Allosteric control of Escherichia coli rRNA promoter complexes by DksA.

The Escherichia coli DksA protein inserts into the RNA polymerase (RNAP) secondary channel, modifying the transcription initiation complex so that promoters with specific kinetic characteristics are regulated by changes in the concentrations of ppGpp and NTPs. We used footprinting assays to determine the specific kinetic intermediate, RP(I), on which DksA acts. Genetic approaches identified substitutions in the RNAP switch regions, bridge helix, and trigger loop that mimicked, reduced, or enhanced DksA function on rRNA promoters.

Sequence-dependent upstream DNA-RNA polymerase interactions in the open complex with lambdaPR and lambdaPRM promoters and implications for the mechanism of promoter interference.

Upstream interactions of Escherichia coli RNA polymerase (RNAP) in an open promoter complex (RPo) formed at the P(R) and P(RM) promoters of bacteriophage lambda have been studied by atomic force microscopy. We demonstrate that the previously described 30-nm DNA compaction observed upon RPo formation at P(R) [Rivetti, C., Guthold, M.

Adenocarcinoma of the lower esophagus with Barrett's esophagus or without Barrett's esophagus: differences in patients' survival after preoperative chemoradiation.

It remains unclear whether the overall survival (OS) of patients with localized esophageal adenocarcinoma (LEA) with Barrett's esophagus (BE) (Barrett's-positive) and those with LEA without BE (Barrett's-negative) following preoperative chemoradiation is different. Based on the published differences in the molecular biology of the two entities, we hypothesized that the two groups will have a different clinical biology (and OS). In this retrospective analysis, all patients with LEA had surgery following preoperative chemoradiation.

Color M-mode echocardiography is more reproducible than conventional M-mode echocardiography for septal-to-posterior wall motion delay measurements.

Objective: To compare the reproducibility of conventional gray-scale M-mode to color Doppler M-mode assessment of the septal-to-posterior wall motion delay (SPWMD) which is used as a marker of left ventricular mechanical dyssynchrony.

Methods: Forty-two SPWMD datasets were interpreted by two experienced cardiologists and the inter- and intraobserver correlation coefficients were determined. Subgroup analysis was performed on patients with severe septal wall motion abnormalities.

Analysis of RNA polymerase-promoter complex formation.

Bacterial promoter identification and characterization is not as straightforward as one might presume. Promoters vary widely in their similarity to the consensus recognition element sequences, in their activities, and in their utilization of transcription factors, and multiple approaches often must be used to provide a framework for understanding promoter regulation. Characterization of RNA polymerase-promoter complex formation in the absence of additional regulatory factors (basal promoter function) can provide a basis for understanding the steps in transcription initiation that are ultimately targeted by nutritional or environmental factors.

Insulin sensitivity is normalized in the third generation (F3) offspring of developmentally programmed insulin resistant (F2) rats fed an energy-restricted diet.

Background/aims: The offspring and grandoffspring of female rats fed low protein diets during pregnancy and lactation, but fed nutritionally adequate diets thereafter, have been shown to exhibit altered insulin sensitivity in adulthood. The current study investigates the insulin sensitivity of the offspring and grandoffspring of female rats fed low protein diets during pregnancy, and then maintained on energy-restricted diets post weaning over three generations.

Methods: Female Sprague Dawley rats (F0) were mated with control males and protein malnourished during pregnancy/lactation.

Prognosis of oocyte donation cycles: a prospective comparison of the in vitro fertilization-embryo transfer cycles of recipients who used shared oocytes versus those who used altruistic donors.

Objective: To prospectively compare the prognosis of IVF-ET cycles using oocyte sharing vs. cycles using altruistic donors.

Design: Prospective cohort prognostic study.

Preoperative gemcitabine and cisplatin followed by gemcitabine-based chemoradiation for resectable adenocarcinoma of the pancreatic head.

Purpose: We conducted a phase II trial of preoperative gemcitabine and cisplatin chemotherapy in addition to chemoradiation (Gem-Cis-XRT) and pancreaticoduodenectomy (PD) for patients with stage I/II pancreatic adenocarcinoma.

Patients And Methods: Chemotherapy consisted of gemcitabine (750 mg/m(2)) and cisplatin (30 mg/m(2)) given every 2 weeks for four doses. Chemoradiation consisted of four weekly infusions of gemcitabine (400 mg/m(2)) combined with radiation therapy (30 Gy in 10 fractions administered over 2 weeks) delivered 5 days per week.

A new method for simultaneous determination of cyclic antidepressants and their metabolites in urine using enzymatic hydrolysis and fast GC-MS.

A method for the simultaneous determination of six commonly prescribed cyclic antidepressants and their major metabolites in urine is presented. This method can be used for quantitation of amitriptyline, nortriptyline, imipramine, desipramine, doxepin, desmethyldoxepin, and maprotiline in human urine, in addition to the qualitative determination of their hydroxylated metabolites. This method is suitable for confirmation of drug abuse in health care professionals and overdose cases where the identity of the abused cyclic antidepressant may not be known.

Advances in bacterial promoter recognition and its control by factors that do not bind DNA.

Early work identified two promoter regions, the -10 and -35 elements, that interact sequence specifically with bacterial RNA polymerase (RNAP). However, we now know that several additional promoter elements contact RNAP and influence transcription initiation. Furthermore, our picture of promoter control has evolved beyond one in which regulation results solely from activators and repressors that bind to DNA sequences near the RNAP binding site: many important transcription factors bind directly to RNAP without binding to DNA.

Significance of thromboembolic phenomena occurring before and during chemoradiotherapy for localized carcinoma of the esophagus and gastroesophageal junction.

Thromboembolic event (TEE) is the most common complication and a second cause of mortality in cancer patients. Multiple hypotheses for occurrence of TEE have been proposed. There are no reports on the frequency/impact of TEE in localized gastroesophageal cancer patients.

Ovarian activity is differentially regulated across the breeding season in immature compared with adult American crows (Corvus brachyrhynchos).

American crow (Corvus brachyrhynchos) reproduction is seasonal. While photoperiod alters reproductive physiology and behavior in nesting adults, whether seasonal photoperiod changes alter ovarian activity in nonnesting adult and immature birds was not known. Ovarian follicular composition was examined in immature and nonnesting adult crows.

Rate of bilirubin regression after stenting in malignant biliary obstruction for the initiation of chemotherapy: how soon should we repeat endoscopic retrograde cholangiopancreatography?

Background: This study was conducted to evaluate the rate of regression of bilirubin after stent placement for malignant biliary obstruction.

Methods: Records were reviewed from October 2002 to September 2005 for patients who underwent endoscopic retrograde cholangiopancreatography with stent placement. The time to achieve a bilirubin level View Article and Find Full Text PDF

Combined EUS with FNA and ERCP for the evaluation of patients with obstructive jaundice from presumed pancreatic malignancy.

Background: An EUS-guided FNA (EUS-FNA) and a therapeutic ERCP are frequently required for the evaluation of patients who were seen for an obstructing periampullary lesion.

Objective: To determine the feasibility and outcomes of combining an EUS-FNA and a therapeutic ERCP into a single session.

Design: Retrospective single-center study.

Standardization of the clinical diagnosis of the dementia syndrome and its subtypes in a cross-national study: the Ni-Hon-Sea experience.

Background: Clinical investigators from Seattle, Honolulu, Tokyo, and Hiroshima participated in two standardization exercises in which data were collected on independent assessments. Exercises were conducted to evaluate the interobserver agreement on clinical diagnoses of dementia and dementia subtypes in a cross-national study of dementia prevalence and incidence rates in the United States and Japan.

Method: Fifteen clinicians from four participating sites assessed the diagnosis of 85 patients based on standardized summaries of clinical and diagnostic test data on each patient.

Fine structure of the promoter-sigma region 1.2 interaction.

We recently proposed that a nontemplate strand base in the discriminator region of bacterial promoters, the region between the -10 element and the transcription start site, makes sequence-specific contacts to region 1.2 of the sigma subunit of Escherichia coli RNA polymerase (RNAP). Because rRNA promoters contain sequences within the discriminator region that are suboptimal for interaction with sigma1.

Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation.

Identification of the RNA polymerase (RNAP) binding site for ppGpp, a central regulator of bacterial transcription, is crucial for understanding its mechanism of action. A recent high-resolution X-ray structure defined a ppGpp binding site on Thermus thermophilus RNAP. We report here effects of ppGpp on 10 mutant Escherichia coli RNAPs with substitutions for the analogous residues within 3-4 A of the ppGpp binding site in the T.

Lymphovascular invasion as a tool to further subclassify T1b esophageal adenocarcinoma.

Background: Lymphovascular invasion (LVI) and/or lymph node metastases (LNM) adversely influence the overall survival (OS) of patients with T1 esophageal adenocarcinoma. Although endoscopic therapy may be adequate for patients with T1a cancer, patients with T1b cancer require esophagectomy/lymphadenectomy. The authors hypothesized that LVI status would subclassify T1b cancers and facilitate new therapeutic strategies.

Pneumatic retinopexy, scleral buckling, and vitrectomy surgery in the management of pseudophakic retinal detachments.

Background: To review the indications for and results of pneumatic retinopexy, scleral buckling, combined pars plana vitrectomy and scleral buckling surgery, and primary pars plana vitrectomy in the management of pseudophakic retinal detachment.

Methods: We retrospectively reviewed a series of 100 pseudophakic retinal detachments in 98 patients who were referred to a tertiary care centre for management over a 3-year period.

Results: Forty-one cases were treated with retinopexy procedures; 38 underwent scleral buckling surgery; 19 underwent combined pars plana vitrectomy and scleral buckling procedures; and 2 cases underwent vitrectomy only.

Value of endoscopic ultrasound staging in conjunction with the evaluation of lymphovascular invasion in identifying low-risk esophageal carcinoma.

Background: With increasing emphasis on endoscopic therapy (ET) for T1 esophageal carcinoma, the identification of low-risk patients is critical. It was hypothesized that endoscopic ultrasonography (EUS) in concert with detailed histopathologic evaluation would identify low-risk cancers for an appropriate but organ-preserving strategy.

Methods: All patients who had pretreatment EUS and underwent esophagectomy as primary therapy for esophageal cancer between 1999 and 2006 were analyzed retrospectively.

Dendritic properties of turtle pyramidal neurons.

The six-layered mammalian neocortex evolved from the three-layered paleocortex, which is retained in present-day reptiles such as the turtle. Thus the turtle offers an opportunity to examine which cellular and circuit properties are fundamental to cortical function. We characterized the dendritic properties of pyramidal neurons in different cortical regions of mature turtles, Pseudemys scripta elegans, using whole cell recordings and calcium imaging from the axon, soma, and dendrites in a slice preparation.