methods of optimizing genetically modified bacteria for the production of a metabolite.
In this work genetic algorithm was proposed to solve fuel loading pattern optimization problem in thorium fueled heavy water reactor. The objective function of optimization was to maximize the conversion ratio and minimize power peaking factor. Those objectives were simultaneously optimized using non-dominated Pareto-based population ranking optimal method. Members of non-dominated population were assigned selection probabilities based on their rankings in a manner similar to Baker's single criterion ranking selection procedure. A selected non-dominated member was bred through simple mutation or one-point crossover process to produce a new member. The genetic algorithm program was developed in FORTRAN 90 while neutronic calculation and analysis was done by COREBN code, a module of core burn-up calculation for SRAC. (authors)
Genetically engineered Foot and Mouth Disease Virus (FMDV) and related engineered proteins and polynucleotides, nanolipoprotein particles, compositions, methods and systems are described. The genetically engineered FMDV is modified by the strategic insertion of a protein tag into select regions of the FMDV genome which encode viral proteins that are exposed on the surface of the FMDV viral capsid. The inserted protein tag is displayed as a decoration or attachment on the viral capsid surface.
The structure of the adult skeleton is determined, in large part, by its genome. Whether genetic variations may influence the effectiveness of interventions to combat skeletal diseases remains unknown. The differential response of trabecular bone to an anabolic (low-level mechanical vibration) and a catabolic (disuse) mechanical stimulus were evaluated in three strains of adult mice. In low bone-mineral-density C57BL/6J mice, the low-level mechanical signal caused significantly larger bone formation rates (BFR) in the proximal tibia, but the removal of functional weight bearing did not significantly alter BFR. In mid-density BALB/cByJ mice, mechanical stimulation also increased BFR, whereas disuse significantly decreased BFR. In contrast, neither anabolic nor catabolic mechanical signals influenced any index of bone formation in high-density C3H/HeJ mice. Together, data from this study indicate that the sensitivity of trabecular tissue to both anabolic and catabolic stimuli is influenced by the genome. Extrapolated to humans, these results may explain in part why prophylaxes for low bone mass are not universally effective, yet also indicate that there may be a genotypic indication of people who are at reduced risk of suffering from bone loss.
Mutation of the Lazy-2 (Lz-2) gene in tomato (Lycopersicon esculentum mill.) produces a phytochrome-dependent reversal of shoot gravitropism, providing a unique genetic resource for investigating how signals from light modulate gravitropism. We mapped the Lz-2 gene using RFLPs and a PCR-based technique to assess the feasibility of positional cloning. Analysis of a 1338 plant backcross population between L. esculentum and L. pennellii placed Lz-2 within a 1.2 cM interval on chromosome 5, 0.4 cM from TG504-CT201A interval. The inabililty to resolve these markers indicates that Lz-2 resides in a centromeric region in which recombination is highly suppressed. Lazy-2 is tightly linked to but does not encode the gene for ACC4, an enzyme involved in ethylene biosynthesis. We also observed that Lz-2 is partially dominant under certain conditions and stages of development.
A diversification of the genetic code based on the number of codons available for the proteinous amino acids is established. Three groups of amino acids during evolution of the code are distinguished. On the basis of their chemical complexity those amino acids emerging later in a translation process are derived. Codon number and chemical complexity indicate that His, Phe, Tyr, Cys and either Lys or Asn were introduced in the second stage, whereas the number of codons alone gives evidence that Trp and Met were introduced in the third stage. The amino acids of stage 1 use purine-rich codons, while all the amino acids introduced in the second stage, in contrast, use pyrimidines in the third position of their codons. A low abundance of pyrimidines during early translation is derived. This assumption is supported by experiments on non-enzymatic replication and interactions of hairpin loops with a complementary strand. A back extrapolation concludes a high purine content of the first nucleic acids, which gradually decreased during their evolution. Amino acids independently available from prebiotic synthesis were thus correlated to purine-rich codons. Implications on the prebiotic replication are discussed also in the light of recent codon usage data.
Classical and advanced hybridization methods are employed in the control literature to calibrate the tuning parameters of internal model control (IMC) and proportional-integral-derivative (PID) controllers. This paper presents an alternative tuning design for the generalized predictive controller (GPC) that is based on both the positional process model and cost function. The proposed method involves the selection of an integral polynomial weighting filter for reference and output signals to deal with reference tracking, disturbance rejection, model-plant mismatch (MPM), minimum control energy and closed-loop robustness. The filter positional GPC (FP-GPC) obtained is transformed into a two-degree-of-freedom polynomial filtered RST structure and then into filtered internal model control (F-IMC) and PID controllers. Also, a multi-objective optimization based on genetic algorithm is applied to tune the filter parameters. Numerical and experimental essays show the effectiveness of the proposed control methodology.
Metal-organic frameworks (MOFs) are promising materials for CO 2 capture with the potential to use less energy than current industrial CO 2 capture methods. MOFs are highly versatile sorbents, and there is an almost unlimited number of MOFs that could be synthesized. In this work, we used a genetic algorithm (GA) and grand canonical Monte Carlo (GCMC) simulations to efficiently search for high-performing MOFs for CO 2 capture. We analyzed the effects of important GA parameters, including the mutation probability, the number of MOFs per generation and the number of GA generations, on the GA performance. Here, we performed GCMC simulations on-the-fly during the GA procedure to determine the performance of proposed MOFs and optimized their structures using multiple objective functions across different topologies. The GA was able to determine top-performing MOFs balancing CO 2 selectivity versus working capacity and reduced the cost of molecular simulations by a factor of 25 versus brute-force screening of an entire database of structures.
The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.
These are slides on genetic algorithm for nuclear data evaluation. The following is covered: initial population, fitness (outer loop), calculate fitness, selection (first part of inner loop), reproduction (second part of inner loop), solution, and examples.
A signaling game is developed in order to derive the equilibrium conditions under which special interest groups (SIGs) involved in the controversial debate over genetically engineered (GE) foods have the incentive to truthfully reveal their information or spin facts regarding the health impact of GE foods. Consumers can choose to inspect information provided by SIGs at a cost. The risk of spinning facts is much higher for pro-GE groups, because if it turns out that a certain GE food is unsafe, the penalty will be severe. However, anti-GE groups can still spin facts at low risk even if consumers choose to inspect. This helps explain why some pro-GE groups, particularly the biotech industry, tend to remain silent. Revealing information regarding the safety of GE foods could be counterproductive given pre-existing public skepticism. Consumers may not make “better” decisions with more information provided because more information increases their inspection costs. When it is costlier for consumers to inspect, it is more likely that anti-GE groups will continue to spin facts about the negative health impact of GE foods.
A comprehensive assessment of lignin configuration in transgenic and mutant plants is long overdue. This review thus undertook the systematic analysis of trends manifested through genetic and mutational manipulations of the various steps associated with monolignol biosynthesis; this included consideration of the downstream effects on organized lignin assembly in the various cell types, on vascular function/integrity, and on plant growth and development. As previously noted for dirigent protein (homologs), distinct and sophisticated monolignol forming metabolic networks were operative in various cell types, tissues and organs, and form the cell-specific guaiacyl (G) and guaiacyl-syringyl (G-S) enriched lignin biopolymers, respectively. Regardless of cell type undergoing lignification, carbon allocation to the different monolignol pools is apparently determined by a combination of phenylalanine availability and cinnamate-4-hydroxylase/"p-coumarate-3-hydroxylase" (C4H/C3H) activities, as revealed by transcriptional and metabolic profiling. Downregulation of either phenylalanine ammonia lyase or cinnamate-4-hydroxylase thus predictably results in reduced lignin levels and impaired vascular integrity, as well as affecting related (phenylpropanoid-dependent) metabolism. Depletion of C3H activity also results in reduced lignin deposition, albeit with the latter being derived only from hydroxyphenyl (H) units, due to both the guaiacyl (G) and syringyl (S) pathways being blocked. Apparently the cells affected are unable to compensate for reduced G/S levels by increasing the amounts of H-components. The downstream metabolic networks for G-lignin enriched formation in both angiosperms and gymnosperms utilize specific cinnamoyl CoA O-methyltransferase (CCOMT), 4-coumarate:CoA ligase (4CL), cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) isoforms: however, these steps neither affect carbon allocation nor H/G designations, this being determined by C4H/C3H activities. Such enzymes thus fulfill subsidiary processing roles, with all (except CCOMT) apparently being bifunctional for both H and G substrates. Their severe downregulation does, however, predictably result in impaired monolignol biosynthesis, reduced lignin deposition/vascular integrity, (upstream) metabolite build-up and/or shunt pathway metabolism. There was no evidence for an alternative acid/ester O-methyltransferase (AEOMT) being involved in lignin biosynthesis.The G/S lignin pathway networks are operative in specific cell types in angiosperms and employ two additional biosynthetic steps to afford the corresponding S components, i.e. through introduction of an hydroxyl group at C-5 and its subsequent O-methylation. [These enzymes were originally classified as ferulate-5-hydroxylase (F5H) and caffeate O-methyltransferase (COMT), respectively.] As before, neither step has apparently any role in carbon allocation to the pathway; hence their individual downregulation/manipulation, respectively, gives either a G enriched lignin or formation of the well-known S-deficient bm3 "lignin" mutant, with cell walls of impaired vascular integrity. In the latter case, COMT downregulation/mutation apparently results in utilization of the isoelectronic 5-hydroxyconiferyl alcohol species albeit in an unsuccessful attempt to form G-S lignin proper. However, there is apparently no effect on overall G content, thereby indicating that deposition of both G and S moieties in the G/S lignin forming cells are kept spatially, and presumably temporally, fully separate. Downregulation/mutation of further downstream steps in the G/S network [i.e. utilizing 4CL, CCR and CAD isoforms] gives predictable effects in terms of their subsidiary processing roles: while severe downregulation of 4CL gave phenotypes with impaired vascular integrity due to reduced monolignol supply, there was no evidence in support of increased growth and/or enhanced cellulose biosynthesis. CCR and CAD downregulation/mutations also established that a depletion in monolignol supply reduced both lignin contents supply reduced both lignin contents and vascular integrity, with a concomitant shift towards (upstream) metabolite build-up and/or shunting.The extraordinary claims of involvement of surrogate monomers (2-methoxybenzaldehyde, feruloyl tyramine, vanillic acid, etc.) in lignification were fully disproven and put to rest, with the investigators themselves having largely retracted former claims. Furthermore analysis of the well-known bm1 mutation, a presumed CAD disrupted system, apparently revealed that both G and S lignin components were reduced. This seems to imply that there is no monolignol specific dehydrogenase, such as the recently described sinapyl alcohol dehydrogenase (SAD) for sinapyl alcohol formation. Nevertheless, different CAD isoforms of differing homology seem to be operative in different lignifying cell types, thereby giving the G-enriched and G/S-enriched lignin biopolymers, respectively. For the G-lignin forming network, however, the CAD isoform is apparently catalytically less efficient with all three monolignols than that additionally associated with the corresponding G/S lignin forming network(s), which can more efficiently use all three monolignols. However, since CAD does not determine either H, G, or S designation, it again serves in a subsidiary role-albeit using different isoforms for different cell wall developmental and cell wall type responses.The results from this analysis contrasts further with speculations of some early investigators, who had viewed lignin assembly as resulting from non-specific oxidative coupling of monolignols and subsequent random polymerization. At that time, though, the study of the complex biological (biochemical) process of lignin assembly had begun without any of the (bio)chemical tools to either address or answer the questions posed as to how its formation might actually occur. Today, by contrast, there is growing recognition of both sophisticated and differential control of monolignol biosynthetic networks in different cell types, which serve to underscore the fact that complexity of assembly need not be confused any further with random formation. Moreover, this analysis revealed another factor which continues to cloud interpretations of lignin downregulation/mutational analyses, namely the serious technical problems associated with all aspects of lignin characterization, whether for lignin quantification, isolation of lignin-enriched preparations and/or in determining monomeric compositions. For example, in the latter analyses, some 50-90% of the lignin components still cannot be detected using current methodologies, e.g. by thioacidolysis cleavage and nitrobenzene oxidative cleavage. This deficiency in lignin characterization thus represents one of the major hurdles remaining in delineating how lignin assembly (in distinct cell types) and their configuration actually occurs.
The root cap is increasingly appreciated as a complex and dynamic plant organ. Root caps sense and transmit environmental signals, synthesize and secrete small molecules and macromolecules, and in some species shed metabolically active cells. However, it is not known whether root caps are essential for normal shoot and root development. We report the identification of a root cap-specific promoter and describe its use to genetically ablate root caps by directing root cap-specific expression of a diphtheria toxin A-chain gene. Transgenic toxin-expressing plants are viable and have normal aerial parts but agravitropic roots, implying loss of root cap function. Several cell layers are missing from the transgenic root caps, and the remaining cells are abnormal. Although the radial organization of the roots is normal in toxin-expressing plants, the root tips have fewer cytoplasmically dense cells than do wild-type root tips, suggesting that root meristematic activity is lower in transgenic than in wild-type plants. The roots of transgenic plants have more lateral roots and these are, in turn, more highly branched than those of wild-type plants. Thus, root cap ablation alters root architecture both by inhibiting root meristematic activity and by stimulating lateral root initiation. These observations imply that the root caps contain essential components of the signaling system that determines root architecture.
Sam Hazen of the University of Massachusetts on "Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, CA.
Magnetic nanoparticles have proven invaluable for biomechanical investigations due to their ability to exert localized forces. However, cellular delivery of exogenous magnetic agents often results in endosomal entrapment, thereby limiting their utility for manipulating subcellular structures. This study characterizes and exploits fully genetically controlled biomineralization of iron-oxide cores inside encapsulin nanocompartments to enable magnetic-activated cell sorting (MACS) and magnetic cell manipulation. The fraction of MACS-retained cells showed substantial overexpression of encapsulins and exhibited both para- and ferrimagnetic responses with magnetic moments of 10 -15 A m 2 per cell, comparable to standard exogenous labels for MACS. Electron microscopy revealed that MACS-retained cells contained densely packed agglomerates of ≈30 nm iron oxide cores consisting of ultrafine quasicrystalline ordered nuclei within an amorphous matrix of iron, oxygen, and phosphorus. Scanning transmission X-ray microscopy, X-ray absorption spectroscopy, and Raman microspectroscopy confirmed that the iron-oxide species are consistent with ferric oxide (Fe 2 O 3 ). In addition, the encapsulin-overexpressing MACS-retained cells can be manipulated by a magnetic needle and regrown in patterns determined by magnetic gradients. This study demonstrates that the formation of quasicrystalline iron oxide with mixed para/ferrimagnetic behavior in the cytosol of mammalian cells enables magnetic manipulation without the delivery of exogenous agents.
Genetic transformation via Agrobacterium-mediated methodology has been used in many sorghum studies. However, the transformation efficiency still varies significantly due to high dependence on sorghum genotypes and technical expertise. In this article, we describe a sorghum transformation procedure in sufficient detail using a public genotype, P898012. This system utilizes a standard binary transgenic vector carrying the bar gene as a selectable marker and immature embryos as starting explants. Glufosinate is employed as the selective agent during callus and shoot induction. Further, this procedure is relatively rapid, efficient, highly reproducible, and should be applicable for many other sorghum genotypes
14–3–3 proteins are central hub regulators of hundreds of phosphorylated “client” proteins. They are subject to over 60 post–translational modifications (PTMs), yet little is known how these PTMs alter 14–3–3 function and its ability to regulate downstream signaling pathways. An often neglected, but well–documented 14–3–3 PTM found under physiological and immune–stimulatory conditions is the conversion of tyrosine to 3–nitro–tyrosine at several Tyr sites, two of which are located at sites considered important for 14–3–3 function: Y130 (β–isoform numbering) is located in the primary phospho–client peptide–binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14–3–3/client complex formation and client regulation. By genetically encoding 3–nitro–tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14–3–3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14–3–3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14–3–3. But, in contrast to other client–binding deficient variants, it did not localize to the nucleus. Further, the 1.9 Å resolution structure of 14–3–3 nitrated at Y213 revealed unusual flexibility of its C–terminal α–helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest that nitration of 14–3–3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14–3–3 interactome.