Anti-amebic effects of Chinese rhubarb (Rheum palmatum) leaves' extract, the anthraquinone rhein and related compounds.

Entamoeba histolytica infects 50 million people worldwide and causes 55 thousand fatalities every year. Current anti-amebic drugs (e.g. paromomycin) work either at the level of the intestinal lumen (where trophozoites proliferate via cell divisions) or on the invasive trophozoites that have penetrated the gut or colonized internal organs (e.g. metronidazole). Some of these drugs are highly toxic to patients, have generated trophozoite resistance, or caused mutations and cancer in laboratory animals. Thus, alternative anti-amebic compounds need to be identified to minimize the side effects (on patients) or resistance (by amebas) to current treatments. The literature suggests that anthraquinones (chemicals found in medicinal plants) have antibacterial, antiparasitic, anti-inflammatory and antioxidant properties. Here we provide experimental evidence that Chinese rhubarb (Rheum palmatum) leaves' extract (rich in the anthraquinone rhein) inhibits E. histolytica trophozoite growth in vitro. In addition, from a set of ten isolated/synthetic anthraquinones (which we suspected to have anti-amebic properties), four analogs (rhein; AHHDAC = 1-amino-4-hydroxy-9, 10-dioxo-9, 10-dihydro-anthracene-2-carboxylic acid; unisol blue AS; and sennoside B) efficiently inhibited amebic growth at EIC50 concentrations comparable to metronidazole. The mechanism of action of these compounds still needs to be determined, although anthraquinones might enhance the production of toxic oxygen metabolites as it has been suggested for various protists (e.g. Leishmania, Plasmodium, Trypanosoma). Our research is the first to explore anti-amebic effects of Chinese rhubarb leaves' extract and isolated/synthetic anthraquinones on pathogenic Entamoeba.

Bioinformatics Structural and Phylogenetic Characterization of Entamoeba histolytica Alcohol Dehydrogenase 2 (EhADH2).

An amitochondriate parasite, Entamoeba histolytica, has a bifunctional ADHE enzyme (EhADH2) that contains separate acetaldehyde (ALDH) and alcohol (ADH) dehydrogenase activities. In a cluster of 25 bifunctional enzymes of single cell eukaryotes and bacteria, we present a phylogenetic analysis that suggests a lateral gene transfer event (prokaryotic ancestor to single-cell eukaryotic ancestor) and a complex structure that aligns with key homologs in the ADHE evolutionary history based on their similarity with bacterial alcohol dehydrogenases. We show that the ADHE in Entamoeba lineage diverged independently but shows significant similarities to the structure of ADHE in Fusobacterium, and a complex model that maps its ALDH and ADH domain well with bacteria such as Geobaccillus thermoglucosidasius. Our analyses likely support a lateral acquisition of an EhADH2-like ancestral gene from bacteria. Several evolutionary analyses software programs reveal that the enzyme structure is highly conserved, and maintains a similar function within a diverse set of pathogens, including Escherichia coli and Clostridium spp.

Discrimination Experiments in Entamoeba and Evidence from Other Protists Suggest Pathogenic Amebas Cooperate with Kin to Colonize Hosts and Deter Rivals.

Entamoeba histolytica is one of the least understood protists in terms of taxa, clone, and kin discrimination/recognition ability. However, the capacity to tell apart same or self (clone/kin) from different or nonself (nonclone/nonkin) has long been demonstrated in pathogenic eukaryotes like Trypanosoma and Plasmodium, free-living social amebas (Dictyostelium, Polysphondylium), budding yeast (Saccharomyces), and in numerous bacteria and archaea (prokaryotes). Kin discrimination/recognition is explained under inclusive fitness theory; that is, the reproductive advantage that genetically closely related organisms (kin) can gain by cooperating preferably with one another (rather than with distantly related or unrelated individuals), minimizing antagonism and competition with kin, and excluding genetic strangers (or cheaters = noncooperators that benefit from others' investments in altruistic cooperation). In this review, we rely on the outcomes of in vitro pairwise discrimination/recognition encounters between seven Entamoeba lineages to discuss the biological significance of taxa, clone, and kin discrimination/recognition in a range of generalist and specialist species (close or distantly related phylogenetically). We then focus our discussion on the importance of these laboratory observations for E. histolytica's life cycle, host infestation, and implications of these features of the amebas' natural history for human health (including mitigation of amebiasis).

Study of the Huntington's disease IT-15 gene in different ethnic groups in Ecuador.

This study aims to establish the current state of the IT-15 (HTT) gene in different Ecuadorian ethnic groups and patients by determining CAG triplet repeats, compared with the ethnicity of individuals. A total of 412 individuals were studied using nested polymerase chain reaction and Sanger sequencing: 75 individuals were indigenous (Kichwas), 211 mestizos, and 65 Afro-Ecuadorians. We included 31 patients who were clinically diagnosed with Huntington's disease (HD) and relatives of the affected patients (n = 30). Moreover, we correlated the presence of HD in Ecuadorian patients with 46 genetic ancestry-informative insertion-deletion polymorphic markers. We found that 77.20% had <28 CAG repetitions, 18.80% had mutable alleles, 2.27% had incomplete penetrance, and 1.70% reflected >39 repetitions. The average of CAG repetitions was 24 ± 3 for indigenous people; 28 ± 2 for mestizos; and 24 ± 3.2 repetitions for the Afro-Ecuadorians. The ancestral component showed that the main ancestry corresponded to Native Americans (0.873) and European ascendants (0.145), Africans were less represented in the evaluated population (0.018). There was a significant difference between the number of CAG repeats in mestizos and indigenous people (P < .01), suggesting that the Ecuadorian mestizo population has a risk factor for the gene mutation.

Entamoeba Clone-Recognition Experiments: Morphometrics, Aggregative Behavior, and Cell-Signaling Characterization.

Studies on clone- and kin-discrimination in protists have proliferated during the past decade. We report clone-recognition experiments in seven Entamoeba lineages (E. invadens IP-1, E. invadens VK-1:NS, E. terrapinae, E. moshkovskii Laredo, E. moshkovskii Snake, E. histolytica HM-1:IMSS and E. dispar). First, we characterized morphometrically each clone (length, width, and cell-surface area) and documented how they differed statistically from one another (as per single-variable or canonical-discriminant analyses). Second, we demonstrated that amebas themselves could discriminate self (clone) from different (themselves vs. other clones). In mix-cell-line cultures between closely-related (E. invadens IP-1 vs. E. invadens VK-1:NS) or distant-phylogenetic clones (E. terrapinae vs. E. moshkovskii Laredo), amebas consistently aggregated with same-clone members. Third, we identified six putative cell-signals secreted by the amebas (RasGap/Ankyrin, coronin-WD40, actin, protein kinases, heat shock 70, and ubiquitin) and which known functions in Entamoeba spp. included: cell proliferation, cell adhesion, cell movement, and stress-induced encystation. To our knowledge, this is the first multi-clone characterization of Entamoeba spp. morphometrics, aggregative behavior, and cell-signaling secretion in the context of clone-recognition. Protists allow us to study cell-cell recognition from ecological and evolutionary perspectives. Modern protistan lineages can be central to studies about the origins and evolution of multicellularity.

Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards.

During four decades (1960-1990s), the conceptualization and experimental design of studies in kin recognition relied on work with multicellular eukaryotes, particularly Unikonta (including invertebrates and vertebrates) and some Bikonta (including plants). This pioneering research had an animal behavior approach. During the 2000s, work on taxa-, clone- and kin-discrimination and recognition in protists produced genetic and molecular evidence that unicellular organisms (e.g. Saccharomyces, Dictyostelium, Polysphondylium, Tetrahymena, Entamoeba and Plasmodium) could distinguish between same (self or clone) and different (diverse clones), as well as among conspecifics of close or distant genetic relatedness. Here, we discuss some of the research on the genetics of kin discrimination/recognition and highlight the scientific progress made by switching emphasis from investigating multicellular to unicellular systems (and backwards). We document how studies with protists are helping us to understand the microscopic, cellular origins and evolution of the mechanisms of kin discrimination/recognition and their significance for the advent of multicellularity. We emphasize that because protists are among the most ancient organisms on Earth, belong to multiple taxonomic groups and occupy all environments, they can be central to reexamining traditional hypotheses in the field of kin recognition, reformulating concepts, and generating new knowledge.

Unravelling the relationship between protein sequence and low-complexity regions entropies: Interactome implications.

Low-complexity regions are sub-sequences of biased composition in a protein sequence. The influence of these regions over protein evolution, specific functions and highly interactive capacities is well known. Although protein sequence entropy has been largely studied, its relationship with low-complexity regions and the subsequent effects on protein function remains unclear. In this work we propose a theoretical and empirical model integrating the sequence entropy with local complexity parameters. Our results indicate that the protein sequence entropy is related with the protein length, the entropies inside and outside the low-complexity regions as well as their number and average size. We found a small but significant increment in the sequence entropy of hubs proteins. In agreement with our theoretical model, this increment is highly dependent of the balance between the increment of protein length and average size of the low-complexity regions. Finally, our models and proteins analysis provide evidence supporting that modifications in the average size is more relevant in hubs proteins than changes in the number of low-complexity regions.

Variation in the Presence of Anti-Batrachochytrium dendrobatidis Bacteria of Amphibians Across Life Stages and Elevations in Ecuador.

Amphibian populations are decreasing worldwide due to a variety of factors. In South America, the chytrid fungus Batrachochytrium dendrobatidis (Bd) is linked to many population declines. The pathogenic effect of Bd on amphibians can be inhibited by specific bacteria present on host skin. This symbiotic association allows some amphibians to resist the development of the disease chytridiomycosis. Here, we aimed (1) to determine for the first time if specific anti-Bd bacteria are present on amphibians in the Andes of Ecuador, (2) to monitor anti-Bd bacteria across developmental stages in a focal amphibian, the Andean marsupial tree frog, Gastrotheca riobambae, that deposits larvae in aquatic habitats, and (3) to compare the Bd presence associated with host assemblages including 10 species at sites ranging in biogeography from Amazonian rainforest (450 masl) to Andes montane rainforest (3200 masl). We sampled and identified skin-associated bacteria of frogs in the field using swabs and a novel methodology of aerobic counting plates, and a combination of morphological, biochemical, and molecular identification techniques. The following anti-Bd bacteria were identified and found to be shared among several hosts at high-elevation sites where Bd was present at a prevalence of 32.5%: Janthinobacterium lividum, Pseudomonas fluorescens, and Serratia sp. Bd were detected in Gastrotheca spp. and not detected in the lowlands (sites below 1000 masl). In G. riobambae, recognized Bd-resistant bacteria start to be present at the metamorphic stage. Overall bacterial abundance was significantly higher post-metamorphosis and on species sampled at lower elevations. Further metagenomic studies are needed to evaluate the roles of host identity, life-history stage, and biogeography of the microbiota and their function in disease resistance.

Evolution Controversy: A Phenomenon Prompted by the Incompatibility between Science and Religious Beliefs.

The incompatibility between science and the belief in supernatural causation helps us understand why people do not accept evolution. Belief disrupts, distorts, delays, or stops (3Ds + S) the acceptance of scientific evidence. Here we examine the evolution controversy under three predictions of the incompatibility hypothesis. First, chronological-conflict-and-accommodation, which explains the historical re-emergence of antagonism between evolution and religion when advances in science continue to threaten the belief in supernatural causation; in such situations, creationists' rejection of and subsequent partial acceptance of the new scientific discoveries are expected. Second, change in evolution's acceptance as function of educational attainment, which explains the positive association between acceptance of evolution and level of education. And third, change in evolution's acceptance as function of religiosity, which explains the negative association between acceptance of evolution and level of religious beliefs. We rely on an ample assessment of the attitudes toward evolution by highly-educated audiences (i.e. research faculty, educators of prospective teachers, and college students in the United States) to characterize the associations among the understanding of science and evolution, personal religious convictions, and conservative ideology. We emphasize that harmonious coexistence between science and religion is illusory. If co-persisting in society, their relationship will fluctuate from moderate to intense antagonism.

Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications.

Unicellular eukaryotes, or protists, are among the most ancient organisms on Earth. Protists belong to multiple taxonomic groups; they are widely distributed geographically and in all environments. Their ability to discriminate among con- and heterospecifics has been documented during the past decade. Here we discuss exemplar cases of taxa-, clone-, and possible kin-discrimination in five major lineages: Mycetozoa (Dictyostelium, Polysphondylium), Dikarya (Saccharomyces), Ciliophora (Tetrahymena), Apicomplexa (Plasmodium) and Archamoebae (Entamoeba). We summarize the proposed genetic mechanisms involved in discrimination-mediated aggregation (self versus different), including the csA, FLO and trg (formerly lag) genes, and the Proliferation Activation Factors (PAFs), which facilitate clustering in some protistan taxa. We caution about the experimental challenges intrinsic to studying recognition in protists, and highlight the opportunities for exploring the ecology and evolution of complex forms of cell-cell communication, including social behavior, in a polyphyletic, still superficially understood group of organisms. Because unicellular eukaryotes are the evolutionary precursors of multicellular life, we infer that their mechanisms of taxa-, clone-, and possible kin-discrimination gave origin to the complex diversification and sophistication of traits associated with species and kin recognition in plants, fungi, invertebrates and vertebrates.

Association of genetic variants of membrane receptors related to recognition and induction of immune response with Helicobacter pylori infection in Ecuadorian individuals.

Helicobacter pylori (Hp) has a worldwide distribution showing its higher prevalence of infection in developing countries. Toll-like receptors (TLRs) and C-type lectin receptors (CLRs) are proteins that recognize pathogen-associated molecular patterns (PAMPs) and initiate an innate immune response by promoting growth and differentiation of specialized hematopoietic cells for host defense. Gastric infections led by Hp induce a Th-1 cellular immune response, regulated mainly by the expression of IFN-γ. In this retrospective case-control study, we evaluated the TLR1 1805T/G, TLR2 2029C/T, TLR4 896A/G, CD209 -336A/G and IFNGR1 -56C/T polymorphisms and their relationship with susceptibility to Hp infection. TLR1 1805T/G showed statistical differences when the control (Hp-) and infected (Hp+) groups (P = 0.041*) were compared; the TLR1 1805G allele had a protective effect towards infection (OR = 0.1; 95% CI = 0.01-0.88, P = 0.033*). Similarly, the IFNGR1 -56C/T polymorphism showed statistical differences between Hp+ and Hp- (P = 0.018*), and the IFNGR1 -56TT genotype exhibited significant risk to Hp infection (OR = 2.9, 95% CI = 1.27-6.54, P = 0.018*). In conclusion, the pro-inflammatory TLR1 1805T and IFNGR1 -56T alleles are related with susceptibility to Hp infection in Ecuadorian individuals. The presence of these polymorphisms in individuals with chronic infection increases the risk of cellular damage and diminishes the cellular immune response efficiency towards colonizing agents.

Galapagos III World Evolution Summit: why evolution matters.

There is no place on Earth like the Galapagos Islands and no better destination to discuss the reality of evolution. Under the theme 'Why Does Evolution Matter', the University San Francisco of Quito (USFQ), Ecuador, and its Galapagos Institute for the Arts and Sciences (GAIAS), organized the III World Evolution Summit in San Cristóbal Island. The 200-attendee meeting took place on 1 to 5 June 2013; it included 12 keynote speakers, 20 oral presentations by international scholars, and 31 posters by faculty, postdocs, and graduate and undergraduate students. The Summit encompassed five sessions: evolution and society, pre-cellular evolution and the RNA world, behavior and environment, genome, and microbes and diseases. USFQ and GAIAS launched officially the Lynn Margulis Center for Evolutionary Biology and showcased the Galapagos Science Center, in San Cristóbal, an impressive research facility conceptualized in partnership with the University of North Carolina at Chapel Hill, USA. USFQ and GAIAS excelled at managing the conference with exceptional vision and at highlighting the relevance of Galapagos in the history of modern evolutionary thinking; Charles Darwin's visit to this volcanic archipelago in 1835 unfolded unprecedented scientific interest in what today is a matchless World Heritage.

Discrimination, crypticity, and incipient taxa in entamoeba.

Persistent difficulties in resolving clear lineages in diverging populations of prokaryotes or unicellular eukaryotes (protistan polyphyletic groups) are challenging the classical species concept. Although multiple integrated approaches would render holistic taxonomies, most phylogenetic studies are still based on single-gene or morphological traits. Such methodologies conceal natural lineages, which are considered "cryptic." The concept of species is considered artificial and inadequate to define natural populations. Social organisms display differential behaviors toward kin than to nonrelated individuals. In "social" microbes, kin discrimination has been used to help resolve crypticity. Aggregative behavior could be explored in a nonsocial protist to define phylogenetic varieties that are considered "cryptic." Two Entamoeba invadens strains, IP-1 and VK-1:NS are considered close populations of the same "species." This study demonstrates that IP-1 and VK-1:NS trophozoites aggregate only with alike members and discriminate members of different strains based on behavioral and chemical signals. Combined morphological, behavioral/chemical, and ecological studies could improve Archamoebae phylogenies and define cryptic varieties. Evolutionary processes in which selection acted continuously and cumulatively on ancestors of Entamoeba populations gave rise to chemical and behavioral signals that allowed individuals to discriminate nonpopulation members and, gradually, to the emergence of new lineages; alternative views that claim a "Designer" or "Creator" as responsible for protistan diversity are unfounded.

Introduction: why people do not accept evolution: using protistan diversity to promote evolution literacy.

The controversy evolution vs. creationism is inherent to the incompatibility between scientific rationalism/empiricism and the belief in supernatural causation. To test this hypothesis, we conceptualized a Cartesian landscape where the dependent variable acceptance of evolution was plotted as function of three factors, each represented by an index (value range 0 to 3): Religiosity Index (RI), Science Index (SI), and Evolution Index (EI). The indexes summarized an individual's personal religious convictions, familiarity with the processes and forces of change in organisms (= concept of evolution), and understanding the essence of science (= method to explore reality). We compared and contrasted acceptance of evolution among four populations of variable educational attainment: 244 professors of New England, United States (93% Ph.D./doctorate holders), 50 protistologists from 25 countries (70% Ph.D./doctorate holders), 62 educators of prospective teachers (83% Ph.D./doctorate holders), and 827 college students. The New England faculty held the highest acceptance of evolution position (RI = 0.49; SI = 2.49; EI = 2.49), followed by the protistologists (RI = 0.46; SI = 2.30; EI = 2.48), the educators of prospective teachers (RI = 0.83; SI = 1.96; EI = 1.96), and the students (RI = 0.89; SI = 1.80; EI = 1.60); therefore, the data supported our hypothesis. Proper science education, public outreach and robust debate over the controversy "evolution versus creationism" should suffice to improve society's evolution literacy, and qualified scholars ought to lead this mission.

Educators of Prospective Teachers Hesitate to Embrace Evolution Due to Deficient Understanding of Science/Evolution and High Religiosity.

Acceptance of evolution by educators of prospective teachers remains superficially studied despite their role in having mentored schoolteachers whose weak support of evolution is known. Here, we contrast the views of New England educators of prospective teachers (n=62; 87% Ph. D./doctorate holders in 32 specializations) with those of the general faculty (n=244; 93% Ph.D./doctorate holders in 40 disciplines), both members of 35 colleges and universities, and with college students (n=827; subsample of the 35 institutions) who were polled on: (1) the controversy evolution vs. creationism vs. intelligent design (ID), (2) their understanding of how science/evolution works, and (3) their religiosity. The educators held intermediate positions in respect to the general faculty and the students: 94% of the general faculty, 75% of the educators, and 63% of the students said they accepted evolution openly; and 82% of the general faculty, 71% of the educators, and 58% of the students thought that evolution is definitely true. Only 3% of the general faculty in comparison to 19% of the educators and 24% of the students thought that evolution and creationism are in harmony. Although 93% of the general faculty, educators, and students knew that evolution relies on common ancestry, 26% of the general faculty, 45% of the educators, and 35% of the students did not know that humans are apes. Remarkably, 15% of the general faculty, 32% of the educators, and 35% of the students believed, incorrectly, that the origin of the human mind cannot be explained by evolution; and 30% of the general faculty, 59% of the educators, and 75% of the students were Lamarckian (=believed in inheritance of acquired traits). For science education: 96% of the general faculty, 86% of the educators, and 71% of the students supported the exclusive teaching of evolution, while 4% of the general faculty, 14% of the educators, and 29% of the students favored equal time to evolution, creationism and ID; note that 92% of the general faculty, 82% of the educators, and 50% of the students perceived ID as either not scientific and proposed to counter evolution based on false claims or as religious doctrine consistent with creationism. The general faculty was the most knowledgeable about science/evolution and the least religious (science index, SI=2.49; evolution index, EI= 2.49; and religiosity index, RI=0.49); the educators reached lower science/evolution but higher religiosity indexes than the general faculty (SI=1.96, EI=1.96, and RI=0.83); and the students were the least knowledgeable about science/ evolution and the most religious (SI=1.80, EI=1.60, and RI=0.89). Understanding of science and evolution were inversely correlated with level of religiosity, and understanding of evolution increased with increasing science literacy. Interestingly, ≈36% of the general faculty, educators and students considered religion to be very important in their lives, and 17% of the general faculty, 34% of the educators, and 28% of the students said they prayed daily. Assessing the perception of evolution by educators of prospective teachers vs. the general faculty and the students of New England, one of the historically most progressive regions in the U.S., is crucial for determining the magnitude of the impact of creationism and ID on attitudes toward science, reason, and education in science.

On the Theory of Evolution Versus the Concept of Evolution: Three Observations.

Here we address three misconceptions stated by Rice et al. in their observations of our article Paz-y-Miño and Espinosa (Evo Edu Outreach 2:655-675, 2009), published in this journal. The five authors titled their note "The Theory of Evolution is Not an Explanation for the Origin of Life." First, we argue that it is fallacious to believe that because the formulation of the theory of evolution, as conceived in the 1800s, did not include an explanation for the origin of life, nor of the universe, the concept of evolution would not allow us to hypothesize the possible beginnings of life and its connections to the cosmos. Not only Stanley Miller's experiments of 1953 led scientists to envision a continuum from the inorganic world to the origin and diversification of life, but also Darwin's own writings of 1871. Second, to dismiss the notion of Rice et al. that evolution does not provide explanations concerning the universe or the cosmos, we identify compelling scientific discussions on the topics: Zaikowski et al. (Evo Edu Outreach 1:65-73, 2008), Krauss (Evo Edu Outreach 3:193-197, 2010), Peretó et al. (Orig Life Evol Biosph 39:395-406, 2009) and Follmann and Brownson (Naturwissenschaften 96:1265-1292, 2009). Third, although we acknowledge that the term Darwinism may not be inclusive of all new discoveries in evolution, and also that creationists and Intelligent Designers hijack the term to portray evolution as ideology, we demonstrate that there is no statistical evidence suggesting that the word Darwinism interferes with public acceptance of evolution, nor does the inclusion of the origin of life or the universe within the concept of evolution. We examine the epistemological and empirical distinction between the theory of evolution and the concept of evolution and conclude that, although the distinction is important, it should not compromise scientific logic.

New England Faculty and College Students Differ in Their Views About Evolution, Creationism, Intelligent Design, and Religiosity.

Public acceptance of evolution in Northeastern U.S. is the highest nationwide, only 59%. Here, we compare perspectives about evolution, creationism, intelligent design (ID), and religiosity between highly educated New England faculty (n=244; 90% Ph.D. holders in 40 disciplines at 35 colleges/universities) and college students from public secular (n=161), private secular (n=298), and religious (n=185) institutions: 94/3% of the faculty vs. 64/14% of the students admitted to accepting evolution openly and/or privately, and 82/18% of the faculty vs. 58/42% of the students thought that evolution is definitely true or probably true, respectively. Only 3% of the faculty vs. 23% of the students thought that evolution and creationism are in harmony. Although 92% of faculty and students thought that evolution relies on common ancestry, one in every four faculty and one in every three students did not know that humans are apes; 15% of the faculty vs. 34% of the students believed, incorrectly, that the origin of the human mind cannot be explained by evolution, and 30% of the faculty vs. 72% of the students was Lamarckian (believed in inheritance of acquired traits). Notably, 91% of the faculty was very concerned (64%) or somehow concerned (27%) about the controversy evolution vs creationism vs ID and its implications for science education: 96% of the faculty vs. 72% of the students supported the exclusive teaching of evolution while 4% of the faculty vs. 28% of the students favored equal time to evolution, creationism and ID; 92% of the faculty vs. 52% of the students perceived ID as not scientific and proposed to counter evolution or as doctrine consistent with creationism. Although ≈30% of both faculty and students considered religion to be very important in their lives, and ≈20% admitted to praying daily, the faculty was less religious (Religiosity Index faculty=0.5 and students=0.75) and, as expected, more knowledgeable about science (Science Index faculty=2.27 and students=1.60) and evolution (Evolution Index faculty=2.48 and students=1.65) than the students. Because attitudes toward evolution correlate (1) positively with understanding of science/evolution and (2) negatively with religiosity/political ideology, we conclude that science education combined with vigorous public debate should suffice to increase acceptance of naturalistic rationalism and decrease the negative impact of creationism and ID on society's evolution literacy.

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random.

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke "design creationism" to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane's hydrophobic/philic nature; a selective "pore" for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the "jackprot," which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the "jackprot," or highest-fitness complete-peptide sequence, required cumulative smaller "wins" (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons ("jackdons" that led to "jackacids" that led to the "jackprot"). The "jackprot" is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide "edition" and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.

Integrating horizontal gene transfer and common descent to depict evolution and contrast it with "common design".

Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of life's diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD(+) as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking "common design" (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded.

Effects of iron depletion on Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2) and trophozoite growth: implications for antiamoebic therapy.

OBJECTIVES: The purpose of this study was to determine the mechanism by which iron chelation affects the trophozoite survival of Entamoeba histolytica. Fe2+ is a cofactor for E. histolytica alcohol dehydrogenase 2 (EhADH2), an essential bifunctional enzyme [alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH)] in the glycolytic pathway of E. histolytica. METHODS: We tested the effects of iron depletion on trophozoite growth, the kinetics of iron binding to EhADH2, and the activities of ADH and ALDH. RESULTS: Growth of E. histolytica trophozoites, and ADH and ALDH enzymatic activities were directly inhibited by iron chelation. Kinetics of iron binding to EhADH2 reveals the differential iron affinity of ADH (higher) and ALDH (lower). CONCLUSIONS: This study demonstrates that iron chelation interrupts the completion of the fermentative pathway of E. histolytica by removing the metal cofactor indispensable for the structural and functional stability of EhADH2, thus affecting trophozoite survival. We propose that iron-starvation-based strategies could be used to treat amoebiasis.