Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer

With the properties of aggressive cancer and heterogeneous tumor biology, triple-negative breast cancer (TNBC) is a type of breast cancer known for its poor clinical outcome. The lack of estrogen, progesterone, and human epidermal growth factor receptor in the tumors of TNBC leads to fewer treatment options in clinics. The incidence of TNBC is higher in African American (AA) women compared with European American (EA) women with worse clinical outcomes. The significant factors responsible for the racial disparity in TNBC are socioeconomic lifestyle and tumor biology. The current study considered the open-source gene expression data of triple-negative breast cancer samples' racial information. We implemented a state-of-the-art classification Support Vector Machine (SVM) method with a recurrent feature elimination approach to the gene expression data to identify significant biomarkers deregulated in AA women and EA women. We also included Spearman's rho and Ward's linkage method in our feature selection workflow. Our proposed method generates 24 features/genes that can classify the AA and EA samples 98% accurately. We also performed the Kaplan-Meier analysis and log-rank test on the 24 features/genes. We only discussed the correlation between deregulated expression and cancer progression with a poor survival rate of 2 genes, KLK10 and LRRC37A2, out of 24 genes. We believe that further improvement of our method with a higher number of RNA-seq gene expression data will more accurately provide insight into racial disparity in TNBC.

Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants

Background

Many biological analysis tasks require extraction of families of genetically similar sequences from large datasets produced by Next-generation Sequencing (NGS). Such tasks include detection of viral transmissions by analysis of all genetically close pairs of sequences from viral datasets sampled from infected individuals or studying of evolution of viruses or immune repertoires by analysis of network of intra-host viral variants or antibody clonotypes formed by genetically close sequences. The most obvious naïeve algorithms to extract such sequence families are impractical in light of the massive size of modern NGS datasets.

Results

In this paper, we present fast and scalable k-mer-based framework to perform such sequence similarity queries efficiently, which specifically targets data produced by deep sequencing of heterogeneous populations such as viruses. It shows better filtering quality and time performance when comparing to other tools. The tool is freely available for download at https://github.com/vyacheslav-tsivina/signature-sj

Conclusion

The proposed tool allows for efficient detection of genetic relatedness between genomic samples produced by deep sequencing of heterogeneous populations. It should be especially useful for analysis of relatedness of genomes of viruses with unevenly distributed variable genomic regions, such as HIV and HCV. For the future we envision, that besides applications in molecular epidemiology the tool can also be adapted to immunosequencing and metagenomics data.

HCV adaptation to HIV coinfection

Human immunodeficiency virus (HIV) infection is rising as a leading cause of morbidity and mortality among hepatitis C virus (HCV)-infected patients. Both viruses interact in co-infected hosts, which may affect their intra-host evolution, potentially leading to differing genetic composition of viral populations in co-infected (CIP) and mono-infected (MIP) patients. Here, we investigate genetic differences between intra-host variants of the HCV hypervariable region 1 (HVR1) sampled from CIP and MIP. Nucleotide (nt) sequences of intra-host HCV HVR1 variants (N = 28,622) obtained from CIP (N = 112) and MIP (n = 176) were represented using 148 physical-chemical (PhyChem) indexes of DNA nt dimers. Significant (p < .0001) differences in the means and frequency distributions of 7 PhyChem properties were found between HVR1 variants from both groups. Linear projection analysis of 29 PhyChem features extracted from such PhyChem properties showed that the CIP and MIP HVR1 variants have a distinct distribution in the modeled 2D-space, with only ~1.3% of PhyChem profiles (N = 6782), shared by all HVR1 variants, being found in both groups. Probabilistic neural network (PNN) and naïve Bayesian (NB) classifiers trained on the PhyChem features accurately classified HVR1 variants by the group in cross-validation experiments (AUROC ≥ 0.96). Similarly, both models showed a high accuracy (AUROC ≥ 0.95) when evaluated on a test dataset of HVR1 sequences obtained from 10 patients, data from whom were not used for model building. Both models performed at the expected lower accuracy on randomly labeled datasets in cross-validation experiments (AUROC = 0.50). The random-label trained PNN showed a similar drop in accuracy on the test dataset (AUROC = 0.48), indicating that the detected associations were unlikely due to random correlations. Marked differences in genetic composition of HCV HVR1 variants sampled from CIP and MIP suggest differing intra-host HCV evolution in the presence of HIV infection. PhyChem features identified here may be used for detection of HIV infection from intra-host HCV variants alone in co-infected patients, thus facilitating monitoring for HIV introduction to high-risk populations with high HCV prevalence.

GHOST: global hepatitis outbreak and surveillance technology

Background

Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Effective HCV outbreak investigation requires comprehensive surveillance and robust case investigation. We previously developed and validated a methodology for the rapid and cost-effective identification of HCV transmission clusters. Global Hepatitis Outbreak and Surveillance Technology (GHOST) is a cloud-based system enabling users, regardless of computational expertise, to analyze and visualize transmission clusters in an independent, accurate and reproducible way.

Results

We present and explore performance of several GHOST implemented algorithms using next-generation sequencing data experimentally obtained from hypervariable region 1 of genetically related and unrelated HCV strains. GHOST processes data from an entire MiSeq run in approximately 3 h. A panel of seven specimens was used for preparation of six repeats of MiSeq libraries. Testing sequence data from these libraries by GHOST showed a consistent transmission linkage detection, testifying to high reproducibility of the system. Lack of linkage among genetically unrelated HCV strains and constant detection of genetic linkage between HCV strains from known transmission pairs and from follow-up specimens at different levels of MiSeq-read sampling indicate high specificity and sensitivity of GHOST in accurate detection of HCV transmission.

Conclusions

GHOST enables automatic extraction of timely and relevant public health information suitable for guiding effective intervention measures. It is designed as a virtual diagnostic system intended for use in molecular surveillance and outbreak investigations rather than in research. The system produces accurate and reproducible information on HCV transmission clusters for all users, irrespective of their level of bioinformatics expertise. Improvement in molecular detection capacity will contribute to increasing the rate of transmission detection, thus providing opportunity for rapid, accurate and effective response to outbreaks of hepatitis C. Although GHOST was originally developed for hepatitis C surveillance, its modular structure is readily applicable to other infectious diseases. Worldwide availability of GHOST for the detection of HCV transmissions will foster deeper involvement of public health researchers and practitioners in hepatitis C outbreak investigation.

The effect of a single early high-dose vitamin D supplement on fracture union in patients with hypovitaminosis D: a prospective randomised trial

AIMS

To evaluate the effect of a single early high-dose vitamin D supplement on fracture union in patients with hypovitaminosis D and a long bone fracture.

PATIENTS AND METHODS

Between July 2011 and August 2013, 113 adults with a long bone fracture were enrolled in a prospective randomised double-blind placebo-controlled trial. Their serum vitamin D levels were measured and a total of 100 patients were found to be vitamin D deficient (< 20 ng/ml) or insufficient (< 30 ng/mL). These were then randomised to receive a single dose of vitamin D₃ orally (100 000 IU) within two weeks of injury (treatment group, n = 50) or a placebo (control group, n = 50). We recorded patient demographics, fracture location and treatment, vitamin D level, time to fracture union and complications, including vitamin D toxicity. Outcomes included union, nonunion or complication requiring an early, unplanned secondary procedure. Patients without an outcome at 15 months and no scheduled follow-up were considered lost to follow-up. The t-test and cross tabulations verified the adequacy of randomisation. An intention-to-treat analysis was carried out.

RESULTS

In all, 100 (89%) patients had hypovitaminosis D. Both treatment and control groups had similar demographics and injury characteristics. The initial median vitamin D levels were 16 ng/mL (interquartile range 5 to 28) in both groups (p = 0.885). A total of 14 patients were lost to follow-up (seven from each group), two had fixation failure (one in each group) and one control group patient developed an infection. Overall, the nonunion rate was 4% (two per group). No patient showed signs of clinical toxicity from their supplement.

CONCLUSIONS

Despite finding a high level of hypovitaminosis D, the rate of union was high and independent of supplementation with vitamin D₃. Cite this article: Bone Joint J 2017;99-B:1520-5.

Efficient detection of viral transmissions with Next-Generation Sequencing data

BACKGROUND

Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Molecular analysis has been frequently used in the study of HCV outbreaks and transmission chains; helping identify a cluster of sequences as linked by transmission if their genetic distances are below a previously defined threshold. However, HCV exists as a population of numerous variants in each infected individual and it has been observed that minority variants in the source are often the ones responsible for transmission, a situation that precludes the use of a single sequence per individual because many such transmissions would be missed. The use of Next-Generation Sequencing immensely increases the sensitivity of transmission detection but brings a considerable computational challenge because all sequences need to be compared among all pairs of samples.

METHODS

We developed a three-step strategy that filters pairs of samples according to different criteria: (i) a k-mer bloom filter, (ii) a Levenhstein filter and (iii) a filter of identical sequences. We applied these three filters on a set of samples that cover the spectrum of genetic relationships among HCV cases, from being part of the same transmission cluster, to belonging to different subtypes.

RESULTS

Our three-step filtering strategy rapidly removes 85.1% of all the pairwise sample comparisons and 91.0% of all pairwise sequence comparisons, accurately establishing which pairs of HCV samples are below the relatedness threshold.

CONCLUSIONS

We present a fast and efficient three-step filtering strategy that removes most sequence comparisons and accurately establishes transmission links of any threshold-based method. This highly efficient workflow will allow a faster response and molecular detection capacity, improving the rate of detection of viral transmissions with molecular data.

Accurate Genetic Detection of Hepatitis C Virus Transmissions in Outbreak Settings

Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections are associated with unsafe injection practices, drug diversion, and other exposures to blood and are difficult to detect and investigate. Here, we developed and validated a simple approach for molecular detection of HCV transmissions in outbreak settings. We obtained sequences from the HCV hypervariable region 1 (HVR1), using end-point limiting-dilution (EPLD) technique, from 127 cases involved in 32 epidemiologically defined HCV outbreaks and 193 individuals with unrelated HCV strains. We compared several types of genetic distances and calculated a threshold, using minimal Hamming distances, that identifies transmission clusters in all tested outbreaks with 100% accuracy. The approach was also validated on sequences obtained using next-generation sequencing from HCV strains recovered from 239 individuals, and findings showed the same accuracy as that for EPLD. On average, the nucleotide diversity of the intrahost population was 6.2 times greater in the source case than in any incident case, allowing the correct detection of transmission direction in 8 outbreaks for which source cases were known. A simple and accurate distance-based approach developed here for detecting HCV transmissions streamlines molecular investigation of outbreaks, thus improving the public health capacity for rapid and effective control of hepatitis C.

Antepartum eclampsia <34 weeks case series: advisable to postpone delivery to administer corticosteroids for fetal pulmonary benefit?

OBJECTIVE

To determine if postponement of delivery to administer fetal lung maturation corticosteroids (PDACs) in mothers with antepartum eclampsia <34 weeks gestation benefits the fetus without compromising the mother.

STUDY DESIGN

A case series of 37 maternal-perinatal pairs over a 9-year period with antepartum eclampsia between 24 and 34 weeks gestation from a single tertiary center were reviewed retrospectively. Duration of PDAC, clinical course and maternal-fetal outcomes, including impact of duration of PDAC on neonatal pulmonary function, were recorded for each case. Group assignment was based on length of corticosteroid treatment course before delivery: Group A, 0 to ≤ 24 h, n=28; B, 24 to <48 h, n=5; C, ≥ 48 h, n=4. Data were collected and analyzed by one-way analysis of variance (ANOVA), ANOVA on ranks, χ(2)-test and Fisher's exact tests where appropriate; statistical significance was determined by a P-value <0.05.

RESULT

Overall, 37 of 68 eclampsia patients in 1999 to 2007 met inclusion criteria. No adverse maternal or fetal event occurred while delivery was postponed. Immediate neonatal intubation or continuous positive airway pressure was required for 23/28 in A, 4/5 in B and 2/4 in C; room air was sufficient at birth for 5/28 in A, 1/5 in B and 2/4 in C. No newborn >33 weeks gestation required INI. Prolonged (that is, >1 day) mechanical ventilation was not required for any infant with a gestational age ≥ 32 weeks or PDAC ≥ 48 h. Two of three neonatal deaths in group A were attributed to pulmonary insufficiency.

CONCLUSION

PDAC for antepartum preterm eclampsia, especially ≤ 32 weeks gestation, appears to offer notable fetal pulmonary benefit without significantly increasing maternal or fetal risk.

The LRC haplotype project: a resource for killer immunoglobulin-like receptor-linked association studies

There is increasing evidence for epistatic interactions between gene products (e.g. KIR) encoded within the Leukocyte Receptor Complex (LRC) with those (e.g. HLA) of the Major Histocompatibility Complex (MHC), resulting in susceptibility to disease. Identification of such associations at the DNA level requires comprehensive knowledge of the genetic variation and haplotype structure of the underlying loci. The LRC haplotype project aims to provide this knowledge by sequencing common LRC haplotypes.

The DNA sequence and biological annotation of human chromosome 1

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

The genomic sequence and analysis of the swine major histocompatibility complex

We describe the generation and analysis of an integrated sequence map of a 2.4-Mb region of pig chromosome 7, comprising the classical class I region, the extended and classical class II regions, and the class III region of the major histocompatibility complex (MHC), also known as swine leukocyte antigen (SLA) complex. We have identified and manually annotated 151 loci, of which 121 are known genes (predicted to be functional), 18 are pseudogenes, 8 are novel CDS loci, 3 are novel transcripts, and 1 is a putative gene. Nearly all of these loci have homologues in other mammalian genomes but orthologues could be identified with confidence for only 123 genes. The 28 genes (including all the SLA class I genes) for which unambiguous orthology to genes within the human reference MHC could not be established are of particular interest with respect to porcine-specific MHC function and evolution. We have compared the porcine MHC to other mammalian MHC regions and identified the differences between them. In comparison to the human MHC, the main differences include the absence of HLA-A and other class I-like loci, the absence of HLA-DP-like loci, and the separation of the extended and classical class II regions from the rest of the MHC by insertion of the centromere. We show that the centromere insertion has occurred within a cluster of BTNL genes located at the boundary of the class II and III regions, which might have resulted in the loss of an orthologue to human C6orf10 from this region.

Analysis of the genomic region containing the tammar wallaby (Macropus eugenii) orthologues of MHC class III genes

Major histocompatibility complex (MHC) molecules are central to development and regulation of the immune system in all jawed vertebrates. MHC class III cytokine genes from the tumor necrosis factor core family, including tumor necrosis factor (TNF) and lymphotoxin alpha and beta (LTA, LTB), are well studied in human and mouse. Orthologues have been identified in several other eutherian species and the cDNA sequences have been reported for a model marsupial, the tammar wallaby. Comparative genomics can help to determine gene function, to understand the evolution of a gene or gene family, and to identify potential regulatory regions. We therefore cloned the genomic region containing the tammar LTB, TNF, and LTA orthologues by "genome walking", using primers designed from known tammar sequences and regions conserved in other species. We isolated two tammar BAC clones containing all three genes. These tammar genes show similar intergenic distances and the same transcriptional orientation as in human and mouse. Gene structures and sequences are also very conserved. By comparing the tammar, human and mouse genomic sequences we were able to identify candidate regulatory regions for these genes in mammals. Full length sequencing of BACs containing the three genes has been partially completed, and reveals the presence of a number of other tammar MHC III orthologues in this region.

The DNA sequence and comparative analysis of human chromosome 20

The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Evidence from a novel human cell clone that adult vascular smooth muscle cells can convert reversibly between noncontractile and contractile phenotypes

Smooth muscle cells (SMCs) perform diverse functions that can be categorized as contractile and synthetic. A traditional model holds that these distinct functions are performed by the same cell, by virtue of its capacity for bidirectional modulation of phenotype. However, this model has been challenged, in part because there is no physiological evidence that an adult synthetic SMC can acquire the ability to contract. We sought evidence for this by cloning adult SMCs from human internal thoracic artery. One clone, HITB5, expressed smooth muscle alpha-actin, smooth myosin heavy chains, heavy caldesmon, and calponin and showed robust calcium transients in response to histamine and angiotensin II, which confirmed intact transmembrane signaling cascades. On serum withdrawal, these cells adopted an elongated and spindle-shaped morphology, random migration slowed, extracellular matrix protein production fell, and cell proliferation and [(3)H]thymidine incorporation fell to near 0. Cell viability was not compromised, however; in fact, apoptosis rate fell significantly. In this state, agonist-induced elevation of cytoplasmic calcium was even more pronounced and was accompanied by SMC contraction. Readdition of 10% serum completely returned HITB5 cells to a noncontractile, proliferative phenotype. Contractile protein expression increased after serum withdrawal, although modestly, which suggested that the switch to contractile function involved reorganization or sensitization of existing contractile structures. To our knowledge, the physiological properties of HITB5 SMCs provide the first direct demonstration that cultured human adult SMCs can convert between a synthetic, noncontracting state and a contracting state. HITB5 cells should be valuable for characterizing the basis of this critical transition.

Does a year make a difference? Changes in physician satisfaction and perception in an increasingly capitated environment

BACKGROUND

Although capitation has become an increasingly common method of payment for heath care, little is known about changes in physician satisfaction as they become more experienced working in a capitated environment.

METHODS

We surveyed the members of a physician hospital organization at an urban teaching hospital in the summers of 1996 and 1997. In 1996, fully capitated contracts covered <5% of patients under 65 years of age, but that figure increased to nearly 25% by 1997. We assessed physicians' satisfaction with their practice, compared satisfaction under fee-for-service and capitated payment, and evaluated ethical issues related to capitation.

RESULTS

In 1996, we surveyed 587 physicians with direct patient care responsibilities, of whom 62% responded; 51% of 520 physicians responded in 1997. Overall satisfaction was 57% in 1996 and 71% in 1997. Among physicians who responded in both years, overall satisfaction was unchanged, but increases in satisfaction were noted for patient load (an increase of 0.5 points on a five-point scale, P <0.01), time to discuss patient needs (an increase of 0.3 points, P <0.01), and helpfulness of care coordination (an increase of 0.5 points, P = 0.02). In a direct comparison between fee-for-service and capitation, physicians were more satisfied with both methods of payment in 1997 than they were in 1996, but they were much more satisfied with fee-for-service in both years. For many individual indicators, the difference in satisfaction between fee-for-service and capitation increased between 1996 and 1997.

CONCLUSION

When introduced to capitation, physicians had strong negative perceptions about it. After a year's experience, satisfaction with capitation improved, but perceived differences between capitation and fee-for-service grew even larger. Thus, physicians have serious concerns about capitation that may not be alleviated by experience with it.

Capitation and its effects on physician satisfaction

OBJECTIVE

Capitation is an increasingly common method of paying physicians, but few data exist on its impact on physician satisfaction. This study examines the perceived effects of capitation on physician satisfaction at a large, academic medical center.

STUDY DESIGN

Survey of physicians at a single, tertiary care hospital.

METHODS

Physicians in a physician hospital organization were surveyed at an urban teaching hospital which received capitation for 5% of patients at the time of the survey but was preparing for a sharp increase in capitation. We used a 5-point Likert scale to assess physicians' satisfaction with their practice, and to compare satisfaction under fee-for-service and expected satisfaction under capitation.

RESULTS

Of the 734 physicians surveyed, 147 were excluded because they had no direct patient care responsibilities. Of the remaining 587 physicians, 363 replied, giving a response rate of 62%. Overall, 57% of physicians were satisfied with their practice. Compared to their satisfaction under fee-for-service reimbursement, they were much less satisfied with their ability to care for capitated patients (17 of 19 questions, p < 0.05). The greatest differences were for freedom to order necessary tests and freedom to obtain referrals (0.9 and 0.8 on the 5-point scale, respectively, both p < 0.0001). Multiple logistic regression analyses revealed four independent predictors of overall satisfaction: patient load (OR = 2.7, 95% CI = 1.9-3.9), efficiency in resource utilization (OR = 1.5, 95% CI = 1.1-2.1), perceived employment stability (OR = 1.7, 95% CI = 1.3-2.2), and control over clinical time schedule (OR = 1.6, 95% CI = 1.2-2.0).

CONCLUSIONS

Physicians initially encountering capitation payment have strong negative perceptions about it, even for areas in which some policy experts expect capitation to benefit patient care. Physician education and focusing on management relations may help smooth the transition to capitated reimbursement.

Immobilization of calcium phosphate nano-clusters into alkoxy-derived porous TiO2 coatings

Alkoxy-derived porous coatings of titanium oxide were fabricated on commercially pure titanium substrates by an electrochemical method in methanolic electrolytes. Nano-clusters of brushite (CaHPO4. 2H2O) were immobilized into the pores of the oxide network by reacting these coatings in acidic calcium phosphate solutions at 50 degrees C. The acid-base reaction between calcium phosphate solutions and the hydroxyl groups of the oxide network resulted in the formation of nano-clusters of brushite crystals immobilized inside the oxide pores. This treatment resulted in the conversion of the porous oxide network into a coherent mass with improved physical integrity. Nano-clusters of brushite crystals immobilized in the oxide matrix were converted into amorphous calcium phosphate (ACP) and poorly crystallized hydroxyapatite (HA) by further treatment of the oxide in alkaline solutions. The porous oxide coating also reacted strongly with concentrated phosphoric acid. The phosphate-modified oxide resulting from this reaction was further treated in calcium hydroxide solution to form nano-clusters of poorly crystallized HA within the oxide network.

Synaptic code for sensory modalities revealed by C. elegans GLR-1 glutamate receptor

How does the nervous system encode environmental stimuli as sensory experiences? Both the type (visual, olfactory, gustatory, mechanical or auditory) and the quality of a stimulus (spatial position, intensity or frequency) are represented as a neural code. Here we undertake a genetic analysis of sensory modality coding in Caenorhabditis elegans. The ASH sensory neurons respond to two distinct sensory stimuli (nose touch and osmotic stimuli). A mutation in the glr-1 (glutamate receptor) gene eliminates the response to nose touch but not to osmotic repellents. The predicted GLR-1 protein is roughly 40% identical to mammalian AMPA-class glutamate receptor (GluR) subunits. Analysis of glr-1 expression and genetic mosaics indicates that GLR-1 receptors act in synaptic targets of the ASH neurons. We propose that discrimination between the ASH sensory modalities arises from differential release of ASH neurotransmitters in response to different stimuli.

Roles of catalase and cytochrome c in hydroperoxide-dependent lipid peroxidation and chemiluminescence in rat heart and kidney mitochondria

A recent report (Radi et al., J. Biol. Chem. 266:22028-22034, 1991) showed that rat heart mitochondria contain catalase. The protective role of mitochondrial catalase was tested by exposing heart or kidney mitochondria and mitoplasts to two oxidants (H2O2) or tert-butyl hydroperoxide, t-BOOH), estimating lipid peroxidation (as thiobarbituric acid-reactive substances, TBARS) and overall oxidative stress (as chemiluminescence). Additional controls included heart and kidney preparations from aminotriazole-treated (catalase-depleted) rats. Both oxidants increased TBARS in catalase-free preparations to similar extents over their respective controls (between 200 to 350%). In catalase-containing preparations, H2O2 lipid peroxidation increased by only 40 to 96% over controls. Similar qualitative results were obtained when measuring chemiluminescence. The catalytic role of cytochrome c in mitochondrial lipid peroxidation was investigated by exposing either control or cytochrome-c-depleted kidney mitoplasts (catalase free) to either H2O2 or t-BOOH. Hydrogen-peroxide-dependent mitochondrial lipid peroxidation varied with cytochrome c concentration, remaining close to controls when cytochrome c concentration decreased by 66%, even though there was no catalase present. Tert-butyl hydroperoxide-dependent lipid peroxidation was less affected by cytochrome c remaining 2.3-fold above controls under the same conditions, suggesting that organic peroxides are more likely to remain in the less polar membrane environment being decomposed by heme or nonheme iron imbedded in the inner mitochondrial membrane. Chemiluminescence was less affected by cytochrome c depletion. Comparing control and cytochrome-c-deficient mitochondria, chemiluminescence was 1.7-fold and 2.8-fold higher when control preparations were challenged with t-BOOH or H2O2, respectively.

Identification of a complex formed between nuclear proteins and the transcriptional enhancer of interferon-inducible genes that is present in the peripheral blood myeloid cells of CML but not normal individuals

Interferon-alpha (INF-alpha) induces cytogenetic remissions in 20% of chronic myelogenous leukemia (CML) patients. To clarify the mechanisms through which this antiproliferative action of IFN is mediated in the CML cell, a modification of the mobility-shift assay was used to follow the formation of complexes between nuclear proteins and IFN-inducible transcriptional enhancers involved in mediating the cellular effects of IFN-alpha. These studies identified a complex that was present in the myeloid cells of 18/24 (75%) of chronic-phase CML patients tested whose cells contained 100% Philadelphia chromosome positive (Ph+) cells, while the proteins of none of the samples tested from normal peripheral blood samples and only 22% (2/9) of the CML patients in an IFN-induced major cytogenetic remission (less than 30% Ph+ cells) contained these complexes. These studies suggest that the mobility-shift assay detects changes in the CML myeloid cell that distinguish it from the normal myeloid cell.

Activation of class I HLA expression by TNF-alpha and gamma-interferon is mediated through protein kinase C-dependent pathway in CML cell lines

The combination of tumour necrosis factor alpha (TNF alpha) and gamma-interferon induced transcription of class I HLA genes in chronic myelogenous leukaemia (CML) cell lines through the formation of a complex between nuclear proteins and the transcriptional enhancers associated with these genes. Although gamma-interferon or TNF-alpha stimulated expression of class I HLA antigens in the EM2 and K562 CML cell lines when used alone, the effect of the combination of TNF-alpha and gamma-interferon was greater than that observed with either agent alone. The induction of class I HLA expression by gamma-interferon and TNF-alpha was inhibited completely by the isoquinoline sulfonamide H7, an inhibitor of protein kinase C. We conclude that the enhancement of the gamma-interferon induced transcriptional activation of class I HLA gene expression by TNF-alpha involves a protein kinase C-dependent pathway.

Professional nursing roles. The reintegration of patient teaching

This article stresses the critical nature of the education function of the nurse and suggests strategies for reintegrating teaching as a professional role. It is important that administrators value teaching and that staff development departments assist nurses in refining teaching skills.

Characterization of nuclear proteins which bind to interferon-inducible transcriptional enhancers in hematopoietic cells

Nuclear proteins isolated from untreated lymphoid cells formed complexes with the interferon-inducible transcriptional enhancer (IITE) containing a 73- and an 84-kDa protein, whereas the nuclear proteins of untreated myeloid cells formed complexes with the IITE which contained 50-, 65-, and 73-, but not 84-kDa nuclear proteins. The difference in the molecular masses of the nuclear proteins binding to the IITE in lymphoid and myeloid cells was due to a phosphatase present in the cytoplasm of the myeloid cells. Induction of transcriptional activation by interferon was accompanied by the binding of a 95-kDa nuclear protein to the IITE 1-4 h after the start of exposure to interferon. Cycloheximide did not inhibit the binding of the 95-kDa nuclear protein or the transcriptional activation of alpha-interferon-inducible genes. These data suggest that the induction of gene transcription by alpha-interferon in hematopoietic cells may be associated with post-translational changes in a 95-kDa nuclear protein that binds to IITE, thereby leading to transcriptional activation.

A phosphatase activity present in peripheral blood myeloid cells of chronic myelogenous leukemia patients but not normal individuals alters nuclear protein binding to transcriptional enhancers of interferon-inducible genes

Cytoplasmic protein from peripheral blood myeloid cells of chronic myelogenous leukemia (CML) patients altered the electrophoretic mobility of complexes formed between nuclear proteins and interferon-inducible transcriptional enhancers. Immature myeloid marrow cells (blasts and promyelocytes) have a higher level of this activity than do mature myeloid marrow cells (bands and polys). This activity, which is not detectable in the peripheral blood cells of normal individuals, is at least 50-fold higher in CML marrow blasts and promyelocytes than that found in marrow blasts and promyelocytes of normal individuals. This activity was inhibited by in vivo incubation of immature myeloid cells with the phosphatase inhibitor, sodium orthovanadate (0.2 mM), and by adding orthovanadate (20 mM) directly to cytoplasmic proteins of myeloid cells. Interferon-alpha (1,000 U/ml) reduced the effects of the CML myeloid cell cytoplasmic protein on the electrophoretic mobility of nuclear protein-DNA complexes. These data suggest that a unique phosphatase may be involved in the abnormalities in CML which are modulated by interferon-alpha.

Evaluation of two approaches to educating elementary schoolteachers about insulin-dependent diabetes mellitus

Two approaches to better educate elementary schoolteachers about children with diabetes were tested. One group of teachers was given a program consisting of a video, pamphlets, and a question-and-answer session. The second group was informed that these materials were available to them in the media center. A 22-point questionnaire was used before intervention and 8 to 10 weeks later. Although both groups showed significant improvement compared with the control group, the improvement was slight and not felt to be clinically satisfactory. We conclude that mass education of elementary schoolteachers is ineffective and that other approaches need to be developed.

Chromosome banding in Amphibia. VIII. An unusual XY/XX-sex chromosome system in Gastrotheca riobambae (Anura, Hylidae)

The mitotic and meiotic chromosomes of the marsupial frog Gastrotheca riobambae were analysed with various banding techniques. The karyotype of this species is distinguished by considerable amounts of constitutive heterochromatin and unusual, heteromorphic XY sex chromosomes. The Y chromosome is considerably larger than the X chromosome and almost completely heterochromatic. The analysis of the banding patterns obtained with GC- and AT-base-pair-specific fluorochromes shows that the constitutive heterochromatin in the Y chromosome consists of at least three different structural categories. The only nucleolus organizer region (NOR) of the karyotype is localized in the short arm of the X chromosome. This causes a sex-specific difference in the number of NOR: female animals have two NORs in diploid cells, male animals one. No cytological indications were found for the inactivation of one of the two X chromosomes in the female cells. In male meiosis, the heteromorphic sex chromosomes form a characteristic sex-bivalent by pairing their telomeres in an end-to-end arrangement. The significance of the XY/XX sex chromosomes of G. riobambae for the study of X-linked genes in Amphibia, the evolution of sex chromosomes and their specific DNA sequences, and the significance of the meiotic process of sex chromosomes are discussed.

Gap junctions: their presence and necessity in myometrium during parturition

Thin sections of longitudinal and circular muscle of myometrium obtained from rats during pregnancy, at term, during delivery, and postpartum were quantitatively examined in the electron microscope. Gap junctions (low resistance pathways) were only present during or immediately prior to delivery and immediately postpartum. The absence of gap junctions during gestation may be necessary for maintenance of pregnancy, while their occurrence during parturition may lead to effective termination of pregnancy.

Oxygen consumption changes with stored blood infusions

Stored blood contains microaggregates, often implicated in the pathogenesis of post-traumatic pulmonary insufficiency. This study was an attempt to further elucidate the effect of autologous stored, filtered and non-filtered blood infusions and homologous stored and fresh blood infusions on pulmonary function and hemodynamics. Inconsistent changes in pulmonary hemodynamics and blood oxygenation were noted. The one significant finding was an increase in oxygen consumption, which occurred with unfiltered autologous or homologous blood but not with fresh or filtered blood. Since an increased oxygen consumption results in an oxygen demand which is difficult to meet in the face of multiple other injuries, it is conceivable that this observation implicates massive stored blood transfusion as a major contributing factor in the development of so-called irreversible shock.