PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes

Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential for many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have focused on specific clades, with greatest attention paid to plants, animals, and fungi. The rapid increase in high-throughput sequencing (HTS) data from diverse lineages now provides opportunities to estimate evolutionary relationships and gene family evolution across the eukaryotic tree of life. At the same time, these types of data are known to be error-prone (e.g., substitutions, contamination). To address these opportunities and challenges, we have refined a phylogenomic pipeline, now named PhyloToL, to allow easy incorporation of data from HTS studies, to automate production of both MSAs and gene trees, and to identify and remove contaminants. PhyloToL is designed for phylogenomic analyses of diverse lineages across the tree of life (i.e., at scales of >100 My). We demonstrate the power of PhyloToL by assessing stop codon usage in Ciliophora, identifying contamination in a taxon- and gene-rich database and exploring the evolutionary history of chromosomes in the kinetoplastid parasite Trypanosoma brucei, the causative agent of African sleeping sickness. Benchmarking PhyloToL’s homology assessment against that of OrthoMCL and a published paper on superfamilies of bacterial and eukaryotic organellar outer membrane pore-forming proteins demonstrates the power of our approach for determining gene family membership and inferring gene trees. PhyloToL is highly flexible and allows users to easily explore HTS data, test hypotheses about phylogeny and gene family evolution and combine outputs with third-party tools (e.g., PhyloChromoMap, iGTP).

The ties that bind: perceived social support, stress, and IBS in severely affected patients

BACKGROUND

This study assessed the association between social support and the severity of irritable bowel syndrome (IBS) symptoms in a sample of severely affected IBS patients recruited to an NIH-funded clinical trial. In addition, we examined if the effects of social support on IBS pain are mediated through the effects on stress.

METHODS

Subjects were 105 Rome II diagnosed IBS patients (F = 85%) who completed seven questionnaires which were collected as part of a pretreatment baseline assessment.

KEY RESULTS

Partial correlations were conducted to clarify the relationships between social support and clinically relevant variables with baseline levels of psychopathology, holding constant number of comorbid medical diseases, age, gender, marital status, ethnicity, and education. Analyses indicated that social support was inversely related to IBS symptom severity. Social support was positively related with less severe pain. A similar pattern of data was found for perceived stress but not quality of life impairment. Regression analyses examined if the effects of social support on pain are mediated by stress. The effects of social support on bodily pain were mediated by stress such that the greater the social support the less stress and the less pain. This effect did not hold for symptom severity, quality of life, or psychological distress.

CONCLUSIONS & INFERENCES

This study links the perceived adequacy of social support to the global severity of symptoms of IBS and its cardinal symptom (pain). It also suggests that the mechanism by which social support alleviates pain is through a reduction in stress levels.

The ties that bind: perceived social support, stress, and IBS in severely affected patients

BACKGROUND

This study assessed the association between social support and the severity of irritable bowel syndrome (IBS) symptoms in a sample of severely affected IBS patients recruited to an NIH-funded clinical trial. In addition, we examined if the effects of social support on IBS pain are mediated through the effects on stress.

METHODS

Subjects were 105 Rome II diagnosed IBS patients (F = 85%) who completed seven questionnaires which were collected as part of a pretreatment baseline assessment.

KEY RESULTS

Partial correlations were conducted to clarify the relationships between social support and clinically relevant variables with baseline levels of psychopathology, holding constant number of comorbid medical diseases, age, gender, marital status, ethnicity, and education. Analyses indicated that social support was inversely related to IBS symptom severity. Social support was positively related with less severe pain. A similar pattern of data was found for perceived stress but not quality of life impairment. Regression analyses examined if the effects of social support on pain are mediated by stress. The effects of social support on bodily pain were mediated by stress such that the greater the social support the less stress and the less pain. This effect did not hold for symptom severity, quality of life, or psychological distress.

CONCLUSIONS & INFERENCES

This study links the perceived adequacy of social support to the global severity of symptoms of IBS and its cardinal symptom (pain). It also suggests that the mechanism by which social support alleviates pain is through a reduction in stress levels.

Motility of the antroduodenum in healthy and gastroparetics characterized by wireless motility capsule

BACKGROUND

The wireless motility capsule (WMC) measures intraluminal pH and pressure, and records transit time and contractile activity throughout the gastrointestinal tract. Our hypothesis is that WMC can differentiate antroduodenal pressure profiles between healthy people and patients with upper gut motility dysfunctions. This study aims to analyze differences in the phasic pressure profiles of the stomach and small intestine in healthy and gastroparetic subjects.

METHODS

Data from 71 healthy and 42 gastroparetic subjects were analyzed. The number of contractions (Ct), area under the pressure curve and motility index (MI = Ln (Ct *sum amplitudes +1)) were analyzed for 60 min before gastric emptying of the capsule (GET), (gastric window) and after GET (small bowel window) and results between groups were compared with the Wilcoxon rank sum test.

KEY RESULTS

Significant differences were observed between healthy and gastroparetic subjects for Ct and MI (P < 0.05). Median values of the motility parameters in gastric window were Ct = 72, MI = 11.83 for healthy and Ct = 47, MI = 11.12 for gastroparetics. In the small bowel, median values were Ct = 144.5, MI = 12.78 for healthy and Ct = 93, MI = 12.12 for gastroparetics. Diabetic subjects with gastroparesis showed significantly lower Ct and MI compared with healthy subjects in both gastric and small bowel windows while idiopathic gastroparetic subjects did not show significant differences.

CONCLUSIONS & INFERENCES

The WMC is able to differentiate between healthy and gastroparetic subjects based on gastric and small bowel motility profiles.

The assessment of regional gut transit times in healthy controls and patients with gastroparesis using wireless motility technology

BACKGROUND

Wireless pH and pressure motility capsule (wireless motility capsule) technology provides a method to assess regional gastrointestinal transit times.

AIMS

To analyse data from a multi-centre study of gastroparetic patients and healthy controls and to compare regional transit times measured by wireless motility capsule in healthy controls and gastroparetics (GP).

METHODS

A total of 66 healthy controls and 34 patients with GP (15 diabetic and 19 idiopathic) swallowed wireless motility capsule together with standardized meal (255 kcal). Gastric emptying time (GET), small bowel transit time (SBTT), colon transit time (CTT) and whole gut transit time (WGTT) were calculated using the wireless motility capsule.

RESULTS

Gastric emptying time, CTT and WGTT but not SBTT were significantly longer in GP than in controls. Eighteen percent of gastroparetic patients had delayed WGTT. Both diabetic and idiopathic aetiologies of gastroparetics had significantly slower WGTT (P < 0.0001) in addition to significantly slower GET than healthy controls. Diabetic gastroparetics additionally had significantly slower CTT than healthy controls (P = 0.0054).

CONCLUSIONS

In addition to assessing gastric emptying, regional transit times can be measured using wireless motility capsule. The prolongation of CTT in gastroparetic patients indicates that dysmotility beyond the stomach in GP is present, and it could be contributing to symptom presentation.

Comparison of gastric emptying of a nondigestible capsule to a radio-labelled meal in healthy and gastroparetic subjects

BACKGROUND

Gastric emptying scintigraphy (GES) using a radio-labelled meal is used to measure gastric emptying. A nondigestible capsule, SmartPill, records luminal pH, temperature, and pressure during gastrointestinal transit providing a measure of gastric emptying time (GET).

AIMS

To compare gastric emptying time and GES by assessing their correlation, and to compare GET and GES for discriminating healthy subjects from gastroparetics.

METHODS

Eighty-seven healthy subjects and 61 gastroparetics enrolled with simultaneous SmartPill and GES. Fasted subjects were ingested capsule and [(99m)Tc]-SC radio-labelled meal. Images were obtained every 30 min for 6 h. Gastric emptying time and percentage of meal remaining at 2/4 h were determined for each subject. The sensitivity/specificity and receiver operating characteristic analysis of each measure were determined for each subject.

RESULTS

Correlation between GET and GES-4 h was 0.73 and GES-2 h was 0.63. The diagnostic accuracy from the receiver operating characteristic curve between gastroparetics and healthy subjects was GET = 0.83, GES-4 h = 0.82 and GES-2 h = 0.79. The 300-min cut-off time for GET gives sensitivity of 0.65 and specificity of 0.87 for diagnosis of gastroparesis. The corresponding sensitivity/specificity for 2 and 4 h standard GES measures were 0.34/0.93 and 0.44/0.93, respectively.

CONCLUSION

SmartPill GET correlates with GES and discriminates between healthy and gastroparetic subjects offering a nonradioactive, standardized, ambulatory alternative to scintigraphy.

Non-Mendelian inheritance of paralogs of 2 cytoskeletal genes in the ciliate Chilodonella uncinata

Recognition of the role of non-Mendelian inheritance is on the rise, particularly as epigenetic phenomena are shown to shape the transformation of genomes into phenotypes. Ciliates provide a model system in which to explore the role of epigenetics because ciliates have both a germ line (micronuclear) and somatic (macronuclear) genome within every cell. In the ciliate Chilodonella uncinata, the macronucleus is extensively fragmented such that many genes end up on their own chromosomes. Hence, it is possible to track the fate of unlinked genes within macronuclei of C. uncinata. Here we demonstrate that the pattern of inheritance in isolates of C. uncinata is complex and involves both Mendelian transmission between micronuclei and macronuclei and epigenetic phenomena. The macronuclei from 2 isolates of C. uncinata and their progeny share identical rDNA loci and 2 identical beta-tubulin paralogs, yet have different actin paralogs and some beta-tubulin paralogs that are not shared. We propose a model in which all the divergent paralogs are present in the ciliate micronuclei. Under this model, different paralogs are retained in developing macronuclei following conjugation. We further speculate that an epigenetic mechanism, such as RNA interference, is involved in selective retention of specific paralogs within lines. This system allows the exploration of epigenetic phenomena that shape somatic genomes and provides parallels to studies of the development of somatic nuclei within animals.

Repeat surfactant therapy for postsurfactant slump

OBJECTIVE

To evaluate repeat surfactant therapy for the treatment of respiratory failure associated with postsurfactant slump in extremely low birth weight infants (ELBW) by characterizing the population of premature infants who develop postsurfactant slump and measuring their response to a secondary course of surfactant therapy.

STUDY DESIGN

A retrospective analysis of a cohort of all patients admitted over a 3-year period with birth weights <1000 g (ELBW infants). Information was collected by chart review and the patients were categorized into three distinct groups for analysis. Initial surfactant only, patients who received surfactant replacement therapy only for respiratory distress syndrome (RDS); repeat surfactant, patients who received both initial surfactant replacement for RDS and repeat surfactant therapy for postsurfactant slump (defined as respiratory failure after 6 days of age), and no surfactant, patients in whom no surfactant was ever administered. A respiratory severity score (RSS) was used to measure the severity of lung disease and response to surfactant therapy.

RESULTS

Over 3 years, there were 165 ELBW infants who could develop postsurfactant slump and be eligible for repeat surfactant therapy. There were 39 infants who never received any surfactant therapy estimated gestational age (EGA) 27.7 +/- 1.7, birth weight 856 +/- 109 g) either at birth or after 6 days of life. There were 126 patients treated for RDS with initial surfactant replacement therapy (EGA 25.6 +/- 1.9 weeks, birth weight 713 +/- 179 g). Out of these RDS patients, 101 improved with an initial course of surfactant therapy (EGA 26 +/- 1.8, birth weight 751 +/- 143 g), but 25 (20% of the patients with RDS) developed postsurfactant slump and received a repeat course of surfactant therapy (EGA 24.7 +/- 1.2, birth weight 647 +/- 120 g). The repeat surfactant group (postsurfactant slump) was significantly more premature and had significantly lower birth weights compared to both the initial surfactant only group and the no surfactant ever group. Logistic regression analysis revealed that lack of antenatal steroids, earlier gestational age, and the receiving of 2 or more doses of surfactant to treat the initial RDS were significantly associated with receiving repeat surfactant therapy for postsurfactant slump. Of the 25 patients treated with a repeat course of surfactant therapy more than 70% of patients (n = 18) had an improvement in their lung disease with a 15% reduction in their RSS. This improvement was significant at all time points evaluated (12, 24, and 48 h).

CONCLUSION

We found that a repeat course of surfactant therapy, after day of life 6, led to a significant improvement in hypoxemic respiratory failure in premature infants with postsurfactant slump. Infants who received repeat surfactant therapy were born at a significantly earlier gestational age, had significantly smaller birth weight and had significantly worse lung disease. They were significantly less likely to have received antenatal steroids and were significantly more likely to have received multiple doses of surfactant to treat their initial RDS. A repeat course of surfactant therapy for patients with postsurfactant slump appeared beneficial in the short-term. These initial findings would support performing randomized control trials of repeat surfactant therapy for postsurfactant slump.

Mutations in PITX2 may contribute to cases of omphalocele and VATER-like syndromes

Omphalocele is a congenital anomaly with substantial morbidity. Rieger syndrome, an autosomal dominant disorder, is characterized by craniofacial abnormalities and abdominal wall defects. PITX2 mutations are etiologic in >40% of cases of Rieger syndrome. We demonstrate that the birth prevalence of omphalocele is significantly higher in Rieger syndrome than in the general population, with omphaloceles found in 0.03% in the Iowa newborn population and 4.3% of patients with Rieger syndrome. Our objective was to screen coding and conserved non-coding regions of PITX2 for mutations in 209 patients with omphalocele. We identified remarkable evolutionarily conserved regions by comparing the 3'UTR of Pitx2 in 13 vertebrate and 3 invertebrate species. No mutations changing the amino acid sequence were found within the omphalocele population. In one case of omphalocele with VATER-like additional anomalies, a three nucleotide deletion was found in the 3'UTR. This deletion was not seen in 1,186 controls. Also in the 3'UTR, we identified a single nucleotide polymorphism at a highly conserved residue. Our findings suggest additional studies of PITX2 conserved regions will be valuable. We also screened the omphalocele cases for mutations in exon 5 of the gene FLNA. Mutations in FLNA have been shown to cause a broad range of congenital malformations, including otopalatodigital syndrome type 2 in which a missense mutation occurring in exon 5 of FLNA results in omphalocele as part of the phenotype. We did not find any mutations in exon 5 of FLNA in 179 omphalocele cases studied.

Genetic structure of the blue ridge dusky salamander (Desmognathus orestes): inferences from allozymes, mitochondrial dna, and behavior

The plethodontid salamander Desmognathus orestes, a member of the D. ochrophaeus species complex, is distributed in southwestern Virginia, eastern Tennessee, and western North Carolina. Previous allozyme analyses indicate that D. orestes consists of two distinct groups of populations (D. orestes 'B' and D. orestes 'C') with extensive intergradation and probable gene flow between these two groups. Spatially varying allele frequencies can reflect historical associations, current gene flow, or a combination of population-level processes. To differentiate among these processes, we use multiple markers to further characterize divergence among populations of D. orestes and assess the degree of intergradation between D. orestes 'B' and D. orestes 'C', specifically investigating variation in allozymes, mitochondrial DNA (mtDNA), and reproductive behavior among populations. On a broad scale, the mtDNA genealogies reconstruct haplotype clades that correspond to the species identified from previous allozyme analyses. However, at a finer geographic scale, the distributions of the allozyme and mtDNA markers for D. orestes 'B' and D. orestes 'C' are discordant. MtDNA haplotypes corresponding to D. orestes 'B' are more broadly distributed across western North Carolina than predicted by allozyme data, and the region of intergradation with D. orestes 'C' indicates asymmetric gene flow of these markers. Asymmetric mating may contribute to observed discordance in nuclear versus cytoplasmic markers. Results support describing D. orestes as a single species and emphasize the importance of using multiple markers to examine fine-scale patterns and elucidate evolutionary processes affecting gene flow when making species-level taxonomic decisions.

Phylogenetic position of Sorogena stoianovitchae and relationships within the class Colpodea (Ciliophora) based on SSU rDNA sequences

The ciliate Sorogena stoianovitchae, which can form a multicellular fruiting body, has been classified based upon its ultrastructure and morphology: the oral and somatic infraciliature of S. stoianovitchae most closely resemble those of members of the order Cyrtolophosidida in the class Colpodea. We characterized the small subunit ribosomal DNA (SSU rDNA) gene sequence from S. stoianovitchae and compared this sequence with those from representatives of all ciliate classes. These analyses placed S. stoianovitchae as either sister to members of the class Nassophorea or Colpodea. In an in-group analysis, including all SSU rDNA sequences from members of the classes Nassophorea and Colpodea and representatives of appropriate outgroups, S. stoianovitchae was always sister to Platyophrya vorax (class Colpodea, order Cyrtolophosidida). However, our analyses failed to support the monophyly of the class Colpodea. Instead, our data suggest that there are essentially three unresolved clades: (1) the class Nassophorea; (2) Bresslaua vorax, Colpoda inflata, Pseudoplatyophrya nana, and Bursaria truncatella (class Colpodea); and (3) P. vorax and S. stoianovitchae (class Colpodea).

Widespread distribution of extensive chromosomal fragmentation in ciliates

Ciliates are a diverse group of eukaryotes characterized by their division of nuclear function into a "germ line" micronucleus and a "somatic" macronucleus. After conjugation, chromosomes in the transcriptionally active macronucleus develop by fragmentation, elimination, and amplification of germ line chromosomes. Extensive chromosomal processing that generates a macronucleus with gene-sized fragments has thus far been well documented in members of only one class of ciliates, the Spirotrichea. Here we establish the broad distribution of extensive fragmentation among members of the class Phyllopharyngea and the genera Metopus (order Armophorida) and Nyctotherus (order Clevelandellida). Moreover, analyses of small-subunit rDNA genealogies indicate that gene-sized chromosomes occur in members of the three separate clades: (1) the class Spirotrichea, (2) the class Phyllopharyngea, and (3) the two orders Clevelandellida and Armophorida. Together, these data indicate that the generation of gene-sized chromosomes is widespread and demonstrate multiple origins of extensive fragmentation within ciliates.

Evolution of nuclear dualism in ciliates: a reanalysis in light of recent molecular data

Ciliates are defined by the presence of dimorphic nuclei. Following conjugation, both the functional macronucleus (MAC) and the transcriptionally inactive germline micronucleus (MIC) develop from a zygotic nucleus. As the MAC develops, germline chromosomes are processed by excision of internal sequences, fragmentation and amplification of the remaining chromosomes. The extent of processing varies among lineages and, in all but one class of ciliates, the resulting MACs divide by an unusual process termed 'amitosis'. Research on these chromosomal rearrangements, largely from studies of only a handful of taxa from two of the nine classes of ciliates, has failed to find evidence of homologous processing among ciliate lineages. This observation, coupled with the structural diversity of MAC genomes among ciliates, led to the hypothesis of multiple origins of at least two MAC properties: (1) the ability to divide and (2) the mechanisms underlying chromosomal processing. Applying this logic to a more inclusive analysis of ciliate lineages, where an even greater diversity of MAC structure is observed, increases the potential number of origins of these MAC characteristics. Here, it is proposed that a single origin of a relatively plastic mechanism underlying MAC development better explains the observed diversity in MAC structure and processing among ciliates. Such a mechanism is suggested by the demonstration of epigenetic effects during MAC development in Paramecium and Tetrahymena.

Survival after multimodality treatment for stage IIIC endometrial cancer

OBJECTIVE

Our purpose was to review our results of multimodality treatment of lymph node metastasis in endometrial cancer (stage IIIC).

STUDY DESIGN

All patients underwent surgical staging for endometrial cancer with complete pelvic and aortic lymphadenectomy. All macroscopic nodal metastases were resected. Patients with microscopic nodal metastasis received adjuvant teletherapy, whereas those with macroscopic nodal metastasis received chemotherapy (carboplatin AUC 5 and paclitaxel 135 mg/m2 every 3 weeks for 6 courses) followed by teletherapy.

RESULTS

Twenty-one patients had stage IIIC disease, and one had stage IVB (inguinal nodal metastasis). Sixty-four percent of tumors were poorly differentiated. Fifty-five percent of patients had pelvic nodal metastasis only and 41% had macroscopic nodal metastasis. At a median follow-up of 3.8 years, 32% of patients had recurrence, all extrapelvic. Overall mean survival was 48 months and progression-free survival was 40 months. Overall survival for microscopic nodal metastasis was >60 months versus 35 months for macroscopic metastasis. Overall survival for pelvic nodal metastasis was 53 months versus 42 months for aorticinguinal metastasis. There were no complications from lymphadenectomy, a 22% chemotherapeutic toxicity, and a 14% radiation toxicity.

CONCLUSION

Our surgical, chemotherapeutic, and radiation treatment protocol for stage IIIC endometrial cancer produced minimal toxicity and good survival.

The Tangled Web: Gene Genealogies and the Origin of Eukaryotes

Accessing data from the genomes of organisms (individual genes) and analyzing these data using sophisticated alignment and phylogenetic methods led to the expectation that we would be able to paint a clear picture of the evolution of eukaryotes. Previous analyses based on morphology and ultrastructure failed to pinpoint both the sister taxon to eukaryotes and the branching order of eukaryotic lineages. However, the expectation that molecular data would provide resolution has not been met since a growing number of gene genealogies present conflicting hypotheses for the origin and diversification of eukaryotes. Instead of reconstructing a simple bifurcating tree of life, these gene genealogies have generated a complex picture of eukaryotic genomes whereby ancient lateral transfers (of individual genes or perhaps even entire genomes) has tangled the evolutionary history of eukaryotes. Resolution of these conflicting genealogies comes in recognizing that eukaryotes are chimeric, containing genetic information from multiple ancestral lineages.

Principles of dialysis: special issues in women

Nephrologists are frequently responsible for the primary care of their female patients. As such, they must be aware of medical issues that are unique to women. Although many of the medical considerations are similar to those in women without renal disease, there are a number of special considerations unique to end-stage renal disease (ESRD) patients. Women comprise a smaller proportion of the dialysis population and have better survival rates than men do. The improved survival is less marked than seen in the general population and may be function of differential susceptibility to disease processes, socio-cultural factors, or gender differences in acceptance or transplantation rates. A variety of factors are important in choosing dialysis modality including lifestyle issues and previous abdominal surgery. Women with ESRD are at high risk of both sexual and gonadal dysfunction, for which the latter may be treated with replacement hormones. Pregnancy is rare and requires an increase in the dose of dialysis and the care of a team of experienced physicians. Finally, awareness and implementation of routine health maintenance recommendations is essential in the care of female dialysis patients.

Prevention and Treatment of Hypertension Study (PATHS): effects of an alcohol treatment program on blood pressure

OBJECTIVE

To determine whether blood pressure is reduced for at least 6 months with an intervention to lower alcohol intake in moderate to heavy drinkers with above optimal to slightly elevated diastolic blood pressure, and whether reduction of alcohol intake can be maintained for 2 years.

DESIGN

A randomized controlled trial.

METHODS

Six hundred forty-one outpatient veterans with an average intake of 3 or more alcoholic drinks per day in the 6 months before entry into the study and with diastolic blood pressure 80 to 99 mm Hg were randomly assigned to a cognitive-behavioral alcohol reduction intervention program or a control observation group for 15 to 24 months. The goal of the intervention was the lower of 2 or fewer drinks daily or a 50% reduction in intake. A subgroup with hypertension was defined as having a diastolic blood pressure of 90 to 99 mm Hg, or 80 to 99 mm Hg if recently taking medication for hypertension.

RESULTS

Reduction in average weekly self-reported alcohol intake was significantly greater (P<.001) at every assessment from 3 to 24 months in the intervention group vs the control group: levels declined from 432 g/wk at baseline by 202 g/wk in the intervention group and from 445 g/wk by 78 g/wk in the control group in the first 6 months, with similar reductions after 24 months. The intervention group had a 1.2/0.7-mm Hg greater reduction in blood pressure than the control group (for each, P = .17 and P = .18) for the 6-month primary end point; for the hypertensive stratum the difference was 0.9/0.7 mm Hg (for each, P = .58 and P = .44).

CONCLUSIONS

The 1.3 drinks per day average difference between changes in self-reported alcohol intake observed in this trial produced only small nonsignificant effects on blood pressure. The results from the Prevention and Treatment of Hypertension Study (PATHS) do not provide strong support for reducing alcohol consumption in nondependent moderate drinkers as a sole method for the prevention or treatment of hypertension.

Characterization of the phosphoglucose isomerase gene from crickets: an analysis of phylogeny, amino acid conservation and nucleotide composition

Although electrophoretic variation in phosphoglucose isomerase (PGI) is often detected in allozyme studies, the Pgi gene has rarely been characterized. Here, I present the cDNA sequence of the Pgi gene from two species of field cricket, Gryllus pennsylvanicus (U65475) and G. veletis (U65476), in which the PGI protein is suspected of being under balancing selection. Phylogenetic analyses support the conclusion that these sequences are truly cricket Pgi. The cricket amino acid sequences are compared to sequences from other taxa to determine conserved residues that may be essential for the function of the protein. Such analysis is necessary as there is no well-resolved structure of the PGI protein. In addition, the compositional bias of cricket Pgi is different from the other animal Pgi genes characterized to date.

Balancing selection on electrophoretic variation of phosphoglucose isomerase in two species of field cricket: Gryllus veletis and G. offnsylvanicus

Two species of crickets, Gryllus veletis and G. pennsylvanicus, share six electrophoretic mobility classes for the enzyme phosphoglucose isomerase (PGI), despite evidence from other genetic markers that the two species are not closely related within eastern North American field crickets. Moreover, the frequencies of the two most common PGI electrophoretic classes (PGI-100 and PGI-65) covary in sympatric populations of these species in the eastern United States, suggesting that PGI may be subject to trans-specific balancing selection. To determine the molecular basis of the electrophoretic variation, we characterized the DNA sequence of the Pgi gene from 29 crickets (15 G. veletis and 14 G. pennsylvanicus). Amino acid substitutions that distinguish the electrophoretic classes are not the same in the two species, and there is no evidence that specific replacement substitutions represent trans-specific polymorphism. In particular, the amino acids that diagnose the PGI-65 allele relative to the PGI-100 allele differ both between G. veletis and G. pennsylvanicus and within G. pennsylvanicus. The heterogeneity among electrophoretic classes that covary in sympatric populations coupled with analysis of patterns of nucleotide variation suggest that Pgi is not evolving neutrally. Instead, the data are consistent with balancing selection operating on an emergent property of the PGI protein.

Transkingdom transfer of the phosphoglucose isomerase gene

Previous analysis of the gene encoding phosphoglucose isomerase (Pgi) suggests that this gene may have been transferred between a eukaryote and a bacterium. However, excluding the alternative hypothesis of ancient gene duplication has proven difficult because of both insufficient sampling of taxa and an earlier misidentification of a bacterial Pgi sequence. This paper presents a phylogenetic analysis of published complete Pgi sequences together with analysis of new partial Pgi sequences from six species of bacteria. The data identify a group of bacterial Pgi sequences, including sequences from Escherichia coli and Haemophilus influenzae, which are more closely related to eukaryotic Pgi sequences than to other bacterial sequences. The topology of gene trees constructed using several different methods are all consistent with the hypothesis of lateral gene transfer and not ancient gene duplication. Furthermore, an estimate of a molecular clock for Pgi dates the divergence of the E. coli and H. influenzae sequences from the animal sequences to between 470 and 650 million years ago, well after other estimates of the divergence between eukaryotes and bacteria. This study provides the most convincing evidence to date of the transkingdom transfer of a nuclear gene.

The small group consensus process for changing physician practices: influenza vaccination

OBJECTIVE

To evaluate the effectiveness of a small group consensus process in enhancing compliance with guidelines for influenza vaccination among older HMO members.

DESIGN

A controlled study of the practice of primary care physicians, with pre/post comparisons and a 2-year follow-up.

SETTING

An 84,000 member prepaid staff model HMO group practice.

PARTICIPANTS

Primary care clinicians (N = 36) practicing in a staff model HMO.

INTERVENTION

A small-group process, including opinion leader, feedback, and group decision making.

MAIN OUTCOME MEASURE

Percentage of patients in a given physician-panel who received influenza immunization.

RESULTS

Improvement in vaccination rate from 60.8% to 72.35% (with further increases over 2 successive years), in the intervention group as compared with improvement in the control from 60.7% to 65.93%.

CONCLUSION

In this model, the small group consensus process resulted in an alteration in physician practice pattern, yielding a significant improvement in immunization rates above the already-established level of 60%.

Receptor-mediated transcytosis of IgA in MDCK cells is via apical recycling endosomes

Classically, the polymeric immunoglobulin receptor and its ligand, IgA, are thought to be sorted from basolateral early endosomes into transcytotic vesicles that directly fuse with the apical plasma membrane. In contrast, we have found that in MDCK cells IgA is delivered from basolateral endosomes to apical endosomes and only then to the apical cell surface. When internalized from the basolateral surface of MDCK cells IgA is found to accumulate under the apical plasma membrane in a compartment that is accessible to two apically added membrane markers: anti-secretory component Fab fragments, and avidin internalized from the biotinylated apical pole of the cell. This accumulation occurs in the presence of apical trypsin, which prevents internalization of the ligand from the apical cell surface. Using a modification of the diaminobenzidine density-shift assay, we estimate that approximately 80% of basolaterally internalized IgA resides in the apical endosomal compartment. In addition, approximately 50% of basolaterally internalized transferrin, a basolateral recycling protein, has access to this apical endosomal compartment and is efficiently recycled back to the basolateral surface. Microtubules are required for the organization of the apical endosomal compartment and it is dispersed in nocodazole-treated cells. Moreover, this compartment is largely inaccessible to fluid-phase markers added to either pole of the cell, and therefore seems analogous to the recycling endosome described in nonpolarized cells. We propose a model in which transcytosis is not a specialized pathway that uses unique transcytotic vesicles, but rather combines portions of pathways used by non-transcytosing molecules.

Combined alpha/beta-blockade versus beta 1-selective blockade in essential hypertension in black and white patients

The purpose of this multicenter investigation was to determine the efficacy and safety of the alpha/beta-blocker labetalol versus the beta 1-selective beta-blocker atenolol in white and black patients with essential hypertension. Equal numbers of black and white patients were enlisted to form four treatment groups (white patients taking either labetalol or atenolol and black patients taking either labetalol or atenolol). Two hundred ninety-two patients (152 white and 140 black patients) with essential hypertension characterized by a standing diastolic blood pressure of 105 to 119 mm Hg (inclusive) were recruited for this trial. Patients were randomized to either labetalol (dosage titrated from 200 to 1600 mg/day) or atenolol (dosage titrated from 50 to 100 mg/day). The therapeutic goal was achievement of a standing diastolic blood pressure of 90 mm Hg or less or a fall of 15 mm Hg in diastolic pressure from baseline value at the end of the placebo run in period. At the end of the study there were no significant differences in blood pressure or heart rate changes in the supine position between the labetalol and atenolol groups. In contrast, labetalol produced greater reduction in both the standing systolic and diastolic blood pressure (-12/-13 mm Hg, respectively) compared with atenolol (-7/-9 mm Hg; p less than 0.05; p less than 0.005, respectively). The greatest decrease in blood pressure was observed in white patients receiving labetalol. In black patients the decrease in blood pressure was greater in those treated with labetalol compared with atenolol, particularly with respect to the systolic blood pressure. We conclude that the alpha 1-blocking property of labetalol provides an additional lowering of the blood pressure over that seen with beta 1-blockade alone, especially in the standing position, and this enhanced efficacy is not confined to one radical group.

Multicenter trial of L-carnitine in maintenance hemodialysis patients. I. Carnitine concentrations and lipid effects

Previous studies have reported conflicting results of carnitine supplementation on plasma lipids in patients with chronic renal failure. We therefore performed a four center, double-blind placebo controlled trial to evaluate the effects of post-hemodialysis intravenous injection of L-carnitine in ESRD patients on maintenance hemodialysis. Thirty-eight patients received up to six months of L-carnitine infusions (20 mg/kg) post-dialysis and 44 patients received placebo infusions. In both groups of patients, baseline pre-dialysis plasma and red blood cell total carnitine levels were normal, but pre-dialysis plasma-free carnitine concentrations and free/total ratios were subnormal, and plasma acyl levels were elevated. Post-dialysis plasma free and total carnitine concentrations were also subnormal. Plasma and red blood cell total carnitine levels rose eightfold in carnitine recipients, but were unchanged from baseline in those receiving placebo. There were no significant changes observed in plasma triglycerides, HDL-cholesterol or other lipoprotein parameters in either the carnitine or placebo treated groups. We conclude that carnitine metabolism is altered in uremia. Furthermore, in a randomly-selected hemodialysis population, L-carnitine injection at the dose of 20 mg/kg results in significant increases in blood (and perhaps tissue) carnitine levels, but this is not associated with any major effects on lipid profiles.

Multicenter trial of L-carnitine in maintenance hemodialysis patients. II. Clinical and biochemical effects

Since carnitine deficiency has been reported in some patients undergoing maintenance hemodialysis, we studied the effects of intravenous infusion of L-carnitine or placebo at the end of each dialysis treatment. The trial, which lasted seven months (one month baseline, 6 months treatment) was multicenter, double blind, placebo controlled, and randomized. Eighty-two long-term hemodialysis patients, who were given either carnitine (N = 38) or placebo (N = 44), completed this study. In each group, clinical and biochemical parameters during treatment were compared with baseline values. Intra-dialytic hypotension and muscle cramps were reduced only in the carnitine treated group, while improvement in post-dialysis asthenia was noticed in both carnitine and placebo groups. Maximal oxygen consumption, measured during a progressive work exercise test, improved significantly in the carnitine group (111 +/- 50 ml/min. P less than 0.03) and was unchanged in the placebo group. L-carnitine treatment was associated with a significant drop in pre-dialysis concentrations of serum urea nitrogen, creatinine and phosphorus (means +/- SEM, 101 +/- 4.5 to 84 +/- 3.9, 16.7 +/- 0.67 to 14.7 +/- 0.64, and 6.4 +/- 0.3 to 5.5 +/- 0.4 mg/dl, respectively, P less than 0.004). No significant changes in any of these variables were noticed in the placebo group. Mid-arm circumference and triceps skinfold thickness were measured in 11 carnitine and 13 placebo treated patients. Calculated mid-arm muscle area increased in the carnitine patients (41.37 +/- 2.68 to 45.6 +/- 2.82 cm2, P = 0.05) and remained unchanged in the placebo patients.(ABSTRACT TRUNCATED AT 250 WORDS)

The hierarchical structure of geriatric patient satisfaction. An Older Patient Satisfaction Scale designed for HMOs

This paper describes an instrument design effort aimed at measuring patient-satisfaction among older (65 years and over) subscribers of HMOs. The study was conducted in a multi-satellite prepaid group practice in Buffalo, New York. In order to be able to construct a satisfaction measure that would reflect the interests of the actual consumers of HMO-services, a series of four focused group interviews were held with 24 randomly selected elderly enrollees. The substantive content of these interviews was systematically analyzed for both topics and ideas, yielding a total of 173 distinct ideas about the perceived satisfaction with the services received expressed over 3,176 lines of narrative. From this substantive pool, sixty attitudinal statements were constructed with the ideas represented in these statements being proportional to the number of lines of transcribed discussion devoted to each topic. This 60-item Older Patient Satisfaction Scale (OPSS) was submitted to a systematic sample of 229 elderly HMO subscribers. They also were asked to complete two existing scales: the Ware PSQ, and the Larsen CSQ-8. Factor analysis performed on the OPSS-items yielded 14 primary factors of geriatric patient satisfaction, two second-order and one third order general factor. As the second-order factors accounted for the largest proportion of the common variance, those items of the original 60-item OPSS were identified that had highest loadings on these second-order factors, yielding 7 such items for one and 5 for the other. These scales had alpha-reliabilities of .83 and .80, respectively. It was also found that the OPSS had good convergent validity with the PSQ and CSQ-8. The overall psychometric properties identified for the OPSS, as well as the fact that it was constructed from a health-care consumer's perspective, makes it well suited for use with a unique and rapidly expanding geriatric patient population.

Relation between phosphate metabolites and oxygen consumption of heart in vivo

The relation between induced increases in cardiac work and phosphate metabolites was investigated in the canine heart in vivo to evaluate the role of ATP hydrolysis products, ADP and inorganic phosphate (Pi), in the control of myocardial oxygen consumption (MVO2). In these studies, myocardial blood flow and oxygen consumption were simultaneously measured with the 31P-nuclear magnetic resonance (NMR)-detected phosphate metabolites. Three protocols were used to increase myocardial work: pacing, epinephrine, and phenylephrine infusions. When these protocols were used, no or only slight changes in myocardial ATP, Pi, and creatine phosphate were observed with a greater than threefold increase in MVO2. The calculated intracellular free Mg concentration, ADP, and pH were also only slightly affected by these increases in work. These data indicate that a simple model involving the feedback of cytosolic ADP and Pi to the mitochondria regulating respiration is inadequate to explain respiratory control in vivo. These data suggest that some other parameters or cooperativity effects involving the phosphate metabolites must play a role in the feedback between respiration and work in the heart in vivo.

Challenges in therapy of hypertension in the elderly

Treating older hypertensive patients presents special challenges. The physiological effects of aging result in hemodynamic and pharmacokinetic changes. Geriatric patients are more likely to have concomitant diseases than younger patients. Treatment regimens should be individualized; monotherapy should be the goal. While most antihypertensive agents can be used, each class of drugs has advantages and disadvantages. Diuretics are both effective and inexpensive but their metabolic side effects (especially hypokalemia) may be quite serious in the geriatric population. Sympatholytics, beta-blockers, alpha-blockers, and direct vasodilators may not be tolerated. The angiotension-converting enzyme inhibitors, captopril and enalapril, are good choices because they have favorable hemodynamics, renin and nonrenin-dependent mechanisms of action and are associated with minimal biochemical alterations. In a recent multicenter study, captopril (25 mg twice daily) was given to 99 geriatric patients with seated diastolic blood pressure (BP) of 92-110 mm Hg. Patients whose blood pressures were not controlled after two weeks of therapy were randomized to either Capozide (captopril, 25 mg with 15 mg hydrochlorothiazide) or captopril, 50 mg twice daily. The average decrease in BP was 16.9/11.9 mm Hg; 75.8% of patients responded to treatment. Black and white patients had equal responses. Only five patients withdrew from the study due to adverse reactions, none of which was serious. Geriatric hypertensives should be treated. Because captopril and Capozide are well-tolerated, effective medications in elderly patients with mild, moderate, or severe hypertension, they should be considered as initial therapy for geriatric hypertension.

Treating black hypertensives with capozide

Twenty-four black men with mild to moderate essential hypertension were enrolled in an open-label trial comparing the efficacy of two doses of Capozide (captopril and hydrochlorothiazide). All antihypertensive drugs were discontinued and patients then received placebo for 2 weeks. Twenty-two patients, mean age 59.1 +/- 14.3 years, with sitting diastolic blood pressure (BP) 92 to 110 mm Hg, entered the 6-week active-drug phase. Eleven patients (Group A) were randomized to Capozide 25/15 and 11 (Group B) to Capozide 50/15. Baseline mean BPs were 151.0/100.7 mm Hg in Group A and 153.1/100.7 mm Hg in Group B. At week 6, mean BPs were 128.7/84.4 mm Hg in Group A and 126.8/82.7 mm Hg in Group B. Uric acid, blood urea nitrogen and creatinine levels rose slightly in both groups. There were no adverse events. Eighteen patients had normal BPs at study completion. Twice-daily Capozide treatment is effective and well tolerated in blacks; patients responded equally well to both doses.

Intracellular pH and inorganic phosphate content of heart in vivo: a 31P-NMR study

Studies were performed to determine the contribution of red blood cells to the 31P-nuclear magnetic resonance (NMR) spectrum of the canine heart in vivo and the feasibility of measuring myocardial intracellular phosphate and pH. This was accomplished by replacing whole blood with a perfluorochemical perfusion emulsion blood substitute, Oxypherol, and noting the difference in the 31P-NMR spectrum of the heart. NMR data were collected with a NMR transmitter-receiver coil on the surface of the distal portion of the left ventricle. These studies demonstrated that a small (approximately 10%) contribution from 2,3-diphosphoglycerate (2,3-DPG) and phosphodiesters in the blood could be detected. The magnitude and shift of these blood-borne signals permitted the relative quantification of intracellular inorganic phosphate (Pi) content as well as intracellular pH. Under resting conditions, the intracellular ATP/Pi was 7.0 +/- 0.8 (n = 19). This corresponds to a free intracellular Pi content of approximately 0.8 mumol/g wet wt. The intracellular pH was 7.10 +/- 0.01 (n = 19). Acute respiratory alkalosis and acidosis, with the arterial pH ranging from approximately 7.0 to 7.7, resulted in only small changes in the intracellular pH (approximately 0.1 pH unit). These latter results demonstrate an effective myocardial intracellular proton-buffering mechanism in vivo.

Activation of dehydrogenase activity and cardiac respiration: a 31P-NMR study

31P-NMR studies were performed to determine the tissue phosphate and oxygen consumption effects of known maneuvers on the activation of pyruvate dehydrogenase during work jumps in the perfused rat heart. In control studies of the glucose-perfused heart, work jumps, with pacing, resulted in a 32% increase in oxygen consumption (QO2) from 1.72 +/- 0.09 to 2.29 +/- 0.12 mmol O2.h-1.g dry wt-1. During this transition no significant change in the high energy phosphates were detected. In contrast, work jumps did cause changes in the phosphates when the activation of pyruvate dehydrogenase was blocked with 2.5 micrograms of ruthenium red per milliliter or maximally stimulated with 11 mM pyruvate before the increase in work. The observed increase in QO2 and inorganic phosphate and calculated increase in ADP are consistent with these phosphates controlling mitochondrial respiration under these conditions. These results suggest that the activation of pyruvate dehydrogenase and/or other dehydrogenases may be an important step in the orchestration of work and QO2.

Determination of pyridine nucleotide fluorescence from the perfused heart using an internal standard

Mitochondrial reduced nicotinamide adenine dinucleotide (NADH) is a key intermediate in energy metabolism in the heart, which can be qualitatively monitored using nondestructive surface fluorescence techniques. However, this optical technique is subject to artifacts from alterations in tissue absorbance, motion of the heart, and variations in excitation intensity. In this study rapid-scan fluorescence emission spectroscopy was used in conjunction with an internal fluorescence standard to compensate for these optical artifacts. The fluorescence spectra obtained from heart had a maximum at 460 nm and a shoulder at 415 nm. Dilution of heart homogenates resulted in a fluorescent spectrum characteristic of suspensions of mitochondria, indicating that absorption of fluorescence by tissue components produces an inner filter effect. This internal filter was characterized, and isobestic points with regard to O2 were found at 425 and 450 nm. Alterations in the inner filter effect due to changes in tissue oxygenation were eliminated by monitoring the NADH at 425 nm. Motion artifacts and excitation source fluctuations were corrected by loading heart cells with an internal fluorescent standard, 5(6)-carboxy-2',7'-dichlorofluorescein (ClCF). Motion of the heart and changes in excitation intensity altered the fluorescence detected from both NADH and ClCF. The use of the NADH-to-ClCF ratio detected at isobestic wavelengths (425 nm NADH and 520 nm ClCF) gives a relative measure of NADH fluorescence, which adequately compensates for both internal absorbance and motion artifacts.

Respiratory control in the glucose perfused heart. A 31P NMR and NADH fluorescence study

The phosphate metabolites, adenosine diphosphate (ADP), inorganic phosphate (Pi), and adenosine triphosphate (ATP), are potentially important regulators of mitochondrial respiration in vivo. However, previous studies on the heart in vivo and in vitro have not consistently demonstrated an appropriate correlation between the concentration of these phosphate metabolites and moderate changes in work and respiration. Recently, mitochondrial NAD(P)H levels have been proposed as a potential regulator of cardiac respiration during alterations in work output. In order to understand better the mechanism of respiratory control under these conditions, we investigated the relationship between the phosphate metabolites, the NAD(P)H levels, and oxygen consumption (Q02) in the isovolumic perfused rat heart during alterations in work output with pacing. ATP, creatine phosphate (CrP), Pi and intracellular pH were measured using 31P NMR. Mitochondrial NAD(P)H levels were monitored using spectrofluorometric techniques. Utilizing glucose as the sole substrate, an increase in paced heart rate led to an increase in Q02 from 1.73 +/- 0.09 to 2.29 +/- 0.12 mmol Q2/h per g dry wt. No significant changes in the levels of Pi, PCr, ATP, or the calculated ADP levels were detected. Under identical conditions, an increase in heart rate was associated with a 23 + 3% increase in NAD(P)H fluorescence. Thus, under the conditions of these studies, an increase in Q02 was not associated with an increase in ADP or Pi. In contrast, increases in Q02 were associated with an increase in NAD(P)H. These data are consistent with the notion that increases in the mitochondrial NADH redox state regulate steady-state levels of respiration when myocardial work is increased.

Primary prevention of gastrointestinal diseases

In the belief that available information can provide reasonable guidance, we review the evidence identifying factors which increase or decrease the risk of developing several gastrointestinal diseases. In the absence of controlled studies, we review case control and other studies. As results from animal studies cannot be readily transferred to humans, we interpret them cautiously. We recommend appropriate personal behavior to reduce risk when they seem reasonably justified by the evidence.

Amyloidosis in subcutaneous heroin abusers ("skin poppers' amyloidosis")

Systemic amyloidosis has recently emerged as a major cause of nephropathy among heroin abusers in New York City. Although focal glomerulosclerosis is typically seen in intravenous drug abusers who present with the nephrotic syndrome, those who escape this complication are at risk for the later development of amyloidosis related to their use of the subcutaneous route. Twenty such addicts identified between 1981 and 1984 are described. Patients typically present with chronic suppurative skin infections, edema, the nephrotic syndrome, benign urinary sediment, and normal-sized or enlarged kidneys. Tubular dysfunction, particularly renal tubular acidosis and diabetes insipidus, is frequent. Progression of renal insufficiency is characteristically rapid. Prolonged survival of heroin abusers and exhaustion of intravenous access requiring recourse to the subcutaneous route underlie the occurrence of amyloidosis in the addict population. Chronic suppurative skin infection consequent to repeated subcutaneous injection appears to be the underlying cause.