bluuebunny/crossref_metadata_2025 huggingface dataset:
Percutaneous Transcatheter Closure of Patent Foramen Ovale in Patients With Paradoxical Embolism
Authors: Martín Francisco , Sánchez Pedro L. , Doherty Elizabeth , Colon-Hernandez Pedro J. , Delgado Gabriel , Inglessis Ignacio , Scott Nandita , Hung Judy , King Mary Etta E. , Buonanno Ferdinando , Demirjian Zareh , de Moor Michael , Palacios Igor F.
Published: August 2002

Background—

Percutaneous transcatheter closure of patent foramen ovale (PFO) is used as an alternative to surgery or long-term anticoagulation for the treatment of patients with paradoxical embolism and PFO.

Methods and Results—

We report the immediate and long-term clinical and echocardiographic outcome of 110 consecutive patients (58 males, mean age 47±14 years) who underwent transcatheter closure of PFO because of paradoxical embolism between 1995 and 2001. Procedural success, defined as successful deployment of the device and effective occlusion (no, or trivial, shunt after device placement), was achieved in all (100%) patients. There was no in-hospital mortality, 1 device migration requiring surgical intervention (0.9%), and 1 episode of cardiac tamponade (0.9%) requiring pericardiocentesis. A progressive increment in full occlusion was observed (44%, 51%, 66%, and 71% at 1 day, 6 months, and 1 and 2 years, respectively, after device placement). At a mean follow-up of 2.3 years, 2 patients experienced recurrent neurological events (1 fatal stroke and 1 transient ischemic attack), representing an annual risk of recurrence of 0.9%. In addition, 4 (3.6%) of the patients required reintervention for device malalignment or significant shunt. Kaplan-Meier analysis showed a freedom from recurrent embolic events and reintervention of 96% and 90% at 1 and 5 years, respectively.

Conclusions—

Transcatheter closure of PFO is a safe and effective therapy for patients with paradoxical embolism and PFO. It is associated with a high success rate, low incidence of hospital complications, and low frequency of recurrent systemic embolic events.
Tripling Survival From Sudden Cardiac Arrest Via Early Defibrillation Without Traditional Education in Cardiopulmonary Resuscitation
Authors: Capucci Alessandro , Aschieri Daniela , Piepoli Massimo F. , Bardy Gust H. , Iconomu Efrosini , Arvedi Maurizio
Published: August 2002

Background—

Early defibrillation is the most important intervention affecting survival from sudden cardiac arrest (SCA). To improve public access to early defibrillation, we established Piacenza Progetto Vita (PPV), the first system of out-of-hospital early defibrillation by first-responder volunteers.

Methods and Results—

The system serves a population of 173 114 residents in the Piacenza region of Italy. Equipment for the system comprises 39 semiautomatic external biphasic defibrillators (AEDs): 12 placed in high-risk locations, 12 in lay-staffed ambulances, and 15 in police cars; 1285 lay volunteers trained in use of the AED, without traditional education in cardiac pulmonary resuscitation, responded to all cases of suspected SCA, in coordination with the Emergency Medical System (EMS). During the first 22 months, 354 SCA occurred (72±12 years, 73% witnessed). The PPV volunteers treated 143 SCA cases (40.4%), with an EMS call-to-arrival time of 4.8±1.2 minutes (versus 6.2±2.3 minutes for EMS,
P
=0.05). Overall survival rate to hospital discharge was tripled from 3.3% (7 of 211) for EMS intervention to 10.5% (15 of 143) for PPV intervention (
P
=0.006). The survival rate for witnessed SCA was tripled by PPV: 15.5% versus 4.3% in the EMS-treated group (
P
=0.002). A “shockable” rhythm was present in 23.8% (34 of 143) of the PPV patients versus 15.6% (33 of 211) of the EMS patients (
P
=0.055). The survival rate from shockable dysrhythmias was higher for PPV versus EMS: 44.1% (15 of 34) versus 21.2% (7 of 33),
P
=0.046. The neurologically intact survival rate was higher in PPV-treated versus EMS-treated patients: 8.4% (12 of 143) versus 2.4% (5 of 211),
P
=0.009.

Conclusions—

Broad dissemination of AEDs for use by nonmedical volunteers enabled early defibrillation and tripled the survival rate for out-of-hospital SCA.
Disproportionate Decrease in α- Compared With β-Adrenergic Sensitivity in the Dorsal Hand Vein in Pregnancy Favors Vasodilation
Authors: Landau Ruth , Dishy Victor , Wood Alastair J.J. , Stein C. Michael , Smiley Richard M.
Published: August 2002

Background—

Altered vascular responses to adrenergic agonists during pregnancy are thought to play an important role in the regulation of blood pressure and placental blood flow. Because α
1
-adrenergic and β
2
-adrenergic sensitivity act in opposing directions to determine vascular tone, we simultaneously evaluated α-adrenergic–mediated vasoconstriction and β-adrenergic–mediated vasodilation in dorsal hand veins during and after pregnancy.

Methods and Results—

Twenty healthy pregnant women were studied at 32 to 37 weeks of gestation and again 12 weeks after delivery. Vascular response to phenylephrine (PE) and isoproterenol (ISO) was measured in a dorsal hand vein using the linear variable differential transformer technique. The dose of PE resulting in 50% constriction (CD
50
) was determined. The response to ISO was measured after the PE preconstriction. Pregnant and postpartum values, expressed as geometric mean (95% CI), were compared by paired
t
test. α-Adrenergic sensitivity during pregnancy (CD
50
2.7 μg/min [95% CI, 1.5 to 5.0]) was markedly decreased, ≈7-fold, compared with postpartum (0.4 μg/min [95% CI, 0.3 to 0.7] [
P
<0.01]). β-Adrenergic vasodilation was also attenuated during pregnancy. The ED
50
of ISO (dose of ISO resulting in 50% of the maximal response, E
max
) was greater during pregnancy (20 ng/min [95% CI, 11 to 35]) than postpartum (8 ng/min [95% CI, 5 to 12]) (
P
<0.05). ISO E
max
was also significantly less during pregnancy (81% [95% CI, 65 to 97] compared with postpartum (105% [95% CI, 97 to 113]) (
P
<01.01).

Conclusions—

Normal pregnancy is characterized by decreased venous sensitivity to both α
1
-adrenoceptor–mediated vasoconstriction and β
2
-adrenoceptor–mediated vasodilation. The greater decrease in α
1
compared with β
2
response may contribute to the vasodilated state characteristic of human pregnancy.
Influenza Infection Promotes Macrophage Traffic Into Arteries of Mice That Is Prevented by D-4F, an Apolipoprotein A-I Mimetic Peptide
Authors: Van Lenten Brian J. , Wagner Alan C. , Anantharamaiah G.M. , Garber David W. , Fishbein Michael C. , Adhikary Lopa , Nayak Debi P. , Hama Susan , Navab Mohamad , Fogelman Alan M.
Published: August 2002

Background—

We reported that HDL loses its antiinflammatory properties during acute influenza A infection in mice, and we hypothesized that these changes might be associated with increased trafficking of macrophages into the artery wall. The present study tested this hypothesis.

Methods and Results—

D-4F, an apolipoprotein A-I mimetic peptide, or vehicle in which it was dissolved (PBS) was administered daily to LDL receptor–null mice after a Western diet and after influenza infection. D-4F treatment increased plasma HDL cholesterol and paraoxonase activity compared with PBS and inhibited increases in LDL cholesterol and peak levels of interleukin-6 after infection. Lung viral titers were reduced by 50% in mice receiving D-4F. Injection of female mice with male macrophages, which were detected with real-time polymerase chain reaction to measure the male
Sry
gene, revealed a marked increase in macrophage traffic into the aortic arch and innominate arteries after infection that was prevented by administration of D-4F.

Conclusions—

We conclude that loss of antiinflammatory properties of HDL after influenza infection in mice is associated with increased arterial macrophage traffic that can be prevented by administration of D-4F.
Elevated Plasma Aldosterone Levels Despite Complete Inhibition of the Vascular Angiotensin-Converting Enzyme in Chronic Heart Failure
Authors: Jorde Ulrich P. , Vittorio Timothy , Katz Stuart D. , Colombo Paolo C. , Latif Farhana , Le Jemtel Thierry H.
Published: August 2002

Background—

Plasma aldosterone levels are elevated in patients with chronic heart failure (CHF) taking angiotensin-converting enzyme (ACE) inhibitors. Elevated aldosterone levels may reflect incomplete inhibition of the vascular converting enzyme during long-term ACE inhibition. We simultaneously measured plasma aldosterone levels and the degree of inhibition of the vascular converting enzyme in patients with CHF.

Methods and Results—

Thirty-four subjects with CHF receiving the maximum recommended doses of ACE inhibitors for a duration of 3 to 105 months were studied. The pressor response to exogenous angiotensin I (AI) was measured and normalized for the pressor response to angiotensin II (AII) to assess inhibition of the vascular converting enzyme (AII/AI ratio). Aldosterone levels were determined by solid-phase radioimmunoassay. Eleven of the 34 subjects had plasma aldosterone levels above the upper limit of normal, ie, >15.0 ng/dL. Seven of these 11 subjects (64%) had an AII/AI ratio ≤0.05, indicating complete inhibition of the vascular converting enzyme. In the entire cohort, the AII/AI ratio did not correlate with the duration of ACE inhibitor therapy.

Conclusions—

Plasma aldosterone levels are elevated in patients with CHF during long-term ACE inhibitor therapy despite complete inhibition of the vascular converting enzyme. Complete inhibition of the vascular converting enzyme does not obviate the need for aldosterone receptor blockade in patients with CHF.
Persistent Infarct–Related Artery Occlusion Is Associated With an Increased Myocardial Apoptosis at Postmortem Examination in Humans Late After an Acute Myocardial Infarction
Authors: Abbate Antonio , Bussani Rossana , Biondi-Zoccai Giuseppe G.L. , Rossiello Raffaele , Silvestri Furio , Baldi Feliciano , Biasucci Luigi M. , Baldi Alfonso
Published: August 2002

Background—

Myocardial apoptosis persists beyond the acute phases of acute myocardial infarction (AMI) and is associated with left ventricular (LV) remodeling. Infarct-related artery (IRA) patency is considered a favorable prognostic factor after AMI and may be associated with more favorable LV remodeling because of reduced apoptosis at the site of AMI. The aim of this study was to assess the influence of IRA status on apoptotic rate (AR) in the hearts of subjects dying late after AMI.

Methods and Results—

We used colocalization for in situ end-labeling of DNA fragmentation and immunohistochemistry for caspase-3 to calculate the AR at time of death (12 to 62 days after AMI) in 16 hearts with persistently occluded IRAs and in 8 hearts with patent IRAs. No significant differences were found when comparing the clinical characteristics of the 2 groups. Occluded IRA was associated with significantly higher AR at site of infarction (25.8% [interquartile range 20.9% to 28.5%] versus 2.3% [interquartile range 0.6% to 5.0%],
P
<0.001). This strong correlation between IRA occlusion and AR remained statistically significant even after correction for clinical characteristics such as sex, age, history of previous additional AMI or heart failure, transmural AMI, anterior AMI, fibrinolytic treatment, time from AMI to death, trauma as cause of death, and multivessel coronary disease (
P
=0.003).

Conclusions—

A significantly higher AR was associated with persistent IRA occlusion late post-AMI. These data may suggest that the post-AMI benefits observed with a patent IRA (the “open-artery hypothesis”) may in part be due to reduced myocardial apoptosis.
Recommendations of the National Heart, Lung, and Blood Institute Heart and Lung Xenotransplantation Working Group
Authors: Platt Jeffrey , DiSesa Verdi , Gail Dorothy , Massicot-Fisher Judith
Published: August 2002

The National Heart, Lung, and Blood Institute (NHLBI) recently convened the Heart and Lung Xenotransplantation Working Group to identify hurdles to the clinical application of xenotransplantation, defined as the use of animal organs or tissue for transplantation, and to recommend possible solutions to these problems. The group consisted of experts in xenotransplantation from academia, industry, and federal agencies, and the discussions focused on those areas within the mission of the NHLBI. The areas covered included immunologic and physiological barriers to xenotransplantation, the limitations of the current animal models, the need for collaboration among groups, the high costs of studies using nonhuman primates and genetic engineering of pigs, and the unique problems of lung xenotransplantation. This report is a summary of those discussions.
Glucocorticoid Receptors in Hippocampal Neurons that Do Not Engage Proteasomes Escape from Hormone-Dependent Down-Regulation but Maintain Transactivation Activity
Authors: Wang Xinjia , Pongrac Julie L. , DeFranco Donald B.
Published: August 2002

The glucocorticoid receptor (GR) protein is subjected to hormone-dependent down-regulation in most cells and tissues. This reduction in receptor levels that accompanies chronic hormone exposure serves to limit hormone responsiveness and operates at transcriptional, posttranscriptional, and posttranslational levels. The ability of glucocorticoid hormones to trigger GR down-regulation may be not universal, particularly in mature and developing neurons in which conflicting results regarding hormone control of GR protein have been reported. We find that endogenous GR is not down-regulated in the HT22 mouse hippocampal cell line and in primary hippocampal neurons derived from embryonic rats. Because GR has the capacity to be ubiquitylated in HT22 cells, receptor down-regulation must be limited by defects in either targeting of polyubiquitylated receptor to the proteasome or processing of the targeted receptor by the proteasome. Despite the lack of GR down-regulation in the HT22 cells, glucocorticoid-induced transcription from transiently transfected templates is attenuated upon prolonged hormone treatment. This termination of GR transactivation is not due to inefficient nuclear import or nuclear retention of the receptor. Furthermore, GR efficiently exports from HT22 cell nuclei in hormone-withdrawn cells, indicating that the receptor has access to both nuclear and cytoplasmic degradation pathways. Our results suggest that appropriate maturation of proteasomal degradative or targeting activities may be required, particularly in hippocampal neurons, for hormone-dependent down-regulation of GR.
Induction of Cyclooxygenase-2 Gene in Pancreatic β-Cells by 12-Lipoxygenase Pathway Product 12-Hydroxyeicosatetraenoic Acid
Authors: Han Xiao , Chen Songyuan , Sun Yujie , Nadler Jerry L. , Bleich David
Published: August 2002

Cyclooxygenase-2 (COX-2) gene and 12-lipoxygenase (12-LO) gene are preferentially expressed over other types of cyclooxygenase and lipoxygenase in pancreatic β-cells. Inhibition of either COX-2 or 12-LO can prevent cytokine-induced pancreatic β-cell dysfunction as defined by inhibition of glucose-stimulated insulin secretion. As cellular stress induces both genes and their respective end products in pancreatic β-cells, we evaluated the role of 12-hydroxyeicosatetraenoic acid (HETE) on COX-2 gene expression, protein expression, and prostaglandin E2 (PGE2) production.

We demonstrate that 12-HETE significantly increases COX-2 gene expression and consequent product formation, whereas a closely related lipid, 15-HETE, does not. In addition, IL-1β-stimulated prostaglandin E2 production is completely inhibited by a preferential lipoxygenase inhibitor cinnaminyl-3,4-dihydroxy-α-cyanocinnamate.

We then evaluated IL-1β-induced PGE2 production in islets purified from control C57BL/6 mice and 12-LO knockout mice lacking cytokine-inducible 12-HETE. IL-1β stimulated an 8-fold increase in PGE2 production in C57BL/6 islets but failed to stimulate PGE2 in 12-LO knockout islets. Addition of 12-HETE to 12-LO knockout islet cells produced a statistically significant rise in PGE2 production. Furthermore, 12-HETE, but not 15-HETE, stimulated COX-2 promoter and activator protein-1 binding activity. These data demonstrate that 12-HETE mediates cytokine-induced COX-2 gene transcription and resultant PGE2 production in pancreatic β-cells.
Persistent Parity-Induced Changes in Growth Factors, TGF-β3, and Differentiation in the Rodent Mammary Gland
Authors: D’Cruz Celina M. , Moody Susan E. , Master Stephen R. , Hartman Jennifer L. , Keiper Elizabeth A. , Imielinski Marcin B. , Cox James D. , Wang James Y. , Ha Seung I. , Keister Blaine A. , Chodosh Lewis A.
Published: August 2002

Epidemiological studies have repeatedly demonstrated that women who undergo an early first full-term pregnancy have a significantly reduced lifetime risk of breast cancer. Similarly, rodents that have previously undergone a full-term pregnancy are highly resistant to carcinogen-induced breast cancer compared with age-matched nulliparous controls. Little progress has been made, however, toward understanding the biological basis of this phenomenon. We have used DNA microarrays to identify a panel of 38 differentially expressed genes that reproducibly distinguishes, in a blinded manner, between the nulliparous and parous states of the mammary gland in multiple strains of mice and rats. We find that parity results in the persistent down-regulation of multiple genes encoding growth factors, such as amphiregulin, pleiotrophin, and IGF-1, as well as the persistent up-regulation of the growth-inhibitory molecule, TGF-β3, and several of its transcriptional targets. Our studies further indicate that parity results in a persistent increase in the differentiated state of the mammary gland as well as lifelong changes in the hematopoietic cell types resident within the gland. These findings define a developmental state of the mammary gland that is refractory to carcinogenesis and suggest novel hypotheses for the mechanisms by which parity may modulate breast cancer risk.
The Effect of Suppressor of Cytokine Signaling 3 on GH Signaling in β-Cells
Authors: Rønn Sif G. , Hansen Johnny A. , Lindberg Karen , Karlsen Allan E. , Billestrup Nils
Published: August 2002

GH is an important regulator of cell growth and metabolism. In the pancreas, GH stimulates mitogenesis as well as insulin production in β-cells. The cellular effects of GH are exerted mainly through activation of the Janus kinase-signal transducer and activator of transcription (STAT) pathway. Recently it has been found that suppressors of cytokine signaling (SOCS) proteins are able to inhibit GH-induced signal transduction. In the present study, the role of SOCS-3 in GH signaling was investigated in the pancreatic β-cell lines RIN-5AH and INS-1 by means of inducible expression systems. Via stable transfection of the β-cell lines with plasmids expressing SOCS-3 under the control of an inducible promoter, a time- and dose-dependent expression of SOCS-3 in the cells was obtained. EMSA showed that SOCS-3 is able to inhibit GH-induced DNA binding of both STAT3 and STAT5 in RIN-5AH cells. Furthermore, using Northern blot analysis it was shown that SOCS-3 can completely inhibit GH-induced insulin production in these cells. Finally, 5-bromodeoxyuridine incorporation followed by fluorescence-activated cell sorting analysis showed that SOCS-3 inhibits GH-induced proliferation of INS-1 cells. These findings support the hypothesis that SOCS-3 is a major regulator of GH signaling in insulin-producing cells.
The Mineralocorticoid Receptor May Compensate for the Loss of the Glucocorticoid Receptor at Specific Stages of Mammary Gland Development
Authors: Kingsley-Kallesen Michelle , Mukhopadhyay Sudit S. , Wyszomierski Shannon L. , Schanler Susan , Schütz Günther , Rosen Jeffrey M.
Published: August 2002

To study the role of glucocorticoid receptor (GR) at different stages of mammary gland development, mammary anlage were rescued from GR−/− mice by transplantation into the cleared fat pad of wild-type mice. In virgin mice, GR−/− outgrowths displayed abnormal ductal morphogenesis characterized by distended lumena, multiple layers of luminal epithelial cells in some regions along the ducts, and increased periductal stroma. In contrast, the loss of GR did not result in overt phenotypic changes in mammary gland development during pregnancy, lactation, and involution. Surprisingly, despite the known synergism between glucocorticoids and prolactin in the regulation of milk protein gene expression, whey acidic protein and β-casein mRNA levels were unaffected in GR−/− transplants as compared with wild-type transplants. That mineralocorticoid receptor (MR) might compensate for the loss of GR was suggested by the detection of MR in the mammary gland at d 1 of lactation. This hypothesis was tested using explant cultures derived from the GR−/− transplants in which the mineralocorticoid fludrocortisone was able to synergistically induce β-casein gene expression in the presence of prolactin and insulin. These studies suggest that MR may compensate for the absence of GR at some, but not at all stages of mammary gland development.
Ubc6p and Ubc7p Are Required for Normal and Substrate-Induced Endoplasmic Reticulum-Associated Degradation of the Human Selenoprotein Type 2 Iodothyronine Monodeiodinase
Authors: Botero Diego , Gereben Balazs , Goncalves Carla , de Jesus Lucia A. , Harney John W. , Bianco Antonio C.
Published: August 2002

The type 2 monodeiodinase (D2) is an endoplasmic reticulum-resident membrane selenoprotein responsible for catalyzing the first step in thyroid hormone action, T4 deiodination to T3. Its short half-life is due to ubiquitination and proteolysis by proteasomes, a mechanism that is accelerated by D2 interaction with T4. To identify proteins involved in D2 ubiquitination, a FLAG-tagged selenocystine133-to-Cys mutation of the human D2 (CysD2) was created and expressed in Saccharomyces cerevisiae using the GAL1 gene promoter. CysD2 activity was detected in the microsomes, indistinguishable from transiently expressed CysD2 in vertebrate cells. Treatment with 100 mg/ml cycloheximide or 30 μm T4 caused rapid loss of CysD2 (t1/2 = ∼30 min). Clasto-lactacystin β-lactone not only increased galactose-inducible CysD2 but also stabilized CysD2 in the presence of cycloheximide or T4. Immunoprecipitation with anti-FLAG antibody combined with Western analysis with antiubiquitin revealed that CysD2 is heavily ubiquitinated. Expression of CysD2 in yeast strains that lack the ubiquitin conjugases Ubc6p or Ubc7p stabilized CysD2 half-life by markedly reducing CysD2 ubiquitination, whereas no difference was detected in Ubc1p-deficient mutants. Similarly, expression of CysD2 in UBC6 and UBC7 mutants also impaired the substrate-induced loss of CysD2 activity and protein. In conclusion, Ubc6p and Ubc7p are required for normal and substrate-induced ubiquitination and proteolysis of D2.
GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming
Authors: Howe Kevin L. , Chothia Tom , Durbin Richard
Published: September 2002

We describe a method (implemented in a program, GAZE) for assembling arbitrary evidence for individual gene components (features) into predictions of complete gene structures. Our system is generic in that both the features themselves, and the model of gene structure against which potential assemblies are validated and scored, are external to the system and supplied by the user. GAZE uses a dynamic programming algorithm to obtain the highest scoring gene structure according to the model and posterior probabilities that each input feature is part of a gene. A novel pruning strategy ensures that the algorithm has a run-time effectively linear in sequence length. To demonstrate the flexibility of our system in the incorporation of additional evidence into the gene prediction process, we show how it can be used to both represent nonstandard gene structures (in the form oftrans-spliced genes in Caenorhabditis elegans), and make use of similarity information (in the form of Expressed Sequence Tag alignments), while requiring no change to the underlying software. GAZE is available athttp://www.sanger.ac.uk/Software/analysis/GAZE.
Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region
Authors: Toyoda Atsushi , Noguchi Hideki , Taylor Todd D. , Ito Takehiko , Pletcher Mathew T. , Sakaki Yoshiyuki , Reeves Roger H. , Hattori Masahira
Published: September 2002

Comprehensive knowledge of the gene content of human chromosome 21 (HSA21) is essential for understanding the etiology of Down syndrome (DS). Here we report the largest comparison of finished mouse and human sequence to date for a 1.35-Mb region of mouse chromosome 16 (MMU16) that corresponds to human chromosome 21q22.2. This includes a portion of the commonly described “DS critical region,” thought to contain a gene or genes whose dosage imbalance contributes to a number of phenotypes associated with DS. We used comparative sequence analysis to construct a DNA feature map of this region that includes all known genes, plus 144 conserved sequences ≥100 bp long that show ≥80% identity between mouse and human but do not match known exons. Twenty of these have matches to expressed sequence tag and cDNA databases, indicating that they may be transcribed sequences from chromosome 21. Eight putative CpG islands are found at conserved positions. Models for two human genes, DSCR4 and DSCR8, are not supported by conserved sequence, and close examination indicates that low-level transcripts from these loci are unlikely to encode proteins. Gene prediction programs give different results when used to analyze the well-conserved regions between mouse and human sequences. Our findings have implications for evolution and for modeling the genetic basis of DS in mice.

[Sequence data described in this paper have been submitted to the DDBJ/GenBank under accession nos. AP003148through AP003158, and AB066227. Supplemental material is available athttp://www.genome.org.]
Patterns of Positive Selection in the Complete NBS-LRR Gene Family of Arabidopsis thaliana
Authors: Mondragón-Palomino Mariana , Meyers Blake C. , Michelmore Richard W. , Gaut Brandon S.
Published: September 2002

Plant disease resistance genes have been shown to be subject to positive selection, particularly in the leucine rich repeat (LRR) region that may determine resistance specificity. We performed a genome-wide analysis of positive selection in members of the nucleotide binding site (NBS)-LRR gene family of Arabidopsis thaliana. Analyses were possible for 103 of 163 NBS-LRR nucleotide sequences in the genome, and the analyses uncovered substantial evidence of positive selection. Sites under positive selection were detected and identified for 10 sequence groups representing 53 NBS-LRR sequences. Functionally characterized Arabidopsis resistance genes were in these 10 groups, but several groups with extensive evidence of positive selection contained no previously characterized resistance genes. Amino acid residues under positive selection were identified, and these residues were mapped onto protein secondary structure. Positively selected positions were disproportionately located in the LRR domain (P < 0.001), particularly a nine–amino acid β-strand submotif that is likely to be solvent exposed. However, a substantial proportion (30%) of positively selected sites were located outside LRRs, suggesting that regions other than the LRR may function in determining resistance specificity. Because of the unusual sequence variability in the LRRs of this class of proteins, secondary-structure analysis identifies LRRs that are not identified by similarity analyses alone. LRRs also contain substantial indel variation, suggesting elasticity in LRR length could also influence resistance specificity.
Genome-Wide Analysis of the Odorant-Binding Protein Gene Family in Drosophila melanogaster
Authors: Hekmat-Scafe Daria S. , Scafe Charles R. , McKinney Aimee J. , Tanouye Mark A.
Published: September 2002

Olfaction is of considerable importance to many insects in behaviors critical for survival and reproduction, including location of food sources, selection of mates, recognition of colony con-specifics, and determination of oviposition sites. An ubiquitous, but poorly understood, component of the insect's olfactory system is a group of odorant-binding proteins (OBPs) that are present at high concentrations in the aqueous lymph surrounding the dendrites of olfactory receptor neurons. OBPs are believed to shuttle odorants from the environment to the underlying odorant receptors, for which they could potentially serve as odorant presenters. Here we show that the Drosophilagenome carries 51 potential OBP genes, a number comparable to that of its odorant-receptor genes. We find that the majority (73%) of these OBP-like genes occur in clusters of as many as nine genes, in contrast to what has been observed for the Drosophila odorant-receptor genes. Two of the presumptive OBP gene clusters each carries an odorant-receptor gene. We also report an intriguing subfamily of 12 putative OBPs that share a unique C-terminal structure with three conserved cysteines and a conserved proline. Members of this subfamily have not previously been described for any insect. We have performed phylogenetic analyses of the OBP-related proteins inDrosophila as well as other insects, and we discuss the duplication and divergence of the genes for this large family.

[The sequence data from this study have been submitted to FlyBase. Annotations for these sequences are available as supplementary material at http://www.genome.org.]
Detection and Visualization of Compositionally Similar cis-Regulatory Element Clusters in Orthologous and Coordinately Controlled Genes
Authors: Jegga Anil G. , Sherwood Shawn P. , Carman James W. , Pinski Andrew T. , Phillips Jerry L. , Pestian John P. , Aronow Bruce J.
Published: September 2002

Evolutionarily conserved noncoding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. However, detecting and visualizing compositionally similarcis-element clusters in the context of conserved sequences is challenging. We have explored potential solutions and developed an algorithm and visualization method that combines the results of conserved sequence analyses (BLASTZ) with those of transcription factor binding site analyses (MatInspector) (http://trafac.chmcc.org). We define hits as the density of co-occurring cis-element transcription factor (TF)-binding sites measured within a 200-bp moving average window through phylogenetically conserved regions. The results are depicted as a Regulogram, in which the hit count is plotted as a function of position within each of the two genomic regions of the aligned orthologs. Within a high-scoring region, the relative arrangement of sharedcis-elements within compositionally similar TF-binding site clusters is depicted in a Trafacgram. On the basis of analyses of several training data sets, the approach also allows for the detection of similarities in composition and relative arrangement ofcis-element clusters within nonorthologous genes, promoters, and enhancers that exhibit coordinate regulatory properties. Known functional regulatory regions of nonorthologous and less-conserved orthologous genes frequently showed cis-element shuffling, demonstrating that compositional similarity can be more sensitive than sequence similarity. These results show that combining sequence similarity with cis-element compositional similarity provides a powerful aid for the identification of potential control regions.
Function ofPseudomonasPorins in Uptake and Efflux
Authors: Hancock Robert E. W. , Brinkman Fiona S. L.
Published: September 2002

▪ Abstract  Porins are proteins that form water-filled channels across the outer membranes of Gram-negative bacteria and thus make this membrane semipermeable. There are four types of porins: general/nonspecific porins, substrate-specific porins, gated porins, and efflux porins (also called channel-tunnels). The recent publication of the genomic sequence of Pseudomonas aeruginosa PAO1 has dramatically increased our understanding of the porins of this organism. In particular this organism has 3 large families of porins: the OprD family of specific porins (19 members), the OprM family of efflux porins (18 members), and the TonB-interacting family of gated porins (35 members). These familial relationships underlie functional similarities such that well-studied members of these families become prototypes for other members. We summarize here the latest information on these porins.
Bioterrorism: From Threat to Reality
Authors: Atlas Ronald M.
Published: September 2002

▪ Abstract  The fears and predictions of attacks with biological weapons, which were increasing at the close of the twentieth century, were transformed into reality not long after September 11, 2001, when several anthrax-laden letters were sent through the U.S. postal system. The attack challenged our medical preparedness and scientific understanding of the epidemiology of biothreat agents. It is fortunate that this was not a massive aerosol release that could have exposed hundreds of thousands. Rapid diagnoses and medical treatments limited casualties and increased survival rates, but tragically some individuals died of inhalational anthrax. Even as physicians tested new treatment regimes and scientists employed new ways of detecting anthrax and decontaminating the mail, new predictions were made for potentially even more devastating attacks with anthrax, smallpox, plague, tularemia, botulism, or hemorrhagic fever viruses. Fear gripped the nation. Law enforcement sought to find the villain(s) who sent the anthrax letters and to deter future bioterrorist attacks. The biomedical community began to seek new ways of protecting against such future threats of bioterrorism.
Bacterial Chromosome Segregation
Authors: Draper Geoffrey C. , Gober James W.
Published: September 2002

▪ Abstract  Recent studies have made great strides toward our understanding of the mechanisms of microbial chromosome segregation and partitioning. This review first describes the mechanisms that function to segregate newly replicated chromosomes, generating daughter molecules that are viable substrates for partitioning. Then experiments that address the mechanisms of bulk chromosome movement are summarized. Recent evidence indicates that a stationary DNA replication factory may be responsible for supplying the force necessary to move newly duplicated DNA toward the cell poles. Some factors contributing to the directionality of chromosome movement probably include centromere-like-binding proteins, DNA condensation proteins, and DNA translocation proteins.
Inteins: Structure, Function, and Evolution
Authors: Gogarten J. Peter , Senejani Alireza G. , Zhaxybayeva Olga , Olendzenski Lorraine , Hilario Elena
Published: September 2002

▪ Abstract  Inteins are genetic elements that disrupt the coding sequence of genes. However, in contrast to introns, inteins are transcribed and translated together with their host protein. Inteins appear most frequently in Archaea, but they are found in organisms belonging to all three domains of life and in viral and phage proteins. Most inteins consist of two domains: One is involved in autocatalytic splicing, and the other is an endonuclease that is important in the spread of inteins. This review focuses on the evolution and technical application of inteins and only briefly summarizes recent advances in the study of the catalytic activities and structures of inteins. In particular, this review considers inteins as selfish or parasitic genetic elements, a point of view that explains many otherwise puzzling aspects of inteins.
Microbial Degradation of Polyhydroxyalkanoates
Authors: Jendrossek Dieter , Handrick René
Published: September 2002

▪ Abstract  Polyesters such as poly(3-hydroxybutyrate) (PHB) or other polyhydroxyalkanoates (PHA) have attracted commercial and academic interest as new biodegradable materials. The ability to degrade PHA is widely distributed among bacteria and fungi and depends on the secretion of specific extracellular PHA depolymerases (e-PHA depolymerases), which are carboxyesterases (EC 3.1.1.75 and EC 3.1.1.76), and on the physical state of the polymer (amorphous or crystalline). This contribution provides a summary of the biochemical and molecular biological characteristics of e-PHA depolymerases and focuses on the intracellular mobilization of storage PHA by intracellular PHA depolymerases (i-PHA depolymerases) of PHA-accumulating bacteria. The importance of different assay systems for PHA depolymerase activity is also discussed.
Genome Remodeling in Ciliated Protozoa
Authors: Jahn Carolyn L. , Klobutcher Lawrence A.
Published: September 2002

▪ Abstract  The germline genomes of ciliated protozoa are dynamic structures, undergoing massive DNA rearrangement during the formation of a functional macronucleus. Macronuclear development involves chromosome fragmentation coupled with de novo telomere synthesis, numerous DNA splicing events that remove internal segments of DNA, and, in some ciliates, the reordering of scrambled gene segments. Despite the fact that all ciliates share similar forms of DNA rearrangement, there appears to be great diversity in both the nature of the rearranged DNA and the molecular mechanisms involved. Epigenetic effects on rearrangement have also been observed, and recent work suggests that chromatin differentiation plays a role in specifying DNA segments either for rearrangement or for elimination.
The Class Mesomycetozoea: A Heterogeneous Group of Microorganisms at the Animal-Fungal Boundary
Authors: Mendoza Leonel , Taylor John W. , Ajello Libero
Published: September 2002

▪ Abstract  When the enigmatic fish pathogen, the rosette agent, was first found to be closely related to the choanoflagellates, no one anticipated finding a new group of organisms. Subsequently, a new group of microorganisms at the boundary between animals and fungi was reported. Several microbes with similar phylogenetic backgrounds were soon added to the group. Interestingly, these microbes had been considered to be fungi or protists. This novel phylogenetic group has been referred to as the DRIP clade (an acronym of the original members: Dermocystidium, rosette agent, Ichthyophonus, and Psorospermium), as the class Ichthyosporea, and more recently as the class Mesomycetozoea. Two orders have been described in the mesomycetozoeans: the Dermocystida and the Ichthyophonida. So far, all members in the order Dermocystida have been pathogens either of fish (Dermocystidium spp. and the rosette agent) or of mammals and birds (Rhinosporidium seeberi), and most produce uniflagellated zoospores. Fish pathogens also are found in the order Ichthyophonida, but so are saprotrophic microbes. The Ichthyophonida species do not produce flagellated cells, but many produce amoeba-like cells. This review provides descriptions of the genera that comprise the class Mesomycetozoea and highlights their morphological features, pathogenic roles, and phylogenetic relationships.
The Bittersweet Interface of Parasite and Host: Lectin-Carbohydrate Interactions During Human Invasion by the ParasiteEntamoeba histolytica
Authors: Petri William A. , Haque Rashidul , Mann Barbara J.
Published: September 2002

▪ Abstract  Entamoeba histolytica, as its name suggests, is an enteric parasite with a remarkable ability to lyse host tissues. However, the interaction of the parasite with the host is more complex than solely destruction and invasion. It is at the host-parasite interface that cell-signaling events commit the parasite to (a) commensal, noninvasive infection, (b) developmental change from trophozoite to cyst, or (c) invasion and potential death of the human host. The molecule central to these processes is an amebic cell surface protein that recognizes the sugars galactose (Gal) and N-acetylgalactosamine (GalNAc) on the surface of host cells. Engagement of the Gal/GalNAc lectin to the host results in cytoskeletal reorganization in the parasite. The parasite cytoskeleton regulates the extracellular adhesive activity of the lectin and recruits to the host-parasite interface factors required for parasite survival within its host. If the parasite lectin attaches to the host mucin glycoproteins lining the intestine, the result is commensal infection. In contrast, attachment of the lectin to a host cell surface glycoprotein leads to lectin-induced host cell calcium transients, caspase activation, and destruction via apoptosis. Finally, trophozoite quorum sensing via the lectin initiates the developmental pathway resulting in encystment. The structure and function of the lectin that controls these divergent cell biologic processes are the subject of this review.
Heavy Metal Mining Using Microbes
Authors: Rawlings Douglas E.
Published: September 2002

▪ Abstract  The use of acidiphilic, chemolithotrophic iron- and sulfur-oxidizing microbes in processes to recover metals from certain types of copper, uranium, and gold-bearing minerals or mineral concentrates is now well established. During these processes insoluble metal sulfides are oxidized to soluble metal sulfates. Mineral decomposition is believed to be mostly due to chemical attack by ferric iron, with the main role of the microorganisms being to reoxidize the resultant ferrous iron back to ferric iron. Currently operating industrial biomining processes have used bacteria that grow optimally from ambient to 50°C, but thermophilic microbes have been isolated that have the potential to enable mineral biooxidation to be carried out at temperatures of 80°C or higher. The development of higher-temperature processes will extend the variety of minerals that can be commercially processed.
Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome
Authors: Zavolan Mihaela , van Nimwegen Erik , Gaasterland Terry
Published: September 2002

We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed draft of the mouse genome. Using this mapping, we identified 3674 mouse genes with multiple transcripts, of which 1098 have splice variants. All but 532 of 21,076 clones (97.5%) mapped to the genome assembly. Alignments of cDNA clone sequences with proteins show that much of the detected splice variation alters coding regions and affects the translated protein. We developed novel analytical techniques to classify observed splice variation and to assess the relation between splice variation and alternative transcription. This analysis indicates that an alternative choice of transcription start or polyadenylation signal frequently induces splice variation.
Temperature-Regulated Transcription in the Pathogenic Fungus Cryptococcus neoformans
Authors: Steen Barbara R. , Lian Tian , Zuyderduyn Scott , MacDonald William Kim , Marra Marco , Jones Steven J.M. , Kronstad James W.
Published: September 2002

The basidiomycete fungus Cryptococcus neoformans is an opportunistic pathogen of worldwide importance that causes meningitis, leading to death in immunocompromised individuals. Unlike many basidiomycete fungi, C. neoformans is thermotolerant, and its ability to grow at 37°C is considered to be a virulence factor. We used serial analysis of gene expression (SAGE) to characterize the transcriptomes of C. neoformans strains that represent two varieties with different polysaccharide capsule serotypes. These include a serotype D strain of the C. neoformans varietyneoformans and a serotype A strain of variety grubii. In this report, we describe the construction and characterization of SAGE libraries from each strain grown at 25°C and 37°C. The SAGE data reveal transcriptome differences between the two strains, even at this early stage of analysis, and identify sets of genes with higher transcript levels at 25°C or 37°C. Notably, growth at the lower temperature increased transcript levels for histone genes, indicating a general influence of temperature on chromatin structure. At 37°C, we noted elevated transcript levels for several genes encoding heat shock proteins and translation machinery. Some of these genes may play a role in temperature-regulated phenotypes in C. neoformans, such as the adaptation of the fungus to growth in the host and the dimorphic transition between budding and filamentous growth. Overall, this work provides the most comprehensive gene expression data available forC. neoformans; this information will be a critical resource both for gene discovery and genome annotation in this pathogen.

[This paper is dedicated to the memory of Michael Smith, founding director of the Biotechnology Laboratory and the British Columbia Genome Sciences Centre. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: Brendan Loftus, Claire Fraser, Richard Hyman, Eula Fung, Don Rowley, Ron Davis , Bruce A. Roe, Doris Kupfer, Jennifer Lewis, Sola Yu, Kent Buchanan, Dave Dyer, and Juneann Murphy.]
Menacing Mold: The Molecular Biology of Aspergillus fumigatus
Authors: Brakhage Axel A. , Langfelder Kim
Published: September 2002

▪ Abstract  Infections with mold pathogens have emerged as an increasing risk faced by patients under sustained immunosuppression. Species of the Aspergillus family account for most of these infections, and in particular Aspergillus fumigatus may be regarded as the most important airborne pathogenic fungus. The improvement in transplant medicine and the therapy of hematological malignancies is often complicated by the threat of invasive aspergillosis. Specific diagnostic methods are still limited as are the possibilities of therapeutic intervention, leading to the disappointing fact that invasive aspergillosis is still associated with a high mortality rate that ranges from 30% to 90%. In recent years considerable progress has been made in understanding the genetics of A. fumigatus, and molecular techniques for the manipulation of the fungus have been developed. Molecular genetics offers not only approaches for the detailed characterization of gene products that appear to be key components of the infection process but also selection strategies that combine classical genetics and molecular biology to identify virulence determinants of A. fumigatus. Moreover, these methods have a major impact on the development of novel strategies leading to the identification of antimycotic drugs. This review summarizes the current knowledge on the biology, molecular genetics, and genomics of A. fumigatus.
What are Bacterial Species?
Authors: Cohan Frederick M.
Published: September 2002

▪ Abstract  Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.