Static Stability and Swim Bladder Volume in the Bluegill Sunfish (Lepomis macrochirus).

Static stability is a property inherent to every organism. More stable bodies benefit from a lower energy cost associated with maintaining a desired orientation, while less stable bodies can be more maneuverable. The static stability of a fish is determined by the relative locations of its center of mass (COM) and center of buoyancy (COB), which may change with changes in swim bladder volume. We hypothesized, however, that fish would benefit from consistent static stability, and predicted that changes in swim bladder volume would not alter the overall pattern of COM and COB locations. We used micro-computed tomography to estimate the locations of the COM and COB in bluegill sunfish (Lepomis macrochirus). Using this technique, we were able to find a small but significant difference between the location of the COM and COB for a given orientation. We found that the swim bladder can change shape within the body cavity, changing relative locations of the COM and COB. At one extreme, the COB is located 0.441 ± 0.007 BL from the snout and 0.190 ± 0.010 BL from the ventral surface of the pelvic girdle, and that the COM is 0.0030 ± 0.0020 BL posterior and 0.0006 ± 0.0005 BL ventral to the COB, a pattern that causes a nose-up pitching torque. At the other extreme, the COM is anterior and dorsal to the COB, a pattern that causes the opposite torque. These changes in location seems to be caused by changes in the shape and centroid location of the swim bladder within the body: The centroid of the swim bladder is located significantly more posteriorly in fish oriented head-down. The air in the bladder "rises" while heavier tissues "sink," driving a change in tissue distribution and changing the location of the COM relative to the COB. Supporting our hypothesis, we found no correlation between swim bladder volume and the distance between the COM and COB. We conclude that bluegill are statically unstable, requiring them to expend energy constantly to maintain their normal orientation, but that the pitch angle of the body could alter the relative locations of COM and COB, changing their static stability.

Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.

We have utilized computational biology to screen GenBank for the presence of recently integrated Ya5 and Yb8 Alu family members. Our analysis identified 2640 Ya5 Alu family members and 1852 Yb8 Alu family members from the draft sequence of the human genome. We selected a set of 475 of these elements for detailed analyses. Analysis of the DNA sequences from the individual Alu elements revealed a low level of random mutations within both subfamilies consistent with the recent origin of these elements within the human genome. Polymerase chain reaction assays were used to determine the phylogenetic distribution and human genomic variation associated with each Alu repeat. Over 99 % of the Ya5 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates, confirming the recent origin of these Alu subfamilies in the human genome. Approximately 1 % of the analyzed Ya5 and Yb8 Alu family members had integrated into previously undefined repeated regions of the human genome. Analysis of mosaic Yb8 elements suggests gene conversion played an important role in generating sequence diversity among these elements. Of the 475 evaluated elements, a total of 106 of the Ya5 and Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity.

Alu insertion polymorphisms for the study of human genomic diversity.

Genomic database mining has been a very useful aid in the identification and retrieval of recently integrated Alu elements from the human genome. We analyzed Alu elements retrieved from the GenBank database and identified two new Alu subfamilies, Alu Yb9 and Alu Yc2, and further characterized Yc1 subfamily members. Some members of each of the three subfamilies have inserted in the human genome so recently that about a one-third of the analyzed elements are polymorphic for the presence/absence of the Alu repeat in diverse human populations. These newly identified Alu insertion polymorphisms will serve as identical-by-descent genetic markers for the study of human evolution and forensics. Three previously classified Alu Y elements linked with disease belong to the Yc1 subfamily, supporting the retroposition potential of this subfamily and demonstrating that the Alu Y subfamily currently has a very low amplification rate in the human genome.

Evidence for alternate splicing within the mRNA transcript encoding the DNA damage response kinase ATR.

Proper cellular response to genotoxic insult often requires the activity of one or more members of a family of high-molecular weight protein kinases referred to as phosphatidylinositol-3 kinase (PIK)-like proteins. While catalytic activity is an indispensable part of PIK-like protein function, little is currently known about factors that control their activity and/or functions. This deficiency stems, in large part, from our lack of knowledge concerning functionally significant subdomains within the large non-catalytic domain of these proteins. We have determined that the transcript encoding the PIK-like protein ATR undergoes alternate splicing within the region of the mRNA encoding its non-catalytic domain. This conclusion is based on the sequencing of a human expressed sequence tag clone encoding a portion of the ATR cDNA, and is supported by the results of reverse transcriptase-polymerase chain reaction (RT-PCR) assays conducted on total and polyA+ RNA, as well as sequencing of cloned RT-PCR products. Cloning and sequencing of a segment of human genomic DNA indicated that this event arises from splicing of a single 192 bp exon within the ATR gene. Analysis of several human tissues indicated that alternate ATR transcripts are differentially expressed, suggesting that this region of the ATR protein may be of functional importance.

Differentiation of Coxiella burnetii isolates by sequence determination and PCR-restriction fragment length polymorphism analysis of isocitrate dehydrogenase gene.

The isocitrate dehydrogenase (icd) gene of Coxiella burnetii was cloned and sequenced to differentiate between isolates with various geographic origins and phenotypic properties. Based on the gene sequences all 19 isolates studied could be divided into three groups. Group 1 contained isolates originating from acute cases of Q fever, ticks and cows. Groups 2 and 3 included isolates from chronic Q fever patients and a prototype strain from an aborted goat. Although the icd gene profiles were different among isolates of the latter two groups, there were two base differences common for both groups which could be used as markers to distinguish them from group 1 isolates. Based on one of the markers a simple method using PCR-restriction fragment length polymorphism analysis was developed for rapid differentiation of C. burnetii isolates as well as for direct detection and differentiation of the bacterium in human serum samples. Taken together, the study results suggest that the icd-based differentiation method may be useful in clinical investigation of Coxiella infections.

Sequence comparison of the VP2 variable region of infectious bursal disease virus isolates from Vietnam.

The variable region in the VP2 gene of twenty-three infectious bursal disease virus (IBDV) isolates, collected in Vietnam in 1997 and 1998, was amplified as cDNA by using the reverse transcription-polymerase chain reaction and sequenced. Analysis of amino acid substitutions and phylogenetic relationships of the deduced amino acid sequences (residues 206-350) showed that the nineteen Vietnamese vv IBDVs clustered with the European vv IBDVs, Japanese vv IBDVs and Chinese vv strains, and that the four vietnamese virulent strains were closely related to European virulent strain 52/70. These results suggest that Vietnamese vv IBDVs, European vv IBDVs, Japanese vv IBDVs and Chinese vv strains have the same origin.

Spin-exchange collisions of submerged shell atoms below 1 Kelvin.

Angular momentum changing collisions can be suppressed in atoms whose valence electrons are submerged beneath filled shells of higher principle quantum number. To determine whether spin-exchange collisions are suppressed in these "submerged shell" atoms, we measured collisional rates for six hyperfine states of Mn at T < 1 K. Although the 3d valence electrons in Mn are submerged beneath a filled 4s orbital, we find spin-exchange rate coefficients similar to Na and H (both nonsubmerged shell atoms).

High-flux beam source for cold, slow atoms or molecules.

We demonstrate and characterize a high-flux beam source for cold, slow atoms or molecules. The desired species is vaporized using laser ablation, then cooled by thermalization in a cryogenic cell of buffer gas. The beam is formed by particles exiting a hole in the buffer gas cell. We characterize the properties of the beam (flux, forward velocity, temperature) for both an atom (Na) and a molecule (PbO) under varying buffer gas density, and discuss conditions for optimizing these beam parameters. Our source compares favorably to existing techniques of beam formation, for a variety of applications.

Hypoxia regulates the expression of the adrenomedullin and HIF-1 genes in cultured HL-1 cardiomyocytes.

Adrenomedullin (AM) is a hypotensive protein expressed in a variety of cells and tissues. We observed previously that the expression of the adrenomedullin gene increases substantially in the developing rat heart and in cultured adult rat ventricular cardiac myocytes in response to hypoxia as a function of time. An adrenomedullin promoter-luciferase reporter construct was used to show that this increase in adrenomedullin mRNA resulted from increased transcription in response to hypoxia. We report here additional evidence documenting that this hypoxia-induced transcription of the adrenomedullin gene is regulated by the hypoxia-inducible factor-1 (HIF-1) transcription factor. We used Northern blot analysis to show an increase in the levels of AM and HIF-1alpha mRNA but not HIF-1beta mRNA in the HL-1 cardiac myocyte cell line in response to hypoxia. Furthermore, Western blot analysis revealed that the levels of both HIF-1alpha and HIF-1beta protein increased under hypoxic conditions. Data from electrophoretic mobility shift assays indicate that the heterodimeric HIF-1 complex binds to the HIF-1-responsive elements. Combined data from these studies demonstrate that the AM gene is regulated by hypoxia-responsive elements localized in the AM promoter region.

Adrenomedullin gene expression is developmentally regulated and induced by hypoxia in rat ventricular cardiac myocytes.

Adrenomedullin is a recently discovered hypotensive peptide that is expressed in a variety of cell and tissue types. Using the technique of differential display, the adrenomedullin gene was observed to be differentially expressed in developing rat heart. Reverse transcription-polymerase chain reaction analysis revealed that the level of adrenomedullin mRNA was significantly higher in adult ventricular cardiac muscle as compared with embryonic day 17 ventricular cardiac muscle. Adrenomedullin receptor mRNA was constitutively expressed throughout development of the ventricular heart. Two potential hypoxia-inducible factor-1 (HIF-1) consensus binding sites were identified in the mouse adrenomedullin promoter at -1095 and -770 nucleotides from the transcription start site. Exposure of cultured adult rat ventricular cardiac myocytes to hypoxia (1% O2) resulted in a significant, time-dependent increase in adrenomedullin mRNA levels. Transfection studies revealed that the 5'-flanking sequence of adrenomedullin was capable of mediating a hypoxia-inducible increase in transcription. Mutation of the putative HIF-1 consensus binding sites revealed that the major regulatory sequence that mediates the hypoxia-inducible transcriptional response is located at -1095. These data demonstrate that the adrenomedullin gene is developmentally regulated in ventricular cardiomyocytes, that adrenomedullin transcription can be induced by hypoxia, and that this response is primarily mediated by HIF-1 consensus sites in the adrenomedullin promoter.

Characterization of the Coxiella burnetti sucB gene encoding an immunogenic dihydrolipoamide succinyltransferase.

The Coxiella burnetii sucB gene encoding the dihydrolipoamide succinyltransferase (E2o) enzyme was cloned by immunological screening of a lambda EMBL3 genomic library prepared from strain Nine Mile DNA and sequenced. The homology of the cloned gene product to the counterpart in Escherichia coli was 54.3%, but the homology of the N-terminal region was only 42%. The gene was expressed in E. coli as an independent unit from its own promoter, producing an immunoreactive protein of about 50 kDa on SDS-PAGE which reacted with antisera from laboratory animals and sera from human patients with acute Q fever. The study results suggest that the C. burnetii E2o enzyme may serve as a potential target antigen for diagnostic assays for Q fever.

Standardization of methods for measuring plasminogen activator inhibitor activity in human plasma.

We have standardized the measurement of plasminogen activator inhibitor type 1 (PAI-1) activity in plasma. One-chain tissue-type plasminogen activator (t-PA; EC 3.4.21.31; final activity, 5 int. units/mL) was incubated with plasma (final dilutions 1:4 to 1:40) in phosphate buffer (pH 7.4, ionic strength = 0.15) for 15 min at 37 degrees C, followed by acidification and measurement of residual t-PA activity by an amidolytic method. The PAI-1 activity assay was 98% specific for PAI-1 activity in samples from both pregnancy and nonpregnancy, and varied linearly with added plasma volume when the percent inhibition of t-PA was between 8% and 50%. For the standardized method, analytical recovery was 93 +/- 5%, the detection limit was 1.6 arbitrary units per milliliter (1 arb. unit of PAI-1 activity = inhibition of 1 int. unit of t-PA activity), and total imprecision was 10.2 (SD 0.7) arb. units/mL (CV = 7%, n = 20). The average PAI-1 activity in 10 healthy individuals drawn between 0800 and 1000 hours was 23.9 +/- 15.4 arb. units/mL. Compared with the standardized assay, two of three previously described assays underestimated PAI-1 activity in plasma by 77% and 85%, respectively.

Zeeman effect in CaF(2Pi(3/2)).

The Zeeman effect in the excited A 2Pi(3/2) state of CaF is measured and analyzed over a wide range of magnetic fields. It is found that the splitting of the Zeeman levels is largely determined by the coupling between different rotational states and there are no low-field seeking states in the J=3/2 manifold of Zeeman levels at high magnetic fields. A model of the Zeeman spectrum based on the ligand-field theory of CaF is shown to be accurate in the interval of magnetic fields 0-5 Tesla. This demonstrates that the magnetic moment of the CaF(A 2Pi(3/2)) molecule is effectively determined by the spin angular momentum of a single electron and the orbital motion of the valence electron around the Ca2+ core. An analysis of the Zeeman spectrum as a function of the molecular rotational constant indicates that 2Pi(3/2) molecules should have significant rotational constants (at least as large as twice the rotational constant of CaF) to be amenable to magnetic trapping in high fields.

Rapid method for detection of Coxiella burnetii antibodies using high-density particle agglutination.

A high-density particle agglutination test, using erythrocyte-sensitizing substance from phase II Coxiella burnetii adsorbed to high-density composite particles, was developed for rapid serodiagnosis of Q fever. The test was compared with the microimmunofluorescence test for sensitivity and specificity by using 3,036 human serum samples collected in Gifu Prefecture, Japan. An excellent agreement was found between the two tests for the acute-phase group and paired serum samples, but some discordant results were observed in the single-sample group. The sensitivity and specificity of the high-density particle agglutination test were both 100% in the former group and 81.6 and 99.9%, respectively, in the latter group. The test is a very promising tool for routine serodiagnosis of Q fever because of its simplicity, sensitivity, and specificity.

Evaluation of the high-density agglutination test for Coxiella burnetii antibodies in animals.

The usefulness of the high-density particle agglutination (HDPA) test as a potential tool for the detection of anti-Coxiella burnetii antibodies in animal sera was studied by using 619 cow, 589 dog, and 150 cat serum samples and antisera from rabbits, guinea pigs, and mice. The sensitivity and specificity of the test versus those of the reference microimmunofluorescence test were determined at two different threshold titer values. At the cutoff value of 1:16, the sensitivities of the HDPA test for cow, dog, and cat sera were 94.3, 95, and 91.3%, respectively, and the specificities were 95.5, 95.3, and 91.3%, respectively. At the cutoff value of 1:32, the sensitivities were 86.7, 88.3, and 82.6%, respectively, and the specificities were 99, 99.2, and 98.4%, respectively. For the group of immune laboratory animals all samples from rabbits, guinea pigs, and mice were positive by the HDPA test. The erythrocyte-sensitizing substance from phase II C. burnetii was found to contain protein and carbohydrate, and both fractions are immunoreactive. The study results show that the HDPA test is a useful tool in the epizootiological survey of Coxiella infection in animals.

Recently integrated human Alu repeats: finding needles in the haystack.

Alu elements undergo amplification through retroposition and integration into new locations throughout primate genomes. Over 500,000 Alu elements reside in the human genome, making the identification of newly inserted Alu repeats the genomic equivalent of finding needles in the haystack. Here, we present two complementary methods for rapid detection of newly integrated Alu elements. In the first approach we employ computational biology to mine the human genomic DNA sequence databases in order to identify recently integrated Alu elements. The second method is based on an anchor-PCR technique which we term Allele-Specific Alu PCR (ASAP). In this approach, Alu elements are selectively amplified from anchored DNA generating a display or 'fingerprint' of recently integrated Alu elements. Alu insertion polymorphisms are then detected by comparison of the DNA fingerprints generated from different samples. Here, we explore the utility of these methods by applying them to the identification of members of the smallest previously identified subfamily of Alu repeats in the human genome termed Ya8. This subfamily of Alu repeats is composed of about 50 elements within the human genome. Approximately 50% of the Ya8 Alu family members have inserted in the human genome so recently that they are polymorphic, making them useful markers for the study of human evolution.

Phylogenetic analysis of the Friedreich ataxia GAA trinucleotide repeat.

Friedreich ataxia is an autosomal recessive neurodegenerative disorder associated with a GAA repeat expansion in the first intron of the gene (FRDA) encoding a novel, highly conserved, 210 amino acid protein known as frataxin. Normal variation in repeat size was determined by analysis of more than 600 DNA samples from seven human populations. This analysis showed that the most frequent allele had nine GAA repeats, and no alleles with fewer than five GAA repeats were found. The European and Syrian populations had the highest percentage of alleles with 10 or more GAA repeats, while the Papua New Guinea population did not have any alleles carrying more than 10 GAA repeats. The distributions of repeat sizes in the European, Syrian, and African American populations were significantly different from those in the Asian and Papua New Guinea populations (p < 0.001). The GAA repeat size was also determined in five nonhuman primates. Samples from 10 chimpanzees, 3 orangutans, 1 gorilla, 1 rhesus macaque, 1 mangabey, and 1 tamarin were analyzed. Among those primates belonging to the Pongidae family, the chimpanzees were found to carry three or four GAA repeats, the orangutans had four or five GAA repeats, and the gorilla carried three GAA repeats. In primates belonging to the Cercopithecidae family, three GAA repeats were found in the mangabey and two in the rhesus macaque. However, an AluY subfamily member inserted in the poly(A) tract preceding the GAA repeat region in the rhesus macaque, making the amplified sequence approximately 300 bp longer. The GAA repeat was also found in the tamarin, suggesting that it arose at least 40 million years ago and remained relatively small throughout the majority of primate evolution, with a punctuated expansion in the human genome.

Antigenic characteristics of polypeptides of Coxiella burnetii isolates.

Eighteen Coxiella burnetii strains from a variety of clinical and geographical sources were screened for antigenic variation of polypeptides by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) coupled with Coomassie brilliant blue (CBB) staining or immunoblotting. These polypeptide profiles showed the greatest variability in the region from 33 to 8.1 kDa. Such differences in the antigenicity of the polypeptides were also recognized by immunoblotting with 15 various mouse anti-C. burnetii antisera. In addition, we detected a polypeptide at about 28 kDa which was immunodominant in strains from human cases of acute Q fever, milk and ticks but not immunogenic in strains from human cases of chronic Q fever. These findings suggest that this polypeptide is a marker to distinguish between acute and chronic strains.

Clinical evaluation of a new PCR assay for detection of Coxiella burnetii in human serum samples.

A nested PCR method was developed for the detection of Coxiella burnetii in human serum samples. Two pairs of oligonucleotide primers were designed to amplify a 438-bp fragment of the com1 gene encoding a 27-kDa outer membrane protein of C. burnetii. The primers amplified the predicted fragments of 21 various strains of C. burnetii but did not react with DNA samples from other microorganisms. The 438-bp amplification products could be digested with restriction enzymes SspI and SalI. The utility of the nested PCR was evaluated by testing human serum samples. The com1 gene fragment was amplified from 135 (87%) of 155 indirect immunofluorescence test (IF)-positive serum samples and from 11 (11%) of 100 IF-negative serum samples. The nested PCR with primers targeted to the com1 gene appeared to be a sensitive, specific, and useful method for the detection of C. burnetii in serum samples.