Hierarchical phenotypic and epigenetic variation in cloned swine

Cloning by somatic cell nuclear transfer can result in the birth of animals with phenotypic and gene expression abnormalities. We compared adult cloned pigs and adult pigs from naturally bred control females using a series of physiological and genetic parameters, including detailed methylation profiles of selected genomic regions. Phenotypic and genetic analyses indicated that there are two classes of traits, one in which the cloned pigs have less variation than controls and another characterized by variation that is equally high in cloned and control pigs. Although cloning creates animals within the normal phenotypic range, it increases the variability associated with some traits. This finding is contrary to the expectation that cloning can be used to reduce the size of groups involved in animal experimentation and to reproduce an animal, including a pet, with a homogenous set of desired traits.     

Variation in abundance and feeding impact of tarnished plant bug (Hemiptera: Miridae) for different cultivars of strawberry: role of flowering phenology and yield attributes

The current study evaluated whether flowering phenology and yield attributes of different strawberry cultivars affect the abundance and feeding impact of tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), as well as behavioral decisions made by feeding nymphs and ovipositing adults. The distribution of emerged nymphs in cage experiments involving nine different cultivars of June-bearing strawberry cultivars suggests that females lay more eggs on plants with numerous flower receptacles, while cultivar per se did not influence their oviposition behavior. A large number of nymphs emerged from receptacles of strawberry plants, while the distribution of emerged nymphs among receptacles, petioles, leaves, and stems varied for different cultivars. These results suggest that the relative intensity of damage caused by ovipositing females may vary for different cultivars. Foraging nymphs did not exhibit a preference for any strawberry cultivar per se, although the abundance of nymphs increased with the weight of receptacles, especially for late instars. Evaluating the density and feeding impact of L. lineolaris for different cultivars under field conditions revealed that some host plant attributes affect the abundance of plant bugs, such as early flowering season and high productivity. Decreasing number of emerged nymphs per flower per plant with increasing density of receptacles per plant suggests that females lay relatively more eggs per receptacle on plants with few receptacles; this pattern of oviposition may explain, in part, why patches with low density of plants typically have high incidence of damage. Planting a high yielding early season cultivar such as 'Cavendish' may contribute to reduce the incidence of damage by L. lineolaris.     

A comparative proteomics resource: proteins of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Using an integrative genome annotation pipeline (iGAP) for proteome-wide protein structure and functional domain assignment, we analyzed all the proteins of Arabidopsis thaliana. Three-dimensional structures at the level of the domain are assigned by fold recognition and threading based on a novel fold library that extends common domain classifications. iGAP is being applied to proteins from all available proteomes as part of a comparative proteomics resource. The database is accessible from the web.     

Segments missing from the draft human genome sequence can be isolated by transformation-associated recombination cloning in yeast

The reported draft human genome sequence includes many contigs that are separated by gaps of unknown sequence. These gaps may be due to chromosomal regions that are not present in the Escherichia coli libraries used for DNA sequencing because they cannot be cloned efficiently, if at all, in bacteria. Using a yeast artificial chromosome (YAC)/ bacterial artificial chromosome (BAC) library generated in yeast, we found that approximately 6% of human DNA sequences tested transformed E. coli cells less efficiently than yeast cells, and were less stable in E. coli than in yeast. When the ends of several YAC/BAC isolates cloned in yeast were sequenced and compared with the reported draft sequence, major inconsistencies were found with the sequences of those YAC/BAC isolates that transformed E. coli cells inefficiently. Two human genomic fragments were re-isolated from human DNA by transformation-associated recombination (TAR) cloning. Re-sequencing of these regions showed that the errors in the draft are the results of both missassembly and loss of specific DNA sequences during cloning in E. coli. These results show that TAR cloning might be a valuable method that could be widely used during the final stages of the Human Genome Project.     

Organic solvents order the dynamic switch II in Ras crystals

Room temperature crystal structures of crosslinked H-Ras bound to GMPPNP were solved in 50% 2,2,2-trifluoroethanol, 60% 1,6-hexanediol, and 50% isopropanol. The disordered switch II region of Ras is ordered in the presence of 2,2,2-trifluoroethanol or 1,6-hexanediol. The overall backbone conformation of switch II in these organic solvents is the same as in the Ras-GMPPNP complexes with RalGDS, PI(3) kinase, and RasGAP, indicating a biologically relevant form. Key polar interactions that stabilize the ordered switch are enhanced in the presence of hydrophobic cosolvents. These results suggest that hydrophobic solvents can be used in general to order short biologically relevant segments of disordered regions in protein crystals by favoring H-bonding interactions between atoms that are highly solvated and mobile in aqueous solution.     

Psychophysics in functional strength and power training: review and implementation framework

Functional training is considered to be training that attempts to mimic the specific physiological demands of real-life activities. Most approaches to functional training, though, omit important factors that contribute to physiological and neuromotor adaptations. Cognitive factors related to sports influence physiological performance, and subsequently, physiological and neuromotor adaptations. We present a rationale and a theoretical framework by which to create effective functional training methods that incorporate cognitive factors. This framework draws upon recent developments and strong empirical evidence in the areas of dynamic systems theory, perceptual skills training, and motor learning/control. Emphasized within rigorous physical training are practice-related techniques and motor-learning strategies. In particular, mental effort, attention, and intention manipulated in a discovery-learning paradigm provide a framework for functional strength and power training. This framework is suggested to help maximize sport-specific physiological adaptations, and subsequently, sports performance.     

The effects of 8 weeks of creatine monohydrate and glutamine supplementation on body composition and performance measures

Twenty-nine (17 men, 12 women) collegiate track and field athletes were randomly divided into a creatine monohydrate (CM, n = 10) group, creatine monohydrate and glutamine (CG, n = 10) group, or placebo (P, n = 9) group. The CM group received 0.3 g creatine.kg body mass per day for 1 week, followed by 0.03 g creatine.kg body mass per day for 7 weeks. The CG group received the same creatine dosage scheme as the CM group plus 4 g glutamine.day(-1). All 3 treatment groups participated in an identical periodized strength and conditioning program during preseason training. Body composition, vertical jump, and cycle performances were tested before (T1) and after (T2) the 8-week supplementation period. Body mass and lean body mass (LBM) increased at a greater rate for the CM and CG groups, compared with the P treatment. Additionally, the CM and CG groups exhibited significantly greater improvement in initial rate of power production, compared with the placebo treatment. These results suggest CM and CG significantly increase body mass, LBM, and initial rate of power production during multiple cycle ergometer bouts.     

Synthesis and application of charge-modified dye-labeled dideoxynucleoside-5'-triphosphates to 'direct-load' DNA sequencing

A novel series of charge-modified, dye-labeled 2′,3′-dideoxynucleoside-triphosphate terminators were synthesized and evaluated as reagents for DNA sequencing. These terminators possess an advantage over existing reagents in that no purification is required to remove unreacted nucleotide or associated breakdown products prior to electrophoretic separation of the sequencing fragments. This obviates the need for a time consuming post-reaction work up, allowing direct loading of DNA sequencing reaction mixtures onto a slab gel. Thermo Sequenase™ II DNA polymerase poorly incorporates the charge-modified terminators compared with regular dye-labeled terminators. However, extending the linker arm between dye and nucleotide and using a mutant form of a related DNA polymerase can in part mitigate the decrease in substrate efficiency. We also present evidence that these charge-modified terminators can relieve gel compression artefacts when used with dGTP in sequencing reactions.