Impact of Peripheral Hydrogen Bond on Electronic Properties of the Primary Acceptor Chlorophyll in the Reaction Center of Photosystem I

Photosystem I (PS I) is a photosynthetic pigment-protein complex that absorbs light and uses the absorbed energy to initiate electron transfer. Electron transfer has been shown to occur concurrently along two (A- and B-) branches of reaction center (RC) cofactors. The electron transfer chain originates from a special pair of chlorophyll a molecules (P700), followed by two chlorophylls and one phylloquinone in each branch (denoted as A-1, A0, A1, respectively), converging in a single iron-sulfur complex Fx. While there is a consensus that the ultimate electron donor-acceptor pair is P700+A0-, the involvement of A-1 in electron transfer, as well as the mechanism of the very first step in the charge separation sequence, has been under debate. To resolve this question, multiple groups have targeted electron transfer cofactors by site-directed mutations. In this work, the peripheral hydrogen bonds to keto groups of A0 chlorophylls have been disrupted by mutagenesis. Four mutants were generated: PsaA-Y692F; PsaB-Y667F; PsaB-Y667A; and a double mutant PsaA-Y692F/PsaB-Y667F. Contrary to expectations, but in agreement with density functional theory modeling, the removal of the hydrogen bond by Tyr → Phe substitution was found to have a negligible effect on redox potentials and optical absorption spectra of respective chlorophylls. In contrast, Tyr → Ala substitution was shown to have a fatal effect on the PS I function. It is thus inferred that PsaA-Y692 and PsaB-Y667 residues have primarily structural significance, and their ability to coordinate respective chlorophylls in electron transfer via hydrogen bond plays a minor role.

P1415Wide antral circumferential pulmonary vein isolation ablation using a novel balloon cryoablation catheter

Background

Pulmonary vein isolation using cryotherapy is an established treatment for the management of patients with paroxysmal atrial fibrillation. Ablation using the commercially available balloon cryocatheter has been shown to create wide antral pulmonary vein isolation. A novel balloon cryocatheter (BCC) has been designed to maintain uniform pressure and size during ablation, potentially improving contact with the antral anatomy. The extent of ablation created using the novel BCC has not previously been established.

Purpose

To determine the anatomical extent of pulmonary vein isolation using electroanatomical mapping when performing catheter ablation for paroxysmal atrial fibrillation using the novel BCC.

Methods

Nine consecutive patients underwent pre-procedure computed tomography angiography of the left atrium to quantify the chamber dimensions. An electroanatomical map was created using the cryoablation system mapping catheter and a high definition mapping system. A bipolar voltage map was obtained following ablation to determine the extent of pulmonary vein isolation ablation. A volumetric technique was used to quantify the extent of vein and posterior wall electrical isolation in addition to traditional techniques for proving entrance and exit block.

Results

All patients had paroxysmal atrial fibrillation, mean age 56 years, 7 (78%) male. Electrical isolation was achieved for 100% of the pulmonary veins; mean total procedure time was 109 min (+/- 26 SD), and fluoroscopy time 14.9 min (+/- 2.4 SD). The median treatment applications per vein was one (range one - four), and median treatment duration 180 sec (range 180 -240). Left atrial volume 32 mL/m2 (+/- 7 SD), and mean left atrial posterior wall area 22 cm2 (+/- 4 SD). Data was available for quantitative assessment of the extent of ablation for eight patients. No lesions (0 of 32) were ostial in nature. The antral surface area of ablation was not statistically different between the left and right sided pulmonary veins (p 0.63), which were 5.9 (1.6 SD) and 5.4 (2.1 SD) cm2 respectively. In total 50% of the posterior left atrial wall was ablated. 

Conclusion

Pulmonary vein isolation using a novel BCC provides a wide and antral lesion set. There is significant debulking of the posterior wall of the left atrium.

Abstract Figure.

A hydrochemically guided landscape classification system for modelling spatial variation in multiple water quality indices: Process-attribute mapping

Spatial variation in landscape attributes can account for much of the variability in water quality relative to land use on its own. Such variation results from the coupling between the dominant processes governing water quality, namely hydrological, redox, and weathering and gradients in key landscape attributes, such as topography, geology, and soil drainage. Despite the importance of 'process-attribute' gradients (PAG), few water quality models explicitly account for their influence. Here a processes-based water quality modelling framework is presented that more completely accounts for the role of landscape variability over water quality - Process-Attribute Mapping (PoAM). Critically, hydrochemical measures form the basis for the identification and mapping of effective landscape attributes, producing PAG maps that attempt to replicate the natural landscape gradients governing each dominant process. Application to the province of Southland (31,824 km²), New Zealand, utilised 12 existing geospatial datasets and a total of 28,626 surface water, groundwater, spring, soil water, and precipitation analyses to guide the identification and mapping of 11 individual PAG. The ability of PAGs to replicate regional hydrological, redox, and weathering gradients was assessed on the accuracy with which the hydrochemical indicators of each dominant process (e.g. hydrological tracers, redox indicators) were estimated across 93 long-term surface water monitoring sites (cross-validated R² values of 0.75-0.95). Given hydrochemical evidence that PAGs replicate actual landscape gradients governing the dominant processes, they were combined with a land use intensity layer and used to estimate steady-state surface water quality. Cross-validated R² values ranged between 0.81 and 0.92 for median total nitrogen, total oxidised nitrogen, total phosphorus and dissolved reactive phosphorus. Models of particulate species E. coli and total suspended sediment, although reasonable (R² 0.72-0.73), were less accurate, suggesting finer-grained land use, landscape attribute, and/or flow normalised measures are required to improve estimation.

Contact X-ray Brachytherapy as an Adjunct to a Watch and Wait Approach is an Affordable Alternative to Standard Surgical Management of Rectal Cancer for Patients with a Partial Clinical Response to Chemoradiotherapy

AIMS

Emerging evidence suggests that contact X-ray brachytherapy (CXB) may increase the clinical complete response rate and durability when administered after standard chemoradiotherapy in patients with rectal cancer. The addition of CXB in partial responders is therefore probably cost-effective. The affordability of widening access to CXB in the UK, however, has not been evaluated.

MATERIALS AND METHODS

Decision analytical modelling with Monte Carlo simulation was used to evaluate long-term costs for the management of patients with rectal cancers who were given a CXB boost when a clinical complete response was not initially achieved following chemoradiotherapy in order to facilitate a watch and wait approach. A third-party payer (National Health Service) perspective was adopted, probabilistic sensitivity analysis was carried out and a scenario analysis was performed to investigate the effect of the number of referral centres and number of patients treated with CXB.

RESULTS

We estimate that 818 (95% confidence interval 628-1021) patients per year are eligible for CXB as an adjunct to a watch and wait approach in England and Wales. As this management is less costly than surgical management for each individual patient, the more patients treated, the more affordable the technology. Even if as few as 125 patients are treated nationally in 15 centres, the cost of implementing this technology would be less than £4 million. If the average number of patients treated in each centre is 30, this technology would be cost saving within 5 years.

CONCLUSIONS

The cost of CXB is not prohibitive according to the National Institute for Health and Care Excellence threshold for implementation of new technology and may even be cost saving within 5 years compared with standard surgical management, depending on the uptake of the technology and the number of referral centres.

The Nasonov pheromone of the honeybeeApis mellifera L. (Hymenoptera, Apidae). Part II. Bioassay of the components using foragers

The Nasonov pheromone of the honeybee comprises seven components, (Z)-citral, nerol, geraniol, nerolic acid, geranic acid, and (E,E)-farnesol. Bioassay of individual components showed each attracted foraging bees. A mixture of components in proportions present in the honeybee was as attractive as the natural secretion, and each component contributed to the attractiveness of the mixture. Honeybees responded anemotactically to the source of Nasonov odor. The presence of footprint pheromone enhanced the attractiveness of the synthetic Nasonov mixture. Nasonov and footprint pheromones may prove useful in attracting honeybees to crops needing pollination.

Nasonov pheromone of the honey bee,Apis mellifera L. (Hymenoptera, Apidae). part III. : Regulation of pheromone composition and production

GC and GC-MS analyses of the multicomponent Nasonov pheromone of the honey bee, and of the air above insects releasing the pheromone, show that constant composition is maintained during release, despite differing volatilities of the components. The regulating mechanism may involve a specific enzyme process, detected in excised Nasonov glands, which converts the major component geraniol into the more volatile (E)-citral. Analysis of honey bees of known ages and at different times of year shows that maximum secretion occurs when foraging is most likely.

Nasonov pheromone of the honeybee.Apis mellifera L. (Hymenoptera, Apidae) : IV. Comparative electroantennogram responses

Electroantennogram (EAG) responses from worker honeybee antennae were obtained for each Nasonov component. Response amplitudes to 10 μg of components correlated well with reported relative abilities to attract foragers in the field. EAG responses of worker, queen, and drone antennae to natural pheromone were consistently greater than to synthetic pheromone, a difference only partly explained by enzymic conversion of geraniol to (E)-citral during preparation of natural extracts.

CXCL13 expression in the gut promotes accumulation of IL-22-producing lymphoid tissue-inducer cells, and formation of isolated lymphoid follicles

The chemokine CXCL13 is overexpressed in the intestine during inflammation. To mimic this condition, we created transgenic mice-expressing CXCL13 in intestinal epithelial cells. CXCL13 expression promoted a marked increase in the number of B cells in the lamina propria and an increase in the size and number of lymphoid follicles in the small intestine. Surprisingly, these changes were associated with a marked increase in the numbers of RORgammat(+)NKp46(-)CD3(-)CD4(+) and RORgammat(+)NKp46(+) cells. The RORgammat(+)NKp46(-)CD3(-)CD4(+) cells expressed CXCR5, the receptor for CXCL13, and other markers of lymphoid tissue-inducer cells, such as LTalpha, LTbeta, and TNF-related activation-induced cytokine (TRANCE). RORgammat(+)NKp46(-)CD3(-)CD4(+) gut LTi cells produced IL-22, a cytokine implicated in epithelial repair; and expressed the IL-23 receptor, a key regulator of IL-22 production. These results suggest that overexpression of CXCL13 in the intestine during inflammatory conditions favors mobilization of B cells and of LTi and NK cells with immunomodulatory and reparative functions.

Comparison of histidine-tryptophan-ketoglutarate solution and University of Wisconsin solution in adult liver transplantation

BACKGROUND

A safe and effective preservation solution is a precondition for successful orthotopic liver transplantation (OLT). This study compared University of Wisconsin (UW) and histidine-tryptophan-ketoglutarate (HTK) solutions in OLT.

PATIENTS AND METHODS

We retrospectively reviewed the medical records of 137 primary cadaveric. OLT performed between January 2003 and December 2006 at our institution. Sixty-eight grafts were harvested using UW and 69 using HTK. Recipients were managed similarly in regard to operative techniques and immunosuppression. We collected donor data including serum transaminases, serum sodium, ICU stay and assessed macroscopic liver quality. Recipient serum transaminases were collected on postoperative days 1, 7, 14, and 30. We compared biliary and vascular complications, as well as patient and graft survivals.

RESULTS

Mean serum bilirubin levels were slightly higher in the HTK group at 1,7,14, and 30 days after transplantation, whereas transaminases were higher in the UW group. Primary nonfunction occurred in 1 patient in each group. Retransplantation was performed in 5 patients in the UW and in 9 patients in the HTK group. Biliary complication rates were similar in the UW and HTK groups (22% and 17%, respectively). Six arterial complications occurred in the HTK (8.7%) and 2 in the UW group (2.9%; P < .05). Mean follow-up was 25 months. Graft survival at 1, 12, and 36 months was 90%, 78%, and 75% versus 90%, 71%, and 71% in the UW versus HTK groups, respectively. One-, 12-, and 36-month patient survival rates were 93%, 78%, and 75% versus 93%, 78%, and 78% in the UW versus HTK groups, respectively.

CONCLUSIONS

There were no significant differences in graft and patient survivals between the 2 groups. Whereas the biliary complication rates were comparable in both groups, the arterial complications were clearly higher in the UW group (8.7% vs 2.9%; P < .05%). UW and HTK solutions seemed to be equally safe and effective in the preservation of liver grafts. The high incidence of arterial complications in the UW group requires further prospective studies.

Histomorphometric study of femoral heads in hip osteoarthritis and osteoporosis

During the period from 2000 to 2003, ninety eight samples of femoral heads were collected. In these pieces, two zones were analyzed: a high-load zone (the hard core of the head) and a low-load zone (the round ligamentum teres zone). As control group, 6 femoral heads (3 of women and 3 of men), proceeding from autopsy in peoples without pathological antecedents and youngs, were studied. After the samples had been embedded in methylmethacrylate and stained, they were subjected to an histomorphometric study. By means of histomorphometry, trabecular bone volume (TBV) and osteoid substance (OSV) was determined. Statistically significant differences were found as for peripheral osteoid volume (low-load zone) (p=0.036) and trabecular bone volume, both peripheral and central. Both volumes decreased in osteoporotic samples and in those from women (p=0.000), in comparison with control group. Regarding the relationship between the high-load and low-load zone, significant data were obtained. The high-load zone had a greater trabecular bone volume than the low-load zone, regardless of the pathology and sex, but this increase was more pronounced in the arthrosic samples and in those from men. Additionally, this trabecular bone volume in the high-load zone decreased with increasing age of the donor (p=0.037), when the control group is compared. In sum, we observed a reduction in the formation of TBV and OSV in osteoporosis but also a decrease in the arthrosic, in samples from older subjects, in women, and in the low-load zone of the samples, when the control group is compared. These data suggest the coexistence of both pathologies, which is more pronounced in older subjects and women.

Successful staged kidney and liver transplantation for glycogen storage disease type Ib: A case report

Glycogen storage disease type Ib is a rare metabolic disease caused by a defect of the G6P transporter. Patients suffer from hypoglycemic episodes; growth and developmental delay; osteoporosis; neutropenia; and tendency to infections, ovarian cysts, and liver adenomas. Terminal kidney disease is a rare complication. Liver transplantation has been performed to prevent malignant transformation of hepatic adenomas. We present the case of a female patient with glycogenosis type Ib who had severe hypoglycemic episodes and recurrent infections since early childhood. She became dialysis dependent at the age of 24 years. Kidney transplantation was performed at age 30, and liver transplantation 2 years later. The main indication for liver transplantation were the persistent, therapy-refractory hypoglycemic episodes. The transplanted kidney function is stable. The liver transplantation resulted in the disappearance of hypoglycemic episodes, with the patient leading a normal life and eating a normal diet. The neutropenia did not recover, but there were no more significant infectious episodes after liver transplantation. This is, to the best of our knowledge, the first communication of a dual kidney and liver transplant performed in a patient with glycogenosis type Ib. It confirmed the beneficial effect of liver transplantation on the quality of life of patients with severe hypoglycemia. The transplantation should be attempted earlier in the course of the disease to reduce complications and allow catch-up growth. Hepatocyte transplantation may be considered; however, long-term results seem to be rather poor in the few documented cases.

Emergent features due to grid-cell biology: synchronisation in biophysical models

Modelling studies of upper ocean phenomena, such as that of the spatial and temporal patchiness in plankton distributions, typically employ coupled biophysical models, with biology in each grid-cell represented by a plankton ecosystem model. It has not generally been considered what impact the choice of grid-cell ecosystem model, from the many developed in the literature, might have upon the results of such a study. We use the methods of synchronisation theory, which is concerned with ensembles of interacting oscillators, to address this question, considering the simplest possible case of a chain of identically represented interacting plankton grid-cells. It is shown that the ability of the system to exhibit stably homogeneous (fully synchronised) dynamics depends crucially upon the choice of biological model and number of grid-cells, with dynamics changing dramatically at a threshold strength of mixing between grid-cells. Consequently, for modelling studies of the ocean the resolution chosen, and therefore number of grid-cells used, could drastically alter the emergent features of the model. It is shown that chaotic ecosystem dynamics, in particular, should be used with care.

Global phylogeography of the scalloped hammerhead shark (Sphyrna lewini)

Large marine fishes typically have little population genetic structure. The exceptions are associated with sedentary behaviour, disjunct distributions, or reproductive philopatry. Scalloped hammerhead sharks (Sphyrna lewini) incorporate the contrasting traits of oceanic habitat (usually associated with high dispersal) and possible fidelity to nursery grounds (for reproductive females). To evaluate the expectations of these contrasting behaviours, we examined the global genetic structure of S. lewini based on collections (n = 271 individuals) from 20 nursery areas. A 548-bp fragment of mitochondrial DNA control region revealed 22 polymorphic sites, 24 haplotypes, and three lineages distinguished by 2.56-3.77% sequence divergence. Coalescence analyses based on a provisional molecular clock indicate an origin in the Indo-West Pacific with late Pleistocene radiations into the central Pacific (Hawaii) and eastern Pacific (Central America), as well as recent interchange between oceans via southern Africa. Population subdivisions are strong (overall Phi(ST) = 0.749, P < 0.0001 and among oceans Phi(ST) = 0.598, P < 0.0098). Genetic discontinuity within oceans (Phi(ST) = 0.519, P < 0.0001) is primarily associated with oceanic barriers (migration across oceans M approximately 0), with much less structure along continental margins (M > 10). We conclude that nursery populations linked by continuous coastline have high connectivity, but that oceanic dispersal by females is rare. Although we cannot rule out philopatry to natal nurseries, oceanic barriers appear to have a much stronger influence on the genetic architecture of this species and may indicate a mechanism for recent evolutionary radiations in the genus Sphyrna.

Sirolimus conversion after liver transplantation: improvement in measured glomerular filtration rate after 2 years

METHODS

We reviewed our prospectively maintained database of 2005 liver transplantations. Therapy was either started de novo or converted from calcineurin inhibitors (CNIs) to sirolimus as the main immunosuppressive agent for nephrotoxicity or rejection. Glomerular filtration rate (GFR) was determined with iodine 125-labeled sodium isthalamate (Glofil-125), and serum creatinine concentration was obtained before and 3 months after transplantation, and yearly in both groups. Sirolimus levels were 10 to 15 ng/mL in patients at less than 3 months after transplantations and 5 to 10 ng/mL in the remaining patients. All patients received mycophenolate mofetil as maintenance therapy.

RESULTS

Data for 29 patients in the de novo group and 35 in the conversion group were reviewed. Patients in the de novo group demonstrated an acute cellular rejection rate of 17.2%, 40% of which were steroid resistant. In this group, 48.2% discontinuation of sirolimus was necessary because of adverse effects. Patients in the conversion group demonstrated an acute cellular rejection rate of 2.8% and a 34.3% rate of sirolimus discontinuation. Seventeen (56.7%) patients at 1 year and 8 (44.4%) patients at 2 years demonstrated continued improvement in GFR. In the conversion group, case-control analysis did not demonstrate a significant difference in GFR and serum creatinine concentration (P > .05) at 1 and 2 years after conversion. At the time of review, no patients in the conversion group required hemodialysis.

CONCLUSIONS

Conversion to sirolimus therapy is an effective strategy in improving renal function in patients with CNI-induced nephrotoxicity and can be done without increased rejection. Most of our patients (65.7%) tolerated sirolimus conversion. Of these, 56.7% and 44.4% demonstrated continued increase in GFR with the CNI-free regimen at 1 and 2 years, respectively. Long-term, large-population, prospective, randomized, controlled studies should further validate these results.

An interspecific comparison of foraging range and nest density of four bumblebee (Bombus) species

Bumblebees are major pollinators of crops and wildflowers in northern temperate regions. Knowledge of their ecology is vital for the design of effective management and conservation strategies but key aspects remain poorly understood. Here we employed microsatellite markers to estimate and compare foraging range and nest density among four UK species: Bombus terrestris, Bombus pascuorum, Bombus lapidarius, and Bombus pratorum. Workers were sampled along a 1.5-km linear transect across arable farmland. Eight or nine polymorphic microsatellite markers were then used to identify putative sisters. In accordance with previous studies, minimum estimated maximum foraging range was greatest for B. terrestris (758 m) and least for B. pascuorum (449 m). The estimate for B. lapidarius was similar to B. pascuorum (450 m), while that of B. pratorum was intermediate (674 m). Since the area of forage available to bees increases as the square of foraging range, these differences correspond to a threefold variation in the area used by bumblebee nests of different species. Possible explanations for these differences are discussed. Estimates for nest density at the times of sampling were 29, 68, 117, and 26/km2 for B. terrestris, B. pascuorum, B. lapidarius and B. pratorum, respectively. These data suggest that even among the most common British bumblebee species, significant differences in fundamental aspects of their ecology exist, a finding that should be reflected in management and conservation strategies.

Spatial variation in Streptomyces genetic composition and diversity in a prairie soil

Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m2). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.

A Malthusian curb on spatial structure in microorganism populations

That all organisms are born in the company of a parent but die alone is a fundamental biological asymmetry. It has been suggested that this provides a deep-rooted source of spatial pattern formation for microorganisms even at the scale of the population. Such a theory, however, neglects the strong influence in nature of the limited and spatially variable availability of food. The tendency, first recognized by Thomas Malthus in the 18th century, of a population to out-strip its food resources will eventually lead, through local starvation, to the suppression of a heterogeneity growing within a population. Using a generic model it is demonstrated that including local food limitation of breeding strongly dampens spatial structure otherwise resulting from birth and death. The extent of this damping is shown to be a function of the strength of the coupling between organisms and their food and of the total abundance of organic material. Moreover, this work provides an example of a density-dependent process acting to diminish spatial structure rather than to create it and highlights the rich variety of behaviour that is missed by continuum models which fail to represent such local dynamics.

Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution

Integrons are horizontal gene transfer (HGT) systems containing elements necessary for site-specific recombination and expression of foreign DNA. The overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. This report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. First, using culture-independent techniques, we explored the diversity of integrons and integron-transferred genes in heavy-metal-contaminated mine tailings. Using degenerate primers, we amplified integron integrase genes from the tailings. We discovered 14 previously undescribed integrase genes, including six novel gene lineages. In addition, we found 11 novel gene cassettes in this sample. One of the gene cassettes that we sequenced is similar to a gene that codes for a step in a pathway for nitroaromatic catabolism, a group of compounds associated with mining activity. This suggests that integrons may be important for gene transfer in response to selective pressures other than the presence of antibiotics. We also investigated the evolution of integrons by statistically comparing the phylogenies of 16S rRNA and integrase genes from the same organisms, using sequences from GenBank and various sequencing projects. We found significant differences between the organismal (16S rRNA) and integrase trees, and we suggest that these differences may be due to HGT.

Molecular and metabolic characterization of cold-tolerant alpine soil Pseudomonas sensu stricto

Alpine soils undergo dramatic temporal changes in their microclimatic properties, suggesting that the bacteria there encounter uncommon shifting selection gradients. Pseudomonads constitute important members of the alpine soil community. In order to characterize the alpine Pseudomonas community and to assess the impact of shifting selection on this community, we examined the ability of cold-tolerant Pseudomonas isolates to grow on a variety of carbon sources, and we determined their phylogenetic relationships based on 16S ribosomal DNA sequencing. We found a high prevalence of Pseudomonas in our soil samples, and isolates from these soils exhibited extensive metabolic diversity. In addition, our data revealed that many of our isolates form a unique cold-adapted clade, representatives of which are also found in the Swedish tundra and Antarctica. Our data also show a lack of concordance between the metabolic properties and 16S phylogeny, indicating that the metabolic diversity of these organisms cannot be predicted by phylogeny.

Choosing among alternative trees of multigene families

Estimation of gene trees is the first step in testing alternative hypotheses about the evolution of multigene families. The standard practice for inferring gene family history is to construct trees that meet some objective criteria based on the fit of the character state changes (nucleotide or amino acid changes) to the gene tree. Unfortunately, analysis of character state data can be misleading. In addition, this approach ignores information about the relationships of the species from which the genes have been sampled. In this paper I explore using statistics of fit between the character data and gene trees and the reconciliation of the gene and species trees for choosing among alternative evolutionary hypotheses of gene families. In particular, I advocate a two-pronged strategy for choosing among alternative gene trees. First, the character data are used to define a set of acceptable gene trees (i.e., trees that are not significantly different from the minimum length tree). Next, the set of acceptable gene trees is reconciled with a known species tree, and the gene tree requiring the fewest number of gene duplications and losses is adopted as the best estimate of evolutionary history. The approach is illustrated using three gene families: BMP, EGR, and LDH.

Regional endemism and cryptic species revealed by molecular and morphological analysis of a widespread species of Neotropical catfish

The lower Central American landscape was fully emergent approximately three million years ago, an event which marked the beginning of the Great American biotic interchange. Freshwater fishes participated in the biotic interchange. Because primary freshwater fishes are restricted to freshwater, they provide an excellent system for investigating the interplay of historical and recent processes on the assembly, structure and diversity of the regions' aquatic ecosystems. We focused on examining the history of diversification for a species of catfish (Pimelodella chagresi) whose distribution spans multiple, isolated drainage basins across the Isthmian landscape and into north-western South America. Analysis of mitochondrial DNA haplotypes and morphological traits indicated that P. chagresi, as currently recognized, comprises a species complex. In addition, along the Pacific slope of Panama, repeated dispersion, diversification, extinction and possibly hybridization are thought to underlie a complex distribution of haplotypes. Overall, the results underscore the tremendous importance of historical processes on regional biodiversity.

Substitution rates of organelle and nuclear genes in sharks: implicating metabolic rate (again)

Rates of nucleotide substitution for nuclear genes are thought to be governed primarily by the number of germ line replication events (the so-called "generation time" hypothesis). In contrast, rates of mitochondrial DNA evolution appear to be set primarily by DNA damage pathways of mutation mediated by mutagenic by-products of oxidative phosphorylation (the so-called "metabolic-rate" hypothesis). Comparison of synonymous substitution rates estimated for the mitochondrial cytochrome b gene and nuclear-encoded dlx, hsp70, and RAG-1 genes in mammals and sharks shows that rates of molecular evolution for sharks are approximately an order of magnitude slower than those for mammals for both nuclear and mitochondrial genes. In addition, there is significant positive covariation of substitution rate for mitochondrial and nuclear genes within sharks. These results, interpreted in light of the pervasiveness of DNA damage by mutagenic by-products of oxygen metabolism to both nuclear and mitochondrial genes and coupled with increasing evidence for cross-genome activity of DNA repair enzymes, suggest that molecular clocks for mitochondrial and nuclear genes may be set primarily by common mutational mechanisms.

Comparative mtDNA phylogeography of neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America

Historical biogeography seeks to explain contemporary distributions of taxa in the context of intrinsic biological and extrinsic geological and climatic factors. To decipher the relative importance of biological characteristics vs. environmental conditions, it is necessary to ask whether groups of taxa with similar distributions share the same history of diversification. Because all of the taxa will have shared the same climatic and geological history, evidence of shared history across multiple species provides an estimate of the role of extrinsic factors in shaping contemporary biogeographic patterns. Similarly, differences in the records of evolutionary history across species will probably be signatures of biological differences. In this study, we focus on inferring the evolutionary history for geographical populations and closely related species representing three genera of primary freshwater fishes that are widely distributed in lower Central America (LCA) and northwestern Colombia. Analysis of mitochondrial gene trees provides the opportunity for robust tests of shared history across taxa. Moreover, because mtDNA permits inference of the temporal scale of diversification we can test hypotheses regarding the chronological development of the Isthmian corridor linking North and South America. We have focused attention on two issues. First, we show that many of the distinct populations of LCA fishes diverged in a relatively brief period of time thus limiting the phylogenetic signal available for tests of shared history. Second, our results provide reduced evidence of shared history when all drainages are included in the analysis because of inferred dispersion events that obscure the evolutionary history among drainage basins. When we restrict the analysis to areas that harbour endemic mitochondrial lineages, there is evidence of shared history across taxa. We hypothesize that there were two to three distinct waves of invasion into LCA from putative source populations in northwestern Colombia. The first probably happened in the late Miocene, prior to the final emergence of the Isthmus in the mid-Pliocene; the second was probably coincident with the rise of the Isthmus in the mid-Pliocene, and the third event occurred more recently, perhaps in the Pleistocene. In each case the geographical scale of the dispersion of lineages was progressively more limited, a pattern we attribute to the continuing development of the landscape due to orogeny and the consequent increase in the insularization of drainage basins. Thus, the fisheye view of LCA suggests a complex biogeographic history of overlaid cycles of colonization, diversification, sorting and extinction of lineages.

Systematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequences

Central American cichlids allied to the genus "Cichlasoma" are thought to be of South American ancestry. The group has apparently undergone extensive morphological, ecological, and behavioral differentiation in Central America following colonization. Uncertainties regarding the systematics of the group and the timing of colonization complicate interpretation of the biological history of cichlids in Central America. We determined complete cytochrome b gene sequences for 54 individual cichlids representing 21 species to test hypotheses regarding the time of origin and pattern of diversification of lower Central American cichlids. The data also bear on issues relating to the systematics and taxonomy of heroine cichlids. Our results suggest that cichlids have been in Central America since the middle to late Miocene. Moreover, the data provide evidence of a rapid radiation early in the history of the group. Similar ecomorphological types have evolved multiple times. Inferences of convergent morphological evolution may, in part, explain a lack of concordance between the mitochondrial gene tree and previous inferences of phylogenetic relationships based on observable characteristics. Phylogenetic inferences based on the molecular data provide support for the recognition of "sections" [erected by Regan (1905) and others] as distinct genera and suggest that thorough revision of Central American cichlids is necessary before the extent of biological diversity within the group can be fully appreciated.

Mitochondrial DNA sequence evolution in sharks: rates, patterns, and phylogenetic inferences

Abundant representation of sharks in the fossil record makes this group a superb system in which to investigate rates and patterns of molecular evolution and to explore the strengths and weaknesses of phylogenetic inferences from molecular data. In this report, the molecular evolution of the cytochrome b gene in sharks is described and the information related to results from phylogenetic analysis of the data evaluated in the light of a phylogeny derived independently of the molecular data. Across divergent lineages of sharks there is evidence for significant substitution rate variation, departure from compositional equilibrium, and substantial homoplasy; nevertheless, the signal of evolutionary history is evident in patterns of shared transversions and amino acid replacements.

Metabolic rate and directional nucleotide substitution in animal mitochondrial DNA

There is marked heterogeneity of nucleotide composition in mitochondrial DNA across divergent animals. Differences in nucleotide composition presumably reflect differences in directional nucleotide substitution for A+T or G+C nucleotides. In mitochondrial DNA, there is A+T directional nucleotide substitution in most (if not all) animals surveyed, and the magnitude of directional A+T nucleotide substitution differs greatly within and among groups. Differences in directional nucleotide substitution among lineages of mammals can be explained by changes in metabolic physiology. This relationship is thought to be mediated by the effect of oxygen radicals because these toxic compounds are by-products of aerobic metabolism and are known mutagens. Association between metabolism and nucleotide composition provides additional evidence in favor of the hypothesis that rates and patterns of nucleotide substitution in mitochondrial DNA can be influenced by factors that impinge on rates of endogenous DNA damage.

Protein evolution in different cellular environments: cytochrome b in sharks and mammals

DNA sequences for the mitochondrial cytochrome b gene were determined for 13 species of sharks. Rates and patterns of amino acid replacement are compared for sharks and mammals. Absolute rates of cytochrome b evolution are six times slower in sharks than in mammals. Bivariate plots of the number of nonsynonymous and silent transversions are indistinguishable in the two groups, however, suggesting that the differences in amino acid replacement rates are due primarily to differences in DNA substitution rates. Patterns of amino acid replacement are also similar in the two groups. Conserved and variable regions occur in the same parts of the cytochrome b gene, and there is little evidence that the types of amino acid changes are significantly different between the groups. Similarity in the relative rates and patterns of protein change between the two groups prevails despite dramatic differences in the cellular environments of sharks and mammals. Poor penetrance of physiological differences through to rates of protein evolution provides support for the neutral theory and suggests that, for cytochrome b, patterns of evolution have been relatively constant throughout much of vertebrate history.

Body size, metabolic rate, generation time, and the molecular clock

There is increasing evidence for variation in rates of nucleotide substitution among divergent taxonomic groups. Here, we summarize published rate data and show a strong relationship between substitution rate and body size. For instance, rates of nuclear and mtDNA evolution are slow in whales, intermediate in primates, and fast in rodents. A similar relationship exists for poikilothermic vertebrates. However, these taxa have slower mtDNA substitution rates overall than do homeotherms of similar size. A number of physiological and life history variables are highly correlated with body size. Of these, generation time and metabolic rate explain some patterns of rate heterogeneity equally well. In many cases, however, differences in metabolic rate explain important exceptions to the generation time model. Correlation between metabolic rate and nucleotide substitution may be mediated by (i) the mutagenic effects of oxygen radicals that are abundant by-products of aerobic respiration, and (ii) increased rates of DNA synthesis and nucleotide replacement in organisms with higher metabolic rates. Both of these factors increase mutation rate by decreasing the "nucleotide generation time," the average length of time before a nucleotide is copied either through replication or repair. Reconsideration of the generation time hypothesis to include physiological effects such as metabolic rate improves the theoretical underpinnings of molecular evolution.

Rates of mitochondrial DNA evolution in sharks are slow compared with mammals

The rate of mitochondrial DNA (mtDNA) evolution has been carefully calibrated only in primates. Similarity between the primate calibration and rates estimated for other vertebrates has led to widespread assumption of a constant molecular clock in vertebrates even though this has never been rigorously tested. We report here the examination of mtDNA sequence variation for 13 species of sharks from two orders that are well represented in the fossil record to test the constancy hypothesis. Nucleotide substitution rates in the cytochrome b and cytochrome oxidase I genes in sharks are seven- to eightfold slower than in primates or ungulates. This difference in substitution rate cannot be explained by nucleotide composition bias, codon-usage bias, selection, or choice of genes sequenced, and was confirmed by comparing species recently separated by the rise of the Isthmus of Panama. Such differences in mtDNA substitution rates among taxa indicate that it is inappropriate to use a calibration for one group to estimate divergence times or demographic parameters for another group. High-resolution studies of molecular evolutionary rates require taxon-specific calibrations.

Anatomical barriers in endodontics

Endodontic therapy can be challenging at the diagnostic and technical levels. The more one can advance one's accomplishments, the more that would-be barriers cease to be so. Difficult aspects of tooth isolation and assessment of root integrity can be rendered less problematic by some relatively simple methods. Gaining a clear awareness of the internal layout of a coronal chamber and any possible inclusions can be assisted by use of a modified endodontic explorer. It can be usefully employed to resolve with certainty the common dilemma of whether openings at the base of a molar or maxillary premolar coronal access cavity are exposures in the pulp chamber roof or orifices in the chamber floor. Locating and then gaining full working length entry into partly calcified canals, even when they are not radiographically discernible, remains one of the difficult tasks in endodontic therapy, but methods can be implemented that maximize their successful negotiation and management. The use of fine engine-driven reamers, but absolutely restricted to a reciprocating action handpiece, is described.

Effect of aging on the oxidative phosphorylation pathway

The proposed study was undertaken to investigate the effect of aging on control of the oxidative phosphorylation pathway. Flux control coefficients for adenine nucleotide translocase and cytochrome c oxidase were determined using the procedure of Groen et al. [J. Biol. Chem., 257 (1982) 137-144]. Hepatic mitochondrial fractions from Fischer 344 rats were isolated from control (average age 6.5 months), and aged (average age 27.3 months) groups. No aging-related changes in the extent of control of respiration by the oxidase were obtained, however, differences were observed for the translocase. For the control group of animals, the greatest regulation occurred at 80-85% maximal respiratory rates, and declined at higher rates. For the aged group, a similar flux control coefficient was obtained at 80-85% respiration, but was maintained as respiration increased to maximal rates. It is proposed that changes in the flux control coefficients at maximal respiratory rates are associated with an aging-related decrease in translocase activity. Evaluation of translocase content revealed no significant differences between the two groups supporting the concept that the decreased activity was not due to decreased content. During the course of these experiments, it also became apparent that there was a significant aging-related decrease in the rate of succinate oxidation providing an adequate supply of ADP was present. No significant changes in respiratory rates, or RCR, were evident at suboptimal concentrations of ADP as reported previously from this laboratory [Vorbeck, M.L. et al., Arch. Biochem. Biophys., 214 (1982) 67-79]. Since similar decreases in respiration were obtained upon addition of an uncoupler, the aging-related changes in respiration are attributed to differences at the level of the electron transport system, including its associated reactions. The aging-related differences in respiratory rates, and extent of control of respiration, were both observed under conditions of maximal stimulation of respiration. This suggests an inability of mitochondria from aged animals to respond to the increased demands of oxidation. Basic to these differences may be the lipid-membrane associated changes seen during aging.

Influence of Ca2+ on the plasma membrane potential and electrogenic uptake of glycine by myeloma cells. Involvement of a Ca2+-activated K+ channel

The involvement of Ca2+-activated K+ channels in the regulation of the plasma membrane potential and electrogenic uptake of glycine in SP 2/0-AG14 lymphocytes was investigated using the potentiometric indicator 3,3'-diethylthiodicarbocyanine iodide. The resting membrane potential was estimated to be -57 +/- 6 mV (n = 4), a value similar to that of normal lymphocytes. The magnitude of the membrane potential and the electrogenic uptake of glycine were dependent on the extracellular K+ concentration, [K+]o, and were significantly enhanced by exogenous calcium. The apparent Vmax of Na+-dependent glycine uptake was doubled in the presence of calcium, whereas the K0.5 was not affected. Ouabain had no influence on the membrane potential under the conditions employed. Additional criteria used to demonstrate the presence of Ca2+-activated K+ channels included the following: (1) addition of EGTA to calcium supplemented cells elicited a rapid depolarization of the membrane potential that was dependent on [K+]o; (2) the calmodulin antagonist, trifluoperazine, depolarized the membrane potential in a dose-dependent and saturable manner with an IC50 of 9.4 microM; and (3) cells treated with the Ca2+-activated K+ channel antagonist, quinine, demonstrated an elevated membrane potential and depressed electrogenic glycine uptake. Results from the present study provide evidence for Ca2+-activated K+ channels in SP 2/0-AG14 lymphocytes, and that their involvement regulates the plasma membrane potential and thereby the electrogenic uptake of Na+-dependent amino acids.

An ELISA for screening hybridoma cultures for monoclonal antibodies against a detergent solubilized integral membrane protein

A method is described for the binding of a detergent solubilized integral membrane protein to polystyrene immunoassay plates. Addition of Bouin's fluid, a histochemical fixative, to wells of plates containing the detergent solubilized antigen, followed by low speed centrifugation, is sufficient to promote binding of antigen in the presence of Triton X-100 concentrations as high as 1.75%. The binding of antigen is rapid and the entire binding procedure, including removal of fixative and washing of the plates, can be accomplished in less than 15 min. Immunological specificity of the bound antigen is retained. This method has been used to effectively screen hybridoma cultures for specific antibodies.

Ca2+ release from energetically coupled tumor mitochondria

A Na+/Ca2+ exchange activity for Ca2+ efflux has been identified in isolated Ehrlich ascites tumor mitochondria. Further, under conditions favoring cycling of Ca2+ across the mitochondrial inner membrane, extramitochondrial [Ca2+] also was shown to be Na+-dependent. The Na+/Ca2+ exchange showed sigmoidal kinetics with a mean (+/-SD) [Na+] required for half maximal stimulation of Ca2+ efflux of 8.4 +/- 3.8 mM and a Hill coefficient of 1.6. Na+/Ca2+ exchange was very sensitive to inhibition by the Ca2+ antagonist diltiazem (56% inhibition at 7.5 nmoles X mg protein-1) whereas a number of other compounds, including verapamil, nupercaine, and trifluoperazine were less effective in inhibiting Ca2+ efflux. These data demonstrate for the first time the presence of a pathway in tumor mitochondria for unidirectional Ca2+ efflux induced by Na+, and provide a mechanism for regulation of tumor intra- and extramitochondrial [Ca2+]. Results of the present study support the need for further study of intracellular Na+ and its role in regulation of Ca2+ homeostasis in tumor cells.

Ca2+-dependent depolarization of energized mitochondrial membrane potential by chlortetracycline (aureomycin)

The addition of chlortetracycline (CTC) to succinate-energized rat liver mitochondria resulted in depolarization of the membrane potential and decreased respiratory control. CTC inhibited both processes at concentrations that were half maximally effective at approximately 13 and 16 microM, respectively. These inhibitory effects were prevented by either the Ca2+ chelator, ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid, or the inhibitor of mitochondrial Ca2+ influx, ruthenium red. These findings are consistent with the formation of a membrane associated calcium-CTC complex and suggest that CTC can alter mitochondrial energy metabolism during transmembrane Ca2+ cycling.