Genome Sequencing of up to 6,000-Year-Old Citrullus Seeds Reveals Use of a Bitter-Fleshed Species Prior to Watermelon Domestication.

Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions. Phylogenomic and population-genomic analyses reveal that (1) much of the nuclear genome of both ancient seeds is traceable to West African seed-use "egusi-type" watermelon (Citrullus mucosospermus) rather than domesticated pulp-use watermelon (Citrullus lanatus ssp. vulgaris); (2) the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh as today found in C. mucosospermus, given alleles in the bitterness regulators ClBT and in the red color marker LYCB; and (3) both ancient genomes showed admixture from C. mucosospermus, C. lanatus ssp. cordophanus, C. lanatus ssp. vulgaris, and even South African Citrullus amarus, and evident introgression between the Libyan seed (UMB-6) and populations of C. lanatus. An unexpected new insight is that Citrullus appears to have initially been collected or cultivated for its seeds, not its flesh, consistent with seed damage patterns induced by human teeth in the oldest Libyan material.

Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication.

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.

A systematic methodology to assess the identity of plants in historical texts: A case study based on the Byzantine pharmacy text John the Physician's Therapeutics.

ETHNOPHARMACOLOGICAL RELEVANCE: In recent decades, the study of historical texts has attracted research interest, particularly in ethnopharmacology. All studies of the materia medica cited in ancient and medieval texts share a concern, however, as to the reliability of modern identifications of these substances. Previous studies of European or Mediterranean texts relied mostly on authoritative dictionaries or glossaries providing botanical identities for the historical plant names in question. Several identities they suggest, however, are questionable and real possibility of error exists. AIM OF THE STUDY: This study aims to develop and document a novel and interdisciplinary methodology providing more objective assessment of the identity of the plants (and minerals) described in these resources. MATERIALS AND METHODS: We developed an iterative experimental approach, using the 13th century Byzantine recipe text John the Physician's Therapeutics in its Commentary version (JC) as a case study. The methodology has six stages and relies on comparative analyses including statistical evaluation of botanical descriptions and information about medicinal uses drawn from both historical and modern sources. Stages 1-4 create the dataset, stage 5 derives the primary outcomes to be reviewed by experts in stage 6. RESULTS: Using Disocorides' De Materia Medica (DMM) (1st century CE) as the culturally related reference text for the botanical descriptions of the plants cited in JC, allowed us to link the 194 plants used medicinally in JC with 252 plants cited in DMM. Our test sample for subsequent analyses consisted of the 50 JC plant names (corresponding to 61 DMM plants) for which DMM holds rich morphological information, and the 130 candidate species which have been suggested in the literature as potential botanical identities of those 50 JC plant names. Statistical evaluation of the comparative analyses revealed that in the majority of the cases, our method detected the candidate species having a higher likelihood of being the correct attribution from among the pool of suggested candidates. Final assessment and revision provided a list of the challenges associated with applying our methodology more widely and recommendations on how to address these issues. CONCLUSIONS: We offer this multidisciplinary approach to more evidence-based assessment of the identity of plants in historical texts providing a measure of confidence for each suggested identity. Despite the experimental nature of our methodology and its limitations, its application allowed us to draw conclusions about the validity of suggested candidate plants as well as to distinguish between alternative candidates of the same historical plant name. Fully documenting the methodology facilitates its application to historical texts of any kind of cultural or linguistic background.

Identification of Dactylopius cochineal species with high-performance liquid chromatography and multivariate data analysis.

Identification of American cochineal species (Dactylopius genus) can provide important information for the study of historical works of art, entomology, cosmetics, pharmaceuticals and foods. In this study, validated species of Dactylopius, including the domesticated cochineal D. coccus, were analysed by high-performance liquid chromatography with a diode array detector (HPLC-DAD) and submitted to multivariate data analysis, in order to discriminate the species and hence construct a reference library for a wide range of applications. Principal components analysis (PCA) and partial least squares discriminant analysis (PLSDA) models successfully provided accurate species classifications. This library was then applied to the identification of 72 historical insect specimens of unidentified species, mostly dating from the 19th century, and belonging to the Economic Botany Collection, Royal Botanic Gardens, Kew, England. With this approach it was possible to identify anomalies in how insects were labelled historically, as several of them were revealed not to be cochineal. Nevertheless, more than 85% of the collection was determined to be species of Dactylopius and the majority of the specimens were identified as D. coccus. These results have shown that HPLC-DAD, in combination with suitable chemometric methods, is a powerful approach for discriminating related cochineal species.

Interpreting materia medica. A case study on Ioannes Archiatrus.

Background: Premodern medical texts are an invaluable source for scholars from humanities and sciences. However, they are usually not accessible as few scientists with an interest in premodern materia medica are also qualified philologists. Therefore, a balance has to be struck to translate these texts while preserving information on how reliable we believe a given translation to be. In this paper, we conduct a case study on the vernacular version of Ioannes archiatrus. Methods: The present study forms part of the output of a multidisciplinary Wellcome Trust Collaborative Award combining humanities and sciences. We deployed a multi-layer tagging system to systematise pharmaceutical terminology and to translate these terms while providing confidence factors for individual words. In a second step, we used AntConc, a freeware concordance software, to analyse our primary source and visualise patterns in the text. Results: Our methodology created a readable text that made it possible for the reader to check confidence factors. It also allows our translation and tagging to be recycled for further research. Conclusions: Our methods provide a tool that allows to balance the need to translate and the necessary caution about translated plant and mineral names. Our approach is transferable and it can be modified to suit the needs of other primary sources.

Pharmaceutical Terminology in Ancient and Medieval Time - andrachne, chrysocolla and Others.

Ancient and medieval pharmacological and medical texts contain a substantial amount of plant and mineral names. In some cases, the identification is straightforward. But for the majority of the data, we are unable to identify these ingredients with high certainty. In this paper, we discuss a selection of plant and mineral names both from a humanities and sciences point of view. In one case, the scientists were even able to examine a plant in situ. The conclusion of our paper is that a close collaboration between sciences and humanities is essential to avoid mistakes in the identification of materia medica.

A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research.

The Andean fever tree (Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82% of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree.

Historical chemical annotations of Cinchona bark collections are comparable to results from current day high-pressure liquid chromatography technologies.

ETHNOPHARMACOLOGICAL RELEVANCE: Species of the genus Cinchona (Rubiaceae) have been used in traditional medicine, and as a source for quinine since its discovery as an effective medicine against malaria in the 17th century. Despite being the sole cure of malaria for almost 350 years, little is known about the chemical diversity between and within species of the antimalarial alkaloids found in the bark. Extensive historical Cinchona bark collections housed at the Royal Botanic Gardens, Kew, UK, and in other museums may shed new light on the alkaloid chemistry of the Cinchona genus and the history of the quest for the most effective Cinchona barks. AIM OF THE STUDY: We used High-Pressure Liquid Chromatography (HPLC) coupled with fluorescence detection (FLD) to reanalyze a set of Cinchona barks originally annotated for the four major quinine alkaloids by John Eliot Howard and others more than 150 years ago. MATERIALS AND METHODS: We performed an archival search on the Cinchona bark collections in the Economic Botany Collection housed in Kew, focusing on those with historical alkaloid content information. Then, we performed HPLC analysis of the bark samples to separate and quantify the four major quinine alkaloids and the total alkaloid content using fluorescence detection. Correlations between historic and current annotations were calculated using Spearman's rank correlation coefficient, before paired comparisons were performed using Wilcox rank sum tests. The effects of source were explored using generalized linear modelling (GLM), before the significance of each parameter in predicting alkaloid concentrations were assessed using chi-square tests as likelihood ratio testing (LRT) models. RESULTS: The total alkaloid content estimation obtained by our HPLC analysis was comparatively similar to the historical chemical annotations made by Howard. Additionally, the quantity of two of the major alkaloids, quinine and cinchonine, and the total content of the four alkaloids obtained were significantly similar between the historical and current day analysis using linear regression. CONCLUSIONS: This study demonstrates that the historical chemical analysis by Howard and current day HPLC alkaloid content estimations are comparable. Current day HPLC analysis thus provide a realistic estimate of the alkaloid contents in the historical bark samples at the time of sampling more than 150 years ago. Museum collections provide a powerful but underused source of material for understanding early use and collecting history as well as for comparative analyses with current day samples.

Assessing Extreme Seed Longevity: The Value of Historic Botanical Collections to Modern Research.

Botanical, historical, and archaeological collections have been the source of extraordinarily long-lived seeds, which have been used to revive extinct genotypes or species. The longest-lived example of a viable seed of known age is the date palm, Phoenix dactylifera L., of which an estimated 2000-year-old seed was germinated in 2005. Seed longevity is important for agriculture and biodiversity conservation, and understanding the basis for the extraordinary longevity of seeds from botanical collections could help improve seed banking technology. In this work, we studied the viability and structural features of date palm seeds collected in Baghdad in 1873 and stored in the Economic Botany Collection (EBC) at the Royal Botanic Gardens, Kew, and seeds collected in 2004 and stored dry at -20°C in the Millennium Seed Bank (MSB). Viability was studied by attempted seed germination and in vitro culture of embryos, and structural features were studied by X-rays, transmission electron microscopy, and differential scanning calorimetry. We found that the seeds preserved in the MSB did not decrease in viability, with ultrastructural features similar to those in freshly harvested seeds. In contrast, the 144-year-old seeds were dead, and large ultrastructural changes were observed, particularly in the storage lipids (size, distribution, and melting properties) and other storage constituents. These results contrast with previous reports that date seeds could remain viable for ∼2000 years in uncontrolled storage environments. We did not find that the postharvest treatment of the EBC seeds in the 19th century, or their storage conditions at Kew, was more deleterious than that which was likely encountered by the ∼2000-year-old seeds. These results highlight the role of well-documented collections in establishing whether reports of extraordinary longevity are ordinarily repeatable.

Economic botany collections: A source of material evidence for exploring historical changes in Chinese medicinal materials.

ETHNOPHARMACOLOGICAL RELEVANCE: Many Chinese medicinal materials (CMMs) have changed over centuries of use, particularly in terms of their botanical identity and processing methods. In some cases, these changes have important implications for safety and efficacy in modern clinical practice. As most previous research has focused on clarifying the evolution of CMMs by analyzing traditional Chinese materia medica ("bencao") literature, assessments of historical collections are needed to validate these conclusions with material evidence. AIM OF THE STUDY: Historical collections of Chinese medicines reveal the market materials in circulation at a given moment in time, and represent an underexploited resource for analyzing the evolution of Chinese herbal medicines. This study compares specimens from a rare collection of CMMs from the 1920s with contemporary market materials; by highlighting examples of changes in botanical identity and processing that remain relevant for safe clinical practice in the modern era, this work aims to stimulate further research into previously unexplored historical collections of Chinese medicines. MATERIALS AND METHODS: 620 specimens of CMMs that were collected from Chinese pharmacies in the Malay peninsula in the 1920s were examined macroscopically and compared with current pharmacopoeia specifications and authentic contemporary samples. These historical specimens, which are stored in the UK in the Economic Botany Collections (EBC) of Royal Botanic Gardens Kew, were morphologically examined, photographed, and compared to authentic CMMs stored at the Bank of China (Hong Kong) Chinese Medicines Center at Hong Kong Baptist University, as well as authentic herbarium-vouchered specimens from the Leon Collection (LC) at the Kew EBC. Case studies were selected to illustrate examples of historical changes in botanical identity, used plant parts, and processing methods. RESULTS: This investigation confirmed that confusion due to shared common names and regional variations in the botanical identity of certain CMMs has been a persistent issue over time. Additionally, historical changes in processing methods and the plant parts used were observed for some CMMs. In some cases, these changes have direct implications for the safe clinical practice of Chinese medicine. CONCLUSIONS: This preliminary assessment illustrated the significant potential of collections for clarifying historical changes in CMMs. More research is needed to investigate pre-modern collections of CMMs, including a more comprehensive assessment of the holdings in the Kew EBC and other European collections that have not yet been explored from the perspective of Chinese medicine.

Gait patterns during different walking conditions in older adults with and without knee osteoarthritis--results from the Baltimore Longitudinal Study of Aging.

Biomechanical analysis of lower extremity activities while walking at different speeds and in challenging conditions may help to identify specific gait patterns associated with knee osteoarthritis (knee-OA). We hypothesized that individuals with asymptomatic knee-OA have lower ankle activity, while individuals with symptomatic knee-OA have similar or higher ankle activity compared to individuals without knee-OA, and that such differences are enhanced during challenging gait tasks. We tested this hypothesis by examining gait characteristics in multiple gait tasks using data from 153 Baltimore Longitudinal Study of Aging (BLSA) participants (112 without knee-OA, 41 with knee-OA; 53-87 years, 52% women). All participants who could walk unassisted were evaluated in the BLSA gait lab while walking at self-selected speed (usual-walking), at maximum speed (fast-walking) and again at self-selected speed after 30-min of walking activities (usual-walking-after-30 min). Knee range of motion was lower for knee-OA participants in the fast-walking and usual-walking-after-30 min tasks (p<0.030). Ankle range of motion for symptomatic knee-OA was greater compared to asymptomatic knee-OA for all walking tasks (p<0.050). Symptomatic knee-OA had greater generative MWE of the ankle compared to asymptomatic knee-OA (p=0.034), while keeping similar absorptive MWE of the knee when compared to no-OA controls (p=0.151). Symptomatic knee-OA individuals seem to adapt an ankle kinematic gait pattern aimed at avoiding knee pain, by enhancing forward propulsion so to minimize knee joint load. Whether these conditions represent subsequent steps in the causal pathway from knee-OA to changes in gait is still not clear.

Association of periodontitis and metabolic syndrome in the Baltimore Longitudinal Study of Aging.

BACKGROUND AND AIMS: Metabolic syndrome (MetS) comprises central obesity, insulin resistance, hypertension and dyslipidemia, interrelated metabolic risk factors for diabetes and cardiovascular disease. A state of low-grade systemic inflammation may underlie this constellation of risk factors. Chronic inflammatory conditions, such as periodontal disease, may contribute to systemic inflammation and development of MetS. This study examines the association of periodontitis with MetS with and without consideration of systemic inflammatory status. METHODS: The association of alveolar bone loss (none/slight vs moderate/severe) determined from panoramic radiographs and MetS parameters were analyzed using logistic regression, adjusting for age, sex, ethnicity, and smoking in 112 men and 78 women (mean+/-SD age 56.7+/-13.3 and 60.0+/-12.1, respectively) participating in the Baltimore Longitudinal Study of Aging. RESULTS: Participants with radiographic evidence of moderate to advanced alveolar bone loss were significantly more likely to have MetS than those with minimal or no bone loss (OR 2.61, 95% CI 1.1-6.1, p<0.05). No significant differences in systemic inflammation were found between periodontal groups. CONCLUSIONS: The association of alveolar bone loss to MetS is consistent with the hypothesis that destructive periodontal disease may contribute to the development of MetS and elevations in systemic inflammation. Longitudinal studies are necessary to clarify the role of periodontal disease in the development of MetS and conditions associated with chronic inflammation.

Fourier-transform Raman characterization of brazilwood trees and substitutes.

In this work we have applied Fourier-transform Raman spectroscopy to the analysis of several archival samples of brazilwoods from different geographical origins and of different ages. Samples of Caesalpinia echinata Lam. (from Brazil, South America), Caesalpinia sappan L. (East Indies, Asia), Haematoxylum brasiletto Karsten (Central America) and Haematoxylum campechianum L. (North America) were analysed in order to isolate key Raman biomarker bands which could provide the basis for an identification protocol. Previously recorded Raman spectra of brazilin and brazilein pigments extracted from genuine brazilwood of Brazilian origin provided a foundation for the nondestructive spectral discrimination between a sample of false 'brazilwood', which consisted of an inferior wood substratum stained with genuine pigment, and the true specimens. The provision of well-documented specimens of determinable age from the archival collection facilitated the evaluation of the effects of temporal degradation on the observed spectra, which could be used to further test the experimental protocols for nondestructive verification of samples in the archive with questionable assignment or provenance.