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Among the currently available virus detection assays, those based on the programmable CRISPR-Cas enzymes have the advantage of rapid reporting and high sensitivity without the requirement of thermocyclers. Type III-A CRISPR-Cas system is a multi-component and multipronged immune effector, activated by viral RNA that previously has not been repurposed for disease detection owing in part to the complex enzyme reconstitution process and functionality. Here, we describe the construction and application of a virus detection method, based on an in vivo-reconstituted Type III-A CRISPR-Cas system. This system harnesses both RNA- and transcription-activated dual nucleic acid cleavage activities as well as internal signal amplification that allow virus detection with high sensitivity and at multiple settings. We demonstrate the use of the Type III-A system-based method in detection of SARS-CoV-2 that reached 2000 copies/μl sensitivity in amplification-free and 60 copies/μl sensitivity via isothermal amplification within 30 min and diagnosed SARS-CoV-2-infected patients in both settings. The high sensitivity, flexible reaction conditions, and the small molecular-driven amplification make the Type III-A system a potentially unique nucleic acid detection method with broad applications., (© 2021. The Author(s).)

Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas., Competing Interests: The authors have declared that no competing interests exist.

Chromatin accessibility of a promoter is fundamental in regulating transcriptional activity. The histone variant H2A.Z has been shown to contribute to this regulation, but its role has remained poorly understood. Here, we prepare high-depth maps of the position and accessibility of H2A.Z-containing nucleosomes for all human Pol II promoters in epithelial, mesenchymal and isogenic cancer cell lines. We find that, in contrast to the prevailing model, many different types of active and inactive promoter structures are observed that differ in their nucleosome organization and sensitivity to MNase digestion. Key aspects of an active chromatin structure include positioned H2A.Z MNase resistant nucleosomes upstream or downstream of the TSS, and a MNase sensitive nucleosome at the TSS. Furthermore, the loss of H2A.Z leads to a dramatic increase in the accessibility of transcription factor binding sites. Collectively, these results suggest that H2A.Z has multiple and distinct roles in regulating gene expression dependent upon its location in a promoter.

Presented here are data from Next-Generation Sequencing of differential micrococcal nuclease digestions of formaldehyde-crosslinked chromatin in selected tissues of maize ( Zea mays ) inbred line B73. Supplemental materials include a wet-bench protocol for making DNS-seq libraries, the DNS-seq data processing pipeline for producing genome browser tracks. This report also includes the peak-calling pipeline using the iSeg algorithm to segment positive and negative peaks from the DNS-seq difference profiles. The data repository for the sequence data is the NCBI SRA, BioProject Accession PRJNA44570 8.

Background: This study evaluates a novel bronchodilator, S1226, for its efficacy in reversing allergen-induced bronchoconstriction in subjects with mild, allergic asthma. S1226 is a new class of bronchodilator that is an aerosol/vapor/gas mixture combining pharmacological and biophysical principles for a novel mode of action. It contains a potent bronchodilator gas (carbon dioxide or CO 2 ) and nebulized perflubron (a synthetic surfactant possessing mucolytic properties). It has demonstrated rapid reversal of allergen-induced bronchoconstriction in an ovine study model., Methods: This was a phase IIa proof-of-concept, placebo-controlled, randomized, double-blind, crossover single-dose clinical trial to evaluate the safety, tolerability, and efficacy of S1226 (8% CO 2 ) administered by nebulization following an allergen-induced early asthmatic response in 12 subjects with mild, allergic asthma. Primary safety endpoints were adverse events, vital signs, pulse oximetry, and spirometry. Efficacy endpoints included bronchodilator response (measured as the forced expiratory volume in 1 s or FEV 1 ) over time, the area under the curve of FEV 1 for the early asthmatic response over time, and achievement of responder status, defined as a 12% improvement after the allergen challenge., Results: No significant safety issues were observed. All adverse events were non-serious, mild, and transient. There was a statistically significant decrease in peripheral blood oxygenation levels over time in the placebo group following allergen inhalation, whereas blood oxygenation was maintained at normal levels in the S1226-treated subjects (P = 0.028). This effect was greatest 5 min after start of treatment (P < 0.001). The recovery rate was faster but not significantly so (P = 0.272) for S1226 compared to the placebo at earlier time points (5, 10, and 15 min), as assessed by ≥12% reversal of FEV 1. The recovery of FEV 1 over time was significantly greater (P = 0.04) with S1226 compared to the placebo., Conclusions: S1226 was safe, tolerated well, and provided bronchodilation and improved blood oxygenation in subjects with mild atopic asthma following allergen-induced bronchoconstriction. Additional studies to optimize the therapeutic response are indicated., Trial Registration: ClinicalTrials.gov, NCT02334553 . Registered on 12 November 2014.

Background: Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean values. Despite dozens of algorithms developed to address this problem in genomics research, methods with improved accuracy and speed are still needed to effectively tackle both existing and emerging genomic and epigenomic segmentation problems., Results: We designed an efficient algorithm, called iSeg, for segmentation of genomic and epigenomic profiles. iSeg first utilizes dynamic programming to identify candidate segments and test for significance. It then uses a novel data structure based on two coupled balanced binary trees to detect overlapping significant segments and update them simultaneously during searching and refinement stages. Refinement and merging of significant segments are performed at the end to generate the final set of segments. By using an objective function based on the p-values of the segments, the algorithm can serve as a general computational framework to be combined with different assumptions on the distributions of the data. As a general segmentation method, it can segment different types of genomic and epigenomic data, such as DNA copy number variation, nucleosome occupancy, nuclease sensitivity, and differential nuclease sensitivity data. Using simple t-tests to compute p-values across multiple datasets of different types, we evaluate iSeg using both simulated and experimental datasets and show that it performs satisfactorily when compared with some other popular methods, which often employ more sophisticated statistical models. Implemented in C++, iSeg is also very computationally efficient, well suited for large numbers of input profiles and data with very long sequences., Conclusions: We have developed an efficient general-purpose segmentation tool and showed that it had comparable or more accurate results than many of the most popular segment-calling algorithms used in contemporary genomic data analysis. iSeg is capable of analyzing datasets that have both positive and negative values. Tunable parameters allow users to readily adjust the statistical stringency to best match the biological nature of individual datasets, including widely or sparsely mapped genomic datasets or those with non-normal distributions.

We show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineage-specific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination activating gene (RAG) recombinase. These changes result in establishment of a specific chromatin organization at the RSS that facilitates accessibility of the genomic DNA for the RAG recombinase. In contrast, in mouse embryonic fibroblasts the coding segment is depleted of nucleosomes, which instead cover the RSS, thereby rendering it inaccessible. Pro-T cells exhibit a pattern intermediate between pro-B cells and mouse embryonic fibroblasts. We also find large-scale variations of nucleosome density over hundreds of kilobases, delineating chromosomal domains within IgH, in a cell type-dependent manner. These findings suggest that developmentally regulated changes in nucleosome location and occupancy, in addition to the known chromatin modifications, play a fundamental role in regulating V(D)J recombination. Nucleosome positioning-which has previously been observed to vary locally at individual enhancers and promoters-may be a more general mechanism by which cells can regulate the accessibility of the genome during development, at scales ranging from several hundred base pairs to many kilobases., Competing Interests: The authors declare no conflict of interest.

Histone variants are known to play a central role in genome regulation and maintenance. However, many variants are inaccessible by antibody-based methods or bottom-up tandem mass spectrometry due to their highly similar sequences. For many, the only tractable approach is with intact protein top-down tandem mass spectrometry. Here, ultra-high-resolution FT-ICR MS and MS/MS yield quantitative relative abundances of all detected HeLa H2A and H2B isobaric and isomeric variants with a label-free approach. We extend the analysis to identify and relatively quantitate 16 proteoforms from 12 sequence variants of histone H2A and 10 proteoforms of histone H2B from three other cell lines: human embryonic stem cells (WA09), U937, and a prostate cancer cell line LaZ. The top-down MS/MS approach provides a path forward for more extensive elucidation of the biological role of many previously unstudied histone variants and post-translational modifications.

Background: A major challenge in treating acute asthma exacerbations is the need to open constricted airways rapidly enough to reestablish ventilation and allow delivery of conventional medication to diseased airways. The solution requires a new approach that considers both biophysical and pharmacological aspects of treatments used in acute asthma. The result of testing several formulations was S-1226: carbon dioxide-enriched air delivered in nebulized perflubron, a synthetic surfactant. These agents act synergistically to rapidly reopen closed airways within seconds. The bronchodilator effect is independent of β-adrenergic and cholinergic mediated-signaling pathways, offering a unique mechanism of action. S-1226 has a low toxicity profile and was effective in treating bronchoconstriction in animal models of asthma. The goal of the present study was to evaluate the safety and tolerability of S-1226 in healthy human subjects., Methods: The phase I study was a single-center, randomized, double-blind, placebo-controlled, sequential, single-ascending-dose study conducted in Canada. Thirty-six subjects were distributed into three cohorts. Within each cohort, subjects were randomized to receive a single dose of S-1226 or a matching placebo administered over a 2-minute nebulization period. S-1226 was formulated with perflubron and 4 %, 8 %, or 12 % CO2. The dose of CO2 was sequentially escalated by cohort. The safety and tolerability of S-1226 were evaluated through assessment of adverse events, vital signs, 12-lead electrocardiograms, clinical laboratory parameters, and physical examinations., Results: S-1226 was safe and well tolerated at all three CO2 levels (4 %, 8 %, and 12 %). A total of 28 adverse events were reported, and all were judged mild in severity. Twenty-four adverse events occurred in the S-1226 cohort, of which five were considered remotely related and six possibly related to S-1226., Conclusions: S-1226 is a novel drug being developed for the treatment of acute asthma exacerbations. It consists of CO2-enriched air and perflubron and has potential to offer rapid and potent bronchodilation. The results of the study indicate that S-1226 is safe and well tolerated. All adverse events were mild, reversible, and likely due to known side effects of CO2 inhalation., Trial Registration: ClinicalTrials.gov NCT02616770 . Registered on 25 November 2015.

Altered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Important studies have mapped human nucleosome distributions genome wide, but the role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Transcription Start Site Sequence Capture method (mTSS-seq) to map the nucleosome distribution at human transcription start sites genome-wide in primary human lung and colon adenocarcinoma tissue. Here, we confirm that nucleosome redistribution is an early, widespread event in lung (LAC) and colon (CRC) adenocarcinoma. These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they may serve as important early adenocarcinoma markers. We demonstrate that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. We conclude that DNA-directed nucleosome redistributions are widespread early in cancer progression. We have proposed an entirely new hierarchical model for chromatin-mediated genome regulation.

Nucleosome occupancy is critically important in regulating access to the eukaryotic genome. Few studies in human cells have measured genome-wide nucleosome distributions at high temporal resolution during a response to a common stimulus. We measured nucleosome distributions at high temporal resolution following Kaposi's-sarcoma-associated herpesvirus (KSHV) reactivation using our newly developed mTSS-seq technology, which maps nucleosome distribution at the transcription start sites (TSS) of all human genes. Nucleosomes underwent widespread changes in organization 24 hours after KSHV reactivation and returned to their basal nucleosomal architecture 48 hours after KSHV reactivation. The widespread changes consisted of an indiscriminate remodeling event resulting in the loss of nucleosome rotational phasing signals. Additionally, one in six TSSs in the human genome possessed nucleosomes that are translationally remodeled. 72% of the loci with translationally remodeled nucleosomes have nucleosomes that moved to positions encoded by the underlying DNA sequence. Finally we demonstrated that these widespread alterations in nucleosomal architecture potentiated regulatory factor binding. These descriptions of nucleosomal architecture changes provide a new framework for understanding the role of chromatin in the genomic response, and have allowed us to propose a hierarchical model for chromatin-based regulation of genome response.

Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug naïve positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse.

The unique chromatin signature of ES cells is fundamental to the pluripotency and differentiation of ES cells. One key feature is the poised chromatin state of master developmental genes that are transcriptionally repressed in ES cells but ready to be activated in response to differentiation signals. Poised chromatin in ES cells contains both H3 Lys-4 trimethylation (H3K4me3) and H3 Lys-27 trimethylation (H3K27me3) methylation, indicating activating and repressing potential. However, the contribution of non-covalent chromatin structure to the poised state is not well understood. To address whether remodeling of nucleosomes is important to the poised state, we characterized the function of BAF250a, a key regulatory subunit of the ES cell ATP-dependent Brahma-associated factor (BAF) chromatin remodeling complex (esBAF). Acute deletion of BAF250a disrupted the differentiation potential of ES cells by altering the expression timing of key developmental genes and pluripotent genes. Our genome-wide nucleosome and histone modification analyses indicated that the disruption of gene expression timing was largely due to changes of chromatin structures at poised genes, particularly those key developmental genes mediated by BAF250a. Specifically, BAF250a deletion caused a nucleosome occupancy increase at H3K4me3- and/or H3K27me3-associated promoters. Moreover, H3K27me3 levels and the number of bivalent promoter genes were reduced in BAF250a KO ES cells. We revealed that BAF250a ablation led to elevated Brg1 but reduced Suz12 recruitment at nucleosome occupancy-increased regions, indicating an unexpected and complicated role of BAF250a in regulating esBAF and Polycomb repressive complex (PRC) activities. Together, our studies identified that BAF250a mediates esBAF and PRC functions to establish the poised chromatin configuration in ES cells, which is essential for the proper differentiation of ES cells., (© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.)

In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, nucleosome dynamics during a genome response have not been well characterized [1,2]. We stimulated Drosophila S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the immune response, with the significant nucleosomal loss occurring at 4 h after stimulation. Data have been deposited to the Gene Expression Omnibus (GEO) database repository with the dataset identifier GSE64507.

The regulation of metazoan gene expression occurs in part by pre-mRNA splicing into mature RNAs. Signals affecting the efficiency and specificity with which introns are removed have not been completely elucidated. Splicing likely occurs cotranscriptionally, with chromatin structure playing a key regulatory role. We calculated DNA encoded nucleosome occupancy likelihood (NOL) scores at the boundaries between introns and exons across five metazoan species. We found that (i) NOL scores reveal a sequence-based feature at the introns on both sides of the intron-exon boundary; (ii) this feature is not part of any recognizable consensus sequence; (iii) this feature is conserved throughout metazoa; (iv) this feature is enriched in genes sharing similar functions: ATPase activity, ATP binding, helicase activity, and motor activity; (v) genes with these functions exhibit different genomic characteristics; (vi) in vivo nucleosome positioning data confirm ontological enrichment at this feature; and (vii) genes with this feature exhibit unique dinucleotide distributions at the intron-exon boundary. The NOL scores point toward a physical property of DNA that may play a role in the mechanism of pre-mRNA splicing. These results provide a foundation for identification of a new set of regulatory DNA elements involved in splicing regulation.

In the eukaryotic nucleus, DNA is packaged into chromatin. The fundamental subunit of chromatin is the nucleosome, DNA is wrapped 1.6 times around a histone octamer core. Nuclear processes in eukaryotes are impacted by whether regulatory DNA is occupied by nucleosomes. We used microarrays to measure nucleosome occupancy in human cells post Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation at hundreds of immunity-related loci. The detailed analysis of these technologies can be found in recent publications from our lab (Druliner et al., 2013; Sexton et al., 2014). We found that nucleosome redistributions displayed chromosome specific nucleosome occupancy. This resource can be used to map nucleosome distributions in a variety of biological contexts.

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

The eukaryotic genome is organized into nucleosomes, the fundamental units of chromatin. The positions of nucleosomes on DNA regulate protein-DNA interactions and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in gene expression relate to changes in nucleosome position is poorly understood. We show that in nucleosome occupancy mapping experiments in maize (Zea mays), particular genomic regions are highly susceptible to variation introduced by differences in the extent to which chromatin is digested with micrococcal nuclease (MNase). We exploited this digestion-linked variation to identify protein footprints that are hypersensitive to MNase digestion, an approach we term differential nuclease sensitivity profiling (DNS-chip). Hypersensitive footprints were enriched at the 5' and 3' ends of genes, associated with gene expression levels, and significantly overlapped with conserved noncoding sequences and the binding sites of the transcription factor KNOTTED1. We also found that the tissue-specific regulation of gene expression was linked to tissue-specific hypersensitive footprints. These results reveal biochemical features of nucleosome organization that correlate with gene expression levels and colocalize with functional DNA elements. This approach to chromatin profiling should be broadly applicable to other species and should shed light on the relationships among chromatin organization, protein-DNA interactions, and genome regulation., (© 2014 American Society of Plant Biologists. All rights reserved.)

Background: The low toxicity of perfluorocarbons (PFCs), their high affinity for respiratory gases and their compatibility with lung surfactant have made them useful candidates for treating respiratory diseases such as adult respiratory distress syndrome. We report results for treating acute allergic and non-allergic bronchoconstriction in sheep using S-1226 (a gas mixture containing carbon dioxide and small volumes of nebulized perflubron). The carbon dioxide, which is highly soluble in perflubron, was used to relax airway smooth muscle., Methods: Sheep previously sensitized to house dust mite (HDM) were challenged with HDM aerosols to induce early asthmatic responses. At the maximal responses (characterised by an increase in lung resistance), the sheep were either not treated or treated with one of the following; nebulized S-1226 (perflubron + 12% CO2), nebulized perflubron + medical air, 12% CO2, salbutamol or medical air. Lung resistance was monitored for up to 20 minutes after cessation of treatment., Results: Treatment with S-1226 for 2 minutes following HDM challenge resulted in a more rapid, more profound and more prolonged decline in lung resistance compared with the other treatment interventions. Video bronchoscopy showed an immediate and complete (within 5 seconds) re-opening of MCh-constricted airways following treatment with S-1226., Conclusions: S-1226 is a potent and rapid formulation for re-opening constricted airways. Its mechanism(s) of action are unknown. The formulation has potential as a rescue treatment for acute severe asthma.

Nucleosome occupancy plays a key role in regulating access to eukaryotic genomes. Although various chromatin regulatory complexes are known to regulate nucleosome occupancy, the role of DNA sequence in this regulation remains unclear, particularly in mammals. To address this problem, we measured nucleosome distribution at high temporal resolution in human cells at hundreds of genes during the reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV). We show that nucleosome redistribution peaks at 24 h post-KSHV reactivation and that the nucleosomal redistributions are widespread and transient. To clarify the role of DNA sequence in these nucleosomal redistributions, we compared the genes with altered nucleosome distribution to a sequence-based computer model and in vitro-assembled nucleosomes. We demonstrate that both the predicted model and the assembled nucleosome distributions are concordant with the majority of nucleosome redistributions at 24 h post-KSHV reactivation. We suggest a model in which loci are held in an unfavorable chromatin architecture and "spring" to a transient intermediate state directed by DNA sequence information. We propose that DNA sequence plays a more considerable role in the regulation of nucleosome positions than was previously appreciated. The surprising findings that nucleosome redistributions are widespread, transient, and DNA-directed shift the current perspective regarding regulation of nucleosome distribution in humans.

The nucleosome is a fundamental structural and functional chromatin unit that affects nearly all DNA-templated events in eukaryotic genomes. It is also a biochemical substrate for higher order, cis-acting gene expression codes and the monomeric structural unit for chromatin packaging at multiple scales. To predict the nucleosome landscape of a model plant genome, we used a support vector machine computational algorithm trained on human chromatin to predict the nucleosome occupancy likelihood (NOL) across the maize (Zea mays) genome. Experimentally validated NOL plots provide a novel genomic annotation that highlights gene structures, repetitive elements, and chromosome-scale domains likely to reflect regional gene density. We established a new genome browser (http://www.genomaize.org) for viewing support vector machine-based NOL scores. This annotation provides sequence-based comprehensive coverage across the entire genome, including repetitive genomic regions typically excluded from experimental genomics data. We find that transposable elements often displayed family-specific NOL profiles that included distinct regions, especially near their termini, predicted to have strong affinities for nucleosomes. We examined transcription start site consensus NOL plots for maize gene sets and discovered that most maize genes display a typical +1 nucleosome positioning signal just downstream of the start site but not upstream. This overall lack of a -1 nucleosome positioning signal was also predicted by our method for Arabidopsis (Arabidopsis thaliana) genes and verified by additional analysis of previously published Arabidopsis MNase-Seq data, revealing a general feature of plant promoters. Our study advances plant chromatin research by defining the potential contribution of the DNA sequence to observed nucleosome positioning and provides an invariant baseline annotation against which other genomic data can be compared.

The development and progression of lung adenocarcinoma, one of the most common cancers, is driven by the interplay of genetic and epigenetic changes and the role of chromatin structure in malignant transformation remains poorly understood. We used systematic nucleosome distribution and chromatin accessibility microarray mapping platforms to analyze the genome-wide chromatin structure from normal tissues and from primary lung adenocarcinoma of different grades and stages. We identified chromatin-based patterns across different patients with lung adenocarcinoma of different cancer grade and stage. Low-grade cancers had nucleosome distributions very different compared with the corresponding normal tissue but had nearly identical chromatin accessibility. Conversely, nucleosome distributions of high-grade cancers showed few differences. Substantial disruptions in chromosomal accessibility were seen in a patient with a high-grade and high-stage tumor. These data imply that chromatin structure changes during the progression of lung adenocarcinoma. We have therefore developed a model in which low-grade lung adenocarcinomas are linked to changes in nucleosome distributions, whereas higher-grade tumors are linked to large-scale chromosomal changes. These results provide a foundation for the development of a comprehensive framework linking the general and locus-specific roles of chromatin structure to lung cancer progression. We propose that this strategy has the potential to identify a new class of chromatin-based diagnostic, prognostic and therapeutic markers in cancer progression.

Several 400- to 800-kb murine chromosome domains switch from early to late replication during loss of pluripotency, accompanied by a stable form of gene silencing that is resistant to reprogramming. We found that, whereas enhanced nuclease accessibility correlated with early replication genome-wide, domains that switch replication timing during differentiation were exceptionally inaccessible even when early-replicating. Nonetheless, two domains studied in detail exhibited substantial changes in transcriptional activity and higher-order chromatin unfolding confined to the region of replication timing change. Chromosome conformation capture (4C) data revealed that in the unfolded state in embryonic stem cells, these domains interacted preferentially with the early-replicating chromatin compartment, rarely interacting even with flanking late-replicating domains, whereas after differentiation, these same domains preferentially associated with late-replicating chromatin, including flanking domains. In both configurations they retained local boundaries of self-interaction, supporting the replication domain model of replication-timing regulation. Our results reveal a principle of developmentally regulated, large-scale chromosome folding involving a subnuclear compartment switch of inaccessible chromatin. This unusual level of regulation may underlie resistance to reprogramming in replication-timing switch regions.

Genome-scale mapping of pre-replication complex proteins has not been reported in mammalian cells. Poor enrichment of these proteins at specific sites may be due to dispersed binding, poor epitope availability or cell cycle stage-specific binding. Here, we have mapped sites of biotin-tagged ORC and MCM protein binding in G1-synchronized populations of Chinese hamster cells harboring amplified copies of the dihydrofolate reductase (DHFR) locus, using avidin-affinity purification of biotinylated chromatin followed by high-density microarray analysis across the DHFR locus. We have identified several sites of significant enrichment for both complexes distributed throughout the previously identified initiation zone. Analysis of the frequency of initiations across stretched DNA fibers from the DHFR locus confirmed a broad zone of de-localized initiation activity surrounding the sites of ORC and MCM enrichment. Mapping positions of mononucleosomal DNA empirically and computing nucleosome-positioning information in silico revealed that ORC and MCM map to regions of low measured and predicted nucleosome occupancy. Our results demonstrate that specific sites of ORC and MCM enrichment can be detected within a mammalian initiation zone, and suggest that initiation zones may be regions of generally low nucleosome occupancy where flexible nucleosome positioning permits flexible pre-RC assembly sites.

Background: Laboratory methods for measuring vaccine potency of nebulized aerosol are required to support clinical trials of measles aerosol vaccination., Methods: Measles vaccine containing the Edmonston Zagreb virus strain was reconstituted in sodium fluoride as tracer and nebulized from three devices. Emitted aerosol was collected using an impinger. Aliquots were removed from the impinger chamber for vaccine virus plaque assay and for fluoride measurement to determine aerosol output., Results: Vaccine potency retention results were adjusted to take into account the effect of aerosol output on estimates. Adjusted potency of nebulized vaccine ranged from 88% to 102%., Conclusions: New laboratory methods to measure aerosol vaccine potency retention were reliable and accurate. The results demonstrated that Edmonston Zagreb vaccine remains robust during aerosolisation and imply that this is a viable candidate for further evaluation in the measles aerosol project.

The fundamental building block of chromatin, the nucleosome, occupies 150 bp of DNA in a spaced arrangement that is a primary determinant in regulation of the genome. The nucleosomal organization of some regions of the human genome has been described, but mapping of these regions has been limited to a few kilobases. We have explored two independent and complementary methods for the high-throughput analysis of mammalian chromatin structure. Through adaptations to a protocol used to map yeast chromatin structure, we determined sites of nucleosomal protection over large regions of the mammalian genome using a tiling microarray. By modifying classical primer extension methods, we localized specific internucleosomally cleaved mammalian genomic sequences using a capillary electrophoresis sequencer in a manner that allows high-throughput nucleotide-resolution characterization of nucleosome protection patterns. We developed algorithms for the automated and unbiased analysis of the resulting data, a necessary step toward large-scale analysis. We validated these assays using the known positions of nucleosomes on the mouse mammary tumor virus LTR, and additionally, we characterized the previously unreported chromatin structure of the LCMT2 gene. These results demonstrate the effectiveness of the combined methods for reliable analysis of mammalian chromatin structure in a high-throughput manner.

Concentrations of cadmium, lead, nickel and vanadium were determined in water, surficial sediments and the muscle of three demersal fish species (Epinephelus coioides, Psettodes erumei and Solea elongate) from 15 sampling sites in the northern part of Persian Gulf. Concentrations of the elements were determined using Inductively Coupled Plasma Mass Spectrometer. There were no significant differences among the sampling sites in Cd and Pb levels in the sediments. The highest concentrations of Ni and V in sediments were found near the southern coast of Qeshm Iland and Bandar Lengeh. Concentrations of Cd, Pb and Ni in the sediments were notably higher than global baseline values. Nearly in all cases the element concentrations in the sediments were considerably greater than RSA (ROPME Sea Area) and the ERL (Effects Range Low) guidelines. Significant differences among the sampling sites could be found for concentrations of all the four metals in water. The mean Ni, Pb and Cd levels in the water samples were relatively higher than those in some other regions of the Persian Gulf. Except few cases, the mean concentrations of the elements in muscle of the selected fish species were markedly below the international guidelines for human consumption.

In breast cancer, overexpression of the small heat shock protein, HSP-27, is associated with increased anchorage-independent growth, increased invasiveness, and resistance to chemotherapeutic drugs and is associated with poor prognosis and reduced disease-free survival. Therefore, factors that increase the expression of HSP-27 in breast cancer are likely to affect the prognosis and outcome of treatment. In this study, we show a strong correlation between elevated levels of the Brn-3b POU transcription factor and high levels of HSP-27 protein in manipulated MCF-7 breast cancer cells as well as in human breast biopsies. Conversely, HSP-27 is decreased on loss of Brn-3b. In cotransfection assays, Brn-3b can strongly transactivate the HSP-27 promoter, supporting a role for direct regulation of HSP-27 expression. Brn-3b also cooperates with the estrogen receptor (ER) to facilitate maximal stimulation of the HSP-27 promoter, with significantly enhanced activity of this promoter observed on coexpression of Brn-3b and ER compared with either alone. RNA interference and site-directed mutagenesis support the requirement for the Brn-3b binding site on the HSP-27 promoter, which facilitates maximal transactivation either alone or on interaction with the ER. Chromatin immunoprecipitation provides evidence for association of Brn-3b with the HSP-27 promoter in the intact cell. Thus, Brn-3b can, directly and indirectly (via interaction with the ER), activate HSP-27 expression, and this may represent one mechanism by which Brn-3b mediates its effects in breast cancer cells.

This study investigates the distribution of three trace elements (Cd, Cu and Zn) in tissues (exoskeleton, abdominal muscle and hepatopancreas) of two shrimp species (Penaeus merguiensis and Penaeus semisulcatus). Special emphasis in this study was placed on evaluating the effects of storage conditions on redistribution of the elements and moreover the potential roles of metallothionein in tissue redistribution. The specimens were collected from the northern part of Persian Gulf during September 2001 and January 2002. The concentrations of metals in the tissues were measured using an Inductively Coupled Plasma-Atomic Emission Spectrophotometer (ICP-AES) and an ICP-Mass Spectrometer (ICP-MS). Metallothionein levels were determined using Differential pulse polarography. Results show a similar hierarchy for Cd and Cu concentrations among different tissues as follows: hepatopancreas>exoskeleton>muscle; and for Zn, the hepatopancreas again contained the highest levels, though there were not any significant differences in Zn concentrations between muscle and exoskeleton. Significant differences were found between the species in the case of Cd and Zn concentrations. Cd and Zn levels in P. semisulcatus were markedly higher than in P. merguiensis. In general, there were highly significant differences among the storage conditions from accumulation the selected trace elements and metallothionein in both species point of view, but in most cases, no significant differences could be observed among the fresh, refrigerated and frozen specimens of P. semisulcatus. In regards to Zn and Cu accumulation in edible (muscle) tissues of P. merguiensis, optimum conditions for frozen storage is -30 degrees C as ice-frozen, and in terms of short-term storage, 1-day refrigeration is recommended. The redistribution of Zn and Cu during the storage period can be attributed to the role of metallothionein in their transport from organ(s) to muscle during storage. The variations in pH values measured in the muscle of P. merguiensis in different storage conditions showed a similar trend with metallothionein, Zn and Cu. In contrast, it appears that cadmium is transported from muscle to the other tissues. Exoskeleton is probably one of the recipient tissues of cadmium. The inter-elemental relationships were assessed for each species, separately. A significant positive relationship was observed between the concentrations of Zn and metallothionein in P. semisulcatus, whereas in P. merguiensis, Cd concentrations decreased significantly with increasing metallothionein. Highly significant differences between the sexes in Cu and Zn contents could be detected. The differences between the sexes in the levels of Zn and Cu were significantly greater in P. semisulcatus. Highly significant size-related differences were found in the levels of Cd, Cu and metallothionein in the selected tissues of the shrimp species. Comparison between the mean concentrations of the elements in muscle tissue and existing guidelines indicate that in nearly all cases, the concentrations were well below permissible levels for human consumption. The only exception was observed regarding mean values of Cd, which was somewhat greater than some of the recommended levels.

This study is focused on twenty trace elements (Ag, Ba, Bi, Cd, Co, Cr, Cs, Cu, Ga, In, Mn, Mo, Pb, Rb, Sb, Sn, Sr, Ti, V, Zn) accumulation in muscles of five sturgeon species (Acipenser guldenstaedti, A. persicus, A. nudiventris, A. stellatus and Huso huso) from the southern part of the Caspian Sea. Moreover the relationships between some biological characteristics and the levels of the selected elements as well as inter-elemental relationships were assessed. The samples (10 specimens for each the five species) were collected from two important sturgeon fishery zones located in the Iranian part of the Sea in 2002. Concentrations of the elements were determined using ICP-MS. Only in the case of Cs could significant differences between two selected sampling areas be detected. There were significant differences in levels of Co, Ga, Rb, Sn, Ti, Pb and Bi in muscles of the species. Only in the case of Cd weight related differences among the species were found. The significant length dependent relationships were observed for Ga and Ba. Patterns of elements accumulation were assessed by statistical methods and compared to the other researches. In all the cases, the amounts of toxic trace elements (Cd, Cu, Pb and Zn) were markedly below the international guidelines for human consumption.

The study was conducted between January and December 2002. The main objective of this study was evaluation of effects of refrigerated storage duration on redistribution of three trace elements (Cd, Cu and Zn) in tissues (exoskeleton, abdominal muscle and hepatopancreas) of a shrimp species (Penaeus semisulcatus). Moreover, the possible roles of metallothionein (a kind of metalloprotein) in redistribution of the elements in tissues of the selected species were assessed. The specimens were sampled from northwestern part of the Persian Gulf. The concentrations of metals in the tissues were measured using Inductively Coupled Plasma-Optical Emission Spectrophotometer (ICP-OES). Metallothionein levels were determined by Differential Pulse Polarography (DPP) method. pH of the muscle samples was also measured in different stages. Different statistical methods were used for interpretation of the results. There were no size-dependent differences in metal contents of the species. The results were compared with specimens from other areas of the world and existing guidelines and limits. Concentrations of the metals in the muscle (0.103, 3.418 and 8.977 microg g(-1) wet weight in the case of Cd, Cu and Zn, respectively) samples were below the most guidelines for human consumption. The results were in general agreement with those obtained by some other researchers. There were highly significant differences between sexes in Zn and Cu contents. Levels of Zn in females were significantly higher than males. The reverse case observed for Cu. The highest mean Cu and Zn concentrations (15.939 and 43.394 microg g(-1) wet weight, respectively) were found in hepatopancreas samples, but the highest level of Cd (0.790 microg g(-1) wet weight) was observed in exoskeleton. There were significant differences between the fresh and refrigerated samples from accumulation of Cd and Zn in tissues point of view, which can be attributed to the metal binding properties of metallothioneins as well as their degradation during the storage.

This review is focused on distribution and redistribution of trace elements in various tissues of different shrimp species, especially genus Penaeus. The possible roles of metallothionein in this regard are emphasized. Factors affecting heavy metals uptake and distribution have also been reviewed separately. Moreover, patterns of metals bioaccumulation and their order of occurrence have been evaluated. Another part of this paper deals with comparison of the related data from different aquatic environments as well as existing guidelines and limits for human consumption. Generally, the number of conducted studies in some related context, especially in the case of possible roles of metallothionein during storage of organisms is very limited.

Objective: To determine the accuracy of questions in identifying subjects occupationally exposed to high noise level and those with hearing loss using noise dosimeter and pure-tone air conduction audiometry as the gold standards., Design: A cross-sectional study involving 259 noise-exposed workers selected randomly from two factories in Eastern Saudi Arabia. Personal noise exposure was determined using a noise dosimeter. The hearing impairment for each subject was assessed using otoscopic examination and audiometry. Each subject completed a comprehensive questionnaire including questions about noise exposure and hearing loss., Results: Eighty five percent of the total workers reported exposure to high noise level, compared to 76% found to be exposed to a high noise level defined as more than 85 dB (A) as determined by noise dosimeter. The prevalence of audiometric hearing loss (threshold average of 25 dB HL or more in any ear) was 32.4% for the low frequency average (0.5, 1 and 2 kHz), 47.9% for the all frequency average (0.5, 1, 2. 4 and 8 kHz) and 65.6% for the high frequency average (4 and 8 kHz). However, the percentage of the subjects who reported hearing loss ranged between 3.9% and 85.3% depending on the question used as indicator of hearing loss. The question "Do you consider the noise level where you are working now high?" was the most sensitive in correctly identifying subjects exposed to a noise level of more than 85 dB (A) (sensitivity = 93.4%) and subjects with hearing loss (sensitivity > 86%) compared with other questions evaluated. However, it overestimated the prevalence rate determined by audiometry., Conclusion: We conclude that in industries where facilities for an objective assessment of noise exposure and hearing loss are not available, questions addressing noise exposure and hearing loss might be a useful alternative means for screening subjects exposed to high noise level and those with hearing loss for the purpose of designing and implementing hearing conservation program.

This paper evaluates the suitability of various compressors available in Europe to generate and deliver tobramycin nebulizer solution to cystic fibrosis patients from the PARI LC PLUS jet nebulizer. This evaluation has been undertaken (i) by establishing an in vitro equivalence to the DeVilbiss PulmoAide compressor (operating at 4.6 l/min) proven effective in US clinical trials, and (ii) by determining equivalent in vitro performance of the LC PLUS nebulizer driven by alternative airflows. Equivalent performance is judged as having both an aerosol output and aerosol size within +/-10% of that obtained with the LC PLUS/PulmoAide combination. The two different in vitro methodologies applied to this investigation were based on the British Standard and a European Standard to assess nebulizer output. The results demonstrate that a wide range of compressed airflow rates generate aerosol output from the PARI LC PLUS equivalent to that obtained from the PulmoAide compressor. This range of airflows encompasses many compressors commonly available in Europe.

The delivery of nebulized drugs is poorly controlled and the choice of the most appropriate delivery device is poorly understood, particularly because of off-license prescriptions and a lack of evidence-based medicine. Standardized in vitro methods for measuring nebulizer performance have been adopted in Europe, by the 2001 publication of a European Standard, prEN13544-1. These standardized methods were subsequently incorporated within the European Respiratory Society nebulizer guidelines, which will provide clinicians with useful information to improve nebulizer therapies. Standards for measuring nebulizer performance should be considered in North America and elsewhere. Careful consideration should be given to either adopting the methods embodied in the European Standard or developing the basis for developing that standard further through the International Standards Organization. Either way, confusion among clinicians would be reduced and nebulizer safety and aerosol delivery efficiency increased by standardizing in vitro methods of nebulizer performance assessment.

The choice of a nebulized system for a patient usually depends on the equipment available. To date, there is limited guidance on the selection and use of a nebulizer. We have conducted in vitro tests described within the draft European Standard for Nebulisers (BSEN13544-1; CEN) and correlated these to in vivo pharmacokinetic performance of relative lung and systemic deposition in healthy volunteers. Eight nebulizer systems have been tested. The in vitro analysis used the recommended CEN methods to quantify the total dose available for inhalation as well as the size distribution from which the respirable dose was determined. The draft European Standard methods were slightly modified to use salbutamol rather than a fluoride tracer. For the in vivo study, nine volunteers provided urine samples after 30 min and then pooled for 24 h after the start of each nebulized dose (2.5 mg of salbutamol). Amounts of salbutamol and its metabolite excreted in the urine samples were determined. There was a significant (p = 0.02) correlation between the in vitro respirable dose and the amount of salbutamol excreted in the urine 30 min after the start of nebulization (relative bioavailability of salbutamol to the lung). Also, there was a significant (p < 0.001) correlation between the in vitro dose available for inhalation and the total amount of salbutamol and its metabolites excreted over the 24 h after the start of nebulization (relative bioavailability of salbutamol to the body). The results demonstrate that in vivo/in vitro correlations exist and warrant further investigations. The in vitro methods require further validation with in vivo correlations using patients with different severities of airway obstruction.

The Brn-3a POU domain transcription factor is able to regulate the transcription of promoters containing a Brn-3 response element via its POU domain. In addition, the POU domain of Brn-3a has been shown to functionally interact with the estrogen receptor and regulate transcription from estrogen responsive promoters. The steroid receptor coactivator, Src-1, enhances transcription with a variety of steroid receptors. Here we describe a functional interaction between Brn-3a and Src-1. In glutathione S-transferase pull-down assays Src-1 was shown to specifically interact with Brn-3 proteins. Moreover, Src-1 co-immunoprecipitated from intact cells with Brn-3a. The transactivation potential of the Brn-3a/Src-1 complex was tested on both the Brn-3 responsive SNAP-25 promoter and the estrogen responsive vitellogenin promoter, in each of two different cell lines, the neuronal ND7 cell line, and the kidney BHK21 cell line. Src-1 consistently and strongly potentiated the activation of Brn-3a on the SNAP promoter construct in both the ND7 and BHK21 cell lines. The vitellogenin promoter construct, however, was only weakly activated by the Brn-3/Src-1 complex in the ND7 cells and there was even less effect on this promoter in the BHK21 cells. These results suggest a functional role for Src-1 in enhancing Brn-3a mediated transactivation, seemingly independent of nuclear hormone receptors, thus broadening the transcriptional repertoire of both Brn-3a and Src-1., ((c) 2002 Elsevier Science (USA).)

Previous work has demonstrated that the shield gas composition in gas metal arc welding can have a considerable effect on hexavalent chromium [Cr(VI)] concentration in the fume and on ozone concentrations near the arc. Normally a single shield gas is used. This paper describes a double shroud torch that allows used of concentric shield gases of different compositions. A solid stainless steel wire was used for welding. The double shroud torch used secondary shield gases containing small amounts of the reducing agents NO and C2H4. The Cr(VI) concentration in the fume and ozone concentration at a fixed point relative to the arc were measured and compared with results when using a single shield gas. Use of the reducing agents in secondary shielding using the double shroud torch was found to offer advantages for ozone concentration reduction compared with use in a conventional torch, but this was not found to be an advantage for reducing Cr(VI) concentrations.

Hexavalent chromium [Cr(VI)] and ozone are produced in many arc-welding processes. Cr(VI) is formed when welding with chromium-containing alloys and is a suspected carcinogen. Ozone is formed by the action of ultraviolet light from the arc on oxygen and can cause severe irritation to the eyes and mucous membranes. Previous work has demonstrated that reduction of sodium and potassium in manual metal arc-welding electrodes leads to substantial reductions in Cr(VI) concentrations in the fume as well as a reduction in the fume formation rate. In this paper replacement of potassium by lithium in a tubular wire welding electrode (self-shielding flux-cored) is shown to give reductions in Cr(VI) concentrations and fume formation rates. Previous work has also demonstrated that use of a tubular wire (metal cored) containing 1% zinc can, under certain conditions, result in a reduction in Cr(VI) formation rate and in ozone concentration near the arc but with a rise in the total fume formation rate. The effects of different shield gases and different levels of zinc are examined. An experimental chromium-containing tubular wire with 1% zinc was used with the following shield gases: argon, Argoshield 5, Argoshield 20, Helishield 101, Ar + 2% CO2, Ar + 5% CO2, Ar + 1% O2 and Ar + 2% O2. The wire gave > 98% reduction in Cr(VI) formation rate compared to the control wire provided the shield gas contained no oxygen. When the shield gas did contain oxygen, 1% zinc enhanced Cr(VI) formation rate, resulting in more than double the rates measured when welding with the control wire. Experiments with zinc concentrations, from 0.018 to 0.9% using Helishield 101, gave results indicating that there is an optimum zinc concentration from the point of view of Cr(VI) reduction. Implications of the use of lithium or zinc on the overall exposure risk are discussed.

The Brn-3b POU domain containing transcription factor is expressed in the developing sensory nervous system as well as in epithelial cells of the breast, cervix, and testes. Brn-3b functionally interacts with the estrogen receptor (ER) and in association with the ER, regulates transcription from estrogen responsive genes. In addition, Brn-3b expression is elevated in breast tumours compared to levels in normal mammary cells. To explore the role of Brn-3b in breast cancer, we established stable cell lines derived from the MCF7 human breast cancer cell line which had been transfected with Brn-3b sense or anti-sense constructs. The Brn-3b over-expressing cell lines exhibited increased growth rate, reached confluence at a higher saturation density, had higher proliferative activity, and an enhanced ability to form colonies in soft agar when compared to the control empty vector transfected cells. Likewise, the Brn-3b anti-sense cell lines showed reduced cellular growth and proliferation, reached confluence at a lower density, and exhibited a decreased ability to form colonies in soft agar when compared to the vector controls. Five to ten per cent of the Brn-3b over-expressing cells exhibited a severely altered morphology characterized by reduced adherence to tissue culture plastic, increased cell size, and a vacuolar cell shape. These results thus further indicate a role for the Brn-3b transcription factor in regulating mammary cell growth and suggest that its elevation in breast cancer is of functional significance.

Objective: To determine the prevalence of hearing loss associated with occupational noise exposure and other risk factors., Design: A cross-sectional study involving 269 exposed and 99 non-exposed subjects (non-industrial noise exposed subjects) randomly selected. Current noise exposure was estimated using both sound level meter and noise-dosimeter. Past noise exposure was estimated by interview questionnaire. Otoscopic examination and conventional frequency (0.25-8 kHz) audiometry were used to assess the hearing loss in each subject., Results: 75% (202 subjects) from the exposed group were exposed to a daily Leq above the permissible level of 85 dB(A) and most (61%) of these did not and had never used any form of hearing protection. Hearing loss was found to be bilateral and symmetrical in both groups. Bivariate analysis showed a significant hearing loss in the exposed vs non-exposed subjects with a characteristic dip at 4 kHz. Thirty eight percent of exposed subjects had hearing impairment, which was an 8-fold higher rate than that found for non-exposed subjects. Multivariate analysis indicated exposure to noise was the primary, and age the secondary predictor of hearing loss. Odds of hearing impairment were lower for a small sub-group of exposed workers using hearing protection (N=19) in which logistic regression analysis showed the probability of workers adopting hearing protective devices increased with noise exposure, education, and awareness of noise control. Hearing loss was also greater amongst those who used headphones to listen to recorded cassettes., Conclusion: Gross occupational exposure to noise has been demonstrated to cause hearing loss and the authors believe that occupational hearing loss in Saudi Arabia is a widespread problem. Strategies of noise assessment and control are introduced which may help improve the work environment.

The objective was to investigate the reliability and effects of age and noise on high-frequency hearing thresholds. A cross-sectional study was used involving 187 exposed and 52 non-industrial noise-exposed subjects selected randomly from noise-exposed and non-industrial noise-exposed subjects, respectively. Each subject was tested with both conventional-frequency (0.25-8 kHz) and high-frequency (10-18 kHz) audiometry. Test-retest results showed that high-frequency audiometry (HFA) was as reliable as the conventional procedure. Although the inter-subject variation was large, the intra-subject variation was small, indicating that HFA can be used more reliably than the conventional procedure to monitor individual cases over time. Both the hearing threshold at high frequencies and the upper frequency limit deteriorated as a function of age and frequency. The exposed subjects had significantly higher hearing thresholds than the non-exposed subjects at all the high frequencies tested, the difference between the two groups being greatest at 14 kHz. Multivariate analysis indicated that age was the primary predictor and noise exposure the secondary predictor of hearing thresholds in a high frequency range (10-18 kHz). In contrast, multivariate analysis indicated the reverse order-noise exposure as the primary predictor, then age-for a conventional frequency range (0.25-8 kHz). The results of this study suggest that HFA might be used as an early indicator for noise-induced hearing loss and acoustic trauma rather than audiometry at a conventional frequency (4 kHz), particularly for younger groups.

Inhalation provocation tests were used to assess whether the volatile products of an activated resin had caused occupational asthma in a non-random sample of six asthmatic coal miners. The resin system uses the polymerization of polyester and styrene under the influence of the cross-linking agent dibenzoyl peroxide to secure roof, wall and floor bolts in mine tunnels. The tests were conducted sequentially in a double-blind fashion over a 'dose' range which extended just beyond the maximum likely to have been experienced occupationally during a single day's work. The tests were monitored by symptoms, changes in the forced expiratory volume in 1 s (FEV1) and changes in airway responsiveness. All subjects completed the series of tests without any significant decrements in FEV1 or significant increases in airway responsiveness. We conclude that the use of this resin system is not likely to have been the cause of the asthma in the test subjects, nor in the larger group of miners of which they were a sample, but neither possibility is fully excluded and the participants may not have been adequately representative of other asthmatic coal miners.