Imen Ayadi

Variation of chemical composition of essential oils in wild populations of Thymus algeriensis Boiss. et Reut., a North African endemic Species

BackgroundThymus algeriensis is an endemic aromatic plant to Tunisia largely used in folk medicine and as a culinary herb. The bulks aromatic plants come from wild populations whose essential oils compositions as well as their biological properties are severely affected by the geographical location and the phase of the plant development. Therefore, the aim of the present work is to provide more information on the variation of essential oil composition of T. algeriensis collected during the vegetative and the flowering phases and from eight different geographical regions. Besides, influence of population location and phenological stage on yield and metal chelating activity of essential oils is also assessed.MethodsThe essential oil composition of Thymus algeriensis was determined mainly by GC/FID and GC/MS. The chemical differentiation among populations performed on all compounds was assessed by linear discriminate analysis and cluster analysis based on Euclidean distance.ResultsA total of 71 compounds, representing 88.99 to 99.76% of the total oil, were identified. A significant effect of the population location on the chemical composition variability of T. algeriensis oil was observed. Only 18 out of 71 compounds showed a statistically significant variation among population locations and phenological stages. Chemical differentiation among populations was high. Minor compounds play an important role to distinguish between chemical groups. Five chemotypes according to the major compounds have been distinguished. Chemotypes distribution is linked to the population location and not to bioclimate, indicating that local selective environmental factors acted on the chemotype diversity.ConclusionsThe major compounds at the species level were α-pinene (7.41-13.94%), 1,8-cineole (7.55-22.07%), cis-sabinene hydrate (0.10-12.95%), camphor (6.8-19.93%), 4-terpineol (1.55-11.86%), terpenyl acetate (0-14.92%) and viridiflorol (0-11.49%). Based on major compounds, the populations were represented by (α-pinene/1,8-cineole/cis-sabinene hydrate/camphor/viridiflorol), (1,8-cineole/camphor/terpenyl acetate), (α-pinene/1,8-cineole/camphor), (1,8-cineole/camphor/4-terpineol) and (α-pinene/1,8-cineole/cis-sabinene hydrate/camphor/4-terpineol) chemotypes. Variation of phenological stage did not have a statistically significant effect on the yield and metal chelating activity of the essential oil. These results can be used to investigate the geographical location and the harvesting time of this plant for relevant industries.

Sediment yield variability in central Tunisia: a quantitative analysis of its controlling factors

Abstract This paper refers to the quantification and prediction of the sedimentation rate of 26 hillside-dam reservoirs in Central Tunisia. The objectives of the study are to develop a simple and practical methodology to identify controlling factors of sedimentation, and to propose a regionalization from the study sites. Principal component analysis (PCA) and complementary multi-dimensional statistical methods are used to relate highly variable area-specific sediment yield to hydro-morphometric, lithological, geomorphological and anthropogenic characteristics of catchments. It appears that catchment area is not the main controlling factor of sedimentation in the studied area. The overall slope index, drainage network characteristics and runoff parameters are also important in characterizing sediment yield. Applied to the annual sedimentation rate series, PCA resulted in retaining the first three principal axes, explaining 65% of the total variance. Statistical methods showed that the overall slope index, the total drainage length, the compacity index and the runoff parameters are as important for the sedimentation quantification. This allowed a graphical clustering of the study zone into three distinct groups having similar behaviours: (i) watersheds characterized by high sediment transport rates and high runoff coefficients, (ii) basins distinguished by relatively low values of both flow discharge and sediment transport rates, and (iii) watersheds with an intermediate sediment yield, especially characterized by relatively high relief. In a second step, a multiple regression model including the four characteristic catchment properties was developed, presenting a valuable tool to predict area-specific sediment yield from catchments in central Tunisia. This model shows reasonable efficiency with an absolute prediction error of 81%. Citation Ayadi, I., Abida, H., Djebbar, Y. & Mahjoub, M. R. (2010) Sediment yield variability in central Tunisia: a quantitative analysis of its controlling factors. Hydrol. Sci. J. 55(3), 446–458.

Combining Autosomal and Y-Chromosomal Short Tandem Repeat Data in Paternity Testing with Male Child: Methods and Application*

Abstract:  Paternity testing is being increasingly requested with the aim of challenging presumptive fatherhood. The ability to establish the biological father is usually based on the genotyping of autosomal short tandem repeat (STR) in alleged father, mother and child, but the use of Y‐chromosomal STR has gained interest in the last few years. In this work, we propose a new probabilistic approach that combines autosomal and Y‐chromosomal STR data in paternity testing with father/son pairs taking into account mutation events. We also suggest a new two‐stage approach where we first type Y‐STRs and possibly autosomal STR for the putative father and son, conditional on Y‐STR results. We applied this approach to 22 cases. Our results show that Y‐STRs can identify nonpaternity cases with high accuracy but need to be validated with autosomal STR to establish paternity. Moreover, the two‐stage approach is less costly than the standard approach and is very useful in motherless cases.

Population genetics of 17 Y-STR markers in West Libya (Tripoli region).

Seventeen Y-chromosomal Short Tandem Repeats (Y-STR) included in the AmpFlSTR Y-filer PCR Amplification kit (Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4) were genotyped in a population sample of 176 unrelated males from western Libya (Tripoli region). A total of 142 different haplotypes were found, 124 being unique. Haplotype diversity was 0.9950. Both R(ST) pairwise analyses and multidimensional scaling plot show a close genetic relationship between Tripoli and North African populations.

Genetic structure of Kuwaiti population revealed by Y-STR diversity

In this study, a sample of 126 Kuwaiti was analysed using 12 Y-chromosome short tandem repeat (STR) polymorphisms. A total of 101 different haplotypes were identified, among which 87 were individual specific. The high haplotype diversity (0.994) supports the usefulness of Y-STR markers in Kuwaiti population diversity investigation. Our results suggest a close genetic relationship between Kuwait and other populations of the Arabian Peninsula, and an even more pronounced similarity of Kuwaiti populations and Yemenis and Saudi Arabians.

Haplotype structure of five SNPs within the ACE gene in the Tunisian population

Background: The Angiotensin-Converting Enzyme (ACE) is a candidate gene in the aetiology of several common diseases. The study of the haplotype structure of this gene is of interest in diagnosis and in pharmacogenomics. Aim: The study investigated the haplotype profile of single nucleotide polymorphisms (SNPs) within the ACE gene in the Tunisian population and compared it with other populations. Subjects and methods: Five SNPs (rs1800764, rs4291, rs4309, rs4331, rs4340) covering a region of 15.6 kb of the ACE gene were typed by PCR-digestion in a sample of 100 healthy subjects. Results: All SNPs were polymorphic and in Hardy–Weinberg equilibrium. A total of 21 haplotypes were identified but only eight had a frequency of more than 1%. The four most common haplotypes had a cumulative frequency of 87.4%. The ‘Yin–Yang’ phenomenon (the two major haplotypes are complementary at all sites) was found. Linkage disequilibrium between all pairs of loci was highly significant (p<10−5). A simple and efficient statistical procedure was used to identify three important SNPs. Conclusion: The Tunisian population showed a different haplotype structure from the European one for the ACE gene and three important SNPs were identified. These will be very helpful in future association studies in the Tunisian and North African populations. Résumé. Arrière plan: Le gène de l’enzyme de conversion de l’angiotensine (ECA) peut être potentiellement impliqué dans l’étiologie de plusieurs maladies courantes. L’étude de la structure de son haplotype est donc utile pour la diagnose comme pour les recherches pharmacogénomiques. Objectif: Etudier le profile haplotypique des polymorphismes de nucléotides uniques (PNU) dans le gène ECA de la population tunisienne et le comparer à d’autres populations. Trois PNU importants pour leur emploi dans les futures études d’association ont été identifiés. Sujets et méthodes: Cinq PNU (rs1800764, rs4291, rs4309, rs4331, rs4340) couvrant une région de 15,6 kb du gène ECA ont été typés par PCR-RFLP dans un échantillon de 100 personnes en bonne santé. Résultats: Tous les PNU étaient polymorphiques et en équilibre de Hardy-Weinberg. Un total de 21 haplotypes ont été identifiés, mais seulement huit avaient une fréquence supérieure à 1%. Les quatre haplotypes les plus communs avaient une fréquence cumulée de 87,4%. On a rencontré le phénomène “Yin-Yang ” (les deux haplotypes majeurs sont complémentaires à tous les sites). Le déséquilibre de linkage entre toutes les paires de loci était hautement significatif (p < 10–5). Une méthode statistique simple et efficace a été utilisée pour identifier trois PNU importants. Conclusion: La population tunisienne présente une structure haplotypique différente de celle des européens pour le gène ECA et trois PNU importants ont été identifiés. Ils seront très utiles pour les futures études d’association dans les populations tunisienne et nord-africaines. Zusammenfassung. Hintergrund: Das Angiotensin-Converting Enzym (ACE) ist ein Kandidatengen in der Ätiologie verschiedener häufiger Krankheiten. Die Untersuchung der Haplotypstruktur dieses Gens ist bei der Diagnostik und der Pharmakogenomik von Interesse. Ziel: Die Studie untersuchte das Haplotypprofil von Einzelnukleotidpolymorphismen (single nucleotide polymorphisms, SNPs) innerhalb des ACE-Gens in der Tunesischen Bevölkerung und verglich es mit anderen Populationen. Drei für den späteren Gebrauch in Assoziationsstudien bedeutsame SNPs wurden identifiziert. Probanden und Methoden: Fünf SNPs (rs1800764, rs4291, rs4309, rs4331, rs4340), die sich über eine Region von 15,6 kb des ACE-Gens erstrecken, wurden mit PCR-RFLP in einer Stichprobe von 100 gesunden Probanden typisiert. Ergebnisse: Alle SNPs waren polymorph und im Hardy–Weinberg Gleichgewicht. Insgesamt 21 Haplotypen wurden identifiziert, aber nur acht traten in einer Häufigkeit von über 1% auf. Die vier häufigsten Haplotypen hatten eine kumulative Häufigkeit von 87,4%. Das ‘Yin–Yang’-Phänomen wurde gefunden (die beiden wichtigsten Haplotypen sind allseits komplementär). Das Kopplungsungleichgewicht zwischen den jeweils gepaarten Loci war hochsignifikant (p < 10−5). Ein einfaches und effizientes statistisches Verfahren wurde genutzt, um drei bedeutsame SNPs zu identifizieren. Zusammenfassung: Die Tunesische Bevölkerung zeigte eine gegenüber der Europäischen unterschiedliche Haplotypstruktur des ACE-Gens, und es wurden drei bedeutsame SNPs identifiziert. Diese werden für spätere Assoziationsstudien bei Tunesischen und anderen Nordafrikanischen Populationen hilfreich sein. Resumen Antecedentes: El enzima convertidor de la angiotensina (ECA) es un gen candidato en la etiología de varias enfermedades comunes. El estudio de la estructura haplotípica de este gen es de interés en diagnóstico y farmacogenómica. Objetivos: El estudio investigó el perfil haplotípico de los polimorfismos de nucleótidos simples (SNPs) dentro del gen ECA en la población de Túnez, y lo comparó con otras poblaciones. Se identificaron tres importantes SNPs para su futuro uso en estudios de asociación. Sujetos y métodos: Se tiparon cinco SNPs (rs1800764, rs4291, rs4309, rs4331, rs4340), que cubren una región de 15,6 kb del gen ECA, utilizando PCR-RFLP en una muestra de 100 sujetos sanos. Resultados: Todos los SNPs fueron polimórficos y estaban en equilibrio de Hardy-Weinberg. Se identificaron un total de 21 haplotipos, pero solo ocho presentaban una frecuencia mayor de 1%. Los cuatro haplotipos más comunes presentaban una frecuencia acumulada del 87,4%. Se observó el fenómeno “Yin-Yang” (dos haplotipos mayores son complementarios en todos los sitios). El desequilibrio de ligamiento entre todos los pares de loci fue altamente significativo (p<10−5). Se utilizó un procedimiento estadístico simple y eficiente para identificar tres SNPs importantes. Conclusión: La población de Túnez mostró una estructura haplotípica diferente de la europea para el gen ECA y se identificaron tres SNPs importantes, los cuales serán de gran ayuda en futuros estudios de asociación en poblaciones de Túnez y del norte de África.

Paternal lineages in Libya inferred from Y-chromosome haplogroups.

Many studies based on genetic diversity of North African populations have contributed to elucidate the modelling of the genetic landscape in this region. North Africa is considered as a distinct spatial-temporal entity on geographic, archaeological, and historical grounds, which has undergone the influence of different human migrations along its shaping. For instance, Libya, a North African country, was first inhabited by Berbers and then colonized by a variety of ethnic groups like Phoenicians, Greeks, Romans, Arabs and, in recent times, Italians. In this study, we contribute to clarify the genetic variation of Libya and consequently, of North African modern populations, by the study of Libyan male lineages. A total of 22 Y-chromosome-specific SNPs were genotyped in a sample of 175 Libyan males, allowing the characterization of 18 Y-chromosomal haplogroups. The obtained data revealed a predominant Northwest African component represented by haplogroup E-M81 (33.7%) followed by J(xJ1a,J2)-M304 (27.4%), which is postulated to have a Middle Eastern origin. The comparative study with other populations (∼5,400 individuals from North Africa, Middle East, Sub-Saharan Africa, and Europe) revealed a general genetic homogeneity among North African populations (FST = 5.3 %; P-value < 0.0001). Overall, the Y-haplogroup diversity in Libya and in North Africa is characterized by two genetic components. The first signature is typical of Berber-speaking people (E-M81), the autochthonous inhabitants, whereas the second is (J(xJ1a,J2)-M304), originating from Arabic populations. This is in agreement with the hypothesis of an Arabic expansion from the Middle East, shaping the North African genetic landscape.

Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches *

Endophytic flora plays a vital role in the colonization and survival of host plants, especially in harsh environments, such as arid regions. This flora may, however, contain pathogenic species responsible for various troublesome host diseases. The present study is aimed at investigating the diversity of both cultivable and non-cultivable endophytic fungal floras in the internal tissues (roots and leaves) of Tunisian date palm trees (Phoenix dactylifera). Accordingly, 13 isolates from both root and leaf samples, exhibiting distinct colony morphology, were selected from potato dextrose agar (PDA) medium and identified by a sequence match search wherein their 18S–28S internal transcribed spacer (ITS) sequences were compared to those available in public databases. These findings revealed that the cultivable root and leaf isolates fell into two groups, namely Nectriaceae and Pleosporaceae. Additionally, total DNA from palm roots and leaves was further extracted and ITS fragments were amplified. Restriction fragment length polymorphism (RFLP) analysis of the ITS from 200 fungal clones (leaves: 100; roots: 100) using HaeIII restriction enzyme revealed 13 distinct patterns that were further sequenced and led to the identification of Alternaria, Cladosporium, Davidiella (Cladosporium teleomorph), Pythium, Curvularia, and uncharacterized fungal endophytes. Both approaches confirmed that while the roots were predominantly colonized by Fusaria (members of the Nectriaceae family), the leaves were essentially colonized by Alternaria (members of the Pleosporaceae family). Overall, the findings of the present study constitute, to the authors’ knowledge, the first extensive report on the diversity of endophytic fungal flora associated with date palm trees (P. dactylifera).

Analysis of HLA-A, -B, -C, -DR, -DQ polymorphisms in the South Tunisian population and a comparison with other populations.

Background: The Human Leucocyte Antigen (HLA) system is often used as a genetic marker for analysing populations. HLA antigen distribution among the Tunisian population is not well defined because of the lack of a general population study. Aim: The aim of the present study was to investigate the polymorphism of HLA-A, -B, -C, -DR and -DQ loci in the South Tunisian population. Subjects and methods: This study has investigated HLA-A, -B, -C, -DR and -DQ polymorphisms in 123 unrelated healthy individuals originating from the south of Tunisia. HLA class I was studied by serology and completed by polymerase chain reaction-sequence specific primer (PCR-SSP). HLA class II was performed using PCR-SSP. Results: The most common alleles were A-2 (0.2154), B-44 (0.1179), C7 (0.2114), DR4 (0.1626) and DQ2 (0.313). A1-B-8-C7-DR3-DQ2 (2.84%) was the predominant haplotype in this population. Comparisons with data of other worldwide populations based on phylogenetic tree and multidimensional scaling analysis were done. This study suggests that both HLA class I and class II polymorphism specificities demonstrate a high diversity in this South Tunisian population, which reflects ancient and recent admixture with neighbouring populations. Conclusion: The results provide useful information for further studies of Tunisian population evolution, anthropology and for resolving HLA frequencies when searching for HLA-compatible donors in transplantation and for the analysis of disease associations.

Sample size computation for association studies using case—parents design

One of the most common designs for identification of genes involved in complex human diseases is the transmission disequilibrium test (TDT) design (Spielmann et al. 1993). This design consists in the collection of cases (affected individuals) and their two parents (commonly called triads of case– parents). The analysis of such data is based on comparison of the numbers of transmissions and nontransmissions of alleles for a candidate locus from parents to affected child. Here we mean by a candidate locus any variant or marker near or within the coding sequence of a candidate gene, whose function or position (or both) suggest its involvement in disease aetiology. Differential transmission of alleles, if any, indicates linkage and association between the candidate locus and the disease. Consider, without loss of generality, a candidate locus with two alleles A and a (in the case of multiple alleles such as for STR markers, one would consider testing each allele A against all others pooled in one non-A (a) allele). The expression of the TDT statistic is T = (b − c)2/(b + c), where b (respectively c) is the number of heterozygous parents who transmit the A (respectively a) allele to their affected child. Thus, for a triad to be informative (contribute to T value), at least one parent needs to be heterozygous for the candidate locus. TDT is a test of both linkage and association; the null hypothesis is linkage and/or association and it was shown that the expectation of TDT under the alternative hypothesis is proportional to (1−2θ)δ, where θ is the recombination fraction between the candidate locus and the disease locus and δ the linkage disequilibrium between the two loci. Under the null hypothesis, heterozygous parents transmit either allele (A, a) to an affected offspring with equal probability. For a large number of triads (>20), the distribution of T can be approximated by a chi-square distribution with one degree of freedom (d.f.). Many approximations have been