Functional data analysis approaches for genotype-phenotype association studies from next-generation sequencing

Next-generation DNA sequencing platforms can effectively detect the entire spectrum of genomic variation and is emerging to be a major tool for systematic exploration of the universe of variants and interactions in the entire genome. However, the data produced by next-generation sequencing technologies will suffer from three basic problems: sequence errors, assembly errors, and missing data. Current statistical methods for genetic analysis are well suited for detecting the association of common variants, but are less suitable to rare variants. This raises great challenge for sequence-based genetic studies of complex diseases.^ This research dissertation utilized genome continuum model as a general principle, and stochastic calculus and functional data analysis as tools for developing novel and powerful statistical methods for next generation of association studies of both qualitative and quantitative traits in the context of sequencing data, which finally lead to shifting the paradigm of association analysis from the current locus-by-locus analysis to collectively analyzing genome regions.^ In this project, the functional principal component (FPC) methods coupled with high-dimensional data reduction techniques will be used to develop novel and powerful methods for testing the associations of the entire spectrum of genetic variation within a segment of genome or a gene regardless of whether the variants are common or rare.^ The classical quantitative genetics suffer from high type I error rates and low power for rare variants. To overcome these limitations for resequencing data, this project used functional linear models with scalar response to develop statistics for identifying quantitative trait loci (QTLs) for both common and rare variants. To illustrate their applications, the functional linear models were applied to five quantitative traits in Framingham heart studies. ^ This project proposed a novel concept of gene-gene co-association in which a gene or a genomic region is taken as a unit of association analysis and used stochastic calculus to develop a unified framework for testing the association of multiple genes or genomic regions for both common and rare alleles. The proposed methods were applied to gene-gene co-association analysis of psoriasis in two independent GWAS datasets which led to discovery of networks significantly associated with psoriasis.^

Analysis of participation in the federally mandated coal workers' health surveillance program

The Federal Coal Mine Health and Safety Act of 1969 required that periodic chest radiographs be offered to underground coal miners to protect the miners from the development of Coal Workers' Pneumoconiosis (CWP) and progression of the disease to progressive massive fibrosis (PMF). These examinations are administered by the National Institute for Occupational Safety and Health (NIOSH) through the Coal Workers' Health Surveillance Program (CWHSP). The mine operator is required to provide each miner with the opportunity to have the chest radiograph at no cost to the miner.^ Three rounds of examinations have been conducted since 1969 and the fourth is underway. The decrease in participation over rounds is of great concern if the incidence and progression of CWP are to be understood and controlled.^ This study developed rates of participation for each of 558 West Virginia underground coal mines who submitted or had NIOSH assigned plans for making chest radiographs available during the third round, July 1978 through December 1980. These rates were analyzed in relation to desired levels of participation and to reinforcing, predisposing and enabling factors presumed to affect rates of participation in disease prevention and surveillance programs.^ Two reinforcing factors, size of mine and inclusion of the mine in the National Coal Study (NCS) epidemiology research program, and the enabling factor, use of an on-site radiograph facility, demonstrated highly significant relationships to participation rates.^ The major findings of the study were: (1) Participation in the CWHSP is even lower than previously estimated; (2) CWHSP program evaluation is not systematic and program data base is not complete and comprehensive; and (3) NIOSH program policy is not clear and administration of the CWHSP is fragmented and lacks adequate fiscal and personnel resources. ^

NONLINEAR TIME SERIES/SYSTEM ANALYSIS (STATE-SPACE, DYNAMICS, INTERVENTION, RESILIENCE, KALMAN)

A discussion of nonlinear dynamics, demonstrated by the familiar automobile, is followed by the development of a systematic method of analysis of a possibly nonlinear time series using difference equations in the general state-space format. This format allows recursive state-dependent parameter estimation after each observation thereby revealing the dynamics inherent in the system in combination with random external perturbations.^ The one-step ahead prediction errors at each time period, transformed to have constant variance, and the estimated parametric sequences provide the information to (1) formally test whether time series observations y(,t) are some linear function of random errors (ELEM)(,s), for some t and s, or whether the series would more appropriately be described by a nonlinear model such as bilinear, exponential, threshold, etc., (2) formally test whether a statistically significant change has occurred in structure/level either historically or as it occurs, (3) forecast nonlinear system with a new and innovative (but very old numerical) technique utilizing rational functions to extrapolate individual parameters as smooth functions of time which are then combined to obtain the forecast of y and (4) suggest a measure of resilience, i.e. how much perturbation a structure/level can tolerate, whether internal or external to the system, and remain statistically unchanged. Although similar to one-step control, this provides a less rigid way to think about changes affecting social systems.^ Applications consisting of the analysis of some familiar and some simulated series demonstrate the procedure. Empirical results suggest that this state-space or modified augmented Kalman filter may provide interesting ways to identify particular kinds of nonlinearities as they occur in structural change via the state trajectory.^ A computational flow-chart detailing computations and software input and output is provided in the body of the text. IBM Advanced BASIC program listings to accomplish most of the analysis are provided in the appendix. ^

AN ECONOMIC ANALYSIS OF THE DEMAND FOR CARE IN A FREE-STANDING EMERGENCY CENTER

Free-standing emergency centers (FECs) represent a new approach to the delivery of health care which are competing for patients with more conventional forms of ambulatory care in many parts of the U.S. Currently, little is known about these centers and their patient populations. The purpose of this study, therefore, was to describe the patients who visited two commonly-owned FECs, and determine the reasons for their visits. An economic model of the demand for FEC care was developed to test its ability to predict the economic and sociodemographic factors of use. Demand analysis of other forms of ambulatory services, such as a regular source of care (RSOC), was also conducted to examine the issues of substitution and complementarity.^ A systematic random sample was chosen from all private patients who used the clinics between July 1 and December 31, 1981. Data were obtained by means of a telephone interview and from clinic records. Five hundred fifty-one patients participated in the study.^ The typical FEC patient was a 26 year old white male with a minimum of a high school education, and a family income exceeding $25,000 a year. He had lived in the area for at least twenty years, and was a professional or a clerical worker. The patients made an average of 1.26 visits to the FECs in 1981. The majority of the visits involved a medical complaint; injuries and preventive care were the next most common reasons for visits.^ The analytic results revealed that time played a relatively important role in the demand for FEC care. As waiting time at the patients' regular source of care increased, the demand for FEC care increased, indicating that the clinic serves as a substitute for the patients' usual means of care. Age and education were inversely related to the demand for FEC care, while those with a RSOC frequented the clinics less than those lacking such a source.^ The patients used the familiar forms of ambulatory care, such as a private physician or an emergency room in a more typical fashion. These visits were directly related to the age and education of the patients, existence of a regular source of care, and disability days, which is a measure of health status. ^

A systematic review of clostridium difficile infection in patients with iatrogenic immunesuppression

Background: Incidence of C. difficile infection (CDI) has increased dramatically in the past decade and is the most frequent cause of nosocomial infectious diarrhea. The outcome of infection may range from mild diarrhea to life-threatening pseudomembranous colitis depending on the immunological response of the host, which is highly compromised in this special population that includes bone marrow transplant (BMT), solid organ transplant (SOT) and cancer patients on cytotoxic chemotherapy. ^ Objectives: We conducted a meta-analysis to assess the incidence rates of CDI and the time to onset of infection in patients with iatrogenic immune suppression. ^ Methods: Original studies were identified through an extensive search of electronic databases including PubMed, Ovid Medline (R), RefWorks and Biological Abstracts and their references. The overall incidence rate of CDI in the immune suppressed population was calculated using random effects model and their 95% confidence interval was derived. Differences in the incidence of CDI and time to onset of infection were calculated between the groups and within the groups. Publication bias was assessed using a funnel plot. Results: Twenty nine published articles involving 7,424 patients met the eligibility requirements. The overall incidence of CDI in the immune suppressed population is 11.1% (95% Confidence Interval (CI): 9.2–13.4%). The incidence of CDI was higher in SOT patients (14.2%, 95% CI: 6.8–21.5%); (p-value-0.022) and in cancer patients on cytotoxic chemotherapy (11.4%, 95% CI: 8.4–15.4%); (p = 0.042) than in BMT patients (10.5%, 95% CI: 7.9–13.1%). In a subgroup analysis of BMT population, the incidence of CDI is significantly higher in patients who received allogeneic BMT (15.1%, 95% CI: 11.2–20.0%; p value <0.0001). Similarly, in the SOT population, the incidence of CDI was higher in patients who underwent liver transplantation (11.0%, 95% CI: 5.6–20.3%); (p= 0.0672). The median time to onset of infection was shorter in BMT patients (p=0.0025). ^ Conclusions: It is evident from the combined analysis of these 29 published studies that the incidence of CDI in the immune suppressed population is higher. However, early diagnosis and treatment of CDI will help reduce the morbidity and mortality due to CDI in this special population.^

Access to oral care --- A systematic review of a continuing public health issue among older adults

Oral health is essential for the general well being of the individual and collectively for the health of the population. Oral health can be maintained by routine dental care and visits to dental professionals, but accessing professional dental care may be a continuing difficulty in vulnerable older adult population. Many older adults are not frequent users of dental care, though oral health is crucial to their well-being and overall health. Access to care is the timely use of personal health services to achieve the best possible health outcomes. ^ Objectives: The aims of this review are to (i) to analyze and elucidate the relationship between socio-economic disparities in gender, ethnicity, poverty status, education and the continuing public issue of access to oral care, (ii) to identify the underlying causes through which these factors can affect access to oral care. This review will provide a knowledgeable basis for development of interventions to provide adequate access to oral care in older adults and implementing policies to ensure access to oral care; through highlighting the various socio economic factors that affect access to oral care among older adults. ^ Methods: This paper used a purposeful review of literature on socioeconomic disparities in access to oral care among older adults. The references considered in this review included all the relevant articles, surveys and reports published in English language, since the year 1985 to 2010, in the United States. The articles selected were scrutinized for relevancy to the topic of access to oral care and which included discussions of the effects of gender, ethnicity, poverty status, educational status in accessing oral care. ^ Results: Evidence confirmed the continuing disparity in access to oral care among older adults. The possible links identified were gender inequality, ethnic differences, income levels and educational differences affecting access to oral care. The underlying causes linking these factors with access to oral care were established. ^ Conclusion: The analysis of the literature review findings supported the prevalence of disparities in gender, ethnicity, income and education with its possible links affecting access to oral care. The underlying causes helped to understand the reasons behind this growing issue of inaccessible oral care. Further research is needed to develop policies and target dental public health efforts towards specific problem areas ensuring equitable access to oral services and consequently, improve the health of older adults.^

A systematic review of personalized therapy in patients with advanced cancer

Background: An increased understanding of the pathogenesis of cancer at the molecular level has led to the development of personalized cancer therapy based on the mutation status of the tumor. Tailoring treatments to genetic signatures has improved treatment outcomes in patients with advanced cancer. We conducted a meta-analysis to provide a quantitative summary of the response to treatment on a phase I clinical trial matched to molecular aberration in patients with advanced solid tumors. ^ Methods: Original studies that reported the results of phase I clinical trials in patients with advanced cancer treated with matched anti-cancer therapies between January 2006 and November 2011 were identified through an extensive search of Medline, Embase, Web of Science and Cochrane Library databases. Odds Ratio (OR) with 95% confidence interval (CI) was estimated for each study to assess the strength of an association between objective response rate (ORR) and mutation status. Random effects model was used to estimate the pooled OR and their 95% CI was derived. Funnel plot was used to assess publication bias. ^ Results: Thirteen studies published between January 2006 and November 2011that reported on responses to matched phase I clinical trials in patients with advanced cancer were included in the meta-analysis. Nine studies reported on the responses seen in 538 of the 835 patients with driver mutations responsive to therapy and seven studies on the responses observed in 234 of the 306 patients with mutation predictive for negative response. Random effects model was used to estimate pooled OR, which was 7.767(95% CI = 4.199 − 14.366; p-value=0.000) in patients with activating mutations that were responsive to therapy and 0.287 (95% CI = 0.119 − 0.694; p-value=0.009) in patients with mutation predictive of negative response. ^ Conclusion: It is evident from the meta-analysis that somatic mutations present in tumor tissue of patients are predictive of responses to therapy in patients with advanced cancer in phase I setting. Plethora of research and growing evidence base indicate that selection of patients based on mutation analysis of the tumor and personalizing therapy is a step forward in the war against cancer.^

The success of worksite nutrition and physical activity interventions with environmental modifications A systematic review

Background: As obesity increases among U.S. workers, employers are implementing programs to increase physical activity and improve diets. Although programs to address individual determinants of obesity have been evaluated, less is known about the effects of workplace programs that change environmental factors, because most reviews have not isolated environmental programs; the one that did was published in 2005. ^ Objective: To update the 2005 review to determine the effectiveness of workplace environmental interventions. ^ Methods: The Medline database was searched for published English language reports (2003-2011) of randomized controlled (RCTs) or quasi-experimental trials (NRCTs) that evaluated strategies to modify physical activity opportunities or food services, targeting employees at least 18 years, not including retirees and that provided data for at least one physical activity, dietary, or health risk indicator. Three coders independently extracted study characteristics and scored the quality of study methods. Program effectiveness was determined using the 2005 review's best evidence approach. ^ Results: Seven studies represented in nine reports met eligibility criteria; three focused on diet and the remainder targeted diet and physical activity interventions. All but one study received a high quality score for internal validity. The evidence for the effectiveness of workplace environmental interventions was at best, inconclusive for diet and physical activity and limited for health risk indicators. The outcome constructs were inconsistent across the studies. ^ Conclusions: Limitations in the methods of the 2005 review made it challenging to draw conclusions about findings for this review that include: variation in outcome measures, reliance on distal measures without proximal behavior change measures, no distinction between changes at the workplace versus outside the workplace, and inappropriate analyses of cluster designs that biased findings toward statistical significance. The best evidence approach relied on vote-counting, using statistical significance alone rather than effect size and confidence intervals. Future research should address these limitations and use more rigorous methods; systematic reviews should use methods of meta-analysis to summarize study findings. These recommendations will help employers to better understand how environmental modifications in the workplace can support their efforts to combat the effects of obesity among employees.^

Sudden Infant Death disparities: A systematic review on health education and policy recommendations for decreasing Sudden Infant Death in the African-American community

Objective: To perform a systematic review of the literature on SIDS and SUID deaths concentrated in the African-American community, describe health education and policy recommendations and recommend a new approach that may aid in decreasing the disparity of infant mortality in the African-American community. ^ Methods: The PubMed database was systematically searched to identify relevant articles for final review and analysis. Using the CASP 2006 system to critique literature, twelve articles were found that met inclusion and exclusion criteria. ^ Results: Evidence in the literature confirmed there was a current disparity among African Americans' infant mortality rates in comparison to other US ethnic groups. The underlying reasons for these disparities included the following maternal and infant characteristics: mothers younger than eighteen, having more than one live infant, having a high school education or less, never been married, and have infants born preterm or with low birth weight. Maternal smoking, substance abuse, and breastfeeding did not have a significant impact on infant sleep environments among African Americans. ^ Conclusion: Tailored health education programs at the community level, better access to pre-pregnancy and prenatal care, and increased maternal perception of risk that is relevant to the infants sleeping environment are all possible solutions that may decrease African American infant mortality rates.^

Patenting genes and gene sequences: Analysis of public health implications and the law

At issue is whether or not isolated DNA is patent eligible under the U.S. Patent Law and the implications of that determination on public health. The U.S. Patent and Trademark Office has issued patents on DNA since the 1980s, and scientists and researchers have proceeded under that milieu since that time. Today, genetic research and testing related to the human breast cancer genes BRCA1 and BRCA2 is conducted within the framework of seven patents that were issued to Myriad Genetics and the University of Utah Research Foundation between 1997 and 2000. In 2009, suit was filed on behalf of multiple researchers, professional associations and others to invalidate fifteen of the claims underlying those patents. The Court of Appeals for the Federal Circuit, which hears patent cases, has invalidated claims for analyzing and comparing isolated DNA but has upheld claims to isolated DNA. The specific issue of whether isolated DNA is patent eligible is now before the Supreme Court, which is expected to decide the case by year's end. In this work, a systematic review was performed to determine the effects of DNA patents on various stakeholders and, ultimately, on public health; and to provide a legal analysis of the patent eligibility of isolated DNA and the likely outcome of the Supreme Court's decision. ^ A literature review was conducted to: first, identify principle stakeholders with an interest in patent eligibility of the isolated DNA sequences BRCA1 and BRCA2; and second, determine the effect of the case on those stakeholders. Published reports that addressed gene patents, the Myriad litigation, and implications of gene patents on stakeholders were included. Next, an in-depth legal analysis of the patent eligibility of isolated DNA and methods for analyzing it was performed pursuant to accepted methods of legal research and analysis based on legal briefs, federal law and jurisprudence, scholarly works and standard practice legal analysis. ^ Biotechnology, biomedical and clinical research, access to health care, and personalized medicine were identified as the principle stakeholders and interests herein. Many experts believe that the patent eligibility of isolated DNA will not greatly affect the biotechnology industry insofar as genetic testing is concerned; unlike for therapeutics, genetic testing does not require tremendous resources or lead time. The actual impact on biomedical researchers is uncertain, with greater impact expected for researchers whose work is intended for commercial purposes (versus basic science). The impact on access to health care has been surprisingly difficult to assess; while invalidating gene patents might be expected to decrease the cost of genetic testing and improve access to more laboratories and physicians' offices that provide the test, a 2010 study on the actual impact was inconclusive. As for personalized medicine, many experts believe that the availability of personalized medicine is ultimately a public policy issue for Congress, not the courts. ^ Based on the legal analysis performed in this work, this writer believes the Supreme Court is likely to invalidate patents on isolated DNA whose sequences are found in nature, because these gene sequences are a basic tool of scientific and technologic work and patents on isolated DNA would unduly inhibit their future use. Patents on complementary DNA (cDNA) are expected to stand, however, based on the human intervention required to craft cDNA and the product's distinction from the DNA found in nature. ^ In the end, the solution as to how to address gene patents may lie not in jurisprudence but in a fundamental change in business practices to provide expanded licenses to better address the interests of the several stakeholders. ^

Molecular and genetic analysis of Myxococcus xanthus early *development

To identify more mutations that can affect the early development of Myxococcus xanthus, the synthetic transposon TnT41 was designed and constructed. By virtue of its special features, it can greatly facilitate the processes of mutation screening/selection, mapping, cloning and DNA sequencing. In addition, it allows for the systematic discovery of genes in regulatory hierarchies using their target promoters. In this study, the minimal regulatory region of the early developmentally regulated gene 4521 was used as a reporter in the TnT41 mutagenesis. Both positive (P) mutations and negative (N) mutations were isolated based on their effects on 4521 expression.^ Four of these mutations, i.e. N1, N2, P52 and P54 were analyzed in detail. Mutations N1 and N2 are insertion mutations in a gene designated sasB. The sasB gene is also identified in this study by genetic and molecular analysis of five UV-generated 4521 suppressor mutations. The sasB gene encodes a protein without meaningful homology in the databases. The sasB gene negatively regulates 4521 expression possibly through the SasS-SasR two component system. A wild-type sasB gene is required for normal M. xanthus fruiting body formation and sporulation.^ Cloning and sequencing analysis of the P52 mutation led to the identification of an operon that encodes the M. xanthus high-affinity branched-chain amino acid transporter system. This liv operon consists of five genes designated livK, livH, livM, livC, and livF, respectively. The Liv proteins are highly similar to their counterparts from other bacteria in both amino acid sequences, functional motifs and predicted secondary structures. This system is required for development since liv null mutations cause abnormality in fruiting body formation and a 100-fold decrease in sporulation efficiency.^ Mutation P54 is a TnT41 insertion in the sscM gene of the ssc chemotaxis system, which has been independently identified by Dr. Shi's lab. The sscM gene encodes a MCP (methyl-accepting chemotaxis protein) homologue. The SscM protein is predicted to contain two transmembrane domains, a signaling domain and at least one putative methylation site. Null mutations of this gene abolish the aggregation of starving cells at a very early stage, though the sporulation levels of the mutant can reach 10% that of wild-type cells. ^

A global seasonal surface ocean climatology of phytoplankton types based on CHEMTAX analysis of HPLC pigments

Much advancement has been made in recent years in field data assimilation, remote sensing and ecosystem modeling, yet our global view of phytoplankton biogeography beyond chlorophyll biomass is still a cursory taxonomic picture with vast areas of the open ocean requiring field validations. High performance liquid chromatography (HPLC) pigment data combined with inverse methods offer an advantage over many other phytoplankton quantification measures by way of providing an immediate perspective of the whole phytoplankton community in a sample as a function of chlorophyll biomass. Historically, such chemotaxonomic analysis has been conducted mainly at local spatial and temporal scales in the ocean. Here, we apply a widely tested inverse approach, CHEMTAX, to a global climatology of pigment observations from HPLC. This study marks the first systematic and objective global application of CHEMTAX, yielding a seasonal climatology comprised of ~1500 1°x1° global grid points of the major phytoplankton pigment types in the ocean characterizing cyanobacteria, haptophytes, chlorophytes, cryptophytes, dinoflagellates, and diatoms, with results validated against prior regional studies where possible. Key findings from this new global view of specific phytoplankton abundances from pigments are a) the large global proportion of marine haptophytes (comprising 32 ± 5% of total chlorophyll), whose biogeochemical functional roles are relatively unknown, and b) the contrasting spatial scales of complexity in global community structure that can be explained in part by regional oceanographic conditions. These publicly accessible results will guide future parameterizations of marine ecosystem models exploring the link between phytoplankton community structure and marine biogeochemical cycles.

Ordinary and duplicate analysis from major and trace elements of ODP Holes 146-888B and 168-1027B

Oceanic sediments deposited at high rate close to continents are dominated by terrigenous material. Aside from dilution by biogenic components, their chemical compositions reflect those of nearby continental masses. This study focuses on oceanic sediments coming from the juvenile Canadian Cordillera and highlights systematic differences between detritus deriving from juvenile crust and detritus from old and mature crust. We report major and trace element concentrations for 68 sediments from the northernmost part of the Cascade forearc, drilled at ODP Sites 888 and 1027. The calculated weighted averages for each site can then be used in the future to quantify the contribution of subducted sediments to Cascades volcanism. The two sites have similar compositions but Site 888, located closer to the continent, has higher sandy turbidite contents and displays higher bulk SiO2/Al2O3 with lower bulk Nb/Zr, attributed to the presence of zircons in the coarse sands. Comparison with published data for other oceanic sedimentary piles demonstrates the existence of systematic differences between modern sediments deriving from juvenile terranes (juvenile sediments) and modern sediments derived from mature continental areas (cratonic sediments). The most striking systematic difference is for Th/Nb, Th/U, Nb/U and Th/Rb ratios: juvenile sediments have much lower ratios than cratonic sediments. The small enrichment of Th over Nb in cratonic sediments may be explained by intracrustal magmatic and metamorphic differentiation processes. In contrast, their elevated Th/U and Nb/U ratios (average values of 6.87 and 7.95, respectively) in comparison to juvenile sediments (Th/U ~ 3.09, Nb/U ~ 5.15) suggest extensive U and Rb losses on old cratons. Uranium and Rb losses are attributed to long-term leaching by rain and river water during exposure of the continental crust at the surface. Over geological times, the weathering effects create a slow but systematic increase of Th/U with exposure time.

Component analysis of three TV-guided grab sampler from the Sahul Shelf (NW Australia)

This paper constitutes a first detailed and systematic facies and biota description of an isolated carbonate knoll (Pee Shoal) in the Timor Sea (Sahul Shelf, NW Australia). The steep and flat-topped knoll is characterized by a distinct facies zonation comprising (A) soft sediments with scattered debris and scarce sponges, hydrozoans and crinoids (320-210 m water depth), (B) hardground outcrops (step-like banks, vertical cliffs) that are mainly colonized by octocorals and sponges (210-75 m), and (C) the summit region (75-21 m) where the slopes merge gently into the flat-topped summit that is densely colonized by massive and encrusting zooxanthellate corals and the octocoral Heliopora coerulea. In contrast, the sediments recovered from the summit are dominated by the green alga Halimeda, subordinate components are corals, benthic foraminifers, mollusks, and coralline red algae. Thus, the sediments are classified as chlorozoan grain assemblage. However, non-skeletal grains (fecal pellets, ooids) are almost completely absent. This discrepancy between the living biota and the sediment composition could reflect a disruption by the severe tropical cyclone Ingrid that hit the northern Australian shelf in March 2005, just before the sampling for this study took place (September 2005).

Chemical analysis and Microbial community composition of surface water samples from the Southern Lagoon of Venice

The Lagoon of Venice is a large water basin that exchanges water with the Northern Adriatic Sea through three large inlets. We examined two adjacent sites within the Southern Basin and at the Chioggia inlet in autumn 2007 and summer 2008. A pilot study in June 2007 on a surface water sample from Chioggia with a rather high salinity of 36.9 PSU had revealed a conspicuous bloom of CF319a-positive cells likely affiliated with the Cytophaga /Flavobacteria cluster of Bacteroidetes. These flavobacterial abundances were one to two orders of magnitude higher than in other marine surface waters. DAPI-stained cells were identified as bacteria with the general bacterial probe mixture EUB338 I-III. CARD-FISH counts with group-specific probes confirmed the dominance of Bacteroidetes (CF319a), Alphaproteobacteria (ALF968), and Gammaproteobacteria (GAM42a). CARD-FISH showed thatBetaproteobacteria and Planctomycetes were minor components of the bacterioplankton in the Lagoon of Venice.