Postoperative Nausea and Vomiting Prediction: Machine Learning Insights from a Comprehensive Analysis of Perioperative Data

Postoperative nausea and vomiting (PONV) are common complications after surgery. This study aimed to present the utilization of machine learning for predicting PONV and provide insights based on a large amount of data. This retrospective study included data on perioperative features of patients, such as patient characteristics and perioperative factors, from two hospitals. Logistic regression algorithms, random forest, light-gradient boosting machines, and multilayer perceptrons were used as machine learning algorithms to develop the models. The dataset of this study included 106,860 adult patients, with an overall incidence rate of 14.4% for PONV. The area under the receiver operating characteristic curve (AUROC) of the models was 0.60-0.67. In the prediction models that included only the known risk and mitigating factors of PONV, the AUROC of the models was 0.54-0.69. Some features were found to be associated with patient-controlled analgesia, with opioids being the most important feature in almost all models. In conclusion, machine learning provides valuable insights into PONV prediction, the selection of significant features for prediction, and feature engineering.

Harnessing Machine Learning for Prediction of Postoperative Pulmonary Complications: Retrospective Cohort Design

Postoperative pulmonary complications (PPCs) are significant causes of postoperative morbidity and mortality. This study presents the utilization of machine learning for predicting PPCs and aims to identify the important features of the prediction models. This study used a retrospective cohort design and collected data from two hospitals. The dataset included perioperative variables such as patient characteristics, preexisting diseases, and intraoperative factors. Various algorithms, including logistic regression, random forest, light-gradient boosting machines, extreme-gradient boosting machines, and multilayer perceptrons, have been employed for model development and evaluation. This study enrolled 111,212 adult patients, with an overall incidence rate of 8.6% for developing PPCs. The area under the receiver-operating characteristic curve (AUROC) of the models was 0.699-0.767, and the f1 score was 0.446-0.526. In the prediction models, except for multilayer perceptron, the 10 most important features were obtained. In feature-reduced models, including 10 important features, the AUROC was 0.627-0.749, and the f1 score was 0.365-0.485. The number of packed red cells, urine, and rocuronium doses were similar in the three models. In conclusion, machine learning provides valuable insights into PPC prediction, significant features for prediction, and the feasibility of models that reduce the number of features.

Spin-liquid-like state in pure and Mn-doped TbInO3 with a nearly triangular lattice

Inelastic neutron scattering studies in single crystals of TbInO3 and TbIn0.95Mn0.05O3 with nearly triangular antiferromagnetic lattice are reported. At low energies, a broad and apparently gapless continuum of magnetic excitations, located at the triangular lattice (TL) Brillouin zone boundary, is observed. The data are well described by the uncorrelated nearest-neighbor valence bonds model. At higher energies, a broad excitation branch dispersing from the TL zone boundary is observed. No signs of static magnetic order are found down to the temperatures two orders of magnitude smaller than the effective interaction energy. The fluctuating magnetic moment exceeds two-thirds of the Tb3+ free-ion value and is confined to the TL plane. These observations are consistent with a TL-based spin liquid state in TbInO3.

Stemmed DNA nanostructure for the selective delivery of therapeutics

DNA has emerged as a biocompatible biomaterial that may be considered for various applications. Here, we report tumor cell-specific aptamer-modified DNA nanostructures for the specific recognition and delivery of therapeutic chemicals to cancer cells. Protein tyrosine kinase (PTK)7-specific DNA aptamer sequences were linked to 15 consecutive guanines. The resulting aptamer-modified product, AptG15, self-assembled into a Y-shaped structure. The presence of a G-quadruplex at AptG15 was confirmed by circular dichroism and Raman spectroscopy. The utility of AptG15 as a nanocarrier of therapeutics was tested by loading the photosensitizer, methylene blue (MB), to the G-quadruplex as a model drug. The generated MB-loaded AptG15 (MB/AptG15) showed specific and enhanced uptake to CCRF-CEM cells, which overexpress PTK7, compared with Ramos cells, which lack PTK7, or CCRF-CEM cells treated with a PTK7-specific siRNA. The therapeutic activity of MB/AptG15 was tested by triggering its photodynamic effects. Upon 660 nm light irradiation, MB/AptG15 showed greater reactive oxygen species generation and anticancer activity in PTK7-overexpressing cells compared to cells treated with MB alone, those treated with AptG15, and other comparison groups. AptG15 stemmed DNA nanostructures have significant potential for the cell-type-specific delivery of therapeutics, and possibly for the molecular imaging of target cells.

Comparison of Recipient Outcomes After Kidney Transplantation: In-House Versus Imported Deceased Donors

BACKGROUND

Increased cold ischemia time in cadaveric kidney transplants has been associated with a high rate of delayed graft function (DGF), and even with graft survival. Kidney transplantation using in-house donors reduces cold preservation time. The purpose of this study was to compare the clinical outcomes after transplantation in house and externally.

METHODS

We retrospectively reviewed the medical records of donors and recipients of 135 deceased-donor kidney transplantations performed in our center from March 2009 to March 2016.

RESULTS

Among the 135 deceased donors, 88 (65.2%) received the kidneys from in-house donors. Median cold ischemia time of transplantation from in-house donors was shorter than for imported donors (180.00 vs 300.00 min; P < .001). The risks of DGF and slow graft function were increased among the imported versus in-house donors. Imported kidney was independently associated with greater odds of DGF in multivariate regression analysis (odds ratio, 4.165; P = .038). However, the renal function of recipients at 1, 3, 5, and 7 years after transplantation was not significantly different between the 2 groups.

CONCLUSIONS

Transplantation with in-house donor kidneys was significantly associated with a decreased incidence of DGF, but long-term graft function and survival were similar compared with imported donor kidneys.

Immune-camouflaged graphene oxide nanosheets for negative regulation of phagocytosis by macrophages

Signal regulatory protein alpha (SIRPα) is highly expressed in macrophages of the reticuloendothelial system and in tumor-associated macrophages, whereas tumor cells express the surface membrane protein, CD47, which interacts with SIRPα to negatively regulate phagocytosis. In this study, we modified the surfaces of graphene oxide (GO) nanosheets with a CD47-like SIRPα-binding peptide (SP). The presence of SP on GO nanosheets reduced the macrophage uptake to a greater extent than the PEGylation of such nanosheets. This reduced uptake was found to be mediated by the activation of Src homology region 2 domain-containing phosphatase 1 (SHP-1) and the downstream inhibition of myosin assembly, which is necessary for phagosome formation. Unlike SP-coated GO nanosheets, PEGylated GO nanosheets did not affect myosin assembly or phagocytosis. After in vivo systemic administration, the clearance of SP-coated GO nanosheets was slower than that of PEGylated GO nanosheets, and this difference increased with repeated administration. Finally, SP-coated GO nanosheets showed a higher distribution to tumor tissues than PEGylated GO nanosheets or a physical mixture of SP and GO nanosheets. Our findings indicate that immune-camouflaged GO nanosheets with natural CD47-like SIRPα-binding molecules can reduce the nonspecific loss of such nanosheets through macrophage uptake, thereby enhancing their blood circulation and tumor delivery after multiple injections.

Kidney Donor Risk Index as the Predictor for the Short-term Clinical Outcomes After Kidney Transplant From Deceased Donor With Acute Kidney Injury

BACKGROUND

The Kidney Donor Risk Index (KDRI) scoring system for deceased donors has been widely introduced for postoperative evaluation of graft function. We analyzed the usefulness of the KDRI in deceased donors with acute kidney injury (AKI).

METHODS

Forty-nine recipients from deceased donors with AKI between January 2009 and December 2014 were reviewed retrospectively. Data collected from donor medical records included age, height, weight, hypertension or diabetes history, cause of death, serum creatinine (sCr), and donation after cardiac death. Graft function data including sCr, estimated glomerular filtration rate (eGFR), and acute rejection episodes were monitored for 1 year. Correlations between KDRI score and factors indicating graft function were analyzed. A cutoff value for KDRI score was calculated using a receiver operating characteristic (ROC) curve for significant graft function.

RESULTS

The mean ages of donors and recipients were 46.81 ± 13.13 and 47.69 ± 11.43, respectively. The mean KDRI score was 1.24 ± 0.40. Univariable analysis of KDRI score and factors indicating graft function indicated that sCr at 6 to 12 months, eGFR at 1 year, and slow graft function (SGF) had statistical significance. The ROC curve of KDRI score for SGF showed an optimal cutoff value of 1.20, with sensitivity of 69.2% and specificity of 69.4% (area under the curve = 0.75) in deceased donors with AKI.

CONCLUSIONS

KDRI score in deceased donors with AKI was correlated with postoperative graft values including eGFR and SGF. KDRI could be used as a predictor for the short-term clinical outcome after kidney transplant from deceased donor with AKI.

Comparison of steroid administration methods in patients with idiopathic sudden sensorineural hearing loss: a retrospective observational study

OBJECTIVES

To compare the recovery rates of patients with idiopathic sudden sensorineural hearing loss (ISSHL) treated with oral systemic steroids (PO) or intratympanic steroid injection (IT) or both.

DESIGN

A retrospective observational study.

SETTING

Tertiary referral centre.

PARTICIPANTS

Eight hundred and forty-four patients diagnosed with ISSHL within 14 days of the onset of symptoms. The patients were divided into three groups by treatment modality.

MAIN OUTCOME MEASURES

Threshold of pure-tone tests, age, accompanying symptoms and underlying diseases were compared. The level of final hearing recovery was evaluated by the application of the results of the pure-tone test that was performed at least 3 months after the completion of each treatment.

RESULTS

Final hearing recovery rate differed significantly by the type of treatment (P = 0.031). Recovery rates in the PO and combined groups were significantly higher in patients with mild (85.1% and 88.6%, respectively) than with profound (52.8% and 69.0%, respectively) hearing loss (P < 0.05). In contrast, severity and recovery rate were not significantly correlated in the IT group (P > 0.05). Combined treatment yielded significantly higher recovery rates than other treatment modalities in patients without hypertension (HTN) and diabetes mellitus (DM) (P = 0.021).

CONCLUSION

In the group treated with combined therapy, better hearing improvement was obtained than in the groups treated with systemic steroid only or with intratympanic steroid injection only without complications. These findings suggest that the combination of systemic administration and intratympanic injection may improve patient prognosis.

Magnonlike dispersion of spin resonance in Ni-doped BaFe2As2

Inelastic neutron scattering measurements on Ba(Fe0.963Ni0.037)2As2 manifest a neutron spin resonance in the superconducting state with anisotropic dispersion within the Fe layer. Whereas the resonance is sharply peaked at the antiferromagnetic (AFM) wave vector Q(AFM) along the orthorhombic a axis, the resonance disperses upwards away from Q(AFM) along the b axis. In contrast to the downward dispersing resonance and hourglass shape of the spin excitations in superconducting cuprates, the resonance in electron-doped BaFe2As2 compounds possesses a magnonlike upwards dispersion.

Immature Rubus coreanus Shows a Free Radical-Scavenging Effect and Inhibits Cholesterol Synthesis and Secretion in Liver Cells

Rubus coreanus fruits have been employed as a traditional medicine for centuries in the Asia-Pacific region. Its pharmacological action differs according to the different extraction methods utilized and the degree of fruit ripening. In this study, we determined the cellular effect of different ethanol extracts of mature and immature Rubus coreanus fruits in human hepatic cell line, HepG2 cells. The antioxidant activity, effect on superoxide dismutase activity and cholesterol biosynthesis efficiency was also evaluated. Immature Rubus coreanus extract showed higher antioxidant capability, compared with that of its mature fractions. Cellular antioxidant proteins including HO-1, Cu/Zn-superoxide dismutase and catalase were highly expressed in the presence of Rubus coreanus. Cholesterol levels in HepG2 cells treated with the water fraction of immature Rubus coreanus were significantly reduced. This antihyperlipidaemic action of Rubus coreanus is a consequence of cholesterol biosynthesis and extracellular secretion in HepG2 cells. These results indicate that among different ethanol fraction of mature and immature Rubus coreanus fruit extracts, water extract of immature fruit extract shows higher antioxidant as well as higher antihyperlipidaemic action.

Effects of transition metal substitutions on the incommensurability and spin fluctuations in BaFe2As2 by elastic and inelastic neutron scattering

The spin fluctuation spectra from nonsuperconducting Cu-substituted, and superconducting Co-substituted, BaFe(2)As(2) are compared quantitatively by inelastic neutron scattering measurements and are found to be indistinguishable. Whereas diffraction studies show the appearance of incommensurate spin-density wave order in Co and Ni substituted samples, the magnetic phase diagram for Cu substitution does not display incommensurate order, demonstrating that simple electron counting based on rigid-band concepts is invalid. These results, supported by theoretical calculations, suggest that substitutional impurity effects in the Fe plane play a significant role in controlling magnetism and the appearance of superconductivity, with Cu distinguished by enhanced impurity scattering and split-band behavior.

Clinical manifestations of hypercalcemia and hypophosphatemia after kidney transplantation

INTRODUCTION

Abnormalities of calcium and phosphorus metabolism in end-stage renal disease patients can persist after transplantation. We investigated their natural courses after transplantation, their risk factors for posttransplantation hypercalcemia and hypophosphatemia, and their impacts on allograft outcomes.

METHODS

We retrospectively analyzed a total of 490 adult patients who underwent kidney transplantations between 2000 and 2009.

RESULTS

The serum calcium continued to increase, and reaching a plateau at around 3 months after transplantation. Thereafter it decreased, reaching a stable level by 2 years. Forty-four patients (9.0%) displayed hypercalcemia within 1 year; it persisted longer than that in 23 subjects (4.7%). Both longer dialysis duration (odds ratio [OR] 1.423; 95% confidence interval [CI], 1.192-1.699) and high intact serum parathyroid hormone (iPTH) level before transplantation (OR 1.002; 95% CI, 1.000-1.003) increased the risk for posttransplantation hypercalcemia. After a significant decrease during the first week, the serum phosphorus level increased, becoming stable between 1 and 6 months after transplantation. Hypophsphatemia occurred in 379 patients (77.3%) with 336 patients displaying hypophosphatemia without hypercalcemia. However, neither hypercalcemia nor hypophosphatemia influenced graft outcomes. Eight patients underwent pretransplantation parathyroidectomy, whereas 4 patients underwent posttransplantation parathyroidectomy. Neither group of patients experienced posttransplantation hypercalcemia.

CONCLUSIONS

Both hypercalcemia and hypophosphatemia are common after renal transplantation, especially among patients with a long history of dialysis before transplantation. Strict control of hyperparathyroidism including parathyroidectomy before transplantation may be the appropriate approach to these abnormalities.

Incommensurate spin-density wave order in electron-doped BaFe2 As2 superconductors

Neutron diffraction studies of Ba(Fe(1-x)Co(x))(2)As)(2) reveal that commensurate antiferromagnetic order gives way to incommensurate magnetic order for Co compositions between 0.056 < x < 0.06. The incommensurability has the form of a small transverse splitting (0, ± ε, 0) from the commensurate antiferromagnetic propagation vector Q(AFM) = (1,0,1) (in orthorhombic notation) where ε ≈ 0.02-0.03 and is composition dependent. The results are consistent with the formation of a spin-density wave driven by Fermi surface nesting of electron and hole pockets and confirm the itinerant nature of magnetism in the iron arsenide superconductors.

A pre- and postoperative bacteriological study of chronic suppurative otitis media

BACKGROUND

Although many bacteriological studies on preoperative otorrhea in patients with chronic suppurative otitis media (CSOM) have been performed, there are few studies on postoperative otorrhea. In this study, we analyzed the pathogenic microorganisms, changes in the bacterial species before and after surgery, and the antibiotic sensitivity on preoperative and postoperative cultures.

METHODS

This was a retrospective study of 87 postoperative otorrhea patients who were part of a sample of 1,754 patients with CSOM who underwent tympanomastoidectomy; preoperative and postoperative otorrhea samples were obtained from January 2002 to April 2009. We analyzed patients with postoperative otorrhea divided into two groups: those with early onset (<3 months after surgery, n = 45) and those with late onset (>3 months after surgery, n = 42) otorrhea.

RESULTS

Four species of organisms, methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant S. aureus (MRSA), Pseudomonas, and coagulase-negative Staphylococcus (CNS), showed higher prevalence than others on both the preoperative and postoperative cultures. When we compared the early and late onset otorrhea groups, we found that 'no growth' was significantly higher in the early onset group (n = 19 vs. n = 5), whereas MSSA was significantly higher in the late onset group (n = 1 vs. n = 12). Of the 67 patients with positive preoperative cultures, 15 (22.4%) had the same bacteria after surgery, 34 (50.8%) had other bacteria, 2 (3.0%) had fungi, and 16 (23.8%) showed no growth on postoperative bacteriological testing. MSSA (9%) and MRSA (16.7%) were rarely recultured after surgery, whereas Pseudomonas was recultured frequently (61.5%).

CONCLUSION

Unlike MSSA and MRSA, ciprofloxacin-resistant P. aeruginosa (CRP) occasionally causes early onset postoperative otorrhea due to the lack of highly potent antibiotics against this species. The success rate of infection control by surgery and antibiotics was low for CRP.

Anomalous suppression of the orthorhombic lattice distortion in superconducting Ba(Fe1-xCox)2As2 single crystals

High-resolution x-ray diffraction measurements reveal an unusually strong response of the lattice to superconductivity in Ba(Fe1-xCox)2As2. The orthorhombic distortion of the lattice is suppressed and, for Co doping near x=0.063, the orthorhombic structure evolves smoothly back to a tetragonal structure. We propose that the coupling between orthorhombicity and superconductivity is indirect and arises due to the magnetoelastic coupling, in the form of emergent nematic order, and the strong competition between magnetism and superconductivity.

QSAR modelling of water quality indices of alkylphenol pollutants

The aim of this study was to determine the degradability of 26 Alkylphenols (APs) by Chemical Oxygen Demand (COD) and/or 5-day Biochemical Oxygen Demand (BOD(5)), and to describe these data from Quantitative Structure-activity Relationships (QSARs). Statistical analysis techniques, such as Multiple Linear Regression (MLR), Principal Component Regression (PCR), Partial Least-Squares (PLS) Regression and Neural Network (NN) were carried out to calibrate and validate four-descriptor QSAR models using two different types of descriptor sets. Stable MLR-QSAR models using Leave-One-Out (LOO) were obtained with high predictability performance: r(2) = 0.924, Q(2)(cv) =0.854 for log (1/BOD) model on 24 APs and r(2) = 0.888, Q(2)(cv) = 0.818 for log (1/COD) on all the studied APs. The MLR models, built with four Dragon descriptors selected by Genetic Algorithm (GA), presented the following performances on 24 APs: r(2) = 0.889, Q(2)(cv) = 0.848 for log (1/BOD(5)) and r(2) = 0.885, Q(2)(cv) = 0.834 for log (1/COD) on 26 compounds. From these results, it is expected that the QSAR models generated could be successfully expanded to predict the biological and chemical activities of structurally diverse AP compounds.

OK-432 sclerotherapy of plunging ranula in 21 patients: it can be a substitute for surgery

BACKGROUND AND PURPOSE

Although first-choice therapy for the ranula is surgery, this choice presents technical difficulties and frequent recurrences because of insufficient surgery. We evaluated the efficacy of OK-432 sclerosis of the plunging ranula as a substitute for surgery.

METHODS

Twenty-one patients with plunging ranula were treated with intralesional injection of OK-432. The liquid content of the ranula was aspirated as much as possible, after which OK-432 solution was injected in the same volumes as that drawn out. Patients were followed on sonography or CT.

RESULTS

Seven (33.3%) patients with plunging ranulas showed total shrinkage and resolution, and 4 (19%) patients showed near-total shrinkage (more than 90% of the volume). Four (19%) patients revealed marked shrinkage (more than 70% of the volume), and 3 (14.3%) patients showed partial shrinkage (less than 70% of the volume). Three (14.3%) patients showed recurrence after total shrinkage 1 month after injection. The overall recurrence rate after each injection was 47% (16 of 34 injections in 21 patients), but the recurrence rate after the last sclerotherapy was only 14%. There were no serious side effects except for fever lasting 2-3 days (12 patients) and swelling (10 patients) for 3-5 days. Mild odynophagia for 1-2 days was also noted in 7 patients, and there was 1 severe case of odynophagia.

CONCLUSION

OK-432 sclerotherapy of plunging ranula is a safe and potentially curative procedure that may be used as a primary treatment for plunging ranula before considering surgery.

Layered perovskites with giant spontaneous polarizations for nonvolatile memories

A series of titanate-based layered perovskites having large values of the spontaneous polarization P(s) were developed for their applcations to nonvolatile ferroelectric random access memories. Among these, the Nd-modified bismuth titanate [Bi(4-x)Nd(x)Ti(3)O(12) (BNdT)] system exhibited the most remarkable ferroelectric properties. The c-axis oriented BNdT capacitor was characterized by a switchable remanent polarization 2P(r) of over 100 microC/cm(2) and imprinting and fatigue-free behavior. The active Ti site responsible for the giant P(s) was identified with the help of Rietveld analysis, x-ray absorption near-edge structure study, and ab initio quantum computations.

Intra-articular ganglion cysts of the knee: clinical and MR imaging features

The purpose of this study was to present clinical and MR imaging features of intra-articular ganglion cysts of the knee. Retrospective review of 1685 consecutive medical records and MR examinations of the knee performed at three imaging centers allowed identification of 20 patients (13 men and 7 women; mean age 35 years), in whom evidence of intra-articular ganglion cyst was seen. Of the 20 ganglion cysts, 5 were found in the infrapatellar fat pad, 10 arose from the posterior cruciate ligament, and 5 from the anterior cruciate ligament. Three of five patients with ganglion cyst in the infrapatellar fat pad had a palpable mass. In 7 of 15 patients with ganglion cyst in the intercondylar notch, exacerbation of pain occurred in a squatting position. On four MR arthrographies, ganglion cysts were an intra-articular round, lobulated, low signal intensity lesion. Five cases of fat-suppressed contrast-enhanced T1-weighted SE images demonstrated peripheral thin rim enhancement. The clinical presentation of intra-articular ganglion cyst is varied according to its intra-articular location. The MR appearance of intra-articular ganglion cyst is characteristic and usually associated with the cruciate ligament or the infrapatellar fat pad. Magnetic resonance arthrography has no definite advantage over conventional MR in the evaluation of the lesion. For intra-articular ganglion cyst in the infrapatellar fat pad, fat-suppressed contrast-enhanced MR imaging could be useful, because a thin, rim-enhancing feature of intra-articular ganglion cyst allows it to be distinguished from synovial hemangioma and synovial sarcoma.

Alternative transcriptional initiation and splicing of mouse Lamc2 message

To investigate the mechanism of two forms of messages (5.1 and 2.4 kb) in mouse Lamc2, a gene encoding for the gamma2 chain of epithelial cell-specific laminin 5, we analyzed approximately 40 kb of genomic DNA containing the sequences from the first intron to the 23rd exon to the 3' untranscribed region. With the 5' rapid amplification of cDNA end (RACE) and primer extension technique using RNA from mouse kidney and thymic epithelial cells, we found that the smaller message starts at the 2895th base of the cDNA within the 19th exon. Upstream sequences of this alternative start site showed the promoter activity in the reporter assay with the secreted form of alkaline phosphatase (SEAP). We also identified a novel alternatively spliced exon (exon 19B) that includes two stop codons. These results revealed two possible additional open reading frame that are different from the previously described alternative human gamma2 peptide. Therefore, the mechanism for generating smaller message and the event of alternative splicing are quite distinct between mouse and human Lamc2, although genomic organization is highly conserved. The significance of the presence of alternative message is discussed.

N-terminal processing is essential for release of epithin, a mouse type II membrane serine protease

Epithin was originally identified as a mouse type II membrane serine protease. Its human orthologue membrane type-serine protease 1 (MT-SP1)/matriptase has been reported to be localized on the plasma membrane. In addition, soluble forms of matriptase were isolated from human breast milk and breast cancer cell-conditioned medium. In this paper, we report a processing mechanism that appears to be required for the release of epithin. CHO-K1 or COS7 cells transfected with single full-length epithin cDNA generated two different-sized proteins in cell lysates, 110 and 92 kDa. The 92-kDa epithin was found to be an N-terminally truncated form of the 110-kDa epithin, and it was the only form detected in the culture medium. The 92-kDa epithin was also found on the cell surface, where it was anchored by the N-terminal fragment. The results of in vivo cell labeling experiments indicate that the 110-kDa epithin is rapidly processed to the 92-kDa epithin. Using site-directed mutagenesis experiments, we identified Gly(149) of the GSVIA sequence in epithin as required for the processing and release of the protein. These results suggest that N-terminal processing of epithin at Gly(149) is a necessary prerequisite step for release of the protein.

Identification and genetic mapping of the mouse Fkbp9 gene encoding a new member of FK506-binding protein family

We have isolated a gene from a cDNA library generated from the thymus of a mouse with severe combined immune deficiency, termed FKBP9, that encodes a protein related to FK506-binding protein 6 (65 kDa, FKBP65). FKBP9 contains four peptidyl-prolyl cis-trans isomerase (PPIase) signature and two EF-hand domains which is identical to FKBP6/65 in overall structural organization. However, the two proteins share only 66% amino acid identity. FKBP9 is expressed at high levels in mouse heart, muscle, lung, and kidney. While FKBP6 was previously mapped to chromosome 11, the Fkbp9 gene was mapped to mouse chromosome 6 by analysis of a multilocus cross. These results identify a new member of the mouse FKBP protein family located on a separate chromosome.

Quantitative histopathologic findings of erythromelanosis follicularis faciei et colli

BACKGROUND

Even though only 33 cases of Erythromelanosis follicularis faciei et colli (EFFC) have been reported around the world, there have been no quantitative clinicopathological studies yet. The purpose of this study is to examine quantitatively clinical and histopathological evaluations of EFFC using image analysis system.

METHOD

Clinical grading of its severity was assessed. Many parameters of the horny layer, granular layer, epidermis and the dermal components were measured and compared to controls by image analysis. The correlation between the histological findings and clinical grading was assessed.

RESULT

Thickness and compactness of the horny layer was significantly increased in EFFC. There were no significant differences in the number of melanocytes and severity of pigmentation between EFFC and controls; however, melanization was slightly increased in EFFC. The percent area of the superficial blood vessels was significantly increased and correlated with visual grading of erythema. Diameters of hair shafts and outer root sheaths, and thickness of inner root sheaths were decreased. Basal layer pigmentation was correlated with the clinical features of pigmentation.

CONCLUSION

This study supported the findings of hyperkeratosis and dilatation of superficial dermal blood vessels in EFFC. The pigmentation of the basal layer and the percent area of the inner spaces of the superficial dermal blood vessels may reflect the clinical severity more than the other parameters. Although follicular plugging is a characteristic clinical feature of EFFC, enlargement of hair follicles and hair shafts were not characteristic pathologic changes EFFC in our study.

Ultrastructural and molecular identification of a Wolbachia endosymbiont in a spider, Nephila clavata

Wolbachia-like bacteria were observed in the egg cells of golden orb-weaving spider, Nephila clavata, by means of transmission electron microscopy. The bacteria exhibited the typical morphology of Wolbachia, including three enveloping membranes. Based on the amplification and sequencing of partial 16S rDNA and ftsZ gene, the bacteria were identified as Wolbachia, intracellular, transovarially inherited alpha-proteobacteria in invertebrates. Phylogenetic analysis based on 16S rDNA and ftsZ gene sequences invariably indicated that the intracellular bacteria from N. clavata belonged to group A Wolbachia, which were found only from insects. Clustering of Wolbachia from N. clavata with group A Wolbachia indicates that the bacteria were probably transferred horizontally between insects and the spider.

Cyclic GMP mediates apoptosis induced by sulindac derivatives via activation of c-Jun NH2-terminal kinase 1

Sulindac sulfone (Exisulind) induces apoptosis and exhibits cancer chemopreventive activity, but in contrast to sulindac, it does not inhibit cyclooxygenases 1 or 2. We found that sulindac sulfone and two potent derivatives, CP248 and CP461, inhibited the cyclic GMP (cGMP) phosphodiesterases (PDE) 2 and 5 in human colon cells, and these compounds caused rapid and sustained activation of the c-Jun NH2-terminal kinase 1 (JNK1). Rapid activation of stress-activated protein/ERK kinase 1 (SEK1) and mitogen-activated protein kinase kinase kinase (MEKK1), which are upstream of JNK1, was also observed. Other compounds that increase cellular levels of cGMP also activated JNK1, and an inhibitor of protein kinase G (PKG), Rp-8-pCPT-cGMPS, inhibited JNK1 activation by the sulindac sulfone derivatives. Expression of a dominant-negative JNK1 protein inhibited CP248-induced cleavage of poly(ADP-ribose) polymerase, a marker of apoptosis. Thus, it appears that sulindac sulfone and related compounds induce apoptosis, at least in part, through activation of PKG, which then activates the MEKK1-SEK1-JNK1 cascade. These studies also indicate a role for cGMP and PKG in the JNK pathway.

Identification of viral induced genes in Ig+ leucocytes of Japanese flounder Paralichthys olivaceus, by differential hybridisation with subtracted and un-subtracted cDNA probes

Up-regulated genes of leucocytes expressing immunoglobulin (Ig+ leucocytes) of hirame rhabdovirus (HRV)-infected Japanese flounder were identified by differential hybridisation, using subtracted and un-subtracted cDNA probes. Ig+ leucocytes were separated from apparently healthy and HRV-infected Japanese flounder by the magnetic beads antibody method using mouse anti-Japanese flounder Ig monoclonal antibody (mab). A cDNA library was constructed from HRV-infected Japanese flounder leucocytes, and was screened with subtracted cDNA probes enriched in genes up-regulated by HRV infection. Fifty cDNAs were isolated for further analysis. These included cDNAs coding for homologues of interferon-inducible 56K protein (IFI56), Stat3, CEF-10, RGS5, inducible poly(A) binding protein, prolylcarboxylpeptidase, basigin III (Ig superfamily), MUC-18 (Ig superfamily), proteasome-nexin 1 (SERPIN), herpes virus entry mediator (TNFR family), collagenase III, gelatinase-b, megakaryocyte stimulating factor, Rab8-interacting protein, IgM, IgD and 20 unknown cDNA clones. The majority of these identified genes are reported for the first time in fish. From leucocytes mRNA for homologues of IFI56, CEF-10, Stat3, SERPIN and inducible poly (A) binding protein expression was shown to increase following HRV infection.

Characterization of the mouse gene, human promoter and human cDNA of TSCOT reveals strong interspecies homology

The regulation of gene expression in thymic epithelial cells is critical for T cell development. The mouse thymic epithelial gene Tscot encodes a protein with weak homology to bacterial 12 transmembrane co-transporters. Using competitive reverse transcription-polymerase chain reaction (RT-PCR), we show that low level Tscot expression is detectable in several other tissues. Tscot was mapped to chromosome 4 and was also detected in other mammalian species by Southern blotting. The human cDNA clone showed 77% amino acid identity with the mouse sequence. The highest conservation was in the TM regions and in a small segment of the central cytoplasmic loop. Genomic clones spanning 17164 bases of the Tscot gene revealed four exons with nine of the TM domains encoded in the first exon. The major transcriptional start site in mouse was identified by a primer extension analysis and confirmed by RT-PCR. Comparison of 1.7 kb of the human and mouse promoters identified six conserved possible regulatory elements, one containing a potential binding site for an interferon alpha inducible factor. Finally, as a functional test, 3 kb of the murine promoter was used to create a transgenic mouse that expresses enhanced green fluorescent protein message strongly in the thymus, weakly in the kidney and undetectably in the spleen, liver and heart.

Spatial, a gene expressed in thymic stromal cells, depends on three-dimensional thymus organization for its expression

Although the importance of thymic stroma in thymopoiesis has been recognized, the underlying molecular details regarding stromal cell biology remain obscure. To study this area, we have cloned genes expressed in thymic stromal cells. Spatial is alternatively spliced to generate two mRNAs in thymus and lymph node (LN) but it is not expressed in the spleen. In mouse embryos, the short form begins expression at day 10 while the long form is not detected until day 12. Both mRNAs encode proline rich proteins and their closest homology is to homeobox and POU domain transcription factors. Spatial is not expressed in thymocytes, but it is expressed in 2-deoxyguanosine-treated day 14 fetal thymic organ culture (FTOC) and in reaggregated FTOC. These data suggest that a normal three-dimensional organization of stromal cells is required for Spatial expression. An antiserum raised against a C-terminal peptide detected proteins of 38 and 32 kDa in Western blots of total thymus proteins. In frozen thymus sections, subcapsular epithelial cells were stained with the anti-Spatial antiserum. Paracortical subcapsular cells of unknown function were also stained in the LN. Both forms of Spatial fused to the green fluorescent protein (GFP) localize to the nucleus in transfected cells.

Epithelial cell-specific laminin 5 is required for survival of early thymocytes

The gene LamC2 encoding the gamma2 chain of laminin 5, an epithelial cell-specific extracellular matrix protein, was identified in a PCR-based subtracted cDNA library from mouse thymic stromal cells. The mRNA existed in two alternative forms (5.1 and 2.4 kb). The full-length message was highly expressed in SCID thymus and in a nurse cell line, but not in other thymic epithelial cell lines, while the short form was more widely expressed. In situ hybridization and immunohistochemical staining revealed laminin 5 expression mostly in the subcapsular region of the adult thymus. Addition to fetal thymic organ cultures of a cell adhesion-blocking mAb to the alpha3 chain of laminin 5 interrupted T cell development. There was a 40% reduction in the total yield of thymocytes, and the most profound decrease (75-90%) was seen in the CD25+CD44+ and CD25+CD44-subsets of the CD4-CD8- double negative fraction. Most of the surviving double negative thymocytes expressed Sca-1, and there were significant increases in the number of cells with CD69 expression and in the fraction of annexin V-stained cells. None of these changes were observed with a nonblocking anti-laminin alpha3 chain mAb. These results suggest that the interaction between double negative thymoctyes and laminin 5 made by subcapsular epithelial cells is required for the survival and differentiation of mouse thymocytes.

A putative 12 transmembrane domain cotransporter expressed in thymic cortical epithelial cells

We have isolated a full-length cDNA clone (thymic stromal origin (TSO)-1C12) from a SCID thymus library using a probe from a PCR-based subtractive library enriched for sequences from fetal thymic stromal cells. TSO-1C12 mRNA is expressed mainly in the thymic cortex and is highly enriched in SCID thymus. Expression per cell is highest during fetal thymus development and decreases after day 16. Antipeptide Abs immunoprecipitated a hydrophobic, plasma membrane glycoprotein (thymic stromal cotransporter, TSCOT) whose translated sequence has weak homology to bacterial antiporters and mammalian cation cotransporters with 12 transmembrane domains. TSCOT represents a new member of this superfamily that is highly expressed in thymic cortical epithelial cells.

Synthesis and in vitro cytotoxicity of hexacyclic camptothecin analogues

A series of C(7)-N-alkylaminoethyl-C(10), C(11)-methylenedioxy- and ethylenedioxy-camptothecin (3a-g, 4a-b) were prepared. Their syntheses and in vitro cytotoxicity were reported. Among 15 derivatives, 3a and 3b showed more potent cytotoxicity than Camptothecin, especially in CAOV-3 cell line.

Cloning and chromosomal mapping of a gene isolated from thymic stromal cells encoding a new mouse type II membrane serine protease, epithin, containing four LDL receptor modules and two CUB domains

We cloned and sequenced a mouse gene encoding a new type of membrane bound serine protease (epithin) containing a multidomain structure. The initial cDNA clone was found previously in a polymerase chain reaction (PCR)-based subtractive library generated from fetal thymic stromal cells, and the message was shown to be highly expressed in a thymic epithelial nurse cell line. A clone isolated from a severe combined immunodeficiency (SCID) thymus library and extended to its full length at the 5' end with the RACE technique contains an open reading frame of 902 amino acids. Based on the sequence of this clone, the predicted protein structure is a type II membrane protein with a C-terminal serine protease domain linked to the membrane by four low density lipoprotein receptor modules and two CUB domains. High message expression by northern blotting was detected in intestine, kidney, lung, SCID, and Rag-2(-/-) thymus, and 2-deoxyguanosine-treated fetal thymic rudiment, but not in skeletal muscle, liver, heart, testis, and brain. Sorted MHC class II+ and II- fetal thymic stromal cells were positive for expression by reverse transcriptase-PCR, whereas CD45(+) thymocytes were not. The gene was found in chicken and multiple mammalian species under low stringency Southern hybridization conditions. Under high stringency conditions, only a single gene per haploid genome was identified in the mouse. This gene, Prss14 (protease, serine, 14), was mapped to mouse chromosome 9 and is closely linked to the Fli1 (Friend leukemia integration 1) gene.

Two species of mRNAs for the fyn proto-oncogene are produced by an alternative polyadenylation

Two mRNA species with different sizes (3.8 kb and 2.8 kb) for the fyn proto-oncogene have been noticed during Northern hybridization analysis. However, the difference between the two mRNA species has not been resolved yet. By screening a phage expression library using the monoclonal antibody (mAb) B16-5 which recognizes Src homology 3 (SH3) domains of phospholipase C-gamma and Nck, we have cloned a cDNA encoding the larger species of fyn mRNA. The size of the clone was 3.5 kb and DNA sequencing analysis of the clone showed that it was fyn expressed mainly in T-cells, fyn (T), with an untranslated region 1 kb longer than the previously reported one. The 3'-end fragment of the clone hybridized only to the larger species (3.8 kb) of fyn mRNA but not to the smaller one (2.8 kb) on Northern blot analysis. Furthermore, an additional polyadenylation signal sequence was found at the end of this clone. These results indicate that the two mRNA species for fyn are produced by alternative polyadenylation.

Isolation and characterization of immune-related genes from the fall webworm, Hyphantria cunea, using PCR-based differential display and subtractive cloning

Following injection of bacteria into the hemocoel of the fall webworm, Hyphantria cunea, several inducible genes were identified and characterized using PCR-based differential display (DD-PCR) and subtractive cloning. Ten immune-related cDNA clones (Hdd1, Hdd2, Hdd3, Hdd11, Hdd13, Hdd15, Hdd17, Hdd23, Hs106, Hs302) were isolated and characterized. The deduced amino acid sequence of Hdd2 was shown to be a member of the copper, zinc superoxide dismutase (Cu-Zn SOD) family. The H. cunea Cu-Zn SOD is novel in that it is up-regulated following a bacterial challenge and has a putative signal peptide suggesting its secretion and involvement in the insect immune response. Hdd3 was found to encode a new member of the serpin (serine protease inhibitor) family. The putative lectin corresponding to Hdd15 is of a different kind in that it has two lectin C domains in a single molecule. These two lectin C domains show significant homology to the lectin C domain of Periplaneta lipopolysaccharide binding protein (LPS-BP). Three cloned genes, Hdd17, Hs106 and Hs302, encode a homologue to Bombyx mori Gram negative binding protein, a hemolin-like protein and a attacin-like protein, respectively. The deduced amino acid sequences from Hdd11 showed weak homology with a Locusta migratoria hemolymph protein. On the contrary, Hdd1, Hdd13 and Hdd23 did not reveal any significant homology with known proteins. All of the 10 genes were clearly inducible by E. coli and M. luteus injection. Injection of distilled water only slightly induced mRNA levels. Comparison of temporal mRNA expression following E. coli injection showed three types of expression patterns.

Synthesis and in vitro cytotoxicity of C(20)(RS)-camptothecin analogues modified at both B (or A) and E ring

A series of C(7) and C(20)-substituted camptothecin derivatives (12-14, 16-18) are prepared. Their syntheses and in vitro cytotoxicities are reported.

A subtractive PCR-based cDNA library made from fetal thymic stromal cells

We describe our initial approach to clone and characterize genes expressed preferentially in thymic stromal cells, in an attempt to generate molecular reagents to study the role of these cells in thymopoiesis and thymic function. Thymic stromal cells were prepared from fetal thymic organ cultures by treating them with 2-deoxyguanosine and depleting the remaining hematopoietic cells with anti-CD45 antibody. A cDNA library was then prepared after subtraction and amplification by PCR. The cloned inserts were sequenced and compared for homology with known genes in the data base. Unidentified cDNAs were then examined for expression in normal and SCID thymus and in a set of SV40-transformed thymic epithelial cell lines, by Northern blotting and a dot blot assay. In this report we describe the development of the library and present a general description of the genes identified from the initial 249 cDNAs sequenced. Among these, a relatively high percentage (55%) do not show any homology to previously identified genes. Several genes with a limited expression pattern were selected for further study.

Molecular cloning of chitinase cDNAs from the silkworm, Bombyx mori and the fall webworm, Hyphantria cunea

cDNAs encoding chitinases were cloned and characterized from Bombyx mori and Hyphantria cunea, and their gene expression during the metamorphosis was also studied. The chitinase cDNA from B. mori encodes a protein of 565 amino acids with a calculated molecular mass of 63.4 kDa and the H. cunea chitinase cDNA encodes a protein of 553 amino acids with a calculated molecular mass of 62.0 kDa. Amino acid alignment of the two chitinases revealed 75% homology and 77-80% with M. sexta chitinase. The putative cleavage site of the signal peptide was between amino acid residues 20 and 21 for both chitinases. There were three potential N-glycosylation sites in the chitinase of B. mori at the amino acid residues 86-89, NFTS 304-307, NATG, 398-401, NYTV, whereas two potential N-glycosylation sites were present at the amino acid residues 86-89, NFTA and 304-307, NATG, in that of H. cunea. Southern blot analysis of total genomic DNA suggested that the B. mori genome has only one chitinase gene detectable by the cDNA probe and the H. cunea genome has one or two chitinase gene copies. Northern analysis indicated that gene expression was up-regulated during the molting process, larval-pupal transformation and pupal-adult transformation, when enzymatic degradation of cuticle was occurring.

Cl- secretion induced by 5-hydroxytryptamine and calcitonin gene-related peptide in rat tracheal epithelia

The effects of 5-hydroxytryptamine (5-HT) and calcitonin gene-related peptide (CGRP), which are colocalized in nerve terminals in the airway, on Cl- secretion in rat tracheal epithelia were tested. Short-circuit current (Isc) was measured after rat tracheal epithelial monolayers were cultured on porous filters. In rat tracheal monolayers 5-HT and CGRP increased Isc upon addition to the serosal compartment, in a dose-dependent manner with EC50 values at 5 micromol/l and 5 nmol/l, respectively. The responses were dependent on the presence of Cl- in the bathing solution and were inhibited by 100 micromol/l bumetanide. When 5-HT or CGRP was added after the administration of forskolin, the responses were not observed. 5-HT and CGRP increased the intracellular cAMP concentration. Low-Ca2+ buffer (0.1 mmol/l) and pretreatment with BAPTA/AM (10 micromol/l), thapsigargin (1 micromol/l) or indomethacin (10 micromol/l) did not affect the responses to 5-HT and CGRP. The 5-HT-induced response was not inhibited by 5-HT2 and/or 5-HT4 antagonists. These results indicate that in the rat tracheal epithelia 5-HT and CGRP increase Cl- secretion by an increase in intracellular cAMP concentration via direct activation of basolateral receptors, and that the response to 5-HT is not mediated via 5-HT4 receptors.

Isolation and characterization of the cDNA encoding the prophenoloxidase of fall webworm, hyphantria cunea

Two kinds of cDNA clones encoding prophenoloxidases (ProPO; zymogen of phenoloxidase (monophenol, L-dopa: oxygen oxydoreductase, EC 1.14.18.1)) were isolated by polymerase chain reaction (PCR) followed by screening of cDNA library that was prepared from whole larvae of the fall webworm, Hyphantria cunea (Lepidoptera, Arctiidae). The cDNAs encode 681 and 697 amino acids with molecular masses of 78.2 and 80.2 kDa, respectively. Deduced amino acid sequence homology between the two H. cunea ProPOs are only 49% whereas the homology against other insect ProPOs ranged from about 40 to 72%. The phylogenic analysis showed that the insect ProPOs are grouped mainly into two families. A putative proteolytic cleavage site for enzyme activation was identical to other insect ProPOs. The conserved copper binding sites were 84-62% homologous to arthropod ProPOs. Two additional highly conserved regions were found in the carboxy terminal. Furthermore, like other insect prophenoloxidases, hydrophobic signal peptide sequences were absent in the deduced ProPOs from H. cunea. Southern blot analysis indicated that the H. cunea ProPO1 is present as a single copy in the genome. Northern blot analysis showed that the expression of the ProPO genes were concentrated in mid-instar larvae, but were much lower in other developmental stages.

An alteration in the structure of the minor groove of duplex DNA induced by the formation of an intermolecular d(GA)n:d(GA)n.d(TC)n triplex

A simple homopolymeric purine:purine.pyrimidine, d(GA)n:d(GA)n.d(TC)n, triplex DNA was generated in the presence of magnesium ion at neutral pH. Hydrogen bonding of the N7 positions of guanines and adenines was investigated by 7-deaza base substitutions and protection from chemical modification by dimethyl sulfate (DMS). Chemical modification of this triplex with DMS revealed an unexpected triplex specific hypermodification in the N3 positions of the adenines in addition to the protection in the N7 positions of the guanines. The significance of this increase in the chemical accessibility of the N3 positions of adenines in the minor groove and possible relevance of dehydration to the mechanism of triplex formation and stability is discussed.

Cloning of a SH3 domain-containing proline-rich protein, p85SPR, and its localization in focal adhesion

A mouse thymus cDNA expression library was screened with monoclonal antibody (mAb), B16-5 which binds to common epitope in SH3 domains of phospholipase C-gamma 1 (PLC-gamma 1) and Nck. We have determined the complete nucleotide sequence of one of several positive clones. The 4,172 bp cDNA clone (GenBank Accession No. U96634) encodes a SH3 domain-containing protein of 646 amino acids. Besides the SH3 domain, the predicted protein has a proline-rich region, nuclear localization signals, and leucine zipper motifs. The expressed protein in Sf9 insect cell exhibits a polypeptide of 85 kDa on SDS-PAGE. The protein is widely distributed in rat tissue with an especially high level of expression in brain and testis. Interestingly, the specific antibodies detected four related proteins of different size (75, 85, 90 and 105 kDa) in brain. In A431 cell, p85SPR is enriched at focal adhesion points indicating that the protein may interact with protein(s) in focal complexes.

The presence of a Sar1 gene family in Brassica campestris that suppresses a yeast vesicular transport mutation Sec12-1

Two new members (Bsar1a and Bsar1b) of the Sar1 gene family have been identified from a flower bud cDNA library of Brassica campestris and their functional characteristics were analyzed. The two clones differ from each other at 14 positions of the 193 amino acid residues deduced from their coding region. The amino acid sequences of Bsar1a and Bsar1b are most closely related to the Sar1 family, genes that function early in the process of vesicle budding from the endoplasmic reticulum (ER). The sequences contain all the conserved motifs of the Ras superfamily (G1-G4 motifs) as well as the distinctive structural feature near the C-terminus that is Sar1 specific. Our phylogenetic analysis confirmed that these two clones can indeed be considered members of the Sar1 family and that they have a close relationship to the ARF family. The Bsar1 proteins, expressed in Escherichia coli, cross-reacted with a polyclonal antibody prepared against Saccharomyces cerevisiae Sar1 protein. It also exhibited GTP-binding activity. Genomic Southern blot analysis, using the 3'-gene-specific regions of the Bsar1 cDNAs as probes, revealed that the two cDNA clones are members of a B. campestris Sar1 family that consists of 2 to 3 genes. RNA blot analysis, using the same gene-specific probes, showed that both genes are expressed with similar patterns in most tissues of the plant, including leaf, stem, root, and flower buds. Furthermore, when we placed the two Bsar1 genes under the control of the yeast pGK1 promoter into the temperature-sensitive mutant yeast strain S. cerevisiae Sec12-1, they suppressed the mutation which consists of a defect in vesicle transport. The amino acid sequence similarity, the GTP-binding activity, and the functional suppression of the yeast mutation suggest that the Bsar1 proteins are functional homologues of the Sar1 protein in S. cerevisiae and that they may perform similar biological functions.

Protein purification and nucleotide sequence of a lysozyme from the bacteria-induced larvae of the fall webworm, Hyphantria cunea

A protein with lytic activity against Micrococcus luteus was purified from the hemolymph of the fall webworm, Hyphantria cunea, larvae challenged with live E. coli. A bacteriolytic protein of about 14,000 daltons in mass was purified by cation exchange chromatography and reverse-phased HPLC. The optimum pH and optimum temperature range for activity were around pH 6.2 and 50 degrees C, respectively, in a 100 mM phosphate buffer. The amino-terminal amino acid sequence of this protein was determined and the corresponding cDNA was isolated and analyzed. The deduced protein of 142 amino acid residues was composed of a putative leader sequence of 20 residues and the mature enzyme of 122 residues. The cloned lysozyme gene was strongly induced in response to bacterial injection, implying that the enzyme is a part of the immune response of H. cunea. Comparison with other known lysozyme sequences shows that our lysozyme belongs to the chicken lysozyme.

Expressed sequence tags of Chinese cabbage flower bud cDNA

We randomly selected and partially sequenced cDNA clones from a library of Chinese cabbage (Brassica campestris L. ssp. pekinensis) flower bud cDNAs. Out of 1216 expressed sequence tags (ESTs), 904 cDNA clones were unique or nonredundant. Five hundred eighty-eight clones (48.4%) had sequence homology to functionally defined genes at the peptide level. Only 5 clones encoded known flower-specific proteins. Among the cDNAs with no similarity to known protein sequences (628), 184 clones had significant similarity to nucleotide sequences registered in the databases. Among these 184 clones, 142 exhibited similarities at the nucleotide level only with plant ESTs. Also, sequence similarities were evident between these 142 ESTs and their matching ESTs when compared using the deduced amino acid sequences. Therefore, it is possible that the anonymous ESTs encode plant-specific ubiquitous proteins. Our extensive EST analysis of genes expressed in floral organs not only contributes to the understanding of the dynamics of genome expression patterns in floral organs but also adds data to the repertoire of all genomic genes.

Probing the structure of a putative intermediate in homologous recombination: the third strand in the parallel DNA triplex is in contact with the major groove of the duplex

A three-stranded DNA that is a putative intermediate of homologous recombination is a novel DNA triplex, R-form DNA. In R-form DNA the third strand includes both purines and pyrimidines and is parallel to the identical strand of the duplex. To test and refine our previously proposed R-form base triplets we have used two approaches: (1) dimethyl sulfate protection of R-form DNA; and (2) thermal dissociation of R-form DNAs in which the duplex strands were substituted in a strand-specific manner with either 7-deaza-guanine or 7-deaza-adenine. Together, the footprinting and isosteric substitution results demonstrate that the third strand in R-form DNA is in contact with the purines in the N7 position in the major groove of the Watson-Crick duplex in three ((GC):G, (AT):A and (TA):T) out of the four possible triplets. Furthermore, these results suggest that the N7 positions of the duplex play a significant role in stabilizing the DNA-DNA contacts during the homology recognition process.

Properties of B cell stage specific and ubiquitous nuclear factors binding to immunoglobulin heavy chain gene switch regions

The Ig heavy chain (IgH) constant region (CH) class switch is manifested by DNA deletions which exchange the C mu gene of a functional VDJ-CH rearrangement for a C gamma, C epsilon or C alpha gene. Repetitive sequences (S regions) 5' of each CH gene mediate CH gene switch recombination by an illegitimate mechanism. S mu can be subdivided into S mu 5' (non-repetitive) and S mu 3' (repetitive) components with recombination occurring in either part. Here, we describe the properties of ubiquitous and B cell stage specific S mu binding factors NFS mu-U1 and NFS mu-B1 respectively. U1 only bound to S mu 5' sequences, and B1 to S mu 5', S mu 3' sequences and to other S regions with varying affinities. DMS and OP-Cu footprinting revealed the sequence AAAAAGCATGGCTGA in the U1 site while the B1 S mu 5' site overlapped the 3' end of the U1 binding site and also contained additional 3' flanking S mu repeat motifs (GAGCTGAGATGGGTGGGCT). Binding site competition assays reveal that NFS mu-B1 is either very related or identical to S alpha BP (described by Waters et al., Mol. Cell Biol. 9:5594, 1989) and BSAP (identified by Barberis et al., Genes Devl. 4:849, 1990) which were shown to bind to two sequences upstream of the S alpha repeats and within the promoters of sea urchin histone genes respectively.(ABSTRACT TRUNCATED AT 250 WORDS)