Comparison of in situ hybridization methods for the assessment of HER-2/neu gene amplification status in breast cancer using a tissue microarray

BackgroundThis project compared HER-2/neu gene status in breast cancers, as demonstrated by FISH (fluorescent in situ hybridization) and CISH (chromogenic in situ hybridization) and using a tissue microarray (TMA). The study also aimed to show whether the TMA technique could be used in clinical diagnostics, rather than remain a scientific tool.Materials and methodsA TMA was constructed using 121 breast cancer specimens, 6 cores from each specimen. Demonstration and assessment of HER-2/neu gene status was by FISH (Vysis Path) and CISH (DAKO Duo CISH).ResultsThe 121 breast cancer specimens were divided into 3 groups by HER-2 status, as determined by immunohistochemistry. In the HER-2 negative group no amplification was observed in 36 out of 40 cases. 3 cases showed amplification by both methods and one by CISH alone. The equivocal HER-2 group showed no amplification in 30 out of 41 cases and amplification in 9 cases. One case was FISH negative CISH positive and one was discarded. In the HER-2 positive group, amplification was confirmed in 37 of the 40 cases by both methods. 3 cases were unsuitable for assessment.ConclusionsThis study indicated that CISH is a sensitive alternative to FISH in detecting HER2 gene amplification and may replace FISH in HER2 testing. Good agreement was observed between methods (98.5% – 119 out of 121 cases).Furthermore, as only 4 out of 121 cases were unsuitable for assessment (no signal or missing TMA cores) – it may be feasible to use TMA in diagnostics.     

The development of linear regression models using environmental variables to explain the spatial distribution of Fasciola hepatica infection in dairy herds in England and Wales

Fasciolosis caused by Fasciola hepatica is a major cause of economic loss to the agricultural community worldwide as a result of morbidity and mortality in livestock. Spatial models developed with the aid of Geographic Information Systems (GIS) can be used to develop risk maps for fasciolosis for use in the formulation of disease control programmes. Here we investigate the spatial epidemiology of F. hepatica in dairy herds in England and Wales and develop linear regression models to explain observed patterns of exposure at a small spatial unit, the postcode area. Exposure data used for the analysis were taken from an earlier study of F. hepatica infection, performed in the winter of 2006/7. Climatic, environmental, soil, livestock and pasture variables were considered as potential predictors. The performance of models that used climate variables for 5 years average data, contemporary data and a combination of both for England and Wales, and for England only, was compared. All models explained over 70% of the variation in the prevalence of exposure. The best performing models were those built using 5 year average and contemporary weather data. However, the fit of these models was only slightly better than the fit of models using weather data from one time period only. Rainfall was a consistent predictor in all models. Other model covariates included temperature, the negative predictors of soil pH and slope and the positive predictors of poor quality land, as determined by the Agricultural Land Classification, and very fine sand content of soil. Choroplethic risk maps showed a good match between the observed F. hepatica exposure values and exposure values fitted by the models. The development of these detailed spatial models is the first step towards the development of a spatially specific, temporal forecasting system for liver fluke in the United Kingdom.     

Higher non-return rate associated with Mycobacterium avium subspecies paratuberculosis infection at early stage in Holstein dairy cows

The effects of infection by Mycobacterium avium paratuberculosis (Map) on dairy cows are poorly documented and quite controversial. This retrospective study aimed at quantifying the variation in non-return to service of Holstein dairy cows according to their Map-infection status. Three different statuses were defined based on both individual and herd tests results: ELISA positive cow, all tests negative cow in a negative herd and all tests negative cow in a positive herd. Whatever the age at Map testing, the status was attributed to a cow from its first lactation onwards. Non-return to service was determined at 200 days after first and second services. The study was performed from 1999 to 2007 on 185,950 AI from 48,914 cows in early stage of the infection in 1069 herds by logistic regression controlling for known factors influencing non-return rate. Non-return rate was higher for infected cows compared to negative cows from negative herds (RR of 1.10 or +3.9 points of % of non-return rate). The effect was significant for parities 1 and 2 (RR of 1.11 and 1.12, respectively) but not for higher ones. This effect was lower when comparing positive cows to negative cows in the same herds but relative risks were still above 1. The hypothesis that the effect of Map on non-return depends upon the stage of infection is formulated.     

Correlation between lifetime heterogeneity and kinetics heterogeneity during chlorophyll fluorescence induction in leaves:: 1. Mono-frequency phase and modulation analysis reveals a conformational change of a PSII pigment complex during the IP thermal phase

The relationship between the fluorescence lifetime (τ) and yield (Φ) obtained in phase and modulation fluorometry at 54 MHz during the chlorophyll fluorescence induction in dark-adapted leaves under low actinic light has been investigated. Three typical phases have been identified: (i) linear during the OI photochemical rise, (ii) convex curvature during the subsequent IP thermal rise, and (iii) linear during the PS slow decay. A similar relationship has been obtained in the fluorescence induction for the fluorescence yield measured at 685 nm plotted versus the fluorescence yield measured at 735 nm. A spectrally resolved analysis shows that the curvature of the τ-Φ relationship is not due to chlorophyll fluorescence reabsorption effects. Several other hypotheses are discussed and we conclude that the curvature of the τ-Φ relationship is due to a variable and transitory nonphotochemical quenching. We tentatively propose that this quenching results from a conformational change of a pigment-protein complex of Photosystem II core antenna during the IP phase and could explain both spectral and temporal transitory changes of the fluorescence. A variable blue shift of the 685 nm peak of the fluorescence spectrum during the IP phase has been observed, supporting this hypothesis.     

Simultaneous determination of m-nisoldipine and its three metabolites in rat plasma by liquid chromatography–mass spectrometry

A simple, sensitive and selective liquid chromatography–tandem mass spectrometry (LC–MS/MS) method for the simultaneous determination of m-nisoldipine and its three metabolites in rat plasma has been developed using nitrendipine as an internal standard (IS). Following liquid–liquid extraction, the analytes were separated using an isocratic mobile phase on a reverse phase C₁₈ column and analyzed by MS in the multiple reaction monitoring (MRM) mode. To avoid contamination by residual sample in the injection syringe, a special injection protocol was developed. We found that m-nisoldipine, metabolite M1 and IS could be ionized under positive or negative electrospray ionization conditions, whereas metabolite M and M2 could only be ionized in the positive mode. The mass spectrometry fragmentation pathways for these analytes are analyzed and discussed herein. The total analysis time required less than 5 min per sample. We employed this method successfully to study the metabolism of m-nisoldipine when it was orally administered to rats at a dose of 9 mg/kg. Three metabolites of m-nisoldipine and an unknown compound of molecular weight 386 were found for the first time in rat plasma. The concentration of the potentially active metabolite was approximately equal to its parent compound concentration.     

Detection of Legionella species in potting mixes using fluorescent in situ hybridisation (FISH)

This study used Fluorescent in situ Hybridisation (FISH) with rRNA targeted oligonucleotide probes combined with scanning confocal laser microscopy to successfully detect Legionella spp. in commercially available potting mix. A range of techniques were explored to optimise the FISH method by reducing background fluorescence and preventing non-specific binding of probes. These techniques included the use of a blocking agent, UV light treatment, image subtraction of a nonsense probe and spectral unmixing of specific probes fluorescence and autofluorescence dependent on the specific emission spectra of probe fluorophores.Spectral unmixing was the best microscopy technique for reducing background fluorescence and non-specific binding of probes was not observed. The rapid turnaround time and increased sensitivity of the FISH provides as an alternative to traditional culture methods, which are tedious and often give varied results. FISH is also advantageous compared to PCR methods as it provides information on the structure of the microbial community the bacteria is situated in. This study demonstrates that FISH could provide an alternative method for Legionella detection and enumeration in environmental samples.     

A fluorescence assay for tetradecyltrimethylammonium mono-oxygenase activity that catalyzes the cleavage of the C-N bond with the production of trimethylamine

This article describes a simple fluorescence method for the determination of tetradecyltrimethylammonium mono-oxygenase (TTAB mono-oxygenase) activity involving N-dealkylation of tetradecyltrimethylammonium bromide with concomitant production of trimethylamine (TMA). Activity was determined by measuring the formation of TMA using the morin reagent and aluminum (Al). Morin reacts with Al to form a fluorescent complex, Al-morin. In the presence of TMA, Al is tightly associated with TMA and cannot be sequestered by morin, thus providing evidence for formation of the Al-TMA complex. The concentration of TMA is estimated by calibration graphs constructed by plotting the fluorescence intensity of the Al-morin complex versus TMA concentration. The fluorescence intensities of the Al-morin complexes quenched by TMA are linearly dependent on both the time of the TTAB mono-oxygenase reaction and the amount of protein used in the reaction. The kinetic behavior is characterized by K_0.5 = 4.26 × 10⁻⁴ M, and the apparent Hill coefficient (n_app) = 2.24. These values are both comparable to those determined by GC-MS (K_0.5 = 4.41 × 10⁻⁴ M and n_app = 2.35). The advantages of this assay include rapid and efficient implementation and potential employment for routine accurate determinations of TTAB mono-oxygenase activity over a wide range of substrate concentrations.     

Detection of Staphylococcus enterotoxin B using fluorescent immunoliposomes as label for immunochromatographic testing

Staphylococcus enterotoxin B (SEB) is one of several toxins produced by the gram positive bacterium Staphylococcus aureus. SEB is a major cause of food poisoning and represents a significant biological threat with regard to bioterrorism. A rapid, sensitive, and specific method is required to monitor food and water in cases of both natural and intentional contamination by this toxin. This report presents an improved immunochromatographic test (ICT) using immunoliposomes as label for the detection of SEB. For the first time in an ICT, the signal generated by the sulforhodamine B encapsulated into immunoliposomes was measured by fluorescence, allowing a 15-fold increase in sensitivity compared with that for visual detection of colored labels. The ICT was completed within 30 min, providing a limit of detection close to 20 pg/ml in buffer and showing no cross-reactivity with the other major toxin of the bacterium, Staphylococcus enterotoxin A. This sensitivity was retained when analyzing SEB spiked in various alimentary matrices, mimicking contaminated foods. Due to the use of fluorescent immunoliposomes as label, the present assay offers the inherent simplicity and speed of a dipstick assay while providing detection of low levels of SEB in real samples.     

Bacterial Community Associated with the Intestinal Tract of Chinese Mitten Crab (Eriocheir sinensis) Farmed in Lake Tai,China

Chinese mitten crab (CMC, Eriocheir sinensis) is an economically valuable species in South-East Asia that has been widely farmed in China. Characterization of the intestinal bacterial diversity of CMC will provide insights into the aquaculturing of CMCs. Based on the analysis of cloned 16S rRNA genes from culture-independent CMC gut bacteria, 124 out of 128 different clones reveal ＞95% nucleotide similarity to the species belonging to the four phyla of Tenericutes, Bacteroidetes, Firmicutes and Proteobacteria; one clone shows 91% sequence similarity to the member of TM7 (a candidate phylum without cultured representatives). Fluorescent in situ hybridization also reveals the abundance of Bacteroidetes in crab intestine. Electron micrographs show that spherical and filamentous bacteria are closely associated with the microvillus brush border of the midgut epithelium and are often inserted into the space between the microvilli using a stalk-like cell appendage. In contrast, the predominant rod-shaped bacteria in the hindgut are tightly attached to the epithelium surface by an unusual pili-like structure. Both 16S rRNA gene denaturing gel gradient electrophoresis and metagenome library indicate that the CMC Mollicutes group 2 appears to be present in both the midgut and hindgut with no significant difference in abundance. The CMC Mollicutes group 1, however, was found mostly in the midgut of CMCs. The CMC gut Mollicutes phylotypes appear to be most closely related to Mollicutes symbionts detected in the gut of isopods (Crustacea: Isopoda). Overall, the results suggest that CMCs harbor diverse, novel and specific gut bacteria, which are likely to live in close relationships with the CMC host.     

Observation of the main phase transition of dinervonoylphosphocholine giant liposomes by fluorescence microscopy

The phase heterogeneity of giant unilamellar dinervonoylphosphocholine (DNPC) vesicles in the course of the main phase transition was investigated by confocal fluorescence microscopy observing the fluorescence from the membrane incorporated lipid analog, 1-palmitoyl-2-(N-4-nitrobenz-2-oxa-1,3-diazol)aminocaproyl-sn-glycero-3-phosphocholine (NBDPC). These data were supplemented by differential scanning calorimetry (DSC) of DNPC large unilamellar vesicles (LUV, diameter ∼0.1 and 0.2 μm) and multilamellar vesicles (MLV). The present data collected upon cooling reveal a lack of micron-scale gel and fluid phase coexistence in DNPC GUVs above the temperature of 20.5 °C, this temperature corresponding closely to the heat capacity maxima (T_em) of DNPC MLVs and LUVs (T_em ≈21 °C), measured upon DSC cooling scans. This is in keeping with the model for phospholipid main transition inferred from our previous fluorescence spectroscopy data for DMPC, DPPC, and DNPC LUVs. More specifically, the current experiments provide further support for the phospholipid main transition involving a first-order process, with the characteristic two-phase coexistence converting into an intermediate phase in the proximity of T_em. This at least macroscopically homogenous intermediate phase would then transform into the liquid crystalline state by a second-order process, with further increase in acyl chain trans→gauche isomerization.     

An Assay for Express Screening of Potato Transformants by GFP Fluorescence

An express assay for screening of potato transformants by their GFP fluorescence intensities is developed. In comparison to the widely used methods of transgenic plant screening by PCR, Real-Time RTPCR or Northern-blotting, the GFP fluorescence assay needs no expensive reagents and takes less time. This approach may also be used for nondestructive screening of the T0 transgenic regenerants which can be further grown and used. To prove this assay reliability, the expression of the hGFP gene in the leaves of transgenic potato (cv. Skoroplodny) plants, determined by its mRNA accumulation, was compared to GFP fluorescence intensity in the micro-samples of aseptic plant leaves. The strong correlation between the results of these two methods is the evidence of positive dependence of GFP fluorescence intensity on the target mRNA content.     

Chlorophyll a fluorescence induction (Kautsky curve) in a Venus flytrap (Dionaea muscipula) leaf after mechanical trigger hair irritation

This paper describes experiments on transient changes in chlorophyll a fluorescence in traps of the carnivorous plant Venus flytrap (Dionaea muscipula) that occur in association with mechanical stimulation of trigger hairs and propagation of action potentials (APs). The experiments show the following reproducible effects of APs on the fluorescence induction (Kautsky-, or OJIPSMT curve) in a 100 s low intensity light pulse (i) no change in the OJ phase attributed to release of photochemical quenching, (ii) a small enhancement, if at all of increase in the thermal JIP phase, (iii) a two- to threefold deceleration of the fluorescence decline (quenching) during the PSMT phase in the 2–100 s time range, and (iv) a transient 15–50% increase in variable fluorescence within ∼20 s under steady state light condition with, after ∼80 s, a 10% undershoot that reverses in several tens of seconds to the original steady state. The results are discussed in terms of a hypothesis that the fluorescence decline during the SMT phase of the Kautsky induction curve, attributed to NPQ, is caused by the Δμ_H+-driven increase in proton conductance of the CF_o channel of the ATPase during its activation. A signal-transducing role of Ca²⁺ is suggested.     

In Situ Hybridization of Prochlorococcus and Synechococcus (Marine Cyanobacteria) spp. with rRNA-Targeted Peptide Nucleic Acid Probes

A simple method for whole-cell hybridization using fluorescently labeled rRNA-targeted peptide nucleic acid (PNA) probes was developed for use in marine cyanobacterial picoplankton. In contrast to established protocols, this method is capable of detecting rRNA in Prochlorococcus, the most abundant unicellular marine cyanobacterium. Because the method avoids the use of alcohol fixation, the chlorophyll content of Prochlorococcus cells is preserved, facilitating the identification of these cells in natural samples. PNA probe-conferred fluorescence was measured flow cytometrically and was always significantly higher than that of the negative control probe, with positive/negative ratio varying between 4 and 10, depending on strain and culture growth conditions. Prochlorococcus cells from open ocean samples were detectable with this method. RNase treatment reduced probe-conferred fluorescence to background levels, demonstrating that this signal was in fact related to the presence of rRNA. In another marine cyanobacterium, Synechococcus, in which both PNA and oligonucleotide probes can be used in whole-cell hybridizations, the magnitude of fluorescence from the former was fivefold higher than that from the latter, although the positive/negative ratio was comparable for both probes. In Synechococcus cells growing at a range of growth rates (and thus having different rRNA concentrations per cell), the PNA- and oligonucleotide-derived signals were highly correlated (r = 0.99). The chemical nature of PNA, the sensitivity of PNA-RNA binding to single-base-pair mismatches, and the preservation of cellular integrity by this method suggest that it may be useful for phylogenetic probing of whole cells in the natural environment.     

Presence of pathogenic Leptospira spp. in the reproductive system and fetuses of wild boars (Sus scrofa) in Italy

Leptospirosis is a re-emerging and globally spread zoonosis caused by pathogenic genomospecies of Leptospira. Wild boar (Sus scrofa) are an important Leptospira host and are increasing in population all over Europe. The aim of this investigation was to evaluate Leptospira spp. infection in the reproductive systems of wild boar hunted in two Italian regions: Tuscany and Sardinia. From 231 animals, reproductive system tissue samples (testicles, epididymides, uteri) as well as placentas and fetuses were collected. Bacteriological examination and Real-Time PCR were performed to detect pathogenic Leptospira (lipL32 gene). Leptospires were isolated from the testicles and epididymides of one adult and two subadult wild boar. Four isolates from the two subadult males were identified as Leptospira interrogans serogroup Australis by MLST, whereas Leptospira kirschneri serogroup Grippotyphosa was identified from the adult testicles and epididymis. Using Real-Time PCR, 70 samples were positive: 22 testicles (23.16%) and 22 epididymides (23.16%), 10 uteri (7.35%), 3 placentas (6.66%), and 13 fetuses (28.88%). Amplification of the rrs2 gene identified L. interrogans and L. kirschneri species. The results from this investigation confirmed that wild boar represent a potential source of pathogenic Leptospira spp. Isolation of Leptospira serogroups Australis and Grippotyphosa from the male reproductive system and the positive Real-Time PCR results from both male and female samples could suggest venereal transmission, as already demonstrated in pigs. Furthermore, placentas and fetuses were positive for the lipL32 target, and this finding may be related to a possible vertical transmission of pathogenic Leptospira.     

4FISH-IF,a Four-Color Dual-Gene FISH Combined with p63 Immunofluorescence to Evaluate NKX3.1 and MYC Status in Prostate Cancer

NKX3.1 allelic loss and MYC amplification are common events during prostate cancer progression and have been recognized as potential prognostic factors in prostate cancer after radical prostatectomy or precision radiotherapy. We have developed a 4FISH-IF assay (a dual-gene fluorescence in situ hybridization combined with immunofluorescence) to measure both NKX3.1 and MYC status on the same slide. The 4FISH-IF assay contains four probes complementary to chromosome 8 centromere, 8p telomere, 8p21, and 8q24, as well as an antibody targeting the basal cell marker p63 visualized by immunofluorescence. The major advantages of the 4FISH-IF include the distinction between benign and malignant glands directly on the 4FISH-IF slide and the control of truncation artifact. Importantly, this specialized and innovative combined multiprobe and immunofluorescence technique can be performed on diagnostic biopsy specimens, increasing its clinical relevance. Moreover, the assay can be easily performed in a standard clinical molecular pathology laboratory. Globally, the use of 4FISH-IF decreases analytic time, increases confidence in obtained results, and maintains the tissue morphology of the diagnostic specimen.     

Infection Status of Freshwater Crabs and Crayfish with Metacercariae of Paragonimus westermani in Korea

The present study investigated the infection status of Paragonimus westermani metacercariae in freshwater crabs (n = 363) and crayfish (n = 31) from October 2007 to October 2008 using the crush method. All of the freshwater crabs, Eriocheir japonicus, were negative for P. westermani metacercariae while 10 (32.3%) of the 31 examined crayfish were positive. The 10 positive crayfish were caught in Haenam, Jeollanam-do, and there were 8-59 (mean 28.4) metacrcariae per infected crayfish. These results suggest that P. westermani metacerariae are still transmitted by crayfish enzootically in southern Korea, and that freshwater crabs may transmit metacercariae only on rare occasions.     

Crystal Structure of the Antitoxin-Toxin Protein Complex RelB-RelE from Methanococcus jannaschii

Here we present the crystal structure of the Methanococcus jannaschii RelE-RelB (RelBE) toxin-antitoxin (TA) protein complex determined by the MIRAS (multiple isomorphous replacement with anomalous signal) method. The genes encoding this TA system are located in the chromosome of this archaeon and involved in stress response. RelE acts as an endoribonuclease that cleaves mRNA on the ribosome, and we compare the RelBE complex to the known structures of other TA systems belonging to this group and to endoribonucleases. M. jannaschii RelBE forms a heterotetramer with the antitoxin in the centre of the complex, a configuration that differs vastly from the heterotetramer structure of the previously published RelBE from another archaeon, Pyrococcus horikoshii. The long N-terminal α-helix of the tightly bound M. jannaschii antitoxin RelB covers the presumed active site of the toxin RelE that is formed by a central β-sheet, a loop on one side and a C-terminal α-helix on the other side. The active site of the M. jannaschii toxin RelE harbours positive charges that are thought to neutralize the negative charges of the substrate mRNA, including Arg62 that was changed to Ser62 by the Escherichia coli expression system, thereby leading to inactive toxin RelE. Comparative studies suggest that Asp43 and His79 are also involved in the activity of the toxin.