bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth of high T
c superconducting thin films using molecular beam epitaxy techniques
Authors: Webb C. , Weng S.-L. , Eckstein J. N. , Missert N. , Char K. , Schlom D. G. , Hellman E. S. , Beasley M. R. , Kapitulnik A. , Harris J. S.
Published: July 2002

Thin films of the high-temperature superconductor DyBa2Cu3O7−x have been grown on SrTiO3 substrates using molecular beam epitaxy techniques. Reflection high-energy electron diffraction patterns observed during deposition indicate incomplete oxidation of copper and growth of oriented metallic copper microcrystals in a matrix of amorphous barium and dysprosium oxides. After post-growth anneal the films exhibited sharp superconducting transitions with zero resistance observed as high as 89 K and critical current densities of 4.8×105 A/cm2 at 4.2 K and 3.9×104 A/cm2 at 77 K.
Anomalous oxidation rate of silicon implanted with very high doses of arsenic
Authors: Choi Seong S. , Numan M. Z. , Chu W. K. , Irene E. A.
Published: July 2002

An anomalous increase in oxidation rate was observed during low-temperature thermal oxidation of very high dose (5×1016, 7×1016/cm2) As+ ion implanted silicon. Oxidation of Si at 850 °C was faster than that at 950 °C. This effect was attributed to the snowplowing of arsenic (which was more pronounced at lower temperatures) creating a glassy Si-O-As layer near the Si-SiO2 interface.
Superconductivity and resputtering effects in rf sputtered YBa2Cu3O7−x thin films
Authors: Shah S. I. , Carcia P. F.
Published: July 2002

Superconducting stoichiometric YBa2Cu3O7−x films have been grown by rf sputtering of a single bulk material target in an Ar+10% O2 sputtering atmosphere on a variety of substrates. Films on SrTiO3 substrates exhibited the best post-annealing superconducting properties with the critical onset temperature of 90 K and zero resistance at 67 K. The maximum current density for these samples was 1×105 A/cm2 at 4.2 K. An extensive loss of film underneath the target was observed during the growth of these films which can be attributed to resputtering due to oxygen anion or energetic neutral particle bombardment of the substrate.
Gettering of gold and copper with implanted carbon in silicon
Authors: Wong H. , Cheung N. W. , Chu P. K.
Published: July 2002

The gettering effects of implanted carbon for Au and Cu are studied and compared with the gettering effects of implanted oxygen, nitrogen, BF2, neon, and argon. It is demonstrated that implanted carbon forms strong gettering centers in silicon which are an order of magnitude more effective than implanted oxygen. The amount of gettered Au by implanted carbon is found to be approximately linear with dose in the range from 1015 to 1016 cm−2 and no thermal instability is observed with annealing up to 12 h at 1000 °C. It is found that the gettering effect of carbon is reduced by the addition of oxygen. This indicates that the strong gettering effect of carbon is not due to carbon-enhanced oxygen precipitation but a phenomenon of its own.
Enzyme plus light therapy to repair DNA damage in ultraviolet-B-irradiated human skin
Authors: Stege Helger , Roza Len , Vink Arie A. , Grewe Markus , Ruzicka Thomas , Grether-Beck Susanne , Krutmann Jean
Published: July 2002

Ultraviolet-B (UVB) (290–320 nm) radiation-induced cyclobutane pyrimidine dimers within the DNA of epidermal cells are detrimental to human health by causing mutations and immunosuppressive effects that presumably contribute to photocarcinogenesis. Conventional photoprotection by sunscreens is exclusively prophylactic in nature and of no value once DNA damage has occurred. In this paper, we have therefore assessed whether it is possible to repair UVB radiation-induced DNA damage through topical application of the DNA-repair enzyme photolyase, derived fromAnacystis nidulans, that specifically converts cyclobutane dimers into their original DNA structure after exposure to photoreactivating light. When a dose of UVB radiation sufficient to induce erythema was administered to the skin of healthy subjects, significant numbers of dimers were formed within epidermal cells. Topical application of photolyase-containing liposomes to UVB-irradiated skin and subsequent exposure to photoreactivating light decreased the number of UVB radiation-induced dimers by 40–45%. No reduction was observed if the liposomes were not filled with photolyase or if photoreactivating exposure preceded the application of filled liposomes. The UVB dose administered resulted in suppression of intercellular adhesion molecule-1 (ICAM-1), a molecule required for immunity and inflammatory events in the epidermis. In addition, in subjects hypersensitive to nickel sulfate, elicitation of the hypersensitivity reaction in irradiated skin areas was prevented. Photolyase-induced dimer repair completely prevented these UVB radiation-induced immunosuppressive effects as well as erythema and sunburn-cell formation. These studies demonstrate that topical application of photolyase is effective in dimer reversal and thereby leads to immunoprotection.
Optimizing bioconversion pathways through systems analysis and metabolic engineering
Authors: Stafford Daniel E. , Yanagimachi Kurt S. , Lessard Philip A. , Rijhwani Sushil K. , Sinskey Anthony J. , Stephanopoulos Gregory
Published: July 2002

We demonstrate a general approach for metabolic engineering of biocatalytic systems comprising the uses of a chemostat for strain improvement and radioisotopic tracers for the quantification of pathway fluxes. Flux determination allows the identification of target pathways for modification as validated by subsequent overexpression of the corresponding gene. We demonstrate this method in the indene bioconversion network ofRhodococcusmodified for the overproduction of 1,2-indandiol, a key precursor for the AIDS drug Crixivan.
The
Caenorhabditis elegans
maternal-effect sterile proteins, MES-2, MES-3, and MES-6, are associated in a complex in embryos
Authors: Xu Lei , Fong Youyi , Strome Susan
Published: July 2002

The
Caenorhabditis elegans
maternal-effect sterile genes,
mes-2
,
mes-3
,
mes-4
, and
mes-6
,
encode nuclear proteins that are essential for germ-line development.
They are thought to be involved in a common process because their
mutant phenotypes are similar. MES-2 and MES-6 are homologs of Enhancer
of zeste and extra sex combs, both members of the Polycomb group of
chromatin regulators in insects and vertebrates. MES-3 is a novel
protein, and MES-4 is a SET-domain protein. To investigate whether the
MES proteins interact and likely function as a complex, we performed
biochemical analyses on
C. elegans
embryo extracts.
Results of immunoprecipitation experiments indicate that MES-2, MES-3,
and MES-6 are associated in a complex and that MES-4 is not associated
with this complex. Based on
in vitro
binding assays,
MES-2 and MES-6 interact directly, via the amino terminal portion of
MES-2. Sucrose density gradient fractionation and gel filtration
chromatography were performed to determine the Stokes radius and
sedimentation coefficient of the MES-2/MES-3/MES-6 complex. Based
on those two values, we estimate that the molecular mass of the complex
is ≈255 kDa, close to the sum of the three known components. Our
results suggest that the two
C. elegans
Polycomb group
homologs (MES-2 and MES-6) associate with a novel partner (MES-3) to
regulate germ-line development in
C. elegans
.
Genome evolution of wild barley (
Hordeum spontaneum
) by
BARE
-1 retrotransposon dynamics in response to sharp microclimatic divergence
Authors: Kalendar Ruslan , Tanskanen Jaakko , Immonen Sirkka , Nevo Eviatar , Schulman Alan H.
Published: July 2002

The replicative spread of retrotransposons in the genome creates new insertional polymorphisms, increasing retrotransposon numbers and potentially both their share of the genome and genome size. The
BARE
-1 retrotransposon constitutes a major, dispersed, active component of
Hordeum
genomes, and
BARE
-1 number is positively correlated with genome size. We have examined genome size and
BARE
-1 insertion patterns and number in wild barley,
Hordeum spontaneum
, in Evolution Canyon, Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates.
BARE
-1 has been sufficiently active for its insertional pattern to resolve individuals in a way consonant with their ecogeographical distribution in the canyon and to distinguish them from provenances outside the canyon. On both slopes, but especially on the drier south-facing slope, a simultaneous increase in the
BARE
-1 copy number and a decrease in the relative number lost through recombination, as measured by the abundance of solo long terminal repeats, appear to have driven the
BARE
-1 share of the genome upward with the height and dryness of the slope. The lower recombinational loss would favor maintenance of more full-length copies, enhancing the ability of the
BARE
-1 family to contribute to genome size growth. These local data are consistent with regional trends for
BARE
-1 in
H. spontaneum
across Israel and therefore may reflect adaptive selection for increasing genome size through retrotransposon activity.
IL-7 is critical for homeostatic proliferation and survival of naïve T cells
Authors: Tan Joyce T. , Dudl Eric , LeRoy Eric , Murray Richard , Sprent Jonathan , Weinberg Kenneth I. , Surh Charles D.
Published: July 2002

In T cell-deficient conditions, naïve T cells undergo spontaneous “homeostatic” proliferation in response to contact with self-MHC/peptide ligands. With the aid of anin vitrosystem, we show here that homeostatic proliferation is also cytokine-dependent. The cytokines IL-4, IL-7, and IL-15 enhanced homeostatic proliferation of naïve T cellsin vitro. Of these cytokines, only IL-7 was found to be critical; thus, naïve T cells underwent homeostatic proliferation in IL-4−and IL-15−hosts but proliferated minimally in IL-7−hosts. In addition to homeostatic proliferation, the prolonged survival of naïve T cells requires IL-7. Thus, naïve T cells disappeared gradually over a 1-month period upon adoptive transfer into IL-7−hosts. These findings indicate that naïve T cells depend on IL-7 for survival and homeostatic proliferation.
Diverse roles of the tumor necrosis factor family member TRANCE in skeletal physiology revealed by TRANCE deficiency and partial rescue by a lymphocyte-expressed TRANCE transgene
Authors: Kim Nacksung , Odgren Paul R. , Kim Dong-Ku , Marks Sandy C. , Choi Yongwon
Published: July 2002

Tumor necrosis factor-related, activation-induced cytokine (TRANCE), a tumor necrosis factor family member, mediates survival of dendritic cells in the immune system and is required for osteoclast differentiation and activation in the skeleton. We report the skeletal phenotype of TRANCE-deficient mice and its rescue by the TRANCE transgene specifically expressed in lymphocytes. TRANCE-deficient mice showed severe osteopetrosis, with no osteoclasts, marrow spaces, or tooth eruption, and exhibited profound growth retardation at several skeletal sites, including the limbs, skull, and vertebrae. These mice had marked chondrodysplasia, with thick, irregular growth plates and a relative increase in hypertrophic chondrocytes. Transgenic overexpression of TRANCE in lymphocytes of TRANCE-deficient mice rescued osteoclast development in two locations in growing long bones: excavation of marrow cavities permitting hematopoiesis in the marrow spaces, and remodeling of osteopetrotic woven bone in the shafts of long bones into histologically normal lamellar bone. However, osteoclasts in these mice failed to appear at the chondroosseous junction and the metaphyseal periosteum of long bones, nor were they present in tooth eruption pathways. These defects resulted in sclerotic metaphyses with persistence of club-shaped long bones and unerupted teeth, and the growth plate defects were largely unimproved by the TRANCE transgene. Thus, TRANCE-mediated regulation of the skeleton is complex, and impacts chondrocyte differentiation and osteoclast formation in a manner that likely requires local delivery of TRANCE.
Predicting the local dynamics of epizootic rabies among raccoons in the United States
Authors: Childs James E. , Curns Aaron T. , Dey Meghan E. , Real Leslie A. , Feinstein Lisa , Bjørnstad Ottar N. , Krebs John W.
Published: July 2002

Mathematical models have been developed to explore the population dynamics of viral diseases among wildlife. However, assessing the predictions stemming from these models with wildlife databases adequate in size and temporal duration is uncommon. An epizootic of raccoon rabies that began in the mid-Atlantic region of the United States in the late 1970s has developed into one of the largest and most extensive in the history of wildlife rabies. We analyzed the dynamics of local epizootics at the county level by examining a database spanning more than 20 years and including 35,387 rabid raccoons. The size, number, and periodicity of rabies epizootics among raccoons were compared with predictions derived from a susceptible, exposed, infectious, and recovered model of raccoon rabies [Coyne, J., Smith, G. & McAllister, F. E. (1989)Am. J. Vet. Res.50, 2148–2154]. After our methods for defining epizootics were applied to solutions of the model, the time series revealed recurrent epizootics in some counties, with a median first epizootic period of 48 months. Successive epizootics declined in size and the epizootic period progressively decreased. Our reanalysis of the model predicted the initial-epizootic period of 4–5 years, with a progressive dampening of epizootic size and progressive decrease in epizootic period. The best quantitative agreement between data and model assumed low levels of immunity (1–5%) within raccoon populations, suggesting that raccoons develop little or no rabies immune class. These results encourage the use of data obtained through wildlife surveillance in assessing and refining epidemic models for wildlife diseases.
Directed polar secretion of protease from single cells of
Vibrio cholerae
via the type II secretion pathway
Authors: Scott Maria E. , Dossani Zain Y. , Sandkvist Maria
Published: July 2002

Bacteria have long been thought of as little more than sacks of homogeneously distributed enzymes. However, recent cytological studies indicate that bacteria are compartmentalized with proteins involved in processes such as cell division, motility, chemotaxis, and development located at distinct sites. We have used the green fluorescent protein as a reporter to determine the cellular distribution of the
e
xtracellular
p
rotein
s
ecretion (
eps
)-encoded type II secretion complex responsible for extracellular secretion of cholera toxin and hemagglutinin/protease in
Vibrio cholerae.
Real-time monitoring of green fluorescent protein fused to EpsM in living cells indicated that, like the single polar flagellum, the Eps complex is located at the old pole after cell division. Eps-dependent protease secretion was also visualized in single cells by fluorescence microscopy by using intramolecularly quenched casein. This analysis demonstrated that active protease secretion is focused at the poles and colocalizes with the site of the polar Eps apparatus. These results suggest that the type II secretion complex is responsible for directed delivery of virulence factors during cholera pathogenesis.
Ryanodine sensitizes the cardiac Ca
2+
release channel (ryanodine receptor isoform 2) to Ca
2+
activation and dissociates as the channel is closed by Ca
2+
depletion
Authors: Du Guo Guang , Guo Xinghua , Khanna Vijay K. , MacLennan David H.
Published: July 2002

In single-channel recordings, the rabbit cardiac Ca
2+
release channel (RyR2) is converted to a fully open subconductance state with about 50% of full conductance by micromolar concentrations of ryanodine. At +30 mV, corresponding to a luminal to cytoplasmic cation current, the probability of opening (
P
o
) of ryanodine-modified channels was only marginally altered at pCa 10 (pCa = −log
10
Ca concentration). However, at −30 mV, the
P
o
was highly sensitive to Ca
2+
added to the cis (cytoplasmic) side and, at pCa 10, was reduced to less than 0.27. The EC
50
value for channel opening was about pCa 8. No significant Ca
2+
inactivation was observed for ryanodine-modified channels at either −30 mV or +30 mV. The opening of unmodified Ca
2+
channels is Ca
2+
sensitive, with an EC
50
value of about pCa 6 (two orders of magnitude less sensitive than ryanodine-modified channels) and IC
50
values of pCa 2.2 at −30 mV and 2.5 at +30 mV. Mg
2+
decreased the
P
o
of ryanodine-modified channels at low Ca
2+
concentrations at both −30 and +30 mV. Caffeine, ATP, and ruthenium red were modulators of the
P
o
of ryanodine-modified channels. In a [
3
H]ryanodine binding assay, [
3
H]ryanodine dissociation from the high-affinity binding site was found to be Ca
2+
sensitive, with an IC
50
of pCa 7.1. High concentrations of unlabeled ryanodine prevented [
3
H]ryanodine dissociation, but ruthenium red accelerated dissociation. These results suggest that ryanodine sensitizes Ca
2+
activation of the Ca
2+
release channel and desensitizes Ca
2+
inactivation through an allosteric interaction. [
3
H]Ryanodine dissociates from the high-affinity site when the channel is closed by removal of Ca
2+
, implying that high-affinity ryanodine and Ca
2+
binding sites are linked through either short- or long-range interactions, probably involving conformational changes.
The LIM domain gene
LMO4
inhibits differentiation of mammary epithelial cells
in vitro
and is overexpressed in breast cancer
Authors: Visvader Jane E. , Venter Deon , Hahm Kyungmin , Santamaria Margaret , Sum Eleanor Y. M. , O'Reilly Lorraine , White David , Williams Rachael , Armes Jane , Lindeman Geoffrey J.
Published: July 2002

LMO4 belongs to a family of LIM-only transcriptional
regulators, the first two members of which are oncoproteins in
acute T cell leukemia. We have explored a role for LMO4, initially
described as a human breast tumor autoantigen, in developing mammary
epithelium and breast oncogenesis.
Lmo4
was expressed
predominantly in the lobuloalveoli of the mammary gland during
pregnancy. Consistent with a role in proliferation, forced expression
of this gene inhibited differentiation of mammary epithelial cells.
Overexpression of
LMO4
mRNA was observed in 5 of 10
human breast cancer cell lines. Moreover,
in situ
hybridization analysis of 177 primary invasive breast carcinomas
revealed overexpression of
LMO4
in 56% of
specimens. Immunohistochemistry confirmed overexpression in a high
percentage (62%) of tumors. These studies imply a role for
LMO4
in maintaining proliferation of mammary epithelium
and suggest that deregulation of this gene may contribute to breast
tumorigenesis.
The herpes simplex virus major regulatory protein ICP4 blocks apoptosis induced by the virus or by hyperthermia.
Authors: Leopardi R , Roizman B
Published: July 2002

Cells infected with herpes simplex virus 1 (HSV-1) undergo productive or latent infection without exhibiting features characteristic of apoptosis. In this report, we show that HSV-1 induces apoptosis but has evolved a function that blocks apoptosis induced by infection as well as by other means. Specifically, (i) Vero cells infected with a HSV-1 mutant deleted in the regulatory gene alpha 4 (that encodes repressor and transactivating functions), but not those infected with wild-type HSV-1(F), exhibit cytoplasmic blebbing, chromatin condensation, and fragmented DNA detected as a ladder in agarose gels or by labeling free DNA ends with terminal transferase; (ii) Vero cells infected with wild-type HSV-1(F) or cells expressing the alpha 4 gene and infected with the alpha 4- virus did not exhibit apoptosis; (iii) fragmentation of cellular DNA was observed in Vero cells that were mock-infected or infected with the alpha 4- virus and maintained at 39.5 degrees C, but not in cells infected with wild-type virus and maintained at the same temperature. Wild-type strains of HSV-1 with limited extrahuman passages, such as HSV-1 (F), carry a temperature-sensitive lesion in the alpha 4 gene and at 39.5 degrees C only alpha genes are expressed. These results indicate that the product of the alpha 4 gene is able to suppress apoptosis induced by the virus as well by other means.
RETRACTED: The pfmdr1 gene of Plasmodium falciparum confers cellular resistance to antimalarial drugs in yeast cells.
Authors: Ruetz S , Delling U , Brault M , Schurr E , Gros P
Published: July 2002

The exact role of the pfmdr1 gene in the emergence of drug resistance in the malarial parasite Plasmodium falciparum remains controversial. pfmdr1 is a member of the ATP binding cassette (ABC) superfamily of transporters that includes the mammalian P-glycoprotein family. We have introduced wild-type and mutant variants of the pfmdr1 gene in the yeast Saccharomyces cerevisiae and have analyzed the effect of pfmdr1 expression on cellular resistance to quinoline-containing antimalarial drugs. Yeast transformants expressing either wild-type or a mutant variant of mouse P-glycoprotein were also analyzed. Dose-response studies showed that expression of wild-type pfmdr1 causes cellular resistance to quinine, quinacrine, mefloquine, and halofantrine in yeast cells. Using quinacrine as substrate, we observed that increased resistance to this drug in pfmdr1 transformants was associated with decreased cellular accumulation and a concomitant increase in drug release from preloaded cells. The introduction of amino acid polymorphisms in TM11 of Pgh-1 (pfmdr1 product) associated with drug resistance in certain field isolates of P. falciparum abolished the capacity of this protein to confer drug resistance. Thus, these findings suggest that Pgh-1 may act as a drug transporter in a manner similar to mammalian P-glycoprotein and that sequence variants associated with drug-resistance pfmdr1 alleles behave as loss of function mutations.
NO hyperpolarizes pulmonary artery smooth muscle cells and decreases the intracellular Ca2+ concentration by activating voltage-gated K+ channels.
Authors: Yuan X J , Tod M L , Rubin L J , Blaustein M P
Published: July 2002

NO causes pulmonary vasodilation in patients with pulmonary hypertension. In pulmonary arterial smooth muscle cells, the activity of voltage-gated K+ (Kv) channels controls resting membrane potential. In turn, membrane potential is an important regulator of the intracellular free calcium concentration ([Ca2+]i) and pulmonary vascular tone. We used patch clamp methods to determine whether the NO-induced pulmonary vasodilation is mediated by activation of Kv channels. Quantitative fluorescence microscopy was employed to test the effect of NO on the depolarization-induced rise in [Ca2+]i. Blockade of Kv channels by 4-aminopyridine (5 mM) depolarized pulmonary artery myocytes to threshold for initiation of Ca2+ action potentials, and thereby increased [Ca2+]i. NO (approximately 3 microM) and the NO-generating compound sodium nitroprusside (5-10 microM) opened Kv channels in rat pulmonary artery smooth muscle cells. The enhanced K+ currents then hyperpolarized the cells, and blocked Ca(2+)-dependent action potentials, thereby preventing the evoked increases in [Ca2+]i. Nitroprusside also increased the probability of Kv channel opening in excised, outside-out membrane patches. This raises the possibility that NO may act either directly on the channel protein or on a closely associated molecule rather than via soluble guanylate cyclase. In isolated pulmonary arteries, 4-aminopyridine significantly inhibited NO-induced relaxation. We conclude that NO promotes the opening of Kv channels in pulmonary arterial smooth muscle cells. The resulting membrane hyperpolarization, which lowers [Ca2+]i, is apparently one of the mechanisms by which NO induces pulmonary vasodilation.
Mass extinctions and supernova explosions.
Authors: Crutzen P J , Brühl C
Published: July 2002

In a recent contribution to this journal Ellis and Schramm [Ellis, J. & Schramm, D. N. (1995) Proc. Natl. Acad. Sci. USA 92, 235-238] claim that supernova explosions can cause massive biological extinctions as a result of strongly enhanced stratospheric NOx (NO + NO2) production by accompanying galactic cosmic rays. They suggested that these NOx productions which would last over several centuries and occur once every few hundred million years would result in ozone depletions of about 95%, leading to vastly increased levels of biologically damaging solar ultraviolet radiation. Our detailed model calculations show, however, substantially smaller ozone depletions ranging from at most 60% at high latitudes to below 20% at the equator.
Genetic ablation of parietal cells in transgenic mice: a new model for analyzing cell lineage relationships in the gastric mucosa.
Authors: Canfield V , West A B , Goldenring J R , Levenson R
Published: July 2002

The gastric mucosa of mammalian stomach contains several differentiated cell types specialized for the secretion of acid, digestive enzymes, mucus, and hormones. Understanding whether each of these cell lineages is derived from a common stem cell has been a challenging problem. We have used a genetic approach to analyze the ontogeny of progenitor cells within mouse stomach. Herpes simplex virus 1 thymidine kinase was targeted to parietal cells within the gastric mucosa of transgenic mice, and parietal cells were ablated by treatment of animals with the antiherpetic drug ganciclovir. Ganciclovir treatment produced complete ablation of parietal cells, dissolution of gastric glands, and loss of chief and mucus-producing cells. Termination of drug treatment led to the reemergence of all major gastric epithelial cell types and restoration of glandular architecture. Our results imply the existence of a pluripotent stem cell for the gastric mucosa. Parietal cell ablation should provide a model for analyzing cell lineage relationships within the stomach as well as mechanisms underlying gastric injury and repair.
Vestibular navigation directed by the slope of terrain.
Authors: Moghaddam M , Kaminsky Y L , Zahalka A , Bures J
Published: July 2002

Slope of terrain is an important orienting gradient affecting the goal-directed locomotion of animals. Its significance was assessed in experiment 1 by training rats to find in darkness a feeder on the top of a low cone (80-cm base, 0- to 4-cm high). A computerized infrared tracking system monitoring the rat's position in darkness showed that the path length on the cone surface was inversely proportional to cone height. A device allowing continuous generation of slope-guided locomotion was used in experiment 2. This device consists of a 1-m arena, the floor of which can be supported at a point corresponding to the position of one of three equidistant feeders located 17 cm from its center. The arena is inclined by the locomotion of the rat to a plane passing through the elevated (2- or 4-cm) feeder, the rat's center of gravity, and a point at the edge of the arena resting on the floor. The multitude of such planes generated by the rat's locomotion forms the surface of a virtual cone, the top of which is formed by the feeder. Additional path (difference between distance traveled and shortest distance of the animal from the goal at the onset of inclination) is inversely related to the incline of the arena and is a sensitive measure of performance in this type of vestibular navigation.
Intermediate-term earthquake prediction.
Authors: Keilis-Borok V I
Published: July 2002

An earthquake of magnitude M and linear source dimension L(M) is preceded within a few years by certain patterns of seismicity in the magnitude range down to about (M - 3) in an area of linear dimension about 5L-10L. Prediction algorithms based on such patterns may allow one to predict approximately 80% of strong earthquakes with alarms occupying altogether 20-30% of the time-space considered. An area of alarm can be narrowed down to 2L-3L when observations include lower magnitudes, down to about (M - 4). In spite of their limited accuracy, such predictions open a possibility to prevent considerable damage. The following findings may provide for further development of prediction methods: (i) long-range correlations in fault system dynamics and accordingly large size of the areas over which different observed fields could be averaged and analyzed jointly, (ii) specific symptoms of an approaching strong earthquake, (iii) the partial similarity of these symptoms worldwide, (iv) the fact that some of them are not Earth specific: we probably encountered in seismicity the symptoms of instability common for a wide class of nonlinear systems.
A novel transporter involved in cobalt uptake
Authors: Komeda Hidenobu , Kobayashi Michihiko , Shimizu Sakayu
Published: July 2002

Cobalt is an essential component of a low molecular-mass nitrile hydratase (L-NHase) from
Rhodococcus rhodochrous
J1. We have found a new gene,
nhlF
, in the DNA region sandwiched between
nhlBA
encoding L-NHase and
amdA
encoding amidase, which are involved in the degradation of nitriles. The product of
nhlF
, NhlF, shows a significant sequence similarity with those of
hoxN
from
Alcaligenes eutrophus
,
hupN
from
Bradyrhizobium japonicum
,
nixA
from
Helicobacter pylori
, and
ureH
from
Bacillus
sp., which are considered to be involved in nickel uptake into these cells. Sequence and hydropathy plot analyses have shown that NhlF encodes a 352-amino acid (aa) protein with eight hydrophobic putative membrane-spanning domains.
nhlF
expression in
R. rhodochrous
ATCC 12674 and
Escherichia coli
JM109 confers uptake of
57
Co in their cells, but not of
63
Ni. The expression of both
nhlF
and
nhlBA
in
R. rhodochrous
ATCC 12674 exhibited higher NHase activity than
nhlBA
expression. These findings together with the inhibitory effect by uncouplers (CCCP and SF6847) for the cobalt uptake suggest that NhlF mediates the cobalt transport into the cell energy-dependently finally to provide L-NHase.
Genome scan for teratogen-induced clefting susceptibility loci in the mouse: Evidence of both allelic and locus heterogeneity distinguishing cleft lip and cleft palate
Authors: Diehl Scott R. , Erickson Robert P.
Published: July 2002

Nonsyndromic clefting of the lip and palate in humans has a highly complex etiology, with both multiple genetic loci and exposure to teratogens influencing susceptibility. Previous studies using mouse models have examined only very small portions of the genome. Here we report the findings of a genome-wide search for susceptibility genes for teratogen-induced clefting in the AXB and BXA set of recombinant inbred mouse strains. We compare results obtained using phenytoin (which induces cleft lip) and 6-aminonicotinamide (which induces cleft palate). We use a new statistical approach based on logistic regression suitable for these categorical data to identify several chromosomal regions as possible locations of clefting susceptibility loci, and we review candidate genes located within each region. Because cleft lip and cleft palate do not frequently co-aggregate in human families and because these structures arise semi-independently during development, these disorders are usually considered to be distinct in etiology. Our data, however, implicate several of the same chromosomal regions for both forms of clefting when teratogen-induced. Furthermore, different parental strain alleles are usually associated with clefting of the lip versus that of the palate (i.e., allelic heterogeneity). Because several other chromosomal regions are associated with only one form of clefting, locus heterogeneity also appears to be involved. Our findings in this mouse model suggest several priority areas for evaluation in human epidemiological studies.
Accelerated evolution as a consequence of transitions to mutualism
Authors: Lutzoni François , Pagel Mark
Published: July 2002

Differential rates of nucleotide substitutions among taxa are a common observation in molecular phylogenetic studies, yet links between rates of DNA evolution and traits or behaviors of organisms have proved elusive. Likelihood ratio testing is used here for the first time to evaluate specific hypotheses that account for the induction of shifts in rates of DNA evolution. A molecular phylogenetic investigation of mutualist (lichen-forming fungi and fungi associated with liverworts) and nonmutualist fungi revealed four independent transitions to mutualism. We demonstrate a highly significant association between mutualism and increased rates of nucleotide substitutions in nuclear ribosomal DNA, and we demonstrate that a transition to mutualism preceded the rate acceleration of nuclear ribosomal DNA in these lineages. Our results suggest that the increased rate of evolution after the adoption of a mutualist lifestyle is generalized across the genome of these mutualist fungi.
Homeobox gene
Prx
3 expression in rodent brain and extraneural tissues
Authors: van Schaick Hermien S. A. , Smidt Marten P. , Rovescalli Alessandra Cecilia , Luijten Mirjam , van der Kleij Arno A. M. , Asoh Sadamitsu , Kozak Christine A. , Nirenberg Marshall , Burbach J. Peter H.
Published: July 2002

Different cDNA clones encoding a rat homeobox gene and the mouse homologue
OG-12
were cloned from adult rat brain and mouse embryo mRNA, respectively. The predicted amino acid sequences of the proteins belong to the paired-related subfamily of homeodomain proteins (Prx homeodomains). Hence, the gene was named
Prx3
and the mouse and rat genes are indicated as m
Prx3
and r
Prx3
, respectively. In the mouse as well as in the rat, the predicted Prx3 proteins share the homeodomain but have three different N termini, a 12-aa residue variation in the C terminus, and contain a 14-aa residue motif common to a subset of homeodomain proteins, termed the “aristaless domain.” Genetic mapping of
Prx3
in the mouse placed this gene on chromosome 3.
In situ
hybridization on whole mount 12.5-day-old mouse embryos and sections of rat embryos at 14.5 and 16.5 days postcoitum revealed marked neural expression in discrete regions in the lateral and medial geniculate complex, superior and inferior colliculus, the superficial gray layer of the superior colliculus, pontine reticular formation, and inferior olive. In rat and mouse embryos, nonneuronal structures around the oral cavity and in hip and shoulder regions also expressed the
Prx3
gene. In the adult rat brain,
Prx3
gene expression was restricted to thalamic, tectal, and brainstem structures that include relay nuclei of the visual and auditory systems as well as other ascending systems conveying somatosensory information.
Prx3
may have a role in specifying neural systems involved in processing somatosensory information, as well as in face and body structure formation.
11β-Hydroxysteroid dehydrogenase type 1 knockout mice show attenuated glucocorticoid-inducible responses and resist hyperglycemia on obesity or stress
Authors: Kotelevtsev Yuri , Holmes Megan C. , Burchell Ann , Houston Pamela M. , Schmoll Dieter , Jamieson Pauline , Best Ruth , Brown Roger , Edwards Christopher R. W. , Seckl Jonathan R. , Mullins John J.
Published: July 2002

Glucocorticoid hormones, acting via nuclear receptors, regulate many metabolic processes, including hepatic gluconeogenesis. It recently has been recognized that intracellular glucocorticoid concentrations are determined not only by plasma hormone levels, but also by intracellular 11β-hydroxysteroid dehydrogenases (11β-HSDs), which interconvert active corticosterone (cortisol in humans) and inert 11-dehydrocorticosterone (cortisone in humans). 11β-HSD type 2, a dehydrogenase, thus excludes glucocorticoids from otherwise nonselective mineralocorticoid receptors in the kidney. Recent data suggest the type 1 isozyme (11β-HSD-1) may function as an 11β-reductase, regenerating active glucocorticoids from circulating inert 11-keto forms in specific tissues, notably the liver. To examine the importance of this enzyme isoform
in vivo
, mice were produced with targeted disruption of the 11β-HSD-1 gene. These mice were unable to convert inert 11-dehydrocorticosterone to corticosterone
in vivo
. Despite compensatory adrenal hyperplasia and increased adrenal secretion of corticosterone, on starvation homozygous mutants had attenuated activation of the key hepatic gluconeogenic enzymes glucose-6-phosphatase and phosphoenolpyruvate carboxykinase, presumably, because of relative intrahepatic glucocorticoid deficiency. The 11β-HSD-1 −/− mice were found to resist hyperglycamia provoked by obesity or stress. Attenuation of hepatic 11β-HSD-1 may provide a novel approach to the regulation of gluconeogenesis.
A functional telomerase RNA swap
in vivo
reveals the importance of nontemplate RNA domains
Authors: Bhattacharyya Anamitra , Blackburn Elizabeth H.
Published: July 2002

The ribonucleoprotein (RNP) enzyme telomerase is required for replication of eukaryotic chromosomal termini. The RNA moiety of telomerase is essential for enzyme function and provides the template for telomeric DNA synthesis. However, the roles of its nontemplate domains have not been explored. Here we demonstrate that a novel interspecies telomerase RNA swap
in vivo
creates a functional but aberrant telomerase. Telomerase RNA from the ciliate
Glaucoma chattoni
was expressed in
Tetrahymena thermophila
cells. The telomerase RNAs from these two species have almost superimposable secondary structures. The template region base sequence is identical in the two RNAs, but elsewhere their sequences differ by 49%. This hybrid telomerase RNP was enzymatically active but added only short stretches of telomeric repeat tracts
in vivo
and
in vitro.
This new enzyme also had a strong, aberrant DNA cleavage activity
in vitro
. Thus, molecular interactions in the RNP involving nontemplate RNA domains affect specific aspects of telomerase enzyme function, raising the possibility that they may regulate telomerase activity.
Lucigenin luminescence as a measure of intracellular superoxide dismutase activity in
Escherichia coli
Authors: Liochev Stefan I. , Fridovich Irwin
Published: July 2002

Lucigenin and paraquat are similar in that each can be taken
into
Escherichia coli
and can then mediate O
2⨪
production by cycles of univalent reduction, to the corresponding
monocation radical, followed by autoxidation. Thus, both compounds
caused induction of enzymes that are regulated by the soxRS regulon.
The lucigenin cation radical has the added property of reacting with
O
2⨪
, in a radical–radical addition, to yield an unstable
dioxetane, whose decomposition yields light. Superoxide dismutases
(SOD), by decreasing [O
2⨪
], inhibit light production
and to the same degree inhibit other O
2⨪
-dependent reactions in
the cell. Lucigenin luminescence was used to show that the levels of
SOD in the parental strain provide ≈95% protection of all
O
2⨪
-sensitive targets in
E. coli
. This degree of
protection was so close to the limit of 100% that halving the parental
level of [SOD], or increasing it 5-fold, had only marginal effects on
the intensity of lucigenin-dependent luminescence.
Inositol hexakisphosphate stimulates non-Ca
2+
-mediated and primes Ca
2+
-mediated exocytosis of insulin by activation of protein kinase C
Authors: Efanov Alexandre M. , Zaitsev Sergei V. , Berggren Per-Olof
Published: July 2002

d
-
myo
-inositol 1,2,3,4,5,6-hexakisphosphate (InsP
6
), formed via complex pathways of inositol phosphate metabolism, composes the main bulk of inositol polyphosphates in the cell. Relatively little is known regarding possible biological functions for InsP
6
. We now show that InsP
6
can modulate insulin exocytosis in permeabilized insulin-secreting cells. Concentrations of InsP
6
above 20 μM stimulated insulin secretion at basal Ca
2+
-concentration (30 nM) and primed Ca
2+
-induced exocytosis (10 μM), both effects being due to activation of protein kinase C. Our results suggest that InsP
6
can play an important modulatory role in the regulation of processes such as exocytosis in insulin-secreting cells. The specific role for InsP
6
can then be to recruit secretory granules to the site of exocytosis.
Development of normal mice from metaphase I oocytes fertilized with primary spermatocytes
Authors: Ogura Atsuo , Suzuki Osamu , Tanemura Kentaro , Mochida Keiji , Kobayashi Yoshiro , Matsuda Junichiro
Published: July 2002

Primary spermatocytes are the male germ cells before meiosis I. To examine whether these 4n diploid cells are genetically competent to fertilize oocytes and support full embryo development, we introduced the nuclei of pachytene/diplotene spermatocytes into oocytes that were arrested in prophase I (germinal vesicle stage), metaphase I, or metaphase II (Met II). Both the paternal and maternal chromosomes then were allowed to undergo meiosis synchronously until Met II. In the first and second groups, the paternal and maternal chromosomes had intermingled to form a large Met II plate, which was then transferred into a fresh enucleated Met II oocyte. In the third group, the paternal Met II chromosomes were obtained by transferring spermatocyte nuclei into Met II oocytes twice. After activation of the Met II oocytes that were produced, those microfertilized at metaphase I showed the best developmental ability
in vitro
, and three of these embryos developed into full-term offspring after embryo transfer. Two pups (one male and one female) were proven to be fertile. This finding provides direct evidence that the nuclei of male germ cells acquire the ability to fertilize oocytes before the first meiotic division.
Glucocorticoids are insufficient for neonatal gene induction in the liver
Authors: Sassi Habib , Pictet Raymond , Grange Thierry
Published: July 2002

Glucocorticoids and their receptor (GR) play a key role in perinatal gene induction. In the liver, the GR is essential for the neonatal induction of a number of genes, including that coding for tyrosine aminotransferase (TAT). To assess the function of the GR in the perinatal period, we have compared the activity of two types of glucocorticoid responsive elements in transgenic mice; one is the
Tat
gene glucocorticoid-responsive unit (GRU), an assembly of numerous binding sites for transcription factors, including the GR; the other is a simple dimer of high-affinity GR binding sites (GREs). Both elements confer strong glucocorticoid response in the adult liver. However, only the
Tat
GRUs are able to promote neonatal induction; the GRE dimer is unresponsive. Because this dimer is responsive to glucocorticoid administration in the neonate, the absence of neonatal induction is not due to the inactivity of the GR at this stage. At birth, the neonate has to withstand a brief period of starvation and hypoglycemia, a nutritional and hormonal situation that resembles fasting in the adult. In transgenic mice, the responses at birth and after fasting in the adult are similar: the
Tat
GRUs but not the dimeric GREs are activated. Our results show that, in rodents, glucocorticoids are not sufficient for neonatal gene induction in the liver and support the conclusion that the hypoglycemia at birth is the main trigger for expression.
Prothrombin deficiency results in embryonic and neonatal lethality in mice
Authors: Sun William Y. , Witte David P. , Degen Jay L. , Colbert Melissa C. , Burkart Melissa C. , Holmbäck Kenn , Xiao Qing , Bugge Thomas H. , Degen Sandra J. F.
Published: July 2002

The conversion of prothrombin (FII) to the serine protease, thrombin (FIIa), is a key step in the coagulation cascade because FIIa triggers platelet activation, converts fibrinogen to fibrin, and activates regulatory pathways that both promote and ultimately suppress coagulation. However, several observations suggest that FII may serve a broader physiological role than simply stemming blood loss, including the identification of multiple G protein-coupled, thrombin-activated receptors, and the well-documented mitogenic activity of FIIa in
in vitro
test systems. To explore in greater detail the physiological roles of FII
in vivo
, FII-deficient (FII
−/−
) mice were generated. Inactivation of the FII gene leads to partial embryonic lethality with more than one-half of the FII
−/−
embryos dying between embryonic days 9.5 and 11.5. Bleeding into the yolk sac cavity and varying degrees of tissue necrosis were observed in many FII
−/−
embryos within this gestational time frame. However, at least one-quarter of the FII
−/−
mice survived to term, but ultimately they, too, developed fatal hemorrhagic events and died within a few days of birth. This study directly demonstrates that FII is important in maintaining vascular integrity during development as well as postnatal life.
Acetyl-
l
-carnitine fed to old rats partially restores mitochondrial function and ambulatory activity
Authors: Hagen Tory M. , Ingersoll Russell T. , Wehr Carol M. , Lykkesfeldt Jens , Vinarsky Vladimir , Bartholomew James C. , Song Mi-Hye , Ames Bruce N.
Published: July 2002

Mitochondrial function and ambulatory activity were monitored after feeding old rats acetyl-
l
-carnitine (ALCAR). Young (3–5 mo) and old (22–28 mo) rats were given a 1.5% (wt/vol) solution of ALCAR in their drinking water for 1 mo, were sacrificed, and their liver parenchymal cells were isolated. ALCAR supplementation significantly reverses the age-associated decline of mitochondrial membrane potential, as assessed by rhodamine 123 staining. Cardiolipin, which declines significantly with age, is also restored. ALCAR increases cellular oxygen consumption, which declines with age, to the level of young rats. However, the oxidant production per oxygen consumed, as measured by 2′,7′-dichlorofluorescin fluorescence levels, is ≈30% higher than in untreated old rats. Cellular glutathione and ascorbate levels were nearly 30% and 50% lower, respectively, in cells from ALCAR-supplemented old rats than in untreated old rats, further indicating that ALCAR supplementation might increase oxidative stress. Ambulatory activity in young and old rats was quantified as a general measure of metabolic activity. Ambulatory activity, defined as mean total distance traveled, in old rats is almost 3-fold lower than in young animals. ALCAR supplementation increases ambulatory activity significantly in both young and old rats, with the increase being larger in old rats. Thus, ALCAR supplementation to old rats markedly reverses the age-associated decline in many indices of mitochondrial function and general metabolic activity, but may increase oxidative stress.
Mouse Deformed epidermal autoregulatory factor 1 recruits a LIM domain factor, LMO-4, and CLIM coregulators
Authors: Sugihara Tod M. , Bach Ingolf , Kioussi Chrissa , Rosenfeld Michael G. , Andersen Bogi
Published: July 2002

Nuclear LIM domains interact with a family of coregulators referred to as Clim/Ldb/Nli. Although one family member, Clim-2/Ldb-1/Nli, is highly expressed in epidermal keratinocytes, no nuclear LIM domain factor is known to be expressed in epidermis. Therefore, we used the conserved LIM-interaction domain of Clim coregulators to screen for LIM domain factors in adult and embryonic mouse skin expression libraries and isolated a factor that is highly homologous to the previously described LIM-only proteins LMO-1, -2, and -3. This factor, referred to as LMO-4, is expressed in overlapping manner with Clim-2 in epidermis and in several other regions, including epithelial cells of the gastrointestinal, respiratory and genitourinary tracts, developing cartilage, pituitary gland, and discrete regions of the central and peripheral nervous system. Like LMO-2, LMO-4 interacts strongly with Clim factors via its LIM domain. Because LMO/Clim complexes are thought to regulate gene expression by associating with DNA-binding proteins, we used LMO-4 as a bait to screen for such DNA-binding proteins in epidermis and isolated the mouse homologue of
Drosophila
Deformed epidermal autoregulatory factor 1 (DEAF-1), a DNA-binding protein that interacts with regulatory sequences first described in the Deformed epidermal autoregulatory element. The interaction between LMO-4 and mouse DEAF-1 maps to a proline-rich C-terminal domain of mouse DEAF-1, distinct from the helix–loop–helix and GATA domains previously shown to interact with LMOs, thus defining an additional LIM-interacting domain.