Horizontal Gene Transfer and the History of Life

Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today.The discovery of the existence of prokaryotic microbes dates back more than 300 years. Since then, our picture of our distant microscopic relatives has undergone several revolutions: from being the living “proofs” of the existence of spontaneous generation, they became later the “archaic” representatives of our distant ancestors, to finally be legitimately recognized as exceptionally diverse organisms, keystone to any ecosystem, including the most familiar and the most hostile environments on Earth. Similarly, although they were first seen as elementary and unbreakable bricks of life, they are now seen as genetically composite bodies, heavyweight champions of “gene robbery.” The most recent of these revolutions has indeed been the realization of their unparalleled ability to integrate genetic material coming from more or less evolutionarily distant organisms. This mechanism is called “horizontal gene transfer” as opposed to vertical transmission from mother to daughter cell.     

Primary Events, Energy Transfer, and Reactions in Photosynthetic Units: A Connected Model of the Photosynthetic Unit

The concept of photosynthetic unit (PSU) is reviewed in the light of the authors' results in the fields of fluorescence and luminescence (delayed light). Models of PSU are mainly distinguished by the amount of exciton exchange which is allowed between units. The “separate” model, with its “first-order” character, is not consistent with fluorescence kinetic data. The sigmoidal rise of fluorescence under actinic light is best explained by “nonseparate” models; however, most of these models assume a delocalization of excitons or centers. The “connected” model introduced here is not subject to this criticism. It discloses a new effect (the “îlot” effect): a nonrandom grouping of fluorescent units the consequences of which are discussed. It is noted that a “two-quantum” model for the photochemical reaction gives results very similar to those of the connected model. A relation between luminescence intensity and fluorescence yield is seen as a necessary consequence of the PSU concept. Its meaning is different in separate and nonseparate models. This relation is discussed in connection with the true system II fluorescence emission.     

Analysis and Prediction of the Metabolic Stability of Proteins Based on Their Sequential Features,Subcellular Locations and Interaction Networks

The metabolic stability is a very important idiosyncracy of proteins that is related to their global flexibility, intramolecular fluctuations, various internal dynamic processes, as well as many marvelous biological functions. Determination of protein''s metabolic stability would provide us with useful information for in-depth understanding of the dynamic action mechanisms of proteins. Although several experimental methods have been developed to measure protein''s metabolic stability, they are time-consuming and more expensive. Reported in this paper is a computational method, which is featured by (1) integrating various properties of proteins, such as biochemical and physicochemical properties, subcellular locations, network properties and protein complex property, (2) using the mRMR (Maximum Relevance & Minimum Redundancy) principle and the IFS (Incremental Feature Selection) procedure to optimize the prediction engine, and (3) being able to identify proteins among the four types: “short”, “medium”, “long”, and “extra-long” half-life spans. It was revealed through our analysis that the following seven characters played major roles in determining the stability of proteins: (1) KEGG enrichment scores of the protein and its neighbors in network, (2) subcellular locations, (3) polarity, (4) amino acids composition, (5) hydrophobicity, (6) secondary structure propensity, and (7) the number of protein complexes the protein involved. It was observed that there was an intriguing correlation between the predicted metabolic stability of some proteins and the real half-life of the drugs designed to target them. These findings might provide useful insights for designing protein-stability-relevant drugs. The computational method can also be used as a large-scale tool for annotating the metabolic stability for the avalanche of protein sequences generated in the post-genomic age.     

Some personal and historical notes on the utility of “deep-etch” electron microscopy for making cell structure/function correlations

This brief essay talks up the advantages of metal replicas for electron microscopy and explains why they are still the best way to image frozen cells in the electron microscope. Then it explains our approach to freezing, namely the Van Harreveld trick of “slamming” living cells onto a supercold block of metal sprayed with liquid helium at −269ºC, and further talks up this slamming over the alternative of high-pressure freezing, which is much trickier but enjoys greater favor at the moment. This leads me to bemoan the fact that there are not more young investigators today who want to get their hands on electron microscopes and use our approach to get the most “true to life” views of cells out of them with a minimum of hassle. Finally, it ends with a few perspectives on my own career and concludes that, personally, I''m permanently stuck with the view of the “founding fathers” that cell ultrastructure will ultimately display and explain all of cell function, or as Palade said in his Nobel lecture,electron micrographs are “irresistible and half transparent … their meaning buried under only a few years of work,” and “reasonable working hypotheses are already suggested by the ultrastructural organization itself.”     

Ordered Regions of Channel Nucleoporins Nup62, Nup54, and Nup58 Form Dynamic Complexes in Solution

Three out of ∼30 nucleoporins, Nup62, Nup54, and Nup58, line the nuclear pore channel. These “channel” nucleoporins each contain an ordered region of ∼150–200 residues, which is predicted to be segmented into 3–4 α-helical regions of ∼40–80 residues. Notably, these segmentations are evolutionarily conserved between uni- and multicellular eukaryotes. Strikingly, the boundaries of these segments match our previously reported mapping and crystal data, which collectively identified two “cognate” segments of Nup54, each interacting with cognate segments, one in Nup58 and the other one in Nup62. Because Nup54 and Nup58 cognate segments form crystallographic hetero- or homo-oligomers, we proposed that these oligomers associate into inter-convertible “mid-plane” rings: a single large ring (40–50 nm diameter, consisting of eight hetero-dodecamers) or three small rings (10–20 nm diameter, each comprising eight homo-tetramers). Each “ring cycle” would recapitulate “dilation” and “constriction” of the nuclear pore complex''s central transport channel. As for the Nup54·Nup62 interactome, it forms a 1:2 triple helix (“finger”), multiples of which project alternately up and down from mid-plane ring(s). Collectively, our previous crystal data suggested a copy number of 128, 64, and 32 for Nup62, Nup54, and Nup58, respectively, that is, a 4:2:1 stoichiometry. Here, we carried out solution analysis utilizing the entire ordered regions of Nup62, Nup54, and Nup58, and demonstrate that they form a dynamic “triple complex” that is heterogeneously formed from our previously characterized Nup54·Nup58 and Nup54·Nup62 interactomes. These data are consistent both with our crystal structure-deduced copy numbers and stoichiometries and also with our ring cycle model for structure and dynamics of the nuclear pore channel.     

An Evolutionary Cascade Model for Sauropod Dinosaur Gigantism - Overview,Update and Tests

Sauropod dinosaurs are a group of herbivorous dinosaurs which exceeded all other terrestrial vertebrates in mean and maximal body size. Sauropod dinosaurs were also the most successful and long-lived herbivorous tetrapod clade, but no abiological factors such as global environmental parameters conducive to their gigantism can be identified. These facts justify major efforts by evolutionary biologists and paleontologists to understand sauropods as living animals and to explain their evolutionary success and uniquely gigantic body size. Contributions to this research program have come from many fields and can be synthesized into a biological evolutionary cascade model of sauropod dinosaur gigantism (sauropod gigantism ECM). This review focuses on the sauropod gigantism ECM, providing an updated version based on the contributions to the PLoS ONE sauropod gigantism collection and on other very recent published evidence. The model consist of five separate evolutionary cascades (“Reproduction”, “Feeding”, “Head and neck”, “Avian-style lung”, and “Metabolism”). Each cascade starts with observed or inferred basal traits that either may be plesiomorphic or derived at the level of Sauropoda. Each trait confers hypothetical selective advantages which permit the evolution of the next trait. Feedback loops in the ECM consist of selective advantages originating from traits higher in the cascades but affecting lower traits. All cascades end in the trait “Very high body mass”. Each cascade is linked to at least one other cascade. Important plesiomorphic traits of sauropod dinosaurs that entered the model were ovipary as well as no mastication of food. Important evolutionary innovations (derived traits) were an avian-style respiratory system and an elevated basal metabolic rate. Comparison with other tetrapod lineages identifies factors limiting body size.     

Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute,Walnut Creek,CA, March 27, 2013

The Prokaryotic Super Program Advisory Committee met on March 27, 2013 for their annual review the Prokaryotic Super Program at the DOE Joint Genome Institute. As is the case with any site visit or program review, the objective is to evaluate progress in meeting organizational objectives, provide feedback to from the user-community and to assist the JGI in formulating plans for the coming year. The advisors want to commend the JGI for its central role in developing new technologies and capabilities, and for catalyzing the formation of new collaborative user communities. Highlights of the post-meeting exchanges among the advisors focused on the importance of programmatic initiatives including:• GEBA, which serves as a phylogenetic “base-map” on which our knowledge of functional diversity can be layered.• FEBA, which promises to provide new insights into the physiological capabilities of prokaryotes under highly standardized conditions.• Single-cell genomics technology, which is seen to significantly enhance our ability to interpret genomic and metagenomic data and broaden the scope of the GEBA program to encompass at least a part of the microbial “dark-matter”.• IMG, which is seen to play a central role in JGI programs and is viewed as a strategically important asset in the JGI portfolio.On this latter point, the committee encourages the formation of a strategic relationship between IMG and the Kbase to ensure that the intelligence, deep knowledge and experience captured in the former is not lost. The committee strongly urges the DOE to continue its support for maintaining this critical resource.     

Deciphering clock cell network morphology within the biological master clock,suprachiasmatic nucleus: From the perspective of circadian wave dynamics

The biological master clock, suprachiasmatic nucleus (of rat and mouse), is composed of ~10,000 clock cells which are heterogeneous with respect to their circadian periods. Despite this inhomogeneity, an intact SCN maintains a very good degree of circadian phase (time) coherence which is vital for sustaining various circadian rhythmic activities, and it is supposedly achieved by not just one but a few different cell-to-cell coupling mechanisms, among which action potential (AP)-mediated connectivity is known to be essential. But, due to technical difficulties and limitations in experiments, so far very little information is available about the morphology of the connectivity at a cellular scale. Building upon this limited amount of information, here we exhaustively and systematically explore a large pool (~25,000) of various network morphologies to come up with some plausible network features of SCN networks. All candidates under consideration reflect an experimentally obtained ‘indegree distribution’ as well as a ‘physical range distribution of afferent clock cells.’ Then, importantly, with a set of multitude criteria based on the properties of SCN circadian phase waves in extrinsically perturbed as well as in their natural states, we select out appropriate model networks: Some important measures are, 1) level of phase dispersal and direction of wave propagation, 2) phase-resetting ability of the model networks subject to external circadian forcing, and 3) decay rate of perturbation induced “phase-singularities.” The successful, realistic networks have several common features: 1) “indegree” and “outdegree” should have a positive correlation; 2) the cells in the SCN ventrolateral region (core) have a much larger total degree than that of the dorsal medial region (shell); 3) The number of intra-core edges is about 7.5 times that of intra-shell edges; and 4) the distance probability density function for the afferent connections fits well to a beta function. We believe that these newly identified network features would be a useful guide for future explorations on the very much unknown AP-mediated clock cell connectome within the SCN.     

Memory for Expectation-Violating Concepts: The Effects of Agents and Cultural Familiarity

Previous research has shown that ideas which violate our expectations, such as schema-inconsistent concepts, enjoy privileged status in terms of memorability. In our study, memory for concepts that violate cultural (cultural schema-level) expectations (e.g., “illiterate teacher”, “wooden bottle”, or “thorny grass”) versus domain-level (ontological) expectations (e.g., “speaking cat”, “jumping maple”, or “melting teacher”) was examined. Concepts that violate cultural expectations, or counter-schematic, were remembered to a greater extent compared with concepts that violate ontological expectations and with intuitive concepts (e.g., “galloping pony”, “drying orchid”, or “convertible car”), in both immediate recall, and delayed recognition tests. Importantly, concepts related to agents showed a memory advantage over concepts not pertaining to agents, but this was true only for expectation-violating concepts. Our results imply that intuitive, everyday concepts are equally attractive and memorable regardless of the presence or absence of agents. However, concepts that violate our expectations (cultural-schema or domain-level) are more memorable when pertaining to agents (humans and animals) than to non-agents (plants or objects/artifacts). We conclude that due to their evolutionary salience, cultural ideas which combine expectancy violations and the involvement of an agent are especially memorable and thus have an enhanced probability of being successfully propagated.     

Human Quadrupeds,Primate Quadrupedalism,and Uner Tan Syndrome

Since 2005, an extensive literature documents individuals from several families afflicted with “Uner Tan Syndrome (UTS),” a condition that in its most extreme form is characterized by cerebellar hypoplasia, loss of balance and coordination, impaired cognitive abilities, and habitual quadrupedal gait on hands and feet. Some researchers have interpreted habitual use of quadrupedalism by these individuals from an evolutionary perspective, suggesting that it represents an atavistic expression of our quadrupedal primate ancestry or “devolution.” In support of this idea, individuals with “UTS” are said to use diagonal sequence quadrupedalism, a type of quadrupedal gait that distinguishes primates from most other mammals. Although the use of primate-like quadrupedal gait in humans would not be sufficient to support the conclusion of evolutionary “reversal,” no quantitative gait analyses were presented to support this claim. Using standard gait analysis of 518 quadrupedal strides from video sequences of individuals with “UTS”, we found that these humans almost exclusively used lateral sequence–not diagonal sequence–quadrupedal gaits. The quadrupedal gait of these individuals has therefore been erroneously described as primate-like, further weakening the “devolution” hypothesis. In fact, the quadrupedalism exhibited by individuals with UTS resembles that of healthy adult humans asked to walk quadrupedally in an experimental setting. We conclude that quadrupedalism in healthy adults or those with a physical disability can be explained using biomechanical principles rather than evolutionary assumptions.     

Re-Examination of Globally Flat Space-Time

In the following, we offer a novel approach to modeling the observed effects currently attributed to the theoretical concepts of “dark energy,” “dark matter,” and “dark flow.” Instead of assuming the existence of these theoretical concepts, we take an alternative route and choose to redefine what we consider to be inertial motion as well as what constitutes an inertial frame of reference in flat space-time. We adopt none of the features of our current cosmological models except for the requirement that special and general relativity be local approximations within our revised definition of inertial systems. Implicit in our ideas is the assumption that at “large enough” scales one can treat objects within these inertial systems as point-particles having an insignificant effect on the curvature of space-time. We then proceed under the assumption that time and space are fundamentally intertwined such that time- and spatial-translational invariance are not inherent symmetries of flat space-time (i.e., observable clock rates depend upon both relative velocity and spatial position within these inertial systems) and take the geodesics of this theory in the radial Rindler chart as the proper characterization of inertial motion. With this commitment, we are able to model solely with inertial motion the observed effects expected to be the result of “dark energy,” “dark matter,” and “dark flow.” In addition, we examine the potential observable implications of our theory in a gravitational system located within a confined region of an inertial reference frame, subsequently interpreting the Pioneer anomaly as support for our redefinition of inertial motion. As well, we extend our analysis into quantum mechanics by quantizing for a real scalar field and find a possible explanation for the asymmetry between matter and antimatter within the framework of these redefined inertial systems.     

Gene Expression Profiling as a Tool for Positional Cloning of Genes-Shortcut or the Longest Way Round

The identification of quantitative trait loci, QTL, in arthritis animal models is a straight forward process. However, to identify the underlying genes is a great challenge. One strategy frequently used, is to combine QTL analysis with genomic/proteomic screens. This has resulted in a number of publications where carefully performed genomic analyses present likely candidate genes for their respective QTL´s. However, seldom the findings are reconnected to the QTL controlled phenotypes. In this review, we use our own data as an illustrative example that “very likely candidate genes” identified by genomic/proteomics is not necessarily the same as true QTL underlying genes.     

Analysis of Cannabis Seizures in NSW,Australia: Cannabis Potency and Cannabinoid Profile

Recent analysis of the cannabinoid content of cannabis plants suggests a shift towards use of high potency plant material with high levels of Δ⁹-tetrahydrocannabinol (THC) and low levels of other phytocannabinoids, particularly cannabidiol (CBD). Use of this type of cannabis is thought by some to predispose to greater adverse outcomes on mental health and fewer therapeutic benefits. Australia has one of the highest per capita rates of cannabis use in the world yet there has been no previous systematic analysis of the cannabis being used. In the present study we examined the cannabinoid content of 206 cannabis samples that had been confiscated by police from recreational users holding 15 g of cannabis or less, under the New South Wales “Cannabis Cautioning” scheme. A further 26 “Known Provenance” samples were analysed that had been seized by police from larger indoor or outdoor cultivation sites rather than from street level users. An HPLC method was used to determine the content of 9 cannabinoids: THC, CBD, cannabigerol (CBG), and their plant-based carboxylic acid precursors THC-A, CBD-A and CBG-A, as well as cannabichromene (CBC), cannabinol (CBN) and tetrahydrocannabivarin (THC-V). The “Cannabis Cautioning” samples showed high mean THC content (THC+THC-A = 14.88%) and low mean CBD content (CBD+CBD-A = 0.14%). A modest level of CBG was detected (CBG+CBG-A = 1.18%) and very low levels of CBC, CBN and THC-V (<0.1%). “Known Provenance” samples showed no significant differences in THC content between those seized from indoor versus outdoor cultivation sites. The present analysis echoes trends reported in other countries towards the use of high potency cannabis with very low CBD content. The implications for public health outcomes and harm reduction strategies are discussed.     

Wet-dry-wet drug screen leads to the synthesis of TS1, a novel compound reversing lung fibrosis through inhibition of myofibroblast differentiation

Therapies halting the progression of fibrosis are ineffective and limited. Activated myofibroblasts are emerging as important targets in the progression of fibrotic diseases. Previously, we performed a high-throughput screen on lung fibroblasts and subsequently demonstrated that the inhibition of myofibroblast activation is able to prevent lung fibrosis in bleomycin-treated mice. High-throughput screens are an ideal method of repurposing drugs, yet they contain an intrinsic limitation, which is the size of the library itself. Here, we exploited the data from our “wet” screen and used “dry” machine learning analysis to virtually screen millions of compounds, identifying novel anti-fibrotic hits which target myofibroblast differentiation, many of which were structurally related to dopamine. We synthesized and validated several compounds ex vivo (“wet”) and confirmed that both dopamine and its derivative TS1 are powerful inhibitors of myofibroblast activation. We further used RNAi-mediated knock-down and demonstrated that both molecules act through the dopamine receptor 3 and exert their anti-fibrotic effect by inhibiting the canonical transforming growth factor β pathway. Furthermore, molecular modelling confirmed the capability of TS1 to bind both human and mouse dopamine receptor 3. The anti-fibrotic effect on human cells was confirmed using primary fibroblasts from idiopathic pulmonary fibrosis patients. Finally, TS1 prevented and reversed disease progression in a murine model of lung fibrosis. Both our interdisciplinary approach and our novel compound TS1 are promising tools for understanding and combating lung fibrosis.Subject terms: Drug discovery, Respiratory tract diseases     

Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions

Situations where individuals have to contribute to joint efforts or share scarce resources are ubiquitous. Yet, without proper mechanisms to ensure cooperation, the evolutionary pressure to maximize individual success tends to create a tragedy of the commons (such as over-fishing or the destruction of our environment). This contribution addresses a number of related puzzles of human behavior with an evolutionary game theoretical approach as it has been successfully used to explain the behavior of other biological species many times, from bacteria to vertebrates. Our agent-based model distinguishes individuals applying four different behavioral strategies: non-cooperative individuals (“defectors”), cooperative individuals abstaining from punishment efforts (called “cooperators” or “second-order free-riders”), cooperators who punish non-cooperative behavior (“moralists”), and defectors, who punish other defectors despite being non-cooperative themselves (“immoralists”). By considering spatial interactions with neighboring individuals, our model reveals several interesting effects: First, moralists can fully eliminate cooperators. This spreading of punishing behavior requires a segregation of behavioral strategies and solves the “second-order free-rider problem”. Second, the system behavior changes its character significantly even after very long times (“who laughs last laughs best effect”). Third, the presence of a number of defectors can largely accelerate the victory of moralists over non-punishing cooperators. Fourth, in order to succeed, moralists may profit from immoralists in a way that appears like an “unholy collaboration”. Our findings suggest that the consideration of punishment strategies allows one to understand the establishment and spreading of “moral behavior” by means of game-theoretical concepts. This demonstrates that quantitative biological modeling approaches are powerful even in domains that have been addressed with non-mathematical concepts so far. The complex dynamics of certain social behaviors become understandable as the result of an evolutionary competition between different behavioral strategies.     

Mass-Produced,Assembly-Line Abortion—A Prime Example of Unethical,Unscientific Medicine

The incidence of psychologic sequelae associated with abortion cannot be established scientifically, and so continues to be disputed. Since there are no truly scientific criteria on which to make a prediction as to the psychologic outcome, it seems only proper that elective abortion be labeled “experimental,” rather than “therapeutic.”This uncertainty as to therapeutic benefit is compounded by the fact that adequate studies and information about physical sequelae are also lacking. Furthermore, preliminary statistics from the Population Council indicate that the morbidity rate of abortion performed even under proper medical auspices is unacceptably high.Viewed in this light and in relation to our own ethical code, the current practice of performing innumerable, mechanized, elective abortions can only be considered unethical. If it is argued that abortion can be ethically validated merely by surrounding it with the same controls used in other experimental procedures, then the medical profession should insist on such controls forthwith.     

The Epidemiologist's Dilemma: A Position Paper on the Role of Epidemiology in Canadian Research

Canadian epidemiology is currently in transition from being primarily interested in infectious disease to becoming active in investigating causes of non-infectious disease. Generally, epidemiologists limit their work to “field”, “basic”, or “theoretical” epidemiology. In all three fields there appears to be a shortage of qualified personnel which is likely to become even more acute because of new roles that epidemiologists will probably play in the future. A minimum of 40 full-time epidemiologists is currently required in Canada.Departments other than departments of preventive medicine at medical schools and teaching hospitals are currently spending 79.5% of all funds allocated for non-microbiological epidemiological research in Canada. Since epidemiology is by its very nature population orientated, rather than clinically orientated, clinicians require consultative advice from epidemiologists at many stages of their research. Epidemiological facilities in departments of preventive medicine should therefore be strengthened in order to provide research training and didactic courses needed as the numbers of physicians, nurses and paramedical persons are increased.     

I Choose,Therefore I Like: Preference for Faces Induced by Arbitrary Choice

Behavioral choice alters one’s preference rather than simply reflecting it. This effect to fit preferences with past choice, is known as “choice-induced preference change.” After making a choice between two equally attractive options, one tends to rate the chosen option better than they initially did and/or the unchosen option worse. The present study examined how behavioral choice changes subsequent preference, using facial images for the choice options as well as blind choice techniques. Participants rated their facial preference for each face, and chose between two equally preferred faces and subsequently rated their facial preference. Results from four experiments demonstrated that randomly chosen faces were more preferred only after participants were required to choose “a preferred face,” (in Experiment 1) but not “an unpreferred face,” (in Experiment 2) or “a rounder face” (in Experiment 3). Further, preference change was still observed after participants were informed that choices were actually random (in Experiment 4). Our findings provide new and important implications characterizing the conditions under which random choice changes preference, and show that people are tempted to make a biased evaluation even after they know that they did not make the choice for themselves.