bluuebunny/crossref_metadata_2025 huggingface dataset:
Colonialism's Civilizing Mission: The Case of the Indian Hemp Drug Commission
Authors: Shamir Ronen , Hacker Daphna
Published: August 2006

This paper examines a particular episode in the history of British imperialism in India: the appointment of the Indian Hemp Drug Commission in 1893. We analyze the way a quasi-judicial investigation into the consumption of drugs was differently conceived and executed as a civilizing mission by, on the one hand, British colonizers, and, on the other hand, an aspiring colonized elite. By bringing together the ideological dimensions of a civilizing mission (e.g., the reliance on scientific knowledge, groper procedures, legal techniques) with its social ones (e.g., collaboration between colonizers and a local elite), we show how the very notion of a civilizing mission became a site of struggle over meaning, identity, and desirable forms of governance. The analysis reveals a local elite struggling to position itself at once on a par with British criteria of scientific competence and yet not as a mere proxy for British interests; at once able to articulate itself in terms of enlightenment concepts such as reason and modernity and yet celebrating its own distinct cultural authenticity.
Genetics of Ischaemic Stroke; Single Gene Disorders
Authors: Flossmann Enrico
Published: August 2006

Examples of single gene disorders have been described for all major subtypes of ischaemic stroke: accelerated atherosclerosis and subsequent thrombo-embolism (e.g. homocysteinuria), weakening of connective tissue resulting in arterial dissections (e.g. Ehler–Danlos type IV), disorders of cerebral small vessels (e.g. cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy and the collagen COL4A1 mutation), disorders increasing the thrombogenic potential of the heart through affecting the myocardium or the heart valves or through disturbance of the heart rhythm (e.g. hypertrophic cardiomyopathy), mitochondrial cytopathies increasing cerebral tissue susceptibility to insults (e.g. mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes), and finally disorders of coagulation that can either directly cause stroke or act synergistically with the aforementioned abnormalities (e.g. sickle cell disease). Most of these disorders are rare but they are important to consider particularly in young patients with stroke, those with a family history or those who have other characteristics of a particular syndrome.
Reducing Stroke Risk in Hypertensive Patients: Asian Consensus Conference Recommendations
Authors: Liu Li Sheng , Caguioa Eduardo S. , Park Chang-Gyu , Quek David Kwang Leng , Saito Ikuo , Venketasubramanian Narayanaswamy , Wong Ka Sing Lawrence , Reid John L.
Published: August 2006

Stroke results in substantial morbidity and mortality globally. Asia-Pacific countries bear a disproportionate share of the burden of stroke, a burden that will grow as their populations' life expectancies rise. Hypertension is the single most important reversible risk factor for stroke, and effective measures to reduce blood pressure contribute significantly to reducing the incidence of stroke. The Asia-Pacific Consensus Conference on Stroke Prevention in Hypertensive Patients assembled leading experts from the region to reach an actionable consensus aimed at reducing stroke-induced morbidity and mortality in Asia through the evidence-based treatment of hypertension. The discussions of the group focused on how best to improve blood pressure control, how to promote lifestyle changes at the population level, and how to reduce the clinical and health system barriers and other challenges facing developing and low-income countries. The experts concluded that physicians must place an increased priority on reducing their patients' risk of stroke and recognise that all hypertensive patients are at greater risk of having a stroke compared with nonhypertensive individuals. They advocated that physicians must educate hypertensive patients about the risk of stroke, promote lifestyle modification to all patients diagnosed with hypertension, and prescribe rigorous antihypertensive treatment to get patients to recommended blood pressure goals.
Medical and Surgical Management of Symptomatic Carotid Stenosis
Authors: Rothwell Peter M.
Published: August 2006

Carotid bifurcation stenosis is an important cause of ischaemic stroke, particularly in patients with recent transient ischaemic attack or minor stroke. Large randomized trials of endarterectomy have shown that surgery reduces the risk of stroke in patients with ≥ 50% recently symptomatic carotid stenosis, and more recent research has gone some way to wards identifying which patients benefit the most. Individual risk modelling has been shown to be useful in selecting patients with the most to gain from endarterectomy for symptomatic stenosis, although timely surgery and optimal medical treatment are of equal importance.
Production of β‐Cryptoxanthin, a Provitamin‐A Precursor, by Flavobacterium Lutescens
Authors: Serrato‐Joya O. , Jiménez‐Islas H. , Botello‐Álvarez E. , Rico‐Martínez R. , Navarrete‐Bolaños J.L.
Published: August 2006

ABSTRACT:  Vitamin A deficiency (VAD) is the leading cause of preventable blindness in children and raises the risk of disease and death from severe infections. Some plant foods contain darkly colored pigments with provitamin A activity (α‐carotene, β‐carotene, and β‐cryptoxanthin) that can be converted to vitamin A. In this work, a process is described for β‐cryptoxanthin production by Flavobacterium lutescens ITCB008 using fermentation technology. The critical process variables associated with batch fermentation production in a stirred vessel were evaluated and quantified based on experimental design strategies. An ad hoc mathematical model was constructed and used to identify the operating conditions (agitation 190 rpm, aeration 0.086 VVM [air volume/broth volume per minute], and temperature 27.6 °C, pH 7.3) that maximized β‐cryptoxanthin synthesis (770 mg of β‐cryptoxanthin/kg biomass; dry weight) in a short processing time (28 h). In addition, downstream‐processing studies were performed revealing that extraction of β‐cryptoxanthin can be achieved with a polar solvent that produces cell lysis, such as methanol or ethanol, in only 1 step. High performance liquid chromatography analysis showed that β‐cryptoxanthin represents nearly 95% of the total carotenoid content in the obtained product. The process described could be a commercial alternative for producing β‐cryptoxanthin additives, as supplement in food formulation, thus assisting VAD prevention.
Enhancement of Omega‐3 Fatty Acid Content in Rainbow Trout (Oncorhynchus mykiss) Fillets
Authors: Chen Y.C. , Nguyen J. , Semmens K. , Beamer S. , Jaczynski J.
Published: August 2006

ABSTRACT:  A commercial diet for rainbow trout (Oncorhynchus mykiss) was supplemented with 0 (control), 8.5%, or 15.0% (w/w) of flaxseed oil (FO). Trouts were harvested on days 0, 30, 60, 90, and 120. Boneless skinless trout fillets were recovered from fish and analyzed for fatty acid profile (FAP) and total fat. While the total fat levels of fillets were not (P > 0.05) affected by FO supplementation, the FAP was. The lowest (P < 0.05) proportion of saturated fatty acids was obtained from 15%, followed by 8.5% FO group, and the control group. The opposite results were observed for the unsaturated fatty acids. The highest (P < 0.05) content of omega‐3 fatty acids (ω‐3 FA) in fillets was determined in the 15.0%, followed by the 8.5% FO group, and the control group. While the 15.0% and 8.5% of FO supplementation increased (P < 0.05) concentration of linolenic acid (ALA, 18:3n3) in fillets, the eicosapentaenoic (EPA, 20:5n3) and docosahexaenoic acids (DHA, 22:6n3) contents decreased (P < 0.05). At the same time, higher (P < 0.05) concentration of linoleic (L, 18:2n6) and lower (P < 0.05) concentration of arachidonic acids (AN, 20:4n6) in fillets were obtained in the 15.0% FO group compared with the control group. The ω‐3/ω‐6 FA ratio was also improved (P < 0.05) by supplementing basal diet with 15.0% FO. Our results suggest that trout fillets with enhanced content of ω‐3 FA can be developed from trout raised in aquaculture systems fed diets supplemented with 15.0% FO. These fillets could be a basis to develop novel functional aquatic foods for some niche markets.
Amino Acid Absorption in Portal Blood After Duodenal Infusions of a Soy Protein Hydrolysate Prepared by a Novel Soybean Protease D3
Authors: Kodera Tomohiro , Hara Hiroshi , Nishimori Yuki , Nio Noriki
Published: August 2006

ABSTRACT:  The intestinal absorption of amino acids from decapeptide was investigated in rats under unrestrained conditions. The soy protein hydrolysate utilized in the experiment was produced by a novel soybean protease D3. The enzymatic features of protease D3 showed high homology with cathepsin L and cathepsin K and the average molecular weight of D3 hydrolysate is approximately 1200. We compared the intestinal absorption of D3 hydrolysate in portal blood with that of an amino acids mixture and soy protein with the same amino acid composition by determining the concentration of individual amino acids after a single administration of a nitrogen source. The absorptive velocity and intensity of each amino acid were calculated from its rate of elevation in the portal blood. And in most cases, these were higher in the D3 hydrolysate than in amino acids mixture and protein. The proportion of the amount of each amino acid absorbed in portal blood from D3 hydrolysate was much more like the composition of the administrated amino acids than like that from the amino acids mixture. The result of in vitro digestion assay indicated that D3 hydrolysate was hydrolyzed easier than the hydrolysates produced by microbial proteases. This is the first report to demonstrate that the D3 hydrolysate, which contains decapeptide as a dominant fraction, was more rapidly utilized than the amino acids mixture and protein as is the case with di‐, tripeptides. This suggested that this hydrolysate could be available for nutraceutical use as well as use in nutritious foods for athletes and patients.
Reduction of Aflatoxins by Extrusion‐Cooking of Rice Meal
Authors: Castells Miren , Marín Sonia , Sanchis Vicente , Ramos Antonio J.
Published: August 2006

ABSTRACT:  The objective of this work was to determine the reduction of aflatoxin B1 (AFB1), B2 (AFB2), G1 (AFG1), and G2 (AFG2) as a function of initial moisture content of samples (24%, 27%, and 30%), barrel temperature (140, 170, and 200 °C), and residence time (30 to 70 s) when artificially contaminated rice meal was extrusion‐cooked. Extruded and unextruded samples were analyzed by high‐performance liquid chromatography (HPLC). Extrusion‐cooking was observed to reduce aflatoxin (AF) content, which ranged from 51% to 95% depending on the type of AF and the studied variables. Only in the case of AFG2 was it found that the higher the temperature, the higher the moisture content, and the longer the residence time, the greater the reduction. Moisture content had a significant influence on reducing AFB2, AFG1, and AFG2 whereas it was not a significant factor affecting the levels of AFB1. Regardless of the type of AF, the lowest reductions were achieved at a temperature of 140 °C. Even though theoretically greater losses would be expected at highest temperature, AFB1 and AFB2 were more reduced by 170 °C than by 200 °C while AFG1 reductions were not statistically different when processing at 170 °C and 200 °C. The decrease of AF followed 1st‐order kinetics; the fastest treatment in reducing AF was that at 200 °C when samples containing AFG2 were wetted to 24% and when samples containing AFB1, AFB2, and AFG1 were hydrated to 27%. By contrast, the slowest treatments were observed at a barrel temperature of 140 °C.
Placement of a long term tracheal cannula in a Thoroughbred racehorse with bilateral laryngeal dysfunction
Authors: SCHAAF KL , KANNEGIETER NJ , LOVELL DK
Published: August 2006

A Thoroughbred horse with bilateral laryngeal dysfunction was treated by placement of a long term tracheal cannula in order to restore full athletic function. The horse initially presented with right‐sided arytenoid dysfunction that was considered to be due to a congenital malformation of the laryngeal cartilage. This was corrected by a right‐sided laryngoplasty and ventriculectomy. The horse re‐presented 1 year later with idiopathic left laryngeal hemiplegia. The decision was made to place a long‐term tracheal cannula due to the low success rate and high complication rate associated with other surgeries used to correct bilateral arytenoid dysfunction.

A three‐piece tracheotomy cannula and stopper were positioned under general anaesthesia. The horse rapidly adjusted to the tracheal cannula and no post‐surgical complications were encountered. The horse resumed training 4 weeks postoperatively. Due to the rules governing racing in Australia the horse was exported to New Zealand where he continued his racing career.

It was concluded that tracheotomy is a straightforward technique associated with minimal complications and can provide an excellent prognosis for return of full airway function in racing horses. It is recognised that many issues need to be considered prior to more general acceptance of this technique, including assessment of animal welfare issues and public perception. In appropriate cases consideration should be given to using long term placement of a tracheotomy cannula as a treatment option to restore maximal airflow in horses with upper airway obstruction.
Genetic Diversity of
Borrelia burgdorferi
Sensu Stricto in
Peromyscus leucopus
, the Primary Reservoir of Lyme Disease in a Region of Endemicity in Southern Maryland
Authors: Anderson Jennifer M. , Norris Douglas E.
Published: August 2006

In the north central and northeastern United States,
Borrelia burgdorferi
sensu stricto, the etiologic agent of Lyme disease (LD), is maintained in an enzootic cycle between the vector,
Ixodes scapularis
, and the primary reservoir host,
Peromyscus leucopus
. Genetic diversity of the pathogen based on sequencing of two plasmid-located genes, those for outer surface protein A (
ospA
) and outer surface protein C (
ospC
), has been examined in both tick and human specimens at local, regional, and worldwide population scales. Additionally, previous studies have only been conducted with tick or human specimens at the local population level in areas with high LD transmission rates. This study examined the genetic diversity of circulating borreliae in the reservoir population from a large region of the western coastal plains of southern Maryland, where moderate numbers of human LD cases are reported. Six
ospA
mobility classes, including two that were not previously described, and eight
ospC
groups were found among the
P. leucopus
samples. Twenty-five percent of all specimens were infected with more than one
ospA
or
ospC
variant. The frequency distribution of variants was homogeneous, both locally and spatially. The spirochete diversity found in Maryland was not as high as that observed among northern tick populations, yet similar genotypes were observed in both populations. These results also show that mice are important for maintaining
Borrelia
variants, even rare variants, and that reservoir populations should therefore be considered when assessing the diversity of
B. burgdorferi
.
Isolation and Identification ofRickettsia massiliaefromRhipicephalus sanguineusTicks Collected in Arizona
Authors: Eremeeva Marina E. , Bosserman Elizabeth A. , Demma Linda J. , Zambrano Maria L. , Blau Dianna M. , Dasch Gregory A.
Published: August 2006

TwentyRhipicephalus sanguineusticks collected in eastern Arizona were tested by PCR assay to establish their infection rate with spotted fever group rickettsiae. With a nested PCR assay which detects a fragment of theRickettsiagenus-specific 17-kDa antigen gene (htrA), five ticks (25%) were found to contain rickettsial DNA. One rickettsial isolate was obtained from these ticks by inoculating a suspension of a triturated tick into monolayers of Vero E6 monkey kidney cells and XTC-2 clawed toad cells, and its cell culture and genotypic characteristics were determined. Fragments of the 16S rRNA, GltA, rOmpA, rOmpB, and Sca4 genes had 100%, 100%, 99%, 99%, and 99%, respectively, nucleotide similarity toRickettsia massiliaestrain Bar29, previously isolated fromR. sanguineusin Catalonia, Spain (L. Beati et al., J. Clin. Microbiol.34:2688-2694, 1996). The new isolate, AZT80, does not elicit cytotoxic effects in Vero cells and causes a persistent infection in XTC-2 cells. The AZT80 strain is susceptible to doxycycline but resistant to rifampin and erythromycin. WhetherR. massiliaeAZT80 is pathogenic or infectious for dogs and humans or can cause seroconversion to spotted fever group antigens in the United States is unknown.
Molecular Profiling of theClostridium leptumSubgroup in Human Fecal Microflora by PCR-Denaturing Gradient Gel Electrophoresis and Clone Library Analysis
Authors: Shen Jian , Zhang Baorang , Wei Guifang , Pang Xiaoyan , Wei Hua , Li Min , Zhang Yan , Jia Wei , Zhao Liping
Published: August 2006

A group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with group-specific clone library analysis to investigate the diversity of theClostridium leptumsubgroup in human feces. PCR products (length, 239 bp) were amplified usingC. leptumcluster-specific primers and were well separated by DGGE. The DGGE patterns of fecal amplicons from 11 human individuals revealed host-specific profiles; the patterns for fecal samples collected from a child for 3 years demonstrated the structural succession of the population in the first 2 years and its stability in the third year. A clone library was constructed with 100 clones consisting of 1,143-bp inserts of 16S rRNA gene fragments that were amplified from one adult fecal DNA with one forward universal bacterial primer and one reverse group-specific primer. Eighty-six of the clones produced the 239-bpC. leptumcluster-specific amplicons, and the remaining 14 clones did not produce these amplicons but still phylogenetically belong to the subgroup. Sixty-four percent of the clones were related toFaecalibacterium prausnitzii(similarity, 97 to 99%), 6% were related toSubdoligranulum variabile(similarity, ∼99%), 2% were related to butyrate-producing bacterium A2-207 (similarity, 99%), and 28% were not identified at the species level. The identities of most bands in the DGGE profiles for the same adult were determined by comigration analysis with the 86 clones that harbored the 239-bp group-specific fragments. Our results suggest that DGGE combined with clone library analysis is an effective technique for monitoring and analyzing the composition of this important population in the human gut flora.
Biodegradation of Ether Pollutants by
Pseudonocardia
sp. Strain ENV478
Authors: Vainberg Simon , McClay Kevin , Masuda Hisako , Root Duane , Condee Charles , Zylstra Gerben J. , Steffan Robert J.
Published: August 2006

A bacterium designated
Pseudonocardia
sp. strain ENV478 was isolated by enrichment culturing on tetrahydrofuran (THF) and was screened to determine its ability to degrade a range of ether pollutants. After growth on THF, strain ENV478 degraded THF (63 mg/h/g total suspended solids [TSS]), 1,4-dioxane (21 mg/h/g TSS), 1,3-dioxolane (19 mg/h/g TSS),
bis
-2-chloroethylether (BCEE) (12 mg/h/g TSS), and methyl
tert
-butyl ether (MTBE) (9.1 mg/h/g TSS). Although the highest rates of 1,4-dioxane degradation occurred after growth on THF, strain ENV478 also degraded 1,4-dioxane after growth on sucrose, lactate, yeast extract, 2-propanol, and propane, indicating that there was some level of constitutive degradative activity. The BCEE degradation rates were about threefold higher after growth on propane (32 mg/h/g TSS) than after growth on THF, and MTBE degradation resulted in accumulation of
tert
-butyl alcohol. Degradation of 1,4-dioxane resulted in accumulation of 2-hydroxyethoxyacetic acid (2HEAA). Despite its inability to grow on 1,4-dioxane, strain ENV478 degraded this compound for >80 days in aquifer microcosms. Our results suggest that the inability of strain ENV478 and possibly other THF-degrading bacteria to grow on 1,4-dioxane is related to their inability to efficiently metabolize the 1,4-dioxane degradation product 2HEAA but that strain ENV478 may nonetheless be useful as a biocatalyst for remediating 1,4-dioxane-contaminated aquifers.
Quantitative Detection of the
nosZ
Gene, Encoding Nitrous Oxide Reductase, and Comparison of the Abundances of 16S rRNA,
narG
,
nirK
, and
nosZ
Genes in Soils
Authors: Henry S. , Bru D. , Stres B. , Hallet S. , Philippot L.
Published: August 2006

Nitrous oxide (N
2
O) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. In order to quantify bacteria capable of N
2
O reduction, we developed a SYBR green quantitative real-time PCR assay targeting the
nosZ
gene encoding the catalytic subunit of the nitrous oxide reductase. Two independent sets of
nosZ
primers flanking the
nosZ
fragment previously used in diversity studies were designed and tested (K. Kloos, A. Mergel, C. Rösch, and H. Bothe, Aust. J. Plant Physiol. 28:991-998, 2001). The utility of these real-time PCR assays was demonstrated by quantifying the
nosZ
gene present in six different soils. Detection limits were between 10
1
and 10
2
target molecules per reaction for all assays. Sequence analysis of 128 cloned quantitative PCR products confirmed the specificity of the designed primers. The abundance of
nosZ
genes ranged from 10
5
to 10
7
target copies g
−1
of dry soil, whereas genes for 16S rRNA were found at 10
8
to 10
9
target copies g
−1
of dry soil. The abundance of
narG
and
nirK
genes was within the upper and lower limits of the 16S rRNA and
nosZ
gene copy numbers. The two sets of
nosZ
primers gave similar gene copy numbers for all tested soils. The maximum abundance of
nosZ
and
nirK
relative to 16S rRNA was 5 to 6%, confirming the low proportion of denitrifiers to total bacteria in soils.
Screening for and Identification of Starch-, Amylopectin-, and Pullulan-Degrading Activities in Bifidobacterial Strains
Authors: Ryan Sinéad M. , Fitzgerald Gerald F. , van Sinderen Douwe
Published: August 2006

Forty-two bifidobacterial strains were screened for α-amylase and/or pullulanase activity by investigating their capacities to utilize starch, amylopectin, or pullulan. Of the 42 bifidobacterial strains tested, 19 were capable of degrading potato starch. Of these 19 strains, 11 were able to degrade starch and amylopectin, as well as pullulan. These 11 strains, which were shown to produce extracellular starch-degrading activities, included 5 strains of
Bifidobacterium breve
, 1
B. dentium
strain, 1
B. infantis
strain, 3 strains of
B. pseudolongum
, and 1 strain of
B. thermophilum
. Quantitative and qualitative enzyme activities were determined by measuring the concentrations of released reducing sugars and by high-performance thin-layer chromatography, respectively. These analyses confirmed both the inducible nature and the extracellular nature of the starch- and pullulan-degrading enzyme activities and showed that the five
B. breve
strains produced an activity that is consistent with type II pullulanase (amylopullulanase) activity, while the remaining six strains produced an activity with properties that resemble those of type III pullulan hydrolase.
Deletion Mutations Caused by DNA Strand Slippage in
Acinetobacter baylyi
Authors: Gore Jeremy M. , Ran F. Ann , Ornston L. Nicholas
Published: August 2006

Short nucleotide sequence repetitions in DNA can provide selective benefits and also can be a source of genetic instability arising from deletions guided by pairing between misaligned strands. These findings raise the question of how the frequency of deletion mutations is influenced by the length of sequence repetitions and by the distance between them. An experimental approach to this question was presented by the heat-sensitive phenotype conferred by
pcaG1102
, a 30-bp deletion in one of the structural genes for
Acinetobacter baylyi
protocatechuate 3,4-dioxygenase, which is required for growth with quinate. The original
pcaG1102
deletion appears to have been guided by pairing between slipped DNA strands from nearby repeated sequences in wild-type
pcaG
. Placement of an in-phase termination codon between the repeated sequences in
pcaG
prevents growth with quinate and permits selection of sequence-guided deletions that excise the codon and permit quinate to be used as a growth substrate at room temperature. Natural transformation facilitated introduction of 68 different variants of the wild-type repeat structure within
pcaG
into the
A. baylyi
chromosome, and the frequency of deletion between the repetitions was determined with a novel method, precision plating. The deletion frequency increases with repeat length, decreases with the distance between repeats, and requires a minimum amount of similarity to occur at measurable rates. Deletions occurred in a
recA
-deficient background. Their frequency was unaffected by deficiencies in
mutS
and was increased by inactivation of
recG
.
Occurrence of Ammonia-Oxidizing Archaea in Wastewater Treatment Plant Bioreactors
Authors: Park Hee-Deung , Wells George F. , Bae Hyokwan , Criddle Craig S. , Francis Christopher A.
Published: August 2006

We report molecular evidence that ammonia-oxidizing archaea (AOA) occur in activated sludge bioreactors used to remove ammonia from wastewater. Using PCR primers targeting archaeal ammonia monooxygenase subunit A (
amoA
) genes, we retrieved and compared 75 sequences from five wastewater treatment plants operating with low dissolved oxygen levels and long retention times. All of these sequences showed similarity to sequences previously found in soil and sediments, and they were distributed primarily in four major phylogenetic clusters. One of these clusters contained virtually identical
amoA
sequences obtained from all five activated sludge samples (from Oregon, Wisconsin, Pennsylvania, and New Jersey) and accounted for 67% of all the sequences, suggesting that this AOA phylotype may be widespread in nitrifying bioreactors.
Hyperthermophilic DNA Methyltransferase M.PabI from the Archaeon
Pyrococcus abyssi
Authors: Watanabe Miki , Yuzawa Harumi , Handa Naofumi , Kobayashi Ichizo
Published: August 2006

Genome sequence comparisons among multiple species of
Pyrococcus
, a hyperthermophilic archaeon, revealed a linkage between a putative restriction-modification gene complex and several large genome polymorphisms/rearrangements. From a region apparently inserted into the
Pyrococcus abyssi
genome, a hyperthermoresistant restriction enzyme [PabI; 5′-(GTA/C)] with a novel structure was discovered. In the present work, the neighboring methyltransferase homologue, M.PabI, was characterized. Its N-terminal half showed high similarities to the M subunit of type I systems and a modification enzyme of an atypical type II system, M.AhdI, while its C-terminal half showed high similarity to the S subunit of type I systems. M.PabI expressed within
Escherichia coli
protected PabI sites from RsaI, a PabI isoschizomer. M.PabI, purified following overexpression, was shown to generate 5′-GTm6AC, which provides protection against PabI digestion. M.PabI was found to be highly thermophilic; it showed methylation at 95°C and retained at least half the activity after 9 min at 95°C. This hyperthermophilicity allowed us to obtain activation energy and other thermodynamic parameters for the first time for any DNA methyltransferases. We also determined the kinetic parameters of
k
cat
,

K
m

, DNA
, and

K
m

, AdoMet
. The activity of M.PabI was optimal at a slightly acidic pH and at an NaCl concentration of 200 to 500 mM and was inhibited by Zn
2+
but not by Mg
2+
, Ca
2+
, or Mn
2+
. These and previous results suggest that this unique methyltransferase and PabI constitute a type II restriction-modification gene complex that inserted into the
P. abyssi
genome relatively recently. As the most thermophilic of all the characterized DNA methyltransferases, M.PabI may help in the analysis of DNA methylation and its application to DNA engineering.
Diversity of
Bacillus anthracis
Strains in Georgia and of Vaccine Strains from the Former Soviet Union
Authors: Merabishvili Maya , Natidze Merab , Rigvava Sergo , Brusetti Lorenzo , Raddadi Noura , Borin Sara , Chanishvili Nina , Tediashvili Marina , Sharp Richard , Barbeschi Maurizio , Visca Paolo , Daffonchio Daniele
Published: August 2006

Despite the increased number of anthrax outbreaks in Georgia and the other Caucasian republics of the former Soviet Union, no data are available on the diversity of the
Bacillus anthracis
strains involved. There is also little data available on strains from the former Soviet Union, including the strains previously used for vaccine preparation. In this study we used eight-locus variable-number tandem repeat analyses to genotype 18 strains isolated from infected animals and humans at different sites across Georgia, where anthrax outbreaks have occurred in the last 10 years, and 5 strains widely used for preparation of human and veterinary vaccines in the former Soviet Union. Three different genotypes affiliated with the A3.a cluster were detected for the Georgian isolates. Two genotypes were previously shown to include Turkish isolates, indicating that there is a regional strain pattern in the South Caucasian-Turkish region. Four of the vaccine strains were polymorphic, exhibiting three different patterns of the cluster A1.a genotype and the cluster A3.b genotype. The genotype of vaccine strain 71/12, which is considered an attenuated strain in spite of the presence of both of the virulence pXO plasmids, appeared to be a novel genotype in the A1.a cluster.
Occurrence of
Cryptosporidium
Oocysts and
Giardia
Cysts in Sewage in Norway
Authors: Robertson L. J. , Hermansen L. , Gjerde B. K.
Published: August 2006

Samples of sewage influent from 40 sewage treatment works (STW) throughout Norway were examined for
Cryptosporidium
oocysts and
Giardia duodenalis
cysts. Both parasites were detected frequently (80% of STW were
Cryptosporidium
positive; 93% of STW were
Giardia
positive) and at maximum concentrations of >20,000 parasites/liter. The data suggest giardiasis is more widespread, and/or occurs with greater infection intensity, than cryptosporidiosis in Norway. STW serving higher person equivalents were more likely to be positive and had higher parasite concentrations. Parasite concentrations were used to estimate the proportion of contributing populations that could be clinically infected. For
Cryptosporidium
, the highest estimates were up to 5 per 100,000 individuals for two populations in eastern Norway. For
Giardia
, the highest estimate was 40 infected per 100,000 persons (approximately five times the usual national annual average) contributing to an STW in western Norway. As this population experienced a large waterborne giardiasis outbreak 6 months after sampling, it can be speculated that regular challenge with
Giardia
may occur here. Most
Giardia
isolates in sewage influent were assemblage A, although some assemblage B isolates were detected. There was substantial heterogeneity, but most samples contained isolates similar to genotype A3. Removal efficiencies at two STW with secondary treatment processes were estimated to be approximately 50% for
Cryptosporidium
and >80% for
Giardia
. An STW with minimal treatment had negligible removal of both parasites. Many STW in Norway have minimal treatment and discharge effluent into rivers and lakes, thus, risk of contamination of water courses by
Cryptosporidium
and
Giardia
is considerable.
Discovery of a Marine Bacterium Producing 4-Hydroxybenzoate and Its Alkyl Esters, Parabens
Authors: Peng Xue , Adachi Kyoko , Chen Choryu , Kasai Hiroaki , Kanoh Kaneo , Shizuri Yoshikazu , Misawa Norihiko
Published: August 2006

Chemically synthesized 4-hydroxybenzoate (4HBA) is widely used in the chemical and electrical industries as a material for producing polymers such as those of the liquid crystal type. Its alkyl esters, called parabens, have been the most widely used preservatives by the food and cosmetic industries. We report here for the first time a microorganism, a marine bacterium, which biosynthesizes these petrochemical products. The marine bacterial strain, A4B-17, which was found to belong to the genus
Microbulbifer
on the basis of its rRNA and
gyrB
sequences, was isolated from an ascidian in the coastal waters of Palau. Strain A4B-17 was, surprisingly, found to produce 10 mg/liter of 4HBA, together with its butyl (24 mg/liter), heptyl (0.4 mg/liter), and nonyl (6 mg/liter) esters. We therefore characterized 23 other marine bacteria belonging to the genus
Microbulbifer
, which our institute had previously isolated from various marine environments, and found that these bacteria also produced 4HBA, although with low production levels (less than one-fifth of that produced by A4B-17). We also show that the alkyl esters of 4HBA produced by strain A4B-17 were effective in preventing the growth of yeasts, molds, and gram-positive bacteria.
Eukaryotic Community Distribution and Its Relationship to Water Physicochemical Parameters in an Extreme Acidic Environment, Río Tinto (Southwestern Spain)
Authors: Aguilera Angeles , Manrubia Susanna C. , Gómez Felipe , Rodríguez Nuria , Amils Ricardo
Published: August 2006

The correlation between water physicochemical parameters and eukaryotic benthic composition was examined in Río Tinto. Principal component analysis showed a high inverse relationship between pH and most of the heavy metals analyzed as well as
Dunaliella
sp., while
Chlamydomonas
sp. abundance was positively related. Zn, Cu, and Ni clustered together and showed a strong inverse correlation with the diversity coefficient and most of the species analyzed. These eukaryotic communities seem to be more influenced by the presence of heavy metals than by the pH.
Engineering of Promoter Replacement Cassettes for Fine-Tuning of Gene Expression in
Saccharomyces cerevisiae
Authors: Nevoigt Elke , Kohnke Jessica , Fischer Curt R. , Alper Hal , Stahl Ulf , Stephanopoulos Gregory
Published: August 2006

The strong overexpression or complete deletion of a gene gives only limited information about its control over a certain phenotype or pathway. Gene function studies based on these methods are therefore incomplete. To effect facile manipulation of gene expression across a full continuum of possible expression levels, we recently created a library of mutant promoters. Here, we provide the detailed characterization of our yeast promoter collection comprising 11 mutants of the strong constitutive
Saccharomyces cerevisiae TEF1
promoter. The activities of the mutant promoters range between about 8% and 120% of the activity of the unmutated
TEF1
promoter. The differences in reporter gene expression in the 11 mutants were independent of the carbon source used, and real-time PCR confirmed that these differences were due to varying levels of transcription (i.e., caused by varying promoter strengths). In addition to a CEN/ARS plasmid-based promoter collection, we also created promoter replacement cassettes. They enable genomic integration of our mutant promoter collection upstream of any given yeast gene, allowing detailed genotype-phenotype characterizations. To illustrate the utility of the method, the
GPD1
promoter of
S. cerevisiae
was replaced by five
TEF1
promoter mutants of different strengths, which allowed analysis of the impact of glycerol 3-phosphate dehydrogenase activity on the glycerol yield.
The Lactic Acid-Induced Acid Tolerance Response in
Salmonella enterica
Serovar Typhimurium Induces Sensitivity to Hydrogen Peroxide
Authors: Greenacre E. J. , Lucchini S. , Hinton J. C. D. , Brocklehurst T. F.
Published: August 2006

Transcriptome analyses of
Salmonella enterica
serovar Typhimurium revealed that 15 genes were significantly up-regulated after 2 h of adaptation with lactic acid.
cadB
was the most highly up-regulated gene and was shown to be an essential component. Lactic acid-adapted cells exhibited sensitivity to hydrogen peroxide, likely due to down-regulation of the OxyR regulon.
Ecological Advantages of Autolysis during the Development and Dispersal of
Pseudoalteromonas tunicata
Biofilms
Authors: Mai-Prochnow Anne , Webb Jeremy S. , Ferrari Belinda C. , Kjelleberg Staffan
Published: August 2006

In the ubiquitous marine bacterium
Pseudoalteromonas tunicata
, subpopulations of cells are killed by the production of an autocidal protein, AlpP, during biofilm development. Our data demonstrate an involvement of this process in two parameters, dispersal and phenotypic diversification, which are of importance for the ecology of this organism and for its survival within the environment. Cell death in
P. tunicata
wild-type biofilms led to a major reproducible dispersal event after 192 h of biofilm development. The dispersal was not observed with a ΔAlpP mutant strain. Using flow cytometry and the fluorescent dye DiBAC
4
(3), we also show that
P. tunicata
wild-type cells that disperse from biofilms have enhanced metabolic activity compared to those cells that disperse from ΔAlpP mutant biofilms, possibly due to nutrients released from dead cells. Furthermore, we report that there was considerable phenotypic variation among cells dispersing from wild-type biofilms but not from the ΔAlpP mutant. Wild-type cells that dispersed from biofilms showed significantly increased variations in growth, motility, and biofilm formation, which may be important for successful colonization of new surfaces. These findings suggest for the first time that the autocidal events mediated by an antibacterial protein can confer ecological advantages to the species by generating a metabolically active and phenotypically diverse subpopulation of dispersal cells.
Bacteria Associated with Mucus and Tissues of the Coral
Oculina patagonica
in Summer and Winter
Authors: Koren Omry , Rosenberg Eugene
Published: August 2006

The relative abundance of bacteria in the mucus and crushed tissue of the Mediterranean coral
Oculina patagonica
was determined by analyses of the 16S rRNA genes of isolated colonies and from a 16S rRNA clone library of extracted DNA. By SYBR gold staining, the numbers of bacteria in mucus and tissue samples were 6.2 × 10
7
and 8.3 × 10
8
/cm
2
of coral surface, respectively, 99.8% of which failed to produce colonies on Marine Agar. From analysis of mucus DNA, the most-abundant bacterium was
Vibrio splendidus
, representing 68% and 50% of the clones from the winter and summer, respectively. After removal of mucus from coral by centrifugation, analyses of DNA from the crushed tissue revealed a large diversity of bacteria, with
Vibrio
species representing less than 5% of the clones. The most-abundant culturable bacteria were a
Pseudomonas
sp. (8 to 14%) and two different α-proteobacteria (6 to 18%). Out of a total 1,088 16S rRNA genes sequenced, 400 different operational taxonomic units were identified (>99.5% identity). Of these, 295 were novel (<99% identical to any sequences in the GenBank database). This study provides a comprehensive database for future examinations of changes in the bacterial community during bleaching events.
Development of a Dinoflagellate-Oriented PCR Primer Set Leads to Detection of Picoplanktonic Dinoflagellates from Long Island Sound
Authors: Lin Senjie , Zhang Huan , Hou Yubo , Miranda Lilibeth , Bhattacharya Debashish
Published: August 2006

We developed dinoflagellate-specific 18S rRNA gene primers. PCR amplification using these oligonucleotides for a picoplanktonic DNA sample from Long Island Sound yielded 24 clones, and all but one of these clones were dinoflagellates primarily belonging to undescribed and
Amoebophrya
-like lineages. These results highlight the need for a systematic investigation of picodinoflagellate diversity in both coastal and oceanic ecosystems.
The
Bacillus subtilis nrdEF
Genes, Encoding a Class Ib Ribonucleotide Reductase, Are Essential for Aerobic and Anaerobic Growth
Authors: Härtig Elisabeth , Hartmann Anja , Schätzle Manuela , Albertini Alessandra M. , Jahn Dieter
Published: August 2006

Ribonucleotide reductases (RNRs) are essential for the biosynthesis of the deoxyribonucleoside triphosphates of DNA. Recently, it was proposed that externally supplied deoxyribonucleosides or DNA is required for the growth of
Bacillus subtilis
under strict anaerobic conditions (M. J. Folmsbee, M. J. McInerney, and D. P. Nagle, Appl. Environ. Microbiol.
70:
5252-5257, 2004). Cultivation of
B. subtilis
on minimal medium in the presence of oxygen indicators in combination with oxygen electrode measurements and viable cell counting demonstrated that growth occurred under strict anaerobic conditions in the absence of externally supplied deoxyribonucleosides. The
nrdEF
genes encode the only obvious RNR in
B. subtilis
. A temperature-sensitive
nrdE
mutant failed to grow under aerobic and anaerobic conditions, indicating that this oxygen-dependent class I RNR has an essential role under both growth conditions. Aerobic growth and anaerobic growth of the
nrdE
mutant were rescued by addition of deoxynucleotides. The
nrd
locus consists of an
nrdI-nrdE-nrdF-ymaB
operon. The 5′ end of the corresponding mRNA revealed transcriptional start sites 45 and 48 bp upstream of the translational start of
nrdI
. Anaerobic transcription of the operon was found to be dependent on the presence of intact genes for the ResDE two-component redox regulatory system. Two potential ResD binding sites were identified approximately 62 bp (site A) and 50 bp (site B) upstream of the transcriptional start sites by a bioinformatic approach. Only mutation of site B eliminated
nrd
expression. Aerobic transcription was ResDE independent but required additional promoter elements localized between 88 and 275 bp upstream of the transcriptional start.
Carbon Isotope Fractionation during Acetoclastic Methanogenesis by
Methanosaeta concilii
in Culture and a Lake Sediment
Authors: Penning Holger , Claus Peter , Casper Peter , Conrad Ralf
Published: August 2006

The isotope enrichment factors (ε) in
Methanosaeta concilii
and in a lake sediment, where acetate was consumed only by
Methanosaeta
spp., were clearly less negative than the ε usually observed for
Methanosarcina
spp. The fraction of methane produced from acetate in the sediment, as determined by using stable isotope signatures, was 10 to 15% lower when the appropriate ε of
Methanosaeta
spp. was used.
Bacterioplankton Community Composition along a Salinity Gradient of Sixteen High-Mountain Lakes Located on the Tibetan Plateau, China
Authors: Wu Qinglong L. , Zwart Gabriel , Schauer Michael , Kamst-van Agterveld Miranda P. , Hahn Martin W.
Published: August 2006

The influence of altitude and salinity on bacterioplankton community composition (BCC) in 16 high-mountain lakes located at altitudes of 2,817 to 5,134 m on the Eastern Qinghai-Xizang (Tibetan) Plateau, China, spanning a salinity gradient from 0.02% (freshwater) to 22.3% (hypersaline), was investigated. Three different methods, fluorescent in situ hybridization, denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing, and reverse line blot hybridization (RLB) with probes targeting 17 freshwater bacterial groups, were used for analysis of BCC. Furthermore, the salt tolerances of 47 strains affiliated with groups detected in or isolated from the Tibetan habitats were investigated. Altitude was not found to influence BCC significantly within the investigated range. Several groups of typical freshwater bacteria, e.g., the ACK-M1 cluster and the
Polynucleobacter
group, were detected in habitats located above 4,400 m. Salinity was found to be the dominating environmental factor controlling BCC in the investigated lakes, resulting in only small overlaps in the BCCs of freshwater and hypersaline lakes. The relative abundances of different classes of
Proteobacteria
showed a sharp succession along the salinity gradient. Both DGGE and RLB demonstrated that a few freshwater bacterial groups, e.g., GKS98 and LD2, appeared over wide salinity ranges. Six freshwater isolates affiliated with the GKS98 cluster grew in ecophysiological experiments at maximum salinities of 0.3% to 0.7% (oligosaline), while this group was detected in habitats with salinities up to 6.7% (hypersaline). This observation indicated ecologically significant differences in ecophysiological adaptations among members of this narrow phylogenetic group and suggested ecological significance of microdiversity.
Forensic Application of Microbiological Culture Analysis To Identify Mail Intentionally Contaminated with
Bacillus anthracis
Spores
Authors: Beecher Douglas J.
Published: August 2006

The discovery of a letter intentionally filled with dried
Bacillus anthracis
spores in the office of a United States senator prompted the collection and quarantine of all mail in congressional buildings. This mail was subsequently searched for additional intentionally contaminated letters. A microbiological sampling strategy was used to locate heavy contamination within the 642 separate plastic bags containing the mail. Swab sampling identified 20 bags for manual and visual examination. Air sampling within the 20 bags indicated that one bag was orders of magnitude more contaminated than all the others. This bag contained a letter addressed to Senator Patrick Leahy that had been loaded with dried
B. anthracis
spores. Microbiological sampling of compartmentalized batches of mail proved to be efficient and relatively safe. Efficiency was increased by inoculating culture media in the hot zone rather than transferring swab samples to a laboratory for inoculation. All mail sampling was complete within 4 days with minimal contamination of the sampling environment or personnel. However, physically handling the intentionally contaminated letter proved to be exceptionally hazardous, as did sorting of cross-contaminated mail, which resulted in generation of hazardous aerosol and extensive contamination of protective clothing. Nearly 8 × 10
6
CFU was removed from the most highly cross-contaminated piece of mail found. Tracking data indicated that this and other heavily contaminated envelopes had been processed through the same mail sorting equipment as, and within 1 s of, two intentionally contaminated letters.
Aggregative Behavior of Bacteria Isolated from Canine Dental Plaque
Authors: Elliott David R. , Wilson Michael , Buckley Catherine M. F. , Spratt David A.
Published: August 2006

Interbacterial adhesion of bacteria isolated from canine dental plaque was assessed by performing a visual coaggregation assay. Using conditions mimicking those likely to be encountered in vivo, the entire cultivable plaque microbiota from a single dog was assessed, and eight (6.7%) unique coaggregation interactions were detected for 120 crosses. Transmission electron microscopy was used to visualize several of the bacteria in isolation and as coaggregates, which revealed surface structures that may be involved in adhesion and coaggregation. The results of this study indicate that the prevalence of coaggregating pairs of dental plaque bacteria in dogs is similar to the prevalence of coaggregating pairs of dental plaque bacteria reported in humans. In addition, genera found in both hosts generally exhibited similar coaggregation reactions; however, autoaggregation was found to be more common among oral bacteria isolated from dogs.