Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses

Cassava is infected by numerous geminiviruses in Africa and India that cause devastating losses to poor farmers. We here describe the molecular diversity of seven representative cassava mosaic geminiviruses (CMGs) infecting cassava from multiple locations in Tanzania. We report for the first time the presence of two isolates in East Africa: (EACMCV-[TZ1] and EACMCV-[TZ7]) of the species East African cassava mosaic Cameroon virus, originally described in West Africa. The complete nucleotide sequence of EACMCV-[TZ1] DNA-A and DNA-B components shared a high overall sequence identity to EACMCV-[CM] components (92% and 84%). The EACMCV-[TZ1] and -[TZ7] genomic components have recombinations in the same genome regions reported in EACMCV-[CM], but they also have additional recombinations in both components. Evidence from sequence analysis suggests that the two strains have the same ancient origin and are not recent introductions. EACMCV-[TZ1] occurred widely in the southern part of the country. Four other CMG isolates were identified: two were close to the EACMV-Kenya strain (named EACMV-[KE/TZT] and EACMV-[KE/TZM] with 96% sequence identity); one isolate, TZ10, had 98% homology to EACMV-UG2Svr and was named EACMV-UG2 [TZ10]; and finally one isolate was 95% identical to EACMV-[TZ] and named EACMV-[TZ/YV]. One isolate of African cassava mosaic virus with 97% sequence identity with other isolates of ACMV was named ACMV-[TZ]. It represents the first ACMV isolate from Tanzania to be sequenced. The molecular variability of CMGs was also evaluated using partial B component nucleotide sequences of 13 EACMV isolates from Tanzania. Using the sequences of all CMGs currently available, we have shown the presence of a number of putative recombination fragments that are more prominent in all components of EACMV than in ACMV. This new knowledge about the molecular CMG diversity in East Africa, and in Tanzania in particular, has led us to hypothesize about the probable importance of this part of Africa as a source of diversity and evolutionary change both during the early stages of the relationship between CMGs and cassava and in more recent times. The existence of multiple CMG isolates with high DNA genome diversity in Tanzania and the molecular forces behind this diversity pose a threat to cassava production throughout the African continent.     

Classification of <Emphasis Type="Italic">Rhizoctonia</Emphasis> spp. using rDNA-ITS sequence analysis supports the genetic basis of the classical anastomosis grouping

Currently, rDNA-ITS sequence analysis seems to be the most appropriate method for comprehensive classification of Rhizoctonia spp. Our previous review article was concerned with detailed analysis of multinucleate Rhizoctonia (MNR), and the current review complements the previous one with detailed analysis of binucleate Rhizoctonia (BNR) (teleomorphs: Ceratobasidium spp. and Tulasnella spp.) and uninucleate Rhizoctonia (UNR) (teleomorph: C. bicorne). Data of all the appropriate BNR and UNR accumulated in GenBank were analyzed together in neighbor-joining (NJ) trees supplemented with percent sequence similarity within and among the anastomosis groups (AGs) and subgroups. Generally, the clusters of the isolate sequences supported the genetic basis for the AG based on hyphal fusion anastomosis. Comprehensive interrelationships among all the currently available MNR, BNR, and UNR groups and subgroups in GenBank were subsequently analyzed in NJ and maximum-parsimony (MP) trees, showing the genetic relatedness among the different groups and indicating possible bridging groups between MNR, BNR, and UNR. The review also indicates serious inaccuracies in designation of sequences of some isolates deposited in GenBank. Several additional teleomorph genera with Rhizoctonia spp. anamorphs have also been reported in the literature. However, as they have not been intensively studied, there were no available data on their rDNA-ITS sequences that could be included in this review.     

PhySIC_IST: cleaning source trees to infer more informative supertrees

Background  

Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene coalescence. When topological conflicts occur among source trees, liberal methods infer supertrees containing the most frequent alternative, while veto methods infer supertrees not contradicting any source tree, i.e. discard all conflicting resolutions. When the source trees host a significant number of topological conflicts or have a small taxon overlap, supertree methods of both kinds can propose poorly resolved, hence uninformative, supertrees.     

Effects of estradiol and FSH on maturation of the testis in the hypogonadal (hpg) mouse

Background  

The hypogonadal (hpg) mouse is widely used as an animal model with which to investigate the endocrine regulation of spermatogenesis. Chronic treatment of these GnRH-deficient mice with estradiol is known to induce testicular maturation and restore qualitatively normal spermatogenesis. The aim of the current studies was to investigate whether these effects of estradiol are direct effects in the testis, or indirect actions via paradoxical stimulation of FSH secretion from the pituitary gland.     

Delayed blockade of the kinin B1 receptor reduces renal inflammation and fibrosis in obstructive nephropathy

Renal fibrosis is the common histological feature of advanced glomerular and tubulointerstitial disease leading to end-stage renal disease (ESRD). However, specific antifibrotic therapies to slow down the evolution to ESRD are still absent. Because persistent inflammation is a key event in the development of fibrosis, we hypothesized that the proinflammatory kinin B1 receptor (B1R) could be such a new target. Here we show that, in the unilateral ureteral obstruction model of renal fibrosis, the B1R is overexpressed and that delayed treatment with an orally active nonpeptide B1R antagonist blocks macrophage infiltration, leading to a reversal of the level of renal fibrosis. In vivo bone marrow transplantation studies as well as in vitro studies on renal cells show that part of this antifibrotic mechanism of B1R blockade involves a direct effect on resident renal cells by inhibiting chemokine CCL2 and CCL7 expression. These findings suggest that blocking the B1R is a promising antifibrotic therapy.     

Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants

Background  

Toxoplasma gondii is a zoonotic parasite of global importance. In common with many protozoan parasites it has the capacity for sexual recombination, but current evidence suggests this is rarely employed. The global population structure is dominated by a small number of clonal genotypes, which exhibit biallelic variation and limited intralineage divergence. Little is known of the genotypes present in Africa despite the importance of AIDS-associated toxoplasmosis.     

Incorporation of genotype effects into animal model evaluations when only a small fraction of the population has been genotyped

The method of Israel and Weller (Estimation of candidate gene effects in dairy cattle populations. Journal of Dairy Science 1998, 81, 1653-1662) to estimate quantitative trait locus (QTL) effects when only a small fraction of the population was genotyped was investigated by simulation. The QTL effect was underestimated in all cases, but bias was greater for extreme allelic frequencies, and increased with the number of generations included in the simulations. Apparently, as the fraction of animals with inferred genotypes increases, the genotype probabilities tend to 'mimic' the effect of relationships. Unbiased estimates of QTL effects were derived by a modified 'cow model' without the inclusion of the relationship matrix on simulated data, even though only a small fraction of the population was genotyped. This method yielded empirically unbiased estimates for the effects of the genes DGAT1 and ABCG2 on milk production traits in the Israeli Holstein population. Based on these results, an efficient algorithm for marker-assisted selection in dairy cattle was proposed. Quantitative trait loci effects are estimated and subtracted from the cows' records. Genetic evaluations are then computed for the adjusted records. Animals are then selected based on the sum of their polygenic genetic evaluations and QTL effects. This scheme differs from a traditional dairy cattle breeding scheme in that all bull calves were considered candidates for selection. At year 10, total genetic gain was 20% greater by the proposed algorithm as compared to the selection based on a standard animal model for a locus with a substitution effect of 0.5 phenotypic standard deviations. The proposed method is easy to apply, and all required software are 'on the shelf.' It is only necessary to genotype breeding males, which are a very small fraction of the entire population. The method is flexible with respect to the model used for routine genetic evaluation. Any number of genetic markers can be easily incorporated into the algorithm, and the reduction in genetic gain due to incorrect QTL determination is minimal.     

Identification of a lithium interaction site in the gamma-aminobutyric acid (GABA) transporter GAT-1

The sodium- and chloride-dependent electrogenic gamma-aminobutyric acid (GABA) transporter GAT-1, which transports two sodium ions together with GABA, is essential for synaptic transmission by this neurotransmitter. Although lithium by itself does not support GABA transport, it has been proposed that lithium can replace sodium at one of the binding sites but not at the other. To identify putative lithium selectivity determinants, we have mutated the five GAT-1 residues corresponding to those whose side chains participate in the sodium binding sites Na1 and Na2 of the bacterial leucine-transporting homologue LeuT(Aa). In GAT-1 and in most other neurotransmitter transporter family members, four of these residues are conserved, but aspartate 395 replaces the Na2 residue threonine 354. At varying extracellular sodium, lithium stimulated sodium-dependent transport currents as well as [3H]GABA uptake in wild type GAT-1. The extent of this stimulation was dependent on the GABA concentration. In mutants in which aspartate 395 was replaced by threonine or serine, the stimulation of transport by lithium was abolished. Moreover, these mutants were unable to mediate the lithium leak currents. This phenotype was not observed in mutants at the four other positions, although their transport properties were severely impacted. Thus at saturating GABA, the site corresponding to Na2 behaves as a low affinity sodium binding site where lithium can replace sodium. We propose that GABA participates in the other sodium binding site, just like leucine does in the Na1 site, and that at limiting GABA, this site determines the apparent sodium affinity of GABA transport.