Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe

To investigate which aspects of contemporary human Y-chromosome variation in Europe are characteristic of primary colonization, late-glacial expansions from refuge areas, Neolithic dispersals, or more recent events of gene flow, we have analyzed, in detail, haplogroup I (Hg I), the only major clade of the Y phylogeny that is widespread over Europe but virtually absent elsewhere. The analysis of 1,104 Hg I Y chromosomes, which were identified in the survey of 7,574 males from 60 population samples, revealed several subclades with distinct geographic distributions. Subclade I1a accounts for most of Hg I in Scandinavia, with a rapidly decreasing frequency toward both the East European Plain and the Atlantic fringe, but microsatellite diversity reveals that France could be the source region of the early spread of both I1a and the less common I1c. Also, I1b*, which extends from the eastern Adriatic to eastern Europe and declines noticeably toward the southern Balkans and abruptly toward the periphery of northern Italy, probably diffused after the Last Glacial Maximum from a homeland in eastern Europe or the Balkans. In contrast, I1b2 most likely arose in southern France/Iberia. Similarly to the other subclades, it underwent a postglacial expansion and marked the human colonization of Sardinia ~9,000 years ago.     

Founder mutations in Tunisia: implications for diagnosis in North Africa and Middle East

Cystinuria (OMIM 220100) is an inborn congenital disorder characterised by a defective cystine metabolism resulting in the formation of cystine stones. Among the heterogeneous group of kidney stone diseases, cystinuria is the only disorder which is exclusively caused by gene mutations. So far, two genes responsible for cystinuria have been identified: SLC3A1 (chromosome 2p21) encodes the heavy subunit rBAT of a renal b^0,+ transporter while SLC7A9 (chromosome 19q12) encodes its interacting light subunit b^0,+AT. Mutations in SLC3A1 are generally associated with an autosomal-recessive mode of inheritance whereas SLC7A9 variants result in a broad clinical variability even within the same family. The detection rate for mutations in these genes is larger than 85%, but it is influenced by the ethnic origin of a patient and the pathophysiological significance of the mutations. In addition to isolated cystinuria, patients suffering from the hypotonia-cystinuria syndrome have been reported carrying deletions including at least the SLC3A1 and the PREPL genes in 2p21. By extensive molecular screening studies in large cohort of patients a broad spectrum of mutations could be identified, several of these variants were functionally analysed and thereby allowed insights in the pathology of the disease as well as in the renal trafficking of cystine and the dibasic amino acids. In our review we will summarize the current knowledge on the physiological and the genetic basis of cystinuria as an inborn cause of kidney stones, and the application of this knowledge in genetic testing strategies.     

Genetic variation of salt-stressed durum wheat (Triticum turgidum subsp. durum Desf.) genotypes under field conditions and gynogenetic capacity

Agriculture has new challenges against the climate change: the preservation of genetic resources and the rapid creation of new varieties better adapted to abiotic stress, specially salinity. In this context, the agronomic performance of 25 durum wheat (Triticum turgidum subsp. durum Desf.) genotypes (nineteen landraces and six improved varieties), cultivated in two semi-arid regions in the center area of Tunisia, were assessed. These sites (Echbika, 2.2?g?l^?1; Barrouta, 4.2?g?l^?1) differ by their degree of salinity of the water irrigation. The results showed that most of the agronomic traits (e.g. spike per meter square, thousand kernels weight and grain yield) were reduced by salinity. Durum wheat landraces, Mahmoudi and Hmira, and improved varieties, Maali and Om Rabia showed the widest adaptability to different quality of irrigation water. Genotypes including Jneh Kotifa and Arbi were estimated as stable genotypes under adverse conditions. Thereafter, salt-tolerant (Hmira and Jneh Khotifa) and the most cultivated high-yielding (Karim, Razzak and Khiar) genotypes were tested for their gynogenetic ability to obtain haploids and doubled haploid lines. Genotypes with good induction capacity had not necessarily a good capacity of regeneration of haploid plantlets. In our conditions, Hmira and Khiar exhibited the best gynogenetic ability (3.1% and 2.9% of haploid plantlets, respectively).     

PTGS2 (COX-2) −765 G > C functional promoter polymorphism and its association with risk and lymph node metastasis in nasopharyngeal carcinoma

Cyclooxygenase-2 (Cox-2) is a key enzyme in the conversion of arachidonic acid to prostaglandins that has been shown to have a particular importance in the progression of several malignancies including nasopharyngeal carcinoma (NPC). In the current report, we designed a case-controlled study to evaluate the susceptibility and prognostic implications of the functional −765 G > C genetic variation in NPC. A PCR and restriction fragment length polymorphism analysis was used to determine the polymorphism in a Tunisian population of patients with NPC (n = 180) and in healthy control subjects (n = 169). A higher risk for NPC was observed for carriers of COX-2 −765 C allele (OR = 1.76; P = 0.01). This association remains significant after adjustments for age and sex (OR = 1.89; P = 0.008). Regarding prognostic indicators, a significant association was found between −765 C allele carriers and the presence of lymph node metastasis (OR = 2.28; P = 0.01), as well as, with tumor stage (OR = 2.73; P = 0.03). This is the first report on the studies of COX-2 SNPs in NPC and our data suggest that this genetic variant may play a role in mediating susceptibility to NPC, as well as, in neoplastic progression, a finding which further supports the involvement of COX-2 in NPC etiology. Hela Ben Nasr and Karim Chahed contributed equally to the study.     

Tests of adaptation: functional studies of pollen removal and estimates of natural selection on anther position in wild radish

Background

There are a number of difficulties associated with the study of adaptation. One is a lack of variation in the trait, which is common in adaptations because past selection has removed unfit variants. This lack of variation makes it difficult to determine the relationship between trait variation and fitness. Another difficulty is proving causation in this trait–fitness relationship, because a correlated trait might be the actual adaptation. These difficulties can be ameliorated at least partially by combining studies of natural variation with studies of experimentally manipulated traits and traits whose variance has been augmented by artificial selection.

Scope

We review here a number of our studies on the adaptive value of two aspects of anther position in wild radish (Raphanus raphanistrum, Brassicaceae): anther exsertion, i.e. the degree to which anthers protrude from the mouth of the corolla tube, and anther height dimorphism, i.e. the difference in lengths of the filaments between the two short and four long stamens. We have used both functional analyses, in which the response variable is pollen removal, and measurements of selection, in which the response variable is lifetime male fitness estimated by molecular genetic paternity analyses. In these studies we use both the natural variation in populations as well as manipulated variation, the latter through both stamen removal and artificial selection, to re-create the ancestral trait conditions.

Conclusions

Our work provides convincing evidence that intermediate anther exsertion values are adaptive, and that this is probably an adaptation to a subset of the pollinator fauna, small bees. The picture for anther height dimorphism is much less clear, as the weight of current evidence suggests that current values of this trait might actually be maladaptive; however, if this is true it is difficult to understand how the dimorphism is maintained across the family Brassicaceae.Key words: Wild radish, Raphanus raphanistrum, adaptation, natural selection, anther position, pollination, pollen removal     

Malachite green decolourization and detoxification by the laccase from a newly isolated strain of Trametes sp.

The decolourization and detoxification of the triarylmethane dye Malachite green (MG) by laccase from Trametes sp. were investigated. The laccase decolorized efficiently the dye down to 97% of 50 mg L^?1 initial concentration of MG when only 0.1 U mL^?1 of laccase was used in the reaction mixture. The effects of different physicochemical parameters were tested and optimal decolourization rates occurred at pH 6 and at temperatures between 50 and 60 °C. Decolourization of MG occurred in the presence of metal ions which could be found in textile industry effluent. 1-hydroxybenzotriazole (HBT) affected positively the decolourization of MG. The presence of some phenolic compounds namely ferulic, coumaric, gallic, and tannic acids was found to be inhibiting for the decolourization at a concentration of 10 mM.The effect of laccase inhibitors in the decolourization of MG was tested with l-cysteine, and ethylene diamine tetra-acetic acid (EDTA) at concentrations of 0.1, 1 and 10 mM. It was demonstrated that l-cysteine and EDTA inhibited the decolourization starting from 1 mM concentration. However, for NaCl a concentration of 100 mM was needed for the inhibition of laccase. The decolourization of MG resulted in the removal of its toxicity against Phanerochaete chrysosporium.The stability of the laccase toward temperature and HBT free radicals was also assessed during MG decolourization. It was shown that laccase was stable at 50 °C but in the presence of the laccase mediator HBT, the stability of the enzyme was severely affected resulting in a loss of 50% of the activity after 3 h incubation.     

Broad-range PCR,cloning and sequencing of the full 16S rRNA gene for detection of bacterial DNA in synovial fluid samples of Tunisian patients with reactive and undifferentiated arthritis

Introduction

Broad-range rDNA PCR provides an alternative, cultivation-independent approach for identifying bacterial DNA in reactive and other form of arthritis. The aim of this study was to use broad-range rDNA PCR targeting the 16S rRNA gene in patients with reactive and other forms of arthritis and to screen for the presence of DNA from any given bacterial species in synovial fluid (SF) samples.

Methods

We examined the SF samples from a total of 27 patients consisting of patients with reactive arthritis (ReA) (n = 5), undifferentiated arthritis (UA) (n = 9), rheumatoid arthritis (n = 7), and osteoarthritis (n = 6) of which the latter two were used as controls. Using broad-range bacterial PCR amplifying a 1400 bp fragment from the 16S rRNA gene, we identified and sequenced at least 24 clones from each SF sample. To identify the corresponding bacteria, DNA sequences were compared to the EMBL (European Molecular Biology Laboratory) database.

Results

Bacterial DNA was identified in 20 of the 27 SF samples (74, 10%). Analysis of a large number of sequences revealed the presence of DNA from more than one single bacterial species in the SF of all patients studied. The nearly complete sequences of the 1400 bp were obtained for most of the detected species. DNA of bacterial species including Shigella species, Escherichia species, and other coli-form bacteria as well as opportunistic pathogens such as Stenotrophomonas maltophilia and Achromobacter xylosoxidans were shared in all arthritis patients. Among pathogens described to trigger ReA, DNA from Shigella sonnei was found in ReA and UA patients. We also detected DNA from rarely occurring human pathogens such as Aranicola species and Pantoea ananatis. We also found DNA from bacteria so far not described in human infections such as Bacillus niacini, Paenibacillus humicus, Diaphorobacter species and uncultured bacterium genera incertae sedis OP10.

Conclusions

Broad-range PCR followed by cloning and sequencing the entire 16S rDNA, allowed the identification of the bacterial DNA environment in the SF samples of arthritic patients. We found a wide spectrum of bacteria including those known to be involved in ReA and others not previously associated with arthritis.     

Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit

Background

Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.

Principal Findings

In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.

Conclusions

Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.