Susceptibility of shellfish aquaculture species in the Chesapeake Bay and Maryland coastal bays to ostreid herpesvirus 1 microvariants.

Ostreid herpesvirus 1 (OsHV-1) and its microvariants (µVars) cause economically devastating mass mortalities of oysters and pose a threat to the shellfish aquaculture industry globally. OsHV-1 outbreaks can cause up to 100% mortality in the Pacific oyster Crassostrea gigas. However, OsHV-1 and its variants have a broad host range and can infect at least 7 bivalve species, including bay scallops Argopecten irradians and eastern oysters C. virginica. Determining the susceptibility of economically and ecologically important bivalve species to OsHV-1 is critical for improving biosecurity and disease management to protect the aquaculture industry. Surveys of eastern oysters were conducted in June to August 2021 in the Maryland portion of the Chesapeake Bay to determine the prevalence and viral load of OsHV-1 at 5 aquaculture farms. Using quantitative PCR, OsHV-1 was not detected at any sites. Experiments examined the susceptibility of single stocks of eastern oysters and hard clams Mercenaria mercenaria to the virus and their ability to horizontally transmit it using OsHV-1 µVar SD (San Diego, California) and OsHV-1 µVar FRA (Marennes-Olreon, France). Results showed that OsHV-1 µVars did not cause mortality or symptomatic infection in the single stocks of eastern oysters and hard clams used in these experiments using natural infection pathways. However, the eastern oyster stock, when injected with OsHV-1, did transmit the virus to naïve Pacific oysters. Further experimentation using additional stocks and lines and establishment of surveillance programs along the east and Gulf coasts of the USA are necessary to prepare for the potential spread and impact of OsHV-1 related disease.

Occupational asthma in teachers.

BACKGROUND: Work-related asthma symptoms are common in teachers and teaching assistants, there are few studies evaluating their causes. AIMS: To identify causes of occupational asthma in teachers and teaching assistants referred to the Birmingham Occupational Lung Disease clinic 2000-20 using evaluation of serial Peak Expiratory Flow (PEF) records. METHODS: Teachers and teaching assistants with possible occupational asthma were asked to record PEF 2-hourly at home and work for 4 weeks. Their records were evaluated with the Oasys programme. Those with a positive score for any of the three scores (area between curves (ABC), timepoint and Oasys score from discriminant analysis) were included. Repeat records were made as indicated to help identify the cause and the effects of remedial actions. RESULTS: Thirty-eight teachers or teaching assistants met the inclusion criteria with all three Oasys scores positive in 24, 2/3 scores in nine and 1/3 in five. The building was the likely cause in 17 (in new builds particularly acrylates from carpet adhesives and in old buildings mould and construction dust), bystander exposure to agents in the schools in 12 (cleaning agents, acrylates from photocopiers and chloramines from indoor pools) and materials used in the classroom in 9 (most commonly MDF in design and technology classes). We illustrate how the PEF records helped identify the cause. CONCLUSIONS: Oasys analysis of PEF records is a useful method of evaluating occupational asthma in teachers and identified difficult to confirm causes where successful remediation or redeployment was achieved.

Dichotomy between Regulation of Coral Bacterial Communities and Calcification Physiology under Ocean Acidification Conditions.

Ocean acidification (OA) threatens the growth and function of coral reef ecosystems. A key component to coral health is the microbiome, but little is known about the impact of OA on coral microbiomes. A submarine CO2 vent at Maug Island in the Northern Mariana Islands provides a natural pH gradient to investigate coral responses to long-term OA conditions. Three coral species (Pocillopora eydouxi, Porites lobata, and Porites rus) were sampled from three sites where the mean seawater pH is 8.04, 7.98, and 7.94. We characterized coral bacterial communities (using 16S rRNA gene sequencing) and determined pH of the extracellular calcifying fluid (ECF) (using skeletal boron isotopes) across the seawater pH gradient. Bacterial communities of both Porites species stabilized (decreases in community dispersion) with decreased seawater pH, coupled with large increases in the abundance of Endozoicomonas, an endosymbiont. P. lobata experienced a significant decrease in ECF pH near the vent, whereas P. rus experienced a trending decrease in ECF pH near the vent. In contrast, Pocillopora exhibited bacterial community destabilization (increases in community dispersion), with significant decreases in Endozoicomonas abundance, while its ECF pH remained unchanged across the pH gradient. Our study shows that OA has multiple consequences on Endozoicomonas abundance and suggests that Endozoicomonas abundance may be an indicator of coral response to OA. We reveal an interesting dichotomy between two facets of coral physiology (regulation of bacterial communities and regulation of calcification), highlighting the importance of multidisciplinary approaches to understanding coral health and function in a changing ocean.IMPORTANCE Ocean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e., calcification) and disrupting associated bacterial communities. Coral-associated bacteria are important for host health, but it remains unclear how coral-associated bacterial communities will respond to future OA conditions. We document changes in coral-associated bacterial communities and changes to calcification physiology with long-term exposure to decreases in seawater pH that are environmentally relevant under midrange IPCC emission scenarios (0.1 pH units). We also find species-specific responses that may reflect different responses to long-term OA. In Pocillopora, calcification physiology was highly regulated despite changing seawater conditions. In Porites spp., changes in bacterial communities do not reflect a breakdown of coral-bacterial symbiosis. Insights into calcification and host-microbe interactions are critical to predicting the health and function of different coral taxa to future OA conditions.

Can serial PEF measurements separate occupational asthma from allergic alveolitis?

BACKGROUND: Occupational asthma commonly results in work-related changes in serial peak expiratory flow (PEF) measurements. Whether alveolitis can result in similar changes is unknown. AIMS: To identify differences and similarities of serial PEF between workers with occupational alveolitis and asthma seen during an outbreak investigation in a factory with metal-working fluid exposure. METHODS: Workers with respiratory symptoms and rest-day improvement were identified by questionnaire. Each was asked to measure PEF 8 times daily for 4 weeks at home and work. Alveolitis was subsequently diagnosed from a validated scoring system including radiological changes, carbon monoxide diffusing capacity, bronchoalveolar lavage and biopsy results. Occupational asthma was confirmed with a positive Oasys score >2.5 and a mean rest-work PEF >16 l/min from serial 2-hourly PEF measurements. The Oasys PEF plotter calculated differences between rest and workdays for mean PEF, diurnal variation and the scores were used to confirm an occupational effect (Oasys, area between curve and time point). Records were compared between the alveolitis group and the group with occupational asthma without alveolitis. RESULTS: Forty workers with occupational asthma and 16 with alveolitis had indistinguishable PEF changes on workdays in terms of magnitude (median reduction 18.5 and 16.1 l/min, respectively) and diurnal variation. Immediate reactions were more common with occupational asthma and late reactions more common with alveolitis. CONCLUSIONS: PEF responses to metal-working fluid aerosols do not distinguish occupational asthma from alveolitis except in timing. They can be used to identify the workplace as the cause of asthma and also alveolitis.

Description of viral assemblages associated with the Gorgonia ventalina holobiont.

The diversity and function of viruses in coral holobionts has only recently received attention. The non-reef building gorgonian octocoral, Gorgonia ventalina, is a major constituent of Caribbean reefs. We investigated viral communities associated with G. ventalina tissues to understand their role in gorgonian ecology. Pyrosequencing was used to prepare a total of 514,632 sequence reads of DNA- and RNA-based mixed-community viral genomes (metaviromes). RNA viral assemblages were comprised of primarily unidentifiable reads, with most matching host transcripts and other RNA metaviromes. DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Only ~5% of contigs matched viral proteins that were primarily cyanophage and viruses of Chlorella and Ostreococcus. Our results confirm that DNA and RNA viruses comprise a component of the gorgonian holobiont, suggesting that they may play a role in the ecology of G. ventalina.

An ABC estimate of pedigree error rate: application in dog, sheep and cattle breeds.

On the basis of correlations between pairwise individual genealogical kinship coefficients and allele sharing distances computed from genotyping data, we propose an approximate Bayesian computation (ABC) approach to assess pedigree file reliability through gene-dropping simulations. We explore the features of the method using simulated data sets and show precision increases with the number of markers. An application is further made with five dog breeds, four sheep breeds and one cattle breed raised in France and displaying various characteristics and population sizes, using microsatellite or SNP markers. Depending on the breeds, pedigree error estimations range between 1% and 9% in dog breeds, 1% and 10% in sheep breeds and 4% in cattle breeds.

An outbreak of occupational asthma due to chromium and cobalt.

BACKGROUND: Five metal turners employed by an aerospace manufacturer presented to the Birmingham Chest Clinic occupational lung disease unit. Four cases of occupational asthma (OA) due to chromium salt (3) and cobalt (1) were diagnosed by serial peak-expiratory flow measurements and specific inhalation challenge testing. AIMS: To measure the extent of the outbreak and to provide epidemiological data to ascertain the aetiology. METHODS: Participants answered a detailed, self-administered questionnaire, designed to detect occupational lung disease. Urine chromium and cobalt excretion, spirometry and exhaled nitric oxide measurements were taken. Those with possible, probable or definite non-OA or OA, after questionnaire, were invited to undertake two-hourly peak flow measurements and received specialist follow-up. RESULTS: A total of 62 workers (95% of workforce) participated. Sixty-one per cent of employees were working in higher metalworking fluid (MWF) exposure areas. Ninety per cent of workers had urinary chromium excretion indicating occupational exposure. Sixty-six per cent of workers reported active respiratory symptoms, although there were no significant differences between exposure groups. Two further workers with probable OA were identified and had significantly higher urinary chromium and cobalt concentration than asymptomatic controls. Eighteen cases of occupational rhinitis (OR) were identified, with significantly raised urinary chromium concentration compared with asymptomatic controls. CONCLUSIONS: Chromium salt and cobalt can be responsible for OA and OR in workers exposed to MWF aerosols. Onset of symptoms in those with positive specific challenges followed change in MWF brand. Workers with OA had increased urinary concentrations of chromium and cobalt, and those with OR had increased urinary concentrations of chromium.

Shift work effects on serial PEF measurements for occupational asthma.

BACKGROUND: Diurnal variation (DV) affects lung function but the changes are thought to be related to sleep patterns rather than time of day. When diagnosing occupational asthma (OA), serial peak expiratory flow (PEF) measurements are the recommended first line investigation, but could be confounded by shift work. AIMS: The aim of the study was to investigate the effects of shift work on PEF measurements used for diagnosing OA. METHODS: PEF records containing more than one shift pattern with ≥ 4 days per shift were identified. OA diagnosis was based on an Oasys-2 score ≥ 2.51 and non-OA on having an alternative clinical diagnosis and Oasys-2 score <2.51. The mean area between curves (ABC) score, mean PEF DV and cross-shift PEF changes were calculated for each shift. RESULTS: Records from 123 workers with OA and 69 without OA satisfied inclusion criteria. In the OA group, PEF declined more on afternoon and night shifts than days (P < 0.001). The ABC score was lower in the OA group on night (P < 0.05) and afternoon shifts (P < 0.05) as compared with days, without significant differences in DV. Among those without OA, cross-shift PEF increased more on day shifts (mean + 25 l/min) than afternoon or night shifts (+1 l/min) (P < 0.001). The sensitivity for the ABC score and DV were good and similar across shifts, but specificity was reduced using DV (DV mean 39%; ABC 98%). CONCLUSIONS: PEF responses between work and rest show small differences according to shift type. The ABC score has a high sensitivity and specificity for all shifts; differences in DV have lower specificity.

Evolution of the genetic variability of eight French dairy cattle breeds assessed by pedigree analysis.

A pedigree analysis was performed on eight French dairy cattle breeds to assess their change in genetic variability since a first analysis completed in 1996. The Holstein, Normande and Montbéliarde breeds are selected internationally with over hundreds of thousands cows registered in the performance recording system. Three breeds are internationally selected but with limited numbers of cows in France (Brown Swiss, French Simmental and French Red Pied). The last two remaining breeds (Abondance and Tarentaise) are raised at regional level. The effective numbers of ancestors of cows born between 2004 and 2007 varied between 15 (Abondance and Tarentaise) and 51 (French Red Pied). The effective population sizes (classical approach) varied between 53 (Abondance) and 197 (French Red Pied). This article also compares the genetic variability of the ex situ (collections of the French National Cryobank) and in situ populations. The results were commented in regard to the recent history of gene flows in the different breeds as well as the existence of more or less stringent bottlenecks. Our results showed that whatever the size of the breeds, their genetic diversity impoverished quite rapidly since 1996 and they all could be considered as quite poor from a genetic diversity point of view. It shows the need for setting up cryobanks as gene reservoirs as well as sustainable breeding programmes that include loss of genetic diversity as an integrated control parameter.

Ex situ conservation of Holstein-Friesian cattle: comparing the Dutch, French, and US germplasm collections.

Holstein-Friesian (HF) gene bank collections were established in France, the Netherlands, and the United States to conserve genetic diversity for this breed. Genetic diversity of HF collections within and between countries was assessed and compared with active male HF populations in each country by using pedigree data. Measures of genetic diversity such as probability of gene origin inbreeding and kinship were calculated. The cryobanks have captured substantial amounts of genetic diversity for the HF compared with the current populations. A substantial part of the US, French, and Dutch collections seems to be genetically similar. On the other hand, the US collection in particular represents an interesting reservoir of HF genes of the past. Gene banks can play an important role in conserving genetic diversity within livestock breeds over time, and may support industry in the future when needed.

Impact of conservation measures on demography and genetic variability of livestock breeds.

Conservation of animal genetic resources requires regular monitoring and interventions to maintain population size and manage genetic variability. This study uses genealogical information to evaluate the impact of conservation measures in Europe, using (i) data from the Domestic Animal Diversity Information System (DAD-IS) and (ii) a posteriori assessment of the impact of various conservation measures on the genetic variability of 17 at-risk breeds with a wide range of interventions. Analysis of data from DAD-IS showed that 68% of national breed populations reported to receive financial support showed increasing demographic trends, v. 51% for those that did not. The majority of the 17 at-risk breeds have increased their numbers of registered animals over the last 20 years, but the changes in genetic variability per breed have not always matched the trend in population size. These differences in trends observed in the different metrics might be explained by the tensions between interventions to maintain genetic variability, and development initiatives which lead to intensification of selection.

Diagnosis of occupational asthma from time point differences in serial PEF measurements.

BACKGROUND: The diagnosis of occupational asthma requires objective confirmation. Analysis of serial measurements of peak expiratory flow (PEF) is usually the most convenient first step in the diagnostic process. A new method of analysis originally developed to detect late asthmatic reactions following specific inhalation testing is described. This was applied to serial PEF measurements made over many days in the workplace to supplement existing methods of PEF analysis. METHODS: 236 records from workers with independently diagnosed occupational asthma and 320 records from controls with asthma were available. The pooled standard deviation for rest day measurements was obtained from an analysis of variance by time. Work day PEF measurements were meaned into matching 2-hourly time segments. Time points with mean work day PEF statistically lower (at the Bonferroni adjusted 5% level) than the rest days were counted after adjusting for the number of contributing measurements. RESULTS: A minimum of four time point comparisons were needed. Records with >or=2 time points significantly lower on work days had a sensitivity of 67% and a specificity of 99% for the diagnosis of occupational asthma against independent diagnoses. Reducing the requirements to >or=1 non-waking time point difference increased sensitivity to 77% and reduced specificity to 93%. The analysis was only applicable to 43% of available records, mainly due to differences in waking times on work and rest days. CONCLUSION: Time point analysis complements other validated methods of PEF analysis for the diagnosis of occupational asthma. It requires shorter records than are required for the Oasys score and can identify smaller changes than other methods, but is dependent on low rest day PEF variance.

Serial PEF measurement is superior to cross-shift change in diagnosing occupational asthma.

Cross-shift measurements of peak expiratory flow (PEF) are commonly employed in the diagnosis of occupational asthma, although evidence for this approach is lacking. The current paper presents an evaluation of the technique. Mean changes in PEF across morning/day shifts were compared between workers with occupational asthma, confirmed using specific challenge testing, and non-working asthmatics. Individuals were divided into a development set, used to identify the optimum cross-shift change for diagnosing occupational asthma, and an evaluation set, used to test the sensitivity and specificity of this value. Comparative analysis of serial PEF records was performed using the Oasys-2 computerised system. A cross-shift decrease in PEF of 5 L.min(-1) achieved acceptable specificity in the development set. Applied to the evaluation set, this cut-off had a specificity of 90.9% and a sensitivity of 50%. Sensitivity could not be improved without unacceptable compromise to specificity. Analysis of serial PEF records using linear discriminant analysis identified occupational asthma with a sensitivity of 83.3% and a specificity of 90.9%. Serial analysis using mean work/rest day PEF comparison had a sensitivity of 66.7% and a specificity of 100%. Cross-shift changes in PEF in morning/day-shift workers have poor sensitivity in diagnosing occupational asthma, and are inferior to serial techniques.

Dinucleotide relative abundance extremes: a genomic signature.

Early biochemical experiments established that the set of dinucleotide odds ratios or 'general design' is a remarkably stable property of the DNA of an organism, which is essentially the same in protein-coding DNA, bulk genomic DNA, and in different renaturation rate and density gradient fractions of genomic DNA in many organisms. Analysis of currently available genomic sequence data has extended these earlier results, showing that the general designs of disjoint samples of a genome are substantially more similar to each other than to those of sequences from other organisms and that closely related organisms have similar general designs. From this perspective, the set of dinucleotide odds ratio (relative abundance) values constitute a signature of each DNA genome, which can discriminate between sequences from different organisms. Dinucleotide-odds ratio values appear to reflect not only the chemistry of dinucleotide stacking energies and base-step conformational preferences, but also the species-specific properties of DNA modification, replication and repair mechanisms.

Finding the genes in genomic DNA.

Genome sequencing efforts will soon generate hundreds of millions of bases of human genomic DNA containing thousands of novel genes. In the past year, the accuracy of computational gene-finding methods has improved significantly, to the point where a reasonable approximation of the gene structures within an extended genomic region can often be predicted in advance of more detailed experimental studies.

Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species.

In humans, the clinical and molecular characterization of sporadic syndromes is often hindered by the small number of patients and the difficulty in developing animal models for severe dominant conditions. Here we show that the availability of large data sets of whole-genome sequences, high-density SNP chip genotypes and extensive recording of phenotype offers an unprecedented opportunity to quickly dissect the genetic architecture of severe dominant conditions in livestock. We report on the identification of seven dominant de novo mutations in CHD7, COL1A1, COL2A1, COPA, and MITF and exploit the structure of cattle populations to describe their clinical consequences and map modifier loci. Moreover, we demonstrate that the emergence of recessive genetic defects can be monitored by detecting de novo deleterious mutations in the genome of bulls used for artificial insemination. These results demonstrate the attractiveness of cattle as a model species in the post genomic era, particularly to confirm the genetic aetiology of isolated clinical case reports in humans.

Phase I study of liposomal vincristine.

PURPOSE: A phase I study of vincristine encapsulated inside 120-nm-diameter distearoylphosphatidylcholine-cholesterol liposomes was performed. The primary objectives were to determine the maximum-tolerated dose (MTD), recommended phase II dose, toxicity, and pharmacokinetics of liposomal vincristine (ONCO-TCS). PATIENTS AND METHODS: Twenty-five patients with histologically confirmed malignancies were enrolled and assessable. Vincristine doses were increased from 0.5 mg/m2 to 1.0, 1.5, 2.0, 2.4, and 2.8 mg/m2 with cohorts of three or more patients per dose level. A total of 64 courses of ONCO-TCS were administered intravenously once every 3 weeks. The pharmacokinetics of total vincristine content in plasma were determined using a high-performance liquid chromatography method. RESULTS: Patients were treated with vincristine doses up to 2.8 mg/m2; however, 2.4 mg/m2 was defined as the MTD and 2.0 mg/m2 as the phase II recommended dose. Pain and obstipation were the dose-limiting toxicites. Other toxicities were fever, rigors, fatigue, myalgias, and peripheral neuropathy. Hematologic toxicity was mild. All patients who were treated with doses above 1.5 mg/m2 received in excess of 2.0 mg of vincristine, with doses as high as 6.2 mg. One partial response was seen in a patient with pancreatic cancer. Tumor response not meeting partial response criteria was seen in two other patients. Pharmacokinetic studies revealed significantly elevated concentrations of total vincristine, but parameters varied and were not directly correlated with toxicity or response. CONCLUSION: The ability to administer elevated doses of vincristine, as well as indications of efficacy, suggests that ONCO-TCS warrants further clinical investigation in a phase II setting.

Prediction of complete gene structures in human genomic DNA.

We introduce a general probabilistic model of the gene structure of human genomic sequences which incorporates descriptions of the basic transcriptional, translational and splicing signals, as well as length distributions and compositional features of exons, introns and intergenic regions. Distinct sets of model parameters are derived to account for the many substantial differences in gene density and structure observed in distinct C + G compositional regions of the human genome. In addition, new models of the donor and acceptor splice signals are described which capture potentially important dependencies between signal positions. The model is applied to the problem of gene identification in a computer program, GENSCAN, which identifies complete exon/intron structures of genes in genomic DNA. Novel features of the program include the capacity to predict multiple genes in a sequence, to deal with partial as well as complete genes, and to predict consistent sets of genes occurring on either or both DNA strands. GENSCAN is shown to have substantially higher accuracy than existing methods when tested on standardized sets of human and vertebrate genes, with 75 to 80% of exons identified exactly. The program is also capable of indicating fairly accurately the reliability of each predicted exon. Consistently high levels of accuracy are observed for sequences of differing C + G content and for distinct groups of vertebrates.

An efficient algorithm for identifying matches with errors in multiple long molecular sequences.

An efficient algorithm is described for finding matches, repeats and other word relations, allowing for errors, in large data sets of long molecular sequences. The algorithm entails hashing on fixed-size words in conjunction with the use of a linked list connecting all occurrences of the same word. The average memory and run time requirement both increase almost linearly with the total sequence length. Some results of the program's performance on a database of Escherichia coli DNA sequences are presented.