Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels.

Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean's primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom's metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels. This transcriptional regulatory network was integrated with a recently published genome-scale metabolic model of Phaeodactylum tricornutum to explore the connectivity of the regulatory network and shared metabolites. The integrated regulatory and metabolic model revealed highly connected modules within carbon and nitrogen metabolism. P. tricornutum's response to rising carbon levels was analyzed by using the recent genome-scale metabolic model with cross comparison to experimental manipulations of carbon dioxide. IMPORTANCE Using a systems biology approach, we studied the response of the marine diatom Phaeodactylum tricornutum to changing atmospheric carbon concentrations on an ocean-wide scale. By integrating an available genome-scale metabolic model and a newly developed transcriptional regulatory network inferred from transcriptome sequencing expression data, we demonstrate that carbon metabolism and nitrogen metabolism are strongly connected and the genes involved are coregulated in this model diatom. These tight regulatory constraints could play a major role during the adaptation of P. tricornutum to increasing carbon levels. The transcriptional regulatory network developed can be further used to study the effects of different environmental perturbations on P. tricornutum's metabolism

Real-time ultrasound elastography in 180 axillary lymph nodes: elasticity distribution in healthy lymph nodes and prediction of breast cancer metastases

BACKGROUND: To determine the general appearance of normal axillary lymph nodes (LNs) in real-time tissue sonoelastography and to explore the method′s potential value in the prediction of LN metastases. METHODS: Axillary LNs in healthy probands (n=165) and metastatic LNs in breast cancer patients (n=15) were examined with palpation, B-mode ultrasound, Doppler and sonoelastography (assessment of the elasticity of the cortex and the medulla). The elasticity distributions were compared and sensitivity (SE) and specificity (SP) were calculated. In an exploratory analysis, positive and negative predictive values (PPV, NPV) were calculated based upon the estimated prevalence of LN metastases in different risk groups. RESULTS: In the elastogram, the LN cortex was significantly harder than the medulla in both healthy (p=0.004) and metastatic LNs (p=0.005). Comparing healthy and metastatic LNs, there was no difference in the elasticity distribution of the medulla (p=0.281), but we found a significantly harder cortex in metastatic LNs (p=0.006). The SE of clinical examination, B-mode ultrasound, Doppler ultrasound and sonoelastography was revealed to be 13.3%, 40.0%, 14.3% and 60.0%, respectively, and SP was 88.4%, 96.8%, 95.6% and 79.6%, respectively. The highest SE was achieved by the disjunctive combination of B-mode and elastographic features (cortex >3mm in B-mode or blue cortex in the elastogram, SE=73.3%). The highest SP was achieved by the conjunctive combination of B-mode ultrasound and elastography (cortex >3mm in B-mode and blue cortex in the elastogram, SP=99.3%). CONCLUSIONS: Sonoelastography is a feasible method to visualize the elasticity distribution of LNs. Moreover, sonoelastography is capable of detecting elasticity differences between the cortex and medulla, and between metastatic and healthy LNs. Therefore, sonoelastography yields additional information about axillary LN status and can improve the PPV, although this method is still experimental

Arabian Dugongs of Qatar: Updates from a Renewed Research Initiative

Dugongs ("bugarah al bahr" or "cow of the sea") in Qatar and the wider Arabian Gulf, are animals of both historic and cultural significance to the people in the region. Historically hunted in Qatar, today they are seen as a symbol for conservation in a country that is trying to balance rapid modernization and coastal development with protection of marine biodiversity, as outlined in the Qatar National Vision 2030. Qatar and the Arabian Gulf are home to the largest population of dugongs outside of Australia and is the most important region for dugongs in the western portion of their range. As long-lived large mammals with low reproductive output dugongs are vulnerable to exploitation and are listed as Vulnerable to Extinction by the IUCN (International Union for the Conservation of Nature). Currently, dugongs in Qatar face many threats including incidental fisheries bycatch and habitat degradation. The extreme marine and physical environment of the Arabian Gulf, as well as the northern limit of dugong distribution, likely means that their life-history differs from populations in Australia. However, there are virtually no life history data for Qatari dugongs and the species remains mostly unstudied. A solid understanding of dugong natural history is necessary to develop a successful management and conservation program. Our knowledge of dugong natural history in Qatar and the Arabian Gulf is poor compared to our knowledge of dugongs in Australia (where the largest population exists). Although approximately 6000 dugongs were estimated to live in the Arabian Gulf including Qatar, this number has not been verified. Sporadic research has been conducted on the Qatari population, including work in 1986 which recorded the largest single dugong group of 577 individuals in the waters between Qatar and Bahrain. More recently, in 2008, the Qatar Ministry of Environment conducted surveys that expanded the area around Qatar where dugongs were observed. Our current study applies similar techniques from the past (boat-based and beach surveys) with newer techniques (aerial surveys using Unmanned Aerial Vehicles [UAVs], histological analyses) to provide an updated understanding of when, where, and how many dugongs are present in Qatari waters, along with preliminary information on their population demographics. From our 2014-2015 surveys, we have enumerated individuals in a large herd, consistently spotted in the winter months in similar areas to the 1986 and 2008 surveys. A total of 508 individuals (including 51 cow-calf pairs) were counted using images taken from a UAV. Underwater surveys verified that the major activity was foraging upon a mixed stand of seagrasses, Halodule univernis and Halophila ovalis, in clear, shallow water)qscienc

The Indigenous Qatari Marine Copepod, Euterpina Acutifrons: A Promising Marine Invertebrate Model Organism for Aquatic Eco-Toxicological Studies

An important objective of aquatic toxicological assessments is to evaluate the effects of water-borne toxic compounds on organisms which play a crucial role in aquatic communities. In marine ecosystems, copepods have a major impact on essential ecological processes: they exert grazing pressure on phytoplankton, and are a significant food source for several fish and macro crustaceans. Euterpina acutifrons, a harpacticoid copepod, is an abundant species in the Arabian Gulf, including the coast of Qatari peninsula. Its high content of poly unsaturated fatty acids make it a nutritionally superior live feed for larval fish in aquaculture, an industry developing fast in Qatar. With its ubiquitous distribution worldwide, inter-and intra-sexual dimorphism, well-defined life cycle, short generation time, and anamorphic developmental stages, this species meets many of the criteria to become a suitable model for toxicity studies. The present study defines protocols for establishing a successful laboratory culture of Euterpina acutifrons and for its acute toxicity testing with four toxicants. This study will add to the refinement of a suite of bioassay techniques being developed at ExxonMobil Research Qatar using a gamut of vertebrate and invertebrate indigenous marine species. A sustainable culture of Euterpina acutifrons was established by rearing ovigerous individuals of this native species isolated from local waters. A few gravid individuals were used to include the natural genetic variability in the population. Through a series of planned trials, a simple protocol was established for culturing and maintaining the species in the laboratory. A temperature of 22 ± 2°C, photoperiod of 12 h light: 12 h darkness, salinity at 40 ± 2 ppt, and a 3:1 microalgal mixture of Chaetoceros sp. (diatom) and Synechococcus sp. (blue-green algae) as food, fed twice every week, was found to give an optimum survival and fecundity in the laboratory. In order to investigate the efficacy of this species as a ecotoxicity test organism, a series of static, acute 24 h and 48 h toxicity tests were performed using three widely used reference toxicants, sodium dodecyl sulfate (SDS, an anionic surfactant used widely in cleaning and hygiene products), 3, 4-dichloroaniline (DCA, a metabolite of several herbicides), and Zinc (heavy metal) at 22 ± 2°C. Impact of chlorine, an anti-biofouling agent used in industrial cooling waters globally, was tested in a semi-static set up, where chlorine dose was renewed at regular intervals. Similar-sized copepodite stages used for these tests were procured through laboratory culture synchronization. The 24 h/48 h LC50 values were calculated based on the end point of the tests, which was mortality or total cessation of mobility. The copepod showed dose-dependent responses and different sensitivity towards the four toxicants; toxicity ranking increasing from DCA, SDS, Zinc to Chlorine. The differences in toxicities can be attributed to different mechanisms of action of the four compounds. The sensitivity of this species compared favorably with other established marine invertebrate models for ecotoxicity testing. Given, the feasibility of culturing, continuous egg production throughout the year, and high reproducibility of the toxicity responses in this study, it is advocated to further explore the use of Euterpina acutifrons as a model organism to assess long- and short-term effects of potential water-borne contaminants in the Arabian Gulf.qscienc

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications

Site-fidelity and spatial movements of western North Pacific gray whales on their summer range off Sakhalin, Russia

The Western North-Pacific (WNP) gray whale feeding grounds are off the northeastern coast of Sakhalin Island, Russia and is comprised of a nearshore and offshore component that can be distinguished by both depth and location. Spatial movements of gray whales within their foraging grounds were examined based on 13 years of opportunistic vessel and shore-based photo-identification surveys. Site fidelity was assessed by examining annual return and resighting rates. Lagged Identification Rates (LIR) analyses were conducted to estimate the residency and transitional movement patterns within the two components of their feeding grounds. In total 243 individuals were identified from 2002-2014, among these were 94 calves. The annual return rate over the period 2002-2014 was 72%, excluding 35 calves only seen one year. Approximately 20% of the individuals identified from 2002-2010 were seen every year after their initial sighting (including eight individuals that returned for 13 consecutive years). The majority (239) of the WNP whales were observed in the nearshore area while only half (122) were found in the deeper offshore area. Within a foraging season, there was a significantly higher probability of gray whales moving from the nearshore to the offshore area. No mother-calf pairs, calves or yearlings were observed in the offshore area, which was increasingly used by mature animals. The annual return rates, and population growth rates that are primarily a result of calf production with little evidence of immigration, suggest that this population is demographically self-contained and that both the nearshore and offshore Sakhalin feeding grounds are critically important areas for their summer annual foraging activities. The nearshore habitat is also important for mother-calf pairs, younger individuals, and recently weaned calves. Nearshore feeding could also be energetically less costly compared to foraging in the deeper offshore habitat and provide more protection from predators, such as killer whales

The ovarian follicle of ruminants: The path from conceptus to adult

This review resulted from an international workshop and presents a consensus view of critical advances over the past decade in our understanding of follicle function in ruminants. The major concepts covered include: (1) the value of major genes; (2) the dynamics of fetal ovarian development and its sensitivity to nutritional and environmental influences; (3) the concept of an ovarian follicle reserve, aligned with the rise of anti-Müllerian hormone as a controller of ovarian processes; (4) renewed recognition of the diverse and important roles of theca cells; (5) the importance of follicular fluid as a microenvironment that determines oocyte quality; (6) the \u27adipokinome\u27 as a key concept linking metabolic inputs with follicle development; and (7) the contribution of follicle development to the success of conception. These concepts are important because, in sheep and cattle, ovulation rate is tightly regulated and, as the primary determinant of litter size, it is a major component of reproductive efficiency and therefore productivity. Nowadays, reproductive efficiency is also a target for improving the \u27methane efficiency\u27 of livestock enterprises, increasing the need to understand the processes of ovarian development and folliculogenesis, while avoiding detrimental trade-offs as greater performance is sought

NADH Dehydrogenases in Pseudomonas aeruginosa Growth and Virulence

Pseudomonas aeruginosa is an opportunistic human pathogen with a complex respiratory chain. The bacterium is predicted to express three NADH:ubiquinone oxidoreductases (NDH-1, NDH-2 and Nqr). We created deletions strains of the predicted NADH:ubiquinone oxidoreductases alone, and in combination to determine the respective roles of the NADH dehydrogenases in growth and virulence. NDH-1 and NDH-2 were largely redundant under aerobic conditions. Aerobic NADH dehydrogenase enzymatic activity assay was lost with deletion of both NDH-1 and NDH-2. Under anaerobic conditions, NDH-1 was required for robust growth, and overexpression of NDH-2 rescued the NDH-1 anaerobic growth defect in rich media. There was not compensatory upregulation of NDH-2 under anaerobic conditions in NDH-1 deletion strains. To test which genes were required for in vivo virulence, we used both an insect and plant disease model. In the Galleria mellonella model, neither deletion of NDH-1 nor NDH-2 led to a change in median lethal dose, although death occurred more slowly in the NDH-1 deletion infections. In a lettuce model of virulence, loss of NDH-1 caused a decrease in recovered viable bacteria and a decrease in visual tissue damage. The compound deletion of NDH-1/NDH-2 causes a severe growth defect, both under aerobic and anaerobic conditions, and was avirulent in a lettuce model. Together, these results demonstrate the redundancy of the P. aeruginosa respiratory chain at the NADH dehydrogenase level in aerobic growth and virulence

Evaluation Of The Sensitivity Of Qatari Marine Microalgae Synechococcus Sp, To Three Reference Toxicants

Background Marine phytoplankton form the basis of the marine food chain and are essential for the normal functioning of ecosystems. Any disturbance to this component, due to the release and accumulation of toxic compounds can have an impact on higher trophic levels. In this study, we investigate the impact of toxicants on the microalgae isolated from Qatari seawater and cultured under controlled laboratory conditions. Objectives * Develop a toxicity test for Synechococcus sp that can be added to the suite of tests currently available for marine invertebrates and fish. * Perform chronic toxicity tests of three reference toxicants (DCA, SDS and Zn) * Evaluate the sensitivity of Synechococcus sp to three reference toxicants and compare sensitivity to other species used in toxicity tests. Methodology Chronic toxicity tests were carried out in 24-well microplate for a period of 3 days for the DCA and Zn tests and 7 days for SDS test. Algal cultures in logarithmic growth phase (cell density of about 3.105 cells mL?1) were used as inoculum. Each test consisted of at least five test concentrations and a control, in triplicate. A different range of concentrations were used to estimate the range findings for each toxicant. * Cell counting using an hemocytometer was conducted to evaluate the inhibition of microalgal growth * The average specific growth rate and the percent inhibition of growth rate were calculated, the lowest observed effect concentration (LOEC) and the no observed effect concentration (NOEC) were statistically determined. Results A growth inhibition toxicity test was successfully developed for Synechococcus sp, which was isolated from Qatari coastal waters. Prior to conducting the toxicity testing, key environmental parameters including light, temperature and nutrients were optimized to obtain acceptable algal growth rates over 72 hours. Results showed that Synechococcus sp was more sensitive to DCA than SDS and Zn. The growth of Synechococcus sp was found to be stimulated by the SDS at the beginning of the test. The growth inhibition by the SDS on Synechococcus sp was shown by day 3 of the experiment. At a longer exposure time, significant values of the percent inhibition of growth rate were reached compared to the control. Conclusion and Discussion Controlled experiments on microalgae under laboratory conditions provide an opportunity to understand the action of these toxicants in the ecosystem. The growth stimulation in the Synechococcus sp test sample seems to be related to the ability of the microalgae to use the SDS as a source of carbon. Inhibition of cell growth under the influence of high concentrations of SDS may result from the destruction of cellular structures and disruptions of metabolism. The findings in this study showed that Synechococcus sp possess a number of desirable characteristics for use in toxicity assessment. In particular, the algae's high sensitivity to environmentally relevant toxicants makes it a suitable choice for site-specific testing. Therefore, we recommend that they be considered, along with other local organisms, as part toxicity tests in the region.qscienc

The Yin-Yang of the Green Fluorescent Protein:Impact on Saccharomyces cerevisiae stress resistance

International audienceAlthough fluorescent proteins are widely used as biomarkers (Yin), no study focuses on their influence on the microbial stress response. Here, the Green Fluorescent Protein (GFP) was fused to two proteins of interest in Saccharomyces cerevisiae. Pab1p and Sur7p, respectively involved in stress granules structure and in Can1 membrane domains. These were chosen since questions remain regarding the understanding of the behavior of S. cerevisiae facing different heat kinetics or oxidative stresses. The main results showed that Pab1p-GFP fluorescent mutant displayed a higher resistance than that of the wild type under a heat shock. Moreover, fluorescent mutants exposed to oxidative stresses displayed changes in the cultivability compared to the wild type strain. In silico approaches showed that the presence of the GFP did not influence the structure and so the functionality of the tagged proteins meaning that changes in yeast resistance were certainly related to GFP ROS-scavenging ability (Yang)