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PubMed2026

Soil Acidification Enriches Antibiotic Resistome.

Soil acidification represents a critical global change issue. Its impacts on antibiotic resistance genes (ARGs), however, remain poorly understood. Here we first analyzed a published global dataset comprising 1012 sampling sites and found a significant negative correlation between soil pH and the total richness and relative abundance of ARGs. To validate the observed pattern, we subjected three soils (with initial pH 7.8-7.9) each to 4 acidification levels (pH 7, 6, 5, and 4) for 30 days and subsequent recovery for another 30 days in microcosms. Shotgun metagenomic sequencing revealed that acidification (pH 6, 5, and 4) significantly increased the total richness and relative abundance of ARGs, as well as the relative abundances of 175 ARG subtypes, across all three soils. These 175 acidification-enriched ARGs together accounted for more than 70% of all the ARGs under severely acidified conditions (pH 5 and 4). Moreover, 93% of the bacteria carrying acidification-enriched ARGs also carried various virulence factor genes homologs associated with pathogenicity in reference databases, resulting in increased risk score. The total relative abundance of the acidification-enriched ARGs was primarily associated with changes in bacterial community traits (community composition, acidification-enriched metabolic functions, and genome size), followed by the increase in availability of toxic metals. When soil recovered from severe acidification (pH 5 and 4), the total relative abundance of the acidification-enriched ARGs significantly declined, demonstrating that the effect of soil acidification is partially reversible. This study reveals an underrecognized risk of ARGs caused by soil acidification, highlighting that the prevention and mitigation of soil acidification are crucial for combating antibiotic resistance.

Hydrogen-Ion Concentration↗

PubMedDate not supplied

Perceived risk of heart attack: a function of gender?

TOPIC: The influence of gender on women's risk beliefs for heart attack. PURPOSE: To inform healthcare providers how women's beliefs and attitudes contribute to treatment-seeking delay in the event of a heart attack, and to establish the importance of risk beliefs in women. SOURCES: Published literature in MEDLINE and CINAHL computerized databases, reference lists of obtained articles. CONCLUSIONS: Women's perceived risk beliefs for heart attack are influenced by the effects of media, cultural, and gender roles and the modeling of bias in health care. There is a need for healthcare providers to change their focus from acting on (etic) a patient to interacting within (emic) the belief systems of their patients to optimize positive outcomes.

Cultural Characteristics↗

PubMed2006

Efficacy and safety of 'wet-wrap' dressings as an intervention treatment in children with severe and/or refractory atopic dermatitis: a critical review of the literature.

BACKGROUND: During the last two decades wet-wrap treatment (WWT) has been advocated as a relatively safe and effective treatment modality in children with severe and/or refractory atopic dermatitis (AD). Unfortunately, there are still many unsolved issues concerning the use of wet-wrap dressings in patients with AD. OBJECTIVES: To make an inventory of the different methodologies and to evaluate the currently available evidence for the use of WWT as an intervention treatment in children with severe and/or refractory AD. METHODS: We performed a search of the literature via the online PubMed database. Reference lists from relevant articles were scanned for additional publications. Publications describing a treatment modality for children with severe and/or refractory AD, which included the application of wet dressings, were collected and evaluated using the guidelines of the NHS Centre for Reviews and Dissemination, University of York. RESULTS: Twenty-four publications were included for evaluation. Eleven of the publications detailed original clinical studies (study design level 2-4), while 13 revealed expert opinions (study design level 5). Evidence levels did not exceed level 4. CONCLUSIONS: Large prospective studies evaluating the efficacy and safety profile of WWT are lacking. We were able to formulate the following conclusions with a grade C of recommendation. (i) WWT using cream or ointment and a double layer of cotton bandages, with a moist first layer and a dry second layer, is an efficacious short-term intervention treatment in children with severe and/or refractory AD. (ii) The use of wet-wrap dressings with diluted topical corticosteroids is a more efficacious short-term intervention treatment in children with severe and/or refractory AD than wet-wrap dressings with emollients only. (iii) The use of wet-wrap dressings with diluted topical corticosteroids for up to 14 days is a safe intervention treatment in children with severe and/or refractory AD, with temporary systemic bioactivity of the corticosteroids as the only reported serious side-effect. (iv) Lowering the absolute amount of applied topical corticosteroid to once daily application and further dilution of the product can reduce the risk of systemic bioactivity.

Adolescent↗

PubMed2006

Analysis of fungal diversity of grapes by application of temporal temperature gradient gel electrophoresis - potentialities and limits of the method.

AIMS: Fungi could be responsible for several problems in wines but the fungal ecosystem of grapes remains little known. The use of traditional methods does not allow to describe quickly this ecosystem. Therefore, we need to improve the knowledge about these fungi to prevent defects in wine. This study aims at evaluating the potentialities of the temporal temperature gradient gel electrophoresis (TTGE) method to describe the fungal ecosystem of grapes. METHODS AND RESULTS: The internal transcribed spacer (ITS) region was amplified and analysed using TTGE. A reference database of 56 fungal species was set up to evaluate the discrimination power of the method. The database was used for the direct identification of the fungal species present in complex samples. The sensitivity of the method is below 10(4) spores per ml. CONCLUSIONS: This method allows to describe the fungal diversity of grapes, but does not always allow to directly identify all fungal species, because of the taxonomic resolution of the ITS sequences. However, this identification strategy is less time consuming than traditional analysis by cloning and sequencing the bands. SIGNIFICANCE AND IMPACT OF THE STUDY: With this method, it will be possible to compare the fungal species present in different vineyards and to connect the presence of some fungi with particular defects in wine.

DNA, Fungal↗

PubMedDate not supplied

A concept analysis of effective breastfeeding.

OBJECTIVE: To provide a concept analysis of effective breastfeeding. DATA SOURCES: Medline and CINAHL electronic databases, reference lists from selected articles, and 7 breastfeeding assessment tools. Search terms included the following: breastfeeding and effective, adequate, successful. STUDY SELECTION: Literature was selected according to whether the concept of effective breastfeeding was defined or described. DATA EXTRACTION: Literature was reviewed and data organized as definitions or descriptions, with descriptions grouped into categories sharing similar characteristics. DATA SYNTHESIS: Four characteristics were chosen as essential attributes of effective breastfeeding: positioning, latch, sucking, and milk transfer. CONCLUSIONS: The concept of effective breastfeeding requires further concept development to define and describe effective positioning, latch, sucking, and milk transfer. Future research is needed to determine the relationships between the antecedents, attributes, and consequences of effective breastfeeding.

Breast Feeding↗

PubMed1996

The relationship of sustained exercise training and bone mineral density in aging male runners.

Fifty-six men aged 42-73 years (50.2 +/- 10.0 years), who were competitive distance runners 20-25 years previously, were examined for bone mineral density (BMD) to determine the relationship between sustained distance running and BMD. Subjects were classified as being highly trained (HT, n = 17), moderately trained (MT, n = 29) or untrained (UT, n = 10) according to their training in recent years. Subjects in each group were of similar age (HT 46.5 +/- 2.01, MT 53.0 +/- 1.51, UT 46.7 +/- 2.44 years) and lean body mass. Total body weight (kg) and percentage fat, however, were significantly greater (P < 0.05) in the UT group than in either the MT or HT groups (UT 80.6 +/- 2.44 kg, 22.0 +/- 1.16%; MT 74.9 +/- 1.51 kg, 17.5 +/- 0.61%; HT 70.5 +/- 1.71 kg, 13.5 +/- 0.59%). Lumbar vertebrae and hip region BMD (g.cm-2) was determined via dual energy X-ray absorptiometry (DEXA). No differences in BMD were found among the three groups in either the lumbar (HT 1.00 +/- 0.02, MT 1.02 +/- 0.03, UT 1.07 +/- 0.04 g.cm-2) or the hip regions (HT 0.99 +/- 0.03, MT 0.98 +/- 0.02, UT 1.06 +/- 0.04 g.cm-2). Furthermore, none of the groups had BMD that was significantly different from age-matched normative values taken from a reference database. A moderate correlation was found between body weight and BMD when combining all subjects (r = 0.38 for lumbar and r = 0.41 for hip). These results indicate that middle-aged to older males who have sustained exercise training in the form of running do not have significantly different lumbar vertebrae or hip region BMD compared to individuals who run less or not at all.

Absorptiometry, Photon↗

PubMed2006

Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes.

A versatile software tool, VIRTUALMSLAB, is presented that can perform advanced complex virtual proteomic experiments with mass spectrometric analyses to assist in the characterization of proteins. The virtual experimental results allow rapid, flexible and convenient exploration of sample preparation strategies and are used to generate MS reference databases that can be matched with the real MS data obtained from the equivalent real experiments. Matches between virtual and acquired data reveal the identity and nature of reaction products that may lead to characterization of post-translational modification patterns, disulfide bond structures, and cross-linking in proteins or protein complexes. The most important unique feature of this program is the ability to perform multistage experiments in any user-defined order, thus allowing the researcher to vary experimental approaches that can be conducted in the laboratory. Several features of VIRTUALMSLAB are demonstrated by mapping both disulfide bonds and artificially introduced protein cross-links. It is shown that chemical cleavage at aspartate residues in the protease resistant RNase A, followed by tryptic digestion can be optimized so that the rigid protein breaks up into MALDI-MS detectable fragments, leaving the disulfide bonds intact. We also show the mapping of a number of chemically introduced cross-links in the NK1 domain of hepatocyte growth factor/scatter factor. The VIRTUALMSLAB program was used to explore the limitation and potential of mass spectrometry for cross-link studies of more complex biological assemblies, showing the value of high performance instruments such as a Fourier transform mass spectrometer. The program is freely available upon request.

Disulfides↗

PubMed2005

Effects of perioperative hypothermia and warming in surgical practice.

Perioperative hypothermia is common and adversely affects clinical outcomes due to its effect on a range of homeostatic functions. Many of these adverse consequences are preventable by the use of warming techniques. A literature search was conducted to identify relevant published articles on perioperative hypothermia and warming. The databases searched include MEDLINE (1966 to February 2005), EMBASE (1974 to February 2005), CINAHL, the Cochrane library and the health technology assessment database. Reference lists of key articles were also searched. The primary beneficial effects of warming are mediated through increased blood flow and oxygen tension at tissue level. Reduction in wound infection, blood loss and perioperative pain with warming is promising. However, more evidence from good-quality prospective randomised controlled trials is needed to evaluate the role of warming in improving overall morbidity, mortality and hospital stay as well as to clarify its role as an adjunct to resuscitation and during the pre-hospital transport phase of critically ill patients. Awareness of the risks of perioperative hypothermia is the key to prevention. Achieving normothermia throughout the patient's journey is a worthwhile goal in surgical patients.

Body Temperature Regulation↗

PubMed2025

The Role of Community Science in DNA-Based Biodiversity Monitoring.

The mutual interest in nature by the general public and scientists has led to many collaborations, past and present. Community science shows great potential for monitoring species occurrences and distributions, especially in combination with scalable and (semi)-automated methods such as DNA-based monitoring, helping to obtain data from a broader geographic and temporal range than would be possible by the scientific community alone. Here, we present an overview of the complementarity between community science and DNA-based biomonitoring through examples from ongoing projects. The involvement of hobby experts is particularly crucial for building up the necessary species reference databases that enable DNA-based monitoring. Based on this overview, we identify some key points related to learning opportunities and participant recognition to maximise the success, impact and benefit of community participants in DNA-based monitoring.

Biodiversity↗

PubMed1999

Radial dose distribution, dose to water and dose rate constant for monoenergetic photon point sources from 10 keV to 2 MeV:EGS4 Monte Carlo model calculation.

A comprehensive set of dose distributions from monoenergetic photon-emitting isotropic point sources in a medium can be used as a reference database for the dosimetry of photon emitter sources in that medium. Data of this type for water over the photon energy range from 15 keV to 2 MeV have been published based on calculations using a one-dimensional photon transport model. The present work, based on a previously published EGS4 Monte Carlo code, updates the classic data set of Berger and provides more extensive calculations than previously available. Air kerma strength per unit photon emission rate from an isotropic point emitter is obtained as a function of energy using published data for mass energy absorption coefficients. The TG-43 dose rate constant for water as a function of energy is calculated for monoenergetic photon emitters as the ratio of dose rate to water at 1 cm to air kerma strength for unit photon emission rate. Results for the radial dose distribution agree well with the data of Berger between 40 and 400 keV. For energies > or =500 keV, a previously undescribed buildup region for the radial dose function is identified. Thickness of the buildup region ranges from 1 mm at 500 keV to 8 mm at 2 MeV. Between 15 and 30 keV, the radial dose function within a few millimeters of the emitter is calculated to be 4%-5% higher than values derived from Berger's data. The maximum dose rate constant for monoenergetic photon emitters occurs at an energy of 60 keV, and has the value 1.355 cGy h(-1)U(-1), where U is the unit of air kerma strength, 1 microGy m2 h(-1). This would correspond to the maximum hypothetical dose rate constant for a brachytherapy photon source emitting photons of energy < or =2 MeV.

Dose-Response Relationship, Radiation↗

PubMed1991

Population genetics in forensic DNA typing.

Variable number of tandem repeat (VNTR) sequences are used to link defendants with crimes by matching DNA patterns. The probative value of a match is often calculated by multiplying together the estimated frequencies with which each particular VNTR pattern occurs in a reference database. However, this method is liable to potentially serious errors because ethnic subgroups within major racial categories exhibit genetic differences that are maintained by endogamy. The multiplication procedure currently in use can be made scientifically valid only by extensive sampling of VNTR frequency distributions in a variety of ethnic groups, similar to the ethnic studies of various blood groups done in the past. Alternative approaches for dealing with subpopulation heterogeneity are discussed.

Alleles↗

PubMed1999

Identification of Epichloë endophytes in planta by a microsatellite-based PCR fingerprinting assay with automated analysis.

Epichloë endophytes are a group of filamentous fungi that include both sexual (Epichloë) and asexual (Neotyphodium) species. As a group they are genetically diverse and form both antagonistic and mutualistic associations with temperate grasses. We report here on the development of a microsatellite-based PCR system for fingerprinting this group of fungi with template isolated from either culture or infected plant material. M13mp19 partial genomic libraries were constructed for size-fractionated genomic DNA from two endophyte strains. These libraries were screened with a mixture of DIG-labeled dinucleotide and trinucleotide repeat probes. Positive clones were sequenced, and nine unique microsatellite loci were identified. An additional microsatellite was serendipitously identified in the 3' untranscribed region of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase gene from N. lolii Lp19. Primers were designed for each locus and a panel of endophytes, from different taxonomic groupings, was screened to determine the degree of polymorphism. On the basis of these results a multiplex assay was developed for strain identification with fluorescently labeled primers for five of these loci. Using this system the size of the products amplified can be precisely determined by automated analysis, and an allele profile for each strain can be readily generated. The assay was shown to resolve endophyte groupings to the level of known isozyme phenotype groupings. In a blind test the assay was used successfully to identify a set of endophytes in planta. A reference database of allele sizes has been established for the panel of endophytes examined, and this will be expanded as new strains are analyzed.

Alleles↗

PubMed2002

Extensive profiling of a complex microbial community by high-throughput sequencing.

Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.

Animals↗

PubMed2004

Molecular fingerprinting of dairy microbial ecosystems by use of temporal temperature and denaturing gradient gel electrophoresis.

Numerous microorganisms, including bacteria, yeasts, and molds, constitute the complex ecosystem present in milk and fermented dairy products. Our aim was to describe the bacterial ecosystem of various cheeses that differ by production technology and therefore by their bacterial content. For this purpose, we developed a rapid, semisystematic approach based on genetic profiling by temporal temperature gradient electrophoresis (TTGE) for bacteria with low-G+C-content genomes and denaturing gradient gel electrophoresis (DGGE) for those with medium- and high-G+C-content genomes. Bacteria in the unknown ecosystems were assigned an identity by comparison with a comprehensive bacterial reference database of approximately 150 species that included useful dairy microorganisms (lactic acid bacteria), spoilage bacteria (e.g., Pseudomonas and Enterobacteriaceae), and pathogenic bacteria (e.g., Listeria monocytogenes and Staphylococcus aureus). Our analyses provide a high resolution of bacteria comprising the ecosystems of different commercial cheeses and identify species that could not be discerned by conventional methods; at least two species, belonging to the Halomonas and Pseudoalteromonas genera, are identified for the first time in a dairy ecosystem. Our analyses also reveal a surprising difference in ecosystems of the cheese surface versus those of the interior; the aerobic surface bacteria are generally G+C rich and represent diverse species, while the cheese interior comprises fewer species that are generally low in G+C content. TTGE and DGGE have proven here to be powerful methods to rapidly identify a broad range of bacterial species within dairy products.

Animals↗

PubMed2004

Raw cow milk bacterial population shifts attributable to refrigeration.

We monitored the dynamic changes in the bacterial population in milk associated with refrigeration. Direct analyses of DNA by using temporal temperature gel electrophoresis (TTGE) and denaturing gradient gel electrophoresis (DGGE) allowed us to make accurate species assignments for bacteria with low-GC-content (low-GC%) (<55%) and medium- or high-GC% (>55%) genomes, respectively. We examined raw milk samples before and after 24-h conservation at 4 degrees C. Bacterial identification was facilitated by comparison with an extensive bacterial reference database ( approximately 150 species) that we established with DNA fragments of pure bacterial strains. Cloning and sequencing of fragments missing from the database were used to achieve complete species identification. Considerable evolution of bacterial populations occurred during conservation at 4 degrees C. TTGE and DGGE are shown to be a powerful tool for identifying the main bacterial species of the raw milk samples and for monitoring changes in bacterial populations during conservation at 4 degrees C. The emergence of psychrotrophic bacteria such as Listeria spp. or Aeromonas hydrophila is demonstrated.

Animals↗

PubMed2005

Comparison of ileum microflora of pigs fed corn-, wheat-, or barley-based diets by chaperonin-60 sequencing and quantitative PCR.

We have combined the culture-independent methods of high-throughput sequencing of chaperonin-60 PCR product libraries and quantitative PCR to profile and quantify the small-intestinal microflora of pigs fed diets based on corn, wheat, or barley. A total of 2,751 chaperonin-60 PCR product clones produced from samples of ileum digesta were examined. The majority (81%) of these clones contained sequences independently recovered from all three libraries; 372 different nucleotide sequences were identified, but only 14% of the 372 different sequences were recovered from all three libraries. Taxonomic assignments of the library sequences were made by comparison to a reference database of chaperonin-60 sequences combined with phylogenetic analysis. The taxa identified are consistent with previous reports of pig ileum microflora. Frequencies of each sequence in each library were calculated to identify taxa that varied in frequency between the corn, barley, and wheat libraries. The chaperonin-60 sequence inventory was used as a basis for designing PCR primer sets for taxon-specific quantitative PCR. Results of quantitative PCR analysis of ileum digesta confirmed the relative abundances of targeted taxa identified with the library sequencing approach. The results of this study indicate that chaperonin-60 clone libraries can be valid profiles of complex microbial communities and can be used as the basis for producing quantitative PCR assays to measure the abundance of taxa of interest during experimentally induced or natural changes in a community.

Animal Feed↗

PubMed2001

Francisella tularensis strain typing using multiple-locus, variable-number tandem repeat analysis.

Francisella tularensis, the etiological agent of tularemia, is found throughout the Northern hemisphere. After analyzing the F. tularensis genomic sequence for potential variable-number tandem repeats (VNTRs), we developed a multilocus VNTR analysis (MLVA) typing system for this pathogen. Variation was detected at six VNTR loci in a set of 56 isolates from California, Oklahoma, Arizona, and Oregon and the F. tularensis live vaccine strain. PCR assays revealed diversity at these loci with total allele numbers ranging from 2 to 20, and Nei's diversity index values ranging from 0.36 to 0.93. Cluster analysis identified two genetically distinct groups consistent with the current biovar classification system of F. tularensis. These findings suggest that these VNTR markers are useful for identifying F. tularensis isolates at this taxonomic level. In this study, biovar B isolates were less diverse than those in biovar A, possibly reflecting the history of tularemia in North America. Seven isolates from a recent epizootic in Maricopa County, Ariz., were identical at all VNTR marker loci. Their identity, even at a hypervariable VNTR locus, indicates a common source of infection. This demonstrates the applicability of MLVA for rapid characterization and identification of outbreak isolates. Future construction of reference databases will allow faster outbreak tracking as well as providing a foundation for deciphering global genetic relationships.

Animals↗

PubMed2003

Use of 18S rRNA gene-based PCR assay for diagnosis of acanthamoeba keratitis in non-contact lens wearers in India.

Identification of Acanthamoeba cysts and trophozoites in ocular tissues requires considerable expertise and is often time-consuming. An 18S rRNA gene-based PCR test, highly specific for the genus Acanthamoeba, has recently been reported in the molecular diagnosis of Acanthamoeba keratitis. This PCR assay was compared with conventional microbiological tests for the diagnosis of Acanthamoeba keratitis. In a pilot study, the PCR conditions with modifications were first tested on corneal scrapings from patients with culture-proven non-contact lens-related Acanthamoeba, bacterial, and fungal keratitis. This was followed by testing of corneal scrapings from 53 consecutive cases of microbial keratitis to determine sensitivity, specificity, and predictive values of the assay. All corneal scrapings from patients with proven Acanthamoeba keratitis showed a 463-bp amplicon, while no amplicon was obtained from patients with bacterial or fungal keratitis. Some of these amplified products were sequenced and compared with EMBL database reference sequences to validate these to be of Acanthamoeba origin. Out of 53 consecutive cases of microbial keratitis included for evaluating the PCR, 10 (18.9%) cases were diagnosed as Acanthamoeba keratitis on the basis of combined results of culture, smear, and PCR of corneal scrapings. Based on culture results as the "gold standard," the sensitivity of PCR was the same as that of the smear (87.5%); however, the specificity and the positive and negative predictive values of PCR were marginally higher than the smear examination (97.8 versus 95.6%, 87.5 versus 77.8%, and 97.8 versus 97.7%) although the difference was not significant. This study confirms the efficacy of the PCR assay and is the first study to evaluate a PCR-based assay against conventional methods of diagnosis in a clinical setting.

Acanthamoeba↗