Showing papers in "Science in 2001"
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Abstract: A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
TL;DR: Film and powders of TiO2-x Nx have revealed an improvement over titanium dioxide (TiO2) under visible light in optical absorption and photocatalytic activity such as photodegradations of methylene blue and gaseous acetaldehyde and hydrophilicity of the film surface.
Abstract: To use solar irradiation or interior lighting efficiently, we sought a photocatalyst with high reactivity under visible light. Films and powders of TiO 2- x N x have revealed an improvement over titanium dioxide (TiO 2 ) under visible light (wavelength 2 has proven to be indispensable for band-gap narrowing and photocatalytic activity, as assessed by first-principles calculations and x-ray photoemission spectroscopy.
TL;DR: This review describes a new paradigm of electronics based on the spin degree of freedom of the electron, which has the potential advantages of nonvolatility, increased data processing speed, decreased electric power consumption, and increased integration densities compared with conventional semiconductor devices.
Abstract: This review describes a new paradigm of electronics based on the spin degree of freedom of the electron. Either adding the spin degree of freedom to conventional charge-based electronic devices or using the spin alone has the potential advantages of nonvolatility, increased data processing speed, decreased electric power consumption, and increased integration densities compared with conventional semiconductor devices. To successfully incorporate spins into existing semiconductor technology, one has to resolve technical issues such as efficient injection, transport, control and manipulation, and detection of spin polarization as well as spin-polarized currents. Recent advances in new materials engineering hold the promise of realizing spintronic devices in the near future. We review the current state of the spin-based devices, efforts in new materials fabrication, issues in spin transport, and optical spin manipulation.
TL;DR: It is proposed that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.
Abstract: Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states. The combinatorial nature of histone amino-terminal modifications thus reveals a “histone code” that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.
TL;DR: Room-temperature ultraviolet lasing in semiconductor nanowire arrays has been demonstrated and self-organized, <0001> oriented zinc oxide nanowires grown on sapphire substrates were synthesized with a simple vapor transport and condensation process.
Abstract: Room-temperature ultraviolet lasing in semiconductor nanowire arrays has been demonstrated The self-organized, oriented zinc oxide nanowires grown on sapphire substrates were synthesized with a simple vapor transport and condensation process These wide band-gap semiconductor nanowires form natural laser cavities with diameters varying from 20 to 150 nanometers and lengths up to 10 micrometers Under optical excitation, surface-emitting lasing action was observed at 385 nanometers, with an emission linewidth less than 03 nanometer The chemical flexibility and the one-dimensionality of the nanowires make them ideal miniaturized laser light sources These short-wavelength nanolasers could have myriad applications, including optical computing, information storage, and microanalysis
TL;DR: This work focuses primarily on the periodic and anomalous components of variability over the early portion of this era, as constrained by the latest generation of deep-sea isotope records.
Abstract: Since 65 million years ago (Ma), Earth's climate has undergone a significant and complex evolution, the finer details of which are now coming to light through investigations of deep-sea sediment cores. This evolution includes gradual trends of warming and cooling driven by tectonic processes on time scales of 10(5) to 10(7) years, rhythmic or periodic cycles driven by orbital processes with 10(4)- to 10(6)-year cyclicity, and rare rapid aberrant shifts and extreme climate transients with durations of 10(3) to 10(5) years. Here, recent progress in defining the evolution of global climate over the Cenozoic Era is reviewed. We focus primarily on the periodic and anomalous components of variability over the early portion of this era, as constrained by the latest generation of deep-sea isotope records. We also consider how this improved perspective has led to the recognition of previously unforeseen mechanisms for altering climate.
TL;DR: These experiments directly confirm the predictions of Maxwell's equations that n is given by the negative square root ofɛ·μ for the frequencies where both the permittivity and the permeability are negative.
Abstract: We present experimental scattering data at microwave frequencies on a structured metamaterial that exhibits a frequency band where the effective index of refraction (n) is negative. The material consists of a two-dimensional array of repeated unit cells of copper strips and split ring resonators on interlocking strips of standard circuit board material. By measuring the scattering angle of the transmitted beam through a prism fabricated from this material, we determine the effective n, appropriate to Snell's law. These experiments directly confirm the predictions of Maxwell's equations that n is given by the negative square root of epsilon.mu for the frequencies where both the permittivity (epsilon) and the permeability (mu) are negative. Configurations of geometrical optical designs are now possible that could not be realized by positive index materials.
TL;DR: The small size and capability of these semiconductor nanowires for sensitive, label-free, real-time detection of a wide range of chemical and biological species could be exploited in array-based screening and in vivo diagnostics.
Abstract: Boron-doped silicon nanowires (SiNWs) were used to create highly sensitive, real-time electrically based sensors for biological and chemical species. Amine- and oxide-functionalized SiNWs exhibit pH-dependent conductance that was linear over a large dynamic range and could be understood in terms of the change in surface charge during protonation and deprotonation. Biotin-modified SiNWs were used to detect streptavidin down to at least a picomolar concentration range. In addition, antigen-functionalized SiNWs show reversible antibody binding and concentration-dependent detection in real time. Lastly, detection of the reversible binding of the metabolic indicator Ca2+ was demonstrated. The small size and capability of these semiconductor nanowires for sensitive, label-free, real-time detection of a wide range of chemical and biological species could be exploited in array-based screening and in vivo diagnostics.
TL;DR: The beltlike morphology appears to be a distinctive and common structural characteristic for the family of semiconducting oxides with cations of different valence states and materials of distinct crystallographic structures, which could be an ideal system for fully understanding dimensionally confined transport phenomena in functional oxides.
Abstract: Ultralong beltlike (or ribbonlike) nanostructures (so-called nanobelts) were successfully synthesized for semiconducting oxides of zinc, tin, indium, cadmium, and gallium by simply evaporating the desired commercial metal oxide powders at high temperatures. The as-synthesized oxide nanobelts are pure, structurally uniform, and single crystalline, and most of them are free from defects and dislocations. They have a rectanglelike cross section with typical widths of 30 to 300 nanometers, width-to-thickness ratios of 5 to 10, and lengths of up to a few millimeters. The beltlike morphology appears to be a distinctive and common structural characteristic for the family of semiconducting oxides with cations of different valence states and materials of distinct crystallographic structures. The nanobelts could be an ideal system for fully understanding dimensionally confined transport phenomena in functional oxides and building functional devices along individual nanobelts.
University of California, San Diego1, Smithsonian Tropical Research Institute2, State Street Corporation3, University of Florida4, University of California, Davis5, Bates College6, Australian National University7, University of Oregon8, University of California, Santa Cruz9, James Cook University10, University of Chicago11, University of North Carolina at Chapel Hill12, National Museum of Natural History13, University of Maine14, University of California, Santa Barbara15
Abstract: Ecological extinction caused by overfishing precedes all other pervasive human disturbance to coastal ecosystems, including pollution, degradation of water quality, and anthropogenic climate change. Historical abundances of large consumer species were fantastically large in comparison with recent observations. Paleoecological, archaeological, and historical data show that time lags of decades to centuries occurred between the onset of overfishing and consequent changes in ecological communities, because unfished species of similar trophic level assumed the ecological roles of overfished species until they too were overfished or died of epidemic diseases related to overcrowding. Retrospective data not only help to clarify underlying causes and rates of ecological change, but they also demonstrate achievable goals for restoration and management of coastal ecosystems that could not even be contemplated based on the limited perspective of recent observations alone.
TL;DR: It is shown that the interaction between human pVHL and a specific domain of the HIF-1α subunit is regulated through hydroxylation of a proline residue by an enzyme the authors have termed Hif-α prolyl-hydroxylase (HIF-PH).
Abstract: Hypoxia-inducible factor (HIF) is a transcriptional complex that plays a central role in the regulation of gene expression by oxygen. In oxygenated and iron replete cells, HIF-alpha subunits are rapidly destroyed by a mechanism that involves ubiquitylation by the von Hippel-Lindau tumor suppressor (pVHL) E3 ligase complex. This process is suppressed by hypoxia and iron chelation, allowing transcriptional activation. Here we show that the interaction between human pVHL and a specific domain of the HIF-1alpha subunit is regulated through hydroxylation of a proline residue (HIF-1alpha P564) by an enzyme we have termed HIF-alpha prolyl-hydroxylase (HIF-PH). An absolute requirement for dioxygen as a cosubstrate and iron as cofactor suggests that HIF-PH functions directly as a cellular oxygen sensor.
TL;DR: It is shown that many 21- and 22-nt expressed RNAs, termed microRNAs, exist in invertebrates and vertebrates and that some of these novel RNAs are highly conserved, which suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by smallRNAs are more general than previously appreciated.
Abstract: In Caenorhabditis elegans, lin-4 and let-7 encode 22- and 21-nucleotide (nt) RNAs, respectively, which function as key regulators of developmental timing. Because the appearance of these short RNAs is regulated during development, they are also referred to as small temporal RNAs (stRNAs). We show that many 21- and 22-nt expressed RNAs, termed microRNAs, exist in invertebrates and vertebrates and that some of these novel RNAs, similar to let-7 stRNA, are highly conserved. This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated.
TL;DR: It is found that human pVHL binds to a short HIF-derived peptide when a conserved proline residue at the core of this peptide is hydroxylated, which may play a key role in mammalian oxygen sensing.
Abstract: HIF (hypoxia-inducible factor) is a transcription factor that plays a pivotal role in cellular adaptation to changes in oxygen availability. In the presence of oxygen, HIF is targeted for destruction by an E3 ubiquitin ligase containing the von Hippel-Lindau tumor suppressor protein (pVHL). We found that human pVHL binds to a short HIF-derived peptide when a conserved proline residue at the core of this peptide is hydroxylated. Because proline hydroxylation requires molecular oxygen and Fe(2+), this protein modification may play a key role in mammalian oxygen sensing.
Abstract: The invention concerns a quantum cascade laser comprising in particular a gain region (14) consisting of several layers (20) each including: alternating strata of a first type (28) defining each an AllnAs quantum barrier and strata of a second type (28) defining each an InGaAs quantum barrier, and injection barriers (22), interposed between two of the layers (20). The layers of the gain region (14) form each an active zone extending from one to the other of the injection barriers (22) adjacent thereto. The strata (26, 28) are dimensioned such that: each of the wells comprises, in the presence of an electric field, at least a first upper subband, a second median subband, and a third lower subband, and the probability of an electron being present in the first subband is highest in the proximity of one of the adjacent injection barriers, in the second subband in the median part of the zone and in the third subband in the proximity of the other adjacent barriers. The laser is formed by a succession of active zones and injection barriers, without interposition of a relaxation zone.
Abstract: Multiple death signals influence mitochondria during apoptosis, yet the critical initiating event for mitochondrial dysfunction in vivo has been unclear. tBID, the caspase-activated form of a "BH3-domain-only" BCL-2 family member, triggers the homooligomerization of "multidomain" conserved proapoptotic family members BAK or BAX, resulting in the release of cytochrome c from mitochondria. We find that cells lacking both Bax and Bak, but not cells lacking only one of these components, are completely resistant to tBID-induced cytochrome c release and apoptosis. Moreover, doubly deficient cells are resistant to multiple apoptotic stimuli that act through disruption of mitochondrial function: staurosporine, ultraviolet radiation, growth factor deprivation, etoposide, and the endoplasmic reticulum stress stimuli thapsigargin and tunicamycin. Thus, activation of a "multidomain" proapoptotic member, BAX or BAK, appears to be an essential gateway to mitochondrial dysfunction required for cell death in response to diverse stimuli.
TL;DR: Larger numbers of species are probably needed to reduce temporal variability in ecosystem processes in changing environments and to determine how biodiversity dynamics, ecosystem processes, and abiotic factors interact.
Abstract: The ecological consequences of biodiversity loss have aroused considerable interest and controversy during the past decade. Major advances have been made in describing the relationship between species diversity and ecosystem processes, in identifying functionally important species, and in revealing underlying mechanisms. There is, however, uncertainty as to how results obtained in recent experiments scale up to landscape and regional levels and generalize across ecosystem types and processes. Larger numbers of species are probably needed to reduce temporal variability in ecosystem processes in changing environments. A major future challenge is to determine how biodiversity dynamics, ecosystem processes, and abiotic factors interact.
TL;DR: The functional architecture of the object vision pathway in the human brain was investigated using functional magnetic resonance imaging to measure patterns of response in ventral temporal cortex while subjects viewed faces, cats, five categories of man-made objects, and nonsense pictures, and a distinct pattern of response was found for each stimulus category.
Abstract: The functional architecture of the object vision pathway in the human brain was investigated using functional magnetic resonance imaging to measure patterns of response in ventral temporal cortex while subjects viewed faces, cats, five categories of man-made objects, and nonsense pictures. A distinct pattern of response was found for each stimulus category. The distinctiveness of the response to a given category was not due simply to the regions that responded maximally to that category, because the category being viewed also could be identified on the basis of the pattern of response when those regions were excluded from the analysis. Patterns of response that discriminated among all categories were found even within cortical regions that responded maximally to only one category. These results indicate that the representations of faces and objects in ventral temporal cortex are widely distributed and overlapping.
TL;DR: Two small temporal RNAs, lin-4 andlet-7, control developmental timing in Caenorhabditis elegans and are found to be members of a large class of 21- to 24-nucleotide noncodingRNAs, called microRNAs (miRNAs), which imply that, as a class, miRNAs have broad regulatory functions in animals.
Abstract: Two small temporal RNAs (stRNAs), lin-4 and let-7, control developmental timing in Caenorhabditis elegans. We find that these two regulatory RNAs are members of a large class of 21- to 24-nucleotide noncoding RNAs, called microRNAs (miRNAs). We report on 55 previously unknown miRNAs in C. elegans. The miRNAs have diverse expression patterns during development: a let-7 paralog is temporally coexpressed with let-7; miRNAs encoded in a single genomic cluster are coexpressed during embryogenesis; and still other miRNAs are expressed constitutively throughout development. Potential orthologs of several of these miRNA genes were identified in Drosophila and human genomes. The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals.
TL;DR: This book aims to investigate elementary forms of learning and memory at a cellular molecular level—as specific molecular activities within identified nerve cells withinidentified nerve cells.
Abstract: One of the most remarkable aspects of an animal's behavior is the ability to modify that behavior by learning, an ability that reaches its highest form in human beings. For me, learning and memory have proven to be endlessly fascinating mental processes because they address one of the fundamental features of human activity: our ability to acquire new ideas from experience and to retain these ideas over time in memory. Moreover, unlike other mental processes such as thought, language, and consciousness, learning seemed from the outset to be readily accessible to cellular and molecular analysis. I, therefore, have been curious to know: What changes in the brain when we learn? And, once something is learned, how is that information retained in the brain? I have tried to address these questions through a reductionist approach that would allow me to investigate elementary forms of learning and memory at a cellular molecular level-as specific molecular activities within identified nerve cells.
TL;DR: It is argued that moral dilemmas vary systematically in the extent to which they engage emotional processing and that these variations in emotional engagement influence moral judgment.
Abstract: The long-standing rationalist tradition in moral psychology emphasizes the role of reason in moral judgment. A more recent trend places increased emphasis on emotion. Although both reason and emotion are likely to play important roles in moral judgment, relatively little is known about their neural correlates, the nature of their interaction, and the factors that modulate their respective behavioral influences in the context of moral judgment. In two functional magnetic resonance imaging (fMRI) studies using moral dilemmas as probes, we apply the methods of cognitive neuroscience to the study of moral judgment. We argue that moral dilemmas vary systematically in the extent to which they engage emotional processing and that these variations in emotional engagement influence moral judgment. These results may shed light on some puzzling patterns in moral judgment observed by contemporary philosophers.
TL;DR: Should past dependences of the global environmental impacts of agriculture on human population and consumption continue, 109 hectares of natural ecosystems would be converted to agriculture by 2050, accompanied by 2.4- to 2.7-fold increases in nitrogen- and phosphorus-driven eutrophication of terrestrial, freshwater, and near-shore marine ecosystems.
Abstract: During the next 50 years, which is likely to be the final period of rapid agricultural expansion, demand for food by a wealthier and 50% larger global population will be a major driver of global environmental change. Should past dependences of the global environmental impacts of agriculture on human population and consumption continue, 10(9) hectares of natural ecosystems would be converted to agriculture by 2050. This would be accompanied by 2.4- to 2.7-fold increases in nitrogen- and phosphorus-driven eutrophication of terrestrial, freshwater, and near-shore marine ecosystems, and comparable increases in pesticide use. This eutrophication and habitat destruction would cause unprecedented ecosystem simplification, loss of ecosystem services, and species extinctions. Significant scientific advances and regulatory, technological, and policy changes are needed to control the environmental impacts of agricultural expansion.
TL;DR: Important insights into the mechanisms of inflammatory responses, pain, and fever have been gleaned from the current understanding of eicosanoid biology.
Abstract: Prostaglandins and leukotrienes are potent eicosanoid lipid mediators derived from phospholipase-released arachidonic acid that are involved in numerous homeostatic biological functions and inflammation. They are generated by cyclooxygenase isozymes and 5-lipoxygenase, respectively, and their biosynthesis and actions are blocked by clinically relevant nonsteroidal anti-inflammatory drugs, the newer generation coxibs (selective inhibitors of cyclooxygenase-2), and leukotriene modifiers. The prime mode of prostaglandin and leukotriene action is through specific G protein-coupled receptors, many of which have been cloned recently, thus enabling specific receptor agonist and antagonist development. Important insights into the mechanisms of inflammatory responses, pain, and fever have been gleaned from our current understanding of eicosanoid biology.
TL;DR: Human activities are releasing tiny particles (aerosols) into the atmosphere that enhance scattering and absorption of solar radiation, which can lead to a weaker hydrological cycle, which connects directly to availability and quality of fresh water, a major environmental issue of the 21st century.
Abstract: Human activities are releasing tiny particles (aerosols) into the atmosphere. These human-made aerosols enhance scattering and absorption of solar radiation. They also produce brighter clouds that are less efficient at releasing precipitation. These in turn lead to large reductions in the amount of solar irradiance reaching Earth's surface, a corresponding increase in solar heating of the atmosphere, changes in the atmospheric temperature structure, suppression of rainfall, and less efficient removal of pollutants. These aerosol effects can lead to a weaker hydrological cycle, which connects directly to availability and quality of fresh water, a major environmental issue of the 21st century.
TL;DR: This light-driven process results in a colloid with distinctive optical properties that directly relate to the nanoprism shape of the particles, which could be useful in developing multicolor diagnostic labels on the basis of nanoparticle composition and size but also of shape.
Abstract: A photoinduced method for converting large quantities of silver nanospheres into triangular nanoprisms is reported. The photo-process has been characterized by time-dependent ultraviolet-visible spectroscopy and transmission electron microscopy, allowing for the observation of several key intermediates in and characteristics of the conversion process. This light-driven process results in a colloid with distinctive optical properties that directly relate to the nanoprism shape of the particles. Theoretical calculations coupled with experimental observations allow for the assignment of the nanoprism plasmon bands and for the first identification of two distinct quadrupole plasmon resonances for a nanoparticle. Unlike the spherical particles they are derived from that Rayleigh light-scatter in the blue, these nanoprisms exhibit scattering in the red, which could be useful in developing multicolor diagnostic labels on the basis not only of nanoparticle composition and size but also of shape.
TL;DR: The facile assembly of key electronic device elements from well-defined nanoscale building blocks may represent a step toward a "bottom-up" paradigm for electronics manufacturing.
Abstract: Because semiconductor nanowires can transport electrons and holes, they could function as building blocks for nanoscale electronics assembled without the need for complex and costly fabrication facilities. Boron- and phosphorous-doped silicon nanowires were used as building blocks to assemble three types of semiconductor nanodevices. Passive diode structures consisting of crossed p- and n-type nanowires exhibit rectifying transport similar to planar p-n junctions. Active bipolar transistors, consisting of heavily and lightly n-doped nanowires crossing a common p-type wire base, exhibit common base and emitter current gains as large as 0.94 and 16, respectively. In addition, p- and n-type nanowires have been used to assemble complementary inverter-like structures. The facile assembly of key electronic device elements from well-defined nanoscale building blocks may represent a step toward a "bottom-up" paradigm for electronics manufacturing.
TL;DR: It is found that drug resistance is associated with the reactivation of BCR-ABL signal transduction in all cases examined and a strategy for identifying inhibitors of STI-571 resistance is suggested.
Abstract: Clinical studies with the Abl tyrosine kinase inhibitor STI-571 in chronic myeloid leukemia demonstrate that many patients with advanced stage disease respond initially but then relapse. Through biochemical and molecular analysis of clinical material, we find that drug resistance is associated with the reactivation of BCR-ABL signal transduction in all cases examined. In six of nine patients, resistance was associated with a single amino acid substitution in a threonine residue of the Abl kinase domain known to form a critical hydrogen bond with the drug. This substitution of threonine with isoleucine was sufficient to confer STI-571 resistance in a reconstitution experiment. In three patients, resistance was associated with progressive BCR-ABL gene amplification. These studies provide evidence that genetically complex cancers retain dependence on an initial oncogenic event and suggest a strategy for identifying inhibitors of STI-571 resistance.
TL;DR: Using bioinformatics and cDNA cloning, this work found 15 new miRNA genes in C. elegans that express small transcripts that vary in abundance during larval development, and three of them have apparent homologs in mammals and/or insects.
Abstract: The lin-4 and let-7 antisense RNAs are temporal regulators that control the timing of developmental events in Caenorhabditis elegans by inhibiting translation of target mRNAs. let-7 RNA is conserved among bilaterian animals, suggesting that this class of small RNAs [microRNAs (miRNAs)] is evolutionarily ancient. Using bioinformatics and cDNA cloning, we found 15 new miRNA genes in C. elegans. Several of these genes express small transcripts that vary in abundance during C. elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse.
TL;DR: Two genes encode ubiquitin ligases that are potential drug targets for the treatment of muscle atrophy, and mice deficient in either MAFbx orMuRF1 were found to be resistant to atrophy.
Abstract: Skeletal muscle adapts to decreases in activity and load by undergoing atrophy. To identify candidate molecular mediators of muscle atrophy, we performed transcript profiling. Although many genes were up-regulated in a single rat model of atrophy, only a small subset was universal in all atrophy models. Two of these genes encode ubiquitin ligases: Muscle RING Finger 1 (MuRF1), and a gene we designate Muscle Atrophy F-box (MAFbx), the latter being a member of the SCF family of E3 ubiquitin ligases. Overexpression of MAFbx in myotubes produced atrophy, whereas mice deficient in either MAFbx or MuRF1 were found to be resistant to atrophy. These proteins are potential drug targets for the treatment of muscle atrophy.
TL;DR: These distinctive in vivo 3D-matrix adhesions differ in structure, localization, and function from classically described in vitro adhesion, and as such they may be more biologically relevant to living organisms.
Abstract: Adhesions between fibroblastic cells and extracellular matrix have been studied extensively in vitro, but little is known about their in vivo counterparts. Here, we characterized the composition and function of adhesions in three-dimensional (3D) matrices derived from tissues or cell culture. "3D-matrix adhesions" differ from focal and fibrillar adhesions characterized on 2D substrates in their content of alpha5beta1 and alphavbeta3 integrins, paxillin, other cytoskeletal components, and tyrosine phosphorylation of focal adhesion kinase (FAK). Relative to 2D substrates, 3D-matrix interactions also display enhanced cell biological activities and narrowed integrin usage. These distinctive in vivo 3D-matrix adhesions differ in structure, localization, and function from classically described in vitro adhesions, and as such they may be more biologically relevant to living organisms.
TL;DR: In Drosophila melanogaster a developmentally regulated precursor RNA is cleaved by an RNA interference-like mechanism to produce mature let-7 stRNA, which regulates developmental timing in Caenorhabditis elegans and probably in other bilateral animals.
Abstract: The 21-nucleotide small temporal RNA (stRNA) let-7 regulates developmental timing in Caenorhabditis elegans and probably in other bilateral animals We present in vivo and in vitro evidence that in Drosophila melanogaster a developmentally regulated precursor RNA is cleaved by an RNA interference-like mechanism to produce mature let-7 stRNA Targeted destruction in cultured human cells of the messenger RNA encoding the enzyme Dicer, which acts in the RNA interference pathway, leads to accumulation of the let-7 precursor Thus, the RNA interference and stRNA pathways intersect Both pathways require the RNA-processing enzyme Dicer to produce the active small-RNA component that represses gene expression