A novel FUT1 allele was identified in a Chinese individual with para-Bombay phenotype

BACKGROUND

The para-Bombay phenotype is characterised by H-deficient or H partially deficient red blood cells (RBCs) in individuals who secrete ABH antigens in their saliva. Samples from an individual whose RBCs had an apparent para-Bombay phenotype and his family members were investigated and a novel FUT1 allele was identified.

MATERIALS AND METHODS

RBCs' phenotype was characterised by standard serologic technique. Genomic DNA was sequenced with primers that amplified the coding sequence of FUT1 and FUT2, respectively. Routine ABO genotyping analysis was performed. Haplotypes of FUT1 were identified by TOPO cloning sequencing. Recombination expression vectors of FUT1 mutation alleles were constructed and transfected into COS-7 cells. The pα-(1,2)-fucosyltransferase activity of expression protein was determined.

RESULTS

B101/O02 genotype of the proband was correlated with ABH substances in saliva. The proband carried a new FUT1 allele which showed 35C/T, 235G/C and 682A/G heterozygote by directly DNA sequencing. Two haplotypes, 235C and 35T+682G, were identified by TOPO cloning sequencing and COS-7 cells transfected with five recombination vectors including wild-type, 35T, 235C, 682G and 35T+682G alleles were established respectively. The α-(1,2)-fucosyltransferase activities of cell lysates which had transfected with 35T, 235C, 682G and 35T+682G recombination vectors showed 79·45, 16·23, 80·32 and 24·59%, respectively, compared with that of the wild-type FUT1-transfected cell lysates.

CONCLUSION

A novel FUT1 allele 235C was identified, which greatly diminished the activity of α-(1,2)-fucosyltransferase.

Sequence variation and genetic diversity in the giant panda

About 336-444 bp mitochondrial D-loop region and tRNA gene were sequenced for 40 individuals of the giant panda which were collected from Mabian, Meigu, Yuexi, Baoxing, Pingwu, Qingchuan, Nanping and Baishuijiang, respectively. 9 haplotypes were found in 21 founders. The results showed that the giant panda has low genetic variations, and that there is no notable genetic isolation among geographical populations. The ancestor of the living giant panda population perhaps appeared in the late Pleistocene, and unfortunately, might have suffered bottleneck attacks. Afterwards, its genetic diversity seemed to recover to some extent.

Analysis of the complete cDNA sequences of HLA-DRB1 alleles with group-specific amplification primers in the Chinese Han population

Currently for the majority of HLA-DRB1 alleles the focus has been mainly on exon 2 and complete cDNA sequences of HLA-DRB1 alleles are rare. In this study, we analyzed the complete coding sequences of partial alleles of HLA-DRB1 locus. The cDNA was amplified by polymerase chain reaction using the group-specific primers located in the 5'- and 3'-untranslated regions to obtain the complete coding sequences. The amplification products were sequenced using an ABI BigDye® Terminator Cycle Sequencing kit. The HLA-DRB1 allele phylogenetic tree was analyzed by dnaman software. Full-length cDNA sequences of 22 HLA-DRB1 alleles were obtained in this study. HLA-DRB1*08:09, DRB1 *12:02:01, and DRB1*13:12 alleles were first reported for complete coding sequences. The sequences of exon 1 of HLA-DRB1*04:06:01, DRB1*08:03:02, and DRB1 *14:07:01 were newly presented. The complete coding sequences of HLA-DRB1 *01:01:01, DRB1*03:01:01:01, DRB1*04:01:01, DRB1*04:05:01, DRB1*07:01:01: 01, DRB1*09:01:02, DRB1*10:01:01, DRB1*11:01:01, DRB1*12:01:01, DRB1*13: 01:01, DRB1*13:02:01, DRB1*14:04, DRB1*14:54, DRB1*15:01:01:01, DRB1*15: 02:01, and DRB1*16:02:01 were identical to those previously reported. Forty polymorphic positions in complete coding sequences outside exon 2 of these HLA-DRB1 alleles were confirmed. According to the phylogenetic tree of full-length coding sequence, the HLA-DRB1 allele was classified into seven major allelic lineages. In conclusion, a protocol for HLA-DRB1 cDNA amplification and sequencing was improved and the data may help to determine the polymorphism of coding sequences outside exon 2.

Human platelet antigen allele frequencies and new mutations on platelet glycoprotein genes in the Chinese Han population

BACKGROUND AND OBJECTIVES

The frequencies of human platelet antigens (HPAs) vary between different populations. In this study, we determined the HPA allele frequencies in the Chinese Han population and identified situation of incompatibility possibly leading to alloimmunisation.

METHODS

A total of 750 volunteer blood donors of the Chinese Han population were genotyped for HPA-1 to -17w systems. HPA genotyping was determined by polymerase chain reaction sequence-based typing.

RESULTS

Among the 17 HPA systems, the allele frequency is different from other populations. We noted the absence of HPA-7bw to HPA-14bw, HPA-16bw and HPA-17bw alleles in the population. The estimated incompatibility probabilities regarding platelet antigens 1 to 6w and 15 systems after transfusion of random donor platelet were from 0·004 to 0·373. Thirteen glycoprotein alleles were observed in the population. In addition, we identified 16 novel mutations on the glycoprotein genes separated from HPA polymorphisms, including GP1BA (517-525delAAC), ITGA2B (2722C>T and IVS26+85T>C), ITGA2 (1521C>T, 2474T>G and IVS20+10 G>C), ITGB3 (1476G>A, IVS10+19C>A, 1813G>A, IVS11+21G>A, IVS11+152A>G and IVS11-104T>C), GP1BB (IVS1-79G>A, IVS1-27C>T and 129G>A) and CD109 (2139A>G). Five of them could lead to amino acid deletion, substitution or premature stop codon in corresponding glycoprotein.

CONCLUSIONS

There was a high degree of polymorphism of the membrane glycoprotein genes related to human platelet alloantigen-1 to -17w systems in the Chinese Han population. These data could have some impact on the diagnosis, prevention and treatment of alloimmune thrombocytopenia.

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

Sequence-derived structural and physicochemical features have been extensively used for analyzing and predicting structural, functional, expression and interaction profiles of proteins and peptides. PROFEAT has been developed as a web server for computing commonly used features of proteins and peptides from amino acid sequence. To facilitate more extensive studies of protein and peptides, numerous improvements and updates have been made to PROFEAT. We added new functions for computing descriptors of protein–protein and protein–small molecule interactions, segment descriptors for local properties of protein sequences, topological descriptors for peptide sequences and small molecule structures. We also added new feature groups for proteins and peptides (pseudo-amino acid composition, amphiphilic pseudo-amino acid composition, total amino acid properties and atomic-level topological descriptors) as well as for small molecules (atomic-level topological descriptors). Overall, PROFEAT computes 11 feature groups of descriptors for proteins and peptides, and a feature group of more than 400 descriptors for small molecules plus the derived features for protein–protein and protein–small molecule interactions. Our computational algorithms have been extensively tested and used in a number of published works for predicting proteins of specific structural or functional classes, protein–protein interactions, peptides of specific functions and quantitative structure activity relationships of small molecules. PROFEAT is accessible free of charge at http://bidd.cz3.nus.edu.sg/cgi-bin/prof/protein/profnew.cgi.

Association of race and socioeconomic status and outcomes with patients with rectal cancer

376

Background: Few studies have evaluated disparities of race and SES with outcomes in RC patients. We hypothesize that disparities exist in treatment and outcomes of RC.

Methods: Medical records were retrospectively reviewed of RC patients treated from 2000-2009 at an NCI cancer center and an urban academic center. SES was estimated using census data. Quartiles of income and education based on zip codes were calculated. Lowest vs. other quartiles were compared. Clinicopathologic variables included: initial stage, chemotherapy refusal, sphincter preservation, and overall survival (OS).

Results: 748 patients were included (581 white, 135 black, 6 other, 26 unknown). Patients with Medicaid were more likely to present with advanced disease (Table). Initial stage did not differ by race, income, or education. Non-white (NW) patients and low education were more likely to refuse chemotherapy. 7 patients refused radiation. After excluding stage IVpatients; sphincter preservation was higher among those with higher income. Median OS for all stages was worse for NW patients (31 months vs. 50 months, p<0.001), low income and education and most pronounced among NW patients with advanced disease. Insurance was not associated with survival difference. Advanced age, stage, and NW race (HR 1.49, 95% CI 1.10-2.02, p=0.01) were independent predictors of survival.

Conclusions: Disparity exists in treatment acceptance and outcomes in patients with RC. NW race and lower SES is associated with advanced disease, lower rates of sphincter preservation, chemotherapy refusal, and worse OS in patients with RC.

[Table: see text]

[Table: see text]

Trends in the exploration of anticancer targets and strategies in enhancing the efficacy of drug targeting

A number of therapeutic targets have been explored for developing anticancer drugs. Continuous efforts have been directed at the discovery of new targets as well as the improvement of therapeutic efficacy of agents directed at explored targets. There are 84 and 488 targets of marketed and investigational drugs for the treatment of cancer or cancer related illness. Analysis of these targets, particularly those of drugs in clinical trials and US patents, provides useful information and perspectives about the trends, strategies and progresses in targeting key cancer-related processes and in overcoming the difficulties in developing efficacious drugs against these targets. The efficacy of anticancer drugs directed at these targets is frequently compromised by counteractive molecular interactions and network crosstalk, negative and adverse secondary effects of drugs, and undesired ADMET profiles. Multi-component therapies directed at multiple targets and improved drug targeting methods are being explored for alleviating these efficacy-reducing processes. Investigation of the modes of actions of these combinations and targeting methods offers clues to aid the development of more effective anticancer therapies.

Trends in the exploration of anticancer targets and strategies in enhancing the efficacy of drug targeting

A number of therapeutic targets have been explored for developing anticancer drugs. Continuous efforts have been directed at the discovery of new targets as well as the improvement of therapeutic efficacy of agents directed at explored targets. There are 84 and 488 targets of marketed and investigational drugs for the treatment of cancer or cancer related illness. Analysis of these targets, particularly those of drugs in clinical trials and US patents, provides useful information and perspectives about the trends, strategies and progresses in targeting key cancer-related processes and in overcoming the difficulties in developing efficacious drugs against these targets. The efficacy of anticancer drugs directed at these targets is frequently compromised by counteractive molecular interactions and network crosstalk, negative and adverse secondary effects of drugs, and undesired ADMET profiles. Multi-component therapies directed at multiple targets and improved drug targeting methods are being explored for alleviating these efficacy-reducing processes. Investigation of the modes of actions of these combinations and targeting methods offers clues to aid the development of more effective anticancer therapies.

The allogeneic but not syngeneic dendritic cells effectively generated regulatory T cells from total CD4+ population without exogenous cytokines

Dendritic cells (DC) play a critical role in both the expansion of natural regulatory T cells (nTreg) and conversion of induced Treg (iTreg) from their precursors. In the present study, we evaluated the potential of DC to generate Treg from total CD4(+) population which contains both nTreg and the precursors, and found that allogeneic (allo-DC) but not syngeneic DC (syn-DC) could effectively generated Foxp3(+) Treg from total CD4(+) population in the absence of exogenous cytokines. Compared with freshly purified CD4(+) T cells, allo-DC-stimulated CD4(+) T cells showed increased percentage of CD4(+)CD25(+)Foxp3(+) Treg by 5-7-folds while syn-DC-stimulated CD4(+) T cells did not. Furthermore, we demonstrated that the significant amounts of endogenous IL-2 and TGF-beta, at least partially, contributed to the expansion of nTreg and conversion of iTreg in this cocultural system, respectively. Importantly, similar to nTreg, these allo-DC-generated Treg were capable of suppressing T cell response in vitro. Thus, our research provides a novel and efficient strategy for generation of Treg from total CD4(+) population.

Distribution of ABO blood group allele and identification of three novel alleles in the Chinese Han population

BACKGROUND

The ABO blood group system is clinically important in blood transfusion. The molecular characterization of ABO blood group has clinical and anthropological importance. Here, we determined the ABO alleles distribution and identified three novel alleles in the Chinese Han population.

STUDY DESIGN AND METHODS

Four hundred and seventeen Chinese Han individuals were determined by standard serologic techniques for the ABO blood group phenotypes. The ABO genotypes and alleles were analysed by polymerase chain reaction sequence-based typing (PCR-SBT) for sequencing exon 6 to 7 of the ABO gene. The polymorphisms of intron 5 and 6 of the ABO gene were also analysed by PCR-SBT. The two haplotypes including new alleles were separated by a Dynabeads M-270 Streptavidin protocol.

RESULTS

All ABO genotypes of the samples were consistent with the phenotypes. Fourteen alleles were identified based on the nucleotide sequences of exon 6 and 7, with five common alleles (A101, A102, B101, O01 and O02), six known rare alleles (A205, B110, O04, O05, O07 and O50) and three novel alleles (B112, CisAB06 and 061). The three new alleles appeared with the frequencies of 0.12%, 0.12% and 0.36%, respectively.

CONCLUSION

The detailed frequencies distribution of ABO alleles was studied in the Chinese Han population. We identified 14 alleles, including 3 novel alleles.

Analysis of the complete genomic sequence of HLA-A alleles in the Chinese Han population

To analyse the complete genomic sequences and investigate the intron polymorphism of the human leucocyte antigen (HLA)-A locus, the full-length nucleotide sequences of each major allelic group of HLA-A in the Chinese Han population were determined, including HLA-A*01, A*02, A*03, A*11, A*23, A*24, A*26, A*29, A*30, A*31, A*32, A*33, A*34, A*68, A*69. More than 3.0-kb DNA fragment of HLA-A locus was amplified from 5'-untranslated region to 3'-noncoding region for sequencing. Full-length sequences of the HLA-A alleles were determined using an ABI BigDye((R)) Terminator Cycle Sequencing kit and the HLA-A phylogenetic tree was analysed by dnaman software. Full-length nucleotide sequences of 15 HLA-A alleles (GenBank Accession numbers EU445470-EU445484) were obtained. HLA-A*110101, A*2301, A*300101, A*310102, A*330301, A*340101, A*680102 and A*6901 alleles were firstly reported for complete genomic sequences. Total 247 polymorphism positions were found in the complete genomic sequences of HLA-A alleles and a insertion of 17 nucleotides within intron 3 was observed in several allelic groups. According to the phylogenetic tree of the full-length nucleotide sequences, HLA-A locus was classified into seven major allelic lineages. In this study, complete genomic sequences of common HLA-A alleles were obtained and the data will help us understand the evolution of HLA-A.

Intra-arterial thrombolysis for acute central retinal artery occlusion

OBJECTIVE

In this study, we aimed at exploring the effect and safety of local intra-arterial thrombolysis on acute central retinal artery occlusion.

METHODS

Retrospective data analysis of 49 consecutive acute central retinal occlusion patients was performed. All the patients were treated with urokinase perfusion through the ophthalmology artery within the first 6 hours after central retinal artery occlusion attack. Conventional treatments including intra-ocular pressure decreasing, microcirculation improvement, neuroprotection and antiplatelet aggregation were conducted. The visual acuity (with International Snellen Chart) and field of vision were detected after thrombolysis. The complications and adverse events were observed.

RESULTS

Recanalization was found in 71% of patients. The visual acuity improvement was greater in the recanalization group (n=35) than in the non-recanalization group (n=14). The averaged visual acuity was 0.15+/-0.02, 0.25+/-0.03 and 0.4+/-0.05 after 2, 28 days and 6 months, respectively. Of the patients, 24.5% regained >0.6 of visual acuity, and the visual field deficit was less than 30% in 34.7% of patients after 28 days. Six months later, 36.7% patients regained visual acuity of >0.6, and the field deficit was less than 30% in 44.9% of patients. The difference between visual acuity in recanalization (0.6+/-0.04) and non-recanalization (0.002+/-0.0012) patients after 6 months after thrombolysis was significant (p>0.05).

CONCLUSIONS

Intra-arterial thrombolysis could obviously improve the short- and long-term visual function for patients with acute central retinal artery occlusion within 6 hours of symptom onset.

The HLA-G 14 bp insertion/deletion polymorphism is a putative susceptible factor for active human cytomegalovirus infection in children

Human leukocyte antigen-G (HLA-G) expression is a potential factor for the pathogenesis of virus infection. A 14 bp insertion/deletion polymorphism (rs16375) in the 3'-untranslated region of the HLA-G gene is involved in the stability of HLA-G mRNA and HLA-G protein expression. Therefore, the HLA-G 14 bp polymorphism might be involved in human cytomegalovirus (hCMV) infection. To test a possible association between the HLA-G 14 bp deletion/insertion polymorphism and the active hCMV infection, in this study, a total of 54 patients with active hCMV infection and 165 age- and sex-matched, unrelated, normal Chinese Han population were genotyped for the 14 bp insertion/deletion polymorphism. Association of 14 bp polymorphism with hCMV urine DNA copies and the odds ratio (OR) of the polymorphism as a risk factor for active hCMV infection were analyzed. Our results showed that the prevalence of -14 bp/ -14 bp genotype in active hCMV patients was markedly increased [P(c) = 0.00034, OR = 3.31, 95% confidence interval (CI): 1.77-6.18], and similar significance was also observed for the frequency of -14 bp allele (P c = 0.0023, OR = 2.24, 95% CI: 1.38-3.64) when compared with that of healthy controls. Furthermore, urine hCMV DNA copies in patients with the -14 bp/ -14 bp genotype were significantly higher than those in patients with the +14 bp/ +14 bp genotype (P = 0.041). Our findings support a potential role of HLA-G 14 bp insertion/deletion polymorphism as a susceptible factor for the active hCMV infection.

Diabetes, pre-diabetes and associated risks on Minnesota code-indicated major electrocardiogram abnormality among Chinese: a cross-sectional diabetic study in Fujian province, southeast China

The goal of this study was to determine the prevalence of diabetes mellitus (DM), impaired glucose regulation (IGR) and related metabolic disorders (overweight, obesity and hypertension) in a Chinese population (20-74 years old). An additional goal was to investigate the relationship between glucose metabolism and the Minnesota code-indicated major abnormal electrocardiogram (MA-ECG). There were 3960 individuals selected from urban and rural areas of Fujian, China from July 2007 to May 2008 by multistage-stratified sampling. Ultimately, data from 3208 subjects (20-74 years old) were analysed (including physical measurements, blood biochemical analysis, oral glucose tolerance test and 12-lead resting ECG). According to World Health Organization diagnostic criteria, the prevalence rates of DM and IGR were 9.51% (male, 10.08%; female, 9.14%) and 14.40% (male, 14.48%; female, 14.35%) respectively. Newly diagnosed DM was found in 53.44% of the diabetic subjects. Based on the 2000 China census, the age-standardized prevalence rates of DM and IGR were 7.19% (male, 7.74%; female, 6.61%) and 11.96 % (male, 12.35%; female, 11.56%) respectively. The age-standardized prevalence rates of DM and IGR in urban areas (7.74% and 12.97% respectively) were slightly but no significantly higher than in rural areas (6.67%, 10.86%). The prevalence rates of overweight, obesity and hypertension were 25.50%, 3.52% and 28.52% respectively (age- and sex- standardized rates: 23.69%, 3.02 % and 22.45 %). After adjusting for other confounding risk factors, multiple logistic regression analysis showed that DM and impaired glucose tolerance were independent risk factors for MA-ECG. Non-diabetic subjects with increased 30-min plasma glucose (PG) after an oral glucose load had a higher risk of MA-ECG after adjusting for other risk factors, especially in those with normal glucose tolerance but with 30-min PG >or= 7.8 mmol L(-1) (odds ratio = 1.371 [1.055-1.780]). The prevalence rates of DM and IGR as well as other metabolic disorders have increased dramatically in the last decade in China, especially in rural areas, with many undiagnosed cases of DM. Even slightly elevated PG levels may predict early cardiovascular events.

Use of quantum dots to detect human papillomavirus in oral squamous cell carcinoma

OBJECTIVE

To examine the association of oral squamous cell carcinoma with human papillomavirus (HPV) using quantum dots (QD) in situ hybridization (ISH).

METHODS

Expression of HPV16/18 was analyzed in a representative collection of 21 oral squamous cell carcinomas by tissue microarrays. The presence of HPV16/18 high risk was detected by applying QDISH which is compared with conventional ISH.

RESULTS

Seven cases out of 21 (33.3%) were positive for QDISH while 1 out of 21 (4.8%) was positive for ISH, although all of HPV DNA were localized in the nuclei in the spinous and basal cell layer of the epithelium. The difference between these two methods was significant (P < 0.05).

CONCLUSIONS

These results demonstrate that the QD might be an efficient method for determination of HPV infection and HPV-associated oral squamous cell carcinoma.

Assessment of body composition in dialysis patients by arm bioimpedance compared to MRI and 40K measurements

This study used multi-frequency bioimpedance spectroscopy (BIS) of the arm and whole body to estimate muscle mass (MM) and subcutaneous adipose tissue (SAT) in 31 hemodialysis (HD) patients comparing these results with magnetic resonance imaging (MRI) and body potassium ((40)K) as gold standards. Total body and arm MM (MM(MRI)) and SAT (SAT(MRI)) were measured by MRI. All measurements were made before dialysis treatment. Regression models with the arm (aBIS) and whole body (wBIS) resistances were established. Correlations between gold standards and the BIS model were high for the arm SAT (r(2) = 0.93, standard error of estimate (SEE) = 3.6 kg), and whole body SAT (r(2) = 0.92, SEE = 3.5 kg), and for arm MM (r(2) = 0.84, SEE = 2.28 kg) and whole body MM (r(2) = 0.86, SEE = 2.28 kg). Total body MM and SAT can be accurately predicted by arm BIS models with advantages of convenience and portability, and it should be useful to assess nutritional status in HD patients.

C/EBPbeta represses p53 to promote cell survival downstream of DNA damage independent of oncogenic Ras and p19(Arf)

CCAAT/enhancer-binding protein-beta (C/EBPbeta) is a mediator of cell survival and tumorigenesis. When C/EBPbeta(-/-) mice are treated with carcinogens that produce oncogenic Ras mutations in keratinocytes, they respond with abnormally elevated keratinocyte apoptosis and a block in skin tumorigenesis. Although this aberrant carcinogen-induced apoptosis results from abnormal upregulation of p53, it is not known whether upregulated p53 results from oncogenic Ras and its ability to induce p19(Arf) and/or activate DNA-damage response pathways or from direct carcinogen-induced DNA damage. We report that p19(Arf) is dramatically elevated in C/EBPbeta(-/-) epidermis and that C/EBPbeta represses a p19(Arf) promoter reporter. To determine whether p19(Arf) is responsible for the proapoptotic phenotype in C/EBPbeta(-/-) mice, C/EBPbeta(-/-);p19(Arf-/-) mice were generated. C/EBPbeta(-/-);p19(Arf-/-) mice responded to carcinogen treatment with increased p53 and apoptosis, indicating p19(Arf) is not essential. To ascertain whether oncogenic Ras activation induces aberrant p53 and apoptosis in C/EBPbeta(-/-) epidermis, we generated K14-ER:Ras;C/EBPbeta(-/-) mice. Oncogenic Ras activation induced by 4-hydroxytamoxifen did not produce increased p53 or apoptosis. Finally, when C/EBPbeta(-/-) mice were treated with differing types of DNA-damaging agents, including alkylating chemotherapeutic agents, they displayed aberrant levels of p53 and apoptosis. These results indicate that C/EBPbeta represses p53 to promote cell survival downstream of DNA damage and suggest that inhibition of C/EBPbeta may be a target for cancer cotherapy to increase the efficacy of alkylating chemotherapeutic agents.

Homology-free prediction of functional class of proteins and peptides by support vector machines

Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive performance for predicting a wide range of protein and peptide classes including certain low- and non- homologous sequences. This method serves as a new and valuable addition to complement the extensively-used alignment-based, clustering-based, and structure-based functional prediction methods. This article evaluates the strategies, current progresses, reported prediction performances, available software tools, and underlying difficulties in using SVM for predicting the functional class of proteins and peptides.

Sequences variations in 5'-flanking region of ABO gene and correlation with ABO alleles in the indigenous Chinese

BACKGROUND AND OBJECTIVES

5'-flanking sequences of the ABO gene play important role in the regulation of gene expression, but polymorphism of 5'-flanking sequence of ABO gene is rarely known. Here, we further characterize the molecular genetic basis and ABO allele-related polymorphism of the 5'-untranslated regions (5'-UTR) of the human ABO gene.

MATERIALS AND METHODS

Collecting blood samples from 72 blood donors in Hangzhou, China, we analysed sequences of exons 6 and 7 of ABO gene and amplified an enhanced segment of 43 bp repeats in the 5'-UTR. Subsequently, we selected 25 homozygotes [of genotypes A101/A101 (two), A102/A102 (seven), B101/B101 (seven) and O01/O01 (nine)] and five heterozygotes [A102/O01 (two), B101/O01 (two) and O01/O105 (one)] for sequencing 5 -kb amplicons spanning the 5'-UTR and partial exon 1 of the ABO gene. We sequenced the amplicons bidirectionally and, when pertinent, analysed selected haplotypes by cloning.

RESULTS

As a result, we identified 11 new polymorphic sites (10 point mutations, one 8-bp deletion) in the 5'-UTR of the A102, B101 and O01 alleles of common ABO phenotypes. Five A102 alleles carry four tandem repeats of a 43-bp minisatellite unit that deviated from previous reports.

CONCLUSION

The results revealed the DNA polymorphisms in the 5'-UTRs correlated with the common ABO alleles. Elucidation of the diversity of the 5'-UTRs is an important supplement to existing methods for increasing our understanding of the molecular basis of the ABO blood group system.

Characterization of two novel cytochrome P450 genes in insecticide-resistant house-flies

Two novel P450 cDNAs, CYP6A36 and CYP6A37, were isolated from house-flies. Putative protein sequences deduced from the cDNA sequences shared 58% identity. Predicted protein sequences of CYP6A36 and CYP6A37 from pyrethroid-resistant ALHF house-flies were identical to their corresponding orthologues in susceptible aabys flies. Expression of CYP6A36 was developmentally regulated with significant overexpression in ALHF compared with susceptible CS flies. Overexpression of CYP6A36 was detected in ALHF abdomen, where the primary detoxification organs of the midgut and fat body are located. CYP6A37, however, was expressed in all tested life stages, with no significant difference in expression between ALHF and CS. Genetic linkage analysis located CYP6A36 on autosome 5; overexpression of CYP6A36 was linked to the factors on autosomes 1 and 2, corresponding to the linkage of P450-mediated resistance in ALHF. This evidence suggests the importance of CYP6A36 in detoxification of insecticides and evolution of insecticide resistance in ALHF.

A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor

Support vector machines (SVM) and other machine-learning (ML) methods have been explored as ligand-based virtual screening (VS) tools for facilitating lead discovery. While exhibiting good hit selection performance, in screening large compound libraries, these methods tend to produce lower hit-rate than those of the best performing VS tools, partly because their training-sets contain limited spectrum of inactive compounds. We tested whether the performance of SVM can be improved by using training-sets of diverse inactive compounds. In retrospective database screening of active compounds of single mechanism (HIV protease inhibitors, DHFR inhibitors, dopamine antagonists) and multiple mechanisms (CNS active agents) from large libraries of 2.986 million compounds, the yields, hit-rates, and enrichment factors of our SVM models are 52.4-78.0%, 4.7-73.8%, and 214-10,543, respectively, compared to those of 62-95%, 0.65-35%, and 20-1200 by structure-based VS and 55-81%, 0.2-0.7%, and 110-795 by other ligand-based VS tools in screening libraries of >or=1 million compounds. The hit-rates are comparable and the enrichment factors are substantially better than the best results of other VS tools. 24.3-87.6% of the predicted hits are outside the known hit families. SVM appears to be potentially useful for facilitating lead discovery in VS of large compound libraries.