Molecular analysis of SMN, NAIP and P44 genes of SMA patients and their families

Mutations of the telomeric survival motor neuron gene (SMN1) are related to spinal muscular atrophy (SMA). However, no phenotype-genotype correlation has been observed since the SMN1 gene is lacking in the majority of patients affected with either the severe form (type I) or the milder forms (types II and III). Here, we analyze the SMN, NAIP and P44 genes in 132 Chinese SMA patients and their families. At least three types of normal allele, and four types of mutant allele were found in this study. The combination of one normal allele with one mutant allele resulted in carriers of different types, and the combination of different mutant alleles accounted for the different genotypes among different types of SMA. Deletions of mutant alleles can be further subgrouped into four types, which includes involving SMN1, SMN1 and NAIP(T) (telomeric portion of NAIP gene), SMN1 and NAIP(T) and P44(T) (telomeric portion of P44 gene), and SMN1 and SMN2 (centromeric portion of SMN gene). Some of the severe (type I) SMA cases correlated with the extent of deletions in the SMN, NAIP and P44 genes or the dosage of SMN gene when both SMN1 and SMN2 are deleted. We also found two novel point mutations, an A insertion at codon 8 (AGT-->AAGT) and an A substitution at codon 228 (TTA-->TAA).

Signaling events in the hypoxic induction of alcohol dehydrogenase gene in Arabidopsis

Expression of the alcohol dehydrogenase gene (ADH) of Arabidopsis is induced during hypoxia. Because many plants increase their ethylene production in response to hypoxic stress, we examined in this report whether ethylene is involved in the hypoxic induction of ADH in Arabidopsis. We found that the hypoxic induction of ADH can be partially inhibited by aminooxy acetic acid, an inhibitor of ethylene biosynthesis. This partial inhibition can be reversed by the addition of 1-aminocyclopropane-1-carboxylic acid, a direct precursor of ethylene. In addition, the hypoxic induction of the ADH gene is also reduced in etr1-1 and ein2-1, two ethylene insensitive mutants in ethylene-signaling pathways, whereas the addition of exogenous ethylene or an increase in cellular ethylene alone does not induce ADH under normoxic conditions. Kinetic analyses of ADH mRNA accumulation indicated that an ethylene signal is required for the induction of ADH during later stages of hypoxia. Therefore, we conclude that ethylene is needed, but not sufficient for, the induction of ADH in Arabidopsis during hypoxia.

Promoter analysis of the nuclear gene encoding the chloroplast glyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsis thaliana

The promoter of the nuclear gene, GAPB, which encodes the B subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase (GADPH) of Arabidopsis thaliana, was previously shown to contain four direct repeats (Gap boxes, located between -237 and -181) that were necessary but not sufficient for light-activated gene transcription. To identify additional elements located between the Gap boxes and TATA box, various GAPB promoter fragments driving the beta-glucuronidase (GUS) reporter gene were constructed in transgenic Arabidopsis. We found a 23 bp element (the XXIII element), centered at -119, that is essential for promoter activity. Mutations in the XXIII element abolished transcription of GAPB completely. Furthermore, we have identified three additional elements, PI, Tboxes, and PII that serve as positive modulators in the light-activated transcription of GAPB. Mutations in any of these three elements resulted in the reduction in light inducibility of the GAPB gene. The PI, XXIII, Tboxes and PII sequences are novel cis-acting elements that are not present in the closely related GAPA promoter or other promoters that are similarly regulated by light. In our current study, we found that transgenic Arabidopsis containing a GAPB promoter::GUS construct with all four Gap boxes deleted exhibited significant GUS expression albeit reduced to 42% of the optimal expression level. In contrast, in previous studies on transgenic tobacco, total abolishment of GUS expression was seen when the Gap boxes were deleted. This suggests that different trans-acting factors present in heterologous systems may result in variability of the expression of the transgene.

Genetic characterization of the rotaviruses associated with a nursery outbreak

G1P[6] rotaviruses were demonstrated previously to be associated with the neonatal nursery outbreak of gastroenteritis in Changhua Christian Hospital that is located in the central region of Taiwan, from September 1994 to May 1995. Meanwhile, rotaviruses were detected in children hospitalized for acute gastroenteritis. Our study characterizes the rotaviruses associated with the nursery outbreak by using genetic approaches. Nucleotide sequence analysis revealed that the VP7 genes of the nursery rotaviruses were distinct from those of the strains circulating in the community. The G1P[6] rotaviruses recovered from the nursery were closely related to another neonatal G1P[6] strain from the northern region of Taiwan in both the VP4 and VP7 genes. The VP4 genes of these nursery strains differed from those of the P[6] human reference strains 1076, M37, RV3, and ST3. Apparently, these nursery rotaviruses were distinct from the strains circulating in the community and seemed to be a variant when compared with P[6] strains reported previously.

Antagonism of free-radical-induced damage of adlay seed and its antiproliferative effect in human histolytic lymphoma U937 monocytic cells

The goal of our current research was to investigate the antioxidative effects of methanolic extracts from different parts of adlay seed and their antiproliferative activity in malignant human cells. The methanolic extracts from different parts of adlay seeds were from the hull (AHM), testa (ATM), bran (ABM), and polished adlay (PAM). AHM exhibited greater capacity to scavenge superoxide anion radicals in the PMS-NADH system than ATM, ABM, or PAM. The scavenging capacities of AHM and ATM on hydrogen peroxides were about 20% at a dose of 250 microg/mL. Using the method of deoxyribose degradation to assess damage caused by hydroxyl radicals, AHM was found to inhibit damage in deoxyribose at a higher concentration. However, ATM, ABM, and PAM exhibited prooxidative activity at the same concentration. The inhibitory effect on enzymatic oxidation of xanthine to uric acid was found to follow the order AHM > ATM =. ABM. However, PAM was inactive. All test samples were positive for inhibition of TPA-induced free radical formation on neutrophil-like leukocytes and were found to follow the order AHM > ATM > ABM > PAM. When human histolytic lymphoma U937 monocytic cells were exposed to tert-butyl hydroperoxide, AHM protected the cells against the cytotoxicity caused by tert-butyl hydroperoxide. In addition, AHM exhibited antiproliferative activity against human histolytic lymphoma U937 monocytic cells in a dose-dependent manner. The antiproliferative properties of AHM appear to be attributable to its induction of apoptotic cell death as determined by flow cytometry. These results show that AHM displays multiple antioxidant effects and induces apoptosis of malignant human cells.

Allele-sharing among affected relatives: non-parametric methods for identifying genes

Non-parametric linkage analysis examines similarities among affected relatives in alleles of one or more genetic markers (pieces of DNA at known locations on a chromosome). The objective is to evaluate departures from the null hypothesis that the markers are not near a disease gene. Under the null hypothesis, Mendel's laws give the probabilities that a set of relatives exhibits a particular allele-sharing pattern, and the null hypothesis is rejected if the extent of allele sharing among affected relatives exceeds Mendelian expectation. Because the rationale for allele-sharing methods is intuitively plausible and easily grasped, geneticists have used these methods for more than 30 years, well before the advent of the large sets of polymorphic markers that have made linkage analysis so fruitful today. Here we describe methods for assessing whether the extent of marker allele sharing among affected relatives exceeds Mendelian expectation. We first quantify the notion of allele sharing and the probabilities of allele sharing in various sets of relatives. Then we describe allele sharing methods for affected sibs and more general sets of relatives. We also discuss related issues of test size and power. We conclude with a brief discussion of areas in need of further research.

Mutation analysis of the putative tumor suppressor gene PTEN/MMAC1 in hepatocellular carcinoma

Loss of heterozygosity of chromosome 10q has been reported in hepatoma. Areas with a high rate of loss of genetic material could harbor putative tumor suppressor genes. PTEN/MMAC1, a candidate tumor suppressor gene located at chromosome 10q23.3, has recently been identified and found to be homozygously deleted or mutated in several different types of human tumors. To determine whether the PTEN/MMAC1 gene is a target of 10q loss of heterozygosity in hepatoma, we examined 42 primary hepatomas for mutations in PTEN/MMAC1 by using nested reverse transcriptase polymerase chain reaction (RT-PCR) of the RNA and single-stranded conformation polymorphism (SSCP) analysis of all genomic exons. Although 2 of 42 hepatoma tissues had aberrant transcripts, 5 matched noncancerous liver tissues also had aberrant transcripts. Southern blot analysis of the entire genomic DNA revealed no genomic change. Therefore, like the TSG101 or FHIT gene, aberrant transcripts of PTEN/MMAC1 using the nested RT-PCR method were a common phenomenon for both cancerous and noncancerous liver tissues, which may not be related to oncogenesis. None of the 42 cases had small deletions, point mutations, or insertions. Our results suggest that the PTEN/MMAC1 gene may not play a role in the pathogenesis of hepatoma.

Genomic typing of human red cell miltenberger glycophorins in a Taiwanese population

BACKGROUND

Antigens in the human red cell Miltenberger series are glycophorin variants of the MN (MNS) blood group system that are due to the rearrangement of glycophorin A (GPA) and glycophorin B (GPB) genes.

STUDY DESIGN AND METHODS

Taking advantage of the differences between the GPA and GPB genes, a polymerase chain reaction-based method was developed to detect all the Miltenberger glycophorin variants and St(a) subtype. GPA- and GPB-specific primers were used to amplify the GPA or GPB gene, and the amplified products were used to recognize the different hybrid genes after restriction enzyme digestions.

RESULTS

Among 264 Taiwanese subjects studied, Mi.III and St(a) are the most common types of Miltenberger variants found. Mi.III was present in 13 (4.92%) of 264, and St(a) was found in 8 (3. 03%) of 264; 1 case (0.4%) of Mi.V was also identified from the study group.

CONCLUSION

This is the first polymerase chain reaction-based method of detecting most of the Miltenberger variants and St(a). The genomic typing results were confirmed by control DNA of identified Miltenberger phenotypes. The prevalence rates of Mi. III and St(a) in this study were also consistent with other previous reports using different methods.

Mutation analysis of the putative tumor suppression gene PTEN/MMAC1 in sporadic breast cancer

PTEN/MMAC1, a potential human tumor suppressor gene, has been found to have inactivating mutations in several types of cancer, including breast cancer. The incidence of breast cancer in Chinese is quite low in comparison with Caucasians, and genetic factors may play some roles. To further determine the role of PTEN/MMAC1 in breast cancer in Chinese, we used loss of heterozygosity (LOH), single strand conformation polymorphism (SSCP) with direct sequencing of variant bands, and Southern blot analysis methods to analyze mutations in PTEN/MMAC1 in 52 cases of breast cancer. None had LOH at chromosome 10q23.3. One mutation was identified, a somatic 3-base deletion, in one case. Our results suggest PTEN/MMAC1 does not play a major role in the development of sporadic breast cancer.

Mutations affecting induction of glycolytic and fermentative genes during germination and environmental stresses in Arabidopsis

Expression of the alcohol dehydrogenase gene (ADH) of Arabidopsis is known to be induced by environmental stresses and regulated developmentally. We used a negative-selection approach to isolate mutants that were defective in regulating the expression of the ADH gene during seed germination; we then characterized three recessive mutants, aar1-1, aar1-2, and aar2-1, which belong to two complementation groups. In addition to their defects during seed germination, mutations in the AAR1 and AAR2 genes also affected anoxic and hypoxic induction of ADH and other glycolytic genes in mature plants. The aar1 and aar2 mutants were also defective in responding to cold and osmotic stress. The two allelic mutants aar1-1and aar1-2 exhibited different phenotypes under cold and osmotic stresses. Based on our results we propose that these mutants are defective in a late step of the signaling pathways that lead to increased expression of the ADH gene and glycolytic genes.

Cis-acting elements essential for light regulation of the nuclear gene encoding the A subunit of chloroplast glyceraldehyde 3-phosphate dehydrogenase in Arabidopsis thaliana

We report the characterization of cis-acting elements involved in light regulation of the nuclear gene (GapA) that encodes the A subunit of glyceraldehyde 3-phosphate dehydrogenase in Arabidopsis thaliana. Our previous deletion analyses indicate that the -277 to -195 upstream region of GapA is essential for light induction of the beta-glucuronidase reporter gene in transgenic tobacco (Nicotiana tabacum) plants. This region contains three direct repeats with the consensus sequence 5'-CAAATGAA(A/G)A-3' (Gap boxes). Our results show that 2-bp substitutions of the last four nucleotides (AA or GA) of the Gap boxes by CC abolish light induction of the beta-glucuronidase reporter gene in vivo and affect binding of the Gap box binding factor in vitro. We have also identified an additional cis-acting element, AE (Activation Element) box, that is involved in regulation of GapA. A combination of a Gap box trimer and an AE box dimer can confer light responsiveness of the cauliflower mosaic virus 35S promoter containing the -92 to +6 upstream sequence, whereas oligomers of Gap boxes or AE boxes alone cannot confer light responsiveness on the same promoter. These results suggest that Gap boxes and AE boxes function together as the light-responsive element of GapA.

Computed tomography in the diagnosis of organic bowel obstruction

BACKGROUND

This study examined the usefulness of computed tomography (CT) scan for cases of organic intestinal obstruction, with two simple criteria.

METHODS

One hundred and thirteen patients with clinical suspicion of bowel obstruction were referred for CT scans. A line was drawn between the dilated proximal, and the collapsed distal bowels. A careful search was conducted on this line for obstructive lesions. The results were reported to be organic obstruction if there was an abrupt change of caliber (Criterion I) or a soft tissue mass around the dilated bowel (Criterion II). The judgement based on the CT findings.

RESULTS

Eighty-eight cases proved to have bowel obstruction. With Criterion I, the sensitivity was 59.1%, and specificity, 88% with Criterion II, the sensitivity was 56.3% and specificity 100%. If either of them was considered to be a positive sign of organic obstruction, the sensitivity was 100%, the specificity 88% and the accuracy 97.3%. The nature of the obstructions were precisely predicted in 76 patients (86%).

CONCLUSIONS

With these two simple criteria, CT scan can achieve high accuracy and is a recommendation in virtually every instance when intestinal obstruction is suspected.

Effects of light and chloroplast functional state on expression of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in long hypocotyl (hy) mutants and wild-type Arabidopsis thaliana

In a previous study of Arabidopsis thaliana (J. Dewdney, T.R. Conley, M.-C. Shih, H.M. Goodman [1993] Plant Physiol 103: 1115-1121), it was postulated that both blue light receptor- and phytochrome-mediated pathways contribute to regulation of the nuclear genes encoding A and B subunits of glyceraldehyde-3-phosphate dehydrogenase (GAPA and GAPB). Here were report on the involvement of a nuclear gene encoding a putative blue-light receptor (HY4) and of a nuclear gene encoding phytochrome A apoprotein (PHYA) in regulation of the GAPA and GAPB genes in response to blue and far-red light. Continuous light irradiation experiments with the hy4 mutant demonstrate that the HY4 gene product is required for full expression of GAPA, GAPB, and one or more of the nuclear genes encoding small subunits of of ribulose-1,5-bisphosphate carboxylase/oxygenase. Continuous light irradiation and fluence-response studies with the phyA-101 mutant show that phytochrome A functions in far-red light regulation of GAPA, GAPB, nuclear genes encoding small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase, and CAB genes. Phytochromes A and B alone either do not participate in red light-mediated gene regulation or have redundant functions, as shown by analysis of phyA-101 and phyB-1 single mutants. In addition, the hypothesis that chloroplast-nucleus interactions affect GAPA and GAPB gene regulation was tested. Herbicide-mediated photooxidative damage to chloroplasts in A thaliana seedlings strongly decreased the maximum amount of GAPA and GAPB steady-state mRNA detected in continuous-light irradiation experiments. Full expression of the GAPB genes is dependent on the presence of functional chloroplasts.

A rapid method to study the relationship between IDDM and HLA-DQ beta 57 Asp

We have developed a rapid and simple method to detect the relation between HLA-DQ beta 57 Asp and Chinese IDDM patients. The method involved the selective amplification of a DNA fragment from the HLA-DQ B1 gene by using the mutagenic primers. After PCR, if the HLA-DQ beta 57 was Asp, then there was an artificially created restriction enzyme cutting site. We then can accurately obtain the results by enzyme digestion and electrophoresis. Sixty-nine IDDM patients and 30 nondiabetic control subjects were analyzed using this method. Twenty-two (42%) IDDM patients had non-Asp 57 homozygous, 31/45%) were Asp/non-Asp 57 heterozygous, and 9 (13%) had Asp-57 homozygous. Of the 30 control subjects, the number of cases for these three types were 6 (20%), 18 (60%), and 6 (20%), respectively. The relative risk of homozygous DQ beta 57 non-Asp in our group was 2.9 and the p value was greater than 0.05. Using this kind of approach, we were able to provide a simple, rapid, and non-radioactive method to detect whether the HLA DQ beta 57 was Asp or not.

Identification of a light-responsive region of the nuclear gene encoding the B subunit of chloroplast glyceraldehyde 3-phosphate dehydrogenase from Arabidopsis thaliana

We report here the identification of a cis-acting region involved in light regulation of the nuclear gene (GapB) encoding the B subunit of chloroplast glyceraldehyde 3-phosphate dehydrogenase from Arabidopsis thaliana. Our results show that a 664-bp GapB promoter fragment is sufficient to confer light induction and organ-specific expression of the Escherichia coli beta-glucuronidase reporter gene (Gus) in transgenic tobacco (Nicotiana tabacum) plants. Deletion analysis indicates that the -261 to -173 upstream region of the GapB gene is essential for light induction. This region contains four direct repeats with the consensus sequence 5'-ATGAA(A/G)A-3' (Gap boxes). Deletion of all four repeats abolishes light induction completely. In addition, we have linked a 109-bp (-263 to -152) GapB upstream fragment containing the four direct repeats in two orientations to the -92 to +6 upstream sequence of the cauliflower mosaic virus 35S basal promoter. The resulting chimeric promoters are able to confer light induction and to enhance leaf-specific expression of the Gus reporter gene in transgenic tobacco plants. Based on these results we conclude that Gap boxes are essential for light regulation and organ-specific expression of the GapB gene in A. thaliana. Using gel mobility shift assays we have also identified a nuclear factor from tobacco that interacts with GapA and GapB DNA fragments containing these Gap boxes. Competition assays indicate that Gap boxes are the binding sites for this factor. Although this binding activity is present in nuclear extracts from leaves and roots of light-grown or dark-treated tobacco plants, the activity is less abundant in nuclear extracts prepared from leaves of dark-treated plants or from roots of greenhouse-grown plants. In addition, our data show that this binding factor is distinct from the GT-1 factor, which binds to Box II and Box III within the light-responsive element of the RbcS-3A gene of pea.

Characterization of cis-acting elements in light regulation of the nuclear gene encoding the A subunit of chloroplast isozymes of glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana

We have characterized cis-acting elements involved in light regulation of the nuclear gene (GapA) encoding the A subunit of chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in Arabidopsis thaliana. Our results show that a 1.1-kb promoter fragment of the GapA gene is sufficient to confer light inducibility and organ specificity in transgenic Nicotiana tabacum (tobacco) plants, using the beta-glucuronidase gene of Escherichia coli as the reporter gene. Deletion analysis indicates that the -359 to -110 bp region of the GapA gene is necessary for light responsiveness. Within this region there are three copies of a decamer repeat (termed the Gap box) having the consensus sequence 5'-CAAATGAA(A/G)A-3', which has not been characterized in the promoter regions of other light-regulated genes. A deletion (to -247) producing loss of one copy of these elements from the GapA promoter reduces light induction by two- to threefold compared with a promoter deletion (to -359) with all three Gap boxes present, while deletion of all three Gap boxes (to -110) abolishes light induction completely. Gel mobility shift experiments using tobacco nuclei as the source of nuclear proteins show that GapA promoter fragments that contain these repeats bind strongly to a factor in the nuclear extract and that binding can be abolished by synthetic competitors consisting only of a monomer or dimer of the Gap box. Furthermore, a trimer, dimer, and monomer of the Gap box show binding activity and, like the authentic GapA promoter-derived probes, show binding activities that are correlated with Gap box copy number. These results strongly suggest that these repeats play important roles in light regulation of the GapA gene of A. thaliana.

Effects of blue and red light on expression of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase of Arabidopsis thaliana

We have characterized the effects of different light spectra on expression of the nuclear genes (GapA and GapB) encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in Arabidopsis thaliana. Steady-state mRNA levels for both genes in etiolated seedlings increased after a short exposure to red or blue light. However, these increases could not be reversed by immediate far-red light following the initial light treatment. In mature plants, a short light pulse, regardless of its spectrum, had no apparent effect on GapA or GapB mRNA levels in dark-adapted plants. In contrast, continuous exposure to red, blue, or white light resulted in increases of GapA and GapB mRNA levels, with blue and white light being far more efficient than red light. Similarly, continuous exposure of etiolated seedlings to red, blue, or white light also resulted in increased GapA and GapB mRNA levels. In addition, we show that illumination of red light-saturated Arabidopsis plants with continuous blue light results in further increases of GapA and GapB mRNA levels. Based on these results, we conclude that both blue light photoreceptor- and phytochrome-mediated pathways are involved in light regulation of GapA and GapB genes in Arabidopsis, with blue light acting as the dominant regulator.

Stress responses and metabolic regulation of glyceraldehyde-3-phosphate dehydrogenase genes in Arabidopsis

We report here effects of three environmental conditions, heat shock, anaerobic treatment, and carbon source supply, on expression of nuclear genes encoding chloroplast (GapA and GapB) and cytosolic (GapC) glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana. The steady-state mRNA level of the GapC increased when Arabidopsis plants were transferred from normal growth condition to heat-shock, anaerobiosis, or increased sucrose supply conditions. In contrast, the steady-state mRNA levels for GapA and GapB genes were unaffected or decreased transiently under the same treatments. To identify the cis-acting regulatory elements, transgenic tobacco plants containing a 820-bp GapC 5'-flanking DNA fragment and beta-glucuronidase (Gus) fusion were constructed. Analyses of these transgenic plants indicate that this 820-bp DNA fragment is sufficient to confer both heat-shock and anaerobic responses. These results suggest that transcriptional level control is involved in regulation of GapC expression under these stress conditions. Histochemical analysis of Gus activity indicates that expression of the GapC is cell-type specific and is probably linked to the metabolic activity of the cells.

Cloning and chromosomal mapping of nuclear genes encoding chloroplast and cytosolic glyceraldehyde-3-phosphate-dehydrogenase from Arabidopsis thaliana

Both cDNA and genomic clones for the nuclear genes encoding chloroplast (cp) (gapA and gapB) and cytosolic (gapC) glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Arabidopsis thaliana have been isolated and characterized. Genomic Southern-blot analyses indicate that there is only one copy of each gapA, gapB and gapC gene in A. thaliana. Comparison of the deduced amino acid (aa) sequences shows that the A and B subunits are highly similar (80% positional aa identity), while there is less similarity between the cp and cytosolic subunits (45% aa identity). These relationships are consistent with the idea that the cp and cytosolic GAPDHs evolved from different lineages, as suggested in our previous study of tobacco GAPDHs [Shih et al., Cell 47 (1986) 73-80]. In addition, the chromosomal locations for the three gap genes were determined by restriction fragment length polymorphism mapping; the three gap genes are not closely linked, gapA (55.8 cM) and gapC (0.0 cM) are on chromosome 3, and gapB (51.3 cM) is on chromosome 1.