Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs

Background  

Combining microarray results and biological pathway information will add insight into biological processes. Pathway information is widely available in databases through the internet.     

Cupressus sempervirens L.

The online version of the original article can be found at     

Actin filaments elongate from their membrane-associated ends

In limulus sperm an actin filament bundle 55 mum in length extends from the acrosomal vacuole membrane through a canal in the nucleus and then coils in a regular fashion around the base of the nucleus. The bundle expands systematically from 15 filaments near the acrosomal vacuole to 85 filaments at the basal end. Thin sections of sperm fixed during stages in spermatid maturation reveal that the filament bundle begins to assemble on dense material attached to the acrosomal vacuole membrane. In micrographs fo these early stages in maturation, short bundles are seen extending posteriorly from the dense material. The significance is that these short, developing bundles have about 85 filaments, suggesting that the 85-filament end of the bundle is assembled first. By using filament bundles isolated and incubated in vitro with G actin from muscle, we can determine the end “preferred” for addition of actin monomers during polymerization. The end that would be associated with the acrosomal vacuole membrane, a membrane destined to be continuous with the plasma membrane, is preferred about 10 times over the other, thicker end. Decoration of the newly polymerized portions of the filament bundle with subfragment 1 of myosin reveals that the arrowheads point away from the acrosomal vacuole membrane, as is true of other actin filament bundles attached to membranes. From these observations we conclude that the bundle is nucleated from the dense material associated with the acrosomal vacuole and that monomers are added to the membrane-associated end. As monomers are added at the dense material, the thick first-made end of the filament bundle is pushed down through the nucleus where, upon reaching the base of the nucleus, it coils up. Tapering is brought about by the capping of the peripheral filaments in the bundle.     

Polarity of microtubules nucleated by centrosomes and chromosomes of Chinese hamster ovary cells in vitro

The structural and growth polarities of centrosomal and chromosomal microtubules were studied by analyzing the kinetics of growth of these microtubules and those initiated by flagellar seeds. By comparing rates of elongation of centrosomal and flagellar-seeded microtubules, we determined whether the centrosomal microtubules were free to grow at their plus ends only, minus ends ony, or at both ends. Our results show that centrosomal microtubules elongate at a rate corresponding to the addition of subunits at the plus end only. The depolymerization rate was also equivalent to that for the plus end only. Chromosomal microtubule elongation was similar to the centrosome-initiated growth. Since the data do not support the hypothesis that both ends of these spindle microtubules are able to interact with monomer in solution, then growth must occur only distal or only proximal to the organizing centers, implying tha the opposite ends in unavailable for exchange of subunits. Experiments with flagellar-seeded microtubules serving as internal controls indicated that the inactivity of the minus end could not be accounted for by a diffusible inhibitor, suggesting a structural explanation. Since there is no apparent way in which the distal ends may be capped, whereas the proximal ends are embedded in the pericentriolar cloud, we conclude that centrosomal microtubules are oriented with their plus ends distal to the site of nucleation. A similar analysis for chromosomal microtubules suggests that they too must be oriented with their plus ends distal to the site of initiation.     

Antigenic analysis of potato virus A particles and coat protein

Five monoclonal antibodies (MAbs) were prepared to particles of potato virus A (PVA), isolate B11. In immunoblots, MAbs A1D8 and A5B6 reacted only with full length molecules of PVA coat protein (CP). Pepscan tests with overlapping octapeptides representing the whole sequence of PVA CP showed that the epitope detected by MAb A5B6 is contained in its N-terminal octapeptide. MAbs A9A4, A3H4 and A6B8 reacted with CP molecules that lacked about 5 kD of sequence at their end(s) and detected epitopes at residues 52 to 62, 64 to 73 and 75 to 82 respectively, all of which lie in the protease-resistant core of the CP. The epitope which reacts with MAb A3H4 is in a region predicted to be hydrophobic and is not detected in intact virus particles, indicating it is a cryptotope. In contrast, MAbs A6B8 and A9A4 reacted with freshly purified PVA particles but more strongly with partially degraded ones. Pepscan tests with polyclonal antibodies to PVA isolate B11 identified five additional immunogenic sequences in PVA CP and showed that regions at the N-termini of the intact and core molecules are immunodominant. PVA isolate B11 was not transmitted by aphids, and its CP N-terminal octapeptide contains the sequence DAS, which is associated with aphid-non-transmissibility in other potyviruses. MAb A5B6, which detects this region, reacted strongly in ELISA with three out of four other aphid-non-transmissible PVA isolates but only weakly with three aphid-transmissible ones, suggesting that differences in N-terminal sequence may underlie most of the differences in aphid transmissibility.     

Flora Palinologica Italiana,Sezione Aeropalinologica: S 205 -Pinus pinea L. (Pinaceae)

Summary According to the program Palynological Italian Flora, Aeropalynological section, the pollen morphological card ofPinus pinea L. is presented. The study is carried out on pollen coming from three Italian localities and regards fresh and acetolyzed pollen. For each sample, measurements are carried out on 30 fresh pollen grains in glicerol jelly with fuchsin and on 30 acetolyzed pollen grains in water/glicerol (1/1); general observations regard 1000 fresh and 1000 acetolyzed pollen grains/sample. Some observations on the main differences between fresh and acetolyzed pollen are mentioned.

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Riassunto Nell'ambito della Flora Palinologica Italiana, Sezione Aeropalinologica, è presentata la scheda morfopalinologica diPinus pinea L. nella versione su polline fresco e polline acetolizzato, su tre campioni di diversa provenienza. Vengono notate le principali differenze tra polline fresco e polline acetolizzato.

     

Metabolic Differences in Response to a High-Fat vs. a High-Carbohydrate Diet

Energy expenditure was measured in a group of 7 subjects who received two isocaloric isonitrogenous diets for a period of 9–21 days with a 4–10-day break between diets. Diet 1 was a high-fat diet (83.5 ± 3.6% of total energy). Diet 2 was a high carbohydrate diet (83.1 ± 3.7% of total energy). Resting and postprandial resting metabolic rate were measured by open circuit indirect calorimetry 2–4 times during each metabolic period. Total energy expenditure (TEE) was measured by the doubly labeled water method over an 8–13-day period. The respiratory quotient was measured 2–4 hours after a meal during each metabolic period for the calculation of total energy expenditure by the doubly labeled water method. Levels of total T₃ (TT₃), T₃ uptake, free thyroid index and T₄ were measured at the end of each metabolic period. No significant changes in resting metabolic rate (RMR) were apparent on the two diets (1567 ± 426 kcal/d high-fat diet and 1503 ± 412 kcal/d high-carbohydrate diet n=7, p<0.15). Total energy expenditure measured in 5 subjects was significantly higher during the high-carbohydrate phase of the diet (2443 ± 422 vs. 2078 ± 482 kcal/d p<0.05). Activity estimated from TEE/RMR was greater on the high-carbohydrate diet but only approached statistical significance (p<0.06). Total T₃ was significantly lower and free thyroid index and T₃ uptake were significantly higher at the end of the high fat diet in comparison to the high-carbohydrate diet. These data suggest that individual tolerance to a high-fat diet varies considerably and may significantly lower TEE by changing levels of physical activity. The explanation for changes in thyroid hormone levels independent of changes in metabolic rate remains unclear.     

Carboxamide SIRT1 inhibitors block DBC1 binding via an acetylation-independent mechanism

SIRT1 is an NAD⁺-dependent deacetylase that counteracts multiple disease states associated with aging and may underlie some of the health benefits of calorie restriction. Understanding how SIRT1 is regulated in vivo could therefore lead to new strategies to treat age-related diseases. SIRT1 forms a stable complex with DBC1, an endogenous inhibitor. Little is known regarding the biochemical nature of SIRT1-DBC1 complex formation, how it is regulated and whether or not it is possible to block this interaction pharmacologically. In this study, we show that critical residues within the catalytic core of SIRT1 mediate binding to DBC1 via its N-terminal region, and that several carboxamide SIRT1 inhibitors, including EX-527, can completely block this interaction. We identify two acetylation sites on DBC1 that regulate its ability to bind SIRT1 and suppress its activity. Furthermore, we show that DBC1 itself is a substrate for SIRT1. Surprisingly, the effect of EX-527 on SIRT1-DBC1 binding is independent of DBC1 acetylation. Together, these data show that protein acetylation serves as an endogenous regulatory mechanism for SIRT1-DBC1 binding and illuminate a new path to developing small-molecule modulators of SIRT1.     

Characterization of Toxoplasma gondii from raccoons (Procyon lotor), coyotes (Canis latrans), and striped skunks (Mephitis mephitis) in Wisconsin identified several atypical genotypes

During 2005-2006, sera and tissues from raccoons (Procyon lotor), coyotes (Canis latrans), and skunks (Mephitis mephitis) from the state of Wisconsin were tested for Toxoplasma gondii infection. Antibodies to T. gondii were found in 32 of 54 (59.2%) raccoons, 18 of 35 (51.4%) coyotes, and 5 of 7 (71.4%) skunks using the modified agglutination test and a cut-off titer of 1:20. Pooled tissues (brains, hearts, and tongues) from 30 raccoons, 15 coyotes, and 1 skunk were bioassayed for T. gondii infection in mice or cats. Viable T. gondii was isolated from 5 of 30 (16.7%) raccoons, 6 of 15 (40.0%) coyotes, and the skunk. Genetic characterization of the 12 parasite isolates by multilocus PCR-RFLP markers revealed 6 different genotypes including 5 atypical and I archetypal II lineages. The results indicate the prevalence of T. gondii in wildlife mammals is high and that these animals may serve as an important reservoir for transmission of T. gondii.