Whole exome sequencing study identifies candidate loss of function variants and locus heterogeneity in familial cholesteatoma

Cholesteatoma is a rare progressive disease of the middle ear. Most cases are sporadic, but some patients report a positive family history. Identifying functionally important gene variants associated with this disease has the potential to uncover the molecular basis of cholesteatoma pathology with implications for disease prevention, surveillance, or management. We performed an observational WES study of 21 individuals treated for cholesteatoma who were recruited from ten multiply affected families. These family studies were complemented with gene-level mutational burden analysis. We also applied functional enrichment analyses to identify shared properties and pathways for candidate genes and their products. Filtered data collected from pairs and trios of participants within the ten families revealed 398 rare, loss of function (LOF) variants co-segregating with cholesteatoma in 389 genes. We identified six genes DENND2C, DNAH7, NBEAL1, NEB, PRRC2C, and SHC2, for which we found LOF variants in two or more families. The parallel gene-level analysis of mutation burden identified a significant mutation burden for the genes in the DNAH gene family, which encode products involved in ciliary structure. Functional enrichment analyses identified common pathways for the candidate genes which included GTPase regulator activity, calcium ion binding, and degradation of the extracellular matrix. The number of candidate genes identified and the locus heterogeneity that we describe within and between multiply affected families suggest that the genetic architecture for familial cholesteatoma is complex.

Quality Control in Metagenomics Data

Experiments involving metagenomics data are become increasingly commonplace. Processing such data requires a unique set of considerations. Quality control of metagenomics data is critical to extracting pertinent insights. In this chapter, we outline some considerations in terms of study design and other confounding factors that can often only be realized at the point of data analysis.In this chapter, we outline some basic principles of quality control in metagenomics, including overall reproducibility and some good practices to follow. The general quality control of sequencing data is then outlined, and we introduce ways to process this data by using bash scripts and developing pipelines in Snakemake (Python).A significant part of quality control in metagenomics is in analyzing the data to ensure you can spot relationships between variables and to identify when they might be confounded. This chapter provides a walkthrough of analyzing some microbiome data (in the R statistical language) and demonstrates a few days to identify overall differences and similarities in microbiome data. The chapter is concluded by discussing remarks about considering taxonomic results in the context of the study and interrogating sequence alignments using the command line.

Combining Molecular Subtypes with Multivariable Clinical Models Has the Potential to Improve Prediction of Treatment Outcomes in Prostate Cancer at Diagnosis

Clinical management of prostate cancer is challenging because of its highly variable natural history and so there is a need for improved predictors of outcome in non-metastatic men at the time of diagnosis. In this study we calculated the model score from the leading clinical multivariable model, PREDICT prostate, and the poor prognosis DESNT molecular subtype, in a combined expression and clinical dataset that were taken from malignant tissue at prostatectomy (n = 359). Both PREDICT score (p < 0.0001, IQR HR = 1.59) and DESNT score (p < 0.0001, IQR HR = 2.08) were significant predictors for time to biochemical recurrence. A joint model combining the continuous PREDICT and DESNT score (p < 0.0001, IQR HR = 1.53 and 1.79, respectively) produced a significantly improved predictor than either model alone (p < 0.001). An increased probability of mortality after diagnosis, as estimated by PREDICT, was characterised by upregulation of cell-cycle related pathways and the downregulation of metabolism and cholesterol biosynthesis. The DESNT molecular subtype has distinct biological characteristics to those associated with the PREDICT model. We conclude that the inclusion of biological information alongside current clinical prognostic tools has the potential to improve the ability to choose the optimal treatment pathway for a patient.

The Urine Biomarker PUR-4 Is Positively Associated with the Amount of Gleason 4 in Human Prostate Cancers

The Prostate Urine Risk (PUR) biomarker is a four-group classifier for predicting outcome in patients prior to biopsy and for men on active surveillance. The four categories correspond to the probabilities of the presence of normal tissue (PUR-1), D’Amico low-risk (PUR-2), intermediate-risk (PUR-3), and high-risk (PUR-4) prostate cancer. In the current study we investigate how the PUR-4 status is linked to Gleason grade, prostate volume, and tumor volume as assessed from biopsy (n = 215) and prostatectomy (n = 9) samples. For biopsy data PUR-4 status alone was linked to Gleason Grade group (GG) (Spearman’s, ρ = 0.58, p < 0.001 trend). To assess the impact of tumor volume each GG was dichotomized into Small and Large volume cancers relative to median volume. For GG1 (Gleason Pattern 3 + 3) cancers volume had no impact on PUR-4 status. In contrast for GG2 (3 + 4) and GG3 (4 + 3) cancers PUR-4 levels increased in large volume cancers with statistical significance observed for GG2 (p = 0.005; Games-Howell). These data indicated that PUR-4 status is linked to the presence of Gleason Pattern 4. To test this observation tumor burden and Gleason Pattern were assessed in nine surgically removed and sectioned prostates allowing reconstruction of 3D maps. PUR-4 was not correlated with Gleason Pattern 3 amount, total tumor volume or prostate size. A strong correlation was observed between amount of Gleason Pattern 4 tumor and PUR-4 signature (r = 0.71, p = 0.034, Pearson’s). These observations shed light on the biological significance of the PUR biomarker and support its use as a non-invasive means of assessing the presence of clinically significant prostate cancer.

Functional annotation of human long noncoding RNAs via molecular phenotyping

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

HOXC8 regulates self-renewal, differentiation and transformation of breast cancer stem cells

BACKGROUND

Homeobox genes are master regulators of cell fate during embryonic development and their expression is altered in cancer. By regulating the balance between cell proliferation and differentiation, they maintain homeostasis of normal tissues. Here, we screened the expression of homeobox genes in mammary stem cells to establish their role in stem cells transformation in breast cancer.

METHODS

Using a Homeobox Genes PCR array, we screened 83 homeobox genes in normal cancer breast stem/progenitor cells isolated by flow cytometry. The candidate gene HOXC8 epigenetic regulation was studied by DNA methylation and miRNA expression analyses. Self-renewal and differentiation of HOXC8-overexpressing or knockdown cells were assessed by flow cytometry and mammosphere, 3D matrigel and soft agar assays. Clinical relevance of in vitro findings were validated by bioinformatics analysis of patient datasets from TCGA and METABRIC studies.

RESULTS

In this study we demonstrate altered expression of homeobox genes in breast cancer stem/progenitor cells. HOXC8 was consistently downregulated in stem/progenitor cells of all breast molecular subtypes, thus representing an interesting tumour suppressor candidate. We show that downregulated expression of HOXC8 is associated with DNA methylation at the gene promoter and expression of miR196 family members. Functional studies demonstrated that HOXC8 gain of function induces a decrease in the CD44⁺/CD24^-/low cancer stem cell population and proportion of chemoresistant cells, with a concomitant increase in CD24⁺ differentiated cells. Increased HOXC8 levels also decrease the ability of cancer cells to form mammospheres and to grow in anchorage-independent conditions. Furthermore, loss of HOXC8 in non-tumorigenic mammary epithelial cells expands the cancer stem/progenitor cells pool, increases stem cell self-renewal, prevents differentiation induced by retinoic acid and induces a transformed phenotype.

CONCLUSIONS

Taken together, our study points to an important role of homeobox genes in breast cancer stem/progenitor cell function and establishes HOXC8 as a suppressor of stemness and transformation in the mammary gland lineage.

Initial experience in sentinel lymph node detection in pancreatic cancer

BACKGROUND

The local recurrence of pancreatic cancer is around 30% when complete resection can be achieved. Extended lymphatic resections may improve survival, but increases severe morbidity. As accurate patient selection should be mandatory, a new method is presented for pancreatic sentinel lymph node (SLN) detection with lymphoscintigraphy and gamma probe.

MATERIALS AND METHODS

Seven patients with cT2N0M0 pancreatic head cancer were enrolled between 2009 and 2012 in this prospective study. One day prior to surgery, preoperative lymphoscintigraphy with echoendoscopic intratumoural administration of Tc(99m)-labelled nanocolloid was performed, with planar and SPECT-CT images obtained 2h later. Gamma probe detection of SLN was also carried out during surgery.

RESULTS

Radiotracer administration was feasible in all patients. Scintigraphy images showed inter-aortocaval lymph nodes in 2 patients, hepatoduodenal ligament lymph nodes in 1, intravascular injection in 3, intestinal transit in 5, and main pancreatic duct visualisation in 1. Surgical resection could only be achieved in 4 patients owing to locally advanced disease. Intraoperative SLN detection was accomplished in 2 patients, both with negative results. Only in one patient could SLN be confirmed as truly negative by final histopathological analysis.

CONCLUSIONS

This new method of pancreatic SLN detection is technically feasible, but challenging. Our preliminary results with 7 patients are not sufficient for clinical validation.

Regulation of vascular endothelial growth factor in prostate cancer

Prostate cancer (PCa) is the most common malignancy affecting men in the western world. Although radical prostatectomy and radiation therapy can successfully treat PCa in the majority of patients, up to ~30% will experience local recurrence or metastatic disease. Prostate carcinogenesis and progression is typically an androgen-dependent process. For this reason, therapies for recurrent PCa target androgen biosynthesis and androgen receptor function. Such androgen deprivation therapies (ADT) are effective initially, but the duration of response is typically ≤24 months. Although ADT and taxane-based chemotherapy have delivered survival benefits, metastatic PCa remains incurable. Therefore, it is essential to establish the cellular and molecular mechanisms that enable localized PCas to invade and disseminate. It has long been accepted that metastases require angiogenesis. In the present review, we examine the essential role for angiogenesis in PCa metastases, and we focus in particular on the current understanding of the regulation of vascular endothelial growth factor (VEGF) in localized and metastatic PCa. We highlight recent advances in understanding the role of VEGF in regulating the interaction of cancer cells with tumor-associated immune cells during the metastatic process of PCa. We summarize the established mechanisms of transcriptional and post-transcriptional regulation of VEGF in PCa cells and outline the molecular insights obtained from preclinical animal models of PCa. Finally, we summarize the current state of anti-angiogenesis therapies for PCa and consider how existing therapies impact VEGF signaling.

Interactions between FGF18 and retinoic acid regulate differentiation of chick embryo limb myoblasts

During limb development Pax3 positive myoblasts delaminate from the hypaxial dermomyotome of limb level somites and migrate into the limb bud where they form the dorsal and ventral muscle masses. Only then do they begin to differentiate and express markers of myogenic commitment and determination such as Myf5 and MyoD. However the signals regulating this process remain poorly characterised. We show that FGF18, which is expressed in the distal mesenchyme of the limb bud, induces premature expression of both Myf5 and MyoD and that blocking FGF signalling also inhibits endogenous MyoD expression. This expression is mediated by ERK MAP kinase but not PI3K signalling. We also show that retinoic acid (RA) can inhibit the myogenic activity of FGF18 and that blocking RA signalling allows premature induction of MyoD by FGF18 at HH19. We propose a model where interactions between FGF18 in the distal limb and retinoic acid in the proximal limb regulate the timing of myogenic gene expression during limb bud development.

Epidemiology of American tegumentary leishmaniasis in domestic dogs in an endemic zone of western Venezuela

Domestic dogs are not only reservoir hosts of the American zoonotic visceral leishmaniasis (ZVL) but of the American zoonotic tegumentary leishmaniasis (ATL) as well, for different reasons. However it is still controversial to state that dogs are incriminated as ATL reservoir hosts as there is evidence that humans and dogs are likely to be exposed in the same way to sandfly vector. In Venezuela this issue has not been completely addressed, for this reason we selected a location inside Trujillo city to study eco-epidemiological conditions as well as to survey a significant sample of dogs by Montenegro Skin Test (MST). Antigen was prepared according to standard procedure using Leishmania (V) braziliensis promastigotes (80 microg/ml); response was read 48 hours post-inoculation with an induration size > 5 mm being considered as positive. The study place is an endemic mountainous semi-urban area located at 850-950 masl with an average rainfall of 150 mm/year. We evaluated 61 dogs in 46 houses with 168 human beings. Among the human population 27 cases of ATL were reported (16.1%). With the MST we found 19 positive-reaction dogs (31%) (mean MST size of 9.58 mm, 95% CI: 8.41-10.75) in 13 houses (28%). Multivariate analysis did not reveal significant association between domestic MST positive-dog ownership and human ATL cases (RR = 1.48, p = 0.28). Although some studies have indicated that dog ownership and dog infection rates are associated with an increased risk of human disease in different evaluated places, this question has not been completely answered in Venezuelan studied zones, further research is necessary.

Cell motility and local viscoelasticity of fibroblasts

Viscoelastic changes of the lamellipodial actin cytoskeleton are a fundamental element of cell motility. Thus, the correlation between the local viscoelastic properties of the lamellipodium (including the transitional region to the cell body) and the speed of lamellipodial extension is studied for normal and malignantly transformed fibroblasts. Using our atomic force microscopy-based microrheology technique, we found different mechanical properties between the lamellipodia of malignantly transformed fibroblasts (H-ras transformed and SV-T2 fibroblasts) and normal fibroblasts (BALB 3T3 fibroblasts). The average elastic constants, K, in the leading edge of SV-T2 fibroblasts (0.48 +/- 0.51 kPa) and of H-ras transformed fibroblasts (0.42 +/- 0.35 kPa) are significantly lower than that of BALB 3T3 fibroblasts (1.01 +/- 0.40 kPa). The analysis of time-lapse phase contrast images shows that the decrease in the elastic constant, K, for malignantly transformed fibroblasts is correlated with the enhanced motility of the lamellipodium. The measured mean speeds are 6.1 +/- 4.5 microm/h for BALB 3T3 fibroblasts, 13.1 +/- 5.2 microm/h for SV-T2 fibroblasts, and 26.2 +/- 11.5 microm/h for H-ras fibroblasts. Furthermore, the elastic constant, K, increases toward the cell body in many instances which coincide with an increase in actin filament density toward the cell body. The correlation between the enhanced motility and the decrease in viscoelastic moduli supports the Elastic Brownian Ratchet model for driving lamellipodia extension.

Effect of tauroursodeoxycholate and S-adenosyl-L-methionine on 17beta-estradiol glucuronide-induced cholestasis

BACKGROUND/AIMS

S-adenosyl-L-methionine (SAMe) and tauroursodeoxycholate (TUDC) exert an additive ameliorating effect on taurolithocholate (TLC)-induced cholestasis. The aims were to investigate the protective effect of SAMe on 17beta-estradiol-glucuronide (17betaEG) cholestasis and to find out whether SAMe and TUDC may exert an additive, ameliorating effect.

METHODS

Hepatocyte couplet function was assessed by canalicular vacuolar accumulation (cVA) of cholyllysylfluorescein (CLF). Cells were co-treated with 17betaEG and SAMe, TUDC, or both (protection study), or treated with 17betaEG and then with SAMe, TUDC or both (reversion study) before CLF uptake. Couplets were also co-treated with SAMe and dehydroepiandrosterone (DHEA), a competitive substrate for the sulfotransferase involved in 17betaEG detoxification. The effects of 17betaEG, SAMe and TUDC were also examined on intracellular distribution of F-actin.

RESULTS

Both SAMe and TUDC significantly protected against, and reversed, 17betaEG-induced cholestasis, but their effects were not additive. DHEA abolished the protective effect of SAMe. 17BetaEG did not affect the uptake of CLF into hepatocytes at the concentrations used, and also, it did not affect the intracellular distribution of F-actin.

CONCLUSIONS

17BetaEG does not affect the uptake of CLF into hepatocytes. SAMe and TUDC protect and reverse 17betaEG-induced cholestasis, but without an additive effect. Protection by SAMe may involve facilitating the sulfation of 17betaEG.

Visualization of the transport of primary and secondary bile acids across liver tissue in rats: in vivo study with fluorescent bile acids

BACKGROUND/AIMS

Lysyl fluorescein conjugated bile acid analogues (LFCBAA) closely parallel their natural counterparts. To assess LFCBAA as a tool for the visualization of bile acid transport within liver tissue.

METHODS

Wistar rats were administered physiological concentrations of the primary bile acid analogue cholyllysyl fluoroscein (CLF) and of the secondary bile acid analogue lithocholyllysyl fluorescein (LLF) and serial liver biopsies were taken at fixed intervals. Both compounds were also injected retrogradely into the biliary tree. Frozen sections were examined by fluorescence microscopy.

RESULTS

Both CLF and LLF were rapidly taken up from sinusoidal blood but differed significantly in their hepatic handling. CLF was rapidly transported into bile, whereas LLF transport was slower and produced significantly more bile duct fluorescence. LLF clearance showed a lobular gradient with last remaining bile acid being confined largely to zone 3. Both compounds were avidly taken up by cholangiocytes after injection intravenously or retrogradely into the biliary tree.

CONCLUSIONS

Visualization of LFCBAA by fluorescence microscopy may yield further information regarding hepatobiliary bile acid localization during studies of physiological and pathological mechanisms involved in transport of bile acids. The presence of both compounds within cholangiocytes strongly suggests that they may undergo a degree of chole-hepatic recirculation.

Somatostatin family of peptides and its receptors in fish

Somatostatin (SRIF or SS) is a phylogenetically ancient, multigene family of peptides. SRIF-14 is conserved with identical primary structure in species of all classes of vertebrates. The presence of multiple SRIF genes has been demonstrated in a number of fish species and could extend to tetrapods. Three distinct SRIF genes have been identified in goldfish. One of these genes, which encodes [Pro2]SRIF-14, is also present in sturgeon and African lungfish, and is closely associated with amphibian [Pro2,Met13]SRIF-14 gene and mammalian cortistatin gene. The post-translational processing of SRIF precursors could result in multiple forms of mature SRIF peptides, with differential abundance and tissue- or cell type-specific patterns. The main neuroendocrine role of SRIF-14 peptide that has been determined in fish is the inhibition of pituitary growth hormone secretion. The functions of SRIF-14 variant or larger forms of SRIF peptide and the regulation of SRIF gene expression remain to be explored. Type 1 and type 2 SRIF receptors have been identified from goldfish and a type 3 SRIF receptor has been identified from an electric fish. Fish SRIF receptors display considerable homology with mammalian counterparts in terms of primary structure and negative coupling to adenylate cyclase. Although additional types of receptors remain to be determined, identification of the multiple gene family of SRIF peptides and multiple types of SRIF receptors opens a new avenue for the study of physiological roles of SRIF, and the molecular and cellular mechanisms of SRIF action in fish.

Molecular cloning and expression of a type-two somatostatin receptor in goldfish brain and pituitary

Somatostatin (SRIF or SS) exerts diverse inhibitory actions through binding to specific receptors. In this study, a SRIF receptor cDNA was cloned and sequenced from goldfish brain using PCR and cDNA library screening. The cDNA encodes a 380-amino acid goldfish type-two SRIF receptor (designated as sst(2)), with seven putative transmembrane domains (TMD) and YANSCANP motif in the seventh TMD, a signature sequence for the mammalian SRIF receptor (sst) family. In addition, the amino acid sequence of the receptor has 61-62% homology to mammalian sst(2), 41-47% homology to other mammalian sst subtypes and 41-43% homology to recently identified fish sst(1) and sst(3) receptors. Both SRIF-14 and [Pro(2)]SRIF-14, two of the native goldfish SRIF forms, but not a putative goldfish SRIF-28, significantly inhibited forskolin-stimulated adenosine 3':5'-cyclic monophosphate (cAMP) release in COS-7 cells transiently expressing goldfish sst(2), suggesting functional coupling of the receptor to adenylate cyclase. None of the three peptides affected inositol phosphate production in the same receptor expression system. Northern blot showed that mRNA for the sst(2) receptor is widely distributed in goldfish brain, and highly expressed in the pituitary. The decrease in pituitary sst(2) mRNA levels following estradiol implantation suggests the presence of a negative feedback mechanism on sst(2) gene expression.

Biphasic changes in nitric oxide generation in hemodialyzed patients with end-stage renal disease treated with recombinant human erythropoietin

BACKGROUND

Use of recombinant human erythropoietin (rHuEpo) in patients with end-stage renal disease (ESRD) improves anemia and reduces the need for blood transfusions. However, one third of patients on rHuEpo develop hypertension, aggravation of preexistent hypertension, or other complications. Nitric oxide (NO) plays a role in blood pressure (BP) regulation. Whether rHuEpo treatment in ESRD is accompanied by alterations in NO production was explored in patients undergoing hemodialysis.

METHODS

Of 121 consecutive patients in a hemodialysis clinic, 107 were treated with rHuEpo and 14 were untreated. Plasma was collected before and after hemodialysis for quantification of nitrite and nitrate (NOx). Findings were correlated with various routinely monitored parameters.

RESULTS

Predialysis NOx levels were lower in the treated than the untreated group; postdialysis NOx levels were virtually the same. Thus, the change was less in the treated group. Urea reduction ratios (URR) and ultrafiltrate volumes were similar. The mean predialysis systolic BP was higher in the treated group than in the untreated group. The dose of rHuEpo did not correlate with the plasma NOx or the predialysis BPs. No correlation was found between NOx levels and Hb or gender. Of the 107 treated patients, 12 had an increased postdialysis NOx without differences in ultrafiltrate volumes or URR. This group had higher total serum calcium levels, faster pulses, and greater BP reductions than other treated patients. No difference was found in the use of calcium-channel blockers and serum phosphorus and intact parathyroid hormone concentrations did not differ significantly among these groups.

CONCLUSIONS

Intermittently hemodialyzed ESRD patients treated with rHuEpo accumulate less NOx in the plasma before dialysis but generate more NOx during dialysis than untreated patients. About 11% of treated patients generated excessive amounts of NOx, thereby maintaining plasma concentrations at the predialysis level or higher. This group experienced significant hemodynamic consequences characteristic of the excessive action of NO.

Characterization and distribution of somatostatin binding sites in goldfish brain

Somatostatin (SRIF) binding sites were characterized in goldfish brain. Binding of (125)I-[Tyr(11)]-SRIF-14 to a brain membrane preparation was found to be saturable, reversible, and time-, temperature-, and pH-dependent. Binding was also displaceable by different forms of SRIF. Under optimal conditions (22 degrees C, pH 7.2), the equilibrium binding of (125)I-[Tyr(11)]-SRIF-14 to goldfish brain membranes was achieved after 60 min incubation. Analysis of saturable equilibrium binding revealed a one-site model fit with K(a) of 1.3 nM. SRIF-14, mammalian SRIF-28, and salmon SRIF-25 displaced (125)I-[Tyr(11)]-SRIF-14 binding with similar affinity, whereas other neuropeptides, e.g., substance P, were unable to displace (125)I-[Tyr(11)]-SRIF-14. Autoradiography studies demonstrated that (125)I-[Tyr(11)]-SRIF-14 binding sites are found throughout the goldfish brain. A high density of (125)I-[Tyr(11)]-SRIF-14 binding sites was found in the forebrain, including the nucleus preopticus, nucleus preopticus periventricularis, nucleus anterioris periventricularis, nucleus lateralis tuberis, nucleus dorsomedialis thalami, nucleus dorsolateralis thalami, nucleus ventromedialis thalami, and nucleus diffusus lobi inferioris. In midbrain, (125)I-[Tyr(11)]-SRIF-14 binding sites were found in the optic tectum. The facial and vagal lobes and the mesencephalic-cerebellar tract were found to have a high density of binding sites. This study provides the first characterization and distribution of specific binding sites for SRIF in a fish brain.

Hemodialysis hypotension: interaction of inhibitors, iNOS, and the interdialytic period

Hypotension during hemodialysis in end-stage renal disease (ESRD) not explained by excessive ultrafiltration has been linked to an apparent increase in the synthesis of nitric oxide (NO). The authors tested whether the induction of NO synthase (iNOS) by cytokines or differences in the concentrations of inhibitors of NOS or both could account for variability in the amount of NO synthesized during hemodialysis. Plasma levels of an inhibitor of NOS, asymmetric dimethylarginine (ADMA), L-arginine, the substrate for NOS, the end-products N02+N03, iNOS activity in circulating buffy coat cells, and their interdialytic changes were measured in 10 patients during three treatments. Predialysis (0') levels of ADMA were markedly elevated with a mean of 0.008+/-0.002 micromol/mL of deproteinized plasma, compared to controls where ADMA is present in trace amounts. ADMA levels from 30 minutes to the end of dialysis correlated directly with the drop in blood pressure (BP), with levels being much higher in patients with severe hypotension. Postdialysis ADMA levels correlated directly with the 0' systolic BP and the drop in BP at the next dialysis treatment. NOS activity was detected in two thirds of the predialysis buffy coat samples, and appeared to increase as dialysis progressed. 0' iNOS activity correlated inversely with the 0' BP, but activities did not differ based on percent drop in BP. iNOS activity in the 0' samples correlated inversely with the time since the last dialysis, reflecting the greater accumulation of dialyzable inhibitors of NOS as the interval is prolonged. The interdialytic change in iNOS activity correlated inversely with the drop in BP. The isoform detected immunochemically in the buffy coat samples had an Mr of 130 kDa and was reactive with antihuman iNOS. Thus, iNOS is already induced in the cells of the buffy coat in many intermittently hemodialyzed ESRD subjects, but its expression may be masked by inhibitors. After 60 minutes of dialysis (too brief a time for the de novo induction of iNOS,) the appearance of or increase in iNOS activity suggests that an inhibitor had been removed. Because ADMA levels are associated with higher predialysis systolic BPs that result in a greater severity of hypotension, reduction in ADMA concentrations would appear to play a major role in the resumption of NO synthesis by various isoforms.

Long-term outcome of neonatal macular hemorrhage

BACKGROUND

We studied long-term visual acuity in children who had macular hemorrhages at birth.

METHODS

Of 11 involved children, seven had eye examinations at about age 10. Two were contacted by telephone; two were lost to follow up.

RESULTS

Of the seven examined children, six had normal visual acuities. One had reduced vision in the eye with the macular hemorrhage, possibly related to deprivation amblyopia secondary to slow resorption of the hemorrhage. The two patients contacted by telephone reported normal vision.

CONCLUSION

Although macular hemorrhages generally resolve without any lasting damage, the outcome may be less favorable in some patients.

Endogenous reactive oxygen metabolites mediate sublethal endothelial cell dysfunction during reoxygenation

PURPOSE

Endothelial cells (EC) secrete vasoactive eicosanoids, which maintain organ blood flow. Because EC are a major source of eicosanoids, we studied the effects of reoxygenation on EC prostacyclin production.

METHODS

Bovine aortic EC cultures were exposed to 2 hours of normoxia, then 1 hour of hypoxia (PO2 = 10 +/- 3.5 mm Hg), followed by 1.5 hours of reoxygenation in either normal medium or medium plus either superoxide dismutase (SOD, 300 units/ml), catalase (1200 units/ml), allopurinol (5.0 x 10(-4) mol/L), or dinitrophenol (10(-4) mol/L).

RESULTS

Prostacyclin production decreased to 40% (p < 0.05) of basal prostacyclin production after 1 hour of hypoxia. EC reoxygenated with control medium recovered to 48% of basal prostacyclin production. EC reoxygenated in SOD resulted in recovery (p < 0.05) to 154% of basal prostacyclin production after 60 minutes. Catalase treatment resulted in recovery to 105% (p < 0.05) of basal prostacyclin production within 30 minutes of reoxygenation. Allopurinol treatment resulted in 77% recovery (p < 0.05) of basal prostacyclin production only during 30 minutes of reoxygenation. Dinitrophenol treatment resulted in significant (> or = 85%, p < 0.05) sustained recovery of basal prostacyclin production at 30, 60, and 90 minutes of experimental reperfusion.

CONCLUSIONS

The hypoxia-induced decrease in EC prostacyclin does not recover during reoxygenation. Catalase/SOD allowed return to baseline prostacyclin production during reoxygenation, implicating reactive oxygen metabolites as mediators of decreased eicosanoid biosynthesis. Recovery of prostacyclin production after 60 minutes reoxygenation with dinitrophenol but not allopurinol suggests a mitochondrial origin of the oxygen metabolites responsible for decreased prostacyclin biosynthesis.

Stability and fluctuations of the potato carboxypeptidase A protein inhibitor fold: a molecular dynamics study

A 120ps non-inertial solvent (NIS) molecular dynamics (MD) trajectory of the potato carboxypeptidase A protein inhibitor (PCI) was calculated and analyzed. It is shown that, in spite of a very low content of regular secondary structure, the PCI fold has a large degree of stability, judged from the fairly good agreement between the average MD and X-ray structures. The N-terminal and C-terminal regions behave differently, both in their isoatomic positional shifts with respect to the X-ray structure, and in atomic fluctuation pattern. Positional shifts up to 9A are detected in the exposed N-terminal region as it folds back on the inhibitor's core. This large deviation is most likely caused by the absence of the receptor protein or by the lack of supporting solvent molecules. In contrast, the C-terminal region, which is the primary contact site with the enzyme, has an average structure similar to the X-ray conformation; this feature is probably due to a hydrogen bond network to the central core of PCI. The C-terminal tail shows larger fluctuations than the core. The secondary contact site retains its structure in this simulation. The results evidence an intrinsically stable PCI fold which favors a spatially well defined, fairly flexible, structuration of the primary and secondary contact sites that optimizes PCI's interaction with its target enzyme.

A molecular dynamics study of a model built Pro-36-Gly mutant derived from the potato carboxypeptidase A inhibitor protein

A 120ps molecular dynamics (MD) trajectory was calculated and analyzed for a putative Pro-36-Gly mutant of the potato carboxypeptidase A (CPA) protein inhibitor (PCIm). The mutant protein's fold shows a large degree of stability, judged from its low alpha-carbon r.m.s. deviation from the X-ray structure of the wild type PCI (PCIw). The N-terminal tail of PCIm differs slightly less from the X-ray structure than it does in PCIw, while the mutant's C-terminal tail (the primary contact site with CPA) and residues 13-17 present deviations as they approach each other. Differences in fluctuation pattern exist between PCIm and PCIw in residues 2-4 (the N-terminal tail), 13-17, 22-23, 28-31 (the secondary contact site with CPA) and 37-38 (the C-terminal tail); the latter region is rigidified in PCIm. Results show that the MD method is able to sense local perturbative effects produced by amino acid substitutions in flexible regions of protein molecules. The simulation suggests that the conformation of the C-terminal tail is less favorable for interaction with the target protein in the mutant than it is in the wild type protein. The Pro-36-Gly mutant is predicted to be a less potent inhibitor.

Circulating colony-forming units of granulocytes and monocytes/macrophages in systemic lupus erythematosus

In systemic lupus erythematosus (SLE) patients, in vitro bone marrow (BM) colony-forming units of granulocytes and monocytes/macrophages (CFU-GM) are decreased, suggesting that granulomonopoietic failure may play an important role in the mechanism of peripheral blood (PB) depletion of neutrophils and monocytes. No information concerning CFU-GM in PB of patients with SLE is available. The present study was undertaken in order to determine whether SLE itself and the inactive or active stage of disease would modify the number of GFU-GM in PB samples from 20 treatment-free SLE women, 12 inactive and eight active. CFU-GM growth was significantly decreased in both inactive (P = 0.018) and active (P = 0.008) SLE patients as compared with controls (n = 8). The difference in CFU-GM growth between SLE groups was not significant. These results indicate that the number of circulating CFU-GM is significantly reduced in patients with SLE regardless of disease activity or remission.

Measurement of right and left ventricular ejection fractions by gated equilibrium scintigraphy using Fourier functional images

Left and right ventricular ejection fractions (LVEF and RVEF) were calculated by gated equilibrium scintigraphy in 28 normal controls and in 21 patients with heart disease. Regions of interest (ROIs) for the ventricles were assigned on the amplitude and phase Fourier images. Two methods of preprocessing of data were compared. In Method 1 the resolution was improved and the statistical noise was reduced, while in Method 2 only the statistical noise was reduced. There were no differences between the results of the two methods for the left ventricle. The mean LVEF for normal subjects was 0.63 +/- 0.06. For the right ventricle, Method 1 showed higher sensitivity in detecting reduced RVEF in pathological situations. The mean RVEF by Method 1 for normal controls was 0.56 +/- 0.07, which is significantly different (p less than 0.001) than that found by Method 2 (0.36 +/- 0.05), and similar to those reported by others employing the firstpass method. The results show the usefulness of the phase Fourier image and the importance of a suitable preprocessing of data for determining RVEF by gated equilibrium scintigraphy.

Measurement of Right and Left Ventricular Ejection Fractions by Gated Equilibrium Scintigraphy Using Fourier Functional Images

Left and right ventricular ejection fractions (LVEF and RVEF) were calculated by gated equilibrium scintigraphy in 28 normal controls and in 21 patients with heart disease. Regions of interest (ROIs) for the ventricles were assigned on the amplitude and phase Fourier images. Two methods of preprocessing of data were compared. In Method 1 the resolution was improved and the statistical noise was reduced, while in Method 2 only the statistical noise was reduced. There were no differences between the results of the two methods for the left ventricle. The mean LVEF for normal subjects was 0.63 ± 0.06. For the right ventricle, Method 1 showed higher sensitivity in detecting reduced RVEF in pathological situations. The mean RVEF by Method 1 for normal controls was 0.56 ± 0.07, which is significantly different (p < 0.001) than that found by Method 2 (0.36 ± 0.05), and similar to those reported by others employing the firstpass method. The results show the usefulness of the phase Fourier image and the importance of a suitable preprocessing of data for determining RVEF by gated equilibrium scintigraphy.

New method for obtaining IgA-specific protease

A simple method for obtaining an active preparation of IgA-specific protease from a bacterial source is presented. In this method Streptococcus sanguis was inoculated onto the surface of a dialysis membrane on nutrient agar. Following growth, the membrane was removed from the agar surface and washed in a small volume of buffer. A solution with protease activity against IgA1 monoclonal proteins was obtained by clarification of the wash and appeared to be similar to enzyme preparations obtained by other methods.

Ozone and vitamin E

Vitamin E deficiency in rats is associated with a greater susceptibility to lethal levels of ozone. Exposure of rats to sublethal ozone concentrations produces an accelerated decline in serum vitamin E levels. These findings are consistent with the possibility that lipid peroxidation is a mechanism of ozone toxicity.

Relation of light reflectance to histological and physical evaluations of cotton leaf maturity

Cotton plants were grown hydroponically with controlled environment. Third, growth chamber grown true leaves of cotton plants were tagged on the day they became macroscopically visible. Beginning 3.0 days after tagging,five leaf harvests representing maturity dates were made at successive 2- or 3-day intervals. Measurements with a spectrophotometer made on the leaves showed that the largest increase in reflectance, about 5%, and decrease in transmittance, about 8%, occurred between average values for after-tagging-ages of 3.5 days and 8.0 days over the 0.75-1.35-micro wavelength interval. Between after-tagging-ages of 3.5 days and 8.0 days, leaves expanded approximately fivefold, numbers of intercellular spaces approximately doubled, and thicknesses increased 14%. The theory of diffuse reflectance and transmittance of a compact leaf of equivalent water thickness (EWT) specified by D is generalized to include also the noncompact leaf characterized by many intercellular air spaces, can be regarded as a pile of N compact layers separated by infinitesimal air spaces. The void area index (VAI) of a noncompact leaf is given by N - 1, where N is not necessarily an integer. Predictions from the generalized theory include a measure of the water, air, and plant pigments in a leaf. An effective dispersion curve associated with the leaf surfaces is also obtained. A derived parameter D/N largely determines the reflectance and transmittance of a typical leaf over the 1.40-2.50-micro spectral range. A cotton leaf is highly compact when it first unfolds. At this point D/N ~ 180 micro. This value is essentially the leaf thickness. Intercellular air spaces develop rapidly during the next few days, and D/N decreases in value to about 130 micro Subsequently, the leaf cells increase in size with no substantial further increase in the number of intercellular air spaces. This final growth phase is characterized by a slight increase in D/N to a maximum value of about 140 micro. Maximum reflectance of the leaf corresponds to a minimum value of D/N. The parameter D/N is highly correlated with the amount of intercellular air spaces in a leaf.