Evolution by the birth-and-death process in multigene families of the vertebrate immune system

Concerted evolution is often invoked to explain the diversity and evolution of the multigene families of major histocompatibility complex (MHC) genes and immunoglobulin (Ig) genes. However, this hypothesis has been controversial because the member genes of these families from the same species are not necessarily more closely related to one another than to the genes from different species. To resolve this controversy, we conducted phylogenetic analyses of several multigene families of the MHC and Ig systems. The results show that the evolutionary pattern of these families is quite different from that of concerted evolution but is in agreement with the birth-and-death model of evolution in which new genes are created by repeated gene duplication and some duplicate genes are maintained in the genome for a long time but others are deleted or become nonfunctional by deleterious mutations. We found little evidence that interlocus gene conversion plays an important role in the evolution of MHC and Ig multigene families.

Distinct aspects of neuronal differentiation encoded by frequency of spontaneous Ca2+ transients

Stimulation of transient increases in intracellular calcium (Cai2+) activates protein kinases, regulates transcription and influences motility and morphology. Developing neurons generate spontaneous Cai2+ transients, but their role in directing neuronal differentiation and the way in which they encode information are unknown. Here we image Ca2+ in spinal neurons throughout an extended period of early development, and find that two types of spontaneous events, spikes and waves, are expressed at distinct frequencies. Neuronal differentiation is altered when they are eliminated by preventing Ca2+ influx. Reimposing different frequency patterns of Ca2+ elevation demonstrates that natural spike activity is sufficient to promote normal neurotransmitter expression and channel maturation, whereas wave activity is sufficient to regulate neurite extension. Suppression of spontaneous Ca2+ elevations by BAPTA loaded intracellularly indicates that they are also necessary for differentiation. Ca2+ transients appear to encode information in their frequency, like action potentials, although they are 10(4) times longer in duration and less frequent, and implement an intrinsic development programme.

Changes in the prevalence of chronic disability in the United States black and nonblack population above age 65 from 1982 to 1999

Survey evidence through the early 1990s generally suggests a reduction in disability in the elderly population of the United States. Because the evidence is not fully consistent, several authors have speculated about whether disability declines will continue. This paper reports results from the 1999 National Long-Term Care Survey on disability trends from 1982 through 1999. It is found that disability continued to decline in the 1994 to 1999 period, and that the decline was greater in the 1990s than in the 1980s. The disability decline from 1982 to 1989 was 0.26% per year, from 1989 to 1994 it was 0.38% per year, and from 1994 to 1999 it was 0.56% per year. In addition, disability declined by a greater percentage for blacks than for nonblacks over the 1989 to 1999 period.

Statistical methods for testing functional divergence after gene duplication

Functional innovations after gene duplication may result in altered functional constraints between member gene clusters of a gene family. This type (type I) of functional divergence is measured by the coefficient of functional divergence (theta lambda), which can be interpreted as the decrease in rate correlation between gene clusters, or the probability that the evolutionary rate at a site is statistically independent between two gene clusters. A simple stochastic model has been developed for estimating theta lambda and testing its statistical significance. The current model includes the model of rate variation among sites as a special case when theta lambda = 0. Moreover, we have developed a site-specific profile based on the hidden Markov model to identify critical amino acid residues that are responsible for these functional differences between two gene clusters, which may have great potential in functional genomics.

Vascular endothelial growth factor signals endothelial cell production of nitric oxide and prostacyclin through flk-1/KDR activation of c-Src

Vascular endothelial growth factor (VEGF) is a potent endothelial cell-specific mitogen that promotes angiogenesis, vascular hyperpermeability, and vasodilation by autocrine mechanisms involving nitric oxide (NO) and prostacyclin (PGI(2)) production. These experiments used immunoprecipitation and immunoassay procedures to characterize the signaling pathways by which VEGF induces NO and PGI(2) formation in cultured endothelial cells. The data showed that VEGF stimulates complex formation of the flk-1/kinase-insert domain-containing receptor (KDR) VEGF receptor with c-Src and that Src activation is required for VEGF induction of phospholipase C gamma1 activation and inositol 1,4,5-trisphosphate formation. Reporter cell assays showed that VEGF promotes a approximately 50-fold increase in NO formation, which peaks at 5-20 min. This effect is mediated by a signaling cascade initiated by flk-1/KDR activation of c-Src, leading to phospholipase C gamma1 activation, inositol 1,4,5-trisphosphate formation, release of [Ca(2+)](i) and nitric oxide synthase activation. Immunoassays of VEGF-induced 6-keto prostaglandin F(1alpha) formation as an indicator of PGI(2) production revealed a 3-4-fold increase that peaked at 45-60 min. The PGI(2) signaling pathway follows the NO pathway through release of [Ca(2+)](i), but diverges prior to NOS activation and also requires activation of mitogen-activated protein kinase. These results suggest that NO and PGI(2) function in parallel in mediating the effects of VEGF.

Claudins regulate the intestinal barrier in response to immune mediators

BACKGROUND & AIMS

To determine the functional role of immune mediators in the formation of the intestinal barrier, we have examined the regulation of claudin expression by interleukin (IL)-17 in human intestinal epithelial cells.

METHODS

Expression of claudins, extracellular signal-related (ERK) mitogen-activated protein kinases (MAPKs), and activated ERK MAPKs was determined by immunoblotting. Claudin membrane association was assessed by immunohistochemistry and claudin messenger RNA expression by Northern blot analysis. Intestinal epithelial barrier function was characterized through transepithelial electrical resistance and mannitol tracer flux.

RESULTS

IL-17 induced the development of a paracellular barrier of T84 cell monolayers. Inhibition of ERK activation with the MEK inhibitor PD98059 blocked IL-17 as well as basal development of tight junctions in T84 cells. IL-17 induced formation of tight junctions correlated with up-regulation of claudin-1 and claudin-2 gene transcription. Inhibition of MEK reduced the activated and basal expression of claudin-2 messenger RNA and protein expression. Functional MEK was required for the expression and membrane association of claudin-2 but not claudin-1 in T84 cells.

CONCLUSIONS

MEK activity is required for claudin-mediated formation of tight junctions. IL-17 is able to regulate the intestinal barrier through the ERK MAPK pathway.

Epinephrine absorption in adults: intramuscular versus subcutaneous injection

We report a prospective, randomized, blinded, placebo-controlled, 6-way crossover study of intramuscular versus subcutaneous injection of epinephrine in young men. Peak plasma epinephrine concentrations were significantly higher (P < .01) after epinephrine was injected intramuscularly into the thigh than after epinephrine was injected intramuscularly or subcutaneously into the upper arm. We recommend intramuscular injection of epinephrine into the thigh as the preferred route and site of injection of this life-saving medication in the initial treatment of anaphylaxis.

Epinephrine absorption in children with a history of anaphylaxis

BACKGROUND

Prompt injection of epinephrine is the cornerstone of systemic anaphylaxis treatment. The rate of epinephrine absorption has not been reported previously in allergic children.

OBJECTIVE

Our objective was to study the clinical pharmacology of epinephrine in this population.

METHODS

We performed a prospective, randomized, blinded, parallel-group study in 17 children with a history of anaphylaxis to food, Hymenoptera venom, or other substances. We injected 0.01 ml/kg epinephrine solution (maximum 0.3 ml [0.3 mg]) subcutaneously, or 0.3 mg epinephrine intramuscularly from an autoinjector. Plasma epinephrine concentrations, heart rate, blood pressure, and adverse effects were monitored.

RESULTS

In nine children who received epinephrine subcutaneously, the mean maximum plasma epinephrine concentration (+/- SEM) was 1802 +/- 214 pg/ml, achieved at a mean time of 34 +/- 14 minutes (range, 5 to 120 minutes). Only two of the nine children achieved maximum plasma concentrations by 5 minutes. In eight children who received epinephrine intramuscularly, the mean maximum plasma concentration was 2136 +/- 351 pg/ml, achieved at a mean time of 8 +/- 2 minutes, which was significantly faster than the mean time at which maximum plasma concentrations were achieved after subcutaneous epinephrine injection (p < 0.05). Six of the eight children achieved maximum plasma concentrations by 5 minutes. The terminal elimination half-life was 43 +/- 15 minutes. No serious adverse effects were noted in any child.

CONCLUSIONS

In children, recommendations for subcutaneous epinephrine injection are based on anecdotal experience, and should be reevaluated in view of our finding of delayed epinephrine absorption when this route is used. This delay might have important clinical implications during an episode of systemic anaphylaxis. The intramuscular route of injection is preferable.

Maximum-likelihood approach for gene family evolution under functional divergence

According to the observed alignment pattern (i.e., amino acid configuration), we studied two basic types of functional divergence of a protein family. Type I functional divergence after gene duplication results in altered functional constraints (i.e., different evolutionary rate) between duplicate genes, whereas type II results in no altered functional constraints but radical change in amino acid property between them (e.g., charge, hydrophobicity, etc.). Two statistical approaches, i.e., the subtree likelihood and the whole-tree likelihood, were developed for estimating the coefficients of (type I or type II) functional divergence. Numerical algorithms for obtaining maximum-likelihood estimates are also provided. Moreover, a posterior-based site-specific profile is implemented to predict critical amino acid residues that are responsible for type I and/or type II functional divergence after gene duplication. We compared the current likelihood with a fast method developed previously by examples; both show similar results. For handling altered functional constraints (type I functional divergence) in the large gene family with many member genes (clusters), which appears to be a normal case in postgenomics, the subtree likelihood provides a solution that is computationally feasible and robust against the uncertainty of the phylogeny. The cost of this feasibility is the approximation when frequencies of amino acids are very skewed. The potential bias and correction are discussed.

The efficient cellular uptake of high density lipoprotein lipids via scavenger receptor class B type I requires not only receptor-mediated surface binding but also receptor-specific lipid transfer mediated by its extracellular domain

The class B type I scavenger receptor, (SR-BI), is a member of the CD36 superfamily of proteins and is a physiologically relevant, high affinity cell surface high density lipoprotein (HDL) receptor that mediates selective lipid uptake. The mechanism of selective lipid uptake is fundamentally different from that of classic receptor-mediated uptake via coated pits and vesicles (e.g. the low density lipoprotein receptor pathway) in that it involves efficient transfer of the lipids, but not the outer shell proteins, from HDL to cells. The abilities of SR-BI and CD36, both of which are class B scavenger receptors, to bind HDL and mediate cellular uptake of HDL-associated lipid when transiently expressed in COS cells were examined. For these experiments, the binding of HDL to cells was assessed using either 125I- or Alexa (a fluorescent dye)-HDL in which the apolipoproteins on the surface of the HDL particles were covalently modified. Lipid transfer was measured using HDL noncovalently labeled by the fluorescent lipid 1,1'-dioctadecyl-3,3, 3',3'-tetramethylindocarbocyanine perchlorate. Although both mSR-BI and human CD36 (hCD36) could mediate the binding of HDL in a punctate pattern across the surfaces of cells, only mSR-BI efficiently mediated the transfer of lipid to the cells. Analysis of point mutants established that the major sites of fatty acylation of mSR-BI are Cys462 and Cys470 and that fatty acylation is not required for receptor clustering, HDL binding, or efficient lipid transfer. Generation of mSR-BI/hCD36 domain swap chimeras showed that the differences in lipid uptake activities between mSR-BI and hCD36 were not due to differences between their two sets of transmembrane and cytoplasmic domains but rather result from differences in their large extracellular loop domains. These results show that high affinity binding to a cell surface receptor is not sufficient to ensure efficient cellular lipid uptake from HDL. Thus, SR-BI-mediated binding combined with SR-BI-dependent facilitated transfer of lipid from the HDL particle to the cell appears to be the most likely mechanism for the bulk of the selective uptake of cholesteryl esters from HDL to the liver and steroidogenic tissues.

Transvenous closure of secundum atrial septal defects: preliminary results with a new self-expanding nitinol prosthesis in a swine model

BACKGROUND

Our purpose was to evaluate a new prosthesis for percutaneous closure of secundum atrial septal defects (ASDs).

METHODS AND RESULTS

Percutaneous closure of surgically created fossa ovalis ASD was attempted in 15 minipigs. The mean balloon-stretched ASD diameter was 12.3+/-2.3 mm (range, 10 to 16 mm). The self-expanding prosthesis was braided from 0.005-in Nitinol wires in the shape of two flat buttons with a short connecting waist with a diameter corresponding to that of the defect to be closed. Polyester filling was added to enhance thrombogenicity. Pulmonary arteriography with levo-phase was obtained before placement; immediately after placement; and at 1-week, 1-month, and 3-month follow-ups. Four animals were killed at 1 week, 1 month, and 3 months for histopathological correlation. Three deaths resulted from ventricular fibrillation (one during anesthesia and two during the placement procedure). Successful placement of the prosthesis was achieved in the remaining 12 animals. Overall immediate ASD closure on angiography occurred in 7 of 12 animals (all polyester-filled prostheses). Absent or trace shunt by angiography was present in 11 of 12 devices at 1 week, with the remaining one demonstrating a small shunt. All septal defects were completely closed at 1 month with the exception of one case in which delayed partial dislodgment of an undersized prosthesis into the right atrium had developed. Closure rate at 3 months was 100%. Neoendothelialization and fibrous incorporation of the prosthesis were completed within 1 to 3 months.

CONCLUSIONS

Effective and permanent occlusion of secundum ASDs is feasible with a device that offers the advantages of easy placement, self-centering, and repositionability.

Scavenger receptor class B, type I-mediated [3H]cholesterol efflux to high and low density lipoproteins is dependent on lipoprotein binding to the receptor

The murine scavenger receptor class B, type I (mSR-BI) is a receptor for high density lipoprotein (HDL), low density lipoprotein (LDL), and acetylated LDL (AcLDL). It mediates selective uptake of lipoprotein lipid and stimulates efflux of [(3)H]cholesterol to lipoproteins. SR-BI-mediated [(3)H]cholesterol efflux was proposed to be independent of ligand binding. In this study, using anti-mSR-BI antibody KKB-1 and two mSR-BI mutants with altered ligand binding properties, we demonstrated that SR-BI-mediated [(3)H]cholesterol efflux to lipoproteins was correlated with ligand binding and lipid uptake activities of the receptor. The KKB-1 antibody, which blocked lipoprotein binding without substantially altering the cholesterol oxidase-accessible cellular [(3)H]cholesterol, also blocked [(3)H]cholesterol efflux to HDL and LDL. One of the SR-BI mutants, which has a double substitution of arginines for glutamines at positions 402 and 418 (Q402R/Q418R), exhibited a high level of LDL binding and lipid uptake from LDL, but lost most of the corresponding HDL receptor activity. This mutant could mediate efficient [(3)H]cholesterol efflux to LDL, but not to HDL. Another mutant, M158R, with an arginine in place of methionine at position 158, exhibited reduced HDL and LDL receptor activities, but apparently normal AcLDL receptor activity. This mutant could mediate efficient [(3)H]cholesterol efflux to AcLDL, but not to HDL or LDL. These results suggest that SR-BI-stimulated [(3)H]cholesterol efflux to lipoproteins critically depends on ligand binding to this receptor and raise the possibility that the mechanisms of selective lipid uptake and [(3)H]cholesterol efflux may be intimately related.

Androgen receptors in thymic epithelium modulate thymus size and thymocyte development

Castration of normal male rodents results in significant enlargement of the thymus, and androgen replacement reverses these changes. Androgen-resistant testicular feminization (Tfm) mice also show significant thymus enlargement, which suggests that these changes are mediated by the androgen receptor (AR). The cellular targets of androgen action in the thymus are not known, but may include the lymphoid cells (thymocytes) as well as nonlymphoid epithelial cells, both of which have been believed to express AR. In the present study immunohistochemical analysis and hormone binding assays were used to demonstrate the presence of AR in thymic epithelial cells. The physiological significance of this epithelial cell AR expression was defined by further studies performed in vivo using chimeric mice, produced by bone marrow transplantation, in which AR expression was limited to either lymphoid or epithelial components of the thymus. Chimeric C57 mice engrafted with Tfm bone marrow cells (AR(+) epithelium and AR(-) thymocytes) had thymuses of normal size and showed the normal involutional response to androgens, whereas chimeric Tfm mice engrafted with C57 bone marrow cells (AR(-) epithelium and AR(+) thymocytes) showed thymus enlargement and androgen insensitivity. Furthermore, phenotypic analyses of lymphocytes in mice with AR(-) thymic epithelium showed abrogation of the normal responses to androgens. These data suggest that AR expressed by thymic epithelium are important modulators of thymocyte development.

Balance and physical impairments after stroke

OBJECTIVE

To investigate the relationship among laboratory and clinical balance measures and physical impairments.

DESIGN

A descriptive correlational study.

SETTING

Research laboratory.

PARTICIPANTS

Thirty subjects with stroke, recruited through convenience sampling.

MAIN OUTCOME MEASURES

Postural sway was calculated in terms of center of pressure (COP) parameters including spectral characteristics. Clinical balance was measured using the Balance Scale. The assessed physical impairments included stages of lower limb motor recovery, ankle proprioception, and passive dorsiflexion range of the involved limb.

RESULTS

The Balance Scale was correlated with COP speed (r = -.57), COP root mean square speed (r = -.50), and COP mean frequency (r = -.50) in the anterior-posterior direction only. Moderate to high correlations were found among most of the COP parameters except spectral characteristics. Significant differences in postural sway were found among different stance in eyes-open (p = .00 to .02) and eyes-closed conditions (p = .00 to .04). Subjects with impaired ankle proprioception had significantly increased postural sway and decreased Balance Scale scores when compared with the subjects with intact ankle proprioception.

CONCLUSIONS

Some of the clinical and laboratory balance assessments were related, indicating that some components of the tests are similar, but some measured different aspects of balance. Postural sway was related to visual condition, stance position, and proprioception.

Identification of a novel virus in pigs--Bungowannah virus: a possible new species of pestivirus

In 2003 an outbreak of sudden deaths occurred in 3-4-week-old piglets on a farm in New South Wales, Australia. There was a marked increase in the birth of stillborn foetuses. Pathological changes consisted of a multifocal non-suppurative myocarditis. A viral infection was suspected but a wide range of known agents were excluded. A modified sequence independent single primer amplification (SISPA) method was used to identify a novel virus associated with this outbreak. Conserved 5'UTR motifs, the presence of a putative N(pro) coding region and limited antigenic cross-reactivity with other members of the Pestivirus genus, support the placement of this virus in the Pestivirus genus. Phylogenetic analysis of the 5'UTR, N(pro) and E2 coding regions showed this virus to be the most divergent pestivirus identified to date.

Increased protein kinase C and isozyme redistribution in pressure-overload cardiac hypertrophy in the rat

Protein kinase C (PKC) activity and isozyme distribution were evaluated during development of pressure-overload-induced cardiac hypertrophy. Three-week-old rats were loosely banded on the ascending aorta (left ventricular hypertrophy [LVH] group). Two weeks later, when left ventricular mass was 50% greater than in the sham-operated control group and cardiac mass was still rapidly increasing beyond that of normal growth, PKC activity and [3H]phorbol 12,13-dibutyrate (PDBu) binding capacity were determined. In LVH, PKC activity was 119 +/- 14%, 158 +/- 17%, and 152 +/- 9% of the control value in cytosol, membrane, and nuclear-cytoskeletal fractions, respectively (n = 9 or 10). [3H]PDBu binding assay revealed increased PKC concentration in LVH cytosolic (control, 0.51 +/- 0.06 pmol/L per milligram; LVH, 0.78 +/- 0.09 pmol/L per milligram; n = 5; P < .05) and membrane fractions (control, 1.33 +/- 0.15; LVH, 2.32 +/- 0.39; n = 5; P < .05). Scatchard analysis indicated no difference in Kd values between control and LVH groups. Immunoblot analysis using PKC isoform-specific antibodies showed that both Ca(2+)-dependent (alpha and beta) and Ca(2+)-independent (delta, epsilon, and zeta) isoforms were present in the left ventricle. Compared with the control value, there was increased concentration in the membrane and nuclear-cytoskeletal fractions for beta 1,2 and epsilon and in the cytosol for beta 1,2. PKC-delta could be detected only in the nuclear-cytoskeletal fraction and was not changed in LVH. PKC-alpha and -zeta were present in all three fractions but were not altered in LVH. These data indicate that PKC activity and concentration increase during development of LVH induced by pressure overload. The increased PKC isozymes were mainly limited to PKC-beta 1,2 and PKC-epsilon, and the increase was present mainly in the membrane and nuclear-cytoskeletal fractions.

Elastocapillary self-assembled neurotassels for stable neural activity recordings

Implantable neural probes that are mechanically compliant with brain tissue offer important opportunities for stable neural interfaces in both basic neuroscience and clinical applications. Here, we developed a Neurotassel consisting of an array of flexible and high-aspect ratio microelectrode filaments. A Neurotassel can spontaneously assemble into a thin and implantable fiber through elastocapillary interactions when withdrawn from a molten, tissue-dissolvable polymer. Chronically implanted Neurotassels elicited minimal neuronal cell loss in the brain and enabled stable activity recordings of the same population of neurons in mice learning to perform a task. Moreover, Neurotassels can be readily scaled up to 1024 microelectrode filaments, each with a neurite-scale cross-sectional footprint of 3 × 1.5 μm², to form implantable fibers with a total diameter of ~100 μm. With their ultrasmall sizes, high flexibility, and scalability, Neurotassels offer a new approach for stable neural activity recording and neuroprosthetics.

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites

This paper presents a maximum likelihood approach to estimating the variation of substitution rate among nucleotide sites. We assume that the rate varies among sites according to an invariant+gamma distribution, which has two parameters: the gamma parameter alpha and the proportion of invariable sites theta. Theoretical treatments on three, four, and five sequences have been conducted, and computer program have been developed. It is shown that rho = (1 + theta alpha)/(1 + alpha) is a good measure for the rate heterogeneity among sites. Extensive simulations show that (1) if the proportion of invariable sites is negligible, i.e., theta = 0, the gamma parameter alpha can be satisfactorily estimated, even with three sequences; (2) if the proportion of invariable sites is not negligible, the heterogeneity rho can still be suitably estimated with four or more sequences; and (3) the distances estimated by the proposed method are almost unbiased and are robust against violation of the assumption of the invariant + gamma distribution.

A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst

tRNA pseudouridine synthase I catalyzes the conversion of uridine to pseudouridine at positions 38, 39, and/or 40 in the anticodon loop of many tRNAs. Pseudouridine synthase I was cloned behind a T7 promoter and expressed in Escherichia coli to about 20% of total soluble proteins. Fluorouracil-substituted tRNA caused a time-dependent inactivation of pseudouridine synthase I and formed a covalent complex with the enzyme that involved the FUMP at position 39. Asp60, conserved in all known and putative pseudouridine synthases, was mutated to amino acids with diverse side chains. All Asp60 mutants bound tRNA but were catalytically inactive and failed to form covalent complexes with fluorouracil-substituted tRNA. We conclude that the conserved Asp60 is essential for pseudouridine synthase activity and propose mechanisms which involve this residue in important catalytic roles.

Vascular endothelial growth factor activates STAT proteins in aortic endothelial cells

Vascular endothelial growth factor (VEGF) intracellular signaling in endothelial cells is initiated by the activation of distinct tyrosine kinase receptors, VEGFR1 (Flt-1) and VEGFR2 (Flk-1/KDR). Because the tyrosine kinase-dependent transcription factors known as STAT (signal transducers and activators of transcription) proteins are important modulators of cell growth responses induced by other growth factor receptors, we have determined the effects VEGF of on STAT activation in BAEC (bovine aortic endothelial cells). Here, we show that VEGF induces tyrosine phosphorylation and nuclear translocation of STAT1 and STAT6. VEGF also stimulates STAT3 tyrosine phosphorylation, but nuclear translocation does not occur. We found that placenta growth factor, which selectively activates VEGFR1, has no effect on the STATs. However, upon VEGF stimulation, STAT1 associates with the VEGFR2 in a tyrosine kinase-dependent manner, indicating that VEGF-induced STAT1 activation is mediated primarily by VEGFR2. Thus, our study shows for the first time that VEGF activates the STAT pathway through VEGFR2. Because the growth-promoting activity of VEGF depends upon VEGFR2 activation, these findings suggest a role for the STATs in the regulation of gene expression associated with the angiogenic effects of VEGF.

Highly simplified device for ultrashort-pulse measurement

We show that a frequency-resolved optical gating device using (1) a thick nonlinear crystal to replace the usual thin crystal and spectrometer and (2) a Fresnel biprism to replace the beam splitter and delay line yields a remarkably simple single-shot ultrashort-pulse intensity-and-phase measurement device with no sensitive alignment parameters and significantly greater sensitivity.

A simple method for estimating the parameter of substitution rate variation among sites

When the rate variation among sites is described by a gamma distribution, an important problem is how to estimate the shape parameter alpha, which is an index of the degree of among-site rate variation. The parsimony-based methods for estimating alpha are simple but biased, i.e., alpha tends to be overestimated. On the other hand, the likelihood-based methods are asymptotically unbiased but take a huge amount of computational time. In this paper, we have developed a new method to solve this problem: we first estimate the expected number of substitutions at each site, which is corrected for multiple hits, and then estimate the parameter alpha. Our method is computationally as fast as the parsimony method, and the estimation accuracy is much higher than that of parsimony and similar to that of the likelihood method.

Breaking the code: regulation of neuronal differentiation by spontaneous calcium transients

Calcium ions play critical roles in neuronal development. Stimulation of transient elevations of intracellular calcium (Ca2+i) activates protein kinases, regulates transcription and influences motility and morphology. Embryonic Xenopus spinal neurons exhibit a Ca(2+)-sensitive period in culture; removing extracellular Ca2+ during this period affects several aspects of neuronal differentiation. However, both the mechanisms that generate natural fluctuations in Ca2+i and the signals they transduce are not well understood. Spontaneous, transient and repeated elevations of Ca2+i in embryonic Xenopus spinal neurons have been observed over periods up to 5 h in vitro and in vivo, confocally imaging fluo 3-loaded cells. Developing neurons generate two distinctive types of spontaneous Ca2+i transients, calcium spikes and calcium waves. We have investigated the mechanisms by which they are generated and their roles in directing neuronal differentiation. Spikes are generated by spontaneous action potentials, and thus are rapidly propagated throughout entire neurons. Ca2+ entry triggers Ca2+ release from intracellular stores, and spikes have a characteristic double exponential decay. In contrast, the generation of waves does not involve conventional voltage-dependent Ca2+ channels, but an unknown Ca2+ entry pathway that can be blocked by Ni2+ at a higher concentration than required to block classical voltage-dependent Ca2+ channels. Waves rise and decay slowly, and unlike spikes, are local events. However both spikes and waves are abolished by removal of extracellular Ca2+. Developmentally, the incidence and frequency of spikes decrease while the incidence and frequency of waves are constant. To study the roles of Ca2+ transients, we have imaged Ca2+ in spinal neurons throughout an extended period of early development, and find that spikes and waves are expressed at distinct frequencies. Neuronal differentiation is altered when they are eliminated by preventing Ca2+ influx. By reimposing different frequency patterns of Ca2+ transients, we demonstrate that natural spike activity is sufficient to promote normal neurotransmitter expression and channel maturation, while wave activity at growth cones is sufficient to regulate neurite extension. On the other hand, suppression of spontaneous Ca2+ elevations with BAPTA, a rapid Ca2+ chelator, indicates that they are also necessary to direct differentiation. Ca2+ transients appear to encode information in their frequency. Thus, they act like action potentials, although they are 10(4) times longer in duration and less frequent and implement an intrinsic development program.

The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment

The size distributions of deletions, insertions, and indels (i.e., insertions or deletions) were studied, using 78 human processed pseudogenes and other published data sets. The following results were obtained: (1) Deletions occur more frequently than do insertions in sequence evolution; none of the pseudogenes studied shows significantly more insertions than deletions. (2) Empirically, the size distributions of deletions, insertions, and indels can be described well by a power law, i.e., fk = Ck-b, where fk is the frequency of deletion, insertion, or indel with gap length k, b is the power parameter, and C is the normalization factor. (3) The estimates of b for deletions and insertions from the same data set are approximately equal to each other, indicating that the size distributions for deletions and insertions are approximately identical. (4) The variation in the estimates of b among various data sets is small, indicating that the effect of local structure exists but only plays a secondary role in the size distribution of deletions and insertions. (5) The linear gap penalty, which is most commonly used in sequence alignment, is not supported by our analysis; rather, the power law for the size distribution of indels suggests that an appropriate gap penalty is wk = a + b ln k, where a is the gap creation cost and blnk is the gap extension cost. (6) The higher frequency of deletion over insertion suggests that the gap creation cost of insertion (ai) should be larger than that of deletion (ad); that is, ai - ad = ln R, where R is the frequency ratio of deletions to insertions.