An Experimental Framework for Generating Evolvable Chemical Systems in the Laboratory

Most experimental work on the origin of life has focused on either characterizing the chemical synthesis of particular biochemicals and their precursors or on designing simple chemical systems that manifest life-like properties such as self-propagation or adaptive evolution. Here we propose a new class of experiments, analogous to artificial ecosystem selection, where we select for spontaneously forming self-propagating chemical assemblages in the lab and then seek evidence of a response to that selection as a key indicator that life-like chemical systems have arisen. Since surfaces and surface metabolism likely played an important role in the origin of life, a key experimental challenge is to find conditions that foster nucleation and spread of chemical consortia on surfaces. We propose high-throughput screening of a diverse set of conditions in order to identify combinations of “food,” energy sources, and mineral surfaces that foster the emergence of surface-associated chemical consortia that are capable of adaptive evolution. Identification of such systems would greatly advance our understanding of the emergence of self-propagating entities and the onset of adaptive evolution during the origin of life.     

Darwin’s legacy in <Emphasis Type="Italic">Platanthera</Emphasis>: are there more than two species in the <Emphasis Type="Italic">Platanthera bifolia/chlorantha</Emphasis> group?

In Central Europe, the genus Platanthera traditionally comprised two species, P. chlorantha Cust. ex Rchb. (Pc) and P. bifolia (L.) Rich. (Pb). They are morphologically characterized by a wide and narrow separation of anthers, respectively. However, a third form with intermediate anther distance has repeatedly been hypothesized but only hesitantly accepted. In addition, intermediate morphology has been also used as the main character of P. × hybrida. However, the status of some purported hybrid populations is challenged by the local lack of parental species, their successful reproduction and non-intermediate traits. Despite this unclear situation, detailed genetic and morphological analyses are lacking. Here, we studied morphology and molecular markers within the P. chlorantha/bifolia group in Central Europe. Three morphological groups emerged representing Pc, Pb and a third form, here informally referred to as non-hybrid intermediates (Pn). The latter is characterized, among other trait differences, by intermediate distance between anthers [(0.7)–1–2.2 mm] and long spurs (28–40 mm). Three gene pools were identified, which largely corresponded to the three morphological groups. The Pn gene pool had several high-frequency private alleles substantiating its genetic independence. Some of the Pn populations were previously interpreted as P. × hybrida suggesting that Pn was overlooked hitherto and mistaken to represent hybrids. The non-perfect fit between morphological and genetic groups highlights the potential for fast morphological evolution. Overall, the finding of three distinct lineages within the bifolia/chlorantha group necessitates a thorough reanalysis of reported taxa and a reevaluation of our understanding of their distribution, ecology and evolution.     

Molecular confirmation of the genomic constitution of <Emphasis Type="Italic">Douglasdeweya</Emphasis> (Triticeae: Poaceae): demonstration of the utility of the 5S rDNA sequence as a tool for haplome identification

A new genus Douglasdeweya containing the two species, Douglasdeweya deweyi and D. wangii was published in 2005 by Yen et al. based upon the results of cytogenetical and morphological findings. The genome constitution of Douglasdeweya-PPStSt-allowed its segregation from the genus Pseudoroegneria which contains the StSt or StStStSt genomes. Our previous work had demonstrated the utility of using 5S rDNA units, especially the non-transcribed spacer sequence variation, for the resolution of genomes (haplomes) previously established by cytology. Here, we show that sequence analysis of the 5S DNA units from these species strongly supports the proposed species relationships of Yen et al. (Can J Bot 83:413-419, 2005), i.e., the PP genome from Agropyron and the StSt genome from Pseudoroegneria. Analysis of the 5S rDNA units constitutes a powerful tool for genomic research especially in the Triticeae.     

Parasitism proteins in nematode-plant interactions

The current battery of candidate parasitism proteins secreted by nematodes to modify plant tissues for parasitism includes cell-wall-modifying enzymes of potential prokaryotic origin, multiple regulators of host cell cycle and metabolism, proteins that can localize to the plant cell nucleus, potential suppressors of host defense, mimics of plant molecules, and a relatively large cadre of predicted novel nematode parasitism proteins. Phenotypic effects of expressing nematode parasitism proteins in transformed plant tissues, protein-protein interaction assays, and RNA-mediated interference (RNAi) analyses are currently providing exciting evidence of the biological role of candidate nematode secreted parasitism proteins and identifying potential novel means of developing transgenic resistance to nematodes in crops.     

Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley

A ‘core set’ of 28 simple sequence repeat (SSR) and 28 single nucleotide polymorphism (SNP) markers for barley was developed after screening six diverse genotypes (DGs) representing six countries (Afghanistan, Pakistan, Algeria, Egypt, Jordan and Syria) with 50 SSR and 50 SNP markers derived from expressed sequence tags (ESTs). The markers of the core set are single locus with very high quality amplifications, high polymorphism information content (PIC) and are distributed across the barley genome. PIC values for the selected SSR and SNP markers ranged between 0.32–0.72 (average 0.58) and 0.28–0.50 (average 0.42), respectively. To make the SNP genotyping cost effective, CAPS (cleaved amplified polymorphic sequence) and indel assays were developed for 23 markers and the remaining 5 SNP markers were optimized for pyrosequencing. A high coefficient of correlations (r = 0.96, P < 0.005) between the genetic similarity matrices of SSR and SNP genotyping data of the core set on diverse genotypes (DGs) and their similar groupings according to the geographical distribution in both SSR and SNP phenograms with high bootstrap values underline the utility and reliability of the core set. A comparative allelic and sequence diversity for SSR and SNP markers between the DGs and six elite parental genotypes (PGs) of mapping populations showed comparable diverse nature of two germplasm sets. However, unique SNPs and indels were observed in both germplasm sets providing more datapoints for analysing haplotypes in a better way for the corresponding SNP marker. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A malaria parasite formin regulates actin polymerization and localizes to the parasite-erythrocyte moving junction during invasion

Malaria parasites invade host cells using actin-based motility, a process requiring parasite actin filament nucleation and polymerization. Malaria and other apicomplexan parasites lack Arp2/3 complex, an actin nucleator widely conserved across eukaryotes, but do express formins, another type of actin nucleator. Here, we demonstrate that one of two malaria parasite formins, Plasmodium falciparum formin 1 (PfFormin 1), and its ortholog in the related parasite Toxoplasma gondii, follows the moving tight junction between the invading parasite and the host cell, which is the predicted site of the actomyosin motor that powers motility. Furthermore, in vitro, the PfFormin1 actin-binding formin homology 2 domain is a potent nucleator, stimulating actin polymerization and, like other formins, localizing to the barbed end during filament elongation. These findings support a conserved molecular mechanism underlying apicomplexan parasite motility and, given the essential role that actin plays in cell invasion, highlight formins as important determinants of malaria parasite pathogenicity.     

C. elegans AP-2 and retromer control Wnt signaling by regulating mig-14/Wntless

While endocytosis can regulate morphogen distribution, its precise role in shaping these gradients is unclear. Even more enigmatic is the role of retromer, a complex that shuttles proteins between endosomes and the Golgi apparatus, in Wnt gradient formation. Here we report that DPY-23, the C. elegans mu subunit of the clathrin adaptor AP-2 that mediates the endocytosis of membrane proteins, regulates Wnt function. dpy-23 mutants display Wnt phenotypes, including defects in neuronal migration, neuronal polarity, and asymmetric cell division. DPY-23 acts in Wnt-expressing cells to promote these processes. MIG-14, the C. elegans homolog of the Wnt-secretion factor Wntless, also acts in these cells to control Wnt function. In dpy-23 mutants, MIG-14 accumulates at or near the plasma membrane. By contrast, MIG-14 accumulates in intracellular compartments in retromer mutants. Based on our observations, we propose that intracellular trafficking of MIG-14 by AP-2 and retromer plays an important role in Wnt secretion.     

Dendrimer-epidermal growth factor conjugate displays superagonist activity

Binding of ligands on to epidermal growth factor receptor (EGFR) can stimulate cell growth; therefore, any application employing EGF as a targeting ligand for a "drug carrier" must evaluate the effect of the conjugate on cell growth. We report the synthesis and in vitro biological activity of EGF molecules coupled to a fluorescein-labeled polyamidoamine dendrimer. The conjugate bound and internalized into several EGFR-expressing cell lines in a receptor-specific fashion. The conjugate effectively induced EGFR phosphorylation and acted as a superagonist by stimulating cell growth to a greater degree than free EGF. Concomitant administration of the chemotherapeutic drug methotrexate completely inhibited cell growth to a degree similar to its effect in the absence of the conjugate. Thus, dendrimer-EGF conjugates serve as EGFR superagonists, but this activity can be overcome by chemotherapeutic drugs. The agonist activity of these materials must be taken into consideration when using EGF conjugates for imaging applications.