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Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches – analyses of chloroplast genomes and genome‐wide proportions of private variants – we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north‐eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post‐domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool. [ABSTRACT FROM AUTHOR]

For ancient types of barley at sites in the Scottish Isles, Faroes, and Iceland, we calculated minimum temperature requirements for grain production (grain production threshold, GPT) as accumulated degree days over the cropping season. Site suitability for barley from AD 1200 to 2000 was investigated by comparing these thresholds with reconstructions of annual cropping season degree days (CSDD) using temperature and tree-ring data. In Iceland, between AD 1200 and 1500, reconstructed CSDD were more favorable in the southwest (Reykjavik), with fewer years below the GPT, than in the North, East and West, but there were two periods (1340–1389 and 1426–1475) with low average CSDD and several years below the GPT which possibly influenced the abandonment of barley cultivation around this time. Reconstructed CSDD for the Faroes (Tórshavn) had only one year below the GPT, but 15 periods of four or more consecutive years with low CSDD which would have challenged barley cultivation, especially in the thirteenth century. Reconstructed CSDD were highest for the Scottish Isles, allowing a more prominent role of barley in the farming system and economy. Nevertheless, years with poor harvests or famines were common and about half were associated with low CSDD, resulting in a significant temperature link but also demonstrating the important contribution of other factors. Despite frequent unfavorable years in both the Faroes and Scottish Isles, resilient production systems, well-adapted barley strains and socio-economic factors allowed barley cultivation to continue, and some ancient types to survive to the present day. [ABSTRACT FROM AUTHOR]

We used genotyping-by-sequencing to investigate the evolutionary history of bere, the oldest barley variety still cultivated in Britain and possibly in all of Europe. With a panel of 203 wild and 401 cultivated barley accessions, including 35 samples identified as bere, we obtained filtered datasets comprising up to 1,946,469 single nucleotide polymorphisms (SNPs). The beres formed two genetically-distinct groups, the larger of which included beres from Orkney and the Scottish Western Isles, as well as varieties not identified as bere from the Faroe Islands. This group of beres was distinct from other British barleys, but had a close genetic affiliation with Scandinavian accessions. Although the data were partly compatible with the traditional view that bere was introduced to Scotland by the Vikings during the eighth century AD, the evidence as whole suggested that the bere and Scandinavian barleys are sister groups descended from a more distant common progenitor, possibly dating to the Bronze Age when hulled barleys first become common in northern Europe. More recently, there has been gene flow from these beres into Polish barleys, possibly following export of grain to the Baltic region during periods when Orkney was under Norwegian or Danish rule. A second, smaller group of beres, which included a traditional Welsh variety, was genetically distinct from the main group and probably represents a more recent introduction of barley from central Europe. Our results emphasize the uniqueness of bere barley and its importance as a heritage crop and a potential source of germplasm for breeding programmes. [ABSTRACT FROM AUTHOR]

Background: Nonsuicidal self‐injury (NSSI) is associated with high levels of distress, co‐morbid mental health issues, and elevated risk of suicide. Previous literature indicates that emotion regulation is the most endorsed function of NSSI. Experience Sampling Methodology (ESM) provides a powerful tool for investigating the moment‐to‐moment associations between emotional states and NSSI thoughts and behaviours. The aim of the current study was to systematically review and evaluate ESM research concerning the relationship between momentary emotional states and NSSI. Methods: A systematic search of electronic databases from date of inception to 16th April 2021 was conducted. This was supplemented through backwards citation tracking. A risk of bias assessment was completed prior to data synthesis. Results: Nineteen eligible studies were identified for inclusion in the review. Heightened negative affect was found to typically precede instances of NSSIT thoughts and behaviour. Results were less consistent for positive affect. Limitations: Sample sizes across studies were often small, meaningful effect sizes were not always reported, and non‐validated measures of NSSI thoughts and behaviour were used during ESM assessments. Conclusions: The results support affect regulation models of NSSI, and demonstrate the value of ESM studies, specifically those sampling more than once per day, in plotting the temporal, "in‐the‐moment" characteristics of these processes. [ABSTRACT FROM AUTHOR]

Background: Occupational problems are common for adults experiencing chronic pain, but occupational therapists are not always accessed as part of the multidisciplinary team. Despite evidence of benefit for work-focused interventions, there is limited evidence for broader benefit from occupational therapy interventions within the context of multidisciplinary pain management. The aim of this study was to explore the experiences of programme attendees who received structured intervention from an occupational therapist as part of a multidisciplinary pain management programme, and gain an understanding as to how they felt it influenced changes they made to occupational participation. Method: A qualitative approach was undertaken with 9 individual patients recruited from a group pain management programme for adults with chronic low back pain. Semi-structured interviews were carried out, recorded and transcribed. Thematic analysis was used to identify themes in the data. Results: Three key themes were identified: 1) the helpfulness of activity pacing techniques 2) the value of participating in a therapeutic activity-based session and 3) an increased understanding of the importance of leisure and creative activities in the context of their lives. Conclusion: Participants perceived the specific occupational therapy content of the programme to be helpful in a number of different ways. The findings suggest that occupational therapy can be important in facilitating patients to apply theoretical techniques in the real world, thereby increasing the likelihood of long term benefit. [ABSTRACT FROM AUTHOR]

Background: Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is 'non-brittleness' of the rachis (the stem of the inflorescence), which facilitates harvesting of the crop. Other phenotypic differences appear to result from facultative or regional selective pressures. The population structure resulting from these regional events has been interpreted as evidence for multiple domestications or a mosaic ancestry involving genetic interaction between multiple wild or proto-domesticated lineages. However, each of the three mutations that confer non-brittleness originated in the western Fertile Crescent, arguing against multiregional origins for the crop. Results: We examined exome data for 310 wild, cultivated and hybrid/feral barley accessions and showed that cultivated barley is structured into six genetically-defined groups that display admixture, resulting at least in part from two or more significant passages of gene flow with distinct wild populations. The six groups are descended from a single founding population that emerged in the western Fertile Crescent. Only a few loci were universally targeted by selection, the identity of these suggesting that changes in seedling emergence and pathogen resistance could represent crucial domestication switches. Subsequent selection operated on a regional basis and strongly contributed to differentiation of the genetic groups. Conclusions: Identification of genetically-defined groups provides clarity to our understanding of the population history of cultivated barley. Inference of population splits and mixtures together with analysis of selection sweeps indicate descent from a single founding population, which emerged in the western Fertile Crescent. This founding population underwent relatively little genetic selection, those changes that did occur affecting traits involved in seedling emergence and pathogen resistance, indicating that these phenotypes should be considered as 'domestication traits'. During its expansion out of the western Fertile Crescent, the crop underwent regional episodes of gene flow and selection, giving rise to a modern genetic signature that has been interpreted as evidence for multiple domestications, but which we show can be rationalized with a single origin. [ABSTRACT FROM AUTHOR]

We used genotyping-by-sequencing (GBS) to investigate the evolutionary history of domesticated tetraploid wheats. With a panel of 189 wild and domesticated wheats, we identified 1,172,469 single nucleotide polymorphisms (SNPs) with a read depth ≥3. Principal component analyses (PCAs) separated the Triticum turgidum and Triticum timopheevii accessions, as well as wild T. turgidum from the domesticated emmers and the naked wheats, showing that SNP typing by GBS is capable of providing robust information on the genetic relationships between wheat species and subspecies. The PCAs and a neighbour-joining analysis suggested that domesticated tetraploid wheats have closest affinity with wild emmers from the northern Fertile Crescent, consistent with the results of previous genetic studies on the origins of domesticated wheat. However, a more detailed examination of admixture and allele sharing between domesticates and different wild populations, along with genome-wide association studies (GWAS), showed that the domesticated tetraploid wheats have also received a substantial genetic input from wild emmers from the southern Levant. Taking account of archaeological evidence that tetraploid wheats were first cultivated in the southern Levant, we suggest that a pre-domesticated crop spread from this region to southeast Turkey and became mixed with a wild emmer population from the northern Fertile Crescent. Fixation of the domestication traits in this mixed population would account for the allele sharing and GWAS results that we report. We also propose that feralization of the component of the pre-domesticated population that did not acquire domestication traits has resulted in the modern wild population from southeast Turkey displaying features of both the domesticates and wild emmer from the southern Levant, and hence appearing to be the sole progenitor of domesticated tetraploids when the phylogenetic relationships are studied by methods that assume a treelike pattern of evolution. [ABSTRACT FROM AUTHOR]

As-for-Sb and Sb-for-As anion exchange reactions have been investigated by the exposure of GaSb surfaces to As2 and As4 species and by the exposure of GaAs to Sb2, respectively. The effect of surface temperature, anion soak time, and anion species (either As2 or As4) on the chemistry governing the anion exchange reactions during GaAsySb1-y/GaSb and GaSbyAs1-y/GaAs heterostructure formation by molecular beam epitaxy is examined. It is found that when GaSb surfaces are exposed to arsenic, the anion exchange reaction competes with the formation of isoelectronic compounds, AsSby, which form clusters precipitating in the GaAsySb1-y/GaSb heterostructures. The relative amount of GaAs and AsSby depends on the surface temperature, the As soak time, and on the As species, i.e., As2 or As4. We observe specific process conditions that minimize AsSby formation, yielding more abrupt heterojunction interfaces. In the case of the Sb2/GaAs system, the Sb-for-As anion exchange does not occur to a significant degree, but surface segregation of antimony is found. A chemical model for the As-for-Sb anion exchange reaction is proposed. [ABSTRACT FROM AUTHOR]

The fundamental chemical and kinetic surface processes governing the P-for-As exchange reaction during epitaxial layer synthesis are investigated. Exposure of a GaAs surface to phosphorus molecular beams (P2) is carried out to create superlattice structures realized by surface reactions. The impact of the GaAs surface reconstruction, the P-soak time, and the surface temperature on the extent of intermixing and on the mechanism governing the anion exchange has been studied using x-ray diffraction, spectroscopic ellipsometry, x-ray photoelectron spectroscopy, and atomic force microscopy. It is found that As-rich GaAs surface reconstructions inhibit P-for-As exchange. The extent of the anion exchange increases with temperature. Furthermore, the P-for-As exchange is not controlled by P diffusion into the GaAs. We propose a chemical model that includes P chemisorption and indiffusion, and the competition between P-for-As anion exchange and the formation of AsP isoelectronic compounds. [ABSTRACT FROM AUTHOR]

In this study we examine the possible reasons for the firing of ad agencies and relate these reasons to the stock price consequences of the firings using event-study methodology. After analyzing a variety of performance measures for profitability, sales, and market share of the client firms prior to the firing, we find that firms that fire their ad agencies have lost market share in the two quarters immediately preceding the firing. We report here, for the first time, that the fall in the stock price of client firms is significantly related to the fall in market share preceding the firing. Previously published research on ad agency firings has shown that the stock price of client firms falls just prior to the announcement of the ad agency firing. We confirm that result using a larger sample of firms over a longer period of time and then extend it to include the stock price impact on fired ad agencies (price falls) and their replacement ad agencies (price rises). In addition, the managerial implications of our results for ad agencies, for their clients, and for researchers are discussed. [ABSTRACT FROM AUTHOR]

The cytokinin dehydrogenase gene HvCKX2.1 is the regulatory target for the most abundant heterochromatic small RNAs in drought-stressed barley caryopses. We investigated the diversity of HvCKX2.1 in 228 barley landraces and 216 wild accessions and identified 14 haplotypes, five of these with ten or more members, coding for four different protein variants. The third largest haplotype was abundant in wild accessions (51 members), but absent from the landrace collection. Protein structure predictions indicated that the amino acid substitution specific to haplotype 3 could result in a change in the functional properties of the HvCKX2.1 protein. Haplotypes 1–3 have overlapping geographical distributions in the wild population, but the average rainfall amounts at the collection sites for haplotype 3 plants are significantly higher during November to February compared to the equivalent data for plants of haplotypes 1 and 2. We argue that the likelihood that haplotype 3 plants were excluded from landraces by sampling bias that occurred when the first wild barley plants were taken into cultivation is low, and that it is reasonable to suggest that plants with haplotype 3 are absent from the crop because these plants were less suited to the artificial conditions associated with cultivation. Although the cytokinin signalling pathway influences many aspects of plant development, the identified role of HvCKX2.1 in the drought response raises the possibility that the particular aspect of cultivation that mitigated against haplotype 3 relates in some way to water utilization. Our results therefore highlight the possibility that water utilization properties should be looked on as a possible component of the suite of physiological adaptations accompanying the domestication and subsequent evolution of cultivated barley. [ABSTRACT FROM AUTHOR]

Domestication of barley and other cereals was accompanied by an increase in seed size which has been ascribed to human selection, large seeds being preferred by early farmers or favoured by cultivation practices such as deep sowing. An alternative suggestion is that the increase in seed size was an indirect consequence of selection for plants with more vigorous growth. To begin to address the latter hypothesis we studied the diversity of HvWAK1, a wall-associated kinase gene involved in root proliferation, in 220 wild barley accessions and 200 domesticated landraces. A 3655-bp sequence comprising the gene and upstream region contained 69 single nucleotide polymorphisms (SNPs), one indel and four short tandem repeats. A network of 50 haplotypes revealed a complex evolutionary relationship, but with landraces largely restricted to two parts of the topology. SNPs in the HvWAK1 coding region resulted in nonsynonymous substitutions at nine positions in the translation product, but none of these changes were predicted to have a significant effect on the protein structure. In contrast, the region upstream of the coding sequence contained five SNPs that were invariant in the domesticated population, fixation of these SNPs decreasing the likelihood that the upstream of a pair of TATA boxes and transcription start sites would be used to promote transcription of HvWAK1. The sequence diversity therefore suggests that the cis-regulatory region of HvWAK1 might have been subject to selection during barley domestication. The extent of root proliferation has been linked with traits such as above-ground biomass, so selection for particular cis-regulatory variants of HvWAK1 would be consistent with the hypothesis that seed size increases during domestication were the indirect consequence of selection for plants with increased growth vigour. [ABSTRACT FROM AUTHOR]

The tetraploid wheat species Triticum turgidum and Triticum timopheevii are morphologically similar, and misidentification of material collected from the wild is possible. We compared published sequences for the Ppd-A1, Ppd-B1 and Ppd-G1 genes from multiple accessions of T. turgidum and T. timopheevii and devised a set of four polymerase chain reactions (PCRs), two specific for Ppd-B1 and two for Ppd-G1. We used these PCRs with 51 accessions of T. timopheevii and 20 of T. turgidum. Sixty of these accessions gave PCR products consistent with their taxon identifications, but the other eleven accessions gave anomalous results: ten accessions that were classified as T. turgidum were identified as T. timopheevii by the PCRs, and one T. timopheevii accession was typed as T. turgidum. We believe that these anomalies are not due to errors in the PCR tests because the results agree with a more comprehensive analysis of genome-wide single nucleotide polymorphisms, which similarly suggest that these eleven accessions have been misclassified. Our results therefore show that the accepted morphological tests for discrimination between T. turgidum and T. timopheevii might not be entirely robust, but that species identification can be made cheaply and quickly by PCRs directed at the Ppd-1 gene. [ABSTRACT FROM AUTHOR]

The aromatic group of Asian cultivated rice is a distinct population with considerable genetic diversity on the Indian subcontinent and includes the popular Basmati types characterized by pleasant fragrance. Genetic and phenotypic associations with other cultivated groups are ambiguous, obscuring the origin of the aromatic population. From analysis of genome-wide diversity among over 1,000 wild and cultivated rice accessions, we show that aromatic rice originated in the Indian subcontinent from hybridization between a local wild population and examples of domesticated japonica that had spread to the region from their own center of origin in East Asia. Most present-day aromatic accessions have inherited their cytoplasm along with 29–47% of their nuclear genome from the local Indian rice. We infer that the admixture occurred 4,000–2,400 years ago, soon after japonica rice reached the region. We identify aus as the original crop of the Indian subcontinent, indica and japonica as later arrivals, and aromatic a specific product of local agriculture. These results prompt a reappraisal of our understanding of the emergence and development of rice agriculture in the Indian subcontinent. [ABSTRACT FROM AUTHOR]

A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include Sh4, Rc, PROG1 and LABA1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the 'domestication alleles' of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the rc and laba1 alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the prog1 and sh4 domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the rc, laba1, prog1 and sh4 alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered. [ABSTRACT FROM AUTHOR]

The nonbrittle rachis, resulting in a seed head which does not shatter at maturity, is one of the key phenotypes that distinguishes domesticated barley from its wild relatives. The phenotype is associated with two loci, Btr1 and Btr2, with all domesticated barleys thought to have either a 1 bp deletion in Btr1 or an 11 bp deletion in Btr2., We used a PCR genotyping method with 380 domesticated barley landraces to identify those with the Btr1 deletion and those with the Btr2 deletion., We discovered two landraces, from Serbia and Greece, that had neither deletion. Instead these landraces possess a novel point mutation in Btr1, changing a leucine to a proline in the protein product. We confirmed that plants carrying this mutation have the nonbrittle phenotype and identified wild haplotypes from the Gaziantep region of southeast Turkey as the closest wild relatives of these two landraces., The presence of a third mutation conferring the nonbrittle phenotype of domesticated barley shows that the origin of this trait is more complex than previously thought, and is consistent with recent models that view the transition to agriculture in southwest Asia as a protracted and multiregional process. [ABSTRACT FROM AUTHOR]

We assessed the ability of whole genome amplification (WGA) to improve the efficiency of downstream polymerase chain reactions (PCRs) directed at ancient DNA (aDNA) of members of the Mycobacterium tuberculosis complex (MTBC). Using extracts from a variety of bones and a tooth from human skeletons with or without lesions indicative of tuberculosis, from multiple time periods, we obtained inconsistent results. We conclude that WGA does not provide any advantage in studies of MTBC aDNA. The sporadic nature of our results are probably due to the fact that WGA is itself a PCR-based procedure which, although designed to deal with fragmented DNA, might be inefficient with the low concentration of templates in an aDNA extract. As such, WGA is subject to similar, if not the same, restrictions as PCR when applied to aDNA. [ABSTRACT FROM AUTHOR]

ABSTRACT The introduction of next-generation sequencing methods has broadened the scope and utility of ancient DNA (aDNA) research, and is opening up exciting new applications in Quaternary science. Palaeogenomes - partial or complete genome sequences for extinct taxa - are now available for Neanderthals and Denisovans, various megafauna, and preserved microorganisms. The analysis of aDNA in sediments, including cores in which there are no visible macro- or microfossils, is helping to reconstruct past ecosystems, especially in Arctic regions where aDNA preservation is relatively good. In this review we follow the development of aDNA research over the last 30 years, showing how the problems caused by contamination of ancient samples with modern DNA have gradually been overcome, and highlighting those technical challenges that still exist. We then survey the current standing of palaeogenomics and sedimentary aDNA studies, and indicate how these fields might be developed further in coming years. [ABSTRACT FROM AUTHOR]

The scope and ambition of biomolecular archaeology is undergoing rapid change due to the development of new 'next generation' sequencing (NGS) methods for analysis of ancient DNA in archaeological specimens. These methods have not yet been applied extensively to archaeobotanical material but their utility has been demonstrated with desiccated, waterlogged and charred remains. The future use of NGS is likely to open up new areas of investigation that have been difficult or impossible with the traditional approach to aDNA sequencing. Species identification should become more routine with archaeobotanical explants, not just with charred grain but with most if not all species likely to be encountered in an archaeobotanical setting. Distinctions between different subspecies groups such as cereal landraces will also be possible in the near future. Phenotypic characterization, in which aDNA sequencing is used to infer the biological characteristics of an archaeological specimen, will become possible, improving our understanding of traits such as flowering behaviour of cereals, and when combined with studies of preserved RNA and protein will enable complex phenotypes such as environmental tolerance and nutritional quality to be assessed. The sequencing of entire ancient plant genomes is also likely to have significant impact. As with past studies of ancient plant DNA, realization of the new potential provided by NGS will require productive collaboration between archaeologists and geneticists within the archaeobotanical research community. [ABSTRACT FROM AUTHOR]

The essay discusses poets including Seamus Heaney and W. B. Yeats. Topics discussed include poem "Paudeen" by Yeats, Irish poets and poet William Wordsworth. Other topics such as poet W. H. Auden, history of Ireland and good governance are also discussed. Poetry as an art and Anglo-Irish elitism are mentioned.

ABSTRACT Tuberculosis is known to have afflicted humans throughout history and re-emerged towards the end of the 20th century, to an extent that it was declared a global emergency in 1993. The aim of this study was to apply a rigorous analytical regime to the detection of Mycobacterium tuberculosis complex (MTBC) DNA in 77 bone and tooth samples from 70 individuals from Britain and continental Europe, spanning the 1st-19th centuries AD. We performed the work in dedicated ancient DNA facilities designed to prevent all types of modern contamination, we checked the authenticity of all products obtained by the polymerase chain reaction, and we based our conclusions on up to four replicate experiments for each sample, some carried out in an independent laboratory. We identified 12 samples that, according to our strict criteria, gave definite evidence for the presence of MTBC DNA, and another 22 that we classified as 'probable' or 'possible.' None of the definite samples came from vertebrae displaying lesions associated with TB. Instead, eight were from ribs displaying visceral new bone formation, one was a tooth from a skeleton with rib lesions, one was taken from a skeleton with endocranial lesions, one from an individual with lesions to the sacrum and sacroiliac joint and the last was from an individual with no lesions indicative of TB or possible TB. Our results add to information on the past temporal and geographical distribution of TB and affirm the suitability of ribs for studying ancient TB. Am J Phys Anthropol 153:178-189, 2014. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Results about a phylogenetic analysis of the genus Onobrychis Mill., tribe Hedysareae DC. are presented. The systematic knowledge of tribe Hedysareae is still incomplete, with difficult circumscription of genera and species. Analyses were undertaken using both nuclear (ITS) and chloroplast (matK) markers for a set of 78 accessions covering 41 Onobrychis species, besides previously sequenced Hedysareae accessions. The phylogenetic methods used were maximum parsimony, maximum likelihood, and Bayesian analyses to produce phylogenetic trees and robustness indices. The genus Onobrychis was resolved as paraphyletic, with species of the genera Eversmannia Bunge and Hedysarum L. nested within it. The position of the section Membranacea of genus Hedysarum was as a sister group to Onobrychis and Eversmannia, separated from other accessions of Hedysarum. Variation in the 2 markers was sufficient to resolve infrageneric groups in Onobrychis and Hedysarum, but we were unable to completely resolve certain species in Onobrychis, particularly those within the sect. Onobrychis. The cause of this difficult species delimitation may be related to recent speciation, hybridization, and introgression events, particularly between cultivated species and their wild relatives, and the presence of cryptospecies as suggested by intraspecific polyploid series. [ABSTRACT FROM AUTHOR]

Sainfoin ( Onobrychis viciifolia Scop.) is a perennial forage legume that possesses beneficial properties in the context of sustainable agriculture. A germplasm collection of O. viciifolia was assembled from many geographic regions, as well as a collection of Onobrychis species that might be crossed with O. viciifolia to improve its biological and agronomic properties. The objective of the present study was to obtain cytological information for a broad range of O. viciifolia varieties and related species, in order to confirm and extend previous findings. The study set was 143 accessions of O. viciifolia as well as 34 accessions of 17 other species from the Onobrychis genus. Three of the O. viciifolia accessions were diploid (2n = 2x = 14) and the remainder tetraploid (2n = 4x = 28). Chromosomes were <5 μm in length. Among the other Onobrychis species, roughly half were found to be diploid and the other half tetraploid, with two species, O. arenaria (Kit.) DC. and O. alba subsp. laconica (Orph. ex Boiss.) Hayek, including a mixture of diploid and tetraploid accessions. The basic number of chromosomes was seven, except for O. aequidentata (Sm.) d'Urv. and O. crista- galli Lam., where it was eight. The 2C value for O. viciifolia was estimated at 2.5 pg. These cytological data will be valuable as part of a pre-breeding programme aimed at the eventual production of improved O. viciifolia varieties for use in sustainable agriculture. [ABSTRACT FROM AUTHOR]

Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae) preserved in ‘Anthropocene’ Colombian copal, dated to ‘post-Bomb’ and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal. [ABSTRACT FROM AUTHOR]

Chloroplast microsatellites (SSRs) are conserved within wheat species, yet are sufficiently polymorphic between and within species to be useful for evolutionary studies. This study describes the relationships among a very large set of accessions of Triticum urartu Thum. ex Gandil., T. dicoccoides (Körn. ex Asch. et Graebn.) Schweinf., T. dicoccon Schrank, T. durum Desf., T. spelta L., and T. aestivum L. s. str. based on their cpSSR genotypes. By characterising the chloroplast diversity in each wheat species in the evolutionary series, the impact on diversity of major evolutionary events such as domestication and polyploidyisation was assessed. We detected bottlenecks associated with domestication, polyploidisation and selection, yet these constrictions were partially offset by mutations in the chloroplast SSR loci that generated new alleles. The discrete cpSSR alleles and haplotypes observed in T. urartu and Aegilops tauschii, combined with other species specific polymorphisms, provide very strong evidence that concur with current opinion that neither species was the maternal and thus cytoplasmic donor for polyploid wheats. Synthetic hexaploid wheats possessed the same chloroplast haplotypes as their tetraploid progenitors demonstrating how the novel synthetic wheat lines have captured chloroplast diversity from the maternal parents, the chloroplast is maternally inherited and novel alleles are not created by genomic rearrangements triggered by the polyploidisation event. [ABSTRACT FROM AUTHOR]

Ancient biomolecules including DNA, proteins, and lipids are often preserved in archaeological skeletons or artifacts such as potsherds from cooking vessels. Techniques for analyzing these molecules have improved dramatically in recent years, though challenges remain in ensuring that results are authentic and not confused by the presence of contaminating modern biomolecules. Ancient DNA (aDNA) can be used to identify the sex, kinship relationships, and population affinities of human skeletons, and also to detect the presence of disease-causing organisms such as the plague and tuberculosis bacteria. Stable isotope ratios in collagen and other skeletal proteins enable past diets to be studied, and similar work with lipids from potsherds have revealed that dairying in Europe began 2,000 years earlier than previously thought. Biomolecular archaeology has therefore developed into a mature discipline that is making a significant contribution to different aspects of our understanding of the human past. [ABSTRACT FROM AUTHOR]

The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited -- perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication. [ABSTRACT FROM AUTHOR]

Emmer wheat, Triticum dicoccon Schrank was one of the founder crops of Neolithic agriculture. Though its cultivation was largely replaced by hexaploid wheats 2000 years ago, pockets of small scale cultivation can still be found. One such area is the Asturias region of Northern Spain, where emmer wheat remains a traditional crop for high value specialist culinary uses, and farmers grow locally adapted landraces. In order to study the diversity of these landraces, we sampled emmer wheat from different regions of Asturias, and genotyped multiple plants from each village using nuclear and chloroplast microsatellites. A high level of variation was observed with markers from both genomes, including a novel chloroplast haplotype. A strong geographic structure was observed in the Asturian emmer wheats in both the chloroplast markers and the nuclear microsatellite data. [ABSTRACT FROM AUTHOR]

Sainfoin ( Onobrychis viciifolia Scop.) is a perennial forage legume that possesses beneficial properties in the context of sustainable agriculture. In order to initiate a pre-breeding programme, we have assembled a germplasm collection of O. viciifolia from many geographic regions, as well as a collection of Onobrychis species that might be crossed with O. viciifolia to improve its biological and agronomic properties. The objective of this study was to obtain DNA sequences from a representative sample of these accessions in order to characterise their genetic diversity and to assess the robustness of the Onobrychis taxonomy. Because of potential problems with copurification of tannins and polyphenols from Onobrychis leaf tissue, three methods for DNA extraction were assessed and the most appropriate one identified. DNA sequences were obtained for the nuclear internal transcribed spacer region and the trnH- psbA and trnT- trnL intergenic spacers of the chloroplast genome. Neighbour joining trees were constructed and accessions were assigned to operational taxonomic units. The results indicated that there is substantial genetic diversity among Onobrychis species. Redundancies in species nomenclature were identified, as well as possible overlap between some of the sections into which the Onobrychis genus has been divided. A genetic distinction was apparent between O. viciifolia accessions from western Europe and those from eastern Europe and Asia, reflecting a similar division based on agronomic properties. Recognition of these different though related germplasms will be valuable in the design of breeding programmes for the rational improvement of sainfoin as a forage crop for sustainable agriculture. [ABSTRACT FROM AUTHOR]

The use of ancient DNA in paleopathological studies of tuberculosis has largely been restricted to confirmation of disease identifications made by skeletal analysis; few attempts at obtaining genotype data from archaeological samples have been made because of the need to perform different PCRs for each genetic locus being studied in an ancient DNA extract. We used a next generation sequencing approach involving hybridization capture directed at specific polymorphic regions of the Mycobacterium tuberculosis genome to identify a detailed genotype for a historic strain of M. tuberculosis from an individual buried in the 19th century St. George's Crypt, Leeds, West Yorkshire, England. We obtained 664,500 sequencing by oligonucleotide ligation and detection (SOLiD) reads that mapped to the targeted regions of the M. tuberculosis genome; the coverage included 218 of 247 SNPs, 10 of 11 insertion/deletion regions, and the repeat elements IS1081 and IS6110. The accuracy of the SOLiD data was checked by conventional PCRs directed at 11 SNPs and two insertion/deletions. The data placed the historic strain of M. tuberculosis in a group that is uncommon today, but it is known to have been present in North America in the early 20th century. Our results show the use of hybridization capture followed by next generation sequencing as a means of obtaining detailed genotypes of ancient varieties of M. tuberculosis, potentially enabling meaningful comparisons between strains from different geographic locations and different periods in the past. [ABSTRACT FROM AUTHOR]

Specialty stores typically sell only one or a few closely related product lines but offer a wide choice within that line. This article establishes specialty store expertise as an important factor influencing customer satisfaction and examines the role of various factors in determining the share of wallet obtained by the store. A mail survey with 210 participants finds that customer perceptions of store expertise increase satisfaction and share of wallet, while distance to the store has a non-linear relationship with share of wallet. Managerial implications include the need for specialty store owners to develop expertise by careful hiring, training and retaining of employees. In addition, they are encouraged to promote store expertise to potential customers thus positioning themselves on this attribute and helping avoid price competition with mass market retailers. [ABSTRACT FROM AUTHOR]

The Onobrychis genus comprises a few agronomically important forage legume species, with sainfoin (Onobrychis viciifolia) being the most widespread. O. viciifolia has a long history of traditional culture worldwide, but its use has declined in western countries over the last decades. It suffers from low productivity and is more difficult to maintain than other legumes but is known to have valuable characteristics such as palatability and drought tolerance. Recent studies suggest that it has several other highly beneficial properties due to its unique tannin and polyphenol composition. Condensed tannins present in Onobrychis species have been shown to confer anthelmintic properties, increase protein utilization and prevent bloating; they may also have the potential to reduce greenhouse gas emissions. Positive effects on wildlife and honey production could also be advantageous in the context of sustainable farming. Modern breeding programmes have not been a priority, leading to a lack of genetic knowledge in comparison to extensively used forage legumes. It is expected that potential for O. viciifolia improvements could be achieved by rigorous characterization of the available germplasm and utilization of characters derived from close relatives of the genus. Breeding priorities for the future would include enhanced germination and improved early establishment, allied to the best anthelmintic properties observed in some varieties. [ABSTRACT FROM PUBLISHER]

This essay considers the impact of Dylan Thomas on a number of Irish poets and how Thomas has been represented in the critical observations and writings of these poets. It notes how for Patrick Kavanagh the reputation of Dylan Thomas might have seemed a Welsh example of a kind of poetic posturing (for which the Kavanagh deployed the term 'the bucklep') that he associated with the Irish poets W.R. Rodgers and F.R. Higgins. By contrast Louis MacNeice respected these poets as he admired and defended Thomas' poetry. His own work during the Second World War was influenced by that of Thomas especially in its existential humanism which shared the Welsh poet's proccupatiuon with death as a theme. Following Thomas' own death MacNeice became a critical advocate for Thomas' verse, celebrating the poet as a skilled craftsman. The essay concludes by considering Thomas's reputation as it is assessed by Seamus Heaney and Derek Mahon. It notes how Heaney's reading is affected by a frame of reference drawn from Kavanaagh's writings while by contrast Mahon supplies a more enthusiastic critique, especially to Thomas' later work, which is seen to explore female sexuality, mature love and marriage. [ABSTRACT FROM AUTHOR]

Until recently, domestication has been interpreted as a rapid process with little predomestication cultivation and a relatively rapid rise of the domestication syndrome. This interpretation has had a profound effect on the biological framework within which investigations into crop origins have been carried out. A major underlying assumption has been that artificial selection pressures were substantially stronger than natural selection pressures, resulting in genetic patterns of diversity that reflect genetic independence of geographic localities. Recent archaeobotanical evidence has overturned the notion of a rapid transition, resulting in a protracted model that undermines these assumptions. Conclusions of genome-wide multilocus studies remain problematic in their support of a rapid-transition model by indicating that domesticated crops appear to be associated by monophyly with only a single geographic locality. Simulations presented here resolve this conflict, indicating that the results observed in such studies are inevitable over time at a rate that is largely influenced by the long-term population size. Counterintuitively, multiple origin crops are shown to be more likely to produce monophyletic clades than crops of a single origin. Under the protracted transition, the importance of the rise of the domestication syndrome becomes paramount in producing the patterns of genetic diversity from which crop origins may be deduced. We identify four different interacting levels of organization that now need to be considered to track crop origins from modern genetic diversity, making crop origins a problem that could be addressed through system-based approaches. [ABSTRACT FROM AUTHOR]

Purpose — This research aims to measure the financial and operating impact for US retailers that adopted quick response (QR). It specifically looks at the impact of QR on profitability, cost efficiency, and inventory management. Design/methodology/approach — The research analyzed data from the CRSP/Compustat data base of US publicly held corporations to compare adopters of QR with non-adopters before and after adoption. Findings — The results indicated that adopters of QR did not benefit as expected. Adopters, on average, did not improve their performance to a statistically significant degree with respect to profitability, cost efficiency, or inventory levels. Research limitations/implications — The main limitations of the research include the fairly small number of firms studied (11 adopters and 16 non-adopters) and the lack of evidence identifying the reasons for the adopters poor performance. Another limitation is the fact that only the manufacturers perceptions have been considered. It would be beneficial in future research to consider the opinion of retailers about their own management of these brands. Originality/value — The research uses objective actual financial results before and after adoption of QR and avoids the practice of using subjective management opinions of success. The research design includes before and after analysis with a control group — the strongest design possible given the inability to randomly assign firms to the adopter and non-adopter categories. [ABSTRACT FROM AUTHOR]

Background: Visualising the evolutionary history of a set of sequences is a challenge for molecular phylogenetics. One approach is to use undirected graphs, such as median networks, to visualise phylogenies where reticulate relationships such as recombination or homoplasy are displayed as cycles. Median networks contain binary representations of sequences as nodes, with edges connecting those sequences differing at one character; hypothetical ancestral nodes are invoked to generate a connected network which contains all most parsimonious trees. Quasi-median networks are a generalisation of median networks which are not restricted to binary data, although phylogenetic information contained within the multistate positions can be lost during the preprocessing of data. Where the history of a set of samples contain frequent homoplasies or recombination events quasi-median networks will have a complex topology. Graph reduction or pruning methods have been used to reduce network complexity but some of these methods are inapplicable to datasets in which recombination has occurred and others are procedurally complex and/or result in disconnected networks. Results: We address the problems inherent in construction and reduction of quasi-median networks. We describe a novel method of generating quasi-median networks that uses all characters, both binary and multistate, without imposing an arbitrary ordering of the multistate partitions. We also describe a pruning mechanism which maintains at least one shortest path between observed sequences, displaying the underlying relations between all pairs of sequences while maintaining a connected graph. Conclusion: Application of this approach to 5S rDNA sequence data from sea beet produced a pruned network within which genetic isolation between populations by distance was evident, demonstrating the value of this approach for exploration of evolutionary relationships. [ABSTRACT FROM AUTHOR]

We present n method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1-2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1-2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1-2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5ala, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen. [ABSTRACT FROM AUTHOR]

To investigate the evolution and geographical origins of hexaploid wheat, we examined a 284 bp sequence from the promoter region of the GluDy locus, coding for the y subunit of high-molecular-weight glutenin. Fourteen different alleles were found in 100 accessions of Aegilops tauschii and 169 of Triticum aestivum. Two alleles were present in both species; the other 7 alleles from Ae. tauschii and 5 from T. aestivum were unique to their respective species. The two shared alleles differed at only one nucleotide position within the region sequenced, but their apparent association with the common haplotypes GluD1a and GluD1d, which have substantial differences within their GluDy coding regions, makes it unlikely that the alleles evolved independently in Ae. tauschii and T. aestivum. The results therefore support previous studies which suggest that there were at least two Ae. tauschii sources that contributed germplasm to the D genome of T. aestivum. The number of alleles present in T. aestivum, and the nucleotide diversity of these alleles, indicates that this region of the D genome has undergone relatively rapid change since polyploidisation. Ae. tauschii from Syria and Turkey had relatively high nucleotide diversity and possessed all the major GluDy alleles, indicating that these populations are probably ancient and not the result of adventive spread. The presence in the Turkish population of both of the shared alleles suggests that hexaploid wheat is likely to have originated in southeast Turkey or northern Syria, within the Fertile Crescent and near to the farming villages at which archaeological remains of hexaploid wheats are first found. A second, more recent, hexaploidisation probably occurred in Iran. [ABSTRACT FROM AUTHOR]

A hybrid neural network model is constructed by characterizing the growth of GaAs1 -yPy-GaAs superlattices (SLs) grown on (001) GaAs substrates by molecular beam epitaxy. These heterostructures are formed by the P2 exposure of an As-stabilized GaAs surface, and a situ high-resolution X-ray diffraction (HRXRD) is performed to determine the phosphorus composition at the interfaces: A first-order kinetic model is then developed to describe the mechanisms of anion exchange, surface desorption, and diffusion. A semi-empirical hybrid neural network is used to estimate the parameters of the kinetic model and analyze the microscopic processes occurring at the interfaces of the mixed anion III-V heterostructures. The phosphorus diffusion process in GaAs is estimated to have a diffusion coefficient of D = 1.4 × 10-14 exp(-0.11 eV/kBTs) cm² ∙ s-1 for samples with PAS4 = 4 × 10-6 torr and exhibits enhanced phosphorus intermixing for samples with lower As-stabilizing fluxes. [ABSTRACT FROM AUTHOR]

Amplified fragment length polymorphism (AFLP) datasets have been used to construct neighbor-joining trees from which monophyletic origins for crops such as einkorn wheat, barley, and emmer wheat have been inferred. We simulated several different multiple domestication scenarios for an imaginary cereal crop and examined the resulting domesticated populations. The simulations showed that the population biology aspects of the domestication process can result in independently domesticated populations merging in such a way that a monophyletic origin is erroneously inferred when the resulting population is examined by AFLP genotyping and neighbor-joining analysis. The results bring into question the use of this method to infer the origins of real crops. [ABSTRACT FROM AUTHOR]

Compares five silica-based methods for their efficiency at extracting DNA from human bones in London, England. Description of the bones used in the study; Discussion on the DNA extraction methods; Precautionary measures used when working with ancient material.