The quest for molecular mechanisms that guide axons or specify synaptic contacts has largely focused on molecules that intuitively relate to the idea of an “instruction.” By contrast, “permissive” factors are traditionally considered background machinery without contribution to the information content of a molecularly executed instruction. In this essay, I recast this dichotomy as a continuum from permissive to instructive actions of single factors that provide relative contributions to a necessarily collaborative effort. Individual molecules or other factors do not (...) constitute absolute instructions by themselves; they provide necessary context for each other, thereby creating a composite that defines the overall instruction. The idea of composite instructions leads to two main conclusions: first, a composite of many seemingly permissive factors can define a specific instruction even in the absence of a single dominant contributor; second, individual factors are not necessarily related intuitively to the overall instruction or phenotypic outcome. (shrink)

Radio Frequency Identification (RFID) systems identify and track objects, animals and, in principle, people. The ability to gather information obtained by tracking consumer goods, government documents, monetary transactions and human beings raises a number of interesting and important privacy issues. Moreover, RFID systems pose an ensemble of other ethical challenges related to appropriate uses and users of such systems. This paper reviews a number of RFID applications with the intention of identifying the technology’s benefits and possible misuses. We offer (...) an overview and discussion of the most important ethical issues concerning RFID, and describes and examine some methods of protecting privacy. (shrink)

This article reviews the use of implantable radiofrequency identification (RFID) tags in humans, focusing on the VeriChip (VeriChip Corporation, Delray Beach, FL) and the associated VeriMed patient identification system. In addition, various nonmedical applications for implanted RFID tags in humans have been proposed. The technology offers important health and nonhealth benefits, but raises ethical concerns, including privacy and the potential for coercive implantation of RFID tags in individuals. A national discussion is needed to identify the limits of acceptable (...) use of implantable RFID tags in humans before their use becomes widespread and it becomes too late to prevent misuse of this useful but ethically problematic technology. (shrink)

A cell's biochemistry is now known to be the biochemistry of molecular machines, that is, protein complexes that are assembled and dismantled in particular locations within the cell as needed. One important element in our understanding has been the ability to begin to see where proteins are in cells and what they are doing as they go about their business. Accordingly, there is now a strong impetus to discover new ways of looking at the workings of proteins in living (...) cells. Although the use of fluorescent tags to track individual proteins in cells has a long history, the availability of laser-based confocal microscopes and the imaginative exploitation of the green fluorescent protein from jellyfish have provided new tools of great diversity and utility. It is now possible to watch a protein bind its substrate or its partners in real time and with submicron resolution within a single cell. The importance of processes of self-organisation represented by protein folding on the one hand and subcellular organelles on the other are well recognised. Self-organisation at the intermediate level of multimeric protein complexes is now open to inspection. BioEssays 22:180–187, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

Rett syndrome (RTT) is an X‐linked dominant neurodevelopmental disorder affecting almost exclusively girls. Although mutations in methyl‐CpG‐binding protein (MeCP2) are known to be associated with RTT, gene expression patterns are not significantly altered in MeCP2‐deficient cells. A recent study1 identified MeCP2‐mediated histone modification and formation of a higher‐order chromatin loop structure specifically associated with silent chromatin at the Dlx5–Dlx6 locus in normal cells, and its absence thereof in RTT patients. This altered expression of Dlx5 through loss of silent chromatin loop (...) formation provides a molecular mechanism underlying RTT and proposes a novel role for MeCP2 in chromatin organization and imprinting. © 2005 Wiley Periodicals, Inc. BioEssays 27:676–680, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

This paper extends previous arguments against the assumption that the study of variation at the molecular level was instigated with a view to solving an internal conflict between the balance and classical schools of population genetics. It does so by focusing on the intersection of basic research in protein chemistry and the molecular approach to disease with the enactment of global health campaigns during the Cold War period. The paper connects advances in research on protein structure and function (...) as reflected in Christian Anfinsen’s The molecular basis of evolution, with a political reading of Emilé Zuckerkandl and Linus Pauling’s identification of molecular disease and evolution. Beyond atomic fallout, these advances constituted a rationale for the promotion of genetic surveys of human populations in the Third World, in connection with international health programs. Light is shed not only on the experimental roots of the molecular challenge but on the broader geopolitical context where the rising role of biomedicine and public health had an impact on evolutionary biology. (shrink)

The aim of this study is to investigate radio frequency identification tagging as a form of sociotechnical experimentation and the kinds of sociotechnical futures at stake in this experimentation. For this purpose, a detailed analysis of a publicly available promotional video by a tag producer for the fashion industry, a sector widely using RFID tags, was analysed in detail. The results of the study indicated that the sociotechnical imaginary of RFID tagging gravitates around the core value of perfect sociotechnical (...) efficiency. This demands a high degree of readiness to engage in standardization efforts, which performs a specific materialized understanding of ethics by other means. Furthermore, the analysis points to the importance of considering the spatiotemporal dimensions in which RFID tags work when reflecting on how this technology matters to society. Finally, the analysis shows a tacit effort to keep RFID technology and thus any questions of responsible innovation confined to the shop floor. However, given the spreading of the use of RFIDs, much wider-ranging considerations are called for. (shrink)

Duchenne muscular dystrophy (DMD) is a progressive and lethal neuromuscular disorder caused by a defective gene on the X chromosome. There is no effective treatment and the biochemical defect is yet unknown. Mapping of the DMD locus to band Xp21 in the short arm of the X chromosome has given rise to strategies to clone the gene from its known location in the chromosome. Two cloning strategies have led to the isolation of a gene that is the largest of any (...) yet described. Portions of the gene are deleted in about 8% of affected males, and rare translocations that disrupt the gene cause the disease in females. The isolation of expressed sequences from the DMD locus will undoubtedly lead to isolation of the gene product and ultimately to an understanding of the basic defect. In the meantime, DNA probes from the DMD locus provide a new and accurate approach for carrier identification and prenatal diagnosis of this dreaded disease. (shrink)

The lymphatic vasculature plays a critical role in the regulation of body fluid volume and immune function. Extensive research into the molecular mechanisms that control blood vessel growth has led to identification of molecules that also regulate development and growth of the lymphatic vessels. This is generating a great deal of interest in the molecular control of the lymphatics in the context of embryogenesis, lymphatic disorders and tumor metastasis. Studies in animal models carried out over the past (...) three years have shown that the soluble protein growth factors, vascular endothelial growth factor (VEGF)‐C and VEGF‐D, and their cognate receptor tyrosine kinase, VEGF receptor‐3 (VEGFR‐3), are critical regulators of lymphangiogenesis. Furthermore, disfunction of VEGFR‐3 has recently been shown to cause lymphedema. The capacity to induce lymphangiogenesis by manipulation of the VEGF‐C/VEGF‐D/VEGFR‐3 signaling pathway offers new opportunities to understand the function of the lymphatic system and to develop novel treatments for lymphatic disorders. BioEssays 24:1030–1040, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

How we age and what we can do about it have been uppermost in human thought since antiquity. The many false starts have frustrated experimentalists and theoretical arguments pronouncing the inevitability of the process have created a nihilistic climate among scientists and the public. The identification of single gene alterations that substantially extend life span in nematodes and flies however, have begun to reinvigorate the field. Drosophila's long history of contributions to aging research, rich storehouse of genetic information, and (...) powerful molecular techniques make it an excellent system for studying the molecular mechanisms underlying the process of aging. In recent years, Drosophila has been used to test current theories on aging and explore new directions of potential importance to the biology of aging. One such example is the surprising finding that, as opposed to the commonly held assumption that adult life is a period of random passive decline in which all things are thought to fall apart, the molecular life of the adult fly appears to be a state of dynamic well‐regulated change. In the fly, the level of expression of many different genes changes in an invariant, often age‐dependent, manner. These as well as other molecular genetic studies and demographic analyses using the fly have begun to challenge widely held ideas about aging providing evidence that aging may be a much more dynamic and malleable process than anticipated. With the enormous success that Drosophila molecular genetics has demonstrated in helping understand complex biological phenomena such as development there is much optimism that similar approaches can be adapted to assist in understanding the process of aging. BioEssays 25:134–141, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Chemotaxis and thermotaxis in Caenorhabditis elegans are based on the chemical senses (smell and taste) and the thermal sense, respectively, which are important for the life of the animal. Laser ablation experiments have allowed identification of sensory neurons and some interneurons required for these senses. Many mutants that exhibit various abnormalies have been isolated and analyzed. These studies have predicted novel signaling pathways whose components include a putative odorant specific transmembrane receptor (ODR‐10) and a cyclic nucleotide‐gated channel (TAX‐4/TAX‐2) functioning (...) in taste and thermosensation as well as in smell. The emerging picture of the mechanisms of sensory transduction in C. elegans seems to be basically similar to what is known of visual and olfactory sensory transduction in vertebrates. Thus, molecular and cellular analyses of chemotaxis and thermotaxis in C. elegans have proved useful and will continue to provide significant implications for the molecular basis of sensory systems in higher animals. (shrink)

The hardest part of replicating a genome is the beginning. The first step of DNA replication (called “initiation”) mobilizes a large number of specialized proteins (“initiators”) that recognize specific sequences or structural motifs in the DNA, unwind the double helix, protect the exposed ssDNA, and recruit the enzymatic activities required for DNA synthesis, such as helicases, primases and polymerases. All of these components are orderly assembled before the first nucleotide can be incorporated. On the occasion of the 50th anniversary of (...) the discovery of the DNA structure, we review our current knowledge of the molecular mechanisms that control initiation of DNA replication in eukaryotic cells, with particular emphasis on the recent identification of novel initiator proteins. We speculate how these initiators assemble molecular machines capable of performing specific biochemical tasks, such as loading a ring‐shaped helicase onto the DNA double helix. BioEssays 25:1158–1167, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

The development of new approaches is critical to gain further insights into biological processes that cannot be obtained by existing methods or technologies. The detection of protein–protein interaction is often challenging, especially for weak and transient interactions or for membrane proteins. Over the last decade, several proximity‐tagging methodologies have been developed to explore protein interactions in living cells. Among those, the most efficient are based on protein partner modification, such as biotinylation or pupylation. Such technologies are based on engineered variants (...) of enzymes like peroxidases or ligases that release reactive molecules, in the presence of specific substrates, that bind surrounding proteins. Fusing a protein of interest (POI) to these enzymes allows the definition of an unbiased “proxisome,” that is, all of the proteins in interaction or in close vicinity of the POI. Here, the different proximity‐labeling tools available are described and comprehensive comparison to discuss advantages and limitations is provided. (shrink)

Genome‐wide identification of transcription factor binding sites with the ChIP‐seq method is an extremely important scientific endeavor − one that should ideally be performed for every transcription factor in as many cell types as possible. A major hurdle on the way to this goal is the necessity for a specific, ChIP‐grade antibody for each transcription factor of interest, which is often not available. Here, we describe CETCh‐seq, a recently published method utilizing genome engineering with the CRISPR/Cas9 system to circumvent (...) the need for a specific antibody. Using the CETCh‐seq method, targeted genomic editing results in an epitope‐tagged transcription factor, which is recognized by a well‐characterized, standard antibody, efficacious for ChIP‐seq. We have used CETCh‐seq in human cancer cell lines as well as mouse embryonic stem cells. We find that roughly 60% of transcription factors tagged using CETCh‐seq produce a high quality ChIP‐seq map, a significant improvement over traditional antibody‐based methods. (shrink)

In this article we discuss the molecular signaling mechanisms that coordinate interactions between Schwann cells and the neurons of the peripheral nervous system. Such interactions take place perpetually during development and in adulthood, and are critical for the homeostasis of the peripheral nervous system (PNS). Neurons provide essential signals to control Schwann cell functions, whereas Schwann cells promote neuronal survival and allow efficient transduction of action potentials. Deregulation of neuron–Schwann cell interactions often results in developmental abnormalities and diseases. Recent (...) investigations have shown that during development, neuronally provided signals, such as Neuregulin, Jagged, and Wnt interact to fine‐tune the Schwann cell lineage progression. In adult, the signal exchange between neurons and Schwann cells ensures proper nerve function and regeneration. Identification of the mechanisms of neuron–Schwann cell interactions is therefore essential for our understanding of the development, function and pathology of the peripheral nervous system as a whole. -/- . (shrink)

Animals use their chemosensory systems to detect and discriminate among chemical cues in the environment. Remarkable progress has recently been made in our knowledge of the molecular and cellular basis of chemosensory perception in insects, based largely on studies in Drosophila. This progress has been possible due to the identification of gene families for olfactory and gustatory receptors, the use of electro‐physiological recording techniques on sensory neurons, the multitude of genetic manipulations that are available in this species, and (...) insights from several insect model systems. Recent studies show that the superfamily of chemoreceptor proteins represent the essential elements in chemosensory coding, endowing chemosensory neurons with their abilities to respond to specific sets of odorants, tastants or pheromones. Investigating how insects detect chemicals in their environment can show us how receptor protein structures relate to ligand binding, how nervous systems process complex information, and how chemosensory systems and genes evolve. BioEssays 28:23–34, 2006. © 2005 Wiley Periodicals, Inc. (shrink)

In the context of 1960s research on biological membranes, scientists stumbled upon a curiously coloured material substance, which became called the “purple membrane.” Interactions with the material as well as chemical analyses led to the conclusion that the microbial membrane contained a photoactive molecule similar to rhodopsin, the light receptor of animals’ retinae. Until 1975, the find led to the formation of novel objects in science, and subsequently to the development of a field in the molecular life sciences that (...) comprised biophysics, bioenergetics as well as membrane and structural biology. Furthermore, the purple membrane and bacteriorhodopsin, as the photoactive membrane transport protein was baptized, inspired attempts at hybrid bio-optical engineering throughout the 1980s. A central motif of the research field was the identification of a functional biological structure, such as a membrane, with a reactive material substance that could be easily prepared and manipulated. Building on this premise, early purple membrane research will be taken as a case in point to understand the appearance and transformation of objects in science through work with material substances. Here, the role played by a perceptible material and its spontaneous change of colour, or reactivity, casts a different light on objects and experimental practices in the late twentieth century molecular life sciences. With respect to the impact of chemical working and thinking, the purple membrane and rhodopsins represent an influential domain straddling the life and chemical sciences as well as bio- and material technologies, which has received only little historical and philosophical attention. Re-drawing the boundary between the living and the non-enlivened, these researches explain and model organismic activity through the reactivity of macromolecular structures, and thus palpable material substances. (shrink)

Skeletal muscle formation is studied in vitro with myogenic cell lines and primary muscle cell cultures, and in vivo with embryos of several species. We review several of the notable advances obtained from studies of cultured cells, including the recognition of myoblast diversity, isolation of the MyoD family of muscle regulatory factors, and identification of promoter elements required for muscle‐specific gene expression. These studies have led to the ideas that myoblast diversity underlies the formation of the multiple types of (...) fast and slow muscle fibers, and that myogenesis is controlled by a combination of ubiquitous and muscle‐specific transcriptional regulators that may be different for each gene. We further review some unexpected results that have been obtained when ideas from work in culture have been tested in developing animals. The studies in vivo point to additional molecular and cellular mechanisms that regulate muscle formation in the animal. (shrink)

Enough is known about pattern formation in development to encourage investigations at the molecular level. A pressing need is to understand the molecular basis of positional value, which is similar to determination. It is suggested here that there is a molecular entity which varies in such a way that it corresponds with cell position. Other problems in pattern formation include thresholds, identification of morphogens, and the origin of handedness.

The cellular machinery responsible for conveying proteins between the endoplasmic reticulum and the Golgi is being investigated using genetics and biochemistry. A role for vesicles in mediating protein traffic between the ER and the Golgi has been established by characterizing yeast mutants defective in this process, and by using recently developed cell‐free assays that measure ER to Golgi transport. These tools have also allowed the identification of several proteins crucial to intracellular protein trafficking. The characterization and possible functions of (...) several GTP‐binding proteins, peripheral membrane proteins, and an integral membrane protein during ER to Golgi transport are discussed here. (shrink)

Mutations that disrupt biological rhythms have existed in microbial and metazoan eukaryotes for some time. They have recently begun to be studied with increasing intensity, both in terms of phenotypic effects of the relevant genetic variants, and with regard to molecular isolation and analysis of the genes defined by two of the ‘clock mutations’. These genetic loci, called period (per) in Drosophila and frequency (frq) in Neurospora, influence not only the basic characteristics of circadian rhythmicity, but also temperature compensation (...) of such daily cycle durations, ‘re‐setting’ of the rhythms' phases, and (for the per mutants) behavioral oscillations associated with much shorter than circadian periodicities. Molecular cloning of Drosophila's per gene, accompanied crucially by the locus's identification in germ‐line transformants, has led to information on its expression ‐ temporally, spatially, and in regard to heterogeneity of mRNA types. Nucleotide‐sequencing analyses of genomic DNA (and/or cDNA) from normal and mutated per alleles have (1) led to the suggestion that this clock gene encodes a family of proteoglycans (which was further indicated by application of antibody reagents obtained by manipulation of one of the gene's exons); and (2) shown that the three types of per mutations ‐ which shorten or lengthen rhythm periodicities or appear to eliminate them ‐ are associated with interesting amino‐acid substitutions or a stop codon, respectively. Analogous molecular findings are awaited from Neurospora, whose frq gene has very recently been cloned and definitively identified, in part via transformation experiments. (shrink)

Of the many genes mutated on the road to tumor formation, few have received as much attention as p53. The gene has come to occupy center stage for the simple reason that it is more frequently altered in human tumors than any other known gene, undergoing mutation at a significant rate in almost every tumor type in which it has been studied. This association between p53 mutation and tumorigenesis has spurred a flurry of research attempting to delineate the normal function (...) of p53 and, by extension, the role of p53 mutation in tumor formation. At the cellular level, p53 has been shown to suppress growth. Recent efforts to further discern the function of p53 have centered on the underlying molecular basis for this growth suppression. In particular, research has focused on the identification of cellular molecules (specifically DNA and proteins) with which the p53 protein associates. p53 has now been shown to bind DNA in a sequence‐specific manner, and mounting evidence suggests that p53 acts as a transcription factor, perhaps regulating the expression levels of genes involved in the inhibition of cell growth. The logical next step in understanding p53 function involves the resolution of two questions: (1) what are the physiological transcriptional targets of p53, and (2) what cellular proteins regulate or mediate the ability of p53 to modulate transcription? Some initial clues to these puzzles are now emerging, and these form the subject of this review. (shrink)

Cancer stem cells (CSC) represent malignant cell subsets in hierarchically organized tumors, which are selectively capable of tumor initiation and self‐renewal and give rise to bulk populations of non‐tumorigenic cancer cell progeny through differentiation. Robust evidence for the existence of prospectively identifiable CSC among cancer bulk populations has been generated using marker‐specific genetic lineage tracking of molecularly defined cancer subpopulations in competitive tumor development models. Moreover, novel mechanisms and relationships have been discovered that link CSC to cancer therapeutic resistance and (...) clinical tumor progression. Importantly, proof‐of‐principle for the potential therapeutic utility of the CSC concept has recently been provided by demonstrating that selective killing of CSC through a prospective molecular marker can inhibit tumor growth. Herein, we review these novel and translationally relevant research developments and discuss potential strategies for CSC‐targeted therapy in the context of resistance mechanisms and molecular pathways preferentially operative in CSC. (shrink)

To ensure their survival in natural habitats, plants must recognize and respond to a wide variety of insect herbivores. Aphids and other Hemiptera pose a particular challenge, because they cause relatively little direct tissue damage when inserting their slender stylets intercellularly to feed from the phloem sieve elements. Plant responses to this unusual feeding strategy almost certainly include recognition of aphid salivary components and the induction of phloem‐specific defenses. Due to the excellent genetic and genomic resources that are available for (...) Arabidopsis thaliana (Arabidopsis), this plant was chosen as a model system to study the metabolic and transcriptional responses to infestation by two aphids, Myzus persicae (green peach aphid, a broad generalist) and Brevicoryne brassicae (cabbage aphid, a crucifer‐feeding specialist). Future research on Arabidopsis–aphid interactions will lead to the identification of aphid‐specific elicitors, components of the defense‐signaling pathway, and additional metabolic responses that are induced by aphid infestation. BioEssays 29:871–883, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

In contrast to the great majority of mycobacterial species that are harmless saprophytes, Mycobacterium tuberculosis and other closely related tubercle bacilli have evolved to be among the most important human and animal pathogens. The need to develop new strategies in the fight against tuberculosis (TB) and related diseases has fuelled research into the evolutionary success of the M. tuberculosis complex members. Amongst the various disciplines, genomics and functional genomics have been instrumental in improving our understanding of these organisms. In this (...) review we will present some of the recent key findings on molecular determinants of mycobacterial pathogenicity and attenuation, the evolution of M. tuberculosis, genome dynamics, antigen mining for improved diagnostic and subunit antigens, and finally the identification of novel drug targets. The genomics revolution has changed the landscape of TB research, and now underpins our renewed efforts to defeat this deadly pathogen. (shrink)

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat, to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci (...) in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes. (shrink)

Data-sharing among genomic researchers is promoted for its potential to accelerate our understanding of the molecular basis of cancer. However, with genomic data sharing the risks of re-identifying study participants, revealing personal genomic information and data misuse might increase. This study aims at exploring perceptions of patients and physicians in Oncology regarding their assessment of the informational risks resulting from participating in whole genomic research studies in order to improve the informed consent process. For this purpose, we conducted a (...) qualitative focus group study at the National Center for Tumor Diseases. Patients and oncologists assessed the informational risks either as minimal or as greater than minimal, depending on the context factors of occupational status, age, and patients’ prognosis. Interestingly, even patients who assumed a greater risk did not refrain from participating in genomic research, provided that certain informational and institutional safeguards are implemented. Moreover, they expected comprehensive disclosure of the risks resulting from genomic data sharing. These results suggest comprehensive disclosure of the risks of genomic research to potential study participants in genomic research to facilitate risk assessment and sound decision making, establishing independent governance entities in order to minimize the informational risks of genomic research, and implementing data sharing policies which offer guidance for physicians and researchers involved in genomic research. (shrink)

The molecular biology of viruses can be effectively described by kinetic logic as several feedback loops are implicated in all viral cycles and as viral proteins generally display several functions. We applied this method to the study of the rhabdovirus cycle.Formally, the dynamics of the model are explored on the basis of a discrete caricature (kinetic logic), with special emphasis on the role of the constitutive feedback loops to determine the essential dynamical behaviour of the viral cycle. From a (...) biological point of view, our model accounts for several stable regimes or attractors: healthy cells, acute infection and different kinds of persistent infections, a multistationarity in good agreement with the existence of several positive feedback loops in our system. (shrink)

In a Common Law system, legal practitioners need frequent access to prior case documents that discuss relevant legal issues. Case documents are generally very lengthy, containing complex sentence structures, and reading them fully is a strenuous task even for legal practitioners. Having a concise overview of these documents can relieve legal practitioners from the task of reading the complete case statements. Legal catchphrases are (multi-word) phrases that provide a concise overview of the contents of a case document, and automated generation (...) of catchphrases is a challenging problem in legal analytics. In this paper, we propose a novel supervised neural sequence tagging model for the extraction of catchphrases from legal case documents. Specifically, we show that incorporating document-specific information along with a sequence tagging model can enhance the performance of catchphrase extraction. We perform experiments over a set of Indian Supreme Court case documents, for which the gold-standard catchphrases (annotated by legal practitioners) are obtained from a popular legal information system. The performance of our proposed method is compared with that of several existing supervised and unsupervised methods, and our proposed method is empirically shown to be superior to all baselines. (shrink)

Data-sharing among genomic researchers is promoted for its potential to accelerate our understanding of the molecular basis of cancer. However, with genomic data sharing the risks of re-identifying study participants, revealing personal genomic information and data misuse might increase. This study aims at exploring perceptions of patients and physicians in Oncology regarding their assessment of the informational risks resulting from participating in whole genomic research studies in order to improve the informed consent process. For this purpose, we conducted a (...) qualitative focus group study at the National Center for Tumor Diseases (NCT). Patients and oncologists assessed the informational risks either as minimal or as greater than minimal, depending on the context factors of occupational status, age, and patients’ prognosis. Interestingly, even patients who assumed a greater risk did not refrain from participating in genomic research, provided that certain informational and institutional safeguards are implemented. Moreover, they expected comprehensive disclosure of the risks resulting from genomic data sharing. These results suggest (1) comprehensive disclosure of the risks of genomic research to potential study participants in genomic research to facilitate risk assessment and sound decision making, (2) establishing independent governance entities in order to minimize the informational risks of genomic research, and (3) implementing data sharing policies which offer guidance for physicians and researchers involved in genomic research. (shrink)

Many biologically active compounds including neurotransmitters, metabolic precursors, and certain drugs are accumulated intracellularly by transporters that are coupled to the transmembrane Na+ gradient. Amino acid neurotransmitter transporters play a key role in the regulation of extracellular amino acid concentrations and termination of neurotransmission in the CNSAbbreviations: CNS, central nervous system; GABA, γ‐aminobutyric acid; cDNA, complementary deoxyribonucleic acid; mRNA, messenger ribonucleic acid; NMDA, N‐methyl‐D‐aspartate; PKC, protein kinase C; PMA, phorbol 12‐myristate 13‐acetate; DAG, diacyl glycerol; R59022, DAG kinase inhibitor; AA, arachidonic (...) acid; ACHC, cis‐3‐aminocyclohexanecarboxylic acid; GAT‐A, ACHC‐sensitive GABA transporter; GAT‐B, β‐alanine‐sensitive GABA transporter; GLY‐1 and GLYT‐1, glycine transporters; PROT‐1, proline transporter; BGT‐1, betaine transporter.. Transporters for the major amino acid neurotransmitters glutamate, GABA, and glycine are found in both neurons and glial cells. Recent work has resulted in the identification of cDNAs encoding several amino acid neurotransmitter transport proteins, all of which belong to the Na+‐and Cl−‐dependent transporter gene family. The diversity of this family suggests a degree of transporter heterogeneity that is greater than that indicated by biochemical and pharmacological studies. (shrink)

Radio Frequency Identification, or RFID, is a technology which has been receiving considerable attention as of late. It is a fairly simple technology involving radio wave communication between a microchip and an electronic reader, in which an identification number stored on the chip is transmitted and processed; it can frequently be found in inventory tracking and access control systems. In this paper, we examine the current uses of RFID, as well as identifying potential future uses of the technology, (...) including item-level tagging, human implants and RFID-chipped passports, while discussing the impacts that each of these uses could potentially have on personal privacy. Possible guidelines for RFID’s use, including Fair Information Principles and the RFID Bill of Rights are then presented, as well as technological solutions to personal privacy problems, such as tag killing and blocker tags, as well as simple aluminum foil shields for passports. It is then claimed, though, that guidelines and technological solutions will be ineffective for privacy protection, and that legislation will be necessary to guard against the threats posed by the RFID. Finally, we present what we believe to be the most important legislative points that must be addressed. (shrink)

This chapter contains sections titled: Historical and Legal Background Philosophical Foundations Radio Frequency Identity Chips Item‐Level Tagging Human Implants RFID‐Chipped Identification Is RFID a Threat to Privacy?

Molecular interactions are at the origin of life. How molecules get at different locations in the cell and how they locate their partners is a major and partially unresolved question in biology that is paramount to signaling. Spatio‐temporal correlations of fluctuating fluorescently tagged molecules reveal how they move, interact, and bind in the different cellular compartments. Methods based on fluctuations represent a remarkable technical advancement in biological imaging. Here we discuss image analysis methods based on spatial and temporal correlation (...) of fluctuations, raster image correlation spectroscopy, number and brightness, and spatial cross‐correlations that give us information about how individual molecules move in cells and interact with partners at the single molecule level. These methods can be implemented with a standard laser scanning microscope and produce a cellular level spatio‐temporal map of molecular interactions. (shrink)

This chapter focuses on the experimental practices and reasoning strategies employed in nineteenth century investigations on the causal origin of the phenomenon of Brownian movement. It argues that there was an extensive and sophisticated experimental work done on the phenomenon throughout the nineteenth century. Investigators followed as rigorously as possible the methodological standards of their time to make causal claims and advance causal explanations of Brownian movement. Two major methodological strategies were employed. The first was the experimental strategy of varying (...) the circumstances. Suspected causal factors were varied and the resulting effect on Brownian movement was studied. The main goal of this strategy was the identification of difference-making factors, i.e., factors having a causal influence on the phenomenon. The second was the so-called method of hypothesis. Rather than relying exclusively on the ability of experiments to identify difference-making factors, its proponents tried to show how the independently developed tenets of the new kinetic-molecular conception of matter provided a plausible causal explanation of Brownian movement. Each one of these methodological strategies had its distinctive practices and notions of control. None of these strategies could, on its own, establish molecular motion as the cause of Brownian movement. It was only the fruitful combination of the two strategies and of their accompanying practices and notions of control that led, at the end of the nineteenth century, to the recognition of molecular motion as the most probable cause of Brownian movement. (shrink)

The consolidation of the informational paradigm in molecular biology research concluded on a system to convert the epistemic object into an operational technological object and a stable epistemic product. However, the acceptance of the informational properties of genetic acids failed to clarify the meaning of the concept of information. The “information”’ as a property of the genetic molecules remained as an informal notion that allows the description of the mechanism of inheritance, but it was not specified in a logic–semantic (...) structure. The metaphorical implications associated with the idea of genes as molecules with meaning, questioned the linguistics that seemed too foreign to molecular biology. A reformulation of the concept of information in molecular biology was developed upon the theory of Claude Shannon. The node for the structural coupling between biology, physics and information theory was the identification of an analog structure between the coded messages of Shannon’s theory. (shrink)

Identification of the molecular mechanisms underlying axonal branching in vivo has begun in several neuronal systems, notably the projections formed by dorsal root ganglion (DRG) neurons or retinal ganglion cells (RGC). cGMP signalling is essential for sensory axon bifurcation at the spinal cord, whereas brain‐derived neurotrophic factor (BDNF) and ephrinA signalling establish position‐dependent branching of RGC axons. In the latter system, the degradation of specific signalling components, via the ubiquitin‐proteasome system, may provide an additional mechanism involved in axon (...) branching of RGC. The process of arborisation is essential for neurons to innervate multiple targets and to build topographic maps. The various forms of branching found in different types of neurons are regulated by distinct signalling pathways activated by multiple extracellular cues in addition to axonal guidance factors. These signalling cascades, together with transcriptional programs, most likely interact and trigger the polymerisation or depolymerisation of the actin and tubulin cytoskeleton to regulate branching. (shrink)

The identification of Smad proteins as molecular components of the transforming growth factor-β (TGF-β) signaling cascade has enhanced our understanding of how ligand-mediated activation of TGF-β receptors leads to modulation of target gene transcription. Recent studies have identified a distinct, structurally related class of Smads which inhibits, rather than transduces, TGF-β family signals. The molecular mechanism of action and the exact signaling pathways that are targeted by antagonistic Smads are not completely understood. These proteins appear to participate (...) in autoregulatory negative feedback loops in which signaling initiated by specific TGF-β family ligands induces the expression of an inhibitory Smad that then functions to modulate the amplitude or duration of signaling. Negative feedback circuits such as these play important roles in fine-tuning the activity of multifunctional signaling molecules during embryonic patterning and in response to pathologic stimuli in adults. BioEssays 21:382–390, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

The identification of neural substrates underlying the long lasting debilitating impact of drug cues is critical for developing novel therapeutic tools. Metabolic coupling has long been considered a key mechanism through which astrocytes and neurons actively interact in response of neuronal activity, but recent findings suggested that disrupting metabolic coupling may represent an innovative approach to prevent memory formation, in particular drug‐related memories. Here, we review converging evidence illustrating how memory and addiction share neural circuitry and molecular mechanisms (...) implicating lactate‐mediated metabolic coupling between astrocytes and neurons. With several aspects of addiction depending on mnemonic processes elicited by drug experience, disrupting lactate transport involved in the formation of a pathological learning, linking the incentive, and motivational effects of drugs with drug‐conditioned stimuli represent a promising approach to encourage abstinence. (shrink)

Identification of Pygopus in Drosophila as a dedicated component of the Wg (fly homolog of mammalian Wnt) signaling cascade initiated many inquiries into the mechanism of its function. Surprisingly, the nearly exclusive role for Pygopus in Wg signal transduction in flies is not seen in mice, where Pygopus appears to have both Wnt‐related and Wnt‐independent functions. This review addresses the initial findings of Pygopus as a Wg/Wnt co‐activator in light of recent data from both fly and mammalian studies. We (...) compare and contrast the developmental phenotypes of pygopus mutants to those characterized for known Wg/Wnt transducers and explore the data regarding a role for mammalian Pygopus 2 in tumorigenesis. We further analyze the roles of the two conserved domains of Pygopus proteins in transcription, and propose a model for the molecular mechanism of Pygopus function in both Wg/Wnt signaling and Wnt‐independent transcriptional regulation. BioEssays 30:448–456, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

In this paper I want to argue for the optimal way to characterise the logical and semantical behaviour of the singular term ‘God’ used in religious language. The relevance of this enterprise to logical theory is the main focus as well. Doing this presupposes to outline the two rivaling approaches of well-definition of singular terms: Kripke’s (“rigid designators”) and Hintikka’s (“world-lines”). ‘God’ as a “rigid designator” is purified from all real-life-language-games of identification and only spells out a metaphysical tag, (...) which favours the view of “anything goes”. Instead, ‘God’ as a “world-line,” plus two ways of quantification, is much more flexible to theological traditions, teachings of the church, religious practices and personal feelings. Thus, it provides a sufficiently well-defined singular term for the purposes of logical theory. (shrink)

Indirect identification of innovations in wild populations involves inferring past, unobserved behavioral events. Such historical inference can make simple use of present distribution patterns of differently behaving individuals, but population genetic studies are a potential source of complementary relevant information. Methodological lessons can be taken from phylogeography, that is, molecular approaches to the history of population spatial distribution patterns and gene flows. Opportunities for such studies in primates should increase with the developing population genetic studies used for management (...) and conservation purposes. (shrink)

AMBIS is a complete identification system which includes (1) a highly reproducible electrophoresis unit; (2) a beta‐scanner with the ability to rapidly locate and measure beta particle emission data from a variety of isotopes and surfaces; and (3) an IBM computer with a massive data storage capacity for the emission data plus subsequent manipulation of that data. Hence it provides a rapid facility for (1) classification of all types of micro‐organisms, (2) examination of cells of multicellular plants and animals, (...) (3) routine determination of molecular weights of one or more proteins in a complex mixture, (4) quantification of single or mixed compounds in a band, (5) scanning and quantification of dot and other blots, immunodiffusion precipitates and probes, (6) direct counting of radioactive solutions from RIA, column fractions, etc., without the need of expensive scintillation fluids with their consequent hazards, (7) circumventing the need of much time‐consuming auto‐radiography, and (8) setting up databases plus exchange and transference of data between AMBIS systems in different locations via floppy disk, modem or other forms of rapid transmission. (shrink)

The discovery of the molecular structure of deoxyribonucleic acid and the science of molecular biology have profoundly changed medicine’s diagnostic capability and promise to transform the therapeutic realm. When some genetic disorders are diagnosed, physicians can intervene for prevention or treatment. While the basic structure of DNA is the same for all human beings, no two individuals, other than identical twins, have the same DNA sequence. This discovery has had important repercussions in the criminal justice system, where DNA (...) can serve as an identification tool.At the crossroads of these different uses of DNA, there are great concerns about potential misuses of genetic information. Preventing disease, curing illness, and convicting criminals are all seen as worthwhile uses of the technology, but concerns of potential misuse in medicine or in the criminal justice system are not unfounded. A 1998 American Medical Association study showed that 68 percent of patients had fears that their genetic test results would be used against them by their employers or insurers. Others, pointing to racial profiling, have suggested that we may now face genetic profiling. (shrink)

The discovery of the molecular structure of deoxyribonucleic acid and the science of molecular biology have profoundly changed medicine’s diagnostic capability and promise to transform the therapeutic realm. When some genetic disorders are diagnosed, physicians can intervene for prevention or treatment. While the basic structure of DNA is the same for all human beings, no two individuals, other than identical twins, have the same DNA sequence. This discovery has had important repercussions in the criminal justice system, where DNA (...) can serve as an identification tool.At the crossroads of these different uses of DNA, there are great concerns about potential misuses of genetic information. Preventing disease, curing illness, and convicting criminals are all seen as worthwhile uses of the technology, but concerns of potential misuse in medicine or in the criminal justice system are not unfounded. A 1998 American Medical Association study showed that 68 percent of patients had fears that their genetic test results would be used against them by their employers or insurers. Others, pointing to racial profiling, have suggested that we may now face genetic profiling. (shrink)