Proliferation-dependent pattern of expression of a dihydrofolate reductase-thymidylate synthase gene from Daucus carota

The pattern of expression of a carrot dhfr-ts gene was evaluated in different plant organs, in somatic embryos, and in hypocotyl explants induced to dedifferentiate in vitro by the addition of the synthetic auxin 2,4 dichorophenoxyacetic acid. The promoter of this gene was also placed upstream of a uidA (GUS) reporter gene and, using biolistic and protoplasts transient expression assays, was shown to drive a particularly high level of expression in actively growing suspension cells. The results from these expression analyses combined with the presence of putative cell cycle-related cis-acting elements in the dhfr-ts promoter, strongly point to a cell division-dependent expression of this gene.

Development of a pyrosequencing approach for rapid screening of rifampin, isoniazid and ethambutol-resistant Mycobacterium tuberculosis

SETTING

The need to minimize the transmission of drug-resistant Mycobacterium tuberculosis requires rapid identification procedures.

OBJECTIVE

To develop a pyrosequencing approach for rapid screening of rifampin, isoniazid and ethambutol-resistant M. tuberculosis based on characterization of resistance-associated hot mutations.

DESIGN

Three pairs of PCR primers and three pyrosequencing sequencing primers for detecting mutations at codon 526 and 531 of the rpoB gene, codon 315 of the katG gene, and codon 306 of the embB gene were chosen. The sensitivity of the pyrosequencing approach was determined by assaying PCR products generated from 10-fold serial dilutions of the DNA from the H37Rv strain. The efficacy of the pyrosequencing approach was evaluated by analyzing clinical isolates with a known antibiotic phenotype.

RESULTS

Resistance-associated hot mutations could be determined within 2 h after PCR amplification using pyrosequencing. About 45 fg DNA per reaction was required to obtain sufficient PCR products to produce a clear, accurate pyrosequencing pattern. No mutations were found in all 20 drug-susceptible clinical isolates, while all isolates with mutations showed corresponding drug resistances.

CONCLUSION

This pyrosequencing approach can be used for rapid screening of rifampin-, isoniazid- and ethambutol-resistant M. tuberculosis prior to standard drug susceptibility testing.

Crystallization and preliminary X-ray diffraction studies of the Saccharomyces cerevisiae phospholipid-transfer protein Sec14p

The Saccharomyces cerevisiae phosphatidylinositol-transfer protein Secl4p catalyzes the exchange of phosphatidylinositol or phosphatidylcholine between membrane bilayers in vitro, and is an essential protein required for the budding of secretory vesicles from the yeast Golgi complex in vivo. At issue is the fundamental question of how the dual phospholipid ligand specificity of Sec 14p translates to in vivo function. In an attempt to determine the structural basis for how Secl4p binds each of its phopholipid ligands, Secl4p occupied with phosphatidylcholine has been purified and the complex crystallized in the presence of the mild detergent n-octyl beta-D-glucopyranoside. The Secl4p crystals diffract to 2.7 A and belong to space group P3(1)21 or P3(2)21 with unit-cell dimensions of a = b = 88.79, c = 111.21 A, alpha = beta = 90, gamma = 120 degrees. As Secl4p exhibits significant primary sequence homology to mammalian retinaldehyde binding proteins and the noncatalytic domain of human MEG2 protein tyrosine phosphatase, is is anticipated that solution of the Secl4p crystal structure will provide new functional insights for a family of interesting proteins.

Structure of a monoclonal anti-ICAM-1 antibody R6.5 Fab fragment at 2.8 A resolution

The specific binding of the monoclonal murine anti-intercellular adhesion molecule-1 (anti-ICAM-1) antibody, R6.5, inhibits the attachment of neutrophils to endothelium and prevents the attachment of major group human rhinovirus (HRV) to ICAM-1. This binding interferes with the host immune system and, as a result, the R6.5 antibody has been developed as a therapeutic anti-inflammatory and perhaps anti-HRV agent. The variable-region amino-acid sequence of R6.5 was determined from the anti-ICAM-1 cDNA. The crystallization conditions of the Fab fragment of R6.5 were established and the three-dimensional structure was determined by X-ray crystallography. The crystal space group is orthorhombic P2(1)2(1)2(1), a = 40.36, b = 137.76, c = 91.32 A, and the highest resolution of recorded reflections is 2.7 A. The molecular-replacement method using known Fab structures was employed to solve the R6.5 Fab structure. The final R-factor is 18.8% for a total of 3320 non-H protein atoms, 39 water molecules and 10 606 unique reflections. The protein exhibits the typical immunoglobulin fold. The surface contour of the antigen-combining site of the R6.5 antibody has a wide groove which resembles more the structure of an anti-polypeptide antibody than the structure of an anti-protein antibody.

Identification of four novel HLA-B alleles, B*1590, B*1591, B*2726, and B*4705, from an East African population by high-resolution sequence-based typing

We report here four novel HLA-B alleles, B*1590, B*1591, B*2726, and B*4705, identified from an East African population during sequence-based HLA-B typing. The novel alleles were confirmed by sequencing two separate polymerase chain reaction products, and by molecular cloning and sequencing multiple clones. B*1590 is identical to B*1510 at exon 2 and exon 3, except for a difference (GCCGTC) at codon 158. Sequence differences at codon 152 (GAGGTG) and codon 167 (TGGTCG) differentiate B*1591 from B*1503 at exon 3. B*2726 is identical to B*2708 at exon 2 and exon 3, except for a difference (AAGCAG) at codon 70. B*4705 was identified in three Kenyan women. The allele is identical to B*47010101/02 at exon 2 and exon 3, except for differences at codon 97 (AGGAAT) and codon 99 (TTTTAT). These new alleles have been named by the WHO Nomenclature Committee. Identification of these novel HLA-B alleles reflects the genetic diversity of this East African population.

Upstream regions of the estrogen receptor alpha proximal promoter transcript regulate ER protein expression through a translational mechanism

Estrogen receptor alpha (ER) mRNA is primarily transcribed from two promoters, the two transcripts share identical sequence encoding the same ER protein but differ in upstream regions. The 5' region of the two transcripts contain upstream open reading frames (uORFs) encoding potential peptides of 20 and 18 amino acids. The peptides have five C-terminal residues in common. These studies were undertaken to determine if the uORFs and encoded peptides differentially affected expression of ER. Expression of green fluorescent protein (GFP) reporter constructs containing upstream proximal promoter transcript sequences with the first 18 codons of ER fused to GFP was tested in HeLa cells. The cells expressed reduced levels of GFP as compared to the pEGFP-N1 parent vector; the effect was dependent on the presence of an intact proximal ER transcript uORF. Similar regulation by the uORF was seen in transfected MCF-7, MDA MB-231 and Ishikawa cells. Only protein expression was affected by eliminating the uORF; RNA levels were unchanged. This indicates the mechanism is translational rather than being an effect of the introduced point mutations on either mRNA stability or transcription. Eliminating the uORF did not significantly increase expression from similar distal promoter transcript ER-GFP constructs. However, study of in-frame fusions of GFP to the entire proximal and distal uORFs and to their translational start motifs showed that the translational start region of the distal uORF was inherently better at initiating translation than the AUG environment of the proximal promoter transcript uORF. The data indicate there are regulatory properties suppressing expression from the ER translation start which are specific to the unique regions of the ER proximal promoter transcript and these are likely associated with the proximal transcript uORF peptide product.

High-resolution sequence-based DPA1 typing identified two novel DPA1 alleles, DPA1*010303 and DPA1*0303, from a Kenyan population

We report here two novel DPA1 alleles, DPA1*010303 and DPA1*0303, identified from a Kenyan population during sequence-based HLA-DPA1 typing. Molecular cloning and sequencing of multiple clones confirmed that one of the new DPA1 alleles is identical to DPA1*010301 at exon 2, except for a single nucleotide substitution (ACG ACC) at codon 15. The new allele has been named by the WHO Nomenclature Committee as DPA1*010303. The second novel DPA1 allele is identical to DPA1*0301, except for a single nucleotide difference (GAA GAC) at codon 28 that changed the amino acid from Glu to Asp. The new allele has been named by the WHO Nomenclature Committee as DPA1*0303. Identification of the two novel DPA1 alleles reflects the genetic diversity of this East African population.

Structural genomics ofCaenorhabditis elegans: structure of the BAG domain

Binding of the BAG domain to the eukaryotic chaperone heat-shock protein (Hsp70) promotes ATP-dependent release of the protein substrate from Hsp70. Although the murine and human BAG domains have been shown to form an antiparallel three-helix bundle, the Caenorhabditis elegans BAG domain is formed by two antiparallel helices, while the third helix is extended away and stabilized by crystal-packing interactions. A small beta-sheet between helices 2 and 3 interferes with formation of the intramolecular three-helix bundle. However, intermolecular three-helix bundles are observed throughout the crystal packing and suggest that stable functional dimers and tetramers can be formed in solution. The structure may represent a new folding type of the BAG domain.

Identification of a novel HLA-DQA1 null allele, DQA1*0403N, from an East African woman

We report a novel DQA1 allele (DQA1*0403N) identified during sequence-based HLA-DQA1 typing of a Kenyan population. The new allele is identical to DQA1*0401 at exon 2 except for a single-nucleotide substitution at codon 53, changing it from lysine to a stop codon (CAA-->TAA). The substitution at codon 53 was confirmed by sequencing two separate polymerase chain reaction products and by sequencing multiple clones obtained following TOPO-TA cloning. The resulting stop codon at position of codon 53 in exon 2 is predicted to produce a non-functional DQA1 alpha-chain. The new allele has been named by the WHO nomenclature committee as DQA1*0403N. This is the first report of a null allele detected in the DQA1 gene.

Detection of the differentially expressed gene IGF-binding protein-related protein-1 and analysis of its relationship to fasting glucose in Chinese colorectal cancer patients

IGF-binding protein-related protein-1 (IGFBP-rP1) is a member of the IGF axis. In our previous work, we separated cDNA fragments of IGFBP-rP1 from colonic adenocarcinoma and normal mucosa cDNA subtraction libraries. In this study, we compared the expression of IGFBP-rP1 by semi-quantitative RT-PCR and immunohistochemistry among colorectal cancer, adenoma, normal tissue adjacent to cancer site, and normal tissue. Associations between IGFBP-rP1 and plasma glucose were further explored. We found that the mRNA level of IGFBP-rP1 was highest in cancer, moderate in adenoma and tissue adjacent to the cancer site and lowest in normal tissue (P<0.05). A significant difference was found in the immunoreactivity of IGFBP-rP1 between paired normal and cancer tissue (P<0.05). Tumor samples with upregulated expression of IGFBP-rP1 in invading tumor cells showed an increased frequency of metastasis to the lymph node, an increased depth of infiltration and stronger staining of IGFBP-rP1 compared with other samples (P<0.05). The fasting glucose level was significantly correlated with the staining of IGFBP-rP1 in cancer tissue (Spearman's rho=0.4, P<0.000). Thus, we concluded overexpression of IGFBP-rP1 might play an important role in the initiation and promotion of colorectal cancer. IGFBP-rP1 expression may also be associated with fasting glucose level and the presence of diabetes mellitus.

High resolution sequence-based DPB1 typing identified two novel DPB1 alleles, DPB1*9401 and DPB1*9501, from a Kenyan population

Two novel DPB1 alleles, DPB1*9401 and DPB1*9501, were identified from a Kenyan population during sequence-based HLA-DPB1 typing. Molecular cloning and sequencing of multiple clones confirmed that one of the new DPB1 alleles is identical to DPB1*0402 at exon 2 except for a single nucleotide substitution (CGG -->TGG), changing codon 70 from Arg to Trp. The new allele has been named DPB1*9401. This is the first report of polymorphism at codon 70 of HLA-DPB1 alleles. New codon combinations have been identified in another novel DPB1 allele named DPB1*9501. The extensive diversity at DPB1 locus of this East African population is being revealed by high resolution sequence-based DPB1 typing.

Leukotriene synthesis by epithelial cells

Leukotrienes (LTs) are intercellular signaling molecules that evoke a variety of responses. They are best known as potent promoters of inflammation. Normally, LTs are produced primarily by leukocytes. As a result, current models regarding the production of LTs in the context of disease focus on the leukocytes as the site of production. Structural cells, including epithelial cells, are typically relegated to supportive roles. It is recognized that epithelial cells normally contain all the components necessary for LT synthesis except the enzyme 5-lipoxygenase (5-LO). There is accumulating evidence that some populations of epithelial cells normally express low levels of 5-LO and can synthesize LTs autonomously. Moreover, certain factors, including bacterial and viral infection, can promote the expression of 5-LO in airway, gastrointestinal and skin epithelial cells. The appearance of active 5-LO enzyme in epithelial cells at these sites may contribute to diseases like cancer, colitis and psoriasis. This paper reviews the state of our knowledge regarding the expression of 5-LO in epithelial cells, the factors that modify that expression, and the implications regarding pathogenesis.

New genomic resources for the honey bee(Apis mellifera L.): development of a deep-coverage BAC library and a preliminary STC database

We have constructed a bacterial artificial chromosome (BAC) library for a European honey bee strain using the cloning enzyme HindIII in order to develop resources for structural genomics research. The library contains 36,864 clones (ninety-six 384-well plates). A random sampling of 247 clones indicated an average insert size of 113 kb (range = 27 to 213 kb) and 2% empty vectors. Based on an estimated genome size of 270 Mb, this library provides approximately 15 haploid genome equivalents, allowing >99% probability of recovering any specific sequence of interest. High-density colony filters were gridded robotically using a Genetix Q-BOT in a 4 x 4 double-spotted array on 22.5-cm2 filters. Screening of the library with four mapped honey bee genomic clones and two bee cDNA probes identified an average of 21 positive signals per probe, with a range of 7-38 positive signals per probe. An additional screening was performed with nine aphid gene fragments and one Drosophila gene fragment resulting in seven of the nine aphid probes and the Drosophila probe producing positive signals with a range of 1 to 122 positive signals per probe (average of 45). To evaluate the utility of the library for sequence tagged connector analysis, 1152 BAC clones were end sequenced in both forward and reverse directions, giving a total of 2061 successful reads of high quality. End sequences were queried against SWISS-PROT, insect genomic sequence GSS, insect EST, and insect transposable element databases. Results in spreadsheet format from these searches are publicly available at the Clemson University Genomics Institute (CUGI) website in a searchable format (http://www.genome.clemson.edu/projects/stc/bee/AM__Ba/).

[A new method for evaluating malaria surveillance effectiveness--establishment and application of an index system]

AIM

To establish a comprehensive index system which is suitable for evaluating the effectiveness of malaria surveillance schemes.

METHODS

Delphi method was used to screen the existed effectiveness evaluation indices by experts to determine key indices and weighted coefficients.

RESULTS

Three indices, i.e. autochthonous incidence, ratio of cases detected (ROCD) and ratio of introduced/imported cases were selected. Their weighted coefficients were 0.36, 0.31 and 0.33, respectively. An index system named the malaria surveillance effectiveness index (MSEI) was built up and formulated as [formula: see text] which was applied to study cost-effectiveness of the two malaria surveillance schemes (A and B). According to the formula, the MSEIs in the study areas using the schemes A and B were 48.56 and 45.93, respectively. However, the cost for increasing a score of MSEI by implementing the scheme A was four times as high as that by implementing the scheme B.

CONCLUSION

The MSEI is practicable for evaluating the overall effectiveness of malaria surveillance schemes, especially in the cost-effectiveness analysis and health-economic evaluation.

[Diagnosis of Falciparum malaria by immunochromatographic test]

AIM

To evaluate the applicability of rapid immunochromatographic test(ICT) for diagnosing falciparum malaria in outpatient clinics in endemic area.

METHODS

With thick blood smear method as control, ICT was used for the detection of P. falciparum.

RESULTS

The sensitivity and specificity of ICT in detecting P. falciparum was 94.7% and 90.3%, respectively. No cross-reaction with P. vivax was found (P > 0.05).

CONCLUSION

ICT is much more rapid and simple than thick blood smear method for the diagnosis of falciparum malaria, and can be applied in the outpatient clinics in endemic area.

[Follow-up study of human herpesvirus 6 and human cytomegalovirus infection in organ transplantation recipients]

OBJECTIVE

To trace the study of the prevalence and adverse factors of human herpesvirus 6(HHV-6) and human cytomegalovirus(HCMV) infection in organ transplantation recipients.

METHOD

Blood and urine specimens were detected by virus isolation, polymerase chain reaction(PCR), and indirect immunofluorescent assay.

RESULT

HCMV and HHV-6 isolation rate were 25.8% and 32.3%, respectively. Anti-HCMV IgM and anti-HHV-6 IgM positive rates before operation were 0% and 3.2%, their positive rates after operation were 19.4% and 25.8%, respectively. HCMV-DNA and HHV-6-DNA positive rates before operation were 35.5% and 45.2%; their positive rates after operation were 45.2% and 61.3%, and kept the high positive rates for a long period. The patients who died within 3 months were all complicated by HCMV and/or HHV-6 productive infection. The productive infection rates of HCMV and HHV-6 were 25.8% and 32.2%, respectively.

CONCLUSION

The majority of HCMV and HHV-6 infection are reactivation. Productive infection attack at 2 weeks after operation, reaches the peak at 3-4 weeks after operation, and attacks at anytime within 3 months. HCMV and/or HHV-6 productive infection are fatal to recipients.

[Examination of human herpesvirus-6 antibody in blood patients serum]

To know the infection state of human herpesvirus-6(HHV-6) in leukemia, lymphoma, myeloproliferative disorder syndrome, and multiple myeloma, indirect fluoroimmunoassay was taken to examine the rate of HHV-6's antibody. The results were that: the patient's rate of HHV-6 antibody was 75.6% (149/197), the blood donor's rate was 45.6% (115/252), there was a significant difference between them (P < 0.01). The results show that the examined patients are infected by HHV-6, which has a good relationship with leukemia, lymphoma, myeloproliferative disorder syndrome, and multiple myeloma.

HLA-A and HLA-B in Kenya, Africa: allele frequencies and identification of HLA-B*1567 and HLA-B*4426

HLA-A and HLA-B alleles of a population from Kenya, Africa were examined by sequencing exon 2 and exon 3 DNA and typing using a Taxonomy-based Sequence-analysis (TBSA) method. Extensive diversities were observed at both HLA-A and HLA-B loci in this population. Forty-one HLA-A alleles were identified from 159 unrelated individuals. The most frequently observed alleles were A*6802 (11.64%), A*02011/09 (9.75%), A*7401/02 (9.43%), A*3001 (7.86%), A*3002 (7.23%) and A*3601 (6.6%). Forty-nine HLA-B alleles were identified in 161 unrelated individuals, including two novel alleles, B*1567 and B*4426. The most frequently observed HLA-B alleles were B*5301 (9.01%), B*5801 (8.38%), B*4201 (7.76%), B*1503 (7.14%), B*1801 (6.21%), and B*5802 (5.90%). The most frequently observed HLA-A-B haplotypes were A*3601-B*5301 (3.55%) and A*3001-B*4201 (3.19%), followed by A*7401/02-B*5801 (2.84%), A*7401/02-B*5802 (2.84%) and A*02011/09-B*1503 (2.13%). Linkage disequilibrium and chi2 analysis showed the association of these HLA-A-B haplotypes at the antigen level to be significant. The frequencies of HLA-A and HLA-B alleles from the Kenyan population were compared with that of a population from Cameroon. The difference in allele and haplotype frequency distributions partly reflected the different ethnic composition of these two African populations.

Phenacetin O-deethylation in extrahepatic tissues of rats

Phenacetin O-deethylation is a marker reaction of CYP450 1A2 activity. The drug-metabolizing enzyme is constitutively expressed in liver. In this study, an in vivo rat model for assessment of extrahepatic metabolism was used to investigate phenacetin O-deethylation and the alterations in the disposition of phenacetin due to the loss of liver function. Rats were divided into the model and normal control groups. The model was established according to our previously described method. The concentrations of phenacetin and its major metabolites acetaminophen, glucuronate-acetaminophen and sulfate-acetaminophen in plasma and urine were determined by HPLC. 30 min after intravenous administration of 0.16% phenacetin 10 mg x kg(-1), plasma acetaminophen in the model group was only 3.6% of that in the control group (0.09+/-0.04 microg x mL(-1) vs 2.49+/-0.85 microg x mL(-1), n = 8). 30 min after intragastric injection of 0.4% phenacetin 30 mg x kg(-1), plasma acetaminophen formation was very slight, about 8.6% of plasma phenacetin in the model group (0.74+/-0.43 microg x mL(-1) acetaminophen vs 8.57+/-8.42 microg x mL(-1) phenacetin) and 6.8% in the control group (1.06+/-0.59 microg x mL(-1) acetaminophen vs 15.47+/-7.21 microg x mL(-1) phenacetin, n = 8); no significant differences were observed in plasma phenacetin, total acetaminophen and the ratio of acetaminophen to phenacetin between control and model groups. In the urine collected for 3 h after intravenous administration of 0.16% phenacetin 10 mg x kg(-1), the total recovery of acetaminophen (as free, glucuronate- and sulfate-acetaminophen ) in the model group was 4.6% of that in the control group (4.47+/-4.27 microg vs 96.63+/-8.50 microg, n = 6), but phenacetin recovery in the model group was 9 times higher than that in the control group (15.03+/-17.72 microg vs 1.66+/-0.50 microg). The results indicate that phenacetin O-deethylation in the extrahepatic tissues and the first-pass metabolism of the probe compound seem to be negligible in rats, but the renal excretion of phenacetin, as a compensation, dramatically increases in model rats.

Control of early seed development

Seed development requires coordinated expression of embryo and endosperm and has contributions from both sporophytic and male and female gametophytic genes. Genetic and molecular analyses in recent years have started to illuminate how products of these multiple genes interact to initiate seed development. Imprinting or differential expression of paternal and maternal genes seems to be involved in controlling seed development, presumably by controlling gene expression in developing endosperm. Epigenetic processes such as chromatin remodeling and DNA methylation affect imprinting of key seed-specific genes; however, the identity of many of these genes remains unknown. The discovery of FIS genes has illuminated control of autonomous endosperm development, a component of apomixis, which is an important developmental and agronomic trait. FIS genes are targets of imprinting, and the genes they control in developing endosperm are also regulated by DNA methylation and chromatin remodeling genes. These results define some exciting future areas of research in seed development.

Response correlation maps of neurons in the mammalian olfactory bulb

To define the relationship between glomerular activation patterns and neuronal olfactory responses in the main olfactory bulb, intracellular recordings were combined with optical imaging of intrinsic signals. Response correlation maps (RCMs) were constructed by correlating the fluctuations in membrane potential and firing rate during odorant presentations with patterns of glomerular activation. The RCMs indicated that mitral/tufted cells were excited by activation of a focal region surrounding their principal glomerulus and generally inhibited by activation of more distant regions. However, the structure of the RCMs and the relative contribution of excitatory and inhibitory glomerular input evolved and even changed sign during and after odorant application. These data suggest a dynamic center-surround organization of mitral/tufted cell receptive fields.

[Preliminary study on citral impaires the Aspergillus flavus membrane]

Compared with the normally growing A. flauas, the content as below was determined: the utilization ratio to protein and reducing sugar of hyphostroma poisened by citral, the activity of [Na+, K+]-ATPase capable of decomposition ATP, and the seepagevity ratio of electrolyte. In addition, the shape change in spore was observed via the scanning electron microscope (SEM) and the fast multi-channel micro-spectrophotomer (FMCM). The result above all suggested facts as following after it's poised by the citral in MIC. The surface of hyphostroma and spore turned into be porous and rough. The pass trace on spore shriveled and closed. The rate of conduct electricity increased by 52.8%. The utilization ratio to protein and reducing sugar respectively decreased 61.5% and 44.3%. The rate of spore's sprout dropped to 61.4%. The molecular structure of membrane was so distinctly changed that it lost the selective permeability. There was inhibition on hyphostroma growth and spore sprout.