Whole-blood 3-gene Signature as a Decision Aid for Rifapentine-based TB Preventive Therapy

Background

Systemic drug reaction (SDR) is a major safety concern with weekly rifapentine plus isoniazid for 12 doses (3HP) for latent tuberculosis infection (LTBI). Identifying SDR predictors and at-risk participants before treatment can improve cost-effectiveness of the LTBI program.

Methods

We prospectively recruited 187 cases receiving 3HP (44 SDRs and 143 non-SDRs). A pilot cohort (8 SDRs and 12 non-SDRs) was selected for generating whole-blood transcriptomic data. By incorporating the hierarchical system biology model and therapy–biomarker pathway approach, candidate genes were selected and evaluated using reverse-transcription quantitative polymerase chain reaction (RT-qPCR). Then, interpretable machine learning models presenting as SHapley Additive exPlanations (SHAP) values were applied for SDR risk prediction. Finally, an independent cohort was used to evaluate the performance of these predictive models.

Results

Based on the whole-blood transcriptomic profile of the pilot cohort and the RT-qPCR results of 2 SDR and 3 non-SDR samples in the training cohort, 6 genes were selected. According to SHAP values for model construction and validation, a 3-gene model for SDR risk prediction achieved a sensitivity and specificity of 0.972 and 0.947, respectively, under a universal cutoff value for the joint of the training (28 SDRs and 104 non-SDRs) and testing (8 SDRs and 27 non-SDRs) cohorts. It also worked well across different subgroups.

Conclusions

The prediction model for 3HP-related SDRs serves as a guide for establishing a safe and personalized regimen to foster the implementation of an LTBI program. Additionally, it provides a potential translational value for future studies on drug-related hypersensitivity.

CoMI: consensus mutual information for tissue-specific gene signatures

Background

The gene signatures have been considered as a promising early diagnosis and prognostic analysis to identify disease subtypes and to determine subsequent treatments. Tissue-specific gene signatures of a specific disease are an emergency requirement for precision medicine to improve the accuracy and reduce the side effects. Currently, many approaches have been proposed for identifying gene signatures for diagnosis and prognostic. However, they often lack of tissue-specific gene signatures.

Results

Here, we propose a new method, consensus mutual information (CoMI) for analyzing omics data and discovering gene signatures. CoMI can identify differentially expressed genes in multiple cancer omics data for reflecting both cancer-related and tissue-specific signatures, such as Cell growth and death in multiple cancers, Xenobiotics biodegradation and metabolism in LIHC, and Nervous system in GBM. Our method identified 50-gene signatures effectively distinguishing the GBM patients into high- and low-risk groups (log-rank p = 0.006) for diagnosis and prognosis.

Conclusions

Our results demonstrate that CoMI can identify significant and consistent gene signatures with tissue-specific properties and can predict clinical outcomes for interested diseases. We believe that CoMI is useful for analyzing omics data and discovering gene signatures of diseases.

Transcriptomic and Proteomic Profiling of Human Mesenchymal Stem Cell Derived from Umbilical Cord in the Study of Preterm Birth

OBJECTIVE

Mesenchymal stem cells (MSCs) hold great therapeutic potential in morbidities associated with preterm birth. However, the molecular expressions of MSCs in preterm birth infants are not systematically evaluated. In this study, the dual-omics analyses of umbilical-cord (UC)-derived MSCs to identify the dysregulated cellular functions are presented.

MATERIALS AND METHODS

The UC-MSCs are collected from ten full-term and eight preterm birth infants for microarray and iTRAQ-based proteome profiling.

RESULTS

The integrative analysis of dual-omics data discovered 5615 commonly identified genes/proteins of which 29 genes/proteins show consistent up- or downregulation in preterm birth. The Gene Ontology analysis reveals that dysregulation of mitochondrial translation and cellular response to oxidative stress are mainly enriched in 290 differential expression proteins (DEPs) while the 412 differential expression genes (DEGs) are majorly involved in single-organism biosynthetic process, cellular response to stress, and mitotic cell cycle in preterm birth. Besides, a 13-protein module involving CUL2 and CUL3 is identified, which plays an important role in cullin-RING-based ubiquitin ligase complex, as potential mechanism for preterm birth.

CONCLUSION

The dual-omics data not only provide new insights to the molecular mechanism but also identify panel of candidate markers associated with preterm birth.

A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations

BACKGROUND

One of the crucial steps toward understanding the associations among molecular interactions, pathways, and diseases in a cell is to investigate detailed atomic protein-protein interactions (PPIs) in the structural interactome. Despite the availability of large-scale methods for analyzing PPI networks, these methods often focused on PPI networks using genome-scale data and/or known experimental PPIs. However, these methods are unable to provide structurally resolved interaction residues and their conservations in PPI networks.

RESULTS

Here, we reconstructed a human three-dimensional (3D) structural PPI network (hDiSNet) with the detailed atomic binding models and disease-associated mutations by enhancing our PPI families and 3D-domain interologs from 60,618 structural complexes and complete genome database with 6,352,363 protein sequences across 2274 species. hDiSNet is a scale-free network (γ = 2.05), which consists of 5177 proteins and 19,239 PPIs with 5843 mutations. These 19,239 structurally resolved PPIs not only expanded the number of PPIs compared to present structural PPI network, but also achieved higher agreement with gene ontology similarities and higher co-expression correlation than the ones of 181,868 experimental PPIs recorded in public databases. Among 5843 mutations, 1653 and 790 mutations involved in interacting domains and contacting residues, respectively, are highly related to diseases. Our hDiSNet can provide detailed atomic interactions of human disease and their associated proteins with mutations. Our results show that the disease-related mutations are often located at the contacting residues forming the hydrogen bonds or conserved in the PPI family. In addition, hDiSNet provides the insights of the FGFR (EGFR)-MAPK pathway for interpreting the mechanisms of breast cancer and ErbB signaling pathway in brain cancer.

CONCLUSIONS

Our results demonstrate that hDiSNet can explore structural-based interactions insights for understanding the mechanisms of disease-associated proteins and their mutations. We believe that our method is useful to reconstruct structurally resolved PPI networks for interpreting structural genomics and disease associations.

Template-based scoring functions for visualising biological insights of H-2Kb-peptide-TCR complexes

Major Histocompatibility Complex (MHC), peptide and T-Cell Receptor (TCR) play an essential role of adaptive immune responses. Many prediction servers are available for identification of peptides that bind to MHC class I molecules but often lack detailed interacting residues for analysing MHC-peptide-TCR interaction mechanisms. This study considers both the interface similarity and the interacting force for identifying binding models. Our model, considering both the MHC-peptide and the peptide-TCR interfaces, is able to provide visualisation and the biological insights of binding models. We believe that our model is useful for the development of peptide-based vaccines.

Genome-wide structural modelling of TCR-pMHC interactions

Background

The adaptive immune response is antigen-specific and triggered by pathogen recognition through T cells. Although the interactions and mechanisms of TCR-peptide-MHC (TCR-pMHC) have been studied over three decades, the biological basis for these processes remains controversial. As an increasing number of high-throughput binding epitopes and available TCR-pMHC complex structures, a fast genome-wide structural modelling of TCR-pMHC interactions is an emergent task for understanding immune interactions and developing peptide vaccines.

Results

We first constructed the PPI matrices and iMatrix, using 621 non-redundant PPI interfaces and 398 non-redundant antigen-antibody interfaces, respectively, for modelling the MHC-peptide and TCR-peptide interfaces, respectively. The iMatrix consists of four knowledge-based scoring matrices to evaluate the hydrogen bonds and van der Waals forces between sidechains or backbones, respectively. The predicted energies of iMatrix are high correlated (Pearson's correlation coefficient is 0.6) to 70 experimental free energies on antigen-antibody interfaces. To further investigate iMatrix and PPI matrices, we inferred the 701,897 potential peptide antigens with significant statistic from 389 pathogen genomes and modelled the TCR-pMHC interactions using available TCR-pMHC complex structures. These identified peptide antigens keep hydrogen-bond energies and consensus interactions and our TCR-pMHC models can provide detailed interacting models and crucial binding regions.

Conclusions

Experimental results demonstrate that our method can achieve high precision for predicting binding affinity and potential peptide antigens. We believe that iMatrix and our template-based method can be useful for the binding mechanisms of TCR-pMHC complexes and peptide vaccine designs.

Inferring homologous protein-protein interactions through pair position specific scoring matrix

Background

The protein-protein interaction (PPI) is one of the most important features to understand biological processes. For a PPI, the physical domain-domain interaction (DDI) plays the key role for biology functions. In the post-genomic era, to rapidly identify homologous PPIs for analyzing the contact residue pairs of their interfaces within DDIs on a genomic scale is essential to determine PPI networks and the PPI interface evolution across multiple species.

Results

In this study, we proposed "pair Position Specific Scoring Matrix (pairPSSM)" to identify homologous PPIs. The pairPSSM can successfully distinguish the true protein complexes from unreasonable protein pairs with about 90% accuracy. For the test set including 1,122 representative heterodimers and 2,708,746 non-interacting protein pairs, the mean average precision and mean false positive rate of pairPSSM were 0.42 and 0.31, respectively. Moreover, we applied pairPSSM to identify ~450,000 homologous PPIs with their interacting domains and residues in seven common organisms (e.g. Homo sapiens, Mus musculus, Saccharomyces cerevisiae and Escherichia coli).

Conclusions

Our pairPSSM is able to provide statistical significance of residue pairs using evolutionary profiles and a scoring system for inferring homologous PPIs. According to our best knowledge, the pairPSSM is the first method for searching homologous PPIs across multiple species using pair position specific scoring matrix and a 3D dimer as the template to map interacting domain pairs of these PPIs. We believe that pairPSSM is able to provide valuable insights for the PPI evolution and networks across multiple species.

Steric recognition of T-cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes

MHC class I-restricted CD8 T-lymphocyte epitopes comprise anchor motifs, T-cell receptor (TCR) contact residues and the peptide backbone. Serial variant epitopes with substitution of amino acids at either anchor motifs or TCR contact residues have been synthesized for specific interferon-γ responses to clarify the TCR recognition mechanism as well as to assess the epitope prediction capacity of immunoinformatical programmes. CD8 T lymphocytes recognise the steric configuration of functional groups at the TCR contact side chain with a parallel observation that peptide backbones of various epitopes adapt to the conserved conformation upon binding to the same MHC class I molecule. Variant epitopes with amino acid substitutions at the TCR contact site are not recognised by specific CD8 T lymphocytes without compromising their binding capacity to MHC class I molecules, which demonstrates two discrete antigen presentation events for the binding of peptides to MHC class I molecules and for TCR recognition. The predicted outcome of immunoinformatical programmes is not consistent with the results of epitope identification by laboratory experiments in the absence of information on the interaction with TCR contact residues. Immunoinformatical programmes based on the binding affinity to MHC class I molecules are not sufficient for the accurate prediction of CD8 T-lymphocyte epitopes. The predictive capacity is further improved to distinguish mutant epitopes from the non-mutated epitopes if the peptide-TCR interface is integrated into the computing simulation programme.

MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates

A module is a fundamental unit forming with highly connected proteins and performs a certain kind of biological functions. Modules and module–module interaction (MMI) network are essential for understanding cellular processes and functions. The MoNetFamily web server can identify the modules, homologous modules (called module family) and MMI networks across multiple species for the query protein(s). This server first finds module candidates of the query by using BLASTP to search the module template database (1785 experimental and 1252 structural templates). MoNetFamily then infers the homologous modules of the selected module candidate using protein–protein interaction (PPI) families. According to homologous modules and PPIs, we statistically calculated MMIs and MMI networks across multiple species. For each module candidate, MoNetFamily identifies its neighboring modules and their MMIs in module networks of Homo sapiens, Mus musculus and Danio rerio. Finally, MoNetFamily shows the conserved proteins, PPI profiles and functional annotations of the module family. Our results indicate that the server can be useful for MMI network (e.g. 1818 modules and 9678 MMIs in H. sapiens) visualizations and query annotations using module families and neighboring modules. We believe that the server is able to provide valuable insights to determine homologous modules and MMI networks across multiple species for studying module evolution and cellular processes. The MoNetFamily sever is available at http://monetfamily.life.nctu.edu.tw.

PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes

One of the most adaptive immune responses is triggered by specific T-cell receptors (TCR) binding to peptide-major histocompatibility complexes (pMHC). Despite the availability of many prediction servers to identify peptides binding to MHC, these servers are often lacking in peptide-TCR interactions and detailed atomic interacting models. PAComplex is the first web server investigating both pMHC and peptide-TCR interfaces to infer peptide antigens and homologous peptide antigens of a query. This server first identifies significantly similar TCR-pMHC templates (joint Z-value ≥ 4.0) of the query by using antibody-antigen and protein-protein interacting scoring matrices for peptide-TCR and pMHC interfaces, respectively. PAComplex then identifies the homologous peptide antigens of these hit templates from complete pathogen genome databases (≥10(8) peptide candidates from 864,628 protein sequences of 389 pathogens) and experimental peptide databases (80,057 peptides in 2287 species). Finally, the server outputs peptide antigens and homologous peptide antigens of the query and displays detailed interacting models (e.g. hydrogen bonds and steric interactions in two interfaces) of hitTCR-pMHC templates. Experimental results demonstrate that the proposed server can achieve high prediction accuracy and offer potential peptide antigens across pathogens. We believe that the server is able to provide valuable insights for the peptide vaccine and MHC restriction. The PAComplex sever is available at http://PAcomplex.life.nctu.edu.tw.

3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes

Background

Comprehensive exploration of protein-protein interactions is a challenging route to understand biological processes. For efficiently enlarging protein interactions annotated with residue-based binding models, we proposed a new concept "3D-domain interolog mapping" with a scoring system to explore all possible protein pairs between the two homolog families, derived from a known 3D-structure dimmer (template), across multiple species. Each family consists of homologous proteins which have interacting domains of the template for studying domain interface evolution of two interacting homolog families.

Results

The 3D-interologs database records the evolution of protein-protein interactions database across multiple species. Based on "3D-domain interolog mapping" and a new scoring function, we infer 173,294 protein-protein interactions by using 1,895 three-dimensional (3D) structure heterodimers to search the UniProt database (4,826,134 protein sequences). The 3D- interologs database comprises 15,124 species and 283,980 protein-protein interactions, including 173,294 interactions (61%) and 110,686 interactions (39%) summarized from the IntAct database. For a protein-protein interaction, the 3D-interologs database shows functional annotations (e.g. Gene Ontology), interacting domains and binding models (e.g. hydrogen-bond interactions and conserved residues). Additionally, this database provides couple-conserved residues and the interacting evolution by exploring the interologs across multiple species. Experimental results reveal that the proposed scoring function obtains good agreement for the binding affinity of 275 mutated residues from the ASEdb. The precision and recall of our method are 0.52 and 0.34, respectively, by using 563 non-redundant heterodimers to search on the Integr8 database (549 complete genomes).

Conclusions

Experimental results demonstrate that the proposed method can infer reliable physical protein-protein interactions and be useful for studying the protein-protein interaction evolution across multiple species. In addition, the top-ranked strategy and template interface score are able to significantly improve the accuracies of identifying protein-protein interactions in a complete genome. The 3D-interologs database is available at http://3D- interologs.life.nctu.edu.tw.

PCFamily: a web server for searching homologous protein complexes

The proteins in a cell often assemble into complexes to carry out their functions and play an essential role of biological processes. The PCFamily server identifies template-based homologous protein complexes [called protein complex family (PCF)] and infers functional modules of the query proteins. This server first finds homologous structure complexes of the query using BLASTP to search the structural template database (11 263 complexes). PCFamily then searches the homologous complexes of the templates (query) from a complete genomic database (Integr8 with 6 352 363 protein sequences in 2274 species). According to these homologous complexes across multiple species, this sever infers binding models (e.g. hydrogen-bonds and conserved amino acids in the interfaces), functional modules, and the conserved interacting domains and Gene Ontology annotations of the PCF. Experimental results demonstrate that the PCFamily server can be useful for binding model visualizations and annotating the query proteins. We believe that the server is able to provide valuable insights for determining functional modules of biological networks across multiple species. The PCFamily sever is available at http://pcfamily.life.nctu.edu.tw.

PPISearch: a web server for searching homologous protein-protein interactions across multiple species

As an increasing number of reliable protein–protein interactions (PPIs) become available and high-throughput experimental methods provide systematic identification of PPIs, there is a growing need for fast and accurate methods for discovering homologous PPIs of a newly determined PPI. PPISearch is a web server that rapidly identifies homologous PPIs (called PPI family) and infers transferability of interacting domains and functions of a query protein pair. This server first identifies two homologous families of the query, respectively, by using BLASTP to scan an annotated PPIs database (290 137 PPIs in 576 species), which is a collection of five public databases. We determined homologous PPIs from protein pairs of homologous families when these protein pairs were in the annotated database and have significant joint sequence similarity (E ≤ 10⁻⁴⁰) with the query. Using these homologous PPIs across multiple species, this sever infers the conserved domain–domain pairs (Pfam and InterPro domains) and function pairs (Gene Ontology annotations). Our results demonstrate that the transferability of conserved domain-domain pairs between homologous PPIs and query pairs is 88% using 103 762 PPI queries, and the transferability of conserved function pairs is 69% based on 106 997 PPI queries. The PPISearch server should be useful for searching homologous PPIs and PPI families across multiple species. The PPISearch server is available through the website at http://gemdock.life.nctu.edu.tw/ppisearch/.

3D-partner: a web server to infer interacting partners and binding models

The 3D-partner is a web tool to predict interacting partners and binding models of a query protein sequence through structure complexes and a new scoring function. 3D-partner first utilizes IMPALA to identify homologous structures (templates) of a query from a heterodimer profile library. The interacting-partner sequence profiles of these templates are then used to search interacting candidates of the query from protein sequence databases (e.g. SwissProt) by PSI-BLAST. We developed a new scoring function, which includes the contact-residue interacting score (e.g. the steric, hydrogen bonds, and electrostatic interactions) and the template consensus score (e.g. couple-conserved residue and the template similarity scores), to evaluate how well the interfaces between the query and interacting candidates. Based on this scoring function, 3D-partner provides the statistic significance, the binding models (e.g. hydrogen bonds and conserved amino acids) and functional annotations of interacting partners. The correlation between experimental energies and predicted binding affinities of our scoring function is 0.91 on 275 mutated residues from the ASEdb. The average precision of the server is 0.72 on 563 queries and the execution time of this server for a query is approximately 15 s on average. These results suggest that the 3D-partner server can be useful in protein-protein interaction predictions and binding model visualizations. The server is available online at: http://3D-partner.life.nctu.edu.tw.

Characterization of silane-modified immobilized gold colloids as a substrate for surface-enhanced Raman spectroscopy

Immobilized gold colloid particles coated with a C-18 alkylsilane layer have been characterized as a substrate for surface-enhanced Raman scattering (SERS) studies of adsorption onto hydrophobic surfaces. Atomic force microscopy images, optical extinction spectra, and SERS measurements are reported as a function of accumulation of gold colloid on glass. As the metal particles become increasingly aggregated on the surface, the SERS enhancement increases until the plasmon resonance shifts to wavelengths longer than the excitation laser. The gold colloid substrates are stable and exhibit reproducible SERS enhancement. When octadecyltrimethoxysilane is self-assembled over the gold, the metal surface is protected from exposure to solution-phase species, as evidenced by the inhibition of chemisorption of a disulfide reagent to the overcoated gold surface. The results show that interactions with gold can be blocked by a silane layer so as not to significantly influence physisorption of molecules at the C-18/solution interface. The SERS enhancement from these C-18-overcoated gold substrates is reproducible for different films prepared from the same colloidal suspension; the substrates are also stable with time and upon exposure to laser irradiation.

Solitary fibrous tumor of the liver

Solitary fibrous tumor of the liver is a rare neoplasm. So far, 21 cases have been described in the English literature. We reported an additional case. Our patient, a 75-year-old man, suffered from abdominal fullness and body weight loss of 6 kg over 6 months, and chills and fever for 2 months. Hypoglycemia was noted at admission. Both abdominal sonography and CT showed a huge mass occupying the right lobe of liver. Liver biopsy showed fibrous tumor. Right lobectomy was performed and the tumor was resected. Pathological examination showed spindle-shaped and fibroblast-like cells within the collagenous stroma. On immunohistochemical stains, these spindle tumor cells showed CD34 positive reactivity. The post-operative course was uneventful and there was no more hypoglycemia. The patient recovered smoothly, regained his body weight, and was alive without evidence of disease recurrence at the last follow-up visit in November, 2000.

Expression and activity of epidermal growth factor receptor in late fetal rat lung is cell- and sex-specific

Epidermal growth factor (EGF) augments late fetal lung maturation by advancing the ontogeny of fetal lung development and by stimulating surfactant synthesis. Previous studies have indicated that fibroblastalveolar epithelial cell communications mediate surfactant synthesis in the fetal lung and EGF acts through such a mechanism. We investigated the hypothesis that is differential activity and expression of the epidermal growth factor receptor (EGF-R) in fetal lung fibroblasts during the canalicular stage of lung development mediates EGF effects. To test this hypothesis, we examined fetal rat lung fibroblasts (FLFs) and type II cells of late gestation (canalicular and saccular stages; 17-22 days) by EGF-R binding techniques, SDS-PAGE, and Western blot analysis. Specific EGF binding increased 181% in day 18 female FLFs, with male FLFs exhibiting a similar increase on day 19. In contrast, specific EGF binding was low in type II cells, did not increase during late gestation, and there were no sex-specific differences. SDS-PAGE and Western blot analysis revealed a predominant 170-kDa EGF-R band in fibroblasts that increased with gestation (peak = 19 days), and was stronger in females. Immunoprecipitation of EGF-treated cells demonstrated the tyrosine kinase activity of the identified receptor. In contrast, type II cells showed minimal signal that did not increase until day 21 of gestation. We also examined whole fetal lung sections by immunohistochemistry to determine cell-specific expression of the EGF-R in vivo. Immunohistochemistry revealed specific EGF-R staining in columnar and cuboidal epithelia of small conducting airways and in mesenchyme of epithelial-mesenchymal borders (including subepithelial mesenchyme). In contrast, alveolar epithelia showed minimal staining, while subalveolar mesenchyme EGF-R staining peaked at day 19 of gestation. We conclude that cell-specific and sex-specific differences in EGF-R binding and EGF-R immunolocalization appears in the fetal lung at a developmental stage that is critical for alveolar epithelial cell differentiation. The results suggest a role for EGF-R activation in late fetal alveolar epithelial cell maturation, which is mediated through mesenchymal-epithelial cell communication.

Population heterogeneity of higher-plant mitochondria in structure and function

Mitochondria of rapidly developing mungbean seedlings were fractionated into four populations: two density classes, each from a 1500S and a 150S pellet. Each of the four populations exhibited cytochrome c oxidase (COX) activity and contained mitochondrial DNA and cardiolipin; plastid and glyoxysome content were found to be relatively low. Five mitochondrial membrane proteins, COXII/III, ATPase alpha/beta and porin, and a matrix enzyme, manganese superoxide dismutase (MnSOD), were detected by immunoblots in all four populations. Another matrix enzyme, pyruvate dehydrogenase was detected only in the two respiratory-competent 1500S populations. The two 150S populations contained a previously unidentified organelle that lacked demonstrable respiratory capability. This organelle, which we have tentatively referred to as "slow-sedimenting (ss-) mitochondrion", was small in size (below light-optics resolution, 70-300nm, majority < or =200nm) and possessed a peculiar looking boundary membrane, ribosomes, and an occasional prominent electron-dense spot. Characteristically, ss-mitochondria were almost always in contact with a filament-aligned membrane-like structure of varying length. Cristae structure, while undetected in small ss-mitochondria, appeared in larger individuals. Typical mitochondria were found in the denser 1500S population, while the lighter 1500S population consisted of 300-800 nm mitochondria exhibiting a varying degree of size-dependent inner membrane folding. Using electron microscopy (EM) immunolocalization and serial sectioning, we have identified in situ organelles resembling in size and in fine structure the ss-mitochondria, which also exhibit a size-dependent folding of the inner membrane. These results suggest that small ss-mitochondria may undergo a progressive development in situ. Taken together, our findings demonstrate the existence of a pattern of structure-function-coordinated gross heterogeneity among mitochondria. This pattern of mitochondrial heterogeneity, characterized both in isolated mitochondria and in situ, implies that small ss-mitochondria may represent a type of "nascent mitochondria" derived from a yet unidentified mitochondria-propagation mode operating during rapid seedling growth. Mitochondrial division by binary fission, characterized by the appearance of dumbbell-shaped intermediates, was also detected.

Variation in protein and RNA synthesis activity in isolated mitochondria of the developing rice (Oryza sativa L.) panicle

We have studied variation in mitochondrial protein and RNA synthesis during the development of a specialized rice (Oryza sativa L.) reproductive organ in a bacteria-free environment. Mitochondria were prepared from the maturing panicle during microsporogenesis when meiosis occurred and from etiolated seedlings at two growth stages. We found (1) that there was no discernible qualitative difference among the polypeptides synthesized by these three mitochondrial samples; (2) that the quantity of proteins synthesized by panicle mitochondria was approximately 3 times that of the seedling mitochondria, while the two seedling samples exhibited only a minor quantitative difference; (3) that panicle and seedling mitochondria samples synthesized qualitatively the same RNA but at distinctly different rates and that more RNA products were synthesized by panicle than by seedling mitochondria. These results, taken together, suggest that either the regulation of mitochondrial transcription and translation or the copy number of mitochondrial DNA per mitochondrion change discretely in the developing panicle and consequently that the level of mitochondrial gene expression increases considerably during the development of the reproductive structure in rice.

Molecular characterization of glucose-6-phosphate dehydrogenase deficiency in Chinese infants with or without severe neonatal hyperbilirubinaemia

To characterize mutations in the glucose-6-phosphate dehydrogenase (G6PD) gene in Chinese infants, we studied 213 G6PD-deficient infants without blood exchange transfusion (BET) therapy, and 34 patients who required BET therapy for their severe hyperbilirubinaemia after birth. Nine different point mutations were characterized in all infants. Of these mutations, the G to T substitution at cDNA nucleotide (nt) 1376, which accounts for the mutations in 131 (53.0%) neonates, followed by G to A substitution at nt 1388 in 18 (10.5%) infants, A to G substitution at nt 493 in 17 (6.9%) infants, A to G substitution at nt 95 in 10 (4.1%) infants, C to T substitution at nt 1024 in six (2.4%) infants, and G to T substitution at nt 392 in three (1.2%) infants, G to A substitution at nt 487 in two (0.8%) infants, C to T substitution at nt 1360 in two (0.8%) infants and C to T substitution at nt 592 in two (0.8%) infants. Mutations in 48 (19.5%) G6PD-deficient infants were not characterized. Most (64.7%) mutations in the G6PD-deficient infants who required BET therapy after birth result from a G to T substitution at nt 1376. The enzyme activity of G6PD deficient infants who required BET therapy is significantly lower than for those who did not, even in a group with the same variant (as in 1376 mutation). Severe neonatal jaundice requiring BET therapy can take place with the majority of variants encountered in this area.

Characteristics and radiofrequency ablation therapy of intermediate septal accessory pathway

Fourteen patients (5%) with an intermediate septal accessory pathway were identified among 283 consecutive patients with the Wolff-Parkinson-White syndrome who had electrophysiologic study and radiofrequency ablation therapy. Nine were women and 5 were men (mean age 33 +/- 13 years). The resting electrocardiogram showed ventricular preexcitation in 8 patients and normal PR interval in 6. Anterograde and retrograde mapping studies revealed that the accessory pathway was para-Hisian in 11 patients and paranodal in 3. The accessory pathway was successfully ablated in 10 patients (9 para-Hisian and 1 paranodal) and damaged in 1 (para-Hisian). Treatment of 3 patients was complicated by transient atrioventricular (AV) block, of 1 by intermittent second-degree AV block, and of another by permanent complete AV block requiring implantation of a permanent pacemaker. Six patients underwent a follow-up electrophysiologic study 84 +/- 55 days after ablation; none had induction of tachycardia even after isoproterenol infusion. It is concluded that radiofrequency ablation therapy for intermediate septal accessory pathway is feasible. However, the success rate is only modest (71%), whereas complications with heart block (36%) or complete right bundle branch block (29%) are high. Thus, the procedure should be reserved for patients with life-threatening or troublesome symptomatic tachyarrhythmias.

[Congenital nasopharyngeal teratoma: report of a case and review of the literature]

Teratomas are the most common congenital tumors, but teratomas of the nasopharynx are rare and seen almost exclusively in infants, usually in neonates. An unusual case of a neonate with respiratory distress is presented and a nasopharyngeal mass protruding into the oral cavity. After successful removal of the mass, pathological examination revealed a mature teratoma. The management and differential diagnosis are discussed, accompanied by a review of the literature.

Characterization of protein synthesis by isolated rice mitochondria

Bacteria-free mitochondria were isolated from aseptically grown, etiolated and green seedlings of both cytoplasmic male-sterile (WA-type) and male-fertile rice (Oryza sativa L.). Protein synthesis in these isolated mitochondria was characterized by gel electrophoresis/fluorography and by the incorporation of [(35)S]-methionine into protein. In the presence of cycloheximide, a set of some 25 discrete polypeptides and an electrophoretically unresolved population were synthesized. This pattern of protein synthesis in organello was essentially the same in mitochondria isolated from both male-fertile and malesterile cytoplasms. Our data does not preclude the possibility, however, that the WA-type CMS possesses a tissue-specific and/or a low abundance mitochondrial protein(s), whose synthesis eluded detection under our experimental conditions. The synthesis of the mitochondria-encoded polypeptides by isolated rice mitochondria was inhibited by chloramphenicol and incompletely inhibited by erythromycin. A minor chloramphenicol-insensitive, cycloheximide-sensitive translation activity was found consistently to copurify with the mitochondria. This activity generated a reproducible electrophoretic profile of a poorly resolved, weakly labelled population of polypeptides and of a few conspicuous polypeptides, including a 42 kDa species.

Synthesis and physicochemical properties of sulfamate derivatives as topical antiglaucoma agents

Several imidazolylphenyl sulfamate and (imidazolylphenoxy)alkyl sulfamate derivatives were synthesized and evaluated as topically active carbonic anhydrase inhibitors. Water solubility, pKa, carbonic anhydrase inhibition, and partition coefficient for the compounds were measured. Sulfamic acid 2-[4-(1H-imidazol-1-yl)phenoxy]ethyl ester monohydrochloride (16) has the best combination of properties and showed excellent topical activity in lowering the intraocular pressure in New Zealand white rabbits.

Physiological profiles of Hong Kong élite soccer players

Most physiological profiles of élite soccer players originate from Western Europe and North America. Unfortunately, there is a scarcity of descriptive data on the physical characteristics of Asian soccer players. Therefore, the purpose of this study was to evaluate the physiological profiles of élite soccer players in Hong Kong. It was conducted in conjunction with the selection of the Hong Kong team before the 1990 Beijing Asian Games. In all, 24 professional soccer players were selected from a pool of 180 players as subjects for the study. The following means(s.d.) were observed: height 173.4(4.6) cm; weight 67.7(5.0) kg; body fat 7.3(3.0)%; forced vital capacity (FVC) 5.1(0.6) l; maximum oxygen uptake (VO2max) 59.1(4.9) ml kg-1 min-1; anaerobic threshold (AT 80.0(7.2)% of VO2max; alactic power index 13.5(2.4) W kg-1; lactic work index 298(27) J kg-1; peak isokinetic dominant knee extensor and flexor strengths 2.72(0.36) Nm kg-1 and 1.65(0.20) Nm kg-1. On average the physique of Hong Kong soccer players appeared to be smaller and lighter than those found in Europe, which may be one of the key factors that contribute to the lack of success of Hong Kong soccer teams in international competition.

Quantitative measurement of muscle and subcutaneous fat thickness in newborn by real-time ultrasonography: a useful method for site and depth evaluation in vaccination

In order to quantify muscle thickness and choose the appropriate site for intramuscular injection of vaccines in neonates, we used ultrasonography to measure muscle and subcutaneous fat thickness of anterolateral mid-thigh, upper outer quadrant of buttock and middle area of deltoid in fifty full term (group 1) and thirty low birth weight (group 2) infants. A Hitachi EUB40 real-time scanner and a 5 MHz transducer was used in the study. We delineated the normal distribution of muscle and subcutaneous fat thickness in mid-thigh, buttock and deltoid areas of full term and low birth weight infants. There was no significant difference between male and female infants in the two groups. Muscle and subcutaneous fat thickness in the thigh area was 11.8 +/- 1.9 mm and 3.8 +/- 0.4 mm, respectively, in group 1; 8.6 +/- 1.7 mm and 2.7 +/- 0.5 mm in group 2. Figures in the buttock area were 10. 1 +/- 1.5 mm and 3.7 +/- 0.5 mm in group 1, 6.9 +/- 1.2 mm and 2.7 +/- 0.7 mm in group 2; and in the deltoid area were 5.2 +/- 0.7 mm and 3.4 +/- 1.5 mm in group 1 and 3.8 +/- 0.8 mm and 2.3 +/- 0.6 mm in group 2. There was significant logarithmic correlation between muscle thickness and body weight (r = 0.6, 0.8, 0.6) and muscle thickness and body length (r = 0.4, 0.6, 0.6) in thigh, buttock and deltoid areas of the low birth weight infants. In contrast, there was significant logarithmic correlation only between buttock muscle and body weight (r = 0.5) in the full term infants.(ABSTRACT TRUNCATED AT 250 WORDS)

2-Phenyl-3H-imidazo[4,5-b]pyridine-3-acetamides as non-benzodiazepine anticonvulsants and anxiolytics

A series of 2-phenyl-3H-imidazo[4,5-b]pyridine-3-acetamides were designed and synthesized as non-benzodiazepine anxiolytics based on a molecular disconnection of a typical 1,4-benzodiazepine (BZD). A number of these compounds showed submicromolar potency in a [3H]benzodiazepine binding assay in vitro and good potency in protecting rodents against pentylenetetrazole-induced seizures. Compound 84 appears to be a selective anticonvulsant (pentylenetetrazole) agent when tested against a profile of chemically and electrically induced seizures in mice. In addition, compound 148 appears to be a selective anxiolytic/hypnotic agent on the basis of biochemical and pharmacological characterization. It appears to be a full BZD agonist as assessed by GABA shift ratio and to be effective in punishment and nonpunishment animal models of anxiety. In addition, it shows a lower side-effect profile than diazepam as assessed by rotorod neurotoxicity and potentiation of ethanol-induced sleep time in mice. The chemistry and structure-activity relationships of this series is discussed.

Protein Synthesis in Isolated Mitochondria of Rice (Oryza sativa L.) Seedlings

For studies of in organello mitochondrial protein synthesis in rice, Oryza sativa L., conventional surface-sterilization procedures were demonstrated to be ineffective. Because of the over-whelmingly efficient [(35)S]methionine utilization by contaminating bacteria, even "essentially bacteria-free" rice mitochondria were shown to be unsuitable for the study of in organello protein synthesis. We developed a procedure to obtain a bacteria-free preparation of rice mitochondria. Such mitochondria favored a membrane-dependent ATP-generating system over an external ATP-generating system as the energy supplement for in organello protein synthesis. Two distinct classes of [(35)S]methionine-labeled, cycloheximide-insensitive products were detected: an electrophoretically unresolved population and a set of some 22 to 27 discrete polypeptide species, each with a characteristic electrophoretic mobility and relative abundance.

Echocardiographic left ventricular hypertrophy in Chinese endurance athletes

Most echocardiographic data on the athletic heart syndrome originate from the United States and Western Europe. There are no published data on echocardiographically documented left ventricular hypertrophy in Asian athletes. We investigated the echocardiographic changes which take place with endurance training by studying eight Hong Kong national cyclists. This study confirms that left ventricular hypertrophy and increased left ventricular end-diastolic dimensions are common findings in Chinese endurance athletes as in their Caucasian counterparts. Calculated left ventricular muscle mass exceeded the 95th percentile in seven of eight subjects.

[Clinical studies of neonatal hyperbilirubinemia treated with blood exchange transfusion]

From April 1984 to November 1989, 194 cases of neonatal hyperbilirubinemia treated with blood exchange transfusions (BET) were studied. The patients included 127 male and 67 female neonates, with an age ranged from 13 hours to 16 days. The most common cause was idiopathic (52.6%), followed by G-6-PD deficiency (23.7%), and sepsis (12.9%). Most of the neonates received BET at the 4th day of birth (23.2%), but there were still 30 cases (15.5%) that received BET after 1 week of age. There were 17 cases (8.8%) with maximum serum bilirubin lower than 20 mg/dl before receiving BET, five of them were LBW infants; 11 cases (5.7%) were greater than 40 mg/dl. The mean of maximum serum bilirubin was 26.9 +/- 7.96 mg/dl. Most of the cases received BET once (145 cases) or twice (33 cases). There were two cases that received up to six BET's. One was G-6-PD deficiency and one idiopathic in etiology. No significant difference of BET frequency between sex or body weight (p greater than 0.05) was found. Newborns with higher serum bilirubin due to G-6-PD deficiency, received more BET (p less than 0.05). No significant differences of the pH value (7.33 +/- 0.08 vs 7.35 +/- 0.10) and bicarbonate values (21.20 +/- 3.99 vs 22.00 +/- 3.83 mM/L) occurred before and after blood exchange transfusion (p greater than 0.1). The serum calcium decreased significantly after BET (3.88 +/- 0.91 vs 3.15 +/- 6.97 mEq/L, p less than 0.05). There were 11 deaths in this series, the mortality rate was 5.7%. Three cases (1.5%) were dead within 6 hours after BET.(ABSTRACT TRUNCATED AT 250 WORDS)

Benzo- and pyrido-1,4-oxazepin-5-ones and -thiones: synthesis and structure-activity relationships of a new series of H1 antihistamines

A series of novel benzo- and pyrido-1,4-oxazepinones and -thiones which represents a new structural class of compounds possessing H1 antihistaminic activity was synthesized, and the SARs were evaluated. The antihistaminic activity was determined by blockade of histamine-induced lethality in guinea pigs. The sedative potential was determined by comparison of the EEG profiles of the compounds with those of known sedating and nonsedating antihistamines. Several of the compounds were shown to possess potent H1 antihistaminic activity and to be free of the cortical slowing with synchronized waves and spindling activity found in the EEG of sedative antihistamines. One compound, 2-[2-(dimethylamino)ethyl]-3,4-dihydro-4-methylpyrido[3,2-f]-1,4- oxazepine-5(2H)-thione (rocastine) is currently undergoing clinical evaluation as a nonsedating H1 antihistamine.

[Menkes' kinky hair disease: report of one case]

A male infant, 2-month-old, was delivered normally at term. He weighed 3.0 Kg and was stated to be quite well until convulsion was presented at the age of 1 month. The convulsion was complex partial seizure in character. Physical examinations showed body weight 2.7 Kg (less than 3 percentile), body temperature 35.7 degrees C, opisthotonic in posture, staring of eyes and unawareness of the outside environment. His hair appeared sparse, coarse and light yellowish color. Laboratory examinations showed normal hemogram and cerebrospinal fluid data. Low serum copper (10 mg/dl), ceruloplasmin (13.5 mg/dl) and hair copper (9.73 ppm) were found. The EEG revealed paroxysmal sharp waves with phase reverses at right temporal and occipital area. Fundus examination showed bilateral optic atrophy. Microscopic examination of the hair showed pili torti (twisting) of the hair. The baby was persisted in hypothermia, poor activity and poor weight gain. The convulsion was poorly controlled and progressed in opisthotonus. The baby died of unknown cause at 3 months of age.

Angiographic coronary morphology in postinfarction angina

To investigate the pathophysiologic relevance of angiographically irregular coronary stenoses in postinfarction angina (PIA), we analyzed the clinical course and coronary angiograms of 73 patients studied within 30 days of infarction. Coronary lesions were classified as smooth or irregular. Thirty-six patients had PIA (Group 1) and 37 had an uncomplicated course (Group 2). Irregular lesion(s) in patent infarct-related arteries were found in 77% of Group 1 vs. 24% of Group 2 patients (P less than 0.005). Irregular lesion(s) in any coronary artery were found in 58% of Group 1 versus 19% of Group 2 patients (P less than 0.002). Other univariate predictors of PIA included older age, hypertension, angina before myocardial infarct, lower peak creatine kinase, three-vessel disease, and higher modified Gensini score. Multivariate analysis ranked lesion irregularity as the strongest predictor of PIA. Our data suggests that ruptured atherosclerotic plaques may be important in the pathogenesis of PIA. It is possible that lesion irregularity is associated with an active process and/or a residual thrombus, which may be responsible for postinfarction angina.

Long-segment coronary ulcerations in survivors of sudden cardiac death

Angiographically irregular coronary stenoses usually represent plaque rupture with or without superimposed thrombi. Long-segment coronary stenoses with diffuse irregularities (type IIB morphology) have been shown to be more prevalent than focal irregular lesions (type IIA morphology) in survivors of cardiac arrest without acute myocardial infarction. To further understand the pathogenetic importance of type IIB morphology, the clinical and angiographic characteristics in 59 such patients were analyzed. Type IIB lesions accounted for 63% of all type II lesions. Type IIB patients were older than type IIA patients (p less than 0.05). There was a tendency for type IIB morphology to be associated with more extensive disease than other types of lesion morphology (p less than 0.10). Type IIB morphology probably reflects more advanced atherosclerosis. Platelet microemboli may precipitate spasm and/or acute ischemic ventricular tachyarrhythmias. It is possible that long-segment coronary ulcerations are associated with a higher risk for local coronary thromboembolism, and hence with sudden death, than focal lesions.

Angiographic coronary morphology in survivors of cardiac arrest

Autopsy studies in victims of sudden coronary death revealed intramyocardial platelet aggregates with microscopic myonecrosis downstream from ruptured atherosclerotic plaques. Ruptured plaques usually manifest angiographically as irregularly bordered (type II) lesions. To investigate the possible pathogenic role of ruptured plaques in arrhythmic death, we analyzed clinical, angiographic, and electrophysiologic data from 49 survivors of cardiac arrest without acute myocardial infarction. All patients had greater than or equal to 50% stenoses of greater than or equal to one coronary artery; 16 had type II morphology, and 33 did not. Type II morphology was more prevalent in patients without inducible sustained monomorphic ventricular tachycardia (11 of 22 or 50%) than in those with it (five of 27 or 19%), p less than 0.05, and patients without akinetic or dyskinetic segments (eight of 14 or 57%) than in those with them (eight of 34 or 24%), p less than 0.06. Thus type II morphology is more prevalent in patients without a demonstrable anatomic and/or electrophysiologic substrate for reentrant ventricular tachycardia, indirectly implicating ruptured plaques in the pathogenesis of cardiac arrest in this subset of patients.

Electrophysiologic study in the management of cardiac arrest survivors: a critical review

This review discusses the value and limitations of EPS in the management of cardiac arrest survivors. Uncertainties associated with EPS include a lack of consensus with respect to stimulation protocol, end points for VT suppression during drug testing, significance of induced polymorphic VT or VF, and timing of EPS after myocardial infarction. Despite methodologic shortcomings in most clinical studies, a useful body of knowledge has emerged. In cardiac arrest survivors, incidence of inducible sustained VT ranged from 35% to 75%. Where induced VT (sustained or nonsustained) was successfully suppressed, recurrent arrhythmic events occurred in 0% to 33% of patients over a 1- to 5-year follow-up period. Failed regimens correlated with a high risk of arrhythmic recurrence. EPS also helps to select patients for the implantable defibrillator or electrocardiac surgery. In conclusion, EPS appears empirically useful in the management of cardiac arrest survivors with coronary artery disease; its value in other disease entities is uncertain.

Postinfarction angina

In conclusion, the PIA patient is at high risk, with higher early as well as late mortality. The pathophysiology of PIA is complex and may vary from patient to patient. The concepts of ischemia at a distance and ischemia in the infarct zone have led to a better understanding of early PIA. Coronary spasm may play an important role in most PIA patients as in the general population of patients with angina pectoris. Medical therapy is efficacious in many, although it may on rare occasion aggravate myocardial ischemia. Urgent coronary arteriography is generally safe and should be performed as soon as possible for medically refractory PIA. CABG appears to be safe in experienced hands, but its timing must be individualized. The IABP should be reserved for more unstable patients for fear of vascular complications. Randomized controlled trials such as the BARI Trial will further compare PTCA with CABG.

Intravenous versus intracoronary streptokinase in acute myocardial infarction

Nine studies specifically dealing with the comparison of intravenous streptokinase (IVSK) and intracoronary streptokinase (ICSK) in the treatment of acute myocardial infarction (MI) were analyzed to determine if IVSK is as efficacious as ICSK in achieving thrombolysis. Pooled data from the studies yielded success rates of 73% for IVSK and 72% for ICSK. Considering that the studies which did not perform preintervention angiogram may have overestimated the thrombolytic success rate in IVSK patients, there is a possibility that ICSK may be slightly more effective in achieving acute reperfusion. Bleeding complications were similar, and a systemic lytic state was observed in both treatment groups. No definitive conclusions can be drawn regarding the differences between groups in improvements of left ventricular function and mortality rates. ICSK has the advantage of direct documentation of reperfusion and spares the patient the risk of anticoagulation should the attempt fail. On the other hand, IVSK is cheaper, easier to administer, and can logistically be given earlier (even in the emergency room or ambulance) than ICSK; it is therefore more widely available, and may be the preferred mode of treatment in community hospitals where cardiac catheterization facilities are not readily available, if streptokinase is to be given at all.

In vitro biological activities of 6-isosteric penicillins and 7-isosteric cephalosporins

Antibiotic and penicillinase inhibitor activities of various penicillin and cephalosporin analogs are reported. The compounds include C-6 penicillin and C-7 cephalosporin carbon, oxygen and sulfur analogs obtained by replacing the NH of the amide side chains with CH2, O and S, respectively. In almost all cases, analogs were considerably less active than the standard compounds (benzylpenicillin and cephalothin). However, some of the analogs act as penicillinase inhibitors.