A Spatially Distributed Investigation of Stream Water Temperature in a Contemporary Mixed-Land-Use Watershed

Stream water temperature (◦C) is an important physical variable that influences many biological and abiotic water quality processes. The intermingled mosaic of land-use/land-cover (LULC) types and corresponding variability in stream water temperature (Tw) processes in contemporary mixed-land-use watersheds necessitate research to advance management and policy decisions. Water temperature was analyzed from 21 gauging sites using a nested-scale experimental watershed study design. Results showed that forested land use was negatively correlated (α = 0.05) with mean and maximum Tw. Agricultural land use was significantly positively correlated (α = 0.05) with maximum Tw except during the spring season. Mixed development and Tw were significantly correlated (α = 0.05) at quarterly and monthly timescales. Correlation trends in some reaches were reversed between the winter and summer seasons, contradicting previous research. During the winter season, mixed development showed a negative relationship with minimum Tw and mean Tw. During the summer season, higher minimum, maximum, and mean Tw correlations were observed. Advanced understanding generated through this high-resolution investigation improves land managers’ ability to improve conservation strategies in freshwater aquatic ecosystems of contemporary watersheds

Symmetry of Energy Divergence Anomalies Associated with the El Niño-Southern Oscillation

The El Niño-Southern Oscillation (ENSO) is a dominant source of global climate variability. The effects of this phenomenon alter the flow of heat from tropical to polar latitudes, resulting in weather and climate anomalies that are difficult to forecast. The current work quantified two components of the vertically integrated equation for the total energy content of an atmospheric column, to show the anomalous horizontal redistribution of surface heat flux anomalies. Symmetric and asymmetric components of the vertically integrated latent and sensible heat flux divergence were quantified using ERA-Interim atmospheric reanalysis output on 30 model layers between 1979 and 2016. Results indicate that asymmetry is a fundamental component of ENSO-induced weather and climate anomalies at the global scale, challenging the common assumption that each phase of ENSO is equal and opposite. In particular, a substantial asymmetric component was identified in the relationship between ENSO and patterns of extratropical climate variability that may be proportional to differences in sea surface temperature anomalies during each phase of ENSO. This work advances our understanding of the global distributions of source and sink regions, which may improve future predictions of ENSO-induced precipitation and surface temperature anomalies. Future studies should apply these methods to advance understanding and to validate predictions of ENSO-induced weather and climate anomalies

Investigating the drivers of the spatio-temporal patterns of genetic differences between Plasmodium falciparum malaria infections in Kilifi County, Kenya

Knowledge of how malaria infections spread locally is important both for the design of targeted interventions aiming to interrupt malaria transmission and the design of trials to assess the interventions. A previous analysis of 1602 genotyped Plasmodium falciparum parasites in Kilifi, Kenya collected over 12 years found an interaction between time and geographic distance: the mean number of single nucleotide polymorphism (SNP) differences was lower for pairs of infections which were both a shorter time interval and shorter geographic distance apart. We determine whether the empiric pattern could be reproduced by a simple model, and what mean geographic distances between parent and offspring infections and hypotheses about genotype-specific immunity or a limit on the number of infections would be consistent with the data. We developed an individual-based stochastic simulation model of households, people and infections. We parameterized the model for the total number of infections, and population and household density observed in Kilifi. The acquisition of new infections, mutation, recombination, geographic location and clearance were included. We fit the model to the observed numbers of SNP differences between pairs of parasite genotypes. The patterns observed in the empiric data could be reproduced. Although we cannot rule out genotype-specific immunity or a limit on the number of infections per individual, they are not necessary to account for the observed patterns. The mean geographic distance between parent and offspring malaria infections for the base model was 0.5 km (95% CI 0.3-1.5), for a distribution with 68% of distances shorter than the mean. Very short mean distances did not fit well, but mixtures of distributions were also consistent with the data. For a pathogen which undergoes meiosis in a setting with moderate transmission and a low coverage of infections, analytic methods are limited but an individual-based model can be used with genotyping data to estimate parameter values and investigate hypotheses about underlying processes

Characterisation of Thinopyrum bessarabicum chromosomes through genome-wide introgressions into wheat

Thinopyrum bessarabicum (2n = 2x = 14, JJ) is an important source for new genetic variation for wheat improvement due to its salinity tolerance and disease resistance. Its practical utilisation in wheat improvement can be facilitated through development of genome-wide introgressions leading to a variety of different wheat–Th. bessarabicum translocation lines. In this study, we report the generation of 12 such wheat–Th. bessarabicum recombinant lines, through two different crossing strategies, which were characterized using sequential chromosome single colour and multi-colour genomic in situ hybridization (sc-GISH and mc-GISH), multi-colour fluorescent in situ hybridization (mc-FISH) and single nucleotide polymorphic (SNP) DNA markers. We also detected 13 lines containing different Th. bessarabicum chromosome aberrations through sc-GISH. Through a combination of molecular and cytological analysis of all the 25 lines containing Th. bessarabicum recombinants and chromosome aberrations we were able to physically map 1150 SNP markers onto seven Th. bessarabicum J chromosomes which were divided into 36 segmental blocks. Comparative analysis of the physical map of Th. bessarabicum and the wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed that Th. bessarabicum contains the 4/5 translocation also present in the A genome of wheat. These wheat–Th. bessarabicum recombinant lines and SNP markers provide a useful genetic resource for wheat improvement with the latter having a wider impact as a tool for detection of introgressions from other Thinopyrum species containing the J or a closely-related genome such as Thinopyrum intermedium (JrJrJvsJvsStSt) and Thinopyrum elongatum (EeEe), respectively

Evaluating Impacts of Anthropogenic Disturbance to Wetland Water Quality Functions

Wetland ecosystems play fundamental roles in regulating our freshwater resources, yet they are not comprehensively protected from degradation and loss. West Virginia, USA has wetlands across diverse landscapes and geography that feed into both the Chesapeake Bay and Gulf of Mexico. The state is also comprised of diverse anthropogenic land-use practices. We are assessing 200 wetlands over 2 years to evaluate how anthropogenic disturbance impact wetland water quality functions. Select water quality parameters (20), and relative diversity and abundance of vegetation and macroinvertebrates will be used as bioindicators. They will be compared with GIS assessments of watershed land cover/ land-use practices and climate data to evaluate relationships and determine how they impact a wetland’s ability to carry out select water quality functions. Preliminary results after one year of sampling indicate that wetlands at higher elevation with fewer watershed land-use practices generally had lower E. Coli, heavy metal (Lead and Zinc), and nutrient (Phosphorus and Nitrogen) concentrations relative to wetlands at lower elevations with greater watershed land-use practices. Seasonal conductivity readings increased following precipitation events. Conductivity and salinity readings also decreased along its drainage gradient, indicative of the wetland performing its water quality functions. We also observed that conductivity and nutrient concentrations were highest during the winter and lowest during the summer, coinciding with the bottom and peak periods of primary productivity. The results of this project will be used to develop wetland water quality standards for West Virginia and help advance more comprehensive wetland regulations

Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

Background: Human genetic factors are important determinants of malaria risk. We investigated associations between multiple candidate polymorphisms—many related to the structure or function of red blood cells—and risk for severe Plasmodium falciparum malaria and its specific phenotypes, including cerebral malaria, severe malaria anaemia, and respiratory distress. Methods: We did a case-control study in Kilifi County, Kenya. We recruited as cases children presenting with severe malaria to the high-dependency ward of Kilifi County Hospital. We included as controls infants born in the local community between Aug 1, 2006, and Sept 30, 2010, who were part of a genetics study. We tested for associations between a range of candidate malaria-protective genes and risk for severe malaria and its specific phenotypes. We used a permutation approach to account for multiple comparisons between polymorphisms and severe malaria. We judged p values less than 0·005 significant for the primary analysis of the association between candidate genes and severe malaria. Findings: Between June 11, 1995, and June 12, 2008, 2244 children with severe malaria were recruited to the study, and 3949 infants were included as controls. Overall, 263 (12%) of 2244 children with severe malaria died in hospital, including 196 (16%) of 1233 with cerebral malaria. We investigated 121 polymorphisms in 70 candidate severe malaria-associated genes. We found significant associations between risk for severe malaria overall and polymorphisms in 15 genes or locations, of which most were related to red blood cells: ABO, ATP2B4, ARL14, CD40LG, FREM3, INPP4B, G6PD, HBA (both HBA1 and HBA2), HBB, IL10, LPHN2 (also known as ADGRL2), LOC727982, RPS6KL1, CAND1, and GNAS. Combined, these genetic associations accounted for 5·2% of the variance in risk for developing severe malaria among individuals in the general population. We confirmed established associations between severe malaria and sickle-cell trait (odds ratio [OR] 0·15, 95% CI 0·11–0·20; p=2·61 × 10−58), blood group O (0·74, 0·66–0·82; p=6·26 × 10−8), and –α3·7-thalassaemia (0·83, 0·76–0·90; p=2·06 × 10−6). We also found strong associations between overall risk of severe malaria and polymorphisms in both ATP2B4 (OR 0·76, 95% CI 0·63–0·92; p=0·001) and FREM3 (0·64, 0·53–0·79; p=3·18 × 10−14). The association with FREM3 could be accounted for by linkage disequilibrium with a complex structural mutation within the glycophorin gene region (comprising GYPA, GYPB, and GYPE) that encodes for the rare Dantu blood group antigen. Heterozygosity for Dantu was associated with risk for severe malaria (OR 0·57, 95% CI 0·49–0·68; p=3·22 × 10−11), as was homozygosity (0·26, 0·11–0·62; p=0·002). Interpretation: Both ATP2B4 and the Dantu blood group antigen are associated with the structure and function of red blood cells. ATP2B4 codes for plasma membrane calcium-transporting ATPase 4 (the major calcium pump on red blood cells) and the glycophorins are ligands for parasites to invade red blood cells. Future work should aim at uncovering the mechanisms by which these polymorphisms can result in severe malaria protection and investigate the implications of these associations for wider health. Funding: Wellcome Trust, UK Medical Research Council, European Union, and Foundation for the National Institutes of Health as part of the Bill & Melinda Gates Grand Challenges in Global Health Initiative

Resistance to wheat rusts identified in wheat/Amblyopyrum muticum chromosome introgressions

© 2020 The Authors. Crop Science © 2020 Crop Science Society of America Wheat (Triticum aestivum L.) rusts are a worldwide production problem. Plant breeders have used genetic resistance to combat these fungi. However, single-gene resistance is rapidly overcome as a result of frequent occurrence of new virulent fungal strains. Thus, a supply of new resistance sources is continually needed, and new resistance sources are limited within hexaploid wheat genetic stocks. Wild relatives are able to be a resource for new resistance genes but are hindered because of chromosome incapability with domesticated wheats. Twenty-eight double-haploid hexaploid wheat/Amblyopyrum muticum (Boiss.) Eig introgression lines, with introgressions covering the majority of the T genome, were evaluated for resistance to Puccinia triticina Erikss., P. graminis Pers.:Pers. f.sp. tritici Erikss. & E. Henning, and P. striiformis Westend. f.sp. tritici Erikss. At the seedling level, four lines were resistant to races of P. triticina, six lines were resistant to P. graminis, and 15 lines were resistant to P. striiformis. At the adult stage, 16 lines were resistant to P. triticina. Line 355 had resistance to all three rusts and line 161 had resistance to all tested races of P. triticina. Some of these lines will require further work to reduce the size of the introgressed segment; however, lines 92 and 355 have very small fragments and can be used directly as new resistance donors

Evaluating the performance of malaria genetics for inferring changes in transmission intensity using transmission modelling

Substantial progress has been made globally to control malaria, however there is a growing need for innovative new tools to ensure continued progress. One approach is to harness genetic sequencing and accompanying methodological approaches as have been used in the control of other infectious diseases. However, to utilise these methodologies for malaria we first need to extend the methods to capture the complex interactions between parasites, human and vector hosts, and environment, which all impact the level of genetic diversity and relatedness of malaria parasites. We develop an individual-based transmission model to simulate malaria parasite genetics parameterised using estimated relationships between complexity of infection and age from 5 regions in Uganda and Kenya. We predict that cotransmission and superinfection contribute equally to within-host parasite genetic diversity at 11.5% PCR prevalence, above which superinfections dominate. Finally, we characterise the predictive power of six metrics of parasite genetics for detecting changes in transmission intensity, before grouping them in an ensemble statistical model. The model predicted malaria prevalence with a mean absolute error of 0.055. Different assumptions about the availability of sample metadata were considered, with the most accurate predictions of malaria prevalence made when the clinical status and age of sampled individuals is known. Parasite genetics may provide a novel surveillance tool for estimating the prevalence of malaria in areas in which prevalence surveys are not feasible. However, the findings presented here reinforce the need for patient metadata to be recorded and made available within all future attempts to use parasite genetics for surveillance

Development of a New A –Genome-Specific Single Nucleotide Polymorphism Marker Set for the Molecular Characterization of Wheat– Introgression Lines

© 2019 The Author(s). Cultivated einkorn wheat (Triticum monococcum L. subsp. monococcum, 2n = 2x = 14, AmAm) and its wild relative T. monococcum subsp. aegilopoides are important sources of economically useful genes that can be exploited for wheat (Triticum aestivum L.) breeding. Einkorn has excellent resistance to fungal diseases and gene transfer is relatively simple via standard breeding methods. To fulfill the growing demand by modern prebreeding programs for a cost-effective high-throughpuprocedure for accurately detecting introgressed chromosomes or chromosome segments from T. monococcum into wheat, we used the Axiom Wheat-Relative Genotyping Array and developed a set of Am genome-specific exome-based single nucleotide polymorphism (SNP) markers suitable for rapid identification of T. monococcum chromatin in a wheat background. We identified 1247 polymorphic SNPs between T. monococcum and wheat. We identified 191 markers across all seven chromosomes of T. monococcum that are also present on an existing Triticum urartu Thum. ex Gandil. genetic map and potentially ordered them on the basis of the high macrocollinearity and conservation of marker order between T. monococcum and T. urartu. The marker set has been tested on leaf-rust-resistant BC3 F4 progenies of wheat–T. monococcum hybrids. Two markers (AX-94492165, AX-95073542) placed on the distal end of the chromosome arm 7AL detected a T. monococcum introgression into wheat. The SNP marker set thus proved highly effective in the identification of T. monococcum chromatin in a wheat background, offering a reliable method for screening and selecting wheat–T. monococcum introgression lines, a procedure that could significantly speed up prebreeding programs

Development and characterisation of interspecific hybrid lines with genome-wide introgressions from <i>Triticum timopheevii</i> in a hexaploid wheat background

© 2019 The Author(s). Background: Triticum timopheevii (2n = 4x = 28; AtAtGG), is an important source for new genetic variation for wheat improvement with genes for potential disease resistance and salt tolerance. By generating a range of interspecific hybrid lines, T. Timopheevii can contribute to wheat's narrow gene-pool and be practically utilised in wheat breeding programmes. Previous studies that have generated such introgression lines between wheat and its wild relatives have been unable to use high-throughput methods to detect the presence of wild relative segments in such lines. Results: A whole genome introgression approach, exploiting homoeologous recombination in the absence of the Ph1 locus, has resulted in the transfer of different chromosome segments from both the At and G genomes of T. Timopheevii into wheat. These introgressions have been detected and characterised using single nucleotide polymorphism (SNP) markers present on a high-throughput Axiom® Genotyping Array. The analysis of these interspecific hybrid lines has resulted in the detection of 276 putative unique introgressions from T. Timopheevii, thereby allowing the generation of a genetic map of T. Timopheevii containing 1582 SNP markers, spread across 14 linkage groups representing each of the seven chromosomes of the At and G genomes of T. Timopheevii. The genotyping of the hybrid lines was validated through fluorescence in situ hybridisation (FISH). Comparative analysis of the genetic map of T. Timopheevii and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of inter- and intra-genomic translocations within the At and G genomes of T. Timopheevii that have been previously only detected through cytological techniques. Conclusions: In this work, we report a set of SNP markers present on a high-throughput genotyping array, able to detect the presence of T. Timopheevii in a hexaploid wheat background making it a potentially valuable tool for marker assisted selection (MAS) in wheat pre-breeding programs. These valuable resources of high-density molecular markers and wheat-T. Timopheevii hybrid lines will greatly enhance the work being undertaken for wheat improvement through wild relative introgressions