bluuebunny/crossref_metadata_2025 huggingface dataset:
Blind separation of auditory event-related brain responses into independent components
Authors: Makeig Scott , Jung Tzyy-Ping , Bell Anthony J. , Ghahremani Dara , Sejnowski Terrence J.
Published: July 2002

Averaged event-related potential (ERP) data recorded from the human scalp reveal electroencephalographic (EEG) activity that is reliably time-locked and phase-locked to experimental events. We report here the application of a method based on information theory that decomposes one or more ERPs recorded at multiple scalp sensors into a sum of components with fixed scalp distributions and sparsely activated, maximally independent time courses. Independent component analysis (ICA) decomposes ERP data into a number of components equal to the number of sensors. The derived components have distinct but not necessarily orthogonal scalp projections. Unlike dipole-fitting methods, the algorithm does not model the locations of their generators in the head. Unlike methods that remove second-order correlations, such as principal component analysis (PCA), ICA also minimizes higher-order dependencies. Applied to detected—and undetected—target ERPs from an auditory vigilance experiment, the algorithm derived ten components that decomposed each of the major response peaks into one or more ICA components with relatively simple scalp distributions. Three of these components were active only when the subject detected the targets, three other components only when the target went undetected, and one in both cases. Three additional components accounted for the steady-state brain response to a 39-Hz background click train. Major features of the decomposition proved robust across sessions and changes in sensor number and placement. This method of ERP analysis can be used to compare responses from multiple stimuli, task conditions, and subject states.
The role of thyroid hormone in zebrafish and axolotl development
Authors: Brown Donald D.
Published: July 2002

Exogenous thyroid hormone (TH) induces premature differentiation of the zebrafish pectoral fins, which are analogous to the forelimbs of tetrapods. It accelerates the growth of the pelvic fins but not precociously. Goitrogens, which are chemical inhibitors of TH synthesis by the thyroid gland, inhibit the transition from larva to juvenile fish including the formation of scales, and pigment pattern; they stunt the growth of both pectoral and pelvic paired fins. Inhibition by goitrogens is rescued by the simultaneous addition of thyroxine. The effect of adding TH to the rearing water of the postembryonic Mexican axolotl was reinvestigated under conditions that permit continued growth and development. In addition to morphological changes that have been described, TH greatly stimulates axolotl limb growth causing the resulting larva to be proportioned as an adult in about two months. This study extends the known evolutionary relatedness of tetrapod limbs and fish fins to include the TH stimulation of salamander limb and zebrafish fin growth, and suggests that TH is required to complete the life cycle of a typical bony fish and a salamander at the same developmental stage that it controls anuran and flounder metamorphosis.
Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy
Authors: Chun Tae-Wook , Stuyver Lieven , Mizell Stephanie B. , Ehler Linda A. , Mican Jo Ann M. , Baseler Michael , Lloyd Alun L. , Nowak Martin A. , Fauci Anthony S.
Published: July 2002

Although highly active antiretroviral therapy (HAART) in the form of triple combinations of drugs including protease inhibitors can reduce the plasma viral load of some HIV-1-infected individuals to undetectable levels, it is unclear what the effects of these regimens are on latently infected CD4+T cells and what role these cells play in the persistence of HIV-1 infection in individuals receiving such treatment. The present study demonstrates that highly purified CD4+T cells from 13 of 13 patients receiving HAART with an average treatment time of 10 months and with undetectable (<500 copies HIV RNA/ml) plasma viremia by a commonly used bDNA assay carried integrated proviral DNA and were capable of producing infectious virus upon cellular activationin vitro. Phenotypic analysis of HIV-1 produced by activation of latently infected CD4+T cells revealed the presence in some patients of syncytium-inducing virus. In addition, the presence of unintegrated HIV-1 DNA in infected resting CD4+T cells from patients receiving HAART, even those with undetectable plasma viremia, suggests persistent active virus replicationin vivo.
Molecular evolution of two vertebrate aryl hydrocarbon (dioxin) receptors (AHR1 and AHR2) and the PAS family
Authors: Hahn Mark E. , Karchner Sibel I. , Shapiro Miriam A. , Perera Samanthi A.
Published: July 2002

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor through which halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo
-p-
dioxin (TCDD) cause altered gene expression and toxicity. The AHR belongs to the basic helix–loop–helix/Per-ARNT-Sim (bHLH-PAS) family of transcriptional regulatory proteins, whose members play key roles in development, circadian rhythmicity, and environmental homeostasis; however, the normal cellular function of the AHR is not yet known. As part of a phylogenetic approach to understanding the function and evolutionary origin of the AHR, we sequenced the PAS homology domain of AHRs from several species of early vertebrates and performed phylogenetic analyses of these AHR amino acid sequences in relation to mammalian AHRs and 24 other members of the PAS family. AHR sequences were identified in a teleost (the killifish
Fundulus heteroclitus
), two elasmobranch species (the skate
Raja erinacea
and the dogfish
Mustelus canis
), and a jawless fish (the lamprey
Petromyzon marinus
). Two putative
AHR
genes, designated
AHR1
and
AHR2
, were found both in
Fundulus
and
Mustelus
. Phylogenetic analyses indicate that the
AHR2
genes in these two species are orthologous, suggesting that an
AHR
gene duplication occurred early in vertebrate evolution and that multiple
AHR
genes may be present in other vertebrates. Database searches and phylogenetic analyses identified four putative PAS proteins in the nematode
Caenorhabditis elegans
, including possible AHR and ARNT homologs. Phylogenetic analysis of the PAS gene family reveals distinct clades containing both invertebrate and vertebrate PAS family members; the latter include paralogous sequences that we propose have arisen by gene duplication early in vertebrate evolution. Overall, our analyses indicate that the AHR is a phylogenetically ancient protein present in all living vertebrate groups (with a possible invertebrate homolog), thus providing an evolutionary perspective to the study of dioxin toxicity and AHR function.
A family of genes required for maintenance of cell wall integrity and for the stress response in
Saccharomyces cerevisiae
Authors: Verna James , Lodder Adriana , Lee Kyunghee , Vagts Alicia , Ballester Roymarie
Published: July 2002

The PKC1–MPK1 pathway in yeast functions in the maintenance of
cell wall integrity and in the stress response. We have identified a
family of genes that are putative regulators of this pathway.
WSC1
,
WSC2
, and
WSC3
encode predicted integral membrane proteins with a conserved cysteine
motif and a WSC1–green fluorescence protein fusion protein localizes
to the plasma membrane. Deletion of
WSC
results in
phenotypes similar to mutants in the PKC1–MPK1 pathway and an increase
in the activity of MPK1 upon a mild heat treatment is impaired in a
wsc
Δ mutant. Genetic analysis places the function of
WSC
upstream of
PKC1
, suggesting that
they play a role in its activation. We also find a genetic interaction
between
WSC
and the RAS–cAMP pathway. The RAS–cAMP
pathway is required for cell cycle progression and for the heat shock
response. Overexpression of
WSC
suppresses the heat
shock sensitivity of a strain in which RAS is hyperactivated and the
heat shock sensitivity of a
wsc
Δ strain is rescued by
deletion of
RAS2
. The functional characteristics and
cellular localization of WSC suggest that they may mediate
intracellular responses to environmental stress in yeast.
Mechanism of photosystem II photoinactivation and D1 protein degradation at low light: The role of back electron flow
Authors: Keren Nir , Berg Alexander , van Kan Paul J. M. , Levanon Haim , Ohad Itzhak
Published: July 2002

Light intensities that limit electron flow induce rapid degradation of the photosystem II (PSII) reaction center D1 protein. The mechanism of this phenomenon is not known. We propose that at low excitation rates back electron flow and charge recombination between the Q
B
•−
or Q
A
•−
semiquinone acceptors and the oxidized S
2,3
states of the PSII donor side may cause oxidative damage via generation of active oxygen species. Therefore, damage per photochemical event should increase with decreasing rates of PSII excitation. To test this hypothesis, the effect of the dark interval between single turnover flashes on the inactivation of water oxidation, charge separation and recombination, and the degradation of D1 protein were determined in spinach thylakoids. PSII inactivation per flash increases as the dark interval between the flashes increases, and a plateau is reached at dark intervals, allowing complete charge recombination of the Q
B
•−
/S
2,3
or Q
A
•−
/S
2
states (about 200 and 40 s, respectively). At these excitation rates: (
i
) 0.7% and 0.4% of PSII is inactivated and 0.4% and 0.2% of the D1 protein is degraded per flash, respectively, and (
ii
) the damage per flash is about 2 orders of magnitude higher than that induced by equal amount of energy delivered by excess continuous light. No PSII damage occurs if flashes are given in anaerobic conditions. These results demonstrate that charge recombination in active PSII is promoted by low rates of excitation and may account for a the high quantum efficiency of the rapid turnover of the D1 protein induced by limiting light.
Daidzin inhibits mitochondrial aldehyde dehydrogenase and suppresses ethanol intake of Syrian golden hamsters
Authors: Keung Wing Ming , Klyosov Anatole A. , Vallee Bert L.
Published: July 2002

Daidzin is the major active principle in extracts of
radix puerariae
, a traditional Chinese medication that suppresses the ethanol intake of Syrian golden hamsters. It is the first isoflavone recognized to have this effect. Daidzin is also a potent and selective inhibitor of human mitochondrial aldehyde dehydrogenase (ALDH-2). To establish a link between these two activities, we have tested a series of synthetic structural analogs of daidzin. The results demonstrate a direct correlation between ALDH-2 inhibition and ethanol intake suppression and raise the possibility that daidzin may, in fact, suppress ethanol intake of golden hamsters by inhibiting ALDH-2. Hamster liver contains not only mitochondrial ALDH-2 but also high concentrations of a cytosolic form, ALDH-1, which is a very efficient catalyst of acetaldehyde oxidation. Further, the cytosolic isozyme is completely resistant to daidzin inhibition. This unusual property of the hamster ALDH-1 isozyme accounts for the fact we previously observed that daidzin can suppress ethanol intake of this species without blocking acetaldehyde metabolism. Thus, the mechanism by which daidzin suppresses ethanol intake in golden hamsters clearly differs from that proposed for the classic ALDH inhibitor disulfiram. We postulate that a physiological pathway catalyzed by ALDH-2, so far undefined, controls ethanol intake of golden hamsters and mediates the antidipsotropic effect of daidzin.
Human immune disorder arising from mutation of the α chain of the interleukin-2 receptor
Authors: Sharfe Nigel , Dadi Harjit K. , Shahar Michal , Roifman Chaim M.
Published: July 2002

Profound cellular immunodeficiency occurs as the result of mutations in proteins involved in both the differentiation and function of mature lymphoid cells. We describe here a novel human immune aberration arising from a truncation mutation of the interleukin-2 receptor α chain (CD25), a subunit of the tripartite high-affinity receptor for interleukin 2. This immunodeficiency is characterized by decreased numbers of peripheral T cells displaying abnormal proliferation but normal B cell development. Extensive lymphocytic infiltration of tissues, including lung, liver, gut, and bone, is observed, accompanied by tissue atrophy and inflammation. Although mature T cells are present, the absence of CD25 does affect the differentiation of thymocytes. While displaying normal development of CD2, CD3, CD4, and CD8 expression, CD25-deficient cortical thymocytes do not express CD1, and furthermore they fail to normally down-regulate levels of the anti-apoptotic protein bcl-2.
An apportionment of human DNA diversity
Authors: Barbujani Guido , Magagni Arianna , Minch Eric , Cavalli-Sforza L. Luca
Published: July 2002

It is often taken for granted that the human species is divided in rather homogeneous groups or races, among which biological differences are large. Studies of allele frequencies do not support this view, but they have not been sufficient to rule it out either. We analyzed human molecular diversity at 109 DNA markers, namely 30 microsatellite loci and 79 polymorphic restriction sites (restriction fragment length polymorphism loci) in 16 populations of the world. By partitioning genetic variances at three hierarchical levels of population subdivision, we found that differences between members of the same population account for 84.4% of the total, which is in excellent agreement with estimates based on allele frequencies of classic, protein polymorphisms. Genetic variation remains high even within small population groups. On the average, microsatellite and restriction fragment length polymorphism loci yield identical estimates. Differences among continents represent roughly 1/10 of human molecular diversity, which does not suggest that the racial subdivision of our species reflects any major discontinuity in our genome.
Role of the J-domain in the cooperation of Hsp40 with Hsp70
Authors: Greene Michael K. , Maskos Karol , Landry Samuel J.
Published: July 2002

The
Escherichia coli
Hsp40 DnaJ and Hsp70 DnaK cooperate in the binding of proteins at intermediate stages of folding, assembly, and translocation across membranes. Binding of protein substrates to the DnaK C-terminal domain is controlled by ATP binding and hydrolysis in the N-terminal ATPase domain. The interaction of DnaJ with DnaK is mediated at least in part by the highly conserved N-terminal J-domain of DnaJ that includes residues 2–75. Heteronuclear NMR experiments with uniformly
15
N-enriched DnaJ2–75 indicate that the chemical environment of residues located in helix II and the flanking loops is perturbed on interaction with DnaK or a truncated DnaK molecule, DnaK2–388. NMR signals corresponding to these residues broaden and exhibit changes in chemical shifts in the presence of DnaK(MgADP). Addition of MgATP largely reversed the broadening, indicating that NMR signals of DnaJ2–75 respond to ATP-dependent changes in DnaK. The J-domain interaction is localized to the ATPase domain of DnaK and is likely to be dominated by electrostatic interactions. The results suggest that the J-domain tethers DnaK to DnaJ-bound substrates, which DnaK then binds with its C-terminal peptide-binding domain.
Defining the domains of type I collagen involved in heparin- binding and endothelial tube formation
Authors: Sweeney Shawn M. , Guy Cynthia A. , Fields Gregg B. , Antonio James D. San
Published: July 2002

Cell surface heparan sulfate proteoglycan (HSPG) interactions with type I collagen may be a ubiquitous cell adhesion mechanism. However, the HSPG binding sites on type I collagen are unknown. Previously we mapped heparin binding to the vicinity of the type I collagen N terminus by electron microscopy. The present study has identified type I collagen sequences used for heparin binding and endothelial cell–collagen interactions. Using affinity coelectrophoresis, we found heparin to bind as follows: to type I collagen with high affinity (
K
d
≈ 150 nM); triple-helical peptides (THPs) including the basic N-terminal sequence α1(I)87–92, KGHRGF, with intermediate affinities (
K
d
≈ 2 μM); and THPs including other collagenous sequences, or single-stranded sequences, negligibly (
K
d
≫ 10 μM). Thus, heparin–type I collagen binding likely relies on an N-terminal basic triple-helical domain represented once within each monomer, and at multiple sites within fibrils. We next defined the features of type I collagen necessary for angiogenesis in a system in which type I collagen and heparin rapidly induce endothelial tube formation
in vitro
. When peptides, denatured or monomeric type I collagen, or type V collagen was substituted for type I collagen, no tubes formed. However, when peptides and type I collagen were tested together, only the most heparin-avid THPs inhibited tube formation, likely by influencing cell interactions with collagen–heparin complexes. Thus, induction of endothelial tube morphogenesis by type I collagen may depend upon its triple-helical and fibrillar conformations and on the N-terminal heparin-binding site identified here.
Autoregulation of thyroid-specific gene transcription by thyroglobulin
Authors: Suzuki Koichi , Lavaroni Stefano , Mori Atsumi , Ohta Masanori , Saito Jun , Pietrarelli Michele , Singer Dinah S. , Kimura Shioko , Katoh Ryohei , Kawaoi Akira , Kohn Leonard D.
Published: July 2002

Thyroglobulin (TG), the primary synthetic product of the thyroid, is the macromolecular precursor of thyroid hormones. TG synthesis, iodination, storage in follicles, and degradation control thyroid hormone formation and secretion into the circulation. Thyrotropin (TSH), via its receptor (TSHR), increases thyroid hormone levels by up-regulating expression of the sodium iodide symporter (NIS), thyroid peroxidase (TPO), and TG genes. TSH does this by modulating the expression and activity of several thyroid-specific transcription factors, thyroid transcription factor (TTF)-1, TTF-2, and Pax-8, which coordinately regulate NIS, TPO, TG, and the TSHR. Major histocompatibility complex class I gene expression, which also is regulated by TTF-1 and Pax-8 in the thyroid, is decreased simultaneously. This helps maintain self-tolerance in the face of TSH-increased gene products necessary for thyroid hormone formation. In this report we show that follicular TG counter-regulates TSH-increased, thyroid-specific gene transcription by suppressing expression of the TTF-1, TTF-2, and Pax-8 genes. This decreases expression of the TG, TPO, NIS, and TSHR genes, but increases class I expression. TG acts transcriptionally, targeting, for example, a sequence within 1.15 kb of the 5′ flanking region of TTF-1. TG does not affect ubiquitous transcription factors regulating TG, TPO, NIS, and/or TSHR gene expression. The inhibitory effect of TG on gene expression is not duplicated by thyroid hormones or iodide and may be mediated by a TG-binding protein on the apical membrane. We hypothesize that TG-initiated, transcriptional regulation of thyroid-restricted genes is a normal, feedback, compensatory mechanism that limits follicular function and contributes to follicular heterogeneity.
Computing geodesic paths on manifolds
Authors: Kimmel R. , Sethian J. A.
Published: July 2002

The Fast Marching Method is a numerical algorithm for solving the Eikonal equation on a rectangular orthogonal mesh in
O
(
M
log
M
) steps, where
M
is the total number of grid points. In this paper we extend the Fast Marching Method to triangulated domains with the same computational complexity. As an application, we provide an optimal time algorithm for computing the geodesic distances and thereby extracting shortest paths on triangulated manifolds.
“Hidden” sequence periodicities and protein architecture
Authors: Rackovsky S.
Published: July 2002

I demonstrate the existence in protein domain sequences of sets of statistically significant periodic signals, characteristic of the architectures of those domains. It is shown that, although the frequencies of the signals characteristic of a particular architecture have definite wave numbers, they can occur in any physical property. The characteristic signals define sequence units, which may correspond to specific structural features. Study of signals in different architectures suggests that symmetric structures are characterized by sets of sequence signals, which are members of harmonic series and which therefore impose commensurate periodicities on the structure. Asymmetric structures are characterized by mutually incommensurate sets of sequence signals. It is pointed out that, although these periodic sequence units can be very short, their existence is a property of the entire sequence.
Early establishment of a pool of latently infected, resting CD4
+
T cells during primary HIV-1 infection
Authors: Chun Tae-Wook , Engel Delphine , Berrey M. Michelle , Shea Theresa , Corey Lawrence , Fauci Anthony S.
Published: July 2002

The presence of latently infected, resting CD4
+
T cells carrying replication-competent HIV-1 has been demonstrated in chronically infected individuals who are antiretroviral therapy naive as well as in those who are receiving highly active antiretroviral therapy (HAART). It is not clear, however, whether the establishment of a pool of latently infected CD4
+
T cells can be blocked by early initiation of HAART after primary infection. The present study demonstrates that initiation of HAART in infected individuals as early as 10 days after the onset of symptoms of primary HIV-1 infection did not prevent generation of latently infected, resting CD4
+
T cells carrying integrated HIV-1 DNA as well as infectious HIV-1 despite the successful control of plasma viremia shortly after institution of HAART. Furthermore, there was no correlation between either the duration of HAART at the time of study (range: 0.2–17 months) or the time of initiation of HAART after the onset of symptoms of primary HIV-1 infection (range: 0.3–4 months) and the frequencies of resting CD4
+
T cells carrying either integrated HIV-1 DNA or infectious virus. These results underscore the rapidity with which latent reservoirs are established in primary HIV-1 infection and indicate that it is unlikely that early treatment during primary infection can prevent establishment of a pool of latently infected, resting CD4
+
T cells as long as treatment is initiated after plasma viremia becomes evident.
Coenzyme Q
10
administration increases brain mitochondrial concentrations and exerts neuroprotective effects
Authors: Matthews Russell T. , Yang Lichuan , Browne Susan , Baik Myong , Beal M. Flint
Published: July 2002

Coenzyme Q
10
is an essential cofactor of the electron transport chain as well as a potent free radical scavenger in lipid and mitochondrial membranes. Feeding with coenzyme Q
10
increased cerebral cortex concentrations in 12- and 24-month-old rats. In 12-month-old rats administration of coenzyme Q
10
resulted in significant increases in cerebral cortex mitochondrial concentrations of coenzyme Q
10
. Oral administration of coenzyme Q
10
markedly attenuated striatal lesions produced by systemic administration of 3-nitropropionic acid and significantly increased life span in a transgenic mouse model of familial amyotrophic lateral sclerosis. These results show that oral administration of coenzyme Q
10
increases both brain and brain mitochondrial concentrations. They provide further evidence that coenzyme Q
10
can exert neuroprotective effects that might be useful in the treatment of neurodegenerative diseases.
The nematode resistance geneMiof tomato confers resistance against the potato aphid
Authors: Rossi Magdalena , Goggin Fiona L. , Milligan Stephen B. , Kaloshian Isgouhi , Ullman Diane E. , Williamson Valerie M.
Published: July 2002

Resistance against the aphidMacrosiphum euphorbiaepreviously was observed in tomato and attributed to a novel gene, designatedMeu-1, tightly linked to the nematode resistance gene,Mi.Recent cloning ofMiallowed us to determine whetherMeu-1andMiare the same gene. We show thatMiis expressed in leaves, that aphid resistance is isolate-specific, and that susceptible tomato transformed withMiis resistant to the same aphid isolates as the original resistant lines. We conclude thatMiandMeu-1are the same gene and thatMimediates resistance against both aphids and nematodes, organisms belonging to different phyla.Miis the first example of a plant resistance gene active against two such distantly related organisms. Furthermore, it is the first isolate-specific insect resistance gene to be cloned and belongs to the nucleotide-binding, leucine-rich repeat family of resistance genes.
Generation of mucosal cytotoxic T cells against soluble protein by tissue-specific environmental and costimulatory signals
Authors: Kim Sung-Kwon , Reed Douglas S. , Olson Sara , Schnell Matthias J. , Rose John K. , Morton Phillip A. , Lefrançois Leo
Published: July 2002

We compared peripheral and mucosal primary CD8 T cell responses to inflammatory and noninflammatory forms of antigen in a T cell-adoptive transfer system. Immunization with the soluble antigen, ovalbumin (ova), administered i.p. or orally without adjuvant, activated nonmucosal CD8 T cells but did not induce cytotoxic activity. However, after activation, the transferred cells entered the intestinal mucosa and became potent antigen-specific killers. Thus, exogenous intact soluble protein entered the major histocompatibility complex class I antigen presentation pathway and induced mucosal cytotoxic T lymphocytes. Moreover, distinct costimulatory requirements for activation of peripheral versus mucosal T cells were noted in that the CD28 ligand, B7-1, was critical for activated mucosal T cell generation but not for activation of peripheral CD8 T cells. The costimulator, B7-2, was required for optimum activation of both populations. Infection with a new recombinant vesicular stomatitis virus encoding ovalbumin induced lytic activity in mucosal as well as peripheral sites, demonstrating an adjuvant effect of inflammatory mediators produced during virus infection. Generation of antiviral cytotoxic T lymphocytes was also costimulation-dependent. The results indicated that induction of peripheral tolerance via antigen administration may not extend to mucosal sites because of distinct costimulatory and inflammatory signals in the mucosa.
Mechanisms underlying nonsteroidal antiinflammatory drug-mediated apoptosis
Authors: Chan Timothy A. , Morin Patrice J. , Vogelstein Bert , Kinzler Kenneth W.
Published: July 2002

Nonsteroidal antiinflammatory drugs (NSAIDs) can inhibit colorectal tumorigenesis and are among the few agents known to be useful for the chemoprevention of neoplasia. Here, we show that the tumor suppressive effects of NSAIDs are not likely to be related to a reduction in prostaglandins but rather are due to the elevation of the prostaglandin precursor arachidonic acid (AA). NSAID treatment of colon tumor cells results in a dramatic increase in AA that in turn stimulates the conversion of sphingomyelin to ceramide, a known mediator of apoptosis. These results have significant implications for understanding and improving colon cancer chemoprevention.
Testing the Cambrian explosion hypothesis by using a molecular dating technique
Authors: Bromham Lindell , Rambaut Andrew , Fortey Richard , Cooper Alan , Penny David
Published: July 2002

Molecular studies have the potential to shed light on the origin of the animal phyla by providing independent estimates of the divergence times, but have been criticized for failing to account adequately for variation in rate of evolution. A method of dating divergence times from molecular data addresses the criticisms of earlier studies and provides more realistic, but wider, confidence intervals. The data are not compatible with the Cambrian explosion hypothesis as an explanation for the origin of metazoan phyla, and provide additional support for an extended period of Precambrian metazoan diversification.
Fluctuating silicate:nitrate ratios and coastal plankton food webs
Authors: Turner R. Eugene , Qureshi Naureen , Rabalais Nancy N. , Dortch Quay , Justic Dubravko , Shaw Richard F. , Cope Joseph
Published: July 2002

Marine diatoms require dissolved silicate to form an external shell, and their growth becomes Si-limited when the atomic ratio of silicate to dissolved inorganic nitrogen (Si:DIN) approaches 1:1, also known as the “Redfield ratio.” Fundamental changes in the diatom-to-zooplankton-to-higher trophic level food web should occur when this ratio falls below 1:1 and the proportion of diatoms in the phytoplankton community is reduced. We quantitatively substantiate these predictions by using a variety of data from the Mississippi River continental shelf, a system in which the Si:DIN loading ratio has declined from around 3:1 to 1:1 during this century because of land-use practices in the watershed. We suggest that, on this shelf, when the Si:DIN ratio in the river decreases to less than 1:1, then (
i
) copepod abundance changes from >75% to <30% of the total mesozooplankton, (
ii
) zooplankton fecal pellets become a minor component of the
in situ
primary production consumed, and (
iii
) bottom-water oxygen consumption rates become less dependent on relatively fast-sinking (diatom-rich) organic matter packaged mostly as zooplankton fecal pellets. This coastal ecosystem appears to be a pelagic food web dynamically poised to be either a food web composed of diatoms and copepods or one with potentially disruptive harmful algal blooms. The system is directed between these two ecosystem states by Mississippi River water quality, which is determined by land-use practices far inland.
Large-scale protein structure modeling of the
Saccharomyces cerevisiae
genome
Authors: Sánchez Roberto , Sali Andrej
Published: July 2002

The function of a protein generally is determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging from the many genome projects. To this end, fold assignment, comparative protein structure modeling, and model evaluation were automated completely. As an illustration, the method was applied to the proteins in the
Saccharomyces cerevisiae
(baker’s yeast) genome. It resulted in all-atom 3D models for substantial segments of 1,071 (17%) of the yeast proteins, only 40 of which have had their 3D structure determined experimentally. Of the 1,071 modeled yeast proteins, 236 were related clearly to a protein of known structure for the first time; 41 of these previously have not been characterized at all.
The intrinsic radioresistance of glioblastoma-derived cell lines is associated with a failure of p53 to induce p21
BAX
expression
Authors: Shu Hui-Kuo G. , Kim Moses M. , Chen Pengchin , Furman Felix , Julin Carol M. , Israel Mark A.
Published: July 2002

Radiation is the primary modality of therapy for all commonly occurring malignant brain tumors, including medulloblastoma and glioblastoma. These two brain tumors, however, have a distinctly different response to radiation therapy. Medulloblastoma is very sensitive to radiation therapy, whereas glioblastoma is highly resistant, and the long-term survival of medulloblastoma patients exceeds 50%, while there are few long-term survivors among glioblastoma patients. p53-mediated apoptosis is thought to be an important mechanism mediating the cytotoxic response of tumors to radiotherapy. In this study, we compared the response to radiation of five cell lines that have wild-type p53: three derived from glioblastoma and two derived from medulloblastoma. We found that the medulloblastoma-derived cell lines underwent extensive radiation-induced apoptotic cell death, while those from glioblastomas did not exhibit significant radiation-induced apoptosis. p53-mediated induction of p21
BAX
is thought to be a key component of the pathway mediating apoptosis after the exposure of cells to cytotoxins, and the expression of mRNA encoding p21
BAX
was correlated with these cell lines undergoing radiation-induced apoptosis. The failure of p53 to induce p21
BAX
expression in glioblastoma-derived cell lines is likely to be of biologic significance, since inhibition of p21
BAX
induction in medulloblastoma resulted in a loss of radiation-induced apoptosis, while forced expression of p21
BAX
in glioblastoma was sufficient to induce apoptosis. The failure of p53 to induce p21
BAX
in glioblastoma-derived cell lines suggests a distinct mechanism of radioresistance and may represent a critical factor in determining therapeutic responsiveness to radiation in glioblastomas.
The terminal tail region of a yeast myosin-V mediates its attachment to vacuole membranes and sites of polarized growth
Authors: Catlett Natalie L. , Weisman Lois S.
Published: July 2002

The
Saccharomyces cerevisiae
myosin-V, Myo2p, has been implicated in the polarized movement of several organelles and is essential for yeast viability. We have shown previously that Myo2p is required for the movement of a portion of the lysosome (vacuole) into the bud and consequently for proper inheritance of this organelle during cell division. Class V myosins have a globular carboxyl terminal tail domain that is proposed to mediate localization of the myosin, possibly through interaction with organelle-specific receptors. Here we describe a
myo2
allele whose phenotypes support this hypothesis.
vac15–1/myo2–2
has a single mutation in this globular tail domain, causing defects in vacuole movement and inheritance. Although a portion of wild-type Myo2p fractionates with the vacuole, the
myo2–2
gene product does not. In addition, the mutant protein does not concentrate at sites of active growth, the predominant location of wild-type Myo2p. Although deletion of the tail domain is lethal, the
myo2–2
gene product retains the essential functions of Myo2p. Moreover,
myo2–2
does not cause the growth defects and lethal genetic interactions seen in
myo2–66
, a mutant defective in the actin-binding domain. These observations suggest that the
myo2–2
mutation specifically disrupts interactions with selected myosin receptors, namely those on the vacuole membrane and those at sites of polarized growth.
Nramp
2
is mutated in the anemic Belgrade (
b
) rat: Evidence of a role for Nramp2 in endosomal iron transport
Authors: Fleming Mark D. , Romano Michelle A. , Su Maureen A. , Garrick Laura M. , Garrick Michael D. , Andrews Nancy C.
Published: July 2002

The Belgrade (
b
) rat has an autosomal recessively inherited, microcytic, hypochromic anemia associated with abnormal reticulocyte iron uptake and gastrointestinal iron absorption. The
b
reticulocyte defect appears to be failure of iron transport out of endosomes within the transferrin cycle. Aspects of this phenotype are similar to those reported for the microcytic anemia (
mk
) mutation in the mouse. Recently,
mk
has been attributed to a missense mutation in the gene encoding the putative iron transporter protein Nramp2. To investigate the possibility that
Nramp2
was also mutated in the
b
rat, we established linkage of the phenotype to the centromeric portion of rat chromosome 7. This region exhibits synteny to the chromosomal location of
Nramp2
in the mouse. A polymorphism within the rat
Nramp2
gene cosegregated with the
b
phenotype. A glycine-to-arginine missense mutation (G185R) was present in the
b Nramp2
gene, but not in the normal allele. Strikingly, this amino acid alteration is the same as that seen in the
mk
mouse. Functional studies of the protein encoded by the
b
allele of rat
Nramp2
demonstrated that the mutation disrupted iron transport. These results confirm the hypothesis that Nramp2 is the protein defective in the Belgrade rat and raise the possibility that the phenotype shared by
mk
and
b
animals is unique to the G185R mutation. Furthermore, the phenotypic characteristics of these animals indicate that Nramp2 is essential both for normal intestinal iron absorption and for transport of iron out of the transferrin cycle endosome.
RNA components of
Escherichia coli
degradosome: Evidence for rRNA decay
Authors: Bessarab Dmitri A. , Kaberdin Vladimir R. , Wei Chia-Li , Liou Gunn-Guang , Lin-Chao Sue
Published: July 2002

Recently, we found that a multicomponent ribonucleolytic degradosome complex formed around RNase E, a key mRNA-degrading and 9S RNA-processing enzyme, contains RNA in addition to its protein components. Herein we show that the RNA found in the degradosome consists primarily of rRNA fragments that have a range of distinctive sizes. We further show that rRNA degradation is carried out in the degradosome by RNase E cleavage of A+U-rich single-stranded regions of mature 16S and 23S rRNAs. The 5S rRNA, which is known to be generated by RNase E processing of the 9S precursor, was also identified in the degradosome, but tRNAs, which are not cleaved by RNase E
in vitro
, were absent. Our results, which provide evidence that decay of mature rRNAs occurs in growing
Escherichia coli
cells in the RNA degradosome, implicate RNase E in degradosome-mediated decay.
Proliferation of granule cell precursors in the dentate gyrus of adult monkeys is diminished by stress
Authors: Gould Elizabeth , Tanapat Patima , McEwen Bruce S. , Flügge Gabriele , Fuchs Eberhard
Published: July 2002

Although granule cells continue to be added to the dentate gyrus of adult rats and tree shrews, this phenomenon has not been demonstrated in the dentate gyrus of adult primates. To determine whether neurons are produced in the dentate gyrus of adult primates, adult marmoset monkeys (
Callithrix jacchus
) were injected with BrdU and perfused 2 hr or 3 weeks later. BrdU is a thymidine analog that is incorporated into proliferating cells during S phase. A substantial number of cells in the dentate gyrus of adult monkeys incorporated BrdU and ≈80% of these cells had morphological characteristics of granule neurons and expressed a neuronal marker by the 3-week time point. Previous studies suggest that the proliferation of granule cell precursors in the adult dentate gyrus can be inhibited by stress in rats and tree shrews. To test whether an aversive experience has a similar effect on cell proliferation in the primate brain, adult marmoset monkeys were exposed to a resident-intruder model of stress. After 1 hr in this condition, the intruder monkeys were injected with BrdU and perfused 2 hr later. The number of proliferating cells in the dentate gyrus of the intruder monkeys was compared with that of unstressed control monkeys. We found that a single exposure to this stressful experience resulted in a significant reduction in the number of these proliferating cells. Our results suggest that neurons are produced in the dentate gyrus of adult monkeys and that the rate of precursor cell proliferation can be affected by a stressful experience.
Phospholipid composition of the mammalian red cell membrane can be rationalized by a superlattice model
Authors: Virtanen J. A. , Cheng K. H. , Somerharju P.
Published: July 2002

Although the phospholipid composition of the erythrocyte membrane has been studied extensively, it remains an enigma as to how the observed composition arises and is maintained. We show here that the phospholipid composition of the human erythrocyte membrane as a whole, as well as the composition of its individual leaflets, is closely predicted by a model proposing that phospholipid head groups
tend
to adopt regular, superlattice-like lateral distributions. The phospholipid composition of the erythrocyte membrane from most other mammalian species, as well as of the platelet plasma membrane, also agrees closely with the predictions of the superlattice model. Statistical analyses indicate that the agreement between the observed and predicted compositions is highly significant, thus suggesting that head group superlattices may indeed play a central role in the maintenance of the phospholipid composition of the erythrocyte membrane.
Imaging of multicellular large-scale rhythmic calcium waves during zebrafish gastrulation
Authors: Gilland Edwin , Miller Andrew L. , Karplus Eric , Baker Robert , Webb Sarah E.
Published: July 2002

Oscillations of cytosolic free calcium levels have been shown to influence gene regulation and cell differentiation in a variety of model systems. Intercellular calcium waves thus present a plausible mechanism for coordinating cellular processes during embryogenesis. Herein we report use of aequorin and a photon imaging microscope to directly observe a rhythmic series of intercellular calcium waves that circumnavigate zebrafish embryos over a 10-h period during gastrulation and axial segmentation. These waves first appeared at about 65% epiboly and continued to arise every 5–10 min up to at least the 16-somite stage. The waves originated from loci of high calcium activity bordering the blastoderm margin. Several initiating loci were active early in the wave series, whereas later a dorsal marginal midline locus predominated. On completion of epiboly, the dorsal locus was incorporated into the developing tail bud and continued to generate calcium waves. The locations and timing at which calcium dynamics are most active appear to correspond closely to embryonic cellular and syncytial sites of known morphogenetic importance. The observations suggest that a panembryonic calcium signaling system operating in a clock-like fashion might play a role during vertebrate axial patterning.
Intergalactic cold dust in the NGC 4631 group
Authors: Neininger N. , Dumke M.
Published: July 2002

We have detected extraplanar cold dust at distances out to >10 kiloparsecs, situated in the halo of the interacting galaxy NGC 4631. The dust emission disk is much thinner than the warped H
i
disk, and new structures emerge. In particular, a giant arc has been found that is linked to anomalies in the kinematical structure of the atomic gas. Most of the extraplanar dust is closely associated with H
i
spurs that have been found earlier [Weliachew, L., Sancisi, R. & Guélin, M. (1978)
Astron. Astrophys.
65, 37–45; Rand, R. J. (1994)
Astron. Astrophys.
285, 833–856]. These spurs obviously are traces of the interaction [Combes, F. (1978)
Astron. Astrophys.
65, 47–55]. The dust emission within the plane reaches the border of the optical disk. The activity of the disk of NGC 4631 is moderately enhanced by the interaction, but no gas moving in the
z
-direction could be found [Rand, R. J., Kulkarni, S. R. & Hester, J. J. (1992)
Astrophys. J.
396, 97–103; Golla, G., Dettmar, R.-J. & Domgörgen, H. (1996)
Astron. Astrophys.
313, 439–447]. Hence, it seems unlikely that strong winds have deposited the high-
z
dust. Instead, the coincidence with the H
i
features suggests that we see a track left behind by the interaction. In addition, the H
i
shows a supershell formed by an impact [Rand, R. J. & Stone, J. M. (1996)
Astron. J.
111, 190–196] in the zone where the dust trail crosses the disk. This region is also characterized by disturbances in the distribution of the Hα light. The masses associated with the dust can be estimated only very roughly on the basis of the existing data; they are of the order of a few 10
9
M
⊙
of gas.
Bloom’s syndrome protein, BLM, colocalizes with replication protein A in meiotic prophase nuclei of mammalian spermatocytes
Authors: Walpita Deepika , Plug Annemieke W. , Neff Norma F. , German James , Ashley Terry
Published: July 2002

Bloom’s syndrome (BS) is a rare autosomal recessive disorder of humans characterized by severe pre- and postnatal growth deficiency, immunodeficiency, genomic instability, and a predisposition to a wide variety of neoplasms. The genomic instability is evidenced in BS somatic cells as a high incidence of gaps and breaks, chromatid exchanges, chromosome rearrangements, and locus-specific mutations. BS arises from a mutation in
BLM
, a gene encoding a protein with homology to the RecQ helicase family. Men with BS are sterile; women have reduced fertility and a shortened reproductive span. The current immunocytological study on mouse spermatocytes shows that the BLM protein is first evident as discrete foci along the synaptonemal complexes (SCs) of homologously synapsed autosomal bivalents in late zygonema of meiotic prophase. BLM foci progressively dissociate from the synapsed autosomal axes during early pachynema and are no longer seen in mid-pachynema. BLM colocalizes with the single-stranded DNA binding replication protein A, which has been shown to be involved in meiotic synapsis. However, there is a temporal delay in the appearance of BLM protein along the SCs relative to replication protein A, suggesting that BLM is required for a late step in processing of a subset of genomic DNA involved in establishment of interhomologue interactions in early meiotic prophase. In late pachynema and into diplonema, BLM is more dispersed in the nucleoplasm, especially over the chromatin most intimately associated with the SCs, suggesting a possible involvement of BLM in resolution of interlocks in preparation for homologous chromosome disjunction during anaphase I.
Genetic dissection of the budding yeast Arp2/3 complex: A comparison of the
in vivo
and structural roles of individual subunits
Authors: Winter Dirk C. , Choe Elizabeth Y. , Li Rong
Published: July 2002

In previous work, we identified the yeast Arp2/3 complex, which localizes to cortical actin patches and is required for their motility and integrity
in vivo
. This complex contains proteins homologous to each subunit of the
Acanthamoeba
and human Arp2/3 complex except for a 40-kDa subunit (p40), which was missing from the purified yeast complex. Here, we demonstrate by using immunoprecipitation and gel-filtration analysis that Arc40p, the homolog of p40 identified from the yeast genome database, associates with the yeast Arp2/3 complex. We have carried out gene disruptions of each subunit of the yeast Arp2/3 complex to study each subunit’s role in the function of the complex. Surprisingly, we find that only ARC40 is fully essential for cell viability. Strains lacking each of the other subunits exhibit varying degrees of defects in cell growth and viability and in assembly and polarization of cortical actin patches. We have also examined each subunit’s role in maintaining the structural integrity of the Arp2/3 complex. Arp2p, Arp3p, and Arc40p fall into the monomer pool in Δarc19 and Δarc35 cells, suggesting that Arc19p and Arc35p are the central scaffolding components of the complex. Arp2p and Arp3p do not have major roles in maintaining complex integrity, and Arc15p is required for association of Arp2p and Arc40p, but not other subunits, with the complex. These results provide evidence that each subunit contributes differently to the assembly and function of the Arp2/3 complex.
Wild-type but not Alzheimer-mutant amyloid precursor protein confers resistance against p53-mediated apoptosis
Authors: Xu Xiao , Yang Daseng , Wyss-Coray Tony , Yan Jim , Gan Li , Sun Yi , Mucke Lennart
Published: July 2002

Amyloid precursor proteins (APPs) are expressed in multiple organs and cell types in diverse species. Their conservation across species and high abundance in brain and the association of various APP missense mutations with autosomal dominant forms of familial Alzheimer’s disease (FAD) suggest important roles for APP in the central nervous system. However, the basic functions of APP in the central nervous system remain largely unknown. To assess potential effects of APP on neuronal death and survival, we transfected APP-deficient rat neuroblastoma cells (B103) with DNA constructs encoding wild-type or FAD-mutant human APP. Wild-type, but not FAD-mutant, APP effectively protected cells against apoptosis induced by ultraviolet irradiation, staurosporine, or p53. Wild-type APP also strongly inhibited p53 DNA-binding activity and p53-mediated gene transactivation, whereas FAD-mutant APP did not. We conclude that APP protects neuronal cells against apoptosis by controlling p53 activation at the post-translational level. Disruption of this function by mutations or alterations in APP processing could enhance neuronal vulnerability to secondary insults and contribute to neuronal degeneration.