Out of Africa and back again: nested cladistic analysis of human Y chromosome variation

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.      

Topochemical distribution of lignin and hydroxycinnamic acids in sugar-cane cell walls and its correlation with the enzymatic hydrolysis of polysaccharides

Background  

Lignin and hemicelluloses are the major components limiting enzyme infiltration into cell walls. Determination of the topochemical distribution of lignin and aromatics in sugar cane might provide important data on the recalcitrance of specific cells. We used cellular ultraviolet (UV) microspectrophotometry (UMSP) to topochemically detect lignin and hydroxycinnamic acids in individual fiber, vessel and parenchyma cell walls of untreated and chlorite-treated sugar cane. Internodes, presenting typical vascular bundles and sucrose-storing parenchyma cells, were divided into rind and pith fractions.     

Immunohistochemical expression of p53 in breast carcinoma is associated with the intron 1 BglII polymorphism of the p53 gene

Breast carcinoma is a public health problem worldwide. It is known that both genetic and environmental factors are important for breast carcinogenesis and that structural and/or functional alterations at p53 gene are commonly observed in breast tumors. In addition, polymorphisms of several genes in either their coding or non-coding sequences have been found related to cancer risk and/or clinicopathological characteristics of tumors. In this study we have evaluated the intron 1 BglII polymorphism of the p53 gene with a PCR-based approach in 117 cases of breast cancer and 102 healthy women and its association with the immunohistochemical expression of p53 in the tumors. The results showed that the presence of the polymorphism (allele 2) is highly associated with the tumor expression of p53 (p<0.0001) and that there is a trend for increased frequency of allele 2 in cases than in controls (p=0.2376). These data suggest that the germ-line variation in the intron 1 of the p53 gene could produce functional or structural changes of the protein that is reflected by its abnormal expression.     

The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology

The food industry is constantly striving to develop new products to fulfil the ever changing demands of consumers and the strict requirements of regulatory agencies. For foods based on microbial fermentation, this pushes the boundaries of microbial performance and requires the constant development of new starter cultures with novel properties. Since the use of ingredients in the food industry is tightly regulated and under close scrutiny by consumers, the use of recombinant DNA technology to improve microbial performance is currently not an option. As a result, the focus for improving strains for microbial fermentation is on classical strain improvement methods. Here we review the use of these techniques to improve the functionality of lactic acid bacteria starter cultures for application in industrial-scale food production. Methods will be described for improving the bacteriophage resistance of specific strains, improving their texture forming ability, increasing their tolerance to stress and modulating both the amount and identity of acids produced during fermentation. In addition, approaches to eliminating undesirable properties will be described. Techniques include random mutagenesis, directed evolution and dominant selection schemes.     

6-Substituted quinolines as RORγt inverse agonists

We identified 6-substituted quinolines as modulators of the retinoic acid receptor-related orphan receptor gamma t (RORγt). The synthesis of this class of RORγt modulators is reported, and optimization of the substituents at the quinoline 6-position that produced compounds with high affinity for the receptor is detailed. This effort identified molecules that act as potent, full inverse agonists in a RORγt-driven cell-based reporter assay. The X-ray crystal structures of two full inverse agonists from this chemical series bound to the RORγt ligand binding domain are disclosed, and we highlight the interaction of a hydrogen-bond acceptor on the 6-position substituent of the inverse agonist with Glu379:NH as a conserved binding contact.     

Effects of drought and elevated temperature on biochemical composition of forage plants and their impact on carbon storage in grassland soil

Aims

The objective of this study was to investigate the effects of future warming and drought on (1) the biochemical composition of above-ground biomass of forage plants (Festuca arundinacea and Dactylis glomerata), (2) the potential mineralization of this material in soil, and (3) its priming effect on native soil organic matter.

Methods

We sampled above-ground plant material from spring regrowth and summer regrowth of a climate change experiment. While in spring, the plants were well watered, the summer regrowth was exposed to drought and elevated temperature (+3 °C) by infrared heating of the canopy during 3 weeks. We assessed the elemental and isotopic composition, lignin and non-cellulosic carbohydrate content and composition of plant material grown under all three conditions. Its mineralization potential in soil and priming effects were evaluated during laboratory incubation.

Results

Warming had no significant effect on elemental and stable isotope composition of both plant materials. In contrast, it resulted in reduction of lignin content for both plant species and decrease of the lignin-to-N ratio for F. arundinacea and increased non-cellulosic carbohydrate content for D. glomerata. Summer regrowth was characterised by increase of δ¹³C values, which is consistent with variations in stomatal conductance due to water shortage. Moreover, summer drought induced an increase in N content leading to decrease of the C/N ratio and increase of lignin-to-N ratio of summer regrowth compared to spring regrowth. Differences in decomposition were small, while priming effects were more strongly altered by the different exposure to enviromental.

Conclusion

Our results provide direct experimental evidence that extreme climatic events (high temperature and precipitation deficit) have an influence on soil carbon storage particularly through their effect on priming of native soil organic matter induced by altered plant litter. These effects seem to be governed by alterations of stoichiometry and to a smaller extent by alterations of plant chemical composition.     

The Ma gene for complete-spectrum resistance to Meloidogyne species in Prunus is a TNL with a huge repeated C-terminal post-LRR region

Root-knot nematode (RKN) Meloidogyne species are major polyphagous pests of most crops worldwide, and cultivars with durable resistance are urgently needed because of nematicide bans. The Ma gene from the Myrobalan plum (Prunus cerasifera) confers complete-spectrum, heat-stable, and high-level resistance to RKN, which is remarkable in comparison with the Mi-1 gene from tomato (Solanum lycopersicum), the sole RKN resistance gene cloned. We report here the positional cloning and the functional validation of the Ma locus present at the heterozygous state in the P.2175 accession. High-resolution mapping totaling over 3,000 segregants reduced the Ma locus interval to a 32-kb cluster of three Toll/Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat (LRR) genes (TNL1-TNL3), including a pseudogene (TNL2) and a truncated gene (TNL3). The sole complete gene in this interval (TNL1) was validated as Ma, as it conferred the same complete-spectrum and high-level resistance (as in P.2175) using its genomic sequence and native promoter region in Agrobacterium rhizogenes-transformed hairy roots and composite plants. The full-length cDNA (2,048 amino acids) of Ma is the longest of all Resistance genes cloned to date. Its TNL structure is completed by a huge post-LRR (PL) sequence (1,088 amino acids) comprising five repeated carboxyl-terminal PL exons with two conserved motifs. The amino-terminal region (213 amino acids) of the LRR exon is conserved between alleles and contrasts with the high interallelic polymorphisms of its distal region (111 amino acids) and of PL domains. The Ma gene highlights the importance of these uncharacterized PL domains, which may be involved in pathogen recognition through the decoy hypothesis or in nuclear signaling.