Geographic origin shapes the adaptive divergences of Rotaria rotatoria (Rotifera, Bdelloidea) to thermal stress: Insights from ecology and transcriptomics

Global warming has raised concerns regarding the potential impact on aquatic biosafety and health. To illuminate the adaptive mechanisms of bdelloid rotifers in response to global warming, the ecological and transcriptomic characteristics of two strains (HX and ZJ) of Rotaria rotatoria were investigated at 25°C and 35°C. Our results showed an obvious genetic divergence between the two geographic populations. Thermal stress significantly reduced the average lifespan of R. rotatoria in both strains, but increased the offspring production in the ZJ strain. Furthermore, the expression levels of genes Hsp70 were significantly upregulated in the HX strain, while GSTo1 and Cu/Zn-SOD were on the contrary. In the ZJ strain, the expression levels of genes Hsp70, CAT2, and GSTo1 were upregulated under thermal stress. Conversely, a significant decrease in the expression level of the Mn-SOD gene was observed in the ZJ strain under thermal stress. Transcriptomic profiling analysis revealed a total of 105 and 5288 differentially expressed genes (DEGs) in the HX and ZJ strains under thermal stress, respectively. The PCA results showed clear differences in gene expression pattern between HX and ZJ strains under thermal stress. Interestingly, compared to the HX strain, numerous downregulated DEGs in the ZJ strain were enriched into pathways related to metabolism under thermal stress, suggesting that rotifers from the ZJ strain prioritize resource allocation to reproduction by suppressing costly metabolic processes. This finding is consistent with the life table results. This study provides new insights into the adaptive evolution of aquatic animals in the context of global climate change.

Diversity of Human T-Lymphotropic Virus Type 1 Cosmopolitan Subtype (HTLV-1a) Circulating in Infected Residents in Portugal

Human T-cell lymphotropic virus type 1 (HTLV-1) prevalence in Portugal is low and mainly affects immigrants from endemic areas where human immunodeficiency virus (HIV) infection represents a public health problem. Despite the majority of HTLV-1-infected individuals remains asymptomatic, severe pathologies may develop after prolonged viral persistence, namely an aggressive form of leukemia. An increased mortality rate and faster progression to death is often related to HTLV-1/HIV coinfection. Nevertheless, studies showed that some antiretrovirals used in HIV treatment lead to a positive immune response against HTLV-1. This study aimed to analyze epidemiological and clinical data, and to assess the diversity of HTLV-1 strains circulating in infected residents diagnosed in the Portuguese national reference laboratory between 2010 and 2021. Long terminal repeat and env proviral sequences derived from 20 individuals were used to generate phylogenetic trees along with multiples reference sequences from different geographic origins retrieved from the database. Three samples belong to Portuguese natives and 17 belong to immigrants: 15 from several countries of Africa, 1 from South America, and 1 from Europe; 6 patients (30%, mean age 40.3 years) showed HTLV-1-related diseases, and 6 (30%, mean age 45.2 years) were coinfected with HIV/AIDS. The results show that the Cosmopolitan subtype is circulating in Portugal, with 10 sequences being classified as subgroup A, that include Portuguese and natives from S. Tomé and Príncipe with a mean age of 39.4 years, and 10 sequences that segregated into the Senegal cluster derived from natives born in Guinea-Bissau with a mean age of 43.5 years. A high proportion of HTLV-1-related diseases and HIV/AIDS coinfection was observed. Risk behavior practices and the absence of specific control measures, including diagnostic and treatment, may contribute to a silent dissemination of a broad diversity of HTLV-1 strains and, therefore, the increased rate of progression to debilitating diseases. In this manner, an early diagnostic and a molecular surveillance of HTLV-1 transmission remains necessary in Portugal.

Fatty Acid Profiling as a Tool for Fostering the Traceability of the Halophyte Plant Salicornia ramosissima and Contributing to Its Nutritional Valorization

Salicornia ramosissima, commonly known as glasswort or sea asparagus, is a halophyte plant cultivated for human consumption that is often referred to as a sea vegetable rich in health-promoting n-3 fatty acids (FAs). Yet, the effect of abiotic conditions, such as salinity and temperature, on the FA profile of S. ramosissima remains largely unknown. These factors can potentially shape its nutritional composition and yield unique fatty acid signatures that can reveal its geographical origin. In this context, samples of S. ramosissima were collected from four different locations along the coastline of mainland Portugal and their FAs were profiled through gas chromatography-mass spectrometry. The lipid extracts displayed a high content of essential FAs, such as 18:2n-6 and 18:3n-3. In addition to an epoxide fatty acid exclusively identified in samples from the Mondego estuary, the relative abundance of FAs varied between origin sites, revealing that FA profiles can be used as site-specific lipid fingerprints. This study highlights the role of abiotic conditions on the nutritional profile of S. ramosissima and establishes FA profiling as a potential avenue to trace the geographic origin of this halophyte plant. Overall, the present approach can make origin certification possible, safeguard quality, and enhance consumers' trust in novel foods.

Chemical Composition and Biological Activities of Essential Oils from Origanum vulgare Genotypes Belonging to the Carvacrol and Thymol Chemotypes

The remarkable biological activities of oregano essential oils (EOs) have recently prompted a host of studies aimed at exploring their potential innovative applications in the food and pharmaceutical industries. The chemical composition and biological activities of EOs from two Origanum vulgare genotypes, widely cultivated in Sicily and not previously studied for their biological properties, were characterized. Plants of the two genotypes, belonging to the carvacrol (CAR) and thymol (THY) chemotypes and grown in different cultivation environments, were considered for this study. The chemical profiles, including the determination of enantiomeric distribution, of the EOs, obtained by hydrodistillation from dried leaves and flowers, were investigated by GC-MS. Biological activity was evaluated as antimicrobial properties against different pathogen indicator strains, while intestinal barrier integrity, reduction in pathogen adhesion and anti-inflammatory actions were assayed in the intestinal Caco-2 cell line. The chemical profile of the CAR genotype was less complex and characterized by higher levels of the most active compound, i.e., carvacrol, when compared to the THY genotype. The enantiomeric distribution of chiral constituents did not vary across genotypes, while being markedly different from that observed in Origanum vulgare genotypes from other geographical origins. In general, all EOs showed high antimicrobial activity, both in vitro and in a food matrix challenge test. Representative EOs from the two genotypes resulted not altering epithelial monolayer sealing only for concentrations lower than 0.02%, were able to reduce the adhesion of selected pathogens, but did not exert relevant anti-inflammatory effects. These results suggest their potential use as control agents against a wide spectrum of foodborne pathogens.

Geographic Differentiation of Essential Oil from Rhizome of Cultivated Atractylodes lancea by Using GC-MS and Chemical Pattern Recognition Analysis

The rhizome of Atractylodes lancea (RAL) is a well-known Chinese herbal medicine (CHM) that has been applied in clinical settings for thousands of years. In the past two decades, cultivated RAL has gradually replaced wild RAL and become mainstream in clinical practice. The quality of CHM is significantly influenced by its geographical origin. To date, limited studies have compared the composition of cultivated RAL from different geographical origins. As essential oil is the primary active component of RAL, a strategy combining gas chromatography-mass spectrometry (GC-MS) and chemical pattern recognition was first applied to compare the essential oil of RAL (RALO) from different regions in China. Total ion chromatography (TIC) revealed that RALO from different origins had a similar composition; however, the relative content of the main compounds varied significantly. In addition, 26 samples obtained from various regions were divided into three categories by hierarchical cluster analysis (HCA) and principal component analysis (PCA). Combined with the geographical location and chemical composition analysis, the producing regions of RAL were classified into three areas. The main compounds of RALO vary depending on the production areas. Furthermore, a one-way analysis of variance (ANOVA) revealed that there were significant differences in six compounds, including modephene, caryophyllene, γ-elemene, atractylon, hinesol, and atractylodin, between the three areas. Hinesol, atractylon, and β-eudesmol were selected as the potential markers for distinguishing different areas by orthogonal partial least squares discriminant analysis (OPLS-DA). In conclusion, by combining GC-MS with chemical pattern recognition analysis, this research has identified the chemical variations across various producing areas and developed an effective method for geographic origin tracking of cultivated RAL based on essential oils.

through surfaced enhanced Raman spectrometry and machine learning algorithms

The leaves of Morus alba Linn., which is also known as white mulberry, have been commonly used in many of traditional systems of medicine for centuries. In traditional Chinese medicine (TCM), mulberry leaf is mainly used for anti-diabetic purpose due to its enrichment in bioactive compounds such as alkaloids, flavonoids and polysaccharides. However, these components are variable due to the different habitats of the mulberry plant. Therefore, geographic origin is an important feature because it is closely associated with bioactive ingredient composition that further influences medicinal qualities and effects. As a low-cost and non-invasive method, surface enhanced Raman spectrometry (SERS) is able to generate the overall fingerprints of chemical compounds in medicinal plants, which holds the potential for the rapid identification of their geographic origins. In this study, we collected mulberry leaves from five representative provinces in China, namely, Anhui, Guangdong, Hebei, Henan and Jiangsu. SERS spectrometry was applied to characterize the fingerprints of both ethanol and water extracts of mulberry leaves, respectively. Through the combination of SERS spectra and machine learning algorithms, mulberry leaves were well discriminated with high accuracies in terms of their geographic origins, among which the deep learning algorithm convolutional neural network (CNN) showed the best performance. Taken together, our study established a novel method for predicting the geographic origins of mulberry leaves through the combination of SERS spectra with machine learning algorithms, which strengthened the application potential of the method in the quality evaluation, control and assurance of mulberry leaves.

Genetic Signature of Pinctada fucata Inferred from Population Genomics: Source Tracking of the Invasion in Mischief Reef of Nansha Islands

Among the anthropogenic stresses that marine ecosystems face, biological invasions are one of the major threats. Recently, as a result of increasingly intense anthropogenic disturbance, numerous marine species have been introduced to their non-native ranges. However, many introduced species have uncertain original sources. This prevents the design and establishment of methods for controlling or preventing these introduced species. In the present study, genomic sequencing and population genetic analysis were performed to detect the geographic origin of the introduced Pinctada fucata population in the Mischief Reef of the South China Sea. The results of population genetic structure analysis showed a close relationship between the Mischief Reef introduced population and the Lingshui population, indicating that Lingshui may be the potential geographical origin. Furthermore, lower heterozygosity and nucleotide diversity were observed in the introduced population in Mischief Reef, indicating lower genetic diversity than in other native populations. We also identified some selected genomic regions and genes of the introduced population, including genes related to temperature and salinity tolerance. These genes may play important roles in the adaptation of the introduced population. Our study will improve our understanding of the invasion history of the P. fucata population. Furthermore, the results of the present study will also facilitate further control and prevention of invasion in Mischief Reef, South China Sea.

Geographical discrimination of Cyclocarya paliurus tea for origin traceability based on multielement analysis by ICP-OES and chemometrics multivariate

Objective

This paper focused on the geographical discrimination of Cyclocarya paliurus tea for origin traceability based on multielement analysis by ICP-OES and chemometrics multivariate.

Methods

In this study, eleven trace element concentrations were determined by ICP-OES and processed by multivariate statistical analysis.

Results

Based on ANOVA, the mean concentrations of 10 elements except Co differed significantly among six origins. Pearson's correlation analysis showed that 11 pairs of elements have a positive significant correlation and 12 pairs have a negative significant correlation. The geographical origins were effectively differentiated using the eleven elements combined with PCA. And the S-LDA model offered a 100% differentiation rate.

Conclusion

The overall results suggested that the combination of multielement analysis by ICP-OES and chemometrics multivariate could trace the geographical origins of tea. And the paper can provide reference for quality control and quality evaluation of C. paliurus in the future.

Life History Traits of Sperm Whales Physeter macrocephalus Linnaeus, 1758 Stranded along Italian Coasts (Cetartiodactyla: Physeteridae)

We investigated the relationship between age and body length, and age at sexual maturity of Physeter macrocephalus individuals stranded along the Italian coast. Our molecular analysis shows that all our samples belong to the C.001.002 haplotype, shared between Atlantic and Mediterranean populations. We show that males attain sexual maturity at 10 years, similar to those from other marine areas. However, considering the same body length class, Mediterranean males are older than Atlantic ones. Our finding of a Mediterranean pregnant female of only 6.5 m in length and an assessed age of 24-26 years is particularly noteworthy, considering that females reach sexual maturity at about 9 years and 9 m of total length in other regions. Comparing our results with the literature data, we highlight the positive correlation between lifespan, adult body length and weight of males from the Mediterranean and Atlantic Ocean. Regardless of whether the relatively small size of Mediterranean specimens is a consequence of an inbreeding depression or an adaptation to less favorable trophic conditions, we recommend to closely monitor this population from a conservation perspective. In fact, its low genetic diversity likely corresponds to a relatively limited ability to respond to environmental changes compared with other populations.

Study of Inter- and Intra-varietal Genetic Variability in Grapevine Cultivars

Vitis vinifera includes a large number of cultivars that are further distinguished in biotypes and clones, and it is actually hard to differentiate them, even through complex molecular techniques. In this work, the plant materials of 56 putative Sangiovese and 14 putative Montepulciano biotypes, two of the most widespread black-berried Italian cultivars, were collected in different wine-growing areas of Italy distributed in 13 regions, from north to south. Firstly, the samples were analyzed using SSR markers to have proper varietal identification. According to the results, the genotypes belonged to three different cultivars: Sangiovese, Sanforte, and Montepulciano. Subsequently, the samples were investigated using AFLP, SAMPL, M-AFLP, and I-SSR molecular markers to estimate their intra-varietal genetic variability. The DNA marker-based method used turned out to be performing to bring out the geographic differences among the biotypes screened, and it can therefore be considered as a powerful tool available for all the grapevine varieties.

Comprehensive Betalain Profiling of Djulis (Chenopodium formosanum) Cultivars Using HPLC-Q-Orbitrap High-Resolution Mass Spectrometry

Betalains are water-soluble pigments that may be used as alternatives to artificial colorants in the food industry. In addition, the betalain profile may be of taxonomic significance to some higher plants. Djulis (Chenopodium formosanum) is an emerging crop grown by Taiwan aboriginal communities, and its various cultivars contain different betalain compositions. To develop an authenticity method for evaluating djulis cultivars, we performed comprehensive betalain profiling with HPLC-Q-Orbitrap high-resolution mass spectrometry (HRMS). An HRMS method for betalain annotation was developed and used to identify 68 betalains, including 10 betacyanins, 24 betacyanin derivatives, and 34 betaxanthins. The profile of betacyanins and their derivatives could be utilized to classify different cultivars of djulis, while betaxanthins were less informative. Furthermore, the betalain profiles were indicative of the geographic origin of djulis. This HRMS method and analytical platform for betalains may be helpful to guide further investigations of natural pigments in other plants.

Geographic Origin Discrimination of Millet Using Vis-NIR Spectroscopy Combined with Machine Learning Techniques

Millet is a primary food for people living in the dry and semi-dry regions and is dispersed within most parts of Europe, Africa, and Asian countries. As part of the European Union (EU) efforts to establish food originality, there is a global need to create Protected Geographical Indication (PGI) and Protected Designation of Origin (PDO) of crops and agricultural products to ensure the integrity of the food supply. In the present work, Visible and Near-Infrared Spectroscopy (Vis-NIR) combined with machine learning techniques was used to discriminate 16 millet varieties (n = 480) originating from various regions of China. Five different machine learning algorithms, namely, K-nearest neighbor (K-NN), Linear discriminant analysis (LDA), Logistic regression (LR), Random Forest (RF), and Support vector machine (SVM), were used to train the NIR spectra of these millet samples and to assess their discrimination performance. Visible cluster trends were obtained from the Principal Component Analysis (PCA) of the spectral data. Cross-validation was used to optimize the performance of the models. Overall, the F-Score values were as follows: SVM with 99.5%, accompanied by RF with 99.5%, LDA with 99.5%, K-NN with 99.1%, and LR with 98.8%. Both the linear and non-linear algorithms yielded positive results, but the non-linear models appear slightly better. The study revealed that applying Vis-NIR spectroscopy assisted by machine learning technique can be an essential tool for tracing the origins of millet, contributing to a safe authentication method in a quick, relatively cheap, and non-destructive way.

Microbiome in Blood Samples From the General Population Recruited in the MARK-AGE Project: A Pilot Study

The presence of circulating microbiome in blood has been reported in both physiological and pathological conditions, although its origins, identities and function remain to be elucidated. This study aimed to investigate the presence of blood microbiome by quantitative real-time PCRs targeting the 16S rRNA gene. To our knowledge, this is the first study in which the circulating microbiome has been analyzed in such a large sample of individuals since the study was carried out on 1285 Randomly recruited Age-Stratified Individuals from the General population (RASIG). The samples came from several different European countries recruited within the EU Project MARK-AGE in which a series of clinical biochemical parameters were determined. The results obtained reveal an association between microbial DNA copy number and geographic origin. By contrast, no gender and age-related difference emerged, thus demonstrating the role of the environment in influencing the above levels independent of age and gender at least until the age of 75. In addition, a significant positive association was found with Free Fatty Acids (FFA) levels, leukocyte count, insulin, and glucose levels. Since these factors play an essential role in both health and disease conditions, their association with the extent of the blood microbiome leads us to consider the blood microbiome as a potential biomarker of human health.

Determination of geographical origin of concentrated apple juice through analysis of stable isotopic and mineral elemental fingerprints: preliminary results

BACKGROUND

With increasing attention being paid to food authenticity, the geographic origin of food has become a topic of interest for both consumers and producers. As far as we know, there are relatively few studies on the origin traceability of concentrated apple juice. The most commonly used methods of origin tracing research is by using stable isotopes and mineral elements technology, because these indicators are directly related to local geographical environment.

RESULTS

In this study, a discriminant model was established by determining the content of the stable isotopes (δ¹³ C, δ¹⁸ O) and 13 mineral elements (B, Mn, Co, Ni, Cu, Sr, V, Ba, Fe, Mg, Na, Ca and Cr) in concentrated apple juice. Linear discriminant analysis (LDA), principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were employed for regional classification of samples. After data conversion and correlation analysis, spatial and quantitative prediction models were established using multiple linear regressions. Finally, the experimental results showed that the eight key variables(δ ¹³ C, δ ¹⁸ O, B, Ca, Mg, Cu, Sr and Na) selected by the analysis can be used to further characterize the production area.

CONCLUSION

The results showed that the carbon and oxygen isotopes combined with certain mineral elements can be used to indicate the origin of concentrated apple juice. © 2020 Society of Chemical Industry.

Inorganic Elements in Mytilus galloprovincialis Shells: Geographic Traceability by Multivariate Analysis of ICP-MS Data

The international seafood trade is based on food safety, quality, sustainability, and traceability. Mussels are bio-accumulative sessile organisms that need regular control to guarantee their safe consumption. However, no well-established and validated methods exist to trace mussel origin, even if several attempts have been made over the years. Recently, an inorganic multi-elemental fingerprint coupled to multivariate statistics has increasingly been applied in food quality control. The mussel shell can be an excellent reservoir of foreign inorganic chemical species, allowing recording long-term environmental changes. The present work investigates the multi-elemental composition of mussel shells, including Al, Cu, Cr, Zn, Mn, Cd, Co, U, Ba, Ni, Pb, Mg, Sr, and Ca, determined by inductively-coupled plasma mass-spectrometry in Mytilus galloprovincialis collected along the Central Adriatic Coast (Marche Region, Italy) at 25 different sampling sites (18 farms and 7 natural banks) located in seven areas. The experimental data, coupled with chemometric approaches (principal components analysis and linear discriminant analysis), were used to create a statistical model able to discriminate samples as a function of their production site. The LDA model is suitable for achieving a correct assignment of >90% of individuals sampled to their respective harvesting locations and for being applied to counteract fraud.

Investigation of Genetic Relatedness of Brucella Strains in Countries Along the Silk Road

In this study, MLVA (multiple-locus variable-number tandem repeat analysis) genotype data of Brucella strains from 11 countries along the Silk Road were downloaded from the MLVAbank. MLVA data of strains were applied to the constructed Minimum Spanning Tree to explore the species/biovars distribution, geographic origins, and genetic relationships of the strains analyzed. Moreover, whole-genome sequencing–single-nucleotide polymorphism (WGS-SNP) phylogenetic analysis of the genome of Brucella melitensis strains from GenBank was performed to discriminate the relatedness of strains further and investigate the transmission pattern of B. melitensis brucellosis. A total of 1,503 Brucella strains were analyzed in this study: 431 Brucella abortus strains (29.8%), 1,009 B. melitensis strains (65.7%), and 63 Brucella suis strains (4.5%). B. melitensis biovar 3 was the dominant species and was shown to be widespread in all of the examined regions, suggesting that the prevention and surveillance of the B. melitensis population are a main challenge in these countries. A wide host spectrum was observed for this Brucella population; many animal reservoirs are a potential reason for the continuous brucellosis circulation in these countries. Although the B. abortus strains from the examined regions had common geographic origins, only a few shared genotypes were observed in different countries. These data revealed that the majority of B. abortus strains were spreading within the national borders. However, the B. melitensis strains from Italy originated from a Western Mediterranean lineage; strains from the other 10 countries originated from Eastern Mediterranean lineage, and this lineage was shared by strains from three to nine different countries, suggesting that the introduction and reintroduction of the disease in the 10 countries might have occurred in the past. Furthermore, the most shared MLVA-16 genotypes were formed in the B. melitensis strains from China, Kazakhstan, and Turkey, suggesting that the introduction and trade in sheep and goats have occurred frequently in these countries. WGS-SNP analysis showed that the B. melitensis in this study originated from the Malta (Italy) region. According to their territorial affiliation between four clade strains from these countries in genotype B, the absence of a clear differentiation suggests that strains continuously expand and spread in countries along with Silk Road. Active exchange and trade of animals (sheep and goats) among these countries are reasonable explanations. B. suis strains from different nations showed unique geographic origins and epidemiological characteristics. Therefore, there is an urgent need for the control of transfer and trade of infected sheep (goats) in countries along the Silk Road, namely, the strengthening of the entry–exit quarantine of sheep and goats and improvements in the diagnosis of animal brucellosis.

Geographical and Species Differentiation of Truffles (Tuber spp.) by Means of Stable Isotope Ratio Analysis of Light Elements (H, C, and N)

Truffles (Tuber spp.) are considered the most expensive edible fungi and, therefore, are highly prone to food fraud. In this study, authentic truffles from different countries of origin and species were characterized by the determination of their stable carbon, nitrogen, and hydrogen isotope ratios (bulk δ²H, δ¹³C, and δ¹⁵N values). Chinese truffles from Yunnan or related provinces (n = 19) could be well-separated from all European samples (eight countries; n = 105) by means of their significantly (p < 0.05) more negative δ²H values. Furthermore, samples of the second most expensive European species Tuber magnatum were both more enriched in ¹⁵N and more depleted in ¹³C compared to the remaining samples, which allowed for an unequivocal differentiation. Hence, stable isotope ratio analysis could be of high value in terms of authentication of truffles.

The Use of Stable Isotope Ratio Analysis to Trace European Sea Bass (D. labrax) Originating from Different Farming Systems

Simple Summary

European sea bass is one of the most economically important fish species in the Mediterranean area. The potential effects of farming systems on the final quality of this product and the recent popular demand for labels to certify the animal rearing origin, which is increasingly used as a marketing tool, have raised the use of analytical techniques that make it possible to differentiate this fish product according to the rearing farming system and authenticate their geographical origin. The aim of this study was to determine whether isotopic ratio mass spectrometry (IRMS) can discriminate farmed European sea bass according to different farming systems (concrete tank inland, sea cages, and extensive methods in valleys or salt works) and geographic origins (different locations scattered throughout Italy). The results of this study showed the viability of δ¹³C and δ¹⁵N to discriminate cultured sea bass from different farming systems (extensive vs. intensive) reared at different geographical sites in Italy. Meanwhile, the measurement of δ¹⁸O and δ²H made it possible to distinguish the geographical origin of the sea bass farmed extensively and intensively (in cages).

Abstract

This study aimed to determine whether isotopic ratio mass spectrometry (IRMS) can discriminate farmed European sea bass according to different farming systems and geographic origins. Dicentrarchus labrax of commercial size from three different rearing systems (concrete tank inland, sea cages, and extensive methods in valleys or salt works) were collected at the trading period (autumn–winter). For each farming type, different locations spread over Italy were monitored. Once the fish were harvested, the muscle and feed were sampled. For both muscle and feed, δ¹³C and δ¹⁵N were measured by continuous flow elemental analyzer isotope ratio mass spectrometry (CF-EA-IRMS) with the goal of discriminating samples based on the rearing system. Additional δ²H and δ¹⁸O measurements of fish samples were performed by continuous flow total combustion elemental analyzer isotope ratio mass spectrometry (CF-TC/EA-IRMS) to track the geographical origin. The measurements of δ¹³C and δ¹⁵N made it possible to discriminate cultured sea bass from different farming systems (extensive vs. intensive) reared at different geographical sites in Italy. Additional information was obtained from δ¹⁸O and δ²H, which enabled the geographical areas of origin of the sea bass farmed extensively and intensively (in cages) to be distinguished.

Metabolite Profiling and Chemometric Study for the Discrimination Analyses of Geographic Origin of Perilla (Perilla frutescens) and Sesame (Sesamum indicum) Seeds

Perilla and sesame are traditional sources of edible oils in Asian and African countries. In addition, perilla and sesame seeds are rich sources of health-promoting compounds, such as fatty acids, tocopherols, phytosterols and policosanols. Thus, developing a method to determine the geographic origin of these seeds is important for ensuring authenticity, safety and traceability and to prevent cheating. We aimed to develop a discriminatory predictive model for determining the geographic origin of perilla and sesame seeds using comprehensive metabolite profiling coupled with chemometrics. The orthogonal partial least squares-discriminant analysis models were well established with good validation values (Q² = 0.761 to 0.799). Perilla and sesame seed samples used in this study showed a clear separation between Korea and China as geographic origins in our predictive models. We found that glycolic acid could be a potential biomarker for perilla seeds and proline and glycine for sesame seeds. Our findings provide a comprehensive quality assessment of perilla and sesame seeds. We believe that our models can be used for regional authentication of perilla and sesame seeds cultivated in diverse geographic regions.

Meta-analysis of the differential effects of habitat fragmentation and degradation on plant genetic diversity

Genetic diversity is a key factor for population survival and evolution. However, anthropogenic habitat disturbance can erode it, making populations more prone to extinction. Aiming to assess the global effects of habitat disturbance on plant genetic variation, we conducted a meta-analysis based on 92 case studies obtained from published literature. We compared the effects of habitat fragmentation and degradation on plant allelic richness and gene diversity (equivalent to expected heterozygosity) and tested whether such changes are sensitive to different life-forms, life spans, mating systems, and commonness. Anthropogenic disturbance had a negative effect on allelic richness, but not on gene diversity. Habitat fragmentation had a negative effect on genetic variation, whereas habitat degradation had no effect. When we examined the individual effects in fragmented habitats, allelic richness and gene diversity decreased, but this decrease was strongly dependent on certain plant traits. Specifically, common long-lived trees and self-incompatible species were more susceptible to allelic richness loss. Conversely, gene diversity decreased in common short-lived species (herbs) with self-compatible reproduction. In a wider geographical context, tropical plant communities were more sensitive to allelic richness loss, whereas temperate plant communities were more sensitive to gene diversity loss. Our synthesis showed complex responses to habitat disturbance among plant species. In many cases, the absence of effects could be the result of the time elapsed since the disturbance event or reproductive systems favoring self-pollination, but attention must be paid to those plant species that are more susceptible to losing genetic diversity, and appropriate conservation should be actions taken.

Typicality Assessment of Onions (Allium cepa) from Different Geographical Regions Based on the Volatile Signature and Chemometric Tools

Onion (Allium cepa L.) is one of the main agricultural commodities produced and consumed around the world. In the present work, for the first time, the volatile signature of onions from different geographical regions of Madeira Island (Caniço, Santa Cruz, Ribeira Brava, and Porto Moniz) was tested with headspace solid-phase microextraction (HS-SPME/GC-qMS) and chemometric tools, showing that the volatile signature was affected by the geographical region of cultivation. Sulfur compounds, furanic compounds, and aldehydes are the most dominant chemical groups. Some of the identified volatile organic metabolites (VOMs) were detected only in onions cultivated in specific regions; 17 VOMs were only identified in onions cultivated at Caniço, eight in Porto Moniz, two in Santa Cruz, two in Ribeira Brava, while 12 VOMs are common to all samples from the four regions. Moreover, some VOMs belonging to sulfur compounds (dipropyl disulfide, 3-(acetylthio)-2-methylfuran), furanic compounds (dimethylmethoxyfuranone, ethyl furanone, acetyloxy-dimethylfuranone), and lactones (whiskey lactone isomer), could be applied as potential geographical markers of onions, providing a useful tool to authenticate onions by farming regions where the influence of latitude seems to be an important factor for yielding the chemical profile and may contribute to geographical protection of food and simultaneously benefiting both consumers and farmers.

Investigation of the molecular epizootiological characteristics and tracking of the geographical origins of Brucella canis strains in China

Brucellosis is a global pandemic infectious zoonosis. Brucella canis is a rare source of human brucellosis in China, and its public health significance remains under debate. Moreover, data pertaining to the epizootiological characteristics and geographical origin of B. canis on a nationwide scale are limited, and the risk to public safety posed by B. canis infections is unknown. The MLVA (multilocus variable-number tandem repeat analysis) assay can be helpful to analyse epidemiological correlations among Brucella isolates and to track their geographic origins. To accomplish this task, MLVA-16 was used to analyse the epidemiological links of 63 isolates obtained from dogs and humans. Sixty-three B. canis strains were sorted into three large clusters (A, B and C) and 50 different genotypes (GT1-50), and 43 unique genotypes were represented by single isolates, suggesting that these strains had no obvious epidemiological links and that canine brucellosis is predominantly sporadic in China. The other seven shared genotypes (among a total of 20 isolates) were each represented by two to eight isolates, indicating that strains from each shared genotype were epidemiologically correlated. Five of the shared genotypes were from 16 strains obtained from Beijing, indicating that canine brucellosis in Beijing originates from multipoint outbreaks with multiple sources of infection. Based on comprehensive case analysis of clinical B. canis infection, we preliminarily suggest that human B. canis infections are associated with Mycoplasma pneumoniae infection that results in decreased patient immunity. B. canis may have limited epidemiological significance for the healthy population, but it remains a significant threat to the canine breeding industry and to humans who come into close contact with dogs. Based on MLVA-11 data, B. canis strains were clustered into 16 genotypes and divided into five evolutionary branches; these data confirm that this population covers an extensive geographic area and exhibits characteristics of the origin and evolution of co-existing introduced and locally native lineages. We believe this study will contribute to strengthening efforts to prevent and control canine brucellosis and to improve public understanding of the health risks posed by B. canis.

The Impact of Neighbourhood Deprivation on Embryonic Growth Trajectories: Rotterdam Periconception Cohort

Background: Neighbourhood deprivation is a risk factor for impaired health and adverse pregnancy outcomes. We investigated whether living in a deprived neighbourhood is associated with embryonic growth. Methods: From the Predict cohort, we studied 566 women who underwent repeated first trimester ultrasound examinations. Crown rump length (CRL; n = 1707) and embryonic volume (EV; n = 1462) were measured using three-dimensional techniques. Neighbourhood deprivation was assessed using the neighbourhood status scores (NSS) of the Dutch Social Cultural Planning office. A high NSS represents a non-deprived neighbourhood. Associations between the NSS and embryonic growth were investigated using linear mixed models. Adjustment was performed for individual-level factors: maternal age, geographic origin, educational level, BMI, folic acid supplement use, fruit and vegetable intake, alcohol use and smoking habits. Results: The NSS was negatively associated with embryonic growth: a higher score (a less deprived neighbourhood) was associated with a smaller CRL and EV; adjusted β: −0.025 (95% CI −0.046, −0.003) and adjusted β: −0.015 (95% CI −0.026, −0.003). At 11 weeks of pregnancy, we observed a 0.55 cm³ smaller EV (7.65 cm³ vs. 7.10 cm³) and 1.08 mm smaller CRL (43.14 mm vs. 42.06 mm) in the highest compared to the lowest category. Conclusion: In deprived neighbourhoods, embryos are larger than in non-deprived neighbourhoods.

Chemical composition and antioxidant potential of essential oil and methanol extract from Tunisian and French fennel (Foeniculum vulgare Mill.) seeds

This study was designed to examine the effect of provenance on the phytochemical and antioxidant properties of essential oil and methanolic extract from Tunisian and French fennel seeds (FFS). Analysis of the essential oil showed that although the same main compounds were found in Tunisian and FFS cultivars, some differences were present in their proportions allowing to classify them in two chemotypes. The first class was composed by trans-anethole (63.41%-78.26%) for Tunisian cultivars and the second one by estragole (44.72%-88.92%) for French cultivars. The phenolic composition of all fennel seed extracts was characterized by its richness in quinic acid, 4-O-caffeoylquinic acid, p-coumaric acid, and 4-O-caffeoylquinic acid. All fennel seed extracts showed a better antioxidant potential than their essential oils depending on the origin. Principal component analysis showed a dispersion of the cultivars on three groups depending on the chemotype diversity. PRACTICAL APPLICATIONS: Recently, much attention has been focused on fennel due to the nutritional and health-protective value of their seeds. Several studies have highlighted the importance of fennel seed extracts and essential oils as key ingredients rich in bioactive compounds serving in formulation of new functional food products. This investigation designed to examine the effect of provenance on phytochemical and antioxidant potentials of Tunisian and French fennel seed extracts and essential oils.

Geographic Variation in the Chemical Composition and Antioxidant Properties of Phenolic Compounds from Cyclocarya paliurus (Batal) Iljinskaja Leaves

Cyclocarya paliurus has been widely used as an ingredient in functional foods in China. However, the antioxidant properties of phenolic compounds and the effect of the plant origin remain unclear. The present study evaluated the geographical variation of this plant in term of its phenolic composition and antioxidant activities based on leaf materials collected from five regions. high-performance liquid chromatography (HPLC) analysis showed that there are three major components, quercetin-3-O-glucuronide, kaempferol-3-O-glucuronide, and kaempferol-3-O-rhamnoside, and their contents varied significantly among sampling locations. The investigated phenolic compounds showed substantial antioxidant activities, both in vitro and in vivo, with the highest capacity observed from Wufeng and Jinzhongshan. Correlation analysis revealed that quercetin and kaempferol glycosides might be responsible for the antioxidant activities. Our results indicate the importance of geographic origin, with sunny hours and temperature as the main drivers affecting the accumulation of C. paliurus phenolics and their antioxidant properties.

The Empirical Distribution of Singletons for Geographic Samples of DNA Sequences

Rare variants are important for drawing inference about past demographic events in a species history. A singleton is a rare variant for which genetic variation is carried by a unique chromosome in a sample. How singletons are distributed across geographic space provides a local measure of genetic diversity that can be measured at the individual level. Here, we define the empirical distribution of singletons in a sample of chromosomes as the proportion of the total number of singletons that each chromosome carries, and we present a theoretical background for studying this distribution. Next, we use computer simulations to evaluate the potential for the empirical distribution of singletons to provide a description of genetic diversity across geographic space. In a Bayesian framework, we show that the empirical distribution of singletons leads to accurate estimates of the geographic origin of range expansions. We apply the Bayesian approach to estimating the origin of the cultivated plant species Pennisetum glaucum [L.] R. Br. (pearl millet) in Africa, and find support for range expansion having started from Northern Mali. Overall, we report that the empirical distribution of singletons is a useful measure to analyze results of sequencing projects based on large scale sampling of individuals across geographic space.

Exhaustive Qualitative LC-DAD-MSn Analysis of Arabica Green Coffee Beans: Cinnamoyl-glycosides and Cinnamoylshikimic Acids as New Polyphenols in Green Coffee

Coffee is one of the most consumed beverages in the world, due to its unique aroma and stimulant properties. Although its health effects are controversial, moderate intake seems to be beneficial. The present work deals with the characterization and quantification of polyphenols and methylxanthines in four Arabica green coffee beans from different geographical origins. The antioxidant activity was also evaluated. Forty-three polyphenols (cinnamic acid, cinnamoyl-amide, 5 cinammoyl-glycosides, and 36 cinnamate esters) were identified using LC-MSⁿ. Among these, cinnamate esters of six different chemical groups (including two dimethoxycinnamoylquinic acid isomers, three caffeoyl-feruloylquinic acid isomers, caffeoyl-sinapoylquinic acid, p-coumaroyl-feruloylquinic acid, two caffeoylshikimic acid isomers, and trimethoxycinnamoylshikimic acid) in addition to five isomers of cinnamoyl-glycosides called caffeoyl-2,7-anhydro-3-deoxy-2-octulopyranosic acid (CDOA) are described for the first time in Arabica green coffee beans. Moreover, 38 polyphenols (6-7% w/w) and 2 methylxanthines (1.3% w/w) were quantified by HPLC-DAD. Caffeoylquinic was the most abundant group of compounds (up to 85.5%) followed by dicaffeoylquinic and feruloylquinic acids (up to 8 and 7%, respectively) and the newly identified cinnamoyl-glycosides (CDOA) (up to 2.5%). Caffeine was the main methylxanthine (99.8%), with minimal amounts of theobromine (0.2%). African coffees (from Kenya and Ethiopia) showed higher polyphenolic content than American beans (from Brazil and Colombia), whereas methylxanthine contents varied randomly. Both phenols and methylxanthines contributed to the antioxidant capacity associated with green coffee, with a higher contribution of polyphenols. We conclude that green coffee represents an important source of polyphenols and methylxanthines, with high antioxidant capacity.

Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation

Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs), Eastern Asia (EAs), and Western Africa (WAf) were highly diversified, while those from Western Asia (WAs), Northern Africa (NAf), and Southeastern Africa (SAf) had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions.

Statistical Analysis of Mineral Concentration for the Geographic Identification of Garlic Samples from Sicily (Italy), Tunisia and Spain

We performed a statistical analysis of the concentration of mineral elements, by means of inductively coupled plasma mass spectrometry (ICP-MS), in different varieties of garlic from Spain, Tunisia, and Italy. Nubia Red Garlic (Sicily) is one of the most known Italian varieties that belongs to traditional Italian food products (P.A.T.) of the Ministry of Agriculture, Food, and Forestry. The obtained results suggest that the concentrations of the considered elements may serve as geographical indicators for the discrimination of the origin of the different samples. In particular, we found a relatively high content of Selenium in the garlic variety known as Nubia red garlic, and, indeed, it could be used as an anticarcinogenic agent.

Utility of Stable Isotope and Cytochrome Oxidase I Gene Sequencing Analyses in Inferring Origin and Authentication of Hairtail Fish and Shrimp

Mislabeling of fishery products continues to be a serious threat to the global market. Consequently, there is an urgent necessity to develop tools for authenticating and establishing their true origin. This investigation evaluates the suitability of stable isotopes and cytochrome oxidase I (COI) sequencing in identifying and tracing the origin of hairtail fish and shrimp. By use of COI sequencing, the hairtail fish samples were identified as Trichiurus japonicus and Trichiurus lepturus, while the shrimp samples were identified as Pandalus borealis, Marsupenaeus japonicus, Fenneropenaeus chinensis, Litopenaeus vannamei, Penaeus monodon, and Solenocera crassicornis. Linear discriminant analysis (LDA) of stable isotopes further categorized the individuals of the same species based on the country of origin. Natural and farmed shrimp (from the same country) were distinctly differentiated on the basis of stable isotope values. Therefore, these two methods could be cooperatively utilized to identify and authenticate fishery products, the utilization of which would enhance transparency and fair trade.

Establishing tobacco origin from pollen identification: an approach to resolving the debate

Previous research into pollen content of tobacco resulted in a debate. We address this debate and determine that pollen analysis may be able to assist with identifying geographical origin of tobacco. However, the value of any results should be assessed on a case-by-case regional basis until sufficient database information is available for an objective interpretation to be undertaken on a global basis. As a first step toward developing comparative data for South America, we analyzed a tobacco sample from Brazil in an effort to identify signature taxa from the state of Minas Gerais. We also assessed the role of honey additives to tobacco to assess this issue. Comparing the data to previously published data, we conclude that pollen signatures can distinguish broad geographic areas. We conclude that this forensic interpretation framework needs to be developed in context of the National Academy of Sciences recommendations for tightening methods in forensic science.

Authenticity and traceability of vanilla flavors by analysis of stable isotopes of carbon and hydrogen

Authenticity and traceability of vanilla flavors were investigated using gas chromatography-isotope ratio mass spectrometry (GC-IRMS). Vanilla flavors produced by chemical synthesis (n = 2), fermentation (n = 1), and extracted from two different species of the vanilla orchid (n = 79) were analyzed. The authenticity of the flavor compound vanillin was evaluated on the basis of measurements of ratios of carbon stable isotopes (δ(13)C). It was found that results of δ(13)C for vanillin extracted from Vanilla planifolia and Vanilla tahitensis were significantly different (t test) and that it was possible to differentiate these two groups of natural vanillin from vanillin produced otherwise. Vanilla flavors were also analyzed for ratios of hydrogen stable isotopes (δ(2)H). A graphic representation of δ(13)C versus δ(2)H revealed that vanillin extracted from pods grown in adjacent geographic origins grouped together. Accordingly, values of δ(13)C and δ(2)H can be used for studies of authenticity and traceability of vanilla flavors.

arabica) from different geographic origins

Characterisation of coffees according to their origins is of utmost importance for commercial qualification. In this study, the aroma profiles of different batches of three monoorigin roasted Coffea arabica coffees (Brazil, Ethiopia and Guatemala) were analysed by Proton-Transfer-Reaction-Time of Flight-Mass Spectrometry (PTR-ToF-MS). The measurements were performed with the aid of a multipurpose autosampler. Unsupervised and supervised multivariate data analysis techniques were applied in order to visualise data and classify the coffees according to origin. Significant differences were found in volatile profiles of coffees. Principal component analysis allowed visualising a separation of the three coffees according to geographic origin and further partial least square regression-discriminant analysis classification showed completely correct predictions. Remarkably, the samples of one batch could be used as training set to predict geographic origin of the samples of the other batch, suggesting the possibility to predict further batches in coffee production by means of the same approach. Tentative identification of mass peaks aided characterisation of aroma fractions. Classification pinpointed some volatile compounds important for discrimination of coffees.

Finding your way through Pneumocystis sequences in the NCBI gene database

Pneumocystis sequences can be downloaded from GenBank for purposes as primer/probe design or phylogenetic studies. Due to changes in nomenclature and assignment, available sequences are presented with a variety of inhomogeneous information, which renders practical utilization difficult. The aim of this study was the descriptive evaluation of different parameters of 532 Pneumocystis sequences of mitochondrial and ribosomal origin downloaded from GenBank with regard to completeness and information content. Pneumocystis sequences were characterized by up to four different names. Official changes in nomenclature have only been partly implemented and the usage of the "forma specialis", a special feature of Pneumocystis, has only been established fragmentary in the database. Hints for a mitochondrial or ribosomal genomic origin could be found, but can easily be overlooked, which renders the download of wrong reference material possible. The specification of the host was either not available or variable regarding the used language and the localization of this information in the title or several subtitles, which limits their applicability in phylogenetic studies. Declaration of products and geographic origin was incomplete. The print version of this manuscript is completed by an online database which contains detailed information to every accession number included in the meta-analysis.

Comparison of leafy kale populations from Italy, Portugal, and Turkey for their bioactive compound content: phenolics, glucosinolates, carotenoids, and chlorophylls

BACKGROUND

Kales are primitive leafy Brassica oleracea L. forms, widespread in local farming systems of several European countries and employed in the preparation of traditional recipes. Kales are also potential sources of healthy bioactive phytochemical components. The present study compared the bioactive compound content of kale populations from Italy, Portugal, and Turkey, either from local sources or grown in an experimental field.

RESULTS

Total phenolics, glucosinolates (GLS), carotenoids, and chlorophylls were in the ranges 8310-38 110, 755-8580, 135-2354, and 1740-16,924 mg kg(-1) dry matter, respectively. On average, locally harvested samples showed a total GLS content about twice as high as populations from the experiment. Conversely, pigments were significantly more abundant in experimental than in local kales, owing to the higher soil fertility. Portuguese samples showed higher phenolic and GLS amounts than Italian and Turkish kales, whereas some of the Italian samples were the richest in carotenoids.

CONCLUSION

This paper represented the first cross-country comparison of local kale accessions with respect to bioactive compound amounts. Both geographic origin and growing environment appeared to be remarkable and discriminating factors in determining bioactive levels in leafy kales, with possible effects on their health-promoting and sensorial attributes.

Tracing the geographic origins of weedy Ipomoea purpurea in the southeastern United States

Ipomoea purpurea (common morning glory) is an annual vine native to Mexico that is well known for its large, showy flowers. Humans have spread morning glories worldwide, owing to the horticultural appeal of morning glory flowers. Ipomoea purpurea is an opportunistic colonizer of disturbed habitats including roadside and agricultural settings, and it is now regarded as a noxious weed in the Southeastern US. Naturalized populations in the Southeastern United States are highly polymorphic for a number of flower color morphs, unlike native Mexican populations that are typically monomorphic for the purple color morph. Although I. purpurea was introduced into the United States from Mexico, little is known about the specific geographic origins of US populations relative to the Mexican source. We use resequencing data from 11 loci and 30 I. purpurea accessions collected from the native range of the species in Central and Southern Mexico and 8 accessions from the Southeastern United States to infer likely geographic origins in Mexico. Based on genetic assignment analysis, haplotype composition, and the degree of shared polymorphism, I. purpurea samples from the Southeastern United States are genetically most similar to samples from the Valley of Mexico and Veracruz State. This supports earlier speculation that I. purpurea in the Southeastern United States was likely to have been introduced by European colonists from sources in Central Mexico.