bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of the λ integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation
Authors: Warren David , Sam My D. , Manley Kate , Sarkar Dibyendu , Lee Sang Yeol , Abbani Mohamad , Wojciak Jonathan M. , Clubb Robert T. , Landy Arthur
Published: July 2003

Lambda integrase (Int) is a heterobivalent DNA-binding protein that
together with the accessory DNA-bending proteins IHF, Fis, and Xis, forms the
higher-order protein–DNA complexes that execute integrative and excisive
recombination at specific loci on the chromosomes of phage λ and its
Escherichia coli
host. The large carboxyl-terminal domain of Int is
responsible for binding to core-type DNA sites and catalysis of DNA cleavage
and ligation reactions. The small amino-terminal domain (residues 1–70),
which specifies binding to arm-type DNA sites distant from the regions of
strand exchange, consists of a three-stranded β-sheet, proposed to
recognize the cognate DNA site, and an α-helix. We report here that a
site on this α-helix is critical for both homomeric interactions between
Int protomers and heteromeric interactions with Xis. The mutant E47A, which
was identified by alanine-scanning mutagenesis, abolishes interactions between
Int and Xis bound at adjacent binding sites and reduces interactions between
Int protomers bound at adjacent arm-type sites. Concomitantly, this residue is
essential for excisive recombination and contributes to the efficiency of the
integrative reaction. NMR titration data with a peptide corresponding to Xis
residues 57–69 strongly suggest that the carboxyl-terminal tail of Xis
and the α-helix of the aminoterminal domain of Int comprise the primary
interaction surface for these two proteins. The use of a common site on
λ Int for both homotypic and heterotypic interactions fits well with
the complex regulatory patterns associated with this site-specific
recombination reaction.
The F-box-containing protein UFO and AGAMOUS participate in antagonistic pathways governing early petal development in
Arabidopsis
Authors: Durfee Tim , Roe Judith L. , Sessions R. Allen , Inouye Carla , Serikawa Kyle , Feldmann Kenneth A. , Weigel Detlef , Zambryski Patricia C.
Published: July 2003

The
UNUSUAL FLORAL ORGANS
(
UFO
) gene is required for
multiple processes in the developing
Arabidopsis
flower, including
the proper patterning and identity of both petals and stamens. The gene
encodes an F-box-containing protein, UFO, which interacts physically and
genetically with the Skp1 homolog, ASK1. In this report, we describe four
ufo
alleles characterized by the absence of petals, which uncover
another role for UFO in promoting second whorl development. This UFO-dependent
pathway is required regardless of the second whorl organ to be formed, arguing
that it affects a basic process acting in parallel with those establishing
organ identity. However, the pathway is dispensable in the absence of
AGAMOUS
(
AG
), a known inhibitor of petal development.
In
situ
hybridization results argue that
AG
is not transcribed in
the petal region, suggesting that it acts non-cell-autonomously to inhibit
second whorl development in
ufo
mutants. These results are combined
into a genetic model explaining early second whorl initiation/proliferation,
in which UFO functions to inhibit an
AG
-dependent activity.
Inhibition of bacterial DNA replication by zinc mobilization during nitrosative stress
Authors: Schapiro Jeffrey M. , Libby Stephen J. , Fang Ferric C.
Published: July 2003

Phagocytic cells inhibit the growth of intracellular pathogens by producing
nitric oxide (NO). NO causes cell filamentation, induction of the SOS
response, and DNA replication arrest in the Gram-negative bacterium
Salmonella enterica
. NO also induces double-stranded chromosomal
breaks in replication-arrested
Salmonella
lacking a functional RecBCD
exonuclease. This DNA damage depends on actions of additional DNA repair
proteins, the RecG helicase, and RuvC endonuclease. Introduction of a
recG
mutation restores both resistance to NO and the ability of an
attenuated
recBC
mutant
Salmonella
strain to cause lethal
infection in mice, demonstrating that bacterial DNA replication is inhibited
during host–pathogen interactions. Inhibition of DNA replication during
nitrosative stress is invariably accompanied by zinc mobilization, implicating
DNA-binding zinc metalloproteins as critical targets of NO-related
antimicrobial activity.
Factors modulating conformational equilibria in large modular proteins: A case study with cobalamin-dependent methionine synthase
Authors: Bandarian Vahe , Ludwig Martha L. , Matthews Rowena G.
Published: July 2003

In the course of catalysis or signaling, large multimodular proteins often
undergo conformational changes that reposition the modules with respect to one
another. The mechanisms that direct the reorganization of modules in these
proteins are of considerable importance, but distinguishing alternate
conformations is a challenge. Cobalamin-dependent methionine synthase (MetH)
is a 136-kDa multimodular enzyme with a cobalamin chromophore; the color of
the cobalamin reflects the conformation of the protein. The enzyme contains
four modules and catalyzes three different methyl transfer reactions that
require different arrangements of these modules. Two of these methyl transfer
reactions occur during turnover, when homocysteine is converted to methionine
by using a methyl group derived from methyltetrahydrofolate. The third
reaction is occasionally required for reactivation of the enzyme and uses
S
-adenosyl-
l
-methionine as the methyl donor. The
absorbance properties of the cobalamin cofactor have been exploited to assign
conformations of the protein and to probe the effect of ligands and mutations
on the distribution of conformers. The results imply that the methylcobalamin
form of MetH exists as an ensemble of interconverting conformational states.
Differential binding of substrates or products alters the distribution of
conformers. Furthermore, steric conflicts disfavor conformers that juxtapose a
methyl group on substrate with one on methylcobalamin. These results suggest
that the methylation state of the cobalamin will influence the distribution of
conformers during turnover.
Long-term trends and a sustainability transition
Authors: Kates Robert W. , Parris Thomas M.
Published: July 2003

How do long-term global trends affect a transition to sustainability? We emphasize the “multitrend” nature of 10 classes of trends, which makes them complex, contradictory, and often poorly understood. Each class includes trends that make a sustainability transition more feasible as well as trends that make it more difficult. Taken in their entirety, they serve as a checklist for the consideration of global trends that impact place-based sustainability studies.
Knowledge systems for sustainable development
Authors: Cash David W. , Clark William C. , Alcock Frank , Dickson Nancy M. , Eckley Noelle , Guston David H. , Jäger Jill , Mitchell Ronald B.
Published: July 2003

The challenge of meeting human development needs while protecting the earth's life support systems confronts scientists, technologists, policy makers, and communities from local to global levels. Many believe that science and technology (S&T) must play a more central role in sustainable development, yet little systematic scholarship exists on how to create institutions that effectively harness S&T for sustainability. This study suggests that efforts to mobilize S&T for sustainability are more likely to be effective when they manage boundaries between knowledge and action in ways that simultaneously enhance the salience, credibility, and legitimacy of the information they produce. Effective systems apply a variety of institutional mechanisms that facilitate communication, translation and mediation across boundaries.
Illustrating the coupled human–environment system for vulnerability analysis: Three case studies
Authors: Turner B. L. , Matson Pamela A. , McCarthy James J. , Corell Robert W. , Christensen Lindsey , Eckley Noelle , Hovelsrud-Broda Grete K. , Kasperson Jeanne X. , Kasperson Roger E. , Luers Amy , Martello Marybeth L. , Mathiesen Svein , Naylor Rosamond , Polsky Colin , Pulsipher Alexander , Schiller Andrew , Selin Henrik , Tyler Nicholas
Published: July 2003

The vulnerability framework of the Research and Assessment Systems for Sustainability Program explicitly recognizes the coupled human–environment system and accounts for interactions in the coupling affecting the system's responses to hazards and its vulnerability. This paper illustrates the usefulness of the vulnerability framework through three case studies: the tropical southern Yucatán, the arid Yaqui Valley of northwest Mexico, and the pan-Arctic. Together, these examples illustrate the role of external forces in reshaping the systems in question and their vulnerability to environmental hazards, as well as the different capacities of stakeholders, based on their access to social and biophysical capital, to respond to the changes and hazards. The framework proves useful in directing attention to the interacting parts of the coupled system and helps identify gaps in information and understanding relevant to reducing vulnerability in the systems as a whole.
A framework for vulnerability analysis in sustainability science
Authors: Turner B. L. , Kasperson Roger E. , Matson Pamela A. , McCarthy James J. , Corell Robert W. , Christensen Lindsey , Eckley Noelle , Kasperson Jeanne X. , Luers Amy , Martello Marybeth L. , Polsky Colin , Pulsipher Alexander , Schiller Andrew
Published: July 2003

Global environmental change and sustainability science increasingly recognize the need to address the consequences of changes taking place in the structure and function of the biosphere. These changes raise questions such as: Who and what are vulnerable to the multiple environmental changes underway, and where? Research demonstrates that vulnerability is registered not by exposure to hazards (perturbations and stresses) alone but also resides in the sensitivity and resilience of the system experiencing such hazards. This recognition requires revisions and enlargements in the basic design of vulnerability assessments, including the capacity to treat coupled human–environment systems and those linkages within and without the systems that affect their vulnerability. A vulnerability framework for the assessment of coupled human–environment systems is presented.
Characterizing a sustainability transition: Goals, targets, trends, and driving forces
Authors: Parris Thomas M. , Kates Robert W.
Published: July 2003

Sustainable development exhibits broad political appeal but has proven difficult to define in precise terms. Recent scholarship has focused on the nature of a sustainability transition, described by the National Research Council as meeting the needs of a stabilizing future world population while reducing hunger and poverty and maintaining the planet's life-support systems. We identify a small set of goals, quantitative targets, and associated indicators that further characterize a sustainability transition by drawing on the consensus embodied in internationally negotiated agreements and plans of action. To illustrate opportunities for accelerating progress, we then examine current scholarship on the processes that influence attainment of four such goals: reducing hunger, promoting literacy, stabilizing greenhouse-gas concentrations, and maintaining fresh-water availability. We find that such analysis can often reveal “levers of change,” forces that both control the rate of positive change and are subject to policy intervention.
Single-nucleotide polymorphisms and genome diversity in
Plasmodium vivax
Authors: Feng Xiaorong , Carlton Jane M. , Joy Deirdre A. , Mu Jianbing , Furuya Tetsuya , Suh Bernard B. , Wang Yufeng , Barnwell John W. , Su Xin-Zhuan
Published: July 2003

The study of genetic variation in malaria parasites has practical
significance for developing strategies to control the disease. Vaccines based
on highly polymorphic antigens may be confounded by allelic restriction of the
host immune response. In response to drug pressure, a highly plastic genome
may generate resistant mutants more easily than a monomorphic one.
Additionally, the study of the distribution of genomic polymorphisms may
provide information leading to the identification of genes associated with
traits such as parasite development and drug resistance. Indeed, the age and
diversity of the human malaria parasite
Plasmodium falciparum
has
been the subject of recent debate, because an ancient parasite with a complex
genome is expected to present greater challenges for drug and vaccine
development. The genome diversity of the important human pathogen
Plasmodium vivax
, however, remains essentially unknown. Here we
analyze an ≈100-kb contiguous chromosome segment from five isolates,
revealing 191 single-nucleotide polymorphisms (SNPs) and 44 size
polymorphisms. The SNPs are not evenly distributed across the segment with
blocks of high and low diversity. Whereas the majority (≈63%) of the SNPs
are in intergenic regions, introns contain significantly less SNPs than
intergenic sequences. Polymorphic tandem repeats are abundant and are more
uniformly distributed at a frequency of about one polymorphic tandem repeat
per 3 kb. These data show that
P. vivax
has a highly diverse genome,
and provide useful information for further understanding the genome diversity
of the parasite.
Blockade of advanced glycation end-product formation restores ischemia-induced angiogenesis in diabetic mice
Authors: Tamarat Radia , Silvestre Jean-Sébastien , Huijberts Maya , Benessiano Joelle , Ebrahimian Teni G. , Duriez Micheline , Wautier Marie-Paule , Wautier Jean Luc , Lévy Bernard I.
Published: July 2003

We hypothesized that formation of advanced glycation end products (AGEs)
associated with diabetes reduces matrix degradation by metalloproteinases
(MMPs) and contributes to the impairment of ischemia-induced angiogenesis.
Mice were treated or not with streptozotocin (40 mg/kg) and streptozotocin
plus aminoguanidine (AGEs formation blocker, 50 mg/kg). After 8 weeks of
treatment, hindlimb ischemia was induced by right femoral artery ligature.
Plasma AGE levels were strongly elevated in diabetic mice when compared with
control mice (579 ± 21 versus 47 ± 4 pmol/ml, respectively;
P
< 0.01). Treatment with aminoguanidine reduced AGE plasma levels
when compared with untreated diabetic mice (
P
< 0.001). After 28
days of ischemia, ischemic/nonischemic leg angiographic score, capillary
density, and laser Doppler skin-perfusion ratios were 1.4-, 1.5-, and 1.4-fold
decreased in diabetic mice in reference to controls (
P
< 0.01).
Treatment with aminoguanidine completely normalized ischemia-induced
angiogenesis in diabetic mice. We next analyzed the role of proteolysis in AGE
formation-induced hampered neovascularization process. After 3 days of
ischemia, MMP-2 activity and MMP-3 and MMP-13 protein levels were increased in
untreated and aminoguanidine-treated diabetic mice when compared with controls
(
P
< 0.05). Despite this activation of the MMP pathway,
collagenolysis was decreased in untreated diabetic mice. Conversely, treatment
of diabetic mice with aminoguanidine restored collagenolysis toward levels
found in control mice. In conclusion, blockade of AGE formation by
aminoguanidine normalizes impaired ischemia-induced angiogenesis in diabetic
mice. This effect is probably mediated by restoration of matrix degradation
processes that are disturbed as a result of AGE accumulation.
Specific protein redirection as a transcriptional therapy approach for t(8;21) leukemia
Authors: Steffen Björn , Serve Hubert , Berdel Wolfgang E. , Agrawal Shuchi , Linggi Bryan , Büchner Thomas , Hiebert Scott W. , Müller-Tidow Carsten
Published: July 2003

Important progress has been achieved in the knowledge about the
pathogenesis of cancer. However, despite these advances, the therapeutic
strategies are still limited. Leukemias are often characterized by specific
balanced translocations, with the t(8;21) balanced translocation being the
most frequent chromosomal aberration in acute myeloid leukemia (AML). This
translocation produces the AML1-ETO fusion protein, which binds to AML1 target
promoter sequences. Transcriptional repression of AML1-dependent genes by
AML1-ETO and associated corepressors represents the pathogenetic mechanisms of
t(8;21). Here, we show that targeting of AML1-ETO to essential, MYB-dependent
gene promoters induces t(8;21)-restricted cell death. We constructed a
chimeric protein that contained the MYB DNA-binding domain and the
AML1-binding domain of myeloid Elf-1-like factor (MEF). This protein
associated with AML1-ETO and directed the complex to MYB-responsive promoters
in vitro
and
in vivo
. In the presence of AML1-ETO, the
chimeric protein repressed the activity of MYB-responsive promoters, rapidly
induced apoptosis, and specifically inhibited colony growth. All these effects
occurred only in AML1-ETO-positive cells, whereas no adverse effects were
observed in cells not expressing AML1-ETO. Taken together, this study
demonstrates that redirection of oncogenic proteins can be used as a strategy
to dramatically influence their cellular effects, with the ultimate goal to
design highly specific therapies for cancer.
Quantitative modeling of sensitivity in bacterial chemotaxis: The role of coupling among different chemoreceptor species
Authors: Mello Bernardo A. , Tu Yuhai
Published: July 2003

We propose a general theoretical framework for modeling receptor
sensitivity in bacterial chemotaxis, taking into account receptor
interactions, including those among different receptor species. We show that
our model can quantitatively explain the recent
in vivo
measurements
of receptor sensitivity at different ligand concentrations for both mutant and
wild-type strains. For mutant strains, our model can fit the experimental data
exactly. For the wild-type cell, our model is capable of achieving high gain
while having modest values of Hill coefficient for the response curves.
Furthermore, the high sensitivity of the wild-type cell in our model is
maintained for a wide range of ambient ligand concentrations, facilitated by
near-perfect adaptation and dependence of ligand binding on receptor activity.
Our study reveals the importance of coupling among different chemoreceptor
species, in particular strong interactions between the aspartate (Tar) and
serine (Tsr) receptors, which is crucial in explaining both the mutant and
wild-type data. Predictions for the sensitivity of other mutant strains and
possible improvements of our model for the wild-type cell are also
discussed.
Genomic transcriptional profiling of the developmental cycle of
Chlamydia trachomatis
Authors: Belland Robert J. , Zhong Guangming , Crane Deborah D. , Hogan Daniel , Sturdevant Daniel , Sharma Jyotika , Beatty Wandy L. , Caldwell Harlan D.
Published: July 2003

Chlamydia trachomatis
is one of the most common bacterial
pathogens and is the etiological agent of debilitating sexually transmitted
and ocular diseases in humans. The organism is an obligate intracellular
prokaryote characterized by a highly specialized biphasic developmental cycle.
We have performed genomic transcriptional analysis of the chlamydial
developmental cycle. This approach has led to the identification of a small
subset of genes that control the primary (immediate-early genes) and secondary
(late genes) differentiation stages of the cycle. Immediate-early gene
products initiate bacterial metabolism and potentially modify the bacterial
phagosome to escape fusion with lysosomes. One immediate early gene (CT147) is
a homolog of the human early endosomal antigen-1 that is localized to the
chlamydial phagosome; suggesting a functional role for CT147 in establishing
the parasitophorous vacuole in a nonfusogenic pathway. Late gene products
terminate bacterial cell division and constitute structural components and
remodeling activities involved in the formation of the highly disulfide
cross-linked outer-membrane complex that functions in attachment and invasion
of new host cells. Many of the genes expressed during the immediate-early and
late differentiation stages are
Chlamydia
-specific and have
evolutionary origins in eukaryotic lineages.
Asymmetric localization of flotillins/reggies in preassembled platforms confers inherent polarity to hematopoietic cells
Authors: Rajendran Lawrence , Masilamani Madhan , Solomon Samuel , Tikkanen Ritva , Stuermer Claudia A. O. , Plattner Helmut , Illges Harald
Published: July 2003

Hematopoietic cells have long been defined as round, nonpolar cells that show uniform distribution of cell surface-associated molecules. However, recent analyses of the immunological synapse and the importance of lipid microdomains in signaling have shed new light on the aspect of lymphocyte polarization during the activation processes, but none of the molecules implicated so far in either the activation process or the microdomain residency are known to have a preferential localization in nonactivated cells. Chemical crosslinking and fluorescence resonance energy transfer methods have allowed the visualization of certain glycosylphosphatidylinositol-anchored proteins in lipid rafts but so far no microdomain resident protein has been shown to exist as visible stable platforms in the membrane. We report here that two lipid microdomain resident proteins, flotillins/reggies, form preassembled platforms in hematopoietic cells. These platforms recruit signaling molecules upon activation through lipid rafts. The preassembled platforms significantly differ from the canonical cholesterol-dependent “lipid rafts,” as they are resistant to cholesterol-disrupting agents. Most evidence for the functional relevance of microdomains in living cells remains indirect. Using laser scanning confocal microscopy, we show that these proteins exist as stable, microscopically patent domains localizing asymmetrically to one pole of the cell. We present evidence that the asymmetric concentration of these microdomain resident proteins is built up during cytokinesis.
Differential effects of ethanol antagonism and neuroprotection in peptide fragment NAPVSIPQ prevention of ethanol-induced developmental toxicity
Authors: Wilkemeyer Michael F. , Chen Shao-yu , Menkari Carrie E. , Brenneman Douglas E. , Sulik Kathleen K. , Charness Michael E.
Published: July 2003

NAPVSIPQ (NAP), an active fragment of the glial-derived activity-dependent neuroprotective protein, is protective at femtomolar concentrations against a wide array of neural insults and prevents ethanol-induced fetal wastage and growth retardation in mice. NAP also antagonizes ethanol inhibition of L1-mediated cell adhesion (ethanol antagonism). We performed an Ala scanning substitution of NAP to determine the role of ethanol antagonism and neuroprotection in NAP prevention of ethanol embryotoxicity. The Ser-Ile-Pro region of NAP was crucial for both ethanol antagonism and protection of cortical neurons from tetrodotoxin toxicity (neuroprotection). Ala replacement of either Ser-5 or Pro-7 (P7A-NAP) abolished NAP neuroprotection but minimally changed the efficacy of NAP ethanol antagonism. In contrast, Ala replacement of Ile-6 (I6A-NAP) caused a decrease in potency (>2 logarithmic orders) with only a small reduction (<10%) in the efficacy of NAP neuroprotection but markedly reduced the efficacy (50%) and the potency (5 logarithmic orders) of NAP ethanol antagonism. Ethanol significantly reduced the number of paired somites in mouse whole-embryo culture; this effect was prevented significantly by 100 pM NAP or by 100 pM P7A-NAP, but not by 100 pM I6A-NAP. The structure–activity relation for NAP prevention of ethanol embryotoxicity was similar to that for NAP ethanol antagonism and different from that for NAP neuroprotection. These findings support the hypothesis that NAP antagonism of ethanol inhibition of L1 adhesion plays a central role in NAP prevention of ethanol embryotoxicity and highlight the potential importance of ethanol effects on L1 in the pathophysiology of fetal alcohol syndrome.
Evolutionary deterioration of the vomeronasal pheromone transduction pathway in catarrhine primates
Authors: Zhang Jianzhi , Webb David M.
Published: July 2003

Pheromones are water-soluble chemicals released and sensed by individuals of the same species to elicit social and reproductive behaviors or physiological changes; they are perceived primarily by the vomeronasal organ (VNO) in terrestrial vertebrates. Humans and some related primates possess only vestigial VNOs and have no or significantly reduced ability to detect pheromones, a phenomenon not well understood at the molecular level. Here we show that genes encoding the TRP2 ion channel and V1R pheromone receptors, two components of the vomeronasal pheromone signal transduction pathway, have been impaired and removed from functional constraints since shortly before the separation of hominoids and Old World monkeys ≈23 million years ago, and that the random inactivation of pheromone receptor genes is an ongoing process even in present-day humans. The phylogenetic distribution of vomeronasal pheromone insensitivity is concordant with those of conspicuous female sexual swelling and male trichromatic color vision, suggesting that a vision-based signaling-sensory mechanism may have in part replaced the VNO-mediated chemical-based system in the social/reproductive activities of hominoids and Old World monkeys (catarrhines).
Analysis of the distributed computing approach applied to the folding of a small β peptide
Authors: Paci Emanuele , Cavalli Andrea , Vendruscolo Michele , Caflisch Amedeo
Published: July 2003

In the recently proposed distributed computing approach to protein folding
a very large number of short independent simulations is performed. Using this
method, folding events on a time scale orders of magnitude shorter than the
experimental one have been reported. However, it has also been observed that
the folding process is not an elementary kinetic step and that the presence of
initial lag phases can bias short simulations toward atypical pathways. We
study here a 20-residue three-stranded antiparallel β-sheet peptide whose
equilibrium properties can be characterized by atomistic molecular dynamics
simulations. We found that the folding rate of this peptide is estimated
correctly by the distributed computing approach when trajectories
>≈1/100 of the equilibrium folding time are considered. We also found
that the fastest folding events occur through high-energy pathways, which are
unlikely under equilibrium conditions. These very fast folding pathways do not
relax within the equilibrium denatured state that is stabilized by the
transient presence of both native and nonnative interactions, and they are
characterized by the nearly simultaneous formation of the two β-hairpins
and a very small number of non-native contacts.
Dynamic, yet structured: The cell membrane three decades after the Singer–Nicolson model
Authors: Vereb G. , Szöllősi J. , Matkó J. , Nagy P. , Farkas T. , Vígh L. , Mátyus L. , Waldmann T. A. , Damjanovich S.
Published: July 2003

The fluid mosaic membrane model proved to be a very useful hypothesis in explaining many, but certainly not all, phenomena taking place in biological membranes. New experimental data show that the compartmentalization of membrane components can be as important for effective signal transduction as is the fluidity of the membrane. In this work, we pay tribute to the Singer–Nicolson model, which is near its 30th anniversary, honoring its basic features, “mosaicism” and “diffusion,” which predict the interspersion of proteins and lipids and their ability to undergo dynamic rearrangement via Brownian motion. At the same time, modifications based on quantitative data are proposed, highlighting the often genetically predestined, yet flexible, multilevel structure implementing a vast complexity of cellular functions. This new “dynamically structured mosaic model” bears the following characteristics: emphasis is shifted from fluidity to mosaicism, which, in our interpretation, means nonrandom codistribution patterns of specific kinds of membrane proteins forming small-scale clusters at the molecular level and large-scale clusters (groups of clusters, islands) at the submicrometer level. The cohesive forces, which maintain these assemblies as principal elements of the membranes, originate from within a microdomain structure, where lipid–lipid, protein–protein, and protein–lipid interactions, as well as sub- and supramembrane (cytoskeletal, extracellular matrix, other cell) effectors, many of them genetically predestined, play equally important roles. The concept of fluidity in the original model now is interpreted as permissiveness of the architecture to continuous, dynamic restructuring of the molecular- and higher-level clusters according to the needs of the cell and as evoked by the environment.
A neuronal network model linking subjective reports and objective physiological data during conscious perception
Authors: Dehaene Stanislas , Sergent Claire , Changeux Jean-Pierre
Published: July 2003

The subjective experience of perceiving visual stimuli is accompanied by objective neuronal activity patterns such as sustained activity in primary visual area (V1), amplification of perceptual processing, correlation across distant regions, joint parietal, frontal, and cingulate activation, γ-band oscillations, and P300 waveform. We describe a neuronal network model that aims at explaining how those physiological parameters may cohere with conscious reports. The model proposes that the step of conscious perception, referred to as access awareness, is related to the entry of processed visual stimuli into a global brain state that links distant areas including the prefrontal cortex through reciprocal connections, and thus makes perceptual information reportable by multiple means. We use the model to simulate a classical psychological paradigm: the attentional blink. In addition to reproducing the main objective and subjective features of this paradigm, the model predicts an unique property of nonlinear transition from nonconscious processing to subjective perception. This all-or-none dynamics of conscious perception was verified behaviorally in human subjects.
Inhibiting expression of specific genes in mammalian cells with 5′ end-mutated U1 small nuclear RNAs targeted to terminal exons of pre-mRNA
Authors: Fortes Puri , Cuevas Yolanda , Guan Fei , Liu Peng , Pentlicky Sara , Jung Stephen P. , Martínez-Chantar Maria L. , Prieto Jesús , Rowe David , Gunderson Samuel I.
Published: July 2003

Reducing or eliminating expression of a given gene is likely to require
multiple methods to ensure coverage of all of the genes in a given mammalian
cell. We and others [Furth, P. A., Choe, W. T., Rex, J. H., Byrne, J. C., and
Baker, C. C. (1994)
Mol. Cell. Biol.
14, 5278–5289] have
previously shown that U1 small nuclear (sn) RNA, both natural or with 5′
end mutations, can specifically inhibit reporter gene expression in mammalian
cells. This inhibition occurs when the U1 snRNA 5′ end base pairs near
the polyadenylation signal of the reporter gene's pre-mRNA. This base pairing
inhibits poly(A) tail addition, a key, nearly universal step in mRNA
biosynthesis, resulting in degradation of the mRNA. Here we demonstrate that
expression of endogenous mammalian genes can be efficiently inhibited by
transiently or stably expressed 5′ end-mutated U1 snRNA. Also, we
determine the inhibitory mechanism and establish a set of rules to use this
technique and to improve the efficiency of inhibition. Two U1 snRNAs base
paired to a single pre-mRNA act synergistically, resulting in up to 700-fold
inhibition of the expression of specific reporter genes and 25-fold inhibition
of endogenous genes. Surprisingly, distance from the U1 snRNA binding site to
the poly(A) signal is not critical for inhibition, instead the U1 snRNA must
be targeted to the terminal exon of the pre-mRNA. This could reflect a
disruption by the 5′ end-mutated U1 snRNA of the definition of the
terminal exon as described by the exon definition model.
Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units
Authors: Shi Jinxiu , Xi Huifeng , Wang Ying , Zhang Chenghui , Jiang Zhengwen , Zhang Kuixing , Shen Yayun , Jin Lin , Zhang Kaiyue , Yuan Wentao , Wang Ying , Lin Jie , Hua Qi , Wang Fengqing , Xu Shuhua , Ren Suangxi , Xu Shijie , Zhao Guoping , Chen Zhu , Jin Li , Huang Wei
Published: July 2003

The study of genomic divergence between humans and primates may provide
insight into the origins of human beings and the genetic basis of unique human
traits and diseases. Chromosome 21 is the smallest chromosome in the human
genome, and some of its regions have been implicated in mental retardation and
other diseases. In this study, we sequenced the coding and regulatory regions
of 127 known genes on human chromosome 21 in DNA samples from human and
chimpanzees and a part of the corresponding genes from orangutan, gorilla, and
macaque. Overall, 3,003 nucleotide differences between human and chimpanzee
were identified over ≈400 kb. The differences in coding, promoter, and
exon–intron junction regions were 0.51 ± 0.02%, 0.88 ±
0.03%, and 0.85 ± 0.02%, respectively, much lower than the previously
reported 1.23% in genomic regions, which suggests the presence of purifying
selection. Significant variation in substitution rate among genes was observed
by comparing the divergence between human and chimpanzee. Furthermore, by
implementing a bioinformatics-based approach, we showed that the
identification of genetic variants specific to the human lineage might lead to
an understanding of the mechanisms that are attributable to the phenotypes
that unique to humans, by changing the structure and/or dosage of the proteins
expressed. A phylogenetic analysis unambiguously confirms the conclusion that
chimpanzees were our closest relatives to the exclusion of other primates and
the relative divergence of the
Homo
–
Pan
and that of
(
Homo
–
Pan
)–
Gorilla
are 4.93 million
years and 7.26 million years, respectively.
Male-specific lethal complex of
Drosophila
targets activated regions of the X chromosome for chromatin remodeling
Authors: Sass Georgette L. , Pannuti Antonio , Lucchesi John C.
Published: July 2003

The male-specific lethal (MSL) complex of
Drosophila
is
responsible for the presence of a monoacetylated isoform of histone H4
(H4Ac16), found exclusively on the X chromosome of males. This particular
covalent modification of histone H4 is correlated with a 2-fold enhancement of
the transcription of most X-linked genes in
Drosophila
males, which
is the basis of dosage compensation in this organism. Although widespread
along the X chromosome, the MSL complex is not distributed uniformly, as can
be seen by the indirect cytoimmunofluorescence staining of larval
salivary-gland polytene chromosomes. This distribution pattern has been
interpreted as a reflection of the tissue-specific transcriptional activity of
the larval salivary gland and as an indication that the MSL complex associates
with active chromatin. We have tested this hypothesis by comparing the
chromosomal distribution of the complex in two different tissues. We performed
this comparison by following the pattern of association of the complex at a
specific site on salivary-gland chromosomes during larval development and
determining whether an ectopic promoter located in a complex-devoid region of
the X chromosome is able to attract the complex upon activation. Our results
indicate that, in contrast to other chromatin-remodeling complexes that
enhance transcription, the MSL complex targets active chromatin.
A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells
Authors: Li Zirong , Van Calcar Sara , Qu Chunxu , Cavenee Webster K. , Zhang Michael Q. , Ren Bing
Published: July 2003

Overexpression of c-Myc is one of the most common alterations in human
cancers, yet it is not clear how this transcription factor acts to promote
malignant transformation. To understand the molecular targets of c-Myc
function, we have used an unbiased genome-wide location-analysis approach to
examine the genomic binding sites of c-Myc in Burkitt's lymphoma cells. We
find that c-Myc together with its heterodimeric partner, Max, occupy >15%
of gene promoters tested in these cancer cells. The DNA binding of c-Myc and
Max correlates extensively with gene expression throughout the genome, a
hallmark attribute of general transcription factors. The c-Myc/Max heterodimer
complexes also colocalize with transcription factor IID in these cells,
further supporting a general role for overexpressed c-Myc in global gene
regulation. In addition, transcription of a majority of c-Myc target genes
exhibits changes correlated with levels of c-
myc
mRNA in a diverse
set of tissues and cell lines, supporting the conclusion that c-Myc regulates
them. Taken together, these results suggest a general role for overexpressed
c-Myc in global transcriptional regulation in some cancer cells and point
toward molecular mechanisms for c-Myc function in malignant
transformation.
ERK5 activation of MEF2-mediated gene expression plays a critical role in BDNF-promoted survival of developing but not mature cortical neurons
Authors: Liu Lidong , Cavanaugh Jane E. , Wang Yupeng , Sakagami Hiroyuki , Mao Zixu , Xia Zhengui
Published: July 2003

Extracellular signal-regulated kinase 5 (ERK5) is a member of the
mitogen-activated protein kinase family whose biological function in the CNS
has not been defined. In contrast to ERK1 and ERK2, which are activated by
neurotrophins (NTs), cAMP, and neuronal activity in cortical neurons, ERK5 is
activated only by NTs. Here, we report that ERK5 expression is high in the
brain during early embryonic development but declines as the brain matures to
almost undetectable levels by postnatal day (P) 49. Interestingly, expression
of a dominant-negative ERK5 blocked brain-derived neurotrophic factor
protection against trophic withdrawal in primary cortical neurons cultured
from embryonic day (E) 17 but not P0. Furthermore, expression of a
dominant-negative ERK5 induced apoptosis in E17 but not P0 cortical neurons
maintained in the presence of serum. We also present evidence that ERK5
protection of E17 cortical neurons may be mediated through myocyte enhancer
factor 2-induced gene expression. These data suggest that ERK5 activation of
myocyte enhancer factor 2-induced gene expression may play an important and
novel role in the development of the CNS by mediating NT-promoted survival of
embryonic neurons.
Mouse Vα14inatural killer T cells are resistant to cytokine polarizationin vivo
Authors: Matsuda Jennifer L. , Gapin Laurent , Baron Jody L. , Sidobre Stéphane , Stetson Daniel B. , Mohrs Markus , Locksley Richard M. , Kronenberg Mitchell
Published: July 2003

Under different circumstances, natural killer T (NKT) cells can cause a T helper (Th) 1 or a Th2 polarization of immune responses. We show here, however, that mouse NKT cells with an invariant Vα14 rearrangement (Vα14iNKT cells) rapidly produce both IL-4 and IFN-γ, and this pattern could not be altered by methods that polarize naive CD4+T cells. Surprisingly, although cytokine protein was detected only after activation, resting Vα14iNKT cells contained IL-4 and IFN-γ mRNAs. Despite this finding,in vivopriming of mice with the glycolipid antigen recognized by Vα14iNKT cells resulted in a more Th2-oriented response upon antigen re-exposure. The Vα14iNKT cells from primed mice retain the ability to produce IL-4 and IFN-γ, but they are less effective at activating NK cells to produce IFN-γ. Our data therefore indicate that Vα14iNKT cells have a relatively inflexible immediate cytokine response, but that changes in their ability to induce IFN-γ secretion by NK cells may determine the extent to which they promote Th1 responses.
Reversal of age-related learning deficits and brain oxidative stress in mice with superoxide dismutase/catalase mimetics
Authors: Liu Ruolan , Liu Ingrid Y. , Bi Xiaoning , Thompson Richard F. , Doctrow Susan R. , Malfroy Bernard , Baudry Michel
Published: July 2003

Oxidative stress has been implicated in cognitive impairment in both old
experimental animals and aged humans. This implication has led to the notion
that antioxidant defense mechanisms in the brain are not sufficient to prevent
age-related increase in oxidative damage and that dietary intake of a variety
of antioxidants might be beneficial for preserving brain function. Here we
report a dramatic loss of learning and memory function from 8 to 11 months of
age in mice, associated with marked increases in several markers of brain
oxidative stress. Chronic systemic administration of two synthetic catalytic
scavengers of reactive oxygen species, Eukarion experimental compounds EUK-189
and EUK-207, from 8 to 11 months almost completely reversed cognitive deficits
and increase in oxidative stress taking place during this time period in
brain. In particular, increase in protein oxidation was completely prevented,
whereas increase in lipid peroxidation was decreased by ≈50%. In addition,
we observed a significant negative correlation between contextual fear
learning and levels of protein oxidation in brain. These results further
support the role of reactive oxygen species in age-related learning impairment
and suggest potential clinical applications for synthetic catalytic scavengers
of reactive oxygen species.
Glycation of the amyloid β-protein by a nicotine metabolite: A fortuitous chemical dynamic between smoking and Alzheimer's disease
Authors: Dickerson Tobin J. , Janda Kim D.
Published: July 2003

The origin of Alzheimer's disease (AD) has been subjected to an intense
amount of examination; however, a clear conclusion as to the nature of this
crippling disease has yet to be identified. What is readily accepted is that a
definitive marker of this disease is the aggregation of the amyloid
β-peptide (Aβ) into neuritic plaques. The recent observation that
nicotine exposure leads to delayed onset of AD has stimulated a flurry of
research into the nature of this neuroprotective effect. This phenomenon has
been debated, but no consensus has been reached, and although these studies
have targeted nicotine, the primary alkaloid in tobacco, few studies have
considered the physiological role of nicotine metabolites in disease states.
Nornicotine is a major nicotine metabolite in the CNS and has been shown to
participate in the aberrant glycation of proteins
in vivo
in a
process termed nornicotine-based glycation. Herein is detailed a potentially
fortuitous role of nornicotine-based glycation in relation to the pathology of
AD. Specifically, nornicotine was found to covalently alter Aβ, leading
to reduced peptide aggregation. Potential consequences of this reaction
cascade include reduced plaque formation and/or altered clearance of the
peptide, as well as attenuated toxicity of soluble Aβ aggregates. The
findings described provide an alternative mechanism for nicotine
neuroprotection in AD and a means for the alteration of amyloid folding based
on a covalent chemical event.
phot1 and phot2 mediate blue light-induced transient increases in cytosolic Ca
2+
differently in
Arabidopsis
leaves
Authors: Harada Akiko , Sakai Tatsuya , Okada Kiyotaka
Published: July 2003

Phototropins (phot1 and phot2) are blue light (BL) receptors that mediate
phototropism, chloroplast movements, and stomatal opening in
Arabidopsis
thaliana
. Physiological studies have suggested that Ca
2+
in
the cytoplasm plays a pivotal role in these BL-induced responses. A
phot1-mediated increase in cytosolic Ca
2+
was reported in
deetiolated seedlings of
A. thaliana
; however, the contribution of
phot2 remains unknown. We examined a BL-induced transient increase in
cytosolic free Ca
2+
in leaves of transgenic
A. thaliana
of
WT plants,
phot1
and
phot2
mutants, and
phot1 phot2
double mutants expressing the Ca
2+
-sensitive luminescent protein
aequorin. phot1 and phot2 had different photosensitivities: phot1 increased
cytosolic Ca
2+
at lower fluence rates (0.1–50
μmol·m
-2
·s
-1
) and phot2 increased it at
higher fluence rates (1–250
μmol·m
-2
·s
-1
). By using Ca
2+
channel blockers, Ca
2+
chelating agents, and inhibitors of
phospholipase C, we further demonstrated that both phot1 and phot2 could
induce Ca
2+
influx from the apoplast through the Ca
2+
channel in the plasma membrane, whereas phot2 alone induced phospholipase
C-mediated phosphoinositide signaling, which might result in Ca
2+
release from internal Ca
2+
stores. These results suggest that phot1
and phot2 mediate the BL-induced increase in cytosolic free Ca
2+
differently.
The first half-century of nuclear transplantation
Authors: Gurdon J. B. , Byrne J. A.
Published: July 2003

Fifty years after Briggs and King first succeeded in obtaining normal tadpoles from transplanted embryo nuclei in vertebrates, two general principles have emerged from work in amphibia and mammals. One is the conservation of the genome during cell differentiation. A small percentage of adult or differentiated cells have totipotent nuclei, and a much higher percentage of cells committed to one pathway of cell differentiation have multipotent nuclei. The other is the remarkable reprogramming capacity of cell, and especially egg, cytoplasm. The eventual identification of reprogramming molecules and mechanisms could facilitate a route toward cell replacement therapy in humans.
The matrix-valued hypergeometric equation
Authors: Tirao Juan A.
Published: July 2003

The hypergeometric differential equation was found by Euler [Euler, L. (1769)Opera Omnia Ser. 1, 11–13] and was extensively studied by Gauss [Gauss, C. F. (1812)Comm. Soc. Reg. Sci. II3, 123–162], Kummer [Kummer, E. J. (1836)Riene Ang. Math.15, 39–83; Kummer, E. J. (1836)Riene Ang. Math.15, 127–172], and Riemann [Riemann, B. (1857)K. Gess. Wiss.7, 1–24]. The hypergeometric function known also as Gauss' function is the unique solution of the hypergeometric equation analytic atz= 0 and with value 1 atz= 0. This function, because of its remarkable properties, has been used for centuries in the whole subject of special functions. In this article we give a matrix-valued analog of the hypergeometric differential equation and of Gauss' function. One can only speculate that many of the connections that made Gauss' function a vital part of mathematics at the end of the 20th century will be shared by its matrix-valued version, discussed here.
Elucidation of the molecular logic by which misfolded α1-antitrypsin is preferentially selected for degradation
Authors: Wu Ying , Swulius Matthew T. , Moremen Kelley W. , Sifers Richard N.
Published: July 2003

The exocytic pathway provides a physical route through which newly
synthesized secretory and membrane proteins are deployed to the eukaryote cell
surface. For newly synthesized α1-antitrypsin (AAT), the modification of
its asparagine-linked oligosaccharides by a slow-acting mannosidase partitions
the misfolded monomer into the proteasomal degradation pathway. Herein, we
asked whether, and how, modification by endoplasmic reticulum mannosidase I
(ERManI) contributes to the preferential selection of the misfolded AAT
monomer for proteasomal degradation. Transiently expressed mutant and WT AAT
variants underwent rapid destabilization in response to an artificially
elevated ERManI concentration in the murine hepatoma cell line, Hepa1a. Based
on the mannosidase- and lactacystin-sensitive properties of intracellular
turnover, a stochastic model is proposed in which the delayed onset of the
glycan modification, relative to the duration of nonnative protein structure,
coordinates the preferential degradation of the misfolded monomer and spares
the native molecule from destruction. Newly synthesized endogenous transferrin
underwent degradation in response to an elevated concentration of ERManI,
whereas the nonglycosylated secretory glycoprotein albumin was not affected.
Taken together, these findings indicate that efficient conformational
maturation might function as the initial quality control standard for a broad
population of glycoproteins.