Textiles from Mexico and Central America in the Collections of the Náprstek Museum

Introduction

Most studies on the molecular biology and functional analysis of vesicular stomatitis virus Indiana 1 serotype (VSV-IN1) are based on the only full-length genomic sequence currently deposited in GenBank. This sequence is a composite of several VSV-IN1 laboratory strains passaged extensively in tissue culture over the years and it is not certain that this sequence is representative of strains circulating in nature. We describe here the complete genomic sequence of three natural isolates, each representing a distinct genetic lineage and geographical origin: 98COE (North America), 94GUB (Central America) and 85CLB (South America). Genome structure and organization were conserved, with a 47 nucleotide 3' leader, five viral genes -- N, P, M, G and L -- and a 59 nucleotide 5' trailer. The most conserved gene was N, followed by M, L and G, with the most variable being P. Sequences containing the polyadenylation and transcription stop and start signals were completely conserved among all the viruses studied, but changes were found in the non-transcribed intergenic nucleotides, including the presence of a trinucleotide at the M-G junction of the South American lineage isolate. A 102-189 nucleotide insertion was present in the 5' non-coding region of the G gene only in the viruses within a genetic lineage from northern Central America. These full-length genomic sequences should be useful in designing diagnostic probes and in the interpretation of functional genomic analyses using reverse genetics.

Geographic Origin may Affect Outcomes for Hispanic Patients with Non-Small Cell Lung Cancer in the United States

The Codex Alimentarius Commission defines honey as: “… the natural sweet substance produced by honey bees from the nectar of plants … which the bees collect, transform by combining with specific substances of their own, deposit, dehydrate, store and leave in the honey comb to ripen and mature”. Honey, produced in all regions of the world varies widely in its chemical and physical properties, which depend on the plants the bees visit and on the species of Apis themselves. The Codex sets standards for the composition of honeys, levels of contaminants permitted, and the correct labelling according to floral source and geographic origin. The growth of stingless bee (Meliponidae) domestication in Central and South America, Asia and Australia has led to another significant source of honey, which is very variable in its properties. Here I review of the properties of honeys and the techniques used to analyze the geographical, entomological and botanical origins of honey, discuss some of the properties and features of the honeys made by the stingless bees, and discuss unusual honeys, the so-called “mad honeys”, made from nectar containing toxic compounds, and the effect of toxic nectar on bees (bumble bees) and humans.

Aim Geographic affinities were analysed for nodule bacteria (Bradyrhizobium sp. Jordan) associated with two legume trees indigenous to the Philippines: Pterocarpus indicus (Papilionoideae) and Wallaceodendron celebicum (Mimosoideae).Location Nodule bacteria from Luzon, the Philippines, were compared with reference strains from Central America, eastern North America, Japan, Korea, China and Australia.Methods Two PCR assays targetting length polymorphisms in the rRNA region were carried out on 96 Philippine bacterial isolates. A 496‐bp portion of the 23S rRNA gene was sequenced in 14 representative isolates. Eight strains were analysed in greater depth by sequencing portions of four other genes (16S rRNA [1410 bp], dnaK [603 bp], nifD [822 bp], recA [512 bp]), and phylogenetic trees were constructed by maximum parsimony, neighbour joining and maximum likelihood methods.Results Most of the Philippine Bradyrhizobium strains showed greater similarity to reference strains from Central America than to strains from other source regions included in the analysis. However, phylogenetic trees for the five genes had significantly conflicting topologies, suggesting that lateral gene transfer events had altered genealogical relationships at different loci. In particular, two Philippine strains resembled Bradyrhizobium strains from Central America or China for 16S rRNA, dnaK and recA sequences, but had nifD sequences that clustered with Australian strains (with bootstrap support values of 90–96%).Main conclusions The Philippines have been colonized by Bradyrhizobium strains from multiple source regions. Subsequent lateral gene transfer has resulted in the evolution of Bradyrhizobium strains that combine DNA segments of different geographic origin.

Data on suicidal behaviour in Central and South America has derived from mortality statistics. Suicide rates in most countries of Central and South America are considerably lower than in North America and Europe. The recent increase in suicide rates particularly afflicts young people. An increase in suicide rates have also been reported among indigenous groups, and seem to be related to extreme pressure exerted by Western society, self-devaluation and alcohol misuse. A WHO worldwide initiative for the prevention of suicide (SUPRE-MISS) multi-centre study estimated the life prevalence of suicidal behaviour in a large Brazilian city at 17.1 per cent for suicidal ideation, 4.8 per cent for plans and 2.8 per cent for suicide attempts. Urban violence and high homicide rates have overshadowed the problem of suicidal behaviour in Latin American countries. It is only recently that awareness of suicidal behaviour among adolescents and young adults, as well as violence (including suicide) and prevention policies have received government attention. Apart from Brazil, most countries in that part of the world lack national suicide prevention programmes, however actions are underway in Chile and Argentina.

The physicochemical properties and composition of honey may vary depending on its botanical and geographical origin, bee species, ratio of nectar, vegetation type, flowering period, foraging insect species, beekeepers' production techniques and timing of honey collection, and packaging and storage conditions of honey. In this study, some physicochemical properties of flower (F1, F2, F3 and F4) and pine (P1, P2, P3 and P4) honeys from different geographical origin (Antalya in Türkiye, Hessen in Germany and Lisbon in Portugal) were determined. The average °Brix, pH, and electrical conductivity (EC) values were 82.73, 4.28, and 0.44 mS/cm, respectively, with the ranges of 81.60-84.43 for °Brix, 3.79-4.85 for pH, and 0.15-0.68 mS/cm for EC. The color characteristics of honey were influenced by its botanical source and composition with the averages for CIE L*, a*, and b* were 24.29, 5.74, and 4.26, respectively. The flower and pine honey samples showed distinct UV-vis spectral profiles, especially in the 200-350 nm range, with differences attributed to their chemical composition, including sugar and phenolic contents. On the other hand, FTIR spectroscopy revealed similar spectral patterns for pine and flower honeys indicating shared functional groups and chemical structures in both honey types. Pine honey samples had significantly higher antioxidant activity values due to their phenolic contents (p

Caffeine content is a crucial attribute of coffee. Its concentration and thus maximum cups of Coffea arabica from Africa, Asia, Central America, and South America from different altitudes of growing areas, altitude, and process using different post-harvest processing (dry, wet, and pulped natural). Our results suggest that geographical origin might affect the alkaloid concentration in C. arabica. The caffeine concentration pattern in green samples was as follows: Central America > South America > Asia > Africa. Altitude affected the concentrations, lowlands > midlands > highlands, however, not significantly. Given caffeine is thermostable, the medium roasting process did not affect the concentration of caffeine directly, but a small increase was observed. Scientific opinion on the safety of habitual caffeine consumption of up to 400 mg per day does not raise safety concerns for non-pregnant adults. A cup (7 g coffee in 120 mL of water) was used for recalculation. Results suggest that mostly highlands and midlands coffee from Africa reached levels of caffeine that might be consumed in more than 5.5 cups a day.

Invited Commentary on ‘A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains’, Preston et al. The genome of Plasmodium falciparum 3D7 parasite has been sequenced, and genes from the parasite genome have been used extensively in vaccine development and other studies. One of the questions frequently asked in the malaria research community is where does the 3D7 parasite come from? The parasite was derived from the NF54 isolate initially obtained from a patient living near Schiphol Airport, Amsterdam, who had never left the Netherlands,1 and the origin of this parasite has been a mystery. A recent publication by Preston et al. in Nature Communications2 suggests that the 3D7 parasite originated from Africa. In the study, the authors analyzed the mitochondrion (mt) and apicoplast (apico) genomes of 711 P. falciparum isolates from 14 countries in West Africa, East Africa, Southeast Asia, Oceania, and South America, including the 3D7 parasites, and identified 151 and 488 single nucleotide polymorphisms (SNPs) from the mt and apico genomes, respectively. Clustering analyses of the SNPs revealed grouping of parasites by their geographic origin, similar to results using genome-wide microsatellites,3 genome-wide SNPs4 or mt polymorphisms.5 The dataset used in this study was larger than the dataset used in the previous analysis of the mt genome, and the lack of recombination in mt and apico genomes provided greater power for identifying the parasite origins than genetic makers from the nuclear genome. Among the 290 distinct haplotypes generated from the combined 639 SNPs, 282 (97.2%) were observed in one region only, which allowed prediction of parasite origins with ∼95% accuracy. The authors then identified 23 SNPs that had high prediction value and developed a SNP barcode that had a predictive accuracy of 92%. Haplotype analysis using the barcoded SNPs clearly placed the 3D7 parasite with African parasites. The absence of parasites from India, Central America, Southern Africa, and the Caribbean in this study indicates that these regions cannot be unequivocally ruled out as a source of 3D7; however, previous studies clearly showed that 3D7 is markedly different from parasites of Central America or South Africa.,3,5 The haplotype analysis also supports a hypothesis of P. falciparum radiation from Africa.5 In addition to the barcode for parasite identification, the large dataset also allowed testing of recombination of the maternally inherited elements. Interestingly, the two organelles were found to be mostly co-inherited, supporting previous theoretical prediction based on parasite gametocytogenesis. Intriguingly, the two co-inherited organelles appeared to experience different selection pressures. The mt genome had more synonymous (S) than non-synonymous (NS) substitutions, whereas the apico had more NS than S substitutions. Pressures from anti-malarial drugs may play a role in the high NS/S ratio of the apico SNPs, although these differences may also point to other unknown mechanisms. This SNP barcode will be useful for tracing parasite origins. Building on the promising results from this study, it would be useful to collect and analyze more samples from additional endemic regions such as India and Central America to establish a global database for tracing parasite origins of future outbreaks. For discriminating local isolates, additional markers of high variability such as microsatellites may be required.

A study of 100 MZ and 67 DZ twin pairs aged 18 to 25 years has shown a highly significant genetic contribution to the following measurements: standing and sitting height; height on tragus; arm length; biacromial, biiliac, and bitrochanteric diameter; weight; circumference of thigh and of upper arm relaxed and contracted; and head length and breadth. The twins were brought up together and of the same socioeconomical, geographical, ethnical, and cultural origin. Zygosity diagnosis was based on 22 to 26 blood groups. The means of the measurements were smaller in MZ than in DZ twins, some of them significantly so. The intraclass correlation coefficients of the MZ cotwins were all significant and greater than those of the DZ cotwins. In families of same geographical origin, sib-sib correlations were somewhat smaller than those of the DZ cotwins, but for the three diameters of the body the order was reversed.

Munamochibashira (base-to-ridge-posts) are posts that rise from the ground to directly support the ridge. They are an important object of study in examining the origin, transformation, and spread of an architectural culture. It is already known that buildings with base-to-ridge-posts exist in vernacular architecture from research in Asia and Europe, but this type of building in Central America has not been discussed in previous studies. In 2013, we conducted a field study in Central America and observed this type of building. In Mexico, we frequently found buildings with base-to-ridge-posts in vernacular architecture. Moreover, we found buildings of this type: 1) among wooden buildings designated as UNESCO’s World Heritage Sites on the American continent; 2) in villages around Tapalpa, about 120 km from Guadalajara; and 3) in academic books and research reports in Spanish that we obtained in Mexico and reports in Spanish or English collected afterwards. In this paper, we report the findings of our field and literature studies concerning buildings with base-to-ridge-posts among structures made by the indigenous people of Mexico. We will also demonstrate that the origin of buildings with base-to-ridge-posts on the American continents could be Asia or Europe. Since we directly observed buildings with base-to-ridge-posts in Mexico and established that there are base-to-ridge-post styles of architecture on the American continents, we claim that the continents are part of cultural areas that have buildings with base-to-ridge posts. Consequently, we maintain that Central America is a highly important field of study in investigating the history of buildings with base-to-ridge-posts from the prehistoric era on a worldwide scale.

Stable isotope analysis for green coffee bean: A possible method for geographic origin discrimination

Aromatic hot peppers ( Capsicum chinense Jacq.) are an important agricultural commodity for many small-scale farmers in the Caribbean because it is a commercially viable crop and one that is integral to the cuisines of the region. The large variation in fruit shape, size, color, pungency, and aroma of this species facilitates a diverse range of uses. Using 264 accessions from a Caribbean germplasm collection (representing primarily the Caribbean Basin, Central and South America), this study investigated 1) morphological variation in 13 fruit descriptors of agro-economic importance; and 2) morphological groups based on geographic origin. All 13 fruit descriptors showed significant variation. Fruit color [immature (six states) and mature (12 states)] was the most diverse qualitative fruit trait. Among the quantitative traits, fruit weight and fruit width showed the highest broad-sense heritability (0.81), and fruit weight was highly correlated with fruit width and placenta size. Cluster analysis revealed four main clusters, which did not show a clear separation of accessions based on major geographic regions, but there was a highly significant association ( P < 0.0001) between geographic subgroups and the clusters to which they were assigned. Most accessions of the Northern Caribbean (particularly the Bahamas and Puerto Rico) separated quite distinctly from most accessions of the Southern Caribbean and clustered with most accessions of Central and South America. Accessions of the Southern Caribbean (Lesser Antilles, Trinidad & Tobago) were substantially more similar to each other than they were to most accessions of Central and South America, thereby suggesting genetic differences between accessions of the Southern Caribbean islands and the mainland populations. Collectively, the results show that this germplasm collection contains useful accessions with desired fruit quality traits and a level of genetic variation that can be used to encourage its active conservation and use for further evaluation trials and crop improvement as well as guide ongoing complementary germplasm introductions to augment the collection’s diversity.

Authentication of coffee is highly required. This study aimed to understand the relative abundance of volatiles of green coffee harvested during two years. Using volatiles (GC-MS) and Linear Discriminant Analysis, we focused on the geographical origin identification. We analyzed samples of green Coffea arabica from Africa, Central America, and South America, harvested in 2018 and the same samples harvested in 2019. A total of 215 different volatiles were detected. Based on their chemical structure and the functional chemical group, they were divided into categories: furan derivates, aldehydes, ketones, alcohols, organic acids, hydrocarbons (alkanes, alkenes, alkynes, aromatic hydrocarbons), terpenoids, heterocyclic compounds, nitriles, amines. Green Arabica contained mostly organic acids and esters, aldehydes, hydrocarbons, and alcohols. We observed significant differences in aromatic hydrocarbons and furan derivates by comparing the volatiles profiles of African coffee beans collected in 2018 and 2019. The profile of Central American samples (both years) was homogenous; thus, no significant differences were observed. The aroma profile of South American coffees had significant differences in aromatic hydrocarbons and alkanes (p-value < 0.05). Rao’s approximation and Bartlett’s test proved a significant difference between 3 continents by applying LDA. More than 94% of the variability between Africa, Central, and South America coffees harvested in 2018 was explained by organic acids and esters, alkenes, aldehydes, and ketones. By adding samples from 2019, LDA calculations reduced input parameters to aldehydes and ketones, organic acids and esters, alkenes, terpenoids, and aldehydes. These appear to be useful for geographical authentication regardless of the year of harvesting.

Cucurbita moschata (Duchesne ex Lam.) Duchesne ex Poir. is an important crop in tropical areas. In Spain, the cultivation of this species is mainly based on landraces maintained for centuries. The Center for Conservation and Breeding of Agricultural Diversity (COMAV) maintains a germplasm collection with about 250 C. moschata landraces, primarily from the Canary Islands and the Spanish peninsula, including some accessions from Central and South America. The morphological characterization of 47 accessions showed considerable variability, comparable to that found in different C. moschata centers of diversity. Molecular analysis using AFLP (amplified fragment length polymorphism) markers, which analyze neutral genetic diversity, and SRAP (sequence‐related amplified polymorphism) markers, which preferentially amplify gene regions, showed a genetic diversity concordant with the morphological variability. With both markers, the accessions clustered according to geographical origin: Central America, South America, and Spain, suggesting the existence of two independent domestications in both American areas, and/or introgressions from related species. In the principal coordinate analysis (PCoA), the Central and South American accessions grouped together by AFLPs, separately from the Spanish ones, while with SRAP the South American accessions grouped separately from the other accessions. This could be due to the different information provided by each marker system. The SRAP results agree with the more primitive traits showed by the South American landraces. In addition, the accessions from the Canary Islands grouped separately from those from the Spanish peninsula. This divergence could be due to an earlier adaptation of C. moschata to the tropical climate of the islands, together with a differential germplasm introduction from America.