bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable alteration of pre-mRNA splicing patterns by modified U7 small nuclear RNAs
Authors: Gorman Linda , Suter Daniel , Emerick Victoria , Schümperli Daniel , Kole Ryszard
Published: July 2002

In several forms of β-thalassemia, mutations in the second intron of the β-globin gene create aberrant 5′ splice sites and activate a common cryptic 3′ splice site upstream. As a result, the thalassemic β-globin pre-mRNAs are spliced almost exclusively via the aberrant splice sites leading to a deficiency of correctly spliced β-globin mRNA and, consequently, β-globin. We have designed a series of vectors that express modified U7 snRNAs containing sequences antisense to either the aberrant 5′ or 3′ splice sites in the IVS2–705 thalassemic pre-mRNA. Transient expression of modified U7 snRNAs in a HeLa cell line stably expressing the IVS2–705 β-globin gene restored up to 65% of correct splicing in a sequence-specific and dose-dependent manner. Cell lines that stably coexpressed IVS2–705 pre-mRNA and appropriately modified U7 snRNA exhibited up to 55% of permanent restoration of correct splicing and expression of full-length β-globin protein. This novel approach provides a potential alternative to gene replacement therapies.
Solution structure of a DNA decamer duplex containing the stable 3′ T⋅G base pair of the pyrimidine(6–4)pyrimidone photoproduct [(6–4) adduct]: Implications for the highly specific 3′ T → C transition of the (6–4) adduct
Authors: Lee Joon-Hwa , Hwang Geum-Sook , Choi Byong-Seok
Published: July 2002

The pyrimidine(6–4)pyrimidone photoproduct [(6–4) adduct] is one of the major photoproducts induced by UV irradiation of DNA and occurs at TpT sites. The (6–4) adduct is highly mutagenic and leads most often to a 3′ T → C transition with 85% replicating error frequency [LeClerc, J. E., Borden, A. & Lawrence, C. W. (1991)
Proc. Natl. Acad. Sci. USA
88, 9685–9689]. To determine the origin of the specific 3′ T → C transition of the (6–4) adduct, we have used experimental NMR restraints and molecular dynamics to determine the solution structure of a (6–4)-lesion DNA decamer duplex that contains a mismatched base pair between the 3′ T residue and an opposed G residue. Normal Watson–Crick-type hydrogen bonding is retained at the 5′ T of the lesion site. The O2 carbonyl of the 3′ T residue forms hydrogen bonds with the imino and amino protons of the opposed G residue. This potential hydrogen bonding stabilizes the overall helix and restores the highly distorted conformation of the (6–4) adduct to the typical B-form-like DNA structure. This structural feature can explain the marked preference for the insertion of an A residue opposite the 5′ T and a G residue opposite the 3′ T of the (6–4) lesion during trans-lesion synthesis. Thus these insertions yield the predominant 3′ T → C transition.
Dominant-negative mutation in the β2 and β6 proteasome subunit genes affect alternative cell fate decisions in the
Drosophila
sense organ lineage
Authors: Schweisguth François
Published: July 2002

In
Drosophila
, dominant-negative mutations in the β2 and β6 proteasome catalytic subunit genes have been identified as dominant temperature-sensitive (DTS) mutations. At restrictive temperature, β2 and β6 DTS mutations confer lethality at the pupal stage. I investigate here the role of proteasome activity in regulating cell fate decisions in the sense organ lineage at the early pupal stage. Temperature-shift experiments in β2 and β6 DTS mutant pupae occasionally resulted in external sense organs with two sockets and no shaft. This double-socket phenotype was strongly enhanced in conditions in which Notch signaling was up-regulated. Furthermore, conditional overexpression of the β6 dominant-negative mutant subunit led to shaft-to-socket and to neuron-to-sheath cell fate transformations, which are both usually associated with increased Notch signaling activity. Finally, expression of the β6 dominant-negative mutant subunit led to the stabilization of an ectopically expressed nuclear form of Notch in imaginal wing discs. This study demonstrates that mutations affecting two distinct proteasome catalytic subunits affect two alternative cell fate decisions and enhance Notch signaling activity in the sense organ lineage. These findings raise the possibility that the proteasome targets an active form of the Notch receptor for degradation in
Drosophila
.
Two distinct mechanisms drive protein translocation across the mitochondrial outer membrane in the late step of the cytochrome
b
2
import pathway
Authors: Esaki Masatoshi , Kanamori Takashi , Nishikawa Shuh-ichi , Endo Toshiya
Published: July 2002

The import of cytochrome
b
2
into mitochondria consists of two steps. The translocation of the first part of the presequence across the inner membrane is coupled with the translocation of the tightly folded heme-binding domain across the outer membrane and requires a membrane potential ΔΨ and the functions of mitochondrial Hsp70 (mHsp70) in the matrix. Once the heme-binding domain has passed the outer membrane, the translocation of the rest of the polypeptide chain across the outer membrane becomes independent of ΔΨ and mHsp70. Here we analyzed the late ΔΨ- and mHsp70-independent step in the transport of cytochrome
b
2
fusion proteins into the intermembrane space (IMS). The import of the cytochrome
b
2
fusion proteins containing two protein domains linked by a spacer segment into mitochondria was arrested at a stage at which one domain folded on each side of the outer membrane, along the pathway that is consistent with the stop-transfer model. The mature-size form of the translocation intermediate could move across the outer membrane in both directions, and the stabilization of the protein domain in the IMS promoted the forward translocation. On the other hand, the intermediate-size form of the translocation intermediate, which retains the anchorage to the inner membrane, was transported into the IMS independently of the stability of the protein domain in the IMS. These results suggest that two distinct mechanisms, the Brownian ratchet and the anchor diffusion mechanisms, can operate for the transmembrane movement of the mature-size form and the intermediate-size form, respectively, of cytochrome
b
2
species.
The mycosubtilin synthetase of
Bacillus subtilis
ATCC6633: A multifunctional hybrid between a peptide synthetase, an amino transferase, and a fatty acid synthase
Authors: Duitman Erwin H. , Hamoen Leendert W. , Rembold Martina , Venema Gerard , Seitz Harald , Saenger Wolfram , Bernhard Frank , Reinhardt Richard , Schmidt Manuel , Ullrich Christian , Stein Torsten , Leenders Frank , Vater Joachim
Published: July 2002

Bacillus subtilis
strain ATCC6633 has been identified as a producer of mycosubtilin, a potent antifungal peptide antibiotic. Mycosubtilin, which belongs to the iturin family of lipopeptide antibiotics, is characterized by a β-amino fatty acid moiety linked to the circular heptapeptide Asn-Tyr-Asn-Gln-Pro-Ser-Asn, with the second, third, and sixth position present in the D-configuration. The gene cluster from
B. subtilis
ATCC6633 specifying the biosynthesis of mycosubtilin was identified. The putative operon spans 38 kb and consists of four ORFs, designated
fenF
,
mycA
,
mycB
, and
mycC
, with strong homologies to the family of peptide synthetases. Biochemical characterization showed that MycB specifically adenylates tyrosine, as expected for mycosubtilin synthetase, and insertional mutagenesis of the operon resulted in a mycosubtilin-negative phenotype. The mycosubtilin synthetase reveals features unique for peptide synthetases as well as for fatty acid synthases: (
i
) The mycosubtilin synthase subunit A (MycA) combines functional domains derived from peptide synthetases, amino transferases, and fatty acid synthases. MycA represents the first example of a natural hybrid between these enzyme families. (
ii
) The organization of the synthetase subunits deviates from that commonly found in peptide synthetases. On the basis of the described characteristics of the mycosubtilin synthetase, we present a model for the biosynthesis of iturin lipopeptide antibiotics. Comparison of the sequences flanking the mycosubtilin operon of
B. subtilis
ATCC6633, with the complete genome sequence of
B. subtilis
strain 168 indicates that the fengycin and mycosubtilin lipopeptide synthetase operons are exchanged between the two
B. subtilis
strains.
Cryptocyanin, a crustacean molting protein: Evolutionary link with arthropod hemocyanins and insect hexamerins
Authors: Terwilliger Nora B. , Dangott Lawrence , Ryan Margaret
Published: July 2002

Cryptocyanin, a copper-free hexameric protein in crab (Cancer magister) hemolymph, has been characterized and the amino acid sequence has been deduced from its cDNA. It is markedly similar in sequence, size, and structure to hemocyanin, the copper-containing oxygen-transport protein found in many arthropods. Cryptocyanin does not bind oxygen, however, and lacks three of the six highly conserved copper-binding histidine residues of hemocyanin. Cryptocyanin has no phenoloxidase activity, although a phenoloxidase is present in the hemolymph. The concentration of cryptocyanin in the hemolymph is closely coordinated with the molt cycle and reaches levels higher than hemocyanin during premolt. Cryptocyanin resembles insect hexamerins in the lack of copper, molt cycle patterns of biosynthesis, and potential contributions to the new exoskeleton. Phylogenetic analysis of sequence similarities between cryptocyanin and other members of the hemocyanin gene family shows that cryptocyanin is closely associated with crustacean hemocyanins and suggests that cryptocyanin arose as a result of a hemocyanin gene duplication. The presence of both hemocyanin and cryptocyanin in one animal provides an example of how insect hexamerins might have evolved from hemocyanin. Our results suggest that multiple members of the hemocyanin gene family—hemocyanin, cryptocyanin, phenoloxidase, and hexamerins—may participate in two vital functions of molting animals, oxygen binding and molting. Cryptocyanin may provide important molecular data to further investigate evolutionary relationships among all molting animals.
The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks
Authors: Chuang Ray-Yuan , Kelly Thomas J.
Published: July 2002

The origin recognition complex (ORC) was originally identified in the yeast
Saccharomyces cerevisiae
as a protein that specifically binds to origins of DNA replication. Although ORC appears to play an essential role in the initiation of DNA replication in the cells of all eukaryotes, its interactions with DNA have not been defined in species other than budding yeast. We have characterized a
Schizosaccharomyces pombe
homologue of the ORC subunit, Orc4p. The homologue (Orp4p) consists of two distinct functional domains. The C-terminal domain shows strong sequence similarity to human, frog, and yeast Orc4 proteins, including conserved ATP-binding motifs. The N-terminal domain contains nine copies of the AT-hook motif found in a number of DNA-binding proteins, including the members of the HMG-I(Y) family of chromatin proteins. AT-hook motifs are known from biochemical and structural studies to mediate binding to the minor groove of AT-tracts in DNA. Orp4p is essential for viability of
Sc. pombe
and is expressed throughout the cell cycle. The Orp4 protein (and its isolated N-terminal domain) binds to the
Sc. pombe
replication origin,
ars1
. The DNA binding properties of Orp4p provide a plausible explanation for the characteristic features of
Sc. pombe
origins of replication, which differ significantly from those of
Sa. cerevisiae
.
Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations
Authors: Jin Li , Underhill Peter A. , Doctor Vishal , Davis Ronald W. , Shen Peidong , Cavalli-Sforza L. Luca , Oefner Peter J.
Published: July 2002

Despite mounting genetic evidence implicating a recent origin of modern humans, the elucidation of early migratory gene-flow episodes remains incomplete. Geographic distribution of haplotypes may show traces of ancestral migrations. However, such evolutionary signatures can be erased easily by recombination and mutational perturbations. A 565-bp chromosome 21 region near the
MX1
gene, which contains nine sites frequently polymorphic in human populations, has been found. It is unaffected by recombination and recurrent mutation and thus reflects only migratory history, genetic drift, and possibly selection. Geographic distribution of contemporary haplotypes implies distinctive prehistoric human migrations: one to Oceania, one to Asia and subsequently to America, and a third one predominantly to Europe. The findings with chromosome 21 are confirmed by independent evidence from a Y chromosome phylogeny. Loci of this type will help to decipher the evolutionary history of modern humans.
Enhanced metabolism of halogenated hydrocarbons in transgenic plants containing mammalian cytochrome P450 2E1
Authors: Doty Sharon Lafferty , Shang Tanya Q. , Wilson Angela M. , Tangen Jeff , Westergreen Aram D. , Newman Lee A. , Strand Stuart E. , Gordon Milton P.
Published: July 2002

Chlorinated solvents, especially trichloroethylene (TCE), are the most widespread groundwater contaminants in the United States. Existing methods of pumping and treating are expensive and laborious. Phytoremediation, the use of plants for remediation of soil and groundwater pollution, is less expensive and has low maintenance; however, it requires large land areas and there are a limited number of suitable plants that are known to combine adaptation to a particular environment with efficient metabolism of the contaminant. In this work, we have engineered plants with a profound increase in metabolism of the most common contaminant, TCE, by introducing the mammalian cytochrome P450 2E1. This enzyme oxidizes a wide range of important pollutants, including TCE, ethylene dibromide, carbon tetrachloride, chloroform, and vinyl chloride. The transgenic plants had a dramatic enhancement in metabolism of TCE of up to 640-fold as compared with null vector control plants. The transgenic plants also showed an increased uptake and debromination of ethylene dibromide. Therefore, transgenic plants with this enzyme could be used for more efficient remediation of many sites contaminated with halogenated hydrocarbons.
The drug situation in Thailand: the role of government and the police
Authors: CHEURPRAKOBKIT SUTHAM
Published: July 2002

Thailand has long dealt with the drug problem and has used several strategies to control it, including promulgating and amending drug laws, implementing drug suppression and prevention policies, cooperating with international organizations and, more recently, developing treatment facilities. Although Thailand has recently received positive results regarding reducing the opium cultivation area in the Golden Triangle and in arresting some major drug‐trafficking individuals, three important issues still remain: (1) the continuation of using Thailand's advanced transportation system for the movement of illicit drug activities, (2) the rapid increase of amphetamine use among teenagers and (3) the Thai police officers' lack of concern about the drug problem and insufficient knowledge about drug laws. The article concludes that the Thai government must emphasize drug prevention strategies and the interception of illicit transported drugs and motivate its police officers to more fully enforce drug laws. In addition, more research is needed to measure the effectiveness of the drug prevention strategies and treatment programs.
The Pattern of Disulfide Linkages in the Extracellular Loop Regions of Connexin 32 Suggests a Model for the Docking Interface of Gap Junctions
Authors: Foote Cynthia I. , Zhou Lan , Zhu Xing , Nicholson Bruce J.
Published: July 2002

Connexins, like true cell adhesion molecules, have extracellular domains that provide strong and specific homophilic, and in some cases, heterophilic interactions between cells. Though the structure of the binding domains of adhesion proteins have been determined, the extracellular domains of connexins, consisting of two loops of ∼34–37 amino acids each, are not easily studied in isolation from the rest of the molecule. As an alternative, we used a novel application of site-directed mutagenesis in which four of the six conserved cysteines in the extracellular loops of connexin 32 were moved individually and in all possible pairwise and some quadruple combinations. This mapping allowed us to deduce that all disulfides form between the two loops of a single connexin, with the first cysteine in one loop connected to the third of the other. Furthermore, the periodicity of movements that produced functional channels indicated that these loops are likely to form antiparallel β sheets. A possible model that could explain how these domains from apposed connexins interact to form a complete channel is discussed.
Intercellular Adhesion Molecule-5 Induces Dendritic Outgrowth by Homophilic Adhesion
Authors: Tian Li , Nyman Henrietta , Kilgannon Patrick , Yoshihara Yoshihiro , Mori Kensaku , Andersson Leif C. , Kaukinen Sami , Rauvala Heikki , Gallatin W. Michael , Gahmberg Carl G.
Published: July 2002

Intercellular adhesion molecule-5 (ICAM-5) is a dendritically polarized membrane glycoprotein in telencephalic neurons, which shows heterophilic binding to leukocyte β2-integrins. Here, we show that the human ICAM-5 protein interacts in a homophilic manner through the binding of the immunoglobulin domain 1 to domains 4–5. Surface coated ICAM-5-Fc promoted dendritic outgrowth and arborization of ICAM- 5–expressing hippocampal neurons. During dendritogenesis in developing rat brain, ICAM-5 was in monomer form, whereas in mature neurons it migrated as a high molecular weight complex. The findings indicate that its homophilic binding activity was regulated by nonmonomer/monomer transition. Thus, ICAM-5 displays two types of adhesion activity, homophilic binding between neurons and heterophilic binding between neurons and leukocytes.
Multiple Distinct Targeting Signals in Integral Peroxisomal Membrane Proteins
Authors: Jones Jacob M. , Morrell James C. , Gould Stephen J.
Published: July 2002

Peroxisomal proteins are synthesized on free polysomes and then transported from the cytoplasm to peroxisomes. This process is mediated by two short well-defined targeting signals in peroxisomal matrix proteins, but a well-defined targeting signal has not yet been described for peroxisomal membrane proteins (PMPs). One assumption in virtually all prior studies of PMP targeting is that a given protein contains one, and only one, distinct targeting signal. Here, we show that the metabolite transporter PMP34, an integral PMP, contains at least two nonoverlapping sets of targeting information, either of which is sufficient for insertion into the peroxisome membrane. We also show that another integral PMP, the peroxin PEX13, also contains two independent sets of peroxisomal targeting information. These results challenge a major assumption of most PMP targeting studies. In addition, we demonstrate that PEX19, a factor required for peroxisomal membrane biogenesis, interacts with the two minimal targeting regions of PMP34. Together, these results raise the interesting possibility that PMP import may require novel mechanisms to ensure the solubility of integral PMPs before their insertion in the peroxisome membrane, and that PEX19 may play a central role in this process.
Abnormal Development of Intestinal Intraepithelial Lymphocytes and Peripheral Natural Killer Cells in Mice Lacking the IL-2 Receptor β Chain
Authors: Suzuki Haruhiko , Duncan Gordon S. , Takimoto Hiroaki , Mak Tak W.
Published: July 2002

The interleukin-2 receptor β chain (IL-2Rβ) is expressed on a variety of hematopoietic cell types, including natural killer (NK) cells and nonconventional T lymphocyte subsets such as intestinal intraepithelial lymphocytes (IEL). However, the importance of IL-2Rβ-mediated signaling in the growth and development of these cells has yet to be clearly established. We have investigated IEL and NK cells in mice deficient for IL-2Rβ and describe here striking defects in the development of these cells. IL-2Rβ−/− mice exhibited an abnormal IEL cell population, characterized by a dramatic reduction in T cell receptor αβ CD8αα and T cell receptor γδ lymphocytes. This selective decrease indicates that IEL can be classified into those whose development and/or differentiation is dependent on IL-2Rβ function and those for which IL-2Rβ–mediated signaling is not essential. NK cell development was also found to be disrupted in IL-2Rβ–deficient mice, characterized by a reduction in NK1.1+CD3− cells in the peripheral circulation and an absence of NK cytotoxic activity in vitro. The dependence of NK cells and certain subclasses of IEL cells on IL-2Rβ expression points to an essential role for signaling through this receptor, presumably by IL-2 and/or IL-15, in the development of lymphocyte subsets of extrathymic origin.
Mouse CD94/NKG2A Is a Natural Killer Cell Receptor for the Nonclassical Major Histocompatibility Complex (MHC) Class I Molecule Qa-1b
Authors: Vance Russell E. , Kraft Jennifer R. , Altman John D. , Jensen Peter E. , Raulet David H.
Published: July 2002

Natural killer (NK) cells preferentially lyse targets that express reduced levels of major histocompatibility complex (MHC) class I proteins. To date, the only known mouse NK receptors for MHC class I belong to the Ly49 family of C-type lectin homodimers. Here, we report the cloning of mouse NKG2A, and demonstrate it forms an additional and distinct class I receptor, a CD94/NKG2A heterodimer. Using soluble tetramers of the nonclassical class I molecule Qa-1b, we provide direct evidence that CD94/NKG2A recognizes Qa-1b. We further demonstrate that NK recognition of Qa-1b results in the inhibition of target cell lysis. Inhibition appears to depend on the presence of Qdm, a Qa-1b-binding peptide derived from the signal sequences of some classical class I molecules. Mouse NKG2A maps adjacent to CD94 in the heart of the NK complex on mouse chromosome six, one of a small cluster of NKG2-like genes. Our findings suggest that mouse NK cells, like their human counterparts, use multiple mechanisms to survey class I expression on target cells.
Protection from Respiratory Virus Infections Can Be Mediated by Antigen-Specific Cd4+ T Cells That Persist in the Lungs
Authors: Hogan Robert J. , Zhong Weimin , Usherwood Edward J. , Cookenham Tres , Roberts Alan D. , Woodland David L.
Published: July 2002

Although CD4+ T cells have been shown to mediate protective cellular immunity against respiratory virus infections, the underlying mechanisms are poorly understood. For example, although phenotypically distinct populations of memory CD4+ T cells have been identified in different secondary lymphoid tissues, it is not known which subpopulations mediate protective cellular immunity. In this report, we demonstrate that virus-specific CD4+ T cells persist in the lung tissues and airways for several months after Sendai virus infection of C57BL/6 mice. A large proportion of these cells possess a highly activated phenotype (CD44hi, CD62Llo, CD43hi, and CD25hi) and express immediate effector function as indicated by the production of interferon γ after a 5-h restimulation in vitro. Furthermore, intratracheal adoptive transfer of lung memory cells into β2m-deficient mice demonstrated that lung-resident virus-specific CD4+ T cells mediated a substantial degree of protection against secondary virus infection. Taken together, these data demonstrate that activated memory CD4+ T cells persisting at mucosal sites play a critical role in mediating protective cellular immunity.
T Cell Homeostasis
Authors: Almeida Afonso R.M. , Borghans José A.M. , Freitas António A.
Published: July 2002

We developed a novel experimental strategy to study T cell regeneration after bone marrow transplantation. We assessed the fraction of competent precursors required to repopulate the thymus and quantified the relationship between the size of the different T cell compartments during T cell maturation in the thymus. The contribution of the thymus to the establishment and maintenance of the peripheral T cell pools was also quantified. We found that the degree of thymus restoration is determined by the availability of competent precursors and that the number of double-positive thymus cells is not under homeostatic control. In contrast, the sizes of the peripheral CD4 and CD8 T cell pools are largely independent of the number of precursors and of the number of thymus cells. Peripheral “homeostatic” proliferation and increased export and/or survival of recent thymus emigrants compensate for reduced T cell production in the thymus. In spite of these reparatory processes, mice with a reduced number of mature T cells in the thymus have an increased probability of peripheral T cell deficiency, mainly in the naive compartment.
Endomorphisms of finite full transformation semigroups
Authors: Schein Boris , Teclezghi Beimnet
Published: July 2002

We describe all endomorphisms of finite full transformation semigroups and count their number.
The Schwarzian derivative for maps between manifolds with complex projective connections
Authors: Molzon Robert , Mortensen Karen
Published: July 2002

In this paper we define, in two equivalent ways, the Schwarzian derivative of a map between complex manifolds equipped with complex projective connections. Also, a new, coordinate-free definition of complex projective connections is given. We show how the Schwarzian derivative is related to the projective structure of the manifolds, to projective linear transformations, and to complex geodesics.
Primes in arithmetic progressions
Authors: Ramaré Olivier , Rumely Robert
Published: July 2002

Strengthening work of Rosser, Schoenfeld, and McCurley, we establish explicit Chebyshev-type estimates in the prime number theorem for arithmetic progressions, for all moduli

k
≤
72

k \le 72

and other small moduli.
On the Diophantine equation |𝑎𝑥ⁿ-𝑏𝑦ⁿ|=1
Authors: Bennett Michael , de Weger Benjamin
Published: July 2002

If

a
,
b

a, b

and

n
n

are positive integers with

b
≥
a

b \geq a

and

n
≥
3

n \geq 3

, then the equation of the title possesses at most one solution in positive integers

x
x

and

y
y

, with the possible exceptions of

(
a
,
b
,
n
)

( a, b, n )

satisfying

b
=
a
+
1

b = a + 1

,

2
≤
a
≤
min
{
0.3
n
,
83
}

2 \leq a \leq \min \{ 0.3 n, 83 \}

and

17
≤
n
≤
347

17 \leq n \leq 347

. The proof of this result relies on a variety of diophantine approximation techniques including those of rational approximation to hypergeometric functions, the theory of linear forms in logarithms and recent computational methods related to lattice-basis reduction. Additionally, we compare and contrast a number of these last mentioned techniques.
Regulation of Fab1 Phosphatidylinositol 3-Phosphate 5-Kinase Pathway by Vac7 Protein and Fig4, a Polyphosphoinositide Phosphatase Family Member
Authors: Gary Jonathan D. , Sato Trey K. , Stefan Christopher J. , Bonangelino Cecilia J. , Weisman Lois S. , Emr Scott D.
Published: July 2002

The Saccharomyces cerevisiae FAB1 gene encodes the sole phosphatidylinositol 3-phosphate [PtdIns(3)P] 5-kinase responsible for synthesis of the polyphosphoinositide PtdIns(3,5)P2. VAC7 encodes a 128-kDa transmembrane protein that localizes to vacuolar membranes. Bothvac7 and fab1 null mutants have dramatically enlarged vacuoles and cannot grow at elevated temperatures. Additionally, vac7Δ mutants have nearly undetectable levels of PtdIns(3,5)P2, suggesting that Vac7 functions to regulate Fab1 kinase activity. To test this hypothesis, we isolated a fab1 mutant allele that bypasses the requirement for Vac7 in PtdIns(3,5)P2production. Expression of this fab1 allele in vac7Δmutant cells suppresses the temperature sensitivity, vacuolar morphology, and PtdIns(3,5)P2defects normally exhibited byvac7Δ mutants. We also identified a mutant allele ofFIG4, whose gene product contains a Sac1polyphosphoinositide phosphatase domain, which suppressesvac7Δ mutant phenotypes. Deletion ofFIG4 in vac7Δ mutant cells suppresses the temperature sensitivity and vacuolar morphology defects, and dramatically restores PtdIns(3,5)P2levels. These results suggest that generation of PtdIns(3,5)P2by the Fab1 lipid kinase is regulated by Vac7, whereas turnover of PtdIns(3,5)P2is mediated in part by theSac1 polyphosphoinositide phosphatase family member Fig4.
Inhibitors of COP-mediated Transport and Cholera Toxin Action Inhibit Simian Virus 40 Infection
Authors: Richards Ayanthi A. , Stang Espen , Pepperkok Rainer , Parton Robert G.
Published: July 2002

Simian virus 40 (SV40) is a nonenveloped virus that has been shown to pass from surface caveolae to the endoplasmic reticulum in an apparently novel infectious entry pathway. We now show that the initial entry step is blocked by brefeldin A and by incubation at 20°C. Subsequent to the entry step, the virus reaches a domain of the rough endoplasmic reticulum by an unknown pathway. This intracellular trafficking pathway is also brefeldin A sensitive. Infection is strongly inhibited by expression of GTP-restricted ADP-ribosylation factor 1 (Arf1) and Sar1 mutants and by microinjection of antibodies to βCOP. In addition, we demonstrate a potent inhibition of SV40 infection by the dipeptideN-benzoyl-oxycarbonyl-Gly-Phe-amide, which also inhibits late events in cholera toxin action. Our results identify novel inhibitors of SV40 infection and show that SV40 requires COPI- and COPII-dependent transport steps for successful infection.
A model for prediction of fume formation rate in gas metal arc welding (GMAW), globular and spray modes, DC electrode positive
Authors: Dennis John H. , Hewitt Peter J. , Redding Christopher A. J. , Workman Andrew D.
Published: July 2002

Prediction of fume formation rate during metal arc welding and the composition of the fume are of interest to occupational hygienists concerned with risk assessment and to manufacturers of welding consumables. A model for GMAW (DC electrode positive) is described based on the welder determined process parameters (current, wire feed rate and wire composition), on the surface area of molten metal in the arc and on the partial vapour pressures of the component metals of the alloy wire. The model is applicable to globular and spray welding transfer modes but not to dip mode. Metal evaporation from a droplet is evaluated for short time increments and total evaporation obtained by summation over the life of the droplet. The contribution of fume derived from the weld pool and spatter (particles of metal ejected from the arc) is discussed, as are limitations of the model. Calculated droplet temperatures are similar to values determined by other workers. A degree of relationship between predicted and measured fume formation rates is demonstrated but the model does not at this stage provide a reliable predictive tool.
Analysis of temporal gene expression profiles: clustering by

simulated annealing and determining the optimal number of clusters
Authors: Lukashin Alexander V. , Fuchs Rainer
Published: July 2002

Motivation: Cluster analysis of genome-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and samples. In the present paper, we focus on several important issues related to clustering algorithms that have not yet been fully studied.

Results: We describe a simple and robust algorithm for the clustering of temporal gene expression profiles that is based on the simulated annealing procedure. In general, this algorithm guarantees to eventually find the globally optimal distribution of genes over clusters. We introduce an iterative scheme that serves to evaluate quantitatively the optimal number of clusters for each specific data set. The scheme is based on standard approaches used in regular statistical tests. The basic idea is to organize the search of the optimal number of clusters simultaneously with the optimization of the distribution of genes over clusters. The efficiency of the proposed algorithm has been evaluated by means of a reverse engineering experiment, that is, a situation in which the correct distribution of genes over clusters is known a priori. The employment of this statistically rigorous test has shown that our algorithm places greater than 90% genes into correct clusters. Finally, the algorithm has been tested on real gene expression data (expression changes during yeast cell cycle) for which the fundamental patterns of gene expression and the assignment of genes to clusters are well understood from numerous previous studies.

Availability: The source code of the program implementing the algorithm is available upon request from the authors.

Contact: alex_lukashin@biogen.com

* To whom correspondence should be addressed.
Drosophila tracheal system formation involves FGF‐dependent cell extensions contacting bridge‐cells
Authors: Wolf Christian , Gerlach Nina , Schuh Reinhard
Published: July 2002

Development of the ectodermally derived Drosophila tracheal system is based on branch outgrowth and fusion that interconnect metamerically arranged tracheal subunits into a highly stereotyped three‐dimensional tubular structure. Recent studies have revealed that this process involves a specialized cell type of mesodermal origin, termed bridge‐cell. Single bridge‐cells are located between adjacent tracheal subunits and serve as guiding posts for the outgrowing dorsal trunk branches. We show that bridge‐cell‐approaching tracheal cells form filopodia‐like cell extensions, which attach to the bridge‐cell surface and are essential for the tracheal subunit interconnection. The results of both dominant‐negative and gain‐of‐function experiments suggest that the formation of cell extensions require Cdc42‐mediated Drosophila fibroblast growth factor activity.
Levofloxacin: serum bactericidal activity against methicillin-resistant Staphylococcus aureus isolates
Authors: Muller-Serieys C. , Decré D. , Benoit C. , Bigot C. , Maubert B. , Carbon C.
Published: July 2002

The aim of this study was to assess the serum bactericidal activity (SBA) of levofloxacin compared with that of ofloxacin against methicillin-resistant Staphylococcus aureus (MRSA) isolates. Serum from 10 healthy volunteers (seven females, three males) was collected after a single oral dose of either levofloxacin (500 mg) or ofloxacin (400 mg). Subjects were allocated randomly to treatment after at least a 1 week interval between antibiotic regimens. Three well-defined MRSA strains were tested, each susceptible to levofloxacin and ofloxacin, with different levels of resistance to methicillin (HBD 456, HBD 3 and HBD 2; class 1, 2 and 3 Tomasz heterogeneous resistance, respectively) together with a methicillin-susceptible (MSSA) reference strain ( S. aureus ATCC 25923). SBA was tested in vitro by a microtitration method 15 min before dosing and at 1, 4, 8 and 12 h after drug absorption. Levofloxacin was significantly more bactericidal than ofloxacin against all strains of S. aureus tested (SBA ≥1:2). An SBA was recorded for only a short period with ofloxacin, and thereafter only bacteriostatic activity remained. This study, therefore, confirms the superior activity of levofloxacin over that of ofloxacin against MSSA and MRSA.
Detection and processing of electromagnetic and near–field acoustic signals in elasmobranch fishes
Authors: Kalmijn Ad. J.
Published: July 2002

The acoustic near field of quietly moving underwater objects and the bio–electric field of aquatic animals exhibit great similarity, as both are predominantly governed by Laplace's equation. The acoustic and electrical sensory modalities thus may, in directing fishes to their prey, employ analogous processing algorithms, suggesting a common evolutionary design, founded on the salient physical features shared by the respective stimulus fields. Sharks and rays are capable of orientating to the earth's magnetic field and, hence, have a magnetic sense. The electromagnetic theory of orientation offers strong arguments for the animals using the electric fields induced by ocean currents and by their own motions in the earth's magnetic field. In the animal's frame of reference, in which the sense organs are at rest, the classical concept of motional electricity must be interpreted in relativistic terms. In the ampullae of Lorenzini, weak electric fields cause the ciliated apical receptor–cell membranes to produce graded, negative receptor currents opposite in direction to the fields applied. The observed currents form part of a positive–feedback mechanism, supporting the generation of receptor potentials much larger than the input signal. Acting across the basal cell membranes, the receptor potentials control the process of synaptic transmission.
Chloroplast DNA methylation and inheritance in Chlamydomonas
Authors: Umen James G. , Goodenough Ursula W.
Published: July 2002

When Chlamydomonas reinhardtii cells mate, a zygotic maturation program is activated, part of which leads to destruction of chloroplast DNA (cpDNA) from the mating type minus(mt−) parent, and, therefore, to uniparental inheritance of mating type plus (mt+) cpDNA. A long-standing model that explains the selective destruction ofmt− cpDNA in zygotes invokes a methylation-restriction system. We tested this model by using the potent methylation inhibitor 5-aza-2‘-deoxycytidine (5adc) to hypomethylate parental cpDNA and found that the pattern of cpDNA inheritance is altered by 5adc in a manner that is consistent with the model. Surprisingly, however, hypomethylated mt+cpDNA is not destroyed in zygotes as the methylation-restriction model predicts it should be. Destruction of mt− cpDNA is also unaffected when the parental mt+ cpDNA is hypomethylated. Instead, loss of methylation affects the relative rates of replication of residual mt− cpDNA andmt+ cpDNA in germinating zygotes. The mode of action for 5adc on cpDNA replication in germinating zygotes may be via hypomethylation of mt+ cpDNA, but is also consistent with its action as a DNA-damaging agent. Interestingly, 5adc causes reduced cpDNA replication only in germinating zygotes, not in vegetatively grown cells, indicating that cpDNA replication is qualitatively different in these two stages of the life cycle. Our results demonstrate that methylation is not necessary for protection of the mt+ cpDNA in early zygotes and uncover a novel stage of the Chlamydomonas life cycle when replication of cpDNA is highly susceptible to perturbation. Our data support a model in which differential cpDNA replication in germinating zygotes is used as a mechanism to selectively amplify intact and properly methylated cpDNA molecules.
Verbal and Nonverbal Emotional Memory Following Unilateral Amygdala Damage
Authors: Buchanan Tony W. , Denburg Natalie L. , Tranel Daniel , Adolphs Ralph
Published: July 2002

The amygdala is involved in the normal facilitation of memory by emotion, but the separate contributions of the left and right amygdala to memory for verbal or nonverbal emotional material have not been investigated. Fourteen patients with damage to the medial temporal lobe including the amygdala (seven left, seven right), 18 brain-damaged, and 36 normal controls were exposed to emotional and neutral pictures accompanied by verbal narratives. Memory for both narratives and pictures was assessed with a free recall test 24 h later. Subjects with left amygdala damage failed to show the normally robust enhancement of memory for verbal and nonverbal emotional stimuli. The group with right amygdala damage showed the normal pattern of facilitation of memory by emotion for both verbal and nonverbal stimuli despite an overall reduction in memory performance. Furthermore, subjects with left amygdala damage were disproportionately impaired on memory for emotional narratives as compared with memory for emotional pictures. The latter finding offers partial support for a lateralized and material-specific pattern of the amygdala's contribution to emotional memory.
A simple model for the nonretarded dispersive force between an electrically polarizable atom and a magnetically polarizable one
Authors: Farina C. , Santos F. C. , Tort A. C.
Published: July 2002

It is known that the consideration or not of retardation effects on the dispersive van der Waals force between two electrically polarizable atoms leads to power laws for the forces that differ only by one power: 1/r8 for the retarded force and 1/r7 for the nonretarded one. On the other hand, for the case of an electrically polarizable atom and a magnetically polarizable one, while the retarded force is still proportional to 1/r8, the nonretarded one is proportional to 1/r5. Here, employing the fluctuating dipole model for both atoms, we reobtain this quite unexpected behavior for the nonretarded force mentioned above. A physical interpretation is also given for such a result.
Floquet’s theorem and matrices for parametric oscillators: Theory and demonstrations
Authors: Fameli N. , Curzon F. L. , Mikoshiba S.
Published: July 2002

The restoring force (kx) of a parametric oscillator is proportional to the displacement (x) but the proportionality factor (k) varies periodically with time (t). This fact gives rise to novel dynamic behavior that can be described with elementary mathematics without knowing the specific dependence of k on t. In addition to gathering together previously available results we also treat special cases, including the effects of degeneracy and damping. A particularly simple practical oscillator (the “yendulum”) is described which makes use of five yen Japanese coins for demonstrating the results presented in the theory of the oscillator.
A simple way of understanding the nonadditivity of van der Waals dispersion forces
Authors: Farina C. , Santos F. C. , Tort A. C.
Published: July 2002

Using a semiclassical model for three interacting fluctuating dipoles we introduce a simple scenario in which the nonadditivity of the van der Waals dispersion forces arises in a very transparent way. For simplicity, we illustrate our model in the case of nonretarded dispersion forces. The argument can be straightforwardly generalized to the case of N interacting fluctuating dipoles. For pedagogical reasons, we also give a brief review of some basic points concerning van der Waals forces.
Stern–Gerlach measurements with arbitrary spin: Quantum combs
Authors: Schönhammer K.
Published: July 2002

As in quantum mechanics the operators of different Cartesian components of the angular momentum do not commute these observables cannot simultaneously have sharp values. In this paper we present a simple method to calculate the probability distributions for the measurements of angular momentum components other than ĵz in eigenstates of ĵz with an arbitrary value of j, where ℏ2j(j+1) is the eigenvalue of ĵ2. Surprisingly this method is not found in textbooks, where usually the case j=12 is presented in discussions of Stern–Gerlach experiments. For larger values of j, the probability distributions have a comb-like structure. A detailed discussion of the quasiclassical limit j≫1 is presented for the measurement of ĵx. It yields rather surprising results.
The transformation of a main sequence star into a red-giant star in the core-and-shell model
Authors: Hauptmann H. , Herrmann F. , Schmidt K.
Published: July 2002

As a star evolves from the hydrogen to the helium burning stage, i.e., from the sun-like state to the state of a red-giant star, the temperature of its core increases whereas the volume decreases. At the same time the temperature of its shell decreases while the volume of the shell increases. This behavior of the core and of the shell is explained qualitatively by a simple model. The star is considered to be composed of two homogeneous subsystems: the active core where the heat production takes place and the shell which plays the part of a thermal insulator. Each of these subsystems is stabilized by a feedback mechanism which works thanks to the negative heat capacity of both systems.
State of the art of sonic boom modeling
Authors: Plotkin Kenneth J.
Published: July 2002

Based on fundamental theory developed through the 1950s and 1960s, sonic boom modeling has evolved into practical tools. Over the past decade, there have been requirements for design tools for an advanced supersonic transport, and for tools for environmental assessment of various military and aerospace activities. This has resulted in a number of advances in the understanding of the physics of sonic booms, including shock wave rise times, propagation through turbulence, and blending sonic boom theory with modern computational fluid dynamics (CFD) aerodynamic design methods. This article reviews the early fundamental theory, recent advances in theory, and the application of these advances to practical models.
Comparison of voice F0 responses to pitch-shift onset and offset conditions
Authors: Larson Charles R. , Burnett Theresa A. , Bauer Jay J. , Kiran Swathi , Hain Timothy C.
Published: July 2002

In order to maintain a steady voice fundamental frequency (F0), it is assumed that people compare their auditory feedback pitch with an internal (memory) or external (acoustic) referent. In the present study we examined whether the internal referent is fixed or variable by comparing voice F0 responses to incorrect auditory feedback in two timing conditions. In one condition, the incorrect pitch was introduced during vocalization (ON condition). In the second, the incorrect auditory feedback pitch was presented before vocal onset and then removed during vocalization (OFF condition). These conditions were examined with pitch-shift stimuli of ±25, 100, and 200 cents. There were no differences in response latency or magnitude between the two timing conditions, indicating that for a sustained-pitch vocalization task, the internal referent is not fixed. Several alternative types of referencing are discussed, which include use of a pitch relative to that which existed at the onset of vocalization (a sample and hold strategy) and pitch velocity referencing.
Acoustic dispersion and attenuation in many spherical scatterer systems and the Kramers–Kronig relations
Authors: Ye Zhen
Published: July 2002

This paper presents a theoretical study of the acoustic dispersion in media containing many spherical scatterers. The existing dispersion relation is used to investigate the dispersion in media containing particles such as low acoustic-contrast fluid, rigid and elastic spheres, as well as air bubbles. It is shown that in the case of low acoustic-contrast fluid, rigid and elastic spheres, the presence of scatterers has more profound effects on the acoustic attenuation than on the phase speed, whereas in the bubble case, both the attenuation and phase speed can be affected significantly. Then the dispersion relation is examined via the Kramers–Kronig relations, as they express a general identity for dispersion and are therefore ideal to test the suitability of a specific model for acoustic propagation. Results indicate that although there remain some discrepancies, the existing dispersion relation satisfies the Kramers–Kronig relations reasonably well. Good agreement is particularly apparent in the bubble case. Possible cause for the discrepancies is also discussed in connection with a discussion of the assumptions that lead to the dispersion relation.