bluuebunny/crossref_metadata_2025 huggingface dataset:
Mammalian Scratch: A neural-specific Snail family transcriptional repressor
Authors: Nakakura Eric K. , Watkins D. Neil , Schuebel Kornel E. , Sriuranpong Virote , Borges Michael W. , Nelkin Barry D. , Ball Douglas W.
Published: July 2002

Members of the Snail family of zinc finger transcription factors
are known to play critical roles in neurogenesis in invertebrates, but
none of these factors has been linked to vertebrate neuronal
differentiation. We report the isolation of a gene encoding a mammalian
Snail family member that is restricted to the nervous system. Human and
murine Scratch (Scrt) share 81% and 69% identity to
Drosophila
Scrt and the
Caenorhabditis elegans
neuronal
antiapoptotic protein, CES-1, respectively, across the five
zinc finger domain. Expression of mammalian Scrt is predominantly
confined to the brain and spinal cord, appearing in newly
differentiating, postmitotic neurons and persisting into postnatal
life. Additional expression is seen in the retina and, significantly,
in neuroendocrine (NE) cells of the lung. In a parallel fashion, we
detect hScrt expression in lung cancers with NE features, especially
small cell lung cancer. hScrt shares the capacity of other Snail family
members to bind to E-box enhancer motifs, which are targets of basic
helix–loop–helix (bHLH) transcription factors. We show that hScrt
directly antagonizes the function of heterodimers of the proneural bHLH
protein achaete-scute homolog-1 and E12, leading to active
transcriptional repression at E-box motifs. Thus, Scrt has the
potential to function in newly differentiating, postmitotic neurons and
in cancers with NE features by modulating the action of bHLH
transcription factors critical for neuronal differentiation.
Impaired survival of T helper cells in the absence of CD4
Authors: Strong Julie , Wang Qi , Killeen Nigel
Published: July 2002

Signal transduction in response to ligand recognition by T cell receptors regulates T cell fate within and beyond the thymus. Herein we examine the involvement of the CD4 molecule in the regulation of T helper cell survival. T helper cells that lack CD4 expression are prone to apoptosis and show diminished survival after adoptive transfer to irradiated recipients. The helper lineage in CD4−/−animals shows a higher than normal apparent rate of cell division and is also enriched for cells exhibiting a memory cell phenotype. Thus the data point to a necessary role for CD4 in the regulation of T helper cell survival and homeostasis.
The starch-related R1 protein is an α-glucan, water dikinase
Authors: Ritte Gerhard , Lloyd James R. , Eckermann Nora , Rottmann Antje , Kossmann Jens , Steup Martin
Published: July 2002

To determine the enzymatic function of the starch-related R1 protein it was heterologously expressed in
Escherichia coli
and purified to apparent homogeneity. Incubation of the purified protein with various phosphate donor and acceptor molecules showed that R1 is capable of phosphorylating glucosyl residues of α-glucans at both the C-6 and the C-3 positions in a ratio similar to that occurring naturally in starch. Phosphorylation occurs in a dikinase-type reaction in which three substrates, an α-polyglucan, ATP, and H
2
O, are converted into three products, an α-polyglucan-P, AMP, and orthophosphate. The use of ATP radioactively labeled at either the γ or β positions showed that solely the β phosphate is transferred to the α-glucan. The apparent
K
m
of the R1 protein for ATP was calculated to be 0.23 μM and for amylopectin 1.7 mg⋅ml
−1
. The velocity of
in vitro
phosphorylation strongly depends on the type of the glucan. Glycogen was an extremely poor substrate; however, the efficiency of phosphorylation strongly increased if the glucan chains of glycogen were elongated by phosphorylase. Mg
2+
ions proved to be essential for activity. Incubation of R1 with radioactively labeled ATP in the absence of an α-glucan showed that the protein phosphorylates itself with the β, but not with the γ phosphate. Autophosphorylation precedes the phosphate transfer to the glucan indicating a ping-pong reaction mechanism.
Stimulation of bone formation and prevention of bone loss by prostaglandin E EP4 receptor activation
Authors: Yoshida Keiji , Oida Hiroji , Kobayashi Takuya , Maruyama Takayuki , Tanaka Masaharu , Katayama Teruaki , Yamaguchi Kojiro , Segi Eri , Tsuboyama Tadao , Matsushita Mutsumi , Ito Kosei , Ito Yoshiaki , Sugimoto Yukihiko , Ushikubi Fumitaka , Ohuchida Shuichi , Kondo Kigen , Nakamura Takashi , Narumiya Shuh
Published: July 2002

Bone remodeling, comprising resorption of existing bone and
de novo
bone formation, is required for the maintenance of a constant bone mass. Prostaglandin (PG)E
2
promotes both bone resorption and bone formation. By infusing PGE
2
to mice lacking each of four PGE receptor (EP) subtypes, we have identified EP4 as the receptor that mediates bone formation in response to this agent. Consistently, bone formation was induced in wild-type mice by infusion of an EP4-selective agonist and not agonists specific for other EP subtypes. In culture of bone marrow cells from wild-type mice, PGE
2
induced expression of core-binding factor α1 (Runx2/Cbfa1) and enhanced formation of mineralized nodules, both of which were absent in the culture of cells from EP4-deficient mice. Furthermore, administration of the EP4 agonist restored bone mass and strength normally lost in rats subjected to ovariectomy or immobilization. Histomorphometric analysis revealed that the EP4 agonist induced significant increases in the volume of cancellous bone, osteoid formation, and the number of osteoblasts in the affected bone of immobilized rats, indicating that activation of EP4 induces
de novo
bone formation. In addition, osteoclasts were found on the increased bone surface at a density comparable to that found in the bone of control animals. These results suggest that activation of EP4 induces bone remodeling
in vivo
and that EP4-selective drugs may be beneficial in humans with osteoporosis.
Damage-induced neuronal endopeptidase (DINE) is a unique metallopeptidase expressed in response to neuronal damage and activates superoxide scavengers
Authors: Kiryu-Seo Sumiko , Sasaki Masahiko , Yokohama Hiroya , Nakagomi Saya , Hirayama Teruhisa , Aoki Shunsuke , Wada Keiji , Kiyama Hiroshi
Published: July 2002

We isolated a membrane-bound metallopeptidase, DINE (damage-induced neuronal endopeptidase), by differential display PCR using rat normal and axotomized hypoglossal nuclei. The most marked properties of DINE were neuron-specific expression and a striking response to axonal injury in both the central nervous system and peripheral nervous system. For instance, cranial and spinal nerve transection, ischemia, corpus callosum transection, and colchicine treatment increased DINE mRNA expression in the injured neurons, whereas kainate-induced hyperexcitation, immobilization, and osmotic stress failed to up-regulate DINE mRNA. Expression of DINE in COS cells partially inhibited C2-ceramide-induced apoptosis, probably because of the activation of antioxidant enzymes such as Cu/Zn-superoxide dismutase, Mn-superoxide dismutase, and glutathione peroxidase through the proteolytic activity of DINE. These data provide insight into the mechanism of how injured neurons protect themselves against neuronal death.
A role for intermolecular disulfide bonds in prion diseases?
Authors: Welker Ervin , Wedemeyer William J. , Scheraga Harold A.
Published: July 2002

The key event in prion diseases seems to be the conversion of the
prion protein PrP from its normal cellular isoform (PrP
C
)
to an aberrant “scrapie” isoform (PrP
Sc
). Earlier
studies have detected no covalent modification in the scrapie isoform
and have concluded that the PrP
C
→ PrP
Sc
conversion is a purely conformational transition involving no chemical
reactions. However, a reexamination of the available biochemical data
suggests that the PrP
C
→ PrP
Sc
conversion
also involves a covalent reaction of the (sole) intramolecular
disulfide bond of PrP
C
. Specifically, the data are
consistent with the hypothesis that infectious prions are composed of
PrP
Sc
polymers linked by intermolecular disulfide bonds.
Thus, the PrP
C
→ PrP
Sc
conversion may
involve not only a conformational transition but also a
thiol/disulfide exchange reaction between the terminal thiolate of
such a PrP
Sc
polymer and the disulfide bond of a
PrP
C
monomer. This hypothesis seems to account for several
unusual features of prion diseases.
Actions of PP2A on the MAP kinase pathway and apoptosis are mediated by distinct regulatory subunits
Authors: Silverstein Adam M. , Barrow Christina A. , Davis Anthony J. , Mumby Marc C.
Published: July 2002

Individual subunits of protein phosphatase 2A (PP2A), protein phosphatase 4, and protein phosphatase 5 were knocked out in
Drosophila
Schneider 2 cells by using RNA interference. Ablation of either the scaffold (A) or catalytic (C) subunits of PP2A caused the disappearance of all PP2A subunits. Treating cells with double-stranded RNA targeting all four of the
Drosophila
PP2A regulatory subunits caused the disappearance of both the A and C subunits. The loss of PP2A subunits was associated with decreased protein stability indicating that only the heterotrimeric forms of PP2A are stable in intact cells. Ablation of total PP2A by using double-stranded RNA against either the A or C subunit, or specific ablation of the R2/B regulatory subunit, enhanced insulin-induced ERK activation. These results indicated that the R2/B subunit targets PP2A to the mitogen-activated protein (MAP) kinase cascade in Schneider 2 cells, where it acts as a negative regulator. A severe loss of viability occurred in cells in which total PP2A or both isoforms of the
Drosophila
R5/B56 subunit had been ablated. The reduced viability of these cells correlated with the induction of markers of apoptosis including membrane blebbing and stimulation of caspase-3-like activity. These observations indicated that PP2A has a powerful antiapoptotic activity that is specifically mediated by the R5/B56 regulatory subunits. In contrast to PP2A, ablation of protein phosphatase 4 caused only a slight reduction in cell growth but had no effect on MAP kinase signaling or apoptosis. Depletion of protein phosphatase 5 had no effects on MAP kinase, cell growth, or apoptosis.
Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments
Authors: Orphan Victoria J. , House Christopher H. , Hinrichs Kai-Uwe , McKeegan Kevin D. , DeLong Edward F.
Published: July 2002

No microorganism capable of anaerobic growth on methane as the sole carbon source has yet been cultivated. Consequently, information about these microbes has been inferred from geochemical and microbiological observations of field samples. Stable isotope analysis of lipid biomarkers and rRNA gene surveys have implicated specific microbes in the anaerobic oxidation of methane (AOM). Here we use combined fluorescent
in situ
hybridization and secondary ion mass spectrometry analyses, to identify anaerobic methanotrophs in marine methane-seep sediments. The results provide direct evidence for the involvement of at least two distinct archaeal groups (ANME-1 and ANME-2) in AOM at methane seeps. Although both archaeal groups often occurred in direct physical association with bacteria, they also were observed as monospecific aggregations and as single cells. The ANME-1 archaeal group more frequently existed in monospecific aggregations or as single filaments, apparently without a bacterial partner. Bacteria associated with both archaeal groups included, but were not limited to, close relatives of
Desulfosarcina
species. Isotopic analyses suggest that monospecific archaeal cells and cell aggregates were active in anaerobic methanotrophy, as were multispecies consortia. In total, the data indicate that the microbial species and biotic interactions mediating anaerobic methanotrophy are diverse and complex. The data also clearly show that highly structured ANME-2/
Desulfosarcina
consortia are not the sole entities responsible for AOM at marine methane seeps. Other microbial groups, including ANME-1 archaea, are capable of anaerobic methane consumption either as single cells, in monospecific aggregates, or in multispecies consortia.
Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates
Authors: Tanabe Hideyuki , Müller Stefan , Neusser Michaela , von Hase Johann , Calcagno Enzo , Cremer Marion , Solovei Irina , Cremer Christoph , Cremer Thomas
Published: July 2002

We demonstrate that the nuclear topological arrangement of chromosome territories (CTs) has been conserved during primate evolution over a period of about 30 million years. Recent evidence shows that the positioning of chromatin in human lymphocyte nuclei is correlated with gene density. For example, human chromosome 19 territories, which contain mainly gene-dense and early replicating chromatin, are located toward the nuclear center, whereas chromosome 18 territories, which consist mainly of gene-poor and later replicating chromatin, is located close to the nuclear border. In this study, we subjected seven different primate species to comparative analysis of the radial distribution pattern of human chromosome 18- and 19-homologous chromatin by three-dimensional fluorescence
in situ
hybridization. Our data demonstrate that gene-density-correlated radial chromatin arrangements were conserved during higher-primate genome evolution, irrespective of the major karyotypic rearrangements that occurred in different phylogenetic lineages. The evolutionarily conserved positioning of homologous chromosomes or chromosome segments in related species supports evidence for a functionally relevant higher-order chromatin arrangement that is correlated with gene-density.
Peptide-amphiphile nanofibers: A versatile scaffold for the preparation of self-assembling materials
Authors: Hartgerink Jeffrey D. , Beniash Elia , Stupp Samuel I.
Published: July 2002

Twelve derivatives of peptide-amphiphile molecules, designed to self-assemble into nanofibers, are described. The scope of amino acid selection and alkyl tail modification in the peptide-amphiphile molecules are investigated, yielding nanofibers varying in morphology, surface chemistry, and potential bioactivity. The results demonstrate the chemically versatile nature of this supramolecular system and its high potential for manufacturing nanomaterials. In addition, three different modes of self-assembly resulting in nanofibers are described, including pH control, divalent ion induction, and concentration.
Pitch perception: A dynamical-systems perspective
Authors: Cartwright Julyan H. E. , González Diego L. , Piro Oreste
Published: July 2002

Two and a half millennia ago Pythagoras initiated the scientific study of the pitch of sounds; yet our understanding of the mechanisms of pitch perception remains incomplete. Physical models of pitch perception try to explain from elementary principles why certain physical characteristics of the stimulus lead to particular pitch sensations. There are two broad categories of pitch-perception models: place or spectral models consider that pitch is mainly related to the Fourier spectrum of the stimulus, whereas for periodicity or temporal models its characteristics in the time domain are more important. Current models from either class are usually computationally intensive, implementing a series of steps more or less supported by auditory physiology. However, the brain has to analyze and react in real time to an enormous amount of information from the ear and other senses. How is all this information efficiently represented and processed in the nervous system? A proposal of nonlinear and complex systems research is that dynamical attractors may form the basis of neural information processing. Because the auditory system is a complex and highly nonlinear dynamical system, it is natural to suppose that dynamical attractors may carry perceptual and functional meaning. Here we show that this idea, scarcely developed in current pitch models, can be successfully applied to pitch perception.
On a psychophysical transformed-rule up and down method converging on a 75% level of correct responses
Authors: Zwislocki Jozef J. , Relkin Evan M.
Published: July 2002

Tranformed-rule up and down psychophysical methods have gained great popularity, mainly because they combine criterion-free responses with an adaptive procedure allowing rapid determination of an average stimulus threshold at various criterion levels of correct responses. The statistical theory underlying the methods now in routine use is based on sets of consecutive responses with assumed constant probabilities of occurrence. The response rules requiring consecutive responses prevent the possibility of using the most desirable response criterion, that of 75% correct responses. The earliest transformed-rule up and down method, whose rules included nonconsecutive responses, did not contain this limitation but failed to become generally accepted, lacking a published theoretical foundation. Such a foundation is provided in this article and is validated empirically with the help of experiments on human subjects and a computer simulation. In addition to allowing the criterion of 75% correct responses, the method is more efficient than the methods excluding nonconsecutive responses in their rules.
Stop codons affect 5′ splice site selection by surveillance of splicing
Authors: Li Binghui , Wachtel Chaim , Miriami Elana , Yahalom Galit , Friedlander Gilgi , Sharon Gil , Sperling Ruth , Sperling Joseph
Published: July 2002

Pre-mRNA splicing involves recognition of a consensus sequence at the 5′ splice site (SS). However, only some of the many potential sites that conform to the consensus are true ones, whereas the majority remain silent and are not normally used for splicing. We noticed that in most cases the utilization of such a latent intronic 5′ SS for splicing would introduce an in-frame stop codon into the resultant mRNA. This finding suggested a link between SS selection and maintenance of an ORF within the mRNA. Here we tested this idea by analyzing the splicing of pre-mRNAs in which in-frame stop codons upstream of a latent 5′ SS were mutated. We found that splicing with the latent site is indeed activated by such mutations. Our findings predict the existence of a checking mechanism, as a component of the nuclear pre-mRNA splicing machine, to ensure the maintenance of an ORF. This notion is highly important for accurate gene expression, as perturbations that would lead to splicing at these latent sites are expected to introduce in-frame stop codons into the majority of mRNAs.
Temperature profile for glacial ice at the South Pole: Implications for life in a nearby subglacial lake
Authors: Price P. Buford , Nagornov Oleg V. , Bay Ryan , Chirkin Dmitry , He Yudong , Miocinovic Predrag , Richards Austin , Woschnagg Kurt , Koci Bruce , Zagorodnov Victor
Published: July 2002

Airborne radar has detected ≈100 lakes under the Antarctic ice cap, the largest of which is Lake Vostok. International planning is underway to search in Lake Vostok for microbial life that may have evolved in isolation from surface life for millions of years. It is thought, however, that the lakes may be hydraulically interconnected. If so, unsterile drilling would contaminate not just one but many of them. Here we report measurements of temperature vs. depth down to 2,345 m in ice at the South Pole, within 10 km from a subglacial lake seen by airborne radar profiling. We infer a temperature at the 2,810-m deep base of the South Pole ice and at the lake of −9°C, which is 7°C below the pressure-induced melting temperature of freshwater ice. To produce the strong radar signal, the frozen lake must consist of a mix of sediment and ice in a flat bed, formed before permanent Antarctic glaciation. It may, like Siberian and Antarctic permafrost, be rich in microbial life. Because of its hydraulic isolation, proximity to South Pole Station infrastructure, and analog to a Martian polar cap, it is an ideal place to test a sterile drill before risking contamination of Lake Vostok. From the semiempirical expression for strain rate vs. shear stress, we estimate shear vs. depth and show that the IceCube neutrino observatory will be able to map the three-dimensional ice-flow field within a larger volume (0.5 km
3
) and at lower temperatures (−20°C to −35°C) than has heretofore been possible.
A binding pocket for a small molecule inhibitor of HIV-1 entry within the transmembrane helices of CCR5
Authors: Dragic Tatjana , Trkola Alexandra , Thompson Daniah A. D. , Cormier Emmanuel G. , Kajumo Francis A. , Maxwell Elizabeth , Lin Steven W. , Ying Weiwen , Smith Steven O. , Sakmar Thomas P. , Moore John P.
Published: July 2002

HIV-1 entry into CD4+cells requires the sequential interactions of the viral envelope glycoproteins with CD4 and a coreceptor such as the chemokine receptors CCR5 and CXCR4. A plausible approach to blocking this process is to use small molecule antagonists of coreceptor function. One such inhibitor has been described for CCR5: the TAK-779 molecule. To facilitate the further development of entry inhibitors as antiviral drugs, we have explored how TAK-779 acts to prevent HIV-1 infection, and we have mapped its site of interaction with CCR5. We find that TAK-779 inhibits HIV-1 replication at the membrane fusion stage by blocking the interaction of the viral surface glycoprotein gp120 with CCR5. We could identify no amino acid substitutions within the extracellular domain of CCR5 that affected the antiviral action of TAK-779. However, alanine scanning mutagenesis of the transmembrane domains revealed that the binding site for TAK-779 on CCR5 is located near the extracellular surface of the receptor, within a cavity formed between transmembrane helices 1, 2, 3, and 7.
Collaborative signaling by mixed chemoreceptor teams in
Escherichia coli
Authors: Ames Peter , Studdert Claudia A. , Reiser Rebecca H. , Parkinson John S.
Published: July 2002

Chemoreceptors of the methyl-accepting chemotaxis protein family form clusters, typically at the cell pole(s), in both Bacteria and Archaea. To elucidate the architecture and signaling role of receptor clusters, we investigated interactions between the serine (Tsr) and aspartate (Tar) chemoreceptors in
Escherichia coli
by constructing Tsr mutations at the six hydrophobic and five polar residues implicated in “trimer of dimers” formation. Tsr mutants with proline replacements could not mediate serine chemotaxis, receptor clustering, or clockwise flagellar rotation. Alanine and tryptophan mutants, although also nonchemotactic, formed receptor clusters, and some produced clockwise flagellar rotation, indicating receptor-coupled activation of the signaling CheA kinase. The alanine and tryptophan mutants evidently assemble defective receptor complexes that cannot modulate CheA activity in response to serine stimuli. In cells containing wild-type Tar receptors, tryptophan replacements in Tsr interfered with Tar function, whereas four Tsr mutants with alanine replacements regained Tsr function. These epistatic and rescuable phenotypes imply interactions between Tsr and Tar dimers in higher-order signaling teams. The bulky side chain in tryptophan mutants may prevent stimulus-induced conformational changes in the team, whereas the small side chain in alanine mutants may permit signaling control when teamed with functional receptor molecules. Direct physical interactions between Tsr and Tar molecules were observed by
in vivo
chemical crosslinking. Wild-type Tsr crosslinked to Tar, whereas a clustering-defective proline replacement mutant did not. These findings indicate that bacterial chemoreceptor clusters are comprised of signaling teams, seemingly based on trimers of dimers, that can contain different receptor types acting collaboratively.
Structure of sortase, the transpeptidase that anchors proteins to the cell wall of
Staphylococcus aureus
Authors: Ilangovan Udayar , Ton-That Hung , Iwahara Junji , Schneewind Olaf , Clubb Robert T.
Published: July 2002

Surface proteins of Gram-positive bacteria play important roles
during the pathogenesis of human infections and require sortase for
anchoring to the cell-wall envelope. Sortase cleaves surface proteins
at the LPXTG motif and catalyzes the formation of an amide bond between
the carboxyl group of threonine (T) and the amino group of cell-wall
crossbridges. The NMR structure of sortase reveals a unique β-barrel
structure, in which the active-site sulfhydryl of cysteine-184 is
poised for ionization by histidine-120, presumably enabling the
resultant thiolate to attack the LPXTG peptide. Calcium binding near
the active site stimulates catalysis, possibly by altering the
conformation of a surface loop that recognizes newly translocated
polypeptides. The structure suggests a mechanistic relationship to the
papain/cathepsin proteases and should facilitate the design of new
antiinfective agents.
Human-modified ecosystems and future evolution
Authors: Western David
Published: July 2002

Our global impact is finally receiving the scientific attention it
deserves. The outcome will largely determine the future course of
evolution. Human-modified ecosystems are shaped by our activities and
their side effects. They share a common set of traits including
simplified food webs, landscape homogenization, and high nutrient and
energy inputs. Ecosystem simplification is the ecological hallmark of
humanity and the reason for our evolutionary success. However, the side
effects of our profligacy and poor resource practices are now so
pervasive as to threaten our future no less than that of biological
diversity itself. This article looks at human impact on ecosystems and
the consequences for evolution. It concludes that future evolution will
be shaped by our awareness of the global threats, our willingness to
take action, and our ability to do so. Our ability is presently
hampered by several factors, including the poor state of ecosystem and
planetary knowledge, ignorance of human impact, lack of guidelines for
sustainability, and a paucity of good policies, practices, and
incentives for adopting those guidelines in daily life. Conservation
philosophy, science, and practice must be framed against the reality of
human-dominated ecosystems, rather than the separation of humanity
and nature underlying the modern conservation movement. The steps
scientists can take to imbed science in conservation and conservation
in the societal process affecting the future of ecosystems and human
well-being are discussed.
Nitroxyl and its anion in aqueous solutions: Spin states, protic equilibria, and reactivities toward oxygen and nitric oxide
Authors: Shafirovich Vladimir , Lymar Sergei V.
Published: July 2002

The thermodynamic properties of aqueous nitroxyl (HNO) and its anion (NO
−
) have been revised to show that the ground state of NO
−
is triplet and that HNO in its singlet ground state has much lower acidity, pKa(
1
HNO/
3
NO
−
) ≈ 11.4, than previously believed. These conclusions are in accord with the observed large differences between
1
HNO and
3
NO
−
in their reactivities toward O
2
and NO. Laser flash photolysis was used to generate
1
HNO and
3
NO
−
by photochemical cleavage of trioxodinitrate (Angeli's anion). The spin-allowed addition of
3
O
2
to
3
NO
−
produced peroxynitrite with nearly diffusion-controlled rate (
k
= 2.7 × 10
9
M
−1
⋅s
−1
). In contrast, the spin-forbidden addition of
3
O
2
to
1
HNO was not detected (
k
≪ 3 × 10
5
M
−1
⋅s
−1
). Both
1
HNO and
3
NO
−
reacted sequentially with two NO to generate N
3
O

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as a long-lived intermediate; the rate laws of N
3
O

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formation were linear in concentrations of NO and
1
HNO (
k
= 5.8 × 10
6
M
−1
⋅s
−1
) or NO and
3
NO
−
(
k
= 2.3 × 10
9
M
−1
⋅s
−1
). Catalysis by the hydroxide ion was observed for the reactions of
1
HNO with both O
2
and NO. This effect is explicable by a spin-forbidden deprotonation by OH
−
(
k
= 4.9 × 10
4
M
−1
⋅s
−1
) of the relatively unreactive
1
HNO into the extremely reactive
3
NO
−
. Dimerization of
1
HNO to produce N
2
O occurred much more slowly (
k
= 8 × 10
6
M
−1
⋅s
−1
) than previously suggested. The implications of these results for evaluating the biological roles of nitroxyl are discussed.
Direct observation of extension and retraction of type IV pili
Authors: Skerker Jeffrey M. , Berg Howard C.
Published: July 2002

Type IV pili are thin filaments that extend from the poles of a
diverse group of bacteria, enabling them to move at speeds of a few
tenths of a micrometer per second. They are required for twitching
motility, e.g., in
Pseudomonas aeruginosa
and
Neisseria gonorrhoeae
, and for social gliding motility
in
Myxococcus xanthus
. Here we report direct observation
of extension and retraction of type IV pili in
P.
aeruginosa
. Cells without flagellar filaments were labeled with
an amino-specific Cy3 fluorescent dye and were visualized on a quartz
slide by total internal reflection microscopy. When pili were attached
to a cell and their distal ends were free, they extended or retracted
at rates of about 0.5 μm s
−1
(29°C). They also flexed
by Brownian motion, exhibiting a persistence length of about 5 μm.
Frequently, the distal tip of a filament adsorbed to the substratum and
the filament was pulled taut. From the absence of lateral deflections
of such filaments, we estimate tensions of at least 10 pN.
Occasionally, cell bodies came free and were pulled forward by pilus
retraction. Thus, type IV pili are linear actuators that extend, attach
at their distal tips, exert substantial force, and retract.
l
-Arginine-dependent suppression of apoptosis in
Trypanosoma cruzi
: Contribution of the nitric oxide and polyamine pathways
Authors: Piacenza Lucía , Peluffo Gonzalo , Radi Rafael
Published: July 2002

Until recently, a capacity for apoptosis and
synthesis of nitric oxide (
⋅
NO) were viewed as exclusive to
multicellular organisms. The existence of these processes in
unicellular parasites was recently described, with their biological
significance remaining to be elucidated. We have evaluated
l
-arginine metabolism in
Trypanosoma cruzi
in the context of human serum-induced apoptotic death.
Apoptosis was evidenced by the induction of DNA fragmentation
and the inhibition of [
3
H]thymidine incorporation, which
were inhibited by the caspase inhibitor Ac-Asp-Glu-Val-aspartic acid
aldehyde (DEVD-CHO). In
T. cruzi
exposed to death
stimuli, supplementation with
l
-arginine inhibited DNA
fragmentation, restored [
3
H]thymidine incorporation, and
augmented parasite
⋅
NO production. These effects were inhibited
by the
⋅
NO synthase inhibitor
N
ω
-nitroarginine methyl ester
(
l
-NAME). Exogenous
⋅
NO limited DNA fragmentation
but did not restore proliferation rates. Because
l
-arginine
is also a substrate for arginine decarboxylase (ADC), and its product
agmatine is a precursor for polyamine synthesis, we evaluated the
contribution of polyamines to limiting apoptosis. Addition of
agmatine, putrescine, and the polyamines spermine and spermidine to
T. cruzi
sustained parasite proliferation and inhibited
DNA fragmentation. Also, the ADC inhibitor difluoromethylarginine
inhibited
l
-arginine-dependent restoration of parasite
replication rates, while the protection from DNA fragmentation
persisted. In aggregate, these results indicate that
T.
cruzi
epimastigotes can undergo programmed cell death that can
be inhibited by
l
-arginine by means of (
i
) a
⋅
NO synthase-dependent
⋅
NO production that suppresses
apoptosis and (
ii
) an ADC-dependent production
of polyamines that support parasite proliferation.
Community structure in social and biological networks
Authors: Girvan M. , Newman M. E. J.
Published: July 2002

A number of recent studies have focused on the statistical properties of networked systems such as social networks and the Worldwide Web. Researchers have concentrated particularly on a few properties that seem to be common to many networks: the small-world property, power-law degree distributions, and network transitivity. In this article, we highlight another property that is found in many networks, the property of community structure, in which network nodes are joined together in tightly knit groups, between which there are only looser connections. We propose a method for detecting such communities, built around the idea of using centrality indices to find community boundaries. We test our method on computer-generated and real-world graphs whose community structure is already known and find that the method detects this known structure with high sensitivity and reliability. We also apply the method to two networks whose community structure is not well known—a collaboration network and a food web—and find that it detects significant and informative community divisions in both cases.
The transcriptional profile of early to middle sporulation in
Bacillus subtilis
Authors: Fawcett Paul , Eichenberger Patrick , Losick Richard , Youngman Philip
Published: July 2002

Spore formation by
Bacillus subtilis
is governed by global changes in gene transcription. We used nylon-substrate DNA arrays representing ≈96% of the predicted open reading frames in the
B. subtilis
chromosome to compare the pattern of transcripts from wild-type cells with the pattern from cells mutant for the sporulation transcription factors Spo0A or σ
F
. We found 520 genes whose transcript levels were at least 3-fold dependent on Spo0A but not on σ
F
, and an additional 66 genes whose transcript levels were dependent upon both regulatory proteins. Two strategies were used to help assign genes to the direct control of a particular developmental regulatory protein. In one approach, we analyzed the effects on global gene expression of artificially producing a constitutively active form of Spo0A during growth. In a second approach, Hidden Markov models were used to identify promoters likely to be activated by Spo0A, σ
F
, or a third sporulation transcription factor, σ
E
. In addition to detecting known sporulation genes, we identified many genes of unknown function whose patterns of expression and regulation suggest that they could be involved in sporulation. Disruption of two such newly identified genes,
yabP
and
yabQ
, blocked sporulation at a late stage.
The complete genome of the crenarchaeon
Sulfolobus solfataricus
P2
Authors: She Qunxin , Singh Rama K. , Confalonieri Fabrice , Zivanovic Yvan , Allard Ghislaine , Awayez Mariana J. , Chan-Weiher Christina C.-Y. , Clausen Ib Groth , Curtis Bruce A. , De Moors Anick , Erauso Gael , Fletcher Cynthia , Gordon Paul M. K. , Heikamp-de Jong Ineke , Jeffries Alex C. , Kozera Catherine J. , Medina Nadine , Peng Xu , Thi-Ngoc Hoa Phan , Redder Peter , Schenk Margaret E. , Theriault Cynthia , Tolstrup Niels , Charlebois Robert L. , Doolittle W. Ford , Duguet Michel , Gaasterland Terry , Garrett Roger A. , Ragan Mark A. , Sensen Christoph W. , Van der Oost John
Published: July 2002

The genome of the crenarchaeon
Sulfolobus solfataricus P2
contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable homologs in other sequenced genomes. Moreover, 40% appear to be archaeal-specific, and only 12% and 2.3% are shared exclusively with bacteria and eukarya, respectively. The genome shows a high level of plasticity with 200 diverse insertion sequence elements, many putative nonautonomous mobile elements, and evidence of integrase-mediated insertion events. There are also long clusters of regularly spaced tandem repeats. Different transfer systems are used for the uptake of inorganic and organic solutes, and a wealth of intracellular and extracellular proteases, sugar, and sulfur metabolizing enzymes are encoded, as well as enzymes of the central metabolic pathways and motility proteins. The major metabolic electron carrier is not NADH as in bacteria and eukarya but probably ferredoxin. The essential components required for DNA replication, DNA repair and recombination, the cell cycle, transcriptional initiation and translation, but not DNA folding, show a strong eukaryal character with many archaeal-specific features. The results illustrate major differences between crenarchaea and euryarchaea, especially for their DNA replication mechanism and cell cycle processes and their translational apparatus.
Artificial ecosystem selection
Authors: Swenson William , Wilson David Sloan , Elias Roberta
Published: July 2002

Artificial selection has been practiced for centuries to shape the properties of individual organisms, providing Darwin with a powerful argument for his theory of natural selection. We show that the properties of whole ecosystems can also be shaped by artificial selection procedures. Ecosystems initiated in the laboratory vary phenotypically and a proportion of the variation is heritable, despite the fact that the ecosystems initially are composed of thousands of species and millions of individuals. Artificial ecosystem selection can be used for practical purposes, illustrates an important role for complex interactions in evolution, and challenges a widespread belief that selection is most effective at lower levels of the biological hierarchy.
Carbohydrate self-recognition mediates marine sponge cellular adhesion
Authors: Haseley Simon R. , Vermeer Henricus J. , Kamerling Johannis P. , Vliegenthart Johannes F. G.
Published: July 2002

Sponges (Porifera), the simplest and earliest multicellular organisms, are thought to have evolved from their unicellular ancestors about 1 billion years ago by developing cell-recognition and adhesion mechanisms to discriminate against “non-self.” Consequently, they are used as models for investigating recognition phenomena. Cellular adhesion of marine sponges is an event involving adherence of extracellular proteoglycan-like molecules, otherwise known as aggregation factors (AFs). In a calcium-independent process the AFs adhere to the cell surface, and in a calcium-dependent process they exhibit AF self-association. A mechanism which has been implied but not definitely proven to play a role in the calcium-dependent event is self-recognition of defined carbohydrate epitopes. For the red beard sponge,
Microciona prolifera
, two carbohydrate epitopes, a sulfated disaccharide and a pyruvylated trisaccharide, have been implicated in cellular adhesion. To investigate this phenomenon a system has been designed, by using surface plasmon resonance detection, to mimic the role of carbohydrates in cellular adhesion of
M. prolifera
. The results show self-recognition of the sulfated disaccharide to be a major force behind the calcium-dependent event. The interaction is not simply based on electrostatic interactions, as other sulfated carbohydrates analyzed by using this procedure did not self-associate. Furthermore, the interaction is completely eradicated on substitution of Ca
2+
ions by either Mg
2+
or Mn
2+
ions. This physiologically relevant recognition mechanism confirms the existence of true carbohydrate self-recognition, and may have significant implications for the role of carbohydrates in cellular recognition of higher organisms.
Activation of NF-κB by nontypeable
Hemophilus influenzae
is mediated by toll-like receptor 2-TAK1-dependent NIK–IKKα/β–IκBα and MKK3/6–p38 MAP kinase signaling pathways in epithelial cells
Authors: Shuto Tsuyoshi , Xu Haidong , Wang Beinan , Han Jiahuai , Kai Hirofumi , Gu Xin-Xing , Murphy Timothy F. , Lim David J. , Li Jian-Dong
Published: July 2002

Nontypeable
Hemophilus influenzae
(NTHi) is an important human pathogen in both children and adults. In children, it causes otitis media, the most common childhood infection and the leading cause of conductive hearing loss in the United States. In adults, it causes lower respiratory tract infections in the setting of chronic obstructive pulmonary disease, the fourth leading cause of death in the United States. The molecular mechanisms underlying the pathogenesis of NTHi-induced infections remain undefined, but they may involve activation of NF-κB, a transcriptional activator of multiple host defense genes involved in immune and inflammatory responses. Here, we show that NTHi strongly activates NF-κB in human epithelial cells via two distinct signaling pathways, NF-κB translocation-dependent and -independent pathways. The NF-κB translocation-dependent pathway involves activation of NF-κB inducing kinase (NIK)–IKKα/β complex leading to IκBα phosphorylation and degradation, whereas the NF-κB translocation-independent pathway involves activation of MKK3/6–p38 mitogen-activated protein (MAP) kinase pathway. Bifurcation of NTHi-induced NIK–IKKα/β-IκBα and MKK3/6–p38 MAP kinase pathways may occur at transforming growth factor-β activated kinase 1 (TAK1). Furthermore, we show that toll-like receptor 2 (TLR2) is required for NTHi-induced NF-κB activation. In addition, several key inflammatory mediators including IL-1β, IL-8, and tumor necrosis factor-α are up-regulated by NTHi. Finally, P6, a 16-kDa lipoprotein highly conserved in the outer membrane of all NTHi and
H. influenzae
type b strains, appears to also activate NF-κB via similar signaling pathways. Taken together, our results demonstrate that NTHi activates NF-κB via TLR2–TAK1-dependent NIK–IKKα/β-IκBα and MKK3/6–p38 MAP kinase signaling pathways. These studies may bring new insights into molecular pathogenesis of NTHi-induced infections and open up new therapeutic targets for these diseases.
The sorbin homology domain: A motif for the targeting of proteins to lipid rafts
Authors: Kimura Akiko , Baumann Christian A. , Chiang Shian-Huey , Saltiel Alan R.
Published: July 2002

On phosphorylation of Cbl, the c-Cbl-associated protein (CAP)/Cbl complex dissociates from the insulin receptor and translocates to a lipid raft membrane fraction to form a ternary complex with flotillin. Deletion analyses of the CAP gene identified a 115-aa region responsible for flotillin binding. This region is homologous to the peptide sorbin and is referred to as the sorbin homology (SoHo) domain. This domain is present in two other proteins, vinexin and ArgBP2. Vinexin also interacted with flotillin, and deletion of its SoHo domain similarly blocked flotillin binding. The overexpression of a CAP mutant in which the SoHo domain had been deleted (CAPΔSoHo) prevented the translocation of Cbl to lipid rafts and subsequently blocked the recruitment of CrkII and C3G. Moreover, overexpression of CAPΔSoHo prevented the stimulation of glucose transport and GLUT4 translocation by insulin. These results suggest a mechanism for localization of signaling proteins to the lipid raft that mediates the compartmentalization of crucial signal transduction pathways.
The nonpsychoactive cannabis constituent cannabidiol is an oral anti-arthritic therapeutic in murine collagen-induced arthritis
Authors: Malfait A. M. , Gallily R. , Sumariwalla P. F. , Malik A. S. , Andreakos E. , Mechoulam R. , Feldmann M.
Published: July 2002

The therapeutic potential of cannabidiol (CBD), the major nonpsychoactive component of cannabis, was explored in murine collagen-induced arthritis (CIA). CIA was elicited by immunizing DBA/1 mice with type II collagen (CII) in complete Freund's adjuvant. The CII used was either bovine or murine, resulting in classical acute CIA or in chronic relapsing CIA, respectively. CBD was administered after onset of clinical symptoms, and in both models of arthritis the treatment effectively blocked progression of arthritis. CBD was equally effective when administered i.p. or orally. The dose dependency showed a bell-shaped curve, with an optimal effect at 5 mg/kg per day i.p. or 25 mg/kg per day orally. Clinical improvement was associated with protection of the joints against severe damage.Ex vivo,draining lymph node cells from CBD-treated mice showed a diminished CII-specific proliferation and IFN-γ production, as well as a decreased release of tumor necrosis factor by knee synovial cells.In vitroeffects of CBD included a dose-dependent suppression of lymphocyte proliferation, both mitogen-stimulated and antigen-specific, and the blockade of the Zymosan-triggered reactive oxygen burst by peritoneal granulocytes. It also was found that CBD administration was capable of blocking the lipopolysaccharide-induced rise in serum tumor necrosis factor in C57/BL mice. Taken together, these data show that CBD, through its combined immunosuppressive and anti-inflammatory actions, has a potent anti-arthritic effect in CIA.
Expression and parent-of-origin effects for
FIS2
,
MEA
, and
FIE
in the endosperm and embryo of developing
Arabidopsis
seeds
Authors: Luo Ming , Bilodeau Pierre , Dennis Elizabeth S. , Peacock W. James , Chaudhury Abed
Published: July 2002

The promoters of
MEA
(
FIS1
)
, FIS2,
and
FIE
(
FIS3
), genes that repress seed development in the absence of pollination, were fused to β-glucuronidase (
GUS
) to study their activity pattern. The
FIS2
∷
GUS
product is found in the embryo sac, in each of the polar cell nuclei, and in the central cell nucleus. After pollination, the maternally derived
FIS2
∷
GUS
protein occurs in the nuclei of the cenocytic endosperm. Before cellularization of the endosperm, activity is terminated in the micropylar and central nuclei of the endosperm and subsequently in the nuclei of the chalazal cyst.
MEA
∷
GUS
has a pattern of activity similar to that of
FIS2
∷
GUS
, but
FIE
∷
GUS
protein is found in many tissues, including the prepollination embryo sac, and in embryo and endosperm postpollination. The similarity in mutant phenotypes; the activity of
FIE
,
MEA,
and
FIS2
in the same cells in the embryo sac; and the fact that MEA and FIE proteins interact in a yeast two-hybrid system suggest that these proteins operate in the same system of control of seed development. Maternal and not paternal
FIS2
∷
GUS
,
MEA
∷
GUS,
and
FIE
∷
GUS
show activity in early endosperm, so these genes may be imprinted. When
fis2
,
mea,
and
fie
mutants are pollinated, seed development is arrested at the heart embryo stage. The seed arrest of
mea
and
fis2
is avoided when they are fertilized by a low methylation parent. The wild-type alleles of
MEA
or
FIS2
are not required. The parent-of-origin-determined differential activity of
MEA
,
FIS2
, and
FIE
is not dependent on DNA methylation, but methylation does control some gene(s) that have key roles in seed development.