Search

Background: Platinum-based chemotherapy has long been used in the treatment of a variety of cancers and functions by inducing DNA damage. ERCC1 and ERCC4 are involved in the removal of this damage and have previously been implicated in resistance to platinum compounds. The aim of the current investigation is to determine the presence, frequency and prognostic impact of ERCC1 or ERCC4 gene copy number alterations in colorectal cancer (CRC).Methods: Fluorescent in situ hybridization probes directed at ERCC1 and ERCC4 with relevant reference probes were constructed. Probes were tested in a CRC cell line panel and in tumor sections from 152 stage III CRC chemonaive patients. Relationships between biomarker status and clinical endpoints (overall survival, time to recurrence, and local recurrence in rectal cancer) were analyzed by survival statistics.Results: ERCC1-19q13 copy number alterations were observed in a single cell line metaphase (HT29). In patient material, ERCC1-19q13 copy number gains (ERCC1-19q13/CEN-2 ≥ 1.5) were detected in 27.0% of specimens, whereas ERCC1-19q13 deletions (ERCC1-19q13/CEN-2 < 0.8) were only detected in 1.3%. ERCC1-19q13 gain was significantly associated with longer survival (multivariate analysis, HR: 0.45, 95% CI: 0.20-1.00, p = 0.049) in patients with colon tumors, but not rectal tumors. No ERCC4 aberrations were detected and scoring was discontinued after 50 patients.Conclusions: ERCC1-19q13 copy number gains occur frequently in stage III CRC and influences survival in patients with colon tumors. Future studies will investigate the effect of ERCC1-19q13 aberrations in a platinum-treated patient population with the aim of developing a predictive biomarker profile for oxaliplatin sensitivity in CRC. [ABSTRACT FROM AUTHOR]

Background: Topoisomerase I (Top1) is the target of Top1 inhibitor chemotherapy. The TOP1 gene, located at 20q12-q13.1, is frequently detected at elevated copy numbers in colorectal cancer (CRC). The present study explores the mechanism, frequency and prognostic impact of TOP1 gene aberrations in stage III CRC and how these can be detected by fluorescent in situ hybridization (FISH). Methods: Nine CRC cell line metaphase spreads were analyzed by FISH with a TOP1 probe in combination with a reference probe covering either the centromeric region of chromosome 20 (CEN-20) or chromosome 2 (CEN-2). Tissue sections from 154 chemonaive stage III CRC patients, previously studied with TOP1/CEN-20, were analyzed with TOP1/CEN-2. Relationships between biomarker status and overall survival (OS), time to recurrence (TTR) in CRC and time to local recurrence (LR; rectal cancer only) were determined. Results: TOP1 aberrations were observed in four cell line metaphases. In all cell lines CEN-2 was found to reflect chromosomal ploidy levels and therefore the TOP1/CEN-2 probe combination was selected to identify TOP1 gene gains (TOP1/CEN-2≥1.5). One hundred and three patients (68.2%) had TOP1 gain, of which 15 patients (14.6%) harbored an amplification (TOP1/CEN-20≥2.0). TOP1 gene gain did not have any association with clinical endpoints, whereas TOP1 amplification showed a non-significant trend towards longer TTR (multivariate HR: 0.50, p = 0.08). Once amplified cases were segregated from other cases of gene gain, non-amplified gene increases (TOP1/CEN-2≥1.5 and TOP1/CEN-20<2.0) showed a trend towards shorter TTR (univariate HR: 1.57, p = 0.07). Conclusions: TOP1 gene copy number increase occurs frequently in stage III CRC in a mechanism that often includes CEN-20. Using CEN-2 as a measurement for tumor ploidy levels, we were able to discriminate between different mechanisms of gene gain, which appeared to differ in prognostic impact. TOP1 FISH guidelines have been updated. [ABSTRACT FROM AUTHOR]

Background and aims: Root distribution over the soil profile is important for crop resource uptake. Using machine learning (ML), this study investigated whether measured square root of planar root length density (Sqrt_pRLD) at different soil depths were related to uptake of isotope tracer (15N) and drought stress indicator (13C) in wheat, to reveal root function. Methods: In the RadiMax semi-field root-screening facility 95 winter wheat genotypes were phenotyped for root growth in 2018 and 120 genotypes in 2019. Using the minirhizotron technique, root images were acquired across a depth range from 80 to 250 cm in May, June, and July and RL was extracted using a convolutional neural network. We developed ML models to explore whether the Sqrt_pRLD estimates at different soil depths were predictive of the uptake of deep soil nitrogen - using deep placement of 15N tracer as well as natural abundance of 13C isotope. We analyzed the correlations to tracer levels to both a parametrized root depth estimation and an ML approach. We further analyzed the genotypic effects on root function using mediation analysis. Results: Both parametrized and ML models demonstrated clear correlations between Sqrt_pRLD distribution and resource uptake. Further, both models demonstrated that deep roots at approx. 150 to 170 cm depth were most important for explaining the plant content of 15N and 13C isotopes. The correlations were higher in 2018. Conclusions: The results demonstrated that, parametrized models and ML-based analysis provided complementary insight into the importance of deep rooting for water and nitrogen uptake. [ABSTRACT FROM AUTHOR]

Many butterfly populations respond negatively to land-use intensification in human-dominated landscapes. Networks of protected sites have been established with the aim to halt species loss. We undertook annual surveys of all occurrence sites of 22 uncommon butterfly species in eastern Denmark during the period 2014–2019 and compared to a systematic atlas survey done 1989–1993, in order to assess trends in regional occupancy of species. Three out of 22 species went regionally extinct between 1993 and 2015. One species sustained a single population through the study period. Logistic regression for the remaining 18 species showed 10 to be in strong decline from 1993 to 2015, two showed a declining trend and six had stable trends. For all species except one, the declining trend continued 2015–2019. For five species, a sustained strong decline was evident. In 1993, the total count of occurrence sites for all 22 butterfly species was 565, which by 2019 had declined to 158 sites (a 72 % loss over 26 years). From 2015 to 2019 alone, the total count of occurrence sites shrank from 200 to 158 (a 21 % decline over just four years). Legal protection of areas (Natura 2000 and Danish Nature Protection Act §3) was, unexpectedly, not associated with lower probability of local extinction for butterfly population. The observed sustained decline across species suggests an overall low efficiency of the network of protected sites, probably due to a combination of misguided management regimes and payment of extinction debts from the past. [ABSTRACT FROM AUTHOR]

The coffee research community has maintained a long ongoing debate regarding the implications of shade trees in coffee production. Historically, there has been contrasting results and opinions on this matter, thus recommendations for the use of shade (namely in coffee agroforestry systems) are often deemed controversial, particularly due to potential yield declines and farmers' income. This study is one of the first demonstrating how several Coffea arabica cultivars respond differently to shade with respect to yield. By standardising more than 200 coffee yield data from various in-field trials, we assembled the so-called "Ristretto" data pool, a one of a kind, open-source dataset, consolidating decades of coffee yield data under shaded systems. With this standardised dataset, our meta-analysis demonstrated significant genotypic heterogeneity in response to shade, showing neutral, inverted U-shaped and decreasing trends between yield and shade cover amongst 18 different cultivars. These findings encourage the examination of C. arabica at the cultivar level when assessing suitability for agroforestry systems. Comparison of productivity is also encouraged across a range of low to moderate shade levels (10–40%), in order to help elucidate potential unknown optimal shade levels for coffee production. [ABSTRACT FROM AUTHOR]

• Intrinsic resistance in wild strawberry plantations inhibited generalist aphid population. • Plant genotypes that were resistant against a chewing beetle (Galerucella tenella), conveyed resistance to generalist aphid only. • There were more specialists aphids on high diversity plots. • Anthocorids and Lacewing adults were more on high diversity plots, whereas other specialist predators followed aphid prey. Ecological theory hypothesizes that plant trait diversity may be as important as the presence of specific functional traits (e.g., resistance) for the herbivore and predator communities within a population. We used experimental populations of wild woodland strawberry (Fragaria vesca) to test whether the degree of plant genotypic diversity and/or the existence of specific resistance traits play a role in the host plant's community structure specifically, the community of generalist and specialist aphids and their natural enemies. In 2019, we studied the aphid abundance and relative predator abundance in an experimental field site in Alnarp, Southern Sweden; the field consisted of plots planted with combinations of 20 different wild strawberry genotypes. These strawberry genotypes were previously identified as either susceptible to or resistant against the herbivorous beetle (Galerucella tenella). Two aphid species, Chaetosiphon fragaefolii (specialist) and the exotic Aphis gossypii (generalist) were found in the plots and of the two species A. gossypii was dominant. The abundance of the specialist aphid (C. fragaefolii) was highest in susceptible plots with high genotypic diversity, while the generalist (A. gossypii) was highest in plots with a mix of resistant and susceptible plants with high genotypic diversity. Anthocorid predators, developed significantly higher population densities in strawberry plots with high genotypic diversity. Overall, predator abundance showed a positive correlation with aphid abundance. These results show that the specific functional trait of resistance as well as plant diversity affected aphids. Knowledge about these effects can be important factors to consider when designing strawberry plantings less susceptible to aphids. [ABSTRACT FROM AUTHOR]

Objective To investigate parameters causing canine thromboelastographic hypercoagulability and to investigate whether thromboelastography (TEG) with Cytochalasin D (Cyt D) added is related to parameters of platelet activity. Design Prospective observational study on hemostatic and inflammatory parameters. Data were collected between November 2012 and July 2013. Setting University teaching hospital. Animals Twenty-eight dogs suffering from diseases predisposing to thrombosis and 19 clinically healthy dogs. Diseased dogs were enrolled if they fulfilled inclusion criteria regarding age, size, informed client consent, and obtained a diagnosis of a disease that has been associated with thrombosis or hypercoagulability. Interventions None. Measurements and Main Results Parameters of coagulation and anticoagulation, fibrinolysis, and antifibrinolysis, platelet activity, inflammation, platelet count, and hematocrit were measured using CBC, TEG, platelet aggregation on multiplate, platelet activity on flow cytometry, and hemostatic and inflammatory markers on plasma and serum analyses. ANOVA and multilinear regression analyses indicated that especially hematocrit and the inflammatory parameters C-reactive protein and interleukin-8 showed best association with overall clot strength in diseased dogs with hypercoagulable TEG tracings. Ratios presumed to reflect platelet contribution to the TEG tracing obtained in TEG analyses with Cyt D were related especially with hematocrit and P-selectin expression of platelets measured after γ-Thrombin activation on flow cytometry. Conclusion Overall clot strength in TEG analyses of the hypercoagulable dogs included in the present study appears to be primarily associated with inflammation as well as hematocrit. Furthermore, the ratio between standard TEG analyses and TEG analyses with Cyt D may reflect some degree of platelet activity. [ABSTRACT FROM AUTHOR]

Aim: To understand how the integration of contextual spatial data on land cover and human infrastructure can help reduce spatial bias in sampling effort, and improve the utilization of citizen science-based species recording schemes. By comparing four different citizen science projects, we explore how the sampling design's complexity affects the role of these spatial biases. Location: Denmark, Europe. Methods: We used a point process model to estimate the effect of land cover and human infrastructure on the intensity of observations from four different citizen science species recording schemes. We then use these results to predict areas of under- and oversampling as well as relative biodiversity 'hotspots' and 'deserts', accounting for common spatial biases introduced in unstructured sampling designs. Results: We demonstrate that the explanatory power of spatial biases such as infrastructure and human population density increased as the complexity of the sampling schemes decreased. Despite a low absolute sampling effort in agricultural landscapes, these areas still appeared oversampled compared to the observed species richness. Conversely, forests and grassland appeared undersampled despite higher absolute sampling efforts. We also present a novel and effective analytical approach to address spatial biases in unstructured sampling schemes and a new way to address such biases, when more structured sampling is not an option. Main conclusions: We show that citizen science datasets, which rely on untrained amateurs, are more heavily prone to spatial biases from infrastructure and human population density. Objectives and protocols of mass-participating projects should thus be designed with this in mind. Our results suggest that, where contextual data is available, modelling the intensity of individual observation can help understand and quantify how spatial biases affect the observed biological patterns. [ABSTRACT FROM AUTHOR]

Abstract: Antibodies to Coxiella burnetii have been found in the Danish dairy cattle population with high levels of herd and within herd seroprevalences. However, the prevalence of antibodies to C. burnetii in Danish beef cattle remains unknown. The objectives of this study were to (1) estimate the prevalence and (2) identify risk factors associated with C. burnetii seropositivity in Danish beef and dairy cattle based on sampling at slaughter. Eight hundred blood samples from slaughtered cattle were collected from six Danish slaughter houses from August to October 2012 following a random sampling procedure. Blood samples were tested by a commercially available C. burnetii antibody ELISA kit. A sample was defined positive if the sample-to-positive ratio was greater than or equal to 40. Animal and herd information were extracted from the Danish Cattle Database. Apparent (AP) and true prevalences (TPs) specific for breed, breed groups, gender and herd type; and breed-specific true prevalences with a random effect of breed was estimated in a Bayesian framework. A Bayesian logistic regression model was used to identify risk factors of C. burnetii seropositivity. Test sensitivity and specificity estimates from a previous study involving Danish dairy cattle were used to generate prior information. The prevalence was significantly higher in dairy breeds (AP=9.11%; TP=9.45%) than in beef breeds (AP=4.32%; TP=3.54%), in females (AP=9.10%; TP=9.40%) than in males (AP=3.62%; TP=2.61%) and in dairy herds (AP=15.10%; TP=16.67%) compared to beef herds (AP=4.54%; TP=3.66%). The Bayesian logistic regression model identified breed group along with age, and number of movements as contributors for C. burnetii seropositivity. The risk of seropositivity increased with age and increasing number of movements between herds. Results indicate that seroprevalence of C. burnetii is lower in cattle sent for slaughter than in Danish dairy cows in production units. A greater proportion of this prevalence is attributed to slaughtered cattle of dairy breeds or cattle raised in dairy herds rather than beef breeds. [Copyright &y& Elsevier]

Light is a critical component of indoor plant cultivation, as different wavelengths can influence both the physiology and morphology of plants. Furthermore, fertilization and seeding density can also potentially interact with the light recipe to affect production outcomes. However, maximizing production is an ongoing research topic, and it is often divested from resource use efficiencies. In this study, three species of microgreens-kohlrabi; mustard; and radish-were grown under five light recipes; with and without fertilizer; and at two seeding densities. We found that the different light recipes had significant effects on biomass accumulation. More specifically, we found that Far-Red light was significantly positively associated with biomass accumulation, as well as improvements in height, leaf area, and leaf weight. We also found a less strong but positive correlation with increasing amounts of Green light and biomass. Red light was negatively associated with biomass accumulation, and Blue light showed a concave downward response. We found that fertilizer improved biomass by a factor of 1.60 across species and that using a high seeding density was 37% more spatially productive. Overall, we found that it was primarily the main effects that explained microgreen production variation, and there were very few instances of significant interactions between light recipe, fertilization, and seeding density. To contextualize the cost of producing these microgreens, we also measured resource use efficiencies and found that the cheaper 24-volt LEDs at a high seeding density with fertilizer were the most efficient production environment for biomass. Therefore, this study has shown that, even with a short growing period of only four days, there was a significant influence of light recipe, fertilization, and seeding density that can change morphology, biomass accumulation, and resource input costs.

Animal-level responses to weather variability in US dairy systems are well described, but the potential of housing and other farm management practices (for example, fans and sprinklers) to moderate the impacts of weather remains uncertain. Here we assess the influence of historical variation in the temperature-humidity index (THI) on milk yields using monthly state-level yield data and high-resolution daily weather data over 1981-2018. We find that milk yields are compromised by exposure to both extreme heat (>79 THI) and cold (<39 THI), causing average daily yield decreases of around 3.7% and 6.1%, respectively, relative to optimal conditions (65-69 THI). Colder regions are more sensitive to heat extremes, and warm regions are more sensitive to cold extremes. Sensitivity to THI has reduced dramatically over time. Climate trends contributed modestly (around 0.1% over 38 years) to rising yields in most states via alleviating cold stress, although more extreme future conditions may negate these benefits., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

We determined how conidia of arthropod-pathogenic fungi on leaves affected the behavior of two predators-Orius majusculus (Hemiptera: Anthocoridae) and Phytoseiulus persimilis (Acari: Phytoseiidae)-when offered a choice between preying on two-spotted spider mites, Tetranychus urticae (Acari: Tetranychidae), in the presence or absence of infective conidia of Metarhizium brunneum (Ascomycota: Hypocreales) and Neozygites floridana (Entomophthoromycota: Neozygitaceae). The results indicate no significant relation between the presence of conidia and predator behavior. The only indication of interference is between the generalists O. majusculus and M. brunneum, with a trend towards more time spent feeding and more prey encounters turning into feeding events on leaf discs without conidia than on leaf discs with conidia. Our results show that the presence of fungal conidia does not alter the preying behavior of the predators, and using predators and fungi together is not limited by any interference between organisms in the short term.