Faculty Bibliography

The mechanistic basis of resistance of vertebrate populations to contaminants, including Atlantic tomcod from the Hudson River (HR) to polychlorinated biphenyls (PCBs), is unknown. HR tomcod exhibited variants in the aryl hydrocarbon receptor 2 (AHR2) that were nearly absent elsewhere. In ligand-binding assays, AHR2-1 protein (common in the HR) was impaired as compared to widespread AHR2-2 in binding TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) and in driving expression in reporter gene assays in AHR-deficient cells treated with TCDD or PCB126. We identified a six-base deletion in AHR2 as the basis of resistance and suggest that the HR population has undergone rapid evolution, probably due to contaminant exposure. This mechanistic basis of resistance in a vertebrate population provides evidence of evolutionary change due to selective pressure at a single locus

Shortnose sturgeon Acipenser brevirostrum is federally listed as ''an endangered species threatened with extinction'' in the U.S. but its listing status is currently under review. As part of this process, the U.S. National Marine Fisheries Service will determine if shortnose sturgeon are divided into Distinct Population Segments (DPS) across its distribution. In this regard, we sought to determine if shortnose sturgeon occur in genetically 'discrete population segments,' and if so, the boundaries of each. We used mitochondrial DNA (mtDNA) control region sequence analysis to assess the genetic discreteness of 14 of 19 river populations that were recommended as DPS in the 1998 Final Recovery Plan for Shortnose Sturgeon. Nine of the 14 proposed DPS proved significantly discrete (P < 0.05 after Bonferoni correction) from both of their bracketing populations, the exceptions being those in the Penobscot River, Chesapeake Bay, Cooper River, and Ogeechee River (our sample from the Cape Fear River was insufficient to statistically analyze). Haplotype frequencies in the newly 'rediscovered' Penobscot River collection were almost identical to those in the proximal Kennebec River system. Genetic data in combination with tagging results suggest that shortnose sturgeon in the Penobscot River are probably migrants from the Kennebec. Likewise, shortnose sturgeon found today within the Chesapeake Bay appear to be migrants from the Delaware River. While haplotype frequencies in the remnant Santee River population in Lake Marion differed significantly from those in nearby Winyah Bay, they did not differ significantly from those in the Cooper River. This suggests that the Cooper River harbors descendants of the Santee River population that are unable to access their historical spawning locales. The Ogeechee River collection was not genetically distinct from that in the nearby Savannah River, suggesting that it may host descendants of hatchery-reared individuals of Savannah River ancestry. Our genetic results indicate that most, but not all, rivers with shortnose sturgeon host genetically discrete populations, constituting important information in the consideration of DPS designations. However, shortnose sturgeon migrations through coastal waters to proximal rivers and release of hatchery-reared fish may confound results from genetic studies such as ours and lead to the possible misidentification of discrete population segments

Atlantic cod Gadus morhua in US waters are currently managed as 2 stocks: (1) a Gulf of Maine stock and (2) a Georges Bank and south stock. This designation is decades old and warrants re-evaluation in light of concerns that fisheries management units may not reflect biologically meaningful population units. In this study, we used 10 microsatellite loci, the PanI locus, and 5 single nucleotide polymorphism markers to characterize the population genetic structure of cod in US waters. We found significant differentiation among temporally and spatially divergent populations of cod (global F-ST = 0.0044), primarily stemming from 2 potentially non-neutral loci, and evidence for a population structure that strongly contradicts the current 2-stock management model. This genetic structure was stable over a 5 yr period. Our results indicate that cod in US waters are broadly structured into 3 groups: (1) a northern spring-spawning coastal complex in the Gulf of Maine (GOM), (2) a southern complex consisting of winter-spawning inshore GOM, offshore GOM and sites south of Cape Cod, Massachusetts, and (3) a Georges Bank population. The strongest differentiation occurs between populations in the northern and southern complex (mean F-ST = 0.0085), some of which spawn in the same bays in different seasons. By means of mixture analysis, young-of-the-year fish sampled on juvenile nurseries were assigned to the spawning complex of their origin. Our findings contribute to a growing body of knowledge that Atlantic cod and other marine fish populations are structured on a finer scale than previously thought and that this structure supports biocomplexity and locally adapted populations. As such, it may be warranted to re-evaluate current management units and tailor management plans toward this finer scale

Background: Promoter methylation of tumor suppressor genes is a frequent and early event in breast carcinogenesis. Paired tumor tissue and serum samples from women with breast cancer show that promoter methylation is detectable in both sample types, with good concordance. This suggests the potential for these serum markers to be used for breast cancer detection. Methods: The current study was a case-control study nested within the prospective New York University Women's Health Study cohort aimed to assess the ability of promoter methylation in serum to detect pre-clinical disease. Cases were women with blood samples collected within the 6 months preceding breast cancer diagnosis (n=50). Each case was matched to 2 healthy cancer-free controls and 1 cancer-free control with a history of benign breast disease (BBD). Results: Promoter methylation analysis of four cancer-related genes: -RASSF1A, GSTP1, APC and RARbeta2, - was conducted using quantitative methylation-specific PCR. Results showed that the frequency of methylation was lower than expected among cases and higher than expected among controls. Methylation was detected in the promoter region of: RASSF1A in 22.0%, 22.9% and 17.2% of cases, BBD controls and healthy controls respectively; GSTP1 in 4%, 10.4% and 7.1% respectively; APC in 2.0%, 4.4% and 4.2% respectively and RARbeta2 in 6.7%, 2.3% and 1.1% respectively. Conclusion: Methylation status of the four genes included in this study was unable to distinguish between cases and either control group. This study highlights some methodological issues to be addressed in planning prospective studies to evaluate methylation markers as diagnostic biomarkers

The distribution of natural populations of American mink is restricted to locales that are in proximity to aquatic ecosystems. Because of the lipophilicity and persistence of polychlorinated biphenyls (PCBs) and reliance of mink on aquatic-based diets, mink at contaminated locales often bioacccumulate high levels of PCBs. In addition, in controlled laboratory studies, mink are highly sensitive at reproductive and developmental end points to the toxic effects of environmental PCB mixtures. It is believed that most, if not all, toxic effects of PCBs occur through activation of the aryl hydrocarbon receptor (AHR) pathway. Transcription of cytochrome P4501A1 (CYP1A1) by PCBs is also mediated through activation of AHR. Thus, levels of CYP1A1 mRNA provide a quantitative assay of exposure to and early biologic effect of PCBs on mink and may be predictive of toxicity at higher levels of biologic organization. We developed polymerase chain reaction (PCR) primers to amplify CYP1A1 as well as identified a housekeeping gene from mink cDNA. We used real-time reverse transcription-PCR to quantify and compare levels of hepatic CYP1A mRNA among groups of ranched mink kits and juveniles, which were fed diets or exposed in utero to fish that were low in PCBs (Atlantic herring) or to diets that were contaminated with three different levels of PCBs (carp) from Saginaw Bay, Lake Michigan. We found significant differences in CYP1A1 mRNA expression between mink fed the control diet and those fed a PCB-contaminated carp diet at all three treatment levels and exposure times. CYP1A1 mRNA was significantly induced 5.3- to 6.6-fold and 3.7- to 4.7-fold at 6 and 27 weeks, respectively. In previous studies, dietary exposures to PCB-contaminated carp were shown to cause mild to moderate lesions in the mandible and maxilla of these animals. This study demonstrates that hepatic CYP1A1 mRNA may be a sensitive biomarker of exposure of mink to environmentally relevant levels of PCBs and may be predictive of their effects in natural populations

Several populations of fishes inhabiting contaminated Atlantic Coast estuaries exhibit resistance to early life-stage (ELS) toxicities induced by halogenated aromatic hydrocarbons such as coplanar polychlorinated biphenyls (PCBs). These toxicities include mortality, circulatory failure, edema, and craniofacial malformations. The mechanisms behind resistance to halogenated aromatic hydrocarbon toxicity in these populations are unknown. First and second generation Atlantic tomcod Microgadus tomcod embryos derived from the Hudson River ([HR]; New York, USA) population are highly resistant to PCB-induced cytochrome P4501A (CYP1A) expression and ELS toxicity when compared to embryos of Miramichi River ([MR]; New Brunswick, Canada) and Shinnecock Bay ([SB]; New York, USA) origin. The present study sought to identify novel genes involved in population differences in response to PCB exposure using custom microarrays. Microarray probes consisted of unsequenced inserts of randomly picked clones from a tomcod cardiac cDNA library. Tomcod embryos from three populations (HR, MR, and SB) were exposed to two doses of an environmentally relevant mixture of coplanar PCBs and screened for dose- and population-specific patterns of gene expression. Clones displaying significant differences between populations exposed to the high dose of PCBs were identified by DNA sequencing. Of the 28 identified nonribosomal protein clones, none displayed expression patterns highly similar to CYP1A (altered in MR and SB, but not in HR). However, several transcripts representing biomarkers of cardiomyopathy in mammals (cardiac troponin T2, cathepsin L, and atrial natriuretic peptide) were differentially altered among the three tomcod populations by PCBs. Although the present study did not identify any novel genes associated with PCB resistance in tomcod, several potential molecular biomarkers of PCB exposure were revealed

To evaluate the associations of breast cancer risk with polymorphisms in the XPC and XPD/ERCC2 DNA nucleotide excision repair genes, a case-control study nested within a prospective cohort of 14,274 women was conducted. Genotypes were characterized for 612 incident, invasive breast cancer cases and their 1:1 matched controls. The homozygous variant of a poly(AT) insertion/deletion polymorphism in intron 9 of the XPC gene (XPC-PAT+/+), was associated with breast cancer risk [odds ratio (OR) = 1.45, 95% confidence interval: 1.07-1.97], after adjustment for other breast cancer risk factors. The breast cancer risk associated with XPC-PAT+/+ did not differ by age at diagnosis. There was an indication of an interaction (p = 0.08) between the XPC-PAT+/+ genotype and cigarette smoking. Ever smokers with the XPC-PAT+/+ genotype were at elevated risk of breast cancer (OR = 1.56, CI: 0.95-2.58), but no differences were observed among never smokers. Analyses of the ERCC2 Lys751Gln polymorphism did not show an association with breast cancer risk, either overall or at younger ages. The results suggest that breast cancer risk is related to the XPC haplotype tagged by the XPC-PAT+/+ insertion-deletion polymorphism in intron 9. Further study of the XPC haplotypes and their interactions with smoking in relation to breast cancer risk is needed

The vitamin D receptor (VDR) is a critical mediator of the cellular effects of vitamin D. The associations between four common VDR polymorphisms (BSMI, APAI, TAQI, and FOKI) and risk of epithelial ovarian cancer (EOC) were assessed in a case-control study nested within two prospective cohorts. One hundred seventy incident cases of EOC and 323 individually matched controls were genotyped. Overall, no associations were observed in genotype analyses. Haplotypes combining three SNPs in high linkage disequilibrium (BSMI, APAI, and TAQI) were also not associated with risk. These observations do not support a role for BSMI, APAI, TAQI, and FOKI polymorphisms in epithelial ovarian cancer in a predominantly Caucasian population

Anadromous fishes are believed to make regular circuits of migration in the sea before homing to their natal rivers. Sea lamprey Petromyzon marinus is an anadromous fish that is an exception to this life-history pattern. It also differs from other anadromous fishes in that its adult phase is parasitic, a feeding strategy that should make homing problematic for lamprey cohorts that become widely dispersed through transport by the diverse hosts they parasitize. We sequenced a portion of the mitochondrial DNA control region from sea lampreys collected from 11 North American east coast rivers to test for genetic evidence of homing. There were no significant differences (chi2=235.1, p=0.401) in haplotype frequencies among them, with almost 99 per cent of haplotypic diversity occurring within populations. These findings, together with concordant genetic results from other geographical regions and ancillary information on pheromonal communication, suggest that sea lamprey does not home but rather exhibits regional panmixia while using a novel 'suitable river' strategy to complete its life cycle