Hereditary cancer syndrome-associated pathogenic variants are common in patients with hematologic malignancies subsequent to primary solid cancer

Background: As the number of long-term survivors of solid cancers keeps increasing, risk assessment of secondary hematologic malignancies is important for the prognosis of the patient. Germline genetic predisposition to secondary hematologic malignancy has been studied widely in myeloid neoplasms and rarely in lymphoid neoplasms. This study aimed to profile the mutational spectrums of patients with subsequent lymphoid tissue neoplasm to shed some light on the understudied area. Methods: In total, 39 patients who had primary solid cancer and subsequent hematologic malignancies were enrolled. We performed two next-generation sequencing (NGS) panel tests encompassing hereditary cancer predisposition genes and genes related to clonal hematopoiesis of indeterminate potential (CHIP). All statistical analyses were performed using R 3.5.1. Results: We found 8 of 39 patients with germline mutations in cancer predisposition genes; 4 of 18 patients had therapy-related myeloid neoplasms (22.2%); and 4 of 15 patients had secondary lymphoid malignancies (26.7%). Notably, of 14 patients who initially suffered from thyroid cancer, 5 patients (35.7%) had germline mutations. Malignancy of lymphoid tissue showed no association with radioactive iodine therapy but was observed to a greater extent in germline mutation-positive thyroid cancer patients regardless of their history of treatment. We observed that 24 of 39 patients (61.5%) were CHIP carriers. Patients who had secondary lymphoid malignancy were less likely to have CHIP than those who had myeloid malignancy. Conclusions: In patients with primary solid cancer who are planning to undergo cytotoxic chemotherapy, radiotherapy, or radioactive iodine therapy, an initial assessment with germline mutation testing using an expanded NGS panel, including low, moderate, and high-risk cancer-associated genes, and somatic CHIP mutation testing can screen the patients who are at risk of developing therapy-related myeloid and lymphoid malignancies. Through careful screening and monitoring throughout the treatment process, patients can benefit from the early detection of secondary malignancies and receive proper treatment.

Quantitative and Qualitative QC of Next-Generation Sequencing for Detecting Somatic Variants: An Example of Detecting Clonal Hematopoiesis of Indeterminate Potential

BACKGROUND

Because next-generation sequencing (NGS) for detecting somatic mutations has been adopted in clinical fields, both qualitative and quantitative QC of the somatic variants through whole coding regions detected by NGS is crucial. However, specific applications or guidelines, especially for quantitative QC, are currently insufficient. Our goal was to devise a practical approach for both quantitative and qualitative QC using an example of detecting clonal hematopoiesis of indeterminate potential (CHIP).

METHODS

We applied the QC scheme using commercial reference materials and in-house QC materials (IQCM) composed of haplotype map and cancer cell lines for monitoring CHIP.

RESULTS

This approach efficiently validated a customized CHIP NGS assay. Accuracy, analytical sensitivity, analytical specificity, qualitative precision (concordance), and limit of detection achieved were 99.87%, 98.53%, 100.00%, 100.00%, and 1.00%, respectively. The quantitative precision analysis also had a higher CV percentage at a lower alternative read depth (R2 = 0.749∼0.858). Use of IQCM ensured more than 100-fold reduction in the cost per run compared with that achieved using commercial reference materials.

CONCLUSION

Our approach determined the general analytical performance of NGS for detecting CHIP and recognized limitations such as lower precision at a lower level of variant burden. This approach could also be theoretically expanded to a general NGS assay for detecting somatic variants. Considering the reliable NGS results and cost-effectiveness, we propose the use of IQCM for QC of NGS assays at clinical laboratories.

Prenylflavonoids isolated from Macaranga tanarius stimulate odontoblast differentiation of human dental pulp stem cells and tooth root formation via the mitogen-activated protein kinase and protein kinase B pathways

AIM

To identify odontogenesis-promoting compounds and examine the molecular mechanism underlying enhanced odontoblast differentiation and tooth formation.

METHODOLOGY

Five different nymphaeols, nymphaeol B (NB), isonymphaeol B (INB), nymphaeol A (NA), 3'-geranyl-naringenin (GN) and nymphaeol C (NC) were isolated from the fruit of Macaranga tanarius. The cytotoxic effect of nymphaeols on human DPSCs was observed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The effect of nymphaeols on odontoblast differentiation was analysed with Alizarin Red S staining and odontoblast marker expression was assessed using real-time polymerase chain reaction and Western blot analysis. The molecular mechanism was investigated with Western blot analysis. In order to examine the effect of INB on dentine formation in the developing tooth germ, INB-soaked beads were placed under the tooth bud explants in the collagen gel; thereafter, the tooth bud explant-bead complexes were implanted into the sub-renal capsules for 3 weeks. Tooth root formation was analysed using micro-computed tomography and histological analysis. Data are presented as mean ± standard error (SEM) values of three independent experiments, and results are compared using a two-tailed Student's t-test. The data were considered to have statistical significance when the P-value was less than 0.05.

RESULTS

Three of the compounds, NB, INB, and GN, did not exert a cytotoxic effect on human DPSCs. However, INB was most effective in promoting the deposition of calcium minerals in vitro (P < 0.001) and induced the expression of odontogenic marker genes (P < 0.05). Moreover, this compound strongly induced the phosphorylation of mitogen-activated protein (MAP) kinases and protein kinase B (AKT) (P < 0.05). The inhibition of p38 MAP, c-Jun N-terminal kinase (JNK), and AKT substantially suppressed the INB-induced odontoblast differentiation (P < 0.001). In addition, isonymphaeol B significantly induced the formation of dentine and elongation of the tooth root in vivo (P < 0.05).

CONCLUSIONS

Prenylflavonoids, including INB, exerted stimulatory effects on odontoblast differentiation and tooth root and dentine formation via the MAP kinase and AKT signalling pathways. These results suggest that nymphaeols could stimulate the repair processes for dentine defects or injuries.

DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data

BACKGROUND

Targeted next-generation sequencing (NGS) is increasingly being adopted in clinical laboratories for genomic diagnostic tests.

RESULTS

We developed a new computational method, DeviCNV, intended for the detection of exon-level copy number variants (CNVs) in targeted NGS data. DeviCNV builds linear regression models with bootstrapping for every probe to capture the relationship between read depth of an individual probe and the median of read depth values of all probes in the sample. From the regression models, it estimates the read depth ratio of the observed and predicted read depth with confidence interval for each probe which is applied to a circular binary segmentation (CBS) algorithm to obtain CNV candidates. Then, it assigns confidence scores to those candidates based on the reliability and strength of the CNV signals inferred from the read depth ratios of the probes within them. Finally, it also provides gene-centric plots with confidence levels of CNV candidates for visual inspection. We applied DeviCNV to targeted NGS data generated for newborn screening and demonstrated its ability to detect novel pathogenic CNVs from clinical samples.

CONCLUSIONS

We propose a new pragmatic method for detecting CNVs in targeted NGS data with an intuitive visualization and a systematic method to assign confidence scores for candidate CNVs. Since DeviCNV was developed for use in clinical diagnosis, sensitivity is increased by the detection of exon-level CNVs.

Uterine rupture during labor in women with twice successful vaginal births after cesarean delivery

Uterine rupture during labor is a serious complication resulting in maternal and neonatal morbidity and mortality. We present the extremely rare case of a 38-year-old gravid woman admitted with labor pain at term, about to experience a uterine rupture during labor. She had previously twice delivered vaginally, and during her third pregnancy had a low transverse Cesarean section. Prior to arriving at the hospital with labor pains, she had routine prenatal care with normal prenatal laboratory tests. One day the woman reported to having sudden epigastric pain, and 40 minutes after her admission a pelvic exam was completed. The unborn baby had a persistent revealed, and a live neonate was promptly delivered with an Apgar score of 1 at one minute and 5 at five minutes. On the fifth postoperative day the woman and her baby were discharged home with no maternal and neonatal complications.

Mutations in DDX58, which encodes RIG-I, cause atypical Singleton-Merten syndrome

Singleton-Merten syndrome (SMS) is an autosomal-dominant multi-system disorder characterized by dental dysplasia, aortic calcification, skeletal abnormalities, glaucoma, psoriasis, and other conditions. Despite an apparent autosomal-dominant pattern of inheritance, the genetic background of SMS and information about its phenotypic heterogeneity remain unknown. Recently, we found a family affected by glaucoma, aortic calcification, and skeletal abnormalities. Unlike subjects with classic SMS, affected individuals showed normal dentition, suggesting atypical SMS. To identify genetic causes of the disease, we performed exome sequencing in this family and identified a variant (c.1118A>C [p.Glu373Ala]) of DDX58, whose protein product is also known as RIG-I. Further analysis of DDX58 in 100 individuals with congenital glaucoma identified another variant (c.803G>T [p.Cys268Phe]) in a family who harbored neither dental anomalies nor aortic calcification but who suffered from glaucoma and skeletal abnormalities. Cys268 and Glu373 residues of DDX58 belong to ATP-binding motifs I and II, respectively, and these residues are predicted to be located closer to the ADP and RNA molecules than other nonpathogenic missense variants by protein structure analysis. Functional assays revealed that DDX58 alterations confer constitutive activation and thus lead to increased interferon (IFN) activity and IFN-stimulated gene expression. In addition, when we transduced primary human trabecular meshwork cells with c.803G>T (p.Cys268Phe) and c.1118A>C (p.Glu373Ala) mutants, cytopathic effects and a significant decrease in cell number were observed. Taken together, our results demonstrate that DDX58 mutations cause atypical SMS manifesting with variable expression of glaucoma, aortic calcification, and skeletal abnormalities without dental anomalies.

Top-up operation at Pohang Light Source-II

After three years of upgrading work, PLS-II (S. Shin, Commissioning of the PLS-II, JINST, January 2013) is now successfully operating. The top-up operation of the 3 GeV linear accelerator had to be delayed because of some challenges encountered, and PLS-II was run in decay mode at the beginning in March 2012. The main difficulties encountered in the top-up operation of PLS-II are different levels between the linear accelerator and the storage ring, the 14 narrow gap in-vacuum undulators in operation, and the full energy injection by 3 GeV linear accelerator. Large vertical emittance and energy jitter of the linac were the major obstacles that called for careful control of injected beam to reduce beam loss in the storage ring during injection. The following measures were taken to resolve these problems: (1) The high resolution Libera BPM (see http://www.i-tech.si) was implemented to measure the beam trajectory and energy. (2) Three slit systems were installed to filter the beam edge. (3) De-Qing circuit was applied to the modulator system to improve the energy stability of injected beam. As a result, the radiation by beam loss during injection is reduced drastically, and the top-up mode has been successfully operating since 19th March 2013. In this paper, we describe the experimental results of the PLS-II top-up operation and the improvement plan.

CACG: a database for comparative analysis of conjoined genes

A conjoined gene is defined as one formed at the time of transcription by combining at least part of one exon from each of two or more distinct genes that lie on the same chromosome, in the same or opposite orientation, which translate independently into different proteins. We comparatively studied the extent of conjoined genes in thirteen genomes by analyzing the public databases of expressed sequence tags and mRNA sequences using a set of computational tools designed to identify conjoined genes on the same DNA strand or opposite DNA strands of the same genomic locus. The CACG database, available at http://cgc.kribb.re.kr/map/, includes a number of conjoined genes (7131-human, 2-chimpanzee, 5-orangutan, 57-chicken, 4-rhesus monkey, 651-cow, 27-dog, 2512-mouse, 263-rat, 1482-zebrafish, 5-horse, 29-sheep, and 8-medaka) and is very effective and easy to use to analyze the evolutionary process of conjoined genes when comparing different species.

Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing

Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.

SpiroESTdb: a transcriptome database and online tool for sparganum expressed sequences tags

Background

Sparganum (plerocercoid of Spirometra erinacei) is a parasite that possesses the remarkable ability to survive by successfully modifying its physiology and morphology to suit various hosts and can be found in various tissues, even the nervous system. However, surprisingly little is known about the molecular function of genes that are expressed during the course of the parasite life cycle. To begin to decipher the molecular processes underlying gene function, we constructed a database of expressed sequence tags (ESTs) generated from sparganum.

Findings

SpiroESTdb is a web-based information resource that is built upon the annotation and curation of 5,655 ESTs data. SpiroESTdb provides an integrated platform for expressed sequence data, expression dynamics, functional genes, genetic markers including single nucleotide polymorphisms and tandem repeats, gene ontology and KEGG pathway information. Moreover, SpiroESTdb supports easy access to gene pages, such as (i) curation and query forms, (ii) in silico expression profiling and (iii) BLAST search tools. Comprehensive descriptions of the sparganum content of all sequenced data are available, including summary reports. The contents of SpiroESTdb can be viewed and downloaded from the web (http://pathod.cdc.go.kr/spiroestdb).

Conclusions

This integrative web-based database of sequence data, functional annotations and expression profiling data will serve as a useful tool to help understand and expand the characterization of parasitic infections. It can also be used to identify potential industrial drug targets and vaccine candidate genes.

Feasibility of nonthermal atmospheric pressure plasma for intracoronal bleaching

AIM

To investigate the effect of nonthermal atmospheric pressure plasma on intracoronal tooth bleaching in blood stained human teeth.

METHODOLOGY

Forty extracted single-root and blood stained human teeth were used. The teeth were randomly divided into two groups (n=20): group 1 received 30% HP activated by nonthermal atmospheric pressure plasma in the pulp chamber for 30 min, whilst group 2 received 30% HP alone in the pulp chamber for 30 min. The overall colour changes (ΔE) were assessed using the Commission Internationale de L'Eclairage (CIE) Lab Colour System. The data were analysed using Student's t-test to determine the significant differences.

RESULTS

The temperature of all teeth was maintained at approximately 37 °C during plasma bleaching. The plasma treatment with 30% HP resulted in significantly higher bleaching efficacy compared to 30% HP alone in discoloured teeth (P<0.05). The average ΔE values of group 1 and group 2 were 9.24 (0.37) and 4.47 (1.62), respectively, at 30 min.

CONCLUSIONS

The application of nonthermal atmospheric pressure plasma to intracoronal bleaching could be a novel and efficient therapy in the bleaching of haemorrhagically stained teeth.

Whole human exome capture for high-throughput sequencing

We captured the whole human exome by hybridization using synthesized oligonucleotides, based on a high-density microarray design, and we sequenced those captured human exons using high-throughput sequencing on a Genome Sequencer FLX instrument. Of the uniquely mapped reads, 71% fell within target regions, and these corresponded to coverage of 94% of human genes, 87% of exons, and 70% of the total base-pair length of the CCDS set. Our study provides strong evidence for the practical usefulness of this method on a genome-wide scale, showing the resequenced whole human exome database with 501 microRNAs and 307 novel SNPs.

Comparative genomic analysis of the false killer whale (Pseudorca crassidens) LMBR1 locus

The sequencing and comparative genomic analysis of LMBR1 loci in mammals or other species, including human, would be very important in understanding evolutionary genetic changes underlying the evolution of limb development. In this regard, comparative genomic annotation of the false killer whale LMBR1 locus could shed new light on the evolution of limb development. We sequenced two false killer whale BAC clones, corresponding to 156 kb and 144 kb, respectively, harboring the tightly linked RNF32, LMBR1, and NOM1 genes. Our annotation of the false killer whale LMBR1 gene showed that it consists of 17 exons (1473 bp), in contrast to 18 exons (1596 bp) in human, and it displays 93.1% and 95.6% nucleotide and amino acid sequence similarity, respectively, compared with the human gene. In particular, we discovered that exon 10, deleted in the false killer whale LMBR1 gene, is present only in primates, and this fact strongly implies that exon 10 might be crucial in determining primate-specific limb development. ZRS and TFBS sequences have been well conserved across 11 species, suggesting that these regions could be involved in an important function of limb development and limb patterning. The neighboring gene RNF32 showed several lineage-conserved exons, such as exons 2 through 9 conserved in eutherian mammals, exons 3 through 9 conserved in mammals, and exons 5 through 9 conserved in vertebrates. The other neighboring gene, NOM1, had undergone a substitution (ATG&rarr;GTA) at the start codon, giving rise to a 36 bp shorter N-terminal sequence compared with the human sequence. Our comparative analysis of the false killer whale LMBR1 genomic locus provides important clues regarding the genetic regions that may play crucial roles in limb development and patterning.

Comparative analysis of expressed sequence tags from the white-rot fungi (Phanerochaete chrysosporium)

Comprehensive analysis of the transcriptome of the P. chrysosporium is a useful approach to improve our understanding of its special and unique enzyme system and fungal evolution in molecular and industrial aspects. In order to unveil the functional diversity of this white-rot fungus in gene level and the expression patterns of its genes, in this study we carried out sequencing and annotation of 4,917 P. chrysosporium expressed sequence tags (ESTs). Through our bioinformatic ESTs analysis, we elucidated that 1,751 genes were derived from the present dataset of 4,917 ESTs, based on clustering and comparative genomic analyses of the ESTs. Of the 1,751 unique ESTs, 1,006 (57.5%) had homologues and orthologues in similarity searches. Our P. chrysosporium ESTs showed many genes for encoding 23 secreted proteins, many proteins for the degradation of cellulose and hemicelluloses, and heat shock proteins for stress resistance, which explain the reason why P. chrysosporium is very important and unique white-rot fungus in dealing with contaminated resources and in degrading lignin and in applying this organism to several industrial aspects.In addition, comparative analysis has shed the fresh light on the mystery about how its unique enzyme system and stress resistance have been evolved differently from its closest relatives.

Identification of a Novel Garlic Cellulase Gene

Genes encoding cellulase enzymes have been investigated in various plants due to the importance of cellulase enzymes in industrial applications, especially in the conversion of biomass into biofuels. Although several cellulase genes have been cloned and characterized, little is known about cellulase genes from garlic or enzyme activities of their gene products. In this study, a cellulase gene from garlic was cloned and characterized in gene and protein levels for the first time. The DNA sequence of the garlic cellulase gene showed 81% identity with the sequence of the endo-beta-1,4-glucanase of Pisum sativum. The open reading frame of this gene is 1,506 bp, which corresponds to 501 deduced amino acids. We identified the novel ORF region, which was translated into a 55.2 kDa protein using the protein expression vector, pET28a, in Escherichia coli and we confirmed that this protein has cellulase activity in vitro. Our study demonstrates that garlic is very useful, not only for the culinary and pharmaceutical industries, but also as an excellent natural source of various kinds of important genes and enzymes.

Sarcomatoid renal cell carcinoma in a renal transplant recipient

The incidence of transplanted kidneys derived from elderly donors is increasing because of the larger waiting lists and greater age of patients with end-stage renal failure. Compared with young donors, one of the problems is the heightened risk of neoplasm transmission. We report 2 cases of kidney recipients, both of whom developed a sarcomatoid renal cell carcinoma after receiving a kidney transplant from the same 68-year-old male donor, who did not show signs of a neoplasm on a previous abdominal ultrasound or a pretransplant biopsy. The first recipient was a 66-year-old woman who developed a kidney mass with several urologic obstructive complications, tumor dissemination, and death at 9 months after kidney transplantation. The second recipient was a 48-year-old asymptomatic man with normal renal function, who was studied after the results of the first recipient, revealing another renal tumor. Transplant nephrectomy was performed and a peritoneal implant was resected. The patient is alive without evidence of a neoplasm after 18 months. Herein we have discussed the mechanisms of neoplasm transmission in kidney transplantation and possible strategies for its prevention and treatment.

The effect of pneumoperitoneum in the steep Trendelenburg position on cerebral oxygenation

BACKGROUND

daVinci robot-assisted laparoscopic radical prostatectomy (RALP) requires pneumoperitoneum in the steep Trendelenburg position, which results in increased intracranial pressure and cerebral blood flow. The aim of this study was to evaluate the effect of pneumoperitoneum in a 30 degrees Trendelenburg position on cerebral oxygenation using regional cerebral oxygen saturation (rSO2).

METHODS

Thirty-two male patients of ASA I and II physical status without previous episodes of cerebral ischemia or hemorrhage undergoing daVinci RALP were enrolled. The rSO2 was continuously monitored with near-infrared spectroscopy (INVOS) 5100) during the study period. Measurements were obtained immediately after anesthesia induction (T0; baseline), 5 min after a 30 degrees Trendelenburg position (T1), 5 min after 15 mmHg pneumoperitoneum in a supine position (T2), 30, 60 and 120 min after the pneumoperitoneum in a Trendelenburg position (T3, T4 and T5, respectively) and after desufflation in a supine position (T6).

RESULTS

The change in the left and right rSO2 was statistically significant (Left P=0.004 and Right P=0.023). Both the right and the left rSO2 increased significantly during pneumoperitoneum in a Trendelenburg position (from T3 to T5) and at T6 compared with the baseline value at T0. The partial pressure of carbon dioxide (PaCO2) was increased significantly at T2, T3, T5 and T6 compared with the baseline value at T0.

CONCLUSIONS

During daVinci RALP, cerebral oxygenation, as assessed by rSO2, increased slightly, which suggests that the procedure did not induce cerebral ischemia. The PaCO2 should be maintained within the normal limit during pneumoperitoneum in a Trendelenburg position in patients undergoing daVinci RALP because the rSO2 increased in conjunctions with the increase in PaCO2.

GarlicESTdb: an online database and mining tool for garlic EST sequences

BACKGROUND

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression.

DESCRIPTION

GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The GarlicESTdb web application is freely available at http://garlicdb.kribb.re.kr.

CONCLUSION

GarlicESTdb is the first incorporated online information database of EST sequences isolated from garlic that can be freely accessed and downloaded. It has many useful features for interactive mining of EST contigs and datasets from each library, including curation of annotated information, expression profiling, information retrieval, and summary of statistics of functional annotation. Consequently, the development of GarlicESTdb will provide a crucial contribution to biologists for data-mining and more efficient experimental studies.

PESTAS: a web server for EST analysis and sequence mining

SUMMARY

We have developed a web server for the high-throughput annotation of expressed sequence tags (ESTs) called pipeline for EST analysis service (PESTAS). PESTAS processes entire datasets with an automated pipeline of 13 analytic services, then deposits the data into the MySQL database and transforms it into three kinds of reports: preprocessing, assembling and annotation. All annotated information is provided to the scientist and can be downloaded through a web browser. To get more relevant functional annotation results, a curation function was introduced with which biologists can easily change the best-hit annotation information. We included a gene chip module that detects gene expression differences between libraries by comparing accession number counts from BLAST search results. PESTAS also provides access to the pathway information of KEGG, which is useful for mapping the relationships among networks of annotated enzymes, and is especially valuable for those researchers interested in biological pathways.

AVAILABILITY

PESTAS is available at http://pestas.kribb.re.kr/.

Cubic SiC nano-thin films and nano-wires: high vacuum metal-organic chemical vapor deposition, surface characterization, and application tests

Single-crystalline and epitaxial cubic silicon carbide (beta-SiC) nano-thin films have been deposited on Si(100) substrates at a sample temperature of approximately 900 degrees C using single source precursors by the thermal metal-organic chemical vapor deposition (MOCVD) method. Diethylmethylsilane and 1,3-disilabutane, which contain Si and C atoms in the same molecule, were used as precursors without any carrier or bubbler gas. Upon increasing the deposition temperature from 900 to 950 degrees C, beta-SiC nano-thin films with relatively small crystals and smoother surfaces were created on Si(100) substrates. Moreover, beta-SiC nano-wires with 40 approximately 100 nm in diameter have also been grown selectively on nickel catalyzed Si(100) substrates with dichloromethylvinylsilane by the MOCVD method. The deposition temperature in this case was as low as 800 degrees C under the pressure of 5.0 x 10(-2) Torr. It is worth noting that the initial growth rates of deposited beta-SiC nano-thin films and nano-wires strongly depend on the deposition temperature rather than the time. In order to test the possibility of applications of these materials for electronic components such as field emitter, MEMS, and high-power transistor, we fabricated the nanoelectronic devices using both beta-SiC nano-wires and nano-thin films. With these preliminary application tests, it is expected that SiC nanowires can be used as field emitter and nanoelectronic high-power transistor, and application of the SiC nano-thin films to MEMS is promising as well.

Realization of an e-health system to perceive emergency situations

Emergency situations can occur anywhere and anytime in daily life. In the paper, we present an e-health system to perceive emergency situations of a patient. Using a wearable shirt (BioShirt) and a personal monitoring system (PBM), we obtain the body signals of a user. The monitoring system collects and transmits the vital signs to a personal digital assistant (PDA) via a BlueTooth communication module. To detect emergency from the received data, a simple detection algorithm is performed in the PDA. And the PDA forwards the data to an e-health central monitoring room (ECMR), if necessary. In the ECMR, several operators supervise the registered users based on incoming body signals from each user's device. If an automatic decision-making algorithm generates an emergency alarm, the operators try to contact the corresponding patient and recognize his status. Ultimately if they decide that the patient is an urgent situation, they give phone calls and messages to the emergency center and the patient's medical attendant immediately.

Bran extracts from pigmented rice seeds inhibit tumor promotion in lymphoblastoid B cells by phorbol ester

Using flow cytometry, we quantitatively evaluated anti-tumor-promoting activity of rice bran extracts by measuring inhibition of Epstein-Barr virus early-antigen activation (EBV-EA) induced by the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA). This assay measures anti-tumor-promoting activity and cytotoxicity of target substances using the same batch of cells. Using this short-term procedure, we have determined the anti-tumor-promoting activity of 70% ethanol-water extracts of bran (outer layer) from seeds of five pigmented rice cultivars: Jumlalocal-1, DZ 78, Elwee, LK1-3-6-12-1-1, and LK1A-2-12-1-1. The results show that, compared to an extract from the non-pigmented white cooking rice variety Chuchung, the extracts from the pigmented varieties strongly inhibited phorbol ester-induced tumor promotion in marmoset lymphoblastoid cells B95-8 in vitro. These findings may facilitate development and use of new health-promoting rice varieties.

A novel splice acceptor mutation in the DSPP gene causing dentinogenesis imperfecta type II

The dentin sialophosphoprotein (DSPP) gene (4q21.3) encodes two major noncollagenous dentin matrix proteins: dentin sialoprotein (DSP) and dentin phosphoprotein (DPP). Defects in the human gene encoding DSPP cause inherited dentin defects, and these defects can be associated with bilateral progressive high-frequency sensorineural hearing loss. Clinically, five different patterns of inherited dentin defects are distinguished and are classified as dentinogenesis imperfecta (DGI) types I, II, and III, and dentin dysplasia types I and II. The genetic basis for this clinical heterogeneity is unknown. Among the 11 members recruited from the studied kindred, five were affected with autosomal dominant DGI type II. The mutation (g.1188C-->G, IVS2-3C-->G) lay in the third from the last nucleotide of intron 2 and changed its sequence from CAG to GAG. The mutation was correlated with the affection status and was absent in 104 unaffected individuals (208 alleles) with the same ethnic and geological background. The proband was in the primary dentition stage and presented with multiple pulp exposures. The occlusal surface of his dental enamel was generally abraded, and the dentin was heavily worn and uniformly shaded brown. The dental pulp chambers appeared originally to be within normal limits without any sign of obliteration, but over time (by age 4), the pulp chambers became partially or completely obliterated. The oldest affected member (age 59) showed mild hearing loss at high-frequency (8 kHz). Permanent dentition was severely affected in the adults, who had advanced dental attrition, premature loss of teeth, and extensive dental reconstruction.

Non-linear registration for brain images by maximising feature and intensity similarities with a Bayesian framework

The objective of this work was to provide a new, precise registration of the cortical mantle with a non-linear transformation. Image registration is broadly classified into two types, using intensity similarity and feature similarity. Whereas the former approach has merit in global brain matching, the latter provides a fast registration centred on a region of interest. The hybrid registration proposed in this paper was achieved using a Bayesian framework, which consisted of a likelihood model including intensity similarity and a prior model including feature information and a smoothing constraint. In this approach, each voxel was spatially transformed, so that the distance between corresponding features was shortened and also so that the intensity correlation was maximised. The result of the hybrid method clearly showed a good match of global brain (r = 0.930) by including intensity similarity. Moreover, this method compensated for the approximated sulcus of the feature-based method with intensity information, so that the geometric shape and thickness of the sulcus at the feature-defined region was likely to be registered. The accuracy in the feature-defined area was improved by 33.4% and 7.5% compared with feature-based and intensity-based methods, respectively.

Affinity enrichment of bovine lactoferrin in whey

Bovine lactoferrin was enriched in various whey samples by affinity chromatography using immobilized gangliosides. Bovine gangliosides were isolated from fresh buttermilk using a combination of ultrafiltration and organic extraction. Isolated gangliosides were covalently immobilized onto controlled-pore glass beads. The immobilized matrix contained 66 micrograms of gangliosides per gram of beads. After loading the matrix with reconstituted whey protein isolate (WPI) or whey protein concentrate (WPC), the matrix was washed with sodium phosphate buffer (pH 7) followed by sodium acetate buffer (pH 4) before elution of lactoferrin with 1 M NaCl in sodium acetate buffer. From the intensities of the protein bands in SDS-PAGE, lactoferrin constituted a minimum of 40% of the total protein in the salt eluted sample. WPI, pretrated by heating and ultrafiltration, showed the highest lactoferrin purity among protein sources, while WPI (10% wt/vol) showed the highest recovery. These results show that immobilized gangliosides can be used to enrich the lactoferrin content of whey.

Clinical Features and Prognosis of Lung Cancer with Brain Metastasis

PURPOSE

Brain metastasis is estimated to occur in 20~40% of solid tumor patients and the most common primary tumor is lung cancer. Even though the prognosis of brain metastasis is grave and the 1-year survival rate is only 15%, symptom palliations are made with whole brain radiation therapy. We retrospectively evaluated the clinical features and prognostic factors of lung cancer with brain metastasis.

MATERIALS AND METHODS

From January 1987 to October 1999, 50 lung cancer patients with brain metastasis underwent whole brain radiation therapy. We reviewed the improvement in neurologic symptoms and survival according to the following parameters; performance status, histological type, presence of brain metastasis at the initial diagnosis of lung cancer, presence of extracranial metastasis, multiplicity of brain lesion, presence of primary lung symptom and treatment modalities.

RESULTS

The most frequent symptom with brain metastasis was a headache (50%). Palliation of the headache and other symptoms was achieved in 81% of the patients. Median overall survival after brain metastasis was 21 weeks and the 1 year survival rate was 15%. Patients without extracranial metastasis had a longer median survival than those with, 38 weeks versus 15 weeks, respectively (p=0.01).

CONCLUSION

In lung cancer with brain metastasis, neurologic symptoms can be palliated with whole brain radiation therapy, and in this study among such patients, absence of extracranial metastasis can be a good prognostic factor.

Rapid fractionation of bovine transferrin using immobilized gangliosides

Bovine transferrin (BTF) was fractionated from bovine whey using ganglioside affinity chromatography. After loading the immobilized matrix with a 2% whey solution, the matrix was washed with sodium acetate buffer at pH 4 containing 1 M NaCl before elution of BTF with sodium phosphate buffers at pH 7. Concanavalin-A affinity and ion exchange chromatography were used for further purification. The ganglioside column showed a 74.2% BTF recovery from whey and BTF was enriched to 61% purity with ion exchange chromatography. Bovine transferrin was identified by SDS-PAGE and western analysis. The Concanavalin-A affinity and ion exchange chromatography steps enriched BTF in the samples and removed other whey proteins from ganglioside purified fractions. These results indicate that immobilized ganglioside can be used to fractionate BTF from bovine whey. Our novel ganglioside affinity chromatography is rapid and efficient for the fractionation of BTF from whey.

Differential expression patterns of Runx2 isoforms in cranial suture morphogenesis

Runx2 (previously known as Cbfal/Pebp2alphaA/AML3), a key transcription factor in osteoblast differentiation, has at least two different isoforms using alternative promoters, which suggests that the isoforms might be expressed differentially. Haploinsufficiency of the Runx2 gene is associated with cleidocranial dysplasia (CCD), the main phenotype of which is inadequate development of calvaria. In spite of the biological relevance, Runx2 gene expression patterns in developing calvaria has not been explored previously, and toward this aim we developed three probes: pRunx2, which comprises the common coding sequence of Runx2 and hybridizes with all isoforms; pPebp2alphaA, which specifically hybridizes with the isoform transcribed with the proximal promoter; and pOsf2, which hybridizes with the isoform transcribed with the distal promoter. These probes were hybridized with tissue sections of mouse calvaria taken at various time points in development. Runx2 expression was localized to the critical area of cranial suture closure, being found in parietal bones, osteogenic fronts, and sutural mesenchyme. Pebp2alphaA and Osf2 showed tissue-specific expression patterns. The sites of Pebp2alphaA expression were almost identical to that of pRunx2 hybridization but expression was most intense in the sutural mesenchyme, where undifferentiated mesenchymal cells reside. The Osf2 isoform was strongly expressed in the osteogenic fronts, as well as in developing parietal bones, where osteopontin (OP) and osteocalcin (OC) also were expressed. However, in contrast to Pebp2alphaA, Osf2 expression did not occur in sutural mesenchyme. Pebp2alphaA also was expressed prominently in primordial cartilage that is found under the sutural mesenchyme and is not destined to be mineralized. Thus, Osf2 isoforms contribute to events later in osteoblast differentiation whereas the Pebp2alphaA isoform participates in a wide variety of cellular activities ranging from early stages of osteoblast differentiation to the final differentiation of osteoblasts.

The changes in delivered oxygen fractions using laerdal resuscitator bag with different types of reservoir

One of the disadvantages of the Laerdal resuscitator bag is that it does not deliver a high concentration of oxygen without a reservoir and an appropriate technique of ventilation. With a specific device that is able to compress a resuscitator bag mechanically at a regular volume, ventilator rate, and speed, we evaluated the effects of various factors (the tidal volume, the ventilator rate, the oxygen flow rate, the type of reservoir) of the Laerdal resuscitator bag during positive pressure ventilation that affect the delivered oxygen fraction (FDO2) and also whether 250 mL and 500 mL corrugated tubes could be used as substitutes for the reservoir bag. The 250 mL corrugated tube increased the FDO2 to over 96% with an oxygen flow rate of 15 L/min. The 500 mL corrugated tube increased the FDO2 to over 96% with an oxygen flow rate of 10 L/min regardless of the ventilator rate at a fixed tidal volume of 500 mL. At the identical fixed tidal volume of 500 mL, the 1,600 mL reservoir bag increased the FDO2 to over 92% with an oxygen flow rate of 5 L/min and to over 96% at 7.5 L/min regardless of the ventilator rate. We concluded that the FDO2 of the Laerdal resuscitator bag depends on various factors such as tidal volume, ventilator rate, oxygen flow rate, and type of reservoir and both the 250 mL and 500 mL corrugated tubes can be used as substitutes.

Valgus ankle secondary to acquired fibular pseudoarthrosis in children. Long-term results of the Langenskiöld operation

Nine cases of acquired absence of the fibular shaft were studied to determine the growth contribution of the distal fibula; in 6 cases the absence was caused by osteomyelitis and in 3 cases by trauma. The average valgus and external rotational deformities were 15.2 degrees and 10 degrees, respectively. In 3 of 7 cases surgically treated with Langenskiöld operation or supramalleolar corrective osteotomy, the valgus deformity recurred during the postoperative growth period. The speculated causes of gradual valgus deformity are the loss of physiologic thrust from the proximal to distal fibula, the tethering effect of contracted soft tissue on distal fibula and early physeal closure of the lateral part of the distal tibia due to continuous, uneven axial overloading. The Langenskiöld operation was found effective for the stability of ankle joint in the initial period, but could not prevent the postoperative revascularization of the ankle. However, it is strongly recommended that any types of prophylactic surgery should be carried out before the development of an epiphyseal deformity of distal tibia, and to prevent secondary osteoarthritis of the ankle joint.

The bovine guanylate cyclase GC-E gene and 5' flanking region

The gene encoding the bovine guanylate cyclase isoform E (GC-E) was isolated as a single 18 kb genomic clone and shown to have 20 exons and 19 introns. Comparison of the structure of the GC-E gene with structures of other membrane guanylate cyclase genes indicates that the GC-E is most closely related to the subfamily of sensory guanylate cyclases. Comparison of the GC-E structure with that of the more distantly related guanylate cyclase isoform A (GC-A) gene shows the most divergence in the extracellular and C-terminal regions, but general conservation of introns and exons in the intracellular kinase-like and catalytic domains. RT-PCR from several bovine tissues shows that GC-E is expressed only in the retina. Consistent with this pattern of expression, elements for the retinal-specific transcription factors RET-1, RET-2 and Talpha-1 are located in the 5' flanking promoter region.

Varus and internal rotational deformity of the ankle secondary to distal tibial physeal injury

Nine children who sustained Lauge-Hansen's supination-inversion injury of distal tibial physeal injury with intact distal fibular physis, were followed until their maturity. The average varus deformity was 39 degrees (maximum, 80 degrees) with 23 degrees of internal rotational deformity. The longitudinal growth of the fibula was retarded compared with opposite normal leg. There was early closure of the medial distal tibial physis, gradual upward migration of medial malleolus, and eventually medial subluxation of the ankle; these resulted in gradual varus and internal rotational deformities of the injured ankle. It is thought that the resultant disabling deformity of ankle should be prevented by any means, though presently there are no available effective methods of treatment. It is suggested that the repeated corrective osteotomy should be carried out before epiphyseal deformity of the distal tibia and subluxation of the ankle joint develop.

Markers of bone and cementum formation accumulate in tissues regenerated in periodontal defects treated with expanded polytetrafluoroethylene membranes

Guided tissue regeneration (GTR) is a concept that evolved from the development of membrane-barrier techniques, which allow the repopulation of periodontal wounds by specific cells, resulting in a new attachment apparatus. To help understand the biological mechanisms involved in membrane barrier-led periodontal healing, the present study investigated the macromolecules phenotypic of bone and cementum formation in tissues grown under the GTR barrier by immunolocalization. Periodontal regeneration was initiated by placing barriers on experimentally induced periodontal defects in a Rhesus monkey model. Samples were harvested 6 wk after healing and sections of soft tissues grown under GTR barriers (membrane tissue) were stained with antibodies to bone morphogenetic proteins-2 and 4 (BMP-2, BMP-4), bone morphogenetic protein-7 (OP-1), cementum attachment protein (CAP), osteonectin (OTN) and bone sialoprotein (BSP). Tissues grown in the absence of any barrier device served as a control (control tissue). Membrane periodontal tissues from beneath the ePTFE membrane were comprised of spindle-shaped fibroblast-like cells encased in a dense fibrillar extracellular matrix (ECM). Round-shaped cells aggregated to form nodules. Newly formed hard tissue was conspicuous. A similar, but very disorganized, fiber network was observed in control tissues, but neither nodule formation nor hard tissue was observed. Osteonectin staining was observed in the ECM of membrane tissues and particularly in the area of the connective tissue adjacent to newly formed hard tissue. The dense network of connective tissue fibers was also stained. In control tissues, cells and fiber network had a significantly weaker signal for osteonectin. An intense reaction was observed in membrane tissues stained for BSP, particularly the connective tissue adjacent to the newly formed hard tissue, while the control tissues did not stain for BSP. Cementum attachment protein (CAP) was observed in the connective tissue adjacent to the newly formed hard tissue of the membrane tissues whereas control tissues exhibited no CAP staining. In membrane tissues, BMP-2 and 4 distribution was found to concentrate in nodule areas, in the newly formed hard tissue and in the fiber network, while very faint staining was observed in control sections. The distribution of OP-1 in membrane and control tissues was found to mimic the BMP-2 pattern, but staining was more distributed in hard tissue matrix. When the profile of BMP-2, BMP-4, OP-1, OTN, CAP and BSP staining was analyzed on membrane tissue sections, striking similarities were noted in the connective tissue adjacent to the newly formed hard tissue and in nodular areas. In addition, the localization of BMP-2 and BMP-4 mRNA was investigated in both tissues by in situ hybridization. An intense expression of BMP-2 and 4 transcripts was observed in membrane tissues while control tissues never yielded any positive hybridization signal. The correlation between these histochemical findings strongly suggests that the forming soft tissues under ePTFE membranes contain cells and ECM macromolecules normally associated with bone and cementum.

A status report on helium inductively coupled plasma mass spectrometry

The current status of helium inductively coupled plasma - mass spectrometry (He ICPMS) is examined, its potentials and limitations are reviewed, and a summary of fundamental properties of atmospheric pressure He ICP discharges is presented. Also included are results of He ICPMS studies with a new helium plasma torch (18 mm i.d.) operated at four sets of operating conditions. Under the "cold plasma" condition (600 W forward power), no secondary discharge is observed and ion kinetic energies ranging from 2.0 eV to 9.5 eV for 6 elements (mass range: 39-208) are measured. At higher power levels, the secondary discharge still is strong. In general, detection limits for certain elements are improved by 1-3 orders of magnitude compared to previous data acquired in 1993 with a 13-mm He ICP torch. Elements such as K, Fe, Cr, Mn, Ni, and Co that suffer from spectral interferences in Ar ICPMS can be detected at pg/mL-levels with an analogue detector and a prototype ICPMS instrument having no photon stops or obstacles present in the ion trajectory path.

Characterization of ribosomal frameshifting for expression of pol gene products of human T-cell leukemia virus type I

For study of the pol gene expression of human T-cell leukemia virus type I (HTLV-I), RNA was transcribed in vitro from proviral DNA and translated in rabbit reticulocyte lysates. This cell-free translation resulted in two major translation products representing the Gag and Gag-Pro polyproteins. By contrast, the Gag-Pro-Pol polyprotein could be readily observed only when translation was performed with mutant mRNA in which the protease (pro) reading frame was aligned to gag to eliminate the frameshifting event in the gag-pro overlap. The results indicated that two independent ribosomal frameshifting events are required for expression of the HTLV-I pol gene product. Studies with mutant DNAs facilitated the characterization of the primary structure of the HTLV-I mRNA responsible for the ribosomal frameshift in the pro-pol overlap and demonstrated that the frameshift occurs at the signal sequence UUUAAAC. Direct amino acid sequencing of the transframe protein localized the site of the frameshift to the asparagine codon AAC.

Identification of HTLV-I gag protease and its sequential processing of the gag gene product

The full-length provirus of human T-cell leukemia virus type I (HTLV-I) was isolated from MT-2, a lymphoid cell line producing HTLV-I. In transfected cells, structural proteins of HTLV-I, the gag and env products, were formed and processed in the same manner as observed in MT-2 cells. The nucleotide sequence was determined for a region between the gag and pol genes of the proviral DNA clone containing an open-reading frame. The deduced amino acid sequences show that this open-reading frame encodes a putative HTLV-I protease. The protease gene (pro) of HTLV-I was investigated using a vaccinia virus expression vector. Processing of 53k gag precursor polyprotein into mature p19, p24, and p15 gag structural proteins was detectable with a recombinant plasmid harboring the entire gag- and protease-coding sequence. We demonstrated that the protease processed the gag precursor polyprotein in a trans-action. A change in the sequence Asp(64)-Thr-Gly, the catalytic core sequence among aspartyl proteases, to Gly-Thr-Gly was shown to abolish correct processing, suggesting that HTLV-I protease may belong to the aspartyl protease group. The 76k gag-pro precursor polyprotein was identified, implying that a cis-acting function of HTLV-I protease may be necessary to trigger the initial cleavage event for its own release from a precursor protein, followed by the release of p53 gag precursor protein. The p53 gag precursor protein is then processed by the trans-action of the released protease to form p19, p24, and p15.

Pulse oximetry during shunt surgery in pediatric patients with tetralogy of fallot

Pulse oximetry is a noninvasive technique for measuring O2 saturation (SpO2) continuously. We applied pulse oximetry to 9 pediatric patients with tetralogy of Fallot during shunt surgery. Arterial oxygen tensions (PaO2) and saturations (SaO2) were also measured at the time of postinduction, just before the shunt, after the shunt and at the end of the operation. The SpO2 and SaO2 levels were identically changed in all 4 periods. The PaO2 was increased a little without statistical significance after the shunt procedure and at the end of the operation compared with the values before the shunt. However, SaO2 values increased with statistical significance after the shunt procedure and SpO2 values also showed similar increases with significance. In conclusion, continuous monitoring of SpO2 by pulse oximetry, instead of PaO2, is a very useful and reliable method to assess the improvement of perfusion after shunt, particularly in cyanotic cases.

Direct determination of chromium(III) and chromium(VI) with ion chromatography using direct current plasma emission as element-selective detector

A method is described that utilizes direct current plasma atomic emission spectrometry as an element-selective method of detection for ion chromatographic determination of chromium(III) and chromium(VI) species. The eluting chromium-containing species are detected on the basis of the atomic emission of chromium without any species conversion. Both anion and cation separator columns give similar results when used with varying sample matrices. By employing an on-column preconcentration procedure, the detectable concentrations of the chromium species are reduced to less than 1.0 ppb. This method is applied to the determination of chromium species in human serum, natural water, and industrial process stream samples.

Sequence requirements for nucleolar localization of human T cell leukemia virus type I pX protein, which regulates viral RNA processing

The posttranscriptional regulator (p27x-III) of human T cell leukemia virus type I (HTLV-I) is located predominantly in the cell nucleolus. A highly basic amino-terminal sequence (NH2-Met-Pro-Lys-Thr-Arg-Arg-Arg-Pro-Arg-Arg-Ser-Gln-Arg-Lys-Arg-Pro-Pro -Thr- Pro) in this protein, when fused to the amino termini of beta-galactosidase and p40x of HTLV-I, acts as an autonomous signal capable of directing the hybrid proteins to the cell nucleolus.

Processing of gag precursor polyprotein of human T-cell leukemia virus type I by virus-encoded protease

The biological activity encoded in the putative protease gene (pro) of human T-cell leukemia virus type I was investigated by using a vaccinia virus expression vector. The 53-kilodalton gag precursor polyprotein was processed into the mature p19, p24, and p15 gag proteins when the gag and protease-coding sequence was expressed under the control of a vaccinia virus promoter, suggesting that the protease may be synthesized through the mechanism of ribosomal frame shifting. The processing defect of a protease mutant could be complemented by cointroduction of a wild-type construct into the cell, demonstrating that the pro gene encodes the biologically active protease molecules which are capable of processing the gag precursor polyprotein in vivo in trans. A study involving the use of a variety of mutants constructed in vitro revealed that the protease consists of a nonessential carboxy-terminal region and a part essential for its activity, including the putative catalytic residue, aspartic acid. Furthermore, a cluster of adenine residues positioned at the overlapping region between the gag and pro genes was shown to be involved in the ribosomal frameshifting event for the synthesis of protease. To mimic the formation of the 76-kilodalton gag-pro precursor polyprotein formed by ribosomal slipping, the coding frames of the gag and pro gene were adjusted. The processing of the gag-pro precursor polyprotein depended on an intact protease gene, implying that a cis-acting function of human T-cell leukemia virus type I protease may be necessary to trigger the initial cleavage event that leads to the release of protease from the precursor protein.

Identification of a protease gene of human T-cell leukemia virus type I (HTLV-I) and its structural comparison

We determined the nucleotide sequence of a region between the gag and pol genes of a replication-competent proviral clone of a human T-cell leukemia virus type I (HTLV-I) from MT-2 cells. This region overlapping the gag and pol genes contains an open reading frame with a different phase from others. The deduced amino acid sequences show significant homology with the known protease gene of other retroviruses, and harbors highly conserved amino acid sequences that are well conserved in other retroviral protease domains. These results indicate that this open reading frame encodes a HTLV-I protease.

Structural analysis of p28 adult T-cell leukaemia-associated antigen

The 28,000 mol. wt. polypeptide (p28) of adult T-cell leukaemia-associated antigen encoded by the 24S defective human T-cell leukaemia virus (HTLV-I) is associated with protein kinase activity. We have determined the nucleotide sequence of this defective HTLV-I provirus and found that it contains a portion of the gag gene (p19 and part of p24), the pX region, and two long terminal repeats, one at each end. The predicted p28 gag-pX fused protein consists of 190 amino acids and its mol. wt. was calculated as 21,055. The results of peptide mapping analysis showing that p28 contains p19 supported the nucleotide sequence data. That p28 was encoded by this defective provirus was also demonstrated by transient expression of p28 polypeptide in COS 7 cells transfected with a recombinant plasmid containing a simian virus 40 early promoter and the p28-coding region of the 24S HTLV-I.

Molecular cloning of cDNA encoding gp68 of adult T-cell leukaemia-associated antigen: evidence for expression of the pX IV region of human T-cell leukaemia virus

A 2.3 kb cDNA was cloned from human T-cell leukaemia virus [HTLV(MT-2)] virion RNA using a vector system, as plasmid pHTLV 707. The restriction endonuclease map of pHTLV 707 revealed that the insert contained the 5' half of the env gene and a portion of the pX region of HTLV, corresponding to the subgenomic RNA derived from 32S defective HTLV. Nucleotide sequence analysis of pHTLV 707 indicated that the clone contained an open reading frame for a 60K mol. wt. protein including the upstream and entire pX IV region. A rabbit antibody raised against a synthetic decapeptide deduced from the nucleotide sequence at the carboxyl terminus of the pX IV region immunoprecipitated gp68, and also 80K and 40K proteins.

Bilateral renal malakoplakia

A case of malakoplakia is presented which was confined to the renal parenchyma of both kidneys in a thirty-five-year-old woman in whom fatal renal failure developed in three weeks. Bilateral renal malakoplakia is rare, and unlike malakoplakia of the bladder, it behaves as a progressive, destructive, and fatal disease.