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The COVID-19 pandemic highlighted the relevance of public health professionals all over the world, in particular Environmental Health Practitioners (EHPs), who played a major role in the containment of the novel coronavirus, SARS-CoV-2. However, as in past disasters, their involvement was oriented towards urgent tasks, and did not fully utilize EHPs' competences and skills. Additionally, due to limited resources, during emergencies EHPs may temporarily transition away from their day-to-day role, potentially increasing other public health and safety risk factors without appropriate surveillance or intervention. To overcome this and prepare for possible future pandemics, it is important to identify and discuss the key roles of EHPs in different countries, providing a common framework for practices that can contribute to population safety and health. To this end, an international workgroup was established to discuss current environmental health practices and challenges across different countries during the pandemic. Findings from discussions concluded that, despite the observed differences across the countries, EHPs are one of the main public health emergency preparedness and response actors. However, since resources are still lagging significantly behind need, we argue that the role of these professionals during pandemics should be focused on practices that have higher impact to support population health and safety., (© 2020 Elsevier Ltd. All rights reserved.)

Summary: Gartland type III posterolateral (IIIB) supracondylar humerus fractures are common among the pediatric population and can lead to concomitant injury, including compromise of the brachial artery and median nerve and long-term deformity, such as cubitus varus. These fractures can be difficult to reduce, and there is little consensus regarding the optimal technique for closed reduction and percutaneous pinning. Here, we discuss the management of Gartland III posterolateral supracondylar humerus fractures, including an in-depth technical description of the methods of operative fixation. We describe a lateral pin-only fixation technique for Gartland III posterolateral supracondylar humerus fractures that uses the intact periosteum during reduction of the distal fragment to assist in realigning the medial and lateral columns anatomically. We also discuss a safe method for placing a medial-based pin if there is persistent rotational instability at the fracture site after placement of the laterally based pins., Competing Interests: J. G. Schoenecker is a member of the education advisory board at OrthoPediatrics, receives research funding from OrthoPediatrics, serves as a board member of the Pediatric Society of North America (POSNA), and receives research support from IONIS Pharmaceuticals. The remaining authors report no conflict of interest., (Copyright © 2020 Wolters Kluwer Health, Inc. All rights reserved.)

The kangaroo soft tick, Ornithodoros gurneyi Warburton, 1926, is a poorly studied argasid of the more arid regions of Australia. Anecdotal accounts have stated that this tick species will bite humans, and yet bites have not been described. Herein we report on an instance of parasitism by a nymph of O. gurneyi on a human, and we provide a summary of confirmed instances of parasitism on humans by this tick based on museum specimens., (Crown Copyright © 2020. Published by Elsevier GmbH. All rights reserved.)

Background: The New Environmental Health is an approach to environmental health adopted in 1999. The new approach was in response to emerging health risks from the pressures that development placed on the environment, climate change, and increasing vulnerabilities of local communities. The new approach heralded a change in perception and roles within environmental health. Twenty years on, it seems these changes have not been embraced by local government., Methods: To determine whether this was the case, we assessed the use of the term "environmental health" in local government annual reports, and where environmental health functions sit within the organisational structure of councils., Results: We found that the New Environmental Health has not been adopted by councils and environmental health relates solely to the delivery of statutory services and legislative compliance., Conclusions: One result of this is local environmental health practitioners, who constitute the major health protection capability of councils, are defined by the narrow legislative obligations imposed on councils. This represents a significant lost opportunity as public health is not protected in the way that was envisaged with the adoption of the New Environmental Health.

Current practice for determining the exposure to methamphetamine in contaminated homes relies on the analysis of surface wipe sample to address direct contact exposures. The movement of methamphetamine into the air phase, and the potential for inhalation exposures to occur within residential homes contaminated from former clandestine manufacture or smoking of methamphetamine has been generally poorly characterised and understood. All available risk-based guidelines for determining safe levels of methamphetamine in residential properties do not include any consideration of the inhalation pathway as an exposure route. This study showed that methamphetamine can readily move from contaminated materials in a home into the air phase. This movement of methamphetamine into the air phase provides both an exposure pathway and a mechanism for the transfer of methamphetamine throughout a property. The inhalation exposure pathway has the potential to result in significant intake of methamphetamine, adding to dermal absorption and ingestion exposure routes. Guidelines that are established for the assessment of methamphetamine contaminated properties that ignore inhalation exposures can significantly underestimate exposure and result in guidelines that are not adequately protective of health. This study also demonstrates that sampling methamphetamine in air can be undertaken using commercially available sorption tubes and analytical methods.

Osteogenesis imperfecta (OI) is a rare genetic connective-tissue disorder with bone fragility. To avoid iatrogenic fractures, healthcare providers have traditionally avoided using non-invasive blood pressure (NIBP) cuffs and extremity tourniquets in the OI population in the perioperative setting. Here, we hypothesize that these procedures do not lead to iatrogenic fractures or other complications in patients with OI. A retrospective study of all children with OI who underwent surgery at a single tertiary care children's hospital from 1998 to 2018 was performed. Patient positioning and the use of NIBP cuffs, arterial lines, and extremity tourniquets were documented. Fractures and other complications were recorded. Forty-nine patients with a median age of 7.9 years (range: 0.2-17.7) were identified. These patients underwent 273 procedures, of which 229 were orthopaedic operations. A total of 246 (90.1%) procedures included the use of an NIBP cuff, 61 (22.3%) an extremity tourniquet, and 40 (14.7%) an arterial line. Pediatric patients with OI did not experience any iatrogenic fractures related to hemodynamic monitoring or extremity tourniquet use during the 20-year period of this study. Given the benefits of continuous intra-operative hemodynamic monitoring and extremity tourniquets, we recommend that NIBP cuffs, arterial lines, and tourniquets be selectively considered for use in children with OI.

Background: A number of factors have been shown to affect how surgeons are subjectively viewed, including their appearance in clinic. Patient preference for pediatric orthopaedic surgeon attire has not previously been studied, nor has its influence on initial perception of the surgeon., Methods: At 5 pediatric regional sites across the United States, parents and patients presenting to the pediatric orthopaedic clinic were given anonymous surveys showing 8 photos of surgeons in different clinical dress including in business or scrub dress, each with or without white coat (WC). Subjects reported their demographics, single preferred photo, rated characteristics of the surgeons in each photo on a 5-point Likert scale, and answered specific questions on scrubs and WCs. The first consecutively completed 100 parent and 100 patient surveys were included from each site., Results: One thousand surveys were collected from patients (500) and parents (500). The majority felt a surgeon's clinical dress would not affect how they are cared for (83%), and that it was ok to wear scrubs in clinic (90%). Overall, WC was preferred to those without no matter the age, but there was no difference between scrub and business choices. Of those stating a preference, woman in business and WC (24%) and woman in scrubs and WC (21%) were most selected, with the only geographic difference being the midwest's preference for man in business and WC. Females were more likely to prefer women photographs (P<0.0001)., Conclusions: In general, pediatric orthopaedic patients and parents do not have a strong specific preference toward what their surgeon wears to clinic, including whether or not we are dressed in scrubs, but some initial biases exist. When asked to choose, the traditional WC worn over any attire is preferred, and female patients and parents uncover a preference for a surgeon of their own sex., Level of Evidence: Level III.

The Protein Ontology (PRO) provides an ontological representation of protein-related entities, ranging from protein families to proteoforms to complexes. Protein Ontology Linked Open Data (LOD) exposes, shares, and connects knowledge about protein-related entities on the Semantic Web using Resource Description Framework (RDF), thus enabling integration with other Linked Open Data for biological knowledge discovery. For example, proteins (or variants thereof) can be retrieved on the basis of specific disease associations. As a community resource, we strive to follow the Findability, Accessibility, Interoperability, and Reusability (FAIR) principles, disseminate regular updates of our data, support multiple methods for accessing, querying and downloading data in various formats, and provide documentation both for scientists and programmers. PRO Linked Open Data can be browsed via faceted browser interface and queried using SPARQL via YASGUI. RDF data dumps are also available for download. Additionally, we developed RESTful APIs to support programmatic data access. We also provide W3C HCLS specification compliant metadata description for our data. The PRO Linked Open Data is available at https://lod.proconsortium.org/ .

Campylobacter spp. is one of the most widespread infectious diseases of veterinary and public health significance. Globally, the incidence of campylobacteriosis has increased over the last decade in both developing and developed countries. Squamates (lizards, snakes and amphisbaenians) are a potential reservoir and source of transmission of campylobacteriosis to humans. This systematic review examined studies from the last 20 years that have reported squamate-associated human campylobacteriosis. It was found that C. fetus subsp. testudinum and C. fetus subsp. fetus were the most common species responsible for human campylobacteriosis from a squamate host. The common squamate hosts identified included bearded dragons ( Pogona vitticeps ), green iguana ( Iguana iguana ), western beaked gecko ( Rhynchoedura ornate ) and blotched blue-tongued skink ( Tiliqua nigrolutea ). People with underlying chronic illnesses, the immunocompromised and the elderly were identified as the most vulnerable population. Exposure to pet squamates, wild animals, consumption of reptilian cuisines and cross contamination with untreated water were risk factors associated with Campylobacter infections. Proper hand hygiene practices, responsible pet ownership, 'One Health' education and awareness on zoonotic diseases will help reduce the public health risks arising from Campylobacter exposure through squamates. Continued surveillance using molecular diagnostic methods will also enhance detection and response to squamate-linked campylobacteriosis.

In response to the Coronavirus Disease 2019 (COVID-19) pandemic, current modeling supports the use of masks in community settings to reduce the transmission of SARS-CoV-2. However, concerns have been raised regarding the global shortage of medical grade masks and the limited evidence on the efficacy of fabric masks. This study used a standard mask testing method (ASTM F2101-14) and a model virus (bacteriophage MS2) to test the viral filtration efficiency (VFE) of fabric masks compared with commercially available disposable, surgical, and N95 masks. Five different types of fabric masks were purchased from the ecommerce website Etsy to represent a range of different fabric mask designs and materials currently available. One mask included a pocket for a filter; which was tested without a filter, with a dried baby wipe, and a section of a vacuum cleaner bag. A sixth fabric mask was also made according to the Victorian Department of Health and Human Services (DHHS) guidelines (Australia). Three masks of each type were tested. This study found that all the fabric masks had a VFE of at least 50% when tested against aerosols with an average size of 6.0 µm (VFE (6.0 µm) ). The minimum VFE of fabric masks improved (to 63%) when the larger aerosols were excluded to give and average aerosol size of 2.6 µm (VFE (2.6 µm) ), which better represents inhaled aerosols that can reach the lower respiratory system. The best performing fabric masks were the cotton mask with a section of vacuum cleaner bag (VFE (6.0 µm) = 99.5%, VFE (2.6 µm) = 98.8%) or a dried baby wipe (VFE (6.0 µm) = 98.5%, VFE (2.6 µm) = 97.6%) in the pocket designed for a disposable filter, the mask made using the Victorian DHHS design (VFE (6.0 µm) = 98.6%, VFE (2.6 µm) =99.1%) and one made from a layer of 100% hemp, a layer of poly membrane, and a layer of cheesecloth (VFE (6.0 µm) = 93.6%, VFE (2.6 µm) = 89.0%). The VFE of two surgical masks (VFE (6.0 µm) = 99.9% and 99.6%, VFE (2.6 µm) = 99.5% and 98.5%) and a N95 masks (VFE (6.0 µm) = 99.9%, VFE (2.6 µm) = 99.3%) were comparable to their advertised bacterial filtration efficacy. This research supports the use of fabric masks in the community to prevent the spread of SARS-CoV-2; however, future research is needed to explore the optimum design in ensuring proper fit. There is also a need for mass education campaigns to disseminate this information, along with guidelines around the proper usage and washing of fabric masks.

Late recurrences of breast cancer are hypothesized to originate from disseminated tumor cells that re-activate after a long period of dormancy, ≥5 years for estrogen-receptor positive (ER+) tumors. An outstanding question remains as to what the key microenvironment interactions are that regulate this complex process, and well-defined human model systems are needed for probing this. Here, a robust, bioinspired 3D ER+ dormancy culture model is established and utilized to probe the effects of matrix properties for common sites of late recurrence on breast cancer cell dormancy. Formation of dormant micrometastases over several weeks is examined for ER+ cells (T47D, BT474), where the timing of entry into dormancy versus persistent growth depends on matrix composition and cell type. In contrast, triple negative cells (MDA-MB-231), associated with early recurrence, are not observed to undergo long-term dormancy. Bioinformatic analyses quantitatively support an increased "dormancy score" gene signature for ER+ cells (T47D) and reveal differential expression of genes associated with different biological processes based on matrix composition. Further, these analyses support a link between dormancy and autophagy, a potential survival mechanism. This robust model system will allow systematic investigations of other cell-microenvironment interactions in dormancy and evaluation of therapeutics for preventing late recurrence., (© 2020 Wiley-VCH GmbH.)

Healthcare-associated infections (HAIs) are one of the most common patient complications, affecting 7% of patients in developed countries each year. The rise of antimicrobial resistant (AMR) bacteria has been identified as one of the biggest global health challenges, resulting in an estimated 23,000 deaths in the US annually. Environmental reservoirs for AMR bacteria such as bed rails, light switches and doorknobs have been identified in the past and addressed with infection prevention guidelines. However, water and water-related devices are often overlooked as potential sources of HAI outbreaks. This systematic review examines the role of water and water-related devices in the transmission of AMR bacteria responsible for HAIs, discussing common waterborne devices, pathogens, and surveillance strategies. AMR strains of previously described waterborne pathogens including Pseudomonas aeruginosa, Mycobacterium spp., and Legionella spp. were commonly isolated. However, methicillin-resistant Staphylococcus aureus and carbapenem-resistant Enterobacteriaceae that are not typically associated with water were also isolated. Biofilms were identified as a hot spot for the dissemination of genes responsible for survival functions. A limitation identified was a lack of consistency between environmental screening scope, isolation methodology, and antimicrobial resistance characterization. Broad universal environmental surveillance guidelines must be developed and adopted to monitor AMR pathogens, allowing prediction of future threats before waterborne infection outbreaks occur.

Legionella pneumophila is an opportunistic waterborne pathogen of public health concern. It is the causative agent of Legionnaires' disease (LD) and Pontiac fever and is ubiquitous in manufactured water systems, where protozoan hosts and complex microbial communities provide protection from disinfection procedures. This review collates the literature describing interactions between L. pneumophila and protozoan hosts in hospital and municipal potable water distribution systems. The effectiveness of currently available water disinfection protocols to control L. pneumophila and its protozoan hosts is explored. The studies identified in this systematic literature review demonstrated the failure of common disinfection procedures to achieve long term elimination of L. pneumophila and protozoan hosts from potable water. It has been demonstrated that protozoan hosts facilitate the intracellular replication and packaging of viable L. pneumophila in infectious vesicles; whereas, cyst-forming protozoans provide protection from prolonged environmental stress. Disinfection procedures and protozoan hosts also facilitate biogenesis of viable but non-culturable (VBNC) L. pneumophila which have been shown to be highly resistant to many water disinfection protocols. In conclusion, a better understanding of L. pneumophila -protozoan interactions and the structure of complex microbial biofilms is required for the improved management of L. pneumophila and the prevention of LD., Competing Interests: The authors declare no conflict of interest.

iPTMnet is a bioinformatics resource that integrates protein post-translational modification (PTM) data from text mining and curated databases and ontologies to aid in knowledge discovery and scientific study. The current iPTMnet website can be used for querying and browsing rich PTM information but does not support automated iPTMnet data integration with other tools. Hence, we have developed a RESTful API utilizing the latest developments in cloud technologies to facilitate the integration of iPTMnet into existing tools and pipelines. We have packaged iPTMnet API software in Docker containers and published it on DockerHub for easy redistribution. We have also developed Python and R packages that allow users to integrate iPTMnet for scientific discovery, as demonstrated in a use case that connects PTM sites to kinase signaling pathways., (© The Author(s) 2020. Published by Oxford University Press.)

Contamination of residential homes with methamphetamine is an emerging issue of significant concern to public health. Cooking or smoking methamphetamine in a residential property contaminates the house, furnishings and personal possessions within it, with subsequent exposure through ingestion, dermal absorption and/or inhalation causing adverse health effects. Current guidelines identifying levels of methamphetamine contamination that require remediation vary between countries. There is also no international standard protocol for measuring levels of contamination and research has shown that different materials give rise to different recovery rates of methamphetamine. There are a number of currently used remediation methods; however, they have varying levels of success with limited studies comparing their long-term efficacies. Most importantly, there are few guidelines available that are based on a transparent, health risk-based approach, and there are many uncertainties on exposures and health effects, making it difficult to ensure the health of people residing in homes that have been used to cook or smoke methamphetamine are sufficiently protected. This manuscript presents the current state of knowledge regarding the contamination of residential homes with methamphetamine and identifies the current gaps in knowledge and priority areas for future research. The current regulatory approach to public health protection associated with exposure to residential premises contaminated with methamphetamine in Australia, New Zealand and the USA is also discussed.

Contamination of domestic dwellings from methamphetamine cooking or smoking is an increasing public health problem in many countries. To evaluate the extent of contamination, sampling generally focusses on the collection of surface wipe samples from walls and other surfaces of a potentially contaminated home. Here, we report the contamination levels of many household materials and items sampled from a home that was suspected to be the premises used to cook methamphetamine, it was then sold, lived in for several years by the new owners and then left unattended for several more years. Although the time since the cooking had taken place was significant (over five years), the levels of contamination were extremely high in both household items that were part of the house when cooking was taking place (blinds, carpets, walls, etc.) and also in articles brought to the house post-cooking (rugs, toys, beds, etc.). Both wipe sampling and analysis of bulk samples indicate that the methamphetamine is not breaking down or being removed and is transferred from contaminated to non-contaminated objects. These results raise questions about the adequacy of characterising contamination and of making decisions about the extent of remediation required based solely on surface wipe samples. Without fully understanding the extent of contamination that is present, not only on surfaces but within the building materials, it is difficult to ensure that the correct and most effective remedial approaches are taken to appropriately determine and address the risks to inhabitants.

The extracellular matrix (ECM) is thought to play a critical role in the progression of breast cancer. In this work, we have designed a photopolymerizable, biomimetic synthetic matrix for the controlled, 3D culture of breast cancer cells and, in combination with imaging and bioinformatics tools, utilized this system to investigate the breast cancer cell response to different matrix cues. Specifically, hydrogel-based matrices of different densities and modified with receptor-binding peptides derived from ECM proteins [fibronectin/vitronectin (RGDS), collagen (GFOGER), and laminin (IKVAV)] were synthesized to mimic key aspects of the ECM of different soft tissue sites. To assess the breast cancer cell response, the morphology and growth of breast cancer cells (MDA-MB-231 and T47D) were monitored in three dimensions over time, and differences in their transcriptome were assayed using next generation sequencing. We observed increased growth in response to GFOGER and RGDS, whether individually or in combination with IKVAV, where binding of integrin β1 was key. Importantly, in matrices with GFOGER, increased growth was observed with increasing matrix density for MDA-MB-231s. Further, transcriptomic analyses revealed increased gene expression and enrichment of biological processes associated with cell-matrix interactions, proliferation, and motility in matrices rich in GFOGER relative to IKVAV. In sum, a new approach for investigating breast cancer cell-matrix interactions was established with insights into how microenvironments rich in collagen promote breast cancer growth, a hallmark of disease progression in vivo , with opportunities for future investigations that harness the multidimensional property control afforded by this photopolymerizable system.

Rainwater is consumed for drinking water in many parts of Australia, either preferentially over municipal water or in regional or remote areas, because rainwater is the primary source of water. Previous rainwater studies in other areas in Australia have shown the levels of some metals to be above the Australian Drinking Water Guidelines (ADWG). This study assessed the level of metals in rainwater harvested in the Adelaide region. Water samples were collected from 53 tanks from three different sampling corridors. A total of 365 water samples were analysed for lead, zinc, copper, and cadmium using atomic absorption spectrophotometry. In 47 out of the 53 tanks, lead was above the ADWG of 0.01 ppm in at least one sample (with 180/365 samples above 0.01 ppm). Zinc was above the ADWG (3.0 ppm) in 53/365 samples, copper was above the ADWG (2.0 ppm) in eight samples out of 365 samples, and cadmium was above the ADWG (0.002 ppm) in 19 samples out of 365 samples. These data are consistent with other studies of rainwater quality in Australia. Comparisons of levels of metals and volume of rainfall in the sampling and preceding month, roof material, and tank material, the presence of a first-flush device, sampling corridor, and sample pH showed that the roof material was related to higher levels of metals. There was a significant relationship between sampling corridors and the levels of lead and zinc. Nine of the tanks surveyed had filters installed. There was a small, but statistically significant, decrease in the levels of metals that passed through a filter prior to collection but, in those samples, filters did not remove metals to below guideline concentrations. An estimate of exposure, and a brief discussion of health risks as a result of exposure to metals, is presented.

Using roof harvested rainwater held in domestic rainwater tanks is a common practice in Australia, particularly in rural areas. This rainwater might become contaminated with ash and other contaminants during or after a bushfire. Current advice from Australian Health Departments can include the recommendation that landholders drain their tanks after a bushfire, which can cause additional distress to landholders who have already been through a traumatic event. This study created artificially contaminated water, spiked with chemicals likely to be associated with bushfires, including chromated copper arsenate-treated timber ash and firefighting foam to determine the possibility of contamination. The authors also tested two readily available filter systems and found that they removed some but not all contaminants. The artificially created contaminated water fell within guidelines for nonpotable uses such as irrigation and stock watering. This suggests that advice to landholders should be that tank water following a bushfire is likely to be safe for use for purposes apart from drinking. Landholders should be encouraged to retain and use their water for recovery purposes, but not for potable use.

Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies. We identify 32 functional domains enriched in cancer variants and PTMs and generate mechanistic hypotheses on overlapping variant and PTM sites by aggregating information at the residue, protein, pathway and species level from these resources. We experimentally test the hypothesis that S768 phosphorylation in the C-helix of EGFR is inhibitory by showing that oncogenic variants altering S768 phosphorylation increase basal EGFR activity. In contrast, oncogenic variants altering conserved phosphorylation sites in the 'hydrophobic motif' of PKCβII (S660F and S660C) are loss-of-function in that they reduce kinase activity and enhance membrane translocation. Our studies provide a framework for integrative, consistent, and reproducible annotation of the cancer kinomes.

In Australia, rainwater is an important source of water for many households. Unlike municipal water, rainwater is often consumed untreated. This study investigated the potential contamination of rainwater by microorganisms. Samples from 53 rainwater tanks across the Adelaide region were collected and tested using Colilert™ IDEXX Quanti-Tray*/2000. Twenty-eight out of the 53 tanks (53%) contained Escherichia coli . Samples collected from ten tanks contained E. coli at concentrations exceeding the limit of 150 MPN/100 mL for recreational water quality. A decline in E. coli was observed in samples collected after prolonged dry periods. Rainwater microbiological values depended on the harvesting environment conditions. A relationship was found between mounted TV antenna on rooftops and hanging canopies; and E. coli abundance. Conversely, there was no relationship between seasonality and E. coli or roof and tank structure materials and E. coli . In several tanks used for drinking water, samples collected prior to and after filtration showed that the filtration systems were not always successful at completely removing E. coli . These results differed from a study undertaken in the laboratory that found that a commercially available in-bench 0.45 µm filter cartridge successfully reduced E. coli in rainwater to 0 MPN/100 mL. After running a total of 265 L of rainwater which contained high levels of E. coli through the filter (half of the advertised filter lifespan), the filter cartridge became blocked, although E. coli remained undetected in filtered water. The difference between the laboratory study and field samples could be due to improper maintenance or installation of filters or recontamination of the faucet after filtration. The presence of E. coli in water that is currently used for drinking poses a potential health concern and indicates the potential for contamination with other waterborne pathogens., Competing Interests: The authors declare no conflict of interest.

To address concern regarding water sustainability, the Australian Federal Government and many state governments have implemented regulatory mechanisms and incentives to support households to purchase and install rainwater harvesting systems. This has led to an increase in rainwater harvesting in regional and urban Australia. This review examines the implementation of the regulatory mechanisms across Australia. In addition, the literature investigating the potential health consequences of rainwater consumption in Australia was explored. Studies demonstrated that although trace metals such as arsenic, cadmium, chromium, lead, and iron were present in Australian rainwater, these metallic elements were generally found below the health limit guideline, except in high industrial areas. In addition, pathogenic or indicator microorganisms that include, but are not limited to, Escherichia coli , total and faecal coliforms, Campylobacter , Salmonella , Legionella , Pseudomonas , Cryptosporidium , Enterococci, Giardia , Aeromonas , and Mycobacterium avium Complex (MAC) have been detected in rainwater collected in Australia. However, epidemiological evidence suggests that drinking rainwater does not increase the risk of gastrointestinal disease. It was also identified that there is a need for further research investigating the potential for rainwater to be a source of infection for opportunistic pathogens.

Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species. iPTMnet encompasses data from (i) our PTM-focused text mining tools, RLIMS-P and eFIP, which extract phosphorylation information from full-scale mining of PubMed abstracts and full-length articles; (ii) a set of curated databases with experimentally observed PTMs; and iii) Protein Ontology that organizes proteins and PTM proteoforms, enabling their representation, annotation and comparison within and across species. Presently covering eight major PTM types (phosphorylation, ubiquitination, acetylation, methylation, glycosylation, S-nitrosylation, sumoylation and myristoylation), iPTMnet knowledgebase contains more than 654 500 unique PTM sites in over 62 100 proteins, along with more than 1200 PTM enzymes and over 24 300 PTM enzyme-substrate-site relations. The website supports online search, browsing, retrieval and visual analysis for scientific queries. Several examples, including functional interpretation of phosphoproteomic data, demonstrate iPTMnet as a gateway for visual exploration and systematic analysis of PTM networks and conservation, thereby enabling PTM discovery and hypothesis generation., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Gene expression levels affect biological processes and play a key role in many diseases. Characterizing expression profiles is useful for clinical research, and diagnostics and prognostics of diseases. There are currently several high-quality databases that capture gene expression information, obtained mostly from large-scale studies, such as microarray and next-generation sequencing technologies, in the context of disease. The scientific literature is another rich source of information on gene expression-disease relationships that not only have been captured from large-scale studies but have also been observed in thousands of small-scale studies. Expression information obtained from literature through manual curation can extend expression databases. While many of the existing databases include information from literature, they are limited by the time-consuming nature of manual curation and have difficulty keeping up with the explosion of publications in the biomedical field. In this work, we describe an automated text-mining tool, Disease-Expression Relation Extraction from Text (DEXTER) to extract information from literature on gene and microRNA expression in the context of disease. One of the motivations in developing DEXTER was to extend the BioXpress database, a cancer-focused gene expression database that includes data derived from large-scale experiments and manual curation of publications. The literature-based portion of BioXpress lags behind significantly compared to expression information obtained from large-scale studies and can benefit from our text-mined results. We have conducted two different evaluations to measure the accuracy of our text-mining tool and achieved average F-scores of 88.51 and 81.81% for the two evaluations, respectively. Also, to demonstrate the ability to extract rich expression information in different disease-related scenarios, we used DEXTER to extract information on differential expression information for 2024 genes in lung cancer, 115 glycosyltransferases in 62 cancers and 826 microRNA in 171 cancers. All extractions using DEXTER are integrated in the literature-based portion of BioXpress.Database URL: http://biotm.cis.udel.edu/DEXTER.

Background and aims The aim of this research was to investigate the relationship between alexithymia and loss-chasing behavior in people at risk and not at risk for problem gambling. Methods An opportunity sample of 58 (50 males and 8 females) participants completed the Problem Gambling Severity Index and the Toronto Alexithymia Scale (TAS-20). They then completed the Cambridge Gambling Task from which a measure of loss-chasing behavior was derived. Results Alexithymia and problem gambling risk were significantly positively correlated. Subgroups of non-alexithymic and at or near caseness for alexithymia by low risk and at risk for problem gambling were identified. The results show a clear difference for loss-chasing behavior for the two alexithymia conditions, but there was no evidence that low and at-risk problem gamblers were more likely to loss chase. The emotion-processing components of the TAS-20 were shown to correlate with loss chasing. Discussion and conclusion These findings suggest that loss-chasing behavior may be particularly prevalent in a subgroup of problem gamblers those who are high in alexithymia.

Due to rapid urbanization, solid waste management (SWM) has become a significant issue in several developing countries including Thailand. Policies implemented by the Central Thai Government to manage SWM issues have had only limited success. This article reviews current municipal waste management plans in Thailand and examines municipal waste management at the local level, with focus on the Tha Khon Yang sub-district surrounding Mahasarakham University in Mahasarakham Province. Within two decades this area has been converted from a rural to an urban landscape featuring accommodation for over 45,000 university students and a range of business facilities. This development and influx of people has outpaced the government's ability to manage municipal solid waste (MSW). There are significant opportunities to improve local infrastructure and operational capacity; but there are few mechanisms to provide and distribute information to improve community participation in waste management. Many community-based waste management projects, such as waste recycling banks, the 3Rs (reduce, reuse and recycle), and waste-to-biogas projects have been abandoned. Additionally, waste from Tha Kon Yang and its surrounding areas has been transferred to unsanitary landfills; there is also haphazard dumping and uncontrolled burning of waste, which exacerbate current pollution issues.

Background: Much controversy still exists surrounding graft choice in anterior cruciate ligament (ACL) reconstruction. Over the past decade, an increase in comparative studies with longer follow-up has enhanced our understanding of current graft options and outcomes., Purpose: To describe the long-term comparative outcomes of ACL reconstruction with autograft bone-patellar tendon-bone (BPTB) versus autograft hamstring (HS) ACL reconstruction with regard to clinical and radiographic outcomes., Study Design: Systematic review; Level of evidence, 2., Methods: A search of the PubMed, MEDLINE, Cochrane, and Scopus databases was performed to identify studies in the English language with outcome data comparing ACL reconstruction utilizing autograft BPTB and autograft HS; only studies with a minimum 5-year follow-up were included. Outcome data included failure and complications, manual and instrumented laxity, patient-reported outcomes, and radiographic risk of osteoarthritis., Results: Twelve studies with a total of 953 patients met the inclusion criteria. Of these studies, 8 were level 1 evidence and 2 were level 2. Mean follow-up was 8.96 years (range, 5-15.3 years). No differences in graft failure or manual or instrumented laxity were seen in any studies. Lower clinical outcomes scores and greater motion loss were seen in BPTB patients in 1 and 2 studies, respectively. Two of 4 studies reporting on anterior knee pain, and 3 of 7 that recorded kneeling pain found it more frequently among BPTB patients. One study found significantly increased reoperation rates in HS patients, while another found a similar result in BPTB, and 1 study reported a significant increase in contralateral ACL tears in BPTB patients. Three of 5 studies reporting on radiographic evidence of osteoarthritis noted significantly increased rates in BPTB patients., Conclusion: This systematic review comparing long-term outcomes after ACL reconstruction with either autograft BPTB or autograft HS suggests no significant differences in manual/instrumented laxity and graft failures between graft types. An increase in long-term anterior knee pain, kneeling pain, and higher rates of osteoarthritis were noted with BPTB graft use., Competing Interests: The authors declared that they have no conflicts of interest in the authorship and publication of this contribution.

Protein post-translational modification (PTM) is an essential cellular regulatory mechanism, and disruptions in PTM have been implicated in disease. PTMs are an active area of study in many fields, leading to a wealth of PTM information in the scientific literature. There is a need for user-friendly bioinformatics resources that capture PTM information from the literature and support analyses of PTMs and their functional consequences. This chapter describes the use of iPTMnet ( http://proteininformationresource.org/iPTMnet/ ), a resource that integrates PTM information from text mining, curated databases, and ontologies and provides visualization tools for exploring PTM networks, PTM crosstalk, and PTM conservation across species. We present several PTM-related queries and demonstrate how they can be addressed using iPTMnet.

The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence variants, and post-translationally modified forms), and protein complexes. PRO defines classes of proteins and protein complexes, both species-specific and species nonspecific, and indicates their relationships in a hierarchical framework, supporting accurate protein annotation at the appropriate level of granularity, analyses of protein conservation across species, and semantic reasoning. In the first section of this chapter, we describe the PRO framework including categories of PRO terms and the relationship of PRO to other ontologies and protein resources. Next, we provide a tutorial about the PRO website ( proconsortium.org ) where users can browse and search the PRO hierarchy, view reports on individual PRO terms, and visualize relationships among PRO terms in a hierarchical table view, a multiple sequence alignment view, and a Cytoscape network view. Finally, we describe several examples illustrating the unique and rich information available in PRO.

Post-translational modifications (PTMs) are one of the main contributors to the diversity of proteoforms in the proteomic landscape. In particular, protein phosphorylation represents an essential regulatory mechanism that plays a role in many biological processes. Protein kinases, the enzymes catalyzing this reaction, are key participants in metabolic and signaling pathways. Their activation or inactivation dictate downstream events: what substrates are modified and their subsequent impact (e.g., activation state, localization, protein-protein interactions (PPIs)). The biomedical literature continues to be the main source of evidence for experimental information about protein phosphorylation. Automatic methods to bring together phosphorylation events and phosphorylation-dependent PPIs can help to summarize the current knowledge and to expose hidden connections. In this chapter, we demonstrate two text mining tools, RLIMS-P and eFIP, for the retrieval and extraction of kinase-substrate-site data and phosphorylation-dependent PPIs from the literature. These tools offer several advantages over a literature search in PubMed as their results are specific for phosphorylation. RLIMS-P and eFIP results can be sorted, organized, and viewed in multiple ways to answer relevant biological questions, and the protein mentions are linked to UniProt identifiers.

The Protein Ontology (PRO) defines protein classes and their interrelationships from the family to the protein form (proteoform) level within and across species. One of the unique contributions of PRO is its representation of post-translationally modified (PTM) proteoforms. However, progress in adding PTM proteoform classes to PRO has been relatively slow due to the extensive manual curation effort required. Here we report an automated pipeline for creation of PTM proteoform classes that leverages two phosphorylation-focused text mining tools (RLIMS-P, which detects mentions of kinases, substrates, and phosphorylation sites, and eFIP, which detects phosphorylation-dependent protein-protein interactions (PPIs)) and our integrated PTM database, iPTMnet. By applying this pipeline, we obtained a set of ~820 substrate-site pairs that are suitable for automated PRO term generation with literature-based evidence attribution. Inclusion of these terms in PRO will increase PRO coverage of species-specific PTM proteoforms by 50%. Many of these new proteoforms also have associated kinase and/or PPI information. Finally, we show a phosphorylation network for the human and mouse peptidyl-prolyl cis-trans isomerase (PIN1/Pin1) derived from our dataset that demonstrates the biological complexity of the information we have extracted. Our approach addresses scalability in PRO curation and will be further expanded to advance PRO representation of phosphorylated proteoforms.

Background: MicroRNAs are increasingly being appreciated as critical players in human diseases, and questions concerning the role of microRNAs arise in many areas of biomedical research. There are several manually curated databases of microRNA-disease associations gathered from the biomedical literature; however, it is difficult for curators of these databases to keep up with the explosion of publications in the microRNA-disease field. Moreover, automated literature mining tools that assist manual curation of microRNA-disease associations currently capture only one microRNA property (expression) in the context of one disease (cancer). Thus, there is a clear need to develop more sophisticated automated literature mining tools that capture a variety of microRNA properties and relations in the context of multiple diseases to provide researchers with fast access to the most recent published information and to streamline and accelerate manual curation., Methods: We have developed miRiaD (microRNAs in association with Disease), a text-mining tool that automatically extracts associations between microRNAs and diseases from the literature. These associations are often not directly linked, and the intermediate relations are often highly informative for the biomedical researcher. Thus, miRiaD extracts the miR-disease pairs together with an explanation for their association. We also developed a procedure that assigns scores to sentences, marking their informativeness, based on the microRNA-disease relation observed within the sentence., Results: miRiaD was applied to the entire Medline corpus, identifying 8301 PMIDs with miR-disease associations. These abstracts and the miR-disease associations are available for browsing at http://biotm.cis.udel.edu/miRiaD . We evaluated the recall and precision of miRiaD with respect to information of high interest to public microRNA-disease database curators (expression and target gene associations), obtaining a recall of 88.46-90.78. When we expanded the evaluation to include sentences with a wide range of microRNA-disease information that may be of interest to biomedical researchers, miRiaD also performed very well with a F-score of 89.4. The informativeness ranking of sentences was evaluated in terms of nDCG (0.977) and correlation metrics (0.678-0.727) when compared to an annotator's ranked list., Conclusions: miRiaD, a high performance system that can capture a wide variety of microRNA-disease related information, extends beyond the scope of existing microRNA-disease resources. It can be incorporated into manual curation pipelines and serve as a resource for biomedical researchers interested in the role of microRNAs in disease. In our ongoing work we are developing an improved miRiaD web interface that will facilitate complex queries about microRNA-disease relationships, such as "In what diseases does microRNA regulation of apoptosis play a role?" or "Is there overlap in the sets of genes targeted by microRNAs in different types of dementia?"."

Given the wealth of bioinformatics resources and the growing complexity of biological information, it is valuable to integrate data from disparate sources to gain insight into the role of genes/proteins in health and disease. We have developed a bioinformatics framework that combines literature mining with information from biomedical ontologies and curated databases to create knowledge "maps" of genes/proteins of interest. We applied this approach to the study of beta-catenin, a cell adhesion molecule and transcriptional regulator implicated in cancer. The knowledge map includes post-translational modifications (PTMs), protein-protein interactions, disease-associated mutations, and transcription factors co-activated by beta-catenin and their targets and captures the major processes in which beta-catenin is known to participate. Using the map, we generated testable hypotheses about beta-catenin biology in normal and cancer cells. By focusing on proteins participating in multiple relation types, we identified proteins that may participate in feedback loops regulating beta-catenin transcriptional activity. By combining multiple network relations with PTM proteoform-specific functional information, we proposed a mechanism to explain the observation that the cyclin dependent kinase CDK5 positively regulates beta-catenin co-activator activity. Finally, by overlaying cancer-associated mutation data with sequence features, we observed mutation patterns in several beta-catenin PTM sites and PTM enzyme binding sites that varied by tissue type, suggesting multiple mechanisms by which beta-catenin mutations can contribute to cancer. The approach described, which captures rich information for molecular species from genes and proteins to PTM proteoforms, is extensible to other proteins and their involvement in disease.

MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally validated miRNA gene targets are often reported in the literature. In this paper, we describe miRTex, a text mining system that extracts miRNA-target relations, as well as miRNA-gene and gene-miRNA regulation relations. The system achieves good precision and recall when evaluated on a literature corpus of 150 abstracts with F-scores close to 0.90 on the three different types of relations. We conducted full-scale text mining using miRTex to process all the Medline abstracts and all the full-length articles in the PubMed Central Open Access Subset. The results for all the Medline abstracts are stored in a database for interactive query and file download via the website at http://proteininformationresource.org/mirtex. Using miRTex, we identified genes potentially regulated by miRNAs in Triple Negative Breast Cancer, as well as miRNA-gene relations that, in conjunction with kinase-substrate relations, regulate the response to abiotic stress in Arabidopsis thaliana. These two use cases demonstrate the usefulness of miRTex text mining in the analysis of miRNA-regulated biological processes.

Research within Indigenous communities has been criticised for lacking community engagement, for being exploitative, and for poorly explaining the processes of research. To address these concerns, and to ensure 'best practice', Jamieson, et al. (2012) recently published a summary of principles outlined by the NHMRC (2003) in "one short, accessible document". Here we expand on Jamieson et al.'s paper, which while commendable, lacks emphasis on the contribution that communities themselves can make to the research process and how culturally appropriate engagement, can allow this contribution to be assured, specifically with respect to engagement with remote communities. Engagement started before the research proposal is put forward, and continued after the research is completed, has integrity. We emphasise the value of narratives, of understanding cultural and customary behaviours and leadership, the importance of cultural legitimacy, and of the need for time, not just to allow for delays, but to ensure genuine participatory engagement from all members of the community. We also challenge researchers to consider the outcomes of their research, on the basis that increasing clinical evidence does not always result in better outcomes for the community involved.

Protein phosphorylation is a reversible post-translational modification where a protein kinase adds a phosphate group to a protein, potentially regulating its function, localization and/or activity. Phosphorylation can affect protein-protein interactions (PPIs), abolishing interaction with previous binding partners or enabling new interactions. Extracting phosphorylation information coupled with PPI information from the scientific literature will facilitate the creation of phosphorylation interaction networks of kinases, substrates and interacting partners, toward knowledge discovery of functional outcomes of protein phosphorylation. Increasingly, PPI databases are interested in capturing the phosphorylation state of interacting partners. We have previously developed the eFIP (Extracting Functional Impact of Phosphorylation) text mining system, which identifies phosphorylated proteins and phosphorylation-dependent PPIs. In this work, we present several enhancements for the eFIP system: (i) text mining for full-length articles from the PubMed Central open-access collection; (ii) the integration of the RLIMS-P 2.0 system for the extraction of phosphorylation events with kinase, substrate and site information; (iii) the extension of the PPI module with new trigger words/phrases describing interactions and (iv) the addition of the iSimp tool for sentence simplification to aid in the matching of syntactic patterns. We enhance the website functionality to: (i) support searches based on protein roles (kinases, substrates, interacting partners) or using keywords; (ii) link protein entities to their corresponding UniProt identifiers if mapped and (iii) support visual exploration of phosphorylation interaction networks using Cytoscape. The evaluation of eFIP on full-length articles achieved 92.4% precision, 76.5% recall and 83.7% F-measure on 100 article sections. To demonstrate eFIP for knowledge extraction and discovery, we constructed phosphorylation-dependent interaction networks involving 14-3-3 proteins identified from cancer-related versus diabetes-related articles. Comparison of the phosphorylation interaction network of kinases, phosphoproteins and interactants obtained from eFIP searches, along with enrichment analysis of the protein set, revealed several shared interactions, highlighting common pathways discussed in the context of both diseases., (© The Author(s) 2015. Published by Oxford University Press.)

Accurately quantifying Legionella for regulatory purposes to protect public health is essential. Real-time PCR (qPCR) has been proposed as a better method for detecting and enumerating Legionella in samples than conventional culture method. However, since qPCR amplifies any target DNA in the sample, the technique's inability to discriminate between live and dead cells means that counts are generally significantly overestimated. Propidium monoazide (PMA) has been used successfully in qPCR to aid live/dead discrimination. We tested PMA use as a method to count only live Legionella cells in samples collected from a modified chemostat that generates environmentally comparable samples. Counts from PMA-treated samples that were pretreated with either heat or three types of disinfectants (to kill the cells) were highly variable, with the only consistent trend being the relationship between biofilm mass and numbers of Legionella cells. Two possibilities explain this result: 1. PMA treatment worked and the subsequent muted response of Legionella to disinfection treatment is a factor of biofilm/microbiological effects; although this does not account for the relationship between the amount of biofilm sampled and the viable Legionella count as determined by PMA-qPCR; or 2. PMA treatment did not work, and any measured decrease or increase in detectable Legionella is because of other factors affecting the method. This is the most likely explanation for our results, suggesting that higher concentrations of PMA might be needed to compensate for the presence of other compounds in an environmental sample or that lower amounts of biofilm need to be sampled. As PMA becomes increasingly toxic at higher concentrations and is very expensive, augmenting the method to include higher PMA concentrations is both counterproductive and cost prohibitive. Conversely, if smaller volumes of biofilm are used, the reproducibility of the method is reduced. Our results suggest that using PMA is not an appropriate method for discriminating between live and dead cells to enumerate Legionella for regulatory purposes.

Background: Infants in the newborn intensive care unit (NICU) are exposed to routine procedures that often cause distress and carry a negative burden or load on the infant's neurodevelopment., Aim: A ratio level index is introduced to estimate procedural load so as to begin to develop a system to monitor the intensity of distress associated with common NICU procedures., Study Design: Two psychophysical methods, magnitude estimation (ME) and the general labeled magnitude scale (gLMS) were used to survey 86 clinicians via the internet to estimate the distress associated with 55 common NICU procedures., Results: gLMS and ME estimations correlated highly across all procedures (r = 0.97). gLMS values were used to derive the procedural load index (PLI) as a ratio level estimation of procedural distress., Conclusion: The PLI ranks and differentiates distress among common NICU procedures more precisely than current tools. This methodology, if correlated with infant physiological indices and health outcomes, may be operationalized at the bedside to measure procedural distress, and help to guide the ideal timing to perform procedures and minimize their negative consequence., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Knowledge representation of the role of phosphorylation is essential for the meaningful understanding of many biological processes. However, such a representation is challenging because proteins can exist in numerous phosphorylated forms with each one having its own characteristic protein-protein interactions (PPIs), functions and subcellular localization. In this article, we evaluate the current state of phosphorylation event curation and then present a bioinformatics framework for the annotation and representation of phosphorylated proteins and construction of phosphorylation networks that addresses some of the gaps in current curation efforts. The integrated approach involves (i) text mining guided by RLIMS-P, a tool that identifies phosphorylation-related information in scientific literature; (ii) data mining from curated PPI databases; (iii) protein form and complex representation using the Protein Ontology (PRO); (iv) functional annotation using the Gene Ontology (GO); and (v) network visualization and analysis with Cytoscape. We use this framework to study the spindle checkpoint, the process that monitors the assembly of the mitotic spindle and blocks cell cycle progression at metaphase until all chromosomes have made bipolar spindle attachments. The phosphorylation networks we construct, centered on the human checkpoint kinase BUB1B (BubR1) and its yeast counterpart MAD3, offer a unique view of the spindle checkpoint that emphasizes biologically relevant phosphorylated forms, phosphorylation-state-specific PPIs and kinase-substrate relationships. Our approach for constructing protein phosphorylation networks can be applied to any biological process that is affected by phosphorylation. Database URL: http://www.yeastgenome.org/

As a member of the Open Biomedical Ontologies (OBO) foundry, the Protein Ontology (PRO) provides an ontological representation of protein forms and complexes and their relationships. Annotations in PRO can be assigned to individual protein forms and complexes, each distinguishable down to the level of post-translational modification, thereby allowing for a more precise depiction of protein function than is possible with annotations to the gene as a whole. Moreover, PRO is fully interoperable with other OBO ontologies and integrates knowledge from other protein-centric resources such as UniProt and Reactome. Here we demonstrate the value of the PRO framework in the investigation of the spindle checkpoint, a highly conserved biological process that relies extensively on protein modification and protein complex formation. The spindle checkpoint maintains genomic integrity by monitoring the attachment of chromosomes to spindle microtubules and delaying cell cycle progression until the spindle is fully assembled. Using PRO in conjunction with other bioinformatics tools, we explored the cross-species conservation of spindle checkpoint proteins, including phosphorylated forms and complexes; studied the impact of phosphorylation on spindle checkpoint function; and examined the interactions of spindle checkpoint proteins with the kinetochore, the site of checkpoint activation. Our approach can be generalized to any biological process of interest.

Two empirical models are presented to elucidate the mechanisms driving reductions in the mercury concentration of southern bluefin tuna (SBT) during culture. Model 1 predicts temporal fluctuations in mercury concentration in response to growth dilution. Model 2 predicts the combined effects of growth dilution and linear mercury accumulation. Model 2 was found to be the more accurate model. Over a typical farming period of 136 days, growth dilution resulted in a reduction in mean mercury concentration of SBT edible tissues from 0.51 mg/kg down to 0.33 mg/kg. Extended culture beyond 136 days resulted in an increase in mercury concentration due to the combined effects of mercury accumulation and seasonal lipid depletion. Results indicate that under current industry practice, cultured SBT can be consumed twice as frequently as that of wild caught SBT while maintaining total dietary mercury intake below national recommendations.

The nucleus of the budding yeast S. cerevisiae has to move to the bud neck during mitosis in order for proper DNA segregation to take place. This movement is mediated by spindle and astral microtubules, and it relies on forces generated by microtubule-associated motor proteins. When budding yeast cells express the non-cleavable cohesin subunit, Scc1-RRDD, sister chromatid separation is blocked, preventing the spindle from elongating. Thus, in the presence of Scc1-RRDD nuclear positioning is mediated solely by forces acting through astral microtubules. We have previously shown that under these conditions cells exit mitosis with the nucleus in the mother cells, and that the position of the nucleus is determined, at least in part, by the FEAR pathway, which regulates various aspects of mitotic exit. When the FEAR pathway is inactivated, cells expressing Scc1-RRDD exit mitosis with the nucleus in the daughter cells (referred to as a "daughterly phenotype"). In order to find additional proteins that participate in nuclear positioning, we screened a series of mutant strains for those that displayed a daughterly phenotype when Scc1-RRDD was expressed. The most prominent defects were seen in ase1delta and cin8delta mutant cells. Both Ase1p and Cin8p were previously shown to be nuclear and to be involved in spindle function. We show here that deletion of ASE1 or CIN8 causes a defect in SPB separation and leads to an abnormal number of astral microtubules and a change in their orientation within the cell. Taken together, these results suggest that in budding yeast Ase1p and Cin8p affect nuclear positioning through astral micro-tubule-dependent mechanisms.

Budding yeast securin/Pds1p, an inhibitor of the anaphase activator separase/Esp1p, is involved in several checkpoint pathways and in promoting Esp1p's nuclear localization. Using a modified synthetic genetic array (SGA) screen for genes that become essential in the absence of Pds1p, we uncovered roles for uncharacterized genes in cell cycle processes, including Esp1p activation.

We examined allelic variation at 22 nuclear-encoded markers (21 microsatellites and one anonymous locus) and mitochondrial (mt)DNA in two geographical samples of the endangered cyprinid fish Notropis mekistocholas (Cape Fear shiner). Genetic diversity was relatively high in comparison to other endangered vertebrates, and there was no evidence of small population effects despite the low abundance reported for the species. Significant heterogeneity (following Bonferroni correction) in allele distribution at three microsatellites and in haplotype distribution in mtDNA was detected between the two localities. This heterogeneity may be due to reduced gene flow caused by a dam built in the early 1900 s. Bayesian coalescent analysis of microsatellite variation indicated that effective population size of Cape Fear shiners has declined in recent times (11-25 435 years ago, with highest posterior probabilities between 126 and 2007 years ago) by one-two orders of magnitude, consistent with the observed decline in abundance of the species. A decline in effective size was not indicated by analysis of mtDNA, where sequence polymorphism appeared to carry the signature of an older expansion phase that dated to the Pleistocene ( approximately 12 700 > 1 million years ago). Cape Fear shiners thus appear to have undergone an expansion phase following a glacial cycle but to have declined significantly in more recent times. These results suggest that rapidly evolving markers such as microsatellites may constitute a suitable tool when inferring recent demographic dynamics of populations.

In budding yeast, cells lacking separase function exit mitosis with an undivided nucleus localized to the daughter cell. Here we show that the inability to separate sister chromatids per se is not sufficient to cause the daughter preference. Rather, separase affects nuclear positioning as part of the Cdc14 early anaphase release (FEAR) pathway. The role of the FEAR pathway in nuclear positioning is exerted during anaphase and is not shared by the mitotic exit network. We find that the nuclear segregation defect in FEAR mutants does not stem from nonfunctional spindle poles or the absence of cytoplasmic microtubules. Instead, the concomitant inactivation of sister chromatid separation and the FEAR pathway uncovered a mother-directed force in anaphase that was previously masked by the elongating spindle. We propose that at anaphase onset, the FEAR pathway activates cytoplasmic microtubule-associated forces that facilitate chromosome segregation to the mother cell.