Zebrafish comparative genomics and the origins of vertebrate chromosomes

To help understand mechanisms of vertebrate genome evolution, we have compared zebrafish and tetrapod gene maps. It has been suggested that translocations are fixed more frequently than inversions in mammals. Gene maps showed that blocks of conserved syntenies between zebrafish and humans were large, but gene orders were frequently inverted and transposed. This shows that intrachromosomal rearrangements have been fixed more frequently than translocations. Duplicated chromosome segments suggest that a genome duplication occurred in ray-fin phylogeny, and comparative studies suggest that this event happened deep in the ancestry of teleost fish. Consideration of duplicate chromosome segments shows that at least 20% of duplicated gene pairs may be retained from this event. Despite genome duplication, zebrafish and humans have about the same number of chromosomes, and zebrafish chromosomes are mosaically orthologous to several human chromosomes. Is this because of an excess of chromosome fissions in the human lineage or an excess of chromosome fusions in the zebrafish lineage? Comparative analysis suggests that an excess of chromosome fissions in the tetrapod lineage may account for chromosome numbers and provides histories for several human chromosomes.

A comparative map of the zebrafish genome

Zebrafish mutations define the functions of hundreds of essential genes in the vertebrate genome. To accelerate the molecular analysis of zebrafish mutations and to facilitate comparisons among the genomes of zebrafish and other vertebrates, we used a homozygous diploid meiotic mapping panel to localize polymorphisms in 691 previously unmapped genes and expressed sequence tags (ESTs). Together with earlier efforts, this work raises the total number of markers scored in the mapping panel to 2119, including 1503 genes and ESTs and 616 previously characterized simple-sequence length polymorphisms. Sequence analysis of zebrafish genes mapped in this study and in prior work identified putative human orthologs for 804 zebrafish genes and ESTs. Map comparisons revealed 139 new conserved syntenies, in which two or more genes are on the same chromosome in zebrafish and human. Although some conserved syntenies are quite large, there were changes in gene order within conserved groups, apparently reflecting the relatively frequent occurrence of inversions and other intrachromosomal rearrangements since the divergence of teleost and tetrapod ancestors. Comparative mapping also shows that there is not a one-to-one correspondence between zebrafish and human chromosomes. Mapping of duplicate gene pairs identified segments of 20 linkage groups that may have arisen during a genome duplication that occurred early in the evolution of teleosts after the divergence of teleost and mammalian ancestors. This comparative map will accelerate the molecular analysis of zebrafish mutations and enhance the understanding of the evolution of the vertebrate genome.

Effects of gender, body composition, and menopause on plasma concentrations of leptin

Circulating concentrations of leptin ([leptin]) vary directly with body mass index and percentage body fat, and may thus constitute an afferent limb of a system regulating body fatness. We tested the hypotheses that: 1) Plasma [leptin] vary more directly with absolute fat mass than with fractional body fatness per se: and 2). The relationship between fat mass and [leptin] is significantly affected by gender and by menopausal status. [Leptin] in the post-absorptive state was examined in 67 subjects (26 male, 20 premenopausal female, 21 postmenopausal females; 43 never-obese, 24 obese) at usual body weight. Body composition was determined by hydrodensitometry, and [leptin] was determined by a double antibody ELISA assay. In male and pre-menopausal female subjects, subcutaneous adipose tissue aspirations were performed for determination of adipocyte volume by the osmium fixation method, and a 3 hour oral glucose tolerance tests was performed. At usual body weight, ([leptin]) was better correlated with absolute fat mass than with body mass index (BMI) or percentage body fat. BMI and % body fat did not account for any of the variance in [leptin] beyond that attributable to FM, per se. The regression equations relating FM to [leptin] did not differ significantly between obese and never-obese subjects. [Leptin] and fasting serum insulin concentrations were significantly correlated in males only. [Leptin] was significantly higher in pre- and post-menopausal females compared to males, even when [leptin] was corrected for differences in body composition (pre-menopausal females > post-menopausal females > males). While plasma [leptin], corrected for FM, declines significantly in women post-menopause, this decline is not sufficient to account for the striking sexual dimorphism in the relationship of leptin to fat mass. This sexual dimorphism is apparently also due, in part, to a suppressive effect of circulating androgens on [leptin].

Combination chemotherapy with mastectomy or radiotherapy for stage III breast carcinoma: a Cancer and Leukemia Group B study

One hundred thirteen evaluable patients with previously untreated stage III breast carcinoma were treated with three monthly cycles of cyclophosphamide (CYC), doxorubicin (DOX), 5-fluorouracil (5-FU), vincristine (VCR), and prednisone (PRED) (CAFVP). Subsequently, 91 (81%) were deemed operable. Patients were then randomized to receive surgery or radiotherapy (RT) to determine which of these modalities afforded better local tumor control. All patients also received 2 additional years of CAFVP in a further attempt to eradicate local disease and systemic micrometastases. Forty-one of the randomized patients have relapsed. Approximately half of the initial relapses in each arm were local. The overall duration of disease control was similar following either modality, with a median of 29.2 months for surgery patients and 24.4 months for RT patients. Similarly, there was no major difference in survival related to randomized treatment with an overall median of 39 months (median follow-up 37 months). Pre- or perimenopausal status and inflammatory disease were associated with shorter disease control and survival. Treatment was generally well tolerated and toxicity was acceptable. This study demonstrates that prolonged control of stage III breast carcinoma can be achieved with combined modality therapy in which cytotoxic chemotherapy precedes and follows treatment directly primarily at the breast tumor, using either surgery or RT. Nevertheless, new regimens must be designed if significant advances that may lead to the cure of this disease are to be achieved.

A comparative study of two preoperative radiation regimens with cystectomy for bladder cancer

This report surveys the results of two programs of preoperative irradiation with radical cystectomy for bladder cancer in 205 patients. Irradiating the true pelvis to 4000 rads in 4 weeks with radical cystectomy after 6 weeks was implemented in 119 patients (Group 1) from 1959 to 1965; 2000 rads given in 1 week to the true pelvis and radical cystectomy within the following week was implemented in 86 patients (Group 2) from 1966 to 1970. Determinate survival without evidence of recurrence at 5 years was 43% in Group 1 and 42% in Group 2. Mortality with recurrence of bladder cancer in 5 or more years was 44% in group 1 and 42% in group 2. Pelvic complications occurred in 13% of group 1 and 9% of group 2.

Manual and automated (robotic) high-performance liquid chromatography methods for the determination of mycophenolic acid and its glucuronide conjugate in human plasma

A manual and an automated (Zymark PyTechnology robot) HPLC method for simultaneous determination of plasma mycophenolic acid (MPA) and its glucuronide conjugate (MPAG) are described here. Both methods are reproducible and accurate, and both are equivalent in all respects, including quantification limits (MPA, 0.100 microgram/ml; MPAG, 4.00 micrograms/ml), range (using 0.05-0.5 ml of plasma: MPA, 0.0500-20.0 micrograms/aliquot; MPAG, 2.00-200 micrograms/aliquot), precision, and accuracy. MPA and MPAG were stable under the conditions used with both methods. Results from aliquots of paired control samples, analyzed by the manual method over three years at six analytical laboratories, showed excellent agreement in precision and accuracy.

Toremifene increases bone mineral density in men receiving androgen deprivation therapy for prostate cancer: interim analysis of a multicenter phase 3 clinical study

PURPOSE

We evaluated the effects of toremifene on bone mineral density, a surrogate for fracture risk, in men receiving androgen deprivation therapy for prostate cancer.

MATERIALS AND METHODS

In an ongoing, multicenter, phase 3 fracture prevention study 1,392 men 50 years or older with prostate cancer receiving androgen deprivation therapy were randomized to 80 mg toremifene per day or placebo. Bone mineral density of the lumbar spine, total hip and femoral neck was assessed using dual energy x-ray absorptiometry. In this planned interim analysis of the first 197 subjects we compared bone mineral density changes from baseline to month 12 between the placebo and toremifene groups.

RESULTS

Compared with the placebo group men in the toremifene group had significant increases in bone mineral density at each evaluated skeletal site. Lumbar spine bone mineral density decreased 0.7% in the placebo group and increased 1.6% in the toremifene group (between group comparison p <0.001). Total hip bone mineral density decreased 1.3% in the placebo group and increased 0.7% in the toremifene group (p = 0.001). Femoral neck bone mineral density decreased 1.3% in the placebo group and increased 0.2% in the toremifene group (p = 0.009). Between group differences in the change in bone mineral density from baseline to month 12 were 2.3%, 2.0% and 1.5% for the lumbar spine, total hip and femoral neck, respectively.

CONCLUSIONS

Toremifene significantly increased hip and spine bone mineral density in men receiving androgen deprivation therapy for prostate cancer. The effect of toremifene on the fracture risk is being assessed in the ongoing randomized, controlled trial.

Neutrophil migration through preexisting holes in the basal laminae of alveolar capillaries and epithelium during streptococcal pneumonia

The purpose of this study was to determine whether or not there are preexisting holes in the endothelial and epithelial basal laminae of alveolar walls and to determine the path taken by neutrophils as they migrate from the capillaries to the airspace of the alveoli during inflammation. Using transmission electron microscopy and serial thin sections of normal rabbit and mouse lung, we have demonstrated the presence of slit-like holes in the capillary basal laminae and round holes in the basal laminae of type 2 pneumocytes. The slits in the capillary basal laminae were observed at the intersection of the thick and thin walls where endothelium, pericytes, and fibroblasts make close contact. The round holes in the type 2 cell basal laminae were observed at sites of close contact with fibroblasts. Neutrophils were observed to migrate through these slits and holes during streptococcal pneumonia in rabbit lungs. We conclude that during inflammation in the lung, migrating neutrophils displace pericytes and fibroblasts from the slits in the capillary basal lamina and then crawl through these slits into the alveolar interstitium. We postulate that neutrophils find their way to type 2 pneumocytes by following interstitial fibroblasts. We believe that neutrophils displace fibroblasts from their close contacts with the type 2 cells and then crawl through the holes in the basal lamina into the basal lateral space of the type 2 cells. From there, neutrophils migrate into the alveolar airspace.

Genetic linkage mapping of zebrafish genes and ESTs

Genetic screens in zebrafish (Danio rerio) have isolated mutations in hundreds of genes essential for vertebrate development, physiology, and behavior. We have constructed a genetic linkage map that will facilitate the identification of candidate genes for these mutations and allow comparisons among the genomes of zebrafish and other vertebrates. On this map, we have localized 771 zebrafish genes and expressed sequence tags (ESTs) by scoring single-stranded conformational polymorphisms (SSCPs) in a meiotic mapping panel. Of these sequences, 642 represent previously unmapped genes and ESTs. The mapping panel was comprised of 42 homozygous diploid individuals produced by heat shock treatment of haploid embryos at the one-cell stage (HS diploids). This "doubled haploid" strategy combines the advantages of mapping in haploid and standard diploid systems, because heat shock diploid individuals have only one allele at each locus and can survive to adulthood, enabling a relatively large quantity of genomic DNA to be prepared from each individual in the mapping panel. To integrate this map with others, we also scored 593 previously mapped simple-sequence length polymorphisms (SSLPs) in the mapping panel. This map will accelerate the molecular analysis of zebrafish mutations and facilitate comparative analysis of vertebrate genomes.

Persistent shedding of viable SARS-CoV in urine and stool of SARS patients during the convalescent phase

In order to further the present knowledge of the emerging severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 486 different specimens from 54 patients with a clinical diagnosis of SARS were investigated for the presence of viral RNA, and 314 plasma specimens of 73 patients were examined for IgM and IgG antibodies specific against SARS-CoV using an indirect ELISA. Viral RNA was detectable in 28 of the 54 patients tested. Cumulative data showed that 67 of the 73 SARS patients demonstrated seroconversion by week 5 of illness. In contrast, only 1 of 278 healthy subjects enrolled in the study was found to be positive for the IgG antibody. Coexistence of viral RNA in plasma and specific antibodies was simultaneously observed over three consecutive weeks in two critical cases. In three convalescent patients in particular, cultivable SARS-CoV was detected in stool or urine specimens for longer than 4 weeks (29-36 days). These findings suggest that SARS-CoV may remain viable in the excretions of convalescent patients.

Processing of the intron-containing thymidylate synthase (td) gene of phage T4 is at the RNA level

The interrupted T4 phage td gene, which encodes thymidylate synthase, is the first known example of an intron-containing prokaryotic structural gene. Analysis of td-encoded transcripts provides evidence in favor of maturation at the RNA level. Northern blotting with T4 RNA and with region-specific probes revealed three classes of RNA: diffuse premessage (ca. 2.5 kb), a low-abundance mature mRNA (ca. 1.3 kb), and an abundant free intron RNA (ca. 1.0 kb). The existence of covalently joined mature mRNA was suggested by hybridization and S1 protection experiments and was confirmed by primer extension analysis of the splice junction. In analogy to expression of interrupted eukaryotic genes, these results are consistent with an RNA processing model that would account for the direct gene transcript serving as precursor for both free intron RNA and a spliced mRNA that is colinear with the thymidylate synthase product.

Identification of tyrosine sulfation in Conus pennaceus conotoxins alpha-PnIA and alpha-PnIB: further investigation of labile sulfo- and phosphopeptides by electrospray, matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI mass spectrometry

Liquid chromatography/electrospray ionization mass spectrometry was used to investigate the peptide composition of the venom of Conus pennaceus, a molluscivorous cone shell from the Red Sea. Based on observed M(r)s, this venom contained all known conotoxins previously isolated and identified from this species. Interestingly, the doubly protonated species of only two of these conotoxins, alpha-PnIA and alpha-PnIB, showed additional related ions at +40 m/z (+80 Da), indicating the presence of either sulfation or phosphorylation in both components. High-performance liquid chromatographic (HPLC) fractions containing these two conotoxins were examined by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry in both positive and negative ion modes, as well as by MALDI high-energy collision-induced dissociation. These experiments established the presence of a single sulfated tyrosine residue within both alpha-PnIA and alpha-PnIB. Hence their post-translationally modified sequences are GCCSLPPCAANNPDY(S)C-NH2 (alpha-PnIA) and GCCSLPPCALSNPDY(S)C-NH2 (alpha-PnIB). This assignment was supported by comparison of their mass spectral behavior with that of known sulfated and phosphorylated peptides. This data clarified further the distinguishing features of the ionization and fragmentation of such modified peptides. Selective disulfide folding of synthetic alpha-PnIB demonstrated that both sulfated and non-sulfated toxins co-elute on reversed-phase HPLC and that alpha-PnIB possesses the same disulfide connectivity as other 'classical' alpha-conotoxins reported previously.

Pulmonary edema and acute upper airway obstruction

Pulmonary edema following the relief of acute upper airway obstruction is unusual and unpredictable. The cause is usually attributed to pulmonary and hemodynamic changes resulting from high negative intrathoracic pressures during obstructed respiration. The incidence of this problem is not known. Why pulmonary edema develops in only certain patients is also unclear. We reviewed the records of 27 consecutive adult patients admitted and treated for acute upper airway obstruction. Three of 27 (11%) developed pulmonary edema. Age, sex, diagnosis, duration of obstruction, history of cardiopulmonary disease, and perioperative fluid administration were evaluated. No differences were noted between those who did and those who did not develop pulmonary edema. Pulmonary edema following acute upper airway obstruction appears to be more common than is generally appreciated, however, no specific factors seem related to its occurrence.

Perception of moving, sounding objects by four-month-old infants

Infants and adults were presented with two moving objects accompanied by a single percussive sound. In different experiments, the sound occurred when one object moved through a particular spatial position, when it abruptly changed its direction of movement, or when it made contact with a rigid surface. Infants responded to the sound-object relationship whenever the sound occurred as the object changed direction, irrespective of its impacts with the surface. Adults, in contrast, responded to the sound-object relationship most clearly when sounds were synchronized with impacts. In infancy, perception of auditory-visual relationships thus depends in part on detection of discontinuities in the movement of a visible object.

Effects of weight change on plasma leptin concentrations and energy expenditure

Circulating concentrations of leptin are closely correlated with body fat mass, and may thus constitute an afferent limb of a system regulating body fatness, with efferent limbs that affect energy expenditure and food intake. We studied 50 subjects (27 males, 23 premenopausal females; 31 never-obese, 19 obese) at usual body weight during active weight loss or weight gain and during the maintenance of body weights 10% above usual (WT + 10%) and 10% and/or 20% below usual body weight (Wt -10% and Wt -20%) to test the hypotheses that the dynamic process of weight change and the maintenance of an altered body weight are associated with significant changes in circulating concentrations of leptin and/or the relationship between fat mass and leptin, and such changes in the plasma concentration of leptin are related to changes in energy expenditure at altered body weight. Subjects were admitted to the Rockefeller University Hospital, and energy metabolism (24-h energy expenditure, resting energy expenditure, thermic effect of feeding, and nonresting energy expenditure) and circulating concentrations of leptin and insulin were examined at various weight plateaus (usual body weight, 10% above usual body weight, 10% below usual body weight, and 20% below usual body weight). Plasma leptin was also measured in some subjects during dynamic periods of weight gain or loss. Though both plasma leptin concentrations and fat mass were significantly correlated with resting energy expenditure, only the correlation of fat mass and energy expenditure remained significant in a multiple stepwise linear regression analysis. Neither absolute nor relative changes in plasma leptin between weight plateaus were significantly correlated with any of the observed changes in energy expenditure. Plasma leptin concentrations were significantly lower during weight loss than during weight maintenance at the same body composition. Plasma leptin concentrations, normalized to fat mass, were significantly lower during the maintenance of a reduced body weight in females and higher during the maintenance of an elevated body weight in males than in the same subjects at usual body weight. At all weight plateaus, plasma leptin concentrations normalized to fat mass were significantly higher in females than in males, but gender was not a significant covariate of the relationship between leptin and energy expenditure. Postabsorptive serum concentrations of insulin was a significant covariate of plasma leptin concentration in males, but not females, at Wt initial and Wt + 10%. Although plasma leptin is significantly reduced during dynamic weight loss compared with static weight maintenance at the same body weight, the lack of correlation between changes in plasma leptin and changes in energy expenditure between weight plateaus suggests that leptin is not the primary signal that mediates the changes of energy expenditure that accompany the maintenance of an altered body weight in humans.

High specific activity chemiluminescent and fluorescent markers: their potential application to high sensitivity and 'multi-analyte' immunoassays

The sensitivities of immunoassays relying on conventional radioisotopic labels (i.e. radioimmunoassay (RIA) and immunoradiometric assay (IRMA) permit the measurement of analyte concentrations above ca 10(7) molecules/ml. This limitation primarily derives, in the case of 'competitive' or 'limited reagent' assays, from the 'manipulation errors arising in the system combined with the physicochemical characteristics of the particular antibody used; however, in the case of 'non-competitive' systems, the specific activity of the label may play a more important constraining role. It is theoretically demonstrable that the development of assay techniques yielding detection limits significantly lower than 10(7) molecules/ml depends on: (1) the adoption of 'non-competitive' assays designs; (2) the use of labels of higher specific activity than radioisotopes; (3) highly efficient discrimination between the products of the immunological reactions involved. Chemiluminescent and fluorescent substances are capable of yielding higher specific activities than commonly used radioisotopes when used as direct reagent labels in this context, and both thus provide a basis for the development of 'ultra-sensitive', non-competitive, immunoassay methodologies. Enzymes catalysing chemiluminescent reactions or yielding fluorescent reaction products can likewise be used as labels yielding high effective specific activities and hence enhanced assay sensitivities. A particular advantage of fluorescent labels (albeit one not necessarily confined to them) lies in the possibility they offer of revealing immunological reactions localized in 'microspots' distributed on an inert solid support. This opens the way to the development of an entirely new generation of 'ambient analyte' microspot immunoassays permitting the simultaneous measurement of tens or even hundreds of different analytes in the same small sample, using (for example) laser scanning techniques. Early experience suggests that microspot assays with sensitivities surpassing that of isotopically based methodologies can readily be developed.

Fibroblasts are in a position to provide directional information to migrating neutrophils during pneumonia in rabbit lungs

Previous findings have shown that pulmonary fibroblasts are associated with preexisting holes in the endothelial and epithelial basal laminae through which neutrophils appear to enter and leave the interstitium as they migrate from capillaries to alveoli. To determine their role in neutrophil migration, fibroblast organization within the interstitium was assessed by transmission electron microscope observations of serial-sectioned rabbit lung tissue. Interstitial fibroblasts were found to physically interconnect the endothelial basal lamina holes to epithelial basal lamina holes. Morphometric assessment of rabbit lung tissue instilled with Streptococcus pneumoniae revealed that approximately 70% of the surface area density of migrating neutrophils is in close contact (15 nm or less) with interstitial fibroblasts and extracellular matrix elements (30 and 40%, respectively). Although migrating neutrophils were close enough to adhere to both fibroblasts and extracellular elements, the interstitial fibroblasts are organized in a manner that would allow them to provide directional information to the neutrophils. A model illustrating this process is proposed.