bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical Composition of Six Seahorse Species, Hippocampus sp., from the Chinese Coast
Authors: Lin Qiang , Lin Junda , Lu Junyi , Li Bingji
Published: April 2008

The biochemical composition of six seahorse species from the Chinese coast was analyzed in this study. The crude protein content (% dry weight) of Hippocampus kuda, Hippocampus trimaculatus, Hippocampus kelloggi, Hippocampus spinosissimus, Hippocampus histrix, and Hippocampus comes was 70.70 ± 2.12%, 77.59 ± 1.06%, 78.31 ± 1.74%, 71.15 ± 1.32%, 68.07 ± 1.96%, and 76.59 ± 3.25%, respectively. The major amino acids (>5% of the total) in seahorses were arginine, aspartic acid, glutamic acid, alanine, and glycine, and there were significant differences in essential amino acids (EAA) (as % of total protein) among the six species (P 
< 
0.05). The scores of EAA were balanced in the seahorse species, and the essential amino acid indexes of the six species were 41.63, 40.89, 44.84, 39.60, 39.31 and 45.45, respectively. The content of flavor‐enhancing amino acids of the six seahorse species was generally high, ranging from 28.16 ± 1.12% in H. histrix to 32.90 ± 2.17% in H. kelloggi (P 
< 
0.05). The total lipid content was generally low, ranging from 0.96 ± 0.08% in H. histrix to 2.02 ± 0.24% in H. comes. The most abundant fatty acid was C16:0, ranging from 15.04 ± 0.67% in H. trimaculatus to 31.04 ± 4.32% in H. spinosissimus. The combination of eicosapentaenoic acid and docosahexaenoic acid as the fraction of the total fatty acids was high (0.14–0.35). The polyunsaturated fatty acid/saturated fatty acid ratio ranged from 0.40 in H. kuda to 1.19 in H. histrix. The trace metal concentrations in the seahorses were generally low. The six seahorse species examined provide a food source for humans with low fat, high protein, good levels of EAA, and high beneficial trace elements. These results are valuable in developing diets for culturing seahorse species.
Effects of an Extended Hatchery Phase and Vaccination against Enteric Septicemia of Catfish on the Production of Channel Catfish, Ictalurus punctatus, Fingerlings
Authors: Carrias Abel A. , Terhune Jeffery S. , Sayles Christopher A. , Chappell Jesse A.
Published: April 2008

Abstract.—

The present study was conducted to evaluate production management methods to improve overall survival of channel catfish, Ictalurus punctatus, fry to the fingerling stage by incorporating the use of a live, attenuated vaccine against Edwardsiella ictaluri and employing an extended hatchery phase. In this experiment, four treatments were used. In Treatment 1, 10‐d posthatch (PH) fry were vaccinated and then directly stocked into earthen ponds. In Treatments 2 and 3, 10‐d PH fry were sham‐vaccinated (control) and vaccinated, respectively, kept in nursery tanks for 22 d, and then stocked into earthen ponds. Fry in Treatment 4 were sham‐vaccinated at 10 d PH, kept in nursery tanks for 22 d, and then vaccinated prior to stocking into earthen ponds. Mean fingerling yield at harvest ranged from 4716 kg/ha in Treatment 1 to 8112 kg/ha in Treatment 4. Mean individual fish weight ranged from 38.8 g in Treatment 1 to 40.9 g in Treatment 4, and feed conversion ratios (FCR) ranged from 1.15 in Treatment 4 to 1.51 in Treatment 1. Mean survival ranged from 47.5% in Treatment 1 to 73.4% in Treatment 4. In specific comparisons to evaluate the nursery effect (Treatments 1 and 3), yield and overall survival were significantly different (P < 0.05) between these two treatments. In specific comparisons to evaluate the effect of the use of the vaccine (Treatments 2, 3, and 4), overall survival was significantly different (P < 0.05) between Treatment 2 (sham‐vaccinated control with nursery phase) and Treatment 4 (vaccinated at 32 d PH with nursery phase). No significant differences (P > 0.05) in yield, average weight, and FCR were observed between treatments. Results indicate that implementing an extended hatchery phase and vaccination strategy with older fry can improve overall survival of fingerling fish.
Promoter methylation of P15INK4B gene is possibly associated with parvovirus B19 infection in adult acute leukemias
Authors: YALCIN A. , SERIN M. S. , EMEKDAS G. , TIFTIK N. , ASLAN G. , ESKANDARI G. , TEZCAN S.
Published: April 2008

In this study, we examined the P15INK4B gene promoter methylation in patients with myelodysplastic syndrome and acute leukemia and its possible relationship with parvovirus B19 and Epstein–Barr virus infections. P15INK4B methylation frequency was significantly higher in acute leukemia patients than in that of non‐malignant patients (P < 0.05). When the patients with myelodysplastic syndrome were included, no significant difference was found between these groups regarding the methylation status. The possible correlation between P15INK4B promoter methylation and parvovirus B19 infection was observed in adult acute leukemia patients (P < 0.05). However, no similar relationship in EBV‐infected patients was observed. To the best of our knowledge, this is the first report showing the possible association between P15INK4B promoter methylation and parvovirus B19 infection in acute leukemia.
Incidence, clinical findings and management of intraoperative floppy iris syndrome associated with tamsulosin
Authors: Keklikci Ugur , Isen Kenan , Unlu Kaan , Celik Yusuf , Karahan Mine
Published: April 2008

Purpose:  To determine the risk ratios and incidence of intraoperative floppy iris syndrome (IFIS) during cataract surgery in patients using tamsulosin, and to assess management strategies for IFIS.

Methods:  We performed a non‐randomized, observational, prospective study, in which 594 eyes of 579 patients undergoing cataract surgery were enrolled. Surgeons were masked to the patients’ drug history. Usage or non‐usage of tamsulosin, duration of tamsulosin use, presence or absence of IFIS, management of IFIS and intraoperative complications were recorded in the patients’ theatre notes.

Results:  Twelve of 15 (80%) IFIS patients were taking systemic tamsulosin. Twelve of 23 (52%) patients using tamsulosin showed features of IFIS. The odds ratios (ORs) and relative risk (RR) ratios show strong positive correlations between tamsulosin use and IFIS. The ORs and RR ratios and the 95% confidence intervals (CIs) are as follows: OR 206.5 (95% CI 50.9–836.5); RR 99.3 (95% CI 30.0–327.8). There were no statistically significant differences between patients with or without IFIS, who were using tamsulosin, in terms of age or duration of tamsulosin use (p > 0.05). Seven eyes (46.6%) with IFIS were successfully managed with epinephrine. Eight eyes (53.4%) with IFIS needed iris hooks.

Conclusions:  Patients using tamsulosin appear to be at high risk of IFIS during cataract surgery. The occurrence of IFIS may not be affected by duration of tamsulosin use or age. Epinephrine may be effective in approximately 50% of eyes with IFIS. The iris hook procedure represents an effective management strategy in IFIS.
Growth and development of Potamogeton malaianus in SW Japan
Authors: Wiegleb Gerhard , Kadono Yasuro
Published: April 2008

Growth and development of a population of Potamogeton malaianus were studied over an annual cycle.

An ample description of the morphological structure of this poorly known species is given. In the study site the plants reached their maximum size with up to 13 g dry weight/shoot complex in October. The plant exhibits a complicated growth cycle which is illustrated here by following the development of biomass and number of different plant parts, the successive development of new generations of vertical shoots, and the extension of horizontal shoots. The life cycle is mainly influenced by the water regime of the river which reflects the distribution of rainfall over the year. Both regrowth and constant loss of plant material occur all over the vegetation period. The main portion of standing crop is found in the vertical shoots (between 32.0 and 42.3% in stems and between 44.5 and 71.3% in submersed leaves). Besides vertical growth also horizontal extension (up to 1.2 m from the starting point) is important. The maximum contribution of horizontal shoots was 10.2% of total biomass. Flowering occurred several times over the year, but was never abundant. A very low number of ripe fruits were produced. The maximum proportion of biomass allocated to flowering structures was reached in September with 3.7%. Regrowth in spring starts from tubers or from buds on relic stems, depending on winter temperatures. The plant has several effective means of vegetative reproduction that also contribute to quick regrowth after the spates during the rainy season.
Notes on generic and infrageneric delimitation in the Valerianaceae
Authors: Eriksen Bente
Published: April 2008

The characters used for generic delimitation in Valerianaceae are discussed, and the South American genera Aretiastrum, Astrephia, Belonanthus, Phuodendron, Phyllactis, and Stangea are included in the genus Valeriana. Valeriana subgen. Phyllactis is emended to comprise all South American species with reduced number of anther locules.
Notes on SE Asian Acanthaceae 1
Authors: Hansen B.
Published: April 2008

The taxonomic importance of the rising placenta in capsules of Acanthaceae is briefly discussed, particularly in relation to Justicia versus Rungia. Rungia naoensis is described as a new species. Justicia imlayae and J. internodialis are new names. New combinations are Justicia stolonifera, Pseuderanthemum lapathifolium, P. latifolium, Ptyssiglottis isophylla, P. kunthiana, Rungia adnata, R. burmanica, R. clauda, R. eberhardtii, R. monetaria, R. oligoneura, R. purpurascens, R. selangorensis, R. subtilifolia, R. vegeta. Antheliacanthus is a synonym of Pseuderanthemum and Polytrema a synonym of Ptyssiglottis.
Typification of Cerastium fontanum ssp. vulgare (Caryophyllaceae)
Authors: Jackson Michael B. Wyse
Published: April 2008

The basionym of Cerustium fontanum ssp. vulgare (Hartman) Greuter and Burdet, C. vulgare Hartman, is neotypified, based on a specimen in UPS. Flora Nordica notes No. 14.
Trachyandra triquetra (Asphodelaceae), a new species from the Horn of Africa
Authors: Thulin Mats
Published: April 2008

The new species Trachyandra triquetra, from shady limestone rocks in north‐eastem Somalia, is described and illustrated. This apparently narrow endemic is the only member of this mainly South African genus in eastern and north‐eastem tropical Africa except for the widespread T. saltii.
Notes on SE Asian Acanthaceae 2
Authors: Hansen Bertel
Published: April 2008

Thunbergia colpifera and Staurogyne parvicaulis are described as new species. Staurogyne longeciliata is a synonym of S. lanceolata, and so is S. lanceolata var. scabridula. Ebennaiera subcapitata is still kept in Staurogyne setigera. Staurogyne malaccensis is a synonym of S. setigera, and so is S. malaccensis var. stenophylla.
Synopsis of Hyacinthaceae in tropical East and North‐East Africa
Authors: Stedje Brita , Thulin Mats
Published: April 2008

Nine genera of Hyacinthaceae, Albuca, Bowiea, Dipcadi, Drimia, Drimiopsis, Lede‐bouria, Ornithogalum, Schizobasis and Scilla, with a total of 34 species, are recognized in Ethiopia, Somalia, Djibouti, Uganda, Kenya and Tanzania. One new species, Ledebouria urceolata, is described from Ethiopia. New combinations are Drimia simensis, Drimiopsis fischeri, Ledebouria sornaliensis, L. kirkii, L. edulis and L. cordifolia. Several names are reduced to synonymy and some are lectotypified. Keys to all taxa are given.
On the occurrence of a velamen radicum in Cyperaceae and Velloziaceae
Authors: Porembski Stefan , Barthlott Wilhelm
Published: April 2008

Roots of tree‐like Cyperaceae (Afrotrilepis pilosa, Bulbostylis leucostachya, Coleo‐chloa setifera, Microdracoides squamosus) and Velloziaceae (Vellozia variegata, Xe‐rophyta pinifolia) were examined by light and scanning electron microscopy. For the first time a velamen is reported for Bromeliiflorae and Commeliniflorae. All species studied possess a velamen radicum that is either one‐layered (Microdracoides, Bulbostylis, Coleochloa) or multi‐layered (Afrotrilepis, Vellozia, Xerophyta). Anticlinal walls of the velamen cells of Microdracoides show perforations similar to those found in orchids. A multiple exodermis delimits the velamen towards the cortex. As in epiphytic Orchidaceae, a velamen may be of considerable adaptive value for arborescent Cyperaceae and Velloziaceae. These mainly occur in edaphically and climatologically extreme habitats (e.g. tropical inselbergs) where rapid water uptake is of crucial importance.
Ecological characteristics of scale‐bearing chrysophytes in a small eutrophic pond in The Netherlands
Authors: Suykerbuyk R. E. M. , Roijackers R. M. M. , Houtman S. S. J.
Published: April 2008

In a pool near Nijmegen (The Netherlands) a study was carried out regarding the ecological characteristics of scale‐bearing chrysophytes (species and groups of species). The results confirm the relatively new thought, that chrysophytes are not indicating oligotrophic waters only, but the wider range of oligotrophic to eutrophic water. In this pool ammonia and nitrate appeared to be the most important chemical variables, determinatting the development of chrysophyte species. Total and ortho‐phosphorus were important variables in the second place. From the physical factors, pH‐value here had less influence, while conductivity and alkalinity had none at all. However, some species of Mallomonas are able to develop at higher levels of conductivity than usually assumed. In high concentrations, ammonia could be toxic. Confirming the knowledge from literature, temperature variation is an important factor for the quantitative development of species. In particular, high abundancies occur at temperatures below around 12–14°C, which explains the decrease of chrysophytes in summertime. The presence of organic matter complicates the results and must be taken into account in future studies. For biological assessment of water quality, the results underline the necessity of having knowledge of the ecological characteristics of the individual species.
Systemic lupus erythematosus in a tertiary, east Malaysian hospital: admission, readmission and death
Authors: TEH C. L. , CHAN G. Y. L. , LEE J.
Published: April 2008

Objective:  There are limited data on hospitalization of systemic lupus erythematosus (SLE) patients in Asian countries. Our aim of this study is to describe the characteristics and poor prognostic factors in our patients.

Method:  We performed a retrospective study of SLE hospitalization during a 1‐year period (2006) in our centre.

Results:  There were 125 episodes of hospitalization of 79 patients with SLE. This is the first report of SLE patients from the native population of east Malaysia. The cause of admission was flare of SLE (80.8%), infection (23.2%), renal biopsy (22.4%) and others (4%). There was only one admission for thromboembolism. Patients with both flare of SLE and infection have the longest median length of stay of 11 days (IQR 5,24) requiring more intensive care therapy (P < 0.01). Readmission occurred in 31.4% and was associated with admission for other reasons during the first admission. Flare of SLE was protective against readmission (P < 0.05, OR = 0.36). There were six deaths (4.8% of admissions). The deaths were due to infection in three patients, active SLE in two and acute myocardial infarction in one. The deaths have a higher cumulative prednisolone dose than the survivals (P < 0.01). In multivariate modelling, the only predictor of death was high Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index score (P < 0.05, OR = 9.61 per increase of 1 score).

Conclusion:  Active disease and infection remains the main cause of admission, readmission and death in SLE patients.
Evidence‐based recommendations for the monitoring and treatment of ankylosing spondylitis: results from the Australian 3E initiative in rheumatology
Authors: KAIN Tracey , ZOCHLING Jane , TAYLOR Andrew , MANOLIOS Nicholas , SMITH Malcolm D. , REED Mark D. , BROWN Matthew A. , SCHACHNA Lionel
Published: April 2008

Aim:  To develop a set of Australian recommendations for the monitoring and treatment of ankylosing spondylitis (AS) through systematic literature review combined with the opinion of practicing rheumatologists.

Methods:  A set of eight questions, four in each domain of monitoring and treatment, were formulated by voting and the Delphi method. The results of a systematic literature review addressing each question were presented to the 23 participants of the Australian 3E meeting. All participants were clinical rheumatologists experienced in the daily management of AS.

Results:  After three rounds of breakout sessions to discuss the findings of the literature review, a set of recommendations was finalized after discussion and voting. The category of evidence and strength of recommendation were determined for each proposal. The level of agreement among participants was excellent (mean 84%, range 64–100%).

Conclusions:  The 12 recommendations developed from evidence and expert opinion provide guidance for the daily management of AS patients. For most recommendations, we found a paucity of supportive evidence in the literature highlighting the need for additional clinical studies.
Improvement of juvenile dermatomyositis with calcinosis universalis after treatment with intravenous immunoglobulin
Authors: YANG Ming‐Chun , LEE Jyh‐Hong , YANG Yao‐Hsu , CHIANG Bor‐Luen
Published: April 2008

Juvenile dermatomyositis is a chronic multisystemic disease. It is believed to be of autoimmune aetiology and is characterized by the presence of vasculitis affecting striated muscle and skin. Calcinosis occurs in about 40% of cases. We report a case of a 10‐year‐old girl diagnosed with juvenile dermatomyositis who presented with difficulty in walking and inability to completely extend the four extremities due to calcinosis universalis. Calcinosis had progressed despite a 3‐year administration of diltiazem, hydroxychloroquine, aluminium hydroxide, cyclosporin, and probenecid. The introduction of monthly intravenous immunoglobulin therapy for 15 months lessened disease activity, and markedly regressed calcinosis, and improved functional outcome.
Differential Antibiotic Susceptibility of
Mycobacterium abscessus
Variants in Biofilms and Macrophages Compared to That of Planktonic Bacteria
Authors: Greendyke Rebecca , Byrd Thomas F.
Published: April 2008

Mycobacterium abscessus
causes refractory pulmonary infections requiring surgery for cure. It exists as a smooth biofilm-forming phenotype which is noninvasive and a rough, non-biofilm-forming phenotype which can invade macrophages and cause persistent pulmonary infection in mice. We have postulated that the dissociation of the smooth phenotype to the rough phenotype may lead to invasive lung disease following initial colonization of the airways. Amikacin, cefoxitin, and clarithromycin are standard therapies for this infection. We determined the MICs of these antibiotics against this pathogen in biofilms and macrophages, the niches that it likely occupies in the human host. Our results demonstrate that even though the MICs indicate sensitivity to these antibiotics, the minimal bactericidal concentrations for amikacin and clarithromycin were substantially higher and were out of the range of the concentrations achievable in serum. Cefoxitin demonstrated only bacteriostatic activity. In addition, although amikacin had modest activity against
M. abscessus
in biofilms, clarithromycin demonstrated only minimal activity at the highest concentrations tested. Our results indicate that
M. abscessus
in mature biofilms is in a stationary-phase state and that clarithromycin is relatively inactive against stationary-phase
M. abscessus
. In human macrophages, all three antibiotics were only bacteriostatic for
M. abscessus
variants at 10 times their MICs. These results suggest why treatment failure with antibiotics alone is common in the clinical setting of
M. abscessus
pulmonary infection. Determination of the efficacies of new antibiotics should include an assessment of their activities against the smooth and rough
M. abscessus
morphotypes in biofilms and macrophages.
Potent Synergistic Anti-Human Immunodeficiency Virus (HIV) Effects Using Combinations of the CCR5 Inhibitor Aplaviroc with Other Anti-HIV Drugs
Authors: Nakata Hirotomo , Steinberg Seth M. , Koh Yasuhiro , Maeda Kenji , Takaoka Yoshikazu , Tamamura Hirokazu , Fujii Nobutaka , Mitsuya Hiroaki
Published: April 2008

Aplaviroc (AVC), an experimental CCR5 inhibitor, potently blocks in vitro the infection of R5-tropic human immunodeficiency virus type 1 (R5-HIV-1) at subnanomolar 50% inhibitory concentrations. Although maraviroc is presently clinically available, further studies are required to determine the role of CCR5 inhibitors in combinations with other drugs. Here we determined anti-HIV-1 activity using combinations of AVC with various anti-HIV-1 agents, including four U.S. Food and Drug Administration-approved drugs, two CCR5 inhibitors (TAK779 and SCH-C) and two CXCR4 inhibitors (AMD3100 and TE14011). Combination effects were defined as synergistic or antagonistic when the activity of drug A combined with B was statistically greater or less, respectively, than the additive effects of drugs A and A combined and drugs B and B combined by using the Combo method, described in this paper, which provides (i) a flexible choice of interaction models and (ii) the use of nonparametric statistical methods. Synergistic effects against R5-HIV-1
Ba-L
and a 50:50 mixture of R5-HIV-1
Ba-L
and X4-HIV-1
ERS104pre
(HIV-1
Ba-L/104pre
) were seen when AVC was combined with zidovudine, nevirapine, indinavir, or enfuvirtide. Mild synergism and additivity were observed when AVC was combined with TAK779 and SCH-C, respectively. We also observed more potent synergism against HIV-1
Ba-L/104pre
when AVC was combined with AMD3100 or TE14011. The data demonstrate a tendency toward greater synergism with AVC plus either of the two CXCR4 inhibitors compared to the synergism obtained with combinations of AVC and other drugs, suggesting that the development of effective CXCR4 inhibitors may be important for increasing the efficacies of CCR5 inhibitors.
The Thymidine-Dependent Small-Colony-Variant Phenotype Is Associated with Hypermutability and Antibiotic Resistance in Clinical
Staphylococcus aureus
Isolates
Authors: Besier Silke , Zander Johannes , Kahl Barbara C. , Kraiczy Peter , Brade Volker , Wichelhaus Thomas A.
Published: April 2008

Thymidine-dependent small-colony variants (TD-SCVs) of
Staphylococcus aureus
can be isolated from the airway secretions of patients suffering from cystic fibrosis (CF) and are implicated in persistent and treatment-resistant infections. These characteristics, as well as the variety of mutations in the thymidylate synthase-encoding
thyA
gene which are responsible for thymidine dependency, suggest that these morphological variants are hypermutable. To prove this hypothesis, we analyzed the mutator phenotype of different
S. aureus
phenotypes, in particular CF-derived TD-SCVs, CF-derived isolates with a normal phenotype (NCVs), and non-CF NCVs. The comparative analysis revealed that the CF isolates had significantly higher mutation rates than the non-CF isolates. The TD-SCVs, in turn, harbored significantly more strong hypermutators (mutation rate ≥ 10
−7
) than the CF and non-CF NCVs. In addition, antimicrobial resistance to non-beta-lactam antibiotics, including gentamicin, ciprofloxacin, erythromycin, fosfomycin, and rifampin, was significantly more prevalent in TD-SCVs than in CF and non-CF NCVs. Interestingly, macrolide resistance, which is usually mediated by mobile genetic elements, was conferred in half of the macrolide-resistant TD-SCVs by the point mutation A2058G or A2058T in the genes encoding the 23S rRNA. Sequence analysis of
mutS
and
mutL
, which are involved in DNA mismatch repair in gram-positive bacteria, revealed that in hypermutable CF isolates and especially in TD-SCVs,
mutL
was often truncated due to frameshift mutations. In conclusion, these data provide direct evidence that TD-SCVs are hypermutators. This hypermutability apparently favors the acquisition of antibiotic resistance and facilitates bacterial adaptation during long-term persistence.
Transfer of
embB
Codon 306 Mutations into Clinical
Mycobacterium tuberculosis
Strains Alters Susceptibility to Ethambutol, Isoniazid, and Rifampin
Authors: Safi Hassan , Sayers Brendan , Hazbón Manzour H. , Alland David
Published: April 2008

Implicated as a major mechanism of ethambutol (EMB) resistance in clinical studies of
Mycobacterium tuberculosis
, mutations in codon 306 of the
embB
gene (
embB
306) have also been detected in EMB-susceptible clinical isolates. Other studies have found strong associations between
embB
306 mutations and multidrug resistance, but not EMB resistance. We performed allelic exchange studies in EMB-susceptible and EMB-resistant clinical
M. tuberculosis
isolates to identify the role of
embB
306 mutations in any type of drug resistance. Replacing wild-type
embB
306 ATG from EMB-susceptible clinical
M. tuberculosis
strain 210 with
embB
306 ATA, ATC, CTG, or GTG increased the EMB MIC from 2 μg/ml to 7, 7, 8.5, and 14 μg/ml, respectively. Replacing
embB
306 ATC or GTG from two high-level EMB-resistant clinical strains with wild-type ATG lowered EMB MICs from 20 μg/ml or 28 μg/ml, respectively, to 3 μg/ml. All parental and isogenic mutant strains had identical isoniazid (INH) and rifampin (RIF) MICs. However,
embB
306 CTG mutants had growth advantages compared to strain 210 at sub-MICs of INH or RIF in monocultures and at sub-MICs of INH in competition assays. CTG mutants were also more resistant to the additive or synergistic activities of INH, RIF, or EMB used in different combinations. These results demonstrate that
embB
306 mutations cause an increase in the EMB MIC, a variable degree of EMB resistance, and are necessary but not sufficient for high-level EMB resistance. The unusual growth property of
embB
306 mutants in other antibiotics suggests that they may be amplified during treatment in humans and that a single mutation may affect antibiotic susceptibility against multiple first-line antibiotics.
Comparison of the Essential Cellular Functions of the Two
murA
Genes of
Bacillus anthracis
Authors: Kedar G. C. , Brown-Driver Vickie , Reyes Daniel R. , Hilgers Mark T. , Stidham Mark A. , Shaw Karen Joy , Finn John , Haselbeck Robert J.
Published: April 2008

Targeted antisense and gene replacement mutagenesis experiments demonstrate that only the
murA1
gene and not the
murA2
gene is required for the normal cellular growth of
Bacillus anthracis
. Antisense-based modulation of
murA1
gene expression hypersensitizes cells to the MurA-specific antibiotic fosfomycin despite the normally high resistance of
B. anthracis
to this drug.
Role of Recombination in the Evolution of the Model Plant Pathogen
Pseudomonas syringae
pv. tomato DC3000, a Very Atypical Tomato Strain
Authors: Yan Shuangchun , Liu Haijie , Mohr Toni J. , Jenrette Jenny , Chiodini Rossella , Zaccardelli Massimo , Setubal João C. , Vinatzer Boris A.
Published: April 2008

Pseudomonas syringae
pv. tomato strain DC3000 (PtoDC3000) is one of the most intensively studied bacterial plant pathogens today. Here we report a thorough investigation into PtoDC3000 and close relatives isolated from
Antirrhinum majus
(snapdragon),
Apium graveolens
(celery), and
Solanaceae
and
Brassicaceae
species. Multilocus sequence typing (MLST) was used to resolve the precise phylogenetic relationship between isolates and to determine the importance of recombination in their evolution. MLST data were correlated with an analysis of the locus coding for the type III secreted (T3S) effector AvrPto1 to investigate the role of recombination in the evolution of effector repertoires. Host range tests were performed to determine if closely related isolates from different plants have different host ranges. It was found that PtoDC3000 is located in the same phylogenetic cluster as isolates from several
Brassicaceae
and
Solanaceae
species and that these isolates have a relatively wide host range that includes tomato,
Arabidopsis thaliana
, and cauliflower. All other analyzed tomato isolates from three different continents form a distinct cluster and are pathogenic only on tomato. Therefore, PtoDC3000 is a very unusual tomato isolate. Several recombination breakpoints were detected within sequenced gene fragments, and population genetic tests indicate that recombination contributed more than mutation to the variation between isolates. Moreover, recombination may play an important role in the reassortment of T3S effectors between strains. The data are finally discussed from a taxonomic standpoint, and
P. syringae
pv. tomato is proposed to be divided into two pathovars.
Anaerobic Consumers of Monosaccharides in a Moderately Acidic Fen
Authors: Hamberger Alexandra , Horn Marcus A. , Dumont Marc G. , Murrell J. Colin , Drake Harold L.
Published: April 2008

16S rRNA-based stable isotope probing identified active xylose- and glucose-fermentingBacteriaand activeArchaea, including methanogens, in anoxic slurries of material obtained from a moderately acidic, CH4-emitting fen. Xylose and glucose were converted to fatty acids, CO2, H2, and CH4under moderately acidic, anoxic conditions, indicating that the fen harbors moderately acid-tolerant xylose- and glucose-using fermenters, as well as moderately acid-tolerant methanogens. Organisms of the familiesAcidaminococcaceae,Aeromonadaceae,Clostridiaceae,Enterobacteriaceae, andPseudomonadaceaeand the orderActinomycetales, including hitherto unknown organisms, utilized xylose- or glucose-derived carbon, suggesting that highly diverse facultative aerobes and obligate anaerobes contribute to the flow of carbon in the fen under anoxic conditions. UnculturedEuryarchaeota(i.e.,MethanosarcinaceaeandMethanobacteriaceae) andCrenarchaeotaspecies were identified by 16S rRNA analysis of anoxic slurries, demonstrating that the acidic fen harbors novel methanogens andCrenarchaeotaorganisms capable of anaerobiosis. Fermentation-derived molecules are conceived to be the primary drivers of methanogenesis when electron acceptors other than CO2are absent, and the collective findings of this study indicate that fen soils harbor diverse, acid-tolerant, and novel xylose-utilizing as well as glucose-utilizing facultative aerobes and obligate anaerobes that form trophic links to novel moderately acid-tolerant methanogens.
Conversion Shift of
d
-Fructose to
d
-Psicose for Enzyme-Catalyzed Epimerization by Addition of Borate
Authors: Kim Nam-Hee , Kim Hye-Jung , Kang Dong-Il , Jeong Ki-Woong , Lee Jung-Kul , Kim Yangmee , Oh Deok-Kun
Published: April 2008

The conversion yield of
d
-psicose from
d
-fructose by a
d
-psicose 3-epimerase from
Agrobacterium tumefaciens
increased with increasing molar ratios of borate to fructose, up to a ratio of 0.6. The formation of the psicose-borate complex was the result of the higher binding affinity of borate for psicose than for fructose. The formed psicose-borate complex did not participate in the conversion reaction, acting instead as if the product had been removed. Thus, more fructose was converted to psicose in order to restore the equilibrium. The maximum conversion yield of psicose with borate was about twofold that obtained without borate and occurred at a 0.6 molar ratio of borate to fructose. Above this ratio, the conversion yield decreased with increasing ratios, because the amount of fructose available decreased through the formation of the initial fructose-borate complex. The structures of the two sugar-borate complexes, determined by nuclear magnetic resonance spectroscopy, were α-
d
-psicofuranose
cis
-
C
-3,4 diol borate and β-
d
-fructopyranose
cis
-
C
-4,5 diol borate.
Rapid Species Identification of Cooked Poisonous Mushrooms by Using Real-Time PCR
Authors: Maeta Kazuhiko , Ochi Tomoya , Tokimoto Keisuke , Shimomura Norihiro , Maekawa Nitaro , Kawaguchi Nobuhisa , Nakaya Makoto , Kitamoto Yutaka , Aimi Tadanori
Published: April 2008

Species-specific identification of the major cooked and fresh poisonous mushrooms in Japan was performed using a real-time PCR system. Specific fluorescence signals were detected, and no nonspecific signals were detected. Therefore, we succeeded in developing a species-specific test for the identification of poisonous mushrooms within 1.5 h.
Heterogeneous Selection in a Spatially Structured Environment Affects Fitness Tradeoffs of Plasmid Carriage in Pseudomonads
Authors: Slater Frances R. , Bruce Kenneth D. , Ellis Richard J. , Lilley Andrew K. , Turner Sarah L.
Published: April 2008

Environmental conditions under which fitness tradeoffs of plasmid carriage are balanced to facilitate plasmid persistence remain elusive. Periodic selection for plasmid-encoded traits due to the spatial and temporal variation typical in most natural environments (such as soil particles, plant leaf and root surfaces, gut linings, and the skin) may play a role. However, quantification of selection pressures and their effects is difficult at a scale relevant to the bacterium in situ. The present work describes a novel experimental system for such fine-scale quantification, with conditions designed to mimic the mosaic of spatially variable selection pressures present in natural surface environments. The effects of uniform and spatially heterogeneous mercuric chloride (HgCl
2
) on the dynamics of a model community of plasmid-carrying, mercury-resistant (Hg
r
) and plasmid-free, mercury-sensitive (Hg
s
) pseudomonads were compared. Hg resulted in an increase in the surface area occupied by, and therefore an increase in the fitness of, Hg
r
bacteria relative to Hg
s
bacteria. Uniform and heterogeneous Hg distributions were demonstrated to result in different community structures by epifluorescence microscopy, with heterogeneous Hg producing spatially variable selection landscapes. The effects of heterogeneous Hg were only apparent at scales of a few hundred micrometers, emphasizing the importance of using appropriate analysis methods to detect effects of environmental heterogeneity on community dynamics. Heterogeneous Hg resulted in negative frequency-dependent selection for Hg
r
cells, suggesting that sporadic selection may facilitate the discontinuous distribution of plasmids through host populations in complex, structured environments.
Assessing Genetic Heterogeneity within Bacterial Species Isolated from Gastrointestinal and Environmental Samples: How Many Isolates Does It Take?
Authors: Döpfer D. , Buist W. , Soyer Y. , Munoz M. A. , Zadoks R. N. , Geue L. , Engel B.
Published: April 2008

Strain typing of bacterial isolates is increasingly used to identify sources of infection or product contamination and to elucidate routes of transmission of pathogens or spoilage organisms. Usually, the number of bacterial isolates belonging to the same species that is analyzed per sample is determined by convention, convenience, laboratory capacity, or financial resources. Statistical considerations and knowledge of the heterogeneity of bacterial populations in various sources can be used to determine the number of isolates per sample that is actually needed to address specific research questions. We present data for intestinal
Escherichia coli
,
Listeria monocytogenes
,
Klebsiella pneumoniae
, and
Streptococcus uberis
from gastrointestinal, fecal, or soil samples characterized by ribotyping, pulsed-field gel electrophoresis, and PCR-based strain-typing methods. In contrast to previous studies, all calculations were performed with a single computer program, employing software that is freely available and with in-depth explanation of the choice and derivation of prior distributions. Also, some of the model assumptions were relaxed to allow analysis of the special case of two (groups of) strains that are observed with different probabilities. Sample size calculations, with a Bayesian method of inference, show that from 2 to 20 isolates per sample need to be characterized to detect all strains that are present in a sample with 95% certainty. Such high numbers of isolates per sample are rarely typed in real life due to financial or logistic constraints. This implies that investigators are not gaining maximal information on strain heterogeneity and that sources and transmission pathways may go undetected.
Engineering and Analysis of a
Saccharomyces cerevisiae
Strain That Uses Formaldehyde as an Auxiliary Substrate
Authors: Baerends Richard J. S. , de Hulster Erik , Geertman Jan-Maarten A. , Daran Jean-Marc , van Maris Antonius J. A. , Veenhuis Marten , van der Klei Ida J. , Pronk Jack T.
Published: April 2008

We demonstrated that formaldehyde can be efficiently coutilized by an engineered
Saccharomyces cerevisiae
strain that expresses
Hansenula polymorpha
genes encoding formaldehyde dehydrogenase (
FLD1
) and formate dehydrogenase (
FMD
), in contrast to wild-type strains. Initial chemostat experiments showed that the engineered strain coutilized formaldehyde with glucose, but these mixed-substrate cultures failed to reach steady-state conditions and did not exhibit an increased biomass yield on glucose. Subsequent transcriptome analyses of chemostat cultures of the engineered strain, grown on glucose-formaldehyde mixtures, indicated that the presence of formaldehyde in the feed caused biotin limitations. Further transcriptome analysis demonstrated that this biotin inactivation was prevented by using separate formaldehyde and vitamin feeds. Using this approach, steady-state glucose-limited chemostat cultures were obtained that coutilized glucose and formaldehyde. Coutilization of formaldehyde under these conditions resulted in an enhanced biomass yield of the glucose-limited cultures. The biomass yield was quantitatively consistent with the use of formaldehyde as an auxiliary substrate that generates NADH and subsequently, via oxidative phosphorylation, ATP. On an electron pair basis, the biomass yield increase observed with formaldehyde was larger than that observed previously for formate, which is tentatively explained by different modes of formate and formaldehyde transport in
S. cerevisiae
.
Analysis of theActinobacillus pleuropneumoniaeArcA Regulon Identifies Fumarate Reductase as a Determinant of Virulence
Authors: Buettner Falk F. R. , Bendallah Ibrahim M. , Bosse Janine T. , Dreckmann Karla , Nash John H. E. , Langford Paul R. , Gerlach Gerald-F.
Published: April 2008

The ability of the bacterial pathogenActinobacilluspleuropneumoniaeto grow anaerobically allows the bacterium to persist in the lung. The ArcAB two-component system is crucial for metabolic adaptation in response to anaerobic conditions, and we recently showed that anA. pleuropneumoniae arcAmutant had reduced virulence compared to the wild type (F. F. Buettner, A. Maas, and G.-F. Gerlach, Vet. Microbiol. 127:106-115, 2008). In order to understand the attenuated phenotype, we investigated the ArcA regulon ofA. pleuropneumoniaeby using a combination of transcriptome (microarray) and proteome (two-dimensional difference gel electrophoresis and subsequent mass spectrometry) analyses. We show that ArcA negatively regulates the expression of many genes, including those encoding enzymes which consume intermediates during fumarate synthesis. Simultaneously, the expression of glycerol-3-phosphate dehydrogenase, a component of the respiratory chain serving as a direct reduction equivalent for fumarate reductase, was upregulated. This result, together with the in silico analysis finding thatA. pleuropneumoniaehas no oxidative branch of the citric acid cycle, led to the hypothesis that fumarate reductase might be crucial for virulence by providing (i) energy via fumarate respiration and (ii) succinate and other essential metabolic intermediates via the reductive branch of the citric acid cycle. To test this hypothesis, an isogenicA. pleuropneumoniaefumarate reductase deletion mutant was constructed and studied by using a pig aerosol infection model. The mutant was shown to be significantly attenuated, thereby strongly supporting a crucial role for fumarate reductase in the pathogenesis ofA. pleuropneumoniaeinfection.
Modeling Approaches to Hydration Properties of Aqueous Nonelectrolytes at Elevated Temperatures and Pressures
Authors: Sedlbauer Josef
Published: April 2008

Thermodynamic models describing temperature and pressure evolution of Henry's law constant and related properties of hydration of aqueous nonelectrolyte solutes are reviewed. The included models cover a broad range spanning from simple van't Hoff-like equations used in environmental chemistry over the more elaborate empirical or semiempirical temperature correlations favored for engineering purposes to complete equations-of-state for hydration properties originating in the theory of near-critical phenomena and developed for modeling of hydrothermal systems. For aqueous organic solutes, the methods are often coupled with the group additivity approximation, leading to complex tools for predicting the properties of solutions containing organic species. The various models were subjected to tests documenting their expected range of applicability at elevated pressures (for acid gases) or at high temperatures (for hydrocarbons and oxygen-containing organic solutes). New developments in the field are discussed and some future needs are envisioned.
THE DETERIORATION BY FUNGI OF JACK, RED, AND WHITE PINE KILLED BY FIRE IN ONTARIO
Authors: Basham J. T.
Published: April 2008

The nature, causes, and rate of pathological deterioration of jack, red, and white pine killed by fire in the Mississagi region of Ontario in 1948 were studied to determine the practicability and probable duration of profitable salvage operations in such stands. Blue and brown sapwood stains appeared in all species 1 year after the fire, and became extensive during the succeeding 3 years. Sap rot was first noted 2 years after the fire; 5 years after the fire most of the sapwood was affected, and in some cases this rot extended into the heartwood. Three fungi, Peniophora gigantea (Fries) Massee, Polyporus anceps Peck, and Polyporus abietinus Dicks. ex Fries, were isolated consistently from white sap rots, while Fomes pinicola (Sw.) Cooke and Fomes subroseus (Weir) Overh. were recovered from many of the brown sap rots. The increase in the volume of heart rot encountered during the course of the study, chiefly associated with Fomes pini (Thore) Lloyd, was much greater than that observed in living pine over a similar period, and for this reason the excess was considered as a form of deterioration. The average rate of radial penetration of visible deterioration was significantly faster in trees with widely spaced annual rings in the outer portion of the bole than in slow-growing trees. Variations in the severity of burn in individual trees or stands apparently had little effect on the rate of pathological deterioration.
CYTOGENETIC STUDY ON A TETRAPLOID PLANT AT THE DIPLOID CHROMOSOME LEVEL
Authors: Lesins Karlis
Published: April 2008

It was ascertained that the species from which Grimm alfalfa presumably originated, viz.; Medicago sativa and M. falcata, may freely exchange genetic material without evidence of a sterility barrier. Consequently a polyhaploid obtained of Grimm may be considered as comparable to natural diploids.The polyhaploid showed some impaired morphological and physiological characters and pronounced meiotic abnormalities. The single genome (x = 8) of the polyhaploid was found to be almost non-functional. Inheritance of purple color indicated a potential autotetraploid mode of transmission of characters.The polyhaploid was raised back to the tetraploid chromosome level by chromosome doubling and compared to its original and to Grimm. The somatically chromosome-doubled counterpart was found to be a close replica of the original polyhaploid. An assumption that an accumulation of detrimental recessive genes may remain latent at the tetraploid level, and may be expressed upon later reduction to half of the genic variability as in the polyhaploid and its somatically chromosome-doubled derivative, is advanced to explain the observed phenomena.Phylogenetic, breeding, and culture-historical aspects of the results are discussed.
Prodromus for a revison of the Phacidiaceae and related anamorphs
Authors: Dicosmo Frank , Raj T. R. Nag , Kendrick Bryce
Published: April 2008

An emendation of the Phacidiaceae is presented. Of 24 genera placed in the family by previous authors, only 2, Lophophacidium and Phacidium (=Phacidiostroma) are retained. Four new species are described, and three new combinations made, in Phacidium. The Apostrasseria or Ceuthospora anamorphs of six of these are also described. Phacidium symplocinum is made the type species of a new genus, Ascluella, tentatively maintained in the Dermateaceae. The new combinations, Coccomyces gaultheriae, Odontotrema sieversiae, Pseudophacidium kumaonense, and Schizoxylon hemisphaericum, are introduced.
Studies on the inflorescence of wild oats (Avena fatua)
Authors: Raju M. V. S. , Ramaswamy S. N.
Published: April 2008

Some observations and experiments were carried out on inflorescences of wild oats, Avenafatua L. (Poaceae). Results of these studies indicate that the distal spikelets are initiated and mature earlier than those in the proximal positions. In each spikelet, the primary floret matures earlier than the secondary floret. However, the less mature secondary floret drops from the spikelet sooner. The awn in mature florets is geniculate and shows a characteristic twisting movement depending on the availability of moisture in the atmosphere. The movement of awns results in periodic dislodging of mature florets from spikelets. The basipetal maturity of spikelets in the panicle, the acropetal maturity of florets in each spikelet, and the premature separation of florets aided by the awn movement produce caryopses of variable maturity and are of considerable significance in the reproductive biology of wild oats.
Activités phosphatases et carence phosphatée chez des champignons supérieurs
Authors: Calleja Mireille , D'Auzac Jean
Published: April 2008

Six mycorrhizal and three saprophytic fungi were collected. They were cultivated in a liquid medium with or without a deficiency in phosphate. Different phosphatase activities were measured from the mycelia: phosphatase activities accessible to an external substrate, phosphatase activities in the culture medium, phosphatase activities of the whole homogenate and two parts of this homogenate (parietal and soluble). With both the mycorrhizal and saprophytic fungi, the deficiency in inorganic phosphate induced a large increase in phosphatase activities which were multiplied on the average by a factor of 72, 56, 43, 64, and 26, for the excreted, accessible, total, parietal, and soluble activities, respectively. If the relative proportions of the various activities were considered, the parietal activity, compared with the total phosphatase activity, increased in six out of nine cases under the effect of phosphate deficiency. The superiority of the parietal activity over the soluble activity was either induced by phosphate deficiency or preexisting. The accessible activity represented only a fraction of the parietal activity and this was usually smaller in a phosphate-deprived medium. Various criteria have been considered to class these fungi in terms of their response to phosphate deficiency, such as the intensity of their phosphatase response to the deficiency and the absolute values in a phosphate-deprived medium of various phosphatase activities. These various criteria do not lead to a classification entirely parallel of the different fungi and they do not discriminate between mycorrhizal and saprophytic fungi.