Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution

The megadiverse haplochromine cichlid radiations of the East African lakes, famous examples of explosive speciation and adaptive radiation, are according to recent studies, introgressed by different riverine lineages. This study is based on the first comprehensive mitochondrial and nuclear DNA dataset from extensive sampling of riverine haplochromine cichlids. It includes species from the lower River Congo and Angolan (River Kwanza) drainages. Reconstruction of phylogenetic hypotheses revealed the paradox of clearly discordant phylogenetic signals. Closely related mtDNA haplotypes are distributed thousands of kilometres apart and across major African watersheds, whereas some neighbouring species carry drastically divergent mtDNA haplotypes. At shallow and deep phylogenetic layers, strong signals of hybridization are attributed to the complex Late Miocene/Early Pliocene palaeohistory of African rivers. Hybridization of multiple lineages across changing watersheds shaped each of the major haplochromine radiations in lakes Tanganyika, Victoria, Malawi and the Kalahari Palaeolakes, as well as a miniature species flock in the Congo basin (River Fwa). On the basis of our results, introgression occurred not only on a spatially restricted scale, but massively over almost the whole range of the haplochromine distribution. This provides an alternative view on the origin and exceptional high diversity of this enigmatic vertebrate group.     

Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae

On the basis of functional and phylogenetic criteria, we have identified a total of 229 subfamilies and 111 singletons predicted to carry out transport or other membrane functions in Saccharomyces cerevisiae. We have extended the Transporter Classification (TC) and created a Membrane Classification (MC) for non-transporter membrane proteins. Using the preliminary phylogenetic digits X, Y, Z (for new families, subfamilies, and clusters, respectively), we allocated a five-digit number to 850 proteins predicted to contain more than two transmembrane domains. Compared with a previous TC of the yeast genome, we classified an additional set of 538 membrane proteins (transporters and non-transporters) and identified 111 novel phylogenetic subfamilies. Electronic Publication     

Separate Branches of the uvr Gene-Dependent Excision Repair Process in Ultraviolet-Irradiated Escherichia coli K-12 Cells; Their Dependence upon Growth Medium and the polA, recA, recB, and exrA Genes

The extent of repair of single-strand breaks (incision breaks) induced in the deoxyribonucleic acid (DNA) of Escherichia coli K-12 cells by the uvr gene-dependent excision repair process after ultraviolet (UV) radiation was determined in the wild-type, polA1, recA56, recB21, and exrA strains. The wild-type strain repaired all incision breaks after incident doses of UV radiation (254 nm) of approximately 60 J m(-2) or less when incubated in growth medium, or approximately 15 J m(-2) or less when incubated in buffer. The polA1 strain repaired the incision breaks completely after incident doses of approximately 12 J m(-2) or less when incubated in growth medium, or after approximately 4 J m(-2) when incubated in buffer. The recA13, recB21, and exrA strains showed essentially complete repair after incident doses of 10 to 15 J m(-2) whether the cells were incubated in buffer or growth medium. These results suggest that the uvr gene-dependent excision repair process may be divided into two branches, one which is dependent on the presence of growth medium and also the rec(+)exr(+) genotype, and a second which can occur in buffer (growth medium-independent) and is largely dependent on DNA polymerase I. The presence of chloramphenicol in the growth medium resulted in an inhibition of the growth medium-dependent repair occurring in wild-type and polA1 cells and had little or no effect on the extent of repair observed in recA56, recB21, or exrA cells. The similarities between the growth medium-dependent and -independent branches of excision repair and two known processes for the repair of X-ray-induced single-strand breaks are discussed.     

Inhibition of protein synthesis in a polyribosome-dependent cell-free system by a specific ribonuclease prepared from the follicles of two different stages of development of the silkmothAntherea pernyi

Summary Crude, cell-free protein-synthesizing systems were prepared from follicles of two different stages of development in the ovariole of the silkmothAntherea pernyi. The efficiency of the translation of natural and synthetic mRNAs in these systems was compared with that in a cell-free wheat germ system. A postmitochondrial extract (S-30) from the follicles almost completely inhibited protein synthesis in a polyribosome-dependent, cell-free systems. A specific ribonuclease, obtained from the post mitochondrial extract by ammonium sulphate precipitation, heat denaturation and DEAE-cellulose chromatography, inhibited polyribosome-dependent protein synthesis. The effect of this specific ribonuclease on the structural integrity of radioactive RNAs and ribosomal subunits, which were isolated from Ehrlich ascites tumor cells, was also studied.     

Mapping of a Gene for Long QT Syndrome to Chromosome 4q25-27

Long QT syndrome (LQTS) is a heterogeneous inherited disorder causing syncope and sudden death from ventricular arrhythmias. A first locus for this disorder was mapped to chromosome 11p15.5. However, locus heterogeneity has been demonstrated in several families, and two other loci have recently been located on chromosomes 7q35-36 and 3p21-24. We used linkage analysis to map the locus in a 65-member family in which LQTS was associated with more marked sinus bradycardia than usual, leading to sinus node dysfunction. Linkage to chromosome 11p15.5, 7q35-36, or 3p21-24 was excluded. Positive linkage was obtained for markers located on chromosome 4q25-27. A maximal LOD score of 7.05 was found for marker D4S402. The identification of a fourth locus for LQTS confirms its genetic heterogeneity. Locus 4q25-27 is associated with a peculiar phenotype within the LQTS entity.     

Invasive and adherent bacterial pathogens co-Opt host clathrin for infection

Infection by the bacterium Listeria monocytogenes depends on host cell clathrin. To determine whether this requirement is widespread, we analyzed infection models using diverse bacteria. We demonstrated that bacteria that enter cells following binding to cellular receptors (termed "zippering" bacteria) invade in a clathrin-dependent manner. In contrast, bacteria that inject effector proteins into host cells in order to gain entry (termed "triggering" bacteria) invade in a clathrin-independent manner. Strikingly, enteropathogenic Escherichia coli (EPEC) required clathrin to form actin-rich pedestals in host cells beneath adhering bacteria, even though this pathogen remains extracellular. Furthermore, clathrin accumulation preceded the actin rearrangements necessary for Listeria entry. These data provide evidence for a clathrin-based entry pathway allowing internalization of large objects (bacteria and ligand-coated beads) and used by "zippering" bacteria as part of a general mechanism to invade host mammalian cells. We also revealed a nonendocytic role for clathrin required for extracellular EPEC infections.     

Improved isolation of glucuronan from algae and the production of glucuronic acid oligosaccharides using a glucuronan lyase

A new source for the production of bioactive glucuronic acid oligosaccharides (GlcUAOs) from the depolymerization of green seaweed Ulva lactuca glucuronan (Algal glucuronan) has been investigated. Algal glucuronan purification was optimized by the acidic precipitation method which allowed us to separate the polysaccharide mixture extracted from the cell wall of Ulva lactuca using hot water containing sodium oxalate. A series of the GlcUAOs were obtained by enzyme degradation of algal glucuronan with a glucuronan lyase (GL) isolated from Trichoderma strain. The putative bioactive GlcUAOs generated were then purified by size-exclusion chromatography in gram quantity and characterized by ¹H/¹³C NMR spectroscopy and ESI-Q/TOF-mass spectrometry.     

Tropical soils degraded by slash‐and‐burn cultivation can be recultivated when amended with ashes and compost

In many tropical regions, slash‐and‐burn agriculture is considered as a driver of deforestation; the forest is converted into agricultural land by cutting and burning the trees. However, the fields are abandoned after few years because of yield decrease and weed invasion. Consequently, new surfaces are regularly cleared from the primary forest. We propose a reclamation strategy for abandoned fields allowing and sustaining re‐cultivation. In the dry region of south‐western Madagascar, we tested, according to a split‐plot design, an alternative selective slash‐and‐burn cultivation technique coupled with compost amendment on 30–year‐old abandoned fields. Corn plants (Zea mays L.) were grown on four different types of soil amendments: no amendment (control), compost, ashes (as in traditional slash‐and‐burn cultivation), and compost + ashes additions. Furthermore, two tree cover treatments were applied: 0% tree cover (as in traditional slash‐and‐burn cultivation) and 50% tree cover (selective slash‐and‐burn). Both corn growth and soil fertility parameters were monitored during the growing season 2015 up to final harvest. The amendment compost + ashes strongly increased corn yield, which was multiplied by 4–5 in comparison with ashes or compost alone, reaching 1.5 t/ha compared to 0.25 and 0.35 t/ha for ashes and compost, respectively. On control plots, yield was negligible as expected on these degraded soils. Structural equation modeling evidenced that compost and ashes were complementary fertilizing pathways promoting soil fertility through positive effects on soil moisture, pH, organic matter, and microbial activity. Concerning the tree cover treatment, yield was reduced on shaded plots (50% tree cover) compared to sunny plots (0% tree cover) for all soil amendments, except ashes. To conclude, our results provide empirical evidence on the potential of recultivating tropical degraded soils with compost and ashes. This would help mitigating deforestation of the primary forest by increasing lifespan of agricultural lands.