bluuebunny/crossref_metadata_2025 huggingface dataset:
Review article: prevalence and epidemiology of gastro‐oesophageal reflux disease in Japan
Authors: Fujimoto K.
Published: December 2004

The prevalence of gastro‐oesophageal reflux disease (GERD) in Asian populations is reported to be lower than that in Western populations. However, recent epidemiological studies suggest that the incidence of the disease is increasing, especially in Japan. Endoscopic studies show that the overall prevalence of reflux oesophagitis among the adult population in Japan is in the region of 14–16%. This is similar to the figure reported in Western countries. The increasing prevalence in Japan may be due to a number of factors including increasing awareness of the condition and improved diagnostic techniques. The majority of the diagnosed cases in Japan are mild and these account for the increase in prevalence of the condition. In contrast to the West, where the condition is more prevalent in male members of the population, there is a high incidence of GERD in elderly females in Japan. The increased incidence of kyphosis and osteoporosis in this population may lead to the development of hiatus hernia, a condition known to exacerbate the development of reflux disease. Furthermore, Japanese patients with endoscopically diagnosed GERD appear to be less likely to complain of typical reflux symptoms, such as heartburn and acid reflux than their Western counterparts. In view of the known relationship between asymptomatic GERD and the development of oesophageal cancers there is a strong case for increased vigilance in the detection of GERD in the Japanese population.
Review article: diagnosis and clinical investigation of gastro‐oesophageal reflux disease: a European view
Authors: Heading R. C.
Published: December 2004

In Western populations, many individuals with symptoms of gastro‐oesophageal reflux disease (GERD) do not bother to seek medical attention because their symptoms are mild and acceptably controlled by self‐medication. Among those who do consult physicians, only a minority present with the classical clinical symptoms of heartburn and regurgitation: more often the pattern is a nonspecific combination of upper gastrointestinal complaints that do not permit confident clinical diagnosis. Oesophagitis is now found in less than 50% of GERD patients and those without oesophagitis are sometimes said to have ‘non‐erosive reflux disease’. If a patient's clinical history is inadequate for diagnosis and the oesophageal endoscopic appearances are normal, ambulatory pH monitoring may be required if the diagnostic uncertainty is to be resolved. Despite initial enthusiasm, the ‘Proton Pump test’ for GERD has proved unreliable and has fallen from favour. Intraluminal impedence measurement is currently considered a research tool only. Most European gastroenterologists acknowledge the occurrence of ‘atypical’ presentations of GERD, including noncardiac chest pain, asthma and hoarseness (laryngitis), though confirmation of GERD as the cause of such symptoms in individual patients is often difficult.
Experimental warming and burn severity alter soil CO2 flux and soil functional groups in a recently burned boreal forest
Authors: Bergner Belle , Johnstone Jill , Treseder Kathleen K.
Published: December 2004

Global warming is projected to be greatest in northern regions, where forest fires are also increasing in frequency. Thus, interactions between fire and temperature on soil respiration at high latitudes should be considered in determining feedbacks to climate. We tested the hypothesis that experimental warming will augment soil CO2 flux in a recently burned boreal forest by promoting microbial and root growth, but that this increase will be less apparent in more severely burned areas. We used open‐top chambers to raise temperatures 0.4–0.9°C across two levels of burn severity in a fire scar in Alaskan black spruce forest. After 3 consecutive years of warming, soil respiration was measured through a portable gas exchange system. Abundance of active microbes was determined by using Biolog EcoPlates™ for bacteria and ergosterol analysis for fungi. Elevated temperatures increased soil CO2 flux by 20% and reduced root biomass, but had no effect on bacterial or fungal abundance or soil organic matter (SOM) content. Soil respiration, fungal abundance, SOM, and root biomass decreased with increasing burn severity. There were no significant interactions between temperature and burn severity with respect to any measurement. Higher soil respiration rates in the warmed plots may be because of higher metabolic activity of microbes or roots. All together, we found that postfire soils are a greater source of CO2 to the atmosphere under elevated temperatures even in severely burned areas, suggesting that global warming may produce a positive feedback to atmospheric CO2, even in young boreal ecosystems.
A comparison of drying operations on the rheological properties of whey protein thickening ingredients
Authors: Resch Jeffrey J. , Daubert Christopher R. , Allen Foegeding E.
Published: December 2004

An existing procedure for the alteration of whey proteins into a cold‐set thickening agent was modified by developing a spray‐drying operation to replace the prohibitively expensive freeze‐drying step. The original and the modified derivatization procedures were used with a commercial whey protein concentrate (WPC). The freeze‐dried and spray‐dried derivatized WPC powders, along with polysaccharide thickeners, were reconstituted in water and evaluated by using a range of rheological studies. The effects of temperature, concentration, and shear on viscosity as well as the mechanical spectra were assessed to characterize the ability of the powders to function in food systems. Rheological characterization revealed the modified derivatization procedure yielded an ingredient having the same cold‐set thickening and gelling ability as the original derivatized powder. The modified whey proteins were also able to achieve, at higher usage levels, textural properties similar to several polysaccharide thickeners. Use of a spray‐drying technique created a more economical process for the production of a whey protein ingredient that was suitable for contributing viscosity and texture to a wide range of food systems.
The effect of successive uses of oak barrels on the extraction of oak‐related volatile compounds from wine
Authors: Gómez‐Plaza Encarna , Pérez‐Prieto Luis J. , Fernández‐Fernández Jose I. , López‐Roca Jose M.
Published: December 2004

Changes in the concentration of furfuryl compounds, guaiacol and 4‐methylguaiacol, cis‐ and trans‐oak lactone, and vanillin were studied during the maturation of wines in oak barrels of different origins (French oak and American oak). The rate at which these volatile compounds accumulated in the wines followed a curve that fits to mathematical models. The changes in concentration were usually consistent with diffusion kinetics. When the barrels are new, the concentration gradient between the wood surface and the wine is high, so diffusion occurs quickly, especially in the case of lactones, the extraction rate of which could be fitted to a power curve. After some time of maturation, the concentration gradient is not so large and furthermore, the wood surface may be exhausted of some compounds so the rate of extraction decreases. During the second fill, the rate of accumulation of these compounds in the wine was almost linear, especially during the first 6 months of storage, and the quantities measured in wine were much lower. The concentration of some compounds, increased during the final 3 months (between days 180 and 270), exhibiting a quadratic curve when plotted. Furfuryl aldehydes behaved differently as they are extracted very rapidly from the first millimetres of wood surface and transformed into furfuryl alcohol, a compound with no organoleptic significance.
Decreased expression of CD28 coincides with the down‐modulation of CD3ζ and augmentation of caspase‐3 activity in T cells from hepatocellular carcinoma‐bearing patients and hepatitis C virus‐infected patients
Authors: MAKI AKIRA , MATSUDA MASANORI , ASAKAWA MASAMI , KONO HIROSHI , FUJII HIDEKI , MATSUMOTO YOSHIRO
Published: December 2004

Background and Aim:  Hepatitis C virus (HCV) infection causes chronic inflammation and increases the risk of hepatocellular carcinoma (HCC). This immunosuppressive state may be one reason why HCV‐infected patients often have multicentric cancers. Therefore, the purpose of the present study was to assess the cellular immune function in HCC‐bearing and HCV‐infected patients.

Methods:  The expression of cluster of differentiation (CD)3ζ, CD28 and caspase‐3 activity of peripheral blood T lymphocytes (PBL) from HCC‐bearing patients, HCV‐infected patients and normal subjects was measured by flow cytometric methods. Furthermore, intrahepatic T lymphocytes (IHL) and tumor‐infiltrating T lymphocytes (TIL) from HCC patients were used.

Results:  Decreased expressions of CD3ζ, CD28 and the augmentation of caspase‐3 activity were recognized in PBL from HCC and HCV patients. These phenomena were more dominant in TIL and IHL than in PBL in HCC patients. Furthermore, the down‐modulation of CD3ζ and increased caspase‐3 activity occurred in CD28 down‐modulated T cells.

Conclusion:  These results demonstrate impairment of the cellular immune system in HCC and HCV patients from the viewpoints of the down‐modulation of CD3ζ and CD28 on T cells and T‐cell apoptosis. In addition, the results imply that the down‐modulation of CD3ζ and T‐cell apoptosis take place in activated T cells.
Complete disappearance of pulmonary metastases in a case of hepatocellular carcinoma treated with docetaxel‐based systemic chemotherapy
Authors: ISHIKAWA TORU , ICHIDA TAKAFUMI , YOKOYAMA JUNJI , MATSUDA YASUNOBU , WATANABE TOSHIAKI , ASAKURA HITOSHI
Published: December 2004

A case of the complete shrinkage of pulmonary metastases from multiple hepatocellular carcinomas (HCC) after administration of docetaxel, cisplatin and enteric‐coated tegafur/uracil is reported. A 54‐year‐old Japanese man was diagnosed with recurrent multiple HCC associated with pulmonary metastases and compensated liver cirrhosis. Docetaxel, cisplatin and enteric‐coated tegafur/uracil were given to this patient. After 2 months of treatment, there was a decrease in tumor markers and a shrinkage of the pulmonary metastases. Image analyses such as chest X‐rays and chest computed tomography scans showed a disappearance of the pulmonary metastases, although the multiple HCC did not disappear completely. This was evaluated as a complete remission of metastatic lesions or a partial remission of primary lesions according to the World Health Organization criteria. No recurrence of pulmonary metastasis was seen for 10 months. This combination therapy was well‐tolerated for lung cancer and could represent an effective treatment for pulmonary metastases from HCC.
Sacral nerve stimulation: an emerging treatment for faecal incontinence
Authors: Tjandra Joe J. , Lim Jit Fong , Matzel Klaus
Published: December 2004

Faecal incontinence is common, distressing to the patient and socially incapacitating. The treatment options depend on the severity and aetiology of incontinence. For mild cases of faecal incontinence, medical management and pelvic floor physiotherapy may be adequate. For more severe cases, surgery is often required. Patients who have a distinct sphincter defect are amenable to surgical repair. In many cases, there is a combination of diffuse structural damage of the anal sphincters with pudendal neuropathy. Conventional surgical repairs have a modest degree of success and the results tend to deteriorate with time. Neosphincter procedures such as artificial bowel sphincter and dynamic graciloplasty are potentially morbid and technically complex. Sacral nerve stimulation is innovative and has had a medium‐term success with improvement of quality of life in over 80% of patients treated for faecal incontinence. These results are superior to other techniques in treating patients with severe refractory faecal incontinence, where current maximal therapy has failed. The technique is unique because there is a screening phase, which has a high predictive value. It is also associated with minimal complications that are usually minor. However, most published reports of sacral nerve stimulation for treatment of faecal incontinence were case studies and methods of assessing outcome were variable. Criteria for patient selection are evolving and are yet to be defined. The present paper critically reviews the publications to date on sacral nerve stimulation for treatment of faecal incontinence. This will form the basis for future evaluation of this emerging treatment of severe, intractable faecal incontinence. Randomized clinical trials like that of the Melbourne trial will further clarify the role and indications of sacral nerve stimulation for faecal incontinence.
Is screening for abdominal aortic aneurysm bad for your health and well‐being?
Authors: Spencer Carole A. , Norman Paul E. , Jamrozik Konrad , Tuohy Raywin , Lawrence‐Brown Michael
Published: December 2004

Background:  The purpose of the present paper was to investigate whether screening for abdominal aortic aneurysm (AAA) causes health‐related quality of life to change in men or their partners.

Methods:  A cross‐sectional case−control comparison was undertaken of men aged 65−83 years living in Perth, Western Australia, using questionnaires incorporating three validated instruments (Medical Outcomes Study Short Form−36, EuroQol EQ‐5D and Hospital Anxiety and Depression Scale) as well as several independent questions about quality of life. The 2009 men who attended for ultrasound scans of the abdominal aorta completed a short prescreening questionnaire about their perception of their general health. Four hundred and ninety‐eight men (157 with an AAA and 341 with a normal aorta) were sent two questionnaires for completion 12 months after screening, one for themselves and one for their partner, each being about the quality of life of the respondent.

Results:  Men with an AAA were more limited in performing physical activities than those with a normal aorta (t‐test of means P = 0.04). After screening, men with an AAA were significantly less likely to have current pain or discomfort than those with a normal aorta (multivariate odds ratio: 0.5; 95% confidence interval (CI): 0.3−0.9) and reported fewer visits to their doctor. The mean level of self‐perceived general health increased for all men from before to after screening (from 63.4 to 65.4).

Conclusions:  Apart from physical functioning, screening was not associated with decreases in health and well‐being. A high proportion of men rated their health over the year after screening as being either the same or improved, regardless of whether or not they were found to have an AAA.
Stressor‐related impairment of synaptic transmission in hippocampal slices from α‐synuclein knockout mice
Authors: Martín Eduardo D. , González‐García Carmen , Milán Miguel , Fariñas Isabel , Ceña Valentín
Published: December 2004

The role of alpha‐synuclein (α‐Syn) has recently received considerable attention because it seems to play a role in Parkinson's disease (PD). Missense mutations in the α‐Syn gene were found in autosomal dominant PD and α‐Syn was shown to be a major constituent of protein aggregates in sporadic PD and other synucleinopathies. Under normal conditions, α‐Syn protein is found exclusively in synaptic terminals. However, the potential participation of alpha‐synuclein in maintaining and regulating synaptic efficacy is unknown. We have investigated the excitatory synaptic modulation of alpha‐synuclein in CA1 pyramidal neurons, using the in vitro hippocampal slice technique. The 4‐aminopyridine‐induced increase of both spontaneous excitatory postsynaptic current (EPSC) frequency and amplitude was significantly higher in α‐Syn wild‐type than knockout mice, whereas basal spontaneous EPSC frequency and amplitude was similar in both animals. As the spontaneous synaptic activity was abolished by tetrodotoxin, which indicates that it was a result of action potential‐mediated transmitter release from presynaptic terminals, spontaneous EPSC changes observed in α‐Syn knockout mice suggest that these animals present a modification of synaptic transmission with a presynaptic origin. Presynaptic depression of evoked EPSCs by hypoxia or adenosine was significantly larger in α‐Syn knockout than in wild‐type mice, further supporting the hypothesis of regulation of synaptic transmission by α‐Syn. Together, these observations indicate that the loss of α‐Syn reduces synaptic efficacy when the probability of transmitter release is modified. We conclude that α‐Syn might have important actions on the maintenance of the functional integrity of synaptic transmission and its regulation in hippocampus.
THE ROLE OF COGNITION AND FEELING IN RELIGIOUS EXPERIENCE
Authors: Azari Nina P. , Birnbacher Dieter
Published: December 2004

AbstractInquiry into religious experience is informed by conceptualizations of emotion. Although a long history of theoretical and empirical work has provided considerable insight into the philosophical, psychological, and (more recently) neurobiological structure of emotion, the role of cognition and feeling in religious emotional states remains poorly conceived, and, hence, so does the concept of religious experience. The lack of a clear understanding of the role of emotion in religious experience is a consequence of a lack of an adequate interdisciplinary account of emotions. Our primary aim here is to examine the consequences of a properly interdisciplinary understanding of emotions for the analysis of religious experience. To this end, we note points of convergence between psychological, philosophical, and neuroscientific accounts of emotion and between such accounts and reports on the neurobiology of religious experience, in particular two recent human brain imaging studies. We conclude that emotions are richer phenomena than either pure feeling or pure thought and that, rightly understood, emotion affords religious experience its distinctive content and quality. Accordingly, we argue that religious experience cannot be reduced to pure feeling or pure thought. Rather, on our analysis, religious experience emerges as “thinking that feels like something.”
The neuregulin receptor, ErbB4, is not required for normal development and adult maintenance of the substantia nigra pars compacta
Authors: Thuret Sandrine , Alavian Kambiz N. , Gassmann Martin , Lloyd C. Kent , Smits Simone M. , Smidt Marten P. , Klein Rüdiger , H. Dyck Richard , Simon Horst H.
Published: December 2004

Degeneration of dopaminergic neurons in the substantia nigra is associated with one of the most prominent human neurological disorders, Parkinson's disease. It is therefore of high interest to identify molecules with trophic effects on this neuronal population. We show here that the neuregulin receptor ErbB4 is differentially expressed in mesencephalic dopaminergic neurons, found in the substantia nigra and in a subregion of the ventral tegmentum but not in the retrorubral field. Early developmental onset and continued expression of ErbB4 into the adult and the presence of two high affinity ligands, neuregulin‐1 and betacellulin, in the basal ganglia, suggested that these molecules might participate in the differentiation and/or maintenance of the nigrostriatal system. In order to address this hypothesis, we used a loxP flanked ErbB4 allele in combination with a nestin‐Cre transgene and generated brain‐specific ErbB4 null mice. These mutant animals survived into adulthood. The distribution of dopaminergic cell bodies in the midbrain, the expression of numerous genes specific to mesencephalic dopaminergic neurons, and the axonal projection to the basal ganglia all appeared normal. Finally, an assessment of their motor function revealed no behavioral deficits. The apparent lack of any mutant phenotype suggests the presence of a strong compensatory mechanism.
Phosphorylation of proteins involved in activity‐dependent forms of synaptic plasticity is altered in hippocampal slices maintained in vitro
Authors: Ho Oanh H. , Delgado Jary Y. , O'Dell Thomas J.
Published: December 2004

The acute hippocampal slice preparation has been widely used to study the cellular mechanisms underlying activity‐dependent forms of synaptic plasticity such as long‐term potentiation (LTP) and long‐term depression (LTD). Although protein phosphorylation has a key role in LTP and LTD, little is known about how protein phosphorylation might be altered in hippocampal slices maintained in vitro. To begin to address this issue, we examined the effects of slicing and in vitro maintenance on phosphorylation of six proteins involved in LTP and/or LTD. We found that AMPA receptor (AMPAR) glutamate receptor 1 (GluR1) subunits are persistently dephosphorylated in slices maintained in vitro for up to 8 h. α calcium/calmodulin‐dependent kinase II (αCamKII) was also strongly dephosphorylated during the first 3 h in vitro but thereafter recovered to near control levels. In contrast, phosphorylation of the extracellular signal‐regulated kinase ERK2, the ERK kinase MEK, proline‐rich tyrosine kinase 2 (Pyk2), and Src family kinases was significantly, but transiently, increased. Electrophysiological experiments revealed that the induction of LTD by low‐frequency synaptic stimulation was sensitive to time in vitro. These findings indicate that phosphorylation of proteins involved in N‐methyl‐d‐aspartate (NMDA) receptor‐dependent forms of synaptic plasticity is altered in hippocampal slices and suggest that some of these changes can significantly influence the induction of LTD.
Effects of supra‐physiological changes in human ovarian hormone levels on maximum force production of the first dorsal interosseus muscle
Authors: Elliott Kirsty Jayne , Cable Nigel Timothy , Reilly Thomas , Sefton Victoria , Kingsland Charles , Diver Michael
Published: December 2004

The purpose of this study was to investigate the effects of supra‐physiological changes in ovarian hormone levels on maximum force production in two conditions, one physiological (pregnancy) and one pseudo‐physiological (in vitro fertilization (IVF) treatment). Forty IVF patients were tested at four distinct stages of treatment and 35 women were tested during each trimester of pregnancy and following parturition. Maximum voluntary isometric force per unit cross‐sectional area of the first dorsal interosseus muscle was measured. Plasma concentrations of total and bioavailable oestradiol and testosterone were measured, in addition to the total concentrations of progesterone and human chorionic gonadotropin. Despite significant changes in the concentrations of total progesterone, 17β‐oestradiol, bioavailable oestradiol and testosterone between phases, strength did not change significantly throughout IVF treatment (1.30 ± 0.29, 1.16 ± 0.38, 1.20 ± 0.29 and 1.26 ± 0.34 N mm−2, respectively, in the 4 phases of IVF treatment). Force production was significantly higher during the second trimester of pregnancy than following childbirth (1.33 ± 0.20 N mm−2 at week 12 of pregnancy, 1.51 ± 0.42 N mm−2 at week 20, 1.15 ± 0.26 N mm−2 at week 36 and 0.94 ± 0.31 N mm−2 at week 6 postnatal) but was not significantly correlated with any of the hormones measured. These data suggest that extreme changes in the concentrations of reproductive hormones do not affect the maximum force‐generating capacity of young women.
Revised Proposal of Fatigue Life Correction Factor Fen for Carbon and Low Alloy Steels in LWR Water Environments
Authors: Higuchi Makoto
Published: December 2004

The fatigue life of carbon and low alloy steels decreases with reduction in strain rate in high temperature water such as in the case of a light water reactor coolant. The fatigue life reduction also depends on temperature and dissolved oxygen. The fatigue life correction factor Fen has been proposed as a method to assess the fatigue life reduction in such environments. Three different models for calculating Fen for carbon and low alloy steels have been proposed by Higuchi et al., Chopra et al., and Mehta. These models were compared using considerable environmental fatigue data that were tested and published in Japan and USA and piled up in the database “JNUFAD” by the author. These models give somewhat different results in the specific conditions and a revised model for calculating Fen is thus proposed by remedying the particular drawbacks of each. In this model, the same formula is used for carbon and low alloy steels and S*,T*,O*, and ε˙* are adopted in the formula after reevaluating every parameter. The revised proposal shows better correlation with the test data than the previous models.
The Effect of D/T on the Load Interaction Behavior of a Plain Pipe
Authors: Ayob Amran Bin
Published: December 2004

The objective of the study is to determine the effect of diameter/thickness (D/T) ratio on the interaction of axial force, bending moment, torsion and internal pressure in plain pipes. The Tresca and von Mises criteria are used to determine the first yield behavior of pipes when subjected to combined loads. The results show that for certain load combinations, the load interaction behavior is affected by D/T ratio and some load interaction relations change with a load dominance. The general trend is an increase in effective stress as D/T is increased. Most design codes show slightly conservative pipe design.
Residual Stresses and Distortion in Boiler Tube Panels With Welded Overlay Cladding
Authors: Yildirim B. , Nied H. F.
Published: December 2004

In this study, finite element models are developed to analyze and predict the transient temperature profiles, residual stresses, and distortion incurred during deposition of protective overlay cladding on boiler tube waterwall panels. Plane strain models are used to simulate the evolution of residual stresses on the cross-section of a typical boiler tube panel during deposition of filler metal in sequential weld passes. The results demonstrate how residual stresses from previous weld passes are affected by an adjacent weld bead during the cladding process. Determination of the increment in panel warpage during each weld pass, for a sufficent number of passes, provides the necessary information to estimate of the total panel warpage after cladding coverage on a very large panel surface. It is noted that the total welding induced distortion can be adequately estimated from a relatively small number of weld passes over the typical waterwall cross-section.
Mixed Mode Loading of an Interface Crack Between Graded Creeping Solids
Authors: Gordon Ali P. , McDowell David L.
Published: December 2004

Interface cracks are seldom subjected to pure Mode I conditions. Stationary cracks between two distinct, bonded elastic-creep materials subjected to remotely applied mixed mode loading are simulated using the finite element method (FEM). Plane strain conditions are assumed. In most cases a functionally graded transition layer is included between two homogeneous, yet distinctive, materials. Examples of such systems include bonded structures or repaired components subjected to elevated temperatures. Numerical solutions based on the asymptotic fields of the homogeneous and heterogeneous Arcan-type specimens are presented. Creep ductility-based damage models are used to predict the initial crack propagation trajectory. Incorporation of functionally graded transition layer regions was determined to affect the evolution of time-dependent stress components in the vicinity of the crack tip. The magnitude and direction of crack tip propagation can then be optimized with respect to interface properties.
Interface Structure and Atomic Bonding Characteristics in Silicon Nitride Ceramics
Authors: Ziegler A. , Idrobo J. C. , Cinibulk M. K. , Kisielowski C. , Browning N. D. , Ritchie R. O.
Published: December 2004

Direct atomic resolution images have been obtained that illustrate how a range of rare-earth atoms bond to the interface between the intergranular phase and the matrix grains in an advanced silicon nitride ceramic. It has been found that each rare-earth atom bonds to the interface at a different location, depending on atom size, electronic configuration, and the presence of oxygen at the interface. This is the key factor to understanding the origin of the mechanical properties in these ceramics and will enable precise tailoring in the future to critically improve the materials' performance in wide-ranging applications.
Evidence from Opportunity's Microscopic Imager for Water on Meridiani Planum
Authors: Herkenhoff K. E. , Squyres S. W. , Arvidson R. , Bass D. S. , Bell J. F. , Bertelsen P. , Ehlmann B. L. , Farrand W. , Gaddis L. , Greeley R. , Grotzinger J. , Hayes A. G. , Hviid S. F. , Johnson J. R. , Jolliff B. , Kinch K. M. , Knoll A. H. , Madsen M. B. , Maki J. N. , McLennan S. M. , McSween H. Y. , Ming D. W. , Rice J. W. , Richter L. , Sims M. , Smith P. H. , Soderblom L. A. , Spanovich N. , Sullivan R. , Thompson S. , Wdowiak T. , Weitz C. , Whelley P.
Published: December 2004

The Microscopic Imager on the Opportunity rover analyzed textures of soils and rocks at Meridiani Planum at a scale of 31 micrometers per pixel. The uppermost millimeter of some soils is weakly cemented, whereas other soils show little evidence of cohesion. Rock outcrops are laminated on a millimeter scale; image mosaics of cross-stratification suggest that some sediments were deposited by flowing water. Vugs in some outcrop faces are probably molds formed by dissolution of relatively soluble minerals during diagenesis. Microscopic images support the hypothesis that hematite-rich spherules observed in outcrops and soils also formed diagenetically as concretions.
Conditional Use of Sex and Parthenogenesis for Worker and Queen Production in Ants
Authors: Pearcy Morgan , Aron Serge , Doums Claudie , Keller Laurent
Published: December 2004

The near-ubiquity of sexual reproduction in animal species has long been considered a paradox because sexually reproducing individuals transmit only half of their genome to their progeny. Here, we show that the ant
Cataglyphis cursor
circumvents this cost by using alternative modes of reproduction for the production of reproductive and nonreproductive offspring. New queens are almost exclusively produced by parthenogenesis, whereas workers are produced by normal sexual reproduction. By selectively using sex for somatic growth and parthenogenesis for germline production,
C. cursor
has taken advantage of the ant caste system to benefit from the advantages of both sexual and asexual reproduction.
Initiation of Protein Synthesis by a Labeled Derivative of theLactobacillus caseiDN-114 001 Strain during Transit from the Stomach to the Cecum in Mice Harboring Human Microbiota
Authors: Oozeer R. , Mater D. D. G. , Goupil-Feuillerat N. , Corthier G.
Published: December 2004

Although studies on the survival of bacteria in the digestive tract have been reported in the literature, little data are available on the physiological adaptation of probiotics to the digestive environment. In previous work, a transcriptional fusion system (i.e., luciferase genes under the control of a deregulated promoter) was used to demonstrate that a derivative of theLactobacillus caseiDN-114 001 strain, ingested in a fermented milk and thus exhibiting initially a very weak metabolic activity, synthesized proteins de novo after its transit in the digestive tract of mice harboring human microbiota (known as human-microbiota-associated mice). With the same genetic system and animal model, we here investigate for the first time the ability ofL. caseito reinitiate synthesis in the different digestive tract compartments. In this study, most ingestedL. caseicells transited from the stomach to the duodenum-jejunum within 1 h postingestion. No luciferase activity was observed in these digestive tract compartments after the first hour. At later times, the bulk of bacteria had transited to the ileum and the cecum. Luciferase synthesis was detected between 1.5 and 2.0 h postingestion at the ileal level and from 1.5 h to at least 6.0 h postingestion in the cecum, where the activity remained at a maximum level. These results demonstrate that ingestedL. casei(derivative of the DN-114 001 strain) administered via a fermented milk has already reinitiated protein synthesis when it reaches the ileal and cecal compartments.
Identification of a Novel Dioxygenase Involved in Metabolism ofo-Xylene, Toluene, and Ethylbenzene byRhodococcussp. Strain DK17
Authors: Kim Dockyu , Chae Jong-Chan , Zylstra Gerben J. , Kim Young-Soo , Kim Seong-Ki , Nam Myung Hee , Kim Young Min , Kim Eungbin
Published: December 2004

Rhodococcussp. strain DK17 is able to grow ono-xylene, benzene, toluene, and ethylbenzene. DK17 harbors at least two megaplasmids, and the genes encoding the initial steps in alkylbenzene metabolism are present on the 330-kb pDK2. The genes encoding alkylbenzene degradation were cloned in a cosmid clone and sequenced completely to reveal 35 open reading frames (ORFs). Among the ORFs, we identified two nearly exact copies (one base difference) of genes encoding large and small subunits of an iron sulfur protein terminal oxygenase that are 6 kb apart from each other. Immediately downstream of one copy of the dioxygenase genes (akbA1aandakbA2a) is a gene encoding a dioxygenase ferredoxin component (akbA3), and downstream of the other copy (akbA1bandakbA2b) are genes putatively encoding ameta-cleavage pathway. RT-PCR experiments show that the two copies of the dioxygenase genes are operonic with the downstream putative catabolic genes and that both operons are induced byo-xylene. When expressed inEscherichia coli, AkbA1a-AkbA2a-AkbA3 transformedo-xylene into 2,3- and 3,4-dimethylphenol. These were apparently derived from an unstableo-xylenecis-3,4-dihydrodiol, which readily dehydrates. This indicates a single point of attack of the dioxygenase on the aromatic ring. In contrast, attack of AkbA1a-AkbA2a-AkbA3 on ethylbenzene resulted in the formation of two differentcis-dihydrodiols resulting from an oxidation at the 2,3 and the 3,4 positions on the aromatic ring, respectively.
Genogroup I and II Noroviruses Detected in Stool Samples by Real-Time Reverse Transcription-PCR Using Highly Degenerate Universal Primers
Authors: Richards Gary P. , Watson Michael A. , Fankhauser Rebecca L. , Monroe Stephan S.
Published: December 2004

Genogroup I noroviruses from five genetic clusters and genogroup II noroviruses from eight genetic clusters were detected in stool extracts using degenerate primers and single-tube, real-time reverse transcription-PCR (RT-PCR) with SYBR Green detection. Two degenerate primer sets, designated MON 431-433 and MON 432-434, were designed from consensus sequences from the major clusters of norovirus based on the RNA-dependent RNA polymerase region of the norovirus genome. Viruses were extracted from stool samples within 20 min using a viral RNA extraction kit. Real-time RT-PCR for noroviruses generated semiquantitative results by means of the cycle threshold data and dilution endpoint standard curves. Presumptive product verification was achieved by evaluation of first-derivative melt graphs. Multiple clusters of noroviruses were identified simultaneously in a multiplex fashion by virtue of slight differences in melting temperature. The detection of 13 different genetic clusters suggests that the MON primers may serve as universal primers for most, if not all, of the noroviruses in a multiplex assay. Our technique provides a framework for broad application of real-time RT-PCR in clinical, environmental, and food testing laboratories for a wide range of noroviruses.
Use of 16S rRNA Gene-Targeted Group-Specific Primers for Real-Time PCR Analysis of Predominant Bacteria in Human Feces
Authors: Matsuki Takahiro , Watanabe Koichi , Fujimoto Junji , Takada Toshihiko , Tanaka Ryuichiro
Published: December 2004

16S rRNA gene-targeted group-specific primers were designed and validated for specific detection and quantification of the
Clostridium leptum
subgroup and the
Atopobium
cluster. To monitor the predominant bacteria in human feces by real-time PCR, we used these specific primers together with four sets of group-specific primers for the
Clostridium coccoides
group, the
Bacteroides fragilis
group,
Bifidobacterium
, and
Prevotella
developed in a previous study (T. Matsuki, K. Watanabe, J. Fujimoto, Y. Miyamoto, T. Takada, K. Matsumoto, H. Oyaizu, and R. Tanaka, Appl. Environ. Microbiol.
68:
5445-5451, 2002). Examination of DNA extracted from the feces of 46 healthy adults showed that the
C. coccoides
group was present in the greatest numbers (log
10
10.3 ± 0.3 cells per g [wet weight] [average ± standard deviation]), followed by the
C. leptum
subgroup (log
10
9.9 ± 0.7 cells per g [wet weight]), the
B. fragilis
group (log
10
9.9 ± 0.3 cells per g [wet weight]),
Bifidobacterium
(log
10
9.4 ± 0.7 cells per g [wet weight]), and the
Atopobium
cluster (log
10
9.3 ± 0.7 cells per g [wet weight]). These five bacterial groups were detected in all 46 volunteers.
Prevotella
was found in only 46% of the subjects at a level of log
10
9.7 ± 0.8 cells per g (wet weight). Examination of changes in the population and the composition of the intestinal flora for six healthy adults over an 8-month period revealed that the composition of the flora of each volunteer remained stable throughout the test period.
Novel Physiological Features of
Carboxydothermus hydrogenoformans
and
Thermoterrabacterium ferrireducens
Authors: Henstra Anne M. , Stams Alfons J. M.
Published: December 2004

Carboxydothermus hydrogenoformans
is able to grow by conversion of CO to H
2
and CO
2
. Besides CO, only pyruvate was described as serving as an energy source. Based on 16S rRNA gene sequence similarity,
C. hydrogenoformans
is closely related to
Thermoterrabacterium ferrireducens. T. ferrireducens
is like
C. hydrogenoformans
a gram-positive, thermophilic, strict anaerobic bacterium. However, it is capable of using various electron donors and acceptors for growth. Growth of
C. hydrogenoformans
with multiple electron donors and acceptors was tested.
C. hydrogenoformans
oxidized formate, lactate, glycerol, CO, and H
2
with 9,10-anthraquinone-2,6-disulfonate as an electron acceptor. Sulfite, thiosulfate, sulfur, nitrate, and fumarate were reduced with lactate as an electron donor.
T. ferrireducens
oxidized CO with 9,10-anthraquinone-2,6-disulfonate as an electron acceptor but did not produce H
2
from CO. In contrast to what was published before,
T. ferrireducens
was able to grow on lactate with sulfite, sulfur, and nitrate as electron acceptors.
New Integrative Method To Generate
Bacillus subtilis
Recombinant Strains Free of Selection Markers
Authors: Brans Alain , Filée Patrice , Chevigné Andy , Claessens Aurore , Joris Bernard
Published: December 2004

The novel method described in this paper combines the use of
blaI
, which encodes a repressor involved in
Bacillus licheniformis
BlaP β-lactamase regulation, an antibiotic resistance gene, and a
B. subtilis
strain (BS1541) that is conditionally auxotrophic for lysine. We constructed a BlaI cassette containing
blaI
and the spectinomycin resistance genes and two short direct repeat DNA sequences, one at each extremity of the cassette. The BS1541 strain was obtained by replacing the
B. subtilis
P

lysA

promoter with that of the P

blaP

β-lactamase promoter. In the resulting strain, the cloning of the
blaI
repressor gene confers lysine auxotrophy to BS1541. After integration of the BlaI cassette into the chromosome of a conditionally
lys
-auxotrophic (BS1541) strain by homologous recombination and positive selection for spectinomycin resistance, the eviction of the BlaI cassette was achieved by single crossover between the two short direct repeat sequences. This strategy was successfully used to inactivate a single gene and to introduce a gene of interest in the
Bacillus
chromosome. In both cases the resulting strains are free of selection marker. This allows the use of the BlaI cassette to repeatedly further modify the
Bacillus
chromosome.
In Situ Expression of
nifD
in
Geobacteraceae
in Subsurface Sediments
Authors: Holmes Dawn E. , Nevin Kelly P. , Lovley Derek R.
Published: December 2004

In order to determine whether the metabolic state of
Geobacteraceae
involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of
nifD
, a highly conserved gene involved in nitrogen fixation, was investigated. When
Geobacter sulfurreducens
was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of
nifD
transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of
recA
and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of
Geobacteraceae
and Fe(III) reduction, as well as the expression of
nifD
in
Geobacteraceae
. Levels of
nifD
transcripts in
Geobacteraceae
decreased more than 100-fold within 2 days after the addition of 100 μM ammonium, while levels of
recA
and total bacterial 16S rRNA in
Geobacteraceae
remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that
Geobacteraceae
could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of
Geobacteraceae
species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by
Geobacteraceae
.
Detection and Quantification ofWallemia sebiin Aerosols by Real-Time PCR, Conventional PCR, and Cultivation
Authors: Zeng Qing-Yin , Westermark Sven-Olof , Rasmuson-Lestander Åsa , Wang Xiao-Ru
Published: December 2004

Wallemia sebiis a deuteromycete fungus commonly found in agricultural environments in many parts of the world and is suspected to be a causative agent of farmer's lung disease. The fungus grows slowly on commonly used culture media and is often obscured by the fast-growing fungi. Thus, its occurrence in different environments has often been underestimated. In this study, we developed two sets of PCR primers specific toW. sebithat can be applied in either conventional PCR or real-time PCR for rapid detection and quantification of the fungus in environmental samples. Both PCR systems proved to be highly specific and sensitive forW. sebidetection even in a high background of other fungal DNAs. These methods were employed to investigate the presence ofW. sebiin the aerosols of a farm. The results revealed a high concentration ofW. sebispores, 107m−3by real-time PCR and 106m−3by cultivation, which indicates the prevalence ofW. sebiin farms handling hay and grain and in cow barns. The methods developed in this study could serve as rapid, specific, and sensitive means of detectingW. sebiin aerosol and surface samples and could thus facilitate investigations of its distribution, ecology, clinical diagnosis, and exposure risk assessment.
Quantification of Tetracycline Resistance Genes in Feedlot Lagoons by Real-Time PCR
Authors: Smith Marilyn S. , Yang Richard K. , Knapp Charles W. , Niu Yafen , Peak Nicholas , Hanfelt Margery M. , Galland John C. , Graham David W.
Published: December 2004

A new real-time PCR method is presented that detects and quantifies three tetracycline resistance (Tc
r
) genes [
tet
(O),
tet
(W), and
tet
(Q)] in mixed microbial communities resident in feedlot lagoon wastewater. Tc
r
gene real-time TaqMan primer-probe sets were developed and optimized to quantify the Tc
r
genes present in seven different cattle feedlot lagoons, to validate the method, and to assess whether resistance gene concentrations correlate with free-tetracycline levels in lagoon waters. The method proved to be sensitive across a wide range of gene concentrations and provided consistent and reproducible results from complex lagoon water samples. The log
10
of the sum of the three resistance gene concentrations was correlated with free-tetracycline levels (
r
2
= 0.50,
P
< 0.001;
n
= 18), with the geometric means of individual resistance concentrations ranging from 4- to 8.3-fold greater in lagoon samples with above-median tetracycline levels (>1.95 μg/liter by enzyme-linked immunosorbent assay techniques) than in below-median lagoon samples. Of the three Tc
r
genes tested,
tet
(W) and
tet
(Q) were more commonly found in lagoon water samples. Successful development of this real-time PCR assay will permit other studies quantifying Tc
r
gene numbers in environmental and other samples.
Hypothesis for the Role of Nutrient Starvation in Biofilm Detachment
Authors: Hunt Stephen M. , Werner Erin M. , Huang Baochuan , Hamilton Martin A. , Stewart Philip S.
Published: December 2004

A combination of experimental and theoretical approaches was used to investigate the role of nutrient starvation as a potential trigger for biofilm detachment. Experimental observations of detachment in a variety of biofilm systems were made with pure cultures of
Pseudomonas aeruginosa
. These observations indicated that biofilms grown under continuous-flow conditions detached after flow was stopped, that hollow cell clusters were sometimes observed in biofilms grown in flow cells, and that lysed cells were apparent in the internal strata of colony biofilms. When biofilms were nutrient starved under continuous-flow conditions, detachment still occurred, suggesting that starvation and not the accumulation of a metabolic product was responsible for triggering detachment in this particular system. A cellular automata computer model of biofilm dynamics was used to explore the starvation-dependent detachment mechanism. The model predicted biofilm structures and dynamics that were qualitatively similar to those observed experimentally. The predicted features included centrally located voids appearing in sufficiently large cell clusters, gradients in growth rate within these clusters, and the release of most of the biofilm with simulated stopped-flow conditions. The model was also able to predict biofilm sloughing resulting solely from this detachment mechanism. These results support the conjecture that nutrient starvation is an environmental cue for the release of microbes from a biofilm.