Genotype-phenotype mapping with polyominos made from DNA origami tiles

The correlation between genetic information and characteristics of a living cell—its genotype and its phenotype—constitutes the basis of genetics. Here, we experimentally realize a primitive form of genotype-phenotype mapping with DNA origami. The DNA origami can polymerize into two-dimensional lattices (phenotype) via blunt-end stacking facilitated by edge staples at the seam of the planar DNA origami. There are 80 binding positions for edge staples, which allow us to translate an 80-bit long binary code (genotype) onto the DNA origami. The presence of an edge staple thus corresponds to a “1” and its absence to a “0.” The interactions of our DNA-based system can be reproduced by a polyomino model. Polyomino growth simulations qualitatively reproduce our experimental results. We show that not only the absolute number of base stacks but also their sequence position determine the cluster size and correlation length of the orientation of single DNA origami within the cluster. Importantly, the mutation of a few bits can result in major morphology changes of the DNA origami cluster, while more often, major sequence changes have no impact. Our experimental realization of a correlation between binary information (“genotype”) and cluster morphology (“phenotype”) thus reproduces key properties of genotype-phenotype maps known from living systems.     

Multivariate assessments of activity-related skeletal changes: Interpreting Bell Beaker specialized male archery and social organization in Central Europe

Objectives

The Bell Beaker period witnessed the rise of individual inhumations with “wealthy” burial contexts containing archery-related grave goods, leading archaeologists to label the individuals in these tombs as “archers.” This study looks to (1) compare the skeletons from male “archer” burials with those from male “non-archer” burials—those not having archery-related grave goods—in order to assess a possible link between burial context and physical activity, and (2) apply a biomechanics profile to evaluate whether the individuals associated with these “archer” burials practiced specialized archer activity.

Materials and Methods

The corpus (males only) included 46 “archers” and 40 “non-archers” from Bell Beaker individual inhumations. Osteological data included measurements, scores of entheseal changes, and a diagnosis of certain pathologies. Data analyses involved visual observations, hypothesis tests, dimension reduction, and MANOVA, with approaches aimed at exploring the treatment of data missingness.

Results

Measurement data revealed no differences between the two groups. Evaluations of entheseal changes found that “non-archers” had consistently more instances of bone surface modifications than “archers.” Individual assessments of specialized archer occupation identified 11 possible specialized archers.

Discussion

These findings indicate a possible labor differentiation represented through the presence of a probably prestigious “archer” burial context. This suggests a link between grave good presence and labor, but not between a Bell Beaker archery occupation and an “archer” burial context. Data analyses support the application of biomechanics to osteological analyses in order to assess specialized activity on the skeleton.     

A possible mechanism for the generation and motion of blobs in tokamaks

A possible mechanism for the generation and motion of so-called blobs—peculiar perturbations that are observed in a tokamak edge plasma—is proposed. It is suggested that blobs are self-contracting plasma filaments generated either by the thermal-radiative instability of a plasma with impurities or by the nonradiative resonant charge-exchange instability resulting from the presence of neutral hydrogen atoms near the tokamak wall. Instability occurs in a narrow temperature range in which pressure is a decreasing function of density. Under these conditions, the most typical perturbations are the local ones that originate spontaneously in the form of separate growing hills and wells in the density. The temperature at the centers of the hills is lower than that in the surrounding plasma, but they are denser and, consequently, brighter than the background. The (denser) hills should move (“sink”) toward the separatrix, while the (less dense) wells should “rise” in the opposite direction, as is observed in experiments. It may even be said that they behave in accordance with a peculiar Archimedes' principle.     

Simulating PDGF-Driven Glioma Growth and Invasion in an Anatomically Accurate Brain Domain

Gliomas are the most common of all primary brain tumors. They are characterized by their diffuse infiltration of the brain tissue and are uniformly fatal, with glioblastoma being the most aggressive form of the disease. In recent years, the over-expression of platelet-derived growth factor (PDGF) has been shown to produce tumors in experimental rodent models that closely resemble this human disease, specifically the proneural subtype of glioblastoma. We have previously modeled this system, focusing on the key attribute of these experimental tumors—the “recruitment” of oligodendroglial progenitor cells (OPCs) to participate in tumor formation by PDGF-expressing retrovirally transduced cells—in one dimension, with spherical symmetry. However, it has been observed that these recruitable progenitor cells are not uniformly distributed throughout the brain and that tumor cells migrate at different rates depending on the material properties in different regions of the brain. Here we model the differential diffusion of PDGF-expressing and recruited cell populations via a system of partial differential equations with spatially variable diffusion coefficients and solve the equations in two spatial dimensions on a mouse brain atlas using a flux-differencing numerical approach. Simulations of our in silico model demonstrate qualitative agreement with the observed tumor distribution in the experimental animal system. Additionally, we show that while there are higher concentrations of OPCs in white matter, the level of recruitment of these plays little role in the appearance of “white matter disease,” where the tumor shows a preponderance for white matter. Instead, simulations show that this is largely driven by the ratio of the diffusion rate in white matter as compared to gray. However, this ratio has less effect on the speed of tumor growth than does the degree of OPC recruitment in the tumor. It was observed that tumor simulations with greater degrees of recruitment grow faster and develop more nodular tumors than if there is no recruitment at all, similar to our prior results from implementing our model in one dimension. Combined, these results show that recruitment remains an important consideration in understanding and slowing glioma growth.     

RGS6 and RGS7 Discriminate between the Highly Similar Gαi and Gαo Proteins Using a Two-Tiered Specificity Strategy

RGS6 and RGS7 are regulators of G protein signaling (RGS) proteins that inactivate heterotrimeric (αβγ) G proteins and mediate diverse biological functions, such as cardiac and neuronal signaling. Uniquely, both RGS6 and RGS7 can discriminate between Gα_o and Gα_i1—two similar Gα subunits that belong to the same G_i sub-family. Here, we show that the isolated RGS domains of RGS6 and RGS7 are sufficient to achieve this specificity. We identified three specific RGS6/7 “disruptor residues” that can attenuate RGS interactions toward Gα subunits and demonstrated that their insertion into a representative high-activity RGS causes a significant, yet non-specific, reduction in activity. We further identified a unique “modulatory” residue that bypasses this negative effect, specifically toward Gα_o. Hence, the exquisite specificity of RGS6 and RGS7 toward closely related Gα subunits is achieved via a two-tier specificity system, whereby a Gα-specific modulatory motif overrides the inhibitory effect of non-specific disruptor residues. Our findings expand the understanding of the molecular toolkit used by the RGS family to achieve specific interactions with selected Gα subunits—emphasizing the functional importance of the RGS domain in determining the activity and selectivity of RGS R7 sub-family members toward particular Gα subunits.     

Transportsomes and channelsomes: are they functional units for physiological responses?

Channels and transporters play essential biological roles primarily through the transportation of ions and small molecules that are required to maintain cellular activities across the biomembrane. Secondary to transportation, channels and transporters also integrate and coordinate biological functions at different levels, ranging from the subcellular (nm) to multicellular (μm) scales. This is underpinned by efficient functional coupling within molecular assemblies of channels, transporters, proteins, small molecules, and lipids. Molecular interactions create local microenvironments that, in some cases, uniquely modify the functional properties of the channels and transporters. These molecular assemblies built around a transporter or channel (“transportsomes” and “channelsomes”) can be considered as physiological functional units. In this special issue, we provide an overview of recent progress in our understanding of protein-protein and molecular interactions in transportsomes and channelsomes, which occur through both direct molecular contacts and more distal functional coupling, and examine the validity of these “somes”.     

Chemistry-driven glycoscience

Carbohydrates are the most prominent features of the cell’s exterior—they are the cell’s “face” and serve as the cell’s identification card. The features of cell surface glycans (e.g. glycoproteins, glycolipids, polysaccharides) can be read by proteins, other cells, or organisms. In all of these contexts, glycan-binding proteins typically recognize (“read”) glycan identity. This recognition mediates important host-microbe interactions, as well as critical physiological functions, including fertilization, development, and immune system function. This article focuses on how proteins recognize glycans with an emphasis on three objectives: 1) to understand the molecular basis for carbohydrate recognition, 2) to implement that understanding to develop functional probes of protein-carbohydrate interactions, and 3) to apply those probes to elucidate and exploit the physiological consequences of protein–carbohydrate interactions. In this context, our group has focused on two key aspects of carbohydrate recognition: CH-π and multivalent interactions. We are applying the foundational knowledge gained from our studies for purposes ranging from illuminating host-microbe interactions to probing immune system function.     

Communication and collective action: language and the evolution of human cooperation

All social species face various “collective action problems” (CAPs) or “social dilemmas,” meaning problems in achieving cooperating when the best move from a selfish point of view yields an inferior collective outcome. Compared to most other species, humans are very good at solving these challenges, suggesting that something rather peculiar about human sociality facilitates collective action. This article proposes that language — the uniquely human faculty of symbolic communication — fundamentally alters the possibilities for collective action. I explore these issues using simple game-theoretic models and empirical evidence (both ethnographic and experimental). I review several standard mechanisms for the evolution of cooperation — mutualism, reciprocal altruism, indirect reciprocity and signaling — highlighting their limitations when it comes to explaining large-group cooperation, as well as the ways in which language helps overcome those limitations. Language facilitates complex coordination and is essential for establishing norms governing production efforts and distribution of collective goods that motivate people to cooperate voluntarily in large groups. Language also significantly lowers the cost of detecting and punishing “free riders,” thus greatly enhancing the scope and power of standard conditional reciprocity. In addition, symbolic communication encourages new forms of collectively beneficial displays and reputation management — what evolutionists often term “signaling” and “indirect reciprocity.” Thus, language reinforces existing forces that favor the evolution of cooperation, as well as creating new opportunities for collective action not available even to our closest primate relatives.     

Lifestyle and nutritional imbalances associated with Western diseases: causes and consequences of chronic systemic low-grade inflammation in an evolutionary context

In this review, we focus on lifestyle changes, especially dietary habits, that are at the basis of chronic systemic low grade inflammation, insulin resistance and Western diseases. Our sensitivity to develop insulin resistance traces back to our rapid brain growth in the past 2.5 million years. An inflammatory reaction jeopardizes the high glucose needs of our brain, causing various adaptations, including insulin resistance, functional reallocation of energy-rich nutrients and changing serum lipoprotein composition. The latter aims at redistribution of lipids, modulation of the immune reaction, and active inhibition of reverse cholesterol transport for damage repair. With the advent of the agricultural and industrial revolutions, we have introduced numerous false inflammatory triggers in our lifestyle, driving us to a state of chronic systemic low grade inflammation that eventually leads to typically Western diseases via an evolutionary conserved interaction between our immune system and metabolism. The underlying triggers are an abnormal dietary composition and microbial flora, insufficient physical activity and sleep, chronic stress and environmental pollution. The disturbance of our inflammatory/anti-inflammatory balance is illustrated by dietary fatty acids and antioxidants. The current decrease in years without chronic disease is rather due to “nurture” than “nature,” since less than 5% of the typically Western diseases are primary attributable to genetic factors. Resolution of the conflict between environment and our ancient genome might be the only effective manner for “healthy aging,” and to achieve this we might have to return to the lifestyle of the Paleolithic era as translated to the 21st century culture.     

hERG Function in Light of Structure

The human ether-a-go-go-related gene1 (hERG) ion channel has been the subject of fascination since it was identified as a target of long QT syndrome more than 20 years ago. In this Biophysical Perspective, we look at what makes hERG intriguing and vexingly unique. By probing recent high-resolution structures in the context of functional and biochemical data, we attempt to summarize new insights into hERG-specific function and articulate important unanswered questions. X-ray crystallography and cryo-electron microscopy have revealed features not previously on the radar—the “nonswapped” transmembrane architecture, an “intrinsic ligand,” and hydrophobic pockets off a pore cavity that is surprisingly small. Advances in our understanding of drug block and inactivation mechanisms are noted, but a full picture will require more investigation.     

Lateralized behavior in two captive bottlenose dolphins (Tursiops truncatus)

The study of behavioral laterality in humans and nonhumans can contribute to our understanding of brain evolution and functional similarities across species. Few studies have focused on cetaceans. This report exams lateralized behaviors in two captive bottlenose dolphins (Tursiops truncatus). Observations were made by videotaping through a 90 × 150 cm underwater one-way Plexiglass mirror. Directional bias in swimming, “barrel-roll” maneuvers, and circular head movements was assessed for each subject. There was a strong clockwise bias in swimming direction and direction of “barrel-rolls,” but not circular head movements. The clockwise bias in swimming direction and “barrel-roll” maneuvers may be consistent with a rightward turning bias. Zoo Biol 16:173–177, 1997. © 1997 Wiley-Liss, Inc.     

Whisking as a “voluntary” response: operant control of whisking parameters and effects of whisker denervation

The rat’s ability to vary its whisking “strategies” to meet the functional demands of a discriminative task suggests that whisking may be characterized as a “voluntary” behavior—an operant—and like other operants, should be modifiable by appropriate manipulations of response–reinforcer contingencies. To test this hypothesis we have used high-resolution, optoelectronic “real-time” recording procedures to monitor the movements of individual whiskers and reinforce specific movement parameters (amplitude, frequency). In one operant paradigm (N = 9) whisks with protractions above a specified amplitude were reinforced (Variable Interval 30?s) in the presence of a tone, but extinguished (EXT) in its absence. In a second paradigm (N = 3), rats were reinforced on two different VI schedules (VI-20s/VI-120s) signaled, respectively, by the presence or absence of the tone. Selective reinforcement of whisking movements maintained the behavior over many weeks of testing and brought it under stimulus and schedule control. Subjects in the first paradigm learned to increase responding in the presence of the tone and inhibit responding in its absence. In the second paradigm, subjects whisked at significantly different rates in the two stimulus conditions. Bilateral deafferentation of the whisker pad did not impair conditioned whisking or disrupt discrimination behavior. Our results confirm the hypothesis that rodent whisking has many of the properties of an operant response. The ability to bring whisking movement parameters under operant control should facilitate electrophysiological and lesion/behavioral studies of this widely used “model” sensorimotor system.     

The torus semicircularis in a gekkonid lizard

The cytoarchitecture and neuromorphology of the torus semicircularis in the tokay gecko, Gekko gecko, were examined in Nissl-stained, fiber-stained, and Golgi-impregnated tissues. From a superficial position, the torus semicircularis extends rostrally under the caudal half of the optic tectum. Caudally, the two tori abut upon one another; rostrally, they diverge. The torus semicircularis consists of central, laminar, and superficial nuclei. The central nucleus consists of fusiform, spherical and triangular neurons. Their dendrites are highly branched, with numerous dendritic spines, and are oriented mediolaterally, dorsoventrally, and rostrocaudally. Fusiform and spherical neurons display two dendritic patterns: “single axis,” ramifying in one axis, and “dual axis,” exhibiting higher-order branches perpendicular to the primary dendrites. Triangular neurons exhibit a “radiate” dendritic pattern. In the rostral half of the torus semicircularis, the laminar nucleus caps the central nucleus. The laminar nucleus encircles the central nucleus in the caudal torus semicircularis. The neurons of the laminar nucleus have dendritic arrays oriented parallel to the border of the central nucleus. These dendrites exhibit a paucity of dendritic spines and higher-order branches. Fusiform and spherical neurons exhibit “single axis” and “dual axis” dendritic patterns. Triangular neurons display “radiate” patterns. The caudal superficial nucleus lies dorsal and dorsolateral to the central nucleus. The superficial nucleus is sparsely populated by small fusiform and spherical neurons with moderately branched dendrites and moderate numbers of dendritic spines. These neurons display “single axis” (fusiform neurons) as well as “dual axis” and “radiate” (spherical neurons) dendritic patterns. They are oriented either parallel to or perpendicular to the boundary of the laminar nucleus.     

Habit learning and brain–machine interfaces (BMI): a tribute to Valentino Braitenberg’s “Vehicles”

Brain–Machine Interfaces (BMI) allow manipulation of external devices and computers directly with brain activity without involvement of overt motor actions. The neurophysiological principles of such robotic brain devices and BMIs follow Hebbian learning rules as described and realized by Valentino Braitenberg in his book “Vehicles,” in the concept of a “thought pump” residing in subcortical basal ganglia structures. We describe here the application of BMIs for brain communication in totally locked-in patients and argue that the thought pump may extinguish—at least partially—in those people because of extinction of instrumentally learned cognitive responses and brain responses. We show that Pavlovian semantic conditioning may allow brain communication even in the completely paralyzed who does not show response-effect contingencies. Principles of skill learning and habit acquisition as formulated by Braitenberg are the building blocks of BMIs and neuroprostheses.     

What is an edge species? The implications of sensitivity to habitat edges

For decades, researchers have categorized species as “edge‐loving” or “edge‐avoiding”, but recent studies that show inconsistencies in responses have called these labels into question and led to a sense that edge effects are idiosyncratic and difficult to understand. We suggest that species would be better categorized according to their sensitivity to edges, not the direction of observed responses because no species should be expected to show the same response to all edge types. Measures of edge sensitivity will apply widely across taxa and landscapes and allow metrics that are broadly comparable, making generalities easier to discern. Finally, while the direction of observed edge responses remains a critical (but largely understood) dynamic, most reported edge responses are neutral, so discovering when species are least likely to respond to edges will increase our understanding of edge ecology and associated fragmentation effects. We offer a case study that measures edge sensitivity of 15 butterfly species at 12 edge types. We found that sensitivity is weakly related to vulnerability to predation, but more importantly we show how our results generate new predictions about edge sensitivity that can be explored in future studies.     

Palate morphogenesis: Current understanding and future directions

In the past, most scientists conducted their inquiries of nature via inductivism, the patient accumulation of “pieces of information” in the pious hope that the sum of the parts would clarify the whole. Increasingly, modern biology employs the tools of bioinformatics and systems biology in attempts to reveal the “big picture.” Most successful laboratories engaged in the pursuit of the secrets of embryonic development, particularly those whose research focus is craniofacial development, pursue a middle road where research efforts embrace, rather than abandon, what some have called the “pedestrian” qualities of inductivism, while increasingly employing modern data mining technologies. The secondary palate has provided an excellent paradigm that has enabled examination of a wide variety of developmental processes. Examination of cellular signal transduction, as it directs embryogenesis, has proven exceptionally revealing with regard to clarification of the “facts” of palatal ontogeny—at least the facts as we currently understand them. Herein, we review the most basic fundamentals of orofacial embryology and discuss how functioning of TGFβ, BMP, Shh, and Wnt signal transduction pathways contributes to palatal morphogenesis. Our current understanding of palate medial edge epithelial differentiation is also examined. We conclude with a discussion of how the rapidly expanding field of epigenetics, particularly regulation of gene expression by miRNAs and DNA methylation, is critical to control of cell and tissue differentiation, and how examination of these epigenetic processes has already begun to provide a better understanding of, and greater appreciation for, the complexities of palatal morphogenesis. Birth Defects Research (Part C) 90:133–154, 2010. © 2010 Wiley‐Liss, Inc.     

Secondary invasion: When invasion success is contingent on other invaders altering the properties of recipient ecosystems

Positive interactions between exotic species may increase ecosystem‐level impacts and potentially facilitate the entry and spread of other exotic species. Invader‐facilitated invasion success—”secondary invasion”—is a key conceptual aspect of the well‐known invasional meltdown hypothesis, but remains poorly defined and empirically underexplored. Drawing from heuristic models and published empirical studies, we explore this form of “secondary invasion” and discuss the phenomenon within the recognized conceptual framework of the determinants of invasion success. The term “secondary invasion” has been used haphazardly in the literature to refer to multiple invasion phenomena, most of which have other more accepted titles. Our usage of the term secondary invasion is akin to “invader‐facilitated invasion,” which we define as the phenomenon in which the invasion success of one exotic species is contingent on the presence, influence, and impacts of one or more other exotic species. We present case studies of secondary invasion whereby primary invaders facilitate the entry or establishment of exotic species into communities where they were previously excluded from becoming invasive. Our synthesis, discussion, and conceptual framework of this type of secondary invasion provides a useful reference to better explain how invasive species can alter key properties of recipient ecosystems that can ultimately determine the invasion success of other species. This study increases our appreciation for complex interactions following invasion and highlights the impacts of invasive species themselves as possible determinants of invasion success. We anticipate that highlighting “secondary invasion” in this way will enable studies reporting similar phenomena to be identified and linked through consistent terminology.     

Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4‐helix bundle proteins

To probe the potential for enzymatic activity in unevolved amino acid sequence space, we created a combinatorial library of de novo 4‐helix bundle proteins. This collection of novel proteins can be considered an “artificial superfamily” of helical bundles. The superfamily of 102‐residue proteins was designed using binary patterning of polar and nonpolar residues, and expressed in Escherichia coli from a library of synthetic genes. Sequences from the library were screened for a range of biological functions including heme binding and peroxidase, esterase, and lipase activities. Proteins exhibiting these functions were purified and characterized biochemically. The majority of de novo proteins from this superfamily bound the heme cofactor, and a sizable fraction of the proteins showed activity significantly above background for at least one of the tested enzymatic activities. Moreover, several of the designed 4‐helix bundles proteins showed activity in all of the assays, thereby demonstrating the functional promiscuity of unevolved proteins. These studies reveal that de novo proteins—which have neither been designed for function, nor subjected to evolutionary pressure (either in vivo or in vitro)—can provide rudimentary activities and serve as a “feedstock” for evolution.     

Predicting resilience of ecosystem functioning from co‐varying species' responses to environmental change

Understanding how environmental change affects ecosystem function delivery is of primary importance for fundamental and applied ecology. Current approaches focus on single environmental driver effects on communities, mediated by individual response traits. Data limitations present constraints in scaling up this approach to predict the impacts of multivariate environmental change on ecosystem functioning. We present a more holistic approach to determine ecosystem function resilience, using long‐term monitoring data to analyze the aggregate impact of multiple historic environmental drivers on species' population dynamics. By assessing covariation in population dynamics between pairs of species, we identify which species respond most synchronously to environmental change and allocate species into “response guilds.” We then use “production functions” combining trait data to estimate the relative roles of species to ecosystem functions. We quantify the correlation between response guilds and production functions, assessing the resilience of ecosystem functioning to environmental change, with asynchronous dynamics of species in the same functional guild expected to lead to more stable ecosystem functioning. Testing this method using data for butterflies collected over four decades in the United Kingdom, we find three ecosystem functions (resource provisioning, wildflower pollination, and aesthetic cultural value) appear relatively robust, with functionally important species dispersed across response guilds, suggesting more stable ecosystem functioning. Additionally, by relating genetic distances to response guilds we assess the heritability of responses to environmental change. Our results suggest it may be feasible to infer population responses of butterflies to environmental change based on phylogeny—a useful insight for conservation management of rare species with limited population monitoring data. Our approach holds promise for overcoming the impasse in predicting the responses of ecosystem functions to environmental change. Quantifying co‐varying species' responses to multivariate environmental change should enable us to significantly advance our predictions of ecosystem function resilience and enable proactive ecosystem management.     

THE CONTRIBUTION OF GENE MOVEMENT TO THE “TWO RULES OF SPECIATION”

The two “rules of speciation”—the Large X‐effect and Haldane's rule—hold throughout the animal kingdom, but the underlying genetic mechanisms that cause them are still unclear. Two predominant explanations—the “dominance theory” and faster male evolution—both have some empirical support, suggesting that the genetic basis of these rules is likely multifarious. We revisit one historical explanation for these rules, based on dysfunctional genetic interactions involving genes recently moved between chromosomes. We suggest that gene movement specifically off or onto the X chromosome is another mechanism that could contribute to the two rules, especially as X chromosome movements can be subject to unique sex‐specific and sex chromosome specific consequences in hybrids. Our hypothesis is supported by patterns emerging from comparative genomic data, including a strong bias in interchromosomal gene movements involving the X and an overrepresentation of male reproductive functions among chromosomally relocated genes. In addition, our model indicates that the contribution of gene movement to the two rules in any specific group will depend upon key developmental and reproductive parameters that are taxon specific. We provide several testable predictions that can be used to assess the importance of gene movement as a contributor to these rules in the future.