bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Analyses of Oral Polio Vaccine Samples
Authors: Poinar Hendrik , Kuch Melanie , Pääbo Svante
Published: July 2002

It has been suggested that the human immunodeficiency virus (HIV), and thus the acquired immunodeficiency syndrome (AIDS) it causes, was inadvertently introduced to humans by the use of an oral polio vaccine (OPV) during a vaccination campaign launched by the Wistar Institute, Philadelphia, PA, USA, in the Belgian Congo in 1958 and 1959. The “OPV/AIDS hypothesis” suggests that the OPV used in this campaign was produced in chimpanzee kidney epithelial cell cultures rather than in monkey kidney cell cultures, as stated by H. Koprowski and co-workers, who produced the OPV. If chimpanzee cells were indeed used, this would lend support to the OPV/AIDS hypothesis, since chimpanzees harbor a simian immunodeficiency virus, widely accepted to be the origin of HIV-1. We analyzed several early OPV pools and found no evidence for the presence of chimpanzee DNA; by contrast, monkey DNA is present.
Commensal Host-Bacterial Relationships in the Gut
Authors: Hooper Lora V. , Gordon Jeffrey I.
Published: July 2002

One potential outcome of the adaptive coevolution of humans and bacteria is the development of commensal relationships, where neither partner is harmed, or symbiotic relationships, where unique metabolic traits or other benefits are provided. Our gastrointestinal tract is colonized by a vast community of symbionts and commensals that have important effects on immune function, nutrient processing, and a broad range of other host activities. The current genomic revolution offers an unprecedented opportunity to identify the molecular foundations of these relationships so that we can understand how they contribute to our normal physiology and how they can be exploited to develop new therapeutic strategies.
The Role of
Drosophila
Mushroom Body Signaling in Olfactory Memory
Authors: McGuire Sean E. , Le Phuong T. , Davis Ronald L.
Published: July 2002

The mushroom bodies of the
Drosophila
brain are important for olfactory learning and memory. To investigate the requirement for mushroom body signaling during the different phases of memory processing, we transiently inactivated neurotransmission through this region of the brain by expressing a temperature-sensitive allele of the
shibire
dynamin guanosine triphosphatase, which is required for synaptic transmission. Inactivation of mushroom body signaling through α/β neurons during different phases of memory processing revealed a requirement for mushroom body signaling during memory retrieval, but not during acquisition or consolidation.
Spin Ice State in Frustrated Magnetic Pyrochlore Materials
Authors: Bramwell Steven T. , Gingras Michel J. P.
Published: July 2002

A frustrated system is one whose symmetry precludes the possibility that every pairwise interaction (“bond”) in the system can be satisfied at the same time. Such systems are common in all areas of physical and biological science. In the most extreme cases, they can have a disordered ground state with “macroscopic” degeneracy; that is, one that comprises a huge number of equivalent states of the same energy. Pauling's description of the low-temperature proton disorder in water ice was perhaps the first recognition of this phenomenon and remains the paradigm. In recent years, a new class of magnetic substance has been characterized, in which the disorder of the magnetic moments at low temperatures is precisely analogous to the proton disorder in water ice. These substances, known as spin ice materials, are perhaps the “cleanest” examples of such highly frustrated systems yet discovered. They offer an unparalleled opportunity for the study of frustration in magnetic systems at both an experimental and a theoretical level. This article describes the essential physics of spin ice, as it is currently understood, and identifies new avenues for future research on related materials and models.
ATR and ATRIP: Partners in Checkpoint Signaling
Authors: Cortez David , Guntuku Saritha , Qin Jun , Elledge Stephen J.
Published: July 2002

The checkpoint kinases ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3 related) transduce genomic stress signals to halt cell cycle progression and promote DNA repair. We report the identification of an ATR-interacting protein (ATRIP) that is phosphorylated by ATR, regulates ATR expression, and is an essential component of the DNA damage checkpoint pathway. ATR and ATRIP both localize to intranuclear foci after DNA damage or inhibition of replication. Deletion of ATR mediated by the Cre recombinase caused the loss of ATR and ATRIP expression, loss of DNA damage checkpoint responses, and cell death. Therefore, ATR is essential for the viability of human somatic cells. Small interfering RNA directed against ATRIP caused the loss of both ATRIP and ATR expression and the loss of checkpoint responses to DNA damage. Thus, ATRIP and ATR are mutually dependent partners in cell cycle checkpoint signaling pathways.
Total Synthesis of Ciguatoxin CTX3C
Authors: Hirama Masahiro , Oishi Tohru , Uehara Hisatoshi , Inoue Masayuki , Maruyama Megumi , Oguri Hiroki , Satake Masayuki
Published: July 2002

More than 20,000 people suffer annually from ciguatera seafood poisoning in subtropical and tropical regions. The extremely low content of the causative neurotoxins, designated as ciguatoxins, in fish has hampered the isolation, detailed biological studies, and preparation of anti-ciguatoxin antibodies for detecting these toxins. The large (3 nanometers long) and complicated molecular structure of ciguatoxins has impeded chemists from completing their total synthesis. Our highly convergent strategic approach featuring the chemoselective ring-closing metathesis reaction as a key tactic has enabled the total synthesis of ciguatoxin CTX3C, which will provide a practical supply for further studies.
Mineral Surface Control of Organic Carbon in Black Shale
Authors: Kennedy Martin J. , Pevear David R. , Hill Ronald J.
Published: July 2002

We show that 85% of variation in total organic carbon can be explained by mineral surface area in a black shale deposit from two locations in the late Cretaceous Western Interior Seaway, United States. This relation suggests that, as in modern marine sediments, adsorption of carbon compounds onto clay mineral surfaces played a fundamental role in the burial and preservation of organic carbon. Our data also provide evidence for organic matter within the smectite interlayer. This association implies that organic carbon sequestration in a representative oil-prone black shale facies may be more closely related to patterns of continental weathering and clay mineralogy than to ocean water chemistry or marine productivity.
Flow and Storage in Groundwater Systems
Authors: Alley William M. , Healy Richard W. , LaBaugh James W. , Reilly Thomas E.
Published: July 2002

The dynamic nature of groundwater is not readily apparent, except where discharge is focused at springs or where recharge enters sinkholes. Yet groundwater flow and storage are continually changing in response to human and climatic stresses. Wise development of groundwater resources requires a more complete understanding of these changes in flow and storage and of their effects on the terrestrial environment and on numerous surface-water features and their biota.
Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics
Authors: Murphy William J. , Eizirik Eduardo , O'Brien Stephen J. , Madsen Ole , Scally Mark , Douady Christophe J. , Teeling Emma , Ryder Oliver A. , Stanhope Michael J. , de Jong Wilfried W. , Springer Mark S.
Published: July 2002

Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy of interordinal relationships, including the position of the root. The latter is critical for understanding the early biogeographic history of placentals. We investigated placental phylogeny using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set. Interordinal relationships are almost entirely resolved. The basal split is between Afrotheria and other placentals, at about 103 million years, and may be accounted for by the separation of South America and Africa in the Cretaceous. Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana).
Outbreak of Poliomyelitis in Hispaniola Associated with Circulating Type 1 Vaccine-Derived Poliovirus
Authors: Kew Olen , Morris-Glasgow Victoria , Landaverde Mauricio , Burns Cara , Shaw Jing , Garib Zacarı́as , André Jean , Blackman Elizabeth , Freeman C. Jason , Jorba Jaume , Sutter Roland , Tambini Gina , Venczel Linda , Pedreira Cristina , Laender Fernando , Shimizu Hiroyuki , Yoneyama Tetsuo , Miyamura Tatsuo , van der Avoort Harrie , Oberste M. Steven , Kilpatrick David , Cochi Stephen , Pallansch Mark , de Quadros Ciro
Published: July 2002

An outbreak of paralytic poliomyelitis occurred in the Dominican Republic (13 confirmed cases) and Haiti (8 confirmed cases, including 2 fatal cases) during 2000–2001. All but one of the patients were either unvaccinated or incompletely vaccinated children, and cases occurred in communities with very low (7 to 40%) rates of coverage with oral poliovirus vaccine (OPV). The outbreak was associated with the circulation of a derivative of the type 1 OPV strain, probably originating from a single OPV dose given in 1998–1999. The vaccine-derived poliovirus associated with the outbreak had biological properties indistinguishable from those of wild poliovirus.
Colorectal Cancer in Mice Genetically Deficient in the Mucin Muc2
Authors: Velcich Anna , Yang WanCai , Heyer Joerg , Fragale Alessandra , Nicholas Courtney , Viani Stephanie , Kucherlapati Raju , Lipkin Martin , Yang Kan , Augenlicht Leonard
Published: July 2002

The gastrointestinal tract is lined by a layer of mucus comprised of highly glycosylated proteins called mucins. To evaluate the importance of mucin in intestinal carcinogenesis, we constructed mice genetically deficient in Muc2, the most abundant secreted gastrointestinal mucin. Muc2
−/−
mice displayed aberrant intestinal crypt morphology and altered cell maturation and migration. Most notably, the mice frequently developed adenomas in the small intestine that progressed to invasive adenocarcinoma, as well as rectal tumors. Thus, Muc2 is involved in the suppression of colorectal cancer.
Hybrid Nanorod-Polymer Solar Cells
Authors: Huynh Wendy U. , Dittmer Janke J. , Alivisatos A. Paul
Published: July 2002

We demonstrate that semiconductor nanorods can be used to fabricate readily processed and efficient hybrid solar cells together with polymers. By controlling nanorod length, we can change the distance on which electrons are transported directly through the thin film device. Tuning the band gap by altering the nanorod radius enabled us to optimize the overlap between the absorption spectrum of the cell and the solar emission spectrum. A photovoltaic device consisting of 7-nanometer by 60-nanometer CdSe nanorods and the conjugated polymer poly-3(hexylthiophene) was assembled from solution with an external quantum efficiency of over 54% and a monochromatic power conversion efficiency of 6.9% under 0.1 milliwatt per square centimeter illumination at 515 nanometers. Under Air Mass (A.M.) 1.5 Global solar conditions, we obtained a power conversion efficiency of 1.7%.
Measuring Spacetime: From the Big Bang to Black Holes
Authors: Tegmark Max
Published: July 2002

Space is not a boring static stage on which events unfold over time, but a dynamic entity with curvature, fluctuations, and a rich life of its own. Spectacular measurements of the cosmic microwave background, gravitational lensing, type Ia supernovae, large-scale structure, spectra of the Lyman α forest, stellar dynamics, and x-ray binaries are probing the properties of spacetime over 22 orders of magnitude in scale. Current measurements are consistent with an infinite flat everlasting universe containing about 30% cold dark matter, 65% dark energy, and at least two distinct populations of black holes.
Cell Cycle Control of DNA Replication
Authors: Stillman Bruce
Published: July 2002

The initiation of DNA replication in eukaryotic cells is a highly regulated process that leads to the duplication of the genetic information for the next cell generation. This requires the ordered assembly of many proteins at the origins of DNA replication to form a competent, pre-replicative chromosomal state. In addition to this competent complex, at least two cell cycle regulated protein kinase pathways are required to affect a transition to a post-replicative chromosomal state. Protein kinases required to establish mitosis prevent re-replication of the DNA. As cells exit mitosis, the cell cycle is reset, allowing the establishment of a new, competent replication state.
Geographic Distribution of Endangered Species in the United States
Authors: Dobson A. P. , Rodriguez J. P. , Roberts W. M. , Wilcove D. S.
Published: July 2002

Geographic distribution data for endangered species in the United States were used to locate “hot spots” of threatened biodiversity. The hot spots for different species groups rarely overlap, except where anthropogenic activities reduce natural habitat in centers of endemism. Conserving endangered plant species maximizes the incidental protection of all other species groups. The presence of endangered birds and herptiles, however, provides a more sensitive indication of overall endangered biodiversity within any region. The amount of land that needs to be managed to protect currently endangered and threatened species in the United States is a relatively small proportion of the land mass.
In Search of Africa's Forgotten Forest Elephant
Authors: Tangley Laura
Published: July 2002

Say “African elephant,” and one pictures a vast savanna, where the largest land mammal mingles with lions, giraffes, and gazelles. In fact, about one-third of the continent's elephants live in its dark, often inaccessible rain forests, where the animals are difficult for researchers to spot, let alone study. But now, new research is bringing these huge, elusive creatures out of the shadows and shedding light on their role in rain-forest ecology and their social behavior.
Requirement of the DEAD-Box Protein Ded1p for Messenger RNA Translation
Authors: Chuang Ray-Yuan , Weaver Paul L. , Liu Zheng , Chang Tien-Hsien
Published: July 2002

The
DED1
gene, which encodes a putative RNA helicase, has been implicated in nuclear pre-messenger RNA splicing in the yeast
Saccharomyces cerevisiae
. It is shown here by genetic and biochemical analysis that translation, rather than splicing, is severely impaired in two newly isolated
ded1
conditional mutants. Preliminary evidence suggests that the protein Ded1p may be required for the initiation step of translation, as is the distinct DEAD-box protein, eukaryotic initiation factor 4A (eIF4A). The
DED1
gene could be functionally replaced by a mouse homolog,
PL10
, which suggests that the function of Ded1p in translation is evolutionarily conserved.
‘Real-Time’ Oceanography Adapts to Sea Changes
Authors: Nadis Steve
Published: July 2002

Oceanographic experiments have traditionally been vast data-collecting expeditions with limited flexibility, but last summer, a project in the Haro Strait near Vancouver Island proved out an approach to oceanography that allows researchers to change their plans in midstream—or midocean. Called adaptive sampling, it is based on feedback between instruments positioned in the water and computer modeling onshore. Primed with new data each day, the computer suggested where the next day's efforts should be focused.
Biology: Fractal Geometry Gets the Measure of Life's Scales
Authors: Williams Nigel
Published: July 2002

Living organisms come in a vast range of sizes--from microbes to whales, they span at least 21 orders of magnitude. For more than a century, biologists have been trying to figure out how body size and physiology are related, but so far they have come up with a big conundrum. Now, on
page 122
, a team of researchers reports a new mathematical model--a unique combination of the dynamics of energy transport and the mathematics of fractal geometry--that may finally help solve the puzzle.
An Occurrence of Metastable Cristobalite in High-Pressure Garnet Granulite
Authors: Darling Robert S. , Chou I-Ming , Bodnar Robert J.
Published: July 2002

High-pressure (0.8 gigapascals) granulite facies garnet from Gore Mountain, New York, hosts multiple solid inclusions containing the low-pressure silica polymorph cristobalite along with albite and minor ilmenite. Identification of cristobalite is based on Raman spectra, electron microprobe analysis, and microthermometric measurements on the α/β phase transformation. The cristobalite plus albite inclusions may have originated as small, trapped samples of hydrous sodium-aluminum-siliceous melt. Diffusive loss of water from these inclusions under isothermal, isochoric conditions may have resulted in a large enough internal pressure decrease to promote the metastable crystallization of cristobalite.
Phosphorylation of the Translational Repressor PHAS-I by the Mammalian Target of Rapamycin
Authors: Brunn Gregory J. , Hudson Christine C. , Sekulić Aleksandar , Williams Josie M. , Hosoi Hajime , Houghton Peter J. , Lawrence John C. , Abraham Robert T.
Published: July 2002

The immunosuppressant rapamycin interferes with G
1
-phase progression in lymphoid and other cell types by inhibiting the function of the mammalian target of rapamycin (mTOR). mTOR was determined to be a terminal kinase in a signaling pathway that couples mitogenic stimulation to the phosphorylation of the eukaryotic initiation factor (eIF)-4E–binding protein, PHAS-I. The rapamycin-sensitive protein kinase activity of mTOR was required for phosphorylation of PHAS-I in insulin-stimulated human embryonic kidney cells. mTOR phosphorylated PHAS-I on serine and threonine residues in vitro, and these modifications inhibited the binding of PHAS-I to eIF-4E. These studies define a role for mTOR in translational control and offer further insights into the mechanism whereby rapamycin inhibits G
1
-phase progression in mammalian cells.
Activation of Heat Shock Transcription Factor 3 by c-Myb in the Absence of Cellular Stress
Authors: Kanei-Ishii Chie , Tanikawa Jun , Nakai Akira , Morimoto Richard I. , Ishii Shunsuke
Published: July 2002

In vertebrates, the presence of multiple heat shock transcription factors (HSFs) indicates that these factors may be regulated by distinct stress signals. HSF3 was specifically activated in unstressed proliferating cells by direct binding to the c-
myb
proto-oncogene product (c-Myb). These factors formed a complex through their DNA binding domains that stimulated the nuclear entry and formation of the transcriptionally active trimer of HSF3. Because c-Myb participates in cellular proliferation, this regulatory pathway may provide a link between cellular proliferation and the stress response.
Evidence for Large-Scale Eddy-Driven Gyres in the North Atlantic
Authors: Lozier M. Susan
Published: July 2002

Analysis of a recent climatological database for the North Atlantic has detailed an extensive large-scale recirculation system in the intermediate waters of the North Atlantic basin. The pressure fields that define this recirculation, coupled with the potential vorticity fields associated with the recirculating flow, provide observational evidence for basin-scale eddy-driven flow in the global ocean. The recirculations are intimately tied to the waters carried southward by the Deep Western Boundary Current and are therefore likely to affect the distribution of climatic anomalies in the North Atlantic.
The Isotopic Oxygen Nightglow as Viewed from Mauna Kea
Authors: Slanger T. G. , Huestis D. L. , Osterbrock D. E. , Fulbright J. P.
Published: July 2002

Optical spectra of the terrestrial nightglow in the 520- to 900-nanometer region, as measured by the W. M. Keck telescope on Mauna Kea in Hawaii and the associated high-resolution echelle spectrograph, showed many bands belonging to the important O
2
(
b-X
) Atmospheric Band emission system. Previous ground-based measurements have shown only a single band, from the lowest vibrational level of the emitting state. Of particular interest is the fact that at the 762-nanometer position of the
b-X
0-0 band, where earlier studies have shown only absorption features, these results showed both absorption at the
16
O
16
O line positions and well-resolved emission at the positions of many of the
18
O
16
O and
17
O
16
O lines. These findings show that substantial advances can be made in understanding atmospheric emission phenomena by the use of astronomical tools.
Enhancement of Protein Crystal Nucleation by Critical Density Fluctuations
Authors: Wolde Pieter Rein ten , Frenkel Daan
Published: July 2002

Numerical simulations of homogeneous crystal nucleation with a model for globular proteins with short-range attractive interactions showed that the presence of a metastable fluid-fluid critical point drastically changes the pathway for the formation of a crystal nucleus. Close to this critical point, the free-energy barrier for crystal nucleation is strongly reduced and hence, the crystal nucleation rate increases by many orders of magnitude. Because the location of the metastable critical point can be controlled by changing the composition of the solvent, the present work suggests a systematic approach to promote protein crystallization.
Aggregation of Huntingtin in Neuronal Intranuclear Inclusions and Dystrophic Neurites in Brain
Authors: DiFiglia Marian , Sapp Ellen , Chase Kathryn O. , Davies Stephen W. , Bates Gillian P. , Vonsattel J. P. , Aronin Neil
Published: July 2002

The cause of neurodegeneration in Huntington's disease (HD) is unknown. Patients with HD have an expanded NH
2
-terminal polyglutamine region in huntingtin. An NH
2
-terminal fragment of mutant huntingtin was localized to neuronal intranuclear inclusions (NIIs) and dystrophic neurites (DNs) in the HD cortex and striatum, which are affected in HD, and polyglutamine length influenced the extent of huntingtin accumulation in these structures. Ubiquitin was also found in NIIs and DNs, which suggests that abnormal huntingtin is targeted for proteolysis but is resistant to removal. The aggregation of mutant huntingtin may be part of the pathogenic mechanism in HD.
De Novo Protein Design: Fully Automated Sequence Selection
Authors: Dahiyat Bassil I. , Mayo Stephen L.
Published: July 2002

The first fully automated design and experimental validation of a novel sequence for an entire protein is described. A computational design algorithm based on physical chemical potential functions and stereochemical constraints was used to screen a combinatorial library of 1.9 × 10
27
possible amino acid sequences for compatibility with the design target, a ββα protein motif based on the polypeptide backbone structure of a zinc finger domain. A BLAST search shows that the designed sequence, full sequence design 1 (FSD-1), has very low identity to any known protein sequence. The solution structure of FSD-1 was solved by nuclear magnetic resonance spectroscopy and indicates that FSD-1 forms a compact well-ordered structure, which is in excellent agreement with the design target structure. This result demonstrates that computational methods can perform the immense combinatorial search required for protein design, and it suggests that an unbiased and quantitative algorithm can be used in various structural contexts.
Time-Domain Holographic Digital Memory
Authors: Shen Xiao A. , Nguyen An-Dien , Perry John W. , Huestis David L. , Kachru Ravinder
Published: July 2002

An optical storage technique based on time-domain holography for the rapid recording and readout of page-formatted digital data is demonstrated. Storage of 356 kilobits of data was achieved at a single spatial location in a rare-earth–doped crystal. The digital data were recorded and accurately retrieved at a peak rate of 300 megabits per second without the use of error-correcting codes. The system's raw bit error rate is about 10
−
7
. This low bit error rate was achieved by a detection scheme for extraction of binary data. These results have implications for dynamic optical memory.
The Response of Global Terrestrial Ecosystems to Interannual Temperature Variability
Authors: Braswell B. H. , Schimel D. S. , Linder E. , Moore B.
Published: July 2002

Measurements of atmospheric carbon dioxide and satellite-derived measurements of temperature and the vegetation index were used to investigate relationships among climate, carbon dioxide, and ecosystems. At the global scale, lagged correlations between temperature and carbon dioxide growth rate were found, indicating modulation by biogeochemical feedbacks. Spatial analysis of the temperature and vegetation index data suggests that the global correlations are a composite of individualistic responses of different ecosystems. The existence of biome-specific time scales of response implies that changes in global ecosystem distributions could indirectly alter the relationships between climate and carbon storage.
Role of Vesicle-Associated Syntaxin 5 in the Assembly of Pre-Golgi Intermediates
Authors: Rowe Tony , Dascher Christiane , Bannykh Sergei , Plutner Helen , Balch William E.
Published: July 2002

Syntaxins are thought to function during vesicular transport as receptors on the target membrane and to contribute to the specificity of membrane docking and fusion by interacting with vesicle-associated receptors. Here, syntaxin 5 (Syn5) was shown to be an integral component of endoplasmic reticulum–derived transport vesicles. This pool, but not the target, Golgi-associated Syn5 pool, was essential for the assembly of vesicular-tubular pre-Golgi intermediates and the delivery of cargo to the Golgi. The requirement for vesicle-associated Syn5 in transport suggests a reevaluation of the basis for operation of the early secretory pathway.
Target-Specific Expression of Presynaptic Mossy Fiber Plasticity
Authors: Maccaferri Gianmaria , Tóth Katalin , McBain Chris J.
Published: July 2002

Mossy fiber synaptic transmission at hippocampal CA3 pyramidal cells and interneurons was compared in rat brain slices to determine whether mossy terminals are functionally equivalent. Tetanic stimulation of mossy fibers induced long-term potentiation in pyramidal neurons but was either without effect or it induced depression at synapses onto interneurons. Unlike transmission onto pyramidal neurons, transmission onto interneurons was not potentiated after adenosine 3′,5′-monophosphate (cAMP) activation. Furthermore, metabotropic glutamate receptor depression of transmission onto interneurons did not involve cAMP-dependent pathways. Thus, synaptic terminals arising from a common afferent pathway do not function as a single compartment but are specialized, depending on their postsynaptic target.
Dependence of Germinal Center B Cells on Expression of CD21/CD35 for Survival
Authors: Fischer Michael B. , Goerg Siegfried , Shen LiMing , Prodeus Andrey P. , Goodnow Christopher C. , Kelsoe Garnett , Carroll Michael C.
Published: July 2002

Affinity-driven selection of B lymphocytes within germinal centers is critical for the development of high-affinity memory cells and host protection. To investigate the role of the CD21/CD35 coreceptor in B cell competition for follicular retention and survival within the germinal center, either Cr2
+
or Cr2
null
lysozyme-specific transgenic B cells were adoptively transferred into normal mice immunized with duck (DEL) or turkey (TEL) lysozyme, which bind with different affinities. In mice injected with high-affinity turkey lysozyme, Cr2
null
B cells responded by follicular retention; however, they could not survive within germinal centers. This suggests that CD21 provides a signal independent of antigen that is required for survival of B cells in the germinal center.
Ribonuclease P Protein Structure: Evolutionary Origins in the Translational Apparatus
Authors: Stams Travis , Niranjanakumari S. , Fierke Carol A. , Christianson David W.
Published: July 2002

The crystal structure of
Bacillus subtilis
ribonuclease P protein is reported at 2.6 angstroms resolution. This protein binds to ribonuclease P RNA to form a ribonucleoprotein holoenzyme with optimal catalytic activity. Mutagenesis and biochemical data indicate that an unusual left-handed βαβ crossover connection and a large central cleft in the protein form conserved RNA binding sites; a metal binding loop may comprise a third RNA binding site. The unusual topology is partly shared with ribosomal protein S5 and the ribosomal translocase elongation factor G, which suggests evolution from a common RNA binding ancestor in the primordial translational apparatus.
Water as a Dense Icelike Component in Silicate Glasses
Authors: Richet P. , Polian A.
Published: July 2002

Density and Brillouin-scattering measurements of hydrous andesite glasses at ambient conditions showed that dissolved water has a concentration-independent partial molar volume of 12 ± 0.5 cubic centimeters per mole and a bulk modulus of 18 ± 3 gigapascals. Dissolved as hydroxyl ions or as molecular water, water has volume properties similar to those of ice VII, the densest form of ice. These properties point to hydrogen bonding as an important factor in water dissolution, and they indicate that changes of water speciation are driven by the entropy and not by the volume of the system. Water in a concentration greater than 1 percent by weight also causes a marked decrease of the shear modulus of the glass.
Self-Organized Growth of Three- Dimensional Quantum-Dot Crystals with fcc-Like Stacking and a Tunable Lattice Constant
Authors: Springholz G. , Holy V. , Pinczolits M. , Bauer G.
Published: July 2002

The self-organization of pyramidal PbSe islands that spontaneously form during strained-layer epitaxial growth of PbSe/Pb
1−

x

Eu

x

Te (
x
= 0.05 to 0.1) superlattices results in the formation of three-dimensional quantum-dot crystals. In these crystals, the dots are arranged in a trigonal lattice with a face-centered cubic (fcc)–like A-B-C-A-B-C vertical stacking sequence. The lattice constant of the dot crystal can be tuned continuously by changing the superlattice period. As shown by theoretical calculations, the elastic anisotropy in these artificial dot crystals acts in a manner similar to that of the directed chemical bonds of crystalline solids. The narrow size distribution and excellent control of the dot arrangement may be advantageous for optoelectronic device applications.
Sum Rules and Interlayer Conductivity of High-
T
c
Cuprates
Authors: Basov D. N. , Woods S. I. , Katz A. S. , Singley E. J. , Dynes R. C. , Xu M. , Hinks D. G. , Homes C. C. , Strongin M.
Published: July 2002

Analysis of the interlayer infrared conductivity of cuprate high–transition temperature superconductors reveals an anomalously large energy scale extending up to midinfrared frequencies that can be attributed to formation of the superconducting condensate. This unusual effect is observed in a va- riety of materials, including Tl
2
Ba
2
CuO
6+

x

, La
2−

x

Sr

x

CuO
4
, and YBa
2
Cu
3
O
6.6
, which show an incoherent interlayer response in the normal state. Midinfrared range condensation was examined in the context of sum rules that can be formulated for the complex conductivity. One possible interpretation of these experiments is in terms of a kinetic energy change associated with the superconducting transition.
An ~15,000-Year Record of El Niño-Driven Alluviation in Southwestern Ecuador
Authors: Rodbell Donald T. , Seltzer Geoffrey O. , Anderson David M. , Abbott Mark B. , Enfield David B. , Newman Jeremy H.
Published: July 2002

Debris flows have deposited inorganic laminae in an alpine lake that is 75 kilometers east of the Pacific Ocean, in Ecuador. These storm-induced events were dated by radiocarbon, and the age of laminae that are less than 200 years old matches the historic record of El Niño events. From about 15,000 to about 7000 calendar years before the present, the periodicity of clastic deposition is greater than or equal to 15 years; thereafter, there is a progressive increase in frequency to periodicities of 2 to 8.5 years. This is the modern El Niño periodicity, which was established about 5000 calendar years before the present. This may reflect the onset of a steeper zonal sea surface temperature gradient, which was driven by enhanced trade winds.
Quartzlike Carbon Dioxide: An Optically Nonlinear Extended Solid at High Pressures and Temperatures
Authors: Iota V. , Yoo C. S. , Cynn H.
Published: July 2002

An extended-solid phase, carbon dioxide phase V (CO
2
-V), was synthesized in a diamond anvil cell by laser heating the molecular orthorhombic phase, carbon dioxide phase III, above 40 gigapascals and 1800 kelvin. This new material can be quenched to ambient temperature above 1 gigapascal. The vibration spectrum of CO
2
-V is similar to that of the quartz polymorph of silicon dioxide, indicating that it is an extended covalent solid with carbon-oxygen single bonds. This material is also optically nonlinear, generating the second harmonic of a neodymium–yttrium-lithium-fluoride laser at a wavelength of 527 nanometers with a conversion efficiency that is near 0.1 percent.
An Adiabatic Quantum Electron Pump
Authors: Switkes M. , Marcus C. M. , Campman K. , Gossard A. C.
Published: July 2002

A quantum pumping mechanism that produces dc current or voltage in response to a cyclic deformation of the confining potential in an open quantum dot is reported. The voltage produced at zero current bias is sinusoidal in the phase difference between the two ac voltages deforming the potential and shows random fluctuations in amplitude and direction with small changes in external parameters such as magnetic field. The amplitude of the pumping response increases linearly with the frequency of the deformation. Dependencies of pumping on the strength of the deformations, temperature, and breaking of time-reversal symmetry were also investigated.
Net Primary Production of a Forest Ecosystem with Experimental CO
2
Enrichment
Authors: DeLucia Evan H. , Hamilton Jason G. , Naidu Shawna L. , Thomas Richard B. , Andrews Jeffrey A. , Finzi Adrien , Lavine Michael , Matamala Roser , Mohan Jacqueline E. , Hendrey George R. , Schlesinger William H.
Published: July 2002

The concentration of atmospheric carbon dioxide was increased by 200 microliters per liter in a forest plantation, where competition between organisms, resource limitations, and environmental stresses may modulate biotic responses. After 2 years the growth rate of the dominant pine trees increased by about 26 percent relative to trees under ambient conditions. Carbon dioxide enrichment also increased litterfall and fine-root increment. These changes increased the total net primary production by 25 percent. Such an increase in forest net primary production globally would fix about 50 percent of the anthropogenic carbon dioxide projected to be released into the atmosphere in the year 2050. The response of this young, rapidly growing forest to carbon dioxide may represent the upper limit for forest carbon sequestration.
Multiple Ink Nanolithography: Toward a Multiple-Pen Nano-Plotter
Authors: Hong Seunghun , Zhu Jin , Mirkin Chad A.
Published: July 2002

The formation of intricate nanostructures will require the ability to maintain surface registry during several patterning steps. A scanning probe method, dip-pen nanolithography (DPN), can be used to pattern monolayers of different organic molecules down to a 5-nanometer separation. An “overwriting” capability of DPN allows one nanostructure to be generated and the areas surrounding that nanostructure to be filled in with a second type of “ink.”
Organic-Inorganic Hybrid Materials as Semiconducting Channels in Thin-Film Field-Effect Transistors
Authors: Kagan C. R. , Mitzi D. B. , Dimitrakopoulos C. D.
Published: July 2002

Organic-inorganic hybrid materials promise both the superior carrier mobility of inorganic semiconductors and the processability of organic materials. A thin-film field-effect transistor having an organic-inorganic hybrid material as the semiconducting channel was demonstrated. Hybrids based on the perovskite structure crystallize from solution to form oriented molecular-scale composites of alternating organic and inorganic sheets. Spin-coated thin films of the semiconducting perovskite (C
6
H
5
C
2
H
4
NH
3
)
2
SnI
4
form the conducting channel, with field-effect mobilities of 0.6 square centimeters per volt-second and current modulation greater than 10
4
. Molecular engineering of the organic and inorganic components of the hybrids is expected to further improve device performance for low-cost thin-film transistors.
Hydrogen Storage in Single-Walled Carbon Nanotubes at Room Temperature
Authors: Liu C. , Fan Y. Y. , Liu M. , Cong H. T. , Cheng H. M. , Dresselhaus M. S.
Published: July 2002

Masses of single-walled carbon nanotubes (SWNTs) with a large mean diameter of about 1.85 nanometers, synthesized by a semicontinuous hydrogen arc discharge method, were employed for hydrogen adsorption experiments in their as-prepared and pretreated states. A hydrogen storage capacity of 4.2 weight percent, or a hydrogen to carbon atom ratio of 0.52, was achieved reproducibly at room temperature under a modestly high pressure (about 10 megapascal) for a SWNT sample of about 500 milligram weight that was soaked in hydrochloric acid and then heat-treated in vacuum. Moreover, 78.3 percent of the adsorbed hydrogen (3.3 weight percent) could be released under ambient pressure at room temperature, while the release of the residual stored hydrogen (0.9 weight percent) required some heating of the sample. Because the SWNTs can be easily produced and show reproducible and modestly high hydrogen uptake at room temperature, they show promise as an effective hydrogen storage material.
Three-Dimensional Atomic-Scale Imaging of Impurity Segregation to Line Defects
Authors: Blavette D. , Cadel E. , Fraczkiewicz A. , Menand A.
Published: July 2002

Clouds of impurity atoms near line defects are believed to affect the plastic deformation of alloys. Three-dimensional atom probe techniques were used to image these so-called Cottrell atmospheres directly. Ordered iron-aluminum alloys (40 atomic percent aluminum) doped with boron (400 atomic parts per million) were investigated on an atomic scale along the 〈001〉 direction. A boron enrichment was observed in the vicinity of an 〈001〉 edge dislocation. The enriched region appeared as a three-dimensional pipe 5 nanometers in diameter, tangent to the dislocation line. The dislocation was found to be boron-enriched by a factor of 50 (2 atomic percent) relative to the bulk. The local boron enrichment is accompanied by a strong aluminum depletion of 20 atomic percent.
A Whole-Genome Assembly of
Drosophila
Authors: Myers Eugene W. , Sutton Granger G. , Delcher Art L. , Dew Ian M. , Fasulo Dan P. , Flanigan Michael J. , Kravitz Saul A. , Mobarry Clark M. , Reinert Knut H. J. , Remington Karin A. , Anson Eric L. , Bolanos Randall A. , Chou Hui-Hsien , Jordan Catherine M. , Halpern Aaron L. , Lonardi Stefano , Beasley Ellen M. , Brandon Rhonda C. , Chen Lin , Dunn Patrick J. , Lai Zhongwu , Liang Yong , Nusskern Deborah R. , Zhan Ming , Zhang Qing , Zheng Xiangqun , Rubin Gerald M. , Adams Mark D. , Venter J. Craig
Published: July 2002

We report on the quality of a whole-genome assembly of
Drosophila melanogaster
and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99.99% without manual curation. As such, this initial reconstruction of the
Drosophila
sequence should be of substantial value to the scientific community.
TAF-Containing and TAF-Independent Forms of Transcriptionally Active TBP in Vivo
Authors: Kuras Laurent , Kosa Peter , Mencia Mario , Struhl Kevin
Published: July 2002

Transcriptional activity in yeast strongly correlates with promoter occupancy by general factors such as TATA binding protein (TBP), TFIIA, and TFIIB, but not with occupancy by TBP-associated factors (TAFs). Thus, TBP exists in at least two transcriptionally active forms in vivo. The TAF-containing form corresponds to the TFIID complex, whereas the form lacking TAFs corresponds to TBP itself or to some other TBP complex. Heat shock treatment altered the relative utilization of these TBP forms, with TFIID being favored. Promoter-specific variations in the association of these distinct forms of TBP may explain why only some yeast genes require TFIID for transcriptional activity in vivo.
Distinct Roles of CONSTANS Target Genes in Reproductive Development of
Arabidopsis
Authors: Samach Alon , Onouchi Hitoshi , Gold Scott E. , Ditta Gary S. , Schwarz-Sommer Zsuzsanna , Yanofsky Martin F. , Coupland George
Published: July 2002

In plants, flowering is triggered by endogenous and environmental signals. CONSTANS (CO) promotes flowering of
Arabidopsis
in response to day length. Four early target genes of CO were identified using a steroid-inducible version of the protein. Two of these genes,
SUPPRESSOR OF OVEREXPRESSION OF CO 1
(
SOC1
) and
FLOWERING LOCUS T
(
FT
), are required for CO to promote flowering; the others are involved in proline or ethylene biosynthesis. The
SOC1
and
FT
genes are also regulated by a second flowering-time pathway that acts independently of CO. Thus, early target genes of CO define common components of distinct flowering-time pathways.
Resetting of Circadian Time in Peripheral Tissues by Glucocorticoid Signaling
Authors: Balsalobre Aurélio , Brown Steven A. , Marcacci Lysiane , Tronche François , Kellendonk Christoph , Reichardt Holger M. , Schütz Günther , Schibler Ueli
Published: July 2002

In mammals, circadian oscillators reside not only in the suprachiasmatic nucleus of the brain, which harbors the central pacemaker, but also in most peripheral tissues. Here, we show that the glucocorticoid hormone analog dexamethasone induces circadian gene expression in cultured rat-1 fibroblasts and transiently changes the phase of circadian gene expression in liver, kidney, and heart. However, dexamethasone does not affect cyclic gene expression in neurons of the suprachiasmatic nucleus. This enabled us to establish an apparent phase-shift response curve specifically for peripheral clocks in intact animals. In contrast to the central clock, circadian oscillators in peripheral tissues appear to remain responsive to phase resetting throughout the day.
A Bacterial Toxin That Controls Cell Cycle Progression as a Deoxyribonuclease I-Like Protein
Authors: Lara-Tejero Maria , Galán Jorge E.
Published: July 2002

Many bacterial pathogens encode a multisubunit toxin, termed cytolethal distending toxin (CDT), that induces cell cycle arrest, cytoplasm distention, and, eventually, chromatin fragmentation and cell death. In one such pathogen,
Campylobacter jejuni
, one of the subunits of this toxin, CdtB, was shown to exhibit features of type I deoxyribonucleases. Transient expression of this subunit in cultured cells caused marked chromatin disruption. Microinjection of low amounts of CdtB induced cytoplasmic distention and cell cycle arrest. CdtB mutants with substitutions in residues equivalent to those required for catalysis or magnesium binding in type I deoxyribonucleases did not cause chromatin disruption. CDT holotoxin containing these mutant forms of CdtB did not induce morphological changes or cell cycle arrest.
First-Principles Theory for the H + H
2
O, D
2
O Reactions
Authors: Zhang Dong H. , Collins Michael A. , Lee Soo-Y.
Published: July 2002

A full quantum dynamical study of the reactions of a hydrogen atom with water, on an accurate ab initio potential energy surface, is reported. The theoretical results are compared with available experimental data for the exchange and abstraction reactions in H + D
2
O and H + H
2
O. Clear agreement between theory and experiment is revealed for available thermal rate coefficients and the effects of vibrational excitation of the reactants. The excellent agreement between experiment and theory on integral cross sections for the exchange reaction is unprecedented beyond atom-diatom reactions. However, the experimental cross sections for abstraction are larger than the theoretical values by more than a factor of 10. Further experiments are required to resolve this.
Powering an Inorganic Nanodevice with a Biomolecular Motor
Authors: Soong Ricky K. , Bachand George D. , Neves Hercules P. , Olkhovets Anatoli G. , Craighead Harold G. , Montemagno Carlo D.
Published: July 2002

Biomolecular motors such as F
1
–adenosine triphosphate synthase (F
1
-ATPase) and myosin are similar in size, and they generate forces compatible with currently producible nanoengineered structures. We have engineered individual biomolecular motors and nanoscale inorganic systems, and we describe their integration in a hybrid nanomechanical device powered by a biomolecular motor. The device consisted of three components: an engineered substrate, an F
1
-ATPase biomolecular motor, and fabricated nanopropellers. Rotation of the nanopropeller was initiated with 2 mM adenosine triphosphate and inhibited by sodium azide.
A Global Geometric Framework for Nonlinear Dimensionality Reduction
Authors: Tenenbaum Joshua B. , Silva Vin de , Langford John C.
Published: July 2002

Scientists working with large volumes of high-dimensional data, such as global climate patterns, stellar spectra, or human gene distributions, regularly confront the problem of dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. The human brain confronts the same problem in everyday perception, extracting from its high-dimensional sensory inputs—30,000 auditory nerve fibers or 10
6
optic nerve fibers—a manageably small number of perceptually relevant features. Here we describe an approach to solving dimensionality reduction problems that uses easily measured local metric information to learn the underlying global geometry of a data set. Unlike classical techniques such as principal component analysis (PCA) and multidimensional scaling (MDS), our approach is capable of discovering the nonlinear degrees of freedom that underlie complex natural observations, such as human handwriting or images of a face under different viewing conditions. In contrast to previous algorithms for nonlinear dimensionality reduction, ours efficiently computes a globally optimal solution, and, for an important class of data manifolds, is guaranteed to converge asymptotically to the true structure.
Insulin Resistance and a Diabetes Mellitus-Like Syndrome in Mice Lacking the Protein Kinase Akt2 (PKBβ)
Authors: Cho Han , Mu James , Kim Jason K. , Thorvaldsen Joanne L. , Chu Qingwei , Crenshaw E. Bryan , Kaestner Klaus H. , Bartolomei Marisa S. , Shulman Gerald I. , Birnbaum Morris J.
Published: July 2002

Glucose homeostasis depends on insulin responsiveness in target tissues, most importantly, muscle and liver. The critical initial steps in insulin action include phosphorylation of scaffolding proteins and activation of phosphatidylinositol 3-kinase. These early events lead to activation of the serine-threonine protein kinase Akt, also known as protein kinase B. We show that mice deficient in Akt2 are impaired in the ability of insulin to lower blood glucose because of defects in the action of the hormone on liver and skeletal muscle. These data establish
Akt2
as an essential gene in the maintenance of normal glucose homeostasis.