Single Nucleotide Exchanges Research Articles

Construction of Human Cytomegalovirus Mutants with Markerless BAC Mutagenesis.

To fully understand the function of cytomegalovirus (CMV) genes, it is imperative that they are studied in the context of infection. Therefore, the targeted deletion of individual viral genes and the comparison of these loss-of-function viral mutants to the wild-type virus allow for the identification of the relevance and role for a particular gene in the viral replication cycle. Targeted CMV mutagenesis has made huge advances over the past 20years. The cloning of CMV genomes into Escherichia coli as bacterial artificial chromosomes (BAC) allows for not only quick and efficient deletion of viral genomic regions, individual genes, or single-nucleotide exchanges in the viral genome but also the insertion of heterologous genetic sequences for gain-of-function approaches. The conceptual advantage of this strategy is that it overcomes the restrictions of recombinant technologies in cell culture systems. Namely, recombination in infected cells occurs only in a few clones, and their selection is not possible if the targeted genes are relevant for virus replication and are not able to compete for growth against the unrecombined parental viruses. On the other hand, BAC mutagenesis enables the selection for antibiotic resistance in E. coli, providing selective growth advantage to the recombined genomes and thus clonal selection of viruses with even extremely poor fitness. Here we describe the methods used for the generation of a CMV BAC, targeted mutagenesis of BAC clones, and transfection of human cells with CMV BAC DNA in order to reconstitute the viral infection process.

Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the Pyrococcus furiosus DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription.

Pyrococcus furiosus DSM 3638 is a model organism for hyperthermophilic archaea with an optimal growth temperature near 100°C. The genome was sequenced about 18 years ago. However, some publications suggest that in contrast to other Pyrococcus species, the genome of P. furiosus DSM 3638 is prone to genomic rearrangements. Therefore, we re-sequenced the genome using third generation sequencing techniques. The new de novo assembled genome is 1,889,914 bp in size and exhibits high sequence identity to the published sequence. However, two major deviations were detected: (1) The genome is 18,342 bp smaller than the NCBI reference genome due to a recently described deletion. (2) The region between PF0349 and PF0388 is inverted most likely due an assembly problem for the original sequence. In addition, numerous minor variations, ranging from single nucleotide exchanges, deletions or insertions were identified. The total number of insertion sequence (IS) elements is also reduced from 30 to 24 in the new sequence. Re-sequencing of a 2-year-old “lab culture” using Nanopore sequencing confirmed the overall stability of the P. furiosus DSM 3638 genome even under normal lab conditions without taking any special care. To improve genome annotation, the updated DNA sequence was combined with an RNA sequencing approach. Here, RNAs from eight different growth conditions were pooled to increase the number of detected transcripts. Furthermore, a differential RNA-Seq approach was employed for the identification of transcription start sites (TSSs). In total, 2515 TSSs were detected and classified into 834 primary (pTSS), 797 antisense (aTSS), 739 internal and 145 secondary TSSs. Our analysis of the upstream regions revealed a well conserved archaeal promoter structure. Interrogation of the distances between pTSSs and aTSSs revealed a significant number of antisense transcripts, which are a result of bidirectional transcription from the same TATA box. This mechanism of antisense transcript production could be further confirmed by in vitro transcription experiments. We assume that bidirectional transcription gives rise to non-functional antisense RNAs and that this is a widespread phenomenon in archaea due to the architecture of the TATA element and the symmetric structure of the TATA-binding protein.

Factors targeting MED12 to drive tumorigenesis?

Mediator Complex Subunit 12 (MED12) is part of the transcriptional preinitiation machinery. Mutations of its gene predominantly occur in two types of highly frequent benign tumors, uterine leiomyomas and fibroadenomas of the breast, where they apparently act as driver mutations. Nevertheless, their presence is not restricted to benign tumors having been found at considerable frequencies in uterine leiomyosarcomas, malignant phyllodes tumors, and chronic lymphocytic leukemia also. Most of the mutations are located within exon 2 of the gene but in rare cases the intron 1/exon 2 boundary or exon 1 are affected. As to their type, predominantly single nucleotide exchanges with a hotspot in one codon are found, but small deletions clustering around that hotspot also are not uncommon. These latter deletions are leaving the open reading frame intact. As to the types of mutations, so far no apparent differences between the tumor entities affected have emerged. Interestingly, this pattern with small deletions clustered around the hotspot of single nucleotide exchanges resembles that seen as a result of targeted gene editing. In contrast to other driver mutations the percentage of MED12-mutation positive tumors of independent clonal origin increases with the number of tumors per patient suggesting unknown etiological factors supporting site specific mutagenesis. These factors may act by inducing simultaneous site-specific double strand breaks the erroneous repair of which may lead to corresponding mutations. As inducers of DNA damage and its repair such as foreign nucleic acids of the microbiome displaying sequence homology to the putative target site might play a role. Interestingly, a 16 base pair homology of the hotspot to a putative terminator base-paired hairpin sequence of a Staphylococcus aureus tRNA gene cluster has been noted which might form R-loop like structures with its target sequence thus inducing said changes.

Factors targeting MED12 to drive tumorigenesis?

Mediator Complex Subunit 12 (MED12) is part of the transcriptional preinitiation machinery. Mutations of its gene predominantly occur in two types of highly frequent benign tumors, uterine leiomyomas and fibroadenomas of the breast, where they apparently act as driver mutations. Nevertheless, their presence is not restricted to benign tumors having been found at considerable frequencies in uterine leiomyosarcomas, malignant phyllodes tumors, and chronic lymphocytic leukemia also. Most of the mutations are located within exon 2 of the gene but in rare cases the intron 1/exon 2 boundary or exon 1 are affected. As to their type, predominantly single nucleotide exchanges with a hotspot in one codon are found, but small deletions clustering around that hotspot also are not uncommon. These latter deletions are leaving the open reading frame intact. As to the types of mutations, so far no apparent differences between the tumor entities affected have emerged. Interestingly, this pattern with small deletions clustered around the hotspot of single nucleotide exchanges resembles that seen as a result of targeted gene editing. In contrast to other driver mutations the percentage of MED12-mutation positive tumors of independent clonal origin increases with the number of tumors per patient suggesting unknown etiological factors supporting site specific mutagenesis. These factors may act by inducing simultaneous site-specific double strand breaks the erroneous repair of which may lead to corresponding mutations. As inducers of DNA damage and its repair such as foreign nucleic acids of the microbiome displaying sequence homology to the putative target site might play a role. Interestingly, a 16 base pair homology of the hotspot to a putative terminator base-paired hairpin sequence of a Staphylococcus aureus tRNA gene cluster has been noted which might form R-loop like structures with its target sequence thus inducing said changes.

Factors targeting MED12 to drive tumorigenesis?

Mediator Subcomplex 12 (MED12) is part of the transcriptional preinitiation machinery. Mutations of its gene predominantly occur in two types of highly frequent benign tumors, uterine leiomyomas and fibroadenomas of the breast, where they apparently act as driver mutations. Nevertheless, their presence is not restricted to benign tumors having been found at considerable frequencies in uterine leiomyosarcomas, malignant phyllodes tumors, and chronic lymphocytic leukemia also. Most of the mutations are located within exon 2 of the gene but in rare cases the intron 1/exon 2 boundary or exon 1 are affected. As to their type, predominantly single nucleotide exchanges with a hotspot in one codon are found, but small deletions clustering around that hotspot also are not uncommon. According to their presumed classification as gain-of-function mutations, these latter deletions are leaving the open reading frame intact. As to the types of mutations, so far no apparent differences between the tumor entities affected have emerged. Interestingly, this pattern with small deletions clustered around the hotspot of single nucleotide exchanges resembles that seen as a result of targeted gene editing. In contrast to other driver mutations the percentage of MED12-mutation positive tumors of independent clonal origin increases with the number of tumors per patient suggesting unknown etiological factors supporting site specific mutagenesis. These factors may act by inducing simultaneous site-specific double strand breaks the erroneous repair of which may lead to corresponding mutations. As inducers of DNA damage and its repair such as foreign nucleic acids of the microbiome displaying sequence homology to the putative target site might play a role. Interestingly, a 16 base pair homology of the hotspot to a putative terminator base-paired hairpin sequence of a Staphylococcus aureus tRNA gene cluster has been noted which might form R-loop like structures with its target sequence thus inducing said changes.

Direct andInvertedRepeat stimulatedexcision (DIRex): Simple, single-step, and scar-free mutagenesis of bacterial genes.

The need for generating precisely designed mutations is common in genetics, biochemistry, and molecular biology. Here, I describe a new λ Red recombineering method (Direct and Inverted Repeat stimulated excision; DIRex) for fast and easy generation of single point mutations, small insertions or replacements as well as deletions of any size, in bacterial genes. The method does not leave any resistance marker or scar sequence and requires only one transformation to generate a semi-stable intermediate insertion mutant. Spontaneous excision of the intermediate efficiently and accurately generates the final mutant. In addition, the intermediate is transferable between strains by generalized transductions, enabling transfer of the mutation into multiple strains without repeating the recombineering step. Existing methods that can be used to accomplish similar results are either (i) more complicated to design, (ii) more limited in what mutation types can be made, or (iii) require expression of extrinsic factors in addition to λ Red. I demonstrate the utility of the method by generating several deletions, small insertions/replacements, and single nucleotide exchanges in Escherichia coli and Salmonella enterica. Furthermore, the design parameters that influence the excision frequency and the success rate of generating desired point mutations have been examined to determine design guidelines for optimal efficiency.

Single nucleotide polymorphism analysis reveals heterogeneity within a seedling tree population of a polyembryonic mango cultivar.

Within a polyembryonic mango seedling tree population, the genetic background of individuals should be identical because vigorous plants for cultivation are expected to develop from nucellar embryos representing maternal clones. Due to the fact that the mango cultivar 'Hôi' is assigned to the polyembryonic ecotype, an intra-cultivar variability of ethylene receptor genes was unexpected. Ethylene receptors in plants are conserved, but the number of receptors or receptor isoforms is variable regarding different plant species. However, it is shown here that the ethylene receptor MiETR1 is present in various isoforms within the mango cultivar 'Hôi'. The investigation of single nucleotide polymorphisms revealed that different MiETR1 isoforms can not be discriminated simply by individual single nucleotide exchanges but by the specific arrangement of single nucleotide polymorphisms at certain positions in the exons of MiETR1. Furthermore, an MiETR1 isoform devoid of introns in the genomic sequence was identified. The investigation demonstrates some limitations of high resolution melting and ScreenClust analysis and points out the necessity of sequencing to identify individual isoforms and to determine the variability within the tree population.

Genetic Diversity of the fliC Genes Encoding the Flagellar Antigen H19 of Escherichia coli and Application to the Specific Identification of Enterohemorrhagic E. coli O121:H19.

Enterohemorrhagic Escherichia coli (EHEC) O121:H19 belong to a specific clonal type distinct from other classical EHEC and major enteropathogenic E. coli groups and is regarded as one of the major EHEC serogroups involved in severe infections in humans. Sequencing of the fliC genes associated with the flagellar antigen H19 (fliCH19) revealed the genetic diversity of the fliCH19 gene sequences in E. coli. A cluster analysis of 12 fliCH19 sequences, 4 from O121 and 8 from non-O121 E. coli strains, revealed five different genotypes. All O121:H19 strains fell into one cluster, whereas a second cluster was formed by five non-O121:H19 strains. Cluster 1 and cluster 2 strains differ by 27 single nucleotide exchanges in their fliCH19 genes (98.5% homology). Based on allele discrimination of the fliCH19 genes, a real-time PCR test was designed for specific identification of EHEC O121:H19. The O121 fliCH19 PCR tested negative in 73 E. coli H19 strains that belonged to serogroups other than O121, including 28 different O groups, O-nontypeable H19, and O-rough:H19 strains. The O121 fliCH19 PCR reacted with all 16 tested O121:H19 strains and 1 O-rough:H19 strain which was positive for the O121 wzx gene. A cross-reaction was observed only with E. coli H32 strains which share sequence similarities in the target region of the O121 fliCH19 PCR. The combined use of O-antigen genotyping (O121 wzx) and the detection of O121 fliCH19 allele type contributes to improving the identification and molecular serotyping of EHEC O121:H19 motile and nonmotile strains and variants of these strains lacking stx genes.

Genetic authentication by RFLP versus ARMS? The case of Moldavian dragonhead (Dracocephalum moldavica L.)

Moldavian dragonhead (Dracocephalum moldavica L.), due to its pleasant lemon scent and medical effects, has acquired increasing impact as functional food. The high diversity within the genus, limited supply not keeping pace with the growing demand, the morphological similarity with other Labiatae, and trading under the common name Turkish Melissa invite adulteration by surrogate species. We have developed several verified reference accessions of D. moldavica L. along with potential surrogate species to compare different approaches of authentication, also in commercial samples. We report on three strategies of authentication—a microscopic method, based on the relative size of epidermal pavement cells versus palisade cells, and two strategies of genetic authentication based on the barcoding marker large subunit of ribulose-1,5-bisphosphate carboxylase oxygenase (rbcL). We can detect single-nucleotide exchanges between D. moldavica L. and the potential surrogate species Melissa officinalis L. and Nepeta cataria L. by restriction fragment length polymorphism (RFLP), and we show that we can use this to verify the presence of D. moldavica even in dried and highly fragmented mixtures from commercial samples. We further develop a third strategy derived from the so-called amplification refractory mutation system (ARMS), based on multiplex PCR of the rbcL marker upon addition of specifically designed intermediate primers that will generate a diagnostic second band in case of D. moldavica L., but not for the surrogate species. We demonstrate that this ARMS approach is superior to the RFLP strategy, because it safeguards against experimental fluctuations, can unequivocally verify the presence of D. moldavica in commercial samples declaring its presence, and yields a clear outcome in a one-step protocol.

Isolation, cloning and sequence analysis of lactate dehydrogenase gene from Theileria annulata may lead to design of new antitheilerial drugs

Theileriosis is a serious animal disease that is transmitted by ticks. Theileria species are tick-borne obligate intracellular protozoan parasites that cause severe and mild infections in their hosts. Two of them, Theileria annulata and Theileria parva, cause lymphoproliferative disease with high mortality and morbidity in cattle commonly known as tropical theileriosis and East Coast fever, respectively. Currently available antiparasitic drugs are effective in animals but animals may remain carriers and treatment is most effective in the early stages of the disease. The isolation, cloning and analysis of lactate dehydrogenase from T. annulata was the goal of the present study with the ultimate aim of designing new antiparasitic drugs that will hopefully have a wider mode of action in animals. Blood samples were taken from a four year-old Brown Swiss cow showing signs of acute tropical theileriosis and genomic DNA was extracted following the confirmation of the clinical diagnosis. For the first time, in this study, the lactate dehydrogenase sequence was isolated from from a Theileria species. Following extraction from genomic DNA by PCR the sequence was cloned into the vector pGEM-T easy. Sequencing of the whole gene from both directions indicated that the open reading frame was interrupted by two introns. Several single nucleotide exchanges, deletions and insertions were also observed in the T. annulata lactate dehydrogenase sequence compared to the host. The most remarkable difference between the parasite and host enzyme is a five residue insertion in the active site loop region that might be an attractive target for inhibitors of the enzyme. This study opens a new route to further kinetic and structural studies towards the development of novel inhibitors of T. annulata lactate dehydrogenase.  

Transcription factor 7-like 2 gene polymorphisms and gestational diabetes mellitus

Objective: Transcription factor 7-like 2 (TCF7L2) gene polymorphisms were shown to be associated with insulin resistance. We examined two single nucleotide exchanges in this gene in women with gestational diabetes mellitus (GDM) and in women with normal glucose tolerance. Methods: A total of 1800 unselected women were prospectively screened for GDM by oral glucose tolerance test (OGTT) between 24 and 28 weeks of gestation. Two hundred and fifty Caucasian women of this collective, 125 patients with pathological OGTT and 125 patients with normal glucose tolerance were randomly selected. DNA samples were isolated and TCF7L2 gene polymorphisms (TCF7L2rs12255372 and TCF7L2rs7903146) were analyzed. Results: Women with GDM were significantly older (30.1 ± 3.4 years vs. 28.2 ± 4.8 years, p = 0.01), had a significantly higher body mass index (26.4 kg/m2; interquartile range: 23.33–31.19 vs. 24.6 kg/m2; interquartile range: 21.05–27.28, p = 0.02) and were significantly more often homozygous for the T allele of TCF7L2rs12255372 (17.2% vs. 2.6%, p = 0.002) than patients with normal glucose tolerance. Binary logistic regression analysis showed that the homozygous variant of TCF7L2rs12255372 (T/T) is an independent risk factor for GDM (OR 7.7, 95% CI: 1.71–34.60), but not the homozygous variant of TCF7L2rs7903146 (T/T). Conclusions: TCF7L2rs12255372 variant (T/T) is associated with increased risk of GDM in Caucasian women.

Molecular diagnostics of Lemon Myrtle (Backhousia citriodora versus Leptospermum citratum)

‘Lemon Myrtle’ is becoming increasingly popular in Europe both for use in cuisine and phytotherapy. However, this common name covers two completely different species, Backhousia citriodora F. Muell. and Leptospermum citratum Challinor, Cheel & A.R.Penfold. These species differ with respect to secondary compounds and even can cause, if mixed up and applied in high dose, toxic effects. We describe how the two species can be discriminated microscopically making use of differences in the morphology of leaf pavement cells and the relative size of palisade parenchyma. Based on the large subunit of ribulose-1,5-bisphosphate carboxylase oxygenase (rbcL) as molecular marker, the phylogenetic position of the two species within the Myrtaceae could be clarified. This sequence information was used to develop a simple assay to discriminate the two species even in dried and highly fragmented mixtures as typically occurring in commercial samples. This assay utilises the occurrence of single-nucleotide exchanges between those species that produce different fragments when the rbcL amplificates are restricted with Sac II.

Initial interrogation, confirmation and fine mapping of modifying genes: STAT3, IL1B and IFNGR1 determine cystic fibrosis disease manifestation

We have used a stepwise approach consisting of initial interrogation, confirmation and fine mapping to analyze STAT3, IL1B and IFNGR1 as modifiers of cystic fibrosis disease building upon the data and sample collection of the European Cystic Fibrosis Twin and Sibling Study. We have observed direct correlation between the length of the intronic microsatellite STAT3Sat to STAT3 expression levels among F508del-CFTR homozygous patients (P=0.0075), and an association of longer STAT3Sat-alleles with the presence of CFTR-mediated residual chloride secretion (P=0.0031), measured as the manifestation of the CF basic defect in intestinal tissue. Both, family-based analysis by TDT and case-reference comparison identified consistently the same intragenic IL1B haplotype as a risk variant (P(raw)=0.055 for TDT, P(raw)<0.3 for case-reference comparison). Using haplotype-guided hierarchical fine mapping, we have identified two single nucleotide exchanges for which concordant and discordant sibling pairs differ at a 7 kb-spanning core haplotype in IFNGR1 (P(raw)=0.0113). Taken together, our findings imply that immunorelevant pathways and ion secretion, dominated by CFTR in intestinal and respiratory epithelium, merge at the level of the epithelial cell to integrate the signaling of cytokines due to innate and acquired immune defense.

Phenotypic and genetic characterization of varicella-zoster virus mutants resistant to acyclovir, brivudine and/or foscarnet

The treatment of varicella-zoster virus (VZV) reactivation is based on nucleoside analogues acyclovir (ACV) and bromevinyldeoxyuridine (BVdU) and a phosphonic acid derivative (PFA). Drug-resistant mutants of 3 wild-type (WT) VZV strains were obtained by exposure of human retinal pigment epithelial (hRPE) cells inoculated with cell-free WT virus at increasing concentrations of ACV, BVdU, and PFA. In addition to single-drug resistance, a cross-resistance of isolates vs. ACV was observed for PFA-resistant strains. Single-nucleotide (nt) exchanges resulting in amino acid (aa) substitutions were observed within the DNA polymerase (ORF 28) and/or thymidine kinase (ORF 36) of 3 of 3 ACV-, 2 of 3 BVdU-, and 3 of 3 PFA-resistant strains. Interestingly, aa substitutions were also observed within the immediate-early regulatory protein and major transactivator IE 62 (ORF 62), and the envelope glycoprotein (g) I (ORF 67) of the BVdU-resistant mutant of strain PP. No aa substitutions were observed in the protein sequences of gene products encoded by ORF 5 (gK, a glycoprotein arranging exocytosis of viral-loaded vacuoles), ORF 14 (gC), ORF 31 (gB), ORF 37 (gH), ORF 47 (protein kinase, involved in major phosphorylating processes), ORF 60 (gL, important for syncytia forming of infected cells in combination with gH), ORF 63 (major transactivator, part of the tegument), and ORF 68 (gE, triggers fusion of viral loaded vacuoles with cell membranes by heterodimerizing with gI). Phenotypic analysis revealed a slow-growth phenotype and a formation of smaller plaques of resistant mutants. Future studies should prove the presence of those resistant mutants in herpes zoster patients and the potential consequences of their putative reduced fitness on the success of therapeutical interventions.

Genetic stability (in vivo) of the attenuated oral rabies virus vaccine SAD B19

The distribution of oral rabies vaccine baits containing replication-competent live viruses poses certain environmental safety risks; among others, the possibility of reversion to or an increase in virulence. Hence, the genetic stability of the complete genome of the most widely used oral rabies vaccine virus, SAD B19, was examined after four and 10 serial i.c. passages in foxes and mice, respectively. It was shown that the consensus strain of SAD B19 was extremely stable in vivo. After 10 consecutive passages in mice not a single mutation was observed. In foxes, seven single nucleotide exchanges were found between the first and fourth passage, of which only one resulted in an amino acid exchange at position 9240 of the L-gene. This mutation was not observed during the first three passages and, furthermore, it was shown that this mutation was not linked to enhanced virulence.

Characterization of the porcine multicopy ribosomal protein SA/37-kDa laminin receptor gene family

Prions represent a new class of infectious agents. The pathogenic prion protein (PrP Sc) is known as the trigger of bovine transmissible spongiform encephalopathy (TSE). By contrast, an oral transmission of PrP Sc and an ensuing infection seems to be blocked in non-ruminants such as pigs. Several investigations postulate that the ribosomal protein SA (RPSA) previously named 37-kDa laminin receptor precursor (LRP)/67-kDa laminin receptor (LR) is the candidate for binding and internalization of externally added cellular prion protein in the gut. We isolated a porcine ribosomal protein SA cDNA that consists of 1064 bp with an open reading frame of 885 bp encoding a 295 aa protein. The alignment of vertebrate ribosomal protein SA sequences displayed interspecies differences between cattle and pigs at positions 241 and 272 in the putative indirect PrP interaction site (aa 180–285) on RPSA. A PAC library screen revealed the existence of two processed ribosomal protein SA pseudogenes ( RPSAP1 and RPSAP3) and of one non-processed pseudogene ( RPSAP2). The pseudogenes have been assigned to SSC6 and SSC1 by hybrid panel analyses and FISH. Compared with the porcine cDNA 3, 7, and 13 insdels, 36, 25, and 57 single nucleotide exchanges and 6, 10, and 8 premature stop codons have been deciphered for RPSAP1, RPSAP2, and RPSAP3. In the 5′, 3′, and intron like regions, 2 ( RPSAP1), 10 ( RPSAP2), and 4 ( RPSAP3) repeats have been detected. Basically, the repeats belong to one of the class/family LINE/L1, SINE/tRNA-Glu and DNA/MER1_type. We conclude that the pig genome contains multiple copies of the RPSA sequence probably as a consequence to maintain the multifunctionality of the mature protein.

Primary Pigmented Nodular Adrenocortical Disease (PPNAD) and Pituitary Adenoma in a Boy with Sporadic Carney Complex Due to a Novel, De Novo Paternal PRKARIA Mutation (R96X)

We report the sporadic case of a 9 year-old boy with Carney syndrome, who presented with precocious puberty due to the endocrinological effects of primary pigmented nodular adrenocortical disease (PPNAD) and a synchronous pituitary adenoma. The adrenal tumor was removed surgically. Following unsuccessful treatment with bromocriptine the pituitary adenoma was also resected and a residual tumor irradiated. Thirty months after diagnosis the boy is free of symptoms. Mutation screening of the entire coding region of the PRKAR1A gene identified five single nucleotide exchanges, four of which were either heterozygous or homozygous polymorphic variants that were also present in his parents. However, the hitherto unreported disease-relevant mutation R96X in exon 3 had occurred de novo on the paternal allele.

Multi-exon out of frame deletion of the FBN1 gene leading to a severe juvenile onset cardiovascular phenotype in Marfan syndrome

Marfan syndrome is caused by mutations in fibrillin-1, a large gene spanning ∼ 200 kb of genomic DNA on chromosome 15q21. So far, more than 600 different mutations have been identified, accounting for 60–90% of all Marfan syndrome cases, the vast majority being single nucleotide exchanges as well as small deletions and insertions. Only four major rearrangements have been described in the literature so far. We have screened 11 individuals fulfilling the diagnostic criteria of Marfan syndrome but negative for point mutations in the fibrillin-1 gene by SSCP and/or direct sequencing, for large rearrangements. We report here the largest known de novo and out of frame deletion in the fibrillin-1 gene in a patient fulfilling the diagnostic criteria of Marfan syndrome. We identified the deletion breakpoints at the genomic and transcript levels and studied the expression of the mutated allele at the transcript and protein level. We conclude that large rearrangements may account for a non-negligible proportion of all Marfan cases.

Identification of variations in the human phosphoinositide 3‐kinase p110δ gene in children with primary B‐cell immunodeficiency of unknown aetiology

Our recent study demonstrated that defects in p110delta result in B-cell immunodeficiency that is very similar to that observed in BTK-deficient mice. We revealed that the p110delta fit the B-cell signal transduction complex and played a non-redundant role in the development and function of B cells. In humans, most children with primary B-cell immunodeficiency have mutations in the BTK, whereas a few have defects in the components of the B-cell signal transduction complex. But little is known about the genetic variation of p110delta in children with defects in B-cell immunodeficiency of unknown aetiology. Sixteen patients from 15 unrelated families and 112 normal controls underwent sequence analysis to identify genetic variations of the p110delta. Allele frequency in each group was also analysed and compared. We identified five single base-pair polymorphic nucleotide exchanges in both patient and control groups with similar allele frequencies, which did not contribute to the immunodeficiency. Three of them are novel (m.953A>G, m.1200C>T and m.1561A>G), and the m.953A>G and m.1561A>G nucleotide exchanges are non-synonymous (N253S and T456A, respectively). The novel m.1561A>G was in complete linkage disequilibrium with the known m.873A>G in our study of Taiwanese group. In addition, one novel single base-pair missense mutation, m.3256G>A (E1021K), was identified in one boy with typical clinical features of primary B-cell immunodeficiency and could not be found in either his family or the normal control population. By atomic structural analysis of the amino acid as well as the alignment comparison between species, it resulted in the replacement of the negative-charged amino acid E with the positive-charged amino acid K at codon 1021, located in the highly conservative and important catalytic functional domain. Our findings could shed light on further understanding the polymorphisms of p110delta in B-cell immunodeficiency and different populations. Moreover, the 3256G>A missense mutation raised the attention and warranted further extensive analysis to elucidate the role of p110delta in human immunodeficiency.

Discrimination of Single Mutations in Cancer-Related Gene Fragments with a Surface Acoustic Wave Sensor

Here, we report on using a surface acoustic wave sensor for the highly sensitive and accurate detection of individual point mutations in cancer-related gene DNA fragments from single injections. Our sensor measures both the mass and viscosity signals and, thus, allows discriminating between mass effects resulting from hybridization of short DNA strands and viscosity effects due to increasing amounts of DNA deposited on the sensor. Single nucleotide exchanges or deletions are distinguished reliably and with exceeding simplicity from the wild-type sequences, on the basis of differences in their dissociation or association rates starting at low nanomolar concentrations. Mutant oligonucleotides were identified immediately from viewing the recorded signal and without further processing of the data. Multiple repeated binding cycles were possible over days without affecting sensitivity. To achieve signal amplification, our new bioassay can also apply multiple hybridization steps based on sandwich hybridizations. Kinetic evaluations gave insight into the physicochemical properties of the fragments used that explain the differences in their binding processes.