Microphotometric analysis of NADH-tetrazolium reductase and alpha-glycerophosphate dehydrogenase in human quadriceps muscle.

Synopsis In serial cross-sections of human skeletal muscles stained for either NADH-tetrazolium reductase (NADH-TR) or -glycerophosphate dehydrogenase (-GPD), a linear relation was found between the total content of enzyme in a cell (expressed as the thickness of the section) and the absorbance of the formazan reaction product formed. Little variation (<4.8%) was found in the concentration of formazan (absorbance per unit thickness) when the same cell was measured in serial cross-sections of various thicknesses (2–10 m) along a longitudinal distance of at least 200 m along the cell. The reduction in enzyme activity was found to be negligible after aqueous preincubation. A maximum of 10–12% of the formazan produced in the NADH-TR reaction might be the result of nothing dehydrogenase activity, whereas this unspecific reaction might account for up to 20% of the formazan deposited in the -GPD reactions after 30 min incubation. The diffusion of Nitro BT into the tissue during the incubation period was found to be unhindered. The rates of formazan production decreased with increasing incubation time, especially in the -GPD reaction in both fibre types. The ratio of the mean absorbance of the formazan in type I fibres to that in type II fibres (in the same section) was 1.41 (coefficient of variation, 2.5%) in the NADH-TR reaction and 0.68 (coefficient of variation, 3.8%) in the -GPD reaction. These values were not affected either by variations in the incubation time (5–40 min) or by the thickness of the section (2–8 m). The concentrations of NADH-TR and -GPD seem to be constant along the length of the muscle fibre. The histochemical reactions reported, together with measurements of the thickness of the sections, seem suitable for the microphotometric quantification of the two enzymes in single fibres of human skeletal muscles.     

Radiation damage in tripalmitin layers studied by means of infrared spectroscopy and electron microscopy.

Structural deteriorations in biomembranes, as inevitably induced while structural information is gathered by electron optical methods, were evaluated by infrared spectroscopy. Tripalmitin model membranes were irradiated with 100 keV-electrons in an electron microscope. The intensity decay of group vibrations over the dose reveals the sequence of damage in the polar and nonpolar part of the molecule. The C-C backbone, being the most important structural feature, shows a significant latency effect up to 0.6 e-/A2 and is completely disordered by 3 e-/A2, corresponding to about three inelastic processes per molecule.     

Ovarian and adrenal function during the estrous cycle of the sow.

The concentrations of plasma estrogens, progesterone, and corticosteroids and of urinary pregnanediol, pregnanetriol, ketogenic steroids, and corticosteroids were determined as indicators of ovarian and adrenal function throughout a normal sow's estrous cycle. Two broad peaks of plasma estrogen, one lasting 11–12 days during estrus and another 6-day peak period during the early part of the luteal phase were detected. Plasma progesterone was elevated during the late follicular and luteal phase. Two broad peaks of plasma corticoids appeared, one following the decrease of plasma progesterone and the second 7–14 days later. Those elevations in plasma corticoids occurred when estrogen titres were elevated. Urinary determinations generally reflected plasma findings. Estrogen levels began to rise during the follicular phase while a reasonably high progesterone level was evident. Estrogen titres never decreased to non-detectable levels. An interrelationship between adrenal function and ovarian estrogen production is suggested.     

Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference

Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing five additional data sets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other data sets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.     

Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver

MicroRNA-122 (miR-122) is an abundant liver-specific miRNA, implicated in fatty acid and cholesterol metabolism as well as hepatitis C viral replication. Here, we report that a systemically administered 16-nt, unconjugated LNA (locked nucleic acid)-antimiR oligonucleotide complementary to the 5′ end of miR-122 leads to specific, dose-dependent silencing of miR-122 and shows no hepatotoxicity in mice. Antagonism of miR-122 is due to formation of stable heteroduplexes between the LNA-antimiR and miR-122 as detected by northern analysis. Fluorescence in situ hybridization demonstrated uptake of the LNA-antimiR in mouse liver cells, which was accompanied by markedly reduced hybridization signals for mature miR-122 in treated mice. Functional antagonism of miR-122 was inferred from a low cholesterol phenotype and de-repression within 24 h of 199 liver mRNAs showing significant enrichment for miR-122 seed matches in their 3′ UTRs. Expression profiling extended to 3 weeks after the last LNA-antimiR dose revealed that most of the changes in liver gene expression were normalized to saline control levels coinciding with normalized miR-122 and plasma cholesterol levels. Combined, these data suggest that miRNA antagonists comprised of LNA are valuable tools for identifying miRNA targets in vivo and for studying the biological role of miRNAs and miRNA-associated gene-regulatory networks in a physiological context.     

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Genome‐scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could correctly describe phenotypes that the previous model could not, particularly under high enzymatic pressure conditions, such as yeast growing on different carbon sources in excess, coping with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between and within metabolic pathways. The developed method and model are expected to increase the use of model‐based design in metabolic engineering.     

Long-Term Miscanthus Yields Influenced by Location,Genotype, Row Distance,Fertilization and Harvest Season

Long-term yield studies in perennial crops like miscanthus are important to determine mean annual energy yield and the farmer’s economy. In two Danish field trials, annual yield of two miscanthus genotypes was followed over a 20-year period. The trials were established in 1993 on loamy sand in Foulum and on coarse sand in Jyndevad. Effects of genotype, row distance and fertilization were investigated. In both trials, yield development over time was characterized by an increase during the first years, optimum yields after 7–8 years and a decrease to a lower level which remained relatively constant from year 11 to 20. Spring harvest reduced the yield by 34–42 % compared to autumn harvest. In Foulum annual fertilization with 75 kg ha^?1 N increased the yield of the genotype Goliath (Miscanthus sinensis) by 26 %. Additional N fertilization only increased the yield of Goliath little, and the genotype Giganteus (Miscanthus?×?giganteus) did not respond to fertilization at all. The highest mean yield in Foulum for the period 1997–2012 was obtained with the shortest row distance (～18,000 rather than ～12,000 plants ha^?1) and harvested in late autumn, namely 13.1 and 12.0 Mg ha^?1 DM annually for Giganteus and Goliath, respectively. In Jyndevad, where only Goliath was studied, the highest yield during 1995–2001 was obtained by short row distance, autumn harvest and annual fertilization with 75 kg ha^?1 N, with yield increasing up to 116 % in response to fertilization. A mean yield of 14.4 Mg ha^?1 DM was achieved over the period 1995–2012.     

Tendon collagen synthesis at rest and after exercise in women.

In general, there is a higher incidence of musculoskeletal injuries during physical activity in women than in men. We hypothesized that in women rates of tendon collagen synthesis would be lower than in men at rest and after exercise, especially in the later luteal phase when estrogen and progesterone concentrations are higher than the early follicular phase. We studied tendon collagen fractional synthesis rate (FSR) in 15 young, healthy female subjects in either the early follicular (n = 8) or the late luteal phase (n = 7) 72 h after an acute bout of one-legged exercise (60 min kicking at 67% workload maximum) (72 h) and compared the results with those previously obtained for men. Samples were taken from the patellar tendon in both the exercised and rested legs to determine collagen FSR by the incorporation of [15N]proline into tendon collagen hydroxyproline. There was no effect of menstrual phase on tendon collagen synthesis either at rest or after exercise. However, there was a significant difference between women and men at rest (women = 0.025 +/- 0.002%/h, men = 0.045 +/- 0.008%/h; P < 0.05) and 72 h after exercise (women = 0.027 +/- 0.005%/h; men = 0.058 +/- 0.008%/h). Furthermore, rest and 72-h tendon collagen synthesis were not different in women, whereas in men tendon collagen synthesis remained significantly elevated 72 h after exercise. It is concluded that both in the resting state and after exercise, tendon collagen FSR is lower in women than in men, which may contribute to a lower rate of tissue repair after exercise.