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PubMed2004

Migration of the plastid genome to the nucleus in a peridinin dinoflagellate.

Dinoflagellate algae are important primary producers and of significant ecological and economic impact because of their ability to form "red tides". They are also models for evolutionary research because of an unparalleled ability to capture photosynthetic organelles (plastids) through endosymbiosis. The nature and extent of the plastid genome in the dominant perdinin-containing dinoflagellates remain, however, two of the most intriguing issues in plastid evolution. The plastid genome in these taxa is reduced to single-gene minicircles encoding an incomplete (until now 15) set of plastid proteins. The location of the remaining photosynthetic genes is unknown. We generated a data set of 6,480 unique expressed sequence tags (ESTs) from the toxic dinoflagellate Alexandrium tamarense (for details, see the Experimental Procedures in the Supplemental Data) to find the missing plastid genes and to understand the impact of endosymbiosis on genome evolution. Here we identify 48 of the non-minicircle-encoded photosynthetic genes in the nuclear genome of A. tamarense, accounting for the majority of the photosystem. Fifteen genes that are always found on the plastid genome of other algae and plants have been transferred to the nucleus in A. tamarense. The plastid-targeted genes have red and green algal origins. These results highlight the unique position of dinoflagellates as the champions of plastid gene transfer to the nucleus among photosynthetic eukaryotes.

Amino Acid Sequence↗
PubMed2005

Organization of the genome and gene expression in a nuclear environment lacking histones and nucleosomes: the amazing dinoflagellates.

Dinoflagellates are fascinating protists that have attracted researchers from different fields. The free-living species are major primary producers and the cause of harmful algal blooms sometimes associated with red tides. Dinoflagellates lack histones and nucleosomes and present a unique genome and chromosome organization, being considered the only living knockouts of histones. Their plastids contain genes organized in unigenic minicircles. Basic cell structure, biochemistry and molecular phylogeny place the dinoflagellates firmly among the eukaryotes. They have G1-S-G2-M cell cycles, repetitive sequences, ribosomal genes in tandem, nuclear matrix, snRNAs, and eukaryotic cytoplasm, whereas their nuclear DNA is different, from base composition to chromosome organization. They have a high G + C content, highly methylated and rare bases such as 5-hydroxymethyluracil (HOMeU), no TATA boxes, and form distinct interphasic dinochromosomes with a liquid crystalline organization of DNA, stabilized by metal cations and structural RNA. Without histones and with a protein:DNA mass ratio (1:10) lower than prokaryotes, they need a different way of packing their huge amounts of DNA into a functional chromatin. In spite of the high interest in the dinoflagellate system in genetics, molecular and cellular biology, their analysis until now has been very restricted. We review here the main achievements in the characterization of the genome, nucleus and chromosomes in this diversified phylum. The recent discovery of a eukaryotic structural and functional differentiation in the dinochromosomes and of the organization of gene expression in them, demonstrate that in spite of the secondary loss of histones, that produce a lack of nucleosomal and supranucleosomal chromatin organization, they keep a functional nuclear organization closer to eukaryotes than to prokaryotes.

Animals↗
PubMed2004

Tsunami hazards in Europe.

Tsunami represents one of the most potentially serious forms of coastal flood risk. Although much is known on the recorded history of tsunamis for given areas of the world, very little information is available on the occurrence of palaeotsunamis during prehistory. This is of fundamental importance in calculating tsunami flood risk for any given coastal area. Given sufficient information on past tsunami activity for a particular coastal area, the numerical calculation of aggregate coastal flood risk (including tsunami) for a coastal area is very difficult to estimate since one needs also to take into account the risk of a tsunami and a storm surge taking place simultaneously during a high tide. Estimates of coastal flood risk also need to consider future changes in relative sea level caused by the combined effects of global climate change and vertical movements of the lithosphere.

Disasters↗
PubMed2005

Freshwater discharge from the drainage basin to the Venice Lagoon (Italy).

The twelve major tributaries of the Venice Lagoon (accounting for the 97% of the inputs from the drainage basin) were monitored in the framework of the DRAIN project (1998-2000) in order to obtain a detailed knowledge on the hydrological regimes and to measure the mean annual freshwater discharge from surface runoff. The study represents an essential step in the estimate of the pollutant load delivered to the lagoon that must necessarily be based on a solid understanding of the fluxes of material out of the drainage basin. Due to the influence of the tide in the majority of the gauging sections, a specific methodology for the measurement of the discharge was developed. The main results of the study are described, underlining the differences in the regime of the investigated streams. A rainfall-runoff analysis evidenced the different characteristics of the monitored tributaries, in terms of specific hydrological features, morphology of the individual sub-basins, management of the water resource and spatial distribution of rainfall. An estimate of the maximum peak discharge from the drainage basin is finally obtained from data of an extreme flood event occurred in November 1999.

Cities↗
PubMed2005

Butyltins in the sediments of Kochi and Mumbai harbours, west coast of India.

Surface sediment samples were collected from various locations in the Mumbai and Kochi harbours, west coast of India, to assess the presence of butyltin compounds. Tributyltin (TBT) and dibutyltin (DBT) varied from 16 to 16,816 ng/g dry wt. and from undetected to 469 ng/g dry wt., respectively, of the sediment in Kochi harbour. In Mumbai harbour, the values of TBT and DBT ranged between 4.5 and 1193 ng/g dry wt. and from undetected to 131 ng/g dry wt. of the sediments, respectively. The concentrations of both TBT and DBT showed strong seasonal variation probably due to the effect of tides and currents. Nevertheless, the levels of butyltin compounds were generally higher at sites influenced by shipping activities such as navigation, dry dock and ship-building activities. The presence of DBT indicates the abiotic or microbiological degradation of TBT. Compared to TBT, DBT was relatively less abundant, suggesting either fresh inputs of TBT and/or less degradation of TBT. The concentrations of TBT showed significant positive relationships with organic carbon and lipid, implying that both lipophilic and ionic interactions were probably involved in controlling the abundance of TBT at these sediments. The observed levels of butyltin compounds are much higher than those required to induce toxic effects on marine organisms, suggesting that these sediments were contaminated with butyltin compounds.

Carbon↗
PubMed2006

Initial study on the effects of Prestige oil on human health.

The big oil tanker Prestige wrecked at 130 miles from the coast of Galicia, on the Northwest of Spain, in November 19, 2002. During the accident over 40,000 tons of oil were spilled, and along the next weeks 22,000 more reached the shore in the way of three black tides. A great number of people participated in the cleaning tasks. The objective of this study was to initially evaluate the damage caused by Prestige oil in exposed individuals both from the cytogenetic and the endocrine points of view. Exposure level was determined by analysing volatile organic compounds in the environment and heavy metals in blood. Cytogenetic damage was determined by sister chromatid exchanges (SCE), and plasmatic prolactin and cortisol levels were used as biomarkers of endocrine toxicity. Finally we have determined the possible influence of GST genetic polymorphisms (GSTM1 and GSTT1 deletion polymorphisms, GSTP1 Ala105Val) on the evaluated effects. The exposed population was classified according to the performed cleaning tasks in three groups: volunteers that collaborated for 1 week (N=25), hired manual workers (N=20) and hired high-pressure cleaner workers (N=23). The control population consisted of 42 individuals. Exposure to Prestige oil caused cytogenetic damage in exposed individuals, being its effect influenced by age, sex, tobacco consumption and GSTM1 polymorphism. With regard to endocrine toxicity, our results showed that xenobiotics present in Prestige oil induced alterations in hormonal status, and thus it may be considered as an endocrine disruptor. Therefore, the selected parameters have shown to be good indicators of toxicity related to exposure to Prestige oil. In addition, data obtained point to the importance of using protective devices in preventing the effects related to the exposure.

Endocrine Glands↗
PubMed2006

Environmental changes reflected by sedimentary geochemistry in recent hundred years of Jiaozhou Bay, North China.

Sediment geochemical technique was employed to assess how the sediment records reflect the environmental changes of Jiaozhou Bay, a semi-enclosed bay adjacent to Qingdao, China. In the past hundred years, Jiaozhou Bay has been greatly impacted by human interventions. A dated core sediment by 210Pb chronology was analyzed for trace metals including Li, Cd, Cr, Pb, Cu, Ni, Co, Zn together with C, N, P and BSi. Based on the research, the development of Jiaozhou Bay environment in the past hundred years can be divided into three stages: (1) before the 1980s characterized by relatively low sedimentation rate, weak heavy metal pollution and scarce eutrophication; (2) from the 1980s to 2000, accelerating in the 1990s, during which high sedimentation rates, polluted by heavy metals and the frequent occurrence of red tide; (3) after 2000, the period of the improvement of environment, the whole system has been meliorated including the heavy metal pollution and hypernutrification.

China↗
PubMed2006

Evaluation of the in situ, time-integrated DGT technique by monitoring changes in heavy metal concentrations in estuarine waters.

Various natural and anthropogenic processes influence heavy metal concentrations within estuaries. In situ, time-integrated DGT measurements made over concurrent tidal phases found significantly higher concentrations of Cu (probability p=0.017), Zn (p=0.003) and Ni (p=0.003) during the flood phase, because the incoming tide passes several point sources. DGT-reactive Cu concentrations significantly decreased with increased tidal-flushing and vice versa within a marina (correlation r=-0.788, p=0.02). DGT measurements also recorded significant increases in Cu (4 out of 4 sites, p<0.001) and Zn (3 out of 4 sites, p< or =0.015) after a 24 mm rainfall event. Finally, DGT-reactive Cu increased significantly (p<0.001) during peak boating times, due to increased numbers of Cu-antifouled boats. This study demonstrates that, with judicious selection of deployment times, DGT measurements enable changes in heavy metal concentrations to be related to various cycles and events within estuaries.

Copper↗
PubMed2006

Implication of site quality on mitochondrial electron transport activity and its interaction with temperature in feral Mya arenaria clams from the Saguenay Fjord.

The advent of global warming has given rise to questions about the impact of temperature/pollution interactions on the integrity of certain benthic organisms like bivalves. This interaction was examined in intertidal Mya arenaria clams from the Saguenay Fjord using the concepts of cellular energy allocation and temperature-dependent mitochondrial electron transport (METT) activity. Clams were collected at low tide from six sites (two clean, four polluted) for determinations of condition factor (weight/shell length), growth index (age-to-length ratio), gonadal lipids and maturation index, gonad MET at various habitat temperatures, METT, gill xanthine oxidase and gill DNA damage. Condition factor was generally lower at the four polluted sites, with growth index being severely affected at two of them. Gonadal maturation was also significantly dampened at two of the four pollution-impacted sites. Gill xanthine oxidase (purine bases salvage pathway) and DNA strand breaks were significantly increased at most of the polluted sites, confirming pollution-mediated damage in clams. Moreover, MET at 20 degrees C, METT and gonad lipids were significantly induced at the polluted sites. Clam condition factor was negatively correlated with most of the biomarkers for cellular energy allocation (gonadal lipids, MET and METT), but not with gonadal maturation. DNA damage and xanthine oxidase were positively correlated with MET at 20 degrees C and METT. This is the first report of electron transport in mitochondria being more sensitive to incremental temperature increases in clams under pollution stress. The gradual warming of clam habitats would likely worsen the impacts of pollution in feral clam populations.

Animals↗
PubMed2006

The inhibition of CHO-K1-BH4 cell proliferation and induction of chromosomal aberrations by brevetoxins in vitro.

Brevetoxins (PbTxs) are highly potent trans-syn polyether neurotoxins produced during blooms of several species of marine dinoflagellates, most notably Karenia brevis. These neurotoxins act on voltage-sensitive sodium channels prolonging the active state. During red tides, the commercial fishing and tourism industries experience millions of dollars of lost revenue. Human consumption of shellfish contaminated with PbTxs results in neurotoxic shellfish poisoning (NSP). Additionally, blooms of K. brevis are potentially responsible for adverse human health effects such as respiratory irritation and airway constriction in coastal residents. There is little information regarding the full range of potential toxic effects caused by PbTxs. Recent evidence suggests that PbTxs are genotoxic substances. The purpose of this study was to determine if PbTxs could induce chromosomal aberrations and inhibit cellular proliferation in CHO-K1-BH4 cells, and if so, could the damage be negated or reduced by the PbTx antagonist brevenal. Results from the chromosomal aberrations assay demonstrated that PbTxs are potent inducers of CHO-K1-BH4 chromosome damage. Results from the inhibition of cellular proliferation assays demonstrated that PbTxs inhibit the ability of CHO-K1-BH4 cells to proliferate, an effect which can be reduced with brevenal.

Animals↗
PubMed2005

Yeast community survey in the Tagus estuary.

The yeast community in the waters of the Tagus estuary, Portugal, was followed for over a year in order to assess its dynamics. Yeast occurrence and incidence were measured and this information was related to relevant environmental data. Yeast occurrence did not seem to depend upon tides, but river discharge had a dramatic impact both on the density and diversity of the community. The occurrence of some yeasts was partially correlated with faecal pollution indicators. Yeast isolates were characterized by microsatellite primed PCR (MSP-PCR) fingerprinting and rRNA gene sequencing. The principal species found were Candida catenulata, C. intermedia, C. parapsilosis, Clavispora lusitaniae, Debaryomyces hansenii, Pichia guilliermondii, Rhodotorula mucilaginosa and Rhodosporidium diobovatum. The incidence of these species was evaluated against the environmental context of the samples and the current knowledge about the substrates from which they are usually isolated.

Classification↗
PubMed2026

An oxidative stress - and immunotherapy-related six-gene signature defines immune subtypes and predicts prognosis and immunotherapy response in hepatocellular carcinoma.

BACKGROUND: Oxidative stress and the tumor immune microenvironment jointly shape hepatocellular carcinoma (HCC) progression and response to immunotherapy, yet integrated biomarkers linking these processes are lacking. METHODS: Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were used to identify oxidative stress- and immunotherapyrelated differentially expressed genes (OSIRDEGs). Functional enrichment, weighted gene co-expression network analysis (WGCNA) and LASSO-Cox regression were used to construct a prognostic signature. Consensus clustering, TIDE, CIBERSORT and ssGSEA characterized immune phenotypes. Somatic mutation, copy-number and drug-response data were integrated to assess genomic alterations and drug sensitivity. Expression of model genes was validated by qRT-PCR and western blotting in HCC cell lines. RESULTS: We identified 24 OSIRDEGs enriched in cell-cycle and mitotic pathways. WGCNA intersection yielded 18 module genes, from which a six-gene signature (BUB1B, CDKN2A, CENPE, HMMR, PTTG1, SPP1) was derived. The signature robustly stratified patients into high- and low-risk groups with significantly different progression-free and disease-free survival in both TCGA-LIHC and GSE14520. Based on signature expression, two molecular subtypes were defined, exhibiting distinct survival, immune landscapes and predicted immunotherapy responsiveness. Model genes harbored recurrent alterations and showed significant correlations with anticancer agents. All six genes were upregulated at mRNA and protein levels in metastatic HCC cell lines versus normal hepatocytes. CONCLUSIONS: We systematically explored the landscape of OSIRDEGs in HCC, and proposed a validated six-gene signature that refines prognostic stratification, delineates immunerelevant HCC subtypes and highlights candidate biomarkers for therapeutic selection and mechanistic investigation.

Humans↗
PubMed2005

Angiographic diagnosis and endovascular management of nonvariceal gastrointestinal hemorrhage.

Diagnostic angiography still plays an essential role in the diagnosis of patients,particularly those with acute lower GI bleeding. Transcatheter therapy appears to be a viable treatment alternative in selected patients with GI bleeding. Many interventionists today believe embolotherapy to be more effective initially and to have better long-term results, specifically less rebleeding, than vasopressin infusion with at least equal complication rates. Unfortunately, direct comparison of the two techniques in a randomized, controlled fashion has not been performed. Small patient series, such as those summarized here, suggest that the results of the two techniques are essentially equal, and ischemic complications appear more prevalent with embolotherapy. The use of embolotherapy--either empirically based on endoscopic or surgical findings or directed against a site found to have contrast extravasation-represents the current intervention of choice in the case of upper GI bleeding refractory to endoscopic intervention. Head-to-head studies directly comparing the efficacy, morbidity, and mortality associated with endovascular or surgical correction of bleeding from the upper GI tract is needed. Although the current tide favors embolotherapy in the lower GI tract, infusion of vasoconstricting agents deserves more attention. To that end, there is a great need for scientific data regarding the safety and efficacy of transcatheter therapy for upper and lower GI bleeding.

Angiography↗
PubMed2006

Preventing obesity: a life cycle perspective.

Traditional approaches to treating overweight and obese adults by focusing on individual weight loss have not been effective in stemming the tide of obesity in the population. Recent research has identified critical factors that, as they accumulate and interact over an individual's life span, may put a person at risk for obesity. These factors include rapid weight gain in infancy and childhood, early puberty, and excessive weight gain in pregnancy. Based on this research, a life cycle perspective can be used to develop comprehensive interventions that address the multiple determinants of obesity. Because obesity tracks across generations, it is essential to adopt effective obesity prevention measures now to prevent even higher rates of obesity in future generations. Dietetics professionals can reduce individual risks by providing nutritional services that support appropriate weight gain in childhood and pregnancy. We can also advocate for policies in communities, schools, and worksites that support breastfeeding, ensure access to health-promoting foods, and provide opportunities to be physically active.

Adolescent↗
PubMed2006

Body on the beach...a case of foot and mouth?

The case of a missing person is described whose body was discovered almost 8 months later on a secluded beach on the Solway coast, south west Scotland. The delay in discovery was due to the foot and mouth outbreak in the UK in 2001 and this resulted in conditions favouring the development of partial mummification. The influence of the tides and involvement of HM Coastguard are discussed, along with difficulties in the identification of partially skeletonised remains.

Animals↗
PubMed2006

Models of total and presumed wildlife sources of fecal coliform bacteria in coastal ponds.

Models that accurately predict fecal coliform bacteria (FCB) concentrations, one of the most widely used measures of estuarine water quality, are needed to improve land use decision-making. Rapidly occurring changes in coastal land uses and the influence on water quality increases the urgency of having improved decision tools. For this study, samples were collected monthly from six coastal ponds, two tidal creeks and four shallow water wells for up to 212 years. These data were used along with other measures of environmental conditions and land classes within each watershed to construct quantitative relationships between combinations of variables and both total and presumed wildlife sources of FCB. Linear regression, bootstrapping and generalized additive modeling that incorporates both linear and nonlinear terms were used. Results of repeated simultaneous sampling on the same tide stage of ponds and downstream estuarine creeks suggest that most FCB come from wildlife and that the ponds effectively remove these bacteria except immediately following heavy rainfall. Predictive models for concentrations of total and presumed wildlife bacteria are provided along with simple measures to estimate watershed boundaries. It is proposed that these tools can be used to minimize impacts on receiving water body quality. The models can be used to test alternative development approaches within coastal watersheds similar to that found in the southeastern USA coastal zone as well as to evaluate specific proposed landscape alterations.

Animals↗
PubMedDate not supplied

Mothers, midwives, and HIV/AIDS in Sub-Saharan Africa.

This article reviews clinical and program issues in the prevention of mother to child transmission (PMTCT) of HIV in sub-Saharan Africa. Topics include prevention of infection, voluntary counseling and testing, prenatal care, labor and birth, postpartum, family planning, infant feeding, and the role of traditional birth attendants. Programs providing short-course antiretroviral therapy to prevent infant infection are contrasted with comprehensive programs offering antiretroviral therapy and medical care to mothers, children, and families. Feminization of the epidemic is related to gender inequalities that facilitate the spread of HIV and make pregnant women an especially vulnerable group. Nurses and midwives are the primary health care providers for most of the population in sub-Saharan Africa. They are the backbone of the new PMTCT programs and will be the largest group of health workers available to diagnose and treat opportunistic infections and dispense antiretroviral therapy. But they have received little training and support to provide AIDS care and treatment and are rarely consulted when plans are made about workforce issues and capacity development in the health sector. Clinical training, leadership skills, salary support, expansion of the nursing workforce, and development of expanded roles for nurses and midwives in AIDS care are needed to help them turn the tide of the epidemic.

Adolescent↗
PubMed2004

The use of photooxidized, mushroom-structured osteochondral grafts for cartilage resurfacing--a comparison to photooxidized cylindrical grafts in an experimental study in sheep.

OBJECTIVE: This article addresses the problem of structural design with osteochondral grafts used for cartilage resurfacing. METHODS: Photooxidized cylindrical or mushroom-shaped grafts were surgically implanted in the weight bearing area of the medial and lateral femoral condyles of eight sheep (condyles: N=8/group). Both types of photooxidized grafts contained no viable chondrocytes at the time of implantation. Results were evaluated at 2 and 6 months after surgical implantation of the grafts. Qualitative and quantitative evaluation of the subchondral bone area was performed using plastic embedded sections of non-decalcified bone and cartilage specimens and placing emphasis on graft anchorage, cyst-like lesions at the base of the cartilage junction and at the base of the graft in the subchondral bone region. Cartilage morphology was studied qualitatively focusing on viability of the graft and adjacent host cartilage, while a score system was developed for semi-quantitative evaluation of the overall articular cartilage performance. The semiquantitative scores and histomorphometrical measurements were subjected to statistical analysis using a factorial analysis of variance (ANOVA-test). RESULTS: The photooxidized mushroom-shaped grafts developed less fibrous tissue and cyst-like lesions in the subchondral bone area at 2 and 6 months compared to the cylindrical grafts. Areas of endochondral ossification and bone remodeling were noticeable in the mushroom structured grafts at 2 months, and also bone remodeling was more complete at 6 months than with the cylindrical grafts. Increased numbers of cells were seen in the basal remodeling zones of both graft types increased from the 2 months to the 6 months specimens, but mushroom structured grafts showed better results. In both graft types, however, the midzone of the cartilage matrix was still acellular at 6 months. Cells from the subchondral bone area started to penetrate the calcified cartilage zone and tide mark at 2 months and repopulated the old photooxidized cartilage matrix already at 6 months after implantation. Cartilage repopulation was dependent on a stable subchondral bone area in both types of grafts. Matrix degradation of the adjacent host cartilage was minimal at 2 and 6 months. At 6 months a junction between host and graft cartilage was already noticed in some of the mushroom-shaped grafts. CONCLUSION: This study confirmed the importance of the subchondral bone area for osteochondral graft survival. In addition it demonstrated that the structure of the graft influences considerably the architecture of the subchondral bone, and with this the possibility for the repopulation of the old cartilage matrix including the junction between the host and graft cartilage matrix.

Analysis of Variance↗