Oil biodegradation and bioremediation: A tale of the two worst spills in U.S. history

The devastating environmental impacts of the Exxon Valdez spill in 1989 and its media notoriety made it a frequent comparison to the BP Deepwater Horizon spill in the popular press in 2010, even though the nature of the two spills and the environments impacted were vastly different. Fortunately, unlike higher organisms that are adversely impacted by oil spills, microorganisms are able to consume petroleum hydrocarbons. These oil degrading indigenous microorganisms played a significant role in reducing the overall environmental impact of both the Exxon Valdez and BP Deepwater Horizon oil spills

The rehabilitation enhancing aging through connected health (REACH) study: study protocol for a quasi-experimental clinical trial

Background: Mobility limitations among older adults increase the risk for disability and healthcare utilization. Rehabilitative care is identified as the most efficacious treatment for maintaining physical function. However, there is insufficient evidence identifying a healthcare model that targets prevention of mobility decline among older adults. The objective of this study is to evaluate the preliminary effectiveness of a physical therapy program, augmented with mobile tele-health technology, on mobility function and healthcare utilization among older adults. Methods: This is a quasi-experimental 12-month clinical trial conducted within a metropolitan-based healthcare system in the northeastern United States. It is in parallel with an existing longitudinal cohort study evaluating mobility decline among community-dwelling older adult primary care patients over one year. Seventy-five older adults (≥ 65–95 years) are being recruited using identical inclusion/exclusion criteria to the cohort study. Three aims will be evaluated: the effect of our program on 1) physical function, 2) healthcare utilization, and 3) healthcare costs. Changes in patient-reported function over 1 year in those receiving the intervention (aim 1) will be compared to propensity score matched controls (N = 150) from the cohort study. For aims 2 and 3, propensity scores, derived from logistic regression model that includes demographic and diagnostic information available through claims and enrollment information, will be used to match treatment and control patients in a ratio of 1:2 or 1:3 from a Medicare Claims Registry derived from the same geographic region. The intervention consists of a one-year physical therapy program that is divided between a combination of outpatient and home visits (6–10 total visits) and is augmented on a computerized tablet using of a commercially available application to deliver a progressive home-based exercise program emphasizing lower-extremity function and a walking program. Discussion Incorporating mobile health into current healthcare models of rehabilitative care has the potential to decrease hospital visits and provide a longer duration of care. If the hypotheses are supported and demonstrate improved mobility and reduced healthcare utilization, this innovative care model would be applicable for optimizing the maintenance of functional independence among community-dwelling older adults. Trial registration ClinicalTrial.gov Identifier: NCT02580409 (Date of registration October 14, 2015)

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma

Synovial sarcoma tumours contain a characteristic fusion protein, SS18-SSX, which drives disease development. Targeting oncogenic fusion proteins presents an attractive therapeutic opportunity. However, SS18-SSX has proven intractable for therapeutic intervention. Using a domain-focused CRISPR screen we identified the bromodomain of BRD9 as a critical functional dependency in synovial sarcoma. BRD9 is a component of SS18-SSX containing BAF complexes in synovial sarcoma cells; and integration of BRD9 into these complexes is critical for cell growth. Moreover BRD9 and SS18-SSX co-localize extensively on the synovial sarcoma genome. Remarkably, synovial sarcoma cells are highly sensitive to a novel small molecule degrader of BRD9, while other sarcoma subtypes are unaffected. Degradation of BRD9 induces downregulation of oncogenic transcriptional programs and inhibits tumour progression in vivo. We demonstrate that BRD9 supports oncogenic mechanisms underlying the SS18-SSX fusion in synovial sarcoma and highlight targeted degradation of BRD9 as a potential therapeutic opportunity in this disease

Frequent HPV-independent p16/INK4A overexpression in head and neck cancer

Objectives p16INK4A (p16) is the most widely used clinical biomarker for Human Papillomavirus (HPV) in head and neck squamous cell cancer (HNSCC). HPV is a favourable prognostic marker in HNSCC and is used for patient stratification. While p16 is a relatively accurate marker for HPV within the oropharynx, recent reports suggest it may be unsuitable for use in other HNSCC subsites, where a smaller proportion of tumors are HPV-driven. Materials and methods We integrated reverse phase protein array (RPPA) data for p16 with HPV status based on detection of viral transcripts by RNA-seq in a set of 210 HNSCCs profiled by The Cancer Genome Atlas project. Samples were queried for alterations in CDKN2A, and other pathway genes to investigate possible drivers of p16 expression. Results While p16 levels as measured by RPPA were significantly different by HPV status, there were multiple HPV (?) samples with similar expression levels of p16 to HPV (+) samples, particularly at non-oropharyngeal subsites. In many cases, p16 overexpression in HPV (?) tumors could not be explained by mutation or amplification of CDKN2A or by RB1 mutation. Instead, we observed enrichment for inactivating mutations in the histone H3 lysine 36 methyltransferase, NSD1 in HPV (?)/p16-high tumors. Conclusions RPPA data suggest high p16 protein expression in many HPV (?) non-oropharyngeal HNSCCs, limiting its potential utility as an HPV biomarker outside of the oropharynx. HPV-independent overexpression of wild-type p16 in non-oropharyngeal HNSCC may be linked to global deregulation of chromatin state by inactivating mutations in NSD1

Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill

Conceived and designed the experiments: MJB RJM BM PAS. Performed the experiments: MJB RJM SR JP YMP LMT JDVN. Analyzed the data: MJB RJM YMP LMT GLA TCH JDVN JZ PAS. Contributed reagents/materials/analysis tools: GLA TCH JZ BM PAS. Wrote the paper: MJB RJM PAS.Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems.Yeshttp://www.plosone.org/static/editorial#pee

NOAA's status and trends mussel watch program: Chlorinated pesticides and PCBs in oysters ( Crassostrea virginica) and sediments from the Gulf of Mexico, 1986–1987

Chlorinated pesticides and PCBs were analyzed in more than 590 oyster and sediment samples collected during 1986 and 1987, the first 2 years of the NOAA's Status and Trends Mussel Watch Program established to monitor the current status and temporal trends of these contaminants in the Gulf of Mexico. Chlorinated hydrocarbons in oysters and sediments presented similar distribution patterns; however, their concentrations in oysters were several times higher than the concentration detected in the surrounding sediments. Alpha-chlordane, trans-nonachlor and dieldrin were the most abundant non-DDT pesticides in both types of sample. The major fraction of DDT related compounds measured in oysters and sediments was DDD. Based on average PCB concentrations, penta-, hexa-, and tetrachlorobiphenyls were preferentially accumulated by oysters as compared to the average sediment composition. Although this study was designed to avoid known point-sources of contaminant inputs, the measured concentrations were, in general, within the range of concentrations previously reported for the Gulf of Mexico. After the first 2 years of this program, the geographical distribution of chlorinated hydrocarbons in oysters and sediments is well defined. In contrast, the temporal trends at the different sites are not clear. Continued sampling will allow the identification of long-term trends in concentrations of chlorinated hydrocarbons in the Gulf of Mexico

What Caused the August 2002 Catastrophic Floods in Central Europe?

The catastrophic August 2002 floods in central Europe followed very intense rains over a span of several days, reported over a large region. On Aug. 12 meteorological stations over an elongated swath, from the vicinity of Saltzburg (Austria) in the south to the vicinity of Berlin in the north, reported precipitation exceeding 100 mm/day. Synoptic analysis points to a jet streak in the mid-Atlantic. moving eastward, which reached Spain on about 9th of August. An understanding of the mechanism that ultimately produced the unprecedented rains was derived conveniently from the GEOS 3 Model developed at NASA Goddard Space Flight Center. Examining the scenarios of omega, we observe on Aug. 10, OOZ, a center of ascending vertical motions, stronger than 0.6 Pa/s at the 700 hPa level over the western Mediterranean. Advecting moist and warm air to higher levels from the near-ocean level, the center moved eastward, reaching the northern Adriatic on Aug. 11, OOZ, then continuing northeast to the regions where most intense precipitation was reported on Aug. 12. The omega at 850 hPa shows a closely similar pattern but especially interesting is the 850 omega pattern on Aug. 12, 12Z, which shows descending motions stronger than 0.4 Pa/s over the eastern Po Valley (northern Italy), and an elongated region of ascending motions stronger than 1.0 Pa/s coinciding in extent with the extreme-precipitation region on that day. At that time, the cyclone which formed over the Po Valley, was centered on eastern Czech Republic, producing on its western side these strong ascending motions over the precipitation region. The pattern of the surface-pressure lows provides further insight into the processes, and specifically, the Aug. 12,06Z map, shows a 996 mb low over the western Czech Republic. The flooding following the extreme rains was acerbated by the fact that river-channels were made narrower over the recent decades by the urbanization of river banks