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Probes Specific (probe + specific)

Distribution by Scientific Domains

Life Sciences	52%
Medical Sciences	30%
Chemistry	13%

Selected Abstracts

A Lanthanide-Complex-Based Ratiometric Luminescent Probe Specific for Peroxynitrite

CHEMISTRY - A EUROPEAN JOURNAL, Issue 22 2010
Cuihong Song
Abstract A lanthanide-complex-based ratiometric luminescence probe specific for peroxynitrite (ONOO,), 4,-(2,4-dimethoxyphenyl)-2,2,:6,,2,,-terpyridine-6,6,,-diyl]bis(methylenenitrilo)tetrakis(acetate)-Eu3+/Tb3+ ([Eu3+/Tb3+(DTTA)]), has been designed and synthesized. Both [Eu3+(DTTA)] and [Tb3+(DTTA)] are highly water soluble with large stability constants at ,1020, and strongly luminescent with luminescence quantum yields of 10.0 and 9.9,%, respectively, and long luminescence lifetimes of 1.38 and 0.26,ms, respectively. It was found that the luminescence of [Tb3+(DTTA)] could be quenched by ONOO, rapidly and specifically in aqueous buffers, while that of [Eu3+(DTTA)] did not respond to the addition of ONOO,. Thus, by simply mixing [Eu3+(DTTA)] and [Tb3+(DTTA)] in an aqueous buffer, a ratiometric luminescence probe specific for time-gated luminescence detection of ONOO, was obtained. The performance of [Tb3+(DTTA)] and [Eu3+/Tb3+(DTTA)] as the probes for luminescence imaging detection of ONOO, in living cells was investigated. The results demonstrated the efficacy and advantages of the new ratiometric luminescence probe for highly sensitive luminescence bioimaging application. [source]

Novel natural parabens produced by a Microbulbifer bacterium in its calcareous sponge host Leuconia nivea

ENVIRONMENTAL MICROBIOLOGY, Issue 6 2009
Elodie Quévrain
Summary A broad variety of natural parabens, including four novel structures and known ethyl and butyl parabens, were obtained from culture of a Microbulbifer sp. bacterial strain isolated from the temperate calcareous marine sponge Leuconia nivea (Grant 1826). Their structures were elucidated from spectral analysis, including mass spectrometry and 1D and 2D nuclear magnetic resonance. Their antimicrobial activity evaluated against Staphylococcus aureus was characterized by much higher in vitro activity of these natural paraben compounds 3,9 than commercial synthetic methyl and propyl parabens, usually used as antimicrobial preservatives. Compounds 4 and 9 revealed a bacteriostatic effect and compounds 6 and 7 appeared as bactericidal compounds. Major paraben compound 6 was also active against Gram positive Bacillus sp. and Planococcus sp. sponge isolates and was detected in whole sponge extracts during all seasons, showing its persistent in situ production within the sponge. Moreover, Microbulbifer sp. bacteria were visualized in the sponge body wall using fluorescence in situ hybridization with a probe specific to L4-n2 phylotypes. Co-detection in the sponge host of both paraben metabolites and Microbulbifer sp. L4-n2 indicates, for the first time, production of natural parabens in a sponge host, which may have an ecological role as chemical mediators. [source]

In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth

ENVIRONMENTAL MICROBIOLOGY, Issue 7 2002
Trine Rolighed Thomsen
Summary Among the filamentous bacteria occasionally causing bulking problems in activated sludge treatment plants, three morphotypes with attached microbial growth are common, Eikelboom Type 0041, Type 1851 and Type 1701. A better knowledge of the phylogeny and physiology of these filamentous bacteria is necessary in order to develop control strategies for bulking. In this study we have used a combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR) to investigate the identity and in situ physiology of the Type 0041-morphotype and its attached bacteria in two wastewater treatment plants. Identification and enumeration of Type 0041 using group-specific 16S rRNA-targeted FISH probes revealed that approximately 15% of the filaments hybridized with a gene probe specific for the TM7 group, a recently recognized major lineage in the bacterial domain. All other filaments morphologically identified as Type 0041 only hybridized to the general bacterial EUB338-probe, indicating that they probably do not belong to commonly isolated bacterial phyla such as the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, for which group-specific probes were used. The phylogenetic heterogeneity of Type 0041 again highlights the inadequacy of a morphology-based classification system. Like the filaments, most of the attached microbial cells were not identified beyond their affiliation to the Bacteria using the group-specific FISH probes. However, several different bacterial phyla were represented in the identified fraction suggesting that the attached microorganisms are phylogenetically diverse. The study of the in situ physiology of Type 0041 using MAR-FISH revealed that both the filaments and the attached bacteria on Type 0041 were versatile in the use of organic substrates and electron acceptors. It was observed that all Type 0041 could consume glucose, but none of the filaments were able to consume acetate under any conditions tested, in contrast to some of the attached bacteria. No significant physiological differences were found between TM7,positive and TM7,negative Type 0041 filaments, and only minor differences were observed between the two treatment plants tested. These are the first data on the physiology of the almost entirely uncharacterized TM7 phylum and show that TM7 filamentous bacteria can uptake carbon substrates under aerobic and anaerobic conditions. [source]

A narrow deletion of 7q is common to HCL, and SMZL, but not CLL

EUROPEAN JOURNAL OF HAEMATOLOGY, Issue 6 2004
Claus Lindbjerg Andersen
Abstract: To further characterise the genetic background of the two closely related B-lymphocytic malignancies hairy cell leukaemia (HCL), and splenic marginal zone lymphoma (SMZL) we have identified characteristic copy number imbalances by comparative genomic hybridisation (CGH). Based on these findings, areas of special interest were fine mapped, and relevant probes constructed for use in interphase-fluorescence in situ hybridisation (FISH) investigations. Thus, using the CGH data from 52 HCL and 61 SMZL patients, we identified the characteristic profiles of copy number imbalances for both diseases. These were a gain of 5q13-31 (19%) and loss of 7q22-q35 (6%) for HCL, and gain of 3q25 (28%), loss of 7q31 (16%), and gain of 12q15 (16%) for SMZL. A partial loss of 7q unsual for low-malignant B-cell diseases was found to be common to the two diseases. This loss was therefore fine mapped with BAC/PAC clones. Fine mapping revealed that in SMZL the minimal lost region covers 11.4 Mb spanning from 7q31.33 to 7q33 located between sequence tagged site (STS)-markers SHGC-3275 and D7S725. This area was distinct from the commonly deleted 7q region of myelodysplastic syndrome/acute myeloid leukaemia (MDS/AML). A FISH probe specific for the 7q region was constructed. Using this probe in an interphase-FISH investigation we showed the minimal lost 7q-region of HCL and SMZL to be one and the same. In one HCL case, this investigation furthermore showed the extent of the deleted region to be below the detection limit of CGH, whereas interphase-FISH screening of 36 chronic lymphocytic leukaemia (CLL) cases showed no deletion of the 7q area. In conclusion, we have identified characteristic profiles of copy number imbalances in HCL and SMZL and fine mapped the minimal extent of a commonly lost 7q area of special interest. We hypothesise that this region may contain (a) gene(s) important for the pathology of HCL and SMZL. [source]

A role for nitric oxide in sensory-induced neurogenesis in an adult insect brain

EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 11 2005
M. Cayre
In the adult cricket, neurogenesis occurs in the mushroom bodies, the main integrative structures of the insect brain. Mushroom body neuroblast proliferation is modulated in response to environmental stimuli. However, the mechanisms underlying these effects remain unspecified. In the present study, we demonstrate that electrical stimulation of the antennal nerve mimics the effects of olfactory activation and increases mushroom body neurogenesis. The putative role of nitric oxide (NO) in this activity-regulated neurogenesis was then explored. In vivo and in vitro experiments demonstrate that NO synthase inhibition decreases, and NO donor application stimulates neuroblast proliferation. NADPH-d activity, anti- l -citrulline immunoreactivity, as well as in situ hybridization with a probe specific for Acheta NO synthase were used to localize NO-producing cells. Combining these three approaches we clearly establish that mushroom body interneurons synthesize NO. Furthermore, we demonstrate that experimental interventions known to upregulate neuroblast proliferation modulate NO production: rearing crickets in an enriched sensory environment induces an upregulation of Acheta NO synthase mRNA, and unilateral electrical stimulation of the antennal nerve results in increased l -citrulline immunoreactivity in the corresponding mushroom body. The present study demonstrates that neural activity modulates progenitor cell proliferation and regulates NO production in brain structures where neurogenesis occurs in the adult insect. Our results also demonstrate the stimulatory effect of NO on mushroom body neuroblast proliferation. Altogether, these data strongly suggest a key role for NO in environmentally induced neurogenesis. [source]

A fluorescently-labelled r-RNA targeted oligonucleotide probe for the in situ detection of G-bacteria of the genus Amaricoccus in activated sludge

JOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2000
A.-M. Maszenan
A fluorescently-labelled r-RNAtargeted oligonucleotide probe specific for members of the genus Amaricoccus, which includes one group of the Gram-negative G-Bacteria seen in activated sludge systems, is described. These organisms, previously ,identified' on their distinctive morphology of cocci in tetrads, have been associated with poor performance of biological nutrient removal (EBNR) plants, by out-competing the polyphosphate accumulating bacteria. Methods of sample preparation for probing activated sludge are detailed, and preliminary surveys of 46 plants, using this probe, show that G-Bacteria belonging to the genus Amaricoccus are seen not only in large numbers in EBNR systems but also in conventional plants. The presence of single cells of this organism was common, emphasizing the dangers of relying on morphology and cell arrangement to identify these bacteria. [source]

Ribosomal RNA transcriptional activation and processing in hamster rubrospinal motoneurons: Effects of axotomy and testosterone treatment

THE JOURNAL OF COMPARATIVE NEUROLOGY, Issue 4 2003
Paul D. Storer
Abstract Rubrospinal motoneurons (RSMN) represent a population of androgen receptor-expressing central motoneurons with limited regenerative potential relative to their peripheral counterparts. A key determinant of regenerative capability lies in the nucleolar reaction of injured neurons. To date, characterization of the nucleolar reaction in injured central motoneurons has not been accomplished. Furthermore, it has been documented that testosterone propionate (TP) augments peripheral motoneuron regeneration through regulation of the nucleolar reaction to injury. In this study, the effects of injury alone, or in conjunction with TP, on the nucleolar response of injured RSMN were examined using in situ hybridization (ISH) techniques. Castrated adult male hamsters were subjected to right spinal cord hemisection at the C7/T1 vertebral level. Half the animals were subcutaneously implanted with one Silastic TP capsule, with the other half sham implanted. ISH for precursor 45S and mature 28S rRNA was accomplished with a 3H-labeled ribosomal DNA probe specific to the external transcribed spacer region or to the 28S region of the ribosomal gene, respectively. Postoperative times of 2, 6, and 24 hours were selected for examination of precursor 45S rRNA (i.e., rRNA transcriptional activation) levels and 0.25, 2, 4, and 14 days for examination of mature rRNA (i.e., ribosome) levels. Transcriptional activation of the rRNA gene was rapidly and transiently increased in injured RSMN, analogously to previously documented effects of injury on rRNA transcription in peripheral motoneurons, but, in contrast, this did not translate into an increase in mature ribosomes. TP administration failed to affect positively the nucleolar response of injured RSMN at all. From this study, a key component underlying inherent differences in the regenerative capacity of peripheral vs. central motoneurons has been identified, which can be targeted in future experiments designed to enhance the regenerative potential of selective neuronal populations. J. Comp. Neurol. 458:326,333, 2003. © 2003 Wiley-Liss, Inc. [source]

A Lanthanide-Complex-Based Ratiometric Luminescent Probe Specific for Peroxynitrite

Folate deficiency in human peripheral blood lymphocytes induces chromosome 8 aneuploidy but this effect is not modified by riboflavin

ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 1 2010
Juan Ni
Abstract Chromosome 8 aneuploidy is a common event in certain cancers but whether folate (F) deficiency induces chromosome 8 aneuploidy is not known. Furthermore the impact of riboflavin (R) deficiency, which may alter activity of a key enzyme in folate metabolism, on these events is unknown. Therefore, the aim of our research was to test the following hypotheses: (a) F deficiency induces chromosome 8 aneuploidy; (b) chromosome 8 aneuploidy is affected by F deficiency to a similar degree as chromosome 17 and (c) R deficiency aggravates the risk of aneuploidy caused by F deficiency. These hypotheses were tested in long-term cultures of lymphocytes from twenty female healthy volunteers (aged 30,48 years). Lymphocytes were cultured in each of the four possible combinations of low (L) and high (H) F (LF, 20 nmol/L, HF 200 nmol/L, respectively) and L and H R (LR 1 nmol/L, HR 500 nmol/L, respectively) media (LFLR, LFHR, HFLR, HFHR) for 9 days. Chromosomes 8 and 17 aneuploidy was measured in mononucleated (MONO) and cytokinesis-blocked binucleated (BN) cells using dual-color fluorescence in situ hybridization (FISH) with fluorescent centromeric probes specific for chromosomes 8 and 17. Culture in LF media (LFLR or LFHR) induced significant and similar increases in frequencies of aneuploidy of chromosomes 8 and 17 (P < 0.001) relative to culture in HF media (HFLR or HFHR). There was no significant effect of R concentration on aneuploidy frequency for either chromosome. We conclude that F deficiency is a possible cause of chromosome 8 aneuploidy. Environ. Mol. Mutagen. 2010. © 2009 Wiley-Liss, Inc. [source]

Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology

ENVIRONMENTAL MICROBIOLOGY, Issue 4 2010
Xavier Mayali
Summary Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate. [source]

Widespread occurrence of an intranuclear bacterial parasite in vent and seep bathymodiolin mussels

ENVIRONMENTAL MICROBIOLOGY, Issue 5 2009
Frank U. Zielinski
Summary Many parasitic bacteria live in the cytoplasm of multicellular animals, but only a few are known to regularly invade their nuclei. In this study, we describe the novel bacterial parasite "Candidatus Endonucleobacter bathymodioli" that invades the nuclei of deep-sea bathymodiolin mussels from hydrothermal vents and cold seeps. Bathymodiolin mussels are well known for their symbiotic associations with sulfur- and methane-oxidizing bacteria. In contrast, the parasitic bacteria of vent and seep animals have received little attention despite their potential importance for deep-sea ecosystems. We first discovered the intranuclear parasite "Ca. E. bathymodioli" in Bathymodiolus puteoserpentis from the Logatchev hydrothermal vent field on the Mid-Atlantic Ridge. Using primers and probes specific to "Ca. E. bathymodioli" we found this intranuclear parasite in at least six other bathymodiolin species from vents and seeps around the world. Fluorescence in situ hybridization and transmission electron microscopy analyses of the developmental cycle of "Ca. E. bathymodioli" showed that the infection of a nucleus begins with a single rod-shaped bacterium which grows to an unseptated filament of up to 20 ,m length and then divides repeatedly until the nucleus is filled with up to 80 000 bacteria. The greatly swollen nucleus destroys its host cell and the bacteria are released after the nuclear membrane bursts. Intriguingly, the only nuclei that were never infected by "Ca. E. bathymodioli" were those of the gill bacteriocytes. These cells contain the symbiotic sulfur- and methane-oxidizing bacteria, suggesting that the mussel symbionts can protect their host nuclei against the parasite. Phylogenetic analyses showed that the "Ca. E. bathymodioli" belongs to a monophyletic clade of Gammaproteobacteria associated with marine metazoans as diverse as sponges, corals, bivalves, gastropods, echinoderms, ascidians and fish. We hypothesize that many of the sequences from this clade originated from intranuclear bacteria, and that these are widespread in marine invertebrates. [source]

Bacterial diversity in the bacterioneuston (sea surface microlayer): the bacterioneuston through the looking glass

ENVIRONMENTAL MICROBIOLOGY, Issue 5 2005
Mark P. Franklin
Summary The bacterioneuston is defined as the community of bacteria present within the neuston or sea surface microlayer. Bacteria within this layer were sampled using a membrane filter technique and bacterial diversity was compared with that in the underlying pelagic coastal seawater using molecular ecological techniques. 16S rRNA gene libraries of , 500 clones were constructed from both bacterioneuston and the pelagic water samples and representative clones from each library were sequenced for comparison of bacterial diversity. The bacterioneuston was found to have a significantly lower bacterial diversity than the pelagic seawater, with only nine clone types (ecotaxa) as opposed to 46 ecotaxa in the pelagic seawater library. Surprisingly, the bacterioneuston clone library was dominated by 16S rRNA gene sequences affiliated to two groups of organisms, Vibrio spp. which accounted for over 68% of clones and Pseudoalteromonas spp. accounting for 21% of the library. The dominance of these two 16S rRNA gene sequence types within the bacterioneuston clone library was confirmed in a subsequent gene probing experiment. 16S rRNA gene probes specific for these groups of bacteria were designed and used to probe new libraries of 1000 clones from both the bacterioneuston and pelagic seawater DNA samples. This revealed that 57% of clones from the bacterioneuston library hybridized to a Vibrio sp.-specific 16S rRNA gene probe and 32% hybridized to a Pseudoalteromonas sp.-specific 16S rRNA gene probe. In contrast, the pelagic seawater library resulted in only 13% and 8% of 16S rRNA gene clones hybridizing to the Vibrio sp. and Pseudoalteromonas sp. probes respectively. Results from this study suggest that the bacterioneuston contains a distinct population of bacteria and warrants further detailed study at the molecular level. [source]

Quantum-Dot-Functionalized Poly(styrene- co -acrylic acid) Microbeads: Step-Wise Self-Assembly, Characterization, and Applications for Sub-femtomolar Electrochemical Detection of DNA Hybridization

ADVANCED FUNCTIONAL MATERIALS, Issue 7 2010
Haifeng Dong
Abstract A novel nanoparticle label capable of amplifying the electrochemical signal of DNA hybridization is fabricated by functionalizing poly(styrene- co -acrylic acid) microbeads with CdTe quantum dots. CdTe-tagged polybeads are prepared by a layer-by-layer self-assembly of the CdTe quantum dots (diameter,=,3.07,nm) and polyelectrolyte on the polybeads (diameter,=,323,nm). The self-assembly procedure is characterized using scanning and transmission electron microscopy, and X-ray photoelectron, infrared and photoluminescence spectroscopy. The mean quantum-dot coverage is (9.54,±,1.2),×,103 per polybead. The enormous coverage and the unique properties of the quantum dots make the polybeads an effective candidate as a functionalized amplification platform for labelling of DNA or protein. Herein, as an example, the CdTe-tagged polybeads are attached to DNA probes specific to breast cancer by streptavidin,biotin binding to construct a DNA biosensor. The detection of the DNA hybridization process is achieved by the square-wave voltammetry of Cd2+ after the dissolution of the CdTe tags with HNO3. The efficient carrier-bead amplification platform, coupled with the highly sensitive stripping voltammetric measurement, gives rise to a detection limit of 0.52 fmol L,1 and a dynamic range spanning 5 orders of magnitude. This proposed nanoparticle label is promising, exhibits an efficient amplification performance, and opens new opportunities for ultrasensitive detection of other biorecognition events. [source]

Visualization of Helicobacter Species Within the Murine Cecal Mucosa Using Specific Fluorescence In Situ Hybridization

HELICOBACTER, Issue 2 2005
Vivian Chan
ABSTRACT Background., Members of the genus Helicobacter have been associated with colitis development in a number of immunodeficient animal models. While it is known that these organisms can initiate colitis development, the location and spatial distribution of these bacteria within the intestinal tract is currently unknown. In this study, we developed and optimized fluorescence in situ hybridization (FISH) probes specifically for Helicobacter species. Materials and Methods., Based on 16S-RNA gene alignments, two probes specific for the entire family Helicobacteraceae and two probes specific for Helicobacter ganmani and Helicobacter hepaticus were designed. Evaluation of these probes was determined using ATCC reference strains and cecum samples from ten IL-10 knockout mice. The presence of Helicobacter species was determined using FISH and verified using PCR-DGGE and microscopic examination of silver stained sections. Results., Analysis of the ATCC reference strains revealed that the probes HEL274/HEL717 were specific for the family Helicobacteraceae, while HEP642 was specific for H. hepaticus and GAN1237 for H. ganmani. Using these probes, a pattern of spatial localization of the two different Helicobacter species was observed in the cecum tissues of IL-10 knockout mice. This consistently showed that H. ganmani was localized to the lower regions and H. hepaticus to the mid-upper regions of the crypts. Conclusion., We have developed FISH probes specific for the family Helicobacteraceae as well as two individual Helicobacter species. This study will allow the future use of the FISH to better understand host-pathogen interactions in vitro. [source]

Linkage and mapping analysis of a non-susceptibility gene to densovirus (nsd-2) in the silkworm, Bombyx mori

INSECT MOLECULAR BIOLOGY, Issue 2 2003
D. O. Ogoyi
Abstract Nonsusceptibility to Bombyx mori densovirus type 2 (BmDNV-2) is controlled by a recessive non-susceptibility gene, nsd-2 (non-susceptibility to DNV-2) in B. mori. Taking advantage of a lack of crossing over in females, reciprocal backcrossed F1 (BF1) progeny were used for linkage analysis and mapping of nsd-2 using silkworm strains C124 and 902, which are classified as being highly susceptible and non-susceptible to DNV-2, respectively. BF1 larvae were inoculated twice with DNV-2 virus at the first and second instar stages. DNA was extracted from each of the surviving fifth instar larvae and analysed by RFLP inheritance patterns using probes specific to each of the 28 linkage groups of B. mori. Our results indicated that the non-susceptibility gene was linked to linkage group 17, since all surviving larvae showed the homozygous profile of strain 902 in their genotype. The other linkage groups showed mixtures of heterozygous and homozygous genotypes, indicating an independent assortment. A linkage map of 30.6 cM was constructed for linkage group 17 with nsd-2 mapped at 24.5 cM and three closely linked cDNA markers were identified. [source]

Oligonucleotide microarrays for the detection and identification of viable beer spoilage bacteria

JOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2008
D.G. Weber
Abstract Aims:, The design and evaluation of an oligonucleotide microarray in order to detect and identify viable bacterial species that play a significant role in beer spoilage. These belong to the species of the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Methods and Results:, Oligonucleotide probes specific to beer spoilage bacteria were designed. In order to detect viable bacteria, the probes were designed to target the intergenic spacer regions (ISR) between 16S and 23S rRNA. Prior to hybridization the ISR were amplified by combining reverse transcriptase and polymerase chain reactions using a designed consenus primer. The developed oligonucleotide microarrays allows the detection of viable beer spoilage bacteria. Conclusions:, This method allows the detection and discrimination of single bacterial species in a sample containing complex microbial community. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non growing bacteria. Significance and Impact of the Study:, The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage micro-organisms within a mixed population. [source]

Hypoplastic left heart in a female infant with partial trisomy 4q due to de novo 4;21 translocation

AMERICAN JOURNAL OF MEDICAL GENETICS, Issue 4 2002
Milen Velinov
Abstract We present a female infant with mild dysmorphic features and congenital heart defect: hypoplastic left heart with aortic atresia and hypoplastic aortic arch, ventricular septal defect, and a nonrestrictive atrial communication. Chromosome analysis showed an unbalanced translocation that contained additional material from 4q translocated onto 21q. This resulted in partial trisomy 4 and monosomy for the 21q telomeric region. The derivative chromosome was characterized using G-banding, M-FISH, and whole chromosome painting. The karyotype was described as 46,XX,der(21)t(4;21)(q25;q22.3).ish(wcp4+;wcp21+). Additional analyses with FISH probes specific for 21q 22.3, 21q22.2, 21q21.1, and 21q11.2 did not indicate any chromosome 21 duplication within the derivative chromosome 21. Monosomy for the telomeric portion of 21q was demonstrated using a tel 21q probe (Oncor). The patient underwent stage 1 Norwood procedure to manage her heart defect. Poor feeding and failure to thrive complicated the postsurgical period. The child subsequently underwent funduplication and feeding tube placement, and at 4.5 months of age presented with microcephaly and developmental delay. Hypoplastic left heart was previously reported with increased frequency in relatively common numeric chromosomal aberrations, such as monosomy X, trisomies 21, 18, and 13, and in various structural chromosomal defects. Our report presents new evidence for the co-occurrence of hypoplastic left heart with a duplicated portion of chromosome 4 distal to 4q25. In addition, monosomy for the telomeric region of chromosome 21 may have implications in the phenotype. © 2001 Wiley-Liss, Inc. [source]

Lipolytic and esterolytic activity-based profiling of murine liver

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 17 2008
Ruth Birner-Gruenberger
Abstract In lipid metabolism, the liver acts as a buffer for transient energy fluctuations. It temporarily stores fatty acids as triacylglycerol and secretes them as very low density lipoprotein into the circulation when the period of maximum lipid load has passed. The lipolytic enzymes responsible for mobilization of internal lipid stores in the liver have not been identified yet. We introduced active site-directed chemical probes for lipolytic activity profiling in complex mixtures, known as activity-based proteomics, and employed it for global analysis and functional annotation of lipolytic proteins in mouse adipose tissue. Here we report the combined application of two approaches using fluorescent and biotinylated probes for discovery and discrimination of lipolytic and esterolytic enzymes in mouse liver subproteomes. Proteomes labeled with the fluorescent probes were analyzed by 2-DE while proteomes labeled with the biotinylated probe were subjected to avidin-affinity isolation. Of 37 totally identified proteins, 15 were detected using both approaches while 14 and 8 were solely identified by 2-DE and avidin-affinity isolation, respectively. Moreover, 12 enzymes were classified as potential lipases and/or cholesteryl esterases by their reaction with probes specific for the respective activities directly in their proteomes. [source]

Induction of centrosome amplification and chromosome instability in p53 -deficient lung cancer cells exposed to benzo[a]pyrene diol epoxide (B[a]PDE),

THE JOURNAL OF PATHOLOGY, Issue 3 2008
K Shinmura
Abstract Benzo[a]pyrene diol epoxide (B[a]PDE), the ultimate carcinogenic metabolite of benzo[a] pyrene, has been implicated in the mutagenesis of the p53 gene involved in smoking-associated lung cancer. To further understand the role of B[a]PDE in lung tumour progression, we investigated its effect on the numerical integrity of centrosomes and chromosome stability in lung cancer cells lacking p53. Exposure of p53 -deficient H1299 lung cancer cells to B[a]PDE resulted in S-phase arrest, leading to abnormal centrosome amplification. Analysis of H1299 cells stably expressing fluorescence-tagged centrin (a known centriolar marker) revealed that the centrosome amplification was primarily attributable to excessive centrosome duplication rather than to centriole splitting. Forced expression of POLK DNA polymerase, which has the ability to bypass B[a]PDE,guanine lesions in an error-free manner, suppressed the B[a]PDE-induced centrosome amplification. Fluorescence in situ hybridization analyses with probes specific for chromosomes 2, 3, and 16 revealed that B[a]PDE exposure also led to chromosome instability, which was likely to have resulted from centrosome amplification. We extended these findings to primary lung carcinomas containing non-functional p53, and found a strong association between centrosome amplification and a high level of B[a]PDE,DNA accumulation. Therefore B[a]PDE contributes to neoplasia by inducing centrosome amplification and consequent chromosome destabilization as well as its mutagenic activity. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source]

Differential expression of c- erb B2/neu, epidermal growth factor receptor, cytokeratin 8, and the prostatic steroid-binding protein gene in rat ventral prostate during postnatal development

THE PROSTATE, Issue 3 2001
Louis L. Pisters
Abstract BACKGROUND The development and progression of prostate neoplasia may recapitulate the early developmental pattern of expression of genes in the prostate. The study of prostate development may, therefore, provide insights into the molecular mechanisms important in prostate neoplasia and reveal new markers. METHODS We compared postnatal expression of four genes: neu and epidermal growth factor receptor genes (EGFR), androgen-upregulated in the ventral prostate of adult rats (C-3), and androgen-repressed (CK8) in Sprague,Dawley rats. In situ hybridization was performed on prostate frozen sections collected on postnatal days 1, 5, 10, 15, 20, 30, and 60 from five rats per day. Staining intensities for antisense probes specific for each gene were determined relative to day 1 intensity. RESULTS Growth factor receptors including neu and EGFR may be coordinately regulated in the basal-cell population during prostate development. CK8 and C-3 show evidence of similar androgen regulation during development. CONCLUSIONS CK8 and C-3 have distinct patterns of expression in the postnatal period of development and these genes may be good markers of differentiation. Both neu and EGFR may be involved in androgen-independent growth of basal cell population in prostate. Prostate 47:164,171, 2001. © 2001 Wiley-Liss, Inc. [source]

Diagnosis of common dermatophyte infections by a novel multiplex real-time polymerase chain reaction detection/identification scheme

BRITISH JOURNAL OF DERMATOLOGY, Issue 4 2007
M. Arabatzis
Summary Background, In the absence of a functional dermatophyte-specific polymerase chain reaction (PCR), current diagnosis of dermatophytoses, which constitute the commonest communicable diseases worldwide, relies on microscopy and culture. This combination of techniques is time-consuming and notoriously low in sensitivity. Objectives, Recent dermatophyte gene sequence records were used to design a real-time PCR assay for detection and identification of dermatophytes in clinical specimens in less than 24 h. Patients and methods, Two assays based on amplification of ribosomal internal transcribed spacer regions and on the use of probes specific to relevant species and species-complexes were designed, optimised and clinically evaluated. One assay was for detecting the Trichophyton mentagrophytes species complex plus T. tonsurans and T. violaceum. The second assayed for the T. rubrum species complex, Microsporum canis and M. audouinii. Results, The analytical sensitivity of both assays was 0·1 pg DNA per reaction, corresponding to 2·5,3·3 genomes per sample. The protocol was clinically evaluated over 6 months by testing 92 skin, nail and hair specimens from 67 patients with suspected dermatophytosis. Real-time PCR detected and correctly identified the causal agent in specimens from which T. rubrum, T. interdigitale, M. audouinii or T. violaceum grew in culture, and also identified a dermatophyte species in an additional seven specimens that were negative in microscopy and culture. Conclusions, This highly sensitive assay also proved to have high positive and negative predictive values (95·7% and 100%), facilitating the accurate, rapid diagnosis conducive to targeted rather than empirical therapy for dermatophytoses. [source]

Bacterial artificial chromosome array-based comparative genomic hybridization using paired formalin-fixed, paraffin-embedded and fresh frozen tissue specimens in multiple myeloma

CANCER, Issue 2 2009
Patrick A. Lennon PhD
Abstract BACKGROUND: Multiple myeloma (MM) is a neoplasm of malignant plasma cells that often harbors many chromosomal aberrations. Currently, fresh frozen tissues (FT) are considered the most reliable for molecular genetic analysis; however, formalin-fixed, paraffin-embedded (FFPE) tissues are easily retrievable. Compared with conventional cytogenetics, bacterial artificial chromosome (BAC) array-comparative genomic hybridization (CGH) allows more sensitive detection of chromosomal abnormalities. METHODS: The authors analyzed 7 paired FT and FFPE samples of bone marrow aspirate materials obtained from patients with MM in parallel to determine the efficacy of BAC array-CGH using FFPE. RESULTS: Thirty-four aberrations were identified, including 29 that were observed in both sample types, yielding 85% concordance. Nonrandom anomalies, including gains on 7q, 9q, 15q, and 19p and losses on 8p and 13q, were observed in paired samples from at least 2 patients. To verify these results, fluorescence in situ hybridization (FISH) was performed using probes specific for 7q and 15q, and gains were observed in the 4 samples that were examined. Furthermore, 1 of 3 samples from patients who had monoclonal gammopathy of undetermined significance that were tested also carried gain on 7q, suggesting that this aberration may be an early transforming event. CONCLUSIONS: The current results indicated that BAC array-CGH can be effective using FFPE samples and is a sensitive method for the identification of nonrandom chromosomal aberrations in MM. Cancer 2009. © 2009 American Cancer Society. [source]