bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial distribution of rare species in lotic habitats
Authors: McCREADIE JOHN W. , ADLER PETER H. 
Published: July 2008

Abstract.

Species rarity is a common phenomenon in the biological world. Although rare species have always interested biologists, the meaning of ‘rare’ has not always been clear with the definition of rarity often arbitrary.
In the current study, we investigate rarity in stream ecosystems using black flies (Diptera: Simuliidae). We defined rare species a priori as those species found ≤ 10% of stream sites examined (n = 111 streams for ‘summer collections’; n = 88 collection for ‘spring’ collections). Hence, we are exploring only one axis of rarity, restricted range.
We first consider the distribution of each rare species separately to determine if the mean (euclidian) distance among streams (habitats) for each rare species differs from a random model. We next took a collective approach by pooling all rare species to determine the influence of stream conditions, niche breadth, and distance among habitats on rarity.
Even within this biologically uniform group of flies, dispersal, range limits, and stream conditions all might play a role in rarity, and the importance of each of these factors appear to vary among species. Rather than looking for broad causes of rarity, future studies might be more fruitful if they looked at species‐specific causes.
A randomisation program to compare species‐richness values
Authors: RICHARDSON JEAN M. L. , RICHARDS MIRIAM H. 
Published: July 2008

Abstract.

Comparisons of biodiversity estimates among sites or through time are hampered by a focus on using mean and variance estimates for diversity measures. These estimators depend on both sampling effort and on the abundances of organisms in communities, which makes comparison of communities possible only through the use of rarefaction curves that reduce all samples to the lowest sample size. However, comparing species richness among communities does not demand absolute estimates of species richness and statistical tests of similarity among communities are potentially more straightforward.
This paper presents a program that uses randomisation methods to robustly test for differences in species richness among samples. Simulated data are used to show that the analysis has acceptable type I error rates and sufficient power to detect violations of the null hypothesis. An analysis of published bee data collected in 4 years shows how both sample size and hierarchical structure in sample type are incorporated into the analysis.
The randomisation program is shown to be very robust to the presence of a dominant species, many rare species, and decreased sample size, giving quantitatively similar conclusions under all conditions. This method of testing for differences in biodiversity provides an important tool for researchers working on questions in community ecology and conservation biology.
Water‐energy and the geographical species richness pattern of European and North African dragonflies (Odonata)
Authors: KEIL PETR , SIMOVA IRENA , HAWKINS BRADFORD A. 
Published: July 2008

Abstract.

Environmental correlates of broad‐scale patterns of Odonata species richness were studied in Europe and part of northern Africa using 220 × 220‐km gridded data. Relationships with 11 environmental variables were tested using multiple regression.
Two models were constructed: (i) for the entire data set covering both Europe and northern Africa, and (ii) only for Europe.
Across both regions, actual evapotranspiration had the strongest relationship with richness, followed by weaker associations of potential evapotranspiration (a concave polynomial) and summer vegetation index (a positive linear relationship). Within Europe the strongest predictor was a concave polynomial of potential evapotranspiration, followed by vascular plant species richness (a positive relationship) and annual precipitation (a concave polynomial).
A test of metabolic theory identified strong non‐linearity in the temperature‐richness relationship, and geographically weighted regression indicated consistency with the theory in a very limited part of Europe.
The results are most consistent with the hypothesis that broad‐scale species richness patterns are primarily determined by water–energy balance, similar to many fully terrestrial insect groups.
Importance of Type II Secretion for Survival of
Legionella pneumophila
in Tap Water and in Amoebae at Low Temperatures
Authors: Söderberg Maria A. , Dao Jenny , Starkenburg Shawn R. , Cianciotto Nicholas P. 
Published: July 2008

ABSTRACT

Legionella pneumophila
type II secretion mutants showed reduced survival in both tap water at 4 to 17°C and aquatic amoebae at 22 to 25°C. Wild-type supernatants stimulated the growth of these mutants, indicating that secreted factors promote low-temperature survival. There was a correlation between low-temperature survival and secretion function when 12 additional
Legionella
species were examined.
Baseline Data from a Belgium-Wide Survey of
Campylobacter
Species Contamination in Chicken Meat Preparations and Considerations for a Reliable Monitoring Program
Authors: Habib Ihab , Sampers Imca , Uyttendaele Mieke , Berkvens Dirk , De Zutter Lieven 
Published: July 2008

ABSTRACT

From February to November 2007, chicken meat preparations (
n
= 656) were sampled at 11 processing companies across Belgium. All samples were tested for
Campylobacter
by enrichment culture and by direct plating according to standard methods. Almost half (48.02%) of the samples were positive for
Campylobacter
spp. The mean
Campylobacter
count was 1.68 log
10
CFU/g with a standard deviation of ± 0.64 log
10
CFU/g. The study revealed a statistically significant variation in
Campylobacter
contamination levels between companies; processors with a wider frequency distribution range of
Campylobacter
counts provided chicken meat preparations with higher
Campylobacter
incidences and concentrations. There was no significant difference between the counts of
Campylobacter
spp. in various preparation types. However, the
Campylobacter
counts and incidences in chicken wings were the highest and portioned-form products (legs, wings, and breasts) showed a higher probability of being
Campylobacter
positive compared to minced-form products (sausages, burgers, and minced meat). The proportion of
Campylobacter
-positive samples was significantly higher in July than in other months. Recovery of
Campylobacter
spp. recovery by direct plating was higher (41.0%) compared to detection after enrichment (24.2%). Statistical modeling of the survey data showed that the likelihood of obtaining a positive result by enrichment culture increases with an increase in the
Campylobacter
concentration in the sample. In the present study, we provide the first enumeration data on
Campylobacter
contamination in Belgian chicken meat preparations and address proposals for improving
Campylobacter
monitoring programs.
Isolation of Predation-Deficient Mutants of
Bdellovibrio bacteriovorus
by Using Transposon Mutagenesis
Authors: Tudor John J. , Davis James J. , Panichella Marissa , Zwolak Adam 
Published: July 2008

ABSTRACT

The availability of the complete genome sequence of
Bdellovibrio bacteriovorus
provides an opportunity for investigating genes that play a significant role in predation. Using two independently derived facultatively predatory
Bdellovibrio
strains, we have designed a method to cultivate and screen transposon insertion mutants in 96-well microtiter dishes. Transposon insertion mutants were produced by introducing the plasposon pRL27, which carries a mini-Tn
5
. Mutants have been screened for predatory activity using 96-well plates. Seventeen independent nonpredatory mutants have been isolated, and DNA flanking the insertion has been sequenced. BLAST analysis revealed that most of these interrupted DNA sequences do not code for known proteins or functions. Two of the inactivated genes were analyzed further: one was found to code for a putative serine protease and the other a probable protein involved in secretion through the outer membrane. The methods described here are the first for the generation and isolation of predation-deficient mutants using random-transposon-insertion mutagenesis. As more mutants are isolated and their gene products analyzed, more light will be shed on how this predator carries out its exclusive life processes and perhaps how these products, or the organism itself, can be used for therapeutic, agricultural, and/or other purposes.
Corynebacterium glutamicum
Contains 3-Deoxy-
d
-Arabino-Heptulosonate 7-Phosphate Synthases That Display Novel Biochemical Features
Authors: Liu Ya-Jun , Li Pan-Pan , Zhao Ke-Xin , Wang Bao-Jun , Jiang Cheng-Ying , Drake Harold L. , Liu Shuang-Jiang 
Published: July 2008

ABSTRACT

3-Deoxy-
d
-arabino-heptulosonate 7-phosphate (DAHP) synthase (EC 2.5.1.54) catalyzes the first step of the shikimate pathway that finally leads to the biosynthesis of aromatic amino acids phenylalanine (Phe), tryptophan (Trp), and tyrosine (Tyr). In
Corynebacterium glutamicum
ATCC 13032, two chromosomal genes, NCgl0950 (
aroF
) and NCgl2098 (
aroG
), were located that encode two putative DAHP synthases. The deletion of NCgl2098 resulted in the loss of the ability of
C. glutamicum
RES167 (a restriction-deficient strain derived from
C. glutamicum
ATCC 13032) to grow in mineral medium; however, the deletion of NCgl0950 did not result in any observable phenotypic alteration. Analysis of DAHP synthase activities in the wild type and mutants of
C. glutamicum
RES167 indicated that NCgl2098, rather than NCgl0950, was involved in the biosynthesis of aromatic amino acids. Cloning and expression in
Escherichia coli
showed that both NCgl0950 and NCgl2098 encoded active DAHP synthases. Both the NCgl0950 and NCgl2098 DAHP synthases were purified from recombinant
E. coli
cells and characterized. The NCgl0950 DAHP synthase was sensitive to feedback inhibition by Tyr and, to a much lesser extent, by Phe and Trp. The NCgl2098 DAHP synthase was slightly sensitive to feedback inhibition by Trp, but not sensitive to Tyr and Phe, findings that were in contrast to the properties of previously known DAHP synthases from
C. glutamicum
subsp.
flavum
. Both Co
2+
and Mn
2+
significantly stimulated the NCgl0950 DAHP synthase's activity, whereas Mn
2+
was much more stimulatory than Co
2+
to the NCgl2098 DAHP synthase's activity.
Selective Isolation and Rapid Identification of Members of the Genus
Micromonospora
Authors: Qiu Danheng , Ruan Jisheng , Huang Ying 
Published: July 2008

ABSTRACT

Improved methods for selective isolation of diverse actinomycetes of the genus
Micromonospora
and a genus-specific nested PCR for rapid identification of putative
Micromonospora
isolates were developed. The robustness of both the isolation and the identification approach was underpinned by phylogenetic analysis based on 16S rRNA gene sequences.
Real-Time PCR Detection of Pathogenic Microorganisms in Roof-Harvested Rainwater in Southeast Queensland, Australia
Authors: Ahmed W. , Huygens F. , Goonetilleke A. , Gardner T. 
Published: July 2008

ABSTRACT

In this study, the microbiological quality of roof-harvested rainwater was assessed by monitoring the concentrations of
Escherichia coli
, enterococci,
Clostridium perfringens
, and
Bacteroides
spp. in rainwater obtained from tanks in Southeast Queensland, Australia. Samples were also tested using real-time PCR (with SYBR Green I dye) for the presence of potential pathogenic microorganisms. Of the 27 rainwater samples tested, 17 (63%), 21 (78%), 13 (48%), and 24 (89%) were positive for
E. coli
, enterococci,
C. perfringens
, and
Bacteroides
spp., respectively. Of the 27 samples, 11 (41%), 7 (26%), 4 (15%), 3 (11%), and 1 (4%) were PCR positive for the
Campylobacter coli ceuE
gene, the
Legionella pneumophila mip
gene, the
Aeromonas hydrophila lip
gene, the
Salmonella invA
gene, and the
Campylobacter jejuni mapA
gene. Of the 21 samples tested, 4 (19%) were positive for the
Giardia lamblia
β-giardin gene. The binary logistic regression model indicated a positive correlation (
P
< 0.02) between the presence/absence of enterococci and
A. hydrophila
. In contrast, the presence/absence of the remaining potential pathogens did not correlate with traditional fecal indicators. The poor correlation between fecal indicators and potential pathogens suggested that fecal indicators may not be adequate to assess the microbiological quality of rainwater and consequent health risk.
Short-Term Response of Soil Bacteria to Carbon Enrichment in Different Soil Microsites
Authors: Monard C. , Binet F. , Vandenkoornhuyse P. 
Published: July 2008

ABSTRACT

The response of bacteria in bulk soil and earthworm casts to carbon enrichment was studied by an RNA stable-isotope probing/terminal restriction fragment length polymorphism strategy with
13
C-labeled glucose and acetate. Both the soil microsite status and the carbon enrichment selected rapidly for different active bacterial communities, which resulted in different degradation kinetics. Our study clearly illustrates the biases that are generated by adding C substrates to detect metabolically active bacteria in soil.
Distinct Contributions of the Nisin Biosynthesis Enzymes NisB and NisC and Transporter NisT to Prenisin Production by
Lactococcus lactis
Authors: van den Berg van Saparoea H. Bart , Bakkes Patrick J. , Moll Gert N. , Driessen Arnold J. M. 
Published: July 2008

ABSTRACT

Several
Lactococcus lactis
strains produce the lantibiotic nisin. The dedicated enzymes NisB and NisC and the transporter NisT modify and secrete the ribosomally synthesized nisin precursor peptide. NisB can function in the absence of the cyclase NisC, yielding the dehydrated prenisin that lacks the thioether rings. A kinetic analysis of nisin production by
L. lactis
NZ9700 demonstrated that the prenisin was released from the cell into the medium before the processing of the leader sequence occurred. Upon the deletion of
nisC
, the production of prenisin was reduced by 70%, while in the absence of
nisB
, the production of prenisin was nearly completely abolished. In cells lacking
nisT
, no secretion was observed, while the expression of
nisABC
in these cells resulted in considerable growth rate inhibition caused by the intracellular accumulation of active nisin. Overall, these data indicate that the efficiency of prenisin transport by NisT is markedly enhanced by NisB, suggesting a channeling mechanism of prenisin transfer between the nisin modification enzymes and the transporter.
Bacteriophage P22 and
Staphylococcus aureus
Attenuation on Nonporous Fomites as Determined by Plate Assay and Quantitative PCR
Authors: Masago Yoshifumi , Shibata Tomoyuki , Rose Joan B. 
Published: July 2008

ABSTRACT

Decay rates of bacteriophage P22 and
Staphylococcus aureus
on six types of common household inanimate surfaces were evaluated based on cultivation and quantitative PCR. A much higher level of inactivation was observed using the plate assay, suggesting that detection of the pathogen genome in samples from fomites does not necessarily imply a health risk to humans.
Methylotrophy in Freshwater
Beggiatoa alba
Strains
Authors: Jewell Talia , Huston Sherry L. , Nelson Douglas C. 
Published: July 2008

ABSTRACT

Two freshwater strains of the gammaproteobacterium
Beggiatoa alba
, B18LD and OH75-2a, are able to use methanol as a sole carbon and energy source under microoxic conditions. Genes encoding a methanol dehydrogenase large-subunit homolog and four enzymes of the tetrahydromethanopterin-dependent C
1
oxidation pathway were identified in B18LD. No evidence of methanotrophy was detected.
Molecular Characterization of the Bacterial Communities in the Different Compartments of a Full-Scale Reverse-Osmosis Water Purification Plant
Authors: Bereschenko L. A. , Heilig G. H. J. , Nederlof M. M. , van Loosdrecht M. C. M. , Stams A. J. M. , Euverink G. J. W. 
Published: July 2008

ABSTRACT

The origin, structure, and composition of biofilms in various compartments of an industrial full-scale reverse-osmosis (RO) membrane water purification plant were analyzed by molecular biological methods. Samples were taken when the RO installation suffered from a substantial pressure drop and decreased production. The bacterial community of the RO membrane biofilm was clearly different from the bacterial community present at other locations in the RO plant, indicating the development of a specialized bacterial community on the RO membranes. The typical freshwater phylotypes in the RO membrane biofilm (i.e.,
Proteobacteria
,
Cytophaga-Flexibacter-Bacteroides
group, and
Firmicutes
) were also present in the water sample fed to the plant, suggesting a feed water origin. However, the relative abundances of the different species in the mature biofilm were different from those in the feed water, indicating that the biofilm was actively formed on the RO membrane sheets and was not the result of a concentration of bacteria present in the feed water. The majority of the microorganisms (59% of the total number of clones) in the biofilm were related to the class
Proteobacteria
, with a dominance of
Sphingomonas
spp. (27% of all clones). Members of the genus
Sphingomonas
seem to be responsible for the biofouling of the membranes in the RO installation.
Cryptosporidium
Genotypes and Subtypes in Lambs and Goat Kids in Spain
Authors: Quílez Joaquín , Torres Eucaris , Chalmers Rachel M. , Hadfield Stephen J. , del Cacho Emilio , Sánchez-Acedo Caridad 
Published: July 2008

ABSTRACT

To provide information on the transmission dynamics of cryptosporidial infections in domestic small ruminants and the potential role of sheep and goats as a source for human cryptosporidiosis,
Cryptosporidium
-positive isolates from 137 diarrheic lambs and 17 goat kids younger than 21 days of age were examined by using genotyping and subtyping techniques. Fecal specimens were collected between 2004 and 2006 from 71 sheep and 7 goat farms distributed throughout Aragón (northeastern Spain).
Cryptosporidium parvum
was the only species identified by restriction analyses of PCR products from small-subunit rRNA genes from all 154 microscopy-positive isolates and the sequencing of a subset of 50 isolates. Sequence analyses of the glycoprotein (GP60) gene revealed extensive genetic diversity within the
C. parvum
strains in a limited geographical area, in which the isolates from lambs exhibited 11 subtypes in two subtype families (IId and IIa) and those from goat kids displayed four subtypes within the family IId. Most isolates (98%) belonged to the subtype family IId, whereas only three isolates belonged to the most widely distributed family, IIa. Three of the four most prevalent subtypes (IIdA17G1a, IIdA19G1, and IIdA18G1) were previously identified in humans, and five subtypes (IIdA14G1, IIdA15G1, IIdA24G1, IIdA25G1, and IIdA26G1) were novel subtypes. All IId subtypes were identical to each other in the nonrepeat region, except for subtypes IIdA17G1b and IIdA22G1, which differed by a single nucleotide polymorphism downstream of the trinucleotide repeats. These findings suggest that lambs and goat kids are an important reservoir of the zoonotic
C. parvum
subtype family IId for humans.
Feasibility of Assessing the Community Composition of Prasinophytes at the Helgoland Roads Sampling Site with a DNA Microarray
Authors: Gescher Christine , Metfies Katja , Frickenhaus Stephan , Knefelkamp Britta , Wiltshire Karen H. , Medlin Linda K. 
Published: July 2008

ABSTRACT
The microalgal class Prasinophyceae (Chlorophyta) contains several picoeukaryotic species, which are known to be common in temperate and cold waters and have been observed to constitute major fractions of marine picoplankton. However, reliable detection and classification of prasinophytes are mainly hampered by their small size and few morphological markers. Consequently, very little is known about the abundance and ecology of the members of this class. In order to facilitate the assessment of the abundance of the Prasinophyceae, we have designed and evaluated an 18S rRNA gene-targeted oligonucleotide microarray consisting of 21 probes targeting different taxonomic levels of prasinophytes. The microarray contains both previously published probes from other hybridization methods and new probes, which were designed for novel prasinophyte groups. The evaluation of the probe set was done under stringent conditions with 18S PCR fragments from 20 unialgal reference cultures used as positive targets. This microarray has been applied to assess the community composition of prasinophytes at Helgoland, an island in the North Sea where time series data are collected and analyzed daily but only for the nano- and microplankton-size fractions. There is no identification of prasinophytes other than to record them numerically in the flagellate fraction. The samples were collected every 2 weeks between February 2004 and December 2006. The study here demonstrates the potential of DNA microarrays to be applied as a tool for quick general monitoring of this important picoplanktonic algal group.
Epidemiology, Etiology, Pathogenesis, and Diagnosis of Recurrent Bacterial Meningitis
Authors: Tebruegge Marc , Curtis Nigel 
Published: July 2008

SUMMARYRecurrent bacterial meningitis is a rare phenomenon and generally poses a considerable diagnostic challenge to the clinician. Ultimately, a structured approach and early diagnosis of any underlying pathology are crucial to prevent further episodes and improve the overall outcome for the affected individual. In this article, we are reviewing the existing literature on this topic over the last two decades, encompassing 363 cases of recurrent bacterial meningitis described in 144 publications. Of these cases, 214 (59%) were related to anatomical problems, 132 (36%) were related to immunodeficiencies, and 17 (5%) were related to parameningeal infections. The review includes a detailed discussion of the underlying pathologies and microbiological aspects as well as recommendations for appropriate diagnostic pathways for investigating this unusual entity.
Evidence-Based Biosafety: a Review of the Principles and Effectiveness of Microbiological Containment Measures
Authors: Kimman Tjeerd G. , Smit Eric , Klein Michèl R. 
Published: July 2008

SUMMARYWe examined the available evidence on the effectiveness of measures aimed at protecting humans and the environment against the risks of working with genetically modified microorganisms (GMOs) and with non-GMO pathogenic microorganisms. A few principles and methods underlie the current biosafety practice: risk assessment, biological containment, concentration and enclosure, exposure minimization, physical containment, and hazard minimization. Many of the current practices are based on experience and expert judgment. The effectiveness of biosafety measures may be evaluated at the level of single containment equipment items and procedures, at the level of the laboratory as a whole, or at the clinical-epidemiological level. Data on the containment effectiveness of equipment and laboratories are scarce and fragmented. Laboratory-acquired infections (LAIs) are therefore important for evaluating the effectiveness of biosafety. For the majority of LAIs there appears to be no direct cause, suggesting that failures of biosafety were not noticed or that containment may have been insufficient. The number of reported laboratory accidents associated with GMOs is substantially lower than that of those associated with non-GMOs. It is unknown to what extent specific measures contribute to the overall level of biosafety. We therefore recommend that the evidence base of biosafety practice be strengthened.