bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence and Etiology of Hearing Loss in Rural Nicaraguan Children
Authors: Saunders James E. , Vaz Sharon , Greinwald John H. , Lai James , Morin Leonor , Mojica Karen
Published: March 2007

Objective/Hypothesis: The prevalence and causes of pediatric hearing loss (HL) in the developing world are largely unknown. Infectious sequelae, ototoxic medications, and genetic causes may play a larger role in developing countries. In addition, the significance of GJB2 mutation gene in poorly developed areas remains unclear. The intent of this study is to investigate the prevalence and etiology of HL in children living in a remote, impoverished region of northern Nicaragua.

Study Design: Cross‐sectional study.

Methods: Clinical data from two sources were analyzed: data from screening examinations performed in rural schools in the Department of Jinotega, Nicaragua (group A) and pediatric HL patients seen at the Otolaryngology and Audiology Clinic in Jinotega, Nicaragua (group B). Patients with congenital HL were offered a genetic test for GJB2 mutations. Comparisons were made using parametric (analysis of variance) and nonparametric (Kruskal‐Wallis) tests.

Results: School‐based screening examinations (group A) revealed a high prevalence of significant HL (>30 dB) of 18%. The majority of these children had normal otoscopic examinations (58%). A family history of HL was seen in 24% of children who failed screening exams. Positive family history was more common in patients with HL (P < .01) and in specific schools (P < .05). Clinic‐based evaluations (group B) reveal a population with predominantly severe‐profound HL. Physical dysmorphism was common, yet identifiable syndromic HL was rare. Although familial HL was common (33%), there were no pathologic GJB2 mutations. Other common risk factors in this population were maternal infection during pregnancy, neonatal distress, low birth weight or prematurity, and gentamicin exposure.

Conclusions: HL in this rural, third world environment is more prevalent, and the etiologies responsible in this study group are different from those encountered in industrialized nations. Poor perinatal health care, infectious causes, gentamicin exposure, and hereditary HL are potentially preventable causes that play a major role in this population.
Health‐Related Quality of Life in Thyroid Cancer Survivors
Authors: Tan Lincoln G. L. , Nan Luo , Thumboo Julian , Sundram Felix , Tan Luke K. S.
Published: March 2007

Objective: The study objective was to study the impact of the diagnosis, treatment, and follow‐up of differentiated thyroid cancer (DTC) on the quality of life and related issues in an urban multi‐ethnic Asian population.

Design: A self‐administered questionnaire containing the Short Form 36 Health Survey (SF‐36) and assessing sociodemographic, disease, and treatment‐related status was mailed to patients with DTC.

Main Outcomes: One hundred fifty‐two (52.4%) of 290 patients answered the questionnaire. There was a statistically significant decrease in SF‐36 scores between thyroid cancer survivors and the general population in all domains except for social functioning (SF). Physical functioning (PF) was worse in those survivors who were aged 50 years or older. Mental health (MH) scores were better in those who had more than 12 years of formal education. Being employed had a positive influence on role physical (RP) and role emotional (RE) scores. Being of Malay/Indian ethnicity strongly correlated with lower scores in bodily pain (BP), SF, RE and MH domains.

Conclusion: Although most patients with well‐differentiated thyroid cancer have near normal life expectancy, our study has shown that there is a significant decrease in their quality of life, especially in the elderly and poorer educated. Returning to work should be encouraged to improve the quality of life in DTC survivors.
Hypoxia Stimulates Inflammatory and Fibrotic Responses From Nasal‐Polyp Derived Fibroblasts
Authors: Early S. Brandon , Hise Kathleen , Han Joseph K. , Borish Larry , Steinke John W.
Published: March 2007

Objectives/Hypothesis: Chronic sinusitis is primarily an inflammatory disorder characterized by hyperplasia of immune cells and sinus tissue. Nasal mucosal swelling or polyps can occlude the sinus ostia, decreasing the level of oxygen available to the sinus tissue. Hypoxia in many diseases results in increased recruitment of inflammatory cells and release of cytokines. The role of hypoxia in chronic sinusitis is unknown. We hypothesized that hypoxia induces production of mediators that recruit cells into the sinus tissue and are involved in remodeling of the nasal mucosa.

Methods: We compared data from unstimulated nasal‐polyp derived fibroblasts with those cultured in hypoxic (10% O2) and anoxic (0% O2) environments. Changes in mRNA expression and protein levels of cytokines and chemokines were measured along with changes in cellular proliferation.

Results: Hypoxic conditions did not change the proliferative capacity of fibroblasts, whereas anoxia led to a 40% reduction in cellular proliferation (P < .05). Hypoxia led to increases in secretion of many cytokines including vascular endothelial growth factor and CCL11. As a marker of remodeling, procollagen and fibronectin production were significantly increased under hypoxic conditions.

Conclusions: Hypoxic conditions present in the sinus tissue could increase production of proinflammatory and remodeling cytokines that contribute to the inflammation observed in sinusitis. Surgical intervention may help decrease inflammation by allowing reoxygenation of the sinus cavity and decrease the hypoxic induction of cytokines and remodeling factors.
Epidemiology of Voice Disorders in the Elderly: Preliminary Findings
Authors: Roy Nelson , Stemple Joseph , Merrill Ray M. , Thomas Lisa
Published: March 2007

Objectives: Epidemiologic studies of the prevalence and risk factors of voice disorders in the elderly, nontreatment seeking population are nonexistent. The purpose of this preliminary investigation was to 1) estimate the prevalence of voice disorders, 2) identify variables associated with increased risk of voice disorders, and 3) measure the socioemotional impact of voice disorders on the elderly who live independently.

Study Design: Prospective, cross‐sectional survey.

Methods: One hundred seventeen seniors (39 males and 78 females; mean age, 76.1 yr; SD, 8.5 yr; range, 65–94 yr), residing in Utah and Kentucky, were interviewed using a questionnaire that addressed three areas related to voice disorders: prevalence, potential risk factors, and socioemotional consequences/effects.

Results: The lifetime prevalence of a voice disorder was 47%, with 29.1% of participants reporting a current voice disorder. The majority of respondents (60%) reported chronic voice problems persisting for at least 4 weeks. Seniors who had experienced esophageal reflux, severe neck/back injury, and chronic pain were at increased risk. Voice‐related effort and discomfort, combined with increased anxiety and frustration and the need to repeat oneself, were specific areas that adversely affected quality of life.

Conclusions: This preliminary epidemiologic study confirmed that voice disorders are common among the elderly, and further research is needed to identify additional risk factors contributing to voice disorder vulnerability.
Metalloproteinase Function in Chronic Rhinosinusitis With Nasal Polyposis
Authors: Kostamo Katriina , Tervahartiala Taina , Sorsa Timo , Richardson Malcolm , Toskala Elina
Published: March 2007

Objectives: Chronic rhinosinusitis with nasal polyposis (CRSwNP) and asthma share characteristic inflammatory features and histopathologic findings of airway remodeling. Remodeling, which is controlled by matrix metalloproteinases (MMP), is a key event in the pathogenesis of asthma. The MMP functions have rarely been evaluated in CRSwNP.

Study Design: Prospective and in vivo.

Methods: MMP‐7, MMP‐8, MMP‐9, and tissue inhibitor of metalloproteinase (TIMP)‐1 concentrations were analyzed by enzyme‐linked immunosorbent assay and their molecular forms by Western immunoblotting and gelatin zymography in 24 patients operated on for CRSwNP and in nasal lavages from 19 healthy controls. MMP function, protective or destructive, was evaluated by comparing MMP/TIMP‐1 levels with the disease activity, estimated by tissue eosinophilia and a need for re‐operations.

Results: Significantly increased levels of MMP‐8/TIMP‐1 and MMP‐9/TIMP‐1 were found in patients without tissue eosinophilia relative to eosinophil‐positive CRSwNP patients and controls, as well as in patients who did not require re‐operation in comparison with re‐operated patients. In eosinophil‐positive and re‐operated patients, these parameters were within the same range than in controls.

Conclusions: Proteolytic spectrum is different in eosinophilic and noneosinophilic CRSwNP, suggesting a new mechanism for eosinophil accumulation in the disease pathogenesis. Enhanced MMP‐8 and MMP‐9 expression was associated with a better prognosis/clinical outcome, and thus these results may represent a synergic, protective role of MMP‐8 and MMP‐9 in host response in CRSwNP. Because synthetic MMP inhibitors, capable of equilibrating the unfavorable MMP/TIMP‐ratio, may be of potential therapeutic value in chronic respiratory tract diseases, the MMP functions in inflammatory conditions need to be carefully established.
Biofilms in Ear, Nose, and Throat Infections: How Important are They?
Authors: Vlastarakos Petros V. , Nikolopoulos Thomas P. , Maragoudakis Paul , Tzagaroulakis Antonios , Ferekidis Eleftherios
Published: March 2007

Background: Biofilms present a new challenging concept in sustaining chronic, common antibiotic‐resistant ear, nose, and throat (ENT) infections. They are communities of sessile bacteria embedded in a matrix of extracellular polymeric substances of their own synthesis that adhere to a foreign body or a mucosal surface with impaired host defense. The aim of this paper is to review the literature on ENT diseases that can be attributed to biofilm formation and to discuss options for future treatment.

Materials and Methods: Literature review from Medline and database sources. Electronic links and related books were also included.

Study Selection: Controlled clinical trials, animal models, ex vivo models, laboratory studies, retrospective studies, and systematic reviews.

Data Synthesis: Biofilm formation is a dynamic five‐step process guided by interbacterial communicating systems. Bacteria in biofilms express different genes and have markedly different phenotypes from their planktonic counterparts. Detachment of cells, production of endotoxin, increased resistance to the host immune system, and provision of a niche for the generation of resistant organisms are biofilm processes that could initiate the infection process. Effective prevention and management strategies include interruption of quorum sensing, inhibition of related genes, disruption of the protective extrapolymer matrix, macrolides (clarithromycin and erythromycin), and mechanical debridement of the biofilm‐bearing tissues. With regard to medical indwelling devices, surface treatment of fluoroplastic grommets and redesign of cochlear implants could minimize initial microbial colonization.

Conclusion: As the role of biofilms in human infection becomes better defined, ENT surgeons should be prepared to deal with their unique and tenacious nature.
Cochlear Origin of Early Hearing Loss in Vestibular Schwannoma
Authors: Gouveris Haralampos T. , Victor Anja , Mann Wolf J.
Published: March 2007

Objective: To test whether early hearing loss (HL) is cochlear in origin in patients with vestibular schwannoma (VS).

Study Design: Retrospective case review in an academic tertiary referral center.

Methods: A group of 19 VS patients with normal/symmetrical hearing and a group of 20 VS patients with mild HL (threshold at any tested frequency better than 45 dB HL) on the tumor ear side. Differences of the amplitudes of the distortion products of otoacoustic emissions (DPOAEs) between the tumor ear and the nontumor ear were studied at frequencies of 1, 1.4, 2, 2.8, and 4 kHz. The Wilcoxon test was used to compare the ears for both groups and to test for possible differences in tumor size between groups.

Results: DPOAE amplitudes do not differ strongly between the ears in VS patients with normal/symmetrical hearing (two‐sided P values: .050 at 1 kHz, .182 at 1.4 kHz, .378 at 2 kHz, .293 at 2.8 kHz, and .238 at 4 kHz) but are decreased compared with the nontumor ear at frequencies 1, 1.4, 2, and 2.8 kHz in VS patients with even mild HL (two‐sided P values: .013 at 1 kHz, .007 at 1.4 kHz, .033 at 2 kHz, .010 at 2.8 kHz, and .156 at 4 kHz). Tumor size did not differ significantly between the two groups (P = .436).

Conclusion: Amplitudes of DPOAEs begin to decrease even at the early stages of HL in VS patients, which suggests a cochlear origin of early HL in these patients. DPOAEs may be used in a clinical setting to monitor progression of cochlear damage at the early stages of hearing impairment in VS patients.
Acquisition of Surgical Skills for Endonasal Skull Base Surgery: A Training Program
Authors: Snyderman Carl , Kassam Amin , Carrau Ricardo , Mintz Arlan , Gardner Paul , Prevedello Daniel M.
Published: March 2007

Introduction: Endonasal surgery represents a radical change in the practice of cranial base surgery and requires the acquisition of new knowledge and surgical skills. The optimal training program for surgeons has not been established.

Methods: We reviewed our experience with endonasal cranial base surgery from 1998 to 2006 to develop a training plan for the acquisition of surgical skills. It consists of a modular and incremental approach to endonasal skull base surgery that is designed to train surgeons to function as a team, learn endoscopic skull base anatomy, and develop fundamental endoscopic skills.

Results: Stages of training are established for the otolaryngologist–head and neck surgeon and the neurosurgeon that are based on level of technical difficulty, potential risk of vascular and neural injury, and unfamiliar endoscopic anatomy. Mastery of each level is recommended before attempting procedures at a higher level.

Conclusions: Standardization of training and the adoption of a modular, incremental training program are expected to facilitate the training of endonasal surgeons in both surgical specialties. Adherence to such a program during the growth phase of endoscopic skull base surgery may decrease the risk of complications as the surgeon's knowledge and surgical expertise develop.
Demands on Caring Relatives of Head and Neck Cancer Patients
Authors: Baghi Mehran , Wagenblast Jens , Hambek Markus , Radeloff Andreas , Gstoettner Wolfgang , Scherzed Agmal , Spaenkuch Birgit , Yuan Juping , Hornung Stefan , Strebhardt Klaus , Knecht Rainald
Published: March 2007

Background: Relatives of cancer patients experience high levels of stress that influence the quality of life of these individuals. To investigate whether there is a necessity for simultaneous supportive care of patient relatives, we performed for the first time a study asking the closest relatives of head and neck cancer patients about their needs during and after the treatment to consider how to optimize the situation for such patient groups.

Material and Methods: Patients' relatives were assessed using an anonymous self‐report questionnaire that was established in our department by expanding on a questionnaire for cancer patients' relatives from the psycho‐oncologic society in Switzerland. The evaluation was multidimensional, cancer specific, and relative based.

Results: Relatives feel confronted themselves with cancer, although indirectly. The majority of the respondents were of the opinion that simultaneous psychological care of the patients and for the caring relatives would be helpful to cope with the situation.

Conclusion: This study shows the significant impact of cancer on caring relatives of head and neck cancer patients. In our opinion, health services should become more aware of this potential to ensure that the needs of the involved patient relatives are met as well as those of the patients.
Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth
Authors: Rea Suzanne , Bowman John P. , Popovski Sam , Pimm Carolyn , Wright André-Denis G.
Published: March 2007

Four formate-utilizing methanogens were isolated from ovine (strain KM1H5-1PT) and bovine (strains AK-87, OCP and ZA-10T) rumen contents. Based on 16S rRNA gene sequence analysis, the methanogen strains were found to belong to the orderMethanobacterialesin the genusMethanobrevibacter. Strains ZA-10Tand KM1H5-1PTgained energy for growth by the reduction of CO2to CH4using H2or formate exclusively as electron donors. Increasing formate concentrations to 220 mM in batch cultures increased the growth of strain KM1H5-1PTbut did not affect the growth of strain ZA-10T. Substrate specificity and resistance to cell-wall lysis supported the affiliation of the strains to the genusMethanobrevibacter. Strains ZA-10Tand KM1H5-1PTshowed 16S rRNA gene sequence similarity of 98.0 and 98.6 % to their closest recognized relatives,Methanobrevibacter thaueriCWTandMethanobrevibacter ruminantiumM1T, respectively. DNA–DNA hybridization experiments indicated that the strains were not affiliated at the species level to their closest recognized relatives, with DNA reassociation values of only 28 % between strains ZA-10TandMethanobrevibacter thaueriCWTand <25 % between strains KM1H5-1PTandMethanobrevibacter ruminantiumM1T. Based on the data presented, the new strains are considered to represent two novel species of the genusMethanobrevibacter, for which the namesMethanobrevibacter milleraesp. nov. (type strain ZA-10T=DSM 16643T=OCM 820T) andMethanobrevibacter olleyaesp. nov. (type strain KM1H5-1PT=DSM 16632T=OCM 841T) are proposed.
Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris)
Authors: Kwon Soon-Wo , Kim Byung-Yong , Lee Kang-Hyo , Jang Kab-Yeul , Seok Soon-Ja , Kwon Jang-Sik , Kim Wan-Gyu , Weon Hang-Yeon
Published: March 2007

A mesophilic bacterium, strain 15-52T, was isolated from the rhizosphere of Chinese cabbage (Brassica campestris). On the basis of phenotypic and genotypic characteristics, the bacterium was identified as representing a novel species belonging to the genus Pedobacter. The strain is non-flagellated, non-spore-forming and grows at temperatures in the range 1–37 °C. Physiological tests of the strain showed the presence of oxidase, catalase, protease (gelatin and casein hydrolysis), β-glucosidase and β-galactosidase activities. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter roseus CL-GP80T (97.3 %) and Pedobacter sandarakinus DS-27T (97.2 %). A phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain 15-52T is a member of the genus Pedobacter. DNA–DNA hybridization analysis revealed low levels of relatedness (<42.3 %) between the isolate and two phylogenetically related type strains, P. roseus KCCM 42272T and P. sandarakinus KCTC 12559T. The DNA G+C content is 44.2 mol% and the predominant fatty acids are iso-C15 : 0 (35.4 %), iso-C15 : 0 2-OH and/or C16 : 1
ω7c (27.8 %) and iso-C17 : 0 3-OH (15.8 %). On the basis of these data, strain 15-52T represents a novel species of the genus Pedobacter, for which the name Pedobacter suwonensis sp. nov. is proposed. The type strain is 15-52T (=KACC 11317T=DSM 18130T).
Aeromonas bivalvium sp. nov., isolated from bivalve molluscs
Authors: Miñana-Galbis David , Farfán Maribel , Fusté M. Carme , Lorén J. Gaspar
Published: March 2007

A polyphasic study was performed to determine the taxonomic position of twoAeromonasstrains, 665N and 868ET, isolated from bivalve molluscs, that could not be identified at the species level in a previous numerical taxonomy study. The DNA G+C content of these isolates was 62.3 and 62.6 mol%, respectively. Sequence analysis of the 16S rRNA gene showed that the two new strains were closely related to members of the genusAeromonas. Fluorescence amplified fragment length polymorphism fingerprinting revealed that strains 665N and 868ETclustered together with a similarity of 78 % but did not cluster with any of theAeromonasgenomospecies. DNA–DNA hybridization experiments revealed a high level of relatedness between the two new isolates (76 %) but low levels of relatedness between these and phylogenetically most closely relatedAeromonasgenomospecies (30–44 %). Useful tests for the phenotypic differentiation of strains 665N and 868ETfrom other mesophilicAeromonasspecies included those for gas from glucose, lysine decarboxylase, Voges–Proskauer reaction, acid froml-arabinose, hydrolysis of aesculin and utilization ofl-lactate. On the basis of genotypic and phenotypic evidence, strains 665N and 868ETare considered to represent a novel species of the genusAeromonas, for which the nameAeromonas bivalviumsp. nov. is proposed. The type strain is 868ET(=CECT 7113T=LMG 23376T).
Lentibacillus halodurans sp. nov., a moderately halophilic bacterium isolated from a salt lake in Xin-Jiang, China
Authors: Yuan Sanqing , Ren Peigen , Liu Jun , Xue Yanfen , Ma Yanhe , Zhou Peijin
Published: March 2007

A Gram-positive, rod-shaped, spore-forming and moderately halophilic bacterium (strain 8-1T) was isolated from a sediment sample of a neutral salt lake in Xin-Jiang, China. The strain grew optimally at 30 °C, pH 7.0–7.5 and 8–12 % (w/v) NaCl. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0and anteiso-C17 : 0. The predominant isoprenoid quinone was MK-7 and the cell-wall peptidoglycan containedmeso-diaminopimelic acid. Phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids were found to be the major polar lipid components. The genomic DNA G+C content was 43.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 8-1Twas closely related toLentibacillus salariusKCTC 3911T(98.0 % sequence similarity) and other recognized species within the genusLentibacillus(94.5–95.9 %). The level of DNA–DNA relatedness between strain 8-1TandL. salariusKCTC 3911Twas 40 %. Based on the phenotypic and genotypic data presented, strain 8-1Tis considered to represent a novel species of the genusLentibacillus, for which the nameLentibacillus haloduranssp. nov. is proposed. The type strain is 8-1T(=CGMCC 1.3702T=DSM 18342T).
Labrys neptuniae sp. nov., isolated from root nodules of the aquatic legume Neptunia oleracea
Authors: Chou Yi-Ju , Elliott Geoffrey N. , James Euan K. , Lin Kuan-Yin , Chou Jui-Hsing , Sheu Shih-Yi , Sheu Der-Shyan , Sprent Janet I. , Chen Wen-Ming
Published: March 2007

A bacterium designated strain Liujia-146T was isolated in the Tainan area of southern Taiwan from root nodules of the aquatic legume Neptunia oleracea. 16S rRNA gene sequence analysis indicated that strain Liujia-146T was highly similar to Labrys monachus VKM B-1479T (97.8 %) and Labrys methylaminiphilus JLW10T (95.5 %) and belonged to the order Rhizobiales in the Alphaproteobacteria. On the basis of phylogenetic analysis, DNA–DNA hybridization data, physiological and biochemical characteristics and fatty acid compositions, the organism was shown to belong to the genus Labrys whilst representing a novel species within this genus. We propose to classify strain Liujia-146T (=BCRC 17578T=LMG 23578T) as the type strain of Labrys neptuniae sp. nov.
Salinicoccus jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood
Authors: Aslam Zubair , Lim Ju Hyoung , Im Wan-Taek , Yasir Muhammad , Chung Young Ryun , Lee Sung-Taik
Published: March 2007

A novel, moderately halophilic, Gram-positive coccus, designated strain S2R53-5T, was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. Strain S2R53-5Tgrew in the presence of 0.5–15 % (w/v) NaCl and at pH 6.5–11.0, with optimum growth at 5 % (w/v) NaCl and pH 7.0. The temperature range for growth was 20.0–30.0 °C, with an optimum temperature of 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2R53-5Tbelongs to the familyStaphylococcaceaeand was most closely related toSalinicoccus roseusDSM 5351T(96.8 % gene sequence similarity),Salinicoccus hispanicusDSM 5352T(96.1 %),Salinicoccus alkaliphilusT8T(95.2 %) andJeotgalicoccus halotoleransYKJ-101T(95.1 %). The genomic DNA G+C content was 47.0 mol%, which is in the range of 46–51 mol% that is characteristic for the genusSalinicoccus. Levels of DNA–DNA relatedness between strain S2R53-5TandS. roseusDSM 5351T,S. hispanicusDSM 5352TandS. alkaliphilusKCTC 13928Twere 32.2, 15.4 and 4.6 %, respectively. Chemotaxonomic data (major menaquinone, MK-6; major fatty acids, iso-C15 : 0and anteiso-C15 : 0; cell-wall murein type, Lys and Gly) and 16S rRNA gene sequence analysis supported the affiliation of strain S2R53-5Twith the genusSalinicoccus. The combined evidence from the low DNA–DNA relatedness, physiological, biochemical and other genotypic data indicate that strain S2R53-5Tclearly represents a novel species of the genusSalinicoccus, for which the nameSalinicoccus jeotgalisp. nov. is proposed. The type strain is S2R53-5T(=KCTC 13030T=LMG 23640T).
Thermococcus celericrescens sp. nov., a fast-growing and cell-fusing hyperthermophilic archaeon from a deep-sea hydrothermal vent
Authors: Kuwabara Tomohiko , Minaba Masaomi , Ogi Noriko , Kamekura Masahiro
Published: March 2007

A fast-growing and cell-fusing hyperthermophilic archaeon was isolated from a hydrothermal vent at Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean. Strain TS2T is an irregular, motile coccus that is generally 0.7–1.5 μm in diameter and possesses a polar tuft of flagella. In the mid-exponential phase of growth, cells that appeared black under phase-contrast microscopy fused at room temperature in the presence of a DNA-intercalating dye, as previously observed in Thermococcus coalescens. Cell fusion was not observed in later growth phases. Transmission electron microscopy revealed that the cells in the mid-exponential phase had a 5 nm-thick, electron-dense cell envelope that appeared to associate loosely with the cytoplasmic membrane. As the growth stage progressed, a surface layer developed on the membrane under the envelope and the envelope eventually peeled off. These observations suggest that the surface layer prevents the fusion of cells. Cells of strain TS2T grew at 50–85 °C, pH 5.6–8.3 and at NaCl concentrations of 1.0 to 4.5 %, with optimal growth occurring at 80 °C, pH 7.0 and 3.0 % NaCl. Under optimal growth conditions, strain TS2T grew very fast with an apparent doubling time of 20 min. It is suggested that the biosynthesis of the surface layer cannot catch up with cell multiplication in the mid-exponential phase and thus cells without the surface layer are generated. Strain TS2T was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 54.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belongs to the genus Thermococcus. However, no significant DNA–DNA hybridization was observed between the genomic DNA of strain TS2T and phylogenetically related Thermococcus species. On the basis of this evidence, strain TS2T is proposed to represent a novel species, Thermococcus celericrescens sp. nov., a name chosen to reflect the fast growth of the strain. The type strain is TS2T (=NBRC 101555T=JCM 13640T=DSM 17994T).
Desulfopila aestuarii gen. nov., sp. nov., a Gram-negative, rod-like, sulfate-reducing bacterium isolated from an estuarine sediment in Japan
Authors: Suzuki Daisuke , Ueki Atsuko , Amaishi Aya , Ueki Katsuji
Published: March 2007

A strictly anaerobic, mesophilic, sulfate-reducing bacterial strain (MSL86T) isolated from an estuarine sediment in the Sea of Japan (around the Japanese islands) was characterized phenotypically and phylogenetically. The cells were found to be Gram-negative, motile, non-spore-forming rods. Catalase was not detected. The optimum NaCl concentration for growth was 1.0 % (w/v) and the optimum temperature was 35 °C. Strain MSL86Twas slightly alkaliphilic, with optimum growth at pH 7.5–7.6. Organic electron donors were incompletely oxidized to (mainly) acetate. Strain MSL86Tutilized formate, pyruvate, lactate, fumarate, ethanol, propanol, butanol and glycerol as electron donors for sulfate reduction and did not use acetate, propionate, butyrate, succinate, malate, methanol, glycine, alanine, serine, aspartate, glutamate or H2. Sulfite, thiosulfate and fumarate were used as electron acceptors with lactate as an electron donor. Without electron acceptors, the strain fermented pyruvate and fumarate. The genomic DNA G+C content was 54.4 mol%. Menaquinone MK-8(H4) was the major respiratory quinone. The major cellular fatty acids were C16 : 0, C16 : 1ω7, C16 : 1ω5 and C17 : 1ω6. A phylogenetic analysis based on the 16S rRNA gene sequence placed the strain in the classDeltaproteobacteria. The recognized bacterium most closely related to strain MSL86Twas [Desulfobacterium]catecholicumDSM 3882T(sequence similarity 94.4 %), and the next most closely related recognized species wereDesulfotalea psychrophila(94.2 % sequence similarity with the type strain) andDesulfotalea arctica(93.7 %). As the physiological and chemotaxonomic characteristics of MSL86Twere distinctly different from those of any related species, a novel genus and speciesDesulfopila aestuariigen. nov., sp. nov. are proposed to accommodate the strain. The type strain ofDesulfopila aestuariiis MSL86T(=JCM 14042T=DSM 18488T).
Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb
Authors: Groth Ingrid , Tan Geok Yuan Annie , González Juan M. , Laiz Leonila , Carlsohn Marc René , Schütze Barbara , Wink Joachim , Goodfellow Michael
Published: March 2007

The taxonomic status of two actinomycetes isolated from the wall of a hypogean Roman catacomb was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genusAmycolatopsis. They also shared a range of chemical, molecular and phenotypic markers which served to separate them from representatives of recognizedAmycolatopsisspecies. The new isolates formed a branch in theAmycolatopsis16S rRNA gene sequence tree withAmycolatopsis minnesotensisNRRL B-24435T, but this association was not supported by a particularly high bootstrap value or by the product of the maximum-parsimony tree-making algorithm. The organisms were distinguished readily from closely relatedAmycolatopsisspecies based on a combination of phenotypic properties and from allAmycolatopsisstrains by their characteristic menaquinone profiles, in which tetra-hydrogenated menaquinones with 11 isoprene units predominated. The combined genotypic and phenotypic data indicate that the isolates merit recognition as representing a novel species of the genusAmycolatopsis. The name proposed for this novel species isAmycolatopsis nigrescenssp. nov., with type strain CSC17Ta-90T(=HKI 0330T=DSM 44992T=NRRL B-24473T).
Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’
Authors: Choo Yoe-Jin , Lee Kiyoung , Song Jaeho , Cho Jang-Cheon
Published: March 2007

A Gram-negative, chemoheterotrophic, facultatively anaerobic coccus, designated IMCC1545T, was isolated from the digestive tract of a marine clamworm, Periserrula leucophryna, inhabiting a tidal flat of the Yellow Sea. Cells of strain IMCC1545T are non-motile, dividing by binary fission. The predominant fatty acids are anteiso-C15 : 0 and C18 : 0. The respiratory quinone is menaquinone-7 and the DNA G+C content is 52.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences using three treeing algorithms revealed that the strain formed a novel genus-level lineage within the phylum ‘Verrucomicrobia’. The most closely related named organisms to strain IMCC1545T are ‘Fucophilus fucoidanolyticus’ SI-1234 (86.5 % 16S rRNA gene sequence similarity), Alterococcus agarolyticus ADT3T (81.8 %) and Opitutus terrae PB90-1T (80.3 %), which belong to subdivision 4 of the ‘Verrucomicrobia’. Subdivision 4 of the ‘Verrucomicrobia’ (here named Opitutae classis nov.) was divided into two clades, a clade containing strain IMCC1545T and a clade containing Opitutus terrae. From the taxonomic data obtained in this study, it is proposed that the new marine isolate be placed into a novel genus and species named Puniceicoccus vermicola gen. nov., sp. nov. (the type strain of Puniceicoccus vermicola is IMCC1545T=KCCM 42343T=NBRC 101964T) within Puniceicoccaceae fam. nov and Puniceicoccales ord. nov in the class Opitutae. The family Opitutaceae fam. nov. and order Opitutales ord. nov. are also formally proposed.
Methylobacterium jeotgali sp. nov., a non-pigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood
Authors: Aslam Zubair , Lee Chang Soo , Kim Kyoung-Ho , Im Wan-Taek , Ten Leonid N. , Lee Sung-Taik
Published: March 2007

A novel facultatively methylotrophic, Gram-negative, rod-shaped bacterium, designated strain S2R03-9T, was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, motile by means of a single polar flagellum, non-sporulating and catalase- and oxidase-positive. Strain S2R03-9Tgrew in the presence of 0–1 % (w/v) NaCl and at pH 6.0–10.0, with optimum growth in the absence of NaCl and at pH 7.0. It grew at temperatures in the range 20.0–30.0 °C, with optimum growth at 30 °C. Colonies grown on R2A medium were non-pigmented, opaque and creamy white. Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was most closely related toMethylobacterium organophilumJCM 2833T(96.6 % similarity) and the phylogenetic similarities to all otherMethylobacteriumspecies with validly published names were less than 95.0 %. The DNA G+C content was 64.9 mol%. The phylogenetic analysis, the phenotypic assessment and the chemotaxonomic data (major ubiquinone, Q-10; major fatty acids, C18 : 1and C18 : 0) showed that S2R03-9Trepresents a novel species within the genusMethylobacteriumin the classAlphaproteobacteria, for which the nameMethylobacterium jeotgalisp. nov. is proposed. The type strain is S2R03-9T(=KCTC 12671T=LMG 23639T).
Marinitoga okinawensis sp. nov., a novel thermophilic and anaerobic heterotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough
Authors: Nunoura Takuro , Oida Hanako , Miyazaki Masayuki , Suzuki Yohey , Takai Ken , Horikoshi Koki
Published: March 2007

A novel thermophilic and sulfur-reducing heterotrophic bacterium, strain TFS10-5T, was isolated from a deep-sea hydrothermal field in Yonaguni Knoll IV, Southern Okinawa Trough. Cells of strain TFS10-5Twere motile rods, 1.5–5 μm in length and 0.5–0.8 μm in width. Strain TFS10-5Twas an obligately anaerobic heterotroph and sulfur-reduction stimulated growth. Growth was observed between 30 and 70 °C (optimum at 55–60 °C), pH 5.0–7.4 (optimum at pH 5.5–5.8), 1.0–5.5 NaCl % (optimum at 3.0–3.5 %). The fatty acid content was C16 : 0(71.0 %), C16 : 1(6.0 %), C18 : 0(21.4 %) and C18 : 1(1.6 %). The G+C content of the genomic DNA was 28 mol%. 16S rRNA gene sequence analysis indicated that strain TFS10-5Tbelongs to the genusMarinitoga. Based on the physiological and phylogenetic features of the new isolate, strain TFS10-5Trepresents a novel species in the genusMarinitogafor which the nameMarinitoga okinawensissp. nov. is proposed. The type strain is TFS10-5T(=JCM 13303T=DSM 17373T).
Candida thaimueangensis sp. nov., an anamorphic yeast species from estuarine water in a mangrove forest in Thailand
Authors: Limtong Savitree , Yongmanitchai Wichien , Kawasaki Hiroko , Seki Tatsuji
Published: March 2007

Four yeast strains (TM1-01T, TM1-07, TM3-47 and TM3-49) were isolated by membrane filtration from estuarine water collected from a mangrove forest in Phang-Nga province, southern Thailand. Analysis of the D1/D2 domains of the large-subunit rDNA sequence revealed that the sequences of the four strains were identical. The closest recognized species in terms of pairwise sequence similarity was Pichia deserticola, but the level of nucleotide substitution (4.8 %) was sufficient to justify the description of a separate species. Phylogenetic analysis demonstrated that the four strains occupy a basal position with respect to Pichia membranifaciens and close relatives. The four strains showed identical phenotypic characteristics, including proliferation by multilateral budding, absence of ascospores, arthrospores and ballistospores and negative reactions for Diazonium blue B and urease. The major ubiquinone was Q-7. On the basis of the above findings, these four strains were assigned to a single novel species of the genus Candida, for which the name Candida thaimueangensis sp. nov. is proposed. The type strain is TM1-01T (=CBS 10360T=NBRC 101967T=BCC 21229T).
TheArabidopsis thalianaHomolog of YeastBRE1Has a Function in Cell Cycle Regulation during Early Leaf and Root Growth
Authors: Fleury Delphine , Himanen Kristiina , Cnops Gerda , Nelissen Hilde , Boccardi Tommaso Matteo , Maere Steven , Beemster Gerrit T.S. , Neyt Pia , Anami Sylvester , Robles Pedro , Micol José Luis , Inzé Dirk , Van Lijsebettens Mieke
Published: March 2007

Chromatin modification and transcriptional activation are novel roles for E3 ubiquitin ligase proteins that have been mainly associated with ubiquitin-dependent proteolysis. We identified HISTONE MONOUBIQUITINATION1 (HUB1) (and its homolog HUB2) in Arabidopsis thaliana as RING E3 ligase proteins with a function in organ growth. We show that HUB1 is a functional homolog of the human and yeast BRE1 proteins because it monoubiquitinated histone H2B in an in vitro assay. Hub knockdown mutants had pale leaf coloration, modified leaf shape, reduced rosette biomass, and inhibited primary root growth. One of the alleles had been designated previously as ang4-1. Kinematic analysis of leaf and root growth together with flow cytometry revealed defects in cell cycle activities. The hub1-1 (ang4-1) mutation increased cell cycle duration in young leaves and caused an early entry into the endocycles. Transcript profiling of shoot apical tissues of hub1-1 (ang4-1) indicated that key regulators of the G2-to-M transition were misexpressed. Based on the mutant characterization, we postulate that HUB1 mediates gene activation and cell cycle regulation probably through chromatin modifications.
Arabidopsis MYB26/MALE STERILE35Regulates Secondary Thickening in the Endothecium and Is Essential for Anther Dehiscence
Authors: Yang Caiyun , Xu Zhengyao , Song Jie , Conner Katie , Vizcay Barrena Gema , Wilson Zoe A.
Published: March 2007

The Arabidopsis thaliana  MYB26/MALE STERILE35 (MS35) gene is critical for the development of secondary thickening in the anther endothecium and subsequent dehiscence. MYB26 is localized to the nucleus and regulates endothecial development and secondary thickening in a cell-specific manner in the anther. MYB26 expression is seen in anthers and also in the style and nectaries, although there is no effect on female fertility in the ms35 mutant. MYB26 expression in anthers occurs early during endothecial development, with maximal expression during pollen mitosis I and bicellular stages, indicating a regulatory role in specifying early endothecial cell development. Overexpression of MYB26 results in ectopic secondary thickening in both Arabidopsis and tobacco (Nicotiana tabacum) plants, predominantly within the epidermal tissues. MYB26 regulates a number of genes linked to secondary thickening, including IRREGULAR XYLEM1 (IRX1), IRX3, IRX8, and IRX12. Changes in expression were also detected in two NAC domain genes, NAC SECONDARY WALL–PROMOTING FACTOR1 (NST1) and NST2, which have been linked to secondary thickening in the anther endothecium. These data indicate that MYB26 regulates NST1 and NST2 expression and in turn controls the process of secondary thickening. Therefore, MYB26 appears to function in a regulatory role involved in determining endothecial cell development within the anther and acts upstream of the lignin biosynthesis pathway.
Aberrant expression of TopBP1 in breast cancer
Authors: Going J J , Nixon C , Dornan E S , Boner W , Donaldson M M , Morgan I M
Published: March 2007

Aims:  The TopBP1 protein includes eight BRCT domains (originally identified in BRCA1) and has homology with BRCA1 over the carboxyl terminal half of the protein. The aim of this study was to determine whether TopBP1 is aberrantly expressed in breast cancer.

Methods and results:  Sixty‐one breast carcinomas from an unselected consecutive patient cohort were studied along with 12 samples of breast tissue from cosmetic breast reduction surgery; these were analysed immunohistochemically for TopBP1 expression using a rabbit polyclonal antibody. This antibody was validated in immunoprecipitation and immunofluorescence experiments. Immunohistochemical analysis demonstrated that TopBP1 was expressed almost exclusively in the nuclei of the normal breast epithelium. However, in a significant number of breast carcinomas TopBP1 was aberrantly expressed, as it was detected in the cytoplasm and nucleus of some tumours and exclusively in the cytoplasm of others. In two out of 61 carcinomas investigated, no TopBP1 expression was detected.

Conclusions:  For the first time this report demonstrates aberrant expression of the TopBP1 protein in breast carcinoma. We propose TOPBP1 as a breast cancer susceptibility gene.
Distinguishing angioimmunoblastic T‐cell lymphoma from peripheral T‐cell lymphoma, unspecified, using morphology, immunophenotype and molecular genetics
Authors: Attygalle A D , Chuang S‐S , Diss T C , Du M‐Q , Isaacson P G , Dogan A
Published: March 2007

Aims:  To identify distinguishing histological, immunophenotypic and molecular genetic features between angioimmunoblastic T‐cell lymphoma (AITL) and peripheral T‐cell lymphoma (PTL).

Methods:  Nodal T‐cell lymphomas examined (n =137), included AITL (n = 89), PTL (n = 22), anaplastic large cell lymphoma (n = 16) and ‘AITL/PTL indeterminate’ (n = 10) with overlapping features between AITL and PTL, showing morphology typical of AITL but lacking follicular dendritic cell expansion. Immunohistochemistry for CD3, CD20, CD21 and CD10, in situ hybridization for Epstein–Barr virus encoded RNA (EBER) and polymerase chain reaction for T‐cell and B‐cell clonality analysis were performed.

Results:  Of the AITLs, 74/89 showed typical morphology, whereas 15/89 showed hyperplastic follicles. AITL and ‘AITL/PTL indeterminate’ showed a polymorphous infiltrate and prominent vascularity in all cases. In both groups, CD10 was present in the majority and clear cells and EBER positivity were specific (but not universal) features lacking in PTL. Detection of T‐cell clonality was significantly higher in AITL (90%) compared with PTLu (59%).

Conclusion:  Clear cells and EBV infection (when present) are useful distinguishing features and CD10 a sensitive and specific marker of AITL. Hyperplastic follicles are present in a significant minority of AITL. AITL/PTL indeterminate probably falls within the spectrum of AITL rather than PTL.
Studies of associations between the Arg389Gly polymorphism of the β1‐adrenergic receptor gene (ADRB1) and hypertension and obesity in 7677 Danish white subjects
Authors: Gjesing A. P. , Andersen G. , Albrechtsen A. , Glümer C. , Borch‐Johnsen K. , Jørgensen T. , Hansen T. , Pedersen O.
Published: March 2007

Aims Activation of the β1‐adrenergic receptor (ADRB1) causes increased lipolysis in adipose tissue and enhances cardiac output. Analysis of the association of the functionalADRB1Arg389Gly variant with obesity and hypertension has given ambiguous results. To clarify the potential impact of this variant on obesity and hypertension in the general population, we examined the Arg389Gly variant in a relatively large‐scale population‐based study.

Methods Case‐control studies and quantitative trait analyses were carried out in 7677 Danish Caucasians who were genotyped for the Arg389Gly variant (dbSNP rs1801253) using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry.

Results A weak association between the Gly allele of the Arg389Gly variant and obesity was observed when comparing cases (n = 1540) defined as body mass index (BMI) > 30 kg/m2with control subjects (n = 6108) defined as BMI ≤ 30 kg/m2for both allele frequencies (P = 0.05) and genotype distribution (P = 0.05). Case‐control studies (casesn = 2518; controln = 3981) examining the effect on hypertension showed no association with allele frequencies (P = 0.3) or genotype distribution (P = 0.5); however, in the quantitative trait analyses, individuals carrying the Gly allele had slightly but significantly lower diastolic (Arg/Arg = 81.9 mmHg vs. Gly‐allele carriers = 81.5 mmHg) and systolic (Arg/Arg = 129.4 mmHg vs. Gly‐allele carriers = 128.8 mmHg) blood pressure as well as a lower mean arterial blood pressure.

Conclusion Our results suggest that the Arg389Gly polymorphism does not have any clinically important impact on the pathogenesis of obesity in Danish white subjects. Furthermore, despite the observed minor influence on blood pressure, this variant is most likely not to be a major contributor to the development of hypertension.
Initial monotherapy with either metformin or sulphonylureas often fails to achieve or maintain current glycaemic goals in patients with Type 2 diabetes in UK primary care
Authors: Cook M. N. , Girman C. J. , Stein P. P. , Alexander C. M.
Published: March 2007

Aims  To describe initial achievement of glycaemic targets and subsequent hyperglycaemia in patients with Type 2 diabetes managed with oral agent monotherapy in UK primary care from 1998 to 2004.

Methods  Electronic medical records of patients initiating metformin (n = 3362) or a sulphonylurea agent (n = 3070) in 290 UK primary care practices were retrieved from the General Practice Research Database (GPRD). Patients included had an HbA1c recorded 0–90 days before and 90–365 days after initiating monotherapy. The probability of achieving glycaemic thresholds in the first year, and for those achieving such targets, the probability of inadequate glycaemic control (HbA1c > 6.5%, > 7.0%, > 7.5%) over time is described.

Results  Low baseline HbA1c and drug initiation within 3 months of diabetes diagnosis were the strongest predictors of initial achievement of glycaemic targets. The proportion of patients with diabetes duration ≥ 4 months who achieved HbA1c < 7% in the first year ranged from 24% to 88% for highest to lowest baseline HbA1c category in sulphonylurea initiators and from 19% to 86% in metformin initiators, with slightly higher proportions for newly diagnosed patients. Kaplan–Meier analyses suggested that 55% and 70% of patients who initially achieved glycaemic targets had HbA1c measurements above these targets at 2 and 3 years.

Conclusions  Many patients fail to achieve glycaemic goals with initial monotherapy and, of those who achieve current goals, few consistently maintain these targets over 3 years. Research is needed to evaluate whether more aggressive treatment or alternative treatments can improve the long‐term maintenance of glycaemic control in patients with Type 2 diabetes.