Ovarian follicular dynamics in suckled zebu (Bos indicus) cows monitored by real time ultrasonography

The pattern of follicular growth was studied in 17 suckled zebu cows with average body condition and under extensive management in a tropical environment (23 degrees C, 78% humidity; 2200 mm annual rainfall; 1000 m altitude). The study covered the period from parturition to weaning at 12 months postpartum (PP). Data were collected by transrectal ultrasonography (7.5 MHz) at 48 h intervals, and progesterone (P4) measurements were performed by RIA. The sequential development of ovarian follicles greater than 4 mm was followed until regression or ovulation. Ovarian activity as characterized by growth and regression of follicles of 4 to 6 mm, with sporadic dominance, and a long interdominance interval was observed in every cow and from as early as 26 +/- 2 days PP. This follicular pattern was highly variable during the first 6 months: cows presented 2 to 20 follicular waves (FW) in which a dominant follicle (DF) grew to 8 +/- 1 mm with daily growth rates of 1.1 +/- 0.5 mm/day. The duration of dominance varied from 2 to 8 days and the interdominance time interval was 0 (overlapped waves) to 60 days. Neither behavioural oestrus nor ovulation was observed during this period. From 6 to 12 months PP, cows presented 7 to 20 FW, some with ovulation and/or corpora lutea (CL) formation. The ovulation was preceded by oestrus in some cases (43%). The mean (+/- sem) diameter of DF was 9 +/- 2.7 mm, their mean growth rate 1.4 +/- 0.2 mm/day, their duration of dominance was 2 to 8 days and the interdominance interval was 0 to 14 days. Progesterone concentrations (P4) from 1.0 to 13 ng/ml were found when a CL was present. Once cyclicity re-commenced at 217 to 278 days PP, the cows presented either normal (21 +/- 3 days), short (10 +/- 2 days), or long (50 +/- 4 days) cycles. The resumption of cyclicity was characterized by an increased frequency of emerging follicular waves. Under the conditions of this study, the suckled Bos indicus cows re-commenced ovarian follicular activity as early as described in B. taurus breeds, but the establishment of cyclicity was substantially later. These data add further to the panorama of postpartum reproductive physiology in tropical cattle.     

Evaluation of thermal environment by real time monitoring SET

1. 1. A system, combining a portable data logger and a personal computer with a GP-IB interface, was developed both to measure environmental variables and also to predict human physiological responses to one's thermal environment.

2. 2. An environmental index: Standard Effective Temperature SET^*, can also be computed with the personal computer and displayed on the CRT for the real time monitoring of the thermal environment and comfort sensation.

Non-invasive real time monitoring of yeast volatilome by PTR-ToF-MS

Introduction

Producing a wide range of volatile secondary metabolites Saccharomyces cerevisiae influences wine, beer, and bread sensory quality and hence selection of strains based on their volatilome becomes pivotal. A rapid on-line method for volatilome assessing of strains growing on standard solid media is still missing.

Objectives

Methodologically, the aim of this study was to demonstrate the automatic, real-time, direct, and non-invasive monitoring of yeast volatilome in order to rapidly produce a robust large data set encompassing measurements relative to many strains, replicates and time points. The fundamental scope was to differentiate volatilomes of genetically similar strains of oenological relevance during the whole growing process.

Method

Six different S. cerevisiae strains (four meiotic segregants of a natural strain and two laboratory strains) inoculated onto a solid medium have been monitored on-line by Proton Transfer Reaction—Time-of-Flight—Mass Spectrometry for 11 days every 4 h (3540 time points). FastGC PTR-ToF-MS was performed during the stationary phase on the 5th day.

Results

More than 300 peaks have been extracted from the average spectra associated to each time point, 70 have been tentatively identified. Univariate and multivariate analyses have been performed on the data matrix (3640 measurements?×?70 peaks) highlighting the volatilome evolution and strain-specific features. Laboratory strains with opposite mating type, and meiotic segregants of the same natural strain showed significantly different profiles.

Conclusions

The described set-up allows the on-line high-throughput screening of yeast volatilome of S. cerevisiae strains and the identification of strain specific features and new metabolic pathways, discriminating also genetically similar strains, thus revealing a novel method for strain phenotyping, identification, and quality control.

     

Sensitive in situ monitoring of a recombinant bioluminescent Yersinia enterocolitica reporter mutant in real time on Camembert cheese

Bioluminescent mutants of Yersinia enterocolitica were generated by transposon mutagenesis using a promoterless, complete lux operon (luxCDABE) derived from Photorhabdus luminescens, and their production of light in the cheese environment was monitored. Mutant B94, which had the lux cassette inserted into an open reading frame of unknown function was used for direct monitoring of Y. enterocolitica cells on cheeses stored at 10 degrees C by quantifying bioluminescence using a photon-counting, intensified charge-coupled device camera. The detection limit on cheese was 200 CFU/cm(2). Bioluminescence of the reporter mutant was significantly regulated by its environment (NaCl, temperature, and cheese), as well as by growth phase, via the promoter the lux operon had acquired upon transposition. At low temperatures, mutant B94 did not exhibit the often-reported decrease of photon emission in older cells. It was not necessary to include either antibiotics or aldehyde in the food matrix in order to gain quantitative, reproducible bioluminescence data. As far as we know, this is the first time a pathogen has been monitored in situ, in real time, in a "real-product" status, and at a low temperature.     

Immunofluorescence signal amplification by the enzyme-catalyzed deposition of a fluorescent reporter substrate (CARD)

Progress has been made in improving the immunohistochemical detection of antigens for imaging and flow cytometry. We report the synthesis of a novel fluorescent horseradish peroxidase substrate, Cy3.29-tyramide, and its application in an enzyme-based signal amplification system, catalyzed reporter deposition (CARD). The catalyzed deposition of Cy3.29-tyramide was used to detect cell surface markers such as CD8 and CD25 on tonsil tissue and human lymphocytes. We compared the fluorescence CARD method to standard indirect immunofluorescence detection methods and found that an amplification of up to 15-fold was possible with CARD. The detection of the intracellular protein myosin II in fibroblastic cells and rabbit serum proteins blotted onto nitrocellulose was also improved. Thus, fluorescent CARD is a simple modification that can be made to standard immunofluorescence staining protocols to enhance significantly the detection of antigens.     

Catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH) detection of Dehalococcoides

Members of the genus Dehalococcoides are well-known for their capacity to reductively dechlorinate chlorinated organic pollutants. The availability of quantitative and sensitive detection methods is of major interest for research on the ecology of those environmentally important micro-organisms. In this paper we describe the development of a Catalyzed Reporter Deposition-Fluorescent In Situ Hybridization (CARD-FISH) for detection of Dehalococcoides cells in enrichment cultures using two oligonucleotide sequences which target two different lineages of Dehalococcoides as probes. Both sequences were previously applied in conventional FISH as probes. Conjugation of the probe to horseradish peroxidase (HRP) did not change the specificity of the probes and bright fluorescent signals were obtained. Despite the use of higher concentrations of probe and the application of longer exposure times in the conventional FISH procedure, CARD-FISH resulted in more intense signals. The CARD-FISH method was applied to a vinyl chloride (VC)-reductively-dechlorinating enrichment culture. Only the probe targeting the CBDB1 lineage of Dehalococcoides reacted with the sample which was in agreement with previous nucleic acid based analysis. The culture consisted of 51%+/-8% of Dehalococcoides cells. Furthermore, the CARD-FISH probes for detecting Dehalococcoides were combined with FISH probes for simultaneous detection of either Bacteria or Archaea which should allow rapid insight into the relative dynamics of the different members of dechlorinating communities as a response to environmental changes. Overall, CARD-FISH proved to be a rapid, reliable and convenient method to detect and quantify Dehalococcoides cells.     

Sequencing by hybridization of long targets

Sequencing by Hybridization (SBH) reconstructs an n-long target DNA sequence from its biochemically determined l-long subsequences. In the standard approach, the length of a uniformly random sequence that can be unambiguously reconstructed is limited to n = O(2(l)) due to repetitive subsequences causing reconstruction degeneracies. We present a modified sequencing method that overcomes this limitation without the need for different types of biochemical assays and is robust to error.     

Expression of catalase mRNA and protein in adult rat brain: detection by nonradioactive in situ hybridization with signal amplification by catalyzed reporter deposition (ISH-CARD) and immunohistochemistry (IHC)/immunofluorescence (IF).

Catalase, the classical peroxisomal marker enzyme, decomposes hydrogen peroxide and is involved in the antioxidant defense mechanisms of mammalian cells. In addition, catalase can oxidize, by means of its peroxidatic activity, a variety of substrates such as methanol and ethanol, producing the corresponding aldehydes. The involvement of brain catalase in the oxidation of ethanol is well established, and severe afflictions of the CNS in hereditary peroxisomal diseases (e.g., Zellweger syndrome) are well known. Whereas the distribution of catalase in the CNS has been investigated by enzyme histochemistry and immunohistochemistry (IHC), very little is known about the exact localization of catalase mRNA in brain. Here we report the application of a tyramine/CARD (catalyzed reporter deposition)-enhanced nonradioactive in situ hybridization (ISH) protocol for detection of catalase mRNA in sections of perfusion-fixed, paraffin-embedded rat brain. Catalase mRNA could be demonstrated in a large number of neurons throughout the rat brain as a distinct cytoplasmic staining signal with excellent morphological resolution. Compared to our standard ISH protocol, the CARD-enhanced protocol for catalase mRNA detection in rat brain showed higher sensitivity and significantly better signal-to-noise ratio. In parallel IHC experiments, using an antigen retrieval method consisting of combined trypsin digestion and microwave treatment of paraffin sections, the catalase antigen was found as distinct cytoplasmic granules in most catalase mRNA-positive neurons. In addition, catalase-positive granules, presumably peroxisomes, were found by confocal laser scanning microscopy in glial cells, which were identified by double labeling immunofluorescence for GFAP and CNPase for astroglial cells and oligodentrocytes, respectively. The excellent preservation of morphology and sensitive detection of both mRNA and protein in our preparations warrant the application of the protocols described here for systematic studies of catalase and other peroxisomal proteins in diverse pathological conditions such as Alzheimer's disease and aging.     

mRNA-targeted fluorescent in situ hybridization (FISH) of Gram-negative bacteria without template amplification or tyramide signal amplification

Technologies are needed to study gene expression at the level of individual cells within a population or microbial community. Fluorescent in situ hybridization (FISH) supplies high-resolution spatial information and has been widely applied to study microbial communities at the rRNA level. While mRNA-targeted FISH has been popular for studying gene expression in eukaryotic cells, very little success has been achieved with prokaryotes. At present, detection of specific mRNAs in individual prokaryotic cells requires the use of in situ RT-PCR or tyramide signal amplification (TSA). In this study we used DNA oligonucleotide probes labeled with a single near-infrared dye in FISH assays to detect multi-copy plasmid-based and endogenous mRNA molecules in Escherichia coli and Shewanella oneidensis MR-1. We took advantage of the fact that there is much less background signal produced by biological materials and support matrices in the near-infrared spectrum and thus long camera exposure times could be used. In addition, we demonstrate that a combination of probes targeting both rRNA and mRNA could be successfully employed within the same FISH assay. These results, as well as ongoing R&D improvements in NIR and infrared dyes, indicate that the FISH approach we demonstrated could be applied in certain environmental settings to monitor gene expression in mixed populations.     

Profiling of molecular interactions in real time using acoustic detection

Acoustic sensors that exploit resonating quartz crystals to directly detect the binding of an analyte to a receptor are finding increasing utility in the quantification of clinically relevant analytes. We have developed a novel acoustic detection technology, which we term resonant acoustic profiling (RAP). This technology builds on the fundamental basics of the "quartz crystal microbalance" or "QCM" with several key additional features including two- or four-channel automated sample delivery, in-line referencing and microfluidic sensor 'cassettes' that are pre-coated with easy-to-use surface chemistries. Example applications are described for the quantification of myoglobin concentration and its interaction kinetics, and for the ranking of enzyme-cofactor specificities.     

Fluorescent substrate analog for monitoring chain elongation by undecaprenyl pyrophosphate synthase in real time

Farnesyl pyrophosphate (FPP) is a common substrate for a variety of prenyltransferases for synthesizing isoprenoid compounds. In this study, (2E,6E)-8-O-(N-methyl-2-aminobenzoyl)-3,7-dimethyl-2,6-octandien-1-pyrophosphate (MANT-O-GPP), a fluorescent analog of FPP, was synthesized and demonstrated as a satisfactory substrate for Escherichia coli undecaprenyl pyrophosphate synthase (UPPS) with a K_m of 1.5 μM and a k_cat of 1.2 s⁻¹ based on [¹⁴C]IPP consumption. Interesting, we found that its emission fluorescence intensity at 420 nm increased remarkably during chain elongation, thereby useful for real-time monitoring kinetics of UPPS to yield a K_m of 1.1 μM and a k_cat of 1.0 s⁻¹, consistent with those measured using radiolabeled substrate. Using this assay, the IC₅₀ of a known UPPS inhibitor farnesyl thiopyrophosphate (FsPP) was confirmed. Our studies provide a convenient and environmentally friendly alternative for kinetics and inhibition studies on UPPS drug target.     

Real-time monitoring of rolling-circle amplification using a modified molecular beacon design

We describe a method to monitor rolling-circle replication of circular oligonucleotides in dual-color and in real-time using molecular beacons. The method can be used to study the kinetics of the polymerization reaction and to amplify and quantify circularized oligonucleotide probes in a rolling-circle amplification (RCA) reaction. Modified molecular beacons were made of 2′-O-Me-RNA to prevent 3′ exonucleolytic degradation by the polymerase used. Moreover, the complement of one of the stem sequences of the molecular beacon was included in the RCA products to avoid fluorescence quenching due to inter-molecular hybridization of neighboring molecular beacons hybridizing to the concatemeric polymerization product. The method allows highly accurate quantification of circularized DNA over a broad concentration range by relating the signal from the test DNA circle to an internal reference DNA circle reporting in a distinct fluorescence color.     

Oxidative quenching of spruce thermomechanical pulp fiber autofluorescence monitored in real time by confocal laser scanning microscopy-implications for lignin autofluorescence

Confocal laser scanning microscopy (CLSM) was used to monitor real-time lignin autofluorescence intensities from different cell wall compartments of spruce fibers during oxidation by laccase-2,2'-azinobis-3-ethylbenzthiazoline-6-sulfonate (ABTS) treatment. CLSM data revealed an instant emission quenching from all cell wall compartments, including those not physically accessible to enzyme or ABTS, followed by an additional decrease simultaneously in all cell wall compartments over a 45 min time course. The importance of site-to-site excitation energy transfer in lignin efficient over long distance is suggested.     

Microelectrode chip based real time monitoring of vital MCF-7 mamma carcinoma cells by impedance spectroscopy

Sensorchip based impedance spectroscopy can detect inhibitory effects of human neuropeptide Y (hNPY) on living cells in a non-invasive labelling free way in real time without the need of supporting reagents. Since the discovery that neoplasmatic transformations in breast cancer are correlated with a change of the receptor subtype expression of hNPY in the affected tissue, the hNPY receptor-ligand system has come to the fore of cancer research. Today there are different methods detecting hNPY receptor interactions like fluorescent and radioactive labelling or detecting hNPY-pathway activation like cyclic adenosine monophosphate (cAMP) and G protein-coupled receptor (GPCR)-assays. For all these assays it is necessary to either label related proteins with additional substances, which can affect the nature state of the cell, or the need of producing cell lysate which allows only a snapshot of the investigated cells. To overcome these problems we established a new method to detect hNPY-receptor interactions. Therefore, we monitor the complex electric resistance (impedance) of cells attached to a microelectrode over a wide frequency range. Cell alterations are detected as changes in the impedance spectra. After application of the adenylyl cyclase-stimulating reagent forskolin, impedance is decreased at 5kHz frequency within minutes. This effect can be inhibited by preincubating the cells with hNPY for a time range of 20min. The inhibitory effect of hNPY can be washed out and the same cells can be stimulated by forskolin again.     

Morphological and molecular evidence of natural hybridization in Shorea (Dipterocarpaceae)

Shorea (Dipterocarpaceae) is a large genus in which many closely related species often grow together in Southeast Asian lowland tropical rain forests. Many Shorea species share common pollinators, and earlier studies suggested occurrence of interspecific hybridization and introgression. Here, we show morphological and molecular evidence of hybridization between Shorea species. In the census of all the trees of Shorea curtisii, Shorea leprosula, and Shorea parvifolia (>30 cm dbh) within the 164-ha area of Bukit Timah Nature Reserve in Singapore, we found 21 morphologically recognizable hybrid individuals. All of the putative hybrids could be distinguished obviously from the parental species on the basis of vegetative characters. Population genetic analysis of DNA sequences of two nuclear (GapC and PgiC) and chloroplast (trnL-trnF) regions demonstrated that each of the three species had several species-specific mutations. The nuclear sequences of the putative hybrids were heterozygote at all the species-specific sites between two parental species. Hybrid between S. curtisii and S. leprosula was found most, while S. curtisii × S. parvifolia and S. leprosula × S. parvifolia hybrids were also found. Almost no shared polymorphism between populations of the parental species suggests rarity of introgression. The study indicated that natural hybridization between sympatric Shorea species should not be uncommon, but all of the hybrid individuals were F₁, and the post-F₁ hybrids were considerably rare.     

High-speed broadband monitoring of cell viscoelasticity in real time shows myosin-dependent oscillations

Study of the dynamic evolutions of cell viscoelasticity is important as during cell activities such as cell metastasis and invasion, the rheological behaviors of the cells also change dynamically, reflecting the biophysical and biochemical connections between the outer cortex and the intracellular structures. Although the time variations of the static modulus of cells have been investigated, few studies have been reported on the dynamic variations of the frequency-dependent viscoelasticity of cells. Measuring and monitoring such dynamic evolutions of cells at nanoscale can be challenging as the measurement needs to meet two objectives inherently contradictory to each other—the measurement must be broadband (to cover a large frequency spectrum) but also rapid (to capture the time-elapsed changes). In this study, we exploited a recently developed control-based nanomechanical protocol of atomic force microscope to monitor in real time the dynamic evolutions of the viscoelasticity of live human prostate cancer cells (PC-3 cells) and study its dependence on myosin activities. We found that the viscoelasticity of PC-3 cells, followed the power law, and oscillated at a period of about 200 s. Both the amplitude and the frequency of the oscillation strongly depended on the intracellular calcium and blebbistatin-sensitive motor proteins.     

Detection of rare DNA targets by isothermal ramification amplification.

We described previously a novel DNA amplification technique, termed ramification amplification (RAM) (Zhang et al., Gene 211 (1998) 277). This method was designed to utilize a circular probe (C-probe) that is covalently linked by a DNA ligase when it hybridizes to a target. Then, a DNA polymerase extends the bound forward primer along the C-probe and continuously displaces a downstream strand, generating a multimeric single-stranded DNA (ssDNA), analogous to in vivo 'rolling circle' replication of bacteriophage. This multimeric ssDNA then serves as a template for multiple reverse primers to hybridize, extend, and displace downstream DNA, generating a large ramified (branching) DNA complex, and resulting in an exponential amplification. Previously, we were able to achieve a significant amplification using phi29 DNA polymerase that has a high processivity and strong displacement activity. However, due to the intrinsic limitations of the polymerase, we only achieved a sensitivity of 10,000 target molecules, which is insufficient for most practical uses. Therefore, we tested several DNA polymerases and found that exo(-) Bst DNA polymerase meets the requirement for high sensitivity. By further improving the assay condition and format, we are able to detect fewer than ten targets in 1 h and to apply successfully this method for detection of Epstein-Barr virus in human lymphoma specimens.     

Detection of Clavibacter michiganensis subsp. sepedonicus by AmpliDet RNA,a new technology based on real time monitoring of NASBA amplicons with a molecular beacon

AIMS: To develop a procedure for direct detection of viable cells of Clavibacter michiganensis subsp. sepedonicus (Cms), the causal organism of bacterial ring rot in potato, based on AmpliDet RNA, in which amplicons generated by nucleic acid sequence based amplification (NASBA) are monitored in real time with a molecular beacon. METHODS AND RESULTS: Five methods were evaluated and fine-tuned for extraction of RNA from Cms. The most efficient non-commercial RNA extraction method included an enzymatic breakdown of the cell wall followed by a phenol extraction. AmpliDet RNA enabled detection of 10,000 molecules of purified rRNA per reaction and 100 cfu of Cms per reaction in more complex samples. Two primer pairs were tested with DNA and RNA purified from Cms. One primer pair was able to distinguish live from dead cells. CONCLUSIONS: An AmpliDet RNA was developed which enabled fast and specific detection of viable cells of Cms in complex substrates at a detection limit of 100 cfu per reaction. SIGNIFICANCE AND IMPACT OF THE STUDY: This novel AmpliDet RNA is carried out in sealed tubes, thus reducing the risk of carry-over contamination. The method will be particularly suitable for studies on the epidemiology of Cms in which viable cells should be exclusively detected.