bluuebunny/crossref_metadata_2025 huggingface dataset:
The structure and potential loasaceous affinities of Schismocarpus
Authors: Hufford Larry D.
Published: April 2008

The affinity of Schismocarpus with Loasaceae has been questioned. Characteristic trichomic features are most often used for definition of Loasaceae, and Schismocarpus possesses a distinctly loasaceous syndrome of trichomes. Its inflorescence morphology is similar to that of Eucnide and Mentzelia, and it shares floral features with Eucnide. Although Schismocarpus possesses unique features (e.g., perennating “rootstock” and striate pollen) relative to Loasaceae, it is not aberrant considering the broad range of diversity that has been long accepted within the family. The apparently divergent floral morphology may be explained by its evolution of a “pollen flower” syndrome.
Autecology and distribution of Isoetes longissimum in Europe
Authors: Romero M. I. , Amigo J.
Published: April 2008

Isoetes longissimum is a rare aquatic pteridophyte known only from the northwest Spanish region of Galicia and from Algeria. We mapped the distribution of this species in Galicia, and investigated the relationship between its presence or absence and water quality variables. I. longissimum is present in sixteen 10 times 10 km grid squares in Galicia, largely in the western central part of the region. Within Galicia, I. longissimum shows a significant preference for sites with low sulphate, ammonium and phosphate concentrations.
Morphology, anatomy and reproduction of the eastern Mediterranean coralline Tenarea tortuosa and its relationship to members of the Lithophylloideae and Mastophoroideae (Rhodophyta, Corallinales)
Authors: Athanasiadis A.
Published: April 2008

One of the most characteristic organisms of the Mediterranean flora, the endemic coralline Tenarea tortuosa, has been collected along the Cretan coast and its vegetative and reproductive structures are reassessed. Gametophytes are described for the first time and are rare, observed only in one locality on the south coast. Reproductive structures suggest that the sexual life history is triphasic, but the present collections indicate unequal representation of males, carposporophytes and tetrasporophytes, and a dominance of bisporophytes suggesting that the alga is reproducing mainly asexually. The frond of Tenarea is formed by the coordinated growth of two elements (branches), growing back‐to‐back, each showing a simple Titanodema‐type of organization; i.e. a monostromatic hypothallium of sinuous cells and a single layer of obliquely borne epithallial cells. Contiguous cells of the two opposite branches are not connected by secondary pit‐plugs, and easily glide apart if decalcified. Natural splitting of the lamellae into its two branches may also occur, and single branches may fold regenerating the back‐to‐back organization. Analogous back‐to‐back growths occur in species of the distantly related genera Goniolithon (Lithophylloideae) and Leptophytum (Melobe‐sioideae) and apparently represent cases of convergence. The affinities of Tenarea to related genera are discussed.
WHO‐ILAR‐COPCORD in the Asia‐Pacific: the past, present and future
Authors: HAQ Syed Atiqul , RASKER Johannes J. , DARMAWAN John , CHOPRA Arvind
Published: April 2008

The aim of the Community Oriented Program for Control of Rheumatic Disorders (COPCORD) is reduction of community burden of rheumatic disorders, particularly in developing communities. Stage I entails estimation of prevalence and incidence of musculoskeletal pain and rheumatic disorders. Stage II is dedicated to education of health workers, patients and the community. Stage III deals with identification of risk factors for common rheumatic disorders and development of strategies for their primary and secondary prevention. So far Stage I data have been reported from 15 countries in the Asia‐Pacific countries. The prevalence of musculoskeletal pain has varied from 11.6% to 45.4%. The commonest sites of pain were low back, knee, neck and shoulder. Commonest rheumatic disorders were osteoarthritis of knees, non‐specific low back pain and soft tissue rheumatism. A few scattered educational activities have been reported from Indonesia and India. Systematic case‐controlled or cohort studies aimed at finding out the risk factors for common rheumatic disorders were scanty. However, several associations were reported from cross‐sectional prevalence surveys. It is imperative that the COPCORD investigators in the Asia‐Pacific region focus on finding out the modifiable risk factors for rheumatic disorders with properly designed studies, develop preventive strategies on the basis of identified risk factors and carry out interventional studies to test the efficacy of the strategies with validated outcome instruments.
Access to biologic medicines for the treatment of rheumatic diseases: lessons from Australia
Authors: LU Christine Y. , WILLIAMS Ken , DAY Ric
Published: April 2008

In order to ensure that our patients have access to effective new rheumatic medicines, it is crucial that the issues affecting access are identified and addressed adequately. Patients in Australia are privileged to have subsidized access to new biologic medicines via the national formulary, known as the Pharmaceutical Benefits Scheme. Access to these expensive medicines was an important achievement by various stakeholders in overcoming several major issues. In this paper, we discuss these challenges associated with publicly funded access to biologicals for rheumatic diseases and the strategies that have been taken to overcome them.
Association of IL‐1 beta gene polymorphism with susceptibility to systemic lupus erythematosus
Authors: AFSHARI Jalil Tavakkol , REZAIEYAZDI Zahra , MAZHANI Maryam
Published: April 2008

Background:  The IL‐1β exon5 (+3954) has been related to the pathogenesis of lupus, but the role of IL‐1 polymorphisms in the aetiology of systemic lupus erythematosus (SLE) is unknown.

Method:  We compare the IL‐1 beta +3954 (exon5) gene polymorphism among 52 SLE patients and healthy controls in north‐eastern Iran. Polymorphism of the gene for IL‐1 beta +3954 was typed after the genomic DNA was amplified by polymerase chain reaction‐sequence‐specific‐primers technique.

Results:  Comparing the results show no significant differences in the frequency of IL‐1 beta exon5 allels between patients with SLE and controls. Additionally, we did not detect any association of IL‐1 beta exon5 (+3954) genotype with clinical and laboratory profiles in SLE patients.

Conclusion:  The polymorphism of the IL‐1 beta exon5 allele is not associated with genetic susceptibility to SLE in north‐eastern of Iran.
Significance of anti‐α‐fodrin autoantibody in diagnosis of Sjogren's syndrome
Authors: FEI Yun Yun , ZHAO Yan , DONG Yi , TANG Fu Lin , ZHANG Feng Chun
Published: April 2008

Objective:  Anti‐α‐fodrin autoantibody has been reported to be a highly specific and sensitive test for the diagnosis of Sjogren's syndrome (SS). The objective of our report is to investigate the sensitivity and specificity of anti‐α‐fodrin antibody in patients with SS and its correlation with clinical manifestations.

Methods:  Recombinant human α‐fodrin was used as envelope antigen in enzyme‐linked immunosorbent assay (ELISA) to detect the relatively specific autoantibody in sera of 42 primary SS, 24 secondary SS with systemic lupus erythematosus (SLE) or rheumatoid arthritis (RA), and 40 other connective tissue diseases (CTDs) (SLE 17, RA 8, ankylosing spondylitis 5, dermatomyositis 5, systemic schlerosis 3, mixed connective tissue disease 1, Takayasu's disease 1) patients.

Results:  Antibodies against α‐fodrin were present in 59.5% of primary SS patients, 31.5% of secondary SS patients, 35.0% and 11.3% of other CTD patients and controls, respectively; the specificity of anti‐α‐fodrin antibody was 79.4% in patients with SS. It showed no significant difference between primary and secondary SS (P > 0.05), as well as SS compared with other CTD patients (P > 0.05). The positive rates of antibodies against α‐fodrin in CTD patients were significantly higher than those in non‐CTD patients and normal controls (P < 0.01). The presence of anti‐α‐fodrin antibodies has no significant correlation with clinical manifestations or other autoantibodies, while the levels of sera IgG and erythrocyte sedimentation rate (ESR) are higher in α‐fodrin antibody‐positive patients (IgG: 23.2 vs. 18.6, P < 0.05; ESR: 52.9 vs. 37.1, P < 0.05) than α‐fodrin antibody‐negative patients. Anti‐α‐fodrin antibodies are all negative in anti‐SS antigen A and antinuclear antibody‐negative SS patients.

Conclusion:  The result showed a lower sensitivity and specificity for anti‐α‐fodrin antibody as a diagnostic marker of SS, compared with previous reports. Anti‐α‐fodrin antibodies had no significant association with clinical manifestations, but might be related to the sera IgG level. Antibodies against α‐fodrin played no important roles in diagnosis of antibody‐negative SS patients.
Proprioception, dynamic balance and maximal quadriceps strength in females with knee osteoarthritis and normal control subjects
Authors: MOHAMMADI Farshid , TAGHIZADEH Shohreh , GHAFFARINEJAD Farahnaz , KHORRAMI Mojdeh , SOBHANI Sobhan
Published: April 2008

Background: Osteoarthritis (OA) is one of the most common musculoskeletal complaints worldwide. The knee is the most frequently involved joint of the lower limb in OA. Knee joint proprioception, dynamic balance and maximal quadriceps strength may be impaired in patients with knee OA.

Objective: To investigate whether females with knee OA have reduced knee joint proprioception, balance responses and quadriceps strength compared with normal controls.

Methods: We undertook a cross‐sectional study of 30 females with knee OA and 30 controls. Knee joint proprioception was measured using electrogoniometer. Dynamic balance response was determined using a step test. Quadriceps strength was measured isometrically using a modified Tornvall chair.

Results: Subjects with OA had greater mean error, poorer dynamic balance and less quadriceps strength than non‐symptomatic ones (P < 0.001). Increasing age was associated with a decline in proprioceptive acuity for both controls and patients (r = 0.40,P < 0.001). In subjects with knee OA, decreased dynamic balance was associated with increasing weight (r = 0.30,P < 0.001) and reduced quadriceps strength (r = –0.37,P = 0.002).

Conclusion: Compared with age and sex‐matched controls, females with symptomatic knee OA have reduced knee proprioception, balance responses and quadriceps strength.
Clinical presentation of juvenile idiopathic arthritis in Bangladesh: experience from a tertiary hospital
Authors: RAHMAN Shahana A. , ISLAM Mohammad Imnul , HOSSAIN Mahmuda , TALUKDER Manik Kumar
Published: April 2008

Objective:  To present our experience of juvenile idiopathic arthritis (JIA) patients in terms of clinical presentation and to observe if there is any difference in clinical presentation of our children from that in the Western world.

Methodology:  A cross‐sectional observational study was carried out in the paediatric rheumatology follow‐up clinic run by the Department of Child Health, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh, during the study period of January 2004 to April 2007. A total of 132 patients fulfilling International League against Rheumatism classification criteria were enrolled in the study. Data were collected in a questionnaire containing clinical history, physical findings, relevant investigations and ophthalmologic findings.

Results:  Among the 132 cases 89 were male and 43 were female, M:F ratio being approximately 2:1. Age range of the patients was 1.5 years to 15 years. Maximum number of patients presented in the age group from 7–8 years (12.10%) followed by 10–11 years (11.36%). Duration of illness was more than 12 months in the majority. Polyarticular rheumatoid factor‐negative patients were most frequent (41.70%), followed by persistent oligoarthritis (23.50%). The majority of the patients (51.52%) were diagnosed with rheumatic fever before they reported to us.

Conclusion:  Late diagnosis with long duration of disease and deformities were common. Wrong diagnosis and wrong treatment was also very common. Clinical presentation of our cases differed from Western JIA cases mainly is terms of sex distribution, subtypes and late presentation.
Stopping the rot: the stories behind methotrexate, sulphasalazine and hydroxychloroquine
Authors: MICALLEF Maree , LIM Keith , TRAVERS Richard
Published: April 2008

Untreated rheumatoid arthritis (RA) has devastating effects on joint structure, function and quality of life. Treatment has improved over the last few decades as the emphasis has switched from empiric symptomatic treatment with non‐steroidal anti‐inflammatory drugs to early introduction of disease‐modifying anti‐rheumatic drugs (DMARDs), and in severe disease, biological DMARDs. We review the history of methotrexate, sulphasalazine and hydroxychloroquine and reflect on how individual studies, world events and the discovery of cortisone may have ‘robbed’ a generation of RA patients of the treatments still used today – in particular methotrexate and sulphasalazine.
Diffuse idiopathic skeletal hyperostosis (DISH): an often missed diagnosis
Authors: GARG Shriram , KAPOOR Sanjiv , MALAVIYA Anand Narayan
Published: April 2008

Diffuse idiopathic skeletal hyperostosis (DISH) is a well known and well researched condition. Yet it is not unusual to come across patients with this disease where the diagnosis was missed. Recently we saw a patient with this disease who was misdiagnosed and treated as gout with no improvement in symptoms. This case report highlights salient features of DISH, its diagnosis and the basic principles of management. Readers are reminded to consider this diagnosis in the appropriate clinical setting.
Systemic lupus erythematosus with sickle cell/β0‐thalassemia
Authors: PINTO Lancelot Mark , SAMANT Rohini
Published: April 2008

The coexistence of haemoglobinopathies with systemic lupus erythematosus (SLE) is an occurrence that has been reported infrequently. The symptomatic overlap between the two diseases can make the diagnosis of an SLE flare versus a sickle crisis challenging. The limited reports available do not suggest an association, but the coexistence of the two diseases has been reported to manifest in a more virulent manner necessitating aggressive immunosuppression. The purpose of this report is to highlight the diagnostic challenges faced in a patient with the coexisting diseases, to report the severity and spectrum of the manifestations of SLE in the patient and our experience in treatment of her complications.
Laryngeal rhinosporidiosis in a Belgian warmblood horse
Authors: Nollet H. , Vercauteren G. , Martens A. , Vanschandevijl K. , Schauvliege S. , Gasthuys F. , Ducatelle R. , Deprez P.
Published: April 2008

In Belgium and even in northern Europe Rhinosporidium seeberi has not been reported in autochtonous people or animals. In this paper, the authors report the first observation of laryngeal masses, caused by Rhinosporidium seeberi, in a Belgian Warmblood horse. Moreover, laryngeal rhinosporidiosis is extremely rare since this localisation is only described in four human cases.
Antiparasitic Activities and Toxicities of Individual Enantiomers of the 8-Aminoquinoline 8-[(4-Amino-1-Methylbutyl)Amino]-6-Methoxy-4-Methyl-5-[3,4-Dichlorophenoxy]Quinoline Succinate
Authors: Nanayakkara N. P. Dhammika , Ager Arba L. , Bartlett Marilyn S. , Yardley Vanessa , Croft Simon L. , Khan Ikhlas A. , McChesney James D. , Walker Larry A.
Published: April 2008

8-Aminoquinolines are an important class of antiparasitic agents, with broad utility and excellent efficacy, but also limitations due to hematological toxicities, primarily methemoglobinemia and hemolysis. One representative from this class, (±)-8-[(4-amino-1-methylbutyl)amino]-6-methoxy-4-methyl-5-[3,4-dichlorophenoxy]quinoline succinate (NPC1161C), proved extremely efficacious in animal models of malaria and pneumocystis pneumonia. This racemic mixture was separated into its component enantiomers by chemical and chromatographic means. The enantiomers were evaluated for antiparasitic activity in murine models of
Plasmodium berghei
,
Pneumocystis carinii
, and
Leishmania donovani
infection, as well as the propensity to elicit hematotoxicity in dogs. The (−)-enantiomer NPC1161B was found to be more active (by severalfold, depending on the dosing regimen) than the (+)-enantiomer NPC1161A in all of these murine models. In addition, the (−) enantiomer showed markedly reduced general toxicity in mice and reduced hematotoxicity in the dog model of methemoglobinemia. It is concluded that the configuration at the asymmetric center in the 8-amino side chain differentially affects efficacy and toxicity profiles and thus may be an important determinant of the “therapeutic window” for compounds in this class.
Mutations in Human Immunodeficiency Virus Type 1 Integrase Confer Resistance to the Naphthyridine L-870,810 and Cross-Resistance to the Clinical Trial Drug GS-9137
Authors: Hombrouck Anneleen , Voet Arnout , Van Remoortel Barbara , Desadeleer Christel , De Maeyer Marc , Debyser Zeger , Witvrouw Myriam
Published: April 2008

To gain further insight into the understanding of the antiviral resistance patterns and mechanisms of the integrase strand transfer inhibitor L-870,810, the prototypical naphthyridine analogue, we passaged the human immunodeficiency virus type 1 strain HIV-1(IIIB) in cell culture in the presence of increasing concentrations of L-870,810 (IIIB/L-870,810). The mutations L74M, E92Q, and S230N were successively selected in the integrase. The L74M and E92Q mutations have both been associated in the past with resistance against the diketo acid (DKA) analogues L-708,906 and S-1360 and the clinical trial drugs MK-0518 and GS-9137. After 20, 40, and 60 passages in the presence of L-870,810, IIIB/L-870,810 displayed 22-, 34-, and 110-fold reduced susceptibility to L-870,810, respectively. Phenotypic cross-resistance against the DKA analogue CHI-1043 and MK-0518 was modest but that against GS-9137 was pronounced. Recombination of the mutant integrase genes into the wild-type background reproduced the resistance profile of the resistant IIIB/L-870,810 strains. In addition, resistance against L-870,810 was accompanied by reduced viral replication kinetics and reduced enzymatic activity of integrase. In conclusion, the accumulation of L74M, E92Q, and S230N mutations in the integrase causes resistance to the naphthyridine L-870,810 and cross-resistance to GS-9137. These data may have implications for cross-resistance of different integrase inhibitors in the clinic.
Radiofungicidal Effects of External Gamma Radiation and Antibody-Targeted Beta and Alpha Radiation on
Cryptococcus neoformans
Authors: Bryan Ruth A. , Huang Xianchun , Morgenstern Alfred , Bruchertseifer Frank , Casadevall Arturo , Dadachova Ekaterina
Published: April 2008

We evaluated the clonogenic survival, membrane permeability, metabolic activity (XTT reduction), and apoptosis (FLICA binding) of
Cryptococcus neoformans
cells subjected to gamma rays from an external source, and beta and alpha particles delivered to fungal cells by capsule-specific antibody. We found that gamma, beta, and alpha radiation affected cells through different pathways.
Mechanisms of Macrolide Resistance among
Streptococcus pneumoniae
Isolates from Russia
Authors: Reinert Ralf R. , Filimonova Olga Y. , Al-Lahham Adnan , Grudinina Svetlana A. , Ilina Elena N. , Weigel Linda M. , Sidorenko Sergey V.
Published: April 2008

Among 76 macrolide-nonsusceptible
Streptococcus pneumoniae
isolates collected between 2003 and 2005 from Central Russia, the resistance mechanisms detected in the isolates included
erm
(B) alone (50%),
mef
alone [
mef
(E),
mef
(I), or a different
mef
subclass; 19.7%], or both
erm
(B) and
mef
(E) (30.3%). Isolates with dual resistance genes [
erm
(B) and
mef
(E)] belonged to clonal complex CC81 or CC271.
Delayed Development of Linezolid Resistance in
Staphylococcus aureus
following Exposure to Low Levels of Antimicrobial Agents
Authors: Miller Keith , O'Neill Alexander J. , Wilcox Mark H. , Ingham Eileen , Chopra Ian
Published: April 2008

The development of resistance to linezolid (LZD) in gram-positive bacteria depends on the mutation of a single 23S rRNA gene, followed by homologous recombination and gene conversion of the other alleles. We sought to inhibit this process in
Staphylococcus aureus
using a range of antibacterial agents, including some that suppress recombination. A model for the rapid selection of LZD resistance was developed which allowed the selection of LZD-resistant mutants with G2576T mutations in all five copies of the 23S rRNA gene following only 5 days of subculture. The emergence of LZD-resistant isolates was delayed by exposing cultures to low concentrations of various classes of antibiotics. All antibiotic classes were effective in delaying the selection of LZD-resistant mutants and, with the exception of fusidic acid (FUS) and rifampin (RIF), prolonged the selection window from 5 to ∼15 days. Inhibitors of DNA processing were no more effective than any other class of antibiotics at suppressing resistance development. However, the unrelated antimicrobials FUS and RIF were particularly effective at preventing the emergence of LZD resistance, prolonging the selection window from 5 to 25 days. The enhanced suppressive effect of FUS and RIF on the development of LZD resistance was lost in a
recA
-deficient host, suggesting that these drugs affect
recA
-dependent recombination. Furthermore, FUS and RIF were shown to be effective inhibitors of homologous recombination of a plasmid into the staphylococcal chromosome. We suggest that RIF or FUS in combination with LZD may have a role in preventing the emergence of LZD resistance.
In Vitro Selection and Characterization of Ceftobiprole-Resistant Methicillin-Resistant
Staphylococcus aureus
Authors: Banerjee Ritu , Gretes Michael , Basuino Li , Strynadka Natalie , Chambers Henry F.
Published: April 2008

Methicillin-resistant
Staphylococcus aureus
(MRSA) is resistant to β-lactam antibiotics because it expresses penicillin-binding protein 2a (PBP2a), a low-affinity penicillin-binding protein. An investigational broad-spectrum cephalosporin, ceftobiprole (BPR), binds PBP2a with high affinity and is active against MRSA. We hypothesized that BPR resistance could be mediated by mutations in
mecA
, the gene encoding PBP2a. We selected BPR-resistant mutants by passage in high-volume broth cultures containing subinhibitory concentrations of BPR. We used strain COLnex (which lacks chromosomal
mecA
) transformed with pAW8 (a plasmid vector only), pYK20 (a plasmid carrying wild-type
mecA
), or pYK21 (a plasmid carrying a mutant
mecA
gene corresponding to five PBP2a mutations). All strains became resistant to BPR by day 9 of passaging, but MICs continued to increase until day 21. MICs increased 256-fold (from 1 to 256 μg/ml) for pAW8, 32-fold (from 4 to 128 μg/ml) for pYK20, and 8-fold (from 16 to 128 μg/ml) for pYK21. Strains carrying wild-type or mutant
mecA
developed six (pYK20 transformants) or four (pYK21 transformants) new mutations in
mecA
. The transformation of COLnex with a
mecA
mutant plasmid conferred BPR resistance, and the loss of
mecA
converted resistant strains into susceptible ones. Modeling studies predicted that several of the
mecA
mutations altered BPR binding; other mutations may have mediated resistance by influencing interactions with other proteins. Multiple
mecA
mutations were associated with BPR resistance in MRSA. BPR resistance also developed in the strain lacking
mecA
, suggesting a role for chromosomal genes.
Reduced
Candida glabrata
Susceptibility Secondary to an
FKS1
Mutation Developed during Candidemia Treatment
Authors: Cleary John D. , Garcia-Effron Guillermo , Chapman Stanley W. , Perlin David S.
Published: April 2008

We describe a case of recurring
Candida glabrata
infection in a 68-year-old African-American female on caspofungin therapy. The initial isolate was susceptible, but isolates recovered during following relapses were not. All isolates were clonal, and high-MIC strains contained a mutation in the highly conserved hot spot 1 region of Fks1p.
Repression of the Locus of the Enterocyte Effacement-Encoded Regulator of Gene Transcription of
Escherichia coli
O157:H7 by
Lactobacillus reuteri
Culture Supernatants Is LuxS and Strain Dependent
Authors: Jelčić Ivan , Hüfner Eric , Schmidt Herbert , Hertel Christian
Published: April 2008

Culture supernatants of
Lactobacillus reuteri
ATCC 55730 repressed
ler
expression in
Escherichia coli
O157:H7 cells, but neither the strain's isogenic
luxS
mutant nor the
L. reuteri
100-23C wild-type strain and its
luxS
mutant elicited a comparable effect. Furthermore, the epinephrine-mediated induction of
ler
expression was repressed by secreted substance(s) of
L. reuteri
ATCC 55730.
Coenzyme F
420
-Dependent Sulfite Reductase-Enabled Sulfite Detoxification and Use of Sulfite as a Sole Sulfur Source by
Methanococcus maripaludis
Authors: Johnson Eric F. , Mukhopadhyay Biswarup
Published: April 2008

Coenzyme F
420
-dependent sulfite reductase (Fsr) of
Methanocaldococcus jannaschii
, a sulfite-tolerant methanogen, was expressed with activity in
Methanococcus maripaludis
, a sulfite-sensitive methanogen. The recombinant organism reduced sulfite to sulfide and grew with sulfite as the sole sulfur source, indicating that Fsr is a sulfite detoxification and assimilation enzyme for methanogens and that
M. maripaludis
synthesizes siroheme.
Bioenergy Production via Microbial Conversion of Residual Oil to Natural Gas
Authors: Gieg Lisa M. , Duncan Kathleen E. , Suflita Joseph M.
Published: April 2008

World requirements for fossil energy are expected to grow by more than 50% within the next 25 years, despite advances in alternative technologies. Since conventional production methods retrieve only about one-third of the oil in place, either large new fields or innovative strategies for recovering energy resources from existing fields are needed to meet the burgeoning demand. The anaerobic biodegradation of
n
-alkanes to methane gas has now been documented in a few studies, and it was speculated that this process might be useful for recovering energy from existing petroleum reservoirs. We found that residual oil entrained in a marginal sandstone reservoir core could be converted to methane, a key component of natural gas, by an oil-degrading methanogenic consortium. Methane production required inoculation, and rates ranged from 0.15 to 0.40 μmol/day/g core (or 11 to 31 μmol/day/g oil), with yields of up to 3 mmol CH
4
/g residual oil. Concomitant alterations in the hydrocarbon profile of the oil-bearing core revealed that alkanes were preferentially metabolized. The consortium was found to produce comparable amounts of methane in the absence or presence of sulfate as an alternate electron acceptor. Cloning and sequencing exercises revealed that the inoculum comprised sulfate-reducing, syntrophic, and fermentative bacteria acting in concert with aceticlastic and hydrogenotrophic methanogens. Collectively, the cells generated methane from a variety of petroliferous rocks. Such microbe-based methane production holds promise for producing a clean-burning and efficient form of energy from underutilized hydrocarbon-bearing resources.
Stimulation of Zero-
trans
Rates of Lactose and Maltose Uptake into Yeasts by Preincubation with Hexose To Increase the Adenylate Energy Charge
Authors: Guimarães Pedro M. R. , Multanen Jyri-Pekka , Domingues Lucília , Teixeira José A. , Londesborough John
Published: April 2008

Initial rates of sugar uptake (zero-
trans
rates) are often measured by incubating yeast cells with radiolabeled sugars for 5 to 30 s and determining the radioactivity entering the cells. The yeast cells used are usually harvested from growth medium, washed, suspended in nutrient-free buffer, and stored on ice before they are assayed. With this method, the specific rates of zero-
trans
lactose uptake by
Kluyveromyces lactis
or recombinant
Saccharomyces cerevisiae
strains harvested from lactose fermentations were three- to eightfold lower than the specific rates of lactose consumption during fermentation. No significant extracellular β-galactosidase activity was detected. The ATP content and adenylate energy charge (EC) of the yeasts were relatively low before the [
14
C]lactose uptake reactions were started. A short (1- to 7-min) preincubation of the yeasts with 10 to 30 mM glucose caused 1.5- to 5-fold increases in the specific rates of lactose uptake. These increases correlated with increases in EC (from 0.6 to 0.9) and ATP (from 4 to 8 μmol·g dry yeast
−1
). Stimulation by glucose affected the transport
V
max
values, with smaller increases in

K
m

values. Similar observations were made for maltose transport, using a brewer's yeast. These findings suggest that the electrochemical proton potential that drives transport through sugar/H
+
symports is significantly lower in the starved yeast suspensions used for zero-
trans
assays than in actively metabolizing cells. Zero-
trans
assays with such starved yeast preparations can produce results that seriously underestimate the capacity of sugar/H
+
symports. A short exposure to glucose allows a closer approach to the sugar/H
+
symport capacity of actively metabolizing cells.
Drosophila melanogasterMounts a Unique Immune Response to the RhabdovirusSigma virus
Authors: Tsai C. W. , McGraw E. A. , Ammar E.-D. , Dietzgen R. G. , Hogenhout S. A.
Published: April 2008

Rhabdoviruses are important pathogens of humans, livestock, and plants that are often vectored by insects. Rhabdovirus particles have a characteristic bullet shape with a lipid envelope and surface-exposed transmembrane glycoproteins.Sigma virus(SIGMAV) is a member of theRhabdoviridaeand is a naturally occurring disease agent ofDrosophila melanogaster. The infection is maintained inDrosophilapopulations through vertical transmission via germ cells. We report here the nature of theDrosophilainnate immune response to SIGMAV infection as revealed by quantitative reverse transcription-PCR analysis of differentially expressed genes identified by microarray analysis. We have also compared and contrasted the immune response of the host with respect to two nonenveloped viruses,DrosophilaC virus (DCV) andDrosophilaX virus (DXV). We determined that SIGMAV infection upregulates expression of the peptidoglycan receptor protein genesPGRP-SB1andPGRP-SDand the antimicrobial peptide (AMP) genesDiptericin-A,Attacin-A,Attacin-B,Cecropin-A1, andDrosocin. SIGMAV infection did not inducePGRP-SAand the AMP genesDrosomycin-B,Metchnikowin, andDefensinthat are upregulated in DCV and/or DXV infections. Expression levels of the Toll and Imd signaling cascade genes are not significantly altered by SIGMAV infection. These results highlight shared and unique aspects of theDrosophilaimmune response to the three viruses and may shed light on the nature of the interaction with the host and the evolution of these associations.
Comparison of Transcription-Mediated Amplification and Growth-Based Methods for the Quantitation of
Enterococcus
Bacteria in Environmental Waters
Authors: Morris Ceri A. , Blackwood A. Denene , Kirs Marek , Buttigieg Neil D. , Morgan Rhian R. , Hogan James J. , Weeks Ian , Noble Rachel T.
Published: April 2008

An assay based on transcription-mediated amplification (TMA) technology was used to quantitate
Enterococcus
fecal indicator bacteria in environmental water samples. The results generated by this and two growth-based methods relative to the 104 most-probable-number or CFU-per-100-ml threshold show that the three methods are in good qualitative agreement when tested against a range of water samples taken from different locations. The results demonstrate sensitive and rapid detection (approximately 4 h from sample collection to result) and quantitation of
Enterococcus
bacteria compared to the results with the growth-based methods.
Factors Contributing to Heat Resistance ofClostridium perfringensEndospores
Authors: Orsburn Benjamin , Melville Stephen B. , Popham David L.
Published: April 2008

The endospores formed by strains of type AClostridium perfringensthat produce theC. perfringensenterotoxin (CPE) are known to be more resistant to heat and cold than strains that do not produce this toxin. The high heat resistance of these spores allows them to survive the cooking process, leading to a large number of food-poisoning cases each year. The relative importance of factors contributing to the establishment of heat resistance in this species is currently unknown. The present study examines the spores formed by both CPE+and CPE−strains for factors known to affect heat resistance in other species. We have found that the concentrations of DPA and metal ions, the size of the spore core, and the protoplast-to-sporoplast ratio are determining factors affecting heat resistance in these strains. While the overall thickness of the spore peptidoglycan was found to be consistent in all strains, the relative amounts of cortex and germ cell wall peptidoglycan also appear to play a role in the heat resistance of these strains.
Characterization of Diazotrophs Containing Mo-Independent Nitrogenases, Isolated from Diverse Natural Environments
Authors: Betancourt Doris A. , Loveless Telisa M. , Brown James W. , Bishop Paul E.
Published: April 2008

Molybdenum-independent nitrogenases were first described in the nitrogen-fixing bacterium
Azotobacter vinelandii
and have since been described in other diazotrophic bacteria. Previously, we reported the isolation of seven diazotrophs with Mo-independent nitrogenases from aquatic environments. In the present study, we extend these results to include diazotrophs isolated from wood chip mulch, soil, “paraffin dirt,” and sediments from mangrove swamps. Mo-deficient, N-free media under both aerobic and anaerobic conditions were used for the isolations. A total of 26 isolates were genetically and physiologically characterized. Their phylogenetic placement was determined using 16S rRNA gene sequence analysis. Most of the isolates are members of the gamma subdivision of the class
Proteobacteria
and appear to be specifically related to fluorescent pseudomonads and azotobacteria. Two other isolates, AN1 and LPF4, are closely related to
Enterobacter
spp. and
Paenibacillus
spp., respectively. PCR and/or Southern hybridization were used to detect the presence of nitrogenase genes in the isolates. PCR amplification of
vnfG
and
anfG
was used to detect the genetic potential for the expression of the vanadium-containing nitrogenase and the iron-only nitrogenase in the isolates. This study demonstrates that diazotrophs with Mo-independent nitrogenases can be readily isolated from diverse natural environments.
Identification of Mobile Elements and Pseudogenes in theShewanella oneidensisMR-1 Genome
Authors: Romine Margaret F. , Carlson Timothy S. , Norbeck Angela D. , McCue Lee Ann , Lipton Mary S.
Published: April 2008

Shewanella oneidensisMR-1 is the first of 22 differentShewanellaspp. whose genomes have been or are being sequenced and thus serves as the model organism for studying the functional repertoire of theShewanellagenus. The original MR-1 genome annotation revealed a large number of transposase genes and pseudogenes, indicating that many of the genome's functions may be decaying. Comparative analyses of the sequencedShewanellastrains suggest that 209 genes in MR-1 have in-frame stop codons, frameshifts, or interruptions and/or are truncated and that 65 of the original pseudogene predictions were erroneous. Among the decaying functions are that of one of three chemotaxis clusters, type I pilus production, starch utilization, and nitrite respiration. Many of the mutations could be attributed to members of 41 different types of insertion sequence (IS) elements and three types of miniature inverted-repeat transposable elements identified here for the first time. The high copy numbers of individual mobile elements (up to 71) are expected to promote large-scale genome recombination events, as evidenced by the displacement of thealgApromoter. The ability of MR-1 to acquire foreign genes via reactions catalyzed by both the integron integrase and the ISSod25-encoded integrases is suggested by the presence ofattCsites and genes whose sequences are characteristic of other species downstream of each site. This large number of mobile elements and multiple potential sites for integrase-mediated acquisition of foreign DNA indicate that the MR-1 genome is exceptionally dynamic, with many functions and regulatory control points in the process of decay or reinvention.
Discovering the Hidden Secondary Metabolome of
Myxococcus xanthus
: a Study of Intraspecific Diversity
Authors: Krug Daniel , Zurek Gabriela , Revermann Ole , Vos Michiel , Velicer Gregory J. , Müller Rolf
Published: April 2008

As a monophyletic group, the myxobacteria are known to produce a broad spectrum of secondary metabolites. However, the degree of metabolic diversity that can be found within a single species remains unexplored. The model species
Myxococcus xanthus
produces several metabolites also present in other myxobacterial species, but only one compound unique to
M. xanthus
has been found to date. Here, we compare the metabolite profiles of 98
M. xanthus
strains that originate from 78 locations worldwide and include 20 centimeter-scale isolates from one location. This screen reveals a strikingly high level of intraspecific diversity in the
M. xanthus
secondary metabolome. The identification of 37 nonubiquitous candidate compounds greatly exceeds the small number of secondary metabolites previously known to derive from this species. These results suggest that
M. xanthus
may be a promising source of future natural products and that thorough intraspecific screens of other species could reveal many new compounds of interest.
Community-Level Assessment of the Effects of the Broad-Spectrum Antimicrobial Chlorhexidine on the Outcome of River Microbial Biofilm Development
Authors: Lawrence J. R. , Zhu B. , Swerhone G. D. W. , Topp E. , Roy J. , Wassenaar L. I. , Rema T. , Korber D. R.
Published: April 2008

Chlorhexidine is a common-use antibacterial agent found in a range of personal-care products. We used rotating annular reactors to cultivate river biofilms under the influence of chlorhexidine or its molar equivalent in nutrients. Studies of the degradation of [
14
C]chlorhexidine demonstrated that no mineralization of the compound occurred. During studies with 100 μg liter
−1
chlorhexidine, significant changes were observed in the protozoan and micrometazoan populations, the algal and cyanobacterial biomass, the bacterial biomass, and carbon utilization. Denaturing gradient gel electrophoresis (DGGE) in combination with statistical analyses showed that the communities developing under control and 100 μg liter
−1
chlorhexidine were significantly different. At 10 μg liter
−1
chlorhexidine, there was significantly increased algal and cyanobacterial biomass while the bacterial biomass was not significantly affected (
P
< 0.05). No significant effects on protozoan or metazoan grazing were detected at the 10-μg liter
−1
chlorhexidine level. Fluorescent in situ hybridization indicated a significant reduction in the abundance of betaproteobacteria and gammaproteobacteria (
P
< 0.05). Archaeal cell counts were significantly reduced by both chlorhexidine and nutrient treatments. DGGE and statistical analyses indicated that 10 μg liter
−1
chlorhexidine and molar equivalent nutrient treatments were significantly different from control communities. In contrast to community level observations, toxicological testing with a panel of cyanobacteria, algae, and protozoa indicated no detectable effects at 10, 50, and 100 μg liter
−1
chlorhexidine. Thus, community level assessment indicated a risk of low levels of chlorhexidine in aquatic habitats while conventional approaches did not.
Functional Diversity and Electron Donor Dependence of Microbial Populations Capable of U(VI) Reduction in Radionuclide-Contaminated Subsurface Sediments
Authors: Akob Denise M. , Mills Heath J. , Gihring Thomas M. , Kerkhof Lee , Stucki Joseph W. , Anastácio Alexandre S. , Chin Kuk-Jeong , Küsel Kirsten , Palumbo Anthony V. , Watson David B. , Kostka Joel E.
Published: April 2008

In order to elucidate the potential mechanisms of U(VI) reduction for the optimization of bioremediation strategies, the structure-function relationships of microbial communities were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate. A polyphasic approach was used to assess the functional diversity of microbial populations likely to catalyze electron flow under conditions proposed for in situ uranium bioremediation. The addition of ethanol and glucose as supplemental electron donors stimulated microbial nitrate and Fe(III) reduction as the predominant terminal electron-accepting processes (TEAPs). U(VI), Fe(III), and sulfate reduction overlapped in the glucose treatment, whereas U(VI) reduction was concurrent with sulfate reduction but preceded Fe(III) reduction in the ethanol treatments. Phyllosilicate clays were shown to be the major source of Fe(III) for microbial respiration by using variable-temperature Mössbauer spectroscopy. Nitrate- and Fe(III)-reducing bacteria (FeRB) were abundant throughout the shifts in TEAPs observed in biostimulated microcosms and were affiliated with the genera
Geobacter, Tolumonas, Clostridium, Arthrobacter, Dechloromonas
, and
Pseudomonas
. Up to two orders of magnitude higher counts of FeRB and enhanced U(VI) removal were observed in ethanol-amended treatments compared to the results in glucose-amended treatments. Quantification of citrate synthase (
gltA
) levels demonstrated a stimulation of
Geobacteraceae
activity during metal reduction in carbon-amended microcosms, with the highest expression observed in the glucose treatment. Phylogenetic analysis indicated that the active FeRB share high sequence identity with
Geobacteraceae
members cultivated from contaminated subsurface environments. Our results show that the functional diversity of populations capable of U(VI) reduction is dependent upon the choice of electron donor.
Role of Intestinal Microbiota in Transformation of Bismuth and Other Metals and Metalloids into Volatile Methyl and Hydride Derivatives in Humans and Mice
Authors: Michalke Klaus , Schmidt Annette , Huber Britta , Meyer Jörg , Sulkowski Margareta , Hirner Alfred V. , Boertz Jens , Mosel Frank , Dammann Philip , Hilken Gero , Hedrich Hans J. , Dorsch Martina , Rettenmeier Albert W. , Hensel Reinhard
Published: April 2008

The present study shows that feces samples of 14 human volunteers and isolated gut segments of mice (small intestine, cecum, and large intestine) are able to transform metals and metalloids into volatile derivatives ex situ during anaerobic incubation at 37°C and neutral pH. Human feces and the gut of mice exhibit highly productive mechanisms for the formation of the toxic volatile derivative trimethylbismuth [(CH
3
)
3
Bi] at rather low concentrations of bismuth (0.2 to 1 μmol kg
−1
[dry weight]). An increase of bismuth up to 2 to 14 mmol kg
−1
(dry weight) upon a single (human volunteers) or continuous (mouse study) administration of colloidal bismuth subcitrate resulted in an average increase of the derivatization rate from approximately 4 pmol h
−1
kg
−1
(dry weight) to 2,100 pmol h
−1
kg
−1
(dry weight) in human feces samples and from approximately 5 pmol h
−1
kg
−1
(dry weight) to 120 pmol h
−1
kg
−1
(dry weight) in mouse gut samples, respectively. The upshift of the bismuth content also led to an increase of derivatives of other elements (such as arsenic, antimony, and lead in human feces or tellurium and lead in the murine large intestine). The assumption that the gut microbiota plays a dominant role for these transformation processes, as indicated by the production of volatile derivatives of various elements in feces samples, is supported by the observation that the gut segments of germfree mice are unable to transform administered bismuth to (CH
3
)
3
Bi.
A Diversity-Covering Approach to Immunization with
Plasmodium falciparum
Apical Membrane Antigen 1 Induces Broader Allelic Recognition and Growth Inhibition Responses in Rabbits
Authors: Remarque Edmond J. , Faber Bart W. , Kocken Clemens H. M. , Thomas Alan W.
Published: April 2008

Plasmodium falciparum
apical membrane antigen 1 (PfAMA1), a candidate malaria vaccine, is polymorphic. This polymorphism is believed to be generated predominantly under immune selection pressure and, as a result, may compromise attempts at vaccination. Alignment of 355 PfAMA1 sequences shows that around 10% of the 622 amino acid residues can vary between alleles and that linkages between polymorphic residues occur. Using this analysis, we have designed three diversity-covering (DiCo) PfAMA1 sequences that take account of these linkages and, when taken together, on average incorporate 97% of amino acid variability observed. For each of the three DiCo sequences, a synthetic gene was constructed and used to transform the methylotrophic yeast
Pichia pastoris
, allowing recombinant expression. All three DiCo proteins were reactive with the reduction-sensitive monoclonal antibody 4G2, suggesting the DiCo sequences had conformations similar to those of naturally occurring PfAMA1. Rabbits were immunized with FVO strain PfAMA1 or with the DiCo proteins either individually or as a mixture. Antibody titers and the ability to inhibit parasite growth in vitro were determined. Animals immunized with the DiCo mix performed similarly to animals immunized with FVO AMA1 when measured against FCR3 strain parasites but outperformed animals immunized with FVO AMA1 when assessed against other strains. The levels of growth inhibition (∼70%) induced by the mix of three DiCo proteins were comparable for FVO, 3D7, and HB3, suggesting that a considerable degree of diversity in AMA1 is adequately covered. This suggests that vaccines based upon the DiCo mix approach provide a broader functional immunity than immunization with a single allele.
Role of Integrin αvβ6 in Acute Lung Injury Induced byPseudomonas aeruginosa
Authors: Song Yuanlin , Pittet Jean Francois , Huang Xiaozhu , He Hong , Lynch Susan V. , Violette Shelia M. , Weinreb Paul H. , Horan Gerald S. , Carmago Amua , Sawa Yoriko , Bernstein Xin Liu , Wiener-Kronish Jeanine P.
Published: April 2008

Deletion of integrin αvβ6 has been associated with significant protection in experiments where lung injury was induced by bleomycin, lipophilic polysaccharides, and high tidal volume ventilation. This has led to the suggestion that antibody blockade of this integrin is a novel therapy for acute lung injury. We questioned whether β6 gene deletion would also protect againstPseudomonas aeruginosa-induced acute lung injury. Wild-type and littermate β6-null mice, as well as recombinant soluble TGF-β receptor type II-Fc (rsTGF-βRII-Fc) and anti-αvβ6 treated wild-type mice, were instilled with liveP. aeruginosa. Four or 8 h after bacterial instillation, the mice were euthanized, and either bronchoalveolar lavage fluid or lung homogenates were obtained. Deletion of the β6 gene resulted in an overall increase in inflammatory cells in the lungs. Bacterial numbers from the lung homogenates of infected β6-null mice were significantly decreased compared to the numbers in the wild-type mice (1.6 × 106CFU versus 4.2 × 106CFU [P< 0.01]). There were no significant differences inP. aeruginosa-mediated increases in lung endothelial permeability between wild-type and β6-null mice. Similarly, pretreatment with the αvβ6 antibody or with rsTGF-βRII-Fc did not significantly affect theP. aeruginosa-induced lung injury or rate of survival compared to pretreatment with control immunoglobulin G. We conclude that deletion or inhibition of the integrin αvβ6 didnotprotect animals fromP. aeruginosa-induced lung injury. However, these therapies also did not increase the lung injury, suggesting that host defense was not compromised by this promising new therapy.