Rapid, single-tube method for quantitative preparation and analysis of RNA and DNA in samples as small as one cell

A Comprehensive Comparison of Rapid RNA Extraction Methods for Detection of SARS-CoV-2 as the Infectious Agent of the Upper Respiratory Tract using Direct RT-LAMP Assay

Background

The current COVID-19 pandemic has highlighted the need for faster and more cost-effective diagnostic methods. The RNA extraction step in current diagnostic methods, such as real-time qPCR, increases the cost and time required for testing. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a promising technique for developing diagnostic tests with desired sensitivity and specificity without the need for RNA extraction.

Materials and Methods

An RT-LAMP assay was developed to detect SARS-CoV-2 with a sensitivity of 0.5 copies of positive control plasmid per microliter in 40 min. Several rapid RNA extraction protocols were evaluated using different reagents, including bovine serum albumin, Triton X-100, Tween 20, proteinase K, guanidine hydrochloride, guanidinium isothiocyanate (GITC), and thermal treatment. Finally, the sensitivity and specificity of the developed direct RT-LAMP were determined using 150 upper respiratory tract samples.

Results

Method 10 was selected as the most efficient protocol for the RNA extraction step. The sensitivity and specificity of the developed direct RT-LAMP assay with clinical samples were estimated at 98.4% and 88.8%, respectively.

Conclusion

These results suggest that the combination of GITC and Triton X-100 detergent is a highly efficient method for RNA extraction and direct RT-LAMP detection of SARS-CoV-2 in clinical samples, providing a valuable tool for the rapid and cost-effective diagnosis of COVID-19.

A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs

In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification. The purpose of this review is to collect updated information about lncRNA classification and new findings on their function derived from single-cell analysis. We also retained useful for all researchers to describe the methods available for single-cell analysis and the databases collecting single-cell and lncRNA data. Tables are included to schematize, describe, and compare exposed concepts.

Effects of laser-assisted thinning versus opening on clinical outcomes according to maternal age in patients with repeated implantation failure

Laser-assisted thinning (LAT) and laser-assisted opening (LAO) are performed as part of human in vitro fertilization (IVF) to increase the implantation rate in patients with a poor prognosis and in cases of repeated implantation failure. However, an insufficient number of studies have directly compared LAT and LAO using the same methods. Therefore, we compared the effects of LAT and LAO on clinical outcomes according to maternal age in patients with repeated implantation failure. This retrospective study was performed in 509 IVF cycles (458 patients). The cycles were divided based on maternal age and the method used (< 38 years LAT, n = 119 vs. LAO, n = 179 and ≥ 38 years LAT, n = 72 vs. LAO, n = 139). Cleavage-stage embryos before transfer were either thinned or opened using a 1.46-μm noncontact diode laser. We compared the implantation rates and pregnancy outcomes of cycles between LAT and LAO according to maternal age. The characteristics of patients did not differ significantly among the groups (p > 0.05), with the exception of mixed factor infertility, which was more common in the LAT group than in the LAO group among patients < 38 years of age (10.1% vs. 2.8%, p = 0.008). The LAT and LAO groups showed similar rates of biochemical pregnancy, clinical pregnancy, ongoing pregnancy, abortion, implantation, singleton pregnancy, and twin pregnancy (p > 0.05). In conclusion, LAT and LAO had similar clinical outcomes. Therefore, we did not find any evidence that LAT is superior to LAO. In fact, the patients ≥ 38 years of age who underwent LAO tended to have a lower abortion rate. Further study is necessary to confirm these results in a larger population.

Closed-Tube Barcoding

Here, we present a new approach for increasing the rate and lowering the cost of identifying, cataloging, and monitoring global biodiversity. These advances, which we call Closed-Tube Barcoding, are one application of a suite of proven PCR-based technologies invented in our laboratory. Closed-Tube Barcoding builds on and aims to enhance the profoundly important efforts of the International Barcode of Life initiative. Closed-Tube Barcoding promises to be particularly useful when large numbers of small or rare specimens need to be screened and characterized at an affordable price. This approach is also well suited for automation and for use in portable devices.

Design and construction of a single tube, quantitative endpoint, LATE-PCR multiplex assay for ventilator-associated pneumonia

AIMS

The goal of this study was to develop a molecular diagnostic multiplex assay for the quantitative detection of microbial pathogens commonly responsible for ventilator-associated pneumonia (VAP) and their antibiotic resistance using linear-after-the-exponential polymerase chain reaction (LATE-PCR).

METHOD AND RESULTS

This multiplex assay was designed for the quantitative detection and identification of pathogen genomic DNA of methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii, Pseudomonas aeruginosa, plus a control target from Lactococcus lactis. After amplification, the single-stranded amplicons were detected simultaneously in the same closed tube by hybridization to low-temperature molecular beacon probes labelled with four differently coloured fluorophores. The resulting hybrids were then analysed by determining the fluorescence intensity of each of the four fluorophores as a function of temperature.

CONCLUSIONS

This LATE-PCR single tube multiplex assay generated endpoint fluorescent contours that allowed identification of all microbial pathogens commonly responsible for VAP, including MRSA. The assay was quantitative, identifying the pathogens present in the sample, no matter whether there were as few as 10 or as many 100 000 target genomes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This assay is rapid, reliable and sensitive and is ready for preclinical testing using samples recovered from patients suffering from ventilator-associated pneumonia.

Design and Construction of a Single-Tube, LATE-PCR, Multiplex Endpoint Assay with Lights-On/Lights-Off Probes for the Detection of Pathogens Associated with Sepsis

Aims. The goal of this study was to construct a single tube molecular diagnostic multiplex assay for the detection of microbial pathogens commonly associated with septicemia, using LATE-PCR and Lights-On/Lights-Off probe technology. Methods and Results. The assay described here identified pathogens associated with sepsis by amplification and analysis of the 16S ribosomal DNA gene sequence for bacteria and specific gene sequences for fungi. A sequence from an unidentified gene in Lactococcus lactis subsp. cremoris served as a positive control for assay function. LATE-PCR was used to generate single-stranded amplicons that were then analyzed at endpoint over a wide temperature range in a specific fluorescent color. Each bacterial target was identified by its pattern of hybridization to Lights-On/Lights-Off probes derived from molecular beacons. Complex mixtures of targets were also detected. Conclusions. All microbial targets were identified in samples containing low starting copy numbers of pathogen genomic DNA, both as individual targets and in complex mixtures. Significance and Impact of the Study. This assay uses new technology to achieve an advance in the field of molecular diagnostics: a single-tube multiplex assay for identification of pathogens commonly associated with sepsis.

Quantitative single-cell gene expression measurements of multiple genes in response to hypoxia treatment

Cell-to-cell heterogeneity in gene transcription plays a central role in a variety of vital cell processes. To quantify gene expression heterogeneity patterns among cells and to determine their biological significance, methods to measure gene expression levels at the single-cell level are highly needed. We report an experimental technique based on the DNA-intercalating fluorescent dye SYBR green for quantitative expression level analysis of up to ten selected genes in single mammalian cells. The method features a two-step procedure consisting of a step to isolate RNA from a single mammalian cell, synthesize cDNA from it, and a qPCR step. We applied the method to cell populations exposed to hypoxia, quantifying expression levels of seven different genes spanning a wide dynamic range of expression in randomly picked single cells. In the experiment, 72 single Barrett's esophageal epithelial (CP-A) cells, 36 grown under normal physiological conditions (controls) and 36 exposed to hypoxia for 30 min, were randomly collected and used for measuring the expression levels of 28S rRNA, PRKAA1, GAPDH, Angptl4, MT3, PTGES, and VEGFA genes. The results demonstrate that the method is sensitive enough to measure alterations in gene expression at the single-cell level, clearly showing heterogeneity within a cell population. We present technical details of the method development and implementation, and experimental results obtained by use of the procedure. We expect the advantages of this technique will facilitate further developments and advances in the field of single-cell gene expression profiling on a nanotechnological scale, and eventually as a tool for future point-of-care medical applications.

Detection and quantification of mRNA in single human polar bodies: a minimally invasive test of gene expression during oogenesis

Proteins and mRNA produced in oogenesis support embryonic development until the zygotic transition, 3 days after fertilization. Since polar bodies can be biopsied with little if any harm to the oocyte, we tested the hypothesis that mRNA originating from expression in the meiotic oocyte is present and detectable in a single polar body prior to insemination. Human oocytes were obtained from patients undergoing controlled ovarian hyperstimulation and intracytoplasmic sperm injection. Immature oocytes were cultured overnight and inspected the following day for maturation. Metaphase II oocytes underwent polar body biopsy followed by reverse transcription without RNA isolation. Sibling oocytes were similarly prepared. Complementary DNA from all samples were pre-amplified over 15 cycles for candidate genes using selective primers. Real-time PCR was performed to detect and quantify relative single-cell gene expression. Polar body mRNA was detected in 11 of 12 candidate genes. Transcripts that were present in greater abundance in the oocyte were more likely to be detected in qPCR replicates from single polar bodies. Pre-amplification of cDNA synthesized without RNA isolation can facilitate the quantitative detection of mRNA in single human polar bodies.

The effects of different laser pulse lengths on the embryo biopsy procedure and embryo development to the blastocyst stage

PURPOSE

a laser is commonly used to remove a blastomere from an embryo for genetic testing. The laser uses intense heat which could possibly disrupt embryo development. It is the goal of this study to test the effects of different laser pulse lengths (and consequently heat) on the embryo biopsy procedure and embryo development.

METHODS

each embryo biopsy was performed randomly utilizing laser pulse lengths of 0.604mS (group I), 0.708mS (group II), and 1.010mS (group III).

RESULTS

for groups I, II, and III, 83, 86, and 71 embryos were biopsied, respectively. There was no difference in day 5 embryo quality or lysed blastomeres between groups. Average number of blastomeres biopsied between group I (1.0 ± 0.0), II (1.0 ± 0.2), and III (1.1 ± 0.2) was significant (0.0001).

CONCLUSION

our data demonstrates that laser pulse length does not influence the embryo biopsy procedure or embryo development.

One-step RT-LATE-PCR for mRNA and viral RNA detection and quantification

LATE-PCR is an optimized form of asymmetric PCR that efficiently generates high levels of single-stranded DNA amplicons. Single-stranded amplicons are advantageous because, as shown in this chapter, they can be probed at low temperature(s) with one or more probes. Based on its properties, LATE-PCR is also useful for constructing multiplex assays. Viral RNA or RNA present in cells can be detected and quantified using LATE-PCR preceded by a reverse transcription (RT) step that converts RNA into cDNA. According to the conventional two-step approach, RT is primed using nonspecific random oligonucleotides prior to performing PCR amplification in a separate step. Recently, however, the so-called "one-step" RT-PCR strategy has gained increasing popularity because all reagents needed for both reactions are added together in a single mix, thus reducing the possibility of contamination, a consideration particularly relevant to viral samples analysis. We describe below two protocols using RT-LATE-PCR and provide specific guidelines for the general application of this technique. The first protocol is devised to quantify mRNA from mouse embryos by real-time PCR; the second protocol employs end-point analysis to detect a number of different viral-like sequences in a multiplex reaction.

An improved one-tube RT-PCR protocol for analyzing single-cell gene expression in individual mammalian cells

It is well known that gene expression is regulated at the level of individual cells, and more evidence is now emerging that heterogeneity of cell regulation is orders of magnitude greater than previously thought. In order to detect meaningful variations in transcription levels, it is necessary to measure gene expression at single cell levels rather than in bulk cells, where individual differences or heterogeneity could be lost. In this work, we report an improved reverse-transcriptase polymerase chain reaction (RT-PCR) protocol which allows the direct measurement of gene expression in one tube (5-25 microl of total PCR mixture) at the single mammalian cell level. The protocol employs a new cell lysis buffer, and involves no RNA isolation or nested PCR steps, significantly reducing the possibility of contamination and errors. We successfully applied this protocol in qRT-PCR and linear-after-the-exponential (LATE)-PCR to analyze selected genes of various expression levels from three cell lines. Although further characterization of RNA stability is important, the preliminary results showed that gene expression heterogeneity could be common among members of genetically identical cell populations. The protocol illustrated can be utilized for a wide array of applications without much modification, such as cancer cell analysis and preimplantation genetic diagnostics. In addition, the protocol is based on intercalator-based (SYBR Green PCR) chemistry, which is less expensive and suitable for high-throughput platforms.

Heat shock memory in preimplantation mouse embryos

To investigate the consequences of possible physiologic stress to embryos caused by in vitro fertilization procedures, we used heat shock response in preimplantation mouse embryos as a model. A heat shock "memory" was discovered that renders cleavage-stage embryos more responsive at the transcriptional level to secondary perturbation with very low doses of heat, even several cell cycles after the initial stress has occurred.

Impact of the size of zona pellucida thinning area on vitrified-warmed cleavage-stage embryo transfers: a prospective, randomized study

PURPOSE

The aim of this study was to determine if the size of zona pellucida thinning area by laser assisted hatching could affect the rates of pregnancy and implantation for vitrified-warmed embryo transfers at the cleavage-stage.

METHODS

A total of 120 vitrified-warmed cleavage-stage embryo transfers were randomly assigned to either quarter or half of zona pellucida thinning group.

RESULTS

The rates of clinical pregnancy (46.7 versus 25.0%) and implantation (32.0 versus 16.2%) were significantly greater in the half thinning group than in the quarter thinning group (P = 0.0218 and P = 0.0090, respectively).

CONCLUSIONS

The results of this investigation show that, in vitrified-warmed embryo transfers at the cleavage-stage, the size of zona pellucida thinning area by laser assisted hatching impacts the rate of clinical pregnancy and implantation and that half of zona pellucida thinning significantly increases both of these results compared with quarter of zona pellucida thinning.

Quantitative analysis of gene expression in a single cell by qPCR

We developed a quantitative PCR method featuring a reusable single-cell cDNA library immobilized on beads for measuring the expression of multiple genes in a single cell. We used this method to analyze multiple cDNA targets (from several copies to several hundred thousand copies) with an experimental error of 15.9% or less. This method is sufficiently accurate to investigate the heterogeneity of single cells.

A novel single-cell quantitative real-time RT-PCR method for quantifying foot-and-mouth disease viral RNA

Foot-and-mouth disease virus is a positive-sense, single-stranded RNA virus with a negative strand as its replication intermediate, which can cause severe acute infection in sensitive cell lines. To investigate better the actual state of virus infection, there is a need to measure the amount of FMDV RNA in a single acutely infected cell rather than in a large number of cells. Therefore, in the present study, a strand-specific single-cell quantitative real-time RT-PCR was developed to analyze the RNA or FMDV. This new method uses two techniques in concert with each other: a technique for isolating single cells with micromanipulators, which is coupled to an assay for detecting viral RNA by real-time RT-PCR. In the assay of acute infection, 185 of 224 (82.6%) single-cell samples were positive and contained viral genome copies ranging from several to thousands, and up to 1,000,000 copies. However, not all cells were infected and there were differences in the number of viral RNA copies between cells. A single-cell quantitative RT-PCR was validated to be feasible and effective.

Multiplex rt-PCR expression analysis of developmentally important genes in individual mouse preimplantation embryos and blastomeres

We have developed a microfluidic chip-based qualitative assay for sensitive (10 RNA copies) detection of multiple transcripts in single cells. We determined the expression patterns of 17 developmentally important genes and isoforms in individual mouse preimplantation embryos from superovulated matings and blastomeres. The ubiquitously expressed histone variant H3f3a and the transcription factor Pou5f1 generated mRNA-derived products in all analyzed (1-cell, 2-cell, 4-cell, and morula stage) embryos and in all analyzed blastomeres from 16-cell embryos, indicating a uniform reactivation of pluripotency gene expression during mouse preimplantation development. In contrast, mRNA expression of different methyltransferases for DNA methylation, methylcytosine-binding proteins for chromatin modification, and base excision repair enzymes, which may provide a mechanism for active demethylation, varied considerably between individual cells from the same embryo and even more dramatically between cells from different embryos. We conclude that at a given point in time the transcriptome encoding the reprogramming machinery and, by extrapolation, genome reprogramming differs between blastomeres. By studying the cell-to-cell variability in gene expression, we can distinguish the following two classes: mouse 16-cell embryos in which most cells express the reprogramming machinery and embryos in which most cells do not contain detectable mRNA levels of DNA and chromatin modification genes. Immunolocalization of DNMT3A, MBD3, APEX1, and LIG3 in most or all nuclei of 40-60-cell embryos is a good indicator of functional activity of genes that are activated by the 16-cell stage.

Effect of the size of zona pellucida opening by laser assisted hatching on clinical outcome of frozen cleaved embryos that were cultured to blastocyst after thawing in women with multiple implantation failures of embryo transfer: a retrospective study

PURPOSE

To evaluate the effect of the size of zona pellucida opening by laser assisted hatching for frozen cleaved embryo that were thawed after both fresh and frozen cleaved embryo transfer cycles failed and were cultured to blastocyst after thawing in patients with multiple implantation failures.

MATERIALS AND METHODS

Of 101 consecutive procedures (October 2003 to June 2006), 30 patients declined to perform assisted hatching and were selected as control group, 40 patients had 40 microm opening of the zona (October 2003 to January 2005), 31 patients had 50% of the zona opening (February 2005 to June 2006).

RESULTS

The pregnancy, implantation and delivery rates were significantly higher in 50% opening group (74%, 52% and 65%) compared to control group (17%, 10% and 13%; P < 0.01) and 40 microm opening group (43%, 27% and 38%; P < 0.04).

CONCLUSIONS

The size of the zona pellucida opening may affect the outcome of frozen cleaved embryo transfer.

Single-cell duplex RT-LATE-PCR reveals Oct4 and Xist RNA gradients in 8-cell embryos

BACKGROUND

The formation of two distinctive cell lineages in preimplantation mouse embryos is characterized by differential gene expression. The cells of the inner cell mass are pluripotent and express high levels of Oct4 mRNA, which is down-regulated in the surrounding trophectoderm. In contrast, the trophectoderm of female embryos contains Xist mRNA, which is absent from cells of the inner mass. Prior to blastocyst formation, all blastomeres of female embryos still express both of these RNAs. We, thus, postulated that simultaneous quantification of Oct4 and Xist transcripts in individual blastomeres at the 8-cell stage could be informative as to their subsequent fate. Testing this hypothesis, however, presented numerous technical challenges. We overcame these difficulties by combining PurAmp, a single-tube method for RNA preparation and quantification, with LATE-PCR, an advanced form of asymmetric PCR.

RESULTS

We constructed a duplex RT-LATE-PCR assay for real-time measurement of Oct4 and Xist templates and confirmed its specificity and quantitative accuracy with different methods. We then undertook analysis of sets of blastomeres isolated from embryos at the 8-cell stage. At this stage, all cells in the embryo are still pluripotent and morphologically equivalent. Our results demonstrate, however, that both Oct4 and Xist RNA levels vary in individual blastomeres comprising the same embryo, with some cells having particularly elevated levels of either transcript. Analysis of multiple embryos also shows that Xist and Oct4 expression levels are not correlated at the 8-cell stage, although transcription of both genes is up-regulated at this time in development. In addition, comparison of data from males and females allowed us to determine that the efficiency of the Oct4/Xist assay is unaffected by sex-related differences in gene expression.

CONCLUSION

This paper describes the first example of multiplex RT-LATE-PCR and its utility, when combined with PurAmp sample preparation, for quantitative analysis of transcript levels in single cells. With this technique, copy numbers of different RNAs can be accurately measured independently from their relative abundance in a cell, a goal that cannot be achieved using symmetric PCR. The technique illustrated in this work is relevant to a wide array of applications, such as stem cell and cancer cell analysis and preimplantation genetic diagnostics.

Early onset of heat-shock response in mouse embryos revealed by quantification of stress-inducible hsp70i RNA

Heat shock response is fully established in mouse embryos at the blastocyst stage, but it is unclear when this response first arises during development. To shed light on this question, we used a single-tube method to quantify mRNA levels of the heat shock protein genes hsp70.1 and hsp70.3 (hsp70i) in individual cleavage-stage embryos that had or had not been heat-shocked. While untreated, healthy embryos contained very low copy numbers of hsp70i RNA, heat shock rapidly induced the synthesis of hundreds of hsp70i transcripts per blastomere at both the 4-cell and the 8-cell stages. In addition, we performed hsp70i measurements in embryos that had not been heat-shocked but had been very slow in developing. Quantification of hsp70i RNA and genomic DNA copy numbers in these slow-growing embryos demonstrated the presence of two distinct populations. Some of the embryos contained considerable levels of hsp70i RNA, a finding consistent with the hypothesis of endogenous metabolic stress accompanied by cell cycle arrest and delayed development. Other slow-growing embryos contained no hsp70i RNA and fewer than expected hsp70i gene copies, suggesting the possibility of ongoing apoptosis. In conclusion, this study demonstrates that mouse embryos can activate hsp70i expression in response to sub-lethal levels of stress as early as at the 4-cell stage. Our results also indicate that quantification of hsp70i DNA and RNA copy numbers may provide a diagnostic tool for embryonic health.

Zona pellucida removal and vitrified blastocyst transfer outcome: a preliminary study

The objective of this study was to investigate whether a change in assisted hatching technique from partial opening to total removal of the zona pellucida improved the outcome of vitrified blastocyst transfer. This was a preliminary observational study conducted from November 2003 to April 2006. Partial opening using acid Tyrode's solution was performed in 45 cycles, while total removal using a laser and mechanical pipetting was performed in 57 cycles. The clinical pregnancy, implantation, and delivery rates were higher in the total removal group than in the partial opening group (67% versus 42%, P < 0.02; 55% versus 30%, P < 0.01; 56% versus 36%, P < 0.04, respectively). These results suggest that total removal of the zona pellucida is associated with higher pregnancy, implantation and delivery rates compared with partial opening for vitrified blastocyst transfer.

Quantification of mRNA using real-time RT-PCR

The real-time reverse transcription polymerase chain reaction (RT-qPCR) addresses the evident requirement for quantitative data analysis in molecular medicine, biotechnology, microbiology and diagnostics and has become the method of choice for the quantification of mRNA. Although it is often described as a "gold" standard, it is far from being a standard assay. The significant problems caused by variability of RNA templates, assay designs and protocols, as well as inappropriate data normalization and inconsistent data analysis, are widely known but also widely disregarded. As a first step towards standardization, we describe a series of RT-qPCR protocols that illustrate the essential technical steps required to generate quantitative data that are reliable and reproducible. We would like to emphasize, however, that RT-qPCR data constitute only a snapshot of information regarding the quantity of a given transcript in a cell or tissue. Any assessment of the biological consequences of variable mRNA levels must include additional information regarding regulatory RNAs, protein levels and protein activity. The entire protocol described here, encompassing all stages from initial assay design to reliable qPCR data analysis, requires approximately 15 h.

Early Onset of Heat-Shock Response in Mouse Embryos Revealed by Quantification of Stress-Induciblehsp70iRNA

Heat shock response is fully established in mouse embryos at the blastocyst stage, but it is unclear when this response first arises during development. To shed light on this question, we used a single-tube method to quantify mRNA levels of the heat shock protein genes hsp70.1 and hsp70.3 ( hsp70i) in individual cleavage-stage embryos that had or had not been heat-shocked. While untreated, healthy embryos contained very low copy numbers of hsp70i RNA, heat shock rapidly induced the synthesis of hundreds of hsp70i transcripts per blastomere at both the 4-cell and the 8-cell stages. In addition, we performed hsp70i measurements in embryos that had not been heat-shocked but had been very slow in developing. Quantification of hsp70i RNA and genomic DNA copy numbers in these slow-growing embryos demonstrated the presence of two distinct populations. Some of the embryos contained considerable levels of hsp70i RNA, a finding consistent with the hypothesis of endogenous metabolic stress accompanied by cell cycle arrest and delayed development. Other slow-growing embryos contained no hsp70i RNA and fewer than expected hsp70i gene copies, suggesting the possibility of ongoing apoptosis. In conclusion, this study demonstrates that mouse embryos can activate hsp70i expression in response to sub-lethal levels of stress as early as at the 4-cell stage. Our results also indicate that quantification of hsp70i DNA and RNA copy numbers may provide a diagnostic tool for embryonic health.

Nucleic acid quantification and disease outcome prediction in colorectal cancer

Histopathological stage at diagnosis remains the most important prognostic determinant for colorectal cancer. However, conventional staging is unable to predict disease outcome accurately for each individual patient. This results in considerable prognostic heterogeneity within a given tumor stage and is of particular relevance for a subgroup of patients with stage II disease that would benefit from adjuvant therapy. The recent advances in functional genomics are beginning to have a significant impact on clinical oncology, and there is widespread interest in using molecular techniques for clinical applications. These have focused on two approaches: the use of polymerase chain reaction (PCR)-based methods for the detection of occult disease in lymph nodes, bone marrow and blood and the use of microarrays for the expression profiling of primary tumors. The aim is to develop molecular classifiers that will allow the prediction of disease outcome, thus matching patients with individualized treatment. Despite the obvious attractions of these approaches, there have been significant technical, biological and analytical problems in their translation into clinically relevant practice. This is particularly true for colorectal cancer, the second most common cancer in the western world. Nevertheless, progress is being made and the improved awareness and appreciation of those difficulties is beginning to generate results that should prove useful for clinical oncology.

Laser zona drilling does not induce hsp70i transcription in blastomeres of eight-cell mouse embryos

To assess whether zona drilling with a 1,480-nm laser induces heat shock in eight-cell embryos, we measured hsp70i RNA levels in sets of single blastomeres isolated after laser treatment of mouse embryos that had or had not been heated at 43 degrees C. Unlike heating, laser zona drilling did not stimulate hsp70i expression, even in the blastomeres closest to the laser beam, corroborating the safety of this procedure for assisted reproduction.