Showing papers by "Massachusetts Institute of Technology published in 2007"

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

Abstract: Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.

Nanocarriers as an emerging platform for cancer therapy

Abstract: Nanotechnology has the potential to revolutionize cancer diagnosis and therapy. Advances in protein engineering and materials science have contributed to novel nanoscale targeting approaches that may bring new hope to cancer patients. Several therapeutic nanocarriers have been approved for clinical use. However, to date, there are only a few clinically approved nanocarriers that incorporate molecules to selectively bind and target cancer cells. This review examines some of the approved formulations and discusses the challenges in translating basic research to the clinic. We detail the arsenal of nanocarriers and molecules available for selective tumour targeting, and emphasize the challenges in cancer treatment.

Moses: Open Source Toolkit for Statistical Machine Translation

Abstract: We describe an open-source toolkit for statistical machine translation whose novel contributions are (a) support for linguistically motivated factors, (b) confusion network decoding, and (c) efficient data formats for translation models and language models. In addition to the SMT decoder, the toolkit also includes a wide variety of tools for training, tuning and applying the system to many translation tasks.

Wireless Power Transfer via Strongly Coupled Magnetic Resonances

Abstract: Using self-resonant coils in a strongly coupled regime, we experimentally demonstrated efficient nonradiative power transfer over distances up to 8 times the radius of the coils We were able to transfer 60 watts with ∼40% efficiency over distances in excess of 2 meters We present a quantitative model describing the power transfer, which matches the experimental results to within 5% We discuss the practical applicability of this system and suggest directions for further study

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Abstract: We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Abstract: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences Lysine 4 and lysine 9 trimethylation marks imprinting control regions Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations

Renal clearance of quantum dots.

Abstract: The field of nanotechnology holds great promise for the diagnosis and treatment of human disease. However, the size and charge of most nanoparticles preclude their efficient clearance from the body as intact nanoparticles. Without such clearance or their biodegradation into biologically benign components, toxicity is potentially amplified and radiological imaging is hindered. Using intravenously administered quantum dots in rodents as a model system, we have precisely defined the requirements for renal filtration and urinary excretion of inorganic, metal-containing nanoparticles. Zwitterionic or neutral organic coatings prevented adsorption of serum proteins, which otherwise increased hydrodynamic diameter by >15 nm and prevented renal excretion. A final hydrodynamic diameter <5.5 nm resulted in rapid and efficient urinary excretion and elimination of quantum dots from the body. This study provides a foundation for the design and development of biologically targeted nanoparticles for biomedical applications.

Chemical sensors based on amplifying fluorescent conjugated polymers.

Abstract: The field of chemical sensing is becoming ever more dependent upon novel materials. Polymers, crystals, glasses, particles, and nanostructures have made a profound impact and have endowed modern sensory systems with superior performance. Electronic polymers have emerged as one of the most important classes of transduction materials; they readily transform a chemical signal into an easily measured electrical or optical event. Although our group reviewed this field in 2000,1 the high levels of activity and the impact of these methods now justify a subsequent review as part of this special issue. In this review we restrict our discussions to purely fluorescence-based methods using conjugated polymers (CPs). We further confine our detailed coverage to articles published since our previous review and will only detail earlier research in this Introduction to illustrate fundamental concepts and terminology that underpin the recent literature.

Charge transport in organic semiconductors.

Abstract: 2.2. Materials 929 2.3. Factors Influencing Charge Mobility 931 2.3.1. Molecular Packing 931 2.3.2. Disorder 932 2.3.3. Temperature 933 2.3.4. Electric Field 934 2.3.5. Impurities 934 2.3.6. Pressure 934 2.3.7. Charge-Carrier Density 934 2.3.8. Size/molecular Weight 935 3. The Charge-Transport Parameters 935 3.1. Electronic Coupling 936 3.1.1. The Energy-Splitting-in-Dimer Method 936 3.1.2. The Orthogonality Issue 937 3.1.3. Impact of the Site Energy 937 3.1.4. Electronic Coupling in Oligoacene Derivatives 938

Studying Disorder in Graphite-Based Systems by Raman Spectroscopy

Abstract: Raman spectroscopy has historically played an important role in the structural characterization of graphitic materials, in particular providing valuable information about defects, stacking of the graphene layers and the finite sizes of the crystallites parallel and perpendicular to the hexagonal axis Here we review the defect-induced Raman spectra of graphitic materials from both experimental and theoretical standpoints and we present recent Raman results on nanographites and graphenes The disorder-induced D and D′ Raman features, as well as the G′-band (the overtone of the D-band which is always observed in defect-free samples), are discussed in terms of the double-resonance (DR) Raman process, involving phonons within the interior of the 1st Brillouin zone of graphite and defects In this review, experimental results for the D, D′ and G′ bands obtained with different laser lines, and in samples with different crystallite sizes and different types of defects are presented and discussed We also present recent advances that made possible the development of Raman scattering as a tool for very accurate structural analysis of nano-graphite, with the establishment of an empirical formula for the in- and out-of-plane crystalline size and even fancier Raman-based information, such as for the atomic structure at graphite edges, and the identification of single versus multi-graphene layers Once established, this knowledge provides a powerful machinery to understand newer forms of sp2 carbon materials, such as the recently developed pitch-based graphitic foams Results for the calculated Raman intensity of the disorder-induced D-band in graphitic materials as a function of both the excitation laser energy (Elaser) and the in-plane size (La) of nano-graphites are presented and compared with experimental results The status of this research area is assessed, and opportunities for future work are identified

New Directions for Low-Dimensional Thermoelectric Materials**

Abstract: Many of the recent advances in enhancing the thermoelectric figure of merit are linked to nanoscale phenomena found both in bulk samples containing nanoscale constituents and in nanoscale samples themselves. Prior theoretical and experimental proof-of-principle studies on quantum-well superlattice and quantum-wire samples have now evolved into studies on bulk samples containing nanostructured constituents prepared by chemical or physical approaches. In this Review, nanostructural composites are shown to exhibit nanostructures and properties that show promise for thermoelectric applications, thus bringing together low-dimensional and bulk materials for thermoelectric applications. Particular emphasis is given in this Review to the ability to achieve 1) a simultaneous increase in the power factor and a decrease in the thermal conductivity in the same nanocomposite sample and for transport in the same direction and 2) lower values of the thermal conductivity in these nanocomposites as compared to alloy samples of the same chemical composition. The outlook for future research directions for nanocomposite thermoelectric materials is also discussed.

Mesenchymal stem cells within tumour stroma promote breast cancer metastasis

Abstract: Mesenchymal stem cells have been recently described to localize to breast carcinomas, where they integrate into the tumour-associated stroma. However, the involvement of mesenchymal stem cells (or their derivatives) in tumour pathophysiology has not been addressed. Here, we demonstrate that bone-marrow-derived human mesenchymal stem cells, when mixed with otherwise weakly metastatic human breast carcinoma cells, cause the cancer cells to increase their metastatic potency greatly when this cell mixture is introduced into a subcutaneous site and allowed to form a tumour xenograft. The breast cancer cells stimulate de novo secretion of the chemokine CCL5 (also called RANTES) from mesenchymal stem cells, which then acts in a paracrine fashion on the cancer cells to enhance their motility, invasion and metastasis. This enhanced metastatic ability is reversible and is dependent on CCL5 signalling through the chemokine receptor CCR5. Collectively, these data demonstrate that the tumour microenvironment facilitates metastatic spread by eliciting reversible changes in the phenotype of cancer cells.

In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state

Abstract: Nuclear transplantation can reprogramme a somatic genome back into an embryonic epigenetic state, and the reprogrammed nucleus can create a cloned animal or produce pluripotent embryonic stem cells. One potential use of the nuclear cloning approach is the derivation of 'customized' embryonic stem (ES) cells for patient-specific cell treatment, but technical and ethical considerations impede the therapeutic application of this technology. Reprogramming of fibroblasts to a pluripotent state can be induced in vitro through ectopic expression of the four transcription factors Oct4 (also called Oct3/4 or Pou5f1), Sox2, c-Myc and Klf4. Here we show that DNA methylation, gene expression and chromatin state of such induced reprogrammed stem cells are similar to those of ES cells. Notably, the cells-derived from mouse fibroblasts-can form viable chimaeras, can contribute to the germ line and can generate live late-term embryos when injected into tetraploid blastocysts. Our results show that the biological potency and epigenetic state of in-vitro-reprogrammed induced pluripotent stem cells are indistinguishable from those of ES cells.

Designing Superoleophobic Surfaces

Abstract: Understanding the complementary roles of surface energy and roughness on natural nonwetting surfaces has led to the development of a number of biomimetic superhydrophobic surfaces, which exhibit apparent contact angles with water greater than 150 degrees and low contact angle hysteresis. However, superoleophobic surfaces-those that display contact angles greater than 150 degrees with organic liquids having appreciably lower surface tensions than that of water-are extremely rare. Calculations suggest that creating such a surface would require a surface energy lower than that of any known material. We show how a third factor, re-entrant surface curvature, in conjunction with chemical composition and roughened texture, can be used to design surfaces that display extreme resistance to wetting from a number of liquids with low surface tension, including alkanes such as decane and octane.

Tumour invasion and metastasis initiated by microRNA-10b in breast cancer

Abstract: MicroRNAs have been implicated in regulating diverse cellular pathways. Although there is emerging evidence that some microRNAs can function as oncogenes or tumour suppressors, the role of microRNAs in mediating cancer metastasis remains unexplored. Here we show, using a combination of mouse and human cells, that microRNA-10b (miR-10b) is highly expressed in metastatic breast cancer cells and positively regulates cell migration and invasion. Overexpression of miR-10b in otherwise non-metastatic breast tumours initiates robust invasion and metastasis. Expression of miR-10b is induced by the transcription factor Twist, which binds directly to the putative promoter of mir-10b (MIRN10B). The miR-10b induced by Twist proceeds to inhibit translation of the messenger RNA encoding homeobox D10, resulting in increased expression of a well-characterized pro-metastatic gene, RHOC. Significantly, the level of miR-10b expression in primary breast carcinomas correlates with clinical progression. These findings suggest the workings of an undescribed regulatory pathway, in which a pleiotropic transcription factor induces expression of a specific microRNA, which suppresses its direct target and in turn activates another pro-metastatic gene, leading to tumour cell invasion and metastasis.

The OBO Foundry : coordinated evolution of ontologies to support biomedical data integration

Abstract: The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.

Sociomaterial Practices: Exploring Technology at Work

Abstract: In this essay, I begin with the premise that everyday organizing is inextricably bound up with materiality and contend that this relationship is inadequately reflected in organizational studies that tend to ignore it, take it for granted, or treat it as a special case. The result is an understanding of organizing and its conditions and consequences that is necessarily limited. I then argue for an alternative approach, one that posits the constitutive entanglement of the social and the material in everyday life. I draw on some empirical examples to help ground and illustrate this approach in practice and conclude by suggesting that a reconfiguration of our conventional assumptions and considerations of materiality will help us more effectively recognize and understand the multiple, emergent, and shifting sociomaterial assemblages entailed in contemporary organizing.

Evolution of genes and genomes on the Drosophila phylogeny.

Abstract: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells

Abstract: MicroRNAs are predicted to regulate thousands of mammalian genes, but relatively few targets have been experimentally validated and few microRNA loss-of-function phenotypes have been assigned. As an alternative to chemically modified antisense oligonucleotides, we developed microRNA inhibitors that can be expressed in cells, as RNAs produced from transgenes. Termed 'microRNA sponges', these competitive inhibitors are transcripts expressed from strong promoters, containing multiple, tandem binding sites to a microRNA of interest. When vectors encoding these sponges are transiently transfected into cultured cells, sponges derepress microRNA targets at least as strongly as chemically modified antisense oligonucleotides. They specifically inhibit microRNAs with a complementary heptameric seed, such that a single sponge can be used to block an entire microRNA seed family. RNA polymerase II promoter (Pol II)-driven sponges contain a fluorescence reporter gene for identification and sorting of sponge-treated cells. We envision the use of stably expressed sponges in animal models of disease and development.

Physical unclonable functions for device authentication and secret key generation

Abstract: Physical Unclonable Functions (PUFs) are innovative circuit primitives that extract secrets from physical characteristics of integrated circuits (ICs). We present PUF designs that exploit inherent delay characteristics of wires and transistors that differ from chip to chip, and describe how PUFs can enable low-cost authentication of individual ICs and generate volatile secret keys for cryptographic operations.

Robust Object Recognition with Cortex-Like Mechanisms

Abstract: We introduce a new general framework for the recognition of complex visual scenes, which is motivated by biology: We describe a hierarchical system that closely follows the organization of visual cortex and builds an increasingly complex and invariant feature representation by alternating between a template matching and a maximum pooling operation. We demonstrate the strength of the approach on a range of recognition tasks: From invariant single object recognition in clutter to multiclass categorization problems and complex scene understanding tasks that rely on the recognition of both shape-based as well as texture-based objects. Given the biological constraints that the system had to satisfy, the approach performs surprisingly well: It has the capability of learning from only a few training examples and competes with state-of-the-art systems. We also discuss the existence of a universal, redundant dictionary of features that could handle the recognition of most object categories. In addition to its relevance for computer vision, the success of this approach suggests a plausibility proof for a class of feedforward models of object recognition in cortex

Genome-wide detection and characterization of positive selection in human populations

Abstract: With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes

Abstract: Extensive studies are currently being performed to associate disease susceptibility with one form of genetic variation, namely, single-nucleotide polymorphisms (SNPs). In recent years, another type of common genetic variation has been characterized, namely, structural variation, including copy number variants (CNVs). To determine the overall contribution of CNVs to complex phenotypes, we have performed association analyses of expression levels of 14,925 transcripts with SNPs and CNVs in individuals who are part of the International HapMap project. SNPs and CNVs captured 83.6% and 17.7% of the total detected genetic variation in gene expression, respectively, but the signals from the two types of variation had little overlap. Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans.

Restoration of p53 function leads to tumour regression in vivo

Abstract: The p53 tumour suppressor is either mutated or inactivated by other alterations in most human cancers. Two papers in this issue show that even brief reactivation of the endogenous p53 genes in established tumours can cause cancer regression in some animal models. In some tumours, p53 reactivation causes cellular senescence associated with an innate immune response that contributes to tumour clearance. These experiments used gene manipulation to alter p53 levels, but they lend further support to the idea that p53-boosting drugs could be a useful form of cancer treatment. One of two papers showing that reactivation of the endogenous p53 tumour suppressor genes in established tumours causes cancer regression. In some tumours, p53 reactivation causes cellular senescence associated with an innate immune response that contributes to tumour clearance. Tumorigenesis is a multi-step process that requires activation of oncogenes and inactivation of tumour suppressor genes1. Mouse models of human cancers have recently demonstrated that continuous expression of a dominantly acting oncogene (for example, Hras, Kras and Myc) is often required for tumour maintenance2,3,4,5; this phenotype is referred to as oncogene addiction6. This concept has received clinical validation by the development of active anticancer drugs that specifically inhibit the function of oncoproteins such as BCR-ABL, c-KIT and EGFR7,8,9,10. Identifying additional gene mutations that are required for tumour maintenance may therefore yield clinically useful targets for new cancer therapies. Although loss of p53 function is a common feature of human cancers11, it is not known whether sustained inactivation of this or other tumour suppressor pathways is required for tumour maintenance. To explore this issue, we developed a Cre-loxP-based strategy to temporally control tumour suppressor gene expression in vivo. Here we show that restoring endogenous p53 expression leads to regression of autochthonous lymphomas and sarcomas in mice without affecting normal tissues. The mechanism responsible for tumour regression is dependent on the tumour type, with the main consequence of p53 restoration being apoptosis in lymphomas and suppression of cell growth with features of cellular senescence in sarcomas. These results support efforts to treat human cancers by way of pharmacological reactivation of p53.