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.     

Vitamin D Status Is Positively Correlated with Regulatory T Cell Function in Patients with Multiple Sclerosis

Background

In several autoimmune diseases, including multiple sclerosis (MS), a compromised regulatory T cell (Treg) function is believed to be critically involved in the disease process. In vitro, the biologically active metabolite of vitamin D has been shown to promote Treg development. A poor vitamin D status has been linked with MS incidence and MS disease activity. In the present study, we assess a potential in vivo correlation between vitamin D status and Treg function in relapsing remitting MS (RRMS) patients.

Methodology/Principal Findings

Serum levels of 25-hydroxyvitamin D (25(OH)D) were measured in 29 RRMS patients. The number of circulating Tregs was assessed by flow-cytometry, and their functionality was tested in vitro in a CFSE-based proliferation suppression assay. Additionally, the intracellular cytokine profile of T helper cells was determined directly ex-vivo by flow-cytometry. Serum levels of 25(OH)D correlated positively with the ability of Tregs to suppress T cell proliferation (R = 0.590, P = 0.002). No correlation between 25(OH)D levels and the number of Tregs was found. The IFN-γ/IL-4 ratio (Th1/Th2-balance) was more directed towards IL-4 in patients with favourable 25(OH)D levels (R = −0.435, P = 0.023).

Conclusions/Significance

These results show an association of high 25(OH)D levels with an improved Treg function, and with skewing of the Th1/Th2 balance towards Th2. These findings suggest that vitamin D is an important promoter of T cell regulation in vivo in MS patients. It is tempting to speculate that our results may not only hold for MS, but also for other autoimmune diseases. Future intervention studies will show whether modulation of vitamin D status results in modulation of the T cell response and subsequent amelioration of disease activity.     

Genetic Mechanisms in Apc-Mediated Mammary Tumorigenesis

Many components of Wnt/β-catenin signaling pathway also play critical roles in mammary tumor development, yet the role of the tumor suppressor gene APC (adenomatous polyposis coli) in breast oncongenesis is unclear. To better understand the role of Apc in mammary tumorigenesis, we introduced conditional Apc mutations specifically into two different mammary epithelial populations using K14-cre and WAP-cre transgenic mice that express Cre-recombinase in mammary progenitor cells and lactating luminal cells, respectively. Only the K14-cre–mediated Apc heterozygosity developed mammary adenocarcinomas demonstrating histological heterogeneity, suggesting the multilineage progenitor cell origin of these tumors. These tumors harbored truncation mutation in a defined region in the remaining wild-type allele of Apc that would retain some down-regulating activity of β-catenin signaling. Activating mutations at codons 12 and 61 of either H-Ras or K-Ras were also found in a subset of these tumors. Expression profiles of acinar-type mammary tumors from K14-cre; Apc^CKO/+ mice showed luminal epithelial gene expression pattern, and clustering analysis demonstrated more correlation to MMTV-neu model than to MMTV-Wnt1. In contrast, neither WAP-cre–induced Apc heterozygous nor homozygous mutations resulted in predisposition to mammary tumorigenesis, although WAP-cre–mediated Apc deficiency resulted in severe squamous metaplasia of mammary glands. Collectively, our results suggest that not only the epithelial origin but also a certain Apc mutations are selected to achieve a specific level of β-catenin signaling optimal for mammary tumor development and explain partially the colon- but not mammary-specific tumor development in patients that carry germline mutations in APC.     

Broadband Criticality of Human Brain Network Synchronization

Self-organized criticality is an attractive model for human brain dynamics, but there has been little direct evidence for its existence in large-scale systems measured by neuroimaging. In general, critical systems are associated with fractal or power law scaling, long-range correlations in space and time, and rapid reconfiguration in response to external inputs. Here, we consider two measures of phase synchronization: the phase-lock interval, or duration of coupling between a pair of (neurophysiological) processes, and the lability of global synchronization of a (brain functional) network. Using computational simulations of two mechanistically distinct systems displaying complex dynamics, the Ising model and the Kuramoto model, we show that both synchronization metrics have power law probability distributions specifically when these systems are in a critical state. We then demonstrate power law scaling of both pairwise and global synchronization metrics in functional MRI and magnetoencephalographic data recorded from normal volunteers under resting conditions. These results strongly suggest that human brain functional systems exist in an endogenous state of dynamical criticality, characterized by a greater than random probability of both prolonged periods of phase-locking and occurrence of large rapid changes in the state of global synchronization, analogous to the neuronal “avalanches” previously described in cellular systems. Moreover, evidence for critical dynamics was identified consistently in neurophysiological systems operating at frequency intervals ranging from 0.05–0.11 to 62.5–125 Hz, confirming that criticality is a property of human brain functional network organization at all frequency intervals in the brain's physiological bandwidth.     

A dual resistance gene system prevents infection by three distinct pathogens

Colletotrichum higginsianum causes typical anthracnose lesions on the leaves, petioles, and stems of cruciferous plants. Inoculation of Arabidopsis thaliana ecotype Columbia leaves with C. higginsianum results in fungal growth and disease symptoms reminiscent of those induced in other cruciferous plants. We performed map-based cloning and natural variation analysis of 19 A. thaliana ecotypes to identify a dominant resistance locus against C. higginsianum. We found that the A. thaliana RCH2 (for recognition of C. higginsianum) locus encodes two NB-LRR proteins, both of which are required for resistance to C. higginsianum in the A. thaliana ecotype Ws-0. Both proteins are well-characterized R proteins involved in resistance against bacterial pathogens; RRS1 (resistance to Ralstonia solanacearum 1) confers resistance to strain Rs1000 of R. solanacearum and RPS4 to Pseudomonas syringae pv. tomato strain DC3000 expressing avrRps4 (Pst-avrRps4). Furthermore, we found that both RRS1-Ws and RPS4-Ws genes are required for resistance to Pst-avrRps4 and to Rs1002 R. solanacearum. We therefore demonstrate that a pair of neighboring genes, RRS1-Ws and RPS4-Ws, function cooperatively as a dual R-gene system against at least three distinct pathogens.Key words: R gene, RPS4, RRS1, Colletotrichum higginsianum, Pseudomonas syringae, Ralstonia solanacearumPlants are exposed to various types of potentially invasive organisms, including viruses, bacteria, fungi, nematodes and protozoa, but are able to defend themselves by activating multiple defense mechanisms. The gene-for-gene hypothesis¹ provides a mechanism for specific recognition of the pathogen by the plant. This recognition is mediated by direct or indirect interactions between the product of a plant resistance (R) gene and the corresponding effectors encoded by avirulence genes in the pathogen.² Most R-genes encode non-membrane proteins that contain a conserved nucleotide-binding (NB) site and a carboxy-terminal leucine-rich repeat (LRR) domain.The A. thaliana genome contains about 150 genes coding for NB-LRR-containing proteins.³ This is far less than the number of genes that would be required to respond individually and specifically to all of its potential pathogens. However, plants may have been able to limit the number of required NB-LRR-encoding genes if host proteins perceive sets of distinct pathogens.⁴Colletotrichum species cause devastating anthracnose diseases in a large number of agronomically important crops. These diseases can often be controlled by introduction of genetic resistance traits, but the molecular components of resistance remain unknown. Inoculation of A. thaliana ecotype Columbia (Col-0) leaves with Colletotrichum higginsianum results in fungal growth and disease symptoms reminiscent of those induced in other cruciferous plants.^5,6 Inoculation of a large number of ecotypes with isolates of C. higginsianum showed that A. thaliana has at least two dominant resistance gene loci, designated RCH1 and RCH2 (for recognition of C. higginsianum), indicating that A. thaliana resistance to C. higginsianum is controlled by a “gene-for-gene” interaction.⁵ In a previous study, we identified a single putative R locus, RCH1 on the top of chromosome 4, in the C. higginsianum-resistant A. thaliana ecotype Eil-0.⁵In the present study, the locus named RCH2 maps in an extensive cluster of disease-resistance loci known as MRC-J in the A. thaliana ecotype Ws-0. By analyzing natural variations within the MRC-J region, we found that alleles of RRS1 (resistance to Ralstonia solanacearum 1) from susceptible ecotypes contain single nucleotide polymorphisms that may affect the encoded protein. Consistent with this finding, two susceptible mutants, rrs1-1 and rrs1–2, were identified by screening a T-DNA-tagged mutant library for the loss of resistance to C. higginsianum. The screening identified an additional susceptible mutant (rps4-21), which has a 5-bp deletion in the neighboring gene, RPS4-Ws, a well-characterized R gene that provides resistance to Pseudomonas syringae pv. tomato strain DC3000 expressing avrRps4 (Pst-avrRps4). To assess if RRS1-Ws and RPS4-Ws function in concert, we generated an rps4-21/rrs1-1 double mutant by crossing rps4-21 and rrs1-1 mutants. The susceptibility levels of rps4-21/rrs1-1 double mutant to C. higginsianum were similar to that exhibited by the single mutants, suggesting that RRS1-Ws and RPS-4-Ws function cooperatively. We also found that both RRS1 and RPS4 are required for resistance to R. solanacearum and Pst-avrRps4. Thus, these two adjacent R genes confer resistance, in tandem or individually, to three distinct pathogens with very different infection strategies and virulence mechanisms (Fig. 1).Open in a separate windowFigure 1RPS4 and RRS1 function as a dual resistance gene system that prevents infection by three distinct pathogens (Colletotrichum higginsianum, Ralstonia solanacearum and Pseudomonas syringae pv. tomato strain DC3000 expressing avrRps4).Several examples of two NB-LRR genes acting cooperatively to confer resistance against a pathogen have been reported. For example, A. thaliana RPP2A and RPP2B reside adjacently in the RPP2 locus.⁷ Blast resistance in Pikm-containing rice is conferred by a combination of two NB-LRR encoding genes, Pikm1-TS and Pikm2-TS.⁸ Pi5-mediated resistance against rice blast requires two NB-LRR-encoding genes.⁹ It is not known whether these NB-LRR genes function cooperatively or independently. Because of structural similarity with RRS1/RPS4 genes, it is possible that resistance to the pathogens is conferred by cooperation between the two NB-LRR genes.Several reports have shown that a single R gene/locus can confer resistance to multiple pathogens. For instance, tomato Mi mediates resistance against three distinct types of pests, including root-knot nematodes, potato aphids and sweet potato whitefly.¹⁰ In the present study, we suggest that two distinct R-genes located in a conserved head-to-head organization confer resistance to three distinct pathogen species by acting cooperatively.The tandem function of RRS1-Ws and its neighboring gene RPS4-Ws is also supported by the evolutionary conservation of the gene pair. Close homologs of RPS4 are often physically paired with homologs of RRS1 in a head-to-head (inverted) tandem arrangement.¹¹ The evolutionary conservation of homologous gene pairs in a head-to-head arrangement also supports the idea that cooperative function of two R genes could be a common mechanism of defense against pathogens. Since the two open reading frames are only 264 bp apart, the promoter regions of the gene pairs possibly overlap, leading to co-regulation of the genes. The head-to-head configuration may assure balanced levels of the protein pair to meet a strict stoichiometric requirement to act together, possibly in a complex. As a practical application, this finding may provide a new strategy for creating transgenic plants that express R genes from other plants. Introduction of two R genes in a head-to-head orientation may be necessary for effective pathogen resistance.     

Rat forming incisor requires a rigorous ECM remodeling modulated by MMP/RECK balance

Reversion-inducing-cysteine-rich protein with Kazal motifs (RECK) is a single membrane-anchored MMP-regulator and regulates matrix metalloproteinases (MMP) 2, 9 and 14. In turn, MMPs are endopeptidases that play a pivotal role in remodeling ECM. In this work, we decided to evaluate expression pattern of RECK in growing rat incisor during, specifically focusing out amelogenesis process. Based on different kinds of ameloblasts, our results showed that RECK expression was conducted by secretory and post-secretory ameloblasts. At the secretory phase, RECK was localized in the infra-nuclear region of the ameloblast, outer epithelium, near blood vessels, and in the stellate reticulum. From the transition to the maturation phases, RECK was strongly expressed by non-epithelial immuno-competent cells (macrophages and/or dendritic-like cells) in the papillary layer. From the transition to the maturation stage, RECK expression was increased. RECK mRNA was amplified by RT-PCR from whole enamel organ. Here, we verified the presence of RECK mRNA during all stages of amelogenesis. These events were governed by ameloblasts and by non-epithelial cells residents in the enamel organ. Concluding, we found differential expression of MMPs-2, -9 and RECK in the different phases of amelogenesis, suggesting that the tissue remodeling is rigorously controlled during dental mineralization.     

Florivores decrease pollinator visitation in a self-incompatible plant

Different biotic interactions may influence one another to produce complex patterns of direct and indirect effects, which together influence plant reproductive success. However, so far most studies on plant-animal interactions have focused on single interactions in isolation. In this study, we studied the effect of florivory by the weevil Cionus nigritarsis on pollinator visitation rate in the self-incompatible perennial herb Verbascum nigrum by combining observations of florivory and pollination in natural populations with records of pollinator visitation to plants with different levels of experimentally inflicted damage.Increasing levels of damage through either natural or simulated florivory resulted in fewer pollinator visits per plant and per flower. As expected, the magnitude of the indirect effect of florivory on pollinator visitation was proportional to the intensity of florivory. Our results indicate that biotic non-pollinating agents, such as florivores, may induce substantial changes in pollinator availability. Therefore, studies addressing different plant-animal interactions in parallel are necessary to better comprehend the factors influencing the reproductive performance and demography of flowering plants.     

Caenorhabditis elegans EFA-6 limits microtubule growth at the cell cortex

Microtubules are polymers of tubulin heterodimers that exhibit dynamic instability: periods of growth followed by periods of shrinkage. However, the molecular regulation of dynamic instability remains elusive. Here, we show that EFA-6, a cortically-localized protein, limits the growth of microtubules near the cell cortex of early embryonic cells from Caenorhabditis elegans, possibly by inducing microtubule catastrophes. Compared with wild type, embryos lacking EFA-6 had abnormally long and dense microtubules at the cell cortex, and growing microtubule plus ends resided at the cortex for up to five-fold longer. Loss of EFA-6 also caused excess centrosome separation and displacement towards the cell cortex early in mitosis, and subsequently a loss of anaphase spindle-pole oscillations and increased rates of spindle elongation. The centrosome separation phenotype was dependent on the motor protein dynein, suggesting a possible link between the modulation of microtubule dynamics at the cortex and dynein-dependent force production. EFA-6 orthologues activate ARF6-type GTPases to regulate vesicle trafficking. However, we show that only the C. elegans EFA-6 amino-terminus is both necessary and sufficient to limit microtubule growth along the cortex, and that this function is independent of ARF-6.