Unrecognized volatile and semi-volatile organic compounds from brake wear

Motor vehicles are among the major sources of pollutants and greenhouse gases in urban areas and a transition to "zero emission vehicles" is underway worldwide. However, emissions associated with brake and tire wear will remain. We show here that previously unrecognized volatile and semi-volatile organic compounds, which have a similarity to biomass burning emissions are emitted during braking. These include greenhouse gases or, these classified as Hazardous Air Pollutants, as well as nitrogen-containing organics, nitrogen oxides and ammonia. The distribution and reactivity of these gaseous emissions are such that they can react in air to form ozone and other secondary pollutants with adverse health and climate consequences. Some of the compounds may prove to be unique markers of brake emissions. At higher temperatures, nucleation and growth of nanoparticles is also observed. Regions with high traffic, which are often disadvantaged communities, as well as commuters can be impacted by these emissions even after combustion-powered vehicles are phased out.

Nutrient digestibility, rumen parameters and (cannabinoid) residues in sheep fed a pelleted diet containing green hemp (Cannabis sativa L.) biomass

The feeding value for ruminants of green hemp biomass, from the low Δ⁹-tetrahydrocannabinol (Δ⁹-THC) variety of Cannabis sativa L., is unknown. Twelve Merino ewes were individually penned and randomly allocated on a stratified liveweight basis to one of two pelleted dietary treatments, control (0% hemp, n = 6) or hemp (42% green hemp biomass, n = 6) that delivered a diet meeting the nutrient requirements of the animals. The experimental period consisted of 17 d dietary and housing adaptation, followed by 7 d total urine and feces collection for determination of apparent nutrient digestibility. A ruminal fluid sample was collected on day 27 and assessed for pH, ammonia, volatile fatty acid (VFA), and cannabinoid concentrations. A blood sample from the jugular vein and incisional subcutaneous fat biopsy from an area around the base of the tail were collected on day 28 with additional fat biopsies taken 35 d and 140 d post-feeding to measure cannabinoids. The dry matter (DM), organic matter (OM), and crude protein (CP) digestibilities, along with total VFA concentration did not differ (P = 0.713) between the two diets; however, acid detergent fiber (ADF) and neutral detergent fiber (NDF) digestibilities (P < 0.001), water intake (P = 0.023), and fecal water output (P < 0.001) were significantly lower for the sheep-fed Hemp. Rumen pH did not vary (P = 0.256) between diets, but ruminal ammonia concentration was significantly lower (P = 0.024) for sheep consuming Hemp. Sheep-fed Hemp had significantly greater molar proportions of butyric (P = 0.039) and hexanoic (P = 0.012) acids and lower molar proportions of propionic acid (P = 0.003). There were no differences between diets for N intake (P = 0.175), fecal N output (P = 0.253), and N balance (P = 0.695), with all sheep in positive N balance; however, there was significantly lower (P = 0.001) urinary N output for sheep-fed Hemp. Cannabidiolic acid (CBDA) and tetrahydrocannabinolic acid (THCA) were detected in plasma of all sheep-fed Hemp. ∆⁹-tetrahydrocannabinol was present in the subcutaneous fat of four of the six sheep on the final day of being fed Hemp, and in all (six) sheep 35 d post-feeding and one sheep 140 d post-feeding Hemp. No cannabinoids were detected in the corresponding samples taken from the sheep-fed Control. Thus, despite green hemp biomass being nutritionally a suitable feed for ruminants, under current Food Standards in Australia, the presence of these cannabinoid residues restricts its use in ruminant diets.

Targeting MYCN-expressing triple-negative breast cancer with BET and MEK inhibitors

Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer that does not respond to endocrine therapy or human epidermal growth factor receptor 2 (HER2)-targeted therapies. Individuals with TNBC experience higher rates of relapse and shorter overall survival compared to patients with receptor-positive breast cancer subtypes. Preclinical discoveries are needed to identify, develop, and advance new drug targets to improve outcomes for patients with TNBC. Here, we report that MYCN, an oncogene typically overexpressed in tumors of the nervous system or with neuroendocrine features, is heterogeneously expressed within a substantial fraction of primary and recurrent TNBC and is expressed in an even higher fraction of TNBCs that do not display a pathological complete response after neoadjuvant chemotherapy. We performed high-throughput chemical screens on TNBC cell lines with varying amounts of MYCN expression and determined that cells with higher expression of MYCN were more sensitive to bromodomain and extraterminal motif (BET) inhibitors. Combined BET and MEK inhibition resulted in a synergistic decrease in viability, both in vitro and in vivo, using cell lines and patient-derived xenograft (PDX) models. Our preclinical data provide a rationale to advance a combination of BET and MEK inhibitors to clinical investigation for patients with advanced MYCN-expressing TNBC.

TBCRC 032 IB/II Multicenter Study: Molecular Insights to AR Antagonist and PI3K Inhibitor Efficacy in Patients with AR+ Metastatic Triple-Negative Breast Cancer

PURPOSE

Preclinical data demonstrating androgen receptor (AR)-positive (AR+) triple-negative breast cancer (TNBC) cells are sensitive to AR antagonists, and PI3K inhibition catalyzed an investigator-initiated, multi-institutional phase Ib/II study TBCRC032. The trial investigated the safety and efficacy of the AR-antagonist enzalutamide alone or in combination with the PI3K inhibitor taselisib in patients with metastatic AR+ (≥10%) breast cancer.

PATIENTS AND METHODS

Phase Ib patients [estrogen receptor positive (ER+) or TNBC] with AR+ breast cancer received 160 mg enzalutamide in combination with taselisib to determine dose-limiting toxicities and the maximum tolerated dose (MTD). Phase II TNBC patients were randomized to receive either enzalutamide alone or in combination with 4 mg taselisib until disease progression. Primary endpoint was clinical benefit rate (CBR) at 16 weeks.

RESULTS

The combination was tolerated, and the MTD was not reached. The adverse events were hyperglycemia and skin rash. Overall, CBR for evaluable patients receiving the combination was 35.7%, and median progression-free survival (PFS) was 3.4 months. Luminal AR (LAR) TNBC subtype patients trended toward better response compared with non-LAR (75.0% vs. 12.5%, P = 0.06), and increased PFS (4.6 vs. 2.0 months, P = 0.082). Genomic analyses revealed subtype-specific treatment response, and novel FGFR2 fusions and AR splice variants.

CONCLUSIONS

The combination of enzalutamide and taselisib increased CBR in TNBC patients with AR+ tumors. Correlative analyses suggest AR protein expression alone is insufficient for identifying patients with AR-dependent tumors and knowledge of tumor LAR subtype and AR splice variants may identify patients more or less likely to benefit from AR antagonists.

p73 Is Required for Ovarian Follicle Development and Regulates a Gene Network Involved in Cell-to-Cell Adhesion

We report that p73 is expressed in ovarian granulosa cells and that loss of p73 leads to attenuated follicle development, ovulation, and corpus luteum formation, resulting in decreased levels of circulating progesterone and defects in mammary gland branching. Ectopic progesterone in p73-deficient mice completely rescued the mammary branching and partially rescued the ovarian follicle development defects. Performing RNA sequencing (RNA-seq) on transcripts from murine wild-type and p73-deficient antral follicles, we discovered differentially expressed genes that regulate biological adhesion programs. Through modulation of p73 expression in murine granulosa cells and transformed cell lines, followed by RNA-seq and chromatin immunoprecipitation sequencing, we discovered p73-dependent regulation of a gene set necessary for cell adhesion and migration and components of the focimatrix (focal intra-epithelial matrix), a basal lamina between granulosa cells that promotes follicle maturation. In summary, p73 is essential for ovarian folliculogenesis and functions as a key regulator of a gene network involved in cell-to-cell adhesion and migration.

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p73 is required for murine ovarian folliculogenesis and proper corpus luteum formation

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p73 loss leads to defects in progesterone signaling and mammary gland branching

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In murine ovaries, p73 is expressed specifically in granulosa cells

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p73 regulates components of the granulosa cell focimatrix and migration

Procedural difficulties during successful intubation in octogenarians: A prospective observational study

OBJECTIVE

Octogenarians undergo anatomic and physiopathologic degradation, making airway management problematic, specific to intubation, bag mask ventilation, leading to desaturation and aspiration. Our study's aim was to examine the process of airway management regarding the steps involved in intubation and any deviations or delays in the tasks.

MATERIALS AND METHODS

An institutional review board-approved difficult airway prospective observational study in older adults was conducted. Inclusion criteria included airway features indicative of difficult airway, history of failed intubation, the planned use of specialized airway devices, and/or expected airway complications due to comorbidities. Patients 80 years and older were analyzed. Demographic data collected were age, weight, BMI, gender, ASA classification, airway indices, diagnosis, and procedures. Problems with intubation (INT) (≥3 intubation attempts), laborious assisted ventilation (VEN) (2-person and/or application of CPAP>20cmH₂O), and complications with oxygenation (OXY) (SpO₂<95%) were analyzed.

RESULTS

Of the 41 patients enrolled in the study, 3 (7.3%) had all 3: problematic (INT), laborious (VEN), and desaturated (OXY); 8 (19.5%) patients experienced problematic (INT), 20 (48.8%) were described as laborious (VEN), and 14 (34.1%) experienced complications with (OXY).

CONCLUSION

In octogenarians, we found a low incidence of difficulty with INT-VEN-OXY together. However, bag mask ventilation was found to be laborious with a high incidence of desaturation. Success rate of INT as a sole metric may not accurately describe the process of the intubation. We recommend alternative airway devices and techniques and the establishment of protocols for airway management in the elderly.

Novel Pretreatments of Whole Blood Using Fenton-like Processes for Trace Metal Analysis

Whole blood is a complex mixture of biological and chemical species. Its pretreatment, which is often conducted by dry ashing, is needed before the analyses of trace metals in whole blood. Recently photo-Fenton Advanced Oxidation Process (AOP) process has been used in the pretreatment of whole blood. Two new AOP processes using simple heating and microwave irradiation have been developed in the current work to pretreat blood samples. The treatments are based on a Fenton-like AOP with acid deactivation of the enzyme catalase. The first treatment is performed with a lab oven over 5 h, while the second uses microwave irradiation for 6 min. These methods allow for either cost-effective pretreatment through the use of the lab oven, or time savings through the use of the microwave oven. The degradations of blood and pure hemoglobin samples are compared through UV/visible spectroscopy, and the copper concentration in the treated samples were analyzed via anodic stripping voltammetry as a demonstration of analyzing trace metals in the pretreated whole blood.

Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection

Triple-negative breast cancer (TNBC) is a heterogeneous disease that can be classified into distinct molecular subtypes by gene expression profiling. Considered a difficult-to-treat cancer, a fraction of TNBC patients benefit significantly from neoadjuvant chemotherapy and have far better overall survival. Outside of BRCA1/2 mutation status, biomarkers do not exist to identify patients most likely to respond to current chemotherapy; and, to date, no FDA-approved targeted therapies are available for TNBC patients. Previously, we developed an approach to identify six molecular subtypes TNBC (TNBCtype), with each subtype displaying unique ontologies and differential response to standard-of-care chemotherapy. Given the complexity of the varying histological landscape of tumor specimens, we used histopathological quantification and laser-capture microdissection to determine that transcripts in the previously described immunomodulatory (IM) and mesenchymal stem-like (MSL) subtypes were contributed from infiltrating lymphocytes and tumor-associated stromal cells, respectively. Therefore, we refined TNBC molecular subtypes from six (TNBCtype) into four (TNBCtype-4) tumor-specific subtypes (BL1, BL2, M and LAR) and demonstrate differences in diagnosis age, grade, local and distant disease progression and histopathology. Using five publicly available, neoadjuvant chemotherapy breast cancer gene expression datasets, we retrospectively evaluated chemotherapy response of over 300 TNBC patients from pretreatment biopsies subtyped using either the intrinsic (PAM50) or TNBCtype approaches. Combined analysis of TNBC patients demonstrated that TNBC subtypes significantly differ in response to similar neoadjuvant chemotherapy with 41% of BL1 patients achieving a pathological complete response compared to 18% for BL2 and 29% for LAR with 95% confidence intervals (CIs; [33, 51], [9, 28], [17, 41], respectively). Collectively, we provide pre-clinical data that could inform clinical trials designed to test the hypothesis that improved outcomes can be achieved for TNBC patients, if selection and combination of existing chemotherapies is directed by knowledge of molecular TNBC subtypes.

Abstract 4698: Gene expression profiles of triple negative breast cancer epithelial and stromal cells are predictive of treatment response

Lacking human epithelial growth factor receptor 2 (HER2) amplification as well as estrogen and progesterone receptors, TNBC is a heterogeneous collection of biologically diverse cancers that likely contributes to variable clinical outcomes for patients suffering from this disease. Since TNBC lacks well-defined molecular targets, we recently performed gene expression (GE) analyses and identified six distinct molecular TNBC subtypes with unique biologies. To further decipher the contribution of tumor epithelium and its adjacent stroma to the biology of TNBC and clinical response to treatments, we performed GE analysis on biopsy material from 20 TNBC patients enrolled in a phase II clinical trial [VICC-BRE0904; a neoadjuvant study of cisplatin and paclitaxel±RAD001 (mTOR inhibitor)]. We isolated RNA from both tumor epithelial and stromal cells using laser capture microdissection. Our goal is to determine if GE from tumor epithelial and/or stromal cells is predictive of response to treatment. Our preliminary results indicate that there is differential GE in both tumor epithelial as well as stromal cells in pretreatment biopsies of responders versus non-responders. Patients with higher expression of proliferation genes such as MKI67, KIFCI, AURKB, E2F3, and DNA damage response genes TP53BP2, CHEK1, RPA1, BLM were more responsive to treatment compared to non-responders. Upon completion of the phase II clinical trial and correlative molecular analyses, we anticipate identifying biomarkers of drug sensitivity that will provide insight to novel combination therapies for the different subtypes of TNBC.

Citation Format: Bojana Jovanovic, Steven X. Chen, Brian D. Lehmann, Kimberly N. Johnson, Violeta Sanchez, Maria G. Kuba, Melinda E. Sanders, Ingrid A. Mayer, Harold L. Moses, Jennifer A. Pietenpol. Gene expression profiles of triple negative breast cancer epithelial and stromal cells are predictive of treatment response. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4698. doi:10.1158/1538-7445.AM2013-4698

Abstract 698: Overexpression of the aryl hydrocarbon receptor correlates with high tumor grade in human breast invasive carcinomas

The aryl hydrocarbon receptor (AhR) is a ligand-activated basic helix-loop-helix transcription factor which binds environmental poly aromatic hydrocarbons (PAH) and mediates their carcinogenic effects. Recent reports, including data from our laboratory implicate AhR in breast cancer development and progression independent of the receptor occupancy by PAH. In this study we investigated the potential of AhR as a stage specific marker of breast cancer. We examined the expression of AhR by immunohistochemistry in tissue microarrays (TMA) containing 192 specimens of clinically defined three stages of invasive breast cancer: node-negative (NN), node-positive (NP) and metastatic (Met) carcinoma. The TMA were obtained from the National Cancer Institute Cooperative Breast Cancer Tissue Resource [NCI-CBCTR] and were stained for AhR using high affinity antibody. The AhR staining was then scored by three evaluators, including two pathologists who were blinded to the study. Statistical analysis showed a significant correlation between the AhR expression and the carcinoma case type (NN, NP or Met) (p-value of ANOVA is &lt; 0.0003), and although there is a significant difference of AhR expression among carcinoma case type of white women (p&lt; 0.0017) there is no significant difference for black women (p&lt;0.0968). There is also a strong positive correlation between the receptor expression and the tumor grade (p &lt;0.0001). While there is no correlation with the status of estrogen or progesterone receptors (p= 0.1643 and 0.1884, respectively), there is strong correlation of high AhR expression and invasive breast carcinoma in women over 50 years old (p&lt;0.0043). In conclusion, our findings identify the AhR as a new predictive clinical marker for metastatic breast cancer and a unique target for the design of novel selective inhibitors for therapeutic intervention of metastatic breast cancer. More importantly, the AhR overexpression identifies a subset of patients who could benefit from therapy targeting this receptor.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 698. doi:1538-7445.AM2012-698

Novel p63 target genes involved in paracrine signaling and keratinocyte differentiation

The transcription factor p63 is required for proper epidermal barrier formation and maintenance. Herein, we used chromatin immunoprecipitation coupled with DNA sequencing to identify novel p63 target genes involved in normal human epidermal keratinocyte (NHEKs) growth and differentiation. We identified over 2000 genomic sites bound by p63, of which 82 were also transcriptionally regulated by p63 in NHEKs. Through the discovery of interleukin-1-α as a p63 target gene, we identified that p63 is a regulator of epithelial–mesenchymal crosstalk. Further, three-dimensional organotypic co-cultures revealed TCF7L1, another novel p63 target gene, as a regulator of epidermal proliferation and differentiation, providing a mechanism by which p63 maintains the proliferative potential of basal epidermal cells. The discovery of new target genes links p63 to diverse signaling pathways required for epidermal development, including regulation of paracrine signaling to proliferative potential. Further mechanistic insight into p63 regulation of epidermal cell growth and differentiation is provided by the identification of a number of novel p63 target genes in this study.

Ectopic expression of an endoparasitic wasp venom protein in Drosophila melanogaster affects immune function, larval development and oviposition

Endoparasitic hymenoptera inject maternal factors into the host, along with their eggs, to subvert the host immune system. The venom protein, Vn50, previously characterized from the wasp Cotesia rubecula inhibits prophenoloxidase activation in its host Pieris rapae and in another lepidopteran, Manduca sexta. We generated a stable line in the model insect, Drosophila melanogaster, which ectopically expresses Vn50. Results indicated that Vn50 expression accelerates larval development, increases oviposition and reduces melanization in the haemolymph of the transgenic flies. Since melanization is known to be an important facet of the insect immune response, we examined the impact of Vn50 expression on susceptibility to pathogens. Transgenic Vn50 flies challenged with the fungus Beauveria bassiana had increased mortality compared with control flies, but there was no significant change in survival in flies challenged with the pathogenic bacteria, Serratia marcescens. Interestingly, mortality induced by the natural pathogen Drosophila C virus was significantly delayed in Vn50 expressing flies. This indicates a wider range of potential hosts that may be affected by Vn50 and its potential for manipulation of immune system in insects.

ISG20L1 is a p53 family target gene that modulates genotoxic stress-induced autophagy

Background

Autophagy is characterized by the sequestration of cytoplasm and organelles into multimembrane vesicles and subsequent degradation by the cell's lysosomal system. It is linked to many physiological functions in human cells including stress response, protein degradation, organelle turnover, caspase-independent cell death and tumor suppression. Malignant transformation is frequently associated with deregulation of autophagy and several tumor suppressors can modulate autophagic processes. The tumor suppressor p53 can induce autophagy after metabolic or genotoxic stress through transcriptionally-dependent and -independent mechanisms. In this study we expand on the former mechanism by functionally characterizing a p53 family target gene, ISG20L1 under conditions of genotoxic stress.

Results

We identified a p53 target gene, ISG20L1, and show that transcription of the gene can be regulated by all three p53 family members (p53, p63, and p73). We generated an antibody to ISG20L1 and found that it localizes to the nucleolar and perinucleolar regions of the nucleus and its protein levels increase in a p53- and p73-dependent manner after various forms of genotoxic stress. When ectopically expressed in epithelial cancer-derived cell lines, ISG20L1 expression decreased clonogenic survival without a concomitant elevation in apoptosis and this effect was partially rescued in cells that were ATG5 deficient. Knockdown of ISG20L1 did not alter 5-FU induced apoptosis as assessed by PARP and caspase-3 cleavage, sub-G₁ content, and DNA laddering. Thus, we investigated the role of ISG20L1 in autophagy, a process commonly associated with type II cell death, and found that ISG20L1 knockdown decreased levels of autophagic vacuoles and LC3-II after genotoxic stress as assessed by electron microscopy, biochemical, and immunohistochemical measurements of LC3-II.

Conclusions

Our identification of ISG20L1 as a p53 family target and discovery that modulation of this target can regulate autophagic processes further strengthens the connection between p53 signaling and autophagy. Given the keen interest in targeting autophagy as an anticancer therapeutic approach in tumor cells that are defective in apoptosis, investigation of genes and signaling pathways involved in cell death associated with autophagy is critical.

Identification of markers of taxane sensitivity using proteomic and genomic analyses of breast tumors from patients receiving neoadjuvant paclitaxel and radiation

PURPOSE

To identify molecular markers of pathologic response to neoadjuvant paclitaxel/radiation treatment, protein and gene expression profiling were done on pretreatment biopsies.

EXPERIMENTAL DESIGN

Patients with high-risk, operable breast cancer were treated with three cycles of paclitaxel followed by concurrent paclitaxel/radiation. Tumor tissue from pretreatment biopsies was obtained from 19 of the 38 patients enrolled in the study. Protein and gene expression profiling were done on serial sections of the biopsies from patients that achieved a pathologic complete response (pCR) and compared to those with residual disease, non-pCR (NR).

RESULTS

Proteomic and validation immunohistochemical analyses revealed that alpha-defensins (DEFA) were overexpressed in tumors from patients with a pCR. Gene expression analysis revealed that MAP2, a microtubule-associated protein, had significantly higher levels of expression in patients achieving a pCR. Elevation of MAP2 in breast cancer cell lines led to increased paclitaxel sensitivity. Furthermore, expression of genes that are associated with the basal-like, triple-negative phenotype were enriched in tumors from patients with a pCR. Analysis of a larger panel of tumors from patients receiving presurgical taxane-based treatment showed that DEFA and MAP2 expression as well as histologic features of inflammation were all statistically associated with response to therapy at the time of surgery.

CONCLUSION

We show the utility of molecular profiling of pretreatment biopsies to discover markers of response. Our results suggest the potential use of immune signaling molecules such as DEFA as well as MAP2, a microtubule-associated protein, as tumor markers that associate with response to neoadjuvant taxane-based therapy.

DeltaNp63 antagonizes p53 to regulate mesoderm induction in Xenopus laevis

p63, a homolog of the tumor suppressor p53, is critical for the development and maintenance of complex epithelia. The developmentally regulated p63 isoform, DeltaNp63, can act as a transcriptional repressor, but the link between the transcriptional functions of p63 and its biological roles is unclear. Based on our initial finding that the mesoderm-inducing factor activin A is suppressed by DeltaNp63 in human keratinocytes, we investigated the role of DeltaNp63 in regulating mesoderm induction during early Xenopus laevis development. We find that down-regulation of DeltaNp63 by morpholino injection in the early Xenopus embryo potentiates mesoderm formation whereas ectopic expression of DeltaNp63 inhibits mesoderm formation. Furthermore, we show that mesodermal induction after down-regulation of DeltaNp63 is dependent on p53. We propose that a key function for p63 in defining a squamous epithelial phenotype is to actively suppress mesodermal cell fates during early development. Collectively, we show that there is a distinct requirement for different p53 family members during the development of both mesodermal and ectodermal tissues. These findings have implications for the role of p63 and p53 in both development and tumorigenesis of human epithelia.

The frequent and conserved DR3-B8-A1 extended haplotype confers less diabetes risk than other DR3 haplotypes

AIM

The goal of this study was to develop and implement methodology that would aid in the analysis of extended high-density single nucleotide polymorphism (SNP) major histocompatibility complex (MHC) haplotypes combined with human leucocyte antigen (HLA) alleles in relation to type 1 diabetes risk.

METHODS

High-density SNP genotype data (2918 SNPs) across the MHC from the Type 1 Diabetes Genetics Consortium (1240 families), in addition to HLA data, were processed into haplotypes using PedCheck and Merlin, and extended DR3 haplotypes were analysed.

RESULTS

With this large dense set of SNPs, the conservation of DR3-B8-A1 (8.1) haplotypes spanned the MHC (>/=99% SNP identity). Forty-seven individuals homozygous for the 8.1 haplotype also shared the same homozygous genotype at four 'sentinel' SNPs (rs2157678 'T', rs3130380 'A', rs3094628 'C' and rs3130352 'T'). Conservation extended from HLA-DQB1 to the telomeric end of the SNP panels (3.4 Mb total). In addition, we found that the 8.1 haplotype is associated with lower risk than other DR3 haplotypes by both haplotypic and genotypic analyses [haplotype: p = 0.009, odds ratio (OR) = 0.65; genotype: p = 6.3 x 10(-5), OR = 0.27]. The 8.1 haplotype (from genotypic analyses) is associated with lower risk than the high-risk DR3-B18-A30 haplotype (p = 0.01, OR = 0.23), but the DR3-B18-A30 haplotype did not differ from other non-8.1 DR3 haplotypes relative to diabetes association.

CONCLUSION

The 8.1 haplotype demonstrates extreme conservation (>3.4 Mb) and is associated with significantly lower risk for type 1 diabetes than other DR3 haplotypes.

In vitro rearing of Perkinsiella saccharicida and the use of leaf segments to assay Fiji disease virus transmission

Fiji leaf gall (FLG) is caused by the Reovirus, Fiji disease virus (FDV), which is transmitted to sugarcane by planthoppers of the genus Perkinsiella. Low vector transmission rates and slow disease symptom development make experimentation within the FDV-Perkinsiella-sugarcane system inherently difficult. A laboratory-based technique was devised to rear the vector using sugarcane leaves as a food source. Planthoppers were reared on sugarcane leaf segments embedded in agarose enclosed within plastic containers. To provide a nondestructive assay for determination of the inoculation potential of planthoppers, FDV was detected by reverse transcription-polymerase chain reaction (RT-PCR) in newly infected sugarcane leaf segments following exposure to viruliferous planthoppers. Leaf segment inoculation correlated with development of FLG symptoms in whole plants that were fed on by the same planthoppers. Analysis of FDV RNAs within the planthopper, measured by quantitative RT-PCR (qRT-PCR), indicated that FDV RNA concentration was associated with successful inoculation of the leaf segment, transmission of FDV to sugarcane and subsequent development of FLG in plants. Quantification of FDV RNA within planthoppers provided an additional measure to assess vector competence in individuals.

IGFBP-3 Is a Direct Target of Transcriptional Regulation by ΔNp63α in Squamous Epithelium

DeltaNp63alpha is a nuclear transcription factor that maintains epithelial progenitor cell populations, is overexpressed in several epithelial cancers, and can negatively regulate apoptosis. However, the mechanisms by which DeltaNp63alpha promotes cell survival are unclear. DeltaNp63alpha has been reported to act as a transcriptional repressor, but specific target genes directly repressed by DeltaNp63alpha remain unidentified. Here, we present evidence that DeltaNp63alpha functions to negatively regulate the proapoptotic protein IGFBP-3. Disruption of p63 expression in squamous epithelial cells increases IGFBP-3 expression, whereas ectopic expression of DeltaNp63alpha down-regulates IGFBP-3. DeltaNp63alpha binds to sites in the IGFBP-3 gene in vivo and can modulate transcription through these sites. Furthermore, DeltaNp63alpha and IGFBP-3 expression patterns are inversely correlated in normal squamous epithelium and squamous cell carcinomas. These data suggest that IGFBP-3 is a target of transcriptional repression by DeltaNp63alpha and that this repression represents a mechanism by which tumors that overexpress p63 may be protected from apoptosis.

Recovery of infectious pariacoto virus from cDNA clones and identification of susceptible cell lines

Pariacoto virus (PaV) is a nodavirus that was recently isolated in Peru from the Southern armyworm, Spodoptera eridania. Virus particles are non enveloped and about 30 nm in diameter and have T=3 icosahedral symmetry. The 3.0-A crystal structure shows that about 35% of the genomic RNA is icosahedrally ordered, with the RNA forming a dodecahedral cage of 25-nucleotide (nt) duplexes that underlie the inner surface of the capsid. The PaV genome comprises two single-stranded, positive-sense RNAs: RNA1 (3,011 nt), which encodes the 108-kDa catalytic subunit of the RNA-dependent RNA polymerase, and RNA2 (1,311 nt), which encodes the 43-kDa capsid protein precursor alpha. In order to apply molecular genetics to the structure and assembly of PaV, we identified susceptible cell lines and developed a reverse genetic system for this virus. Cell lines that were susceptible to infection by PaV included those from Spodoptera exigua, Helicoverpa zea and Aedes albopictus, whereas cells from Drosophila melanogaster and Spodoptera frugiperda were refractory to infection. To recover virus from molecular clones, full-length cDNAs of PaV RNAs 1 and 2 were cotranscribed by T7 RNA polymerase in baby hamster kidney cells that expressed T7 RNA polymerase. Lysates of these cells were infectious both for cultured cells from Helicoverpa zea (corn earworm) and for larvae of Galleria mellonella (greater wax moth). The combination of infectious cDNA clones, cell culture infectivity, and the ability to produce milligram amounts of virus allows the application of DNA-based genetic methods to the study of PaV structure and assembly.

The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA

The 3.0 A resolution crystal structure of Pariacoto virus (PaV) reveals extensive interactions between portions of the viral RNA genome and the icosahedral capsid. Under the protein shell of the T = 3 quasi equivalent capsid lies a dodecahedral cage composed of RNA duplex that accounts for approximately 35% of the single-stranded RNA genome. The highly basic N-terminal regions (residues 7-54) of the subunits, forming pentamers (A subunits) are clearly visible in the density map and make numerous interactions with the RNA cage. The C-terminal segments (residues 394-401) of the A subunits lie in channels near the quasi three-fold axes. Electron cryo-microscopy and image reconstruction of PaV particles clearly show the dodecahedral RNA cage.

Characterization and construction of functional cDNA clones of Pariacoto virus, the first Alphanodavirus isolated outside Australasia

Pariacoto virus (PaV) was recently isolated in Peru from the Southern armyworm (Spodoptera eridania). PaV particles are isometric, nonenveloped, and about 30 nm in diameter. The virus has a bipartite RNA genome and a single major capsid protein with a molecular mass of 39.0 kDa, features that support its classification as a Nodavirus. As such, PaV is the first Alphanodavirus to have been isolated from outside Australasia. Here we report that PaV replicates in wax moth larvae and that PaV genomic RNAs replicate when transfected into cultured baby hamster kidney cells. The complete nucleotide sequences of both segments of the bipartite RNA genome were determined. The larger genome segment, RNA1, is 3,011 nucleotides long and contains a 973-amino-acid open reading frame (ORF) encoding protein A, the viral contribution to the RNA replicase. During replication, a 414-nucleotide long subgenomic RNA (RNA3) is synthesized which is coterminal with the 3' end of RNA1. RNA3 contains a small ORF which could encode a protein of 90 amino acids similar to the B2 protein of other alphanodaviruses. RNA2 contains 1,311 nucleotides and encodes the 401 amino acids of the capsid protein precursor alpha. The amino acid sequences of the PaV capsid protein and the replicase subunit share 41 and 26% identity with homologous proteins of Flock house virus, the best characterized of the alphanodaviruses. These and other sequence comparisons indicate that PaV is evolutionarily the most distant of the alphanodaviruses described to date, consistent with its novel geographic origin. Although the PaV capsid precursor is cleaved into the two mature capsid proteins beta and gamma, the amino acid sequence at the cleavage site, which is Asn/Ala in all other alphanodaviruses, is Asn/Ser in PaV. To facilitate the investigation of PaV replication in cultured cells, we constructed plasmids that transcribed full-length PaV RNAs with authentic 5' and 3' termini. Transcription of these plasmids in cells recreated the replication of PaV RNA1 and RNA2, synthesis of subgenomic RNA3, and translation of viral proteins A and alpha.

Reverse transcription of a naturally occurring nonretroviral RNA produces a precise deletion in the majority of its cDNA products

A precise, reproducible deletion made during in vitro reverse transcription of RNA2 from the icosahedral positive-stranded Helicoverpa armigera stunt virus (Tetraviridae) is described. The deletion, located between two hexamer repeats, is a 50-base sequence that includes one copy of the hexamer repeat. Only the Moloney murine leukemia virus reverse transcriptase and its derivative Superscript I, carrying a deletion of the carboxy-terminal RNase H region, showed this response, indicating a template-switching mechanism different from one proposed that involves a RNase H-dependent strand transfer. Superscript II, however, which carries point mutations to reduce RNase H activity, does not cause a deletion. A possible mechanism involves the enzyme pausing at the 3' side of a stem-loop structure and the 3' end of the nascent DNA strand separating from the template and reannealing to the upstream hexamer repeat.

Molecular characterization of Drosophila C virus isolates

Reverse transcription coupled with polymerase chain reaction and restriction enzyme analysis was used to characterize 12 Drosophila C virus isolates from geographically different regions. A 1.2-kb fragment was amplified from cDNA and profiles from digestion with 20 restriction enzymes were generated. Analysis of the restriction fragment data gave estimates of nucleotide divergence of 0-10% between isolates. The isolates were grouped on the basis of genetic distance estimates derived from the restriction data. For the isolates from which a single genotype could be purified, a geographical pattern in the distribution of viral genotypes was identified. The 4 Moroccan isolates were very closely related to each other, differing in only 1 restriction profile. The 2 Australian isolates were each other's closest relatives, as were the 2 isolates first recovered in France. The PCR-RFLP technique used in this study has provided us with a simple procedure which can be used to characterize DCV isolates. A single enzyme, Taq I, generated 5 distinct and diagnostic restriction fragment patterns, which allowed easy assignment of isolates to one of the five viral genotypes identified in this study.

The novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family

The complete nucleotide sequence of the genomic RNA from the insect picorna-like virus Drosophila C virus (DCV) was determined. The DCV sequence predicts a genome organization different to that of other RNA virus families whose sequences are known. The single-stranded positive-sense genomic RNA is 9264 nucleotides in length and contains two large open reading frames (ORFs) which are separated by 191 nucleotides. The 5' ORF contains regions of similarities with the RNA-dependent RNA polymerase, helicase and protease domains of viruses from the picornavirus, comovirus and sequivirus families. The 3' ORF encodes the capsid proteins as confirmed by N-terminal sequence analysis of these proteins. The capsid protein coding region is unusual in two ways: firstly the cistron appears to lack an initiating methionine and secondly no subgenomic RNA is produced, suggesting that the proteins may be translated through internal initiation of translation from the genomic length RNA. The finding of this novel genome organization for DCV shows that this virus is not a member of the Picornaviridae as previously thought, but belongs to a distinct and hitherto unrecognized virus family.

Mechanism and biological significance of constitutive expression of MGSA/GRO chemokines in malignant melanoma tumor progression

By reverse transcriptase-polymerase chain reaction, enzyme-linked immunosorbent assay, and immunohistochemistry, MGSA-alpha, -beta, -gamma, and CXCR2 mRNA expression and proteins are detected in 7 out of 10 human melanoma lesions. The biological consequence of constitutive expression of the MGSA/GRO chemokine in immortalized melanocytes was tested in SCID and nude mouse models. Continuous expression of MGSA/GRO-alpha, -beta, or -gamma in immortalized melan-a mouse melanocytes results in nearly 100% tumor formation for each of the clones tested, whereas clones expressing only the neomycin resistance vector form tumors <10% of the time. Moreover, antibodies to the MGSA/GRO proteins slow or inhibit the formation of tumors in the SCID mouse model and block the angiogenic response to conditioned medium from the tumor-producing clones. Transcription of the MGSA/GRO chemokines is regulated by an enhancesome-like complex comprised of the nuclear factor-kappaB (NF-kappaB), HMG(I)Y, IUR, and Sp1 elements. In Hs294T melanoma cells the half life of the IKB protein is shortened in comparison to normal retinal epithelial cells, facilitating the endogenous nuclear localization of NF-kappaB. We propose that this endogenous nuclear NF-kappaB, working in concert with the 115-kDa IUR-binding factor, promotes constitutive expression of MGSA/GRO genes.

Establishment of breast cell cultures and lines from peoples of African origin

OBJECTIVES

The purpose of our study was to establish breast epithelial cell cultures and cell lines from peoples of African origin (blacks). It is presumed that the biology of breast cancer in women of African origin has unique aspects that can be explored using cultured breast epithelial cells.

STUDY DESIGN

Biopsy specimens were obtained from black women undergoing radical or modified mastectomies. Normal cell cultures were established using tissue from reduction mammaplasties or the milk of lactating mothers. The tissue specimens were lacerated, digested with collagenase solution, and plated on tissue culture plates. To extend the life of the epithelial cells in culture, they are transformed with SV40 virus.

RESULTS

We have maintained breast tumor cells in culture from a 27-year-old black woman for more than 1 month.

CONCLUSION

Despite the difficulty of establishing epithelial cell cultures, we have maintained breast tumor cells from blacks in culture for an extended period to allow characterization.

A molecular taxonomy for cricket paralysis virus including two new isolates from Australian populations of Drosophila (Diptera: Drosophilidae)

Two new isolates of cricket paralysis virus, TAR and SIM, are described that were originally isolated from laboratory colonies of Drosophila melanogaster and Drosophila simulans respectively. Using a combination of biological, serological and molecular characters it was possible to distinguish the SIM isolate from all other isolates and it is thus described as a new strain; CrPVSIM. The TAR isolate however, was indistinguishable from the CrPV reference isolate CrPVVIC/GM/D2(2)/Gm/D2(2) (Teleogryllus commodus, Victoria, Australia, 1968). The molecular characters used in the present study were obtained by combining PCR and restriction endonuclease digestion of the amplified fragments. This work demonstrates that such molecular characters, when used in combination with others, provide a powerful set of taxonomic characters for classifying CrPV isolates and strains and assessing their genetic relatedness.

Forest Planning in an Oregon Case Study: Defining the Problem and Attempting to Meet Goals with a Spatial-Analysis Technique

Five major management goals were identified for the upper Grande Ronde River Basin on the Wallowa-Whitman National Forest in northeastern Oregon: to produce high-quality fish habitat, to maintain elk habitat, to restore and maintain forest conditions within the natural range of viability, and to contribute to community economic stability. From the broad goals, specific goals for stream temperature, habitat effectiveness index (HEI), habitat corridors, maintenance of land in late or old seral stages, and a nondeclining even flow of timber were selected. A case study was undertaken in a small watershed that is under typical societal constraints to determine whether one decision-support tool, SNAP II+, could evaluate the selected goals in a single planning exercise. Three riparian management strategies and two forest road scenarios were used. The exclusion of harvest and road-building from riparian zones in order to increase habitat protection decreased harvest levels and net present value but maintained preactivity stream temperatures. Other resources were generally maintained within prescribed management levels. Although the technique has limitations (e.g., it does not account for riparian zones in calculations of forage and cover for HEI, and it can use the maximum but not minimum acreage goal for some resources), it shows promise for evaluating management tradeoffs in watershed analysis.

The hermit transposable element of the Australian sheep blowfly, Lucilia cuprina, belongs to the hAT family of transposable elements

We report the cloning of hermit, a member of the hAT family of transposable elements from the genome of the Australian sheep blowfly, Lucilia cuprina. Hermit is 2716 bp long and is 49% homologous to the autonomous hobo element, HFL1, at the nucleic acid level. Hermit has 15 bp terminal inverted repeats that share 10 bp with the terminal inverted repeats of HFL1. Conceptual translation reveals a 583 residue open reading frame (ORF) that is 64% similar and 42% identical to the HFL1 ORF. However, the sequence of the hermit element contains two frameshifts within the putative ORF, indication that hermit is an inactive element. Analysis of L. cuprina strains from within and outside Australia suggested that hermit is present as a single copy in all the genomes analysed.

The larger genomic RNA of Helicoverpa armigera stunt tetravirus encodes the viral RNA polymerase and has a novel 3'-terminal tRNA-like structure

In this paper we report the complete nucleotide sequence of the larger segment (5312 nucleotides) of the bipartite RNA genome of Helicoverpa armigera stunt tetravirus (HaSV). HaSV therefore becomes the first member of the Tetraviridae, a virus family with a host range restricted to lepidopteran insects, whose genome has been completely sequenced. HaSV RNA 1 encodes a 187K protein which includes three domains conserved in RNA-dependent RNA polymerases of RNA viruses in the alpha-like superfamily. Analysis of the replicase sequence confirms the status of the Tetraviridae as a distinct family within this superfamily, which includes animal, plant, and insect viruses, and shows the least-distantly related replicase for all three domains to be that of the hepatitis E virus. Another feature of the nonpolyadenylated HaSV genomic RNAs is a well-conserved 3'-terminal tRNA-like structure, the first such structure discerned in an animal virus. However, in contrast to the tRNA-like structures on some plant virus RNAs, the HaSV structure, which has a valine anticodon (CAU), appears to form without a pseudoknot and therefore resembles authentic tRNA(Val) more closely than do the plant viral structures. The implications of these observations for our understanding of RNA virus evolution are discussed.

Sequence of RNA2 of the Helicoverpa armigera stunt virus (Tetraviridae) and bacterial expression of its genes

The complete nucleotide sequence of RNA2 of Helicoverpa armigera stunt virus (HaSV), a member of the Tetraviridae, was determined by characterization of cloned cDNA and PCR products and direct sequencing of genomic RNA. The capped, positive sense, single-stranded RNA is 2478 nucleotides in length and has two overlapping open reading frames (ORFs) likely to be cistrons which are situated between terminal non-coding regions of 282 and 168 bases, 5' and 3', respectively. Extensive secondary structure of the RNA strand is indicated, including a tRNA-like structure at the 3' terminus which is the first such structure discerned in an animal virus. The first ORF encodes a 17 kDa PEST protein (p17) of unknown function while the second ORF encodes the 71 kDa coat protein precursor (p71) that is cleaved at an Asn-Phe site into the 64 kDa and 7 kDa coat proteins. The precursor coat protein is 66% identical to that of another tetravirus, the Nudaurelia omega virus, with most of the difference residing in a 165 amino acid region located in the middle of the sequence. Despite the extensive similarity, no serological relationship was observed between the two viruses, suggesting that the dissimilar region is exposed on the capsid exterior. Expression in bacteria of the two RNA2 gene products shows they are likely to be expressed by a leaky scan-through mechanism. Bacterial expression of p71 did not produce virus-like particles while expression of p17 produced large arrays of mostly hollow, hexagonal tube-like structures.

Preliminary results of proton beam irradiation of macular and paramacular melanomas

Proton beam irradiation has been used for the treatment of 60 eyes with choroidal melanomas located 3 mm or less from the fovea. The average follow-up period was 18 months. 86% of the treated lesions showed regression at the time of this analysis, and the 14% that did not were followed up for less than a year. Visual acuity remained the same in 47% of the treated eyes, improved in 20%, and deteriorated in 33%. 58% of the treated eyes had visual acuity of 20/100 or better at the last follow-up examination. Radiation vasculopathy with macular oedema was the most common complication, and it was observed in 22% of the treated eyes. These preliminary observations suggest that proton beam irradiation may be a reasonable alternative to enucleation even for this group of choroidal melanomas, which is considered unfavourable in respect of the preservation of visual function.

Replicated item level factor analysis of the full MMPI

We completed a comprehensive factor analysis of the full MMPI item pool by using recent advances in computational facilities. Nearly 20,000 MMPI protocols were collected for the analysis, however, we discarded invalid records and protocols with more than 50 missing items. Analyses were computed on a developmental sample of 5,506 subjects and a cross-validation sample of 5,632. Twenty-one replicated factors were found by using an orthogonal varimax solution. The rotated factors were submitted to several experts on MMPI for factor naming. The consensus obtained on the item factors suggests that this analysis provides an unambiguous picture of the major content dimensions in the MMPI item pool.

Proton irradiation of malignant melanoma of the ciliary body

This is our first case of malignant melanoma of the ciliary body treated with proton beam irradiation, a technique that we developed for irradiating choroidal melanomas. After 21 months of follow-up no growth of the tumour has been observed, and shrinkage of the tumour was noted on the follow-up photographs and by ultrasonography. The 32P uptake test, which was positive before treatment, turned negative 14 months after irradiation. The described technique of proton beam irradiation might offer an alternative for the treatment of ciliary body melanomas when the present techniques of iridocyclectomy cannot be applied because of the size of the lesion.

Proton irradiation of choroidal melanomas. Preliminary results

Choroidal malignant melanomas in nine patients were treated with proton beam irradiation at the Harvard Cyclotron Laboratory, Cambridge, Mass. Each patient received five proton beam treatments in eight to ten days, totalling 4,730 to 8,570 rads at the tumor. No complications occurred during the treatment or follow-up period, which, at the time of this writing, ranges from one to 24 months, with an average of 12 months. No further growth of the tumor has been observed in any patient. Different signs of tumor regression have been noted. Resolution of the serous retinal detachments that accompanied some tumors is the earliest finding. Pigment changes over the surface of the tumor and adjacent pigment epithelium is a usual initial tumor response. Fluorescein angiography initially showed decreased leakage of dye; later, destruction of the tumor's vasculature and elimination of fluorescein leakage became evident. Only large choroidal vessels remained patient. Ultrasonography revealed decreased height of the tumors postirradiation, and the radioactive phosphorus (32P) uptake test, repeated in one patient, turned negative on postirradiation measurements.

28. The nursing home project of the Iowa Health Services Data System

The long-term care project of the Iowa Hospital Association has demonstrated the feasibility and utility of a multipurpose data system for nursing homes and related institutions. Important features of the Iowa system are emphasis on the needs and constraints of those providing care and collecting the data; prior establishment of specific criteria for the content of the system; the use of three related forms (admission, evaluation, and discharge) to produce current reports; and ease, flexibility, and transferability. A significant byproduct of the demonstration project was improved record keeping and patient care planning by the 14 participating facilities. Major problems encountered were lack of experience on the part of nursing homes and external regulatory agencies in defining their data needs and using data effectively, and financial support. Contribution to cost by external agencies in return for data and a major commitment to educational programs, both initial and continuing, are seen as essential to the success of long-term care data systems.