bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction with the mammary microenvironment redirects spermatogenic cell fate
in vivo
Authors: Boulanger Corinne A. , Mack David L. , Booth Brian W. , Smith Gilbert H.
Published: March 2007

Previously, we characterized a parity-induced mammary epithelial cell population that possessed the properties of pluripotency and self-renewal upon transplantation. These cells were lineally marked by the expression of β-galactosidase (LacZ) as a result of mammary-specific activation of a reporter gene through Cre-lox recombination during pregnancy. We used this experimental model to determine whether testicular cells would alter their cell fate upon interaction with the mammary gland microenvironment during pregnancy, lactation, and involution. Adult testicular cells, isolated from seminiferous tubules, were mixed with limiting dilutions of dispersed mammary epithelial cells and injected into epithelium-divested mammary fat pads. The host mice were bred 6–8 weeks later and examined 20–30 days postinvolution. This approach allowed for the growth of mammary tissue from the injected cells and transient activation of the whey acidic protein promoter-Cre gene during pregnancy and lactation, leading to Cre-lox recombination and constitutive expression of LacZ from its promoter. Here we show that cells from adult seminiferous tubules interact with mammary epithelial cells during regeneration of the gland. They adopt mammary epithelial progenitor cell properties, including self-renewal and the production of cell progeny, which differentiate into functional mammary epithelial cells. Our results provide evidence for the ascendancy of the tissue microenvironment over the intrinsic nature of cells from an alternative adult tissue.
Yoga as a Complementary Treatment of Depression: Effects of Traits and Moods on Treatment Outcome
Authors: Shapiro David , Cook Ian A. , Davydov Dmitry M. , Ottaviani Cristina , Leuchter Andrew F. , Abrams Michelle
Published: March 2007

Preliminary findings support the potential of yoga as a complementary treatment of depressed patients who are taking anti‐depressant medications but who are only in partial remission. The purpose of this article is to present further data on the intervention, focusing on individual differences in psychological, emotional and biological processes affecting treatment outcome. Twenty‐seven women and 10 men were enrolled in the study, of whom 17 completed the intervention and pre‐ and post‐intervention assessment data. The intervention consisted of 20 classes led by senior Iyengar yoga teachers, in three courses of 20 yoga classes each. All participants were diagnosed with unipolar major depression in partial remission. Psychological and biological characteristics were assessed pre‐ and post‐intervention, and participants rated their mood states before and after each class. Significant reductions were shown for depression, anger, anxiety, neurotic symptoms and low frequency heart rate variability in the 17 completers. Eleven out of these completers achieved remission levels post‐intervention. Participants who remitted differed from the non‐remitters at intake on several traits and on physiological measures indicative of a greater capacity for emotional regulation. Moods improved from before to after the yoga classes. Yoga appears to be a promising intervention for depression; it is cost‐effective and easy to implement. It produces many beneficial emotional, psychological and biological effects, as supported by observations in this study. The physiological methods are especially useful as they provide objective markers of the processes and effectiveness of treatment. These observations may help guide further clinical application of yoga in depression and other mental health disorders, and future research on the processes and mechanisms.
Efficient Estimation of Time-Invariant and Rarely Changing Variables in Finite Sample Panel Analyses with Unit Fixed Effects
Authors: Plümper Thomas , Troeger Vera E.
Published: March 2007

This paper suggests a three-stage procedure for the estimation of time-invariant and rarely changing variables in panel data models with unit effects. The first stage of the proposed estimator runs a fixed-effects model to obtain the unit effects, the second stage breaks down the unit effects into a part explained by the time-invariant and/or rarely changing variables and an error term, and the third stage reestimates the first stage by pooled OLS (with or without autocorrelation correction and with or without panel-corrected SEs) including the time-invariant variables plus the error term of stage 2, which then accounts for the unexplained part of the unit effects. We use Monte Carlo simulations to compare the finite sample properties of our estimator to the finite sample properties of competing estimators. In doing so, we demonstrate that our proposed technique provides the most reliable estimates under a wide variety of specifications common to real world data.
Hearing Levels in Patients With Microtia: Correlation With Temporal Bone Malformation
Authors: Ishimoto Shin‐ichi , Ito Ken , Karino Shotaro , Takegoshi Hideki , Kaga Kimitaka , Yamasoba Tatsuya
Published: March 2007

Objective: To evaluate the relationship between hearing level and temporal bone abnormalities in patients with microtia.

Study Design: Retrospective case series study between 1992 and 2004.

Setting: Academic, tertiary care referral medical center.

Patients: We evaluated 115 ears of 89 patients (68 males, 21 females; mean age, 11 yr; range, 5‐44 yr) with microtia.

Main Outcome Measures: Hearing level was examined in patients with microtia. Developmental abnormalities of the temporal bone were evaluated by Jahrsdoerfer's computed tomography (CT) scoring system using high‐resolution CT (HRCT) scans of the temporal bone. Temporal bone malformation scores were divided into four subgroups: ossicular development, windows connected to the cochlea, aeration of the middle ear cavity, and facial nerve aberration. Patients were divided into the stenosis and atresia groups on the basis of the appearance of the external auditory canal (EAC). We also evaluated the relationships between hearing level and four subtotal scores of the HRCT findings in the stenosis and atresia groups.

Results: There was no relationship between hearing level and total points of HRCT scoring system or between hearing level and severity of microtia scored by Marx classification. With regard to subtotal points related to ossicles (4 points), the hearing level in ears with low scores (<2) (64.7 ± 1.6 dB) was significantly different (P = .03) from that in ears with high scores (≥2) (54.0 ± 2.8 dB) in the stenosis group. In the atresia group, the hearing level was 64.3 ± 2.2 dB in ears with low scores and 62.3 ± 1.1 in ears with high scores (P > .5). As for subtotal points related to the windows connected to cochlea (2 points), the hearing level was 64.8 ± 2.6 dB in ears with low scores (0) and 55.9 ± 2.4 dB in ears with high scores (> = 1) in the stenosis group. In the atresia group, the hearing level was 67.7 ± 2.3 dB in ears with low scores and 61.5 ± 1.0 in ears with high scores. There was significant difference between ears with low and high scores in the stenosis group (P = .03) and atresia group (P = .009). There was no significant difference between ears with low and high scores with respect to the subtotal points related to aeration of the middle ear cavity and aberration of the facial nerve.

Conclusion: The hearing level in microtic ears correlated with the formation of oval/round windows and ossicular development but not with the degree of middle ear aeration, facial nerve aberration, or severity of microtia. The hearing level can also serve as an indictor, such as the HRCT findings, to determine whether a subject's hearing will likely improve after reconstructive surgery.
Quality of Life 17 to 20 Years After Uvulopalatopharyngoplasty
Authors: Goh Yau H. , Mark Ignatius , Fee Willard E.
Published: March 2007

Objectives: To study the long‐term quality of life outcomes of a group of unselected patients for the long‐term effects of uvulopalatopharyngoplasty (UPPP).

Study Design: Retrospective chart review and telephone survey.

Methods: Forty‐nine patients who underwent UPPP between July 1980 and July 1983 and who had their medical records were reviewed and were asked to grade on a visual analogue scale (VAS) the clinical benefits and complications of UPPP after the surgery.

Results: Forty‐three (87.8%) males and six (12.2%) female patients were studied. Improvement in snoring, excessive daytime somnolence, and nocturnal arousals were seen after UPPP with decreased effectiveness after time. The most common complication of UPPP was velopharyngeal insufficiency (VPI) (28.5%); however, dry throat and swallowing difficulty tended to be more severe in those patients who had them. No correlation between the snoring and VPI VAS grades was observed. Forty‐three patients had a preoperative sleep study and 22 patients a postoperative sleep study. There was lack of correlation between the significant subjective clinical improvement and their postoperative polysomnography.

Conclusion: When undertaking UPPP, both subjective and objective benefits should be weighed against the risk of long‐term ill effects. Patients should also be warned that the long‐term side effects such as VPI, dry throat, and abnormal swallowing sensation might be more common than previously expected.
Quality of Life in Laryngopharyngeal Reflux Patients
Authors: Siupsinskiene Nora , Adamonis Kestutis , Toohill Robert J.
Published: March 2007

Objectives: To evaluate and compare quality of life (QL) parameters in patients with laryngopharyngeal reflux (LPR) versus healthy controls, to determine the impact of clinical signs to QL, and to assess changes in QL parameters after treatment.

Study Design: Prospective, open, clinical study.

Material and Methods: One hundred outpatients with LPR and 109 healthy voice controls were enrolled. LPR patients underwent endoscopy and received omeprazole for 3 months. Results of endoscopy revealed 79 patients without esophagitis and 21 with, giving two subgroups of LPR patients. QL was evaluated using voice handicap index (VHI), hospital anxiety and depression scale, disability in social activities, and well‐being in general (W‐BVAS).

Results: The mean scores for total VHI and functional, physical, and emotional functioning domain subscales were found to be significantly higher in LPR patients versus controls (P < .0001), with no difference among LPR subgroups. Abnormal anxiety was one third in both LPR subgroups versus 6.4% of controls (P < .001). Both LPR subgroups patients had significantly reduced social activities and significantly lower mean W‐BVAS score than controls. LPR symptoms had a significant relation with all tested QL parameters, whereas laryngoscopic findings had a significant relation with VHI and W‐BVAS only. All mean QL parameters scores improved after 3‐month omeprazole treatment.

Conclusions: QL in LPR patients with or without esophagitis is impaired significantly in many aspects. Impairment of QL is more associated with symptoms than laryngoscopic findings. Treatment with omeprazole significantly improved QL in both LPR subgroups patients.
Tracheal Regeneration After Partial Resection: A Tissue Engineering Approach
Authors: Yamashita Masaru , Kanemaru Shin‐ichi , Hirano Shigeru , Magrufov Akhmar , Tamaki Hisanobu , Tamura Yoshihiro , Kishimoto Masanao , Omori Koichi , Nakamura Tatsuo , Ito Juichi
Published: March 2007

Objectives: The aims of this study are to investigate the efficiency of a tissue engineering approach to partial tracheal reconstruction and to improve epithelialization of the reconstructed trachea. The trachea must be resected in some cases of cancer or trauma. Various restructuring techniques are used, with no consensus on the best approach. Two problems that arise when treating tracheal defects by conventional techniques are an inability to regenerate ciliated epithelium at the reconstructed site and having to perform multiple procedures to achieve the desired repair. This study is designed to address these problems.

Study Design: Preliminary, an animal experiment.

Methods: Surgery was performed on five adult beagles under anesthesia. After the making of a longitudinal cervical skin incision, the trachea was exposed and a circular defect created. A polypropylene and collagen scaffold preclotted with peripheral blood was inserted to the defect site. Postoperatively, the site was evaluated fiberscopically, histologically, and radiographically.

Results: All dogs did well postoperatively. Fiberscopic examination showed that the implanted scaffolds were completely covered with regenerated mucosa with capillaries in all cases. Histologic data showed ciliated epithelium regenerated at the operated site from 1 month postoperatively. Newly formed cartilage was detected in the specimens from 8 to 12 postoperative months. Computed tomography images revealed the fine luminal contour of the regenerated site.

Conclusions: Good epithelial regeneration was observed after repair of a round tracheal resection using a simple tissue engineering technique, making the technique a good substitute for conventional approaches to tracheal reconstruction in patients with cancer or trauma.
Viscoelasticity of Hyaluronan and Nonhyaluronan Based Vocal Fold Injectables: Implications for Mucosal Versus Muscle Use
Authors: Caton Trace , Thibeault Susan L. , Klemuk Sarah , Smith Marshall E.
Published: March 2007

Objectives: The purpose of this study was to measure and compare biomechanical properties of commonly used vocal fold injectates Cymetra, Radiesse, Restylane, Hylaform, and one investigational injectate, Carbylan‐GSX 5%, to determine suitability for mucosal injection.

Study Design: Rheologic investigation.

Methods: Oscillatory shear stress was applied to five samples of each injectate using a parallel plate controlled stress rheometer. Shear stress, shear strain, and strain rate associated with the oscillatory shear deformation were computed from the prescribed torque and measured angular velocity; viscoelastic data were obtained on the basis of these functions. Values calculated included elastic shear moduli, viscous moduli, and dynamic viscosity as a function of oscillatory frequency (0.01–150 Hz).

Results: Elastic moduli for all samples increased as the frequency increased. Hyaluronan based materials were all comparable with each other and at least an order of magnitude lower than the stiffer and more viscous Cymetra and Radiesse. Carbylan‐GSX 5% was found to have almost identical values to Hylaform with the exception of its mean viscosity, which was noticeably lower.

Conclusions: Hyaluronan based biomaterials offer less resistance to flow and stiffness and may be better suited for injections into the mucosa, whereas Cymetra and Radiesse appear to be appropriate for injections into muscle. Viscoelastic properties of Hylaform and Carbylan‐GSX 5% were found to most resemble that of the human vocal fold mucosa.
Genetic and Acquired Prothrombotic Risk Factors and Sudden Hearing Loss
Authors: Capaccio Pasquale , Ottaviani Francesco , Cuccarini Valeria , Bottero Alessandro , Schindler Antonio , Cesana Bruno Mario , Censuales Salvatore , Pignataro Lorenzo
Published: March 2007

Objectives: Idiopathic sudden sensorineural hearing loss (ISSNHL) is a frequently encountered condition, and various pathogenetic mechanisms have been hypothesized, such as viral infections, autoimmune processes, and ischemic events; however, whatever the cause, impaired cochlear perfusion appears to be the most important event. A number of inherited prothrombotic risk factors and their related genetic alterations have recently been correlated with vascular disorders.

Methods: To investigate the mechanisms of vascular thrombosis of the inner ear leading to sudden HL, we examined 100 patients with SSNHL for the presence of acquired or inherited prothrombotic risk factors and 200 healthy volunteers as controls. All of the subjects underwent hematologic examinations, including MTHFR C677T and A1298C, prothrombin G20210A, platelet GlyIIIaA1/A2, V Leiden G1691A genotyping, fibrinogenemia, cholesterolemia, homocystinemia, and folatemia. Genomic DNA was isolated from peripheral blood leukocytes using standard methods, and gene mutations were investigated using a LightCycler DNA analyser and polymerase chain reaction.

Results: A statistically significant association was found between SSNHL and the MTHFR C677T/A1298C polymorphisms, the prothrombin G20210A transition, and the platelet GlyIIIaA1/A2 and V Leiden G1691A mutations. Furthermore, the SSNHL patients had significantly higher levels of fibrinogenemia, cholesterolemia, and homocystinemia and lower levels of folatemia than the controls (P < .0001).

Conclusions: The association between inherited and acquired prothrombotic factors and sudden HL suggests that the microvascular impairment causing SSNHL may be caused by a multifactorial mechanism. All patients with ISSNHL should undergo a comprehensive hematologic investigation of inherited and acquired prothrombotic factors, including MTHFR polymorphisms, the prothrombin transition, and the platelet and V Leiden mutations, to identify a subset of patients at high risk of recurrent HL.
Repetitive Transcranial Magnetic Stimulation for Tinnitus: A Pilot Study
Authors: Smith Jason A. , Mennemeier Mark , Bartel Twyla , Chelette Kenneth C. , Kimbrell Timothy , Triggs William , Dornhoffer John L.
Published: March 2007

Objectives/Hypothesis: Low‐frequency repetitive transcranial magnetic stimulation (rTMS) has been shown to alleviate tinnitus perception, presumably by inhibiting cortical activity associated with tinnitus. We conducted a pilot study to assess effectiveness of neuronavigated rTMS and its effects on attentional deficits and cortical asymmetry in four patients with chronic tinnitus using objective and subjective measures and employing an optimization technique refined in our laboratory.

Study Design: Randomized, placebo‐controlled (sham stimulation) crossover study.

Methods: Patients received 5 consecutive days of active, low‐frequency rTMS or sham treatment (using a 45‐degree coil‐tilt method) before crossing over. Subjective tinnitus was assessed at baseline, after each treatment, and 4 weeks later. Positron emission tomography/computed tomography (PET/CT) scans were obtained at baseline and immediately after active treatment to examine change in cortical asymmetry. Attentional vigilance was assessed at baseline and after each treatment using a simple reaction time test.

Results: All patients had a response to active (but not sham) rTMS, as indicated by their best tinnitus ratings; however, tinnitus returned in all patients by 4 weeks after active treatment. All patients had reduced cortical activity visualized on PET immediately after active rTMS. Mean reaction time improved (P < .05) after active but not sham rTMS.

Conclusions: rTMS is a promising treatment modality that can transiently diminish tinnitus in some individuals, but further trials are needed to determine the optimal techniques required to achieve a lasting response. It is unclear whether the improved reaction times were caused by tinnitus reduction or a general effect of rTMS. PET/CT scans immediately after treatment suggest that improvement may be related to reduction of cortical asymmetry associated with tinnitus.
Noise Exposure of the Inner Ear During Drilling a Cochleostomy for Cochlear Implantation
Authors: Pau Hans Wilhelm , Just Tino , Bornitz Matthias , Lasurashvilli Nikoloz , Zahnert Thomas
Published: March 2007

Objectives: Inserting an electrode array into the cochlea may cause inner ear trauma, which has to be minimized, particularly in cochlear implant patients with substantial residual hearing. Another potential inner ear trauma has, to a large extent, been neglected so far: the acoustic trauma that can occur during cochleostomy using different techniques. In this study, the noise exposure of the inner ear during the drilling procedure was re‐evaluated. In experiments on temporal bones, quantitative measurements of sound pressure level (SPL) were carried out while a cochleostomy for cochlear implantation was drilled.

Study Design: Experimental study.

Materials and Methods: Acoustic measurements during different drilling procedures were carried out on four human temporal bone preparations equipped with microphones attached to the round window. Special calibrations were carried out, which allowed determination of SPLs affecting the cochlea during the drilling procedure.

Results: The highest SPLs measured on the cochlea were recorded when a still‐intact endosteal membrane was touched by the burr. The SPL exceeded 130 dB and reached a level almost comparable with the situation when the ossicular chain is touched by a running burr.

Conclusions: In the drilling procedure for a cochleostomy, the inner ear may be affected by very high SPLs, particularly if the endosteal membrane is left intact and comes into contact with the running burr. Of course, the resulting SPLs depend on the drilling speed and the size and characteristics of the burr (larger burrs cause higher SPLs); however, we are of the opinion that the cochlear function is at risk, anyway, if special precaution is not exercised. Even when working with reduced drilling speed, the surgeon should be aware of the high risk in the form of an acoustic trauma, which may endanger residual hearing. Recommendations in terms of “soft surgery” are given in the paper (e.g., the use of microhooks instead of a drill to remove the very last shell of bone covering the cochlea).
Functional Optical Hemodynamic Imaging of the Olfactory Cortex
Authors: Kobayashi Eiji , Kusaka Takashi , Karaki Masayuki , Kobayashi Ryuichi , Itoh Susumu , Mori Nozomu
Published: March 2007

Objective: We used multichannel near‐infrared spectroscopy (MNIRS) to monitor the activity of the frontal cortex as mirrored by hemodynamic responses subjected to olfactory stimulation. The aim of this study was to clarify the functional brain imaging of olfactory activity.

Study Design: Prospective study.

Methods: This study was conducted on eight healthy subjects aged from 22 to 39 years (4 men and 4 women; mean age, 28.8 yr). We used a 22‐channel near‐infrared spectroscopy device with eight light‐incident fibers and seven detector fibers, each with an interoptode distance of 2.5 cm on the frontal region. Olfactory stimulation consisted of five repetitions, each lasting 5 seconds and followed by a 55 seconds rest period. Isovaleric acid was used as odor stimulation, and saline was used as a control. We measured the changes in concentrations of oxyhemoglobin [oxyHb], deoxyhemoglobin [deoxyHb], and total hemoglobin [totalHb] from prebaseline values. Furthermore, we divided the frontal cortex into four areas (right upper, left upper, right lower, left lower) and investigated the activity in each area.

Results: Isovaleric acid caused changes, especially in the lower area, but saline caused no changes. [oxyHb] and [totalHb] increased after odor stimulation, but [deoxyHb] did not change. These active areas may be related to the orbitofrontal cortex, corresponding to olfactory cortices.

Conclusion: This study has shown that MNIRS enables evaluation of changes in hemodynamics related to brain activity by olfactory stimulation.
Dysphagia After Endoscopic Repair of Zenker's Diverticulum
Authors: Palmer Andrew D. , Herrington Heather C. , Rad Ionel C. , Cohen James I.
Published: March 2007

Objectives/Hypothesis: To determine whether patient outcomes after endoscopic staple‐assisted diverticulectomy (ESD) were correlated with demographic or disease‐specific patient characteristics.

Study Design: Retrospective chart review with follow‐up.

Methods: A survey was sent to all eligible subjects who had undergone ESD from February 1995 to June 2004 to gather information about their postoperative weight, diet, dysphagia symptoms, distress, and overall satisfaction.

Results: Thirty‐five individuals responded (49% response rate) at a mean of 29 (range, 3–83) months postoperative. There was a significant reduction in the following symptoms: food avoidance, regurgitation, dysphagia for pills, choking, coughing, difficulty finishing a meal, heartburn/reflux, and halitosis. There was no significant difference for dysphonia. Swallow‐related distress had decreased from a preoperative level of 7.86 to 2.23 at follow‐up (P < .001). Overall satisfaction with the surgery was high. There were no significant differences in outcome by any demographic characteristic, duration of preoperative symptoms, presence of gastroesophageal reflux disease, Zenker's diverticulum size, time since surgery, or number of surgeries. Ninety‐one percent of subjects reported improvement in their swallowing after surgery, but 22% reported some decline since that time. Symptomatic subjects reported significantly higher swallow‐related distress and lower satisfaction (P < .01). Preoperative variables were not correlated with a return of symptoms. Individuals who underwent multiple procedures had similar levels of benefit and satisfaction as those who underwent a single ESD procedure.

Conclusion: ESD results in high levels of patient satisfaction, significant reduction in postoperative symptoms, low levels of complications, and the opportunity to safely and successfully repeat the procedure if necessary.
Postirradiation Sinus Mucosa Disease in Nasopharyngeal Carcinoma Patients
Authors: Huang Chi‐Che , Huang Shiang‐Fu , Lee Ta‐Jen , Ng Shu‐Hang , Chang Joseph Tung‐Chieh
Published: March 2007

Objectives/Hypothesis: We sought to determine the incidence, progression, and risk factors for postirradiation sinus mucosa diseases (SMD) incidentally found on follow‐up magnetic resonance images (MRIs) in nasopharyngeal carcinoma (NPC) patients.

Study Design: Retrospective.

Methods: The medical records, pre‐ and postradiotherapy (RT) MRIs were reviewed in NPC patients. Lund‐Mackay system for staging of rhinosinusitis (Lund score) was used as a tool for investigation.

Results: One hundred twelve NPC patients (77 males and 35 females) were recruited in this study. The distribution of tumor staging in these patients were 39 (34.8%) patients in T1, 23(20.5%) in T2, 31(27.7%) in T3, and 19 (17.0%) in T4 by MRI staging before RT. In these 62 patients with normal sinus ventilation before RT, 42 (67.7%) patients returned to having SMDs 3 months after RT. The maxillary, anterior ethmoid, and posterior ethmoid sinuses were most readily affected. In patients with SMDs at 3 months postRT, advanced tumor stage (P = .013) and smoking habit (P = .047) were the two factors that significantly influence Lund score. When comparing Lund score with different times after radiation therapy, a trend of decrease in Lund score could be noted from 3 months to 3 years after irradiation.

Conclusions: The incidence and severity of SMD was found to be highest at 3 months postRT and decreased gradually with time. Conservative management with clinical symptom correlation should be attempted first in these patients. In these NPC patients, advanced tumor stage and smoking habit would predispose them to SMD development.
Multilocus sequence analysis of Ensifer and related taxa
Authors: Martens Miet , Delaere Manuel , Coopman Renata , De Vos Paul , Gillis Monique , Willems Anne
Published: March 2007

Multilocus sequence analysis (MLSA) was performed on representatives ofEnsifer(including species previously assigned to the genusSinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies ofdnaK,gltA,glnA,recA,thrCand 16S rRNA genes were compared. The data confirm that the potential for discrimination ofEnsiferspecies is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected fordnaK,glnAandthrC. Analyses of concatenated sequences ofdnaK,glnAandthrCgenes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to uniteEnsiferandSinorhizobiumin a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should beEnsifer, as proposed by Young [Young, J. M. (2003).Int J Syst Evol Microbiol53, 2107–2110]. Data obtained previously and these new data indicate thatEnsifer adhaerensand ‘Sinorhizobium morelense’ are not heterotypic synonyms, but represent separate species. However, transfer to the genusEnsiferis not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genusEnsiferor a new combination based on a basonym would be created.
Polaromonas hydrogenivorans sp. nov., a psychrotolerant hydrogen-oxidizing bacterium from Alaskan soil
Authors: Sizova Maria , Panikov Nicolai
Published: March 2007

Psychrotolerant (0–25 °C), chemolithotrophic Gram-negative cocci were isolated from Alaskan forest soil. The novel isolate was found to grow autotrophically on H2 : CO2 mixtures and to switch to heterotrophic growth on media containing organic substrates. The novel strain utilized a wide range of organic acids, some simple sugars and alcohols. Naphthalene vapour did not support growth. On the basis of 16S rRNA gene sequence similarity, the novel strain is affiliated to the genus Polaromonas, of the class Betaproteobacteria, and is related to Polaromonas naphthalenivorans (99.6 % gene sequence similarity), Polaromonas aquatica (97.4 %) and Polaromonas vacuolata (96.1 %). The membrane phospholipids contained 16 : 1ω7c/16 : 1ω6c, 16 : 0 and 18 : 1ω7c, similar to the fatty acids found for P. naphthalenivorans, P. aquatica and P. vacuolata. On the basis of DNA–DNA hybridization, physiological and biochemical properties, the hydrogen-oxidizing mixotrophic isolate represents a novel species, for which the name Polaromonas hydrogenivorans sp. nov. is proposed. The type strain is DSM 17735T (=NRRL B-41369T).
Phylogenetic analysis of Helicobacter species based on partial gyrB gene sequences
Authors: Hannula Minna , Hänninen Marja-Liisa
Published: March 2007

Analysis of 16S rRNA gene sequences is one of the most common methods for investigating the phylogeny and taxonomy of bacteria. However, several studies have indicated that the 16S rRNA gene does not distinguish between certainHelicobacterspecies. We therefore selected for phylogenetic analysis an alternative marker,gyrB, encoding gyrase subunit B. The aim of this investigation was to examine the applicability ofgyrBgene fragments (~1100 bp) for the phylogenetic study of 16Helicobacterspecies and a total of 33Helicobacterstrains included in this study. Based on the sequenced fragments, a phylogenetic tree was obtained that contained two distinct clusters, with gastric species forming one cluster and enterohepatic species the other. The only exception was the gastric speciesHelicobacter mustelae, which clustered with the enterohepatic species. The calculated similarity matrix revealed the highest interspecies similarity betweenHelicobacter salomonisandHelicobacter felis(89 %) and the lowest similarity betweenHelicobacter pullorumandH. felis(60 %). The DNA G+C content of the sequenced fragments was ⩽40 mol% in enterohepatic species and >46 mol% in gastric species, excludingHelicobacter pyloriandH. mustelae, with G+C contents of 34 and 42 mol%, respectively. In summary, thegyrBgene fragments provided superior resolution and reliability to the 16S rRNA gene for differentiating between closely relatedHelicobacterspecies. A further outcome of this study was achieved by designinggyrBgene-based species-specific PCR primers for the identification ofHelicobacter bizzozeronii.
Taxonomic status of the intracellular bacterium Wolbachia pipientis
Authors: Lo N. , Paraskevopoulos C. , Bourtzis K. , O'Neill S. L. , Werren J. H. , Bordenstein S. R. , Bandi C.
Published: March 2007

Wolbachia pipientis is a maternally inherited, intracellular bacterium found in more than 20 % of all insects, as well as numerous other arthropods and filarial nematodes. It has been the subject of a growing number of studies in recent decades, because of the remarkable effects it has on its arthropod hosts, its potential as a tool for biological control of arthropods of agricultural and medical importance and its use as a target for treatment of filariasis. W. pipientis was originally discovered in cells of the mosquito Culex pipiens and is the only formally described member of the genus. Molecular sequence-based studies have revealed a number of phylogenetically diverse strains of W. pipientis. Owing to uncertainty about whether W. pipientis comprises more than one species, researchers in the field now commonly refer to W. pipientis simply as Wolbachia. In this note, we briefly review higher-level phylogenetic and recombination studies of W. pipientis and propose that all the intracellular symbionts known to cluster closely with the type strain of W. pipientis, including those in the currently recognized supergroups (A–H), are officially given this name.
Gordonia shandongensis sp. nov., isolated from soil in China
Authors: Luo Hongli , Gu Qiang , Xie Jianping , Hu Changhua , Liu Zhiheng , Huang Ying
Published: March 2007

The taxonomic position of strain SD29T, isolated from soil, was clarified using a polyphasic taxonomic approach. The organism produced an elementary branching mycelium which fragmented into rod/coccus-shaped elements and it possessed meso-diaminopimelic acid, arabinose, galactose as diagnostic diamino acid and sugars, MK-9(H2) as predominant menaquinone, phospholipids of type PII and mycolic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SD29T was most closely related to Gordonia hydrophobica DSM 44015T and Gordonia sihwensis DSM 44576T, forming a distinct but loosely related branch in the phylogenetic tree. A number of physiological properties readily separated the isolate from its nearest neighbours. It is evident from genotypic and phenotypic data that strain SD29T represents a novel species of the genus Gordonia, for which the name Gordonia shandongensis sp. nov. is proposed. The type strain is SD29T (=CGMCC 4.3492T=JCM 13907T).
Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea
Authors: Kim Byung-Yong , Weon Hang-Yeon , Yoo Seung-Hee , Hong Seung-Beom , Kwon Soon-Wo , Stackebrandt Erko , Go Seung-Joo
Published: March 2007

An orange-coloured bacterial strain, designated R2A15-11T, was isolated from greenhouse soil. The strain was found to be strictly aerobic, Gram-negative, non-spore-forming and non-flagellated. The cells were short rods (0.7–0.9×1.0–1.5 μm) and produced flexirubin. Growth of the strain was observed at 10–35 °C, pH 5.0–8.0 and 0–3 % (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1
ω7c). The genomic DNA G+C content was 45.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence of strain R2A15-11T revealed a clear affiliation with the phylum Bacteroidetes, and the highest levels of sequence similarity were found with respect to Terrimonas ferruginea ATCC 13524T (91.5 %), Terrimonas lutea DYT (90.2 %), Niastella yeongjuensis GR20-13T (89.9 %) and Niastella koreensis GR20-10T (89.7 %). On the basis of the polyphasic evidence from this study, strain R2A15-11T represents a novel genus and species, for which the name Niabella aurantiaca gen. nov., sp. nov. is proposed. The type strain of Niabella aurantiaca is R2A15-11T (=KACC 11698T=DSM 17617T).
Vibrio litoralis sp. nov., isolated from a Yellow Sea tidal flat in Korea
Authors: Nam Young-Do , Chang Ho-Won , Park Ja Ryeong , Kwon Hyuk-Yong , Quan Zhe-Xue , Park Yong-Ha , Kim Byung-Chun , Bae Jin-Woo
Published: March 2007

Two Gram-negative, facultatively anaerobic bacterial strains, MANO22DT and MANO22P, were isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. The isolates were rod-shaped and were motile by means of one or more polar flagella. They grew at 1–12 % NaCl, 4–45 °C and pH 4.1–8.8 and were oxidase-positive, arginine dihydrolase-negative and sensitive to the vibriostatic agent O/129. The isolates required Na+ for growth, produced acid, but no gas, from d-glucose under anaerobic conditions and utilized a wide range of compounds as sole carbon and energy sources. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belong to the Gammaproteobacteria and are specifically related to Vibrio species. They were most closely related to Vibrio rumoiensis FERM P-14531T, with which they were found to share 98.65 % 16S rRNA gene sequence similarity. In the phylogenetic tree, the two novel strains comprised a relatively long subline of descent, sharing a branching point with the outlying species V. rumoiensis, and were found to occupy a phylogenetically distant position on the main Vibrio branch. The levels of DNA–DNA hybridization with respect to V. rumoiensis FERM P-14531T, which is their most closely related phylogenetically related Vibrio species, were 7.4 % (MANO22DT) and 3.9 % (MANO22P). Thus, the two novel isolates appear to represent a novel species within the genus Vibrio, for which the name Vibrio litoralis sp. nov. is proposed. The type strain is MANO22DT (=KCTC 12520T=DSM 17657T).
Emended description of Actinobacillus capsulatus Arseculeratne 1962, 38AL
Authors: Kuhnert Peter , Korczak Bożena M. , Christensen Henrik , Bisgaard Magne
Published: March 2007

The taxonomic position ofActinobacillus capsulatus, a member of the familyPasteurellaceaefound in rabbits, hares and hamsters, has been challenged. 16S rRNA gene (rrs) sequence data show the species to be heterogeneous. Using a polyphasic approach, 23 strains that were identified previously as belonging, or closely related, toA. capsulatuswere analysed. Eighty characters were included in the phenotypic analysis. Phylogenetic analysis was done based onrrs,rpoB,infBandrecNsequences. In addition, therecNsequence similarities were used to calculate the whole-genome sequence relatedness of all strains investigated as well as that with other members of the familyPasteurellaceae. The phenotypic analysis allowed identification of five groups. The major group of 17 strains could be classified asA. capsulatus. Two hamster isolates were closely related toA. capsulatusbut differed in a few characters. Single isolates from a rabbit and snowshoe-hare were phenotypically related toActinobacillus suis. One rabbit isolate was related to the genusMannheimia, while another isolate could not be classified phenotypically with known taxa. The phylogenetic analysis confirmed the phenotypic grouping. In contrast to therrs-based tree, theA. capsulatusstrains clustered unambiguously with the type species and related species of the genusActinobacillusin therpoB-,infB- andrecN-based trees. Genome similarity comparison usingrecNfinally confirmed the high genomic relationship of theA. capsulatusstrains with the type species and related species of the genusActinobacillusand allowed a clear assignment of the other unrelated strains to the phenotypic and phylogenetic clusters outlined. The present findings allow the description ofA. capsulatusto be emended and separate it more clearly from other species, both phenotypically and genotypically. The type strain ofA. capsulatusis CCUG 12396T(=Frederiksen 243T=ATCC 51571T=NCTC 11408T=CIP 103283T).
Marixanthomonas ophiurae gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a deep-sea brittle star
Authors: Romanenko Lyudmila A. , Uchino Masataka , Frolova Galina M. , Mikhailov Valery V.
Published: March 2007

An aerobic, Gram-negative, non-motile, yellow-pigmented bacterium, strain KMM 3046T, was isolated from a deep-sea brittle star from the Fiji Sea and was subjected to a polyphasic taxonomic analysis. Strain KMM 3046Tgrew at 5–32 °C and in the presence of 1–12 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and 3-OH i16 : 0, 3-OH i17 : 0 and 3-OH a17 : 0 as the major fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 3046Tforms a distinct evolutionary lineage within the familyFlavobacteriaceae(phylumBacteroidetes), displaying 92.3–91.9 % sequence similarity with respect toSalegentibacterspecies. On the basis of the phenotypic and phylogenetic data, strain KMM 3046Trepresents a novel genus and species of the familyFlavobacteriaceae, for which the nameMarixanthomonas ophiuraegen. nov., sp. nov. is proposed. The type strain ofMarixanthomonas ophiuraeis KMM 3046T(=NRIC 0684T=JCM 14121T).
Williamsia serinedens sp. nov., isolated from an oil-contaminated soil
Authors: Yassin A. F. , Young Chiu Chung , Lai Wei-An , Hupfer H. , Arun A. B. , Shen Fo-Ting , Rekha P. D. , Ho Mann-Jing
Published: March 2007

The taxonomic status of a bacterium designated strain IMMIB SR-4T isolated from an oil-contaminated soil sample was characterized by using a polyphasic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Williamsia and that on pyrolysis GC produce C16 : 0 and C18 : 0 fatty acids, and dihydrogenated menaquinone with nine isoprene units as the predominant menaquinone. The generic assignment was confirmed by 16S rRNA gene sequence analysis. Comparative analysis of the 16S rRNA gene sequence showed that strain IMMIB SR-4T formed a distinct phyletic line within the genus Williamsia, displaying sequence similarities of 95.5–98.1 % with the type strains of recognized Williamsia species. Strain IMMIB SR-4T was distinguished from the type strains of recognized species of the genus Williamsia based on a set of phenotypic features. The genotypic and phenotypic data indicated that strain IMMIB SR-4T represents a novel species of the genus Williamsia, for which the name Williamsia serinedens sp. nov. is proposed. The type strain is IMMIB SR-4T (=DSM 45037T=CCUG 53151T).
Syntrophomonas zehnderi sp. nov., an anaerobe that degrades long-chain fatty acids in co-culture with Methanobacterium formicicum
Authors: Sousa Diana Z. , Smidt Hauke , Alves M. Madalena , Stams Alfons J. M.
Published: March 2007

An anaerobic, mesophilic, syntrophic fatty-acid-oxidizing bacterium, designated strain OL-4T, was isolated as a co-culture with Methanobacterium formicicum DSM 1535NT from an anaerobic expanded granular sludge bed reactor used to treat an oleate-based effluent. Strain OL-4T degraded oleate, a mono-unsaturated fatty acid, and straight-chain fatty acids C4 : 0–C18 : 0 in syntrophic association with Methanobacterium formicicum DSM 1535NT. Even-numbered fatty acids were degraded to acetate and methane whereas odd-numbered fatty acids were degraded to acetate, propionate and methane. Branched-chain fatty acids were not degraded. The bacterium could not grow axenically with any other substrate tested and therefore is considered to be obligately syntrophic. Fumarate, sulfate, thiosulfate, sulfur and nitrate could not serve as electron acceptors for strain OL-4T to degrade oleate or butyrate. Cells of strain OL-4T were curved rods, formed spores and showed a variable response to Gram staining. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OL-4T was most closely related to the fatty-acid-oxidizing, syntrophic bacterium Syntrophomonas sp. TB-6 (95 % similarity), Syntrophomonas wolfei subsp. wolfei DSM 2245T (94 % similarity) and Syntrophomonas erecta DSM 16215T (93 % similarity). In addition to this moderate similarity, phenotypic and physiological characteristics, such as obligate syntrophy, spore formation and utilization of a broader substrate range, differentiated strain OL-4T from these Syntrophomonas species. Therefore strain OL-4T represents a novel species, for which the name Syntrophomonas zehnderi sp. nov. is proposed. The type strain is OL-4T (=DSM 17840T=JCM 13948T).
Mycobacterium seoulense sp. nov., a slowly growing scotochromogenic species
Authors: Mun Ho-Suk , Kim Hyun-Ju , Oh Eun-Ju , Kim Hong , Bai Gil-Han , Yu Hee-Kyung , Park Young-Gil , Cha Chang-Yong , Kook Yoon-Hoh , Kim Bum-Joon
Published: March 2007

A previously undescribed, slowly growing, scotochromogenic mycobacterium was isolated from a patient with symptomatic pulmonary infection during hsp65 sequence-based identification of Korean clinical isolates. Phenetic characteristics of this strain were generally similar to those of Mycobacterium nebraskense and Mycobacterium scrofulaceum. However, some phenetic characteristics differentiated it from these two species. Its 16S rRNA gene sequences were unique and phylogenetic analysis based on 16S rRNA gene sequences placed the organism in the slowly growing Mycobacterium group close to M. nebraskense and M. scrofulaceum. Its unique mycolic acid profiles and the results of phylogenetic analysis based on two independent alternative chronometer molecules, hsp65 and rpoB, confirmed the taxonomic status of this strain as representing a novel species. These data support the conclusion that this strain represents a novel mycobacterial species, for which the name Mycobacterium seoulense sp. nov. is proposed. The type strain is strain 03-19T (=DSM 44998T=KCTC 19146T).
Deefgea rivuli gen. nov., sp. nov., a member of the class Betaproteobacteria
Authors: Stackebrandt Erko , Lang Elke , Cousin Sylvie , Päuker Orsola , Brambilla Evelyne , Kroppenstedt Reiner , Lünsdorf Heinrich
Published: March 2007

Two strains, designated WB 3.4-79T and WB 3.3-25, were isolated from a hard-water sample collected from the Westerhöfer Bach, Lower Saxony, Germany. The strains shared 100 % DNA–DNA relatedness, indicating membership of the same genospecies. This close relationship was supported by identical 16S rRNA gene sequences and high similarities in fatty acid composition and biochemical characteristics. The G+C content of the genomic DNA of strain WB 3.4-79T was 48.5 mol% and the predominant ubiquinone was Q-8. Major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Major fatty acids (>10 %) were C16 : 0 and C16 : 1
ω7c. Polyhydroxybutyrate and polyphosphate granules as well as unidentified enterosomes and a polar organelle are visible by electron microscopy. Comparative 16S rRNA gene sequence analysis indicated that the isolates were placed within the class Betaproteobacteria, remotely related to Chitinibacter tainanensis DSM 15459T, Silvimonas terrae KCTC 12358T, Formivibrio citricus DSM 6150T and Iodobacter fluviatilis DSM 3764T. On the basis of phylogenetic and phenotypic distinctness, we propose a novel genus, Deefgea gen. nov., with Deefgea rivuli sp. nov. as the type species. The type strain of Deefgea rivuli is strain WB 3.4-79T (=DSM 18356T=CIP 109326T).