bluuebunny/crossref_metadata_2025 huggingface dataset:
Nitrolinoleate, a nitric oxide-derived mediator of cell function: Synthesis, characterization, and vasomotor activity
Authors: Lim Dong Gun , Sweeney Scott , Bloodsworth Allison , White C. Roger , Chumley Phillip H. , Krishna N. Rama , Schopfer Francisco , O'Donnell Valerie B. , Eiserich Jason P. , Freeman Bruce A.
Published: December 2002

Nitric oxide (
•
NO) and
•
NO-derived reactive species rapidly react with lipids during both autocatalytic and enzymatic oxidation reactions to yield nitrated derivatives that serve as cell signaling molecules. Herein we report the synthesis, purification, characterization, and bioactivity of nitrolinoleate (LNO
2
). Nitroselenylation of linoleic acid yielded LNO
2
that was purified by solvent extraction, silicic acid chromatography, and reverse-phase HPLC. Structural characterization was performed by IR spectroscopy,
15
N-NMR, LC-negative ion electrospray mass spectroscopy (MS), and chemiluminescent nitrogen analysis. Quantitative MS analysis of cell and vessel LNO
2
metabolism, using L[
15
N]O
2
as an internal standard, revealed that LNO
2
is rapidly metabolized by rat aortic smooth muscle (RASM) monolayers and rat thoracic aorta, resulting in nitrite production and up to 3-fold increases in cGMP (ED
50
= 30 μM for RASM, 50 μM for aorta). LNO
2
induced endothelium-independent relaxation of preconstricted rat aortic rings, which was unaffected by L
G
-nitro-
l
-arginine methyl ester addition and inhibited by the guanylate cyclase inhibitor 1
H
-[1,2,4] oxadiazole[4,3-a]quinoxalin-1-one and the
•
NO scavenger HbO
2
. These results reveal that synthetic LNO
2
, identical to lipid derivatives produced biologically by the reaction of
•
NO and
•
NO-derived species with oxidizing unsaturated fatty acids (e.g., linoleate), can transduce vascular signaling actions of
•
NO.
Structure of the extracellular domains of the human interleukin-6 receptor α-chain
Authors: Varghese J. N. , Moritz R. L. , Lou M.-Z. , van Donkelaar A. , Ji H. , Ivancic N. , Branson K. M. , Hall N. E. , Simpson R. J.
Published: December 2002

Dysregulated production of IL-6 and its receptor (IL-6R) are implicated in the pathogenesis of multiple myeloma, autoimmune diseases and prostate cancer. The IL-6R complex comprises two molecules each of IL-6, IL-6R, and the signaling molecule, gp130. Here, we report the x-ray structure (2.4 Å) of the IL-6R ectodomains. The N-terminal strand of the Ig-like domain (D
1
) is disulfide-bonded to domain D
2
, and domains D
2
and D
3
, the cytokine-binding domain, are structurally similar to known cytokine-binding domains. The head-to-tail packing of two closely associated IL-6R molecules observed in the crystal may be representative of the configuration of the physiological dimer of IL-6R and provides new insight into the architecture of the IL-6R complex.
Hypothalamic gene expression in reproductively photoresponsive and photorefractory Siberian hamsters
Authors: Prendergast Brian J. , Mosinger Bedrich , Kolattukudy Pappachan E. , Nelson Randy J.
Published: December 2002

An interval timing mechanism in the brain governs reproduction in seasonally breeding mammals by triggering refractoriness to inhibitory short photoperiods during midwinter. The neural mechanisms responsible for the timing and induction of photorefractoriness by this seasonal clock are unknown. Using cDNA microarrays and RT-PCR, we identified a class of genes encoding thyroxine (T
4
)-binding proteins (transthyretin, T
4
-binding globulin, albumin) whose expression is associated with reproductive refractoriness to short day lengths. Down-regulation of these genes was associated with reduced hypothalamic T
4
uptake, which was reversed by long-day photoperiod treatments that restored responsiveness to short days. Circulating T
4
concentrations did not vary with states of photoresponsiveness in euthyroid hamsters, but blockade of thyroid function accelerated the onset of photorefractoriness to short days. These data link changes in gene expression in the hypothalamus to the functional output of a seasonal clock. Reproductive inhibition in short days depends on T
4
only late in the nonbreeding season. Down-regulation of genes encoding T
4
-binding proteins in the hypothalamus during this interval may restrict access of a static T
4
signal to hypothalamic target tissues that regulate reproduction, thereby timing annual transitions in reproductive function. Hypothalamic autoregulation of T
4
influx may constitute a critical cellular process involved in the generation and expression of seasonal reproductive rhythms and suggests a previously undescribed mechanism by which neural targets gain access to peripheral hormones.
Differential modulation of BMP signaling promotes the elaboration of cerebral cortical GABAergic neurons or oligodendrocytes from a common sonic hedgehog-responsive ventral forebrain progenitor species
Authors: Yung Shau-Yu , Gokhan Solen , Jurcsak Jennifer , Molero Aldrin E. , Abrajano Joseph J. , Mehler Mark F.
Published: December 2002

During cerebral cortical development, excitatory glutamatergic projection neurons are generated from neural stem cells intrinsic to the early embryonic cortical ventricular zone by a process of radial migration, whereas most inhibitory γ-aminobutyric acid (GABA)ergic interneurons and oligodendrocytes (OLs) appear to be elaborated from ventral forebrain stem cells that initially undergo tangential cortical migration before terminal lineage maturation. In contrast to the more compartmentalized developmental organization of the spinal cord, the generation of neurons and OLs from a common ventral forebrain stem cell would expose these cells to the sequential actions of ventral and dorsal gradient morphogens [sonic hedgehog (Shh) and bone morphogenetic proteins (BMPs)] that normally mediate opposing developmental programs. Here we report that Shh promotes GABAergic neuronal/OL lineage restriction of forebrain stem cells, in part, by activation of the basic helix–loop–helix transcription factors, Olig2 and Mash1. In mutant mice with a generalized defect in tangential cortical migration (Dlx1/2−/−), there is a profound and selective reduction in the elaboration of both cortical GABAergic neurons and OLs. Our studies further demonstrate that the sequential elaboration of cortical GABAergic neurons and OLs from common Shh-responsive ventral forebrain progenitors requires the spatial and temporal modulation of cortical BMP signaling by BMP ligands and the BMP antagonist, noggin, respectively. These findings suggest an integrative model for cerebral cortical GABAergic neuronal and OL lineage maturation that would incorporate the sequential contributions of the ventral and dorsal forebrain, and the potential role of regional developmental cues in modulating transcriptional codes within evolving neural lineage species.
Single pilus motor forces exceed 100 pN
Authors: Maier Berenike , Potter Laura , So Magdalene , Seifert Hank S. , Sheetz Michael P.
Published: December 2002

Force production by type IV pilus retraction is critical for infectivity of
Neisseria gonorrhoeae
and DNA transfer. We investigated the roles of pilus number and the retraction motor, PilT, in force generation
in vivo
at the single-molecule level and found that individual retraction events are generated by a single pilus fiber, and only one PilT complex powers retraction. Retraction velocity is constant at low forces but decreases at forces greater than 40 pN, giving a remarkably high average stall force of 110 ± 30 pN. Further insights into the molecular mechanism of force generation are gained from the effect of ATP-depletion, which reduces the rate of retraction but not the stall force. Energetic considerations suggest that more than one ATP is involved in the removal of a single pilin subunit from a pilus. The results are most consistent with a model in which the ATPase PilT forms an oligomer that disassembles the pilus by a cooperative conformational change.
Memory-specific temporal profiles of gene expression in the hippocampus
Authors: Cavallaro Sebastiano , D'Agata Velia , Manickam Pachiappan , Dufour Franck , Alkon Daniel L.
Published: December 2002

Many experiments in the past have demonstrated the requirement of
de novo
gene expression during the long-term retention of learning and memory. Although previous studies implicated individual genes or genetic pathways in learning and memory, they did not uncover the collective behaviors or patterns of the genes. We have used genome-scale screening to analyze gene expression during spatial learning of rats in the Morris water maze. Our results show distinct temporal gene expression profiles associated with learning and memory. Exogenous administration of one peptide whose sustained increase during memory retention was implicated by microarray analysis, fibroblast growth factor (FGF)-18, improved spatial learning behavior, suggesting that pharmacological modulation of pathways and targets identified may allow new therapeutic approaches for improving learning and memory. Results of this study also suggest that while learning and physical activity involve common groups of genes, the behavior of learning and memory emerges from unique patterns of gene expression across time.
Adoptive T cell therapy using antigen-specific CD8+T cell clones for the treatment of patients with metastatic melanoma:In vivopersistence, migration, and antitumor effect of transferred T cells
Authors: Yee C. , Thompson J. A. , Byrd D. , Riddell S. R. , Roche P. , Celis E. , Greenberg P. D.
Published: December 2002

Adoptive T cell therapy, involving theex vivoselection and expansion of antigen-specific T cell clones, provides a means of augmenting antigen-specific immunity without thein vivoconstraints that can accompany vaccine-based strategies. A phase I study was performed to evaluate the safety,in vivopersistence, and efficacy of adoptively transferred CD8+T cell clones targeting the tumor-associated antigens, MART1/MelanA and gp100 for the treatment of patients with metastatic melanoma. Four infusions of autologous T cell clones were administered, the first without IL-2 and subsequent infusions with low-dose IL-2 (at 0.25, 0.50, and 1.0 × 106units/m2twice daily for the second, third, and fourth infusions, respectively). Forty-three infusions of MART1/MelanA-specific or gp100-specific CD8+T cell clones were administered to 10 patients. No serious toxicity was observed. We demonstrate that the adoptively transferred T cell clones persistin vivoin response to low-dose IL-2, preferentially localize to tumor sites and mediate an antigen-specific immune response characterized by the elimination of antigen-positive tumor cells, regression of individual metastases, and minor, mixed or stable responses in 8 of 10 patients with refractory, metastatic disease for up to 21 mo.
Characteristic genome rearrangements in experimental evolution of
Saccharomyces
cerevisiae
Authors: Dunham Maitreya J. , Badrane Hassan , Ferea Tracy , Adams Julian , Brown Patrick O. , Rosenzweig Frank , Botstein David
Published: December 2002

Genome rearrangements, especially amplifications and deletions, have regularly been observed as responses to sustained application of the same strong selective pressure in microbial populations growing in continuous culture. We studied eight strains of budding yeast (
Saccharomyces cerevisiae
) isolated after 100–500 generations of growth in glucose-limited chemostats. Changes in DNA copy number were assessed at single-gene resolution by using DNA microarray-based comparative genomic hybridization. Six of these evolved strains were aneuploid as the result of gross chromosomal rearrangements. Most of the aneuploid regions were the result of translocations, including three instances of a shared breakpoint on chromosome 14 immediately adjacent to
CIT1
, which encodes the citrate synthase that performs a key regulated step in the tricarboxylic acid cycle. Three strains had amplifications in a region of chromosome 4 that includes the high-affinity hexose transporters; one of these also had the aforementioned chromosome 14 break. Three strains had extensive overlapping deletions of the right arm of chromosome 15. Further analysis showed that each of these genome rearrangements was bounded by transposon-related sequences at the breakpoints. The observation of repeated, independent, but nevertheless very similar, chromosomal rearrangements in response to persistent selection of growing cells parallels the genome rearrangements that characteristically accompany tumor progression.
Visual detection is gated by attending for action: Evidence from hemispatial neglect
Authors: Rafal Robert , Danziger Shai , Grossi Giordana , Machado Liana , Ward Robert
Published: December 2002

We report observations in patients with visual extinction demonstrating that detection of visual events is gated by attention at the level of processing at which a stimulus is selected for action. In one experiment, three patients reported the identity of numerical words and digits presented either in the ipsilesional field, the contralesional field, or both fields. On the critical bilateral trials, extinction was greater when the competing items shared the same meaning and response, regardless of whether the items were visually different (e.g., ONE + 1), or identical (e.g., 1 + 1). A fourth patient was tested in a second experiment in which the competing items on bilateral trials were either different (e.g., ONE + TWO), identical (e.g., ONE + ONE) or homophones that were visually and semantically different but shared the same response (e.g., ONE + WON). Homophones and identical items caused similar extinction with less extinction occurring on different item trials.
Control of PERK eIF2α kinase activity by the endoplasmic reticulum stress-induced molecular chaperone P58
IPK
Authors: Yan Wei , Frank Christopher L. , Korth Marcus J. , Sopher Bryce L. , Novoa Isabel , Ron David , Katze Michael G.
Published: December 2002

P58
IPK
is an Hsp40 family member known to inhibit the interferon (IFN)-induced, double-stranded RNA-activated, eukaryotic initiation factor 2α (eIF2α) protein kinase R (PKR) by binding to its kinase domain. We find that the stress of unfolded proteins in the endoplasmic reticulum (ER) activates

P58
IPK

gene transcription through an ER stress-response element in its promoter region. P58
IPK
interacts with and inhibits the PKR-like ER-localized eIF2α kinase PERK, which is normally activated during the ER-stress response to protect cells from ER stress by attenuating protein synthesis and reducing ER client protein load. Levels of phosphorylated eIF2α were lower in ER-stressed

P58
IPK

-overexpressing cells and were enhanced in P58
IPK
mutant cells. In the ER-stress response, PKR-like ER kinase (PERK)-mediated translational repression is transient and is followed by translational recovery and enhanced expression of genes that increase the capacity of the ER to process client proteins. The absence of P58
IPK
resulted in increased expression levels of two ER stress-inducible genes,
BiP
and
Chop
, consistent with the enhanced eIF2α phosphorylation in the P58
IPK
deletion cells. Our studies suggest that P58
IPK
induction during the ER-stress response represses PERK activity and plays a functional role in the expression of downstream markers of PERK activity in the later phase of the ER-stress response.
Mosaic organization and heterogeneity in frequency of allelic recombination of the
Plasmodium vivax
merozoite surface protein-1 locus
Authors: Putaporntip Chaturong , Jongwutiwes Somchai , Sakihama Naoko , Ferreira Marcelo U. , Kho Weon-Gyu , Kaneko Akira , Kanbara Hiroji , Hattori Tetsuya , Tanabe Kazuyuki
Published: December 2002

The organization and allelic recombination of the merozoite surface protein-1 gene of
Plasmodium vivax
(
PvMsp-1
), the most widely prevalent human malaria parasite, were evaluated in complete nucleotide sequences of 40 isolates from various geographic areas. Alignment of 31 distinct alleles revealed the mosaic organization of
PvMsp-1
, consisting of seven interallele conserved blocks flanked by six variable blocks. The variable blocks showed extensive variation in repeats and nonrepeat unique sequences. Numerous recombination sites were distributed throughout
PvMsp-1
, in both conserved blocks and variable block unique sequences, and the distribution was not uniform. Heterozygosity of
PvMsp-1
alleles was higher in Asia (0.953 ± 0.009) than in Brazil (0.813 ± 0.047). No identical alleles were shared between Asia and Brazil, whereas all but one variable block nonrepeat sequence found in Brazil occurred in Asia. These observations suggest that
P. vivax
populations in Asia are ancestral to Brazilian populations, and that
PvMsp-1
has heterogeneity in frequency of allelic recombination events. Recurrent origins of new
PvMsp-1
alleles by repeated recombination events were supported by a rapid decline in linkage disequilibrium between pairs of synonymous sites with increasing nucleotide distance, with little linkage disequilibrium at a distance of over 3 kb in a
P. vivax
population from Thailand, evidence for an effectively high recombination rate of the parasite. Meanwhile, highly reduced nucleotide diversity was noted in a region encoding the 19-kDa C-terminal epidermal growth factor-like domain of merozoite surface protein-1, a vaccine candidate.
Coordination of kinesin's two heads studied with mutant heterodimers
Authors: Kaseda Kuniyoshi , Higuchi Hideo , Hirose Keiko
Published: December 2002

A conventional kinesin molecule has two identical catalytic domains (heads) and is thought to use them alternately to move processively, with 8-nm steps. To clarify how each head contributes to the observed steps, we have constructed heterodimeric kinesins that consist of two distinct heads. The heterodimers in which one of the heads is mutated in a microtubule-binding loop moved processively, even when the parent mutant homodimers bound too weakly to retain microtubules in microtubule-gliding assays. The velocities of the heterodimers were only slightly higher than those of the mutant homodimers, although mixtures of these weak-binding mutant homodimers and the WT dimers moved microtubules at a velocity similar to the WT. Thus, the mutant head affects the motility of the WT head only when they are in the same molecule. The maximum force a single heterodimer produced in optical trapping nanometry was intermediate between the WT and mutant homodimers, indicating that both heads contribute to the maximum force at the same time. These results demonstrate close collaboration of kinesin's two heads in producing force and motility.
Preferential induction of apoptosis for primary human leukemic stem cells
Authors: Guzman Monica L. , Swiderski Carol F. , Howard Dianna S. , Grimes Barry A. , Rossi Randall M. , Szilvassy Stephen J. , Jordan Craig T.
Published: December 2002

Acute myelogenous leukemia (AML) is typically a disease of stem/progenitor cell origin. Interestingly, the leukemic stem cell (LSC) shares many characteristics with normal hematopoietic stem cells (HSCs) including the ability to self-renew and a predominantly G0cell-cycle status. Thus, although conventional chemotherapy regimens often ablate actively cycling leukemic blast cells, the primitive LSC population is likely to be drug-resistant. Moreover, given the quiescent nature of LSCs, current drugs may not effectively distinguish between malignant stem cells and normal HSCs. Nonetheless, based on recent studies of LSC molecular biology, we hypothesized that certain unique properties of leukemic cells could be exploited to induce apoptosis in the LSC population while sparing normal stem cells. In this report we describe a strategy using treatment of primary AML cells with the proteasome inhibitor carbobenzoxyl-l-leucyl-l-leucyl-l-leucinal (MG-132) and the anthracycline idarubicin. Comparison of normal and leukemic specimens usingin vitroculture andin vivoxenotransplantation assays shows that the combination of these two agents induces rapid and extensive apoptosis of the LSC population while leaving normal HSCs viable. Molecular genetic studies using a dominant-negative allele of inhibitor of nuclear factor κB (IκBα) demonstrate that inhibition of nuclear factor κB (NF-κB) contributes to apoptosis induction. In addition, gene-expression analyses suggest that activation of p53-regulated genes are also involved in LSC apoptosis. Collectively, these findings demonstrate that malignant stem cells can be preferentially targeted for ablation. Further, the data begin to elucidate the molecular mechanisms that underlie LSC-specific apoptosis and suggest new directions for AML therapy.
Nitric oxide preferentially induces type 1 T cell differentiation by selectively up-regulating IL-12 receptor β2 expression via cGMP
Authors: Niedbala Wanda , Wei Xiao-qing , Campbell Carol , Thomson Duncan , Komai-Koma Mousa , Liew Foo Y.
Published: December 2002

Nitric oxide plays an important role in immune regulation. We have shown that although high concentrations of NO generally were immune-suppressive, low concentrations of NO selectively enhanced the differentiation of T helper (Th)1 cells but not Th2 cells. This finding provided an explanation for the crucial role of NO in defense against intracellular pathogens. However, the mechanism for the selective induction of Th1 cells was unknown. We report here that at low concentrations, NO activates soluble guanylyl cyclase, leading to the up-regulation of cGMP, which selectively induces the expression of IL-12 receptor β2 but has no effect on IL-4 receptor. Because IL-12 and IL-4 are the key cytokines for induction of Th1 and Th2 cells, respectively, these results, therefore, provide the mechanism for the selective action of NO on T cell subset differentiation. Furthermore, this selectivity also applies to CD8+cytotoxic and human T cells and, thus, demonstrates the general implication of this observation in immune regulation. Our results also provide an example of the regulation of cytokine receptor expression by NO. The selectivity of such action via cGMP suggests that it is amenable to therapeutic intervention.
Sensitivity of HIV-1 to entry inhibitors correlates with envelope/coreceptor affinity, receptor density, and fusion kinetics
Authors: Reeves Jacqueline D. , Gallo Stephen A. , Ahmad Navid , Miamidian John L. , Harvey Phoebe E. , Sharron Matthew , Pöhlmann Stefan , Sfakianos Jeffrey N. , Derdeyn Cynthia A. , Blumenthal Robert , Hunter Eric , Doms Robert W.
Published: December 2002

HIV entry inhibitors include coreceptor antagonists and the fusion inhibitor T-20. T-20 binds the first helical region (HR1) in the gp41 subunit of the viral envelope (Env) protein and prevents conformational changes required for membrane fusion. HR1 appears to become accessible to T-20 after Env binds CD4, whereas coreceptor binding is thought to induce the final conformational changes that lead to membrane fusion. Thus, T-20 binds to a structural intermediate of the fusion process. Primary viruses exhibit considerable variability in T-20 sensitivity, and determinants outside of HR1 can affect sensitivity by unknown mechanisms. We studied chimeric Env proteins containing different V3 loop sequences and found that gp120/coreceptor affinity correlated with T-20 and coreceptor antagonist sensitivity, with greater affinity resulting in increased resistance to both classes of entry inhibitors. Enhanced affinity resulted in more rapid fusion kinetics, reducing the time during which Env is sensitive to T-20. Reduced coreceptor expression levels also delayed fusion kinetics and enhanced virus sensitivity to T-20, whereas increased coreceptor levels had the opposite effect. A single amino acid change (K421D) in the bridging sheet region of the primary virus strain YU2 reduced affinity for CCR5 and increased T-20 sensitivity by about 30-fold. Thus, mutations in Env that affect receptor engagement and membrane fusion rates can alter entry inhibitor sensitivity. Because coreceptor expression levels are typically limiting
in vivo
, individuals who express lower coreceptor levels may respond more favorably to entry inhibitors such as T-20, whose effectiveness we show depends in part on fusion kinetics.
Dissociation between conflict detection and error monitoring in the human anterior cingulate cortex
Authors: Swick Diane , Turken And U.
Published: December 2002

The relative importance of the anterior cingulate cortex (ACC) for the detection and resolution of response conflicts versus its role in error monitoring remains under debate. One disputed issue is whether conflict detection and error monitoring can be viewed as unitary functions performed by the same region of the ACC, or whether these processes can be dissociated functionally and anatomically. We used a combination of electrophysiological and neuropsychological methods to assess these competing hypotheses. A neurological patient with a rare focal lesion of rostral-to-middorsal ACC was tested in an event-related potential study designed to track the time course of neural activity during conflicts and erroneous responses. Compared with controls, the error-related negativity component after incorrect responses was attenuated in the patient, accompanied by lower error-correction rates. Conversely, the stimulus-locked component on correct conflict trials, the N450, was enhanced, and behavioral performance was impaired. We hypothesize that intact regions of lateral prefrontal cortex were able to detect response conflict, but damage to the dorsal ACC impaired response inhibition, which may be due to disconnection from cingulate and supplementary motor areas. The results implicate rostral-dorsal ACC in error monitoring and suggest this function can be dissociated from conflict-detection processes.
Role of human DNA polymerase κ as an extender in translesion synthesis
Authors: Haracska Lajos , Prakash Louise , Prakash Satya
Published: December 2002

Human DNA polymerase (Pol)κ is a member of the Y family of DNA polymerases. Unlike Polη, another member of this family, which carries out efficient translesion synthesis through various DNA lesions, the role of Polκ in lesion bypass has remained unclear. Recent studies, however, have indicated that Polκ is a proficient extender of mispaired primer termini on undamaged DNAs and also on cis-syn thymine-thymine (T-T) dimer-containing DNA. Here we determine whether Polκ can promote the efficient bypass of DNA lesions by extending from the nucleotides inserted opposite the lesion site by another DNA polymerase. From steady-state kinetic analyses, we find that Polκ is highly inefficient at incorporating nucleotides opposite an
O
6
-methyl guanine (m6G) lesion, but it efficiently extends from the T or C nucleotide incorporated opposite this lesion by Polδ. Opposite an 8-oxoguanine (8-oxoG) lesion, Polκ efficiently inserts an A and then proficiently extends from it. Importantly, for both these DNA lesions, however, the most efficient bypass occurs when Polδ is combined with Polκ; in this reaction, Polκ performs the extension step after the incorporation of nucleotides opposite these lesion sites by Polδ. These studies reveal a role for Polκ in the extension phase of lesion bypass.
Persistent millennial-scale shifts in moisture regimes in western Canada during the past six millennia
Authors: Cumming Brian F. , Laird Kathleen R. , Bennett Joseph R. , Smol John P. , Salomon Anne K.
Published: December 2002

Inferences of past climatic conditions from a sedimentary record from Big Lake, British Columbia, Canada, over the past 5,500 years show strong millennial-scale patterns, which oscillate between periods of wet and drier climatic conditions. Higher frequency decadal- to centennial-scale fluctuations also occur within the dominant millennial-scale patterns. These changes in climatic conditions are based on estimates of changes in lake depth and salinity inferred from diatom assemblages in a well dated sediment core. After periods of relative stability, abrupt shifts in diatom assemblages and inferred climatic conditions occur approximately every 1,220 years. The correspondence of these shifts to millennial-scale variations in records of glacial expansion/recession and ice-rafting events in the Atlantic suggest that abrupt millennial-scale shifts are important to understanding climatic variability in North America during the mid- to late Holocene. Unfortunately, the spatial patterns and mechanisms behind these large and abrupt swings are poorly understood. Similar abrupt and prolonged changes in climatic conditions today could pose major societal challenges for many regions.
The Brownian Web
Authors: Fontes L. R. G. , Isopi M. , Newman C. M. , Ravishankar K.
Published: December 2002

Arratia, [Arratia, R. (1979) Ph.D. thesis (University of Wisconsin, Madison) and unpublished work] and later Toth and Werner [Toth, B. & Werner, W. (1998)
Probab. Theory Relat. Fields
111, 375–452] constructed random processes that formally correspond to coalescing one-dimensional Brownian motions starting from every space-time point. We extend their work by constructing and characterizing what we call the Brownian Web as a random variable taking values in an appropriate (metric) space whose points are (compact) sets of paths. This leads to general convergence criteria and, in particular, to convergence in distribution of coalescing random walks in the scaling limit to the Brownian Web.
AMP kinase is required for mitochondrial biogenesis in skeletal muscle in response to chronic energy deprivation
Authors: Zong Haihong , Ren Jian Ming , Young Lawrence H. , Pypaert Marc , Mu James , Birnbaum Morris J. , Shulman Gerald I.
Published: December 2002

Mitochondrial biogenesis is a critical adaptation to chronic energy deprivation, yet the signaling mechanisms responsible for this response are poorly understood. To examine the role of AMP-activated protein kinase (AMPK), an evolutionarily conserved fuel sensor, in mitochondrial biogenesis we studied transgenic mice expressing a dominant-negative mutant of AMPK in muscle (DN-AMPK). Both DN-AMPK and WT mice were treated with β-guanidinopropionic acid (GPA), a creatine analog, which led to similar reductions in the intramuscular ATP/AMP ratio and phosphocreatine concentrations. In WT mice, GPA treatment resulted in activation of muscle AMPK and mitochondrial biogenesis. However, the same GPA treatment in DN-AMPK mice had no effect on AMPK activity or mitochondrial content. Furthermore, AMPK inactivation abrogated GPA-induced increases in the expression of peroxisome proliferator-activated receptor γ coactivator 1α and calcium/calmodulin-dependent protein kinase IV (both master regulators of mitochondrial biogenesis). These data demonstrate that by sensing the energy status of the muscle cell, AMPK is a critical regulator involved in initiating mitochondrial biogenesis.
The directional atomic solvation energy: An atom-based potential for the assignment of protein sequences to known folds
Authors: Mallick Parag , Weiss Robert , Eisenberg David
Published: December 2002

The Directional Atomic Solvation EnergY (DASEY) is an atom-based description of the environment of an amino acid position within a known 3D protein structure. The DASEY has been developed to align and score a probe amino acid sequence to a library of template protein structures for fold assignment. DASEY is computed by summing the atomic solvation parameters of atoms falling within a tetrahedral sector, or petal, extending 16 Å along each of the four bond axes of each α-carbon atom of the protein. The DASEY discriminates between pairs of structurally equivalent positions and random pairs in protein structures sharing a fold but belonging to different superfamilies, unlike some previous descriptors of protein environments, such as buried area. Furthermore, the DASEY values have characteristic patterns of residue replacement, an essential feature of a successful fold assignment method. Benchmarking fold assignment with DASEY achieves coverage of 56% of sequences with 90% accuracy when probe sequences are matched to protein structural templates belonging to the same fold but to a different superfamily, an improvement of greater than 200% over a previous method.
Retinaldehyde dehydrogenase 2 (RALDH2)- independent patterns of retinoic acid synthesis in the mouse embryo
Authors: Niederreither Karen , Vermot Julien , Fraulob Valérie , Chambon Pierre , Dollé Pascal
Published: December 2002

Knockout of the murine retinoic acid (RA)-synthesizing enzyme retinaldehyde dehydrogenase 2 (RALDH2) gene leads to early morphogenetic defects and embryonic lethality. Using a RA-responsive reporter transgene, we have looked for RA-generating activities in
Raldh2
-null mouse embryos and investigated whether these activities could be ascribed to the other known RALDH enzymes (RALDH1 and RALDH3). To this end, the early defects of
Raldh2
−/−
embryos were rescued through maternal dietary RA supplementation under conditions that do not interfere with the activity of the reporter transgene in WT embryos. We show that RALDH2 is responsible for most of the patterns of reporter transgene activity in the spinal cord and trunk mesodermal derivatives. However, reporter transgene activity was selectively detected in
Raldh2
−/−
embryos within the mesonephric area that expresses RALDH3 and in medial-ventral cells of the spinal cord and posterior hindbrain, up to the level of the fifth rhombomere. The craniofacial patterns of RA-reporter activity were unaltered in
Raldh2
−/−
mutants. Although these patterns correlated with the presence of
Raldh1
and/or
Raldh3
transcripts in eye, nasal, and inner ear epithelia, no such correlation was found within forebrain neuroepithelium. These data suggest the existence of additional RA-generating activities in the differentiating forebrain, hindbrain, and spinal cord, which, along with RALDH1 and RALDH3, may account for the development of
Raldh2
−/−
mutants once these have been rescued for early lethality.
Biliverdin reductase: A major physiologic cytoprotectant
Authors: Barañano David E. , Rao Mahil , Ferris Christopher D. , Snyder Solomon H.
Published: December 2002

Bilirubin, an abundant pigment that causes jaundice, has long lacked any clear physiologic role. It arises from enzymatic reduction by biliverdin reductase of biliverdin, a product of heme oxygenase activity. Bilirubin is a potent antioxidant that we show can protect cells from a 10,000-fold excess of H
2
O
2
. We report that bilirubin is a major physiologic antioxidant cytoprotectant. Thus, cellular depletion of bilirubin by RNA interference markedly augments tissue levels of reactive oxygen species and causes apoptotic cell death. Depletion of glutathione, generally regarded as a physiologic antioxidant cytoprotectant, elicits lesser increases in reactive oxygen species and cell death. The potent physiologic antioxidant actions of bilirubin reflect an amplification cycle whereby bilirubin, acting as an antioxidant, is itself oxidized to biliverdin and then recycled by biliverdin reductase back to bilirubin. This redox cycle may constitute the principal physiologic function of bilirubin.
The autosomal recessive hypercholesterolemia (ARH) protein interfaces directly with the clathrin-coat machinery
Authors: Mishra Sanjay K. , Watkins Simon C. , Traub Linton M.
Published: December 2002

The low density lipoprotein (LDL) receptor plays a pivotal role in cholesterol metabolism. Inherited mutations that disturb the activity of the receptor lead to elevations in plasma cholesterol levels and early-onset coronary atherosclerosis. Defects in either the LDL receptor or apolipoprotein B, the proteinaceous component of LDL particles that binds the LDL receptor, elevate circulating LDL-cholesterol levels in an autosomal-dominant fashion, with heterozygotes displaying values between homozygous and normal individuals. Rarely, similar clinical phenotypes occur with a recessive pattern of inheritance, and several genetic lesions in the autosomal recessive hypercholesterolemia (
ARH
) gene on chromosome 1 have been mapped in this class of patients. ARH has an N-terminal phosphotyrosine-binding (PTB) domain evolutionarily related to that found in Disabled-2 and numb, two endocytic proteins. PTB domains bind to the consensus sequence FXNPXY, corresponding to the internalization motif of the LDL receptor. We show here that in addition to the FXNPXY sequence, ARH binds directly to soluble clathrin trimers and to clathrin adaptors by a mode involving the independently folded appendage domain of the β subunit. At steady state, ARH colocalizes with endocytic proteins in HeLa cells, and the LDL receptor fluxes through peripheral ARH-positive sites before delivery to early endosomes. Because ARH also binds directly to phosphoinositides, which regulate clathrin bud assembly at the cell surface, our data suggest that in ARH patients, defective sorting adaptor function in hepatocytes leads to faulty LDL receptor traffic and hypercholesterolemia.
The average distances in random graphs with given expected degrees
Authors: Chung Fan , Lu Linyuan
Published: December 2002

Random graph theory is used to examine the “small-world phenomenon”; any two strangers are connected through a short chain of mutual acquaintances. We will show that for certain families of random graphs with given expected degrees the average distance is almost surely of order logn/logd̃,whered̃is the weighted average of the sum of squares of the expected degrees. Of particular interest are power law random graphs in which the number of vertices of degreekis proportional to1/kβfor some fixed exponent β. For the case of β > 3, we prove that the average distance of the power law graphs is almost surely of order logn/logd̃.However, many Internet, social, and citation networks are power law graphs with exponents in the range 2 < β < 3 for which the power law random graphs have average distance almost surely of order log logn,but have diameter of order logn(provided having some mild constraints for the average distance and maximum degree). In particular, these graphs contain a dense subgraph, which we call the core, havingnc/log lognvertices. Almost all vertices are within distance log lognof the core although there are vertices at distance lognfrom the core.
Surface crystallization of supercooled water in clouds
Authors: Tabazadeh A. , Djikaev Y. S. , Reiss H.
Published: December 2002

The process by which liquid cloud droplets homogeneously crystallize into ice is still not well understood. The ice nucleation process based on the standard and classical theory of homogeneous freezing initiates within the interior volume of a cloud droplet. Current experimental data on homogeneous freezing rates of ice in droplets of supercooled water, both in air and emulsion oil samples, show considerable scatter. For example, at −33°C, the reported volume-based freezing rates of ice in supercooled water vary by as many as 5 orders of magnitude, which is well outside the range of measurement uncertainties. Here, we show that the process of ice nucleus formation at the air (or oil)-liquid water interface may help to explain why experimental results on ice nucleation rates yield different results in different ambient phases. Our results also suggest that surface crystallization of ice in cloud droplets can explain why low amounts of supercooled water have been observed in the atmosphere near −40°C.
Penelope
retroelements from
Drosophila virilis
are active after transformation of
Drosophila melanogaster
Authors: Pyatkov Konstantin I. , Shostak Natalia G. , Zelentsova Elena S. , Lyozin George T. , Melekhin Michael I. , Finnegan David J. , Kidwell Margaret G. , Evgen'ev Michael B.
Published: December 2002

The
Penelope
family of retroelements was first described in species of the
Drosophila virilis
group. Intact elements encode a reverse transcriptase and an endonuclease of the UvrC type, which may play a role in
Penelope
integration.
Penelope
is a key element in the induction of
D. virilis
hybrid dysgenesis, which involves the mobilization of several unrelated families of transposable elements. We here report the successful introduction of
Penelope
into the germ line of
Drosophila melanogaster
by
P
element-mediated transformation with three different constructs.
Penelope
is actively transcribed in the
D. melanogaster
genome only in lines transformed with a construct containing a full-length
Penelope
clone. The transcript is identical to that detected in
D. virilis
dysgenic hybrids. Most newly transposed
Penelope
elements have a very complex organization. Significant proliferation of
Penelope
copy number occurred in some lines during the 24-month period after transformation. The absence of copy number increase with two other constructs suggests that the 5′ and/or 3′ UTRs of
Penelope
are required for successful transposition in
D. melanogaster
. No insect retroelement has previously been reported to be actively transcribed and to increase in copy number after interspecific transformation.
Ventricular septal defect and cardiomyopathy in mice lacking the transcription factor CHF1/Hey2
Authors: Sakata Yasuhiko , Kamei Caramai N. , Nakagami Hironori , Bronson Roderick , Liao James K. , Chin Michael T.
Published: December 2002

Ventricular septal defects are common in human infants, but the genetic programs that control ventricular septation are poorly understood. Here we report that mice with a targeted disruption of the cardiovascular basic helix–loop–helix factor (
CHF
)
1/Hey2
gene show isolated ventricular septal defects. These defects result primarily in failure to thrive. Mice often succumbed within the first 3 wk after birth and showed pulmonary and liver congestion. The penetrance of this phenotype varied, depending on genetic background, suggesting the presence of modifier genes. Expression patterns of other cardiac-specific genes were not affected. Of the few animals on a mixed genetic background that survived to adulthood, most developed a cardiomyopathy but did not have ventricular septal defects. Our results indicate that CHF1 plays an important role in regulation of ventricular septation in mammalian heart development and is important for normal myocardial contractility. These mice provide a useful model for the study of the ontogeny and natural history of ventricular septal defects and cardiomyopathy.
Brain-derived neurotrophic factor can act as a pronecrotic factor through transcriptional and translational activation of NADPH oxidase
Authors: Kim Sun H. , Won Seok J. , Sohn Seonghyang , Kwon Hyuk J. , Lee Jee Y. , Park Jong H. , Gwag Byoung J.
Published: December 2002

Several lines of evidence suggest that neurotrophins (NTs) potentiate or cause neuronal injury under various pathological conditions. Since NTs enhance survival and differentiation of cultured neurons in serum or defined media containing antioxidants, we set out experiments to delineate the patterns and underlying mechanisms of brain-derived neurotrophic factor (BDNF)–induced neuronal injury in mixed cortical cell cultures containing glia and neurons in serum-free media without antioxidants, where the three major routes of neuronal cell death, oxidative stress, excitotoxicity, and apoptosis, have been extensively studied. Rat cortical cell cultures, after prolonged exposure to NTs, underwent widespread neuronal necrosis. BDNF-induced neuronal necrosis was accompanied by reactive oxygen species (ROS) production and was dependent on the macromolecular synthesis. cDNA microarray analysis revealed that BDNF increased the expression of cytochrome b558, the plasma membrane-spanning subunit of NADPH oxidase. The expression and activation of NADPH oxidase were increased after exposure to BDNF. The selective inhibitors of NADPH oxidase prevented BDNF-induced ROS production and neuronal death without blocking antiapoptosis action of BDNF. The present study suggests that BDNF-induced expression and activation of NADPH oxidase cause oxidative neuronal necrosis and that the neurotrophic effects of NTs can be maximized under blockade of the pronecrotic action.
Lamin A/C speckles mediate spatial organization of splicing factor compartments and RNA polymerase II transcription
Authors: Kumaran R. Ileng , Muralikrishna Bhattiprolu , Parnaik Veena K.
Published: December 2002

The A-type lamins have been observed to colocalize with RNA splicing factors in speckles within the nucleus, in addition to their typical distribution at the nuclear periphery. To understand the functions of lamin speckles, the effects of transcriptional inhibitors known to modify RNA splicing factor compartments (SFCs) were examined. Treatment of HeLa cells with α-amanitin or 5,6-dichlorobenzimidazole riboside (DRB) inhibited RNA polymerase II (pol II) transcription and led to the enlargement of lamin speckles as well as SFCs. Removal of the reversible inhibitor DRB resulted in the reactivation of transcription and a rapid, synchronous redistribution of lamins and splicing factors to normal-sized speckles, indicating a close association between lamin speckles and SFCs. Conversely, the expression of NH2-terminally modified lamin A or C in HeLa cells brought about a loss of lamin speckles, depletion of SFCs, and down-regulation of pol II transcription without affecting the peripheral lamina. Our results suggest a unique role for lamin speckles in the spatial organization of RNA splicing factors and pol II transcription in the nucleus.
The transcription cycle of RNA polymerase II in living cells
Authors: Kimura Hiroshi , Sugaya Kimihiko , Cook Peter R.
Published: December 2002

RNA polymerase II transcribes most eukaryotic genes. Its catalytic subunit was tagged with green fluorescent protein and expressed in Chinese hamster cells bearing a mutation in the same subunit; it complemented the defect and so was functional. Photobleaching revealed two kinetic fractions of polymerase in living nuclei: ∼75% moved rapidly, but ∼25% was transiently immobile (association t1/2 ≈ 20 min) and transcriptionally active, as incubation with 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole eliminated it. No immobile but inactive fraction was detected, providing little support for the existence of a stable holoenzyme, or the slow stepwise assembly of a preinitiation complex on promoters or the nuclear substructure. Actinomycin D decreased the rapidly moving fraction, suggesting that engaged polymerases stall at intercalated molecules while others initiate. When wild-type cells containing only the endogenous enzyme were incubated with [3H]uridine, nascent transcripts became saturated with tritium with similar kinetics (t1/2 ≈ 14 min). These data are consistent with a polymerase being mobile for one half to five sixths of a transcription cycle, and rapid assembly into the preinitiation complex. Then, most expressed transcription units would spend significant times unassociated with engaged polymerases.