Survey of Genomics Approaches to Improve Bioenergy Traits in Maize,Sorghum and Sugarcane

Bioenergy crops currently provide the only source of alternative energy with the potential to reduce the use of fossil transportation fuels in a way that is compatible with existing engine technology,including in developing countries.Even though bioenergy research is currently receiving considerable attention,many of the concepts are not new,but rather build on intense research efforts from 30 years ago.A major difference with that era is the availability of genomics tools that have the potential to acceler...     

Design of the human tumor-associated VNTR(Muc1) antigen gene, fused with streptavidin, its expression in Escherichia coli. Study of properties of the hybrid protein

A gene of human tumor-associated antigen VNTR(MUC1) bound to streptavidin, an expression plasmid, and a highly effective hybrid protein-producing strain were constructed. It was shown that the streptavidin leader peptide ensures an effective secretion of the hybrid protein into the periplasmic space of Escherichia coli cells. The hybrid protein was isolated in a homogeneous state and its immunogenic properties were studied.     

Directed introduction of amino groups by internucleotide phosphate group during solid-phase synthesis of oligodeoxyribonucleotides. Preparation of biotinylated oligonucleotide probes]

An efficient procedure for solid-phase synthesis of amino-oligonucleotides has been developed, leading to direct introduction of an aliphatic primary amino group at the internucleotide phosphate. Amino-oligonucleotides were successfully used for preparation of biotinylated oligonucleotides.     

Study of the role of the insA open reading frame in the IS1 insertion element structure during transposition and resolution of the IS1 mediated cointegrates

In order to elucidate the function of the IS1 insA gene derivatives of plasmid pUC19::Tn9' with insertions of synthetic oligonucleotides were obtained. The latter are equal or multiple of 9 b.p. in length and are located in the Pst1 site within each of the two IS1 copies of the Tn9' transposon. The insertions of the nine base oligonucleotides code for the neutral amino acids and do not shift the reading frame. One of the mutant transposon obtained - Tn9'/X was studied on the ability to form simple insertions and plasmid cointegrates. For this purpose the pUC19 derivatives carrying the wild type and mutant transposon were mobilized by conjugative plasmid pRP3.1. It was found that the damage of the insA gene does not influence the ability of transposon to form simple insertions and plasmid cointegrates in both recA - and rec+ cells of E. coli. However, the frequency of the cointegrate formation in the subsequent transposition of the mutant transposon from pRP3.1::Tn9'/X to pBR322 was by 10-20 times lower in comparison to the wild type transposon. Instable (dissociating) Tn9'/X-mediated plasmid cointegrates formed by interaction pUC19::Tn9'/X and pRP3.1 were obtained. It was shown that in the E. coli recA-cells such cointegrates dissociate, as a rule, "correctly", i.e. they segregate mainly plasmids of types pUC19::Tn9'/X and pUC19::IS1/X. The data obtained correspond with the notion that the gene insA product is not essential for transposition, but is, possibly, involved in the formation of the IS1-generated deletions.     

Improving the performance of the EPT Index to accommodate multiple stressors in Afrotropical streams

The EPT index (Ephemeroptera, Plecoptera and Trichoptera) may be skewed by the wide tolerance to multiple stressors of the Baetid, Caenid and Hydropsychid families, which affects the performance of the EPT index as an indicator of multiple stressors in aquatic ecosystems. The effect of the BCH families on the EPT index was evaluated and alternatives were considered to improve its performance. The hypothesis that the removal of the BCH families improves sensitivity of the EPT index to human-induced stressors in streams and rivers was tested. Macroinvertebrates were collected in January–March 2009 at 22 sites in the Nyando and Nzoia Rivers, Lake Victoria basin, Kenya. Nine derivatives and modifications of the EPT index were tested for responses to a disturbance gradient, ranked into three condition categories (reference, intermediate and impaired). The sensitivity of the proportionate abundance derivative of the EPT index improved when the BCH families were removed, whereas that of the richness derivative improved marginally. Other modifications considered performed poorly when compared with the EPT-BCH metrics. Wide distribution of the BCH across all sites, irrespective of the level of disturbance, reduced the sensitivity of the EPT index in the studied streams. The removal of the BCH families enhanced the sensitivity of the index to multiple stressors in Afrotropical streams and rivers.     

Construction of a gene of the human tumor-associated antigen VNTR(MUC1) bound to streptavidin, its expression inEscherichia coli, and the study of properties of the hybrid protein

A gene of human tumor-associated antigen VNTR(MUC1) bound to streptavidin, an expression plasmid, and a highly effective hybrid protein-producing strain were constructed. It was shown that the streptavidin leader peptide ensures effective secretion of the hybrid protein into the periplasmic space ofEscherichia coli cells. The hybrid protein was isolated in a homogeneous state and its immunogenic properties were studied.     

Satellite RNA for the control of plant diseases caused by cucumber mosaic virus

Two virus-protecting strains, S₅₁ and S₅₂, were obtained for the control of cucumber mosaic virus (CMV) by local lesion selection after adding satellite RNA to the RNA genome of CMV. Both were found to protect pepper plants against a virulent strain of CMV under greenhouse and field conditions. Results from 14 localities in China indicated that the use of protective strains decreased the disease index by 21.6% to 82.8% and increased fruit yields by 10.8% to 55.6%. The host reactions and safety of S₅₁ and S₅₂ were tested, and the effects of the strains on plant growth were also investigated. Possible mechanisms of control of CMV-caused plant diseases by mild strains are discussed.     

Age-related changes in saccadic eye movements in healthy subjects and patients with Parkinson's disease

Age-related changes in characteristics of saccadic eye movements (latency, duration and percentage of multistep saccades) in healthy subjects and patients with Parkinson's disease were evaluated. Healthy volunteers were divided into 6 age groups (17-20 years, 21-30 years, 31-40 years, 41-50 years, 51-60 years, 61-75 years), parkinsonian patients into 3 age groups (41-50 years, 51-60 years, 61-75 years). According to our data, saccade characteristics depend upon age in both healthy subjects and parkinsonian patients. In healthy volunteers the percentage of multistep saccades and the mean saccade latency increase significantly after the age of 60. Values of these characteristics in patients with Parkinson's disease significantly exceed the values in the corresponding age groups of healthy subjects. The "disease" factor (MANOVA) has a greater influence on saccade latency and percentage of multistep saccades then the "age" factor. The duration of single saccades depends on age to a smaller extent and does not change in patients with Parkinson's disease. The peculiarities of neurodegenerative processes during normal aging and aging with Parkinson's disease are discussed.     

A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data

Phylogeny reconstruction is a difficult computational problem, because the number of possible solutions increases with the number of included taxa. For example, for only 14 taxa, there are more than seven trillion possible unrooted phylogenetic trees. For this reason, phylogenetic inference methods commonly use clustering algorithms (e.g., the neighbor-joining method) or heuristic search strategies to minimize the amount of time spent evaluating nonoptimal trees. Even heuristic searches can be painfully slow, especially when computationally intensive optimality criteria such as maximum likelihood are used. I describe here a different approach to heuristic searching (using a genetic algorithm) that can tremendously reduce the time required for maximum-likelihood phylogenetic inference, especially for data sets involving large numbers of taxa. Genetic algorithms are simulations of natural selection in which individuals are encoded solutions to the problem of interest. Here, labeled phylogenetic trees are the individuals, and differential reproduction is effected by allowing the number of offspring produced by each individual to be proportional to that individual's rank likelihood score. Natural selection increases the average likelihood in the evolving population of phylogenetic trees, and the genetic algorithm is allowed to proceed until the likelihood of the best individual ceases to improve over time. An example is presented involving rbcL sequence data for 55 taxa of green plants. The genetic algorithm described here required only 6% of the computational effort required by a conventional heuristic search using tree bisection/reconnection (TBR) branch swapping to obtain the same maximum-likelihood topology.      

Site-directed mutagenesis with the use of addressed fragmentation of single-stranded DNA for obtaining hybrids of homologous proteins]

Site-directed multiple mutagenesis to obtain hybrids of homologous proteins was carried out by means of the oligonucleotide-targeting digestion of ss DNA. The procedure is more convenient, rapid and simple than the step-by-step approach. To demonstrate different approaches to targeting digestion of ss DNA, NcoI, HinfI, FokI endonucleases were used for DNA cleavage. A hydride of the human and porcine IFN-alpha-2-genes has been constructed.