The polymerase chain reaction

A novel near-infrared fluorescent probe for real-time monitoring of leucine aminopeptidase activity and metastatic tumor progression

This article discusses the importance of early tumor detection, particularly in liver cancer, and the role of leucine aminopeptidase (LAP) as a potential marker for liver cancer diagnosis and prognosis assessment. The article highlights the limitations of current tumor markers and the need for new markers and multi-marker approaches to improve accuracy. The authors introduce a novel near-infrared fluorescent probe, NTAP, designed for LAP detection. They describe the synthesis of the probe and evaluate its spectral properties, including the LOD was 0.0038 U/mL, and QY was 0.32 %. The kinetic properties of NTAP, such as the relationship between LAP concentration (0-0.08 U/mL), reaction time (3 min), and fluorescence excitation spectra (475 nm) and emission spectra (715 nm) are investigated. The article also discusses the stability and selectivity of the probe and its ability to detect LAP in complex samples. Cellular imaging experiments demonstrate the NATP specificity and selectivity in detecting LAP activity and its inhibition. Animal models of liver and lung metastasis are used to evaluate the probe's imaging capabilities, showing its ability to accurately locate and detect metastatic lesions. The article concludes by emphasizing the potential applications of the NTAP probe in early tumor diagnosis, treatment monitoring, and the study of tumor metastasis mechanisms.

The Evolution of Diagnostic Techniques in the Paleopathology of Tuberculosis: A Scoping Review

Tuberculosis (TB) is an ancient chronic infectious disease that remains a global health concern. In human remains, the most common and characteristic clinical signs are the skeletal modifications involving the spine, such as in Pott's disease. Diagnosing TB in ancient human remains is challenging. Therefore, in this systematic review, the authors investigated the studies assessing molecular diagnosis of Pott's disease in ancient human remains with the intention to survey the literature, map the evidence, and identify gaps and future perspectives on TB in paleopathology. Our systematic review offers a full contextualization of the history of Pott's disease in ancient times. Our search strategy was performed between August 2022 and March 2023. The authors initially identified 340 records, and 74 studies were finally included and assessed for qualitative analysis. Due to non-specific clinical signs associated with TB, how best to diagnose tuberculosis in human remains still represents a central point. Nevertheless, ancient DNA (aDNA) analysis, lipid biomarkers, and spoligotyping might be extremely useful tools in the study of TB in human remains. Moreover, we propose the extraction and study of immune response genes involved in innate and adaptive immunity versus Mycobacterium spp. as an innovative and vastly overlooked approach in TB paleopathology. Complementary methodologies should be integrated to provide the best approach to the study of TB in human remains.

Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review

Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.

Smart Nanostructured Materials for SARS-CoV-2 and Variants Prevention, Biosensing and Vaccination

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has raised great concerns about human health globally. At the current stage, prevention and vaccination are still the most efficient ways to slow down the pandemic and to treat SARS-CoV-2 in various aspects. In this review, we summarize current progress and research activities in developing smart nanostructured materials for COVID-19 prevention, sensing, and vaccination. A few established concepts to prevent the spreading of SARS-CoV-2 and the variants of concerns (VOCs) are firstly reviewed, which emphasizes the importance of smart nanostructures in cutting the virus spreading chains. In the second part, we focus our discussion on the development of stimuli-responsive nanostructures for high-performance biosensing and detection of SARS-CoV-2 and VOCs. The use of nanostructures in developing effective and reliable vaccines for SARS-CoV-2 and VOCs will be introduced in the following section. In the conclusion, we summarize the current research focus on smart nanostructured materials for SARS-CoV-2 treatment. Some existing challenges are also provided, which need continuous efforts in creating smart nanostructured materials for coronavirus biosensing, treatment, and vaccination.

Biodiversity and ecology of microorganisms in high pressure membrane filtration systems

High-pressure membrane filtration (reverse osmosis and nanofiltration) is used to purify different water sources, including wastewater, surface water, groundwater and seawater. A major concern in membrane filtration is the accumulation and growth of micro-organisms and their secreted polymeric substances, leading to reduced membrane performance and membrane biofouling. The fundamental understanding of membrane biofouling is limited despite years of research, as the means of microbial interactions and response to the conditions on the membrane surface are complicated. Here, we discuss studies that investigated the microbial diversity of fouled high-pressure membranes. High-throughput amplicon sequencing of the 16S rRNA gene have shown that Burkholderiales, Pseudomonadales, Rhizobiales, Sphingomonadales and Xanthomonadales frequently obtain a high relative abundance on fouled membranes. The bacterial communities present in the diverse feed water types and in pre-treatment compartments are different from the communities on the membrane, because high-pressure membrane filtration provides a selective environment for certain bacterial groups. The biofilms that form within the pre-treatment compartments do not commonly serve as an inoculum for the subsequent high-pressure membranes. Besides bacteria also fungi are detected in the water treatment compartments. In contrast to bacteria, the fungal community does not change much throughout membrane cleaning. The stable fungal diversity indicates that they are more significant in membrane biofouling than previously thought. By reviewing the biodiversity and ecology of microbes in the whole high pressure membrane filtration water chain, we have been able to identify potentials to improve biofouling control. These include modulation of hydrodynamic conditions, nutrient limitation and the combination of cleaning agents to target the entire membrane microbiome.

Advanced DNA-Based Point-of-Care Diagnostic Methods for Plant Diseases Detection

Diagnostic technologies for the detection of plant pathogens with point-of-care capability and high multiplexing ability are an essential tool in the fight to reduce the large agricultural production losses caused by plant diseases. The main desirable characteristics for such diagnostic assays are high specificity, sensitivity, reproducibility, quickness, cost efficiency and high-throughput multiplex detection capability. This article describes and discusses various DNA-based point-of care diagnostic methods for applications in plant disease detection. Polymerase chain reaction (PCR) is the most common DNA amplification technology used for detecting various plant and animal pathogens. However, subsequent to PCR based assays, several types of nucleic acid amplification technologies have been developed to achieve higher sensitivity, rapid detection as well as suitable for field applications such as loop-mediated isothermal amplification, helicase-dependent amplification, rolling circle amplification, recombinase polymerase amplification, and molecular inversion probe. The principle behind these technologies has been thoroughly discussed in several review papers; herein we emphasize the application of these technologies to detect plant pathogens by outlining the advantages and disadvantages of each technology in detail.

A PHYLOGENETIC ANALYSIS OF BODY SIZE EVOLUTION AND BIOGEOGRAPHY IN CHUCKWALLAS (SAUROMALUS) AND OTHER IGUANINES

The evolution of body size was reconstructed in chuckwallas (genus Sauromalus), large herbivorous lizards of southwest North America, using a phylogeny derived from sequence variation in the mitochondrial cytochrome b gene. The body mass of two endemic island species (S. hispidus and S. varius) is typically fivefold larger than mainland species. We tested the hypothesis that large body size has evolved on these islands in response to local ecological conditions against the alternative hypothesis that large size is simply retained from large iguanine ancestors. The most parsimonious tree topology depicts the insular gigantic Sauromalus as monophyletic, having diverged from a common ancestor on the Baja California peninsula after the radiation of smaller bodied clades. In a robustness analysis of this topology, we found general support for this tree over alternative topologies representing minimum evolution hypotheses that imply large body size is retained from large iguanine ancestors. The most parsimonious reconstruction of body size evolution implies a change from large to small size after the Sauromalus ancestor diverged from Iguana, and one reversal back to large size within Sauromalus. The large size increase in the gigantic clade contrasts with evolutionary stasis of small body size (for an iguanine) in mainland populations. The gigantic species show 3-4% total sequence divergence from S. obesus populations on the nearby Baja California peninsula, and mainland populations of S. obesus obesus show similar levels of divergence from each other. An analysis of character transitions and comparative behavior implicates predation, and its relaxation on isolated islands, as a strong selective force in Sauromalus. Patterns of genetic differentiation in Sauromalus and biogeographic implications are discussed.

Whole Genome Amplification and Branching Processes

Whole genome amplification is important for multipoint mapping by sperm or oocyte typing and genetic disease diagnosis. Polymerase chain reaction is not suitable for amplifying long DNA sequences. This paper studies a new technique, designated PEP-primer-extension-preamplification, for amplifying long DNA sequences using the theory of branching processes. A mathematical model for PEP is constructed and a closed formula for the expected target yield is obtained. A central limit theorem and a strong law of large numbers for the number of kth generation target sequences are proved.

The evolution of clonality testing in the diagnosis and monitoring of hematological malignancies

Currently, distinguishing between benign and malignant lymphoid proliferations is based on a combination of clinical characteristics, cyto/histomorphology, immunophenotype and the identification of well-defined chromosomal aberrations. However, such diagnoses remain challenging in 10-15% of cases of lymphoproliferative disorders, and clonality assessments are often required to confirm diagnostic suspicions. In recent years, the development of new techniques for clonality detection has allowed researchers to better characterize, classify and monitor hematological neoplasms. In the past, clonality was primarily studied by performing Southern blotting analyses to characterize rearrangements in segments of the IG and TCR genes. Currently, the most commonly used method in the clinical molecular diagnostic laboratory is polymerase chain reaction (PCR), which is an extremely sensitive technique for detecting nucleic acids. This technique is rapid, accurate, specific, and sensitive, and it can be used to analyze small biopsies as well as formalin-fixed paraffin-embedded samples. These advantages make PCR-based approaches the current gold standard for IG/TCR clonality testing. Since the completion of the first human genome sequence, there has been a rapid development of technologies to facilitate high-throughput sequencing of DNA. These techniques have been applied to the deep characterization and classification of various diseases, patient stratification, and the monitoring of minimal residual disease. Furthermore, these novel approaches have the potential to significantly improve the sensitivity and cost of clonality assays and post-treatment monitoring of B- and T-cell malignancies. However, more studies will be required to demonstrate the utility, sensitivity, and benefits of these methods in order to warrant their adoption into clinical practice. In this review, recent developments in clonality testing are examined with an emphasis on highly sensitive systems for improving diagnostic workups and minimal residual disease assessments.

Forensic human identification in the United States and Canada: a review of the law, admissible techniques, and the legal implications of their application in forensic cases

Forensic human identification techniques are successful if they lead to positive personal identification. However, the strongest personal identification is of no use in the prosecution--or vindication--of an accused if the associated evidence and testimony is ruled inadmissible in a court of law. This review examines the U.S. and Canadian legal rulings regarding the admissibility of expert evidence and testimony, and subsequently explores four established methods of human identification (i.e., DNA profiling, forensic anthropology, forensic radiography, forensic odontology) and one complementary technique useful in determining identity, and the legal implications of their application in forensic cases.

GeneMarker® HID: A reliable software tool for the analysis of forensic STR data

GeneMarker(®) HID was assessed as a software tool for the analysis of forensic short tandem repeat (STR) data and as a resource for analysis of custom STR multiplexes. The software is easy to learn and use, and includes design features that have the potential to reduce user fatigue. To illustrate reliability and accuracy, STR data from both single-source and mixture profiles were analyzed and compared to profiles interpreted with another software package. A total of 1898 STR profiles representing 28,470 loci and more than 42,000 alleles were analyzed with 100% concordance. GeneMarker HID was also used to successfully analyze data generated from a custom STR multiplex, with simplified and rapid implementation. Finally, the impact of the user-friendly design features of the software was assessed through a time scale study. The results suggest that laboratories can reduce the time required for data analysis by at least 25% when using GeneMarker HID.

Characterization of a recombinant thermostable dehalogenase isolated from the hot spring thermophile Sulfolobus tokodaii

A putative dehalogenase, L-HAD(ST), from the thermophile Sulfolobus tokodaii, was cloned and expressed in Escherichia coli. The recombinant enzyme catalyzes the stereospecific dehalogenation of L-2-haloacids with similar levels of activity as its homolog from mesophiles. L-HAD(ST) remains fully active after being incubated for 4 h at 70 degrees C and tolerates extreme pH conditions ranging from 4 to 10. Furthermore, it can be purified conveniently without the usage of any chromatography method. The high expression yield and easy purification procedure make the recombinant dehalogenase an excellent candidate for biotechnological applications.

Diagnosis of inherited disease before implantation

The diagnosis of inherited disease in affected embryos before implantation is now possible using in vitro fertilization (IVF), embryo biopsy and DNA analysis. This enables pregnancies to be established with unaffected embryos following transfer to the uterus avoiding the possibility of terminating a pregnancy diagnosed as affected later in gestation. Pregnancies have been established with female embryos in women carrying X-linked recessive genetic defects affecting boys by identifying the sex of embryos either by DNA amplification of Y-specific sequences or by dual fluorescent in situ hybridization (FISH) with X- and Y-specific probes to interphase nuclei. The predominant ΔF508 deletion causing cystic fibrosis (CF) has also been detected by DNA amplification from single cells and the first pregnancy and birth of a child successfully screened for a single gene defect achieved. The prospects for applying preimplantation diagnosis to other chromosomal and single gene defects are reviewed.

Ligation-mediated PCR for genomic sequencing and footprinting

This unit describes how PCR can be used to exponentially amplify segments of DNA located between two specified primer hybridization sites. A single-sided PCR method is used that initially requires specification of only one primer hybridization site; the second is defined by the ligation-based addition of a unique DNA linker. This linker, together with the flanking gene-specific primer, allows exponential amplification of any fragment of DNA. Because a defined, discrete-length sequence is added to every fragment, complex populations of DNA such as sequence ladders can be amplified intact with retention of single-base resolution. The ligation-based protocol was specifically designed for genomic footprinting and direct sequencing reactions, and is described in this context; it can, however, be used for other applications.

The HLA system: genetics, immunology, clinical testing, and clinical implications

The human major histocompatibility complex HLA is located on the short arm of chromosome 6. It is known to be the most polymorphic genetic system in humans. The biological role of the HLA class I and class II molecules is to present processed peptide antigens. The HLA system is clinically important as transplantation antigens. Molecular HLA allele typing is routinely performed to provide HLA class I and class II allele matching in unrelated donor hematopoietic stem cell transplantation. Prospective lymphocyte crossmatching is critical in solid organ transplantation to prevent allograft rejection. HLA alloimmunization causes various problems in transfusion therapy. The HLA system is associated with certain diseases, but its underlying mechanisms are not yet fully explained.

Electrokinetically synchronized polymerase chain reaction microchip fabricated in polycarbonate

This paper presents a novel method for DNA thermal amplification using the polymerase chain reaction (PCR) in an electrokinetically driven synchronized continuous flow PCR (EDS-CF-PCR) configuration carried out in a microfabricated polycarbonate (PC) chip. The synchronized format allowed patterning a shorter length microchannel for the PCR compared to nonsynchronized continuous flow formats, permitting the use of smaller applied voltages when the flow is driven electrically and also allowed flexibility in selecting the cycle number without having to change the microchip architecture. A home-built temperature control system was developed to precisely configure three isothermal zones on the chip for denaturing (95 degrees C), annealing (55 degrees C), and extension (72 degrees C) within a single-loop channel. DNA templates were introduced into the PCR reactor, which was filled with the PCR cocktail, by electrokinetic injection. The PCR cocktail consisted of low salt concentrations (KCl) to reduce the current in the EDS-CF-PCR device during cycling. To control the EOF in the PC microchannel to minimize dilution effects as the DNA "plug" was shuttled through the temperature zones, Polybrene was used as a dynamic coating, which resulted in reversal of the EOF. The products generated from 15, 27, 35, and 40 EDS-CF-PCR amplification cycles were collected and analyzed using microchip electrophoresis with LIF detection for fragment sizing. The results showed that the EDS-CF-PCR format produced results similar to that of a conventional block thermal cycler with leveling effects observed for amplicon generation after approximately 25 cycles. To the best of our knowledge, this is the first report of electrokinetically driven synchronized PCR performed on chip.

Positive and negative regulation of poly(A) nuclease

PAN, a yeast poly(A) nuclease, plays an important nuclear role in the posttranscriptional maturation of mRNA poly(A) tails. The activity of this enzyme is dependent on its Pan2p and Pan3p subunits, as well as the presence of poly(A)-binding protein (Pab1p). We have identified and characterized the associated network of factors controlling the maturation of mRNA poly(A) tails in yeast and defined its relevant protein-protein interactions. Pan3p, a positive regulator of PAN activity, interacts with Pab1p, thus providing substrate specificity for this nuclease. Pab1p also regulates poly(A) tail trimming by interacting with Pbp1p, a factor that appears to negatively regulate PAN. Pan3p and Pbp1p both interact with themselves and with the C terminus of Pab1p. However, the domains required for Pan3p and Pbp1p binding on Pab1p are distinct. Single amino acid changes that disrupt Pan3p interaction with Pab1p have been identified and define a binding pocket in helices 2 and 3 of Pab1p's carboxy terminus. The importance of these amino acids for Pab1p-Pan3p interaction, and poly(A) tail regulation, is underscored by experiments demonstrating that strains harboring substitutions in these residues accumulate mRNAs with long poly(A) tails in vivo.

Identification of factors regulating poly(A) tail synthesis and maturation

Posttranscriptional maturation of the 3' end of eukaryotic pre-mRNAs occurs as a three-step pathway involving site-specific cleavage, polymerization of a poly(A) tail, and trimming of the newly synthesized tail to its mature length. While most of the factors essential for catalyzing these reactions have been identified, those that regulate them remain to be characterized. Previously, we demonstrated that the yeast protein Pbp1p associates with poly(A)-binding protein (Pab1p) and controls the extent of mRNA polyadenylation. To further elucidate the function of Pbp1p, we conducted a two-hybrid screen to identify factors with which it interacts. Five genes encoding putative Pbp1p-interacting proteins were identified, including (i) FIR1/PIP1 and UFD1/PIP3, genes encoding factors previously implicated in mRNA 3'-end processing; (ii) PBP1 itself, confirming directed two-hybrid results and suggesting that Pbp1p can multimerize; (iii) DIG1, encoding a mitogen-activated protein kinase-associated protein; and (iv) PBP4 (YDL053C), a previously uncharacterized gene. In vitro polyadenylation reactions utilizing extracts derived from fir1 Delta and pbp1 Delta cells and from cells lacking the Fir1p interactor, Ref2p, demonstrated that Pbp1p, Fir1p, and Ref2p are all required for the formation of a normal-length poly(A) tail on precleaved CYC1 pre-mRNA. Kinetic analyses of the respective polyadenylation reactions indicated that Pbp1p is a negative regulator of poly(A) nuclease (PAN) activity and that Fir1p and Ref2p are, respectively, a positive regulator and a negative regulator of poly(A) synthesis. We suggest a model in which these three factors and Ufd1p are part of a regulatory complex that exploits Pab1p to link cleavage and polyadenylation factors of CFIA and CFIB (cleavage factors IA and IB) to the polyadenylation factors of CPF (cleavage and polyadenylation factor).

Nonsense-containing mRNAs that accumulate in the absence of a functional nonsense-mediated mRNA decay pathway are destabilized rapidly upon its restitution

Nonsense-mediated mRNA decay (NMD) is a conserved proofreading mechanism that protects eukaryotic cells from the potentially deleterious effects of truncated proteins. Studies of Saccharomyces cerevisiae imply that NMD is a predominantly cytoplasmic decay pathway, while studies of mammalian systems suggest that decay of most substrate mRNAs may occur while they are still associated with the nucleus, possibly during a round of translation that occurs during their export to the cytoplasm. Complete entry of the latter mRNAs into the cytoplasm appears to render them immune to further NMD; i.e., they escape further susceptibility to this decay pathway. To determine if yeast cytoplasmic nonsense-containing mRNAs that evade decay are subsequently immune to NMD, we examined the consequences of placing each of the three UPF/NMD genes under the control of a galactose-inducible promoter. The decay kinetics of ADE2 and PGK1 nonsense-containing mRNAs were then analyzed when expression of UPF1, NMD2, or UPF3 was either repressed or subsequently induced. Results from these experiments demonstrated that activation of NMD caused rapid and immediate degradation of both substrate transcripts, with half-lives of both stable mRNA populations shortened to approximately 7 min. These findings make it unlikely that yeast nonsense-containing mRNAs can escape degradation by NMD and indicate that such mRNAs are available to this decay pathway at each round of translation.

Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing

Dbp2p, a member of the large family of DEAD-box proteins and a yeast homolog of human p68, was shown to interact with Upf1p, an essential component of the nonsense-mediated mRNA decay pathway. Dbp2p:Upf1p interaction occurs within a large conserved region in the middle of Upf1p that is largely distinct from its Nmd2p and Sup35/45p interaction domains. Deletion of DBP2, or point mutations within its highly conserved DEAD-box motifs, increased the abundance of nonsense-containing transcripts, leading us to conclude that Dbp2p also functions in the nonsense-mediated mRNA decay pathway. Dbp2p, like Upf1p, acts before or at decapping, is predominantly cytoplasmic, and associates with polyribosomes. Interestingly, Dbp2p also plays an important role in rRNA processing. In dbp2Delta cells, polyribosome profiles are deficient in free 60S subunits and the mature 25S rRNA is greatly reduced. The ribosome biogenesis phenotype, but not the mRNA decay function, of dbp2Delta cells can be complemented by the human p68 gene. We propose a unifying model in which Dbp2p affects both nonsense-mediated mRNA decay and rRNA processing by altering rRNA structure, allowing specific processing events in one instance and facilitating dissociation of the translation termination complex in the other.

Upf1p, Nmd2p, and Upf3p regulate the decapping and exonucleolytic degradation of both nonsense-containing mRNAs and wild-type mRNAs

In Saccharomyces cerevisiae, rapid degradation of nonsense-containing mRNAs requires the decapping enzyme Dcp1p, the 5'-to-3' exoribonuclease Xrn1p, and the three nonsense-mediated mRNA decay (NMD) factors, Upf1p, Nmd2p, and Upf3p. To identify specific functions for the NMD factors, we analyzed the mRNA decay phenotypes of yeast strains containing deletions of DCP1 or XRN1 and UPF1, NMD2, or UPF3. Our results indicate that Upf1p, Nmd2p, and Upf3p regulate decapping and exonucleolytic degradation of nonsense-containing mRNAs. In addition, we show that these factors also regulate the same processes in the degradation of wild-type mRNAs. The participation of the NMD factors in general mRNA degradation suggests that they may regulate an aspect of translation termination common to all transcripts.

Isolation and identification of male and female DNA on a postcoital condom

BACKGROUND

Identification of male perpetrators of sexual assault may be made from cells and fluids recovered from postcoital condoms. To date, the focus has been on identifying the person who had worn the condom.

OBJECTIVE

To describe a method for scientifically identifying both the male and female participants in a sex act by employing polymerase chain reaction-based technology on swabs taken from the internal and external surfaces of a condom. Fluorescence in situ hybridization may be used to screen for the presence of female cells on a condom.

METHODS

Swabs were taken from the internal and external surfaces of a condom 8 hours postcoitus. DNA was isolated from each swab through standard organic extraction. Extracted DNA was amplified for 8 different genetic loci using the Promega PowerPlex kit and the sex identification amelogenin marker. Amplified samples were electrophoresed on precast sequencing gels and analyzed fluorescently using a Hitachi FMBIO 2 fluorescent scanner and software. Each DNA sample obtained from the condom was compared with male and female buccal controls. At the time of collection, air-dried slides were prepared from the swabs for subsequent multicolor fluorescence in situ hybridization using dual X- and Y-chromosome probes with 4'-6-diamidino-2-phenylindole (DAPI) counterstaining.

RESULTS

A pure sample of female DNA was isolated from the external surface of the condom as determined by exclusive amplification of the X-chromosome-specific 212-base pair amelogenin marker. Swabs taken from the internal surface yielded DNA originating from the male participant. Identification was conclusive at 8 of 8 genetic loci. Fluorescence in situ hybridization identified pure populations of male epithelial cells from the internal surface of the condom and female cells from the external surface.

CONCLUSIONS

Cells shed from a female during sexual intercourse can be retrieved from the external surface of a condom following sexual intercourse. Fluorescence in situ hybridization can be used to screen for the presence of female cells, and positive identification of the female sexual partner can then be made using polymerase chain reaction-based methods. We suggest that swabs taken from both surfaces of a condom used during sexual assault may be used to provide information that will definitively link the victim to the suspect.

Upf1p control of nonsense mRNA translation is regulated by Nmd2p and Upf3p

Upf1p, Nmd2p, and Upf3p regulate the degradation of yeast mRNAs that contain premature translation termination codons. These proteins also appear to regulate the fidelity of termination, allowing translational suppression in their absence. Here, we have devised a novel quantitative assay for translational suppression, based on a nonsense allele of the CAN1 gene (can1-100), and used it to determine the regulatory roles of the UPF/NMD gene products. Deletion of UPF1, NMD2, or UPF3 stabilized the can1-100 transcript and promoted can1-100 nonsense suppression. Changes in mRNA levels were not the basis of suppression, however, since deletion of DCP1 or XRN1 or high-copy-number can1-100 expression in wild-type cells caused an increase in mRNA abundance similar to that obtained in upf/nmd cells but did not result in comparable suppression. can1-100 suppression was highest in cells harboring a deletion of UPF1, and overexpression of UPF1 in cells with individual or multiple upf/nmd mutations lowered the level of nonsense suppression without affecting the abundance of the can1-100 mRNA. Our findings indicate that Nmd2p and Upf3p regulate Upf1p activity and that Upf1p plays a critical role in promoting termination fidelity that is independent of its role in regulating mRNA decay. Consistent with these relationships, Upf1p, Nmd2p, and Upf3p were shown to be present at 1, 600, 160, and 80 molecules per cell, levels that underscored the importance of Upf1p but minimized the likelihood that these proteins were associated with all ribosomes or that they functioned as a stoichiometric complex.

Isolation and identification of female DNA on postcoital penile swabs

After sexual assault, cells originating from the assailant may be recovered from the victim. Through polymerase chain reaction (PCR)-based technology, positive scientific identification of the assailant may be made from these cells. Described is a prospective study describing a method for positively identifying cells from a female sex partner obtained from postcoital swabs of the penis of the male sex partner. Swabs were taken from the penis of a man at 1- to 24-hour intervals after coitus. DNA was isolated from each swab through standard organic extraction methods. The presence of female DNA was detected using the gender-specific amelogenin marker. Extracted DNA was amplified for eight different genetic loci using the Promega PowerPlex kit (Promega) and Amplitaq Gold (Perkin Elmer). Amplified samples were electrophoresed on precast sequencing gels (Hitachi) and were analyzed fluorescently using Hitachi's FMBIO 2 fluorescent scanner and software. Each sample obtained from a penile swab or condom was compared to male and female buccal controls. Female DNA was isolated from all postcoital penile swabs as determined by exclusive amplification of the X-chromosome specific 212 base pair amelogenin marker. In all cases, scientific identification of the female DNA from the swabs was determined by coamplification of eight STR loci (PowerPlex) and was compared to female and male control profiles. Cells shed from a female victim during sexual intercourse can be retrieved from the penis of a male offender after sexual intercourse during a 1- to 24-hour postcoital interval. DNA can be extracted from these cells and can be used to scientifically identify the female sexual participant through PCR-based technology. It is suggested that penile swabs be taken from alleged perpetrators of sexual assaults to associate them with a female victim.

Genetic identification of Candida species in HIV-positive patients using the polymerase chain reaction and restriction fragment length polymorphism analysis of its DNA

The polymerase chain reaction was used to amplify a targeted region: an internal transcribed spacer region of the ribosomal DNA from 114 Candida isolates and 65 reference strains. Unique product sizes were obtained for Candida glabrata, C. guillermondii and C. inconspicua. Isolates of C. albicans, C. tropicalis, C. dubliniensis and C. krusei could be identified following restriction digestion of the PCR products. The methods proved to be both simple and reproducible and may offer potential advantages over phenotyping methods.

Mechanisms of disease and injury: utilization of mutants, monoclonals, and molecular methods

Rapid advances in our ability to localize and quantify macromolecular changes in health and disease are being brought about by the availability of genetically altered animals (mutants), purified reagents such as monoclonal antibodies, and new molecular methods. Targeted gene deletion (knockouts) and gene insertions (transgenics) in animals can allow identification of the importance and function of macromolecules. Monoclonal antibodies and fluorescent labels coupled with advances in microscopy provide exacting and multi-dimensional information about localization and cellular changes in proteins, carbohydrates, and lipids using immunohistochemistry, fluorescent activated cell sorting, and immunoprecipitation. Similarly, new applications of molecular methods can be used to identify and localize nucleic acids in tissues via in situ hybridization, polymerase chain reaction (PCR), reverse transcription (RT) PCR, differential display RT-PCR, RNase protection assays, and microchip arrays. The ligand for CD40 (CD40L), an important immunoregulatory molecule, is an example of the successful application of mutants, monoclonal antibodies, and molecular methods to cloning and biological characterization of new molecules. CD40L knockout mice, monoclonal antibodies, and several molecular methods were used to identify mutations in CD40L as the genetic basis for hyper-IgM syndrome in humans, to provide new insights into the pathobiology of Pneumocystis carinii infection, and to evaluate CD40L for immunotherapy of tumors and opportunistic infections.

Pbp1p, a factor interacting with Saccharomyces cerevisiae poly(A)-binding protein, regulates polyadenylation

The poly(A) tail of an mRNA is believed to influence the initiation of translation, and the rate at which the poly(A) tail is removed is thought to determine how fast an mRNA is degraded. One key factor associated with this 3'-end structure is the poly(A)-binding protein (Pab1p) encoded by the PAB1 gene in Saccharomyces cerevisiae. In an effort to learn more about the functional role of this protein, we used a two-hybrid screen to determine the factor(s) with which it interacts. We identified five genes encoding factors that specifically interact with the carboxy terminus of Pab1p. Of a total of 44 specific clones identified, PBP1 (for Pab1p-binding protein) was isolated 38 times. Of the putative interacting genes examined, PBP1 promoted the highest level of resistance to 3-aminotriazole (>100 mM) in constructs in which HIS3 was used as a reporter. We determined that a fraction of Pbp1p cosediments with polysomes in sucrose gradients and that its distribution is very similar to that of Pab1p. Disruption of PBP1 showed that it is not essential for viability but can suppress the lethality associated with a PAB1 deletion. The suppression of pab1Delta by pbp1Delta appears to be different from that mediated by other pab1 suppressors, since disruption of PBP1 does not alter translation rates, affect accumulation of ribosomal subunits, change mRNA poly(A) tail lengths, or result in a defect in mRNA decay. Rather, Pbp1p appears to function in the nucleus to promote proper polyadenylation. In the absence of Pbp1p, 3' termini of pre-mRNAs are properly cleaved but lack full-length poly(A) tails. These effects suggest that Pbp1p may act to repress the ability of Pab1p to negatively regulate polyadenylation.

Molecular genetics as a diagnostic tool in farm animals

In this review, the importance of molecular genetics for diagnostic applications in animal production and breeding is underlined. Recently, several new techniques and methods based on gene technology have been developed, such as the polymerase chain reaction, fluorescence in situ hybridization, and the use of microsatellite polymorphism. The examples include detection of favourable alleles of genes coding for milk proteins, recognition of negative recessive alleles in hereditary syndromes, the use of microsatellite variants for breeding purposes and parentage control, and application of specific DNA-probes for identification of Y-chromosome-bearing spermatozoa and the sex of embryos. It is to be understood that this list is not complete and more applications will undoubtedly show up in the future. For this review, the authors have mainly selected areas where they themselves or their co-workers have gained experience.

Pep7p provides a novel protein that functions in vesicle-mediated transport between the yeast Golgi and endosome

Saccharomyces cerevisiae pep7 mutants are defective in transport of soluble vacuolar hydrolases to the lysosome-like vacuole. PEP7 is a nonessential gene that encodes a hydrophilic protein of 515 amino acids. A cysteine-rich tripartite motif in the N-terminal half of the polypeptide shows striking similarity to sequences found in many other eukaryotic proteins. Several of these proteins are thought to function in the vacuolar/lysosomal pathway. Mutations that change highly conserved cysteine residues in this motif lead to a loss of Pep7p function. Kinetic studies demonstrate that Pep7p function is required for the transport of the Golgi-precursors of the soluble hydrolases carboxypeptidase Y, proteinase A, and proteinase B to the endosome. Integral membrane hydrolase alkaline phosphatase is transported to the vacuole by a parallel intracellular pathway that does not require Pep7p function. pep7 mutants accumulate a 40-60-nm vesicle population, suggesting that Pep7p functions in a vesicle consumption step in vesicle-mediated transport of soluble hydrolases to the endosome. Whereas pep7 mutants demonstrate no defects in endocytic uptake at the plasma membrane, the mutants demonstrate defects in transport of receptor-mediated macromolecules through the endocytic pathway. Localization studies indicate that Pep7p is found both as a soluble cytoplasmic protein and associated with particulate fractions. We conclude that Pep7p functions as a novel regulator of vesicle docking and/or fusion at the endosome.

Upf1p, Nmd2p, and Upf3p are interacting components of the yeast nonsense-mediated mRNA decay pathway

Rapid turnover of nonsense-containing mRNAs in Saccharomyces cerevisiae is dependent on Upf1p, Nmd2p, and Upf3p, the products of the UPF1, NMD2/UPF2, and UPF3 genes, respectively. We showed previously that Upf1p and Nmd2p interact and that this interaction is required for nonsense-mediated mRNA decay (F. He and A. Jacobson, Genes Dev. 9:437-454, 1995; F. He, A. H. Brown, and A. Jacobson, RNA 2:153-170, 1996). In this study we have used the yeast two-hybrid system to define other protein-protein interactions among the essential components of this decay pathway. Nmd2p-Upf3p and Upf1p-Upf3p interactions were identified, and the respective domains involved in these interactions were delineated by deletion analysis. The domains of Upf1p and Upf3p putatively involved in their mutual interaction were found to correspond to the domains on the two proteins which interact with Nmd2p, suggesting that Nmd2p bridges Upf1p and Upf3p. This conclusion was reinforced by experiments showing that: (i) deletion of NMD2 completely abolishes interactions between Upf1p and Upf3p and (ii) overexpression of full-length Nmd2p or Nmd2p fragments that retain Upf1p- and Upf3p-interacting domains promotes 10- to 200-fold enhancement of Upf1p-Nmd2p-Upf3p complex formation. These results; the observation that cells harboring either single or multiple deletions of UPF1, NMD2, and UPF3 inhibit nonsense-mediated mRNA decay to the same extent; and an analysis of the possible targets of a dominant-negative NMD2 allele indicate that Upf1p, Nmd2p, Upf3p, and at least one other factor are functionally dependent, interacting components of the yeast nonsense-mediated mRNA decay pathway.

The future of PCR technology: diversification of technologies and applications

The polymerase chain reaction has had a major impact on research in molecular biology, on the human genome project and on the diagnosis of disease. In the future, this powerful technique will be increasingly applied to the study of individual genomic variation and to assess the genetic consequences of ecological and demographic events on past and contemporary populations of many organisms.

Detection of Candida albicans DNA with a yeast-specific primer system by polymerase chain reaction

The in vitro and in vivo selectivity and sensitivity of a yeast-specific primer system was investigated. A two-step polymerase chain reaction (PCR) was used: the first amplified a 245-bp fragment of the gene for cytochrome P450L1A1 and the second a product of 193 bp. This nested PCR produced an approximately 1000-fold increase in the sensitivity of the test for Candida albicans DNA compared with the first primer pair. The lower level of sensitivity of the test in physiological saline and tissue homogenate was about 10 C. albicans cells ml-1. On the other hand, the sensitivity of the nested PCR method was reduced by a factor of more than 1000 when C. albicans was fixed with 4% formalin. After i.v. injection of different doses of C. albicans into mice, the yeast could be demonstrated in blood and in six different organs. The nested PCR was to some extent more sensitive than culturing for the detection of the yeast in the specimens of organs such as lung, cardiac muscle, liver, kidneys and brain. In contrast, in blood and spleen the culture was superior to the PCR technique used. Nested PCR is thus a useful additional method for the demonstration of yeasts.

Laboratory probing of oncogenes from human liquid and solid specimens as markers of exposure to toxicants

Recent discoveries regarding the mechanistic role of oncogenes and tumor suppressor genes in cancer development have opened a new era of molecular diagnosis. It has been observed repeatedly that genetic lesions serve as tumor markers in a broad variety of human cancers. The ras gene family, consisting of three related genes, H-ras, K-ras, and N-ras, acquires transforming activity through amplification or mutation in many tissues. If not all, then most types of human malignancies have been found to contain an altered ras gene. Because the ras oncogenes actively participate in both early and intermediate stages of cancer, several highly specific and sensitive approaches have been introduced to detect these genetic alterations as biomarkers of exposure to carcinogens. There is also mounting evidence that implicate chemical-specific alterations of the p53 tumor suppressor gene detected in most human tumors. Therefore, it seems a reliable laboratory approach to identify both altered p53 and ras genes as biomarkers of human chronic or intermittent exposure to toxicants in a variety of occupational settings.

Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen

Rapid turnover of nonsense-containing mRNAs in yeast in dependent on the product of the UPF1 gene (Upf1p). Mutations in UPF1 lead to the selective stabilization of mRNAs containing early nonsense mutations without affecting the decay rates of most other mRNAs. To identify other integral components of this decay pathway, we have employed a two-hybrid screen, seeking those cellular factors that specifically interact with Upf1p. Screening of yeast genomic libraries identified six genes encoding potential Upf1p-interacting proteins. These include four previously uncharacterized genes, NMD1-4 (nonsense-mediated mRNA decay), DBP2, a gene encoding a putative RNA helicase with homology to mammalian p68 RNA helicase, and SNP1, a gene encoding a U1 snRNP 70-kD protein homolog. In this paper we report the identification and characterization of NMD2, a yeast gene that encodes a specific Upf1p-interacting protein. Disruption of NMD2 yields a nonsense-mediated mRNA decay phenotype identical to that obtained in UPF1-deletion strains, indicating that the NMD2 gene product (Nmd2p) is a new factor in the nonsense-mediated mRNA decay pathway. Deletion analysis demonstrated that the acidic carboxyl terminus of Nmd2p constituted the Upf1p-interacting domain. High-level expression of a fragment of Nmd2p containing this domain had a dominant-negative effect on nonsense-mediated mRNA decay when the protein was localized the cytoplasm but not when it was localized to the nucleus, indicating that this decay pathway has a cytoplasmic component. The association of a dominant-negative phenotype with a gene fragment identified in a two-hybrid screen suggests a generalized approach to confirming the function of genes identified in such screens.

The polymerase chain reaction and branching processes

We construct a mathematical model for the polymerase chain reaction and its mutations using the theory of branching processes. Under this model we study the number of mutations in a randomly chosen sequence after n PCR cycles. A method for estimating the mutation is proposed and the variance of this estimator is studied. We also study the distribution of the Hamming distance between two randomly chosen sequences and a method for estimating the mutation rate based on pairwise differences is proposed.