Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated

It has long been known, from the distribution of multiple amino acid replacements, that not all amino acids of a sequence are replaceable. More recently, the phenomenon was observed at the nucleotide level in mitochondrial DNA even after allowing for different rates of transition and transversion substitutions. We have extended the search to globin gene sequences from various organisms, with the following results: (1) Nearly every data set showed evidence of invariable nucleotide positions. (2) In all data sets, substitution rates of transversions and transitions were never in the ratio of 2/1, and rarely was the ratio even constant. (3) Only rarely (e.g., the third codon position of beta hemoglobins) was it possible to fit the data set solely by making allowance for the number of invariable positions and for the relative rates of transversion and transition substitutions. (4) For one data set (the second codon position of beta hemoglobins) we were able to simulate the observed data by making the allowance in (3) and having the set of covariotides (concomitantly variable nucleotides) be small in number and be turned over in a stochastic manner with a probability that was appreciable. (5) The fit in the latter case suggests, if the assumptions are correct and at all common, that current procedures for estimating the total number of nucleotide substitutions in two genes since their divergence from their common ancestor could be low by as much as an order of magnitude. (6) The fact that only a small fraction of the nucleotide positions differ is no guarantee that one is not seriously underestimating the total amount of divergence (substitutions). (7) Most data sets are so heterogeneous in their number of transition and transversion differences that none of the current models of nucleotide substitution seem to fit them even after (a) segregation of coding from noncoding sequences and (b) splitting of the codon into three subsets by codon position. (8) These frequently occurring problems cannot be seen unless several reasonably divergent orthologous genes are examined together.      

Yellow Fever Vaccine. V. Antibody Response in Monkeys Inoculated with Graded Doses of the 17D Vaccine

A dosage equal to or greater than approximately 3.4 Dex (decimal exponent, log(10)) weanling mouse intracerebral 50% lethal dose (LD(50)) was sufficient to elicit a yellow fever antibody response, as determined by the plaque neutralization (PN) test, in better than 90% of vaccinated rhesus monkeys. Lower dosages were progressively less effective in terms of PN titers and the PN and hemagglutination-inhibition serological conversion rates observed. A dose of between 3.4 and 4.2 Dex weanling mouse intracerebral LD(50), or one-tenth to one times the dosage recommended for man, provided an optimal antibody response in monkeys. In rhesus monkeys, in contrast to the findings for man, pre-existing yellow fever antibody did not interfere with the antibody response to yellow fever vaccine. The PN test was felt to be a more sensitive and specific indicator of yellow fever antibody in rhesus monkeys after vaccination than the hemagglutination inhibition or complement fixation tests.     

Multiple gating modes and the effect of modulating factors on the microI sodium channel.

Macroscopic current from the microI skeletal muscle sodium channel expressed in Xenopus oocytes shows inactivation with two exponential components. The major, slower component's amplitude decreases with rapid pulsing. When microI cRNA is coinjected with rat skeletal muscle or brain mRNA the faster component becomes predominant. Individual microI channels switch between two principal gating modes, opening either only once per depolarization, or repeatedly in long bursts. These two modes differ in both activation and inactivation kinetics. There is also evidence for additional gating modes. It appears that the equilibrium among gating modes is influenced by a modulating factor encoded in rat skeletal muscle and brain mRNA. The modal gating is similar to that observed in hyperkalemic periodic paralysis.     

Developmental clustering of ion channels at and near the node of Ranvier.

Voltage-gated Na(+) and K(+) channels are localized to distinct subcellular domains in mammalian myelinated nerve fibers. Specifically, Na(+) channels are clustered in high densities at nodes of Ranvier, while K(+) channels are found in juxtaparanodal zones just beyond regions of axoglial contact where sequential layers of the myelin sheath terminate. Specific targeting, clustering, and maintenance of these channels in their respective domains are essential to achieve high conduction velocities of action potential propagation. The cellular, molecular, and developmental mechanisms that exist to achieve this neuronal specialization are discussed and reviewed. Current evidence points to a prominent role in channel clustering played by myelinating glial cells, and sites of axoglial contact in particular.     

Bayesian adaptive sequence alignment algorithms

The selection of a scoring matrix and gap penalty parameters continues to be an important problem in sequence alignment. We describe here an algorithm, the 'Bayes block aligner, which bypasses this requirement. Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data. We compared the Bayes aligner with the popular Smith-Waterman algorithm with parameter settings from the literature which had been optimized for the identification of structural neighbors, and found that the Bayes aligner correctly identified more structural neighbors. In a detailed examination of the alignment of a pair of kinase and a pair of GTPase sequences, we illustrate the algorithm's potential to identify subsequences that are conserved to different degrees. In addition, this example shows that the Bayes aligner returns an alignment-free assessment of the distance between a pair of sequences.      

Training-induced alterations of carbohydrate metabolism in women: women respond differently from men

We examined the hypothesis that glucose flux wasdirectly related to relative exercise intensity both beforeand after a 12-wk cycle ergometer training program [5days/wk, 1-h duration, 75% peakO₂ consumption(O_{2 peak})] inhealthy female subjects (n = 17; age23.8 ± 2.0 yr). Two pretraining trials (45 and 65% of O_{2 peak})and two posttraining trials [same absolute workload (65% of oldO_{2 peak})and same relative workload (65% of new O_{2 peak})] wereperformed on nine subjects by using a primed-continuous infusion of[1-¹³C]- and[6,6-²H]glucose.Eight additional subjects were studied by using[6,6-²H]glucose.Subjects were studied postabsorption for 90 min of rest and 1 h ofcycling exercise. After training, subjects increased O_{2 peak} by 25.2 ± 2.4%. Pretraining, the intensity effect on glucose kinetics wasevident between 45 and 65% ofO_{2 peak} with rates ofappearance (R_a: 4.52 ± 0.25 vs. 5.53 ± 0.33 mg · kg¹ · min¹),disappearance (R_d: 4.46 ± 0.25 vs. 5.54 ± 0.33 mg · kg¹ · min¹),and oxidation (R_ox: 2.45 ± 0.16 vs. 4.35 ± 0.26 mg · kg¹ · min¹)of glucose being significantly greater(P  0.05) in the 65% thanin the 45% trial. Training reducedR_a (4.7 ± 0.30 mg · kg¹ · min¹),R_d (4.69 ± 0.20 mg · kg¹ · min¹),and R_ox (3.54 ± 0.50 mg · kg¹ · min¹)at the same absolute workload (P  0.05). When subjects were tested at the same relative workload,R_a,R_d, andR_ox were not significantlydifferent after training. However, at both workloads after training,there was a significant decrease in total carbohydrate oxidation asdetermined by the respiratory exchange ratio. These results show thefollowing in young women: 1)glucose use is directly related to exercise intensity;2) training decreasesglucose flux for a given power output;3) when expressed asrelative exercise intensity, training does not affect the magnitude ofblood glucose flux during exercise; but4) training does reduce totalcarbohydrate oxidation.