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Biomedical subjects

William D Grant

Publications and source records attributed to William D Grant.

At least 19 recordsLinked to original sources
PubMed2006

Phylogenetic analysis of bacterial isolates from man-made high-pH, high-salt environments and identification of gene-cassette-associated open reading frames.

Environmental samples were collected from high-pH sites in Pakistan, including a uranium heap set up for carbonate leaching, the lime unit of a tannery, and the Khewra salt mine. Another sample was collected from a hot spring on the shore of the soda lake, Magadi, in Kenya. Microbial cultures were enriched from Pakistani samples. Phylogenetic analysis of isolates was carried out by sequencing 16S rRNA genes. Genomic DNA was amplified by polymerase chain reaction using integron gene-cassette-specific primers. Different gene-cassette-linked genes were recovered from the cultured strains related to Halomonas magadiensis, Virgibacillus halodenitrificans, and Yania flava and from the uncultured environmental DNA sample. The usefulness of this technique as a tool for gene mining is indicated.

Alkalies↗
PubMed2006

Salt-activated endoglucanase of a strain of alkaliphilic Bacillus agaradhaerens.

An endoglucanase was purified to homogeneity from an alkaline culture broth of a strain isolated from seawater and identified here as Bacillus agaradhaerens JAM-KU023. The molecular mass was around 38-kDa and the N-terminal 19 amino acids of the purified enzyme exhibited 100% sequence identity to Cel5A of B. agaradhaerens DSM8721(T). The enzyme activity increased around 4-fold by the addition of 0.2-2.0 M NaCl in 0.1 M glycine-NaOH buffer (pH 9.0). KCl, Na2SO4, NaBr, NaNO3, CH3COONa, LiCl, NH4NO3, and NH4Cl also activated the enzyme up to 2- to 4-fold. The optimal pH and temperature values were pH 7-9.4 and 60 degrees C with 0.2 M NaCl, but pH 6.5-7 and 50 degrees C without NaCl; enzyme activity increased approximately 6-fold at 60 degrees C with 0.2 M NaCl compared to that at 50 degrees C without NaCl in 0.1 M glycine-NaOH buffer (pH 9.0). The thermostability and pH stability of the enzyme were not affected by NaCl. The enzyme was very stable to several chemical compounds, surfactants and metal ions (except for Fe2+ and Hg2+ ions), regardless whether NaCl was present or not.

Amino Acid Sequence↗
PubMed2006

Caldalkalibacillus thermarum gen. nov., sp. nov., a novel alkalithermophilic bacterium from a hot spring in China.

A thermophilic, alkaliphilic and catalase-positive bacterium, designated strain HA6(T), was isolated from a hot spring in China. The strain was aerobic and chemo-organotrophic and grew optimally at 60 degrees C, pH 8.5 and 1.5 % (w/v) NaCl. The cells were Gram-positive rods, forming single terminal endospores. The predominant cellular fatty acids were iso-C(15 : 0) and iso-C(17 : 0). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C content was 45.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain HA6(T) formed a distinct lineage within the family Bacillaceae and was most closely related to Bacillus horti K13(T) and Bacillus smithii DSM 4216(T), with sequence similarities of 91.8 and 93.1 %, respectively. On the basis of its physiological and molecular properties, strain HA6(T) should be placed in a novel genus and species, for which the name Caldalkalibacillus thermarum gen. nov., sp. nov. is proposed. The type strain of Caldalkalibacillus thermarum is strain HA6(T) (=CGMCC 1.4242(T)=JCM 13486(T)).

China↗
PubMed2006

Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples.

Here we describe the application of metagenomic technologies to construct cDNA libraries from RNA isolated from environmental samples. RNAlater (Ambion) was shown to stabilize RNA in environmental samples for periods of at least 3 months at -20 degrees C. Protocols for library construction were established on total RNA extracted from Acanthamoeba polyphaga trophozoites. The methodology was then used on algal mats from geothermal hot springs in Tengchong county, Yunnan Province, People's Republic of China, and activated sludge from a sewage treatment plant in Leicestershire, United Kingdom. The Tenchong libraries were dominated by RNA from prokaryotes, reflecting the mainly prokaryote microbial composition. The majority of these clones resulted from rRNA; only a few appeared to be derived from mRNA. In contrast, many clones from the activated sludge library had significant similarity to eukaryote mRNA-encoded protein sequences. A library was also made using polyadenylated RNA isolated from total RNA from activated sludge; many more clones in this library were related to eukaryotic mRNA sequences and proteins. Open reading frames (ORFs) up to 378 amino acids in size could be identified. Some resembled known proteins over their full length, e.g., 36% match to cystatin, 49% match to ribosomal protein L32, 63% match to ribosomal protein S16, 70% to CPC2 protein. The methodology described here permits the polyadenylated transcriptome to be isolated from environmental samples with no knowledge of the identity of the microorganisms in the sample or the necessity to culture them. It has many uses, including the identification of novel eukaryotic ORFs encoding proteins and enzymes.

Acanthamoeba↗
PubMed2005

Sequence of the gene for a high-alkaline mannanase from an alkaliphilic Bacillus sp. strain JAMB-750, its expression in Bacillus subtilis and characterization of the recombinant enzyme.

A novel alkaline mannanase Man26A has been found in the culture of an alkaliphilic Bacillus sp. strain JAMB-750 and the optimal pH for the mannanase activity of the enzyme was around pH 10 (J Biol Macromol 4: 67-74, 2004). This optimal pH is the highest among those of the mannanases reported to date. The gene man26A coding the enzyme was cloned from the genomic DNA of strain JAMB-750 and sequenced. It encodes a protein of 997 amino acids including a signal peptide. The N-terminal half (Glu27-Val486) of the enzyme exhibited moderate similarities to other mannanases belonging to glycoside hydrolase family 26, such as the enzymes from Cellvibrio japonicus (37% identity), Cellulomonas fimi (33% identity), and Bacillus sp. strain AM-001 (28% identity). The C-terminal half was found to contain four domains. The first, second, third, and fourth domains exhibited similarities to the carbohydrate-binding module, the mannan-binding module, the Homo sapiens collagen type IX alpha I chain, and the membrane anchor region of Gram-positive surface proteins, respectively. Its recombinant mannanase was produced extracellularly using Bacillus subtilis as the host. The optimal pH for the mannanase activity of the recombinant enzyme was around pH 10. The enzyme was very resistant to surfactants, for example, SDS up to 2.0% (w/v).

Amino Acid Sequence↗
PubMed2005

Relationship between antenatal inflammation and antenatal infection identified by detection of microbial genes by polymerase chain reaction.

Although antenatal infection is thought to play an important role in the pathogenesis of preterm labor and neonatal diseases, the exact mechanisms are largely unknown. We sought to clarify the relationship between antenatal infection and intrauterine and neonatal inflammation. Samples were obtained from 41 preterm infants of <33 wk gestation delivered to 36 mothers and analyzed for the presence of 16s ribosomal RNA (16s rRNA) genes using PCR and for the proinflammatory cytokines IL-6 and IL-8. In 16 (44%) mother-baby pairings, at least one sample was found to be positive for the presence of 16s rRNA genes. All but one of the positive samples were from mothers presenting with preterm prelabor rupture of membranes (pPROM) or in spontaneous idiopathic preterm labor. A strong association was found between the presence of 16s rRNA genes and chorioamnionitis and with funisitis. A marked increase in IL-6 and IL-8 was noted in all tissues positive for 16s rRNA genes, including placenta, fetal membranes, cord blood serum, and, where samples were available, in bronchoalveolar lavage fluid (BAL) and in amniotic fluid. Interestingly, gastric fluid was always positive for 16s rRNA genes if any other intrauterine or BAL sample was positive, suggesting that this sample may provide an alternative to amniotic fluid to identify antenatal infection. In conclusion, we have found that microbial genes are particularly prevalent in pPROM and spontaneous preterm labor groups and that their presence is strongly associated with a marked intrauterine inflammatory response.

Amniotic Fluid↗
PubMed2005

Cellulomonas bogoriensis sp. nov., an alkaliphilic cellulomonad.

An alkaliphilic, slightly halotolerant, chemo-organotrophic, Gram-positive, rod-shaped bacterium, strain 69B4(T), was isolated from the sediment of the littoral zone of Lake Bogoria, Kenya. Phylogenetically, it is a member of the genus Cellulomonas, showing less than 97.5 % sequence similarity to the type strains of other Cellulomonas species. The highest level of similarity, albeit moderate, was found with respect to Cellulomonas cellasea DSM 20118(T). Chemotaxonomic properties confirm the 16S rRNA gene-based generic affiliation, i.e. a DNA G+C content of 71.5 mol%, anteiso-C(15:0) and C(16:0) as the major fatty acids, MK-9(H(4)) as the major isoprenoid quinone, a peptidoglycan containing L-ornithine as the diamino acid and D-aspartic acid in the interpeptide bridge and phosphatidylglycerol as the only identified main polar lipid. The strain is aerobic to facultatively anaerobic, being capable of growth under strictly anaerobic conditions. Optimal growth occurs between pH values 9.0 and 10.0. On the basis of its distinct phylogenetic position and metabolic properties, strain 69B4(T) represents a novel species of the genus Cellulomonas, for which the name Cellulomonas bogoriensis sp. nov. is proposed. The type strain is 69B4(T) (=DSM 16987(T)=CIP 108683(T)).

Bacterial Typing Techniques↗
PubMed2005

Halalkalicoccus tibetensis gen. nov., sp. nov., representing a novel genus of haloalkaliphilic archaea.

A haloalkaliphilic archaeon (strain DS12T) isolated from Lake Zabuye, the Tibetan Plateau, China, was characterized to elucidate its taxonomy. The strain was aerobic, chemo-organotrophic, and grew optimally at 40 degrees C, pH 9.5-10.0 and 3.4 M NaCl. Cells of strain DS12T were non-motile cocci and stained Gram-variable. The major polar lipids of strain DS12T were diphytanyl and phytanyl-sesterterpanyl diether derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Phylogenetic analysis revealed that the strain formed a distinct lineage within the family Halobacteriaceae. The low 16S rRNA gene sequence similarity values to its closest relatives (91.5-92.5 %) and its signature bases both suggest that the strain has no close affinity with any members of the family Halobacteriaceae with validly published names. Therefore, it is proposed that strain DS12T (=AS 1.3240T=JCM 11890T) represents the type strain of a novel species in a new genus, Halalkalicoccus tibetensis gen. nov., sp. nov.

Base Sequence↗
PubMed2005

An evidence-based journal club for dental residents in a GPR program.

The journal club offers a significant opportunity to serve as both an educational experience but also as a real-world example of the application of the principles and practices of evidence-based dentistry (EBD). Designed around the American Dental Association's recommended four steps in the implementation of the EBD process, the journal clubs are held once per month for GPR residents. The structured process allows residents to formulate answerable clinical questions, track down with maximum efficiency the best evidence with which to answer the questions, critically appraise the evidence for its validity and usefulness, and apply the results of this appraisal in clinical practice as appropriate.

Databases as Topic↗
PubMed2004

A phylogenetic analysis of Wadi el Natrun soda lake cellulase enrichment cultures and identification of cellulase genes from these cultures.

Samples of sediments and surrounding soda soils (SS) from the extremely saline and alkaline lakes of the Wadi el Natrun in the Libyan Desert, Egypt, were obtained in October 2000. Anaerobic enrichment cultures were grown from these samples, DNA isolated, and the bacterial diversity assessed by 16S rRNA gene clone analysis. Clones derived from lake sediments (LS) most closely matched Clostridium spp., Natronoincola histidinovorans, Halocella cellulolytica, Bacillus spp., and the Cytophaga-Flexibacter-Bacteroides group. Similar clones were identified in the SS, but Bacillus spp. predominated. Many of the clones were most closely related to organisms already identified in alkaline or saline environments. Two genomic DNA libraries were made from the pooled LS enrichments and a single SS-enrichment sample. A novel cellulase activity was identified and characterized in each. The lake cellulase ORF encoded a protein of 1,118 amino acids; BLASTP analysis showed it was most closely related to an endoglucanase from Xanthomonas campestris. The soil-cellulase ORF encoded a protein of 634 amino acids that was most closely related to an endoglucanase from Fibrobacter succinogenes.

Bacillus↗
PubMed2004

Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate.

An alkaline mannanase (EC 3.2.1.78) from the alkaliphilic Bacillus sp. strain JAMB-602 was cloned and sequenced. The deduced amino-acid sequence of the enzyme suggested that the enzyme consists of a catalytic and unknown additional domains. The recombinant enzyme expressed by B. subtilis was crystallized using the hanging-drop vapour-diffusion method at 277 K. X-ray diffraction data were collected to 1.65 A. The crystal belongs to space group P2(1)2(1)2(1), with unit-cell parameters a = 70.7, b = 79.5, c = 80.4 A. The asymmetric unit contains one protein molecule, with a corresponding VM of 2.26 A3 Da(-1) and a solvent content of 45.6%. Molecular replacement for initial phasing was carried out using the three-dimensional structure of a mannanase from Thermomonospora fusca as a search model, which corresponds to the catalytic domain of the alkaline mannanase. It gave sufficient phases to build the unknown domain.

Bacillus↗
PubMed2004

Alkalimonas amylolytica gen. nov., sp. nov., and Alkalimonas delamerensis gen. nov., sp. nov., novel alkaliphilic bacteria from soda lakes in China and East Africa.

Two related novel alkaliphilic and slightly halophilic bacteria are described. They are strain N10 from Lake Chahannor in China and strain 1E1 from Lake Elmenteita in East Africa. Both strains are strictly aerobic, heterotrophic, alkaliphilic, mesophilic, and require NaCl for growth. The optimal conditions for growth were at pH 10-10.5 and 2-3% (w/v) NaCl. Cells of both strains were Gram-negative, rod-shaped, non-spore-forming, and motile with a single polar flagellum. Cellular fatty acids in both strains were predominantly saturated and mono-unsaturated straight-chain fatty acids (16:0, 16:1omega7c and 18:1omega7c). The major isoprenoid quinone of both strains was Q8. The major polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylglycerol phosphate and phosphatidylethanolamine. The guanine plus cytosine (G + C) content of the DNA was 52.5 mol% and 55.4 mol%, respectively. Phylogenetic analysis revealed that the two strains formed a distinct lineage within the gamma-3 subclass of the Proteobacteria. The strains shared a 16S rDNA sequence similarity of 96.1% and showed less than 93.7% of sequence similarity to any other known species. Based on polyphasic data, the two strains were differentiated from currently recognized genera and represent a new genus, Alkalimonas gen. nov., with two species, Alkalimonas amylolytica sp. nov. (type strain is N10T = AS 1.3430) and Alkalimonas delamerensis sp. nov. ( type strain is 1E1(P, T) = CBS 391.94). The GenBank accession numbers for the 16S rRNA gene sequence of strains N10 and 1E1 are AF250323 and X92130, respectively.

Africa, Eastern↗
PubMed2004

Clinical comparison of the Welch Allyn SureSight handheld autorefractor versus cycloplegic autorefraction and retinoscopic refraction.

PURPOSE: To investigate the accuracy of the Welch Allyn SureSight (WASS; Welch Allyn, Skaneateles Falls, New York) hand-held autorefractor in noncyclopleged children and to compare the results with those obtained in cyclopleged children using the Nidek AR-820 (NAR; Nidek, Aichi, Japan) and retinoscopic refraction (RR) of an experienced pediatric ophthalmologist. METHODS: Ninety-one children (mean age 97 months +/- 19, range 37 to 107) whose vision screening, performed by a school nurse and/or by their primary care provider, was unsuccessful were prospectively evaluated in the private practice of a university pediatric ophthalmologist. After completion of a history, each child was refracted using the WASS. A complete ophthalmic examination, including cycloplegic refraction using the NAR and retinoscopic refraction refined to obtain a visual acuity of at least 20/30 diopters, was then performed. The physician was masked to the previous WASS and NAR results. Analysis variables included race, age (months), refraction (sphere, cylinder, axis), and initial and final corrected visual acuity. Only WASS values for which reliability was > or = 8 were used. A coin toss determined which eye would be used for analysis. RESULTS: Using analysis of variance and Scheffé multiple comparison testing, sphere results obtained by the WASS indicated a statistical difference compared with those obtained using the NAR (P =.0027) and retinoscopy (P =.0088). Similarly, spherical equivalence results obtained by the WASS also indicated a statistical difference compared with that of the NAR (P =.0027) and retinoscopy (P =.0056). Myopic sphere and spherical equivalent values were recorded more frequently with the WASS than with the NAR or refined retinoscopy. Cylindrical values comparing the WASS with the NAR, the WASS with RR, and the NAR with RR were statistically similar to each other (P =.9993,.748, and.7261 respectively). Axial results for patients with +0.50 or more of astigmatism were also statistically similar by all 3 methods. CONCLUSIONS: Our data indicate that when the WASS is used on noncyclopleged children as suggested for primary care providers, myopia may be overdiagnosed.

Analysis of Variance↗
PubMed2004

Low back pain in Australian adults: prevalence and associated disability.

OBJECTIVES: To determine the prevalence ranges of low back pain (LBP) together with any related disability in Australian adults. DESIGN: A population-based survey. METHODS: The survey was mailed in June 2001 to a stratified random sample of 3000 Australian adults selected from the Electoral Roll. Demographic variables of respondents were compared with the Australian population. Selective response bias was investigated using wave analysis. A range of prevalence data was derived, as were disability scores using the Chronic Pain Grade. RESULTS: There was a 69% response rate. There was little variation between the sample and the Australian adult population. There was no significant selective response bias found. The sample point prevalence was estimated at 25.6% (95% confidence interval [CI], 23.6-27.5), 12-month prevalence was 67.6% (95% CI, 65.5-69.7), and lifetime prevalence was 79.2%, (95% CI, 77.3-81.0). In the previous 6-month period, 42.6% (95% CI, 40.4-44.8) of the adult population had experienced low-intensity pain and low disability from it. Another 10.9% (95% CI, 9.6-12.3) had experienced high intensity-pain but still low disability from this pain. However, 10.5% (95% CI, 9.2-11.9) had experienced high-disability LBP. CONCLUSION: LBP is a common problem in the Australian adult population, yet most of this is low-intensity and low-disability pain. Nevertheless, over 10% had been significantly disabled by LBP in the past 6 months. Data from this study will provide a better understanding of the magnitude of the LBP problem in Australia, the need for access to health care resources, and also strategic research directions.

Adult↗
PubMed2004

Low back pain in Australian adults. health provider utilization and care seeking.

OBJECTIVE: To determine the characteristics of Australian adults who seek care for low back pain (LBP), including the type of care they choose and any factors associated with making those choices. DESIGN: A population-based mailed survey. SUBJECTS: An age, gender, and state stratified random sample of 2768 Australian adults selected from the Electoral Roll. METHODS: A self-administered, fully structured questionnaire included a series of questions relating to care seeking for LBP, choice of provider, and types of treatment received. In addition, a series of questions were asked relating to demographic characteristics, socioeconomic variables, severity of LBP, cigarette smoking, anthropometric variables, perceived cause of LBP, lifetime emotional distress, job satisfaction, lifetime physical fitness, past 5-year health status, and fear of LBP causing future impairment. RESULTS: The response rate was 69.1%. The sample proved to be similar to the Australian adult population. The majority of respondents with LBP in the past 6 months did not seek care for it (55.5%). Factors that increased care seeking were higher grades of pain and disability severity, fear of the impact of pain on future work and life, and female sex. Factors decreasing the likelihood for seeking care were identified as the cause of pain being an accident at home and also never being married. General medical practitioners and chiropractors are the most popular providers of care. CONCLUSION: This study shows that a majority of people did not seek care for their LBP. The reasons for care seeking proved to be independent of social or economic status.

Adult↗
PubMed2004

Halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from Lake Zabuye in Tibet, China.

A novel haloalkaliphilic archaeon, strain 8W8T, was isolated from Lake Zabuye, on the Tibetan Plateau, China. On the basis of 16S rRNA gene sequence analysis, strain 8W8T was shown to belong to the genus Halorubrum and was related to Halorubrum vacuolatum (96.7% sequence similarity), Halorubrum saccharovorum (96.0%), Halorubrum lacusprofundi (95.4%) and Halorubrum sodomense (95.3%). The phylogenetic distance from any species within the other genera of Halobacteriales was lower than 90%. The major polar lipids of strain 8W8T were C20C20 and C20C25 derivatives of phosphatidylglycerol phosphate and phosphatidylglycerol phosphate methyl ester. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 8W8T from the eight Halorubrum species with validly published names. Therefore, strain 8W8T represents a novel species, for which the name Halorubrum tibetense sp. nov. is proposed, with the type strain 8W8T (=AS 1.3239T=JCM 11889T).

China↗
PubMed2003

Pulmonary Ureaplasma urealyticum is associated with the development of acute lung inflammation and chronic lung disease in preterm infants.

Previously, we have reported marked pulmonary inflammation in infants who develop chronic lung disease of prematurity. We revisited these infants who did not have clinical or laboratory evidence of infection and searched for Ureaplasma urealyticum, group B streptococci, and other microbes by reverse transcription-PCR performed on RNA extracted from 93 bronchoalveolar lavage samples. From infants ventilated for respiratory distress syndrome, 6 (gestation, 28 wk; birthweight, 880 g) were positive for U. urealyticum and 11 (25 wk, 800 g) were negative. Five (83%) positive and four (36%) negative infants developed chronic lung disease. Each infant was colonized with either biovar 1 or biovar 2 but not both. U. urealyticum was very weakly detectable in two infants on d 1 but was detected in five of six infants at d 10. Furthermore, pulmonary neutrophils, alveolar macrophages, soluble intercellular adhesion molecule-1, and IL-1beta on d 10 and IL-6 and IL-8 at d 1 were significantly increased in the positive group. A variety of organisms were identified in six samples between 14 and 21 d of age, but all samples were negative for group B streptococci. Our data suggest that U. urealyticum colonization is associated with the development of pulmonary inflammation in infants who subsequently develop chronic lung disease.

Acute Disease↗