bluuebunny/crossref_metadata_2025_split huggingface dataset:
The linking of burglary crimes using offender behaviour: Testing research cross‐nationally and exploring methodology
Authors: Tonkin M. , Santtila P. , Bull R. 
Published: January 2011

Purpose. The current study tests whether existing behavioural case linkage findings from the United Kingdom (UK) will replicate abroad with a sample of residential burglaries committed in Finland. In addition, a previously discussed methodological issue is empirically explored.Methods. Seven measures of behavioural similarity, geographical proximity, and temporal proximity are calculated for pairs of burglary crimes committed by 117 serial burglars in Finland. The ability of these seven measures to distinguish between pairs of crimes committed by the same offender (linked pairs) and different offenders (unlinked pairs) is tested using logistic regression and receiver operating characteristic (ROC) analysis. Two methodologies for forming the unlinked pairs are compared; one representing the ‘traditional’ approach used by research and, the other, a new approach that represents a potentially more realistic and statistically sound approach to testing case linkage.Results. A wider range of offender behaviours were able to distinguish between linked and unlinked crime pairs in the current Finnish sample than in previous UK‐based research. The most successful features were the kilometre‐distance between crimes (the intercrime distance), the number of days separating offences (temporal proximity), and a combination of target, entry, internal, and property behaviours (the combined domain). There were no statistically significant differences between the two methodological approaches.Conclusions. The current findings demonstrate that a wider range of offender behaviours can be used to discriminate between linked and unlinked residential burglary crimes committed in Finland than in the UK. The use of a more realistic and statistically sound methodology does not lead to substantial changes in case linkage findings.
Thermococcus kodakarensis
as a Host for Gene Expression and Protein Secretion
Authors: Takemasa Ryo , Yokooji Yuusuke , Yamatsu Atsushi , Atomi Haruyuki , Imanaka Tadayuki 
Published: January 2011

ABSTRACT

Taking advantage of the gene manipulation system developed in
Thermococcus kodakarensis
, here, we developed a system for gene expression and efficient protein secretion using this hyperthermophilic archaeon as a host cell. DNA fragments encoding the C-terminal domain of chitinase (ChiAΔ4), which exhibits endochitinase activity, and the putative signal sequence of a subtilisin-like protease (TK1675) were fused and positioned under the control of the strong constitutive promoter of the cell surface glycoprotein gene. This gene cassette was introduced into
T. kodakarensis
, and secretion of the ChiAΔ4 protein was examined. ChiAΔ4 was found exclusively in the culture supernatant and was not detected in the soluble and membrane fractions of the cell extract. The signal peptide was specifically cleaved at the C-terminal peptide bond following the Ala-Ser-Ala sequence. Efficient secretion of the orotidine-5′-monophosphate decarboxylase protein was also achieved with the same strategy. We next individually overexpressed two genes (TK1675 and TK1689) encoding proteases with putative signal sequences. By comparing protein degradation activities in the host cells and transformants in both solid and liquid media, as well as measuring peptidase activity using synthetic peptide substrates, we observed dramatic increases in protein degradation activity in the two transformants. This study displays an initial demonstration of cell engineering in hyperthermophiles.
Poly-α-Glutamic Acid Synthesis Using a Novel Catalytic Activity of RimK from
Escherichia coli
K-12
Authors: Kino Kuniki , Arai Toshinobu , Arimura Yasuhiro 
Published: January 2011

ABSTRACT

Poly-
l
-α-amino acids have various applications because of their biodegradable properties and biocompatibility. Microorganisms contain several enzymes that catalyze the polymerization of
l
-amino acids in an ATP-dependent manner, but the products from these reactions contain amide linkages at the side residues of amino acids: e.g., poly-γ-glutamic acid, poly-ε-lysine, and cyanophycin. In this study, we found a novel catalytic activity of RimK, a ribosomal protein S6-modifying enzyme derived from
Escherichia coli
K-12. This enzyme catalyzed poly-α-glutamic acid synthesis from unprotected
l
-glutamic acid (Glu) by hydrolyzing ATP to ADP and phosphate. RimK synthesized poly-α-glutamic acid of various lengths; matrix-assisted laser desorption ionization-time of flight-mass spectrometry showed that a 46-mer of Glu (maximum length) was synthesized at pH 9. Interestingly, the lengths of polymers changed with changing pH. RimK also exhibited 86% activity after incubation at 55°C for 15 min, thus showing thermal stability. Furthermore, peptide elongation seemed to be catalyzed at the C terminus in a stepwise manner. Although RimK showed strict substrate specificity toward Glu, it also used, to a small extent, other amino acids as C-terminal substrates and synthesized heteropeptides. In addition, RimK-catalyzed modification of ribosomal protein S6 was confirmed. The number of Glu residues added to the protein varied with pH and was largest at pH 9.5.
Antifungal Activity Displayed by Cereulide, the Emetic Toxin Produced by
Bacillus cereus
Authors: Ladeuze Sandy , Lentz Nathalie , Delbrassinne Laurence , Hu Xiaomin , Mahillon Jacques 
Published: January 2011

ABSTRACT

In this study, the fungistatic activity of
Bacillus cereus
cereulide-producing strains was demonstrated against nine fungal species. The role of cereulide was confirmed using plasmid-cured derivatives and
ces
knockout mutants. The fungistatic spectra of cereulide and valinomycin, a chemically related cyclododecadepsipeptide, were also compared and found to be similar but distinct.
Correlation of Quantitative PCR for a Poultry-Specific
Brevibacterium
Marker Gene with Bacterial and Chemical Indicators of Water Pollution in a Watershed Impacted by Land Application of Poultry Litter
Authors: Weidhaas Jennifer L. , Macbeth Tamzen W. , Olsen Roger L. , Harwood Valerie J. 
Published: January 2011

ABSTRACT

The impact of fecal contamination from human and agricultural animal waste on water quality is a major public health concern. Identification of the dominant source(s) of fecal pollution in a watershed is necessary for assessing the safety of recreational water and protecting water resources. A field study was conducted using quantitative PCR (qPCR) for the 16S rRNA gene of
Brevibacterium
sp. LA35 to track feces-contaminated poultry litter in environmental samples. Based on sensitivity and specificity characteristics of the qPCR method, the Bayesian conditional probability that detection of the LA35 marker gene in a water sample represented a true-positive result was 93%. The marker's covariance with fecal indicator bacteria (FIB) and metals associated with poultry litter was also assessed in litter, runoff, surface water, and groundwater samples. LA35 was detected in water and soil samples collected throughout the watershed, and its concentration covaried with concentrations of
Escherichia coli
, enterococci, As, Cu, P, and Zn. Significantly greater concentrations of FIB, As, Cu, P, and Zn were observed in edge-of-field runoff samples in which LA35 was detected, compared to samples in which it was not detected. Furthermore, As, Cu, P, and Zn concentrations covaried in environmental samples in which LA35 was detected and typically did not in samples in which the marker gene was not detected. The covariance of the poultry-specific LA35 marker gene with these known contaminants from poultry feces provides further evidence that it is a useful tool for assessing the impact of poultry-derived fecal pollution in environmental waters.
Novel Virulence Gene and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Multilocus Sequence Typing Scheme for Subtyping of the Major Serovars of
Salmonella enterica
subsp.
enterica
Authors: Liu Fenyun , Barrangou Rodolphe , Gerner-Smidt Peter , Ribot Efrain M. , Knabel Stephen J. , Dudley Edward G. 
Published: January 2011

ABSTRACT

Salmonella enterica
subsp.
enterica
is the leading cause of bacterial food-borne disease in the United States. Molecular subtyping methods are powerful tools for tracking the farm-to-fork spread of food-borne pathogens during outbreaks. In order to develop a novel multilocus sequence typing (MLST) scheme for subtyping the major serovars of
S. enterica
subsp.
enterica
, the virulence genes
sseL
and
fimH
and clustered regularly interspaced short palindromic repeat (CRISPR) loci were sequenced from 171 clinical isolates from nine
Salmonella
serovars,
Salmonella
serovars Typhimurium, Enteritidis, Newport, Heidelberg, Javiana, I 4,[5],12:i:−, Montevideo, Muenchen, and Saintpaul. The MLST scheme using only virulence genes was congruent with serotyping and identified epidemic clones but could not differentiate outbreaks. The addition of CRISPR sequences dramatically improved discriminatory power by differentiating individual outbreak strains/clones. Of particular note, the present MLST scheme provided better discrimination of
Salmonella
serovar Enteritidis strains than pulsed-field gel electrophoresis (PFGE). This method showed high epidemiologic concordance for all serovars screened except for
Salmonella
serovar Muenchen. In conclusion, the novel MLST scheme described in the present study accurately differentiated outbreak strains/clones of the major serovars of
Salmonella
, and therefore, it shows promise for subtyping this important food-borne pathogen during investigations of outbreaks.
Regulatory Control of the
Escherichia coli
O157:H7
lpf1
Operon by H-NS and Ler
Authors: Rojas-López Maricarmen , Arenas-Hernández Margarita M. P. , Medrano-López Abraham , Martínez de la Peña Claudia F. , Puente José Luis , Martínez-Laguna Ygnacio , Torres Alfredo G. 
Published: January 2011

ABSTRACT

Long polar fimbriae 1 (Lpf1) of
Escherichia coli
O157:H7 is a tightly regulated adhesin, with H-NS silencing the transcriptional expression of the
lpf1
operon while Ler (locus of enterocyte effacement-encoded regulator) acts as an antisilencer. We mapped the minimal regulatory region of
lpf1
required for H-NS- and Ler-mediated regulation and found that it is 79% AT rich. Three putative sites for H-NS binding were identified. Two of them, named silencer regulatory sequence 1 (SRS1) and SRS2, are located on a region that covers both of the
lpf1
promoters (P1 and P2). The third putative H-NS binding site is located within the
lpfA1
gene in a region extending from +258 bp to +545 bp downstream of ATG; however, this site does not seem to play a role in
lpfA1
regulation under the conditions tested in this work. Ler was also found to interact with Ler binding sites (LBSs). Ler binding site 1 (LBS1) and LBS2 are located upstream of the two promoters. LBS1 overlaps SRS1, while LBS3 overlaps the P1 promoter and SRS2. Based on the experimental data, we propose that H-NS silences
lpf1
expression by binding to both of the SRSs on the promoter region, forming an SRS-H-NS complex that prevents RNA polymerase-mediated transcription. A model of the regulation of the
lpfA1
operon of
E. coli
O157:H7 by H-NS and Ler is discussed.
Legionella pneumophila
LbtU Acts as a Novel, TonB-Independent Receptor for the Legiobactin Siderophore
Authors: Chatfield Christa H. , Mulhern Brendan J. , Burnside Denise M. , Cianciotto Nicholas P. 
Published: January 2011

ABSTRACT

Gram-negative
Legionella pneumophila
produces a siderophore (legiobactin) that promotes lung infection. We previously determined that
lbtA
and
lbtB
are required for the synthesis and secretion of legiobactin. DNA sequence and reverse transcription-PCR (RT-PCR) analyses now reveal the presence of an iron-repressed gene (
lbtU
) directly upstream of the
lbtAB
-containing operon.
In silico
analysis predicted that LbtU is an outer membrane protein consisting of a 16-stranded transmembrane β-barrel, multiple extracellular domains, and short periplasmic tails. Immunoblot analysis of cell fractions confirmed an outer membrane location for LbtU. Although replicating normally in standard media,
lbtU
mutants, like
lbtA
mutants, were impaired for growth on iron-depleted agar media. While producing typical levels of legiobactin,
lbtU
mutants were unable to use supplied legiobactin to stimulate growth on iron-depleted media and displayed an inability to take up iron. Complemented
lbtU
mutants behaved as the wild type did. The
lbtU
mutants were also impaired for infection in a legiobactin-dependent manner. Together, these data indicate that LbtU is involved in the uptake of legiobactin and, based upon its location, is most likely the
Legionella
siderophore receptor. The sequence and predicted two-dimensional (2D) and 3D structures of LbtU were distinct from those of all known siderophore receptors, which generally contain a 22-stranded β-barrel and an extended N terminus that binds TonB in order to transduce energy from the inner membrane. This observation coupled with the fact that
L. pneumophila
does not encode TonB suggests that LbtU is a new type of receptor that participates in a form of iron uptake that is mechanistically distinct from the existing paradigm.
Identification of Genes Essential for Prey-Independent Growth of
Bdellovibrio bacteriovorus
HD100
Authors: Roschanski Nicole , Klages Sven , Reinhardt Richard , Linscheid Michael , Strauch Eckhard 
Published: January 2011

ABSTRACT

Bdellovibrio bacteriovorus
HD100 is an obligate predatory bacterium that attacks and invades Gram-negative bacteria. The predator requires living bacteria to survive as growth and replication take place inside the bacterial prey. It is possible to isolate mutants that grow and replicate outside prey bacteria. Such mutants are designated host or prey independent, and their nutritional requirements vary. Some mutants are saprophytic and require prey extracts for extracellular growth, whereas other mutants grow axenically, which denotes the formation of colonies on complete medium in the absence of any prey components. The initial events leading to prey-independent growth are still under debate, and several genes may be involved. We selected new mutants by three different methods: spontaneous mutation, transposon mutagenesis, and targeted gene knockout. By all approaches we isolated mutants of the
hit
(host interaction) locus. As the relevance of this locus for the development of prey independence has been questioned, we performed whole-genome sequencing of five prey-independent mutants. Three mutants were saprophytic, and two mutants could grow axenically. Whole-genome analysis revealed that the mutation of a small open reading frame of the
hit
locus is sufficient for the conversion from predatory to saprophytic growth. Complementation experiments were performed by introduction of a plasmid carrying the wild-type
hit
gene into saprophytic mutants, and predatory growth could be restored. Whole-genome sequencing of two axenic mutants demonstrated that in addition to the
hit
mutation the colony formation on complete medium was shown to be influenced by the mutations of two genes involved in RNA processing. Complementation experiments with a wild-type gene encoding an RNA helicase, RhlB, abolished the ability to form colonies on complete medium, indicating that stability of RNA influences axenic growth.
Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions
Authors: Peer Asaf , Margalit Hanah 
Published: January 2011

ABSTRACT
Bacterial small noncoding RNAs have attracted much interest in recent years as posttranscriptional regulators of genes involved in diverse pathways. Small RNAs (sRNAs) are 50 to 400 nucleotides long and exert their regulatory function by directly base pairing with mRNA targets to alter their stability and/or affect their translation. This base pairing is achieved through a region of about 10 to 25 nucleotides, which may be located at various positions along different sRNAs. By compiling a data set of experimentally determined target-binding regions of sRNAs and systematically analyzing their properties, we reveal that they are both more evolutionarily conserved and more accessible than random regions. We demonstrate the use of these properties for computational identification of sRNA target-binding regions with high specificity and sensitivity. Our results show that these predicted regions are likely to base pair with known targets of an sRNA, suggesting that pointing out these regions in a specific sRNA can help in searching for its targets.
Ethical issues related to the access to orphan drugs in Brazil: the case of mucopolysaccharidosis type I
Authors: Boy Raquel , Schwartz Ida V D , Krug Bárbara C , Santana-da-Silva Luiz C , Steiner Carlos E , Acosta Angelina X , Ribeiro Erlane M , Galera Marcial F , Leivas Paulo G C , Braz Marlene 
Published: January 2011

Background/AimsMucopolysaccharidosis type I (MPS I) is a rare lysosomal storage disorder treated with bone marrow transplantation or enzyme replacement therapy with laronidase, a high-cost orphan drug. Laronidase was approved by the US Food and Drug Administration and the European Medicines Agency in 2003 and by the Brazilian National Health Surveillance Agency in 2005. Many Brazilian MPS I patients have been receiving laronidase despite the absence of a governmental policy regulating access to the drug. Epidemiological and treatment data concerning MPS I are scarce. This study aims to present a demographic profile of Brazilian patients with MPS I, describe the routes of access to laronidase in Brazil, and discuss associated ethical issues relating to public funding of orphan drugs.MethodsIn this cross-sectional observational study, data were collected nationwide between January and September 2008 from physicians, public institutions and non-governmental organisations involved with diagnosis and treatment of MPS I, using two data collection instruments specifically designed for this purpose.ResultsThe minimum prevalence of MPS I in Brazil was estimated at 1/2 700 000. Most patients (69.8%) were younger than 15 years; 60 (88.2%) received laronidase. The most common route of access to the drug was through lawsuits (86.6%).ConclusionsIn Brazil, MPS I is predominantly a paediatric illness. Even though the cost of laronidase treatment is not officially covered by the Brazilian government, most MPS I patients receive the drug, usually through litigation. This gives rise to major ethical conflicts concerning drug access in a low-resource context. The Brazilian health policy framework lacks evidence-based clinical protocols for the distribution of orphan drugs.
Novel non-occlusive temporary endoluminal neck protection device to assist in the treatment of aneurysms in a canine model
Authors: Turner Raymond D , Chaudry M Imran , Turk Aquilla S 
Published: January 2011

IntroductionCurrent models for the endovascular treatment of aneurysms often require the use of adjuvant devices. Balloon-assisted techniques require temporary occlusion of the parent vessel. Intravascular stents require the use of antiplatelet medication. A novel device that achieves temporary neck protection without parent vessel occlusion or antiplatelet medication is examined in a canine model.Method20 sidewall wide-necked aneurysms were created in 10 canines, one in each carotid artery, using a vein graft technique, and allowed to mature. In each canine, one aneurysm was catheterized with a microcatheter while the neck protection device (NPD) was unsheathed across the neck of the aneurysm and the aneurysm was coiled. The second aneurysm in each canine was coiled without an adjunctive device. The NPD was assessed for coil herniation, coil entrapment within the device, deployability and retrievability. Five animals were killed immediately and five were killed at 28 days and the carotid artery was explanted and sent for necropsy to assess for injury to the endothelium.ResultsAll aneurysms were successfully treated with no adverse events. The NPD was well visualized and unsheathed and resheathed successfully in all cases. There was no coil entrapment within the device, and there were no cases of coil herniation. There was no evidence of endothelial injury or dissection.ConclusionThe device was technically successful in all devices and further development of this device may be of benefit in endovascular treatment of aneurysms.
Biological monitoring of low-level 2-butoxyethanol exposure in decal transfer workers in bicycle manufacturing factories
Authors: Hung Po-Chen , Cheng Shu-Fang , Liou Saou-Hsing , Tsai Shih-Wei 
Published: January 2011

ObjectivesIn this study, exposures to ethylene glycol monobutyl ether (or 2-butoxyethanol, 2-BE) in decal transfer workers in the bicycle manufacturing industry were investigated. Personal air sampling and biological monitoring were used to assess total uptake through inhalation and dermal exposure. Haemoglobin was also analysed to evaluate the effects of exposure on the haematopoietic system.Methods80 workers in two bicycle factories completed a questionnaire. NIOSH method 1403 was adopted for air sampling and analysis of 2-BE. Prework and postwork urine samples were also collected for determination of total 2-butoxyacetic acid (BAA) after hydrolysis. Haemoglobin tests were performed using an automated haemoglobin analysis system.ResultsThe 31 decal transfer workers whose hands were in direct contact with a dilute aqueous solution of 2-BE, were exposed to an average of 1.7 ppm (8.1 mg/m3) of 2-BE in air. Correlation of 2-BE in air and postshift urinary BAA levels (after hydrolysis) was poor. Postshift total BAA levels in urine on Monday and Friday (446.8 and 619.4 mg/g creatinine) were around 223% and 310% of the ACGIH proposed Biological Exposure Index (BEI; 200 mg/g creatinine). Higher levels of total BAA were observed in the urine of subjects exposed to low-level 2-BE in air, presumably because of direct dermal contact.ConclusionsThe mean preshift BAA on Friday was significantly higher than that on Monday, implying that the more days of exposures, the higher the accumulation. Since accumulation occurred with low-level exposure to 2-BE, it is recommended that urine samples be collected at the end of the working week.