The Effect of Dispersed Oil on the Calcification Rate of the Reef-Building Coral Diploria Strigosa

Hermatypic corals represent environmentally and economically important components of the reef ecosystem. Oil spills and clean-up operations in reef areas are potential sources of pollution impact. This paper presents an evaluation of the calcification rate of specimens of the reef-building coral Diploria strigosa in response to 24 hour treatments of chemically dispersed oil at concentrations of 20 ppm. The concentrations and durations were chosen to represent a scenario of a short-term oil spill treated with dispersant passing over a coral reef. Calcification rates were determined by the buoyant weight technique at several day intervals for up to 29 days following treatment. Results from laboratory experiments (Winter and Summer) conducted in a flow-through seawater system indicate that treated corals, both in comparison to untreated controls as well as to their pretreatment rates, experienced no depression in calcification. In contrast, a possible short-term enhancement of calcification for the treated corals was observed

The Effects of Oil and Oil Dispersants on the Skeletal Growth of the Hermatypic Coral Diploria strigosa

Specimens of the hermatypic coral species Diploria strigosa were exposed to various concentrations (1–50 ppm) of oil or oil plus dispersant for 6–24 h periods in four laboratory and two field experiments. After dosing, corals were transplanted to, or left in, the field and recollected approximately one year later for extension (linear) growth analysis by the alizarin stain method. The experiments were designed to assess the long-term effects of brief low-level concentrations of chemically dispersed oil and oil alone on corals in a situation, for example, where an oil slick (treated and non-treated with dispersants) passes over a reef. No significant differences between extension growth parameters (Septa increase, Columella increase) and a calical shape parameter (New Endotheca Length) of treated corals versus controls were found in any of the experiments. In two summer experiments calical relief (Fossa length) was found to be depressed in corals of some of the experimental treatments

Behavioural Effects of Chemically Dispersed Oil and Subsequent Recovery in Diploria strigosa (Dana)

Survival and behaviour of the hermatypic coral Diploria strigosa was studied during 6–24 h doses with water-accomodated fractions of chemically dispersed crude oil, and for a subsequent recovery period of 1 month. Experiments utilized a flow-through laboratory dosing procedure and incorporated petroleum hydrocarbon measurements in order to simulate a major but short-term oil spill in shallow subtidal benthic reef environments. Chemically dispersed oil treatments consisted of Arabian Light Crude oil with Corexit 9527 or BP1100WD at 1–20 ppm concentrations of oil. In general, effects observed were sub-lethal, temporary, and associated with the highest concentrations tested. Responses to the presence of dispersed oil at 20ppm for 24 h included mesenterial filament extrusion, extreme tissue contraction, tentacle retraction and localized tissue rupture. The nature and severity of reactions during the dosing phase varied between colonies and treatments, but colonies typically resumed normal behaviour within 2 h to 4 d of the recovery period. It therefore seems unlikely that observed biological effects would impair long-term viability

Integrated nutritional intervention in the elderly after hip fracture. A process evaluation

SummaryBackground & aimsWithin a multicentre randomized controlled trial aimed at improving the nutritional status and increase the speed of recovery of elderly hip fracture patients, we performed a process evaluation to investigate the feasibility of the intervention within the present Dutch health care system.MethodsPatients in the intervention group received nutritional counseling during 10 contacts. Oral nutritional supplements were advised as needed until three months after hip fracture surgery. The intervention was evaluated with respect to dieticians’ adherence to the study protocol, content of nutritional counseling, and patients’ adherence to recommendations given.ResultsWe included 66 patients (mean age of 76, range 55–92 years); 74% women. Eighty-three percent of patients received all 10 contacts as planned, but in 62% of the patients one or more telephone calls had to be replaced by face to face contacts. Nutritional counseling was complete in 91% of contacts. Oral nutritional supplementation was needed for a median period of 76 days; 75% of the patients took the oral nutritional supplements as recommended.ConclusionsNutritional counseling in elderly hip fracture patients through face to face contacts and telephone calls is feasible. However, individual tailoring of the intervention is recommended. The majority of hip fracture patients needed >2 months oral nutritional supplements to meet their nutritional requirements.The trial was registered at clincialtrails.gov as NCT00523575

The Feasibility of High-Resolution Peripheral Quantitative Computed Tomography (HR-pQCT) in Patients with Suspected Scaphoid Fractures

Introduction: Diagnosing scaphoid fractures remains challenging. High-resolution peripheral quantitative computed tomography (HR-pQCT) might be a potential imaging technique, but no data are available on its feasibility to scan the scaphoid bone in vivo. Methodology: Patients (≥18 years) with a clinically suspected scaphoid fracture received an HR-pQCT scan of the scaphoid bone (three 10.2-mm stacks, 61-μm voxel size) with their wrist immobilized with a cast. Scan quality assessment and bone contouring were performed using methods originally developed for HR-pQCT scans of radius and tibia. The contouring algorithm was applied on coarse hand-drawn pre-contours of the scaphoid bone, and the resulting contours (AUTO) were manually corrected (sAUTO) when visually deviating from bone margins. Standard morphologic analyses were performed on the AUTO- and sAUTO-contoured bones. Results: Ninety-one patients were scanned. Two out of the first five scans were repeated due to poor scan quality (40%) based on standard quality assessment during scanning, which decreased to three out of the next 86 scans (3.5%) when using an additional thumb cast. Nevertheless, after excluding one scan with an incompletely scanned scaphoid bone, post hoc grading revealed a poor quality in 14.9% of the stacks and 32.9% of the scans in the remaining 85 patients. After excluding two scans with contouring problems due to scan quality, bone indices obtained by AUTO- and sAUTO-contouring were compared in 83 scans. All AUTO-contours were manually corrected, resulting in significant but small differences in densitometric and trabecular indices (<1.0%). Conclusions: In vivo HR-pQCT scanning of the scaphoid bone is feasible in patients with a clinically suspected scaphoid fracture when using a cast with thumb part. The proportion of poor-quality stacks is similar to radius scans, and AUTO-contouring appears appropriate in good- and poor-quality scans. Thus, HR-pQCT may be promising for diagnosis of and microarchitectural evaluations in suspected scaphoid fractures

Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms

Current limitations in technology have prevented an extensive analysis of the connections among neurons, particularly within nonmammalian organisms. We developed a transsynaptic viral tracer originally for use in mice, and then tested its utility in a broader range of organisms. By engineering the vesicular stomatitis virus (VSV) to encode a fluorophore and either the rabies virus glycoprotein (RABV-G) or its own glycoprotein (VSV-G), we created viruses that can transsynaptically label neuronal circuits in either the retrograde or anterograde direction, respectively. The vectors were investigated for their utility as polysynaptic tracers of chicken and zebrafish visual pathways. They showed patterns of connectivity consistent with previously characterized visual system connections, and revealed several potentially novel connections. Further, these vectors were shown to infect neurons in several other vertebrates, including Old and New World monkeys, seahorses, axolotls, and Xenopus. They were also shown to infect two invertebrates, Drosophila melanogaster, and the box jellyfish, Tripedalia cystophora, a species previously intractable for gene transfer, although no clear evidence of transsynaptic spread was observed in these species. These vectors provide a starting point for transsynaptic tracing in most vertebrates, and are also excellent candidates for gene transfer in organisms that have been refractory to other methods

Olfactory Jump Reflex Habituation in Drosophila and Effects of Classical Conditioning Mutations

Habituation is a nonassociative learning mechanism, in which an initial response toward repeated stimuli gradually wanes. This is amongst the simplest and most widespread forms of behavioral plasticity. So far, neither the underlying molecular mechanisms nor the precise neural networks of habituation are well understood. We have developed a novel paradigm to quantify habituation of the olfactory jump reflex in Drosophila. We present data demonstrating several behavioral properties of this phenomenon, generally observed in other species. We also show that the dunce and rutabaga memory mutants behave abnormally in this assay, suggesting that this assay might be used in behavioral screens for new mutants with defects in this simpler form of behavioral plasticity

Cryptic Transcription Mediates Repression of Subtelomeric Metal Homeostasis Genes

Nonsense-mediated mRNA decay (NMD) prevents the accumulation of transcripts bearing premature termination codons. Here we show that Saccharomyces cerevisiae NMD mutants accumulate 5′–extended RNAs (CD-CUTs) of many subtelomeric genes. Using the subtelomeric ZRT1 and FIT3 genes activated in response to zinc and iron deficiency, respectively, we show that transcription of these CD-CUTs mediates repression at the bona fide promoters, by preventing premature binding of RNA polymerase II in conditions of metal repletion. Expression of the main ZRT1 CD-CUT is controlled by the histone deacetylase Rpd3p, showing that histone deacetylases can regulate expression of genes through modulation of the level of CD-CUTs. Analysis of binding of the transcriptional activator Zap1p and insertion of transcriptional terminators upstream from the Zap1p binding sites show that CD-CUT transcription or accumulation also interferes with binding of the transcriptional activator Zap1p. Consistent with this model, overexpressing Zap1p or using a constitutively active version of the Aft1p transcriptional activator rescues the induction defect of ZRT1 and FIT3 in NMD mutants. These results show that cryptic upstream sense transcription resulting in unstable transcripts degraded by NMD controls repression of a large number of genes located in subtelomeric regions, and in particular of many metal homeostasis genes

The CCR4-NOT Complex Physically and Functionally Interacts with TRAMP and the Nuclear Exosome

BACKGROUND: Ccr4-Not is a highly conserved multi-protein complex consisting in yeast of 9 subunits, including Not5 and the major yeast deadenylase Ccr4. It has been connected functionally in the nucleus to transcription by RNA polymerase II and in the cytoplasm to mRNA degradation. However, there has been no evidence so far that this complex is important for RNA degradation in the nucleus. METHODOLOGY/PRINCIPAL FINDINGS: In this work we point to a new role for the Ccr4-Not complex in nuclear RNA metabolism. We determine the importance of the Ccr4-Not complex for the levels of non-coding nuclear RNAs, such as mis-processed and polyadenylated snoRNAs, whose turnover depends upon the nuclear exosome and TRAMP. Consistently, mutation of both the Ccr4-Not complex and the nuclear exosome results in synthetic slow growth phenotypes. We demonstrate physical interactions between the Ccr4-Not complex and the exosome. First, Not5 co-purifies with the exosome. Second, several exosome subunits co-purify with the Ccr4-Not complex. Third, the Ccr4-Not complex is important for the integrity of large exosome-containing complexes. Finally, we reveal a connection between the Ccr4-Not complex and TRAMP through the association of the Mtr4 helicase with the Ccr4-Not complex and the importance of specific subunits of Ccr4-Not for the association of Mtr4 with the nuclear exosome subunit Rrp6. CONCLUSIONS/SIGNIFICANCE: We propose a model in which the Ccr4-Not complex may provide a platform contributing to dynamic interactions between the nuclear exosome and its co-factor TRAMP. Our findings connect for the first time the different players involved in nuclear and cytoplasmic RNA degradation

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

RNA polymerase II synthesizes a diverse set of transcripts including both protein-coding and non-coding RNAs. One major difference between these two classes of transcripts is the mechanism of termination. Messenger RNA transcripts terminate downstream of the coding region in a process that is coupled to cleavage and polyadenylation reactions. Non-coding transcripts like Saccharomyces cerevisiae snoRNAs terminate in a process that requires the RNA–binding proteins Nrd1, Nab3, and Sen1. We report here the transcriptome-wide distribution of these termination factors. These data sets derived from in vivo protein–RNA cross-linking provide high-resolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3′ antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link efficiently to many expected non-coding RNAs but does cross-link to the 3′ end of most pre–mRNA transcripts, suggesting an extensive role in mRNA 3′ end formation and/or termination