Alien plant species composition and associations with anthropogenic disturbance in North American forests

A probability-based sampling scheme was used to survey plant species composition in forests of 16 states in seven geopolitical regions of the United States (California, Colorado, Minnesota, and parts of the Pacific Northwest, Southeast, Mid-Atlantic, and Northeast) in 1994. The proportion of alien species relative to the total species number and to canopy cover in the ground stratum (0–0.6 m height) was evaluated in 279 plots. Visually evident anthropogenic disturbances (e.g., artificial regeneration, logging, prescribed burning, and grazing by livestock), if any, were recorded on each plot. In each of the seven regions we quantified (1) the percentage of the number of species and total cover comprised of alien species, (2) the difference in these percentages for disturbed and undisturbed plots, and (3) the origin or native range for the alien species.The percentage of alien species ranged from approximately 4.5% (Colorado) to approximately 13.2% (California). The percentage of alien species cover ranged from approximately 1.5% in Colorado to 25% in California. In five regions, species introduced from temperate Eurasia comprised the largest proportion of alien species and cover. In the Southeast, species introduced from far eastern and subtropical Asia dominated the alien flora. In the Mid-Atlantic, the majority of alien species was Eurasian and the majority of alien species cover consisted of far eastern and subtropical Asian species.The proportion of plots in which at least one alien species was recorded was significantly higher in disturbed than undisturbed plots in the Southeast and marginally significantly higher ($p=0.053$) in the Northeast. These results are consistent with other published studies that indicate that anthropogenic disturbance affects the structure and composition of both the ground stratum and upper canopy of forest habitats. In other regions, however, no significant differences were found.     

Targeted extended cystic fibrosis mutation testing on known and at-risk patients and relatives

This paper reports mathematically derived residual risks of being a carrier or being affected with cystic fibrosis following various screening scenarios to assist in interpreting test results and advising patients. While parental screening with 23 American College of Medical Genetics (ACMG) cystic fibrosis mutations defines the 64% of affected U.S. Caucasian fetuses with two detectable mutations, newborn screening for elevated immunoreactive trypsinogen (IRT) and sweat chloride identifies an additional 36% of affected newborns with zero or one detected mutation. The relatives of these affected newborns with less than two detectable mutations have higher posterior (after) 23 mutation-negative test risks of carrying undetected mutations. These calculations emphasize how knowledge of the mutations in the related affected patient substantially improves upon the quality of after-test advice to patients. Furthermore, negative tests of the partner without a family history and/or more extensive cystic fibrosis transmembrane conductance regulator (CFTR) gene testing also increases the likelihood that a negative report is truly negative. When a newborn patient with zero or one detected CFTR mutation has an inconclusive sweat test result, the sweat test should be repeated before ordering additional often unnecessary CFTR gene sequencing. Given the same composite mutation panel test accuracy, a higher proportion of reported test results would be correct during parental screening than when testing at-risk fetuses or symptomatic newborns. Prenatal and newborn screening would be enhanced substantially by medical professionals offering copies of all positive parental and newborn test reports to the parents to share with their relatives. These principles are likely to be applicable to other genetic diseases as the most common mutation frequencies are reported.     

The molecular basis for the lack of immunostimulatory activity of vertebrate DNA

Macrophages and B cells are activated by unmethylated CpG-containing sequences in bacterial DNA. The lack of activity of self DNA has generally been attributed to CpG suppression and methylation, although the role of methylation is in doubt. The frequency of CpG in the mouse genome is 12.5% of Escherichia coli, with unmethylated CpG occurring at approximately 3% the frequency of E. coli. This suppression of CpG alone is insufficient to explain the inactivity of self DNA; vertebrate DNA was inactive at 100 micro g/ml, 3000 times the concentration at which E. coli DNA activity was observed. We sought to resolve why self DNA does not activate macrophages. Known active CpG motifs occurred in the mouse genome at 18% of random occurrence, similar to general CpG suppression. To examine the contribution of methylation, genomic DNAs were PCR amplified. Removal of methylation from the mouse genome revealed activity that was 23-fold lower than E. coli DNA, although there is only a 7-fold lower frequency of known active CpG motifs in the mouse genome. This discrepancy may be explained by G-rich sequences such as GGAGGGG, which potently inhibited activation and are found in greater frequency in the mouse than the E. coli genome. In summary, general CpG suppression, CpG methylation, inhibitory motifs, and saturable DNA uptake combined to explain the inactivity of self DNA. The immunostimulatory activity of DNA is determined by the frequency of unmethylated stimulatory sequences within an individual DNA strand and the ratio of stimulatory to inhibitory sequences.     

Triaminotriazine DNA helicase inhibitors with antibacterial activity

Screening of a chemical library in a DNA helicase assay involving the Pseudomonas aeruginosa DnaB helicase provided a triaminotriazine inhibitor with good antibacterial activity but associated cytotoxicity toward mammalian cells. Synthesis of analogs provided a few inhibitors that retained antibacterial activity and demonstrated a significant reduction in cytotoxicity. The impact of serum and initial investigations toward a mode of action highlight several features of this class of compounds as antibacterials.     

Crossing to safety: dispersal,colonization and mate choice in evolutionarily distinct populations of Steller sea lions,Eumetopias jubatus

Population growth typically involves range expansion and establishment of new breeding sites, while the opposite occurs during declines. Although density dependence is widely invoked in theoretical studies of emigration and colonization in expanding populations, few empirical studies have documented the mechanisms. Still fewer have documented the direction and mechanisms of individual transfer in declining populations. Here, we screen large numbers of pups sampled on their natal rookeries for variation in mtDNA (n = 1106) and 16 microsatellite loci (n = 588) and show that new Steller sea lion breeding sites did not follow the typical paradigm and were instead colonized by sea lions from both a declining (Endangered) population and an increasing population. Dispersing individuals colonized rookeries in the distributional hiatus between two evolutionarily distinct ( = 0.222,  = 0.053, K = 2) metapopulations recently described as separate subspecies. Hardy–Weinberg, mixed‐stock and relatedness analysis revealed levels of interbreeding on the new rookeries that exclude (i) assortative mating among eastern and western forms, and (ii) inbreeding avoidance as primary motivations for dispersal. Positive and negative density dependence is implicated in both cases of individual transfer. Migration distance limits, and conspecific attraction and performance likely influenced the sequence of rookery colonizations. This study demonstrates that resource limitation may trigger an exodus of breeding animals from declining populations, with substantial impacts on distribution and patterns of genetic variation. It also revealed that this event is rare because colonists dispersed across an evolutionary boundary, suggesting that the causative factors behind recent declines are unusual or of larger magnitude than normally occur.     

Evolution of Bacterial-Like Phosphoprotein Phosphatases in Photosynthetic Eukaryotes Features Ancestral Mitochondrial or Archaeal Origin and Possible Lateral Gene Transfer

Protein phosphorylation is a reversible regulatory process catalyzed by the opposing reactions of protein kinases and phosphatases, which are central to the proper functioning of the cell. Dysfunction of members in either the protein kinase or phosphatase family can have wide-ranging deleterious effects in both metazoans and plants alike. Previously, three bacterial-like phosphoprotein phosphatase classes were uncovered in eukaryotes and named according to the bacterial sequences with which they have the greatest similarity: Shewanella-like (SLP), Rhizobiales-like (RLPH), and ApaH-like (ALPH) phosphatases. Utilizing the wealth of data resulting from recently sequenced complete eukaryotic genomes, we conducted database searching by hidden Markov models, multiple sequence alignment, and phylogenetic tree inference with Bayesian and maximum likelihood methods to elucidate the pattern of evolution of eukaryotic bacterial-like phosphoprotein phosphatase sequences, which are predominantly distributed in photosynthetic eukaryotes. We uncovered a pattern of ancestral mitochondrial (SLP and RLPH) or archaeal (ALPH) gene entry into eukaryotes, supplemented by possible instances of lateral gene transfer between bacteria and eukaryotes. In addition to the previously known green algal and plant SLP1 and SLP2 protein forms, a more ancestral third form (SLP3) was found in green algae. Data from in silico subcellular localization predictions revealed class-specific differences in plants likely to result in distinct functions, and for SLP sequences, distinctive and possibly functionally significant differences between plants and nonphotosynthetic eukaryotes. Conserved carboxyl-terminal sequence motifs with class-specific patterns of residue substitutions, most prominent in photosynthetic organisms, raise the possibility of complex interactions with regulatory proteins.Reversible protein phosphorylation is a posttranslational mechanism central to the proper function of living organisms (Brautigan, 2013). Governed by two large groups of enzymes, protein kinases and protein phosphatases, this mechanism has been suggested to regulate upwards of 70% of all eukaryotic proteins (Olsen et al., 2010). Protein phosphatases represent one-half of this dynamic regulatory system and have been shown to be highly regulated proteins themselves (Roy and Cyert, 2009; Shi, 2009; Uhrig et al., 2013). Classically, protein phosphatases have been placed into four families defined by a combination of their catalytic mechanisms, metal ion requirements, and phosphorylated amino acid targets (Kerk et al., 2008). These four families are the phosphoprotein phosphatases (PPPs), metallo-dependent protein phosphatases, protein Tyr phosphatases, and Asp-based phosphatases. The PPP protein phosphatases, best known to include PP1, PP2A, PP2B, and PP4 to PP7 (Kerk et al., 2008; Shi, 2009), have been found to regulate a diverse number of biological processes in plants ranging from cell signaling (Ahn et al., 2011; Di Rubbo et al., 2011; Tran et al., 2012) to metabolism (Heidari et al., 2011; Leivar et al., 2011) and hormone biosynthesis (Skottke et al., 2011). The classical PPP protein phosphatase family has been expanded to include three novel classes that show greatest similarity to PPP-like protein phosphatases of prokaryotic origin (Andreeva and Kutuzov, 2004; Uhrig and Moorhead, 2011a; Uhrig et al., 2013). These bacterial-like phosphatase classes were annotated as Shewanella-like (SLP) phosphatases, Rhizobiales-like (RLPH) phosphatases, and ApaH-like (ALPH) phosphatases based on their similarity to prokaryotic sequences from these respective sources (Andreeva and Kutuzov, 2004). Recent characterization of the SLP phosphatases from Arabidopsis (Arabidopsis thaliana) provided biochemical evidence of insensitivity to the classic PPP protein phosphatase inhibitors okadaic acid and microcystin in addition to revealing a lack of genetic redundancy across sequenced plant genomes (Uhrig and Moorhead, 2011a).The characterization of eukaryotic protein evolution can provide insight into individual protein or protein class conservation across the domains of life for biotechnological applications in addition to furthering our understanding of how multicellular life evolved. In particular, investigation into the evolution of key signaling proteins, such as protein kinases and phosphatases from plants, can have wide-ranging agribiotechnological and medical potential. This can include the development of healthier, disease- or stress-resistant crops in addition to treatments for parasitic organisms such as Plasmodium spp. (malaria; Patzewitz et al., 2013) and other chromoalveolates (Kutuzov and Andreeva, 2008; Uhrig and Moorhead, 2011b) that are derived from photosynthetic eukaryotes and maintain a remnant chloroplast (apicoplast; Le Corguillé et al., 2009; Janouskovec et al., 2010; Kalanon and McFadden, 2010; Walker et al., 2011). The existence of proteins that are conserved across diverse eukaryotic phyla but absent in metazoa, such as the majority of bacterial-like PPP protein phosphatases described here, presents unique research opportunities.Conventional understanding of the acquisition by eukaryotes of prokaryotic genes and proteins largely involves ancient endosymbiotic gene transfer events stemming from primary endosymbiosis of α-Proteobacteria and Cyanobacteria to form eukaryotic mitochondria and chloroplasts, respectively (Keeling and Palmer, 2008; Dorrell and Smith, 2011; Tirichine and Bowler, 2011). Over time, however, it has become apparent that alternative modes of eukaryotic gene and protein acquisition exist, such as independent horizontal or lateral gene transfer (LGT) events (Keeling and Palmer, 2008; Keeling, 2009). Targeted studies of protein evolution have seen a steady rise in documented LGT events across a wide variety of eukaryotic organisms, including photosynthetic eukaryotes (Derelle et al., 2006; Raymond and Kim, 2012; Schönknecht et al., 2013), nematodes (Mayer et al., 2011), arthropods (Acuña et al., 2012), fungi (Wenzl et al., 2005), amoebozoa (Clarke et al., 2013), and oomycetes (Belbahri et al., 2008). Each instance documents the integration of a bacterial gene(s) into a eukaryotic organism, seemingly resulting in an adaptive advantage(s) important to organism survival.Utilizing a number of in silico bioinformatic techniques and available sequenced genomes, the molecular evolution of three bacterial-like PPP classes found in eukaryotes is revealed to involve ancient mitochondrial or archaeal origin plus additional possible LGT events. A third, more ancient group of SLP phosphatases (SLP3 phosphatases) is defined in green algae. Subcellular localization predictions reveal distinctive subsets of bacterial-like PPPs, which may correlate with altered functions. In addition, the large sequence collections compiled here have allowed the elucidation of two highly conserved C-terminal domain motifs, which are specific to each bacterial-like PPP class and whose differences are particularly pronounced in photosynthetic eukaryotes. Together, these findings substantially expand our knowledge of the molecular evolution of the bacterial-like PPPs and point the way toward attractive future research avenues.     

Vancomycin-Resistant Gram-Positive Cocci Isolated from the Saliva of Wild Songbirds

We analyzed highly vancomycin-resistant Gram-positive bacteria isolated from the saliva of migratory songbirds captured, sampled, and released from a bird-banding station in western Kansas. Individual bacterial isolates were identified by partial 16S rRNA sequencing. Most of the bacteria in this study were shown to be Staphylococcus succinus with the majority being isolated from the American Robin. Some of these bacteria were shown to carry vanA, vanB, and vanC vancomycin-resistance genes and have the ability to form biofilms. One of the van gene-carrying isolates is also coagulase positive, which is normally considered a virulence factor. Other organisms isolated included Staphylococcus saprophyticus as well as Enterococcus gallinarum. Given the wide range of the American Robin and ease of horizontal gene transfer between Gram-positive cocci, we postulate that these organisms could serve as a reservoir of vancomycin-resistance genes capable of transferring to human pathogens.