bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Benzaldehyde Tolerance in
Zymomonas mobilis
Biofilms and the Potential of Biofilm Applications in Fine-Chemical Production
Authors: Li Xuan Zhong , Webb Jeremy S. , Kjelleberg Staffan , Rosche Bettina 
Published: February 2006

ABSTRACT

Biotransformation plays an increasingly important role in the industrial production of fine chemicals due to its high product specificity and low energy requirement. One challenge in biotransformation is the toxicity of substrates and/or products to biocatalytic microorganisms and enzymes. Biofilms are known for their enhanced tolerance of hostile environments compared to planktonic free-living cells.
Zymomonas mobilis
was used in this study as a model organism to examine the potential of surface-associated biofilms for biotransformation of chemicals into value-added products.
Z. mobilis
formed a biofilm with a complex three-dimensional architecture comprised of microcolonies with an average thickness of 20 μm, interspersed with water channels. Microscopic analysis and metabolic activity studies revealed that
Z. mobilis
biofilm cells were more tolerant to the toxic substrate benzaldehyde than planktonic cells were. When exposed to 50 mM benzaldehyde for 1 h, biofilm cells exhibited an average of 45% residual metabolic activity, while planktonic cells were completely inactivated. Three hours of exposure to 30 mM benzaldehyde resulted in sixfold-higher residual metabolic activity in biofilm cells than in planktonic cells. Cells inactivated by benzaldehyde were evenly distributed throughout the biofilm, indicating that the resistance mechanism was different from mass transfer limitation. We also found that enhanced tolerance to benzaldehyde was not due to the conversion of benzaldehyde into less toxic compounds. In the presence of glucose,
Z. mobilis
biofilms in continuous cultures transformed 10 mM benzaldehyde into benzyl alcohol at a steady rate of 8.11 g (g dry weight)
−1
day
−1
with a 90% molar yield over a 45-h production period.
GIP2, a Putative Transcription Factor That Regulates the Aurofusarin Biosynthetic Gene Cluster in
Gibberella zeae
Authors: Kim Jung-Eun , Jin Jianming , Kim Hun , Kim Jin-Cheol , Yun Sung-Hwan , Lee Yin-Won 
Published: February 2006

ABSTRACT

Gibberella zeae
(anamorph:
Fusarium graminearum
) is an important pathogen of maize, wheat, and rice. Colonies of
G. zeae
produce yellow-to-tan mycelia with the white-to-carmine red margins. In this study, we focused on nine putative open reading frames (ORFs) closely linked to
PKS12
and
GIP1
, which are required for aurofusarin biosynthesis in
G. zeae
. Among them is an ORF designated
GIP2
(for Gi
bberella zeae p
igment gene
2
), which encodes a putative protein of 398 amino acids that carries a Zn(II)
2
Cys
6
binuclear cluster DNA-binding domain commonly found in transcription factors of yeasts and filamentous fungi. Targeted gene deletion and complementation analyses confirmed that
GIP2
is required for aurofusarin biosynthesis. Expression of
GIP2
in carrot medium correlated with aurofusarin production by
G. zeae
and was restricted to vegetative mycelia. Inactivation of the 10 contiguous genes in the Δ
GIP2
strain delineates an aurofusarin biosynthetic gene cluster. Overexpression of
GIP2
in both the Δ
GIP2
and the wild-type strains increases aurofusarin production and reduces mycelial growth. Thus,
GIP2
is a putative positive regulator of the aurofusarin biosynthetic gene cluster, and aurofusarin production is negatively correlated with vegetative growth by
G. zeae
.
Biodiversity of Methanogenic and Other
Archaea
in the Permanently Frozen Lake Fryxell, Antarctica
Authors: Karr Elizabeth A. , Ng Joshua M. , Belchik Sara M. , Sattley W. Matthew , Madigan Michael T. , Achenbach Laurie A. 
Published: February 2006

ABSTRACT

Archaea
were detected in molecular diversity studies of the permanently frozen Lake Fryxell, Antarctica. Two clusters of methanogens were detected in the sediments, and another cluster of possibly methanotrophic
Euryarchaeota
was detected in the anoxic water column just above the sediments. One crenarchaeote was detected in water just below the oxycline. The
Archaea
present in Lake Fryxell are likely involved in the major biogeochemical cycles that occur there.
A
Bacillus megaterium
Plasmid System for the Production, Export, and One-Step Purification of Affinity-Tagged Heterologous Levansucrase from Growth Medium
Authors: Malten Marco , Biedendieck Rebekka , Gamer Martin , Drews Ann-Christin , Stammen Simon , Buchholz Klaus , Dijkhuizen Lubbert , Jahn Dieter 
Published: February 2006

ABSTRACT

A multiple vector system for the production and export of recombinant affinity-tagged proteins in
Bacillus megaterium
was developed. Up to 1 mg/liter of a His
6
-tagged or Strep-tagged
Lactobacillus reuteri
levansucrase was directed into the growth medium, using the
B. megaterium
esterase LipA signal peptide, and recovered by one-step affinity chromatography.
Cumulative Effects of Short-Term Polymetal Contamination on Soil Bacterial Community Structure
Authors: Ranjard L. , Lignier L. , Chaussod R. 
Published: February 2006

ABSTRACT

In this study we evaluated the short-term effects of copper, cadmium, and mercury, added singly or in combination at different doses, on soil bacterial community structure using the bacterial automated ribosomal intergenic spacer analysis (B-ARISA) fingerprinting technique. Principal-component analysis of B-ARISA profiles allowed us to deduce the following order of impact: (Cu + Cd + Hg) >> Hg ≥ Cd > Cu. These results demonstrated that there was a cumulative effect of metal toxicity. Furthermore, the trend of modifications was consistent with the “hump-backed” relationships between biological diversity and disturbance described by Giller et al. (K. E. Giller, E. Witler, and S. P. McGrath, Soil Biol. Biochem.
30:
1389-1414, 1998).
Probing In Vivo Promoter Activities in
Mycoplasma pneumoniae
: a System for Generation of Single-Copy Reporter Constructs
Authors: Halbedel Sven , Stülke Jörg 
Published: February 2006

ABSTRACT

The nucleotide sequences that control transcription initiation and regulation in
Mycoplasma pneumoniae
are poorly understood. In this work, we developed a
lacZ
-based reporter plasmid that can be used to integrate fusions of promoter fragments to a promoterless
lacZ
gene into the chromosome of
M. pneumoniae
.
Diversity of Microorganisms within Rock Varnish in the Whipple Mountains, California
Authors: Kuhlman K. R. , Fusco W. G. , La Duc M. T. , Allenbach L. B. , Ball C. L. , Kuhlman G. M. , Anderson R. C. , Erickson I. K. , Stuecker T. , Benardini J. , Strap J. L. , Crawford R. L. 
Published: February 2006

ABSTRACTRock varnish from Arizona's Whipple Mountains harbors a microbial community containing about 108microorganisms g−1of varnish. Analyses of varnish phospholipid fatty acids and rRNA gene libraries reveal a community comprised of mostlyProteobacteriabut also includingActinobacteria, eukaryota, and a few members of theArchaea. Rock varnish represents a significant niche for microbial colonization.
Characterization of an
Agrobacterium tumefaciens
d
-Psicose 3-Epimerase That Converts
d
-Fructose to
d
-Psicose
Authors: Kim Hye-Jung , Hyun Eun-Kyung , Kim Yeong-Su , Lee Yong-Joo , Oh Deok-Kun 
Published: February 2006

ABSTRACT

The noncharacterized gene previously proposed as the
d
-tagatose 3-epimerase gene from
Agrobacterium tumefaciens
was cloned and expressed in
Escherichia coli
. The expressed enzyme was purified by three-step chromatography with a final specific activity of 8.89 U/mg. The molecular mass of the purified protein was estimated to be 132 kDa of four identical subunits. Mn
2+
significantly increased the epimerization rate from
d
-fructose to
d
-psicose. The enzyme exhibited maximal activity at 50°C and pH 8.0 with Mn
2+
. The turnover number (
k
cat
) and catalytic efficiency (
k
cat
/

K
m

) of the enzyme for
d
-psicose were markedly higher than those for
d
-tagatose, suggesting that the enzyme is not
d
-tagatose 3-epimerase but
d
-psicose 3-epimerase. The equilibrium ratio between
d
-psicose and
d
-fructose was 32:68 at 30°C.
d
-Psicose was produced at 230 g/liter from 700-g/liter
d
-fructose at 50°C after 100 min, corresponding to a conversion yield of 32.9%.
Identification of an
endo
-β-1,4-
d
-Xylanase from
Magnaporthe grisea
by Gene Knockout Analysis, Purification, and Heterologous Expression
Authors: Wu Sheng-Cheng , Halley Jeffrey E. , Luttig Christopher , Fernekes Linda M. , Gutiérrez-Sanchez Gerardo , Darvill Alan G. , Albersheim Peter 
Published: February 2006

ABSTRACT

Magnaporthe grisea
, a destructive ascomycetous pathogen of rice, secretes cell wall-degrading enzymes into a culture medium containing purified rice cell walls as the sole carbon source. From
M. grisea
grown under the culture conditions described here, we have identified an expressed sequenced tag,
XYL-6
, a gene that is also expressed in
M. grisea
-infected rice leaves 24 h postinoculation with conidia. This gene encodes a protein about 65% similar to
endo
-β-1,4-
d
-glycanases within glycoside hydrolase family GH10. A
M. grisea
knockout mutant for
XYL-6
was created, and it was shown to be as virulent as the parent strain in infecting the rice host. The proteins secreted by the parent strain and by the
xyl-6
Δ mutant were each fractionated by liquid chromatography, and the collected fractions were assayed for
endo
-β-1,4-
d
-glucanase or
endo
-β-1,4-
d
-xylanase activities. Two protein-containing peaks with
endo
-β-1,4-
d
-xylanase activity secreted by the parent strain are not detectable in the column eluant of the proteins secreted by the mutant. The two endoxylanases (XYL-6α and XYL-6β) from the parent were each purified to homogeneity. N-terminal amino acid sequencing indicated that XYL-6α is a fragment of XYL-6β and that XYL-6β is identical to the deduced protein sequence encoded by the
XYL-6
gene. Finally,
XYL-6
was introduced into
Pichia pastoris
for heterologous expression, which resulted in the purification of a fusion protein, XYL-6H, from the
Pichia pastoris
culture filtrate. XYL-6H is active in cleaving arabinoxylan. These experiments unequivocally established that the
XYL-6
gene encodes a secreted
endo
-β-1,4-
d
-xylanase.
Reliable and Rapid Identification of
Listeria monocytogenes
and
Listeria
Species by Artificial Neural Network-Based Fourier Transform Infrared Spectroscopy
Authors: Rebuffo Cecilia A. , Schmitt Jürgen , Wenning Mareike , von Stetten Felix , Scherer Siegfried 
Published: February 2006

ABSTRACT

Differentiation of the species within the genus
Listeria
is important for the food industry but only a few reliable methods are available so far. While a number of studies have used Fourier transform infrared (FTIR) spectroscopy to identify bacteria, the extraction of complex pattern information from the infrared spectra remains difficult. Here, we apply artificial neural network technology (ANN), which is an advanced multivariate data-processing method of pattern analysis, to identify
Listeria
infrared spectra at the species level. A hierarchical classification system based on ANN analysis for
Listeria
FTIR spectra was created, based on a comprehensive reference spectral database including 243 well-defined reference strains of
Listeria monocytogenes
,
L. innocua
,
L. ivanovii
,
L. seeligeri
, and
L. welshimeri
. In parallel, a univariate FTIR identification model was developed. To evaluate the potentials of these models, a set of 277 isolates of diverse geographical origins, but not included in the reference database, were assembled and used as an independent external validation for species discrimination. Univariate FTIR analysis allowed the correct identification of 85.2% of all strains and of 93% of the
L. monocytogenes
strains. ANN-based analysis enhanced differentiation success to 96% for all
Listeria
species, including a success rate of 99.2% for correct
L. monocytogenes
identification. The identity of the 277-strain test set was also determined with the standard phenotypical API
Listeria
system. This kit was able to identify 88% of the test isolates and 93% of
L. monocytogenes
strains. These results demonstrate the high reliability and strong potential of ANN-based FTIR spectrum analysis for identification of the five
Listeria
species under investigation. Starting from a pure culture, this technique allows the cost-efficient and rapid identification of
Listeria
species within 25 h and is suitable for use in a routine food microbiological laboratory.
Differential strength of association of child injury prevention attitudes and beliefs on practices: a case for audience segmentation
Authors: Vladutiu C J , Nansel T R , Weaver N L , Jacobsen H A , Kreuter M W 
Published: February 2006

Objective:Many injuries to children cannot be prevented without some degree of active behavior on the part of parents. A better understanding of social and cognitive determinants of parents’ injury prevention behavior and the identification of potential subgroups for targeted message delivery could advance the effectiveness of educational and behavioral interventions. This study assessed the degree to which parents’ injury prevention behavior is associated with theoretical determinants and examined whether this relation differs by age or birth order of child.Design:Cross sectional observational study.Setting:Three Midwestern pediatric clinics.Subjects:594 parents of children ages 0–4 attending routine well child visits.Measures:Injury prevention attitudes, beliefs, and practices.Results:Overall, only modest relations were observed between injury beliefs and attitudes and injury prevention behaviors. However, these relations differed substantially by child age and birth order, with stronger associations observed for parents of older first born children. Outcome expectations and social norms were more strongly related to injury prevention behavior among parents of preschool children than among parents of infants and toddlers, while attitudes were more predictive for parents of first born children than parents of later born children.Conclusions:These findings highlight the complexity of relations between theorized determinants and behavior, and suggest the potential utility of using audience segmentation strategies in behavioral interventions addressing injury prevention.
Accuracy of injury coding under ICD-9 for New Zealand public hospital discharges
Authors: Langley J , Stephenson S , Thorpe C , Davie G 
Published: February 2006

Objective:To determine the level of accuracy in coding for injury principal diagnosis and the first external cause code for public hospital discharges in New Zealand and determine how these levels vary by hospital size.Method:A simple random sample of 1800 discharges was selected from the period 1996–98 inclusive. Records were obtained from hospitals and an accredited coder coded the discharge independently of the codes already recorded in the national database.Results:Five percent of the principal diagnoses, 18% of the first four digits of the E-codes, and 8% of the location codes (5th digit of the E-code), were incorrect. There were no substantive differences in the level of incorrect coding between large and small hospitals.Conclusions:Users of New Zealand public hospital discharge data can have a high degree of confidence in the injury diagnoses coded under ICD-9-CM-A. A similar degree of confidence is warranted for E-coding at the group level (for example, fall), but not, in general, at higher levels of specificity (for example, type of fall). For those countries continuing to use ICD-9 the study provides insight into potential problems of coding and thus guidance on where the focus of coder training should be placed. For those countries that have historical data coded according to ICD-9 it suggests that some specific injury and external cause incidence estimates may need to be treated with more caution.
Specific epitopes of the structural and hypothetical proteins elicit variable humoral responses in SARS patients
Authors: Chow S C S , Ho C Y S , Tam T T Y , Wu C , Cheung T , Chan P K S , Ng M H L , Hui P K , Ng H K , Au D M Y , Lo A W I 
Published: February 2006

Background:Severe acute respiratory syndrome (SARS) is an infectious disease which was caused by a novel coronavirus (SARS-CoV). SARS has caused an outbreak in the world during 2003 and 2004, with 8098 individuals being infected and a death toll of 774 in 28 regions around the world. Specific humoral responses to viral infection remain unclear.Objective:To analyse the antigenicity of the SARS-CoV genome and identify potential antigenic epitopes in the structural proteins.Methods:Potential antigenic epitopes were identified in the structural proteins (nucleocapsid, membrane, spike, and small envelope proteins) and hypothetical proteins (SARS3a, 3b, 6, 7a, and 9b) that are specific for SARS-CoV. A peptide chip platform was created and the profiles of antibodies to these epitopes were investigated in 59 different SARS patients’ sera obtained 6–103 days after the onset of the illness. Serial sera from five additional patients were also studied.Results:Epitopes at the N-terminus of the membrane protein and the C-terminus of nucleocapsid protein elicited strong antibody responses. Epitopes on the spike protein were only moderately immunogenic but the effects were persistent. Antibodies were also detected for some putative proteins, noticeably the C-termini of SARS3a and SARS6.Conclusions:Important epitopes of the SARS-CoV genome that may serve as potential markers for the viral infection are identified. These specific antigenic sites may also be important for vaccine development against this new fatal infectious disease.
Modern management of arrhythmias
Authors: Hall M C S , Todd D M 
Published: February 2006

Abstract
The specialist management of arrhythmias has changed significantly over the past decade. This article outlines current management strategies for atrial flutter and atrial fibrillation, with particular emphasis on curative strategies with catheter ablation and the recent data on rhythm compared with rate control strategies. The expanding role of catheter ablation in the treatment of a wide variety of supraventricular and ventricular arrhythmias is discussed. The current evidence for implantable cardioverter defibrillators in the prevention of sudden cardiac death is summarised. The article also highlights the increasing recognition of a number of inherited syndromes that predispose to sudden cardiac death (for example, Brugada and long QT syndromes).
Incidence and risk factors for development of venous thromboembolism in Indian patients undergoing major orthopaedic surgery: results of a prospective study
Authors: Bagaria V , Modi N , Panghate A , Vaidya S 
Published: February 2006

Abstract

Introduction
The incidence of venous thromboembolism (VTE) in Western populations undergoing major orthopaedic surgery without any thromboprophylaxis has been reported to range from 32% to 88%. There is however limited information on incidence of VTE in Indian patients and most of the Indian patients undergoing these surgeries do not receive any form of prophylaxis regardless of their risk profile.

Methods
A prospective study was performed on 147 patients undergoing major orthopaedic surgery for total knee replacement (TKR), total hip replacement (THR), and proximal femur fracture fixation (PFF) without any prophylaxis. These patients were profiled for presence of the known risk factors responsible for development of VTE. A duplex ultrasound on both lower limbs was done 6 to 10 days after surgery. Twenty three patients underwent THR, 22 patients underwent TKR, and 102 underwent surgery for PFF. The patients were assessed clinically for any signs of deep venous thrombosis (DVT) and pulmonary embolism (PE). A helical CT scan was done in case of suspicion of PE and a duplex ultrasound was done in case of clinical suspicion of DVT irrespective of the stage of study.

Results
The overall incidence of VTE was 6.12% and that of PE was 0.6%. The risk factors that were found to be significantly responsible for development of VTE (p &lt; 0.05) were: immobility greater than 72 hours, malignancy, obesity, surgery lasting more than two hours.

Conclusion
The study reconfirms the belief that DVT has a lower incidence in Indian patients as compared with other ethnic groups.
Diabetic neuropathy
Authors: Bansal V , Kalita J , Misra U K 
Published: February 2006

AbstractDiabetic neuropathy (DN) refers to symptoms and signs of neuropathy in a patient with diabetes in whom other causes of neuropathy have been excluded. Distal symmetrical neuropathy is the commonest accounting for 75% DN. Asymmetrical neuropathies may involve cranial nerves, thoracic or limb nerves; are of acute onset resulting from ischaemic infarction of vasa nervosa. Asymmetric neuropathies in diabetic patients should be investigated for entrapment neuropathy. Diabetic amyotrophy, initially considered to result from metabolic changes, and later ischaemia, is now attributed to immunological changes. For diagnosis of DN, symptoms, signs, quantitative sensory testing, nerve conduction study, and autonomic testing are used; and two of these five are recommended for clinical diagnosis. Management of DN includes control of hyperglycaemia, other cardiovascular risk factors; α lipoic acid and L carnitine. For neuropathic pain, analgesics, non-steroidal anti-inflammatory drugs, antidepressants, and anticonvulsants are recommended. The treatment of autonomic neuropathy is symptomatic.
Retrospective analysis of the use of inferior vena cava filters in routine hospital practice
Authors: Dovrish Z , Hadary R , Blickstein D , Shilo L , Ellis M H 
Published: February 2006

Abstract

Introduction
Characteristics and outcomes of patients undergoing inferior vena cava (IVC) filter insertion are not well reported. Particularly, the role of long term anticoagulation in these patients is unclear.

Aims
(1) To describe in a cohort of patients undergoing IVC filter insertion, underlying diseases, indications for filter insertion, complications, and survival. (2) To determine the effect of long term anticoagulant treatment on thromboembolism and patient survival.

Study design
A retrospective analysis of 109 consecutive patients undergoing IVC filter insertion in two university hospitals.

Results
Average age was 67.4 years. Median duration of follow up was two years. Indications for IVC filter insertion were: contraindication to anticoagulation (n = 61, 56%), prophylactic insertion (n = 29, 27%), thromboembolism while receiving adequate anticoagulation (n = 17, 15%), and non-compliance with anticoagulation (n = 2, 2%). Insertion related complications were groin haematoma in four patients (3.5%) and localised infection at the puncture site in one patient (0.9%). Fifty six patients (51.4%) died during the study period. Of these, 22 received long term anticoagulants and 34 did not. Overall and thrombosis free survival was greater in the anticoagulant treated group (median survival not reached) than in the untreated group (median survival = 12 months). Patients not receiving long term anticoagulation after IVC filter insertion were nearly 2.5-fold more likely to die or experience venous thromboembolism.

Conclusion
IVC filter insertion was a safe procedure and was performed for appropriate indications in the patients studied. In patients surviving for longer than 30 days, prolonged administration of oral anticoagulants was associated with improved survival with no significant increase in haemorrhagic complications.