bluuebunny/crossref_metadata_2025 huggingface dataset:
Porphyry‐Type Mineralization at Selogiri Area, Wonogiri Regency, Central Java, Indonesia
Authors: Imai Akira , Shinomiya Jumpei , Soe Maung Thiha , Setijadji Lucas Donny , Watanabe Koichiro , Warmada I Wayan
Published: June 2007

The Selogiri area, situated in Wonogiri regency, Central Java, is one of several gold prospecting areas in the Southern areas Mountain Range in Java, Indonesia. Three types of dioritic–andesitic intrusive rocks occur in the Selogiri area, namely, hornblende andesite porphyry, hornblende diorite porphyry and hornblende diorite, exposed in a half‐circular depression where volcanic breccia and tuff are widely distributed. The occurrence of stockwork quartz veinlets and associated with magnetite and malachite coating along the cracks in the diorite porphyry suggests porphyry type mineralization. This is also supported by the occurrence of polyphase hypersaline fluid inclusions in the stockwork veinlet quartz. Small‐scale miners are mining NS‐trending quartz veins for gold associated with base metal sulfides. These veins are probably epithermal‐type mineralization that overprinted porphyry‐type mineralization. The Neogene intermediate to silicic hydrous magmatism in Java could have formed the porphyry‐type mineralization in Selogiri, as in the rest of the Sunda–Banda arc.
Clinical significance of fatty liver associated with metabolic syndrome
Authors: Kogiso Tomomi , Moriyoshi Yuriko , Nagahara Hikaru
Published: June 2007

Aim:  Metabolic syndrome (MS) has been recognized as a high‐risk disorder that leads to life‐threatening diseases, such as coronary vascular disease. The aim of the present study was to investigate the association of fatty liver (FL) with MS in order to establish an effective treatment for FL.

Methods:  One thousand two hundred and fifty‐four individuals (694 males, 560 females) who visited the Department of General Medicine, International Medical Center of Japan for a human dry dock annual check‐up from 2000 to 2004 were analyzed.

Results:  FL was diagnosed in 41.5% of the males and 10.7% of the females, with the prevalence rate increasing in postmenopausal females over 55 years old. High body mass index and waist circumference were observed in those with FL, whereas body mass index reduction was strongly correlated with a decrease in alanine aminotransferase level (R = 0.6,P < 0.01). MS complications were more common in subjects with FL and the most common initial events of MS were shown to be obesity, hyperlipidemia and FL, followed by glucose intolerance and hypertension. Subjects with FL showed a higher level of high‐sensitivity C‐reactive protein (hs‐CRP) (normal: FL = 0.38: 0.73 mg/L, P < 0.05), which was strongly correlated with serum markers that indicated lipid and glucose metabolism in females with FL (R = 0.61–0.77, P < 0.05).

Conclusions:  FL could be a part of or, at least, a predictor of MS. Further, bodyweight reduction is an effective treatment for FL.
Double filtration plasmapheresis and interferon combination therapy for chronic hepatitis C patients with genotype 1 and high viral load
Authors: Fujiwara Kenji , Kaneko Shuichi , Kakumu Shinichi , Sata Michio , Hige Shuhei , Tomita Eiichi , Mochida Satoshi ,   The Virus Reduction Therapy Study Group
Published: June 2007

Aim:  The efficacy and safety of double filtration plasmapheresis (DFPP) plus interferon (IFN) combination therapy were compared with those of IFN therapy alone in 193 chronic hepatitis C patients having a high hepatitis C virus ribonucleic acid load of difficult‐to‐treat genotype 1b.

Methods:  All patients received either interferon alpha‐2b (IFN‐α‐2b) monotherapy or combination therapies with ribavirin and IFN‐α‐2b or pegylated interferon alpha‐2b (PEG‐IFN‐α‐2b). Each patient individually decided whether to receive concomitant DFPP. DFPP was immediately followed by IFN treatment, and up to five sessions were given during the first week.

Results:  Sixty patients decided to receive DFPP. In the DFPP plus PEG‐IFN‐α‐2b therapy group (n = 30), viral load reduction at 4 weeks after the start of treatment was greater than innon‐DFPP (n = 74) (2.47 vs 1.52, log, P = 0.010), and the sustained virus response was also higher (77.8% vs 50.0%), even in cases of re‐treated patients (relapsers or non‐responders to previous IFN therapies). Adverse events, mild and transient, were observed in 38.3% of all DFPP‐treated patients.

Conclusion:  DFPP plus IFN combination therapy produced a great reduction of viral load during the early stage of treatment and achieved a high sustained virus response, suggesting that this combination therapy may be a new modality for chronic hepatitis C patients at difficult‐to‐treat states.
Oral branched‐chain amino acid supplementation improves the oxidized/reduced albumin ratio in patients with liver cirrhosis
Authors: Fukushima Hideki , Miwa Yoshiyuki , Shiraki Makoto , Gomi Ikuko , Toda Katsuhisa , Kuriyama Shoko , Nakamura Hironori , Wakahara Toshitatsu , Era Seiichi , Moriwaki Hisataka
Published: June 2007

Aim:  Branched‐chain amino acid (BCAA) supplementation improves hypoalbuminemia in decompensated cirrhotics. Recently, it was clarified that the ratio of oxidized albumin within total albumin rises with progression of liver cirrhosis. We conducted a feasibility study to investigate whether BCAA supplementation might improve this ratio.

Methods:  Seven cirrhotic patients (age: 70 ±> 6 years; M/F = 4/3; etiology: hepatitis C in six and non‐B/non‐C hepatitis virus in one; Child–Pugh classification: A in six and B in one) were enrolled consecutively in this study in October 2004 to March 2005. Patients were given 4 g BCAA after each meal for 8 weeks. Serum total, oxidized and reduced albumin, plasma amino acids, glutathione, zinc, selenium, and lipid peroxide concentrations were measured every 2 weeks.

Results:  Low total albumin, high oxidized albumin, and low reduced albumin levels were observed at entry. After 8 weeksBCAA supplementation, the ratio of oxidized albumin within total albumin decreased significantly and that of reduced albumin increased significantly (P < 0.05, respectively). Total albumin tended to rise and lipid peroxide concentrations tended to fall, but not significantly.

Conclusion:  BCAA supplementation improved the oxidized/reduced state of serum albumin. This intervention is effective to maintain the quality of serum albumin in cirrhotic patients.
Evaluation of long‐term biochemical responses to combination therapy of interferon plus ribavirin in those infected with hepatitis C virus genotype 1b and high baseline viral load
Authors: Sezaki Hitomi , Suzuki Fumitaka , Kawamura Yusuke , Yatsuji Hiromi , Hosaka Tetsuya , Akuta Norio , Kobayashi Masahiro , Suzuki Yoshiyuki , Arase Yasuji , Ikeda Kenji , Kumada Hiromitsu
Published: June 2007

Aim:  The aim of this study was to determine the long‐term effects in non‐responders (NRs) to 48‐week interferon (IFN) and ribavirin combination treatment in patients infected with hepatitis C virus (HCV) genotype 1b and high baseline viral loads.

Methods:  We measured serum alanine aminotransferase (ALT) and HCV‐RNA levels in 52 consecutive patients infected with HCV genotype 1b and high viral loads who received combination therapy for 48 weeks.

Results:  Sustained virologic response (SVR) was noted in 30 patients (57.7%). Virologic response (VR), that is serum HCV‐RNA negativity by the end of treatment and positivity during follow‐up, was noted in nine patients (17.3%). Thirteen (25.0%) patients were NRs. Significantly lower serum albumin (P = 0.007) and ribavirin doses according to body weight (P = 0.021) and higher gamma glutamyl transpeptidase (GGT,P = 0.038) were noted at baseline in the NR group than in the SVR and VR groups. ALT normalization rates at six months after the completion of treatment were 55.6% (5/9) in VR and 61.5% (8/13) in NRs. Sustained ALT normalization at two years after the completion of treatment was noted in 55.6% (5/9) and 58.3% (7/12), respectively.

Conclusion:  Our study indicates a high rate of ALT normalization in patients infected with HCV genotype 1b and high baseline viral loads who received combination therapy and that such a rate could be maintained after the completion of therapy, even in NRs. Our results suggest that combination therapy should be continued in NRs who show ALT normalization in order to prevent potential hepatocarcinogenesis.
Association between hepatic alveolar echinococcosis and frequency of human leukocyte antigen class I and II alleles in Turkish patients
Authors: Aydinli Bulent , Pirim Ibrahim , Polat Kamil Y. , Gursan Nesrin , Atamanalp Sabri S. , Ezer Mehmet , Donmez Ramazan
Published: June 2007

Background:  Human alveolar echinococcosis (AE) is a potentially fatal, chronically progressive hepatic infestation that is characterized by a long asymptomatic period in which an invasive tumor‐like lesion develops. Several studies have suggested that genetic susceptibility to AE may be linked to HLA class II alleles. We investigated the association between AE and antigen HLA‐A, B, C, DR and DQ profiles of patients with hepatic AE (HAE) in the eastern part of Turkey.

Methods:  This case‐controlled study was performed on 44 unrelated patients with HAE and 76 control subjects. The diagnosis was supported by clinical, radiological, and histopathological evidence. The association of class I and class II HLA antigens was examined in the patients with HAE and control subjects.

Results:  There was an increase in the antigen frequencies of HLA‐DRB1*15, HLA‐DQB1*02, 06, 07 in the HAE patientscompared with those in the control group (P < 0.05, P < 0.001, P < 0.01, P < 0.05, respectively). HLA‐DQB1*02, 06, 07 were more frequent in patients with stages III and IV who were classified according to the PNM staging system.

Conclusions:  The present study indicates that susceptibility to HAE in the Turkish population is essentially HLA class II and poorly class I mediated, with HLA‐26, and DRB1*015, DQB1* 02, 06, 07 with more allele distribution in the patient group. Our results are not similar to those of other studies, but contribute to the discussions on the association of HLA class I and class II alleles with AE.
Prolonged engraftment of human hepatocytes in mice transgenic for the deleted form of human hepatocyte growth factor
Authors: Krishnan Anuradha , Viker Kimberly , Rietema Heleen , Telgenkamp Marije , Knudsen Bruce , Charlton Michael
Published: June 2007

Aim:  Small animal models chimeric for human hepatocytes have provided valuable insights into the biology of hepatotropic viral infection and provided a platform for the study of therapeutic agents. Existing models of human hepatocyte transplantation are limited by phenotypic fragility and impaired immunity. We hypothesized that mice transgenic for human hepatocyte growth factor (HGF), a potent human hepatocyte mitogen, would engraft human hepatocytes in the absence of immunodeficiency.

Methods:  A plasmid construct containing the 2.3 kb coding region of the 723 amino acid isoform of HGF cDNA under the transcriptional control of the mouse albumin promoter/enhancer was used to generate transgenic mice. Cryopreserved human hepatocytes were transplanted into nine transgenic and six non‐transgenic mice. Engraftment of human hepatocytes was followed for a period of 12 weeks by immunoblotting for human albumin in mouse serum samples.

Results:  In six out of the nine transgenic mice, abundance of human albumin, following an initial decline, increased andpeaked at > 70 days post transplantation, demonstrating sustained engraftment of transplanted human hepatocytes. In all the non‐transgenic mice, post‐transplant human albumin levels declined sequentially without evidence of sustained engraftment. Immunostaining of mouse liver sections indicated the presence of human hepatocytes adjacent to clusters of non‐staining murine hepatocytes.

Conclusion:  These results demonstrate that sustained engraftment of human hepatocytes in mice is facilitated by expression of the human dHGF transgene. Human hepatocyte engraftment in this model has been achieved on an immunocompetent strain background and merits further study as a candidate for the study of hepatotropic viral infections.
Anti‐hepatitis C virus activity of albinterferon alfa‐2b in cell culture
Authors: Liu Chen , Zhu Haizhen , Subramanian G. Mani , Moore Paul A. , Xu Yiling , Nelson David R.
Published: June 2007

Background:  Interferon‐based combination therapy is the standard treatment for chronic hepatitis C virus (HCV) infection. The weekly administration of long‐acting pegylated interferons (PEG‐IFNα‐2a or PEG‐IFNα‐2b) provides superior antiviral efficacy over standard interferon alfa (IFNα) for the treatment of HCV infection. Albinterferon alfa‐2b (alb‐IFN) is a novel recombinant protein consisting of IFNα‐2b that is genetically fused to human albumin.

Methods:  To test alb‐IFN antiviral efficacy, we compared the antiviral activity of unmodified IFNα with the three modified interferons (PEG‐IFNα‐2a, PEG‐IFNα‐2b, and alb‐IFN) at clinically relevant serum concentrations using liver cell‐based and non‐liver cell‐based HCV replicon cell lines. The EC50 in GSB cells for IFNα‐2b, PEG‐IFNα‐2a, PEG‐IFNα‐2b and alb‐IFN was 7 U/mL, 1.1 ng/mL, 18 ng/mL, and 15 ng/mL, respectively.

Results:  At clinically relevant patient serum concentrations, alb‐IFN exhibits more antiviral activity than the pegylated interferons. Alb‐IFN showed similar inhibition of HCV replication in human liver cells and non‐liver cells, indicating it has anti‐HCV activity in non‐liver cells. The magnitude of induction of interferon‐stimulated genes (MxA, 2′5′OAS1, IFI44, and IFI27) at 6 h and 48 h was comparable for all the modified IFNs in human liver cells at the drug concentrations evaluated.

Conclusion:  The present study indicates that alb‐IFN has a potent, direct anti‐HCV activity in both liver and non‐liver cells.
Changes in viral loads of lamivudine‐resistant mutants during entecavir therapy
Authors: Suzuki Fumitaka , Suzuki Yoshiyuki , Akuta Norio , Yatsuji Hiromi , Sezaki Hitomi , Arase Yasuji , Kawamura Yusuke , Hosaka Tetsuya , Kobayashi Masahiro , Ikeda Kenji , Kobayashi Mariko , Watahiki Sachiyo , Kumada Hiromitsu
Published: June 2007

Aim:  Entecavir therapy is effective against lamivudine‐resistant virus in patients with hepatitis B virus infection. We investigated viral load changes of YMDD mutant virus (rtM204I [YIDD sequence], rtM204V [YVDD]) in serial serum samples during entecavir treatment for lamivudine‐resistant virus and determined changes in viral precore and core promoter mutants.

Methods:  Nineteen patients were treated in randomized, double‐blind phase II clinical trials of entecavir at 0.5 or 1.0 mg for breakthrough hepatitis due to lamivudine‐resistant virus. Viral changes in YMDD mutants (rtM204I, rtM204V), amino acid changes in the polymerase reverse transcriptase region and precore/core promoter mutations at 52 weeks were determined in 18 patients.

Results:  Changes in viral loads of rtM204I and rtM204V were similar. No differences in load changes were seen betweenthe 0.5 and 1.0 mg groups. However, load changes for rtM204I alone were greater than those for the rtM204I + rtM204V mixed‐type (P = 0.042, at both 40 and 52 weeks). Load changes in rtM204I and rtM204V with G1896A tended to be greater than those without. Moreover, G1896A was replaced by wild‐type virus in two patients at 52 weeks.

Conclusion:  RtM204I only or the existence of precore mutation was more sensitive to entecavir therapy against lamivudine‐resistant virus.
Comparative study of NMDA and AMPA/kainate receptors involved in cardiovascular inhibition produced by imidazoline‐like drugs in anaesthetized rats
Authors: Wang Li‐Gang , Zeng Jun , Yuan Wen‐Jun , Su Ding‐Feng , Wang Wei‐Zhong
Published: June 2007

The depressor mechanism of imidazoline‐like drugs is believed to result from activation of I1‐imidazoline receptors (I1R) and/or α2‐adrenoceptors within the central nervous system, which are associated with the glutamatergic system. The rostral ventrolateral medulla (RVLM) has been recognized as a specific target area that mediates the depressor action of imidazoline‐like drugs. The objective of this study was to determine the comparative effects of blockade of the central glutamate receptor subtypes N‐methyl‐d‐aspartate (NMDA) or α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid (AMPA)/kainate on the cardiovascular actions of imidazoline‐like drugs (clonidine and moxonidine) in anaesthetized rats. Intracerebroventricular (i.c.v.) injection of the NMDA receptor antagonist MK801 or the AMPA/kainate receptor antagonist 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione (CNQX) produced similar reductions in blood pressure (BP) and heart rate (HR) to those induced by i.c.v. injection of clonidine. Intracerebroventricular injection of the glutamate receptor antagonist kynurenic acid not only abolished clonidine‐induced hypotension and bradycardia but converted the responses to a pressor action and tachycardia. Unilateral injection of MK801 or CNQX into RVLM significantly attenuated intra‐RVLM clonidine‐induced decreases in BP and HR. We also found that unilateral injection of a selective I1R agonist, moxonidine, significantly decreased BP and HR, which were also attenuated to a similar extent by prior injection of MK801 or CNQX. In conclusion, these data show that blockade of central (RVLM) NMDA and AMPA/kainate receptors produces similar attenuation of the decrease in BP and HR induced by clonidine or moxonidine. It is suggested that both NMDA and AMPA/kainate receptors are involved in the cardiovascular inhibition produced by imidazoline‐like drugs, which is probably at least partly dependent on an I1R mechanism in the RVLM.
Increased thermogenic responsiveness to intravenous β‐adrenergic stimulation in habitually exercising humans is not related to skeletal muscle β2‐adrenergic receptor density
Authors: Stob Nicole R. , Seals Douglas R. , Jensen Jørgen , Van Baak Marleen A. , Steig Amy J. , Lindstrom Rachel C. , Bikman Benjamin T. , Bell Christopher
Published: June 2007

Habitually exercising adults demonstrate greater thermogenic responsiveness to β‐adrenergic receptor (β‐AR) stimulation compared with their sedentary peers, but the molecular mechanisms involved are unknown. To determine the possible role of increased β‐AR density, we studied 32 healthy adults: 17 habitual aerobic exercisers (age 45 ± 5 years, 11 males) and 15 sedentary (49 ± 5 years, 7 males). Maximal oxygen uptake (43.7 ± 2.5 versus 31.6 ± 2.9 ml kg−1 min−1, P= 0.002, mean ±s.e.m.) and vastus lateralis muscle maximal citrate synthase activity (1.70 ± 0.36 versus 0.58 ± 0.11 μmol min−1 g−1, P= 0.008) were higher in the habitually exercising subjects. Resting energy expenditure (EE) adjusted for fat‐free mass (FFM) was similar in the habitually exercising (5903 ± 280 kJ day−1) and sedentary adults (6054 ± 289 kJ day−1, P= 0.43). The percentage increase in EE (ΔEE%; indirect calorimetry, ventilated hood) above resting EE in response to β‐AR stimulation (intravenous isoproterenol at 6, 12 and 24 ng  (kg FFM)−1 min−1) was greater (7.1 ± 1.2, 13.7 ± 1.0, 20.7 ± 1.3 versus 5.9 ± 0.9, 9.9 ± 1.4, 15.9 ± 1.70%, respectively, P= 0.04), and the dose of isoproterenol required to increase EE by 10% above resting EE was lower (8.2 ± 1.5 versus 17.1 ± 4.1 ng (kg FFM)−1 min−1, P= 0.03) in the habitually exercising adults. In contrast, vastus lateralis muscle β2‐AR density was similar in the habitually exercising and sedentary subjects (7.46 ± 0.29 versus 7.44 ± 0.60 fmol  (mg dry weight muscle)−1, P= 0.98), and was not related to ΔEE% (r= 0.02, P= 0.94) or to the isoproterenol dose required to increase EE by 10% above resting EE (r=−0.06, P= 0.76). These findings indicate that increased β2‐AR density is not a mechanism contributing to the greater thermogenic responsiveness to β‐AR stimulation in adult humans who regularly perform aerobic exercise.
Multivariate Analysis of Complex DNA Sequence Electropherograms for High-Throughput Quantitative Analysis of Mixed Microbial Populations
Authors: Trosvik Pål , Skånseng Beate , Jakobsen Kjetill S. , Stenseth Nils C. , Næs Tormod , Rudi Knut
Published: June 2007

High-throughput quantification of genetically coherent units (GCUs) is essential for deciphering population dynamics and species interactions within a community of microbes. Current techniques for microbial community analyses are, however, not suitable for this kind of high-throughput application. Here, we demonstrate the use of multivariate statistical analysis of complex DNA sequence electropherograms for the effective and accurate estimation of relative genotype abundance in cell samples from mixed microbial populations. The procedure is no more labor-intensive than standard automated DNA sequencing and provides a very effective means of quantitative data acquisition from experimental microbial communities. We present results with the
Campylobacter jejuni
strain-specific marker gene
gltA
, as well as the 16S rRNA gene, which is a universal marker across bacterial assemblages. The statistical models computed for these genes are applied to genetic data from two different experimental settings, namely, a chicken infection model and a multispecies anaerobic fermentation model, demonstrating collection of time series data from model bacterial communities. The method presented here is, however, applicable to any experimental scenario where the interest is quantification of GCUs in genetically heterogeneous DNA samples.
High Rates of Sulfate Reduction in a Low-Sulfate Hot Spring Microbial Mat Are Driven by a Low Level of Diversity of Sulfate-Respiring Microorganisms
Authors: Dillon Jesse G. , Fishbain Susan , Miller Scott R. , Bebout Brad M. , Habicht Kirsten S. , Webb Samuel M. , Stahl David A.
Published: June 2007

The importance of sulfate respiration in the microbial mat found in the low-sulfate thermal outflow of Mushroom Spring in Yellowstone National Park was evaluated using a combination of molecular, microelectrode, and radiotracer studies. Despite very low sulfate concentrations, this mat community was shown to sustain a highly active sulfur cycle. The highest rates of sulfate respiration were measured close to the surface of the mat late in the day when photosynthetic oxygen production ceased and were associated with a
Thermodesulfovibrio
-like population. Reduced activity at greater depths was correlated with novel populations of sulfate-reducing microorganisms, unrelated to characterized species, and most likely due to both sulfate and carbon limitation.
A Cyclic AMP Receptor Protein-Regulated Cell-Cell Communication System Mediates Expression of a FecA Homologue in
Stenotrophomonas maltophilia
Authors: Huang Tzu-Pi , Wong Amy C. Lee
Published: June 2007

Stenotrophomonas maltophilia
WR-C possesses an
rpf
/diffusible signal factor (DSF) cell-cell communication system. It produces
cis
-Δ2-11-methyl-dodecenoic acid, a DSF, and seven structural derivatives, which require
rpfF
and
rpfB
for synthesis. Acquisition of iron from the environment is important for bacterial growth as well as the expression of virulence genes. We identified a gene homologous to
fecA
, which encodes a ferric citrate receptor that transports exogenous siderophore ferric citrate from the environment into the bacterial periplasm. Western blot analysis with anti-FecA-His
6
antibody showed that the FecA homologue was induced in the iron-depleted medium supplemented with a low concentration of ferric citrate. Deletion of
rpfF
or
rpfB
resulted in reduced FecA expression compared to the wild type. Synthetic DSF restored FecA expression by the Δ
rpfF
mutant to the wild-type level. Reverse transcription-PCR showed that the
fecA
transcript was decreased in the Δ
rpfF
mutant compared to the wild type. These data suggest that DSF affected the level of
fecA
mRNA. Transposon inactivation of
crp
, which encodes cyclic AMP (cAMP) receptor protein (CRP) resulted in reduced FecA expression and
rpfF
transcript level. Putative CRP binding sites were located upstream of the
rpfF
promoter, indicating that the effect of CRP on FecA is through the
rpf
/DSF pathway and by directly controlling
rpfF
. We propose that CRP may serve as a checkpoint for iron uptake, protease activity, and hemolysis in response to environmental changes such as changes in concentrations of glucose, cAMP, iron, or DSF.
Growth and Mycorrhizal Community Structure ofPinus sylvestrisSeedlings following the Addition of Forest Litter
Authors: Aučina Algis , Rudawska Maria , Leski Tomasz , Skridaila Audrius , Riepšas Edvardas , Iwanski Michal
Published: June 2007

We report the effects of pine and oak litter on species composition and diversity of mycorrhizal fungi colonizing 2-year-oldPinus sylvestrisL. seedlings grown in a bare-root nursery in Lithuania. A layer of pine or oak litter was placed on the surface of the nursery bed soil to mimic natural litter cover. Oak litter amendment appeared to be most favorable for seedling survival, with a 73% survival rate, in contrast to the untreated mineral bed soil (44%). The concentrations of total N, P, K, Ca, and Mg were higher in oak growth medium than in pine growth medium. Relative to the control (pH 6.1), the pH was lower in pine growth medium (5.8) and higher in oak growth medium (6.3). There were also twofold and threefold increases in the C content of growth medium with the addition of pine and oak litter, respectively. Among seven mycorrhizal morphotypes, eight different mycorrhizal taxa were identified:Suillus luteus,Suillus variegatus,Wilcoxina mikolae, aTubersp., aTomentellasp.,Cenococcum geophilum,Amphinema byssoides, and one unidentified ectomycorrhizal symbiont. Forest litter addition affected the relative abundance of mycorrhizal symbionts more than their overall representation. This was more pronounced for pine litter than for oak litter, with 40% and 25% increases in the abundance of suilloid mycorrhizae, respectively. Our findings provide preliminary evidence that changes in the supply of organic matter through litter manipulation may have far-reaching effects on the chemistry of soil, thus influencing the growth and survival of Scots pine seedlings and their mycorrhizal communities.
Effect of Afforestation and Reforestation of Pastures on the Activity and Population Dynamics of Methanotrophic Bacteria
Authors: Singh Brajesh K. , Tate Kevin R. , Kolipaka Gokul , Hedley Carolyn B. , Macdonald Catriona A. , Millard Peter , Murrell J. Colin
Published: June 2007

We investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different New Zealand sites. Methane oxidation was measured in soils from two pine (
Pinus radiata
) forests and one shrubland (mainly
Kunzea ericoides
var.
ericoides
) and three adjacent permanent pastures. The methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. A combination of phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of these soils revealed that different methanotrophic communities were active in soils under the different vegetations. The C
18
PLFAs (signature of type II methanotrophs) predominated under pine and shrublands, and C
16
PLFAs (type I methanotrophs) predominated under pastures. Analysis of the methanotrophs by molecular methods revealed further differences in methanotrophic community structure under the different vegetation types. Cloning and sequencing and terminal-restriction fragment length polymorphism analysis of the particulate methane oxygenase gene (
pmoA
) from different samples confirmed the PLFA-SIP results that methanotrophic bacteria related to type II methanotrophs were dominant in pine forest and shrubland, and type I methanotrophs (related to
Methylococcus capsulatus
) were dominant in all pasture soils. We report that afforestation and reforestation of pastures caused changes in methane oxidation by altering the community structure of methanotrophic bacteria in these soils.
Impact of Alginate Conditioning Film on Deposition Kinetics of Motile and Nonmotile
Pseudomonas aeruginosa
Strains
Authors: de Kerchove Alexis J. , Elimelech Menachem
Published: June 2007

The initial deposition of bacteria in most aquatic systems is affected by the presence of a conditioning film adsorbed at the liquid-solid interface. Due to the inherent complexity of such films, their impact on bacterial deposition remains poorly defined. The aim of this study was to gain a better understanding of the effect of a conditioning film on the deposition of motile and nonmotile
Pseudomonas aeruginosa
cells in a radial stagnation point flow system. A well-defined alginate film was used as a model conditioning film because of its polysaccharide and polyelectrolyte nature. Deposition experiments under favorable (nonrepulsive) conditions demonstrated the importance of swimming motility for cell transport towards the substrate. The impact of the flagella of motile cells on deposition is dependent on the presence of the conditioning film. We showed that on a clean substrate surface, electrostatic repulsion governs bacterial deposition and the presence of flagella increases cell deposition. However, our results suggest that steric interactions between flagella and extended polyelectrolytes of the conditioning film hinder cell deposition. At a high ionic strength (100 mM), active swimming motility and changes in alginate film structure suppressed the steric barrier and allowed conditions favorable for deposition. We demonstrated that bacterial deposition is highly influenced by cell motility and the structure of the conditioning film, which are both dependent on ionic strength.
Differences between Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and Its Mounds
Authors: Fall Saliou , Hamelin Jérôme , Ndiaye Farma , Assigbetse Komi , Aragno Michel , Chotte Jean Luc , Brauman Alain
Published: June 2007

In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by theActinobacteriaphylum, whereas theFirmicutesandProteobacteriaphyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering ofActinobacteriaphylotypes between the mound and the surrounding soil. TheActinobacteriaclones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by theNocardioidaceaefamily. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.
Cloning of a Novel Aldo-Keto Reductase Gene from
Klebsiella
sp. Strain F51-1-2 and Its Functional Expression in
Escherichia coli
Authors: Jiang Hong , Yang Chao , Qu Hong , Liu Zheng , Fu Q. S. , Qiao Chuanling
Published: June 2007

A soil bacterium capable of metabolizing organophosphorus compounds by reducing the P═S group in the molecules was taxonomically identified as
Klebsiella
sp. strain F51-1-2. The gene involved in the reduction of organophosphorus compounds was cloned from this strain by the shotgun technique, and the deduced protein (named AKR5F1) showed homology to members of the aldo-keto reductase (AKR) superfamily. The intact coding region for AKR5F1 was subcloned into vector pET28a and overexpressed in
Escherichia coli
BL21(DE3). Recombinant His
6
-tagged AKR5F1 was purified in one step using Ni-nitrilotriacetic acid affinity chromatography. Assays for cofactor specificity indicated that reductive transformation of organophosphorus compounds by the recombinant AKR5F1 specifically required NADH. The kinetic constants of the purified recombinant AKR5F1 toward six thion organophosphorus compounds were determined. For example, the

K
m

and
k
cat
values of reductive transformation of malathion by the purified recombinant AKR5F1 are 269.5 ± 47.0 μΜ and 25.7 ± 1.7 min
−1
, respectively. Furthermore, the reductive transformation of organophosphorus compounds can be largely explained by structural modeling.
Frataxin, a Conserved Mitochondrial Protein, in the Hydrogenosome of
Trichomonas vaginalis
Authors: Dolezal Pavel , Dancis Andrew , Lesuisse Emmanuel , Sutak Róbert , Hrdý Ivan , Embley T. Martin , Tachezy Jan
Published: June 2007

Recent data suggest that frataxin plays a key role in eukaryote cellular iron metabolism, particularly in mitochondrial heme and iron-sulfur (FeS) cluster biosynthesis. We have now identified a frataxin homologue (
T. vaginalis
frataxin) from the human parasite
Trichomonas vaginalis
. Instead of mitochondria, this unicellular eukaryote possesses hydrogenosomes, peculiar organelles that produce hydrogen but nevertheless share common ancestry with mitochondria.
T. vaginalis
frataxin contains conserved residues implicated in iron binding, and in silico, it is predicted to form a typical α-β sandwich motif. The short N-terminal extension of
T. vaginalis
frataxin resembles presequences that target proteins to hydrogenosomes, a prediction confirmed by the results of overexpression of
T. vaginalis
frataxin in
T. vaginalis
. When expressed in the mitochondria of a frataxin-deficient
Saccharomyces cerevisiae
strain,
T. vaginalis
frataxin partially restored defects in heme and FeS cluster biosynthesis. Although components of heme synthesis or heme-containing proteins have not been found in
T. vaginalis
to date,
T. vaginalis
frataxin was also shown to interact with
S. cerevisiae
ferrochelatase by using a Biacore assay. The discovery of conserved iron-metabolizing pathways in mitochondria and hydrogenosomes provides additional evidence not only of their common evolutionary history, but also of the fundamental importance of this pathway for eukaryotes.
Self-Aggregation of
Cryptococcus neoformans
Capsular Glucuronoxylomannan Is Dependent on Divalent Cations
Authors: Nimrichter Leonardo , Frases Susana , Cinelli Leonardo P. , Viana Nathan B. , Nakouzi Antonio , Travassos Luiz R. , Casadevall Arturo , Rodrigues Marcio L.
Published: June 2007

The capsular components of the human pathogen
Cryptococcus neoformans
are transported to the extracellular space and then used for capsule enlargement by distal growth. It is not clear, however, how the glucuronoxylomannan (GXM) fibers are incorporated into the capsule. In the present study, we show that concentration of
C. neoformans
culture supernatants by ultrafiltration results in the formation of highly viscous films containing pure polysaccharide, providing a novel, nondenaturing, and extremely rapid method to isolate extracellular GXM. The weight-averaged molecular mass of GXM in the film, determined using multiangle laser light scattering, was ninefold smaller than that of GXM purified from culture supernatants by differential precipitation with cetyl trimethyl ammonium bromide (CTAB). Polysaccharides obtained either by ultrafiltration or by CTAB-mediated precipitation showed different reactivities with GXM-specific monoclonal antibodies. Viscosity analysis associated with inductively coupled plasma mass spectrometry and measurements of zeta potential in the presence of different ions implied that polysaccharide aggregation was a consequence of the interaction between the carboxyl groups of glucuronic acid and divalent cations. Consistent with this observation, capsule enlargement in living
C. neoformans
cells was influenced by Ca
2+
in the culture medium. These results suggest that capsular assembly in
C. neoformans
results from divalent cation-mediated self-aggregation of extracellularly accumulated GXM molecules.
Differential Regulation of Two Oligogalacturonate Outer Membrane Channels, KdgN and KdgM, ofDickeya dadantii(Erwinia chrysanthemi)
Authors: Condemine Guy , Ghazi Alexandre
Published: June 2007

The entry of oligogalacturonates intoDickeya dadantiioccurs through the specific channel KdgM. The genome of the bacterium encodes a second member of this family of outer membrane proteins, KdgN. We showed that this protein is also involved in the uptake of oligogalacturonates. When KdgN was reconstituted in proteoliposomes, it formed channels with a conductance of about 450 pS at a positive potential. These channels had weak anionic selectivity. The regulation ofkdgNis complex, and five genes controlling the expression ofkdgNhave been identified:kdgR,pecS,ompR,hns, andcrp. Moreover,kdgNwas regulated by growth phase but only when bacteria were grown in rich medium. Most of these regulators ofkdgNalso controlkdgMexpression, but some of them regulatekdgMin the opposite manner: while PecS and OmpR are repressors ofkdgM, they are activators ofkdgN. This pattern resembles the regulation of theEscherichia coligeneral porins OmpF and OmpC, but such opposite regulation of two specific outer membrane channels has never been described before. KdgN may allow the bacteria to collect oligogalacturonates under saprophytic conditions, when virulence genes, includingkdgM, are not expressed.
Identification of Genes in
Xanthomonas campestris
pv. vesicatoria Induced during Its Interaction with Tomato
Authors: Tamir-Ariel Dafna , Navon Naama , Burdman Saul
Published: June 2007

Xanthomonas campestris
pv. vesicatoria is the causal agent of bacterial spot disease of tomato and pepper. The disease process is interactive and very intricate and involves a plethora of genes in the pathogen and in the host. In the pathogen, different genes are activated in response to the changing environment to enable it to survive, adapt, evade host defenses, propagate, and damage the host. To understand the disease process, it is imperative to broaden our understanding of the gene machinery that participates in it, and the most reliable way is to identify these genes in vivo. Here, we have adapted a recombinase-based in vivo expression technology (RIVET) to study the genes activated in
X. campestris
pv. vesicatoria during its interaction with one of its hosts, tomato. This is the first study that demonstrates the feasibility of this approach for identifying in vivo induced genes in a plant pathogen. RIVET revealed 61 unique
X. campestris
pv. vesicatoria genes or operons that delineate a picture of the different processes involved in the pathogen-host interaction. To further explore the role of some of these genes, we generated knockout mutants for 13 genes and characterized their ability to grow in planta and to cause disease symptoms. This analysis revealed several genes that may be important for the interaction of the pathogen with its host, including a
citH
homologue gene, encoding a citrate transporter, which was shown to be required for wild-type levels of virulence.
Molecular Characterization of Class 3 Integrons fromDelftiaspp
Authors: Xu Hai , Davies Julian , Miao Vivian
Published: June 2007

Two environmental strains,Delftia acidovoransC17 andDelftia tsuruhatensisA90, were found to carry class 3 integrons, which have seldom been reported and then only from pathogens in which they are associated with antibiotic resistance genes. TheDelftiaintegrons comprised a highly conserved class 3 integrase gene, upstream and oppositely oriented from a set of three or four gene cassettes that encoded unidentified functions. The A90 integron had one more gene cassette than the C17 integron, but the two were otherwise the same; furthermore, they were located within regions of sequence identity in both strains and linked to chromosomal genes. A screen of otherDelftiaand related strains did not reveal the presence of additional class 3 integrons. The observations suggest that these integrons were horizontally transferred toDelftiaas part of a larger region and reside as chromosomal elements that probably predate transposon dissemination, as has been proposed for certain class 1 integrons.
A Second Large Plasmid Encodes Conjugative Transfer and Antimicrobial Resistance in O119:H2 and Some Typical O111 Enteropathogenic
Escherichia coli
Strains
Authors: Nwaneshiudu Adaobi I. , Mucci Tania , Pickard Derek J. , Okeke Iruka N.
Published: June 2007

A novel and functional conjugative transfer system identified in O119:H2 enteropathogenic
Escherichia coli
(EPEC) strain MB80 by subtractive hybridization is encoded on a large multidrug resistance plasmid, distinct from the well-described EPEC adherence factor (EAF) plasmid. Variants of the MB80 conjugative resistance plasmid were identified in other EPEC strains, including the prototypical O111:NM strain B171, from which the EAF plasmid has been sequenced. This separate large plasmid and the selective advantage that it confers in the antibiotic era have been overlooked because it comigrates with the virulence plasmid on conventional gels.
Pseudomonas aeruginosa
Type IV Pilus Expression in
Neisseria gonorrhoeae
: Effects of Pilin Subunit Composition on Function and Organelle Dynamics
Authors: Winther-Larsen Hanne C. , Wolfgang Matthew C. , van Putten Jos P. M. , Roos Norbert , Aas Finn Erik , Egge-Jacobsen Wolfgang M. , Maier Berenike , Koomey Michael
Published: June 2007

Type IV pili (TFP) play central roles in the expression of many phenotypes including motility, multicellular behavior, sensitivity to bacteriophages, natural genetic transformation, and adherence. In
Neisseria gonorrhoeae
, these properties require ancillary proteins that act in conjunction with TFP expression and influence organelle dynamics. Here, the intrinsic contributions of the pilin protein itself to TFP dynamics and associated phenotypes were examined by expressing the
Pseudomonas aeruginosa
PilA
PAK
pilin subunit in
N. gonorrhoeae
. We show here that, although PilA
PAK
pilin can be readily assembled into TFP in this background, steady-state levels of purifiable fibers are dramatically reduced relative those of endogenous pili. This defect is due to aberrant TFP dynamics as it is suppressed in the absence of the PilT pilus retraction ATPase. Functionally, PilA
PAK
pilin complements gonococcal adherence for human epithelial cells but only in a
pilT
background, and this property remains dependent on the coexpression of both the PilC adhesin and the PilV pilin-like protein. Since
P. aeruginosa
pilin only moderately supports neisserial sequence-specific transformation despite its assembly proficiency, these results together suggest that PilA
PAK
pilin functions suboptimally in this environment. This appears to be due to diminished compatibility with resident proteins essential for TFP function and dynamics. Despite this, PilA
PAK
pili support retractile force generation in this background equivalent to that reported for endogenous pili. Furthermore, PilA
PAK
pili are both necessary and sufficient for bacteriophage PO4 binding, although the strain remains phage resistant. Together, these findings have significant implications for TFP biology in both
N. gonorrhoeae
and
P. aeruginosa
.
Conjugal Transfer of Chromosomal DNA Contributes to Genetic Variation in the Oral Pathogen
Porphyromonas gingivalis
Authors: Tribble Gena D. , Lamont Gwyneth J. , Progulske-Fox Ann , Lamont Richard J.
Published: June 2007

Porphyromonas gingivalis
is a major oral pathogen that contributes to the development of periodontal disease. There is a significant degree of genetic variation among strains of
P. gingivalis
, and the population structure has been predicted to be panmictic, indicating that horizontal DNA transfer and recombination between strains are likely. The molecular events underlying this genetic exchange are not understood, although a putative type IV secretion system is present in the genome sequence of strain W83, implying that DNA conjugation may be responsible for genetic transfer in these bacteria. In this study, we provide in vitro evidence for the horizontal transfer of DNA using plasmid- and chromosome-based assays. In the plasmid assays,
Bacteroides
-derived shuttle vectors were tested for transfer from
P. gingivalis
strains into
Escherichia coli
. Of the eight strains tested, five were able to transfer DNA into
E. coli
by a mechanism most consistent with conjugation. Additionally, strains W83 and 33277 tested positive for the transfer of chromosomally integrated antibiotic resistance markers. Ten chimeras resulting from the chromosomal transfer assay were further analyzed by Southern hybridization and were shown to have exchanged DNA fragments of between 1.1 and 5.6 kb, but the overall strain identity remained intact. Chimeras showed phenotypic changes in the ability to accrete into biofilms, implying that DNA transfer events are sufficient to generate measurable changes in complex behaviors. This ability to transfer chromosomal DNA between strains may be an adaptation mechanism in the complex environment of the host oral cavity.
Hypoxic preconditioning induces elevated expression of stanniocalcin-1 in the heart
Authors: Westberg Johan A. , Serlachius Martina , Lankila Petri , Andersson Leif C.
Published: June 2007

Animals exposed for a few hours to low oxygen content (8%) develop resistance against further ischemic myocardial damage. The molecular mechanism(s) behind this phenomenon, known as hypoxic preconditioning (HOPC), is still incompletely understood. Stanniocalcin-1 (STC-1) is an evolutionarily conserved glycoprotein originally discovered in fish, in which it regulates calcium/phosphate homeostasis and protects against toxic hypercalcemia. Our group originally reported expression of mammalian STC-1 in brain neurons and showed that STC-1 is a prosurvival factor that guards neurons against hypercalcemic and hypoxic damage. This study investigates the involvement of STC-1 in HOPC-induced cardioprotection. Wild-type mice and IL-6-deficient ( Il-6−/−) mice were kept in hypoxic conditions (8% O2) for 6 h. Myocardial Stc-1 mRNA expression was quantified during hypoxia and after recovery. HOPC triggered a biphasic upregulation of Stc-1 expression in hearts of wild-type mice but not in those of Il-6−/−mice. Treatment of cardiomyocyte cells in culture with hypoxia or IL-6 elicited an Stc-1 response, and ectopically expressed STC-1 in HL-1 cells localized to the mitochondria. Our findings indicate that IL-6-induced expression of STC-1 is one molecular mechanism behind the ischemic tolerance generated by HOPC in the heart.