Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae)

© 2019 Public Library of Science. All rights reserved. Ciguatera fish poisoning (CFP) is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, CFP is prevalent in tropical Queensland and increasingly in sub-tropical regions of Australia, but has a report rate of approximately 10%. Yet the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study, we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species first described from Australia. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, to determine the presence and patchiness of this species across samples from Chnoospora sp., Padina sp. and Sargassum sp. macroalgal hosts

3α-Dimethyl­amino-20-(N-methyl­acetamido)­pregn-5-ene

The title compond, C26H44N2O, is an steroidal alkaloid isolated from the medicinally important plant Sarcococca saligna. The mol­ecule consists of four fused rings (A–D), having chair, half-chair, chair and envelope conformations, respectively. The dimethyl­amino group is axially oriented on ring A, whereas the (N-methyl­acetamido)­ethyl group is attached equatorially on ring D. The crystal structure is stabilized only by van der Waals forces

Plastic Solid Waste (PSW) in the Context of Life Cycle Assessment (LCA) and Sustainable Management

Over the past few decades, life cycle assessment (LCA) has been established as a critical tool for the evaluation of the environmental burdens of chemical processes and materials cycles. The increasing amount of plastic solid waste (PSW) in landfills has raised serious concern worldwide for the most effective treatment. Thermochemical post-treatment processes, such as pyrolysis, seem as the most appropriate method to treat this type of waste in an effective manner. This is because such processes lead to the production of useful chemicals or hydrocarbon oil of high calorific value (i.e. bio-oil in the case of pyrolysis). LCA seems as the most appropriate tool for the process design from an environmental context, however, addressed limitations including initial assumptions, functional unit and system boundaries, as well as lack of regional database and exclusion of socio-economic aspects, may hinder the final decision. This review aims to address the benefits of pyrolysis as a method for PSW treatment and raise the limitations and gaps of conducted research via an environmental standpoint

Glucose deprivation activates a metabolic and signaling amplification loop leading to cell death.

The altered metabolism of cancer can render cells dependent on the availability of metabolic substrates for viability. Investigating the signaling mechanisms underlying cell death in cells dependent upon glucose for survival, we demonstrate that glucose withdrawal rapidly induces supra-physiological levels of phospho-tyrosine signaling, even in cells expressing constitutively active tyrosine kinases. Using unbiased mass spectrometry-based phospho-proteomics, we show that glucose withdrawal initiates a unique signature of phospho-tyrosine activation that is associated with focal adhesions. Building upon this observation, we demonstrate that glucose withdrawal activates a positive feedback loop involving generation of reactive oxygen species (ROS) by NADPH oxidase and mitochondria, inhibition of protein tyrosine phosphatases by oxidation, and increased tyrosine kinase signaling. In cells dependent on glucose for survival, glucose withdrawal-induced ROS generation and tyrosine kinase signaling synergize to amplify ROS levels, ultimately resulting in ROS-mediated cell death. Taken together, these findings illustrate the systems-level cross-talk between metabolism and signaling in the maintenance of cancer cell homeostasis

The Predicting Tree Growth App: an algorithmic approach to modelling individual tree growth

PredictingTreeGrowth is free and open-source application software written in Python 3.7 that allows easy and fast development of predictive models using the Recurrent Neural Network (RNN)/Long Short-Term Memory (LSTM) framework. RNNs have an upgraded architecture able to capture tree growth mechanisms related to time ordering and size dependence. The motivation for this App is to demystify the use of Machine Learning algorithms and allow accessibility of Machine Learning algorithms by the scientific community. Its simple graphical user interface (GUI) provides straightforward tools for building predictive models with the RNN algorithm.Fil: Magalhaes, Juliana G. de S.. University of British Columbia; CanadáFil: Polinko, Adam P.. Mississippi State University.; Estados UnidosFil: Amoroso, Mariano Martin. Universidad Nacional de Río Negro. Sede Andina. Instituto de Investigaciones en Recursos Naturales, Agroecología y Desarrollo Rural; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kohli, Gursimran S.. University Fraser Simon; CanadáFil: Larson, Bruce C.. University of British Columbia; Canad

Violence, uncertainty, and resilience among refugee women and community workers: An evaluation of gender-based violence case management services in the Dadaab refugee camps.

Reports of gender-based violence (GBV) are common in camps for refugees and displaced populations. In the Dadaab refugee camps in north-eastern Kenya, the International Rescue Committee (IRC) and CARE International (CARE) implement programmes that aim to both respond to and prevent GBV. A cornerstone of this work has been to train refugees, known as refugee community workers, to deliver aspects of GBV prevention and response work in order to develop a broader implementation of traditional GBV outreach, community mobilisation, and case management. To date, there has been limited rigorous research on this broader GBV case management plus task sharing approach in the context of a refugee camp setting. To address this key gap in evidence, the London School of Hygiene and Tropical Medicine (LSHTM) and the African Population and Health Research Centre (APHRC), in collaboration with IRC and CARE, have sought to assess this model to understand its feasibility, acceptability, and influence among female survivors of GBV accessing care. Data for this study, funded by UK aid, were collected in the Dadaab refugee camps between 2014 and 2017, which coincided with a temporary decision to close the camp and repatriate Somali refugees. The research confirms the magnitude and complexity of the violence that women and girls experience in the camps in Dadaab. In the year leading up to this study, 47% of women accessing the GBV centres for case management reported experiencing intimate partner violence and 39% reported experiencing non-partner violence. In addition, the study highlights the specific risks, challenges, opportunities and rewards experienced by refugee community workers in their dual role of community members and GBV activists living side-by-side with survivors and perpetrators of violence. Solely related to their work as GBV caseworkers, one in three refugee community workers reported experiencing non-partner violence in the last 12 months. Despite this, 93% of refugee community workers stated their work was rewarding or extremely rewarding. The majority of women (82%) accessing services reported that their interactions with refugee community workers had a positive effect, and that working with them was useful. However, having refugees deliver services to their own community was not without its challenges, and survivors raised issues on confidentiality, mistranslations, and perceived biases on clan differences. The study also provides an insight into the importance of contextual factors in case management, and the impact of the announcement of the (now-delayed) camp closure in Dadaab. Priorities of both the camp population and service providers (GBV and referral services) shifted greatly during this time of uncertainty and affected when and how women were accessing services

Iterative graph cuts for image segmentation with a nonlinear statistical shape prior

Shape-based regularization has proven to be a useful method for delineating objects within noisy images where one has prior knowledge of the shape of the targeted object. When a collection of possible shapes is available, the specification of a shape prior using kernel density estimation is a natural technique. Unfortunately, energy functionals arising from kernel density estimation are of a form that makes them impossible to directly minimize using efficient optimization algorithms such as graph cuts. Our main contribution is to show how one may recast the energy functional into a form that is minimizable iteratively and efficiently using graph cuts.Comment: Revision submitted to JMIV (02/24/13

Elastic constants of nematic liquid crystals of uniaxial symmetry

We study in detail the influence of molecular interactions on the Frank elastic constants of uniaxial nematic liquid crystals composed of molecules of cylindrical symmetry. A brief summary of the status of theoretical development for the elastic constants of nematics is presented. Considering a pair potential having both repulsive and attractive parts numerical calculations are reported for three systems MBBA, PAA and 8OCB. For these systems the length-to-width ratio ${x_0}$ is estimated from the experimentally proposed structure of the molecules. The repulsive interaction is represented by a repulsion between hard ellipsoids of revolution (HER) and the attractive potential is represented by the quadrupole and dispersion interactions. From the numerical results we observe that in the density range of nematics the contribution of the quadrupole and dispersion interactions are small as compared to the repulsive HER interaction. The inclusion of attractive interaction reduces the values of elastic constants ratios. The temperature variation of elastic constants ratios are reported and compared with the experimental values. A reasonably good agreement between theory and experiment is observed

Robust and sensitive amplicon-based whole-genome sequencing assay of respiratory syncytial virus subtype A and B

Prevention of respiratory syncytial virus (RSV) infection is now a global health priority, with a long-acting monoclonal antibody and two RSV vaccines recently licenced for clinical use. Most licenced and candidate interventions target the RSV fusion (RSV-F) protein. New interventions may be associated with the spread of mutations, reducing susceptibility to antibody neutralization in RSV-F. There is a need for ongoing longitudinal global surveillance of circulating RSV strains. To achieve this large-scale genomic surveillance, a reliable, high-throughput RSV sequencing assay is required. Here we report an improved high-throughput RSV whole-genome sequencing (WGS) assay performed directly on clinical samples without additional enrichment, using a 4-primer-pool, short-amplicon PCR-tiling approach that is suitable for short-read sequencing platforms. Using upper respiratory tract (URT) RSV-positive clinical samples obtained from a sentinel network of primary care providers and from hospital patients (29.7% and 70.2%, respectively; n = 1,037), collected over the period 2019 to 2023, this assay had a threshold of approximately 4 × 103 to 8 × 103 copies/mL (RSV-B and RSV-A sub-types, respectively) as the lowest amount of virus needed in the sample to achieve >96% of whole-genome coverage at a high-quality level. Using a Ct value of 31 as an empirical cut-off, the overall assay success rate of obtaining >90% genome coverage at a read depth minimum of 20 was 96.83% for clinical specimens successfully sequenced from a total of 1,071. The RSV WGS approach described in this study has increased sensitivity compared to previous approaches and can be applied to clinical specimens without the requirement for enrichment. The updated approach produces sequences of high quality consistently and cost-effectively, suitable for implementation to underpin national programs for the surveillance of RSV genomic variation.ImportanceIn this paper, we report an improved high-throughput respiratory syncytial virus (RSV) whole-genome sequencing (WGS) assay performed directly on clinical samples, using a 4-primer-pool, short-amplicon PCR-tiling approach that is suitable for short-read sequencing platforms. The RSV WGS approach described in this study has increased sensitivity compared to previous approaches and can be applied to clinical specimens without the requirement for enrichment. The updated approach produces sequences of high quality consistently and cost-effectively, suitable for implementation to underpin national and global programs for the surveillance of RSV genomic variation. The quality of sequence produced is essential for preparedness for new interventions in monitoring antigenic escape, where a single point mutation might lead to a reduction in antibody binding effectiveness and neutralizing activity, or indeed in the monitoring of retaining susceptibility to neutralization by existing and new interventions