Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.

Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.

Environmental impacts of the ultraviolet filter oxybenzone.

Organic UV filters are emerging contaminants with increasing evidence of their negative impact on environmental health and water quality. One of the most common and environmentally relevant organic UV filters is oxybenzone (OBZ). While much of the initial focus has been on investigating the interaction of OBZ with coral reefs, there have been several recent studies that indicate that organic UV filters are affecting other environmental endpoints, including marine animals, algae, and plants. OBZ has been found to bioaccumulate in marine animals such as fish and mussels and then potentially acting as an endocrine disruptor. In plants, exposure to OBZ has been associated with decreased photosynthesis, inhibited seed germination, and impaired plant growth. In this review, we summarize the current state of knowledge regarding the environmental impacts of OBZ and suggest potential future directions.

Monitoring coliphages to reduce waterborne infectious disease transmission in the One Water framework.

Coastal waters, surface waters, and groundwater are impacted by wastewater and stormwater discharges, as well as agricultural flows containing animal waste and nutrients. A One Water approach posits that components of the water system have overlapping and interactive impacts on other aspects of the system, for which a comprehensive approach to water management is needed to further inform public health decisions. Current frameworks for monitoring wastewater effluent and recreational surface waters include the measurement of fecal indicator bacteria. Although viral pathogens are likely to be transported further and can survive longer than bacterial pathogens, virus monitoring is not required for recreational waters. A scientific consensus is emerging that the use of bacterial indicators alone does not account for nor represent the health risks associated with viral pathogens due to the differences in the fate and transport of bacterial versus viral pathogens in wastewater treatment, surface water, and groundwater. Furthermore, it is likely that the public health risk associated with these waterborne pathogens is variable and diverse. For example, under drought conditions, effluents of urban water systems can comprise most of the dry weather flow in downstream waters, which are often used as sources of drinking water. This de facto reuse could increase viral risk for the end users of this water. A One Water approach will aid in protecting the health of the public from waterborne pathogens, regardless of where those pathogens entered the water system. In this review, we assert that monitoring for fecal indicator viruses can complement the monitoring of bacterial indicators, thereby improving public health protections. Bacteriophages have the strongest research foundation and correlation with viral pathogens along with some prediction power for risk to human health. Methods for detecting and quantifying coliphages are briefly summarized, as are challenges in the implementation of testing. Key knowledge gaps and research priorities are discussed so that the potential value and limitations of coliphage monitoring can be better addressed and understood.

Complete Chloroplast Genome Sequence of a Black Spruce (Picea mariana) from Eastern Canada.

Here, we present the chloroplast genome sequence of black spruce (Picea mariana), a conifer widely distributed throughout North American boreal forests. This complete and annotated chloroplast sequence is 123,961 bp long and will contribute to future studies on the genetic basis of evolutionary change in spruce and adaptation in conifers.

Determining the effects of Class I landfill leachate on biological nutrient removal in wastewater treatment.

The disposal of landfill leachate is a chronic problem facing the municipal solid waste industry. The composition of landfill leachate is highly variable and often dependent on site-specific conditions. Due to the potentially disruptive impact on wastewater treatment processes, wastewater treatment plants (WWTP) are reluctant to accept landfill leachate for co-treatment. To improve the ability of WWTPs to screen the impact of landfill leachate and reduce landfill owners' cost of disposal, two bench scale methods were evaluated. First, six landfill leachates were screened with the specific oxygen uptake rate (SOUR) test, and second, the effect of leachate on the efficacy of activated sludge processes using lab scale sequencing batch reactors (SBRs) was determined with volumetric loading rates ranging from 5% to 20%. Results suggested that these tools can be used to estimate the impacts of leachate loading on biological processes. Both tools were able to identify loadings where biological activity was increased and inhibition of biological processes was minimized. The loading that maximized microbial activity was leachate specific and typically ranged from 5% to 10%. Taken together, these results suggest that improved landfill leachate screening and testing may improve outcomes at WWTPs by identifying a "Goldilocks" loading rate that increases biological activity. Nevertheless, our results also demonstrated that the effluent quality was degraded even at loading rates that increased biological activity. It is uncertain at this time if biological acclimation can remedy increased effluent nutrient mass loadings, suggesting further research is needed.

Natural Radiation in the Rocks, Soils, and Groundwater of Southern Florida with a Discussion on Potential Health Impacts.

Southern Florida is underlain by rocks and sediments that naturally contain radioactive isotopes. The primary origin of the radioactive isotopes is Miocene-aged phosphate deposits that can be enriched in uranium-238 and its daughter isotopes. Nodular phosphate containing radionuclides from the Miocene has been reworked into younger formations and is ubiquitous in southern Florida. When the nodular phosphate is exposed to groundwater with geochemical conditions favorable for its dissolution, uranium, radium, and radon may be released into the groundwater system. Uranium concentrations have been measured above the 30 µg/L drinking water standard at only one location in Lee County. Radium226/228 exceedances of the drinking water standard have been documented in numerous wells in Sarasota County. Indoor radon activities have exceeded the 4 piC/L guideline in five southern Florida counties. The exceedance of radioactivity standards in drinking water does not occur in municipal drinking water supplies, but rather only in some domestic self-supply wells. Health risks for exposure to radiation from domestic self-supply wells could be mitigated by testing of well water and, if necessary, switching to the use of a different aquifer or treatment process. While the risk of exposure to radon in indoor air in southern Florida is generally low, some areas are enriched in soil radon that migrates into structures, which could be addressed by improved ventilation.

Habituation of the electrodermal response - A biological correlate of resilience?

Current approaches to quantifying resilience make extensive use of self-reported data. Problematically, this type of scales is plagued by response distortions-both deliberate and unintentional, particularly in occupational populations. The aim of the current study was to develop an objective index of resilience. The study was conducted in 30 young healthy adults. Following completion of the Connor-Davidson Resilience Scale (CD-RISC) and Depression/Anxiety/Stress Scale (DASS), they were subjected to a series of 15 acoustic startle stimuli (95 dB, 50 ms) presented at random intervals, with respiration, skin conductance and ECG recorded. As expected, resilience (CD-RISC) significantly and negatively correlated with all three DASS subscales-Depression (r = -0.66, p<0.0001), Anxiety (r = -0.50, p<0.005) and Stress (r = -0.48, p<0.005). Acoustic stimuli consistently provoked transient skin conductance (SC) responses, with SC slopes indexing response habituation. This slope significantly and positively correlated with DASS-Depression (r = 0.59, p<0.005), DASS-Anxiety (r = 0.35, p<0.05) and DASS-Total (r = 0.50, p<0.005) scores, and negatively with resilience score (r = -0.47; p = 0.006), indicating that high-resilience individuals are characterized by steeper habituation slopes compared to low-resilience individuals. Our key finding of the connection between habituation of the skin conductance responses to repeated acoustic startle stimulus and resilience-related psychometric constructs suggests that response habituation paradigm has the potential to characterize important attributes of cognitive fitness and well-being-such as depression, anxiety and resilience. With steep negative slopes reflecting faster habituation, lower depression/anxiety and higher resilience, and slower or no habituation characterizing less resilient individuals, this protocol may offer a distortion-free method for objective assessment and monitoring of psychological resilience.

Complete plastome sequences from Bertholletia excelsa and 23 related species yield informative markers for Lecythidaceae.

PREMISE OF THE STUDY: The tropical tree family Lecythidaceae has enormous ecological and economic importance in the Amazon basin. Lecythidaceae species can be difficult to identify without molecular data, however, and phylogenetic relationships within and among the most diverse genera are poorly resolved. METHODS: To develop informative genetic markers for Lecythidaceae, we used genome skimming to de novo assemble the full plastome of the Brazil nut tree (Bertholletia excelsa) and 23 other Lecythidaceae species. Indices of nucleotide diversity and phylogenetic signal were used to identify regions suitable for genetic marker development. RESULTS: The B. excelsa plastome contained 160,472 bp and was arranged in a quadripartite structure. Using the 24 plastome alignments, we developed primers for 10 coding and non-coding DNA regions containing exceptional nucleotide diversity and phylogenetic signal. We also developed 19 chloroplast simple sequence repeats for population-level studies. DISCUSSION: The coding region ycf1 and the spacer rpl16-rps3 outperformed plastid DNA markers previously used for barcoding and phylogenetics. Used in a phylogenetic analysis, the matrix of 24 plastomes showed with 100% bootstrap support that Lecythis and Eschweilera are polyphyletic. The plastomes and primers presented in this study will facilitate a broad array of ecological and evolutionary studies in Lecythidaceae.

Evaluating Acquisition of Knowledge about Infertility Using a Whiteboard Video.

OBJECTIVE: Myths about fertility are commonplace in society. Few studies have investigated educational approaches to bridge gaps in knowledge among consumers. We evaluated the effectiveness of an animated, 15-minute whiteboard video to effect change in knowledge about infertility. METHODS: We recruited medical students in their first or second year of training for participation. The students completed the study before their formal lectures on infertility issues. Participants completed questionnaires assessing infertility knowledge immediately before and one week after watching the educational video. Before and after scores (maximum = 50 points) were compared using paired t tests. RESULTS: The study cohort included 101 medical students; 69% (70/101) were female and 31% (31/101) were male. Overall, students increased their score by 4.0/50 (95% CI 3.2 to 4.8, P < 0.001) from 36.5/50 to 40.5/50. Female students improved slightly more in their responses than did male students (mean improvement 4.7/50 vs. 2.5/50). CONCLUSION: A whiteboard video presentation on infertility resulted in short-term improvement in medical students' knowledge of basic reproductive biology, infertility risk factors, treatments, and common myths associated with infertility.

Evaluation of a field appropriate membrane filtration method for the detection of Vibrio cholerae for the measurement of biosand filter performance in the Artibonite Valley, Haiti.

Biosand filters in the Artibonite Valley of Haiti, the epicenter of the cholera epidemic that began in October 2010, were tested for total coliform and Vibrio cholerae removal efficiencies. While coliform are often used as an indicator organism for pathogenic bacteria, a correlation has never been established linking the concentration of coliform and V. cholerae, the causative agent for cholera. Hence, a method for field enumeration of V. cholerae was developed and tested. To this end, a plate count test utilizing membrane filtration technique was developed to measure viable V. cholerae cell concentration in the field. Method accuracy was confirmed by comparing plate count concentrations to microscopic counts. Additionally, biosand filters were sampled and removal efficiencies of V. cholerae and coliform bacteria compared. The correlation between removal efficiency and time in operation, biofilm ("schmutzdecke") composition, and idle time was also investigated. The plate count method for V. cholerae was found to accurately reflect microscope counts and was shown to be effective in the field. Overall, coliform concentration was not an appropriate indicator of V. cholerae concentration. In 90% of the influent samples from the study, coliform underestimated V. cholerae concentration (n = 26). Furthermore, coliform removal efficiency was higher than for V. cholerae hence providing a conservative measurement. Finally, time in operation and idle time were found to be important parameters controlling performance. Overall, this method shows promise for field applications and should be expanded to additional studies to confirm its efficacy to test for V. cholerae in various source waters.

Effects of isoform-selective phosphatidylinositol 3-kinase inhibitors on osteoclasts: actions on cytoskeletal organization, survival, and resorption.

Phosphatidylinositol 3-kinases (PI3K) participate in numerous signaling pathways, and control distinct biological functions. Studies using pan-PI3K inhibitors suggest roles for PI3K in osteoclasts, but little is known about specific PI3K isoforms in these cells. Our objective was to determine effects of isoform-selective PI3K inhibitors on osteoclasts. The following inhibitors were investigated (targets in parentheses): wortmannin and LY294002 (pan-p110), PIK75 (α), GDC0941 (α, δ), TGX221 (ß), AS252424 (γ), and IC87114 (δ). In addition, we characterized a new potent and selective PI3Kδ inhibitor, GS-9820, and explored roles of PI3K isoforms in regulating osteoclast function. Osteoclasts were isolated from long bones of neonatal rats and rabbits. Wortmannin, LY294002, GDC0941, IC87114, and GS-9820 induced a dramatic retraction of osteoclasts within 15-20 min to 65-75% of the initial area. In contrast, there was no significant retraction in response to vehicle, PIK75, TGX221, or AS252424. Moreover, wortmannin and GS-9820, but not PIK75 or TGX221, disrupted actin belts. We examined effects of PI3K inhibitors on osteoclast survival. Whereas PIK75, TGX221, and GS-9820 had no significant effect on basal survival, all blocked RANKL-stimulated survival. When studied on resorbable substrates, osteoclastic resorption was suppressed by wortmannin and inhibitors of PI3Kß and PI3Kδ, but not other isoforms. These data are consistent with a critical role for PI3Kδ in regulating osteoclast cytoskeleton and resorptive activity. In contrast, multiple PI3K isoforms contribute to the control of osteoclast survival. Thus, the PI3Kδ isoform, which is predominantly expressed in cells of hematopoietic origin, is an attractive target for anti-resorptive therapeutics.

Phospholipase C-beta1 signaling affects reproductive behavior, ovulation, and implantation.

Infertility can result from a wide range of defects, from behavioral, through germ cell development and maturation, to fertilization or embryo development. Many of the hormones regulating these processes signal via G protein-coupled receptors, which in turn activate a range of plasma membrane enzymes including phospholipase C (PLC)-beta isoforms. Transgenic mice lacking functional Plc-beta1 (Plc-beta1 KO mice) have been noted to have severely impaired fertility, but there has been little study of the reproductive processes affected by lack of this enzyme. This study examined reproductive behavior, gonadal development, fertilization, and implantation in Plc-beta1 KO mice. Male and female Plc-beta1 KO mice exhibited impaired reproductive behavior. No other defect in reproduction was noted in males, raising the possibility that the reduced fertility of Plc-beta1 KO males could be due solely to impaired behavior. In contrast, female Plc-beta1 KO mice exhibited both behavioral and nonbehavioral defects. Plc-beta1 KO females ovulated only in response to exogenous hormones, with a large proportion of in vivo embryos recovered on embryonic d 4.5 exhibiting abnormal morphology. In addition, uteri of pregnant Plc-beta1 KO females exhibited an implantation defect, with poor embryo attachment and a failure to up-regulate cyclooxygenase-2 mRNA.