Comprehensive analysis of proteins to evaluate their genetic diversity, study their differences, and respond to the tensions is the main subject of an interdisciplinary field of study called proteomics. The main objective of the proteomics is to detect and quantify proteins and study their post-translational modifications and interactions using protein chemistry, bioinformatics, and biology. Any disturbance in proteins interactive network can act as a source for biological disorders and various diseases such as Alzheimer and cancer. Most current computational methods (...) for discovering protein complexes are usually based on specific topological characteristics of protein-protein networks. To identify the protein complexes, in this paper, we, first, present a new encoding method to represent solutions; we then propose a new clustering algorithm based on the genetic algorithm, named PPI-GA, employing a new multiobjective quality function. The proposed algorithm is evaluated on two gold standard and real-world datasets. The result achieved demonstrates that the proposed algorithm can detect important protein complexes, and it provides more accurate results compared with state-of-the-art protein complex identification algorithms. (shrink)

The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2‐type zinc finger domains that specifically bind to DNA. Few well‐studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has revealed a key difference (...) between groups of organisms. Unlike plants, transcription factors in metazoans contain clusters of C2H2 domains typically separated by a linker with the TGEKP consensus sequence. The average size of C2H2 clusters varies substantially, even between genomes of higher metazoans, and with a tendency to increase in combination with SCAN, and especially KRAB domains, reflecting the increasing complexity of gene regulatory networks. (shrink)

Interactions among membrane proteins regulate numerous cellular processes, including cell growth, cell differentiation and apoptosis. We need to understand which proteins interact, where they interact and to which extent they interact. This article describes a set of novel approaches to measure, on the surface of living cells, the number of clusters of proteins, the number of proteins per cluster, the number of clusters or membrane domains that contain pairs of interacting proteins and the fraction of one protein species (...) that interacts with another protein within these domains. These data can then be interpreted in terms of the function of the protein‐protein interactions. BioEssays 26:196–203, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Coronins constitute an evolutionarily conserved family of WD‐repeat actin‐binding proteins, which can be clearly classified into two distinct groups based on their structural features. All coronins possess a conserved basic N‐terminal motif and three to ten WD repeats clustered in one or two core domains. Dictyostelium and mammalian coronins are important regulators of the actin cytoskeleton, while the fly Dpod1 and the yeast coronin proteins crosslink both actin and microtubules. Apart from that, several coronins have been shown to be involved (...) in vesicular transport. C. elegans POD‐1 and Drosophila coro regulate the actin cytoskeleton, but also govern vesicular trafficking as indicated by mutant phenotypes. In both organisms, defects in cytoskeleton and trafficking lead to severe developmental defects ranging from abnormal cell division to aberrant formation of morphogen gradients. Finally, mammalian coronin 7 appears not to execute any cytoskeleton‐related functions, but rather participates in regulating Golgi trafficking. Here, we review recent data providing more insight into molecular mechanisms underlying the regulation of F‐actin structures, cytoskeletal rearrangements and intracellular membrane transport by coronin proteins and the way that they might link cytoskeleton with trafficking in development and disease. BioEssays 27:625–632, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins’ amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism’s biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the GþC content of the first codon position. An (...) unexpected bias is driven, in many proteomes, by the AANbox of the genetic code, suggesting some functional biochemical relationship between asparagine and lysine. Less-significant biases are driven by the rare amino acids, cysteine and tryptophan. Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction. (shrink)

The accurate annotation of an unknown protein sequence depends on extant data of template sequences. This could be empirical or sets of reference sequences, and provides an exhaustive pool of probable functions. Individual methods of predicting dominant function possess shortcomings such as varying degrees of inter-sequence redundancy, arbitrary domain inclusion thresholds, heterogeneous parameterization protocols, and ill-conditioned input channels. Here, I present a rigorous theoretical derivation of various steps of a generic algorithm that integrates and utilizes several statistical methods to (...) predict the dominant function in unknown protein sequences. The accompanying mathematical proofs, interval definitions, analysis, and numerical computations presented are meant to offer insights not only into the specificity and accuracy of predictions, but also provide details of the operatic mechanisms involved in the integration and its ensuing rigor. The algorithm uses numerically modified raw hidden markov model scores of well defined sets of training sequences and clusters them on the basis of known function. The results are then fed into an artificial neural network, the predictions of which can be refined using the available data. This pipeline is trained recursively and can be used to discern the dominant principal function, and thereby, annotate an unknown protein sequence. Whilst, the approach is complex, the specificity of the final predictions can benefit laboratory workers design their experiments with greater confidence. -/- . (shrink)

Chemical kinds (e.g. gold) are generally treated as having timelessly fixed identities. Biological kinds (e.g. goldfinches) are generally treated as evolved and/or evolving entities. So what kind of kind is a biochemical kind? This paper defends the thesis that biochemical molecules are clustered chemical kinds, some of which–namely, evolutionarily conserved units–are also biological kinds.On this thesis, a number of difficulties that have recently occupied philosophers concerned with proteins and kinds are shown to be resolved or dissolved.

The use of super‐resolution imaging techniques in cell biology has yielded a wealth of information regarding cellular elements and processes that were invisible to conventional imaging. Focusing on images obtained by stimulated emission depletion (STED) microscopy, we discuss how the new high‐resolution data influence the ways in which we use and interpret images in cell biology. Super‐resolution images have lent support to some of our current hypotheses. But, more significantly, they have revealed unexpectedly complex processes that cannot be accounted for (...) by the simpler models based on diffraction‐limited imaging. The super‐resolution imaging data challenge cell biologists to change their theoretical framework, by including, for instance, interpretations that describe multiple functions, functional errors or lack of function for cellular elements. In this context, we argue that descriptive research using super‐resolution microscopy is now as necessary as hypothesis‐driven research. (shrink)

Clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR‐associated protein (CRISPR/Cas) system has revolutionized genetic research in the life sciences. Four classes of CRISPR/Cas‐derived genome editing agents, such as nuclease, base editor, recombinase, and prime editor have been introduced for engineering the genomes of diverse organisms. The recently introduced prime editing system offers precise editing without many off‐target effects than traditional CRISPR‐based systems. Many researchers have successfully applied this gene‐editing toolbox in diverse systems for various genome‐editing applications. This review presents the (...) mechanism of prime editing and summarizes the details of the prime editing system applied in plants and mammalian cells for precise genome editing. We also discuss the advantages, limitations, and potential future applications of prime editing in these systems. This review enables the researcher to gain knowledge on prime editing tools and their potential applications in plants and mammalian cells. (shrink)

The discovery of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-mediated protein 9 (CRISPR-Cas9) immediately revealed numerous potential therapeutic applications. Although CRISPR-Cas9 will most likely be useful for addressing issues such as genetic diseases and related medical issues, use of this modality for germline modification generates complex ethical questions regarding the safety and efficacy, human genetic enhancement, and “designer” babies. In this article, the case of the He Jiankui affair is used as an example of the potential (...) for unregulated use of CRISPR-Cas9 technology. In 2018, Dr He Jiankui reported that he had successfully edited human embryos. This work clearly violates all international principles of bioethics. As such, the purpose of this paper is to explore the ethical challenges inherent in the use of CRISPR-Cas9 for human germline editing from the perspectives of the goals of Islamic law (Maqasid al Shari'a) and the major jurisprudential maxims (Qawaid Fiqhiyyah). We argue that from an Islamic standpoint, the therapeutic application of CRISPR-Cas9 for germline editing may be permissible if the safety and efficacy concerns are resolved and if the principles of Maqasid al-Shari'a are fulfilled. (shrink)

With the emergence of clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) as one of the most promising new gene-editing techniques, scientists are now endeavoring to apply it to various domains. Among all the possible applications, gene editing in human embryos has received the most attention. Against this background, this article carries out a philosophical study on the ethical problems of human embryo gene editing or designing. Arguments against human embryo gene designing include that parents should be (...) prohibited from deciding their children’s future; commodifying children should be prohibited; the natural reproductive process should not be disturbed; and human embryo gene designing might foster discrimination. Arguments for human embryo gene designing include that parents should have the freedom to design their own babies and this freedom should not be limited; designing babies can promote the happy life of the baby; and totally forbidding embryo gene editing would drive the practice underground, where it would be performed illegally. This article analyzes all of these arguments and points out that all of them have some flaws. In order to draw a thoughtful conclusion, we turn to Confucianism and find a new perspective to determine whether designing babies with CRISPR technology is ethically permissible. (shrink)

Metallothioneins (MTs) are ubiquitous proteins with the capacity to bind heavy metal ions (mainly Cd, Zn or Cu), and they have been found in animals, plants, eukaryotic and prokaryotic micro‐organisms. We have carried out a comparative analysis of ciliate MTs (Tetrahymena species) to well‐known MTs from other organisms, discussing their exclusive features, such as the presence of aromatic amino acid residues and almost exclusive cysteine clusters (CCC) present in cadmium‐binding metallothioneins (CdMTs), higher heavy metal‐MT stoichiometry values, and a strictly conserved (...) modular–submodular structure. Based on this last feature and an extensive gene duplication, we propose a possible model for the evolutionary history of T. thermophila MTs. We also suggest possible functions for these MTs from consideration of their differential gene expressions and discuss the potential use of these proteins and/or their gene promoters for designing molecular or whole‐cell biosensors for a fast detection of heavy metals in diverse polluted ecosystems. (shrink)

Sorting of membrane proteins is generally mediated by cytosolic coats, which create a scaffold to form coated buds and vesicles and to selectively concentrate cargo by interacting with cytosolic signals. The classical paradigm is the interaction between clathrin coats and associated adaptor proteins, which cluster receptors with characteristic tyrosine and dileucine motifs during endocytosis. Clathrin in association with different sets of adaptors is found in addition at the trans-Golgi network and endosomes. Sequences similar to internalization signals also direct lysosomal (...) and basolateral sorting, which implicates related clathrin-adaptor coats in the respective sorting pathways. This review concentrates on the recognition of sorting signals by clathrin-associated adaptor proteins, an area of significant recent progress due to new methodological and conceptual approaches. BioEssays 21:558–567, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Pathogenic variants occurring in protein‐coding regions underlie human genetic disease through various mechanisms. They can lead to a loss of function (LOF) such as in recessive conditions or in dominant conditions due to haploinsufficiency. Dominant‐negative (DN) effects, counteracting the activity of the normal gene‐product, and gain of function (GOF) are also mechanisms driving dominance. Here, I discuss a few papers on these specific mechanisms. In short, there is accumulating evidence pointing to differences between LOF versus non‐LOF variants (DN and (...) GOF). The latter are thought to have milder effects on protein structure and, as expected, DN variants are enriched at protein interfaces. This tendency to cluster in 3D space can help improve the ability of computational tools to predict the pathogenicity of DN variants, which is currently a challenging issue. More recent results support the hypothesis whereby cotranslational assembly of macromolecular complexes can buffer deleterious consequences of variants that would otherwise lead to DN effects (DNEs). Indeed, subunits the variants of which are responsible for DNEs tend to elude cotranslational assembly, thus poisoning complexes involving wild‐type subunits. The constraints explaining why the buffering of DNEs is not universal require further investigation. (shrink)

Chemical kinds are generally treated as having timelessly fixed identities. Biological kinds are generally treated as evolved and/or evolving entities. So what kind of kind is a biochemical kind? This article defends the thesis that biochemical molecules are clustered chemical kinds, some of which—namely, evolutionarily conserved units—are also biological kinds. On this thesis, a number of difficulties that have recently occupied philosophers concerned with proteins and kinds are shown to be either resolved or dissolved. 1 Introduction2 Conflicting Intuitions about Kinds (...) of Proteins3 Against Permissive Pluralism4 Against Nominalism, Toward a Duality of Kinds5 Biological Kinds, Chemical Kinds, and Their Relations6 Implications for Biological Individuals7 Implications for Monism and Scientific Practice. (shrink)

Systems biology provides alternatives to the strategies to developing mechanistic explanations traditionally pursued in cell and molecular biology and much discussed in accounts of mechanistic explanation. Rather than starting by identifying a mechanism for a given phenomenon and decomposing it, systems biologists often start by developing cell-wide networks of detected connections between proteins or genes and construe clusters of highly interactive components as potential mechanisms. Using inference strategies such as ‘guilt-by-association’, researchers advance hypotheses about functions performed of these mechanisms. I (...) examine several examples of research on budding yeast, first on what are taken to be enduring networks and subsequently on networks that change as cells perform different activities or respond to different external conditions. (shrink)

The exocyst is a conserved octameric complex that physically tethers a vesicle to the plasma membrane, prior to membrane fusion. It is important not only for secretion and membrane delivery but also, in mammalian cells, for cytokinesis, ciliogenesis, autophagy, tumorigenesis, and host defense. The combination of genome editing and advanced light microscopy of exocyst subunits in living cells has recently shown the complex to be much more dynamic than previously appreciated, and exposed how little we still know about its function (...) and regulation. (shrink)

In the wake of the advent of genome editing technology CRISPR-Cas9 (clustered regularly interspaced palindromic repeat (CRISPR)-associated protein 9), there has been a global debate around the implications of manipulating the human genome. While CRISPR-based germline gene editing is new, the debate about the ethics of gene editing is not – for several decades now, scholars have debated the ethics of making heritable changes to the human genome. The arguments that have been raised both for and against the use (...) of genetic technologies in human reproduction reiterate much of the arguments made in the pre-CRISPR debate. As such, it is instructive for South Africa to reflect on these arguments now, in considering our position on the regulation of the use of this novel biotechnology. There are two dominant schools of thought in this area, bioliberalism and bioconservatism. Bioconservatives raise concerns about the risks of genetic manipulation, and argue that it ought to be limited or prohibited to avert these risks to human health and human nature. Bioliberal scholars are more open to the prospect of genetic manipulation, because of its potential utility. In this article, I conclude that in liberal democracies such as our own, bioliberal arguments ought to be seriously considered when formulating policy on human genome editing because of the extent to which they resonate with our Constitutional values and human rights. I further suggest that there is a need for an enquiry into the relevance of African perspectives on the ethical questions that arise concerning germline genome editing. (shrink)

Biochemical kinds present an interesting case study in the philosophical literature on natural kinds and functions, as they fall between chemical kinds, defined by their intrinsic microstructural properties, and biological kinds, which involve functional and evolutionary considerations. Here we examine how the distinct chemical and functional properties of biochemical kinds are unified, as well as their identity criteria. We contend that unification principles are crucial for explaining the clustering of properties shared by members of natural kinds and for establishing identity (...) criteria for such kinds. We consider whether there are specific properties that characterize biochemical kinds. This entails investigating the relationship between biochemical functions and structure. We focus on proteins, particularly on vitamin B12, as a representative example of a biochemical kind. We conclude that if there are unification principles for biochemical kinds, these principles exist at the level of biochemistry itself. This supports the naturalness of biochemical kinds as genuine categories and provides identity conditions for such kinds. (shrink)

Systems biology has provided new resources for discovering and reasoning about mechanisms. In addition to generating databases of large bodies of data, systems biologists have introduced platforms such as Cytoscape to represent protein–protein interactions, gene interactions, and other data in networks. Networks are inherently flat structures. One can identify clusters of highly connected nodes, but network representations do not represent these clusters as at a higher level than their constituents. Mechanisms, however, are hierarchically organized: they can be decomposed (...) into their parts and their activities can be decomposed into component operations. A potent bridge between flat networks and hierarchical mechanisms is provided by biological ontologies, both those curated by hand such as Gene Ontology and those extracted directly from databases such as Network Extracted Ontology. I examine several examples in which by applying ontologies to networks, systems biologists generate new hypotheses about mechanisms and characterize these novel strategies for developing mechanistic explanations. (shrink)

This focus issue considers the normative implications of the recent emergence in genome editing technology known as CRISPR (clustered regularly interspaced short palindromic repeats) or CRISPR‐associated protein 9. Originally discovered in the adaptive immune systems of bacteria and archaea, CRISPR enables researchers to make efficient and site‐specific modifications to the genomes of cells and organisms. More accessible, precise, and economic than previous gene editing technologies, CRISPR holds the promise of not only transforming the fields of genetics, agriculture, and human (...) medicine, but also heralding a new era of democratized biotechnology. However, the speed with which developments in the field have progressed threatens to overwhelm our normative sensibilities about the long‐term practical and ethical implications. The contributors to this focus issue attempt to think through some of the more salient moral and practical consequences of CRISPR in the context of religious ethics, particularly as they relate to themes of autonomy, human flourishing, social justice, and the ethics of enhancement. (shrink)

A major approach to cancer research in the late twentieth century was to search for genes that, when altered, initiated the development of a cell into a cancerous state or failed to stop this development. But as researchers acquired the capacity to sequence tumors and incorporated the resulting data into databases, it became apparent that for many tumors no genes were frequently altered and that the genes altered in different tumors in the same tissue type were often distinct. To address (...) this heterogeneity problem, many researchers looked to a higher level of organization—to mechanisms in which gene products participated. They proposed to reduce heterogeneity by recognizing that multiple gene alterations affect the same mechanism and that it is the altered mechanism that is responsible for the cell developing one or more hallmarks of cancer. I examine how mechanisms figure in this research and focus on two heuristics researchers use to integrate proteins into mechanisms, one focusing on pathways and one focusing on clusters in networks. (shrink)

This article responds to two problems confronting social and human sciences: how to relate to digital data, inasmuch as it challenges established social science methods; and how to relate to life sciences, insofar as they produce knowledge that impinges on our own ways of knowing. In a case study of proteomics, we explore how digital devices grapple with large-scale multiples – of molecules, databases, machines and people. We analyse one particular visual device, a cluster-heatmap, produced by scientists by mining (...) data from a large number of experiments on human blood plasma proteins. These proteins make up a myriad multiple whose identity shifts in many ways. Rather than displaying data about proteins, the heatmap constructs a view of the differences and similarities between experiments. We find this attempt to construct a view on many things at once instructive in thinking about multiples more generally. Instead of flattening molecular ‘life itself’, this visual device superimposes layers of digital devices and techniques from a wide variety of disciplines. This layering suggests a different way of relating to the life sciences more generally: rather than what they know, how they know might be of use to social and human sciences when attending to multiplicities. (shrink)

This paper seeks to expand our appreciation of the gene editing tool, clustered regularly interspaced short palindromic repeats‐associated protein 9 (CRISPR‐Cas9), its function, its benefits and risks, and the challenges of regulating its use. I frame CRISPR's emergence and its current use in the context of 150 years of formal exploration of heredity and genetics. I describe CRISPR's structure and explain how it functions as a useful engineering tool. The contemporary international and domestic regulatory environment governing human genetic interventions (...) is reviewed and shown to be increasingly ineffective in its ability to restrain, guide, and optimize the emerging use of CRISPR. Several reasons for this lack of consensus are discussed. In conclusion, I suggest a number of public policy recommendations that might allow us to simultaneously embrace our most important moral values and manage the inevitable power CRISPR will come to have in our lives. (shrink)

In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator‐like effector proteins, which are easier to engineer to target new DNA sequences than the previously available DNA binding templates, zinc fingers and meganucleases. Recently, the area experimented a quantum leap because of the introduction of the clustered regularly interspaced short palindromic repeats (CRISPR)‐associated protein (Cas) system (clustered regularly interspaced short (...) palindromic sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR‐Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human pathways or to improve key organisms for biotechnological applications, such as plants, livestock genome as well as yeasts and bacterial strains. (shrink)

The integrins are receptors for proteins of the extracellular matrix, both providing a physical link to the cytoskeleton and transducing signals from the extracellular matrix. Activation of integrins leads to tyrosine and serine phosphorylation of a number of proteins, elevation of cytosolic calcium levels, cytoplasmic alkalinization, changes in phospholipid metabolism and, ultimately, changes in gene expression. The recently discovered focal adhesion kinase localizes to focal contacts, which are sites of integrin clustering, and focal adhesion kinase can physically associate with integrins (...) in vitro. As integrins lack intrinsic catalytic activity, focal adhesion kinase is a candidate for a signaling molecule that is recruited by integrins in order to trigger the generation of intracellular second messengers. Thus, focal adhesion kinase may play a central role in signal transduction through integrins. (shrink)

Most cells communicate with their immediate neighbors through the exchange of cytosolic molecules such as ions, second messengers and small metabolites. This activity is made possible by clusters of intercellular channels called gap junctions, which connect adjacent cells. In terms of molecular architecture, intercellular channels consist of two channels, called connexons, which interact to span the plasma membranes of two adjacent cells and directly join the cytoplasm of one cell to another. Connexons are made of structural proteins named connexins, which (...) compose a multigene family. Connexin channels participate in the regulation of signaling between developing and differentiated cell types, and recently there have been some unexpected findings. First, unique ionic‐ and size‐selectivities are determined by each connexin; second, the establishment of intercellular communication is defined by the expression of compatible connexins; third, the discovery of connexin mutations associated with human diseases and the study of knockout mice have illustrated the vital role of cell‐cell communication in a diverse array of tissue functions. (shrink)

TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin‐mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter‐TAD loop formation. Based on the reanalysis of Nano‐C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered (...) CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read‐through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter‐TAD loops is restricted though. We speculate that the DNA‐encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer–promoter loop formation and other genomic processes. (shrink)

The Earth agglomerates and heats. Convection cells within the planetary interior expedite the cooling process. Volcanoes evolve steam, carbon dioxide, sulfur dioxide and pyrophosphate. An acidulous Hadean ocean condenses from the carbon dioxide atmosphere. Dusts and stratospheric sulfurous smogs absorb a proportion of the Sun’s rays. The cooled ocean leaks into the stressed crust and also convects. High temperature acid springs, coupled to magmatic plumes and spreading centers, emit iron, manganese, zinc, cobalt and nickel ions to the ocean. Away from (...) the spreading centers cooler alkaline spring waters emanate from the ocean floor. These bear hydrogen, formate, ammonia, hydrosulfide and minor methane thiol. The thermal potential begins to be dissipated but the chemical potential is dammed. The exhaling alkaline solutions are frustrated in their further attempt to mix thoroughly with their oceanic source by the spontaneous precipitation of biomorphic barriers of colloidal iron compounds and other minerals. It is here we surmise that organic molecules are synthesized, filtered, concentrated and adsorbed, while acetate and methane—separate products of the precursor to the reductive acetyl-coenzyme-A pathway—are exhaled as waste. Reactions in mineral compartments produce acetate, amino acids, and the components of nucleosides. Short peptides, condensed from the simple amino acids, sequester ‘ready-made’ iron sulfide clusters to form protoferredoxins, and also bind phosphates. Nucleotides are assembled from amino acids, simple phosphates carbon dioxide and ribose phosphate upon nanocrystalline mineral surfaces. The side chains of particular amino acids register to fitting nucleotide triplet clefts. Keyed in, the amino acids are polymerized, through acid–base catalysis, to alpha chains. Peptides, the tenuous outer-most filaments of the nanocrysts, continually peel away from bound RNA. The polymers are concentrated at cooler regions of the mineral compartments through thermophoresis. RNA is reproduced through a convective polymerase chain reaction operating between 40 and 100°C. The coded peptides produce true ferredoxins, the ubiquitous proteins with the longest evolutionary pedigree. They take over the role of catalyst and electron transfer agent from the iron sulfides. Other iron–nickel sulfide clusters, sequestered now by cysteine residues as CO-dehydrogenase and acetyl-coenzyme-A synthase, promote further chemosynthesis and support the hatchery—the electrochemical reactor—from which they sprang. Reactions and interactions fall into step as further pathways are negotiated. This hydrothermal circuitry offers a continuous supply of material and chemical energy, as well as electricity and proticity at a potential appropriate for the onset of life in the dark, a rapidly emerging kinetic structure born to persist, evolve and generate entropy while the sun shines. (shrink)

Developed in the past two decades, the clustered regularly interspaced short palindromic repeats‐associated protein 9 (CRISPR‐Cas9) technique offers greater accessibility and efficiency in editing genes. Its immediate success has transformed medical research and treatment in productive ways, but has also left questions about ethical consequences in its wake. These are questions familiar to bioethical inquiry. How do we balance short‐term and long‐term benefits and risks? How do we promote just and equitable access to new medical interventions? How do we (...) protect respect for individual autonomy? These questions require a balance between protecting individuals' liberties and the good of the communities in which they live. In this essay, I am interested in how the principle of respect for autonomy can be interpreted in light of CRISPR‐Cas9. I argue that a relational autonomy framework forges a middle ground between the need to respect individual freedom to pursue genetic treatments and the need to acknowledge the networks of dependence that define our moral worlds. I identify three thematic areas that relational autonomy brings into greater focus: the importance of trust, the acknowledgment of vulnerability/dependence, and the promotion of justice. Autonomy understood relationally allows us to see individual freedom as tethered to communal well‐being. (shrink)

COPII coated vesicles bud from an ER domain termed the transitional ER (tER), but the mechanism that clusters COPII vesicles at tER sites is unknown. tER sites are closely associated with early Golgi or pre‐Golgi structures, suggesting that the clustering of nascent COPII vesicles could be achieved by tethering to adjacent membranes. This model challenges the prevailing view that COPII vesicles are clustered by a scaffolding protein at the ER surface. Although Sec16 was proposed to serve as such a (...) scaffolding protein, recent data suggest that rather than organizing COPII into higher‐order structures, Sec16 acts at the level of individual COPII vesicles to regulate COPII turnover. A plausible synthesis is that tER sites are created by tethering to Golgi membranes and are regulated by Sec16. Meanwhile, the COPII vesicles that bud from tER sites are thought to nucleate new Golgi cisternae. Thus, an integrated self‐organization process may generate tER‐Golgi units. (shrink)

Fractal time fluctuations of the spectral “1/f” form are universal in natural self-organizing systems. Neurobiology is uniquely infused with fractal fluctuations in the form of statistically self-similar clusters or bursts on all levels of description from molecular events such as protein chain fluctuations, ion channel currents and synaptic processes to the behaviors of neural ensembles or the collective behavior of Internet users. It is the thesis of this essay that the brain self-organizes via a vertical collation of these spontaneous (...) events in order to perceive the world and generate adaptive behaviors. REM sleep, which coalesces from self-similar clusters of burst-within-burst behavior during ontogeny, is essential to cognitive-emotional function, and has recurrent fractal organization. Empirical fMRI observations further support the association of fractal fluctuations in the temporal lobes, brainstem and cerebellum during the expression of emotional memory, spontaneous fluctuations of thought and meditative practice. Cognitive-emotional integration arises as amygdaloid-brainstem-cerebellar systems harmonize the vertical “1/f” symphony of coupled isochronous cortical oscillations in the pursuit of mindfulness. (shrink)

In many cells, a nitric oxide (NO) synthase inducible by immunological stimuli produces a sustained flow of NO that lasts a long time. NO is a short‐lived molecule but it is a diffusibel ligand believed to be capable of reaching distal target sites. Further, several lines of evidence indicate that cysteine‐rich motifs of metal‐binding proteins, as well as redox‐sensitive metal clusters of metalloproteins, are natural sensors of bioradicals like NO. In metalloregulatory proteins, metals are often conveniently located at binding sites (...) and bound to cysteine residues. Accordingly, disruption of the metal‐thiolate polymetallic clusters should trigger significant remodelling of the protein structure involved in regulation. We can therefore postulate that the nitrosation reaction occurring at metal centres or cysteine‐rich motifs will preclude correct binding to regulatory sites. Several examples are given of metalloregulatory proteins whose metal is bound to thiols and may then become sensitive to NO. Recent observations indicate that in response to NO synthesis, iron regulatory protein, a eukaryotic bifunctional [Fe‐S] protein, switches from acting as aconitase to being an RNA‐binding regulator, and we suggest that the interplay between NO or a NO‐derived molecule and metal clusters at critical allosteric sites may be a crucial component of the cellular response to environmental stress. (shrink)

The discovery of the signal peptides that direct proteins to localize at the nucleolus is described here. The nucleolar targeting signal termed the NOS consists of clustered basic amino acids organized such that a portion also functions as the nuclear transporting signal. Although a NOS has been identified within the regulatory genes of human retroviruses, HTLV‐I and HIV‐I, signals of similar function in cellular proteins – such as heat shock proteins – may be induced through the configurational change of (...) class='Hi'>protein structure by heat or stress. (shrink)

Phagocytosis is an uptake of large particles governed by the actin-based cytoskeleton. Binding of particles to specific cell surface receptors is the first step of phagocytosis. In higher Eucaryota, the receptors able to mediate phagocytosis are expressed almost exclusively in macrophages, neutrophils, and monocytes, conferring immunodefence properties to these cells. Receptor clustering is thought to occur upon particle binding, that in turn generates a phagocytic signal. Several pathways of phagocytic signal transduction have been identified, including the activation of tyrosine kinases (...) and (or) serine/threonine kinase C in pivotal roles. Kinase activation leads to phosphorylation of the receptors and other proteins, recruited at the sites of phagocytosis. Monomeric GTPases of the Rho and ARF families are likely to be engaged downstream of activated receptors. The GTPases, in cooperation with phosphatidylinositol 4-phosphate 5-kinase and phosphatidylinositol 3-kinase lipid modifying enzymes, can modulate locally the assembly of the submembranous actin filament system leading to particle internalization. BioEssays 21:422–431, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Emerging evidence suggests that microRNA (miRNA)‐mediated post‐transcriptional gene regulation plays an essential role in modulating embryonic stem (ES) cell pluripotency maintenance, differentiation, and reprogramming of somatic cells to an ES cell‐like state. Investigations from ES cell‐enriched miRNAs, such as mouse miR‐290 cluster and human miR‐302 cluster, and ES cell‐depleted miRNAs such as let‐7 family miRNAs, revealed a common theme that miRNAs target diverse cellular processes including cell cycle regulators, signaling pathway effectors, transcription factors, and epigenetic modifiers and shape (...) their protein output. The combinatorial effects downstream of miRNA action allow miRNAs to modulate cell‐fate decisions effectively. Furthermore, the transcription and biogenesis of miRNAs are also tightly regulated. Thus, elucidating the interplay between miRNAs and other modes of gene regulation will shed new light on the biology of pluripotent stem cells and somatic cell reprogramming. (shrink)

We hypothesise that some influenza virus adaptations to poultry may explain why the barrier for human‐to‐human transmission is not easily overcome once the virus has crossed from wild birds to chickens. Since the cluster of human infections with H5N1 influenza in Hong Kong in 1997, chickens have been recognized as the major source of avian influenza virus infection in humans. Although often severe, these infections have been limited in their subsequent human‐to‐human transmission, and the feared H5N1 pandemic has not (...) yet occurred. Here we examine virus adaptations selected for during replication in chickens and other gallinaceous poultry. These include altered receptor binding and increased pH of fusion of the haemagglutinin as well as stalk deletions of the neuraminidase protein. This knowledge could aid the delivery of vaccines and increase our ability to prioritize research efforts on those viruses from the diverse array of avian influenza viruses that have greatest human pandemic potential. (shrink)

Collections are a group of multimeric proteins mostly consisting of 9–18 polypeptides organised into either ‘bundle‐of‐tulips’ or ‘X‐like’ overall structures. Each polypeptide contains a short N‐terminal segment followed by a collagen‐like sequence and then by a C‐terminal lectin domain. A collectin molecule is assembled from identical or very similar polypeptides by disulphide bonds at the N‐terminal segment, formation of triple helices in the collagen‐like region and clusters of three lectin domains at the peripheral ends of triple helices. These proteins can (...) bind to sugar residues on microorganisms via the peripheral lectin domains and subsequently interact, via the collagen‐like triple‐helices, with receptor(s) on phagocytes and/or the complement system to bring about the killing and clearance of the targets without the involvement of antibodies. The collectins can also bind to phagocyte receptor(s) to enhance phagocytosis mediated by other phagocytic receptors. Lack, or low levels, of collectin expression can lead to higher susceptibility to infections, especially during childhood when specific immunity has not fully developed. Therefore, the collectins play important roles in the enhancement of innate immunity. (shrink)

Large deletions and genomic re‐arrangements are increasingly recognized as common products of double‐strand break repair at Clustered Regularly Interspaced, Short Palindromic Repeats ‐ CRISPR associated protein 9 (CRISPR/Cas9) on‐target sites. Together with well‐known off‐target editing products from Cas9 target misrecognition, these are important limitations, that need to be addressed. Rigorous assessment of Cas9‐editing is necessary to ensure validity of observed phenotypes in Cas9‐edited cell‐lines and model organisms. Here the mechanisms of Cas9 specificity, and strategies to assess and mitigate unwanted (...) effects of Cas9 editing are reviewed; covering guide‐RNA design, RNA modifications, Cas9 modifications, control of Cas9 activity; computational prediction for off‐targets, and experimental methods for detecting Cas9 cleavage. Although recognition of the prevalence of on‐ and off‐target effects of Cas9 editing has increased in recent years, broader uptake across the gene editing community will be important in determining the specificity of Cas9 across diverse applications and organisms. (shrink)

The chorion genes of Drosophila are amplified in response to developmental signals in the follicle cells of the ovary prior to their transcription. Their expression is regulated both temporally and spatially within this tissue. They thus serve as models both for the regulation of DNA replication and of developmental transcription. The regulatory elements for DNA amplification have been delineated. Their analysis reveals that amplification is mediated by several regulatory regions and initiates at defined origins within the chorion cluster. Proteins (...) involved in amplification are being identified both by mutations affecting amplification and by DNA binding studies. Regulatory elements for temporal as well as spatial control of chorion gene, expression have been characterized, and two candidate transcription factor genes have been cloned. (shrink)

The developing neuromuscular junction has provided an important paradigm for studying synapse formation. An outstanding feature of neuromuscular differentiation is the aggregation of acetylcholine receptors (AChRs) at high density in the postsynaptic membrane. While AChR aggregation is generally believed to be induced by the nerve, the mechanisms underlying aggregation remain to be clarified. A 43‐kD protein (43k) normally associated with the cytoplasmic aspect of AChR clusters has long been suspected of immobilizing AChRs by linking them to the cytoskeleton. In (...) recent studies, the AChR clustering activity of 43k has, at last, been demonstrated by expressing recombinant AChR and 43k in non‐muscle cells. Mutagenesis of 43k has revealed distinct domains within the primary structure which may be responsible for plasma membrane targeting and AChR binding. Other lines of study have provided clues as to how nerve‐derived (extracellular) AChR‐cluster inducing factors such as agrin might activate 43k‐driven postsynaptic membrane specialization. (shrink)

PDZ (also called DHR or GLGF) domains are found in diverse membraneassociated proteins including members of the MAGUK family of guanylate kinase homologues, several protein phosphatases and kinases, neuronal nitric oxide synthase, and several dystrophin‐associated proteins, collectively known as syntrophins. Many PDZ domain‐containing proteins appear to be localised to highly specialised submembranous sites, suggesting their participation in cellular junction formation, receptor or channel clustering, and intracellular signalling events. PDZ domains of several MAGUKs interact with the C‐terminal polypeptides of a (...) subset of NMDA receptor subunits and/or with Shaker‐type K+ channels. Other PDZ domains have been shown to bind similar ligands of other transmembrane receptors. Recently, the crystal structures of PDZ domains, with and without ligand, have been determined. These demonstrate the mode of ligand‐binding and the structural bases for sequence conservation among diverse PDZ domains. (shrink)

Pericytes, like vascular smooth muscle cells, are perivascular cells closely associated with blood vessels throughout the body. Pericytes are necessary for vascular development and homeostasis, with particularly critical roles in the brain, where they are involved in regulating cerebral blood flow and establishing the blood-brain barrier. A role for pericytes during neurovascular disease pathogenesis is less clear—while some studies associate decreased pericyte coverage with select neurovascular diseases, others suggest increased pericyte infiltration in response to hypoxia or traumatic brain injury. Here, (...) we used an endothelial loss-of-function Recombination signal binding protein for immunoglobulin kappa J region (Rbpj)/Notch mediated mouse model of brain arteriovenous malformation (AVM) to investigate effects on pericytes during neurovascular disease pathogenesis. We tested the hypothesis that pericyte expansion, via morphological changes, and Platelet-derived growth factor B/Platelet-derived growth factor receptor β (Pdgf-B/Pdgfrβ)-dependent endothelial cell-pericyte communication are affected, during the pathogenesis of Rbpj mediated brain AVM in mice. Our data show that pericyte coverage of vascular endothelium expanded pathologically, to maintain coverage of vascular abnormalities in brain and retina, following endothelial deletion of Rbpj. In Rbpj-mutant brain, pericyte expansion was likely attributed to cytoplasmic process extension and not to increased pericyte proliferation. Despite expanding overall area of vessel coverage, pericytes from Rbpj-mutant brains showed decreased expression of Pdgfrβ, Neural (N)-cadherin, and cluster of differentiation (CD)146, as compared to controls, which likely affected Pdgf-B/Pdgfrβ-dependent communication and appositional associations between endothelial cells and pericytes in Rbpj-mutant brain microvessels. By contrast, and perhaps by compensatory mechanism, endothelial cells showed increased expression of N-cadherin. Our data identify cellular and molecular effects on brain pericytes, following endothelial deletion of Rbpj, and suggest pericytes as potential therapeutic targets for Rbpj/Notch related brain AVM. (shrink)

Electrical signaling by neurons depends on the precisely ordered distribution of a wide variety of ion channels on the neuronal surface. The mechanisms underlying the targeting of particular classes of ion channels to specific subcellular sites are poorly understood. Recent studies have identified a new class of protein‐protein interaction mediated by PDZ domains, protein binding modules that recognize specific sequences at the C terminus of membrane proteins. The PDZ domains of a family of synaptic cytoskeleton‐associated proteins, typified (...) by PSD‐95, bind to the intracellular C‐terminal tails of NMDA receptors and Shaker‐type K+ channels. This interaction appears to be important in the clustering and localization of these ion channels at synaptic sites. Recognition of specific C‐terminal peptide sequences by different PDZ domain‐containing proteins may be a general mechanism for differential targeting of proteins to a variety of subcellular locations. (shrink)

Complex functions of the central nervous system such as learning and memory are believed to result from the modulation of the synaptic transmission between neurons. The sequence of events leading to the fusion of synaptic vesicles at the presynaptic active zone and the detection of this signal at the postsynaptic density involve the activity of ion channels and neurotransmitter receptors. Their accumulation and dynamic exchange at synapses are dependent on their interaction with synaptic scaffolds. These are synaptic structures composed of (...) adaptor proteins that provide binding sites for receptors and channels as well as other synaptic proteins. While in its entirety the synaptic scaffold is a relatively stable structure, individual adaptor proteins exchange at a fast time scale. These properties of scaffolds help to ensure the stability of synaptic transmission while permitting the modulation of synaptic strength. Here, we review the dynamics of the synaptic scaffold and of adaptor proteins in relation to their roles in the organisation of the synapse as well as in the clustering and trafficking of receptor proteins. BioEssays 30:1062–1074, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

BackgroundMediation analysis is important to test the theoretical framework underpinning an intervention. We therefore aimed to investigate if the healthy body image intervention’s effect on eating disorder symptomatology and use of muscle building supplements was mediated by the change in risk and protective factors for ED development and muscle building supplement use.MethodsThis study used data from the HBI intervention: a cluster randomized controlled universal intervention aiming to promote positive body image and embodiment and reduce the risk for ED development (...) including 30 schools in Norway. A total of 1,713 participants were included in the analyses. Conditional latent growth curve analyses were performed to test for indirect effects on ED symptomatology and weekly frequency of protein and creatine supplement use measured at the 12-month follow-up via change in the proposed mediators.ResultsIn girls, the reduction in ED symptomatology was mediated by positive changes in protective factors and reductions in risk factor scores. Comparable changes in protective and risk factors among boys played no mediating role.ConclusionInterventions aiming to reduce the risk of ED development in girls may benefit from aiming to enhance self-esteem and body image flexibility and reduce perceived media pressure and thin appearance internalization. Future studies should investigate the casual relationship between muscle building supplement use and risk and protective factors for ED development in both girls and boys. (shrink)