bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineering of Chimeric Class II Polyhydroxyalkanoate Synthases
Authors: Niamsiri Nuttawee , Delamarre Soazig C. , Kim Young-Rok , Batt Carl A. 
Published: November 2004

ABSTRACT

PHA synthase is a key enzyme involved in the biosynthesis of polyhydroxyalkanoates (PHAs). Using a combinatorial genetic strategy to create unique chimeric class II PHA synthases, we have obtained a number of novel chimeras which display improved catalytic properties. To engineer the chimeric PHA synthases, we constructed a synthetic
phaC
gene from
Pseudomonas oleovorans
(
phaC1

Po

) that was devoid of an internal 540-bp fragment. Randomly amplified PCR products (created with primers based on conserved
phaC
sequences flanking the deleted internal fragment) were generated using genomic DNA isolated from soil and were substituted for the 540-bp internal region. The chimeric genes were expressed in a PHA-negative strain of
Ralstonia eutropha
, PHB
−
4 (DSM 541). Out of 1,478 recombinant clones screened for PHA production, we obtained five different chimeric
phaC1

Po

genes that produced more PHA than the native
phaC1

Po

. Chimeras S1-71, S4-8, S5-58, S3-69, and S3-44 exhibited 1.3-, 1.4-, 2.0-, 2.1-, and 3.0-fold-increased levels of in vivo activity, respectively. All of the mutants mediated the synthesis of PHAs with a slightly increased molar fraction of 3-hydroxyoctanoate; however, the weight-average molecular weights (
M
w
) of the PHAs in all cases remained almost the same. Based upon DNA sequence analyses, the various
phaC
fragments appear to have originated from
Pseudomonas fluorescens
and
Pseudomonas aureofaciens
. The amino acid sequence analyses showed that the chimeric proteins had 17 to 20 amino acid differences from the wild-type phaC1
Po
, and these differences were clustered in the same positions in the five chimeric clones. A threading model of PhaC1
Po
, developed based on homology of the enzyme to the
Burkholderia glumae
lipase, suggested that the amino acid substitutions found in the active chimeras were located mostly on the protein model surface. Thus, our combinatorial genetic engineering strategy proved to be broadly useful for improving the catalytic activities of PHA synthase enzymes.
Visualization of Differential Gene Expression by Improved Cyan Fluorescent Protein and Yellow Fluorescent Protein Production in
Bacillus subtilis
Authors: Veening Jan-Willem , Smits Wiep Klaas , Hamoen Leendert W. , Jongbloed Jan D. H. , Kuipers Oscar P. 
Published: November 2004

ABSTRACT

The distinguishable cyan and yellow fluorescent proteins (CFP and YFP) enable the simultaneous in vivo visualization of different promoter activities. Here, we report new cloning vectors for the construction of
cfp
and
yfp
fusions in
Bacillus subtilis
. By extending the N-terminal portions of previously described CFP and YFP variants, 20- to 70-fold-improved fluorescent-protein production was achieved. Probably, the addition of sequences encoding the first eight amino acids of the N-terminal part of ComGA of
B. subtilis
overcomes the slow translation initiation that is provoked by the eukaryotic codon bias present in the original
cfp
and
yfp
genes. Using these new vectors, we demonstrate that, within an isogenic population of sporulating
B. subtilis
cells, expression of the
abrB
and
spoIIA
genes is distinct in individual cells.
Saccharomyces cerevisiae
Engineered for Xylose Metabolism Exhibits a Respiratory Response
Authors: Jin Yong-Su , Laplaza Jose M. , Jeffries Thomas W. 
Published: November 2004

ABSTRACT

Native strains of
Saccharomyces cerevisiae
do not assimilate xylose.
S. cerevisiae
engineered for
d
-xylose utilization through the heterologous expression of genes for aldose reductase (
XYL1
), xylitol dehydrogenase (
XYL2
), and
d
-xylulokinase (
XYL3
or
XKS1
) produce only limited amounts of ethanol in xylose medium. In recombinant
S. cerevisiae
expressing
XYL1
,
XYL2
, and
XYL3
, mRNA transcript levels for glycolytic, fermentative, and pentose phosphate enzymes did not change significantly on glucose or xylose under aeration or oxygen limitation. However, expression of genes encoding the tricarboxylic acid cycle, respiration enzymes (
HXK1
,
ADH2
,
COX13
,
NDI1
, and
NDE1
), and regulatory proteins (
HAP4
and
MTH1
) increased significantly when cells were cultivated on xylose, and the genes for respiration were even more elevated under oxygen limitation. These results suggest that recombinant
S. cerevisiae
does not recognize xylose as a fermentable carbon source and that respiratory proteins are induced in response to cytosolic redox imbalance; however, lower sugar uptake and growth rates on xylose might also induce transcripts for respiration. A petite respiration-deficient mutant (ρ°) of the engineered strain produced more ethanol and accumulated less xylitol from xylose. It formed characteristic colonies on glucose, but it did not grow on xylose. These results are consistent with the higher respiratory activity of recombinant
S. cerevisiae
when growing on xylose and with its inability to grow on xylose under anaerobic conditions.
Identification of Common Subpopulations of Non-Sorbitol-Fermenting, β-Glucuronidase-Negative
Escherichia coli
O157:H7 from Bovine Production Environments and Human Clinical Samples
Authors: Yang Zhijie , Kovar Joy , Kim Jaehyoung , Nietfeldt Joseph , Smith David R. , Moxley Rodney A. , Olson Michael E. , Fey Paul D. , Benson Andrew K. 
Published: November 2004

ABSTRACT

Non-sorbitol-fermenting, β-glucuronidase-negative
Escherichia coli
O157:H7 strains are regarded as a clone complex, and populations from different geographical locations are believed to share a recent common ancestor. Despite their relatedness, high-resolution genotyping methods can detect significant genome variation among different populations. Phylogenetic analysis of high-resolution genotyping data from these strains has shown that subpopulations from geographically unlinked continents can be divided into two primary phylogenetic lineages, termed lineage I and lineage II, and limited studies of the distribution of these lineages suggest there could be differences in their propensity to cause disease in humans or to be transmitted to humans. Because the genotyping methods necessary to discriminate the two lineages are tedious and subjective, these methods are not particularly suited for studying the large sets of strains that are required to systematically evaluate the ecology and transmission characteristics of these lineages. To overcome this limitation, we have developed a lineage-specific polymorphism assay (LSPA) that can readily distinguish between the lineage I and lineage II subpopulations. In the studies reported here, we describe the development of a six-marker test (LSPA-6) and its validation in a side-by-side comparison with octamer-based genome scanning. Analysis of over 1,400 O157:H7 strains with the LSPA-6 demonstrated that five genotypes comprise over 91% of the strains, suggesting that these subpopulations may be widespread.
Relationship of
Vibrio
Species Infection and Elevated Temperatures to Yellow Blotch/Band Disease in Caribbean Corals
Authors: Cervino James M. , Hayes Raymond L. , Polson Shawn W. , Polson Sara C. , Goreau Thomas J. , Martinez Robert J. , Smith Garriet W. 
Published: November 2004

ABSTRACT

The bacterial and temperature factors leading to yellow blotch/band disease (YBD), which affects the major reef-building Caribbean corals
Montastrea
spp., have been investigated. Groups of bacteria isolated from affected corals and inoculated onto healthy corals caused disease signs similar to those of YBD. The 16S rRNA genes from these bacteria were sequenced and found to correspond to four
Vibrio
spp. Elevating the water temperature notably increased the rate of spread of YBD on inoculated corals and induced greater coral mortality. YBD-infected corals held at elevated water temperatures had 50% lower zooxanthella densities, 80% lower division rates, and a 75% decrease in chlorophyll
a
and
c
2
pigments compared with controls. Histological sections indicated that the algal pyrenoid was fragmented into separate segments, along with a reconfiguration and swelling of the zooxanthellae, as well as vacuolization. YBD does not appear to produce the same physiological response formerly observed in corals undergoing temperature-related bleaching. Evidence indicates that YBD affects primarily the symbiotic algae rather than coral tissue.
Long-Chain
N
-Acyltyrosine Synthases from Environmental DNA
Authors: Brady Sean F. , Chao Carol J. , Clardy Jon 
Published: November 2004

ABSTRACT

The heterologous expression of DNA extracted directly from environmental samples (environmental DNA [eDNA]) in easily cultured hosts provides access to natural products produced by previously inaccessible microorganisms. When eDNA cosmid libraries were screened in
Escherichia coli
for antibacterially active clones, long-chain
N
-acyltyrosine-producing clones were found in every eDNA library. These apparently common natural products have not been previously described from screening extracts of cultured bacteria for biologically active natural products. Of the 11 long-chain
N
-acyl amino acid synthases (NASs) that were characterized, 10 are unique sequences. A predicted protein of previously unknown function from
Nitrosomonas europaea
, a gram-negative nitrifying beta-proteobacterium, is 14 to 37% identical to eDNA NASs. When cloned into
E. coli
, this open reading frame confers the production of long-chain
N
-acyltyrosines to the host and is therefore the first NAS from a cultured bacterium to be functionally characterized. Understanding the role that long-chain
N
-acyl amino acids play in soil microbial communities should now be feasible with the identification of a cultured organism that has the genetic capacity to produce these compounds.
Electric Current-Induced Detachment of
Staphylococcus epidermidis
Biofilms from Surgical Stainless Steel
Authors: van der Borden Arnout J. , van der Werf Hester , van der Mei Henny C. , Busscher Henk J. 
Published: November 2004

ABSTRACT

Biomaterial-centered infections of orthopedic percutaneous implants are serious complications which can ultimately lead to osteomyelitis, with devastating effects on bone and surrounding tissues, especially since the biofilm mode of growth offers protection against antibiotics and since removal frequently is the only ultimate solution. Recently, it was demonstrated that as a possible pathway to prevent infections of percutaneous stainless steel implants, electric currents of 60 to 100 μA were effective at stimulating the detachment of initially adhering staphylococci from surgical stainless steel. However, initially adhering bacteria are known to adhere more reversibly than bacteria growing in the later stages of biofilm formation. Hence, the aim of this study was to examine whether a growing
Staphylococcus epidermidis
biofilm can be stimulated to detach from surgical stainless steel by the use of electric currents. In separate experiments, four currents, i.e., 60 and 100 μA of direct current (DC) and 60 and 100 μA of block current (50% duty cycle, 1 Hz), were applied for 360 min to stimulate the detachment of an
S. epidermidis
biofilm that had grown for 200 min. A 100-μA DC yielded 78% detachment, whereas a 100-μA block current under the same experimental conditions yielded only 31% detachment. The same trend was found for 60 μA, with 37% detachment for a DC and 24% for a block current. Bacteria remaining on the surface after the current application were less viable than they were prior to the current application, as demonstrated by confocal laser scanning microscopy. In conclusion, these results suggest that DCs are preferred for curing infections.
Indole-Diterpene Gene Cluster fromAspergillus flavus
Authors: Zhang Shuguang , Monahan Brendon J. , Tkacz Jan S. , Scott Barry 
Published: November 2004

ABSTRACTAflatrem is a potent tremorgenic mycotoxin produced by the soil fungusAspergillus flavusand is a member of a large structurally diverse group of secondary metabolites known as indole-diterpenes. By using degenerate primers for conserved domains of fungal geranylgeranyl diphosphate synthases, we cloned two genes,atmGandggsA(an apparent pseudogene), fromA. flavus. Adjacent toatmGare two other genes,atmCandatmM. These three genes have 64 to 70% amino acid sequence similarity and conserved synteny with a cluster of orthologous genes,paxG,paxC, andpaxM, fromPenicillium paxilliwhich are required for indole-diterpene biosynthesis.atmG,atmC, andatmMare coordinately expressed, with transcript levels dramatically increasing at the onset of aflatrem biosynthesis. A genomic copy ofatmMcan complement apaxMdeletion mutant ofP. paxilli, demonstrating thatatmMis a functional homolog ofpaxM. Thus,atmG,atmC, andatmMare necessary, but not sufficient, for aflatrem biosynthesis byA. flavus. This provides the first genetic evidence for the biosynthetic pathway of aflatrem inA. flavus.
Evaluation of the LIVE/DEAD
Bac
Light Kit for Detection of Extremophilic Archaea and Visualization of Microorganisms in Environmental Hypersaline Samples
Authors: Leuko Stefan , Legat Andrea , Fendrihan Sergiu , Stan-Lotter Helga 
Published: November 2004

ABSTRACT

Extremophilic archaea were stained with the LIVE/DEAD
Bac
Light kit under conditions of high ionic strength and over a pH range of 2.0 to 9.3. The reliability of the kit was tested with haloarchaea following permeabilization of the cells. Microorganisms in hypersaline environmental samples were detectable with the kit, which suggests its potential application to future extraterrestrial halites.
Degradation of a Nonylphenol Single Isomer by
Sphingomonas
sp. Strain TTNP3 Leads to a Hydroxylation-Induced Migration Product
Authors: Corvini P. F. X. , Meesters R. J. W. , Schäffer A. , Schröder H. F. , Vinken R. , Hollender J. 
Published: November 2004

ABSTRACT

Sphingomonas
sp. strain TTNP3 degrades 4(3′,5′-dimethyl-3′-heptyl)-phenol and unidentified metabolites that were described previously. The chromatographic analyses of the synthesized reference compound and the metabolites led to their identification as 2(3′,5′-dimethyl-3′-heptyl)-1,4-benzenediol. This finding indicates that the nonylphenol metabolism of this bacterium involves unconventional degradation pathways where an NIH shift mechanism occurs.
Detection and Enumeration of
Vibrio vulnificus
in Oysters from Two Estuaries along the Southwest Coast of India, Using Molecular Methods
Authors: Parvathi Ammini , Kumar H. Sanath , Karunasagar Indrani , Karunasagar Iddya 
Published: November 2004

ABSTRACT

This study was conducted to understand the seasonal distribution of
Vibrio vulnificus
in oysters from two estuaries and the effect of environmental factors on the abundance of
V. vulnificus
in tropical waters.
V. vulnificus
was detected in 56.6% of the samples tested by colony hybridization with an alkaline phosphatase-labeled oligonucleotide probe (VV-AP), and the counts ranged from <10/g during the summer months to 10
3
/g in the monsoon season at both sites. The density of
V. vulnificus
appeared to be controlled more by salinity than by temperature. A nested PCR used in this study detected
V. vulnificus
in 85% of the samples following 18 h of enrichment in alkaline peptone water.
SIZE DISTRIBUTION AND SOLUBILITY OF 15 ELEMENTS IN ATMOSPHERIC AEROSOLS
Authors: KASAHARA M. , PARK J.H. , CHATANI S. 
Published: November 2004

To investigate the physical and chemical characteristics of atmospheric aerosols, aerosol particles were sampled with classifying into 13 size ranges between 0.01 and 30µm. Collected aerosol particles were separated into the soluble and insoluble components. The concentrations of 15 elements in both components were determined by a PIXE analysis using a 2.0MeV-proton beam. The mass size distribution of each element was illustrated in three types: mono-modal distribution having only one peak in the fine or coarse fraction and the bimodal distribution having one peak each in fine and coarse fractions. The mass mean diameter of 15 elements ranged between 0.62µm of S and 3.15µm of Fe. More than 85% of atmospheric aerosols consists of the lighter elements such as C, N, O, H and Al. The soluble component was dominant in the smaller size range and the insoluble component in the larger size range. Si, Ti and especially Fe existed in high insoluble state. Conversely, Ca, Zn, Br and especially S and Cl were dissolved in water.
See One, Do One, Teach One: Advanced Technology in Medical Education
Authors: Vozenilek John , Huff J. Stephen , Reznek Martin , Gordon James A. 
Published: November 2004

AbstractThe concept of “learning by doing” has become less acceptable, particularly when invasive procedures and high‐risk care are required. Restrictions on medical educators have prompted them to seek alternative methods to teach medical knowledge and gain procedural experience. Fortunately, the last decade has seen an explosion of the number of tools available to enhance medical education: web‐based education, virtual reality, and high fidelity patient simulation. This paper presents some of the consensus statements in regard to these tools agreed upon by members of the Educational Technology Section of the 2004 AEM Consensus Conference for Informatics and Technology in Emergency Department Health Care, held in Orlando, Florida. Findings:
Web‐based teaching: 1) Every ED should have access to medical educational materials via the Internet, computer‐based training, and other effective education methods for point‐of‐service information, continuing medical education, and training. 2) Real‐time automated tools should be integrated into Emergency Department Information Systems [EDIS] for contemporaneous education. Virtual reality [VR]: 1) Emergency physicians and emergency medicine societies should become more involved in VR development and assessment. 2) Nationally accepted protocols for the proper assessment of VR applications should be adopted and large multi‐center groups should be formed to perform these studies. High‐fidelity simulation: Emergency medicine residency programs should consider the use of high‐fidelity patient simulators to enhance the teaching and evaluation of core competencies among trainees. Conclusions: Across specialties, patient simulation, virtual reality, and the Web will soon enable medical students and residents to… see one, simulate many, do one competently, and teach everyone.
Where's the Beef? The Promise and the Reality of Clinical Documentation
Authors: Davidson Steven J. , Zwemer Frank L. , Nathanson Larry A. , Sable Kenneth N. , Khan Abu N.G.A. 
Published: November 2004

AbstractPhysician‐generated emergency department clinical documentation (information obtained from clinician observations and summarized decision processes inclusive of all manner of electronic systems capturing, storing, and presenting clinical documentation) serves four purposes: recording of medical care and communication among providers; payment for hospital and physician; legal defense from medical negligence allegations; and symptom/disease surveillance, public health, and research functions. In the consensus development process described by Handler, these objectives were balanced with the consideration of efficiency, often evaluated as physician time and clinical documentation system costs, in recording the information necessary for their accomplishment. The consensus panel session participants and authors recommend that 1) clinical documentation be electronically retrievable; 2) selection and implementation be evidence‐based and grounded on valid metrics (research is needed to identify these metrics); 3) the user interface be crafted to promote clinical excellence through high‐quality information collection and efficient charting techniques; 4) the priorities for integration of clinical information be standardized and implemented within enterprises and across health and information systems; 5) systems use accepted standards for bidirectional, real‐time clinical data exchange, without limiting the location or number of simultaneous users; 6) systems fully utilize existing electronic sources of specific patient information and general medical knowledge; 7) systems automatically and reliably capture appropriate data that support electronic billing for emergency department services; and 8) systems promote bedside documentation and mobile access.
Disparate Systems, Disparate Data: Integration, Interfaces, and Standards in Emergency Medicine Information Technology
Authors: Barthell Edward N. , Coonan Kevin , Finnell John , Pollock Dan , Cochrane Dennis 
Published: November 2004

AbstractAs part of the broader informatics consensus initiative sponsored by Academic Emergency Medicine, this report addresses the issues of integration, interfaces, and data standards and how they are relevant to information management in emergency medicine. The purpose of this report, and the workgroup that contributed to its content, is to provide emergency physicians and other stakeholders in the emergency informatics community a sense of direction as they design, build, and/or choose systems. Problems are identified, strategies to address these problems are discussed, and consensus recommendations are provided.
Information Technology Principles for Management, Reporting, and Research
Authors: Gillam Michael , Rothenhaus Todd , Smith Vernon , Kanhouwa Meera 
Published: November 2004

AbstractInformation technology holds the promise to enhance the ability of individuals and organizations to manage emergency departments, improve data sharing and reporting, and facilitate research. The Society for Academic Emergency Medicine (SAEM) Consensus Committee has identified nine principles to outline a path of optimal features and designs for current and future information technology systems. The principles roughly summarized include the following: utilize open database standards with clear data dictionaries, provide administrative access to necessary data, appoint and recognize individuals with emergency department informatics expertise, allow automated alert and proper identification for enrollment of cases into research, provide visual and statistical tools and training to analyze data, embed automated configurable alarm functionality for clinical and nonclinical systems, allow multiexport standard and format configurable reporting, strategically acquire mission‐critical equipment that is networked and capable of automated feedback regarding functional status and location, and dedicate resources toward informatics research and development. The SAEM Consensus Committee concludes that the diligent application of these principles will enhance emergency department management, reporting, and research and ultimately improve the quality of delivered health care.
Clinical Information Systems: Instant Ubiquitous Clinical Data for Error Reduction and Improved Clinical Outcomes
Authors: Feied Craig F. , Handler Jonathan A. , Smith Mark S. , Gillam Michael , Kanhouwa Meera , Rothenhaus Todd , Conover Keith , Shannon Tony 
Published: November 2004

AbstractImmediate access to existing clinical information is inadequate in current medical practice; lack of existing information causes or contributes to many classes of medical error, including diagnostic and treatment error. A review of the literature finds ample evidence to support a description of the problems caused by data that are missing or unavailable but little evidence to support one proposed solution over another. A primary recommendation of the Consensus Committee is that hospitals and departments should adopt systems that provide fast, ubiquitous, and unified access to all types of existing data. Additional recommendations cover a variety of related functions and operational concepts, from backups and biosurveillance to speed, training, and usability.