Size Does Matter: Cre-mediated Somatic Deletion Efficiency Depends on the Distance Between the Target <Emphasis Type="Italic">lox</Emphasis>-Sites

Cre/lox recombination in vivo has become an important tool to induce chromosomal rearrangements like deletions. Using a combination of Ds transposition and Cre/lox recombination in two independent experiments on chromosomes 6 and 7 of tomato, two sets of somatic deletions up to a size of 200 kb were obtained. The efficiency of somatic deletion decreased with increasing deletion size. The largest germinally transmitted deletion had a size of only 55 kb. The results show that Cre-mediated deletion in somatic cells is less efficient when the lox sites are separated over larger distances. A further drop of the deletion efficiency after germinal transmission of the larger deletions can be explained by the probable loss of genes that are of vital importance to gametophyte function. Plasmid rescue of an 8.4 kb circularised deleted DNA showed that the Cre-mediated deletion takes place in tomato as expected. Since the circular Cre-deleted DNA could only be PCR amplified in plant cells where the deletion was not complete, the double-stranded DNA circle is assumed to be instable.     

Electron cryomicroscopy of biological machines at subnanometer resolution

Advances in electron cryomicroscopy (cryo-EM) have made possible the structural determination of large biological machines in the resolution range of 6-9 angstroms. Rice dwarf virus and the acrosomal bundle represent two distinct types of machines amenable to cryo-EM investigations at subnanometer resolutions. However, calculating the density map is only the first step, and much analysis remains to extract structural insights and the mechanism of action in these machines. This paper will review the computational and visualization methodologies necessary for analysis (structure mining) of the computed cryo-EM maps of these machines. These steps include component segmentation, averaging based on local symmetry among components, density connectivity trace, incorporation of bioinformatics analysis, and fitting of high-resolution component data, if available. The consequences of these analyses can not only identify accurately some of the secondary structure elements of the molecular components in machines but also suggest structural mechanisms related to their biological functions.     

Evaluation of dietary practices of National Collegiate Athletic Association Division I football players

The objective of this study is to evaluate the dietary practices of 28 football athletes on a National Collegiate Athletic Association (NCAA) Division I team using 3-day diet records. Student athletes completed 3-day diet records at 2 individual points of time, when no training table was available. Diet records were evaluated and were compared with the Third National Health and Nutrition Survey (NHANES III) data for the same ages and gender group. No differences in dietary practices of collegiate football athletes were observed when compared with data for the same ages and gender group culled from NHANES III. Inadequacies in energy intake for activity level were significant (p < 0.05). Influences of fad dieting trends were noted when the diets were mapped onto the United States Department of Agriculture (USDA) food guide pyramid. Changes in diet would be necessary to sustain the activity level of these athletes.     

Sonic hedgehog myocardial gene therapy: tissue repair through transient reconstitution of embryonic signaling

Sonic hedgehog (Shh) is a crucial regulator of organ development during embryogenesis. We investigated whether intramyocardial gene transfer of naked DNA encoding human Shh (phShh) could promote a favorable effect on recovery from acute and chronic myocardial ischemia in adult animals, not only by promoting neovascularization, but by broader effects, consistent with the role of this morphogen in embryogenesis. After Shh gene transfer, the hedgehog pathway was upregulated in mammalian fibroblasts and cardiomyocytes. This resulted in preservation of left ventricular function in both acute and chronic myocardial ischemia by enhanced neovascularization, and reduced fibrosis and cardiac apoptosis. Shh gene transfer also enhanced the contribution of bone marrow-derived endothelial progenitor cells to myocardial neovascularization. These data suggest that Shh gene therapy may have considerable therapeutic potential in individuals with acute and chronic myocardial ischemia by triggering expression of multiple trophic factors and engendering tissue repair in the adult heart.     

Upping the ante on antibodies

The current generation of antibodies has done more than make a few companies rich. It has laid the groundwork for ambitious companies to move to maturity.     

fMRI Hippocampal Activity During a VirtualRadial Arm Maze

Numerous studies have shown that the hippocampus is critical for spatial memory. Within nonhuman research, a task often used to assess spatial memory is the radial arm maze. Because of the spatial nature of this task, this maze is often used to assess the function of the hippocampus. Our goal was to extrapolate this task to humans and examine whether healthy undergraduates utilize their hippocampus while performing a virtual reality version of the radial arm maze task. Thirteen undergraduates performed a virtual radial arm maze during functional magnetic resonance imaging. The brain maps of activity reveal bilateral hippocampal BOLD signal changes during the performance of this task. However, paradoxically, this BOLD signal change decreases during the spatial memory component of the task. Additionally, we note frontal cortex activity reflective of working memory circuits. These data reveal that, as predicted by the rodent literature, the hippocampus is involved in performing the virtual radial arm maze in humans. Hence, this virtual reality version may be used to assess the integrity of hippocampus so as to predict risk or severity in a variety of psychiatric disorders.     

Chemical characterisation of eggs from deep-sea sharks

The chemical characterisation and nutritional value of eggs from the five deep-sea sharks leafscale gulper shark (Centrophorus squamosus), greater lantern shark (Etmopterus princeps), longnose velvet dogfish (Centroscymnus crepidater), Portuguese dogfish (Centroscymnus coelolepis) and black dogfish (Centrocyllium fabricii) captured at Hatton Bank in the North Atlantic were examined. The chemical composition was quite similar for all the eggs studied. The dominant fatty acid in all the eggs was the monounsaturated fatty acid C18:1, which varied from 27-39%. The eggs had a relatively high content of C16:0 (13.0-18.5%) and C22:6n-3 (10.3-15.1%). The two main lipid classes in the eggs were triacylglycerols (36-55%) and phospholipids (34-41%). The eggs had high amounts of vitamin A and E. The shark eggs were particularly rich in the amino acids aspartic acid, glutamic acid, leucine and arginine.     

Improving implicit solvent simulations: a Poisson-centric view

Recent developments in implicit solvent models may be compared in terms of accuracy and computational efficiency. Based on improvements in the accuracy of generalized Born methods and the speed of Poisson-Boltzmann solvers, it appears that the two techniques are converging to a point at which both will be suitable for simulating certain types of biomolecular systems over sizable time and length scales.     

Similar mating and sperm displacement patterns in two highly divergent D. simulans populations from Africa and Europe

The frequency of remating in Drosophila melanogaster is affected by both genetic and ecological factors. We studied the remating behaviour in one European (Italy) and one African (Uganda) Drosophila simulans population using six highly polymorphic microsatellite markers. Despite that the populations were genetically distinct (F(ST) = 0.18) and originated from very dissimilar ecological settings with different population densities, we inferred a very similar mating pattern. The remating parameter alpha was similar in both populations (a = 1.3-1.4). No more than two distinct paternal genotypes per family were detected in each population.     

Oestrogen receptor β is present in both muscle fibres and endothelial cells within human skeletal muscle tissue

Oestrogen receptor β (ERβ) is expressed in human skeletal muscle tissue. In the present study, we have developed an immunohistochemical method to reveal if ERβ is located within the muscle fibres as well as within capillaries. Skeletal muscle biopsies were obtained from m. quadriceps femoris vastus lateralis in four healthy young subjects. Immunohistochemical triple staining was applied to transverse sections of paraffin-wax-embedded tissue. The basement membrane of muscle fibres and capillaries was identified by using an antibody to collagen IV, endothelial cells using an antibody to CD34 and ERβ using a corresponding antibody. The ERβ-positive (ERβ+) nuclei were located within the muscle fibre defined by the localisation of collagen IV. ERβ+ nuclei were also, for the first time, found in endothelial cells of capillaries in skeletal muscle tissue. Quantification was performed on transverse cryostat sections after performing a double staining (collagen IV and ERβ). It was shown that 24% of the ERβ+ nuclei were located within capillaries, and 76% were located within muscle fibres. In conclusion, ERβ in human skeletal muscle tissue is expressed not only in the muscle fibres themselves, but also within the capillary endothelial cells. This observation might improve understanding of the physiological role of oestrogen and its receptor.