bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of divergent genes in microbial aCGH experiments
Authors: Snipen Lars , Repsilber Dirk , Nyquist Ludvig , Ziegler Andreas , Aakra Ågot , Aastveit Are
Published: September 2006

Background

Array-based comparative genome hybridization (aCGH) is a tool for rapid comparison of genomes from different bacterial strains. The purpose of such analysis is to detect highly divergent or absent genes in a sample strain compared to an index strain. Development of methods for analyzing aCGH data has primarily focused on copy number abberations in cancer research. In microbial aCGH analyses, genes are typically ranked by log-ratios, and classification into divergent or present is done by choosing a cutoff log-ratio, either manually or by statistics calculated from the log-ratio distribution. As experimental settings vary considerably, it is not possible to develop a classical discriminant or statistical learning approach.

Methods

We introduce a more efficient method for analyzing microbial aCGH data using a finite mixture model and a data rotation scheme. Using the average posterior probabilities from the model fitted to log-ratios before and after rotation, we get a score for each gene, and demonstrate its advantages for ranking and detecting divergent genes with enlarged specificity and sensitivity.

Results

The procedure is tested and compared to other approaches on simulated data sets, as well as on four experimental validation data sets for aCGH analysis on fully sequenced strains of Staphylococcus aureus and Streptococcus pneumoniae.

Conclusion

When tested on simulated data as well as on four different experimental validation data sets from experiments with only fully sequenced strains, our procedure out-competes the standard procedures of using a simple log-ratio cutoff for classification into present and divergent genes.
Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
Authors: Tharakaraman Kannan , Mariño-Ramírez Leonardo , Sheetlin Sergey L , Landsman David , Spouge John L
Published: September 2006

Background

Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set.

Results

We describe an improvement to the A-GLAM computer program, which predicts regulatory elements within DNA sequences with Gibbs sampling. The improvement adds an optional "scanning step" after Gibbs sampling. Gibbs sampling produces a position specific scoring matrix (PSSM). The new scanning step resembles an iterative PSI-BLAST search based on the PSSM. First, it assigns an "individual score" to each subsequence of appropriate length within the input sequences using the initial PSSM. Second, it computes an E-value from each individual score, to assess the agreement between the corresponding subsequence and the PSSM. Third, it permits subsequences with E-values falling below a threshold to contribute to the underlying PSSM, which is then updated using the Bayesian calculus. A-GLAM iterates its scanning step to convergence, at which point no new subsequences contribute to the PSSM. After convergence, A-GLAM reports predicted regulatory elements within each sequence in order of increasing E-values, so users have a statistical evaluation of the predicted elements in a convenient presentation. Thus, although the Gibbs sampling step in A-GLAM finds at most one regulatory element per input sequence, the scanning step can now rapidly locate further instances of the element in each sequence.

Conclusion

Datasets from experiments determining the binding sites of transcription factors were used to evaluate the improvement to A-GLAM. Typically, the datasets included several sequences containing multiple instances of a regulatory motif. The improvements to A-GLAM permitted it to predict the multiple instances.
Phase distribution of spliceosomal introns: implications for intron origin
Authors: Nguyen Hung D , Yoshihama Maki , Kenmochi Naoya
Published: September 2006

Background

The origin of spliceosomal introns is the central subject of the introns-early versus introns-late debate. The distribution of intron phases is non-uniform, with an excess of phase-0 introns. Introns-early explains this by speculating that a fraction of present-day introns were present between minigenes in the progenote and therefore must lie in phase-0. In contrast, introns-late predicts that the nonuniformity of intron phase distribution reflects the nonrandomness of intron insertions.

Results

In this paper, we tested the two theories using analyses of intron phase distribution. We inferred the evolution of intron phase distribution from a dataset of 684 gene orthologs from seven eukaryotes using a maximum likelihood method. We also tested whether the observed intron phase distributions from 10 eukaryotes can be explained by intron insertions on a genome-wide scale. In contrast to the prediction of introns-early, the inferred evolution of intron phase distribution showed that the proportion of phase-0 introns increased over evolution. Consistent with introns-late, the observed intron phase distributions matched those predicted by an intron insertion model quite well.

Conclusion

Our results strongly support the introns-late hypothesis of the origin of spliceosomal introns.
Development of a Premature Stop Codon-detection method based on a bacterial two-hybrid system
Authors: Real Sebastián M , Marzese Diego M , Gomez Laura C , Mayorga Luis S , Roqué María
Published: September 2006

Background

The detection of Premature Stop Codons (PSCs) in human genes is very useful for the genetic diagnosis of different hereditary cancers, e.g. Familial Breast Cancer and Hereditary Non-Polyposis Colorectal Cancer (HNPCC). The products of these PSCs are truncated proteins, detectable in vitro by the Protein Truncation Test and in vivo by using the living translation machinery of yeast or bacteria. These living strategies are based on the construction of recombinant plasmids where the human sequence of interest is inserted upstream of a reporter gene. Although simple, these assays have their limitations. The yeast system requires extensive work to enhance its specificity, and the bacterial systems yield many false results due to translation re-initiation events occurring post PSCs. Our aim was to design a recombinant plasmid useful for detecting PSCs in human genes and resistant to bacterial translation re-initiation interferences.

Results

A functional recombinant plasmid (pREAL) was designed based on a bacterial two-hybrid system. In our design, the in vivo translation of fused fragments of the Bordetella pertussis adenylate cyclase triggers the production of cAMP giving rise to a selectable bacterial phenotype. When a gene of interest is inserted between the two fragments, any PSC inhibits the enzymatic activity of the product, and translation re-initiation events post-PSC yield separated inactive fragments. We demonstrated that the system can accurately detect PSCs in human genes by inserting mutated fragments of the brca1 and msh2 gene. Western Blot assays revealed translation re-initiation events in all the tested colonies, implying that a simpler plasmid would not be resistant to this source of false negative results. The application of the system to a HNPCC family with a nonsense mutation in the msh2 gene correctly diagnosed wild type homozygous and heterozygous patients.

Conclusion

The developed pREAL is applicable to the detection of PSCs in human genes related to different diseases and is resistant to translation re-initiation events. The diagnosis steps are easy, have a low cost, detect only pathologic mutations, and allow the analysis of separated alleles.
Severe osteomyelitis caused by Myceliophthora thermophila after a pitchfork injury
Authors: Destino Lauren , Sutton Deanna A , Helon Anna L , Havens Peter L , Thometz John G , Willoughby Rodney E , Chusid Michael J
Published: September 2006

Background

Traumatic injuries occurring in agricultural settings are often associated with infections caused by unusual organisms. Such agents may be difficult to isolate, identify, and treat effectively.

Case report

A 4-year-old boy developed an extensive infection of his knee and distal femur following a barnyard pitchfork injury. Ultimately the primary infecting agent was determined to be Myceliophthora thermophila, a thermophilic melanized hyphomycete, rarely associated with human infection, found in animal excreta. Because of resistance to standard antifungal agents including amphotericin B and caspofungin, therapy was instituted with a prolonged course of terbinafine and voriconazole. Voriconazole blood levels demonstrated that the patient required a drug dosage (13.4 mg/kg) several fold greater than that recommended for adults in order to attain therapeutic blood levels.

Conclusion

Unusual pathogens should be sought following traumatic farm injuries. Pharmacokinetic studies may be of critical importance when utilizing antifungal therapy with agents for which little information exists regarding drug metabolism in children.
Development of the Well-being questionnaire short-form in Japanese: the W-BQ12
Authors: Riazi Afsane , Bradley Clare , Barendse Shalleen , Ishii Hitoshi
Published: September 2006

Background

The Well-being Questionnaire (W-BQ) was designed to measure psychological well-being in people with diabetes. This study aimed to develop a Japanese version and a short form of the W-BQ.

Methods

A linguistic validation process produced a preliminary Japanese version of the 22-item W-BQ, which was distributed to 550 patients. Factor structure, reliability (Cronbach's alpha) and aspects of validity (hypothesised group differences and correlations with other measures) were evaluated.

Results

Questionnaires were returned by 464 patients (84.4%). Preliminary factor analysis revealed that the Depression and Anxiety items were dispersed according to the positive or negative direction of the wording. A 12-item W-BQ (Japanese W-BQ12), consisting of three 4-item subscales (Negative Well-being, Energy and Positive Well-being), was constructed that balanced positively and negatively worded items. Cronbach's alpha was high (>0.85) for the 12-item questionnaire and consistently high (>0.82) across sex and treatment subgroups. Cronbach's alpha for subscale scores in the total sample ranged from 0.69 (Energy) to 0.80 (Positive Well-being). Expected subgroup differences indicated significantly poorer well-being in women compared with men and in insulin-treated patients compared with tablet/diet treated patients. Discriminant and convergent validity was supported by minimal correlations between W-BQ12 scores and HbA1c and low-to-moderate correlations with Diabetes Treatment Satisfaction Questionnaire (DTSQ) scores.

Conclusion

The W-BQ12 (Japanese) is a short, reliable and valid measure of psychological well-being that is suitable for use with people with diabetes. The items selected to produce the W-BQ12 (Japanese) have since produced psychometrically sound 12-item short-form measures in other translations for use in diabetes and in other chronic illnesses.
Expression of innate immune complement regulators on brain epithelial cells during human bacterial meningitis
Authors: Canova Cecile , Neal Jim W , Gasque Philippe
Published: September 2006

Background

In meningitis, the cerebrospinal fluid contains high levels of innate immune molecules (e.g. complement) which are essential to ward off the infectious challenge and to promote the infiltration of phagocytes (neutrophils, monocytes). However, epithelial cells of either the ependymal layer, one of the established niche for adult neural stem cells, or of the choroid plexus may be extremely vulnerable to bystander attack by cytotoxic and cytolytic complement components.

Methods

In this study, we assessed the capacity of brain epithelial cells to express membrane-bound complement regulators (ie, CD35, CD46, CD55 and CD59) in vitro and in situ by immunostaining of control and meningitis human brain tissue sections.

Results

Double immunofluorescence experiments for ependymal cell markers (GFAP, S100, ZO-1, E-cadherin) and complement regulators indicated that the human ependymal cell line model was strongly positive for CD55, CD59 compared to weak stainings for CD46 and CD35. In tissues, we found that CD55 was weakly expressed in control choroid plexus and ependyma but was abundantly expressed in meningitis. Anti-CD59 stained both epithelia in apical location while increased CD59 staining was solely demonstrated in inflamed choroid plexus. CD46 and CD35 were not detected in control tissue sections. Conversely, in meningitis, the ependyma, subependyma and choroid plexus epithelia were strongly stained for CD46 and CD35.

Conclusion

This study delineates for the first time the capacity of brain ependymal and epithelial cells to respond to and possibly sustain the innate complement-mediated inflammatory insult.
Short-term arginine deprivation results in large-scale modulation of hepatic gene expression in both normal and tumor cells: microarray bioinformatic analysis
Authors: Leong Hwei Xian , Simkevich Carl , Lesieur-Brooks Anne , Lau Bonnie W , Fugere Celine , Sabo Edmond , Thompson Nancy L
Published: September 2006

Background

We have reported arginine-sensitive regulation of LAT1 amino acid transporter (SLC 7A5) in normal rodent hepatic cells with loss of arginine sensitivity and high level constitutive expression in tumor cells. We hypothesized that liver cell gene expression is highly sensitive to alterations in the amino acid microenvironment and that tumor cells may differ substantially in gene sets sensitive to amino acid availability. To assess the potential number and classes of hepatic genes sensitive to arginine availability at the RNA level and compare these between normal and tumor cells, we used an Affymetrix microarray approach, a paired in vitro model of normal rat hepatic cells and a tumorigenic derivative with triplicate independent replicates. Cells were exposed to arginine-deficient or control conditions for 18 hours in medium formulated to maintain differentiated function.

Results

Initial two-way analysis with a p-value of 0.05 identified 1419 genes in normal cells versus 2175 in tumor cells whose expression was altered in arginine-deficient conditions relative to controls, representing 9–14% of the rat genome. More stringent bioinformatic analysis with 9-way comparisons and a minimum of 2-fold variation narrowed this set to 56 arginine-responsive genes in normal liver cells and 162 in tumor cells. Approximately half the arginine-responsive genes in normal cells overlap with those in tumor cells. Of these, the majority was increased in expression and included multiple growth, survival, and stress-related genes. GADD45, TA1/LAT1, and caspases 11 and 12 were among this group. Previously known amino acid regulated genes were among the pool in both cell types. Available cDNA probes allowed independent validation of microarray data for multiple genes. Among genes downregulated under arginine-deficient conditions were multiple genes involved in cholesterol and fatty acid metabolism. Expression of low-density lipoprotein receptor was decreased in both normal and tumor cells.

Conclusion

Arginine-sensitive regulation appears to be an important homeostatic mechanism to coordinate cell response and nutrient availability in hepatic cells. Genes predicted as arginine-responsive in stringent microarray data analysis were confirmed by Northern blot and RT-PCR. Although the profile of arginine-responsive genes is altered and increased, a considerable portion of the "arginome" is maintained upon neoplastic transformation.
Matrix metalloproteinases, their production by monocytes and macrophages and their potential role in HIV-related diseases
Authors: Webster Nicole L , Crowe Suzanne M
Published: September 2006

Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that are a subfamily of metzincins. Matrix metalloproteinases are responsible for much of the turnover of extra-cellular matrix components and are key to a wide range of processes including tissue remodeling and release of biological factors. Imbalance between the MMPs and endogenous tissue inhibitors of metalloproteinases (TIMPs) can result in dysregulation of many biologic processes and lead to the development of malignancy, cardiovascular disease, and autoimmune and inflammatory disorders. MMP production by monocyte/macrophages is dependent on the cell type, state of differentiation, and/or level of activation and whether they are infected, e.g., by HIV-1. MMP expression by HIV-1 infected monocytes and macrophages may alter cellular trafficking and contribute to HIV-associated pathology such as HIV-associated dementia (HAD). This review will provide a classification of the MMP super-family with particular reference to those produced by monocyte/macrophages, describe their regulation and function within the immune system, and indicate their possible roles in the pathogenesis of disease, including HIV-associated dementia.
Roles of neutrophil-mediated inflammatory response in the bony repair of injured growth plate cartilage in young rats
Authors: Chung Rosa , Cool Johanna C , Scherer Michaela A , Foster Bruce K , Xian Cory J
Published: September 2006

Injured growth plate cartilage is often repaired by bony tissue, resulting in impaired bone growth in children. Previously, injury-induced, initial inflammatory response was shown to be an acute inflammatory event containing predominantly neutrophils. To examine potential roles of neutrophils in the bony repair, a neutrophil-neutralizing antiserum or control normal serum was administered systemically in rats with growth plate injury. The inflammatory response was found temporally associated with increased expression of neutrophil chemotactic chemokine cytokine-induced neutrophil chemoattractant-1 and cytokines TNF-α and IL-1β. Following the inflammatory response, mesenchymal infiltration, chondrogenic and osteogenic responses, and bony repair were observed at the injury site. Neutrophil reduction did not significantly affect infiltration of other inflammatory cells and expression of TNF-α and IL-1β and growth factors, platelet-derived growth factor-B and TGF-β1, at the injured growth plate on Day 1 and had no effects on mesenchymal infiltration on Day 4. By Day 10, however, there was a significant reduction in proportion of mesenchymal repair tissue but an increase (although statistically insignificant) in bony trabeculae and a decrease in cartilaginous tissue within the injury site. Consistently, in antiserum-treated rats, there was an increase in expression of osteoblastic differentiation transcription factor cbf-α1 and bone matrix protein osteocalcin and a decrease in chondrogenic transcription factor Sox-9 and cartilage matrix collagen-II in the injured growth plate. These results suggest that injury-induced, neutrophil-mediated inflammatory response appears to suppress mesenchymal cell osteoblastic differentiation but enhance chondrogenic differentiation, and thus, it may be involved in regulating downstream chondrogenic and osteogenic events for growth plate bony repair.
Surgical Mortality in Patients With Esophageal Cancer: Development and Validation of a Simple Risk Score
Authors: Steyerberg Ewout W. , Neville Bridget A. , Koppert Linetta B. , Lemmens Valery E.P.P. , Tilanus Hugo W. , Coebergh Jan-Willem W. , Weeks Jane C. , Earle Craig C.
Published: September 2006

Purpose

Surgery has curative potential in a proportion of patients with esophageal cancer, but is associated with considerable perioperative risks. We aimed to develop and validate a simple risk score for surgical mortality that could be applied to administrative data.

Patients and Methods

We analyzed 3,592 esophagectomy patients from four cohorts. We applied logistic regression analysis to predict mortality occurring within 30 days after esophagectomy for 1,327 esophageal cancer patients older than 65 years of age, diagnosed between 1991 and 1996 in the linked Surveillance, Epidemiology and End Results (SEER) - Medicare database. A simple score chart for preoperative risk assessment of surgical mortality was developed and validated on three other cohorts, including 714 SEER-Medicare patients diagnosed between 1997 and 1999, 349 patients from a population-based registry in the Netherlands diagnosed between 1993 and 2001, and 1,202 patients from a referral hospital in the Netherlands diagnosed between 1980 and 2002.

Results

Surgical mortality in the four cohorts was 11% (147 of 1,327), 10% (74 of 714), 7% (25 of 349), and 4% (45 of 1,202), respectively. Predictive patient characteristics included age, comorbidity (cardiac, pulmonary, renal, hepatic, and diabetes), preoperative radiotherapy or combined chemoradiotherapy, and a relatively low hospital volume. At validation, the simple score showed good agreement of predicted risks with observed mortality rates (calibration), but low discrimination (area under the receiver operating characteristic curve 0.58 to 0.66).

Conclusion

A simple risk score combining clinical characteristics along with hospital volume to predict surgical mortality after esophagectomy from administrative data may form a basis for risk adjustment in quality of care assessment.
Endothelin-1 Inhibits Apoptosis through a Sphingosine Kinase 1-Dependent Mechanism in Uterine Leiomyoma ELT3 Cells
Authors: Raymond Marie-Noëlle , Bole-Feysot Christine , Banno Yoshiko , Tanfin Zahra , Robin Philippe
Published: September 2006

Uterine leiomyomas, or fibroids, are the most common tumors of the myometrium. The ELT3 cell line, derived from Eker rat leiomyoma, has been successfully used as a model for the study of leiomyomas. We have demonstrated previously the potent mitogenic properties of the peptidic hormone endothelin (ET)-1 in this cell line. Here we investigated the antiapoptotic effect of ET-1 in ELT3 cells. We found that 1) serum starvation of ELT3 cells induced an apoptotic process characterized by cytochrome c release from mitochondria, caspase-3/7 activation, nuclei condensation and DNA fragmentation; 2) ET-1 prevented the apoptotic process; and 3) this effect of ET-1 was fully reproduced by ETB agonists. In contrast, no antiapoptotic effect of ET-1 was observed in normal myometrial cells. A pharmacological approach showed that the effect of ET-1 on caspase-3/7 activation in ELT3 cells was not dependent on phosphatidylinositol 3-kinase, ERK1/2, or phospholipase D activities. However, inhibitors of sphingosine kinase-1 (SphK1), dimethylsphingosine and threo-dihydrosphingosine, reduced the effect of ET-1 by about 50%. Identical results were obtained when SphK1 expression was down-regulated in ELT3 cells transfected with SphK1 small interfering RNA. Furthermore, serum starvation induced a decrease in SphK1 activity that was prevented by ET-1 without affecting the level of SphK1 protein expression. Finally, sphingosine 1-phosphate, the product of SphK activity, was as efficient as ET-1 in inhibiting serum starvation-induced caspase-3/7 activation. Together, these results demonstrate that ET-1 possesses a potent antiapoptotic effect in ELT3 cells that involves sphingolipid metabolism through the activation of SphK1.
Genistein Affects Adipose Tissue Deposition in a Dose-Dependent and Gender-Specific Manner
Authors: Penza M. , Montani C. , Romani A. , Vignolini P. , Pampaloni B. , Tanini A. , Brandi M. L. , Alonso-Magdalena P. , Nadal A. , Ottobrini L. , Parolini O. , Bignotti E. , Calza S. , Maggi A. , Grigolato P. G. , Di Lorenzo D.
Published: September 2006

The soy isoflavone genistein targets adipose tissue and elicits physiological effects that may vary based on dietary intake. We hypothesized that the adipose effects of genistein are dose and gender dependent. Four-week-old C57BL/6 male and female mice received daily oral doses of genistein (50–200,000 μg/kg·d) or 17β-estradiol (E2) (5 μg/kg·d) for 15 d or a diet containing 800 ppm genistein. Genistein increased epididymal and renal fat pad and adipocyte size at doses up to 50,000 μg/kg·d or at 800 ppm in the diet in males but not in females. The alteration in adipocity correlated with changes in peripheral insulin resistance. These treatments increased genistein serum concentrations from 35 ± 6 to 103 ± 26 nm 12 h after treatment and lowered plasma triglycerides and cholesterol levels. The 200,000 μg/kg·d genistein dose decreased adipose tissue weight similarly to E2. This genistein dose down-regulated estrogen receptor (β more than α) and progesterone receptor expression and induced estrogen-dependent adipose differentiation factors; it did not change expression of the minimal consensus estrogen-responsive element in ERE-tK-LUC mice, which was positively modulated in other tissues (e.g. the lung). E2 down-regulated almost all examined adipogenic factors. Gene microarray analysis identified factors in fat metabolism and obesity-related phenotypes differentially regulated by low and high doses of genistein, uncovering its adipogenic and antiadipogenic actions. The lower dose induced the phospholipase A2 group 7 and the phospholipid transfer protein genes; the 200,000 μg/kg·d dose inhibited them. The antiadipogenic action of genistein and down-regulation of adipogenic genes required the expression of ERβ. In conclusion, nutritional doses of genistein are adipogenic in a gender-specific manner, whereas pharmacological doses inhibited adipose deposition.
Developmental Control of Iodothyronine Deiodinases by Cortisol in the Ovine Fetus and Placenta Near Term
Authors: Forhead Alison J. , Curtis Katrina , Kaptein Ellen , Visser Theo J. , Fowden Abigail L.
Published: September 2006

Preterm infants have low serum T4 and T3 levels, which may partly explain the immaturity of their tissues. Deiodinase enzymes are important in determining the bioavailability of thyroid hormones: deiodinases D1 and D2 convert T4 to T3, whereas deiodinase D3 inactivates T3 and produces rT3 from T4. In human and ovine fetuses, plasma T3 rises near term in association with the prepartum cortisol surge. This study investigated the developmental effects of cortisol and T3 on tissue deiodinases and plasma thyroid hormones in fetal sheep during late gestation. Plasma cortisol and T3 concentrations in utero were manipulated by exogenous hormone infusion and fetal adrenalectomy. Between 130 and 144 d of gestation (term 145 ± 2 d), maturational increments in plasma cortisol and T3, and D1 (hepatic, renal, perirenal adipose tissue) and D3 (cerebral), and decrements in renal and placental D3 activities were abolished by fetal adrenalectomy. Between 125 and 130 d, iv cortisol infusion raised hepatic, renal, and perirenal adipose tissue D1 and reduced renal and placental D3 activities. Infusion with T3 alone increased hepatic D1 and decreased renal D3 activities. Therefore, in the sheep fetus, the prepartum cortisol surge induces tissue-specific changes in deiodinase activity that, by promoting production and suppressing clearance of T3, may be responsible for the rise in plasma T3 concentration near term. Some of the maturational effects of cortisol on deiodinase activity may be mediated by T3.
Brainstem Thyrotropin-Releasing Hormone Regulates Food Intake through Vagal-Dependent Cholinergic Stimulation of Ghrelin Secretion
Authors: Ao Yan , Go Vay Liang W. , Toy Natalie , Li Tei , Wang Yu , Song Moon K. , Reeve Joseph R. , Liu Yanyun , Yang Hong
Published: September 2006

The brainstem is essential for mediating energetic response to starvation. Brain stem TRH is synthesized in caudal raphe nuclei innervating brainstem and spinal vagal and sympathetic motor neurons. Intracisternal injection (ic) of a stable TRH analog RX77368 (7.5–25 ng) dose-dependently stimulated solid food intake by 2.4- to 3-fold in freely fed rats, an effect that lasted for 3 h. By contrast, RX77368 at 25 ng injected into the lateral ventricle induced a delayed and insignificant orexigenic effect only in the first hour. In pentobarbital-anesthetized rats, RX77368 (50 ng) ic induced a significant bipeak increase in serum total ghrelin levels from the basal of 8.7 ± 1.7 ng/ml to 13.4 ± 2.4 ng/ml at 30 min and 14.5 ± 2.0 ng/ml at 90 min, which was prevented by either bilateral vagotomy (−60 min) or atropine pretreatment (2 mg/kg, −30 min) but magnified by bilateral adrenalectomy (−60 min). TRH analog ic-induced food intake in freely fed rats was abolished by either peripheral atropine or ghrelin receptor antagonist (d-Lys-3)-GHRP-6 (10 μmol/kg) or ic Y1 receptor antagonist 122PU91 (10 nmol/5 μl). Brain stem TRH mRNA and TRH receptor 1 mRNA increased by 57–58 and 33–35% in 24- and 48-h fasted rats and returned to the fed levels after a 3-h refeeding. Natural food intake in overnight fasted rats was significantly reduced by ic TRH antibody, ic Y1 antagonist, and peripheral atropine. These data establish a physiological role of brainstem TRH in vagal-ghrelin-mediated stimulation of food intake, which involves interaction with brainstem Y1 receptors.
A Comparative Study of the Central Effects of Specific Proopiomelancortin (POMC)-Derived Melanocortin Peptides on Food Intake and Body Weight in Pomc Null Mice
Authors: Tung Y. C. Loraine , Piper Sarah J. , Yeung Debra , O’Rahilly Stephen , Coll Anthony P.
Published: September 2006

Functional disruption of either MC3R or MC4R results in obesity, implicating both in the control of energy homeostasis. The ligands for these receptors are derived from the prohormone proopiomelancortin (POMC), which is posttranslationally processed to produce a set of melanocortin peptides with a range of activities at the MC3R and MC4R. The relative importance of each of these peptides α-MSH, γ3-MSH, γ2-MSH, γ-lipotropin (γ-LPH) and, in man but not in rodents, β-MSH] in the maintenance of energy homeostasis is, as yet, unclear. To investigate this further, equimolar amounts (2 nmol) of each peptide were centrally administered to freely feeding, corticosterone-supplemented, Pomc null (Pomc−/−) mice. After a single dose at the onset of the dark cycle, α-MSH had the most potent anorexigenic effect, reducing food intake to 35% of sham-treated animals. β-MSH, γ-LPH, and γ3- and γ2-MSH all reduced food intake but to a lesser degree. The effects of peptide administration over 3 d were also assessed. Only α-MSH significantly reduced body weight, affecting both fat and lean mass. Other peptides had no significant effect on body weight. Pair-feeding of sham-treated mice to those treated with α-MSH resulted in identical changes in total weight, fat and lean mass indicating that the effects of α-MSH were primarily due to reduced food intake rather than increased energy expenditure. Although other melanocortins can reduce food intake in the short-term, only α-MSH can reduce the excess fat and lean mass found in Pomc−/− mice, mediated largely through an effect on food intake.
Apnetic anesthesia for microlaryngeal surgery
Authors: Nelson Ralph A. , Miller Tom
Published: September 2006

An apneic anesthesia state can be induced and maintained with intravenous thiopental, succinylcholine, and 100 percent oxygen at 6L/min. by catheter. This technique allows an unobstructed view of the endolarynx, avoids trauma of the larynx by an endotracheal tube prior to diagnostic procedures, and precludes seeding the larynx and trachea with malignant cells. The rise in PnCO2 is 3 mm Hg/min. Arrhythmias that occur with laryngeal manipulation bear no relation to the level of arterial carbon dioxide. Patients can tolerate this technique for a minimum of 10 minutes, but eight of 31 patients could not tolerate the condition beyond that time. The subjects with apneic intolerance were found to have relatively low functional residual capacities and were relatively obese. An FRC/WT. above 17 was considered an indicator of high apneic tolerance, and an FRC/WT. below 15 an indicator of a patient who should be monitored closely. WT/IPPB should always be administered postoperatively.
Delayed post‐stapedectomy facial paralysis: A report of five cases
Authors: Althaus Sean R. , House Howard P.
Published: September 2006

Review of a series of 2,307 stapedectomy procedures revealed five cases of delayed facial paralysis. The paralysis was clinically complete in three and incomplete in two cases. Onset of weakness occurred from five to 13 days postoperatively. Complete recovery occurred in all cases within eight weeks and surgical intervention was unnecessary.

The cause of this uncommon complication is felt to be retrograde edema of the chorda tympani nerve into the facial trunk, or edema of a dehiscent facial nerve in the postoperative period. This phenomenon has not been stressed in the otologic literature to date.

Careful evaluation of the patient, close follow‐up with nerve excitability testing in cases of complete paralysis, and steroid and vasodilator therapy is the recommended mode of management. Exploration and decompression of the facial nerve should be strongly considered if the nerve excitability threshold exceeds that of the normal side by 3.5 ma. or more, or should the stimulus threshold be lost altogether.

With preservation of nerve excitability thresholds, the outlook for return of function is good, according to this small series.
Angiofibroma: A treatment approach
Authors: Biller Hugh F. , Sessions Donald G. , Ogura Joseph H.
Published: September 2006

A systematic treatment approach for nasopharyngeal angiofibromas is presented. Surgery, as the primary treatment modality is advocated. Routine pre‐operative angiography is utilized for diagnosis and delineation of tumor extent. The surgical approach or approaches is dependent upon the tumor extent.
Recognition of Natural Expressions of Emotion by CVA Patients with Damage to the Left or Right Hemisphere
Authors: Bowen Rebecca , McDonald Skye
Published: September 2006

The present study investigated the ability of cerebrovascular accident (CVA) patients to perceive emotions portrayed by realistic stimuli. Statistical analyses demonstrated that CVA patients with damage to either the right or left cerebral hemisphere performed, on average, as well as controls did in perceiving emotions. However, a case study of one patient suggested that there may be a subset of CVA patients with right parieto-occipital damage who have deficits in the perception of negative emotions. The performance of this participant also indicated that deficits in emotion perception are ameliorated to some extent when patients are provided with realistic, complex stimuli that include a range of auditory and visual cues.
The methylenetetrahydrofolate reductase C677T gene mutation is associated with hyperhomocysteinemia, cardiovascular disease and plasma B-type natriuretic peptide levels in Korea
Authors: Cho Sung Eun , Sook Hong Ki , Shin Gil Ja , Chung Wha Soon
Published: September 2006

Clin Chem Lab Med 2006;44:1070–5.
Rheumatoid factor interference in the determination of carbohydrate antigen 19-9 (CA 19-9)
Authors: Berth Mario , Bosmans Eugene , Everaert Jacques , Dierick Jan , Schiettecatte Johan , Anckaert Ellen , Delanghe Joris
Published: September 2006

Clin Chem Lab Med 2006;44:1137–9.
Widespread Adaptive Evolution of Drosophila Genes With Sex-Biased Expression
Authors: Pröschel Matthias , Zhang Zhi , Parsch John
Published: September 2006

Many genes in higher eukaryotes show sexually dimorphic expression, and these genes tend to be among the most divergent between species. In most cases, however, it is not known whether this rapid divergence is caused by positive selection or if it is due to a relaxation of selective constraint. To distinguish between these two possibilities, we surveyed DNA sequence polymorphism in 91 Drosophila melanogaster genes with male-, female-, or nonsex-biased expression and determined their divergence from the sister species D. simulans. Using several single- and multilocus statistical tests, we estimated the type and strength of selection influencing the evolution of the proteins encoded by genes of each expression class. Adaptive evolution, as indicated by a relative excess of nonsynonymous divergence between species, was common among the sex-biased genes (both male and female). Male-biased genes, in particular, showed a strong and consistent signal of positive selection, while female-biased genes showed more variation in the type of selection they experience. Genes expressed equally in the two sexes, in contrast, showed no evidence for adaptive evolution between D. melanogaster and D. simulans. This suggests that sexual selection and intersexual coevolution are the major forces driving genetic differentiation between species.
History and Structure of Sub-Saharan Populations ofDrosophila melanogaster
Authors: Pool John E , Aquadro Charles F
Published: September 2006

Drosophila melanogaster is an important model organism in evolutionary genetics, yet little is known about the population structure and the demographic history of this species within sub-Saharan Africa, which is thought to contain its ancestral range. We surveyed nucleotide variation at four 1-kb fragments in 240 individual lines representing 21 sub-Saharan and 4 Palearctic population samples of D. melanogaster. In agreement with recent studies, we find a small but significant level of genetic differentiation within sub-Saharan Africa. A clear geographic pattern is observed, with eastern and western African populations composing two genetically distinct groups. This pattern may have resulted from a relatively recent establishment of D. melanogaster in western Africa. Eastern populations show greater evidence for long-term stability, consistent with the hypothesis that eastern Africa contains the ancestral range of the species. Three sub-Saharan populations show evidence for cosmopolitan introgression. Apart from those cases, the closest relationships between Palearctic and sub-Saharan populations involve a sample from the rift zone (Uganda), suggesting that the progenitors of Palearctic D. melanogaster might have come from this region. Finally, we find a large excess of singleton polymorphisms in the full data set, which is best explained by a combination of population growth and purifying selection.
Mutator Phenotype ofCaenorhabditis elegansDNA Damage Checkpoint Mutants
Authors: Harris Jasper , Lowden Mia , Clejan Iuval , Tzoneva Monika , Thomas James H , Hodgkin Jonathan , Ahmed Shawn
Published: September 2006

DNA damage response proteins identify sites of DNA damage and signal to downstream effectors that orchestrate either apoptosis or arrest of the cell cycle and DNA repair. The C. elegans DNA damage response mutants mrt-2, hus-1, and clk-2(mn159) displayed 8- to 15-fold increases in the frequency of spontaneous mutation in their germlines. Many of these mutations were small- to medium-sized deletions, some of which had unusual sequences at their breakpoints such as purine-rich tracts or direct or inverted repeats. Although DNA-damage-induced apoptosis is abrogated in the mrt-2, hus-1, and clk-2 mutant backgrounds, lack of the apoptotic branch of the DNA damage response pathway in cep-1/p53, ced-3, and ced-4 mutants did not result in a Mutator phenotype. Thus, DNA damage checkpoint proteins suppress the frequency of mutation by ensuring that spontaneous DNA damage is accurately repaired in C. elegans germ cells. Although DNA damage response defects that predispose humans to cancer are known to result in large-scale chromosome aberrations, our results suggest that small- to medium-sized deletions may also play roles in the development of cancer.
A Genetic Linkage Map of the Hermaphrodite Teleost Fish Sparus aurata L.
Authors: Franch Rafaella , Louro Bruno , Tsalavouta Matina , Chatziplis Dimitris , Tsigenopoulos Costas S , Sarropoulou Elena , Antonello Jenny , Magoulas Andonis , Mylonas Constantinos C , Babbucci Massimiliano , Patarnello Tomaso , Power Deborah M , Kotoulas Giorgos , Bargelloni Luca
Published: September 2006

The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60–90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal.
Amh and Dmrta2 Genes Map to Tilapia (Oreochromis spp.) Linkage Group 23 Within Quantitative Trait Locus Regions for Sex Determination
Authors: Shirak Andrey , Seroussi Eyal , Cnaani Avner , Howe Aimee E , Domokhovsky Raisa , Zilberman Noam , Kocher Thomas D , Hulata Gideon , Ron Micha
Published: September 2006

Recent studies have revealed that the major genes of the mammalian sex determination pathway are also involved in sex determination of fish. Several studies have reported QTL in various species and strains of tilapia, regions contributing to sex determination have been identified on linkage groups 1, 3, and 23. Genes contributing to sex-specific mortality have been detected on linkage groups 2, 6, and 23. To test whether the same genes might control sex determination in mammals and fishes, we mapped 11 genes that are considered putative master key regulators of sex determination: Amh, Cyp19, Dax1, Dmrt2, Dmrta2, Fhl3l, Foxl2, Ixl, Lhx9, Sf1, and Sox8. We identified polymorphisms in noncoding regions of these genes and genotyped these sites for 90 individuals of an F2 mapping family. Mapping of Dax1 joined LG16 and LG21 into a single linkage group. The Amh and Dmrta2 genes were mapped to two distinct regions of LG23. The Amh gene was mapped 5 cM from UNH879 within a QTL region for sex determination and 2 cM from UNH216 within a QTL region for sex-specific mortality. Dmrta2 was mapped 4 cM from UNH848 within another QTL region for sex determination. Cyp19 was mapped to LG1 far from a previously reported QTL region for sex determination on this chromosome. Seven other candidate genes mapped to LG4, -11, -12, -14, and -17.
Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of Maize
Authors: Fu Yan , Wen Tsui-Jung , Ronin Yefim I , Chen Hsin D , Guo Ling , Mester David I , Yang Yongjie , Lee Michael , Korol Abraham B , Ashlock Daniel A , Schnable Patrick S
Published: September 2006

A new genetic map of maize, ISU–IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73 × Mo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations (F2, Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.
Comparative Genomics of Host-Specific Virulence in Pseudomonas syringae
Authors: Sarkar Sara F , Gordon Jeffrey S , Martin Gregory B , Guttman David S
Published: September 2006

While much study has gone into characterizing virulence factors that play a general role in disease, less work has been directed at identifying pathogen factors that act in a host-specific manner. Understanding these factors will help reveal the variety of mechanisms used by pathogens to suppress or avoid host defenses. We identified candidate Pseudomonas syringae host-specific virulence genes by searching for genes whose distribution among natural P. syringae isolates was statistically associated with hosts of isolation. We analyzed 91 strains isolated from 39 plant hosts by DNA microarray-based comparative genomic hybridization against an array containing 353 virulence-associated (VA) genes, including 53 type III secretion system effectors (T3SEs). We identified individual genes and gene profiles that were significantly associated with strains isolated from cauliflower, Chinese cabbage, soybean, rice, and tomato. We also identified specific horizontal gene acquisition events associated with host shifts by mapping the array data onto the core genome phylogeny of the species. This study provides the largest suite of candidate host-specificity factors from any pathogen, suggests that there are multiple ways in which P. syringae isolates can adapt to the same host, and provides insight into the evolutionary mechanisms underlying host adaptation.
Can Random Mutation Mimic Design?: A Guided Inquiry Laboratory for Undergraduate Students
Authors: Kalinowski Steven T , Taper Mark L , Metz Anneke M
Published: September 2006

Complex biological structures, such as the human eye, have been interpreted as evidence for a creator for over three centuries. This raises the question of whether random mutation can create such adaptations. In this article, we present an inquiry-based laboratory experiment that explores this question using paper airplanes as a model organism. The main task for students in this investigation is to figure out how to simulate paper airplane evolution (including reproduction, inheritance, mutation, and selection). In addition, the lab requires students to practice analytic thinking and to carefully delineate the implications of their results.
Ribosomal DNA in the GrasshopperPodisma pedestris: Escape From Concerted Evolution
Authors: Keller Irene , Chintauan-Marquier Ioana C , Veltsos Paris , Nichols Richard A
Published: September 2006

Eukaryote nuclear ribosomal DNA (rDNA) typically exhibits strong concerted evolution: a pattern in which several hundred rDNA sequences within any one species show little or no genetic diversity, whereas the sequences of different species diverge. We report a markedly different pattern in the genome of the grasshopper Podisma pedestris. Single individuals contain several highly divergent ribosomal DNA groups. Analysis of the magnitude of divergence indicates that these groups have coexisted in the Podisma lineage for at least 11 million years. There are two putatively functional groups, each estimated to be at least 4 million years old, and several pseudogene groups, many of which are transcribed. Southern hybridization and real-time PCR experiments show that only one of the putatively functional types occurs at high copy number. However, this group is scarcely amplified under standard PCR conditions, which means that phylogenetic inference on the basis of standard PCR would be severely distorted. The analysis suggests that concerted evolution has been remarkably ineffective in P. pedestris. We propose that this outcome may be related to the species' exceptionally large genome and the associated low rate of deletion per base pair, which may allow pseudogenes to persist.