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Recent advances in next-generation sequencing strategies have led to the discovery of many novel disease genes. We describe here a non-consanguineous family with two affected boys presenting with early onset of severe axonal neuropathy, optic atrophy, intellectual disability, auditory neuropathy and chronic respiratory and gut disturbances. Whole-exome sequencing (WES) was performed on all family members and we identified compound heterozygous variants (c.[760C>A];[1528G>C];p.[(Gln254Lys);(Ala510Pro)] in the polyribonucleotide nucleotidyltransferase 1 (PNPT1) gene in both affected individuals. PNPT1 encodes the polynucleotide phosphorylase (PNPase) protein, which is involved in the transport of small RNAs into the mitochondria. These RNAs are involved in the mitochondrial translation machinery, responsible for the synthesis of mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) complexes. Both PNPT1 variants are within highly conserved regions and predicted to be damaging. These variants resulted in quaternary defects in the PNPase protein and a clear reduction in protein and mRNA expression of PNPT1 in patient fibroblasts compared with control cells. Protein analysis of the OXPHOS complexes showed a significant reduction in complex I (CI), complex III (CIII) and complex IV (CIV). Enzyme activity of CI and CIV was clearly reduced in patient fibroblasts compared with controls along with a 33% reduction in total mitochondrial protein synthesis. In vitro rescue experiments, using exogenous expression of wild-type PNPT1 in patient fibroblasts, ameliorated the deficiencies in the OXPHOS complex protein expression, supporting the likely pathogenicity of these variants and the importance of WES in efficiently identifying rare genetic disease genes.

Down syndrome is the most common chromosomal disorder affecting the nervous system in humans. To date, investigations of neural anomalies in Down syndrome have focused on the central nervous system, although dysfunction of the peripheral nervous system is a common manifestation. The molecular and cellular bases underlying peripheral abnormalities have remained undefined. Here, we report the developmental loss of sympathetic innervation in human Down syndrome organs and in a mouse model. We show that excess regulator of calcineurin 1 (RCAN1), an endogenous inhibitor of the calcineurin phosphatase that is triplicated in Down syndrome, impairs neurotrophic support of sympathetic neurons by inhibiting endocytosis of the nerve growth factor (NGF) receptor, TrkA. Genetically correcting RCAN1 levels in Down syndrome mice markedly improves NGF-dependent receptor trafficking, neuronal survival and innervation. These results uncover a critical link between calcineurin signalling, impaired neurotrophin trafficking and neurodevelopmental deficits in the peripheral nervous system in Down syndrome., Down syndrome is associated with both central and peripheral nervous system dysfunction. Here, the authors report reduced sympathetic neural innervation in human Down syndrome tissues and a mouse model, and propose a role for RCAN1 trisomy in disrupted NGF receptor trafficking and neurotrophic support.

Identifying the causative variant from among the thousands identified by whole-exome sequencing or whole-genome sequencing is a formidable challenge. To make this process as efficient and flexible as possible, we have developed a Variant Analysis Module coupled to our previously described Web-based phenotype intake tool, PhenoDB (http://researchphenodb.net and http://phenodb.org). When a small number of candidate-causative variants have been identified in a study of a particular patient or family, a second, more difficult challenge becomes proof of causality for any given variant. One approach to this problem is to find other cases with a similar phenotype and mutations in the same candidate gene. Alternatively, it may be possible to develop biological evidence for causality, an approach that is assisted by making connections to basic scientists studying the gene of interest, often in the setting of a model organism. Both of these strategies benefit from an open access, online site where individual clinicians and investigators could post genes of interest. To this end, we developed GeneMatcher (http://genematcher.org), a freely accessible Website that enables connections between clinicians and researchers across the world who share an interest in the same gene(s).

Objective. Aggressive chemotherapy and radiotherapy or radical oncological surgery in young women with cancer has greatly enhanced these patients' life expectancy, but these treatments often cause infertility or premature ovarian failure due to a massive destruction of the ovarian reserve. The objective of this review is to discuss the effect of the various cancer treatments on fertility and present the various fertility sparing operations and fertility preservation strategies. Method. An extensive survey of the most up-to-date literature was performed. Results. This review discusses the impact of current cancer treatment on fertility potential and the various surgical and assisted-reproduction innovations available today for the most common cancers in young women. Although the ability to retain reproductive potential is becoming a major quality-of-life factor in an increasing number of young female cancer survivors, they are still being poorly counseled with regard to the negative impact of the treatment on their fertility and on their options for fertility preservation. Conclusion. As the emerging discipline of fertility preservation is steadily attracting increasing interest, developments in the near future promise to be very exciting. However, in everyday routine work, better interdisciplinary cooperation between gynecological and pediatric oncologists, surgeons, immunologists, and endocrinologists is necessary so that individualized options for fertility preservation can be offered in advance of surgical procedures or cancer treatments.

There has been much controversy regarding the origins of the natural polycyclic aromatic hydrocarbon (PAH) and chemical biomarker background in Prince William Sound (PWS), Alaska, site of the 1989 Exxon Valdez oil spill. Different authors have attributed the sources to various proportions of coal, natural seep oil, shales, and stream sediments. The different probable bioavailabilities of hydrocarbons from these various sources can affect environmental damage assessments from the spill. This study compares two different approaches to source apportionment with the same data (136 PAHs and biomarkers) and investigate whether increasing the number of coal source samples from one to six increases coal attributions. The constrained least-squares (CLS) source allocation method that fits concentrations meets geologic and chemical constraints better than partial least-squares (PLS) which predicts variance. The field data set was expanded to include coal samples reported by others, and CLS fits confirm earlier findings of low coal contributions to PWS.

Die zunehmende Inzidenz von Rotatorenmanschettendefekten (RMD) mit steigendem Alter stellt den Schulterchirurgen immer haufiger vor die Entscheidung, ob denn auch beim alteren Patienten eine Rekonstruktion sinnvoll und zu empfehlen ist. Anhand einer retrospektiven Analyse soll die Frage geklart werden, inwieweit sich die klinischen Ergebnisse nach offener Rekonstruktion eines RMD, die Defektgrose, Begleitpathologien und Redefektrate bei Patienten ab dem sechzigsten Lebensjahr von denen jungerer Patienten unterscheiden. Bei 76 Patienten mit einem Durchschnittsalter von 65 Jahren (60–78 Jahre) und bei 166 Patienten unter 60 Jahren wurde eine Rekonstruktion eines Rotatorenmanschettendefektes durchgefuhrt. Es erfolgte eine genaue Analyse aller intraoperativ erhobenen Befunde hinsichtlich der Rupturgrose, Affektionen des Acromioclavicular-Gelenks (ACG) und der langen Bizepssehne (LBS). Nach einem Follow-up von mindestens 2 Jahren wurde der Constant-Score erhoben sowie eine klinische und sonographische Nachuntersuchung durchgefuhrt. Die beiden Gruppen unterschieden sich hinsichtlich der intraoperativ gefundenen Rupturgrose (p=0,591) und der Haufigkeit kompletter LBS-Rupturen (p=0,61) sowie der Haufigkeit der sonographisch gefundenen Redefekte (p=0,341) nicht signifikant. Jedoch hatten die Patienten ab 60 Jahren mit einem durchschnittlichen alters- und geschlechtskorrigierten Constant-Score von 90% (13–126%) signifikant bessere Werte (p=0,002) als die Gruppe unter 60 Jahren mit 81,1% (15–116%). Bei den Patienten ab 60 fanden sich signifikant haufiger therapierelevante Affektionen des ACG (p

Good software cost models can significantly help software project managers. With good models, project stakeholders can make informed decisions about how to manage resources, how to control and plan the project, or how to deliver the project on time, on schedule, and on budget. Real-world data sets, such as those coming from software engineering projects, often contain noisy, irrelevant, or redundant variables. We propose that cost modelers should perform data-pruning experiments after data collection and before model building. Such pruning experiments are simple and fast.

Objective To evaluate topical interferon alfa 2b (IFNα2b) as a single therapeutic agent in the treatment of presumed recurrent corneal and conjunctival intraepithelial neoplasia. Design Noncomparative, retrospective case series. Participants Seven consecutive patients with recurrent corneal and conjunctival intraepithelial neoplasia diagnosed at the University of Minnesota from July 2000 to November 2003 were studied retrospectively. All patients had a history of histologically proven primary corneal and conjunctival intraepithelial neoplasia and were treated by surgery, cryotherapy, radiation, and/or topical mitomycin C before recurrence. Intervention Patients with a clinical diagnosis of recurrent corneal and conjunctival intraepithelial neoplasia were treated with recombinant topical IFNα2b drops (1 million IU/ml) 4 times daily until lesion resolution was noted. Main outcome measures A review of medical records was performed to assess the duration of and response to treatment with topical IFNα2b, defined by clinical resolution of corneal and conjunctival intraepithelial neoplasia. Results The average age of the 7 patients at the initiation of topical IFNα2b treatment for presumed recurrent corneal and conjunctival intraepithelial neoplasia was 68.7 years (range, 54–88). Six of 7 patients had successful treatment of recurrent corneal and conjunctival intraepithelial neoplasia lesions with topical IFNα2b treatment. The average length of IFNα2b treatment to resolution of recurrent corneal and conjunctival intraepithelial neoplasia was 14.5 weeks (range, 5–24). After treatment with topical IFNα2b for recurrent corneal and conjunctival intraepithelial neoplasia, 2 patients had another recurrence of corneal and conjunctival intraepithelial neoplasia, noted at 1 year and 2 months, respectively. The average post-treatment follow-up was 11.7 months (range, 8–17) after the resolution of recurrent corneal and conjunctival intraepithelial neoplasia. No side effects of treatment were noted in any patient. Conclusions Topical IFNα2b as a single therapeutic agent is an effective treatment of presumed recurrent corneal and conjunctival intraepithelial neoplasia. It offers the benefits of topical therapy and avoids the risks of surgical or other interventions—specifically, ocular surface toxicity, cicatricial conjunctival changes, and limbal stem cell deficiency. Larger controlled studies with longer follow-up periods are recommended to confirm the long-term efficacy and safety of this topical treatment.

Purpose: HER-2 blocking strategies, for instance with trastuzumab (Herceptin®), have been successfully used in therapy of breast cancer. To study molecular mechanisms and the efficiency of HER-2 blocking therapies we established a mouse tumor model that allows switching-off of HER-2 expression in tumor tissue. Material and Methods: NIH3T3 cells conditionally expressing HER-2 by the TET-OFF system (NIH3T3-HER-2 cells) were subcutaneously injected into the dorsal skin of nude mice. These cells allowed switching-off of HER-2 expression by exposure to anhydrotetracycline. We examined the influence of HER-2 down-regulation on tumor volume of subcutaneously growing tumors in nude mice. Tumor development was studied by magnetic resonance imaging. HER-2 expression was quantified by Western Blot analysis. Results: Eight to ten days after injection of 7 × 10 6 NIH3T3-HER-2 cells small subcutaneously growing tumors became visible. A surprisingly efficient tumor remission was observed already 7 days after switching-off of HER-2 expression: mice with initial tumor volumes of 0.8, 1.2, 3.9 and 14.9 cm 3 showed a decrease in tumor volumes to 1.9, 11.8, 11.3 and 25.8%, respectively, compared to the respective volumes before anhydrotetracycline administration. In contrast, a steady increase in tumor volume was observed for mice not exposed to anhydrotetracyclin. Conclusion: Switching-off of HER-2 expression causes a strong remission already after 7 days. Interestingly, the extent of tumor remission depends on initial tumor size, whereby a stronger remission can be achieved for smaller tumors. Our data support clinical studies testing HER-2 blocking strategies as adjuvant therapy for early breast cancer.

To evaluate the sources, transport, bioremediation, fate, and effects of spilled petroleum and petroleum products, environmental studies often measure parent and alkylated polycyclic aromatic hydrocarbons (PAH), alkanes, and chemical biomarkers (e.g., triterpanes). Accurate data for low analyte concentrations are required when environmental samples contain hydrocarbons from multiple sources that need to be resolved and quantified. The accuracy and usefulness of the analyses can be improved by lowering the method detection limits (MDLs) for these compounds. Misidentification of hydrocarbon source can result when the MDLs are too high. Modifications to standard analytical methods (i.e., U.S. Environmental Protection Agency Method 8270) can lower MDLs by factors ranging from 10 to 1000. This reduction has important implications for ecological-risk assessments. Modifications having the greatest impact on the MDL include GCMS analysis in the selected-ion-monitoring mode (SIM), increased sample size, column cleanup of the extract, and decreased preinjection volume (volume of final extract prior to injection into instrument). In one study in which a benthic sediment sample was spiked with low levels of topped (heated to remove more volatile PAH that are naturally enriched in crude oil) Alaska North Slope crude, MDLs for individual PAH analytes and biomarkers were determined to be less than 0.5 ng/g (ppb) dry weight and less than 5 ppb dry weightfor individual alkanes. Similar results were obtained when the sediment was spiked with the 16 EPA priority pollutants. In addition, a method has been developed to estimate MDLs for source-specific alkylated PAH analytes and chemical biomarker compounds for which standards are not commercially available or are prohibitively expensive. These improved analytical techniques have been used to identify and quantify low levels of hydrocarbons, derived from both natural and anthropogenic sources, found in the benthic sediments of Prince William Sound, AK.

We determined the bioavailability to sediment-dwelling marine worms of polycyclic aromatic hydrocarbons (PAHs) associated with offshore sediments from 3 spill path and 3 non-spill path areas of Prince William Sound (PWS), Alaska, 12 years after the Exxon Valdez oil spill. The PAHs in sediments from 4 sites sampled in 2001 were primarily from a regional natural petrogenic background derived from organic-rich shales and natural oil seeps associated with sources southeast of PWS. Pyrogenic (combustion) PAHs, primarily from former human and industrial activities, were more abundant than petrogenic PAHs in nearshore sediments from 2 bays associated with past and current human activities. We performed sediment bioaccumulation tests with the six sediments and polychaete worms according to standard EPA protocols. All the PAHs had a very low bioavailability, as indicated by low values for biota/sediment accumulation factors (BSAFs) in the worms. Mean BSAFs for total PAHs (sum of 41 analyte groups) ranged from 0.002 to 0.009. The worms exposed to spill path and non-spill path sediments bioaccumulated small amounts of 4- and 5-ring PAHs, particularly fluoranthene and pyrene; these higher molecular weight PAHs are responsible for induction of mixed function oxygenase (MFO) activity in marine fish, birds, and mammals. These results may help to explain in part why fish from throughout PWS exhibit induced MFO activity. Elevated levels of MFO activity cannot be used as evidence of recent exposure by marine fish, birds, and mammals in the sound to Exxon Valdez oil.

Studies of records and data pertaining to anthropogenic and natural sources of petroleum, and specifically of the polycyclic aromatic hydrocarbons (PAH), have indicated a generally constant background, with episodic input spikes of bioavailable PAH to the marine environment of Prince William Sound (PWS), Alaska. The Exxon Valdez oil spill (EVOS) was one such PAH spike. However, hundreds of smaller spills, occurring prior to and since the EVOS, contribute a background of bioavailable petrogenic PAH to PWS. The widespread historical and contemporary uses of PWS by man have left chronic, sizeable, and widespread petrogenic and pyrogenic PAH fingerprints and bioavailable PAH at many locations in PWS. Evidence from mussel samples, taken both prior to and since EVOS, and from subtidal sediments, indicates that bioavailable PAH are a constant feature of the PWS system. While EVOS may continue to add some bioavailable PAH to highly localized areas, most PAH inputs to the PWS marine environment are unrelated to EVOS. Such findings indicate that biological, sublethal effects studies, which rely on tissue body burdens and biomarkers as leading indicators of continuing effects from EVOS (e.g. CYP1A-P450, etc.) may have been misinterpreted, as they are confounded by this easily detectable, significant, and continuing background of bioavailable PAH. Therefore measurements of exposure to PAH as indicating lingering effects from EVOS, 13 years after the spill, are speculative and ignore the baseline PAH from non-EVOS inputs.

The application of petroleum geochemistry to determining the fate and effects of oil spills in the marine environment requires high quality data to allow source identification through fingerprinting methods and unbiased sampling designs that allow valid comparisons to be made to detect spill related effects in the presence of other sources of environmental stress. This is particularly important in long-term studies, where sources of hydrocarbons and other pollutants unrelated to the spill event and non-spill related environmental effects become far more important in defining the environmental status of the spill zone. In studies of the Exxon Valdez oil spill, petroleum geochemistry is used to identify the many sources contributing polycyclic aromatic hydrocarbons (PAH) to the marine environment of Prince William Sound (PWS), including the Exxon Valdez oil spill, oil seep residues, particulates from eroding organic shales and coal formations, forest fire fallout, recent biogenic inputs and past human and industrial activities. A sediment quality triad-based shoreline ecology program (SEP), begun in 1990, includes a random sampling component and worst-case non-random site component that provides chemistry data through 2001 to determine the fate and bioavailability of spill oil residues on the shorelines. Environmental half-life values for the PAH at oiled sites range from 2.0 – 7.4 months for upper intertidal areas. Analysis of mussel tissue samples collected at worst-case spill locations find PAH concentrations in the same range as reference site samples. The results of concurrent sediment toxicity measurements using standard bioassays defines a dose-response relationship for total PAH concentration (TPAH) having a threshold of effect TPAH of 2,600 ng/g (dry wt.) that agrees well with the onset of sublethal ecological stress as defined by reductions in infaunal community structure parameters.

Analytical data must be reliable. Chemical fingerprinting methods, whether based on sample-specific comparisons of profiles, analyses of “diagnostic ratios,” or multivariate statistical analyses, are dependent on good quality analytical chemistry data and are thus vulnerable to data quality problems. Analytical data for the same compounds, but from different laboratories or derived by different methods, can introduce uncertainty in the comparisons. There are many chemical fingerprinting methods, which range from simple profile comparisons of individual samples to sophisticated multivariate analyses. Individual profile comparisons can be useful when the profiles are clearly different. However, the human eye has difficulty detecting subtle patterns between histogram plots of 10 PCDD/F homologs. Multivariate statistical analyses such as hierarchical cluster analysis and PCA are often used to condense and simplify a complex set of variables. These widely used and accepted techniques are scientifically defensible, although the underlying mathematics are complex.

Environmental forensics combines scientific disciplines and historical research methods to reconstruct past contaminating events, in particular, the parties involved and when and how contamination at various locations occurred. This overview of some applications of environmental forensics is based on laws and practices of the United States; however, the methods and framework should be applicable under a variety of international laws. Applications described include apportionment of responsibility for remediation of Superfund and other hazardous waste sites, site investigations for property transfer, environmental litigation between an insured party and insurers, and determination of the causes of personal injury in the context of a toxic tort.

The identification and allocation of multiple hydrocarbon sources in marine sediments is best achieved using an holistic approach. Total organic carbon (TOC) is one important tool that can constrain the contributions of specific sources and rule out incorrect source allocations in cases where inputs are dominated by fossil organic carbon. In a study of the benthic sediments from Prince William Sound (PWS) and the Gulf of Alaska (GOA), we find excellent agreement between measured TOC and TOC calculated from hydrocarbon fingerprint matches of polycyclic aromatic hydrocarbons (PAH) and chemical biomarkers. Confirmation by two such independent source indicators (TOC and fingerprint matches) provides evidence that source allocations determined by the fingerprint matches are robust and that the major TOC sources have been correctly identified. Fingerprint matches quantify the hydrocarbon contributions of various sources to the benthic sediments and the degree of hydrocarbon winnowing by waves and currents. TOC contents are then calculated using source allocation results from fingerprint matches and the TOCs of contributing sources. Comparisons of the actual sediment TOC values and those calculated from source allocation support our earlier published findings ( 5 ) that the natural petrogenic hydrocarbon background in sediments in this area comes from eroding Tertiary shales and associated oil seeps along the northern GOA coast and exclude thermally mature area coals from being important contributors to the PWS background due to their high TOC content.

Prince William Sound (PWS), Alaska has an extensive history of human and industrial activity that has produced a complex organic geochemistry record in subtidal sediments of embayments throughout the sound. In addition to contributions from recent oil spills and a regional background of natural petroleum hydrocarbons originating from active hydrocarbon systems in the northern Gulf of Alaska (GOA), pyrogenic and petrogenic PAH were, and continue to be introduced to subtidal sediments at numerous sites of past and present human activities. These sites include villages, fish hatcheries, fish camps and recreational campsites in addition to abandoned settlements, canneries, sawmills, and mines. A holistic approach is used to fingerprint and quantify hydrocarbon contributions from multiple sources in a sediment sample. It involves acquiring a comprehensive understanding of the history of the area to identify potential sources, collection of representative samples, and accurate quantitative analyses of the sourc...

AIMS To show the ability of magnetic resonance hydrometry (MRH) to quantify the pancreatic secretion after secretin stimulation in order to distinguish between physiological excretion and reduced output in chronic pancreatitis. METHODS MRH images were acquired in a 1.0-T-clinical scanner using a body-array coil and a heavily T2-weighted standard single-shot TSE sequence. Thirty-one patients (14 male/17 female) who routinely underwent ERCP for suspected choledocholithiasis (n = 22), recurring abdominal pain (n = 1), icterus (n = 6 and suspected pancreatitis (n = 2) were included. During the investigation 1 CU/kg BW secretin were administered intravenously. Secreted volume of fluid, start of secretion, achievement of a plateau of secretion and a combined score of these parameters (MRH score) were assessed and evaluated. Sensitivity and specificity were calculated for these parameters. RESULTS 27 patients had no pancreatic pathology, and four suffered from chronic pancreatitis. Patients without pancreatic disorders produced a mean pancreatic fluid volume of 183 plus minus 86 mL, whereas patients with chronic pancreatitis secreted 61 +/- 39 mL. Secretion started after a mean time of 95 +/- 94 seconds (no pancreatic impairment) and 62 +/- 13 seconds (chronic pancreatitis). The MRH score achieved a high accuracy in the detection of chronic pancreatitis. CONCLUSIONS Our study demonstrated the feasibility of measuring pancreatic output by MRH after stimulation with secretin. Moreover, a distinction between normal secretion and patients with chronic pancreatitis is possible.

Weathered oil is a term that is often used without communicating the degree of weathering and components that still remain. The subjective use of vague and often inaccurate weathering terms (i.e., lightly, moderately, heavily, or extensively weathered) often leads to misperceptions or misinformation about potential persistence and potential toxicity of oil residues observed in the environment. A semi-quantitative approach is needed for defining the stages of weathering, without adjectives, for oil released into the environment. MC252 oil from the Deepwater Horizon accident was evaluated to develop such an approach. The weathering of MC252 oil started immediately after release; during its 1,500 meter ascent to the sea surface most of the water soluble components partitioned into the water column. Once on the sea surface, the oil continued to weather via evaporation, dissolution, photo-degradation, and biodegradation. After reaching the shoreline, weathering continued and biodegradation became more pronounced. Extensively weathered and biodegraded MC252 oil samples have been collected on the shoreline and in some cases show a complete loss of resolved n-alkanes and near complete loss of PAH components, while still maintaining identifiable MC252 characteristics. At the same time that compounds have been lost due to degradation, others (e.g., some oxygenated compounds) have been formed as part of the weathering processes. The hydrocarbon chemistry data associated with more than 800 weathered MC252 oil samples were evaluated and quantitative metrics were developed to aid in defining the weathering stages. Sample GC/FID chromatograms were digitized and multiple chromatographic features (e.g., peak height to UCM height) were captured quantitatively. Together, the chemistry and chromatograms were analyzed to define seven (7) stages of weathering providing researchers with an objective means of discussing the weathering for oil after its release to the environment.

Biomimetic surfaces and materials may be utilized in biosensing applications, harnessing material properties that mimic the natural environment of a biomolecule in order to maintain its functionality, artificially create a complex that takes on the form of a biomolecular structure, or modify an environment to promote cellular affinity. Throughout the scientific literature, there are numerous mechanisms by which this concept may be accomplished. Synthetic lipid membranes, meant to mimic a cellular membrane, have been deposited onto sensor platforms for analyte detection with immobilized functional biomolecules. Natural biomolecules may also be immobilized on transducers, with care taken to protect their functionality (e.g., through polymer linkages), allowing them to operate as sensing units. Synthetic molecular constructs have been developed to mimic the activity of biomolecules. Molecularly imprinted polymers have been created, operating as artificial bioaffinity recognition sites for target molecules. Furthermore, whole cells may be immobilized onto sensing surfaces, acting as sensing units or mimics of larger tissue systems. In this chapter, the relevant literature examples are discussed, highlighting the means by which these biomimetic sensing approaches are accomplished.

The presence of polycyclic aromatic hydrocarbons (PAH) in urban sediments around the U.S. is well established. The toxic, mutagenic, and carcinogenic characteristics attributed to this class of hydrocarbons typically warrant their close monitoring, removal (e.g., dredging), or isolation (e.g., capping) in order to protect or revitalize the local urban environments. The high costs and other liabilities associated with any remedial action of urban sediments, combined with the common occurrence of multiple potentially responsible parties (PRPs) with properties bordering urban waterways, is a recipe for legal wrangling among PRPs. Environmental forensic investigations, conducted appropriately, provide the insight necessary to defensibly identify both historic and/or current, point and non-point sources of PAH to an urban water body's sediments. The results from such investigations are sufficiently robust to support technical allocation strategies for determining responsibility among PRPs involved in ...

Beginning in 1989, scientists supported by ExxonMobil conducted a number of scientific studies to assess the fate and effects of the Exxon Valdez oil spill on shorelines in Prince William Sound (PWS), Alaska. The 1990, 1991, and 1993 field programs included concurrent sediment sampling for hydrocarbon chemistry and sediment toxicity. This sediment quality assessment found that spill residues on the oiled shorelines rapidly lost toxicity through weathering. The relative amounts of naphthalenes and chrysenes in the polycyclic aromatic hydrocarbons (PAH) in the sediments were found to be good indicators of weathering and toxicity. Using a standard sediment amphipod bioassay on the field samples increased mortality above background was found at exposure levels above approximately 2,600 ng/g total PAH (TPAH) for oil that had weathered a year or more. For samples with TPAH > 2,600 ng/g, fractions of naphthalenes (R = +0.76) and chrysenes (R = −0.63) significantly correlated with amphipod mortality where samples with high mortalities (> 80%) were dominated by relatively high fractions of naphthalenes (median = 0.26), and the low mortality category (< 30%) was dominated by relatively high fractions of chrysenes (median = 0.24). The amphipod mortality data fit significantly to a logistic model. Estimated LC10 and LC50 values were approximately 4,100 and 10,750 ng/g TPAH, respectively. Sediment grain size and total organic carbon were also found to contribute to increased amphipod mortality and were covariates in the data analysis. As petroleum weathers through exposure to the environment and lighter hydrocarbon fractions are lost, the results of this study show that the Exxon Valdez spill oil rapidly lost toxicity as the fractions of chrysenes increased and fractions of naphthalenes decreased.

A shoreline ecology program was performed in Prince William Sound (PWS), Alaska in 1990 and 1991 (1 and 2 years after the Exxon Valdez oil spill, EVOS) to assess the fate and effects of the oil in the intertidal zone. Major components of the study were repeated in 1998 and 1999. This update included a sediment-sampling program at formerly oiled “worst-case” boulder/cobble (B/C) sites and randomly chosen unoiled B/C reference sites. The samples were analyzed for petroleum hydrocarbons and benthic infaunal community characteristics. This paper focuses on the results of the benthic infaunal community analysis. Analysis of Covariance (ANCOVA) was used to analyze the 1990–1999 infaunal species composition data. Very little effect of oiling was detected in either the analysis of community structure parameters or in individual species abundances. Oiling effects were detected at some sites in 1990 and 1991, but not in 1998 and 1999. Nearly all the change in intertidal community parameters between 1990 and 1999 was attributed to natural interannual variation. The composition of the intertidal community of B/C shores changed over time because of natural factors not related to the spill. A core group of species was found in each of the 4 years. This group of species represented between 9 to 30% of all species identified. Two other groups of species did not co-occur. One group was present in 1990 and 1991, but not in 1998 and 1999; the other group was present in 1998 and 1999, but not in 1990 and 1991. The progressive change in the animal community observed between 1990 and 1999 is very likely related to long-term climatic changes occurring in the study area and not the oil spill. This long-term study demonstrates the importance of study designs that allow separation of oiling effects from natural factors that can affect biological communities.

The dominant sources of the petrogenic hydrocarbon background in benthic sediments of Prince William Sound, AK (PWS), site of the 1989 Exxon-Valdez oil spill, are eroding Tertiary shales and residues of natural oil seepage. Mass balance considerations and statistical analyses of hydrocarbon fingerprints independently indicate that coal contributes generally less than 1% of the polycyclic aromatic hydrocarbons (PAH) and chemical biomarkers in this background. This is environmentally significant because of presumed differences in the bioavailability of PAH in coal, seep oil residues, and shales. Coal particles are present in PWS sediments, but their PAH and chemical biomarker contributions are overwhelmed by those of seep oil residues and organic particles from shales of low-to-high thermally maturity. In the late Tertiary or early Quaternary, the currently exposed and eroding shale formations were heated into the oil-generation window and, consequently, are now relatively rich in extractable PAH and chemical biomarkers. The exposed and eroding coals in the area, in contrast, experienced long hot burial and are now thermally overmature with respect to oil generation. The concentrations of thermally sensitive PAH and biomarker compounds in PWS sediments are not consistent with a mature coal origin but are consistent with the low-to-high maturity shales and seep oils in the area.

X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ABCD1 gene, which encodes a peroxisomal ABC half-transporter (ALDP) involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement. There is no apparent correlation between genotype and phenotype. In males, unambiguous diagnosis can be achieved by demonstration of elevated levels of VLCFA in plasma. In 15 to 20% of obligate heterozygotes, however, test results are false–negative. Therefore, mutation analysis is the only reliable method for the identification of heterozygotes. Since most X-ALD kindreds have a unique mutation, a great number of mutations have been identified in the ABCD1 gene in the last seven years. In order to catalog and facilitate the analysis of these mutations, we have established a mutation database for X-ALD ( http://www.x-ald.nl). In this review we report a detailed analysis of all 406 X-ALD mutations currently included in the database. Also, we present 47 novel mutations. In addition, we review the various X-ALD phenotypes, the different diagnostic tools, and the need for extended family screening for the identification of new patients. Hum Mutat 18:499–515, 2001. © 2001 Wiley-Liss, Inc.

α-Thalassemia double-gene deletions in cis are clinically significant because homozygosity or compound heterozygosity for such deletions leads to fetal demise or death shortly after birth. They account for the majority of cases of hydrops fetalis among couples of Southeast Asian origin. We have sequenced the −−THAI breakpoint junction in a patient and included this allele in a single-tube multiplex-PCR test for detecting common Southeast Asian α-thalassemia determinants. The assay was tested on genomic DNA samples and found to detect the −α3.7, −α4.2, −−FIL, −−SEA, and −−THAI determinants of α-thalassemia. α-Thalassemia is common throughout the tropics and subtropics and accounts for the majority of cases of hydrops fetalis among couples of Southeast Asian origin (1)(2)(3). Couples who are both carriers of a deletion that removes both the adjacent α2- and α1-globin genes on one of their chromosomes 16 (−−) are at 25% risk of having fetuses with hemoglobin (Hb) Barts hydrops fetalis syndrome. Such pregnancies are accompanied by increased risks of maternal complications [reviewed in Ref. (3)]. The −−SEA deletion is the most common double-gene deletion in cis among Southeast Asians, whereas the −−FIL and −−THAI deletions account for a smaller percentage of the double-deletion alleles (3)(4). Unlike the −−SEA deletion, the latter two deletions remove the entire α-globin gene cluster (5)(6)(7), and fetuses homozygous or compound heterozygous for the −−FIL and −−THAI deletions are thought to undergo early fetal demise and abort spontaneously. However, compound heterozygosity of −−SEA with either −−FIL or −−THAI produces Hb Barts hydrops …

This comment addresses the recent paper by Hostettler et al. proposing a new geochemical refractory PAH index, T/C (the ratio of triaromatic steranes to methyl chrysenes), and using the index to indicate that coal is the main source of the natural petrogenic hydrocarbons in marine sediments in Prince William Sound, Alaska. In response Bench et al. argue that coal is only one of several possibilities, and that measurements of vitrinite/kerogen reflectance, hydrocarbon mass balance calculations, and other molecular indicators including biomarkers demonstrate that coal is not the dominant source. The small sample of data used by Hostettler et al., evidence from vitrinite/kerogen reflectance data, beach coal, mass balance constraints, and the limitations of the T/C index are discussed. Selected molecular parameters in the sediments and in the potential sources of the hydrocarbons background are tabulated.

Polycyclic aromatic hydrocarbons (PAH) are sensitive recorders of past human activities in Prince William Sound, Alaska. In the nearshore subtidal sediments of bays, the fingerprints of the pyrogenic (combustion-derived) PAH record numerous sites of both present and historical human activities including active settlements, fish hatcheries, fish camps and recreational campsites, in addition to abandoned settlements, canneries, sawmills, and mining camps. In instances, there are high levels of PAH attributable to past human activities even though there is little remaining visual evidence of these activities on the shorelines. Forest fires are also an important source of pyrogenic PAH in subtidal sediments at certain time periods and locations and pyrogenic PAH from atmospheric fallout forms part of the regional PAH background. These pyrogenic PAH fingerprints are superimposed on a regional background of natural petroleum hydrocarbons derived from seeps in the eastern Gulf of Alaska. In isolated locations, weathered traces of the Exxon Valdez oil spill were detected as a minor part of the total PAH present from all sources.

After the March 24, 1989 grounding of the Exxon Valdez and the release of 258,000 barrels of Alaska North Slope (ANS) crude oil into the marine environment of Prince William Sound (PWS), Alaska, a number of scientific studies were conducted from 1989 to 1998 to assess the fate and effects of the spill. These included the 1990–1991 shoreline ecology program (SEP), which detected little measurable impact of the spill, except at certain heavily oiled sites. In 1998, these 1990 and 1991 studies were updated. The 1998 study found spill small remnants from originally heavily oiled sites represent a minute fraction of the total PWS shoreline area. Any isolated deposits of remaining oil residues from the spill generally were found at the top of the tidal zone and highly weathered and therefore in a form and location unavailable and non-toxic to biota. Between 1991 and 1998, the concentrations of petroleum hydrocarbons at the “worst case” sites studied decreased dramatically. The polycyclic aromatic hydrocarbon (PAH) concentrations measured at these sites in 1998 were at least three times lower than the effects range-low (ER-L) sediment toxicity threshold values of 4,022 ng/g for total PAH. Mussels sampled at heavily oiled “worst case” sites in 1998 also had dramatically lower tissue PAH concentrations compared with samples taken in 1993, indicating low bioavailability of any hydrocarbons present and thus low risk to biota. Natural interannual variability in the structure of the biological infaunal communities is the largest, most consistent signal observed in this study, not any residual oil spill effects. The results of statistical analyses of the data (ANCOVA) indicated no continuing oiling effects in 1998. Consistent differences were observed between oiled and unoiled reference sites, but they were significant in only one analysis. These differences were unrelated to differences in the total PAH present among sites. Any observed differences are more likely related to the fact these “worst case” oiled sites were not selected in an unbiased, random manner.

This study was conducted to assess the subtidal effects of the Exxon Valdez oil spill in a large embayment in Prince William Sound, AK. A stratified random-sampling design was used to compare stations in an oiled bay, the Bay of Isles, with stations in Drier Bay, a bay that received little impact from the spill. The study included sediment chemistry, benthic ecology, and bioaccumulation elements. Only the results on chemistry of the oil in the bottom sediments are reported here. Analyses of sediment samples revealed four types of polycyclic aromatic hydrocarbons (PAH) in the two bays: (1) Alaska North Slope (ANS) crude oil attributable to the spill, (2) natural oil seep-derived background, (3) pyrogenic, and (4) diagenetic. The Bay of Isles subtidal sediments contained significantly higher levels of weathered ANS-PAH attributable to the spill than did Drier Bay. However, the levels of ANS-PAH in the Bay of Isles were generally lower than those of the petrogenic background PAH naturally present in the sub...

We present the development of an electrochemical biosensor based on modified glassy carbon (GC) electrodes using hydrogel-based molecularly imprinted polymers (MIPs) has been fabricated for protein detection. The coupling of pattern recognition techniques via principal component analysis (PCA) has resulted in unique protein fingerprints for corresponding protein templates, allowing for MIP-based protein profiling. Polyacrylamide MIPs for memory imprinting of bovine haemoglobin (BHb), equine myoglobin (EMb), cytochrome C (Cyt C), and bovine serum albumin (BSA), alongside a non-imprinted polymer (NIP) control, were spectrophotometrically, and electrochemically characterised using modified GC electrodes. Rebinding capacities (Q) were revealed to be higher for larger proteins (BHb and BSA, Q ≈ 4.5) while (EMb and Cyt C, Q ≈ 2.5). Electrochemical results show that due to the selective nature of MIPs, protein arrival at the electrode via diffusion is delayed, in comparison to a NIP, by attractive selective interactions with exposed MIP cavities. However, at lower concentrations such discriminations are difficult due to low levels of MIP rebinding. PCA loading plots revealed 5 variables responsible for the separation of the proteins; Ep, Ip, E1/2 , Iat −0.8 V, �Idecay peak current to −0.8 V. Statistical symmetric measures of agreement using Cohen’s kappa coefficient (K) were revealed to be 63% for bare GC, 96% for NIP and 100% for MIP. Therefore, our results show that with the use of PCA such discriminations are achievable, also with the advantage of faster detection rates. The possibilities for this MIP technology once fully developed are vast, including uses in bio-sample clean-up or selective extraction, replacement of biological antibodies in immunoassays, as well as biosensors for medicine, food and the environment.

Advances in environmental chemistry laboratory and data interpretation techniques (i.e. chemical fingerprinting) contributed to a better understanding of the biological impact of the 1989 Exxon Valdez oil spill and the fate of the spilled oil. A review of the evolution of petroleum chemical fingerprinting techniques is presented followed by a summarization of how new approaches were used to characterize and differentiate among different petroleum sources in the Prince William Sound region after the spill. An assessment of the initial data suggested that multiple sources of polycyclic aromatic hydrocarbons (PAH) were present. These findings were further substantiated, even in samples of low part-per-billion PAH concentrations, by using refined and extended laboratory techniques including the analysis of saturate biomarkers. To interpret these mixtures of sources, fingerprint-analysis flow charts and source allocation techniques were developed and applied to the data, leading to the quantification of the spilled oil as a small increment on the natural hydrocarbon background in subtidal sediments.

We examine the impact of targeted disruption of growth hormone-releasing hormone (GHRH) in mice on longevity and the putative mechanisms of delayed aging. GHRH knockout mice are remarkably long-lived, exhibiting major shifts in the expression of genes related to xenobiotic detoxification, stress resistance, and insulin signaling. These mutant mice also have increased adiponectin levels and alterations in glucose homeostasis consistent with the removal of the counter-insulin effects of growth hormone. While these effects overlap with those of caloric restriction, we show that the effects of caloric restriction (CR) and the GHRH mutation are additive, with lifespan of GHRH-KO mutants further increased by CR. We conclude that GHRH-KO mice feature perturbations in a network of signaling pathways related to stress resistance, metabolic control and inflammation, and therefore provide a new model that can be used to explore links between GHRH repression, downregulation of the somatotropic axis, and extended longevity. DOI: http://dx.doi.org/10.7554/eLife.01098.001, eLife digest There is increasing evidence that the hormonal systems involved in growth, the metabolism of glucose, and the processes that balance energy intake and expenditure might also be involved in the aging process. In rodents, mutations in genes involved in these hormone-signaling pathways can substantially increase lifespan, as can a diet that is low in calories but which avoids malnutrition. As well as living longer, such mice also show reductions in age-related conditions such as diabetes, memory loss and cancer. Many of these effects appear to involve the actions of growth hormone. Mice with mutations that disrupt the development of the pituitary gland, which produces growth hormone, show increased longevity, as do mice that lack the receptor for growth hormone. However, these animals also show changes in a number of other hormones, making it difficult to be sure that the reduction in growth hormone signaling is responsible for their increased lifespan. Now, Sun et al. have studied mutant mice that lack a gene called GHRH, which promotes the release of growth hormone. These mice, which have normal levels of all other pituitary hormones, lived for up to 50% longer than their wild-type littermates. They were more active than normal mice and had more body fat, and showed greatly increased sensitivity to insulin. Some of the changes in these mutant mice resembled those seen in animals with a restricted calorie intake, suggesting that the same mechanisms may be implicated in both. However, Sun et al. found that caloric restriction further increased the lifespans of their GHRH knockout mice, indicating that at least some of the effects of caloric restriction are independent of disrupted growth hormone signaling. The results of this study are an important step forward for understanding how growth hormone signaling and caloric restriction regulate aging, both individually and in combination. The GHRH knockout mice are likely to become an important model system for studying these processes and for understanding the complex interactions between diet and hormonal pathways. DOI: http://dx.doi.org/10.7554/eLife.01098.002

A realistic understanding of contaminant sources is required to set appropriate control policy. Forensic chemical methods can be powerful tools in source characterization and identification, but they require a multiple-lines-of-evidence approach. Atmospheric receptor models, such as the US Environmental Protection Agency (USEPA)'s chemical mass balance (CMB), are increasingly being used to evaluate sources of pyrogenic polycyclic aromatic hydrocarbons (PAHs) in sediments. This paper describes the assumptions underlying receptor models and discusses challenges in complying with these assumptions in practice. Given the variability within, and the similarity among, pyrogenic PAH source types, model outputs are sensitive to specific inputs, and parsing among some source types may not be possible. Although still useful for identifying potential sources, the technical specialist applying these methods must describe both the results and their inherent uncertainties in a way that is understandable to nontechnical policy makers. The authors present an example case study concerning an investigation of a class of parking-lot sealers as a significant source of PAHs in urban sediment. Principal component analysis is used to evaluate published CMB model inputs and outputs. Targeted analyses of 2 areas where bans have been implemented are included. The results do not support the claim that parking-lot sealers are a significant source of PAHs in urban sediments.

We have previously linked aging, carcinogenesis, and de novo methylation within the promoter of the estrogen receptor (ER) gene in human colon. We now examine the dynamics of this process for the imprinted gene for insulin-like growth factor II (IGF2). In young individuals, the P2-4 promoters of IGF2 are methylated exclusively on the silenced maternal allele. During aging, this promoter methylation becomes more extensive and involves the originally unmethylated allele. Most adult human tumors, including colon, breast, lung, and leukemias, exhibit increased methylation at the P2-4 IGF2 promoters, suggesting further spreading during the neoplastic process. In tumors, this methylation is associated with diminished or absent IGF2 expression from the methylated P3 promoter but maintained expression from P1, an upstream promoter that is not contained within the IGF2 CpG island. Our results demonstrate a remarkable evolution of methylation patterns in the imprinted promoter of the IGF2 gene during aging and carcinogenesis, and provide further evidence for a potential link between aberrant methylation and diseases of aging.

A natural regional petroleum hydrocarbon background has been identified in the subtidal sediments of Prince William Sound that is readily distinguished from Exxon Valdez spill oil by chemical fingerprinting methods. This hydrocarbon background is derived from natural petroleum seeps in the eastern Gulf of Alaska. The Alaska Coastal Current carries fine-grained sediments and associated hydrocarbons from seep areas to the east into Prince William Sound, where they are deposited on the seafloor. The analysis of age-dated sediment cores indicates that this process has been going on for the past 160 years, and probably for many thousands of years. In addition, results of a stratified random study of nearshore subtidal sediments conducted in 1990 show that this is a general phenomenon throughout the sound and is significant even in shallow water (3 to 30 m). For example, oleanane, a saturate petroleum biomarker found in Prince William Sound prespill background petroleum and seep sources but not in Exxon Valdez petroleum, is present in subtidal sediment samples from locations throughout the sound. This supports the conclusion that seep areas to the east are major sediment sources for the sound. Moreover, polycyclic aromatic hydrocarbon mixing model calculations show that, although Exxon Valdez spill-oil residues are present in nearshore subtidal sediments, they generally form a small increment on the natural background. The recognition of preexisting natural and anthropogenic hydrocarbon sources in a spill area is a fundamentally important component of any natural resource damage assessment.

The grounding of the Exxon Valdez on March 24, 1989, released about 41 million L of crude oil into the waters of Prince William Sound, Alaska, USA, and oiled about 16% of the Prince William Sound shoreline to various degrees. Although winter storms, cleanups, and natural biodegradation have removed the majority of the oil on the shorelines, some residual oil still remains trapped in sediments immediately below mussel beds. This oil was protected from wave action by the dense covering of mussels. Field surveys found that mussels in such beds constituted less than 3% of the mussels available for foraging in two areas that had been extensively oiled in 1989. Levels of polycyclic aromatic hydrocarbons (PAHs) in these mussels were also measured. Mean PAH concentrations in mussel tissues ranged between 20 and 4,000 ng/g dry weight and in sediments between 20 and 26,000 ng/g dry weight. Assuming that the species considered most at risk (i.e., harlequin ducks, black oystercatchers, and sea otters) consumed the mussel proportion of their diets exclusively from such beds (at either the median or 95th percentile of mussel tissue PAH concentration), the estimated PAH dosage they would receive was one to three orders of magnitude below doses known to cause sublethal effects in surrogate species. Considering the low frequency of mussel beds with residual oil, the patchy distribution of remaining weathered oil residues, and the relatively low PAH concentrations in the mussels, the risk of quantifiable injury at the level of an individual bird or otter, or at the population level, is minimal. Furthermore, based on a review of the mussel PAH data in Prince William Sound, the risk to wildlife has been minimal since 1990, 1 year after the spill.