Microdissection and molecular manipulation of single chromosomes in woody fruit trees with small chromosomes using pomelo (Citrus grandis) as a model. II. Cloning of resistance gene analogs from single chromosomes

Amplification of resistance gene analogs (RGAs) is both a useful method for acquiring DNA markers closely linked to disease resistance (R) genes and a potential approach for the rapid cloning of R genes in plants. However, the screening of target sequences from among the numerous amplified RGAs can be very laborious. The amplification of RGAs from specific chromosomes could greatly reduce the number of RGAs to be screened and, consequently, speed up the identification of target RGAs. We have developed two methods for amplifying RGAs from single chromosomes. Method 1 uses products of Sau3A linker adaptor-mediated PCR (LAM-PCR) from a single chromosome as the templates for RGA amplification, while Method 2 directly uses a single chromosomal DNA molecule as the template. Using a pair of degenerate primers designed on the basis of the conserved nucleotide-binding-site motifs in many R genes, RGAs were successfully amplified from single chromosomes of pomelo using both these methods. Sequencing and cluster analysis of RGA clones obtained from single chromosomes revealed the number, type and organization of R-gene clusters on the chromosomes. We suggest that Method 1 is suitable for analyzing chromosomes that are unidentifiable under a microscope, while Method 2 is more appropriate when chromosomes can be clearly identified.

Microdissection and molecular manipulation of single chromosomes in woody fruit trees with small chromosomes using pomelo (Citrus grandis) as a model. I. Construction of single chromosomal DNA libraries

Construction of single chromosomal DNA libraries by means of chromosome microdissection and microcloning will be useful for genomic research, especially for those species that have not been extensively studied genetically. Application of the technology of microdissection and microcloning to woody fruit plants has not been reported hitherto, largely due to the generally small sizes of metaphase chromosomes and the difficulty of chromosome preparation. The present study was performed to establish a method for single chromosome microdissection and microcloning in woody fruit species using pomelo as a model. The standard karyotype of a pomelo cultivar ( Citrus grandis cv. Guanxi) was established based on 20 prometaphase photomicrographs. According to the standard karyotype, chromosome 1 was identified and isolated with fine glass microneedles controlled by a micromanipulator. DNA fragments ranging from 0.3 kb to 2 kb were acquired from the isolated single chromosome 1 via two rounds of PCR mediated by Sau3A linker adaptors and then cloned into T-easy vectors to generate a DNA library of chromosome 1. Approximately 30,000 recombinant clones were obtained. Evaluation based on 108 randomly selected clones showed that the sizes of the cloned inserts varied from 0.5 kb to 1.5 kb with an average of 860 bp. Our research suggests that microdissection and microcloning of single small chromosomes in woody plants is feasible.

Difficulties in maintaining long-term partial nitritation of ammonium-rich sludge digester liquids in a moving-bed biofilm reactor (MBBR)

Nitrogen can be eliminated effectively from sludge digester effluents by anaerobic ammonium oxidation (anammox), but 55-60% of the ammonium must first be oxidized to nitrite. Although a continuous flow stirred tank reactor (CSTR) with suspended biomass could be used, its hydraulic dilution rate is limited to 0.8-1 d(-1) (30 degrees C). Higher specific nitrite production rates can be achieved by sludge retention, as shown here for a moving-bed biofilm reactor (MBBR) with Kaldnes carriers on laboratory and pilot scales. The maximum nitrite production rate amounted to 2.7 gNO2-Nm(-2)d(-1) (3 gO2m(-3)d(-1), 30.5 degrees C), thus doubling the dilution rate compared to CSTR operation with suspended biomass for a supernatant with 700 gNH4-Nm(-3). Whenever the available alkalinity was fully consumed, an optimal amount of nitrite was produced. However, a significant amount of nitrate was produced after 11 months of operation, making the effluent unsuitable for anaerobic ammonium oxidation. Because the sludge retention time (SRT) is relatively long in biofilm systems, slow growth of nitrite oxidizers occurs. None of the selection criteria applied - a high ammonium loading rate, high free ammonia or low oxygen concentration - led to selective suppression of nitrite oxidation. A CSTR or SBR with suspended biomass is consequently recommended for full-scale operation.

The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces

SUMMARY

To make information about protein interactive function easily accessible, we are mining the primary scientific literature for detailed data about protein interfaces. The Binding Interface Database (BID) organizes the vast amount of protein interaction information into tables, graphical contact maps and descriptive functional profiles. Currently data on 170 interacting protein pairs are available with over 1300 mutations described.

AVAILABILITY

The BID database is freely available at http://tsailab.org/BID/ To have your protein of interest entered, contact Tiffany Fischer (tiffbrink@neo.tamu.edu) or Jerry Tsai at the email below

[Observation on efficacy of artemether compound against vivax malaria]

AIM

To observe the efficacy of artemether compound against vivax malaria.

METHODS

Each artemether compound tablet contains 120 mg benflumetolum and 20 mg artemether. 132 patients with vivax malaria were divided into 3 groups. Group A, 36 patients received 8 tablets as an initial dose, followed by 4 tablets daily for 2 days; group B, 41 patients received 8 tablets as an initial dose, followed by 3 tablets daily for 4 days; group C, 55 patients receiving chloroguine-primaquine served as control. Two patients of group A were voluntarily to be bitten by Anopheles dirus before and after medication to observe the influence of artemether compound on the sporogony.

RESULTS

The average defervescence times for groups A, B and C were 22.3 h, 23.2 h and 25.0 h (P > 0.05), respectively, the average parasite clearance times were 33.5 h, 30.5 h and 44.9 h, respectively, the average parasite clearance times of groups A and B were all significantly shorter than that of group C (P < 0.01). The replase rates of groups A, B and C were 84.9%, 78.8% and 22.9%, respectively, followed-up at nine months, the relapse rates of groups A and B were higher than that of group C(P < 0.01).

CONCLUSION

Two regimens of artemether compound have the advantage of high efficacy against vivax malaria.

Analysis of intra-operative bleeding and recurrence of juvenile nasopharyngeal angiofibromas

The purpose of this study is to present our experience with 34 patients diagnosed with juvenile nasopharyngeal angiofibromas and treated in the Chinese PLA General Hospital between 1986 and 1999, and to examine the factors influencing intra-operative bleeding and tumour recurrence. The age of the patient, the duration of symptoms and tumour stage were related to the amount of intra-operative bleeding. The tumours were totally resected in 30 patients and recurred in five patients (16.7%), with a mean follow-up time of 77 months. The mean time to tumour recurrence after operation was 3.2 months (1-6 months). The incidence of recurrence had no correlation with the age of the patient, duration of symptoms, peri-operative treatment or surgical approaches (P > 0.05); but strongly correlated with tumour stage (P < 0.05).

A promoter polymorphism in the gene encoding interleukin-12 p40 (IL12B) is associated with mortality from cerebral malaria and with reduced nitric oxide production

Interleukin-12 (IL-12) is an important regulatory cytokine in infection and immunity. Administration of IL-12 may reduce complications of severe malaria in rodents. Polymorphisms in IL12B, the gene encoding the IL-12 p40 subunit, influence the secretion of IL-12 and susceptibility to Type 1 diabetes. We therefore investigated whether IL12B polymorphisms may affect the outcome of severe malaria. Homozygosity for a polymorphism in the IL12B promoter was associated with increased mortality in Tanzanian children having cerebral malaria but not in Kenyan children with severe malaria. Furthermore, homozygotes for the IL12B promotor polymorphism had decreased production of nitric oxide, which is in part regulated by IL-12 activity. These studies suggest that IL12B polymorphisms, via regulation of IL-12 production, may influence the outcome of malaria infection in at least one African population.

[Evaluation of the effect of causes of death of advanced schistosomiasis patients on the life span of population by using potential years of life lost analysis]

AIM

To evaluate the effect of the causes of death of advanced schistosomiasis patients on the life span of population in an area where schistosomiasis had been under control by applying the indicators of potential years of life lost (PYLL) and rate of PYLL (PYLLR).

METHODS

Using the formula of calculation of PYLL and PYLLR, the causes of death of 487 patients of advanced schistosomiasis in 3 previously endemic townships of Shanghai suburb.

RESULTS

Of 487 cases who died between 1955 and 1995, the PYLLR of all causes of death was 256.3@1000. The main causes of death were hepatic failure (100.3@1000), liver carcinoma (43.4@1000) and cancer of other organs (24.8@1000). In the 1960s, the PYLLR of advanced schistosomiasis complicated with hepatic failure and upper digestive tract hemorrhage was 222.2@1000 and 34.5@1000, the PYLLR of the complications of schistosomal liver cirrhosis, hepatic failure and hemorrhage accounted for 67.5% of the total PYLLR, being apparently higher in the non-splenectomy group than in the splenctomty group. After the schistosomiasis was under control, both PYLL and PYLLR decreased linearly. As compared with the 1960s, the PYLLR of all causes of death and the causes of death of the complications of schistosomal liver cirrhosis in the 1990s has declined by 62.9% and 83.2%, respectively, the PYLLR of upper digestive tract hemorrhage was found only 0.3@1000 in the last 5 years.

CONCLUSION

PYLL and PYLLR analysis could be used to quantify the effect of complications of advanced schistosomiasis and other causes of death on the life span of population.

Polymorphisms in the Il12b gene affect structure and expression of IL-12 in NOD and other autoimmune-prone mouse strains

Interleukin (Il)-12 is a heterodimeric cytokine composed of 35 and 40 kD chains that plays a key role in the induction of Th1 cells, a T cell subset involved in many autoimmune diseases. We report here the cDNA sequence encoding the IL-12 p40 subunit from the autoimmune-prone non-obese diabetic (NOD) mouse, which spontaneously develops type 1 diabetes. Compared with the C57BL/6 sequence, there are two base changes that lead to amino acid replacements. Other autoimmune-prone strains, but not the diabetes-resistant NOR strain, share the same allele as NOD. We found both trans- and cis- allele-dependent effects on levels of basal and induced IL-12p40 expression. Furthermore, we show that one of these changes results in a structural change in the p40 molecule, as evidenced by the failure of a monoclonal antibody to bind NOD IL-12. These findings have implications for the predisposition to autoimmune responses in NOD and other autoimmune-prone mouse strains.

Survival effect of lung transplantation among patients with cystic fibrosis

CONTEXT

Patients with cystic fibrosis (CF) are the second largest group of lung transplant recipients in the United States. The survival effect of transplantation on a general CF population has not previously been measured.

OBJECTIVE

To determine the impact of bilateral lung transplantation on survival in patients with CF.

DESIGN, SETTING, AND PATIENTS

Retrospective observational cohort study of 11 630 CF patients who did not undergo lung transplantation (controls) and 468 transplant recipients with CF from 115 CF centers in the United States, 1992-1998. Patients were stratified into 5 groups based on a 5-year survival prediction model (survival group 1: <30%; survival group 2: 30 to <50%; survival groups 3-5: 50 to <100%.)

MAIN OUTCOME MEASURE

Five-year survival from date of transplantation in 1992-1997 in the transplant group and from January 1, 1993, in the control group.

RESULTS

Lung transplantation increased 5-year survival of CF patients in survival group 1. Survival group 2 had equivocal survival effects, and groups 3-5 had negative survival effects from transplantation. From 1994-1997, there was a mean annual prevalence of 238 patients in survival group 1 and mean annual incidence of 154 patients entering the group, approximately 1.5 times the number of lung transplantations performed each year in CF patients (mean, 104). Use of the criterion of forced expiratory volume in 1 second of less than 30% resulted in an equivocal survival benefit and identified 1458 potential candidates for transplantation in 1993.

CONCLUSIONS

Cystic fibrosis patients in group 1 have improved 5-year survival after lung transplantation. The majority of patients with CF have equivocal or negative survival effects from the procedure. Selection of patients with CF for transplantation based on group 1 survival predictions maximizes survival benefits to individuals and may reduce the demand for scarce donor organs.

[Rat hearing loss and hearing organs mitochondrial DNA4834 deletions associated with hypercholesteremia]

OBJECTIVE

To determine whether or not the rat hypercholesteremia contributes to hearing organs mtDNA4834 deletion and involves in the development of hearing loss.

METHODS

The rat hypercholesteremia model (n = 38) was established by feeding with high cholesterol diet and the control group (n = 22) with common diet for 6 months. The rats were tested for auditory sensitivity using auditory brainstem response (ABR). Twenty-one left cochleae and 27 left cochlear nuclei from experimental group and 10 left cochleae and 13 left cochlear nuclei from control group were harvested. The total DNA of them was extracted. mtDNA was amplified by nest PCR to examine the presence of mtDNA4834 deletion.

RESULTS

Our result showed: (1) There is a significant increase in serum cholesterol level and ABR threshold in the experimental group. (2) The mitochondrially-encoded tRNA and ND1 segments were amplified from all samples, as well as mtDNA4834 deletions. (3) The incidence of mtDNA4834 deletions in hearing organs of hypercholesteremia rats was significantly higher than that of the control group (P < 0.05).

CONCLUSION

Extended hypercholesteremia can induce hearing loss, and mtDNA4834 deletion in hearing organs may be one of the pathogenic mechanisms.

[HCV-PCR-Hybrid.ELISA for the detection of HCV RNA in serum samples from hepatitis patients]

BACKGROUND

To detect HCV RNA in serum samples from hepatitis patients by using the methods of HCV-Reverse transcription polymerase chain reaction and hybrid ELISA.

METHODS

HCV RNA in serum samples was amplified by RT-PCR with one of the primer labeled with biotin. PCR amplified products were detected with microtiter plate hybridization with HCV specific probe, then determined with steptavidin-HRP assay. Anti-HCV in these samples was also detected with ELISA simultaneously.

RESULTS

The positive rates of HCV RNA were 81.8% (72/88) in anti-HCV positive group and 57.9% (88/152) in the whole patients group. Serum HCV RNA and anti-HCV positive rates were compared and the consistent rate was 78.9% (120/152, P>0.05). The positive rate of HCV RNA was higher in H.ELISA (57.9%, 88/152) than that in electrophoresis (35.5%, 54/152)(P<0.01).

CONCLUSIONS

The HCV-PCR-H.ELISA was a sensitive, specific, stable, semi-quantitative and easy to operate method. This HCV RNA detection was especially beneficial to early diagnosis during viramia period and was helpful for the evaluation of anti-HCV therapy.