Genome-Wide Association Study to Identify Possible Candidate Genes of Snap Bean Leaf and Pod Color

Color can be an indicator of plant health, quality, and productivity, and is useful to researchers to understand plant nutritional content in their studies. Color may be related to chlorophyll content and photosynthetic activity and provides information for those studying diseases and mineral nutrition because every nutrient deficiency and many diseases produce symptoms that affect color. In order to identify significant loci related to both leaf and pod color in a snap bean (Phaseolus vulgaris L.) diversity panel, a genome-wide association study (GWAS) was carried out. Leaf color in one and pod traits in multiple environments were characterized using a colorimeter. L*a*b* color data were recorded and used to calculate chroma (C*) and hue angle (H°). Leaves were evaluated at three positions (lower, middle, and upper) in the canopy and both pod exterior and interior colors were obtained. GWAS was conducted using two reference genomes that represent the Andean (G19833) and Middle American (5-593) domestication centers. Narrow sense heritabilities were calculated using the mixed linear model (MLM) method in genome association and prediction integrated tool (GAPIT), and significant single nucleotide polymorphisms (SNPs) for each color parameter were obtained using the Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) GWAS model with two principal components (PCAs). In comparison to pod color traits, narrow sense heritabilities of leaf traits were low and similar for both reference genomes. Generally, narrow sense heritability for all traits was highest in the lower, followed by middle, and then upper leaf positions. Heritability for both pod interior and exterior color traits was higher using the G19833 reference genome compared to 5-593 when evaluated by year and means across years. Forty-five significant SNPs associated with leaf traits and 872 associated with pods, totaling 917 significant SNPs were identified. Only one SNP was found in common for both leaf and pod traits on Pv03 in the 5-593 reference genome. One-hundred thirteen significant SNPs, 30 in leaves and 83 in pods had phenotypic variation explained (PVE) of 10% or greater. Fourteen SNPs (four from G19833 and ten from 5-593) with ≥10 PVE%, large SNP effect, and largest p-value for L* and H° pod exterior was identified on Pv01, Pv02, Pv03, and Pv08. More SNPs were associated with pod traits than with leaf traits. The pod interior did not exhibit colors produced by anthocyanins or flavonols which allowed the differentiation of potential candidate genes associated with chloroplast and photosynthetic activity compared to the pod exterior where candidate genes related to both flavonoids and photosynthesis affected color. Several SNPs were associated with known qualitative genes including the wax pod locus (y), persistent color (pc), purple pods (V), and two genes expressed in seeds but not previously reported to affect other plant tissues (B and J). An evaluation of significant SNPs within annotated genes found a number, within a 200 kb window, involved in both flavonoid and photosynthetic biosynthetic pathways.

Genetic variation in a tepary bean (Phaseolus acutifolius A. Gray) diversity panel reveals loci associated with biotic stress resistance

Tepary bean (Phaseolus acutifolius A. Gray), indigenous to the arid climates of northern Mexico and the Southwest United States, diverged from common bean (Phaseolus vulgaris L.), approximately 2 million years ago and exhibits a wide range of resistance to biotic stressors. The tepary genome is highly syntenic to the common bean genome providing a foundation for discovery and breeding of agronomic traits between these two crop species. Although a limited number of adaptive traits from tepary bean have been introgressed into common bean, hybridization barriers between these two species required the development of bridging lines to alleviate this barrier. Thus, to fully utilize the extant tepary bean germplasm as both a crop and as a donor of adaptive traits, we developed a diversity panel of 422 cultivated, weedy, and wild tepary bean accessions which were then genotyped and phenotyped to enable population genetic analyses and genome-wide association studies for their response to a range of biotic stressors. Population structure analyses of the panel revealed eight subpopulations and the differentiation of botanical varieties within P. acutifolius. Genome-wide association studies revealed loci and candidate genes underlying biotic stress resistance including quantitative trait loci for resistance to weevils, common bacterial blight, Fusarium wilt, and bean common mosaic necrosis virus that can be harnessed not only for tepary bean but also common bean improvement.

A robust SNP-haplotype assay for Bct gene region conferring resistance to beet curly top virus in common bean (Phaseolus vulgaris L.)

Beet curly top virus (BCTV), which is synonymous with curly top virus (CTV), causes significant yield loss in common bean (snap and dry beans) cultivars and several other important crops. Common bean cultivars have been found to be resistant to CTV, but screening for resistance is challenging due to the cyclical nature of epidemics and spotty feeding by the leafhopper that vectors the virus. We used an SNP dataset for the Snap Bean Association Panel (SnAP) agro-inoculated with CTV-Logan (CA/Logan) strain to locate the Bct gene region to a 1.7-Mb interval on chromosome Pv07 using genome-wide association study (GWAS) analysis. Recombinant lines from the SnAP were used to further narrow the Bct region to a 58.0-kb interval. A missense SNP (S07_2970381) in candidate gene Phvul.007G036300 Exonuclease V (EXO5) was identified as the most likely causal mutation, and it was the most significant SNP detected by GWAS in a dry bean population (DBP) naturally infected by the CTV-Worland (Wor) strain. Tm-shift assay markers developed for SNP S07_2970381 and two linked SNPs, S07_2970276 and S07_2966197, were useful for tracking different origins of the Bct EXO5 candidate gene resistance to CTV in common bean. The three SNPs identified four haplotypes, with haplotype 3-1 (Haplo3-1) of Middle American origin associated with the highest levels of CTV resistance. This SNP-haplotype assay will enable breeders to track resistance sources and to develop cultivars with better CTV resistance.

Mapping of the bs5 and bs6 non-race-specific recessive resistances against bacterial spot of pepper

Bacterial spot caused by Xanthomonas euvesicatoria is a major disease of pepper (Capsicum annuum L.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes, bs5 and bs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregating populations for bs5 and bs6 were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5 introgression) or ECW60R (bs6 introgression). Following fine-mapping, bs5 was delimited to a ~535 Kbp interval on chromosome 3, and bs6 to a ~666 Kbp interval in chromosome 6. We identified 14 and 8 candidate resistance genes for bs5 and bs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. This research enhances marker-assisted selection of bs5 and bs6 in breeding programs and is a crucial step towards elucidating the molecular mechanisms underlying the resistances.

Human and dog Bayesian dietary mixing models using bone collagen stable isotope ratios from ancestral Iroquoian sites in southern Ontario

Under the archaeological canine surrogacy approach (CSA) it is assumed that because dogs were reliant on humans for food, they had similar diets to the people with whom they lived. As a result, the stable isotope ratios of their tissues (bone collagen and apatite, tooth enamel and dentine collagen) will be close to those of the humans with whom they cohabited. Therefore, in the absence of human tissue, dog tissue isotopes can be used to help reconstruct past human diets. Here δ¹³C and δ¹⁵N ratios on previously published dog and human bone collagen from fourteenth-seventeenth century AD ancestral Iroquoian village archaeological sites and ossuaries in southern Ontario are used with MixSIAR, a Bayesian dietary mixing model, to determine if the dog stable isotope ratios are good proxies for human isotope ratios in dietary modeling for this context. The modeling results indicate that human dietary protein came primarily from maize and high trophic level fish and dogs from maize, terrestrial animals, low trophic level fish, and human feces. While isotopes from dog tissues can be used as general analogs for human tissue isotopes under CSA, greater insights into dog diets can be achieved with Bayesian dietary mixing models.

The Monongahela tradition in "real time": Bayesian analysis of radiocarbon dates

Despite advances in techniques, methods, and theory, northeastern North American archaeologists continue to use early to mid-twentieth century culture historical taxa as units of analysis and narrative. There is a distinct need to move away from this archaeological practice to enable fuller understandings of past human lives. One tool that enables such a move is Bayesian analysis of radiocarbon dates, which provides a means of constructing continuous chronologies. A large dataset of radiocarbon dates for late prehistoric (ca AD 900/1000–1650) sites in the lower upper Ohio River basin in southwestern Pennsylvania and adjacent portions of Maryland, Ohio, and West Virginia is used here as an example. The results allow a preliminary assessment of how the settlement plans of contemporaneous villages varied considerably, reflecting decisions of the village occupants how to structure built environments to meet their needs.

Phaseolus vulgaris Seeds from the Late Sixteenth–Early Seventeenth Century AD Ancestral Oneida Diable Site, New York

The ethnohistorical, ethnographic, and contemporary literatures all suggest that common bean (Phaseolus vulgaris) was an important component of Northern Iroquoian agronomic systems and diets. Seemingly at odds with this is the sparse occurrence of whole and partial common bean seeds on fourteenth through seventeenth century AD village sites. The recovery of a large quantity of whole and partial bean seeds from the ancestral Oneida Diable site, dated here to between AD 1583 and 1626 with a Bayesian model using seven new AMS radiocarbon dates, provides clues as to when large quantities of rehydrated/cooked common bean seeds may occur in the archaeological record.

Resolving Indigenous village occupations and social history across the long century of European permanent settlement in Northeastern North America: The Mohawk River Valley ~1450-1635 CE

The timeframe of Indigenous settlements in Northeast North America in the 15th-17th centuries CE has until very recently been largely described in terms of European material culture and history. An independent chronology was usually absent. Radiocarbon dating has recently begun to change this conventional model radically. The challenge, if an alternative, independent timeframe and history is to be created, is to articulate a high-resolution chronology appropriate and comparable with the lived histories of the Indigenous village settlements of the period. Improving substantially on previous initial work, we report here high-resolution defined chronologies for the three most extensively excavated and iconic ancestral Kanien'kehá꞉ka (Mohawk) village sites in New York (Smith-Pagerie, Klock and Garoga), and a fourth early historic Indigenous site, Brigg's Run, and re-assess the wider chronology of the Mohawk River Valley in the mid-15th to earlier 17th centuries. This new chronology confirms initial suggestions from radiocarbon that a wholesale reappraisal of past assumptions is necessary, since our dates conflict completely with past dates and the previously presumed temporal order of these three iconic sites. In turn, a wider reassessment of northeastern North American early history and re-interpretation of Atlantic connectivities in the later 15th through early 17th centuries is required. Our new closely defined date ranges are achieved employing detailed archival analysis of excavation records to establish the contextual history for radiocarbon-dated samples from each site, tree-ring defined short time series from wood charcoal samples fitted against the radiocarbon calibration curve ('wiggle-matching'), and Bayesian chronological modelling for each of the individual sites integrating all available prior knowledge and radiocarbon dating probabilities. We define (our preferred model) most likely (68.3% highest posterior density) village occupation ranges for Smith-Pagerie of ~1478-1498, Klock of ~1499-1521, Garoga of ~1550-1582, and Brigg's Run of ~1619-1632.

The tepary bean genome provides insight into evolution and domestication under heat stress

Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.

Using Maize δ15N values to assess soil fertility in fifteenth- and sixteenth-century ad Iroquoian agricultural fields

Native Americans developed agronomic practices throughout the Western Hemisphere adapted to regional climate, edaphic conditions, and the extent of dependence on agriculture for subsistence. These included the mounding or "corn hill" system in northeastern North America. Iroquoian language speakers of present-day New York, USA, and Ontario and Québec, Canada were among those who used this system. While well-known, there has been little archaeological documentation of the system. As a result, there is scant archaeological evidence on how Iroquoian farmers maintained soil fertility in their often-extensive agricultural fields. Using δ15N values obtained on fifteenth- and sixteenth-century AD maize kernels from archaeological sites in New York and Ontario, adjusted to take into account changes that result from charring as determined through experiments, we demonstrate that Iroquoian farmers were successful at maintaining nitrogen in their agricultural fields. These results add to our archaeological knowledge of Iroquoian agronomic practices. Our results also indicate the potential value of obtaining δ15N values on archaeological maize in the investigation of Native American agronomic practices.

Radiocarbon, Bayesian chronological modeling and early European metal circulation in the sixteenth-century AD Mohawk River Valley, USA

European metal artifacts in assemblages from sites predating the physical presence of Europeans in Northern Iroquoia in present-day New York, USA and southern Ontario, Canada have been used as chronological markers for the mid-sixteenth century AD. In the Mohawk River Valley of New York, European metal artifacts at sites pre-dating the physical presence of Europeans have been used by archaeologists as a terminus post quem (TPQ) of 1525 to 1550 in regional chronologies. This has been done under the assumption that these metals did not begin to circulate until after sustained European presence on the northern Atlantic coast beginning in 1517. Here we use Bayesian chronological modeling of a large set of radiocarbon dates to refine our understanding of early European metal circulation in the Mohawk River Valley. Our results indicate that European iron and cuprous metals arrived earlier than previously thought, by the beginning of the sixteenth century, and cannot be used as TPQs. Together with recent Bayesian chronological analyses of radiocarbon dates from several sites in southern Ontario, these results add to our evolving understanding of intra-regional variation in Northern Iroquoia of sixteenth-century AD circulation and adoption of European goods.

Novel, rapid, low-cost screen-printed (bio)sensors for the direct analysis of boar taint compounds androstenone and skatole in porcine adipose tissue: Comparison with a high-resolution gas chromatographic method

This is the first report on the fabrication, characterisation and application of an electrochemical (bio)sensor system for the simultaneous measurement of skatole and androstenone. A biosensor for androstenone was fabricated using a Meldola's Blue modified SPCE (MB-SPCE) by depositing NADH and the enzyme 3α-hydroxysteroid dehydrogenase onto the MB-SPCE surface; samples of adipose tissue were analysed using the biosensors in conjunction with chronoamperometry. Cyclic voltammetry was used to investigate the electrochemical behaviour of skatole at a screen-printed carbon electrode (SPCE vs. Ag/AgCl). An oxidation peak was observed around +0.55 V (vs. Ag/AgCl) and differential pulse voltammetry was applied for quantification of skatole in adipose tissue (in-situ). Quantitative analysis was achieved using calibration plots obtained from fortified meat samples. The concentrations obtained by the electrochemical and gas chromatographic (GC) methods demonstrated a good positive correlation. The (bio)sensor system completed both measurements within 60 s, as compared to several hours for GC, and at a considerably reduced cost and complexity. Consequently, the novel (bio)sensor system should have applications for analysis of carcasses on the abattoir processing line.

An Electrocatalytic Screen-Printed Amperometric Sensor for the Selective Measurement of Thiamine (Vitamin B1) in Food Supplements

An electrocatalytic screen-printed sensor has been investigated for the measurement of the biologically important biomolecule vitamin B1 (thiamine) for the first time in food supplements. Under basic conditions, the vitamin was converted to its electrochemically active thiolate anion species. It was shown that an electrocatalytic oxidation reaction occurred with the screen-printed carbon electrode containing the mediator cobalt phthalocyanine (CoPC-SPCE). This had the advantage of producing an analytical response current at an operating potential of 0 V vs. Ag/AgCl compared to +0.34 V obtained with plain SPCEs. This resulted in improved selectivity and limit of detection. Detailed studies on the underlying mechanism occurring with the sensor are reported in this paper. A linear response was obtained between 0.1 and 20 µg mL⁻¹, which was suitable for the quantification of the vitamin in two commercial products containing vitamin B1. The mean recovery for a multivitamin tablet with a declared content of 5 mg was 101% (coefficient of variation (CV) of 9.6%). A multivitamin drink, which had a much lower concentration of vitamin B1 (0.22 mg/100 mL), gave a mean recovery of 93.3% (CV 7.2%). These results indicate that our sensor holds promise for quality control of food supplements and other food types.

Freshwater reservoir offsets on radiocarbon-dated dog bone from the headwaters of the St. Lawrence River, USA

Isotopic analysis of dog (Canis lupus familiaris) bone recovered from archaeological sites as proxies for human bone is becoming common in North America. Chronological placement of the dogs is often determined through radiocarbon dating of dog bone. The Great Lakes, their tributaries, and nearby lakes and streams were important fisheries for Native Americans prior to and after sustained European presence in the region. Carbon entering the food web in freshwater systems is often not in full isotopic equilibrium with the atmosphere, giving rise to spuriously old radiocarbon ages in fish, other aquatic organisms, and their consumers. These freshwater reservoir offsets (FROs) have been noted on human and dog bone in several areas of the world. Here we report the results of multi-tracer Bayesian dietary modeling using δ¹⁵N and δ¹³C values on dog bone collagen from mid-fifteenth to mid-sixteenth-century Iroquoian village sites at the headwaters of the St. Lawrence River, New York, USA. Results indicate that fish was an important component of dog diets. A comparison of radiocarbon dates on dog bone with dates on deer bone or maize from the same sites indicate FROs ranging from 97 ± 24 to 220 ± 39 ¹⁴Cyr with a weighted mean of 132 ± 8 ¹⁴Cyr. These results suggest that dog bone should not be used for radiocarbon dating in the absence of modeling to determine fish consumption and that previously reported radiocarbon dates on human bone from the larger region are likely to have FROs given the known importance of fish in regional human diets.

A Reagentless, Screen-Printed Amperometric Biosensor for the Determination of Glutamate in Food and Clinical Applications

A reagentless biosensor has been successfully developed to measure glutamate in food and clinical samples. The enzyme, glutamate dehydrogenase (GLDH) and the cofactor, nicotinamide adenine dinucleotide (NAD⁺) are fully integrated onto the surface of a Meldola's Blue screen-printed carbon electrode (MB-SPCE). The biological components are immobilized by utilizing unpurified multi-walled carbon nanotubes (MWCNT's) mixed with the biopolymer chitosan (CHIT), which are drop-coated onto the surface of the MB-SPCE in a layer-by-layer fashion. Meldola's Blue mediator is also incorporated into the biosensor cocktail in order to increase and facilitate electron shuttling between the reaction layers and the surface of the electrode. The loadings of each component are optimized by using amperometry in stirred solution at a low fixed potential of +0.1 V. The optimum temperature and pH are also determined using this technique. Quantification of glutamate in real samples is performed using the method of standard addition. The method of standard addition involves the addition of a sample containing an unknown concentration of glutamate, followed by additions of known concentrations of glutamate to a buffered solution in the cell. The currents generated by each addition are then plotted and the resulting line is extrapolated in order to determine the concentration of glutamate in the sample (Pemberton et al., Biosens Bioelectron 24:1246-1252, 2009). This layer-by-layer approach holds promise as a generic platform for the fabrication of reagentless biosensors.

Alpha-synuclein ferrireductase activity is detectible in vivo, is altered in Parkinson's disease and increases the neurotoxicity of DOPAL

The normal cellular role of α-synuclein is of potential importance in understanding diseases in which an aggregated form of the protein has been implicated. A potential loss or change in the normal function of α-synuclein could play a role in the aetiology of diseases such as Parkinson's disease. Recently, it has been suggested that α-synuclein could cause the enzymatic reduction of iron and a cellular increase in Fe(II) levels. Experiments were carried out to determine if such activity could be measured in vivo. Experiments with rats overexpressing human α-synuclein in nigral dopaminergic neurons demonstrated a correlation between α-synuclein expression and ferrireductase activity. Furthermore, studies on tissue from Parkinson's disease patient brains showed a significant decrease in ferrireductase activity, possibly due to deposition of large amounts of inactive protein. Cellular studies suggest that increase ferrireductase activity results in increased levels of dopamine metabolites and increased sensitivity to the toxicity of DOPAL. These findings demonstrate that α-synuclein ferrireductase activity is present in vivo and its alteration may play a role in neuron loss in disease.

Effects of population dispersal on regional signaling networks: An example from northern Iroquoia

The dispersal of Iroquoian groups from St. Lawrence River valley during the 15th and 16th centuries A.D. has been a source of archaeological inquiry for decades. Social network analysis presented here indicates that sites from Jefferson County, New York at the head of the St. Lawrence River controlled interactions within regional social signaling networks during the 15th century A.D. Measures indicate that Jefferson County sites were in brokerage liaison positions between sites in New York and Ontario. In the network for the subsequent century, to which no Jefferson County sites are assigned, no single group took the place of Jefferson County in controlling network flow. The dispersal of Jefferson County populations effectively ended this brokerage function concomitant with the emergence of the nascent Huron-Wendat and Iroquois confederacies and may have contributed to the escalation of conflict between these entities. These results add to a growing literature on the use of network analyses with archaeological data and contribute new insights into processes of population relocation and geopolitical realignment, as well as the role of borderlands and frontiers in nonstate societies.

Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen

Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).

Recent Advances in the Fabrication and Application of Screen-Printed Electrochemical (Bio)Sensors Based on Carbon Materials for Biomedical, Agri-Food and Environmental Analyses

This review describes recent advances in the fabrication of electrochemical (bio)sensors based on screen-printing technology involving carbon materials and their application in biomedical, agri-food and environmental analyses. It will focus on the various strategies employed in the fabrication of screen-printed (bio)sensors, together with their performance characteristics; the application of these devices for the measurement of selected naturally occurring biomolecules, environmental pollutants and toxins will be discussed.

Nation Building and Social Signaling in Southern Ontario: A.D. 1350-1650

Pottery is a mainstay of archaeological analysis worldwide. Often, high proportions of the pottery recovered from a given site are decorated in some manner. In northern Iroquoia, late pre-contact pottery and early contact decoration commonly occur on collars—thick bands of clay that encircle a pot and extend several centimeters down from the lip. These decorations constitute signals that conveyed information about a pot’s user(s). In southern Ontario the period A.D. 1350 to 1650 witnessed substantial changes in socio-political and settlement systems that included population movement, coalescence of formerly separate communities into large villages and towns, waxing and waning of regional strife, the formation of nations, and finally the development of three confederacies that each occupied distinct, constricted areas. Social network analysis demonstrates that signaling practices changed to reflect these regional patterns. Networks become more consolidated through time ultimately resulting in a “small world” network with small degrees of separation between sites reflecting the integration of communities within and between the three confederacies.

Genotyping-by-Sequencing Enabled Mapping and Marker Development for the By-2 Potyvirus Resistance Allele in Common Bean

Since its emergence in 2001, an aphid-transmitted virus disease complex has caused substantial economic losses to snap bean (Phaseolus vulgaris L.) production and processing in the Great Lakes Region of the United States. The general ineffectiveness of chemical control measures for nonpersistently transmitted viruses established an urgent need for the development and deployment of cultivars with resistance to the component viruses. Our objectives were to further characterize the inheritance of resistance to Bean yellow mosaic virus (BYMV), which is conditioned by the By-2 allele, to adapt genotyping-by-sequencing (GBS) to common bean to discover and genotype genome-wide single nucleotide polymorphisms (SNPs) in a set of recombinant inbred lines (RILs) derived from an introgression program, and to enable and validate marker-assisted selection for By-2. We optimized ApeKI for GBS in common bean and retained 7530 high-quality SNPs that segregated in our introgression RILs. A case-control genome-wide association study (GWAS) was used to discover 44 GBS SNPs that were strongly associated with the resistance phenotype and which delimited a 974 kb physical interval on the distal portion of chromosome 2. Seven of these SNPs were converted to single-marker Kompetitive Allele-Specific Polymerase chain reaction (KASP) assays and were demonstrated to be tightly linked to BYMV resistance in an F₂ population of 185 individuals. This research enables marker-assisted selection of By-2, provides enhanced resolution for fine mapping, and demonstrates the potential of GBS as a highly efficient, high-throughput genotyping platform for common bean breeding and genetics.

Fabrication and evaluation of a micro(bio)sensor array chip for multiple parallel measurements of important cell biomarkers

This report describes the design and development of an integrated electrochemical cell culture monitoring system, based on enzyme-biosensors and chemical sensors, for monitoring indicators of mammalian cell metabolic status. MEMS technology was used to fabricate a microwell-format silicon platform including a thermometer, onto which chemical sensors (pH, O₂) and screen-printed biosensors (glucose, lactate), were grafted/deposited. Microwells were formed over the fabricated sensors to give 5-well sensor strips which were interfaced with a multipotentiostat via a bespoke connector box interface. The operation of each sensor/biosensor type was examined individually, and examples of operating devices in five microwells in parallel, in either potentiometric (pH sensing) or amperometric (glucose biosensing) mode are shown. The performance characteristics of the sensors/biosensors indicate that the system could readily be applied to cell culture/toxicity studies.

Novel reductive-reductive mode electrochemical detection of Rohypnol following liquid chromatography and its determination in coffee

Rohypnol (flunitrazepam) has been successfully determined in coffee by high performance liquid chromatography dual electrode detection (LC-DED) in the dual reductive mode. Initial studies were performed to optimise the chromatographic conditions and these were found to be 50% acetonitrile, 50% 50 mM pH 2.0 phosphate buffer at a flow rate of 0.75 mL min(-1), employing a Hypersil C18, 5 μm, 250 mm × 4.6 mm column. Cyclic voltammetric studies were made to ascertain the redox behaviour of Rohypnol at a glassy carbon electrode over the pH range 2-12. Hydrodynamic voltammetry was used to optimise the applied potential at the generator and detector cells; these were identified to be -2.4 V and +0.8 V for the redox mode and -2.4 V and -0.1 V for the dual reductive mode respectively. A linear range of 0.5-100 μg mL(-1), with a detection limit of 20 ng mL(-1) was obtained for the dual reductive mode. Further studies were then performed to identify the optimum conditions required for the LC-DED determination of Rohypnol in beverage samples. A convenient and rapid method for the determination of Rohypnol in beverage samples was developed using a simple sample pre-treatment procedure. A recovery of 95.5% was achieved for a sample of white coffee fortified at 9.6 μg mL(-1) Rohypnol.

A series of eIF4E alleles at the Bc-3 locus are associated with recessive resistance to Clover yellow vein virus in common bean

Clover yellow vein virus (ClYVV) is capable of causing severe damage to common bean (Phaseolus vulgaris L.) production worldwide. The snap bean market class is particularly vulnerable because infection may lead to distortion and necrosis of the fresh green pods and rejection of the harvest. Three putatively independent recessive genes (cyv, desc, bc-3) have been reported to condition resistance to ClYVV; however, their allelic relationships have not been resolved. We identified, evaluated, and characterized the phenotypic and molecular genetic variation present in 21 informative common bean genotypes for resistance to ClYVV. Allelism testing phenotypes from multiple populations provided clear evidence that the three genes were a series of recessive alleles at the Bc-3 locus that condition unique potyvirus strain- and species-specific resistance spectra. Candidate gene analysis revealed complete association between the recessive resistance alleles and unique patterns of predicted amino acid substitutions in P. vulgaris eukaryotic translation initiation factor 4E (PveIF4E). This led to the discovery and characterization of two novel PveIF4E alleles associated with resistance to ClYVV, PveIF4E (3) , and PveIF4E (4) . We developed KASPar allele-specific SNP genotyping assays and demonstrated their ability to accurately detect and differentiate all of the PveIF4E haplotypes present in the germplasm, allelism testing, and in three separate segregating populations. The results contribute to an enhanced understanding and accessibility of the important potyvirus resistance conditioned by recessive alleles at Bc-3. The KASPar assays should be useful to further enable germplasm exploration, allelic discrimination, and marker-assisted introgression of bc-3 alleles in common bean.

Development of an amperometric screen-printed galactose biosensor for serum analysis

The development of a disposable amperometric biosensor for the measurement of circulating galactose in serum is described. The biosensor comprises a screen-printed carbon electrode (SPCE), incorporating the electrocatalyst cobalt phthalocyanine (CoPC), which is covered by a permselective cellulose acetate (CA) membrane and a layer of immobilized galactose oxidase (GALOX). The optimal response of the biosensor, designated as GALOX-CA-CoPC-SPCE, was obtained by systematically examining the effects of enzyme loading, temperature, pH, and buffer strength. The optimal performance of the biosensor occurred with 2U of GALOX, at 35°C, using 50mM phosphate buffer solution (pH 7.0). The sensitivity was 7.00μAmM(-1)cm(-2) and the linear range from 0.1 to 25mM with a calculated limit of detection (LOD) of 0.02mM; this concentration range and LOD are appropriate to diagnose galactosemia, i.e., concentrations >1.1mM in infants. When the biosensor was used in conjunction with amperometry in stirred solution for the analysis of serum, the precision values obtained on unspiked (endogenous level of 0.153mM) and spiked serum (1mM added) (n=6) were 1.10% and 0.11%, respectively, with a calculated recovery of 99.9%.

Microfabricated glucose biosensor for culture well operation

A water-based carbon screen-printing ink formulation, containing the redox mediator cobalt phthalocyanine (CoPC) and the enzyme glucose oxidase (GOx), was investigated for its suitability to fabricate glucose microbiosensors in a 96-well microplate format: (1) the biosensor ink was dip-coated onto a platinum (Pt) wire electrode, leading to satisfactory amperometric performance; (2) the ink was deposited onto the surface of a series of Pt microelectrodes (10-500 μm diameter) fabricated on a silicon substrate using MEMS (microelectromechanical systems) microfabrication techniques: capillary deposition proved to be successful; a Pt microdisc electrode of ≥100 μm was required for optimum biosensor performance; (3) MEMS processing was used to fabricate suitably sized metal (Pt) tracks and pads onto a silicon 96 well format base chip, and the glucose biosensor ink was screen-printed onto these pads to create glucose microbiosensors. When formed into microwells, using a 340 μl volume of buffer, the microbiosensors produced steady-state amperometric responses which showed linearity up to 5 mM glucose (CV=6% for n=5 biosensors). When coated, using an optimised protocol, with collagen in order to aid cell adhesion, the biosensors continued to show satisfactory performance in culture medium (linear range to 2 mM, dynamic range to 7 mM, CV=5.7% for n=4 biosensors). Finally, the operation of these collagen-coated microbiosensors, in 5-well 96-well format microwells, was tested using a 5-channel multipotentiostat. A relationship between amperometric response due to glucose, and cell number in the microwells, was observed. These results indicate that microphotolithography and screen-printing techniques can be combined successfully to produce microbiosensors capable of monitoring glucose metabolism in 96 well format cell cultures. The potential application areas for these microbiosensors are discussed.

Why We Are What and Where We Are University of California Press, Berkeley, 2012. 327 pp. $60, £41.95. ISBN 9780520272118

Synthesizing anthropology and biogeography, Harcourt discusses how geography has affected our anatomy, physiology, cultures, and population densities.

Development of a sandwich format, amperometric screen-printed uric acid biosensor for urine analysis

A screen-printed carbon electrode (SPCE) incorporating the electrocatalyst cobalt phthalocyanine (CoPC), fabricated using a water-based ink formulation, has been investigated as the base transducer for a uric acid biosensor. A sandwich biosensor was fabricated by first depositing cellulose acetate (CA) onto this transducer (CoPC-SPCE), followed by uricase (UOX) and finally a polycarbonate (PC) membrane; this device is designated PC-UOX-CA-CoPC-SPCE. This biosensor was used in conjunction with chronoamperometry to optimize the conditions for the analysis of urine: temperature, 35°C; buffer, pH 9.2; ionic strength, 50 mM; uricase, 0.6 U; incubation time, 180 s. The proposed biosensor was applied to urine from a healthy subject. The precision determined on unspiked urine (n=6) was 5.82%. Urine was fortified with 0.225 mM UA, and the resulting precision and recovery were 4.21 and 97.3%, respectively. The linear working range of the biosensor was found to be 0.015 to 0.25 mM (the former represents the detection limit), and the sensitivity was calculated to be 2.10 μA/mM.

Teosinte inflorescence phytolith assemblages mirror Zea taxonomy

Molecular DNA analyses of the New World grass (Poaceae) genus Zea, comprising five species, has resolved taxonomic issues including the most likely teosinte progenitor (Zea mays ssp. parviglumis) of maize (Zea mays ssp. mays). However, archaeologically, little is known about the use of teosinte by humans both prior to and after the domestication of maize. One potential line of evidence to explore these relationships is opaline phytoliths produced in teosinte fruit cases. Here we use multidimensional scaling and multiple discriminant analyses to determine if rondel phytolith assemblages from teosinte fruitcases reflect teosinte taxonomy. Our results indicate that rondel phytolith assemblages from the various taxa, including subspecies, can be statistically discriminated. This indicates that it will be possible to investigate the archaeological histories of teosinte use pending the recovery of appropriate samples.

The voltammetric behaviour of lead at a microband screen-printed carbon electrode and its determination in acetate leachates from glazed ceramic plates

Microband screen-printed carbon electrodes (μBSPCEs) without further modification have been investigated as disposable sensors for the measurement of lead in acetate leachates from ceramic glazed plates. Cyclic voltammetry was employed to elucidate the electrochemical behaviour of Pb(2+) at these electrodes in a variety of supporting electrolytes. The anodic peaks obtained on the reverse scans, showed that Pb had been deposited as a thin layer on the surface of the μBSPCE. The anodic peak of greatest magnitude was obtained in 0.1M pH 4.1 acetate buffer containing 13 mM Cl(-). The effect of chromium, copper, phosphate, sulphate and tin was examined and under the conditions employed, no significant change in current was found. The μBSPCEs were evaluated by carrying out lead determinations for acetate leachates from glazed ceramic plates. A highly decorated ornamental plate was found to leach 400 μg Pb(2+) (%CV=1.91%). A second plate, designed for dinnerware was found not to leach any detectable levels of Pb(2+). However, once fortified with 2.10 μg of Pb (equivalent to 100 ng/ml in the leachate), a mean recovery of 82.08% (%CV=4.07%) was obtained. The performance characteristics indicate that reliable data has been obtained for this application which could identify potentially toxic sources of lead.

Impact of stent design on the outcome of intervention for carotid bifurcation stenosis

Over the past several years, there has been continued significant interest in refinement of patient selection, devices, procedures and protocols in an effort to optimize the outcome of percutaneous intervention for carotid bifurcation stenosis, including: ongoing National Institutes of Health and manufacturer trials and registries; the further refinement of existing devices and emergence of new platforms to attain distal embolic protection; ongoing study of what really constitutes a high-risk carotid surgery or stenting patient; and attention to device characteristics and patient-device matching. Within the latter area, considerable interest has focused on stent characteristics that have the potential to impact short and long-term outcome when compared with other stent design strategies when studied in large series. The stent in carotid artery intervention occupies a unique role in that after the embolic protection system has been removed, it is the main line of defense (in concert with aggressive dual antiplatelet therapy) from embolic and thromboembolic complications that may arise from the newly remodeled plaque after post-stent angioplasty. In this review, we aim to update the current status of efforts to relate stent design strategy to outcome in intervention for extracranial carotid artery disease with a focus primarily on the function of "free cell area" (typically lower with closed-cell stents and higher with open-cell stents) in analyses of outcome in carotid artery stenting. Also, the potential role of closed-cell vs. open-cell stent selection in other reports related to carotid artery stenting outcome or complications is reviewed. Rigorous studies have examined the issue of free cell area and arrived at disparate conclusions. Randomized data on the impact of free cell area and cell design strategy on carotid intervention are presently lacking. However, we believe sufficient data and rationale exist 1) to warrant ongoing study of the impact of stent design on outcome in carotid intervention; and 2) to make consideration of closed-cell (low free cell area) stent use a reasonable approach to device selection--when patient factors, lesion characteristics, or device availability make doing so possible.

Amperometric lactate biosensor for flow injection analysis based on a screen-printed carbon electrode containing Meldola's Blue-Reinecke salt, coated with lactate dehydrogenase and NAD+

A biosensor for the measurement of lactate in serum has been developed, which is based on a screen-printed carbon electrode, modified with Meldola's Blue-Reinecke Salt (MBRS-SPCE), coated with the enzyme lactate dehydrogenase NAD(+) dependent (from Porcine heart), and NAD(+). A cellulose acetate layer was deposited on the top of the device to act as a permselective membrane. The biosensor was incorporated into a commercially available, thin-layer, amperometric flow cell operated at a potential of only +0.05 V vs. Ag/AgCl. The mobile phase consisted of 0.2 M phosphate buffer pH 10 containing 0.1 M potassium chloride solution; a flow rate of 0.8 ml min(-1) was used throughout the investigation. The biosensor response was linear over the range 0.55-10 mM lactate; the former represents the detection limit. The precision of the system was determined by carrying out 10 repeat injections of 10 mM l(+)lactic acid standard; the calculated coefficient of variation was 4.28%. It was demonstrated that this biosensor system could be applied to the direct measurement of lactate in serum without pre-treatment; therefore, this would allow high throughput-analysis, at low cost, for this clinically important analyte.

A flow injection system, comprising a biosensor based on a screen-printed carbon electrode containing Meldola's Blue-Reinecke salt coated with glucose dehydrogenase, for the measurement of glucose

A biosensor for the measurement of glucose in serum has been developed, based on a screen-printed carbon electrode modified with Meldola's Blue-Reinecke salt, coated with the enzyme glucose dehydrogenase (from Bacillus sp.), and nicotinamide adenine dinucleotide coenzyme (NAD+). A cellulose acetate layer was deposited on top of the device to act as a permselective membrane. The biosensor was incorporated into a commercially available, thin-layer, amperometric flow cell operated at a potential of only +0.05 V versus Ag/AgCl. The mobile phase consisted of 0.2 M phosphate buffer (pH 7.0) containing 0.1 M potassium chloride solution, and a flow rate of 0.8 ml min(-1) was used throughout the investigation. The biosensor response was linear over the range of 0.075-30 mM glucose, with the former representing the detection limit. The precision of the system was determined by carrying out 20 repeat injections of a 5-mM glucose standard, and the calculated coefficient of variation was 3.9%. It was demonstrated that this biosensor system could be applied to the direct measurement of glucose in serum without pretreatment. Therefore, this would allow high-throughput analysis, at low cost, for this clinically important analyte.

Development of an amperometric assay for phosphate ions in urine based on a chemically modified screen-printed carbon electrode

An amperometric assay for the determination of inorganic phosphate (Pi) in urine has been developed without the need for sample preparation. A screen-printed carbon electrode modified with the electrocatalyst cobalt phthalocyanine (CoPC-SPCE) and covered with a cellulose acetate membrane (CAM) serves as the sensor. The sensor detects hydrogen peroxide (H(2)O(2)), which is produced as a result of the oxidative decarboxylation of pyruvate, catalyzed by pyruvate oxidase (PyOd), in the presence of Pi, oxygen, and cofactors. Following optimization of solution conditions, and in the presence of a urine sample, a linear range was found to exist between the rate of current increase and phosphate concentration over the range of 2.27 x 10(-5) to 1.81 x 10(-4)M, and the limit of detection was found to be 4.27 x 10(-6)M. The assay was applied to the determination of phosphate ions in the urine of a normal subject, and the mean concentration in unspiked urine was found to be 3.40 x 10(-5)M with a coefficient of variation of 8.0% (n=5). The mean recovery of phosphate added to urine samples was 98.7% with a coefficient of variation of 5.5% (n=3). To the authors' knowledge, this is the first report of an amperometric assay for Pi that incorporates a CoPC-SPCE as the sensing device.

Preparation of screen-printed electrochemical immunosensors for estradiol, and their application in biological fluids

The method of fabrication of a prototype electrochemical immunosensor for estradiol (E2) is described. Methodologies are also given for colorimetric assays, which can be used to verify and optimize reagent performance, prior to their use in the electrochemical immunoassay: these include an E2 ELISA and a colorimetric assay performed on the immunosensor surface. The electrochemical immunosensor system uses screen-printed carbon electrodes (SPCEs) upon which antibody against E2 is immobilized. Antibodies (rabbit anti-mouse IgG, then monoclonal mouse anti-E2) are immobilized by passive adsorption onto the working electrode surface. A competitive immunoassay is then performed using an alkaline-phosphatase-labeled E2 conjugate. Electrochemical measurements are performed using differential pulse voltammetry (DPV) to detect the production of 1-naphthol from 1-naphthyl phosphate. The calibration plot of DPV peak current vs. E2 concentration shows a measurable range of 25-500 pg/mL with a detection limit of 50 pg/mL. The immunosensor can be applied to the determination of E2 in spiked serum, following an extraction step with diethyl ether.

Development of an anodic stripping voltammetric assay, using a disposable mercury-free screen-printed carbon electrode, for the determination of zinc in human sweat

This paper reports on the development of a novel electrochemical assay for Zn(2+) in human sweat, which involves the use of disposable screen-printed carbon electrodes (SPCEs). Initially, SPCEs were used in conjunction with cyclic voltammetry to study the redox characteristics of Zn(2+) in a selection of supporting electrolytes. The best defined cathodic and anodic peaks were obtained with 0.1 M NaCl/0.1 M acetate buffer pH 6.0. The anodic peak was sharp and symmetrical which is typical for the oxidation of a thin metal film on the electrode surface. This behaviour was exploited in the development of a differential pulse anodic stripping voltammetric (DPASV) assay for zinc. It was shown that a deposition potential of -1.6 V versus Ag/AgCl and deposition time of 60 s with stirring (10 s equilibration) produced a well-defined stripping peak with E(pa) = -1.2 V versus Ag/AgCl. Using these conditions, the calibration plot was linear over the range 1x10(-8) to 5x10(-6) M Zn(2+). The precision was examined by carrying out six replicate measurements at a concentration of 2x10(-6) M; the coefficient of variation was calculated to be 5.6%. The method was applied to the determination of the analyte in sweat from 10 human volunteers. The concentrations were between 0.39 and 1.56 microg/mL, which agrees well with previously reported values. This simple, low-cost sensitive assay should have application in biomedical studies and for stress and fatigue in sports studies.

Voltammetric behaviour of DNA bases at a screen-printed carbon electrode and its application to a simple and rapid voltammetric method for the determination of oxidative damage in double stranded DNA

Screen-printed carbon electrodes (SPCEs) have been investigated as possible sensors to identify gamma-irradiation induced oxidative damage in double stranded (ds) DNA. Studies were undertaken to explore the possibility of using both cyclic voltammetry and differential pulse voltammetry to identify changes due to oxidative damage. Initially, guanine, adenine and 8-oxoguanosine were examined and it was found possible to differentiate them from their voltammetric responses. The voltammetric response of 8-oxoguanosine was found to be linear over the concentration range 1-400 microM, with a slope of 0.0296 microA microM(-1) (R2 value of 0.9984), in the presence of 2mM concentrations of guanine and adenine. Investigations were made into harnessing these findings to identify oxidative damage in gamma-irradiated dsDNA. The presence of oxidative damage in these samples was readily identifiable, and the magnitude of the voltammetric response was found to be dose dependant (R2=0.9919). A simple sample preparation step involving only the dissolution of double stranded DNA sample in the optimised electrolyte (0.1M acetate buffer pH 4.5) was required. This report appears to be first describing the use of a SPCE to detect DNA damage which can be related to the dose of gamma-radiation used.

A novel, disposable, screen-printed amperometric biosensor for glucose in serum fabricated using a water-based carbon ink

Screen-printed amperometric glucose biosensors have been fabricated using a water-based carbon ink. The enzyme glucose oxidase (GOD) and the electro-catalyst cobalt phthalocyanine were mixed with the carbon ink prior to the screen-printing process; therefore, biosensors are prepared in a one-step fabrication procedure. Optimisation of the biosensor performance was achieved by studying the effects of pH, buffer strength, and applied potential on the analytical response. Calibration studies were performed under optimum conditions, using amperometry in stirred solution, with an operating potential of +500 mV versus SCE. The sensitivity was found to be 1170 nA mM(-1), with a linear range of 0.025-2 mM; the former represents the detection limit. The disposable amperometric biosensor was evaluated by carrying out replicate determinations on a sample of bovine serum. This was achieved by the method of multiple standard additions and included a correction for background currents arising from oxidizable serum components. The mean serum concentration was calculated to be 8.63 mM and compared well with the supplier's value of 8.3 mM; the coefficient of variation was calculated to be 3.3% (n=6).

Voltammetric Behavior of Nitrazepam and Its Determination in Serum Using Liquid Chromatography with Redox Mode Dual-Electrode Detection

A method involving high-performance liquid chromatography with dual-electrode electrochemical detection in the redox mode (LC-DED) has been successfully developed for the determination of the benzodiazepine tranquilizer, nitrazepam, in serum. To elucidate the electrochemical mechanism occurring at a glassy carbon electrode, cyclic voltammetry was preformed with 1 mM solutions of nitrazepam at pH values between 2 and 12, using a potential range from -1.5 to +1.5 V. Two reduction peaks were observed over the whole pH range; the first, designated R1, was consistent with the 4e-, 4H+ reduction of the 7-nitro group to a hydroxylamine species; the second more negative peak, designated R2, was shown to be the result of a 2e-, 2H+ reduction of the 4-5 azomethine group. On the reverse anodic scan, an oxidation signal was observed, designated O1, which was considered to result from a 2e-, 2H+ oxidation of the hydroxylamine to a nitroso group. On the second forward scan, a new reduction peak, designated R3, was observed, which was considered to result from reduction of the nitroso species back to the hydroxylamine species. Studies were then undertaken to exploit the hydroxylamine/nitroso redox couple using LC-DED detection for the measurement of nitrazepam in serum. The optimal chromatographic conditions were found to comprise a mobile phase containing 60% methanol, 40% 50 mM pH 4.1 acetate buffer, in conjunction with a Hypersil C18 250 mm x 4.6 mm column. Hydrodynamic voltammetric studies were undertaken to optimize the operating potentials required for dual-electrode detection. It was found that an applied potential of -2.4 V was optimum for the "generator" cell and +0.5 V for the "detector" cell. The proposed method was evaluated by carrying out replicate nitrazepam determinations on spiked bovine and human serum samples. The former evaluation was preformed at a concentration of 11.2 microg mL(-1), and the latter at 1670 ng mL(-1). For bovine serum, the recovery of nitrazepam was found to be 75.8% and the associated coefficient of variation was 6.1% (n = 6). For human serum, the recovery was 74.1% with a coefficient of variation of 7.8% (n = 7). These data suggest that the method holds promise for applications in toxicology and where an alternative reliable method to confirm drug abuse may be required.