Sensitive and rapid diagnosis of human parvovirus B19 infection by loop-mediated isothermal amplification

BACKGROUND

Human parvovirus B19 (B19) infections exhibit various skin manifestations that are similar to and hence hard to distinguish from many other skin diseases. The virological diagnosis of B19 infection is usually based on time-consuming serological tests and polymerase chain reaction (PCR).

OBJECTIVES

In this study, a DNA amplification method, loop-mediated isothermal amplification (LAMP), was used for the diagnosis of B19 infection and was compared with PCR.

METHODS

Ten patients with acute B19 infection and 16 patients with other skin diseases were enrolled. Sera and pharyngeal swabs were used directly as the templates in LAMP. The LAMP reaction was carried out at 63 degrees C for 1 h in a heat block. The reaction products were judged visually, by adding SYBR Green I into the tubes, and by gel electrophoresis.

RESULTS

B19 DNA was detected by LAMP in 10 sera and all of seven tested pharyngeal swabs of 10 patients with acute B19 infection but not in samples from 16 patients with other skin diseases. The results were in agreement with those obtained by PCR except for one case. The reason for the single discrepancy may be that the sensitivity of LAMP is 10(2) times higher than PCR.

CONCLUSIONS

Detection of B19 DNA by LAMP in serum and especially in the pharynx is a rapid and convenient method for the diagnosis of acute B19 infection.

Acceptability of self-taken vaginal swabs and first-catch urine samples for the diagnosis of urogenital Chlamydia trachomatis and Neisseria gonorrhoeae with an amplified DNA assay in young women attending a public health sexually transmitted disease clinic

OBJECTIVES

Public health efforts are needed to encourage young women to get tested for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC).

GOAL

To assess the acceptability and feasibility of 2 noninvasive diagnostic approaches.

STUDY DESIGN

Participants of this cross-sectional survey were 413 young women (age 16-35) who underwent STD testing by self-taken vaginal swab (SVS) and a first-catch urine sample (FCU) by nucleic acid amplification test (BDProbTec) and filled out a questionnaire.

RESULTS

CT and GC were diagnosed in 10.9% (45/413) and 1.5% (6/413). Eleven percent of the participants who never previously had an STD examination (68%) tested STD positive. SVS and FCU were almost uniformly reported as easy to perform and preferred above gynecologic examination.

CONCLUSIONS

Using SVS combined with FCU can be an important enhancing tool in public health approaches. Acceptability among potential patients is high, enabling the noninvasive detection of STDs that would otherwise remain undetected and untreated.

Genome wide cDNA-AFLP analysis of genes rapidly induced by combined sucrose and ABA treatment in rice cultured cells

We identified 27 genes induced by combined sucrose and ABA treatment from rice cultured cells with cDNA-AFLP. Thirteen of these up-regulated genes were induced 30 min after the co-treatment. This suite of genes includes starch biosynthesis related genes. Type A genes were expressed only in the presence of both sucrose and ABA. Type B genes were expressed in the presence of sucrose or ABA and the expression was dramatically enhanced by the co-treatment of sucrose and ABA. These results indicate that multiple steps of starch biosynthesis and other processes may be regulated by at least two different pathways.

Evolution of teleostean hatching enzyme genes and their paralogous genes

We isolated genes for hatching enzymes and their paralogs having two cysteine residues at their N-terminal regions in addition to four cysteines conserved in all the astacin family proteases. Genes for such six-cysteine-containing astacin proteases (C6AST) were searched out in the medaka genome database. Five genes for MC6AST1 to 5 were found in addition to embryo-specific hatching enzyme genes. RT-PCR and whole-mount in situ hybridization evidenced that MC6AST1 was expressed in embryos and epidermis of almost all adult tissues examined, while MC6AST2 and 3 were in mesenterium, intestine, and testis. MC6AST4 and 5 were specifically expressed in jaw. In addition, we cloned C6AST cDNA homologs from zebrafish, ayu, and fugu. The MC6AST1 to 5 genes were classified into three groups in the phylogenetic positions, and the expression patterns and hatching enzymes were clearly discriminated from other C6ASTs. Analysis of the exon-intron structures clarified that genes for hatching enzymes MHCE and MAHCE were intron-less, while other MC6AST genes were basically the same as the gene for another hatching enzyme MLCE. In the basal Teleost, the C6AST genes having the ancestral exon-intron structure (nine exon/eight intron structure) first appeared by duplication and chromosomal translocation. Thereafter, maintaining such ancestral exon-intron structure, the LCE gene was newly diversified in Euteleostei, and the MC6AST1 to 5 gene orthologs were duplicated and diversified independently in respective fish lineages. The HCE gene lost all introns in Euteleostei, whereas in the lineage to zebrafish, it was translocated from chromosome to chromosome and lost some of its introns.

Detection of EGFR mutations in archived cytologic specimens of non-small cell lung cancer using high-resolution melting analysis

Mutations of the epidermal growth factor receptor (EGFR), particularly deletional mutations (DEL) in exon 19 and L858R in exon 21, are reportedly correlated with clinical outcome in patients with non-small cell lung cancer (NSCLC) receiving the EGFR tyrosine kinase inhibitors gefitinib and erlotinib, suggesting that detection of EGFR mutations would have an important role in clinical decision making. We established and validated an easy, inexpensive, and rapid method for detecting DEL and L858R from cytologic material by high-resolution melting analysis (HRMA). Dilution for sensitivity studies revealed that DEL and L858R were detectable in the presence of at least 10% and 0.1% EGFR-mutant cells, respectively. We analyzed 37 archived cytological slides of specimens from 29 patients with advanced NSCLC and compared the results with direct sequencing data obtained previously. Of 37 samples, 34 (92%) yielded consistent results with direct sequencing, 2 were false negative, and 1 was indeterminate. The sensitivity of this analysis was 90% (19/21) and specificity, 100% (15/15). These results suggest that HRMA of archived cytologic specimens of advanced NSCLC is useful for detecting EGFR mutations in clinical practice.

AFLP fingerprinting for the analysis of genetic diversity within Necator americanus

In the present study, we utilised the method of AFLP to screen for genetic variation within and among individuals of the blood-feeding human hookworm Necator americanus (Nematoda) from Africa, Asia and South America. A total of 45 adult worms (i.e. 20 from Ghana, 16 from Colombia and 9 from Nepal) were subjected to analysis using the restriction enzyme/primer combination HindIII+AG/BglII+AC. Cluster analysis divided N. americanus into multiple, genetically distinct groups, consistent with previous findings using ribosomal and mitochondrial DNA data sets. The results demonstrated the usefulness of AFLP fingerprinting for establishing genetic variation within N. americanus and reinforce its applicability to other parasitic helminths of human and/or veterinary health importance.

Sequence homology of polymorphic AFLP markers in garlic (Allium sativum L.)

Linkage mapping and genetic diversity studies with DNA markers in plant species assume that comigrating bands are identical, or at least that they have homologous sequences. To test this assumption in a plant with a large genome, sequence identities of 7 polymorphic amplified fragment length polymorphism (AFLP) markers of garlic, previously used to estimate similarity in genetic diversity studies, were characterized. Among 37 diverse garlic clones, 87 bands from these 7 polymorphisms were excised, amplicons were cloned, and 2 to 6 colonies were sequenced from each band, to yield a total of 191 DNA amplicons. Of these 87 bands, 83 bands (95.4%) contained AFLP amplicons that were identical or highly homologous to the typical marker of that band; only 4 bands contained amplicons with little homology to the same-sized amplicons of other garlic clones. Of these 83 bands, 64 (73.6%) contained only highly homologous amplicons (>90% sequence identity), whereas 19 (21.8%) contained both homologous and nonhomologous amplicons, with sequence identities less than 60%. Of the 37 nonhomologous amplicons identified, 25 (67.5%) differed in length from other amplicons in the band. Sequence conservation of AFLP amplicons followed patterns similar to phylogenetic relationships among garlic clones, making them useful for developing simple PCR-based markers in genetic mapping and diversity assessment.

[The demonstration of tuberculosis using molecular genetic methods polymerase chain reaction (PCR) and Amplified Mycobacterium tuberculosis direct (AMTD) test]

INTRODUCTION

Tuberculosis is a communicable disease, in most instances with a chronic course. The aetiological agent is Mycobacterium tuberculosis. Its demonstration is based on microscopic investigations and cultures. Microscopy is not sufficiently sensitive, while cultures are lengthy. One of the possibilities of speeding up diagnosis are molecular genetic methods.

PURPOSE OF THE STUDY

To compare the demonstration of mycobacteria using molecular genetic methods with the results of cultures.

METHODS

We used two methods to demonstrate the nucleic acid complex of Mycobacterium tuberculosis-the polymerase chain reaction (PCR) and the Amplified Mycobacterium tuberculosis direct test (AMTD). We investigated 647 samples. Out of these, 275 samples were tested with PCR and 372 were investigated with a AMTD set. At the same time we started for each sample a parallel culture.

RESULTS

In 275 samples, out of a total of 647, which were analysed with PCR, mycobacterial DNA was demonstrated in 18 (6.5 %). Out of the 372 samples investigated with AMTD, mycobacterial RNA was demonstrated in 27 (7 %). Out of the 18 PRC positive samples, 6 (13 %) did not yield a positive mycobacterial culture. Out of the 27 positive results RNA with the AMTD method 17 did not yield positive cultures. On the other hand, a diagnosis of tuberculosis verified by cultures without a positive PCR was found in 2 patients (0.7 %). Disagreement between the results of AMTD and cultures was also found in 2 samples (0.5 %).

CONCLUSIONS

Molecular genetic methods substantially speed up the diagnosis of tuberculosis. These methods are particularly important in cases of paucibacillary material and of unique and unrepeatable samples (tissues biopsies, nodes, cerebrospinal fluid). Given the possibility of false positive results, parallel verification by microscopy and cultures is essential.

PCR-based identification of Burkholderia pseudomallei

DNA amplification techniques are being used increasingly in clinical laboratories to confirm the identity of medically important bacteria. A PCR-based identification method has been in use in our centre for 10 years for Burkholderia pseudomallei and was used to confirm the identity of bacteria isolated from cases of melioidosis in Ceará since 2003. This particular method has been used as a reference standard for less discriminatory methods. In this study we evaluated three PCR-based methods of B. pseudomallei identification and used DNA sequencing to resolve discrepancies between PCR-based results and phenotypic identification methods. The established semi-nested PCR protocol for B. pseudomallei 16-23s spacer region produced a consistent negative result for one of our 100 test isolates (BCC #99), but correctly identified all 71 other B. pseudomallei isolates tested. Anomalous sequence variation was detected at the inner, reverse primer binding site for this method. PCR methods were developed for detection of two other B. pseudomallei bacterial metabolic genes. The conventional lpxO PCR protocol had a sensitivity of 0.89 and a specificity of 1.00, while a real-time lpxO protocol performed even better with sensitivity and specificity of 1.00, and 1.00. This method identified all B. pseudomallei isolates including the PCR-negative discrepant isolate. The phaC PCR protocol detected the gene in all B. pseudomallei and all but three B. cepacia isolates, making this method unsuitable for PCR-based identification of B. pseudomallei. This experience with PCR-based B. pseudomallei identification methods indicates that single PCR targets should be used with caution for identification of these bacteria, and need to be interpreted alongside phenotypic and alternative molecular methods such as gene sequencing.

Increased GABAA-Receptor ?1-Subunit Expression in Hippocampal Dentate Gyrus after Early-life Status Epilepticus

PURPOSE

Previous studies in neonatal (postnatal day 10) and adult rats suggest that status epilepticus (SE) induces changes in the alpha1 subunit of the GABA(A) receptor (GABRA1) in dentate granule neurons (DGNs) that are age dependent and vary inversely with the likelihood of epilepsy development. In the present study, we examined GABRA1 expression after SE at postnatal day 20 (P20), an intermediate age when only a subset of SE-exposed animals develop epilepsy.

METHODS

SE was induced with lithium-pilocarpine or kainate at P20. Animals were video-EEG monitored after SE to determine the presence or absence of spontaneous seizures. GABRA1 mRNA and protein levels were determined 7 days or 3 months later in SE-exposed and control animals by using a combination of aRNA amplification, Western blotting, and immunohistochemistry techniques.

RESULTS

GABRA1 mRNA levels in DGNs of SE-exposed rats that did not become epileptic were higher than those in control rats, but were not different from DGNs in epileptic SE-exposed rats. GABRA1 protein levels in dentate gyrus were significantly increased in both epileptic and nonepileptic SE-exposed rats compared with controls. GABRA1 mRNA changes were region specific and did not occur in CA1 or CA3 areas of hippocampus. GABRA1 alterations were present by 1 week after P20 SE and were similar whether pilocarpine or kainate was used to induced SE.

CONCLUSIONS

P20 SE results in persistent increases in GABRA1 levels selectively in dentate gyrus. These changes preceded the onset of epilepsy, were not model specific, and occurred in both epileptic and nonepileptic animals.

Association of core promoter mutations with viral breakthrough in chronic hepatitis B patients on long-term lamivudine therapy

BACKGROUND AND AIM

Virologic breakthrough (VBTH) during long-term lamivudine therapy is believed to be due to the emergence of rtYM204I/VDD mutants. We observed VBTH in 17 of 67 patients receiving long-term lamivudine therapy. The YMDD mutant at the onset of VBTH and/or subsequently was seen in eight (47%) of 17 such patients. We investigated other potential loci in the viral genome contributing to VBTH.

METHODS

Chronic hepatitis B (CHB) patients (n=17) on long-term (>or=12 months) lamivudine therapy who had at least one episode of VBTH were selected (group I). Age, sex, serology and baseline viral load matched patients on long-term lamivudine without VBTH (n=12) served as controls (group II). Hepatitis B virus (HBV) DNA sequences were analyzed for pre-S, surface, polymerase, core promoter, precore and core regions and were compared with sequences of respective genotypes.

RESULTS

Group I patients with VBTH (n=17) either had rtYM204I/VDD mutations (n=8, group Ia YMDD) or no rtYM204I/VDD mutations (n=9, group Ib non-YMDD). Group Ia patients had median baseline HBV DNA of 2794 pg/mL (range 3-9166 pg/mL) and a mean alanine aminotransferase (ALT) level of 86+/-33 IU/L. In group Ib, the median baseline viral DNA was 916 pg/mL (range 8.3-5787 pg/mL) and the mean ALT was 61+/-38 IU/L. The first VBTH in group Ia and Ib patients was noted at 21+/-9 months and 15.2+/-5.9 months, respectively, with a rise in HBV DNA levels from undetectable limits to 952 pg/mL (range 4.3-4875 pg/mL) and 571 pg/mL (range 1.2-1970 pg/mL), respectively. Core promoter mutations were seen in five of eight (62.5%) and in six of nine (66.6%); classic double mutations (A1762T/G1764A) of core promoter region were detected in two and three patients and novel double mutations of core promoter (G1764T/C1766G) in one patient each of group Ia and Ib patients, respectively. Compared to 11 (68%) of 17 group I patients, only three (25%) of 12 patients in group II had core promoter mutations (P<0.05). No patient in group II had double mutations of the core promoter region. No significant difference in viral mutations was seen in any other region of the viral genome between group I and group II patients. In group I, none of the 15 patients (two died of hepatocellular carcinoma), but five (42%) group II patients achieved hepatitis B e antigen (HBeAg) seroconversion and sustained response by month 24 (P<0.05).

CONCLUSION

Both core promoter and YMDD motif mutation(s) are associated with VBTH in patients on long-term lamivudine therapy. Whether or not these promoter mutations in the absence of YMDD mutations confer drug resistance needs to be studied in an in vitro cell culture system, as they could create novel and stronger binding sites for hepatocyte nuclear factors.

Nonconventional and new methods in the diagnosis of tuberculosis: feasibility and applicability in the field

Tuberculosis (TB) remains one of the major causes of death from a single infectious agent worldwide. Of great concern for TB control is the emergence of drug resistance. Since there is no cure for some multidrug-resistant strains of Mycobacterium tuberculosis, there is concern that they may spread around the world, stressing the need for additional control measures, such as new diagnostics, better drugs for treatment, and a more effective vaccine. Pulmonary TB can be diagnosed by its symptoms, chest radiography, sputum smear microscopy and by cultivation of M. tuberculosis, which is considered as the gold standard. Recent advances in molecular biology and molecular epidemiology, and a better understanding of the molecular basis of drug resistance in TB, have provided new tools for rapid diagnosis; however, the high cost of most of these techniques, and their requirement for sophisticated equipment and skilled personnel have precluded their implementation on a routine basis, especially in low-income countries. Other nonconventional diagnostic approaches proposed include the search for biochemical markers, detection of immunological response and early detection of M. tuberculosis by methods other than colony counting. In the present article, some of these approaches will be reviewed and the feasibility for their implementation in diagnostic laboratories will be discussed.

Comparative analysis of a 3' end tag PCR and a linear RNA amplification approach for microarray analysis

BACKGROUND

Various types of amplification techniques have been developed in order to enable microarray gene expression analysis when the amount of starting material is limited. The two main strategies are linear amplification, using in vitro transcription, and exponential amplification, based on PCR. We have evaluated the performance of a linear and an in-house developed exponential amplification protocol that relies on 3' end tag sequences. We used 100 ng total RNA as starting material for amplification and compared the results with data from hybridizations with unamplified mRNA and total RNA.

RESULTS

Preservation of expression ratios after amplification was examined comparing log(2) ratios obtained with amplification protocols to those obtained with standard labelling of mRNA. The Pearson correlations were 0.61 and 0.84, respectively, for the two linear amplification replicates and 0.76 and 0.80 for the two exponential amplification replicates. The correlations between repeated amplifications was 0.82 with the exponential method and 0.63 with the linear, indicating a better reproducibility with the PCR-based approach.

CONCLUSION

Both amplification methods generated results in agreement with unamplified material. In this study, the PCR-based method was more reproducible than in vitro transcription amplification. Advantages with the in-house developed method are the lower cost since it is non-commercial and that the PCR generated product offers compatibility with both sense and antisense arrays.

Mutation analysis of the FBN1 gene in patients with Marfan syndrome

Marfan syndrome is an autosomal-dominant connective tissue disorder characterized by pleiotropic manifestations involving the skeletal, ocular, and cardiovascular systems and resulting from mutations in the gene for fibrillin, FBN1. The clinical diagnosis is based on a set of well-defined clinical criteria (Ghent nosology). Nevertheless, the age-related nature of some clinical manifestations and the variable phenotypic expression of the disorder may hamper the diagnosis. In those instances, molecular analysis of the FBN1 gene is helpful to identify at-risk individuals. Mutations are spread over the entire FBNJ gene and there are no particular hot spots. Different standard methodologies are available to identify these mutations, however, one of the most sensitive techniques is denaturing high-performance liquid chromatography. This approach allows the performance of the analysis in a semi-automated manner and has a mutation detection rate of approx 95%.

Development of a magnetic capture hybridization-PCR assay for Listeria monocytogenes direct detection in milk samples

AIMS

A rapid and sensitive method for Listeria monocytogenes direct detection from milk was developed. It is based on a magnetic capture hybridization procedure for selective DNA purification, followed by PCR identification. A comparison with two similar commercial systems from Dynal (Dynabeads) was carried out.

METHODS AND RESULTS

The technique used previously developed nanoparticles modified with a 21-mer oligonucleotide. This sequence, sharing homology with all the L. monocytogenes strains, was selected on hlyA gene and located outside the desired specific PCR site to avoid cross-contaminations. Capture probe properties, in term of spacer length and purification, were determined to obtain the highest hybridization efficiency. Its specificity was tested in hybridization experiments with nontarget bacterial species. Any inhibitory effect of the nanoparticles on PCR was also examined. The amplification performed with the purified DNA could reliably identify a 10 CFU ml(-1) contamination rate.

CONCLUSIONS

The optimized purification method showed a high specificity and sensitivity, with a detection level one log more sensitive than PCR carried out with nucleic acids obtained using commercial nanoparticles.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method, avoiding pre-enrichment, provides a rapid alternative to conventional microbiological detection methods. Furthermore, it is suitable for automation and can be proposed for the screening of a large number of samples.

Screening of genetic and expression alterations of SRC1 gene in prostate cancer

BACKGROUND

Genetic alterations of the SRC1 gene have not been thoroughly studied in prostate cancer.

MATERIALS AND METHODS

Five prostate cancer cell lines and 32 xenografts were screened for mutations and gene copy number alterations. Subsequently, frequencies of detected sequence variations were further analyzed in 44 clinical prostate cancers, 6 benign prostate hyperplasias, and 48 normal controls. Finally, the protein expression of SRC1 in 254 clinical prostate tumors was investigated.

RESULTS

Three non-recurrent sequence variations, and one single nucleotide polymorphism in the coding region of SRC1, as well as one case of SRC1 gene amplification were found. The protein expression of SRC1 was higher in androgen ablation resistant than untreated prostate carcinomas, but the difference was not statistically significant (P = 0.0796).

CONCLUSIONS

Genetic alterations of SRC1 are rare in prostate cancer. The nuclear protein accumulation of SRC1 seems to be mildly increased in androgen ablation resistant prostate cancers. .

The large isoform of Drosophila melanogaster heterochromatin protein 2 plays a critical role in gene silencing and chromosome structure

Drosophila melanogaster heterochromatin protein 2 (HP2) interacts with heterochromatin protein 1 (HP1). In polytene chromosomes, HP2 and HP1 colocalize at the chromocenter, telomeres, and the small fourth chromosome. We show here that HP2 is present in the arms as well as the centromeric regions of mitotic chromosomes. We also demonstrate that Su(var)2-HP2 exhibits a dosage-dependent modification of variegation of a yellow reporter transgene, indicating a structural role in heterochromatin formation. We have isolated and characterized 14 new mutations in the Su(var)2-HP2 gene. Using wm4h, many (but not all) mutant alleles show dominant Su(var) activity. Su(var)2-HP2 mutant larvae show a wide variety of mitotic abnormalities, but not the telomere fusion seen in larvae deficient for HP1. The Su(var)2-HP2 gene codes for two isoforms: HP2-L (approximately 365 kDa) and HP2-S (approximately 175 kDa), lacking exons 5 and 6. In general, mutations that affect only the larger isoform result in more pronounced defects than do mutations common to both isoforms. This suggests that an imbalance between large and small isoforms is particularly deleterious. These results indicate a role for HP2 in the structural organization of chromosomes and in heterochromatin-induced gene silencing and show that the larger isoform plays a critical role in these processes.

Matching the origin of an invasive weed for selection of a herbivore haplotype for a biological control programme

The Florida Everglades have been invaded by an exotic weed fern, Lygodium microphyllum. Across its native distribution in the Old World tropics from Africa to Australasia it was found to have multiple location-specific haplotypes. Within this distribution, the climbing fern is attacked by a phytophagous mite, Floracarus perrepae, also with multiple haplotypes. The genetic relationship between mite and fern haplotypes was matched by an overarching geographical relationship between the two. Further, mites that occur in the same location as a particular fern haplotype were better able to utilize the fern than mites from more distant locations. From a biological control context, we are able to show that the weed fern in the Everglades most likely originated in northern Queensland, Australia/Papua New Guinea and that the mite from northern Queensland offers the greatest prospect for control.

Selective acquisition of novel mating type and vegetative incompatibility genes via interspecies gene transfer in the globally invading eukaryote Ophiostoma novo-ulmi

The Dutch elm disease fungus Ophiostoma novo-ulmi, which has destroyed billions of elm trees worldwide, originally invaded Europe as a series of clonal populations with a single mating type (MAT-2) and a single vegetative incompatibility (vic) type. The populations then rapidly became diverse with the appearance of the MAT-1 type and many vegetative incompatibility types. Here, we have investigated the mechanism using isolates from sites in Portugal at which the rapid evolution of O. novo-ulmi populations from clonality to heterogeneity was well established. We show by genetic mapping of vic and MAT loci with AFLP markers and by sequence analysis of MAT loci that this diversification was due to selective acquisition by O. novo-ulmi of the MAT-1 and vic loci from another species, Ophiostoma ulmi. A global survey showed that interspecies transfer of the MAT-1 locus occurred on many occasions as O. novo-ulmi spread across the world. We discuss the possibility that fixation of the MAT-1 and vic loci occurred in response to spread of deleterious viruses in the originally clonal populations. The process demonstrates the potential of interspecies gene transfer for facilitating rapid adaptation of invasive organisms to a new environment.

Hybrid origin and differentiation of two tetraploid Achillea species in East Asia: molecular, morphological and ecogeographical evidence

Achillea (Asteraceae-Anthemideae) offers classical models for speciation by hybridization and polyploidy. Here, we test the suspected allotetraploid origin of two species, Achillea alpina and Achillea wilsoniana between phylogenetically distinct lineages in East Asia. A total of 421 AFLP bands from 169 individuals and 19 populations of five 2x- and two 4x-species were obtained. The data set was analysed with a newly developed model that accounts for polyploidy and assumes lack of recombination between the parental chromosome sets (i.e. disomic inheritance). A. alpina and A. wilsoniana then appear to be allotetraploids between Achillea acuminata-2x (sect. Ptarmica) and Achillea asiatica-2x (sect. Achillea). The two 4x-species share 44% and 48% of their AFLP bands with A. acuminata-2x, and 39% and 38% with A. asiatica-2x, respectively. Eight plastid haplotypes (A-H) were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analyses. A. alpina-4x and A. wilsoniana-4x share haplotype F only with A. asiatica-2x. This is consistent with the hybrid origin(s) involving the latter as the maternal ancestor. This result corroborates our previous DNA sequence data, where A. alpina-4x and A. wilsoniana-4x are also placed close to A. asiatica-2x. Morphology, ecology, and amplified fragment length polymorphism (AFLP) profiles of the two 2x-species are distinct, whereas the two 4x-species, grouped as A. alpina aggregate, form a nearly continuous link between them. Considering all evidence, this 4x-aggregate is regarded as the product of a hybridization between genetically distant 2x-ancestors limited to China and adjacent areas: one A. acuminata-like, and the other A. asiatica-like. The allopolyploid A. alpina agg. exhibits considerable morphological variation and ecological flexibility, and has expanded throughout eastern Asia and to northern North America, far beyond the ranges of their presumed 2x-ancestors.

Detection and sequence-based typing of human adenoviruses using sensitive universal primer sets for the hexon gene

The universal primer sets for identification of human adenovirus (HAdV) targeting hexon gene were designed and applied to 121 clinical samples suspected of HAdV infection. The primer sets amplified at least 20 HAdV reference strains of six species. Of these clinical samples, 81 (66.9%) samples were positive for HAdV. They were classified into 11 serotypes belonging to 5 HAdV species (B-F). The primer sets described here are sensitive and reactive to the broad spectrum of HAdV and are useful for rapid diagnosis of various HAdV infections.

Proof of principle and first cases using preimplantation genetic haplotyping--a paradigm shift for embryo diagnosis

Preimplantation genetic haplotyping (PGH) proof-of-principle was demonstrated by multiple displacement amplification (MDA) of single buccal cells from a female donor and genotyping using 12 polymorphic markers within the dystrophin gene; the known paternal genotype enabled identification of the paternal haplotype in the MDA products despite 27% allele dropout. MDA amplified DNA from 49 single human blastomeres with 100% success. The MDA products were genotyped using a total of 57 polymorphic markers for chromosomes 1, 7, 13, 18, 21, X and Y; 72% of alleles amplified providing results at 90% of the loci tested. A PGH cycle was carried out for Duchenne muscular dystrophy. One embryo was biopsied: PGH showed a non-carrier female, which was transferred with no resulting pregnancy. A PGH cycle was carried out for cystic fibrosis. Seven embryos were biopsied and PGH allowed the exclusion of 2 affected embryos; a carrier and a non-carrier embryo were transferred resulting in an on-going twin pregnancy. PGH represents a paradigm shift in embryo diagnosis, as one panel of markers can be used for all carriers of the same monogenic disease, bypassing the need for development of mutation-specific tests, and widening the scope and availability of preimplantation genetic testing.

Nuclear myosin is ubiquitously expressed and evolutionary conserved in vertebrates

Nuclear myosin I (NMI) is a single-headed member of myosin superfamily localized in the cell nucleus which participates along with nuclear actin in transcription and chromatin remodeling. We demonstrate that NMI is present in cell nuclei of all mouse tissues examined except for cells in terminal stages of spermiogenesis. Quantitative PCR and western blots demonstrate that the expression of NMI in tissues varies with the highest levels in the lungs. The expression of NMI is lower in serum-starved cells and it increases after serum stimulation. The lifespan of NMI is longer than 16 h as determined by cycloheximide translation block. A homologous protein is expressed in human, chicken, Xenopus, and zebrafish as shown by RACE analysis. The analysis of genomic sequences indicates that almost identical homologous NMI genes are expressed in mammals, and similar NMI genes in vertebrates.