zA map for sequence analysis of the Arabidopsis thaliana genome.

Arabidopsis thaliana has emerged as a model system for studies of plant genetics and development, and its genome has been targeted for sequencing by an international consortium (the Arabidopsis Genome Initiative; http://genome-www. stanford.edu/Arabidopsis/agi.html). To support the genome-sequencing effort, we fingerprinted more than 20,000 BACs (ref. 2) from two high-quality publicly available libraries, generating an estimated 17-fold redundant coverage of the genome, and used the fingerprints to nucleate assembly of the data by computer. Subsequent manual revision of the assemblies resulted in the incorporation of 19,661 fingerprinted BACs into 169 ordered sets of overlapping clones ('contigs'), each containing at least 3 clones. These contigs are ideal for parallel selection of BACs for large-scale sequencing and have supported the generation of more than 5.8 Mb of finished genome sequence submitted to GenBank; analysis of the sequence has confirmed the integrity of contigs constructed using this fingerprint data. Placement of contigs onto chromosomes can now be performed, and is being pursued by groups involved in both sequencing and positional cloning studies. To our knowledge, these data provide the first example of whole-genome random BAC fingerprint analysis of a eucaryote, and have provided a model essential to efforts aimed at generating similar databases of fingerprint contigs to support sequencing of other complex genomes, including that of human.

Anatomy of subcritical submarine flows with a lutocline and an intermediate destruction layer.

Turbidity currents are sediment-laden flows that travel over a sloping bed under a stagnant ambient fluid, driven by the density difference between the current and the ambient. Turbidity currents transport large amounts of carbon, nutrients and fresh water through oceans and play an important role in global geochemical cycling and seafloor ecosystems. Supercritical currents are observed in steeper slopes. Subcritical currents are observed in milder slopes, where the near-bed and interface layers are prevented from interacting across the velocity maximum. Past works show the existence of such a barrier to vertical momentum transfer is essential for the body of the subcritical current to extend over hundreds of kilometers in length without much increase in height. Here we observe the body of subcritical currents to have a three layer structure, where the turbulent near-bed layer and the non-turbulent interface layer are separated by an intermediate layer of negative turbulence production. We explain the mechanism by which this layer prevents the near-bed turbulent structures from penetrating into the interface layer by transferring energy back from turbulence to the mean flow.

Gastrojejunal stricture after gastric bypass and efficacy of endoscopic intervention.

The Roux-en-Y gastric bypass procedure (RYGBP) is an effective treatment for morbid obesity. Anastomotic strictures are a common complication after RYGBP. This study examines the frequency of post-RYGBP gastrojejunal strictures (GJS), methods of evaluation, and the outcome of endoscopic intervention. Medical records of patients who had RYGBP for morbid obesity at our institution during four consecutive years were reviewed for patient demographics, medical comorbidities, surgical technique, and outcomes. Radiographic and endoscopic findings of those patients suspected to have GJS were noted. The impact of patient-related variables and surgical technique on risk of GJS, time to diagnosis of GJS, and treatment outcomes for GJS was determined. Of 888 patients, 503 had open RYGBP (57%) and 385 laparoscopic RYGBP (43%). Ninety-four patients (10.6%) underwent esophagogastroduodenoscopy (EGD) for possible GJS and 58 (6.5%) were found to have anastomotic stricture. Laparoscopic RYGBP was associated with increased incidence of GJS (43/385, 11.1%) compared with open RYGBP (15/503 or 2.9%, P = 0.0003). A total of 125 dilations were performed with an average of 2.2 dilations per patient. None of the strictures needed surgical revision. There were four perforations (3.2%) related to EGD. Mean time to diagnosis of GJS was 66.2 days. Eighty-seven of 94 patients underwent radiologic upper gastrointestinal (UGI) evaluation prior to EGD. UGI evaluation demonstrated a positive predictive value (PPV) of only 66% [95% confidence interval (CI) 52-77], and negative predictive value (NPV) of 83% (95% CI 65-93). Laparoscopic GBP is associated with increased risk of GJS. Endoscopic dilation of GJS is an effective treatment with minimal risk. Radiographic studies appear to have poor specificity for diagnosis of GJS and have a low positive predictive value. EGD should be performed in all suspected cases of GJS.

Dose-escalation and pharmacodynamic study of topotecan in combination with cyclophosphamide in patients with refractory cancer.

PURPOSE: Based on preclinical data that demonstrated synergy between alkylating agents and topoisomerase (topo) I poisons, we determined the maximum-tolerated dose (MTD) of topotecan, using a 5 day bolus schedule, that could be given in combination with a single, fixed dose of cyclophosphamide. Pharmacodynamics of this combination were explored by analyzing biochemical effects of treatment in peripheral-blood mononuclear cells (PBMCs). PATIENTS AND METHODS: Patients with refractory cancer were treated with cyclophosphamide 600 mg/m2 on day 1, followed by topotecan given as a 30-minute infusion for 5 consecutive days. Cycles were repeated every 3 weeks. Once the MTD was defined, granulocyte colony-stimulating factor (G-CSF) was added to the regimen in an attempt to escalate further the dose of topotecan. Plasma concentrations of topotecan were determined during the first treatment cycle by high-performance liquid chromatography. PBMCs were sampled at baseline and throughout the 5-day treatment period for analysis of topo I protein concentrations and to determine drug-induced DNA fragmentation. RESULTS: Twenty-six patients were treated with topotecan at doses that ranged from 0.5 mg/m2/d to 1.2 mg/ m2/d for a total of 74 cycles. Reversible neutropenia was dose-limiting, with mild to moderate suppression of the other blood-cell elements commonly occurring. Transfusions of RBCs and platelets were required in 24% and 7% of treatment cycles, respectively. The most prominent nonhematologic toxicities were fatigue and weight loss. Compared with previously published data in which topotecan was administered alone, cyclophosphamide did not appear to alter the pharmacokinetics of topotecan. Significant increases in topo I concentration were identified in PBMCs following the administration of cyclophosphamide on day 1 and there was a significant decrease in topo 1 during the 5-day course of treatment (P < .01, sign test). DNA fragmentation as a result of drug treatment was identified in 11 of 15 (73%) cycles analyzed. CONCLUSION: For previously treated patients, the recommended dose of topotecan in this schedule is 0.75 mg/m2/d without growth factor support and 1.0 mg/ m2/d if it is administered with G-CSF. Biochemical changes in cells induced by exposure to camptothecins can be measured in vivo and these effects may have important implication in the design of combination therapies and the optimal scheduling of this class of agents.