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PubMed2026

The utilization of Salmonella phage in milk and chicken: depolymerase identification and potential for anti-biofilm activity.

Bacteriophage (phage)-based biocontrol presents a promising strategy against foodborne pathogens. In this study, a novel phage, PH215, exhibited lytic activity against seven prevalent Salmonella serotypes, was isolated and characterized. PH215 demonstrated remarkable environmental stability, sustaining infectivity across a wide pH range (2-11) and at temperatures from 4 to 50 °C. The multiplicative potential of PH215 was evidenced by a low multiplicity of infection (MOI) of 10-6, a short latent period of 10 min, and a substantial burst size of approximately 50 PFU per infected cell. Genomic analysis revealed a 43,505 kb double-stranded DNA genome encoding 67 putative proteins. Notably, the product of the Peg38 gene, identified as a tail spike protein (termed PH215Depo), possessed depolymerase activity. We have shown that the cloned expression of PH215Depo exhibited enzymatic activity against various Salmonella serotypes and significantly impeded biofilm formation. Furthermore, in practical application models, PH215 application reduced Salmonella counts in milk and chicken by 2.04 to 5.37 log10 CFU/mL. Our findings highlight the potential of depolymerase-encoding phages like PH215 as effective and broad-spectrum biocontrol agents against Salmonella in the food industry.

Biofilms↗
PubMed2006

The effects of birdsfoot trefoil (Lotus corniculatus) and chicory (Cichorium intybus) when compared with perennial ryegrass (Lolium perenne) on ovine gastrointestinal parasite development, survival and migration.

Two experiments were conducted to investigate the effects of birdsfoot trefoil and chicory on parasitic nematode development, survival and migration when compared with perennial ryegrass. In experiment one, sheep faeces, containing 10,385 Cooperia curticei eggs were added to 25 cm diameter pots containing birdsfoot trefoil, chicory or ryegrass, and the pots maintained under optimal conditions for nematode parasite development. Replicate pots of each forage type were destructively sampled on day 8, 16, 20, 28 and 37 to collect the nematode larvae. When forages were compared on a dry matter basis, by day 16 there were 31% and 19% fewer larvae on birdsfoot trefoil and chicory than on ryegrass, respectively (P<0.01). In the second experiment, replicate 1m(2) field plots of birdsfoot trefoil, chicory and ryegrass were sub-sampled on day 14, 21, 35 and 49 for larval counts following the application of sheep faeces containing 585,000 Teladorsagia circumcincta eggs to each plot on day 0. Results showed there were a minimum of 58% and 63% fewer infective stage parasitic larvae on birdsfoot trefoil and chicory, respectively, compared with ryegrass on day 14 and 35 when forages were compared on a forage dry matter, plot area sampled and leaf area basis (P<0.01). Overall, these results indicate that the number of infective stage larvae on birdsfoot trefoil and chicory pasture was reduced by the effect of their sward structure on the development/survival/migration of ovine parasitic nematodes. These effects may be one of the ways in which these forages may affect parasitic infections in grazing livestock.

Analysis of Variance↗
PubMed1993

A mathematically defined motif for the radial distribution of charged residues on apolipoprotein amphipathic alpha helixes.

Multiple amphipathic alpha-helical candidate domains have been identified in exchangeable apolipoproteins by sequence analysis and indirect experimental evidence. The distribution of charged residues can differ within and between these apolipoproteins. Segrest et al. (Segrest, J. P., H. DeLoof, J. G. Dohlman, C. G. Brouillette, and G. M. Anantharamaiah. 1990. Proteins. 8:103-117.) argued that these differences are correlated with lipid affinity. A mathematically defined motif for the particular charge distribution associated with high lipid affinity (class A) is proposed. Primary sequence data from protein segments proposed previously to have an amphipathic alpha-helical structure are scanned. Counting formulas are presented for determining the conditional probability that the match between an observed charge distribution and the proposed motif would occur by chance. Because the preselected helical segments are short (the modal length is 22) and the motif definition imposes multiple constraints on the acceptable distributions, the computer-based algorithm is quite feasible computationally. 19 of the 20 segments previously assigned to class A match the motif sufficiently well (the remaining one is borderline), while very few others "erroneously" pass the screening test. These results confirm the original assignments of the candidate domains and, thus, support the hypothesis that there is a distinguishable subset of helixes having high lipid affinity. This counting approach is applicable to a growing subset of protein sequence analysis problems in which the segment lengths are short and the motif is complex.

Apolipoproteins↗
PubMed1999

Actual car fleet emissions estimated from urban air quality measurements and street pollution models.

A method to determine emissions from the actual car fleet under realistic driving conditions has been developed. The method is based on air quality measurements, traffic counts and inverse application of street air quality models. Many pollutants are of importance for assessing the adverse impact of the air pollution, e.g. NO2, CO, lead, VOCs and particulate matter. Aromatic VOCs are of special great concern due to their adverse health effects. Measurements of benzene, toluene and xylenes were carried out in central Copenhagen since 1994. Significant correlation was observed between VOCs and CO concentrations, indicating that the petrol engine vehicles are the major sources of VOC air pollution in central Copenhagen. Hourly mean concentrations of benezene were observed to reach values of up to 20 ppb, what is critically high according to the WHOs recommendations. Based on inverse model calculation of dispersion of pollutants in street canyons, an average emission factor of benzene for the fleet of petrol fuelled vehicles was estimated to be 0.38 g/km in 1994 and 0.11 in 1997. This decrease was caused by the reduction of benzene content in Danish petrol since summer 1995 and increasing percentage of cars equipped with three-way catalysts. The emission factors for benzene for diesel-fuelled vehicles were low.

Air Pollutants↗
PubMed2000

Liquid scintillation determination of low level components in complex mixtures of radionuclides

A new approach to simultaneous activity measurements of the complex radionuclide mixtures using liquid scintillation counting, which is applicable to the analysis of the environmental and technological samples, is presented. The method is based on specially developed software 'SpectraDec', realized on a Windows 95/98/NT platform and a spectra library created for different kinds and levels of quenching. The method allows analysis of complex mixtures when the activity ratios of the individual components vary considerably. For example, the radionuclide concentrations were successfully determined in the following complex mixture: 3H, 63Ni, 90Sr + 90Y, 137Cs, 241Am (model mixture), where the 90Sr + 90Y/3H activity ratio was 1/2500 (0.2 Bq/500 Bq) and 90Sr, 137Cs, 134Cs, 232Th, 226Ra (IAEA-reference sample), where the 90Sr/137Cs activity ratio was 1/50 (92 Bq/4515 Bq) with an accuracy of about 20%. The limitations of the given approach to the LS analysis of the radionuclide mixtures are considered.

Journal Article↗
PubMed2000

Pulse loss and counting statistics with a digital spectrometer

A commercially available digital gamma-ray spectrometer is tested at high count rates using a germanium detector and appropriate pulse processing parameters. Correction for pulse loss due to dead time and pileup is done by extending the live time according to the Gedcke-Hale method. The accuracy of this count-loss correction technique is tested experimentally up to saturation count rates. Also the statistical uncertainty applicable to the total number of counts in arbitrary regions of interest in gamma-ray spectra is studied experimentally, for measurements at fixed real time as well as at fixed live time. The results are similar to those found with traditional spectrometers using analog technology.

Journal Article↗
PubMed2001

Micromachined impedance spectroscopy flow cytometer for cell analysis and particle sizing.

A new cytological tool, based on the microCoulter particle counter (microCPC) principle, aimed at diagnostic applications for cell counting and separation in haematology, oncology or toxicology is described. The device measures the spectral impedance of individual cells or particles and allows screening rates over 100 samples s(-1) on a single-cell basis. This analyzer is intended to drive a sorting actuator producing a subsequent cell separation. Size reduction and integration of functions are essential in achieving precise measurements and high throughput. 3D finite element simulations are presented to compare various electrode geometries and their influence on cell parameters estimation. The device is based on a glass-polyimide microfluidic chip with integrated channels and electrodes microfabricated at the length scale of the particles to be investigated (1-20 microm). A laminar liquid flow carries the suspended particles through the measurement area. Each particle's impedance signal is recorded by a differential pair of microelectrodes using the cell surrounding media as a reference. The micromachined chip and processing electronic circuit allow simultaneous impedance measurements at multiple frequencies, ranging from 100 kHz to 15 MHz. In this paper, we describe the microfabrication and characterisation of an on-chip flow-cytometer as the first building block of a complete cell-sorting device. We then discuss the signal conditioning technique and finally impedance measurements of cells and particles of different sizes and types to demonstrate the differentiation of subpopulations in a mixed sample.

Flow Cytometry↗
PubMed2026

Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.

MOTIVATION: Short-read sequencing data can be affected by alignment artifacts in certain genomic regions. Removing reads overlapping these exclusion regions, previously known as Blacklists, help to potentially improve biological signal. Alternatively, "sponge" or decoy sequences have been proposed to reduce alignment artifacts. RESULTS: We examined the widely used Blacklist software and found that pre-generated exclusion sets were difficult to reproduce due to sensitivity to input data, aligner choice, and read length. We further explored the use of "sponge" sequences-unassembled genomic regions such as satellite DNA, ribosomal DNA, and mitochondrial DNA-as an alternative approach. We additionally investigated the effect of the T2T-CHM13 genome assembly on improving biological signals. Aligning reads to a genome that includes sponge sequences reduced signal correlation in ChIP-seq data comparably to Blacklist-derived exclusion sets while preserving biological signal. Sponge-based alignment also had minimal impact on RNA-seq gene counts, suggesting broader applicability beyond chromatin profiling. These results highlight the limitations of fixed exclusion sets, and recommend the use of the T2T-CHM13 assembly or, for the hg38 genome assembly, "sponge" sequences as an alignment-guided strategy for reducing artifacts and improving functional genomics analyses.

Software↗
PubMed1996

Detection of Francisella tularensis by the polymerase chain reaction.

Francisella tularensis is the causative agent of tularaemia. Effective antibiotic treatment of tularaemia is now available, but the early diagnosis of tularaemia remains a problem. Four primers (three pairs) were designed to detect F. tularensis by the polymerase chain reaction (PCR), based on the previously published nucleotide sequence of T-cell epitopes of a F. tularensis membrane protein. Amplification of purified F. tularensis chromosomal DNA with the three pairs of primers resulted in three different products with sizes consistent with those predicted from sequence data (211 bp, 347 bp and 568 bp). The specificity of the PCR was confirmed as no amplification was detected with a range of other bacteria. The sensitivity of the PCR was determined with limiting dilution PCR and viable counts. The preliminary application of the PCR to the detection of F. tularensis in aerosols and experimentally infected mice was investigated. Comparison of the results with those from traditional culture indicated that PCR was more sensitive. The animal challenge test showed that, 24 h after inoculation with 15 cfu of F. tularensis, 38 (82.6%) of 46 blood samples were positive by PCR, whereas only 22 (47.8%) were positive by culture. The results showed that PCR is a helpful tool for the detection of F. tularensis in blood, liver and spleen which should enable the rapid confirmation of clinical diagnoses of tularaemia.

Aerosols↗
PubMed2025

Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches.

Short-read sequencing data can be affected by alignment artifacts in certain genomic regions. Removing reads overlapping these exclusion regions, previously known as Blacklists, help to potentially improve biological signal. Tools like the widely used Blacklist software facilitate this process, but their algorithmic details and parameter choices are not always clearly documented, affecting reproducibility and biological relevance. We examined the Blacklist software and found that pre-generated exclusion sets were difficult to reproduce due to variability in input data, aligner choice, and read length. We also identified and addressed a coding issue that led to over-annotation of high-signal regions. We further explored the use of "sponge" sequences-unassembled genomic regions such as satellite DNA, ribosomal DNA, and mitochondrial DNA-as an alternative approach. Aligning reads to a genome that includes sponge sequences reduced signal correlation in ChIP-seq data comparably to Blacklist-derived exclusion sets while preserving biological signal. Sponge-based alignment also had minimal impact on RNA-seq gene counts, suggesting broader applicability beyond chromatin profiling. These results highlight the limitations of fixed exclusion sets and suggest that sponge sequences offer a flexible, alignment-guided strategy for reducing artifacts and improving functional genomics analyses.

Journal Article↗
PubMed1980

Occurrence of cytophagas in sewage plants.

With the application of plate count methods and of the KOH-flexirubin test, bacteria belonging to the Cytophaga group were proved to occur regularly in samples from biological sewage treatment facilities. Generally, the percentage of Cytophaga colonies of the total heterotrophic colonies was lowest in the inflow sewage water as compared with the values found in activated sludge, trickling filter, and effluent samples. During an observation period of 16 months, the highest percentages of cytophagas were found in winter samples from activated sludge and trickling filters. Furthermore, cytophagas were shown to have high percentages of the bacteria lytic to polymeric substrates such as cellulose, chitin, dextran, pectin, xylan, and gelatin. Thus, it is suggested that cytophagas may contribute to sewage purification, especially at cold temperatures and by polymer breakdown. Cytophaga strains isolated were shown to have gliding motility, flexirubin pigmentation, and a low guanine plus cytosine base ratio in common. The strains were roughly subdivided into a spreading, a nonspreading, and a cellulolytic group.

Journal Article↗
PubMed1974

Evaluation of an automated colony counter.

An automated colony counter was found to readily detect surface and subsurface bacterial colonies of 0.3-mm size or greater with a high degree of precision. On a logarithmic scale, counting efficiency consistently ranged from 89 to 95% of corresponding manual count determinations for plates containing up to 1,000 colonies. In routine application, however, automated plate counts up to approximately 400 colonies were selected as a more practical range for operation. The automated counter was easily interfaced with an automated data acquisition system.

Automation↗
PubMedDate not supplied

Introduction to nuclear physics.

Photons for counting or imaging applications in nuclear medicine result from several processes. Gamma rays are produced from excited state transitions after beta decay and electron capture. Annihilation photons result from positron decay. The de-excitation of the atom after electron capture results in the production of characteristic x rays or Auger electrons. Metastable state transitions result in gamma ray emission or internal conversion electrons. All radiopharmaceuticals used in diagnostic nuclear medicine applications are tagged with radionuclides that emit photons as a result of one of these processes.

Curriculum↗
PubMed2003

Evaluation of FLIPR Calcium 3 Assay Kit--a new no-wash fluorescence calcium indicator reagent.

We have evaluated the FLIPR Calcium 3 Assay Kit (Calcium 3), a new no-wash fluorescence calcium indicator dye reagent, for the measurement of agonist-stimulated calcium signaling in cells expressing the serotonin 2C (5-HT(2C)), metabotropic glutamate receptor 5 (mGluR5) and the vasopressin 2 (V2) G-protein-coupled receptors. Calcium 3 yielded equivalent (5-HT(2C)) or superior (mGluR5 and V2) sensitivity to FLUO-4 as indexed by the change in fluorescence counts following agonist application. Assay variability, indexed by CV, using Calcium 3 or FLUO-4 was equivalent with 5-HT(2C) receptor responses although CVs were reduced using Calcium 3 in the examples of the mGluR5 and V2 receptors. Receptor pharmacologies based on agonist EC(50) values were identical when either Calcium 3 or FLUO-4 were utilized. Our results validate Calcium 3 as a compelling alternative to FLUO-4 in the choice of fluorescent dye reagent for studying G-protein-coupled receptors, providing the advantage of a homogenous, no-wash assay format.

Aniline Compounds↗
PubMed1989

"Going with the flow": a perspective on flow cytometry in gastroenterology.

In this perspective on the applications of flow cytometry in gastroenterology are described the use of flow cytometry in the study of normal physiology, in normal anatomy, and in premalignant and malignant conditions of the digestive tract. The basic principles and applications for cell counting, sorting, cell cycle analysis, and quantitation of cellular characteristics are addressed to emphasize the great potential and availability of flow cytometry.

Cell Separation↗
PubMed1985

Topical chemotherapy of intradermal Walker 256 carcinosarcoma with diaziquone and doxorubicin in the rat.

A model for metastatic skin cancer using intradermal injection of Walker 256 carcinosarcoma has been developed in the rat. Using this model, antitumor activity of topically applied doxorubicin and diaziquone in Vanicream, Plastibase, and dimethyl sulfoxide (DMSO) as vehicles was compared with intraperitoneal injection of the drugs at the same doses beginning 4 days after injection of tumor cells. Doxorubicin applied topically at 0.5 mg/day for 4 days in Vanicream or Plastibase exhibited no antitumor activity, while i.p. administered doxorubicin at 0.5 mg/day for 4 days inhibited tumor growth at day 20 by 66%. Diaziquone applied topically at 0.1 mg/day for 4 days in Vanicream, Plastibase, or DMSO inhibited tumor growth at day 20 by 66, 86, and 43%, respectively, and cured animals of the skin tumor at a dose of 0.5 mg/day. Diaziquone administered i.p. at 0.5 mg/day for 4 days was lethal to rats, and at 0.1 mg/day it produced 93% inhibition of tumor growth at day 20. Diaziquone applied topically at 0.1 mg/day for 4 days in Plastibase cured rats of advanced tumor when treatment was begun 12 days after injection of tumor cells. The area under the plasma radioactivity time curve over 5 h for a single 0.64-mg dose of topically applied [ring-14C]diaziquone in DMSO was 0.01% that of the same dose of [ring-14C]diaziquone administered i.p. in non-tumored rats. The decrease in WBC count following topical application of diaziquone at a dose of 0.1 mg/day for 4 days, compared to the same dose of diaziquone administered i.p., was 62% in Vanicream, 81% in Plastibase and 33% in DMSO. Topical diaziquone was non-toxic to normal skin in the rat and in the domestic pig. It is concluded that topical application of diaziquone offers a therapeutic advantage over systemic treatment for metastatic cancer of the skin.

Absorption↗
PubMedDate not supplied

[The 20 min. iodine uptake in Graves' disease. 1. Technique and reliability (author's transl)].

The 20 minute intravenous radioiodine uptake technique is described in detail and results compared with those from the classical 2 1/2 hour oral uptake in 93 Graves' disease patients. Two methods used in correcting for extrathyroidal radioactivity in the early uptake are similarly compared. The 20 minute uptake was normal (locally less than 8% dose) in only 6,5% of the patients while the 2 1/2 hour uptake was normal (locally less than 35% dose) in 18,5%; in six patients the uptake at 20 min. was higher than at 2 1/2 h, observations indicating the superior sensitivity and diagnostic value of the early uptake. The suppression test performed at 20 minutes was, furthermore, pathological in 97,8% of patients. The comparison of methods to correct for extrathyroidal radioactivity in the 20-minute test showed excellent agreement between thigh count subtraction and application of a formula based on the thyroid uptake at 2 minutes. The former technique, however, was considered to be simpler. We conclude that the 20 minute intravenous iodine uptake technique is not only simpler to perform than the classical oral method, but is also diagnostically more accurate. A high quality scan was obtained 30-60 minutes after the injection of radioiodine in most of these patients.

Administration, Oral↗