bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear theory of unstable fluid mixing driven by shock wave
Authors: Zhang Qiang , Sohn Sung-Ik
Published: July 2002

A shock driven material interface between two fluids of different density is unstable. This instability is known as Richtmyer–Meshkov (RM) instability. In this paper, we present a quantitative nonlinear theory of compressible Richtmyer–Meshkov instability in two dimensions. Our nonlinear theory contains no free parameter and provides analytical predictions for the overall growth rate, as well as the growth rates of the bubble and spike, from early to later times for fluids of all density ratios. The theory also includes a general formulation of perturbative nonlinear solutions for incompressible fluids (evaluated explicitly through the fourth order). Our theory shows that the RM unstable system goes through a transition from a compressible and linear one at early times to a nonlinear and incompressible one at later times. Our theoretical predictions are in excellent agreement with the results of full numerical simulations from linear to nonlinear regimes.
Creation and uses of positron plasmas*
Authors: Greaves R. G. , Tinkle M. D. , Surko C. M.
Published: July 2002

Advances in positron trapping techniques have led to room-temperature plasmas of 107 positrons with lifetimes of 103 s. Improvements in plasma manipulation and diagnostic methods make possible a variety of new experiments, including studies just being initiated of electron–positron plasmas. The large numbers of confined positrons have also opened up a new area of positron annihilation research, in which the annihilation cross sections for positrons with a variety of molecules have been measured, as well as the energy spread of the resulting gamma rays. Such measurements are of interest for fundamental physics and for the modeling of astrophysical plasmas.
Interpenetration and ion separation in colliding plasmas
Authors: Rambo P. W. , Denavit J.
Published: July 2002

The interpenetration of colliding plasmas in the transition regime, where the ion–ion mean-free path is of the same order as the gradient scale length, is studied by one-dimensional simulations and dimensional analysis. Separate fluid equations for multiple species are solved, with coupling between the different species due to the electric field and Coulomb collisions. These simulations show initial interpenetration followed by a ‘‘soft’’ stagnation. For colliding plasmas characteristic of opposing laser heated disks, the stagnation time, the stagnation density and temperature, and the interpenetration distance are shown to depend primarily on a single parameter, defining the ratio of the scale length to the ion–ion mean-free path. Simulations of colliding plasmas from exploding plastic foils with separate ion fluids for the carbon and hydrogen are presented, showing appreciable ion separation. These results may provide a guide for the design of interpenetrating plasma experiments.
The effect of finite ion temperature on solitary waves in a plasma with an ion beam
Authors: Chatterjee Prasanta , Roychoudhury Rajkumar
Published: July 2002

The effect of finite ion and beam ion temperature on the conditions for existence of solitary waves in a beam plasma system is investigated. It is found that a finite ion temperature drastically reduces the region in which solitary waves can exist. This work can be considered as an extension of the work done by Zhang and Kuehl [Phys. Fluids B 4, 2517 (1992)].
Low frequency drift instabilities in a dusty plasma
Authors: Rosenberg M. , Krall N. A.
Published: July 2002

Low frequency drift instabilities are investigated in a dusty magnetized plasma with negatively charged grains in which locally there is an electron density gradient which is opposite in sign to a dust density gradient. Frequencies less than the ion gyrofrequency but much larger than the dust gyrofrequency are considered. Two different equilibria are considered that are characterized by ρd≶Lnd, where ρd is the dust gyroradius and Lnd is the dust density scale length. Instabilities analogous to the universal instability and to the lower-hybrid-drift instability (with the lower-hybrid frequency in this case associated with the dust) are investigated. Possible applications to dusty space plasmas such as the spoke regions of Saturn’s B-ring are discussed.
Radiative recombination coefficient of free carriers in GaAs-AlGaAs quantum wells and its dependence on temperature
Authors: Matsusue Toshio , Sakaki Hiroyuki
Published: July 2002

The radiative recombination coefficient B, defined by dN/dt=dP/dt≡−BNP, of two-dimensional free carriers, N and P, in a selectively doped GaAs/n-Al0.3Ga0.7As quantum well was determined in the temperature range T between 15 and 300 K by measuring the decay time τ of photoluminescence from the quantum well with electron density N0=1×1012/cm2. It is found that B(=1/τN0) is 1.1–1.9×10−4 cm2/s at 300 K and increases as T is lowered, reaching 2.3×10−3 cm2/s (τ∼0.43 ns) at 15 K. The initial increase of B is nearly proportional to 1/T, whereas B tends to saturate at low temperature. These experimental findings are shown to be well explained by the theory of band-to-band recombination of two-dimensional carriers in quantum wells.
Fighting fruit flies: A model system for the study of aggression
Authors: Chen Selby , Lee Ann Yeelin , Bowens Nina M. , Huber Robert , Kravitz Edward A.
Published: July 2002

Despite the importance of aggression in the behavioral repertoire of most animals, relatively little is known of its proximate causation and control. To take advantage of modern methods of genetic analysis for studying this complex behavior, we have developed a quantitative framework for studying aggression in common laboratory strains of the fruit fly,
Drosophila melanogaster
. In the present study we analyze 73 experiments in which socially naive male fruit flies interacted in more than 2,000 individual agonistic interactions. This allows us to (
i
) generate an ethogram of the behaviors that occur during agonistic interactions; (
ii
) calculate descriptive statistics for these behaviors; and (
iii
) identify their temporal patterns by using sequence analysis. Thirty-minute paired trials between flies contained an average of 27 individual agonistic interactions, lasting a mean of 11 seconds and featuring a variety of intensity levels. Only few fights progressed to the highest intensity levels (boxing and tussling). A sequential analysis demonstrated the existence of recurrent patterns in behaviors with some similarity to those seen during courtship. Based on the patterns characterized in the present report, a detailed examination of aggressive behavior by using mutant strains and other techniques of genetic analysis becomes possible.
Highly reduced protection againstStreptococcus pneumoniaeafter deletion of a single heavy chain gene in mouse
Authors: Mi Qing-Sheng , Zhou Li , Schulze Dan H. , Fischer Randy T. , Lustig Ana , Rezanka Louis J. , Donovan David M. , Longo Dan L. , Kenny James J.
Published: July 2002

Phosphocholine (PC) is the immunodominant epitope found on the surface ofStreptococcus pneumoniae(SPn). T15-idiotype Abs, whose heavy (H) chain variable region is encoded by theV1gene, are dominant in the anti-PC response in adult mice and protect mice from lethal pneumococcal infection. The ability of anti-PC Abs using H chains other than theV1H chain to protect against pneumococcal infection remains controversial. We generated V1−/−knockout mice to determine whether protective anti-PC Abs could be produced in the absence of theV1gene. No anti-PC Abs were produced in V1−/−mice immunized with avirulentSPn; however, PC-BSA binding Abs were induced after immunization with PC-keyhole limpet hemocyanin but at significantly lower levels than those in wild-type mice. These Abs provided poor protection against virulentSPn; thus, <25% of V1−/−mice survived challenge with 104bacteria as compared with 100% survival of V1+/+mice. The anti-PC Abs in V1−/−mice were heteroclitic, binding to nitrophenyl-PC better than to PC. None of nine hybridomas produced from V1−/−mice provided passive protection. However, the V1−/−mice produced normal amounts of Ab toSPnproteins that can partially protect mice againstSPn. These data indicate that theV1gene is critical for the production of anti-PC Abs providing optimum protection against infection withSPn, and the V1−/−mice could be useful in unmasking epitopes other than the immunodominant PC epitope onSPncapable of providing cross protection.
Identification of a renal-specific oxido-reductase in newborn diabetic mice
Authors: Yang Qiwei , Dixit Bharat , Wada Jun , Tian Yufeng , Wallner Elisabeth I. , Srivastva Satish K. , Kanwar Yashpal S.
Published: July 2002

Aldose reductase (ALR2), a NADPH-dependent aldo-keto reductase (AKR), is widely distributed in mammalian tissues and has been implicated in complications of diabetes, including diabetic nephropathy. To identify a renal-specific reductase belonging to the AKR family, representational difference analyses of cDNA from diabetic mouse kidney were performed. A full-length cDNA with an ORF of 855 nt and yielding a ≈1.5-kb mRNA transcript was isolated from a mouse kidney library. Human and rat homologues also were isolated, and they had ≈91% and ≈97% amino acid identity with mouse protein.
In vitro
translation of the cDNA yielded a protein product of ≈33 kDa. Northern and Western blot analyses, using the cDNA and antirecombinant protein antibody, revealed its expression exclusively confined to the kidney. Like ALR2, the expression was up-regulated in diabetic kidneys. Its mRNA and protein expression was restricted to renal proximal tubules. The gene neither codistributed with Tamm–Horsfall protein nor aquaporin-2. The deduced protein sequence revealed an AKR-3 motif located near the N terminus, unlike the other AKR family members where it is confined to the C terminus. Fluorescence quenching and reactive blue agarose chromatography studies revealed that it binds to NADPH with high affinity (
K
dNADPH
= 66.9 ± 2.3 nM). This binding domain is a tetrapeptide (Met-Ala-Lys-Ser) located within the AKR-3 motif that is similar to the other AKR members. The identified protein is designated as RSOR because it is renal-specific with properties of an oxido-reductase, and like ALR2 it may be relevant in the renal complications of diabetes mellitus.
Genomewide insertional mutagenesis in
Streptomyces coelicolor
reveals additional genes involved in morphological differentiation
Authors: Gehring Amy M. , Nodwell Justin R. , Beverley Stephen M. , Losick Richard
Published: July 2002

The filamentous soil bacterium
Streptomyces coelicolor
undergoes a complex cycle of morphological differentiation involving the formation of an aerial mycelium and the production of pigmented antibiotics. We have developed a procedure for generating insertional mutants of
S. coelicolor
based on
in vitro
transposition of a plasmid library of cloned
S. coelicolor
DNAs. The insertionally mutated library was introduced into
S. coelicolor
, and transposon insertions were recovered at widely scattered locations around the chromosome. Many of the insertions revealed previously uncharacterized genes, and several caused novel mutant phenotypes, such as altered pigment production, enhanced antibiotic sensitivity, delayed or impaired formation of aerial hyphae, and a block in spore formation. The sporulation mutant harbored an insertion in one of three adjacent genes that are apparently unique to
Streptomyces
but are each represented by at least 20 paralogs at dispersed locations in the chromosome. Individual members of the three families often are found grouped together in a characteristic arrangement, suggesting that they have a common function.
Inhibition of the ubiquitin-proteasome system in Alzheimer's disease
Authors: Lam Y. Amy , Pickart Cecile M. , Alban Andrew , Landon Michael , Jamieson Craig , Ramage Robert , Mayer R. John , Layfield Robert
Published: July 2002

Alzheimer's disease is the most common cause of dementia in the elderly. Although several genetic defects have been identified in patients with a family history of this disease, the majority of cases involve individuals with no known genetic predisposition. A mutant form of ubiquitin, termed Ub
+1
, has been selectively observed in the brains of Alzheimer's patients, including those with nonfamilial Alzheimer's disease, but it has been unclear why Ub
+1
expression should be deleterious. Here we show that Ub
+1
is an efficient substrate for polyubiquitination
in vitro
and in transfected human cells. The resulting polyubiquitin chains are refractory to disassembly by deubiquitinating enzymes and potently inhibit the degradation of a polyubiquitinated substrate by purified 26S proteasomes. Thus, expression of Ub
+1
in aging brain could result in dominant inhibition of the Ub-proteasome system, leading to neuropathologic consequences.
Mice with a targeted mutation in the thyroid hormone β receptor gene exhibit impaired growth and resistance to thyroid hormone
Authors: Kaneshige Masahiro , Kaneshige Kumiko , Zhu Xu-guang , Dace Alexandra , Garrett Lisa , Carter Todd A. , Kazlauskaite Rasa , Pankratz Daniel G. , Wynshaw-Boris Anthony , Refetoff Samuel , Weintraub Bruce , Willingham Mark C. , Barlow Carrolee , Cheng Sheue-yann
Published: July 2002

Patients with mutations in the thyroid hormone receptor β
(
TRβ
) gene manifest resistance to thyroid hormone
(RTH), resulting in a constellation of variable phenotypic
abnormalities. To understand the molecular basis underlying the action
of mutant TRβ
in vivo
, we generated mice with a
targeted mutation in the
TRβ
gene (
TRβ
PV
;
PV, mutant thyroid hormone receptor kindred PV) by using homologous
recombination and the
Cre
/
lox
P system.
Mice expressing a single
PV
allele showed the typical
abnormalities of thyroid function found in heterozygous humans with
RTH. Homozygous
PV
mice exhibit severe dysfunction of the
pituitary–thyroid axis, impaired weight gains, and abnormal bone
development. This phenotype is distinct from that seen in mice with a
null mutation in the
TRβ
gene. Importantly, we
identified abnormal expression patterns of several genes in tissues of
TRβ
PV
mice, demonstrating the interference of the mutant
TR with the gene regulatory functions of the wild-type TR
in
vivo
. These results show that the actions of mutant and
wild-type TRβ
in vivo
are distinct. This model allows
further study of the molecular action of mutant TR
in
vivo
, which could lead to better treatment for RTH patients.
Genetic analysis of calcium spiking responses in nodulation mutants of
Medicago truncatula
Authors: Wais Rebecca J. , Galera Christine , Oldroyd Giles , Catoira Romy , Penmetsa R. Varma , Cook Douglas , Gough Clare , Dénarié Jean , Long Sharon R.
Published: July 2002

The symbiotic interaction between
Medicago
truncatula
and
Sinorhizobium meliloti
results in
the formation of nitrogen-fixing nodules on the roots of the host
plant. The early stages of nodule formation are induced by bacteria via
lipochitooligosaccharide signals known as Nod factors (NFs). These NFs
are structurally specific for bacterium–host pairs and are sufficient
to cause a range of early responses involved in the host developmental
program. Early events in the signal transduction of NFs are not well
defined. We have previously reported that
Medicago
sativa
root hairs exposed to NF display sharp oscillations of
cytoplasmic calcium ion concentration (calcium spiking). To assess the
possible role of calcium spiking in the nodulation response, we
analyzed
M. truncatula
mutants in five complementation
groups. Each of the plant mutants is completely Nod− and is blocked at
early stages of the symbiosis. We defined two genes,
DMI1
and
DMI2
, required in common for
early steps of infection and nodulation and for calcium spiking.
Another mutant, altered in the
DMI3
gene, has a similar
mutant phenotype to
dmi1
and
dmi2
mutants
but displays normal calcium spiking. The calcium behavior thus implies
that the
DMI3
gene acts either downstream of calcium
spiking or downstream of a common branch point for the calcium response
and the later nodulation responses. Two additional mutants, altered in
the
NSP
and
HCL
genes, which show root
hair branching in response to NF, are normal for calcium spiking. This
system provides an opportunity to use genetics to study
ligand-stimulated calcium spiking as a signal transduction event.
A genome-wide screen in
Saccharomyces cerevisiae
for genes affecting UV radiation sensitivity
Authors: Birrell Geoff W. , Giaever Guri , Chu Angela M. , Davis Ronald W. , Brown J. Martin
Published: July 2002

The recent completion of the deletion of essentially all of the ORFs in yeast is an important new resource for identifying the phenotypes of unknown genes. Each ORF is replaced with a cassette containing unique tag sequences that allow rapid parallel analysis of strains in a pool by using hybridization to a high-density oligonucleotide array. We examined the utility of this system to identify genes conferring resistance to UV irradiation by using a pool of 4,627 individual homozygous deletion strains (representing deletions of all nonessential genes). We identified most of the nonessential genes previously shown to be involved in nucleotide excision repair, in cell cycle checkpoints, in homologous recombination, and in postreplication repair after UV damage. We also identified and individually confirmed, by replacing the genes, three new genes, to our knowledge not previously reported to confer UV sensitivity when deleted. Two of these newly identified genes have human orthologs associated with cancer, demonstrating the potential of this system to uncover human genes affecting sensitivity to DNA-damaging agents and genes potentially involved in cancer formation.
Functional testicular tissue does not masculinize development of the zebra finch song system.
Authors: Wade J , Arnold A P
Published: July 2002

Current theories of sexual differentiation maintain that ovarian estrogen prevents masculine development of the copulatory system in birds, whereas estrogen derived from testicular androgens promotes masculine sexual differentiation of neuroanatomy and sexual behavior in mammals. Paradoxically, some data suggest that the neural song system in zebra finches follows the mammalian pattern with estrogenic metabolites of testicular secretions causing masculine development. To test whether the removal of estrogen from males during early development would prevent the development of masculine song systems, zebra finches were treated embryonically with an inhibitor of estrogen synthesis. In addition, this treatment in genetic female zebra finches induced both functional ovarian and testicular tissue to develop, thus allowing the assessment of the direct effects of testicular secretions on song system development. In males, the inhibition of estrogen synthesis before hatching had a small but significant effect in demasculinizing one aspect of the neural song system. In treated females, the song systems remained morphologically feminine. These results suggest that masculinization of the song system is not determined solely by testicular androgens or their estrogenic metabolites.
A specific protein carboxyl methylesterase that demethylates phosphoprotein phosphatase 2A in bovine brain.
Authors: Lee J , Chen Y , Tolstykh T , Stock J
Published: July 2002

Phosphoprotein phosphatase 2A (PP2A) is one of the four major protein serine/threonine phosphatases found in all eukaryotic cells. We have shown that the 36-kDa catalytic subunit of PP2A is carboxyl methylated in eukaryotic cells, and we have previously identified and purified a novel methyltransferase (MTase) that is responsible for this modification. Here, we describe a novel protein carboxyl methyl-esterase (MEase) from bovine brain that demethylates PP2A. The enzyme has been purified to homogeneity as a monomeric 46-kDa soluble protein. The MEase is highly specific for PP2A. It does not catalyze the demethylation of other protein or peptide methylesters. Moreover, MEase activity is dramatically inhibited by nanomolar concentrations of okadaic acid, a specific inhibitor of PP2A. From these results, we conclude that PP2A methylation is controlled by two specific enzymes, a MTase and a MEase. Since PP2A methylation is highly conserved in eukaryotes ranging from human to yeast, it is likely that this system plays an important role in phosphatase regulation.
Infectivity of chimeric human T-cell leukemia virus type I molecular clones assessed by naked DNA inoculation.
Authors: Zhao T M , Robinson M A , Bowers F S , Kindt T J
Published: July 2002

Two human T-cell leukemia virus type I (HTLV-I) molecular clones, K30p and K34p were derived from HTLV-I-infected rabbit cell lines. K30p and K34p differ by 18 bp with changes in the long terminal repeats (LTRs) as well as in the gag, pol, and rex but not tax or env gene products. Cells transfected with clone K30p were infectious in vitro and injection of the K30p transfectants or naked K30p DNA into rabbits leads to chronic infection. In contrast, K34p did not mediate infection in vitro or in vivo, although the cell line from which it was derived is fully infectious and K34p transfectants produce intact virus particles. To localize differences involved in the ability of the clones to cause infection, six chimeric HTLV-I clones were constructed by shuffling corresponding fragments containing the substitutions in the LTRs, the gag/pol region and the rex region between K30p and K34p. Cells transfected with any of the six chimeras produced virus, but higher levels of virus were produced by cells transfected with those constructs containing the K30p rex region. Virus production was transient except in cells transfected with K30p or with a chimera consisting of the entire protein coding region of K30p flanked by K34p LTRs; only the transfectants showing persistent virus production mediated in vitro infection. In vivo infection in rabbits following intramuscular DNA injection was mediated by K30p as well as by a chimera of K30p containing the K34p rex gene. Comparisons revealed that virus production was greater and appeared earlier in rabbits injected with K30p. These data suggest that several defects in the K34p clone preclude infectivity and furthermore, provide systems to explore functions of HTLV-I genes.
Critical contribution of beta chain residue 57 in peptide binding ability of both HLA-DR and -DQ molecules.
Authors: Nepom B S , Nepom G T , Coleman M , Kwok W W
Published: July 2002

Position 57 in the beta chain of HLA class II molecules maintains an Asp/non-Asp dimorphism that has been conserved through evolution and is implicated in susceptibility to some autoimmune diseases. The latter effect may be due to the influence of this residue on the ability of class II alleles to bind specific pathogenic peptides. We utilized highly homologous pairs of both DR and DQ alleles that varied at residue 57 to investigate the impact of this dimorphism on binding of model peptides. Using a direct binding assay of biotinylated peptides on whole cells expressing the desired alleles, we report several peptides that bind differentially to the allele pairs depending on the presence or absence of Asp at position 57. Peptides with negatively charged residues at anchor position 9 bind well to alleles not containing Asp at position 57 in the beta chain but cannot bind well to homologous Asp-positive alleles. By changing the peptides at the single residue predicted to interact with this position 57, we demonstrate a drastically altered or reversed pattern of binding. Ala analog peptides confirm these interactions and identify a limited set of interaction sites between the bound peptides and the class II molecules. Clarification of the impact of specific class II polymorphisms on generating unique allele-specific peptide binding "repertoires" will aid in our understanding of the development of specific immune responses and HLA-associated diseases.
A Carboniferous insect gall: insight into early ecologic history of the Holometabola.
Authors: Labandeira C C , Phillips T L
Published: July 2002

Although the prevalence or even occurrence of insect herbivory during the Late Carboniferous (Pennsylvanian) has been questioned, we present the earliest-known ecologic evidence showing that by Late Pennsylvanian times (302 million years ago) a larva of the Holometabola was galling the internal tissue of Psaronius tree-fern fronds. Several diagnostic cellular and histological features of these petiole galls have been preserved in exquisite detail, including an excavated axial lumen filled with fecal pellets and comminuted frass, plant-produced response tissue surrounding the lumen, and specificity by the larval herbivore for a particular host species and tissue type. Whereas most suggestions over-whelmingly support the evolution of such intimate and reciprocal plant-insect interactions 175 million years later, we provide documentation that before the demise of Pennsylvanian age coal-swamp forests, a highly stereotyped life cycle was already established between an insect that was consuming internal plant tissue and a vascular plant host responding to that herbivory. This and related discoveries of insect herbivore consumption of Psaronius tissues indicate that modern-style herbivores were established in Late Pennsylvanian coal-swamp forests.
Design of artificial sequence-specific DNA bending ligands.
Authors: Liberles D A , Dervan P B
Published: July 2002

Proteins that bend DNA are important regulators of biological processes. Sequence-specific DNA bending ligands have been designed that bind two noncontiguous sites in the major groove and induce a bend in the DNA. An oligonucleotide containing pyrimidine segments separated by a central variable linker domain simultaneously binds by triple helix formation two 15-bp purine tracts separated by 10 bp. Bend angles of 61 degrees, 50 degrees, and 38 degrees directed towards the minor groove were quantitated by phasing analysis for linkers of four, five, and six T residues, respectively. The design and synthesis of nonnatural architectural factors may provide a new class of reagents for use in biology and human medicine.
Gangliosides are neuronal ligands for myelin-associated glycoprotein.
Authors: Yang L J , Zeller C B , Shaper N L , Kiso M , Hasegawa A , Shapiro R E , Schnaar R L
Published: July 2002

Nerve cells depend on specific interactions with glial cells for proper function. Myelinating glial cells are thought to associate with neuronal axons, in part, via the cell-surface adhesion protein, myelin-associated glycoprotein (MAG). MAG is also thought to be a major inhibitor of neurite outgrowth (axon regeneration) in the adult central nervous system. Primary structure and in vitro function place MAG in an immunoglobulin-related family of sialic acid-binding lactins. We report that a limited set of structurally related gangliosides, known to be expressed on myelinated neurons in vivo, are ligands for MAG. When major brain gangliosides were adsorbed as artificial membranes on plastic microwells, only GT1b and GD1a supported cell adhesion of MAG-transfected COS-1 cells. Furthermore, a quantitatively minor ganglioside expressed on cholinergic neurons, GQ1b alpha (also known as Chol-1 alpha-b), was much more potent than GT1b or GD1a in supporting MAG-mediated cell adhesion. Adhesion to either GT1b or GQ1b alpha was abolished by pretreatment of the adsorbed gangliosides with neuraminidase. On the basis of structure-function studies of 19 test glycosphingolipids, an alpha 2,3-N-acetylneuraminic acid residue on the terminal galactose of a gangliotetraose core is necessary for MAG binding, and additional sialic acid residues linked to the other neutral core saccharides [Gal(II) and GalNAc(III)] contribute significantly to binding affinity. MAG-mediated adhesion to gangliosides was blocked by pretreatment of the MAG-transfected COS-1 cells with anti-MAG monoclonal antibody 513, which is known to inhibit oligodendrocyte-neuron binding. These data are consistent with the conclusion that MAG-mediated cell-cell interactions involve MAG-ganglioside recognition and binding.
Transcriptional regulation of the Rhodococcus rhodochrous J1 nitA gene encoding a nitrilase.
Authors: Komeda H , Hori Y , Kobayashi M , Shimizu S
Published: July 2002

The 1.4-kb downstream region from a nitrilase gene (nitA) of an actinomycete Rhodococcus rhodochrous J1, which is industrially in use, was found to be required for the isovaleronitrile-dependent induction of nitrilase synthesis in experiments using a Rhodococcus-Escherichia coli shuttle vector pK4 in a Rhodococcus strain. Sequence analysis of the 1.4-kb region revealed the existence of an open reading frame (nitR) of 957 bp, which would encode a protein with a molecular mass of 35,100. Deletion of the central and 3'-terminal portion of nitR resulted in the complete loss of nitrilase activity, demonstrating that nitR codes for a transcriptional positive regulator in nitA expression. The deduced amino acid sequence of nitR showed similarity to a positive regulator family including XylS from Pseudomonas putida and AraC from E. coli. By Northern blot analysis, the 1.4-kb transcripts for nitA were detected in R. rhodochrous J1 cells cultured in the presence of isovaleronitrile, but not those cultured in the absence of isovaleronitrile. The transcriptional start site for nitA was mapped to a C residue located 26 bp upstream of its translational start site. Deletion analysis to define the nitA promoter region suggested the possible participation of an inverted repeat sequence, centered on base pair -52, in induction of nitA transcription.
Negative regulation of hypoxia-inducible genes by the von Hippel-Lindau protein.
Authors: Iliopoulos O , Levy A P , Jiang C , Kaelin W G , Goldberg M A
Published: July 2002

Inactivation of the von Hippel-Lindau protein (pVHL) has been implicated in the pathogenesis of renal carcinomas and central nervous system hemangioblastomas. These are highly vascular tumors which overproduce angiogenic peptides such as vascular endothelial growth factor/vascular permeability factor (VEGF/VPF). Renal carcinoma cells lacking wild-type pVHL were found to produce mRNAs encoding VEGF/VPF, the glucose transporter GLUT1, and the platelet-derived growth factor B chain under both normoxic and hypoxic conditions. Reintroduction of wild-type, but not mutant, pVHL into these cells specifically inhibited the production of these mRNAs under normoxic conditions, thus restoring their previously described hypoxia-inducible profile. Thus, pVHL appears to play a critical role in the transduction of signals generated by changes in ambient oxygen tension.
Local stress, not systemic factors, regulate gene expression of the cardiac renin-angiotensin system in vivo: a comprehensive study of all its components in the dog.
Authors: Lee Y A , Liang C S , Lee M A , Lindpaintner K
Published: July 2002

Cardiac hypertrophy is associated with altered expression of the components of the cardiac renin-angiotensin system (RAS). While in vitro data suggest that local mechanical stimuli serve as important regulatory modulators of cardiac RAS activity, no in vivo studies have so far corroborated these observations. The aims of this study were to (i) examine the respective influence of local, mechanical versus systemic, soluble factors on the modulation of cardiac RAS gene expression in vivo; (ii) measure gene expression of all known components of the RAS simultaneously; and (iii) establish sequence information and an assay system for the RAS of the dog, one of the most important model organisms in cardiovascular research. We therefore examined a canine model of right ventricular hypertrophy and failure (RVHF) in which the right ventricle (RV) is hemodynamically loaded, the left ventricle (LV) is hemodynamically unloaded, while both are exposed to the same circulating milieu of soluble factors. Using specific competitive PCR assays, we found that RVHF was associated with significant increases in RV mRNA levels of angiotensin converting enzyme and angiotensin II type 2 receptor, and with significant decreases of RV expression of chymase and the angiotensin II type 1 receptor, while RV angiotensinogen and renin remained unchanged. All components remained unchanged in the LV. We conclude that (i) dissociated regional regulation of RAS components in RV and LV indicates modulation by local, mechanical, not soluble, systemic stimuli; (ii) components of the cardiac RAS are independently and differentially regulated; and (iii) opposite changes in the expression of angiotensin converting enzyme and chymase, and of angiotensin II type I and angiotensin II type 2 receptors, may indicate different physiological roles of these RAS components in RVHF.
The E5 gene product of rhesus papillomavirus is an activator of endogenous Ras and phosphatidylinositol-3′-kinase in NIH 3T3 cells
Authors: Ghai Jyotsna , Ostrow Ronald S. , Tolar Jakub , McGlennen Ronald C. , Lemke Todd D. , Tobolt Diane , Liu Zhanjiang , Faras Anthony J.
Published: July 2002

We examined the effect of two rhesus papillomavirus 1 (RhPV)
oncogenes on cytokine-induced signal transduction pathways leading to
the possible activation of Ras protein (p21
ras
) and
phosphatidylinositol kinase. p21
ras
in both the activated
(GTP-bound) and inactivated (GDP-bound) states were quantitated. NIH
3T3 cell lines expressing the RhPV 1
E5
gene or
epidermal growth factor receptor cDNA had about a sixfold higher ratio
of p21
ras
-bound GTP to p21
ras
-bound GDP as
compared with parental NIH 3T3 cells or a cell line expressing the RhPV
1
E7
gene under normal culture conditions, yet expressed
similar levels of p21
ras
. Quiescent cells had dramatically
reduced levels of activated p21
ras
, except those containing
RhPV 1
E7
. Levels were restored by stimulation with
epidermal growth factor or platelet-derived growth factor. Both
epidermal growth factor and platelet-derived growth factor receptor of
RhPV 1
E5
- and
E7
-containing cells
responded to cytokine stimulation. Endogenous
phosphatidylinositol-3′-kinase was up-regulated in NIH 3T3 cells
transformed with the
E5
genes of RhPV 1 and bovine
papillomavirus 1. These results suggest that
E5
genes of
papillomaviruses play a major role in the regulation of transduction
pathways.
NMR of laser-polarized xenon in human blood
Authors: Bifone A. , Song Y.-Q. , Seydoux R. , Taylor R. E. , Goodson B. M. , Pietrass T. , Budinger T. F. , Navon G. , Pines A.
Published: July 2002

By means of optical pumping with laser light it is possible to
enhance the nuclear spin polarization of gaseous xenon by four to five
orders of magnitude. The enhanced polarization has allowed advances in
nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance
imaging (MRI), including polarization transfer to molecules and imaging
of lungs and other void spaces. A critical issue for such applications
is the delivery of xenon to the sample while maintaining the
polarization. Described herein is an efficient method for the
introduction of laser-polarized xenon into systems of biological and
medical interest for the purpose of obtaining highly enhanced NMR/MRI
signals. Using this method, we have made the first observation of the
time-resolved process of xenon penetrating the red blood cells in fresh
human blood—the xenon residence time constant in the red blood cells
was measured to be 20.4 ± 2 ms. The potential of certain
biologically compatible solvents for delivery of laser-polarized xenon
to tissues for NMR/MRI is discussed in light of their respective
relaxation and partitioning properties.
Aspergillus
has distinct fatty acid synthases for primary and secondary metabolism
Authors: Brown D. W. , Adams T. H. , Keller N. P.
Published: July 2002

Aspergillus nidulans
contains two functionally
distinct fatty acid synthases (FASs): one required for primary fatty
acid metabolism (FAS) and the other required for secondary metabolism
(sFAS). FAS mutants require long-chain fatty acids for growth, whereas
sFAS mutants grow normally but cannot synthesize sterigmatocystin (ST),
a carcinogenic secondary metabolite structurally and biosynthetically
related to aflatoxin. sFAS mutants regain the ability to synthesize ST
when provided with hexanoic acid, supporting the model that the ST
polyketide synthase uses this short-chain fatty acid as a starter unit.
The characterization of both the polyketide synthase and FAS may
provide novel means for modifying secondary metabolites.
A targeted mutation of the D3 dopamine receptor gene is associated with hyperactivity in mice.
Authors: Accili D , Fishburn C S , Drago J , Steiner H , Lachowicz J E , Park B H , Gauda E B , Lee E J , Cool M H , Sibley D R , Gerfen C R , Westphal H , Fuchs S
Published: July 2002

While most effects of dopamine in the brain are mediated by the D1 and D2 receptor subtypes, other members of this G protein-coupled receptor family have potentially important functions. D3 receptors belong to the D2-like subclass of dopamine receptors, activation of which inhibits adenylyl cyclase. Using targeted mutagenesis in mouse embryonic stem cells, we have generated mice lacking functional D3 receptors. A premature chain-termination mutation was introduced in the D3 receptor gene after residue Arg-148 in the second intracellular loop of the predicted protein sequence. Binding of the dopamine antagonist [125I]iodosulpride to D3 receptors was absent in mice homozygous for the mutation and greatly reduced in heterozygous mice. Behavioral analysis of mutant mice showed that this mutation is associated with hyperactivity in an exploratory test. Homozygous mice lacking D3 receptors display increased locomotor activity and rearing behavior. Mice heterozygous for the D3 receptor mutation show similar, albeit less pronounced, behavioral alterations. Our findings indicate that D3 receptors play an inhibitory role in the control of certain behaviors.
The phosphatase activity of carbonic anhydrase III is reversibly regulated by glutathiolation.
Authors: Cabiscol E , Levine R L
Published: July 2002

Carbonic anhydrase isozyme III (CAIII) is unique among the carbonic anhydrases because it demonstrates phosphatase activity. CAIII forms a disulfide link between glutathione and two of its five cysteine residues, a process termed S-glutathiolation. Glutathiolation of CAIII occurs in vivo and is increased during aging and under acute oxidative stress. We show that glutathiolation serves to reversibly regulate the phosphatase activity of CAIII. Glutathiolation of Cys-186 is required for phosphatase activity, while glutathiolation of Cys-181 blocks activity. Phosphotyrosine is the preferred substrate, although phosphoserine and phosphothreonine can also be cleaved. Thus, glutathiolation is a reversible covalent modification that can regulate CAIII, a phosphatase that may function in the cellular response to oxidative stress.
Myofibroblasts differentiate from fibroblasts when plated at low density.
Authors: Masur S K , Dewal H S , Dinh T T , Erenburg I , Petridou S
Published: July 2002

Myofibroblasts, defined by their expression of smooth muscle alpha-actin, appear at corneal and dermal incisions and promote wound contraction. We report here that cultured fibroblasts differentiate into myofibroblasts by a cell density-dependent mechanism. Fibroblasts seeded at low density (5 cells per mm2) produced a cell culture population consisting of 70-80% myofibroblasts, 5-7 days after seeding. In contrast, fibroblasts seeded at high density (500 cells per mm2) produced cultures with only 5-10% myofibroblasts. When the myofibroblast-enriched cultures were subsequently passaged at high density, the smooth muscle alpha-actin phenotype was lost within 3 days. Furthermore, initially 60% of the low density-cultured cells incorporated BrdUrd compared to 30% of cells passaged at high density. Media from myofibroblast-enriched cultures had more latent and active transforming growth factor beta (TGF-beta) than did media from fibroblast-enriched cultures. Although there was a trend towards increased numbers of myofibroblasts after addition of exogenous TGF-beta, the results did not reach statistical significance. We conclude that myofibroblast differentiation can be induced in fibroblasts by plating at low density. We propose a cell density-dependent model of myofibroblast differentiation during wounding and healing in which at least two factors interact: loss of cell contact and the presence of TGF-beta.
Functional domains are specified to single-cell resolution in a
Drosophila
epithelium
Authors: Sözen M. Ali , Armstrong J. Douglas , Yang Mingyao , Kaiser Kim , Dow Julian A. T.
Published: July 2002

Specification of pattern is fundamental to the development of a multicellular organism. The Malpighian (renal) tubule of
Drosophila melanogaster
is a simple epithelium that proliferates under the direction of a single tip cell into three morphologically distinct domains. However, systematic analysis of a panel of over 700 P{GAL4} enhancer trap lines reveals unexpected richness for such an apparently simple tissue. Using numerical analysis, it was possible formally to reconcile apparently similar or complementary expression domains and thus to define at least five genetically defined domains and multiple cell types. Remarkably, the positions of domain boundaries and the numbers of both principal and secondary (“stellate”) cell types within each domain are reproducible to near single-cell precision between individual animals. Domains of physiological function were also mapped using transport or expression assays. Invariably, they respect the boundaries defined by enhancer activity. These genetic domains can also be visualized
in vivo
, both in transgenic and wild-type flies, providing an “identified cell” system for epithelial physiology. Building upon recent advances in
Drosophila
Malpighian tubule physiology, the present study confirms this tissue as a singular model for integrative physiology.
Gene cloning, sequence analysis, and expression of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Authors: Chaiyen Pimchai , Ballou David P. , Massey Vincent
Published: July 2002

The gene encoding 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO; EC
1.14.12.4
) was cloned by using an oligonucleotide probe corresponding to the N terminus of the enzyme to screen a DNA library of
Pseudomonas
sp. MA-1. The gene encodes for a protein of 379 amino acid residues corresponding to a molecular mass of 41.7 kDa, the same as that previously estimated for MHPCO. MHPCO was expressed in
Escherichia coli
and found to have the same properties as the native enzyme from
Pseudomonas
sp. MA-1. This study shows that MHPCO is a homotetrameric protein with one flavin adenine dinucleotide bound per subunit. Sequence comparison of the enzyme with other hydroxylases reveals regions that are conserved among aromatic flavoprotein hydroxylases.
Neurotrophin-3 signals redistribute RNA in neurons
Authors: Knowles Roger B. , Kosik Kenneth S.
Published: July 2002

The translocation of specific mRNAs to dendrites and their potential for locally regulated translation are likely to serve as an effector in neuronal plasticity. Whether translation in dendrites is regulated by delivery of the RNA to sites of plasticity or a stationary pool of localized RNA undergoes enhanced translational efficiency is not clear. We show that RNA can translocate into dendrites in response to NT-3. RNA granules were visualized in cultured rat cortical neurons using the dye SYTO 14, which labels poly-ribosome complexes. Long before the morphological effects of NT-3 appeared, there was increased distal translocation of labeled complexes. This effect was blocked by K252a, a potent inhibitor of tyrosine kinase receptors. Therefore, neurons can utilize extracellular signals to alter the distribution of protein synthetic machinery via the active transport of RNA granules.
Microsatellite diversity and the demographic history of modern humans
Authors: Jorde Lynn B. , Rogers Alan R. , Bamshad Michael , Watkins W. Scott , Krakowiak Patrycja , Sung Sandy , Kere Juha , Harpending Henry C.
Published: July 2002

We have examined differences in diversity at 60 microsatellite loci among human population samples from three major continental groups to evaluate the hypothesis of greater African diversity in this rapidly evolving class of loci. Application of a statistical test that assumes equal mutation rates at all loci fails to demonstrate differences in microsatellite diversity, while a randomization test that does not make this assumption finds that Africans have significantly greater microsatellite diversity (
P
< 10
−8
) than do Asians and Europeans. Greater African diversity is most apparent at loci with smaller overall variance in allele size, suggesting that the record of population history has been erased at repeat loci with higher mutation rates. A power analysis shows that only 35–40 microsatellites are needed to establish this difference statistically, demonstrating the considerable evolutionary information contained in these systems. On average, African populations have ≈20% greater microsatellite diversity than do Asian and European populations. A comparison of continental diversity differences in microsatellites and mtDNA sequences suggests earlier demographic expansion of the ancestors of Africans.
Signal transduction and activator of transcription (STAT) protein-dependent activation of angiotensinogen promoter: A cellular signal for hypertrophy in cardiac muscle
Authors: Mascareno Eduardo , Dhar Manya , Siddiqui M. A. Q.
Published: July 2002

The role of the peptide hormone angiotensin (AngII) in promoting myocardial hypertrophy is well documented. Our studies demonstrate that AngII uses a signaling pathway in cardiac myocytes in which the promoter of the gene encoding its prohormone, angiotensinogen, serves as the target site for activated signal transduction and activator of transcription (STAT) proteins. Gel mobility-shift assay revealed that STAT3 and STAT6 are selectively activated by AngII treatment of cardiomyocytes in culture and bind to a sequence motif (St-domain) in the angiotensinogen promoter to activate its transcription in transient transfection assay. We have also observed a dramatic increase in the St-domain binding activity of STAT proteins in the hypertrophied heart of the genetically hypertensive rat relative to that of the aged-matched normotensive strain WKY, providing a compelling argument in favor of the linkage of STAT pathway to the heart tissue autocrine AngII loop. These studies thus uncover a mechanism by which the activation of a selective set of STATs underlies mobilization of the gene activation program intrinsic to cardiac hypertrophy.