Observations and models of emissions of volatile terpenoid compounds from needles of ponderosa pine trees growing in situ: control by light,temperature and stomatal conductance

Terpenoid emissions from ponderosa pine (Pinus ponderosa subsp. scopulorum) were measured in Colorado, USA over two growing seasons to evaluate the role of incident light, needle temperature, and stomatal conductance in controlling emissions of 2-methyl-3-buten-2-ol (MBO) and several monoterpenes. MBO was the dominant daylight terpenoid emission, comprising on average 87 % of the total flux, and diurnal variations were largely determined by light and temperature. During daytime, oxygenated monoterpenes (especially linalool) comprised up to 75 % of the total monoterpenoid flux from needles. A significant fraction of monoterpenoid emissions was dependent on light and ¹³CO₂ labeling studies confirmed de novo production. Thus, modeling of monoterpenoid emissions required a hybrid model in which a significant fraction of emissions was dependent on both light and temperature, while the remainder was dependent on temperature alone. Experiments in which stomata were forced to close using abscisic acid demonstrated that MBO and a large fraction of the monoterpene flux, presumably linalool, could be limited at the scale of seconds to minutes by stomatal conductance. Using a previously published model of terpenoid emissions, which explicitly accounts for the physico-chemical properties of emitted compounds, we were able to simulate these observed stomatal effects, whether induced experimentally or arising under naturally fluctuation conditions of temperature and light. This study shows unequivocally that, under naturally occurring field conditions, de novo light-dependent monoterpenes comprise a significant fraction of emissions in ponderosa pine. Differences between the monoterpene composition of ambient air and needle emissions imply a significant non-needle emission source enriched in Δ-3-carene.     

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data

Background

The use of sequencing technologies to investigate the microbiome of a sample can positively impact patient healthcare by providing therapeutic targets for personalized disease treatment. However, these samples contain genomic sequences from various sources that complicate the identification of pathogens.

Results

Here we present Clinical PathoScope, a pipeline to rapidly and accurately remove host contamination, isolate microbial reads, and identify potential disease-causing pathogens. We have accomplished three essential tasks in the development of Clinical PathoScope. First, we developed an optimized framework for pathogen identification using a computational subtraction methodology in concordance with read trimming and ambiguous read reassignment. Second, we have demonstrated the ability of our approach to identify multiple pathogens in a single clinical sample, accurately identify pathogens at the subspecies level, and determine the nearest phylogenetic neighbor of novel or highly mutated pathogens using real clinical sequencing data. Finally, we have shown that Clinical PathoScope outperforms previously published pathogen identification methods with regard to computational speed, sensitivity, and specificity.

Conclusions

Clinical PathoScope is the only pathogen identification method currently available that can identify multiple pathogens from mixed samples and distinguish between very closely related species and strains in samples with very few reads per pathogen. Furthermore, Clinical PathoScope does not rely on genome assembly and thus can more rapidly complete the analysis of a clinical sample when compared with current assembly-based methods. Clinical PathoScope is freely available at: http://sourceforge.net/projects/pathoscope/.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-262) contains supplementary material, which is available to authorized users.     

Seed Dispersal of Morus macroura (Moraceae) by Two Frugivorous Bats in Xishuangbanna, SW China

The dispersal of Morus macroura seeds by two species of frugivorous bats ( Rousettus leschenaulti and Cynopterus sphinx ) was studied in a forest at Xishuangbanna Tropical Botanical Garden in Southwest China from March to May 2005. Feeding roosts were identified within 500 m around parent trees and the types and number of seed loads under each roost were recorded. We found feeding roost density decreased with increasing distance from the parent, but found no correlation between distance and seed deposition. The effect of bat digestion on seed germination was investigated, and we found that germination percentage of all treatments involving ingestion by bats was significantly lower than control seeds and some germination parameters of seeds from different treatments changed.     

Colorectal cancer cases and relatives of cases indicate similar willingness to receive and disclose genetic information

Context: Recent developments in genetic testing allow us to detect individuals with inherited susceptibility to some cancers. Genetic testing to identify carriers of cancer-related mutations may help lower risk by encouraging preventive behaviors and surveillance. This study assessed willingness of colon cancer cases and relatives to receive genetic information that may indicate an increased risk for cancer, to whom they would disclose genetic information, and whether receiving genetic test results may influence future prevention behaviors among individuals enrolled in the Seattle Colorectal Cancer Family Registry. Methods: Incident invasive colorectal cancer cases were identified from the Puget Sound Surveillance Epidemiology and End Results (SEER) registry. In 2007, a sequential sample of cases and relatives (n = 147) were asked to respond to a questionnaire addressing study aims. The questionnaire was administered during a baseline or 5-year follow-up interview. Results: Patterns of response to each statement were similar between colorectal cancer cases and relatives. Both colorectal cases (95%) and relatives (95%) reported willingness to receive genetic information. Nearly all participants would tell their doctor the results of a genetic test (99% of cases; 98% of relatives), and all married participants would tell their spouses. Cases (96%) anticipated being slightly more likely than relatives (90%) to change their cancer screening behavior, but this difference was not statistically significant (p = 0.33). Conclusions: A high percentage of both colorectal cancer cases and relatives sampled from the Seattle Colorectal Cancer Family Registry are interested in identifying their genetic status, discussing their genetic status with their family and doctor, and adopting behavioral changes that may reduce cancer risk.     

Personality predicts ectoparasite abundance in an asocial sciurid

Parasitism is a consequence of complex interactions between host, parasite, and their shared environment, and host behavior can influence parasite risk. Animal personality (i.e., consistent behavioral differences that are repeatable across time and context) can influence parasitism with more explorative individuals typically hosting greater parasite loads. Host “sociality” is known to impact parasite risk with more social individuals typically at higher risk of acquiring or transmitting parasites, but other behaviors could also be important. We quantified personality in least chipmunks (Tamias minimus), including repeatability of behavioral traits, and determined whether these personality traits affected ectoparasite prevalence and abundance. We measured personality using standardized hole‐board tests and quantified ectoparasitism of 39 least chipmunks over 2 years at a site in southeastern Manitoba, Canada. We found that activity and exploration were repeatable within the context of the hole‐board test for least chipmunks, which suggests that these traits reflect personality. More exploratory individuals hosted a greater abundance of ectoparasites compared to less exploratory individuals. Our results are consistent with past studies implicating personality as a factor in host–parasite dynamics and suggest that exploration may be an important behavioral correlate of parasite acquisition.     

Differential reliance on aquatic prey subsidies influences mercury exposure in riparian arachnids and songbirds

Cross‐ecosystem subsidies move substantial amounts of nutrients between ecosystems. Emergent aquatic insects are a particularly important prey source for riparian songbirds but may also move aquatic contaminants, such as mercury (Hg), to riparian food webs. While many studies focus on species that eat primarily emergent aquatic insects, we instead study riparian songbirds with flexible foraging strategies, exploiting both aquatic and terrestrial prey sources. The goal in this study is to trace reliance on aquatic prey sources and correlate it to Hg concentrations in common riparian arachnids (Families Tetragnathidae, Opiliones, and Salticidae) and songbirds (Common Yellowthroat Geothlypis trichas, Spotted Towhee Pipilo maculatus, Swainson''s Thrush Catharus ustulatus, Song Sparrow Melospiza melodia, and Yellow Warbler Setophaga petechia). We used stable isotopes of δ¹³C and δ¹⁵N and Bayesian mixing models in MixSIAR to determine the reliance of riparian predators on aquatic prey sources. Using mixed effects models, we found that arachnid families varied in their reliance on aquatic prey sources. While songbird species varied in their reliance on aquatic prey sources, songbirds sampled earlier in the season consistently relied more on aquatic prey sources than those sampled later in the season. For both arachnids and songbirds, we found a positive correlation between the amount of the aquatic prey source in their diet and their Hg concentrations. While the seasonal pulse of aquatic prey to terrestrial ecosystems is an important source of nutrients to riparian species, our results show that aquatic prey sources are linked with higher Hg exposure. For songbirds, reliance on aquatic prey sources early in the breeding season (and subsequent higher Hg exposure) coincides with timing of egg laying and development, both of which may be impacted by Hg exposure.     

Widespread contamination of SARS-CoV-2 on highly touched surfaces in Brazil during the second wave of the COVID-19 pandemic

Although SARS-CoV-2 surface contamination has been investigated in health care settings, little is known about the SARS-CoV-2 surface contamination in public urban areas, particularly in tropical countries. Here, we investigated the presence of SARS-CoV-2 on high-touch surfaces in a large city in Brazil, one of the most affected countries by the COVID-19 pandemic in the world. A total of 400 surface samples were collected in February 2021 in the City of Recife, Northeastern Brazil. A total of 97 samples (24.2%) tested positive for SARS-CoV-2 by RT-qPCR using the CDC-USA protocol. All the collection sites, except one (18/19, 94.7%) had at least one environmental surface sample contaminated. SARS-CoV-2 positivity was higher in public transport terminals (47/84, 55.9%), followed by health care units (26/84, 30.9%), beach areas (4/21, 19.0%), public parks (14/105, 13.3%), supply centre (2/21, 9.5%), and public markets (4/85, 4.7%). Toilets, ATMs, handrails, playgrounds and outdoor gyms were identified as fomites with the highest rates of SARS-CoV-2 detection. Taken together, our data provide a real-world picture of SARS-CoV-2 dispersion in highly populated tropical areas and identify critical control points that need to be targeted to break SARS-CoV-2 transmission chains.     

Deprivation and emergency admissions for cancers of colorectum,lung, and breast in south east England: ecological study

Objectives: To examine the relation between deprivation and acute emergency admissions for cancers of the colon, rectum, lung, and breast in south east England. Design: Ecological analysis with data from hospital episode statistics and 1991 census. Setting: North and South Thames Regional Health Authorities (population about 14 million), divided into 10 aggregations of 31 470 census enumeration districts (median population 462). Subjects: 146 639 admissions relating to 76 552 patients aged <100 years on admission, resident in the Thames regions, admitted between 1 April 1992 and 31 March 1995. Results: Residents living in deprived areas were more likely to be admitted as emergencies and has ordinary inpatient admissions and less likely to be admitted as day cases. Adjusted odds of ordinary admissions from the most deprived tenth occurring as emergencies (relative to admissions from the most affluent tenth) were 2.29 (95% confidence interval 2.09 to 2.52) for colorectal cancer, 2.20 (1.99 to 2.43) for lung cancer, and 2.41 (2.17 to 2.67) for female breast cancer; adjusted odds of admissions as day cases were 0.70 (0.64 to 0.76), 0.50 (0.44 to 0.56), and 0.56 (0.50 to 0.62), respectively. Patients from deprived areas with lung or breast cancers were less likely to be recorded as having surgical interventions. Adjusted odds of patients from the most deprived tenth receiving surgery were 0.88 (0.78 to 1.00), 0.58 (0.48 to 0.70), and 0.63 (0.56 to 0.71), respectively. Admissions for colorectal cancer from the most deprived areas were less likely to be to hospitals admitting 100 or more new patients a year; the opposite held true for breast cancer admissions. No association was found for lung cancer admissions. Conclusions: Earlier diagnostic and referral procedures in primary care in deprived areas are required if there are to be significant reductions in mortality from these cancers. A national information strategy is required to ensure the continued availability of population based data on NHS patients and to mandate standardised datasets from the private sector. Rationalisation of acute services, hospital mergers, and plans for bed closures must take into account the increased healthcare needs and inequities in access to treatment and care of residents in areas with high levels of deprivation. Health authorities and primary care groups should re-examine their purchasing intentions, service reviews, and monitoring arrangements in the light of these findings.

Key messages

• A major reorganisation of cancer services is under way in England and Wales with the aim of improving access to and quality of treatment
• Residents with cancers of the bowel, lung, or breast in deprived areas in the Thames region were more likely to be admitted as emergencies and ordinary inpatients than their counterparts from more affluent areas, and patients with lung or breast cancers from deprived areas were less likely to receive surgical treatment
• Patients with colorectal cancer from the most deprived areas were less likely to be seen at hospitals with a large caseload than were patients from affluent areas; the opposite held true for patients with breast cancer, but no association was found for admissions for lung cancer
• More effective early diagnostic and referral procedures in primary care in deprived areas are required if reductions in mortality are to be achieved
• Hospital mergers and plans for service reconfiguration and bed closures must take into account inequities in access to treatment among residents in deprived areas