Sampling Dates Research Articles

CTNI-69. REAL-TIME DRUG SCREENING AND GENOMIC TESTING TO DETERMINE INDIVIDUALIZED TREATMENT PLANS IN CHILDREN AND YOUNG ADULTS WITH RELAPSED MEDULLOBLASTOMA: PRELIMINARY REPORT OF PNOC027

Abstract While current upfront multi-modal treatment for medulloblastoma is effective in many cases, for patients who relapse or don’t respond to initial therapy, effective treatment options are limited and novel therapeutic approaches are needed. The Pacific Pediatric Neuro-Oncology Consortium (PNOC) PNOC027 clinical trial investigates a precision medicine approach that combines real-time drug screening with whole exome and RNA sequencing of fresh tumor tissue to inform individualized treatment recommendations for children and young adults with relapsed medulloblastoma. The primary endpoint is to determine the feasibility of incorporating real time drug screening with DNA/RNA sequencing of tumor to develop a treatment regimen of up to 4-drug of FDA approved agents within 21 business days of tumor acquisition. To this end, freshly isolated cells from relapsed medulloblastoma tumor tissue undergo high-throughput drug screening using a platform of 232 clinically available compounds in parallel with multi-omic genomic analyses to predict individualized tumor response to treatment. Drug responses are assessed after 72 hours of drug exposure and the results yield drug prioritizations based on cytotoxicity and predicted blood-brain barrier permeability. Drugs from different classes are selected based on results from drug screening and molecular analyses combined with patient age, prior treatments, and other medical conditions. Four patients have been enrolled to date and viable tissue samples have been successfully collected and analyzed with treatment recommendations rendered within 21 business days for all patients. The five drug classes with the highest in vitro responses on the drug screen are HDAC inhibitors, proteosome inhibitors, anthracyclines, DNA crosslinkers and kinase inhibitors. PNOC027 demonstrates preliminary feasibility of real-time drug screening combined with DNA/RNA sequencing to inform targeted therapy selection for patients with relapsed medulloblastoma in clinically relevant timeframes. The trial is informing an expanded precision-based approach for relapsed medulloblastoma and the impact of genetic and epigenetic alterations on treatment response.

Impact of cluster thinning and harvest date on berry volatile composition and sensory profile of <i>Vitis</i> sp. Seyval blanc and Vandal-Cliche

Northern conditions are challenging for grape and wine producers. To cope with these challenges, the use of early ripening interspecific hybrid Vitis sp., such as Seyval blanc and Vandal-Cliche, is often preferred to traditional V. vinifera. However, knowledge about cultural practices suitable for interspecific hybrid varieties are still scarce, especially regarding their impact on profiles of volatile compounds and the sensory perception of berries. In this study, the impact of cluster thinning and harvest date on grapevine physiology, must chemical composition and berry sensory attributes of Seyval blanc and Vandal-Cliche was investigated. Three crop loads (100 %, 70 % and 40 % crop) and three harvest dates corresponding to pre-maturity, maturity, and post-maturity were assessed in 2012 and 2013. Cluster thinning significantly decreased the yield of Vandal-Cliche, but not of Seyval blanc, for which it instead improved fruit set without affecting yield. The impact of cluster thinning on must chemical composition was limited for both cultivars, although some significant changes were observed, especially in the cool season of 2013. Clear variations during ripening, in terms of technological parameters and aroma characteristics, were observed depending on the cultivars and the seasons. In Seyval blanc, C6-alcohols and C13-norisoprenoids decreased during ripening, while C6-aldehydes and linalool increased. In Vandal-Cliche, berries from the first and the last sampling dates of the warm season of 2012 showed the highest levels of C13-norisoprenoids, whereas berries from the last sampling date in the cold season of 2013 showed the highest levels of terpenes, C13-norisoprenoids and ethyl esters. Despite its limited impact on fruit chemical composition, cluster thinning significantly impacted the sensory perception of Vandal-Cliche berries in both years. Cluster-thinned berries had softer skin, sweeter and less acidic pulp, and fruitier skin and pulp aroma. Skin softness allowed excellent discrimination of the maturity of both cultivars during the two study years, suggesting that this descriptor could be a suitable maturity marker for these interspecific hybrid varieties. In summary, cluster thinning proves beneficial for enhancing fruit set in Seyval Blanc in a northern climate; however, its influence on fruit quality is minimal for both cultivars.

PSII-15 Effects of Tillage Method and Fertilization Rate on Fall Performance of Stocker Cattle Grazing Wheat Pasture and Stand Performance

Abstract The objectives of this study were to determine the effects of fertilization rate and wheat pasture establishment method on fall stocker and wheat stand performance. Twenty-four, 1.62-ha pastures were utilized, with 8 pastures per fertilizer (N) treatment. Fertilization consisted of urea applied at 50.44, 67.25, or 84.06 kg N/ha. To measure responses associated with tillage method, 2 fields from each N treatment were prepared using clean-till (CT, n = 6), and the remaining fields were prepared with a no-till (NT) method. Beef steers (278.51 ± 29.42 kg) were randomly allocated at a fixed rate of 2.47 steers/ha (4 steers/pasture), with a combined total of 240 steers used in fall of 2021 and 2022. Steers were weighed upon arrival, at turnout, every 28 days, and when pulled off pasture. Steers were pulled off pasture when forage mass (FM) became insufficient, or temperatures became too cold to support forage regrowth. Forage mass sampling was recorded with a 0.25 m2 plate meter. Sampling dates coincided with weigh dates. Twenty plate meter readings were taken in every field (600 readings in total per sampling date) and 0.25 m2 grass clippings were obtained from 15 fields every sampling date to form a regression curve to estimate FM. An analysis of co-variance using the Mixed Model procedure in JMP was used to analyze this data. Tillage method and N rate were fixed categorical and continuous covariates, respectively. Year was modeled as a random effect. Tillage × N interaction was used to examine differences in slope estimates for N rate between CT and NT. Non-significant interactions were removed from the model. Total weight gain per hectare and final weight were both greater in CT compared with NT (P = 0.01), More grazing days was observed with CT (P < 0.01), as well as a trend toward greater mean FM (P = 0.06). Ending FM was also greater for CT pastures (P < 0.05). No significant effects from tillage were found for initial weight, average daily weight gain, initial FM, or FM slope change. No differences (P > 0.1) among responses were associated with a linear response to N rate. In conclusion, CT demonstrated greater performance than NT, with CT having greater FM response, more grazing days, and greater body weight gain per hectare, and N rates greater than 50.4 kg/ha did not appear beneficial for the studied stocking rate and climate conditions.

PSXIII-26 Investigating the Genetic Background of Juniper Consumption in Goats

Abstract Junipers (Juniperus spp.) are woody invasive plants that have caused encroachment problems in the U.S. western rangeland, decreasing forage productivity and biodiversity. A potential solution to this issue is the use of goats in target grazing programs. Selecting goats for juniper consumption is of great interest to rangeland farmers. Therefore, our main objectives were to 1) estimate genetic parameters, including heritability and repeatability, for juniper consumption in Angora (ANG) and Boer x Spanish (BxS) composite population of goats grazing on West Texas rangelands (USA); and, 2) perform a genome-wide association study (GWAS) to identify candidate genes associated with juniper consumption. Fecal samples were collected multiple times between 2008 and 2017 and analyzed using near-infrared reflectance spectroscopy (NIRS) to estimate the percentage of juniper in the diet of goats, using calibration equations previously developed in controlled studies. We analyzed a dataset comprising 2,327 records from 459 ANG and 8,714 records from 1,996 BxS. The pedigree file included 1,601 and 2,426 ANG and BxS goats, respectively. Genomic information for 50,957 single nucleotide polymorphisms (SNP) from 93 ANG and 238 BxS goats was included in the analyses. Sampling date and sex were fitted as categorical fixed effects and age as a linear covariate in the statistical models. Animal direct additive genetic and permanent environment were considered as random effects. Genetic parameters were calculated based on the Restricted Maximum Likelihood method under the single-step genomic BLUP procedure implemented in the BLUPf90+ family of programs. We used de-regressed estimated breeding values and whole-genome sequence data for the GWAS analyses with 8 million SNP for the ANG and 5.3 million SNP for the BxS. The software GCTA was employed for these analyses. Juniper percentage in their diets varied across the years and ranged from 2.14% (± 7.51%) to 14.6% (± 11.0%) for ANG and from 10.5% (± 14.7) to 33.8% (± 18.1) for the BxS population. The heritability estimate for juniper consumption was 0.19 (± 0.038) for ANG and 0.28 (± 0.022) for BxS, indicating that juniper consumption can be increased through selection. The repeatability values were 0.21 for ANG and 0.37 for BxS. The GWAS revealed 1,257 significant SNP located within or close to 220 genes in ANG, and 878 SNP related to 159 genes in BxS, suggesting their association with juniper consumption. These findings suggest that juniper consumption is under genetic control and has a polygenic inheritance pattern influenced by multiple genes of small effect. The heritability and repeatability estimates indicate that genetic improvement of juniper consumption is feasible in both goat populations.

Thirty years of regional groundwater-quality trend studies in the United States: Major findings and lessons learned

Changes in groundwater quality have been evaluated for more than 2,200 wells in 25 Principal Aquifers in the United States based on repeated decadal sampling (once every 10 years) from 1988 to 2021. The purpose of this study is to identify contaminants with changing concentrations, the locations and magnitude of those changes, the factors driving those changes, the obstacles to interpreting the changes, and approaches to ameliorate those obstacles. Sampling was conducted in 89 networks of 20–30 wells each that represent various geographic regions, aquifer types and land use types. Each network, and the wells that comprise them, are sampled on a rotating basis once every 10 years. Of the 28 constituents evaluated for trends, concentrations of Na, Cl, dissolved solids, SO4, and NO3 exhibited statistically significant increases at the network level more frequently than other constituents. Factors affecting trends in Cl and NO3 are emphasized in this study. Regional patterns show large increases of Cl in urban areas in the Northeast and Midcontinent, where road-deicing salt application rates are 10 to 100 times greater than in other regions of the country, and in semiarid and arid regions of the western United States, where evaporation concentrates solutes in recharge. The largest increases in NO3 were in agricultural areas of the semiarid west, arid west and Pacific regions which are characterized by oxic groundwater, long-term increases in nitrogen fertilizer usage, and high rates of irrigation. However, finding a direct relation between increasing contaminant sources and corresponding groundwater quality response, particularly when sampling once every 10 years, can be complicated by factors such as uncertainty in the timing, mass, and location of contaminant sources, groundwater residence time (recharge date), geochemical conditions in the aquifer that affect contaminant transport, and variability in water quality due to climatic factors such as seasonality and hydrologic conditions. Understanding groundwater residence time allows the changes in groundwater quality to be evaluated in the context of recharge date rather than the sample date. Likewise, information on geochemical characteristics of the aquifer can be helpful for understanding relations between contaminant source inputs and groundwater concentrations. For example, oxic geochemical conditions in the aquifer may allow for conservative transport and accumulation of NO3 in groundwater, whereas reducing environments could favor NO3 degradation. Differences in hydrologic conditions (wetter or drier than average) on the date of sampling could impact the statistical results of sampling at decadal intervals and obscure long-term patterns. Samples collected under substantially different hydrologic conditions can be identified, and high-frequency sampling can improve interpretation of measured results in these cases. Although decadal sampling and associated water-quality interpretations have limitations, repeated, scheduled sampling of thousands of wells over multiple decades has great value for identifying and understanding long-term, regional groundwater-quality trends. Despite these limitations, the concepts presented herein provide options that could be used to interpret trends or changes when sampling over longer timespans, which is less common than trend networks with higher frequency sampling intervals.

The effects of annual cycle, source population, and body condition on leukocyte profile and immune challenge in a basal reptile, the tuatara (Sphenodon punctatus).

Leukocyte profiles are broadly used to assess the health status of many species. Reference intervals, and an understanding of the factors that may influence these intervals, are necessary for adequate interpretation of leukograms. Using a data set that spans over three decades, we investigated variation in leukocyte profile in several populations of the evolutionarily unique reptile, the tuatara (Sphenodon punctatus). To do this, we first established reference intervals for each leukocyte type according to best practices. Next, we determined that source population and sampling date were the two most important predictors of leukocyte makeup. We found significant differences in the ratio of heterophils: lymphocytes (H:L) between populations, with tuatara on the more resource-stressed sampling island having a significantly higher ratio of H:L. Finally, we found that sampling location, sex, and life stage did not explain variation in the responses of tuatara to stimulation with Concanavalin A and lipopolysaccharide in both 3-(4,5-dimethylthiazol-2-yl)-2,5-di-phenyltetrazolium bromide and Griess assay experiments. Our results offer important insight into the function of leukocytes in reptiles.

Implementation of a Newborn Screening for Sickle Cell Disease, at the Hospital Materno Infantil Dr Manuel Pedro Azancot De Menezes, Angola

Sickle Cell Disease (SCD) is a hereditary disease, and a worldwide public health problem, with a higher incidence in sub-Saharan Africa, where the prevalence is very high (about 80%). SCD prevalence can reach 3,3 % in Angola, while carriers of the sickle cell trait account for more than 25% of the population. The early identification of patients and their follow-up in consultation are an added value for the reduction of morbidity and mortality of children with SCD. The implementation of early infant screening and follow-up programs for children with SCD showed excellent results in increasing the survival of these children. With this project we intend to implement a Newborn screening in Hospital Materno Infantil Dr Manuel Pedro Azancot de Menezes, a referral of the main maternity in Angola, located in Luanda, the country capital, that could be replicated in other hospitals, giving training to the health professionals, and to the laboratory technicians, in order to diagnose the SCD patients. The objective of this project is to establish a neonatal screening for SCD at a main Hospital in Angola, contributing to reduce the under 5 mortality, and to support for pediatric follow-up consultations of children diagnosed with SCD. Specific aims include: record the data and medical history of babies diagnosed with SCD up to 5 years of age at regular appointments; estimate the prevalence of SCD in the municipality of Camama, Luanda; and to evaluate the costs of neonatal screening and early interventions in Angola, by supporting a registry of SCD. The newborn screening has started in June 2023, with the training of the team at the hospital, and with the creation of all documents and forms needed. The project received ethical approval in June 2023. The study includes every child born in the maternity ward of the Hospital, and also every child that take vaccinations there (in this way we can include newborns delivered at home), that the legal guardians authorize the collection of blood sample by prick heel for screening for SCD. The samples of filter paper duly identified with the sample number and date of collection are being sent to Lisbon (Portugal), for hemoglobin electrophoresis by isoelectric focusing (IEF) carried out in the Migele equipment (acquired with the support of Perkin Elmer, and the ARISE project) (Figure 1). All SS samples are being genotyped for the HbS mutation by PCR-RFLP. Since the start of the newborn screening (June 28 th) we have collected 1000 samples in 4 weeks and have started the IEF analysis with MIGELE (Perkin Elmer). The preliminary results (221 samples, 177 AA, 41 AS and 3 SS) showed a 1.4% prevalence of SS, and 19.5% of AS, confirmed by PCR-RFLP (in all AS and SS). The frequencies were in Hardy-Weinberg equilibrium. Moreover, we are searching for other possible hemoglobinopathies. More results will be presented. All children diagnosed as SS (SCD) are being contacted by the Hospital Materno Infantil Dr Manuel Pedro Azancot de Menezes, Angola, to be followed in consultation. Newborn screening and early interventions for SCD should be a health priority and implemented at national level. It is our plan to catalyze progress toward this aim by demonstrating the high prevalence of neonatal SCD in the Luanda Hospital and demonstrate the feasibility of this screening in reducing under 5 mortalities. The present project has the support of ARISE project “African Research and Innovative initiative for Sickle cell Education: Improving Research Capacity for Service Improvement” project (GA 824021 - ARISE - H2020-MSCA-RISE-2018) by supporting the secondments of Angolan Laboratory technicians in Lisbon (Portugal) to perform the IEF and genetic analysis and be trained. Until now 5 Angolan secondees, and 3 Nigerian secondees have been trained in Lisbon. Perkin Elmer (Revvity) is giving llogistical support by kindly support the low-cost acquisition, installation and training in MIGELE equipment for IEF, and being always available to technical support. Figure 1 - Flow diagram of the methodology followed in the present study.

Surge of lower respiratory tract group A streptococcal infections in England in winter 2022: epidemiology and clinical profile

BackgroundFollowing low incidence of invasive group A streptococcal (iGAS) infections during the COVID-19 pandemic, marked increases were noted in many countries during 2022, particularly in children. In November 2022, severe presentations of lower respiratory tract infections (LRTIs), including empyema, were notified by clinicians across the UK. UKHSA investigated this rise with the aim of informing clinical management and public health response. MethodsWe undertook a case-series analysis using multiple routine data sources, exempted from ethics approval or patient consent. We identified iGAS cases in England in children younger than 15 years with an LRTI reported between Oct 1 and Dec 21, 2022, using UKHSA laboratory surveillance data (GAS detected in LRT specimens) and notifications by clinicians and Health Protection Teams (HPTs). Symptoms, diagnoses, health-care interactions, and outcome (death or recovery) data were obtained from HPT case management notes, the National Child Mortality Database, and the NHS Digital Emergency Care Dataset. FindingsWe identified 147 cases of LRTI iGAS in children across England (77 [52%] male, 70 [48%] female; median age 4 years [IQR 2–6]). Predominant ethnicities were White (74 [65%] of 113 with known ethnicity) and Asian (18 [16%] of 113). Most reported symptoms were fever (90 [75%] of 120 children with ≥1 symptom) and cough (60 [50%] of 120), and 71 (48%) of all 147 children had a diagnosed respiratory viral coinfection (most commonly hMPV and RSV). 127 (86%) of children attended an emergency department, 31% (n=36/114 with onset date) at least twice within 21 days after symptom onset. 37 (25%) of 147 children died, with a median time from symptom onset to death of 4 days (IQR 3–7). Of 32 children with sample dates, 16 (84%) were tested for GAS on or after the day they died. Over half of deaths (21 [57%] of 37 deaths) occurred in the community after rapid deterioration, of whom 18 had previous contact with health-care services documented. InterpretationThe UK saw an unusual rise in iGAS LRTIs in children in late 2022. One in four cases died, over half in the community. Non-specific symptoms, viral symptoms, or positive virology might have lowered suspicion of bacterial infection. Although the use of multiple available data sources expedited the analysis, varying data completeness limited interpretation. Our study highlights the need for earlier detection and identification of effective measures to prevent death. FundingNone.

Mendelian randomization study on the causal effect of serum IgA levels on H7N9 avian influenza A virus susceptibility.

Avian influenza A viruses (IAVs) that cross the species barrier to infect humans have the potential to initiate a new pandemic. However, the host factors influencing avian IAV infection remain poorly understood. To address this knowledge gap, we conducted a two-sample Mendelian randomization (MR) analysis by integrating our in-house genome-wide association study (GWAS) of avian IAV H7N9 susceptibility (with 217 cases and 116 controls) with the largest GWAS of serum IgA levels to date (sample size 41 263). Using the inverse-variance weighted (IVW) method, we discovered that genetically decreased serum IgA levels were associated with an increased risk of H7N9 infection (β = -2.528, 95% confidence interval [CI]: -4.572 to -0.484; p = 0.015). Consistent results were obtained from three other MR methods, including robust IVW estimation (β = -2.506, 95% CI: -4.109 to -0.902; p = 0.002), generalized summary-data-based MR (GSMR) (β = -2.238, 95% CI: -4.106 to -0.602; p = 0.019), and MR-pleiotropy residual sum and outlier (MR-PRESSO) (β = -2.528, 95% CI: -4.396 to -0.892; p = 0.026). In conclusion, our analysis provided compelling evidence support a causal relationship between genetically predicted serum IgA levels and avian IAV H7N9 susceptibility.

Conserved grasslands support similar pollinator diversity as pollinator-specific practice regardless of proximal cropland and pesticide exposure.

Pollinator diversity and abundance are declining globally. Cropland agriculture and the corresponding use of agricultural pesticides may contribute to these declines, while increased pollinator habitat (flowering plants) can help mitigate them. Here we tested whether the relative effect of wildflower plantings on pollinator diversity and counts were modified by proportion of nearby agricultural land cover and pesticide exposure in 24 conserved grasslands in Iowa, USA. Compared with general grassland conservation practices, wildflower plantings led to only a 5% increase in pollinator diversity and no change in counts regardless of the proportion of cropland agriculture within a 1 km radius. Pollinator diversity increased earlier in the growing season and with per cent flower cover. Unexpectedly, neither insecticide nor total pesticide concentrations on above-ground passive samplers were related to pollinator diversity. However, pollinator community composition was most strongly related to date of sampling, total pesticide concentration, and forb or flower cover. Our results indicate very little difference in pollinator diversity between grassland conservation practices with and without wildflower plantings. Given the relatively high economic costs of wildflower plantings, our research provides initial evidence that investment in general grassland conservation may efficiently conserve pollinator diversity in temperate regions of intensive cropland agriculture.

Human herpesvirus 6A and axonal injury before the clinical onset of multiple sclerosis.

Recent research indicates that multiple sclerosis is preceded by a prodromal phase with elevated levels of serum neurofilament light chain (sNfL), a marker of axonal injury. The effect of environmental risk factors on the extent of axonal injury during this prodrome is unknown. Human herpesvirus 6A (HHV-6A) is associated with an increased risk of developing multiple sclerosis. The objective of this study was to determine if HHV-6A serostatus is associated with the level of sNfL in the multiple sclerosis prodrome, which would support a causative role of HHV-6A. A nested case-control study was performed by crosslinking multiple sclerosis registries with Swedish biobanks. Individuals with biobank samples collected before the clinical onset of multiple sclerosis were included as cases. Controls without multiple sclerosis were randomly selected, matched for biobank, sex, sampling date and age. Serostatus of HHV-6A and Epstein-Barr virus was analysed with a bead-based multiplex assay. The concentration of sNfL was analysed with single molecule array technology. The association between HHV-6A serology and sNfL was assessed by stratified t-tests and linear regressions, adjusted for Epstein-Barr virus serostatus and sampling age. Within-pair ratios of HHV-6A seroreactivity and sNfL were calculated for each case and its matched control. To assess the temporal relationship between HHV-6A antibodies and sNfL, these ratios were plotted against the time to the clinical onset of multiple sclerosis and compared using locally estimated scatterplot smoothing regressions with 95% confidence intervals (CI). Samples from 519 matched case-control pairs were included. In cases, seropositivity of HHV-6A was significantly associated with the level of sNfL (+11%, 95% CI 0.2-24%, P = 0.045) and most pronounced in the younger half of the cases (+24%, 95% CI 6-45%, P = 0.007). No such associations were observed among the controls. Increasing seroreactivity against HHV-6A was detectable before the rise of sNfL (significant within-pair ratios from 13.6 years versus 6.6 years before the clinical onset of multiple sclerosis). In this study, we describe the association between HHV-6A antibodies and the degree of axonal injury in the multiple sclerosis prodrome. The findings indicate that elevated HHV-6A antibodies both precede and are associated with a higher degree of axonal injury, supporting the hypothesis that HHV-6A infection may contribute to multiple sclerosis development in a proportion of cases.

High trophic level organisms and the complexity of soil micro-food webs at aggregate scale regulate carbon accumulation in cropland soils

Enhancing soil organic carbon (SOC) levels via improved fertilization strategies can promote soil health and support sustainable crop production. While bacteria and fungi play a key role in SOC accumulation, the effects of soil micro-food webs that include organisms from higher trophic levels remain uncertain. We sought to narrow this knowledge gap by clarifying the associations between SOC accumulation and soil micro-food webs at the aggregate scale under long-term (18 years) fertilization treatments, which included a no-fertilizer control (Ctrl), synthetic fertilizers (NPK), and partial synthetic nitrogen replacement with pig slurry (OMNPK) or crop straw (RSDNPK). The concentration of SOC was significantly increased by fertilization following the order RSDNPK (13.1 g kg−1) > OMNPK (11.4 g kg−1) > NPK (9.1 g kg−1) > Ctrl (6.4 g kg−1). Nematodes and protists accounted for approximately 20% of all nodes in the multitrophic networks. Fertilization increased network complexity at the aggregate scale by 1–4 times across different sampling dates (P < 0.05). In all aggregate classes, the functionally important (FI) nematodes, protists, and bacterial taxa involved in soil carbon cycle had higher relative abundances under the fertilization treatments than under the Ctrl (P < 0.05). Structural equation modeling further indicated that besides soil microbes, network complexity, FI nematodes and protists were important to SOC accumulation. Compared with NPK, the key moments during which these soil biological attributes strongly regulated SOC under OMNPK and RSDNPK were delayed to late growth stages of maize. In conclusion, the increased network complexity and relative abundance of functionally important organisms from higher trophic levels of the soil micro-food webs at certain periods are vital contributors to effective SOC accumulation under fertilization regimes that include organic amendments.

Relating Antimicrobial Resistance and Virulence in Surface-Water E. coli.

The role of the environment in the emergence and spread of antimicrobial resistance (AMR) is being increasingly recognized, raising questions about the public health risks associated with environmental AMR. Yet, little is known about pathogenicity among resistant bacteria in environmental systems. Existing studies on the association between AMR and virulence are contradictory, as fitness costs and genetic co-occurrence can be opposing influences. Using Escherichia coli isolated from surface waters in eastern North Carolina, we compared virulence gene prevalence between isolates resistant and susceptible to antibiotics. We also compared the prevalence of isolates from sub-watersheds with or without commercial hog operations (CHOs). Isolates that had previously been evaluated for phenotypic AMR were paired by matching isolates resistant to any tested antibiotic with fully susceptible isolates from the same sample date and site, forming 87 pairs. These 174 isolates were evaluated by conventional PCR for seven virulence genes (bfp, fimH, cnf-1, STa (estA), EAST-1 (astA), eae, and hlyA). One gene, fimH, was found in 93.1% of isolates. Excluding fimH, at least one virulence gene was detected in 24.7% of isolates. Significant negative associations were found between resistance to at least one antibiotic and presence of at least one virulence gene, tetracycline resistance and presence of a virulence gene, resistance and STa presence, and tetracycline resistance and STa presence. No significant associations were found between CHO presence and virulence, though some sub-significant associations merit further study. This work builds our understanding of factors controlling AMR dissemination through the environment and potential health risks.

Early and long-distance uptake by Eucalyptus grandis of N, K and Ca tracers injected down to a depth of 7 m

Eucalyptus plantations are commonly fertilized at planting to sustain high biomass production over successive rotations in nutrient-poor soils. However, the dynamics of nutrient uptake by tree roots in the early stages of stand development, depending on the lateral distance from the trees and the depth in the soil, are poorly documented. We assessed the potential uptake of N, K and Ca, from 6 to 18 months after planting, by Eucalyptus grandis trees depending on: i) the lateral distance from the tracer injection point and ii) the depth in the soil. At 6 months after planting, we injected 15NO3–, Rb+, Sr2+ and Cs+ tracers at depths of 1, 3, 5, and 7 m, respectively. Recently expanded leaves were then sampled monthly on 16 target E. grandis trees located at lateral distances ranging from 0.75 to 11.1 m from the injection points, and on 4 more distant E. grandis control trees; 15N contents (atom %) and concentrations of Rb, Cs and Sr in the leaves were determined at each sampling date, and compared to those of control trees to detect the dates of tracer uptake for each individual. A LOESS model was applied to account for the temporal trend and inter-tree variability among the control trees. Tracer uptake by a target tree was detected if the measurements exceeded the upper limit of the prediction interval (α = 0.005) generated by the model. Only the 6 target trees located within 2.0 m from the injection point took up the 15NO3– tracer. However, Rb+, Sr2+ and Cs+ tracers were taken up to lateral distances of approx. 11 m from the injection point. Tracer uptake occurred as early as 9, 7, 8 and 9 months after planting for 15NO3–, Rb+, Sr2+ and Cs+, respectively. Four trees located within 2.8 m from the injection point took up the 3 cation tracers, injected between the depths of 3 m and 7 m. All but one of the target trees took up at least one cation tracer. The potential of Eucalyptus trees to take up nutrients early, at long distance and at depth, can be promoted by silvicultural practices enhancing rapid root development after planting, as subsoiling in commercial plantations and large planting holes in smallholder plantations. Our results also suggest that fertilization could be applied only once at planting in Eucalyptus stands established on deep tropical soils, with low risks of nutrient losses by deep drainage.

Dataset: Biodiversity of Ground Beetles (Coleoptera, Carabidae) of the Republic of Mordovia (Russia)

(1) Background: Carabidae is one of the most diverse families of Coleoptera. Many species of Carabidae are sensitive to anthropogenic impacts and are indicators of their environmental state. Some species of large beetles are on the verge of extinction. The aim of this research is to describe the Carabidae fauna of the Republic of Mordovia (central part of European Russia); (2) Methods: The research was carried out in April-September 1979, 1987, 2000, 2001, 2005, 2007–2022. Collections were performed using a variety of methods (light trapping, soil traps, window traps, etc.). For each observation, the coordinates of the sampling location, abundance, and dates were recorded; (3) Results: The dataset contains data on 251 species of Carabidae from 12 subfamilies and 4576 occurrences. A total of 66,378 specimens of Carabidae were studied. Another 29 species are additionally known from other publications. Also, twenty-two species were excluded from the fauna of the region, as they were determined earlier by mistake (4). Conclusions: The biodiversity of Carabidae in the Republic of Mordovia included 280 species from 12 subfamilies. Four species (Agonum scitulum, Lebia scapularis, Bembidion humerale, and Bembidion tenellum) were identified for the first time in the Republic of Mordovia.

Jurassic heritance of the geomorphology in Mid Norway

The age and formation of the Scandinavian mountains and the Norwegian strandflat have long been the subject of dispute. Some researchers argue that the present-day mountains are remains of the Caledonian orogen while others claim that the Caledonian nappes after erosion were buried by Mesozoic sediments and subsequently exhumed. In order to clarify these issues, we have studied remains of chemically weathered rocks (saprolites) from the coast to the interior of central Norway. The multidisciplinary study includes digital topography, electrical resistivity tomography (ERT), XRD, XRF, palynological analyses and K–Ar dating of samples from outcrops, trenches and core drilling. The coastal areas are dominated by an outer strandflat and an inner joint-valley landscape, while the interior is characterised by smoother landscapes referred to as palaeo-surfaces. Remnants of pre–Tertiary weathering occur in the joint valley landscape as well as on the palaeo-surfaces. The saprolites are found within fault- and fracture-zones and at depths exceeding 50 m in drillholes. It is suggested that the old saprolites were strongly eroded along the coast and in the fjords and valleys such as in Orkdalen and Sunndalen. K–Ar dating of mainland clay alteration most frequently yielded Jurassic ages along a profile extending from the coast to the Dovrefjell mountains (c. 1400 m a.s.l.). The formation age of the smectite- and kaolinite-containing saprolites seems to be almost contemporaneous along this profile implying that the entire area was subject to weathering in a warm and humid climate, such as prevailed during the Late Triassic and Jurassic. Palynological residues containing thermally altered Triassic and Jurassic pollen and spores in the clay-infected bedrock lend support to the saprolite interpretation. The Mesozoic landscape in central Norway was consequently shaped by uplift and deep weathering in the Jurassic. The entire Trøndelag county was most likely covered by Mesozoic sedimentary rocks until Cenozoic exhumation. The landscape was modified by Cenozoic tectonic uplift and erosion, and finally reworked by Pleistocene glacial erosion. We therefore conclude that both the observed saprolites and the shape of the present-day landscape in central Norway give a strong impression of the original Jurassic weathering surface.

Horizontal variability and diurnal fluctuation of soil respiration in corn and soybean rows

This study evaluated the horizontal variability and diurnal fluctuation of soil respiration to accurately capture changes in carbon flux during agricultural production in Lishu County, Jilin Province, China. Corn (Zea mays L.) and soybean (Glycine max L.) were planted with 60-cm row spacing in 2020. The soil respiration rate (SRR) was measured at 2-hour intervals on July 1, August 1, and September 25 using a portable, closed chamber at five positions, P0, P15, P30, P45, and P60, denoting specific distances from the crop rows. The SRR between crop rows was affected both by dates and fields with the coefficient of variation ranging between 7.1 and 37.7%. The SRR at P45 was closest to the mean SRR, with a relative deviation of 0.09–4.85% on July 01 and August 01 in corn and soybean fields. On September 25, the optimal position to measure SRR was between P45 and P60. The sampling dates influenced the optimal time for measuring SRR but were mostly concentrated between 9:00 and 11:00 (24-hour clock) for corn and between 11:00 and 13:00 for soybean. The root biomass of crop rows and diurnal soil temperature were the main factors affecting horizontal variability and diurnal fluctuation of SRR, respectively. We recommend an SRR sampling strategy at P45 between 9:00 and 11:00 for corn and between 11:00 and 13:00 for soybean to decrease the effects of horizontal variability and diurnal fluctuation of SRR.

The Transmission Effectiveness of the Dissolved Nutrients (N, P, Si) Through a South Mediterranean Estuary (Seybouse, Algeria) Under Large Anthropogenic Forcing

The Seybouse Estuary (SE) is the downstream of the second great river in Algeria draining one of the main country’s watersheds (6471 km2, 1.5 million inhabitants). This study highlights the effect of the estuarine part on the distribution and the flux of dissolved nitrogen (N), phosphorus (P) and silicon (Si) through the SE. Surface water sampling was taken and analysed in the dry (September 2016) and wet (April 2017) seasons. Physical parameters and water discharge data were jointly recorded in parallel to sampling dates. Very low flows varying between 0.3 and 4.7 m3 s-1 were recorded at the outlet in dry and wet seasons, respectively. The SE outlet waters were 2.6 and 10 folds higher than upstream in dissolved inorganic nitrogen (DIN) and phosphates (PO4) levels, respectively. However, the silicates (SiO4) levels decreased by about 1/2 in the outlet waters. In terms of flux, the SE delivered to the coast 84 t·yr-1, 9 t·yr-1 and 56 t·yr-1 of DIN, PO4 and SiO4, respectively. The high DIN:PO4 = 137 and low SiO4:DIN = 0.52 molar ratios classify SE as one of the strong anthropised estuaries. The estuarine part amply modifies cycles and budgets of riverine nutrients introduced to the coast.

Comparison of phenolic composition in date (Phoenix dactylifera L.) flesh and seeds extracted by an ultrasonic-assisted and conventional method

ABSTRACT Date palm (Phoenix dactylifera L.) is an important fruit of the Middle East and North Africa with a high content of phenolic compounds. This study applied ultrasonic-assisted and conventional methods to extract phenolic compounds from date flesh and seed. The efficacy of the extraction methods is compared in terms of quantity, content, and antioxidant capacity of phenolic compounds. The highest total phenolic content (TPC) was found in ultrasonic-assisted date seed samples extracted by ethanol (18.53 mg GAE/g). In contrast, the TPC content of conventionally extracted seed samples ranged from 1.30 to 14.46 mg GAE/g. The TPC and antioxidant capacity values of phenolic compounds extracted from date flesh samples were lower than those extracted from seed samples. Liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF-MS/MS) was used to characterize phenolic compounds. A total of 47 different phenolic compounds were identified, including 21 phenolic acids, 21 flavonoids, and 5 other polyphenols. High-performance liquid chromatography equipped with a photodiode array detector (HPLC-PDA) was used to quantify the phenolic compounds in different date samples. The highest content was found in ultrasonic-assisted date seed samples extracted in methanol solvent. The extract also contained epicatechin (36.12 μg/g), coumaric acid (27.05 μg/g), p-hydroxybenzoic acid (21.03 μg/g), syringic acid (19.85 μg/g), and epicatechin gallate (11.67 μg/g). The results showed that ultrasonic-assisted extraction could significantly increase the quantities of functional components of the extracts obtained from fresh date fruit samples.

Did Captain Beechey see a living Mandarina luhuana, an extinct land snail species?

ABSTRACT Knowledge about prehuman biotas and the impact of early human contact, particularly on land snails inhabiting oceanic islands, is still poor. One specific example of interest is Mandarina luhuana, which was first collected from the Chichijima Islands of the Ogasawara Archipelago in 1827 during Captain Frederick William Beechey's expedition. The initial description of M. luhuana included an image of a shell with dark brown pigmentation, which contrasts with current understanding, with all known specimens being considered to lack dark colouration. Traditionally, it is believed that M. luhuana represents a fossil species that became extinct on the island before human arrival. However, I propose that the specimen collected for the original description was either recently dead or still alive at the time of collection. Furthermore, I hypothesize that M. luhuana faced extinction after human arrival on Ogasawara, which began during the 17th century. To test this hypothesis, I used accelerator mass spectrometry dating to determine the extinction dates of subfossil samples of M. luhuana. The results of this study suggest that M. luhuana became extinct after the 17th century, with the species having possibly survived until the early 19th century. It is likely that the extinction of M. luhuana occurred shortly after human arrival in the islands. These findings underscore the need for further research to understand the impact of human arrival on island ecosystems and to uncover the original diversity of land snail faunas on islands.