bluuebunny/crossref_metadata_2025 huggingface dataset:
Underground Globalization: Mapping the Space of Flows of the Internet Adult Industry
Authors: Zook Matthew A
Published: July 2003

This paper develops a case study of the Internet adult industry in order to study the ways in which electronic commerce interacts with geography. Digital products, low barriers to entry, cost differentials, and sensitivity to regulation have created a pervasive and complex geography of models, webmasters, and consumers around the globe. With a series of specially developed datasets on the location of content production, websites, and hosting it is shown that the online adult industry offers people and places outside major metropolitan areas opportunities to become active purveyors of this type of electronic commerce. The roles of these actors, however, are not simply determined by a spaceless logic of cyber-interaction but by histories and economies of the physical places they inhabit. In short, the ‘space of flows’ cannot be understood without reference to the ‘space of places’ to which it connects. This geography also provides a valuable counterpoint to mainstream electronic commerce and highlights the ability of socially marginal and underground interests to use the Internet to form and connect in global networks.
Chips, Bits, and the Law: An Economic Geography of Internet Gambling
Authors: Wilson Mark
Published: July 2003

Online gambling offers valuable insights into the relationship between real and virtual places. Gambling in most countries is highly regulated, with its geography reflecting the licensing of gambling to specific activities and locations. The ability to use the Internet challenges the legal foundation for gambling by offering access in an efficient and private way from distant locations. The heaviest concentration of gambling websites is found in North America and the Caribbean, with the leading locations for gambling-domain-name registrations being the United States, Canada, Antigua and Barbuda, Costa Rica, the United Kingdom, and St Kitts and Nevis. In this paper I explore the location and operation of Internet-gambling websites, with emphasis on the legal and economic geography of this activity.
Structural Change in a Local Urban Housing Market
Authors: Jones Colin , Leishman Chris , Watkins Craig
Published: July 2003

This paper addresses the structural change in a local urban housing market within a submarket framework. There is a voluminous literature examining the economic structure and operation of urban housing submarkets, with much of the associated empirical work based on static cross-sectional studies. Analysis of the temporal dynamics of local markets has tended to be perfunctory. As such, our understanding of structural change over time remains underdeveloped. In this paper we construct repeat-sale indices at the urban submarket level and deploy cointegration analysis to examine the stability of spatially defined housing submarkets within Glasgow between 1984 and 1997. Specifically, we consider whether price differences between submarkets have been eroded by a process of arbitrage operating through supply-side responses and/or migration flows. The empirical analysis shows that a stable system of housing submarkets persists throughout the study period.
The Geographies of Online Job Search: Preliminary Findings from Worcester, MA
Authors: Niles Sarah , Hanson Susan
Published: July 2003

For those who have online access, the Internet significantly reduces the cost and time of transferring information over distance. This paper explores the potential of the Internet to improve people's employment opportunities by increasing their access to job information beyond that provided via their grounded social networks. Information circulating through grounded social networks is biased socially and geographically toward the life experiences of network members. The tendency for those members to have similar life experiences dampens the variability in the information exchanged in such networks. What is the potential for the Internet to expand people's access to information about jobs and employers' information about workers? We report on a pilot study undertaken in Worcester, Massachusetts, that examined employers' use of Internet recruiting for employees. The results of this qualitative study indicate that these employers use the Internet strategically to enhance the volume of applications when the labor market is tight and to segment the applicant pool when the market loosens and the number of resumes is overwhelming. As a result, we conclude that many grounded social relations that have been integral to the hiring process are resilient to the Internet; pre-Internet geographies shape Internet geographies, and grounded social relations continue to define access to information about job opportunities even online.
Tethered Connectivity? The Spatial Distribution of Wireless Infrastructure
Authors: Gorman Sean P , McIntee Angela
Published: July 2003

At current growth rates, the number of wireless subscribers will surpass that of fixed telephones in the middle of the first decade of the 21st century. This fundamental shift in telecommunications has led many to believe that wireless technologies will break the ‘tyranny of geography’, help close the digital divide between core and periphery locations, and allow firms to be more footloose. This paper will examine the spatial distribution of wireless infrastructure in the United States to determine if the core–periphery relationship of cities is altered by wireless technologies. To do so the analysis will compare wireless infrastructure with Internet infrastructure and telephone switch infrastructure with a focus on data infrastructure in all three categories. The infrastructure datasets will be then compared with population distributions to determine their impacts on a spatial digital divide. The results of the study will provide a snapshot of the geography of wireless technologies, a comparison with other terrestrial communications, and insight into the policy of infrastructure delivery.
Gene expression of a gene family in maize based on noncollinear haplotypes
Authors: Song Rentao , Messing Joachim
Published: July 2003

Genomic regions of nearly every species diverged into different haplotypes,
mostly based on point mutations, small deletions, and insertions that do not
affect the collinearity of genes within a species. However, the same genomic
interval containing the
z1C
gene cluster of two inbred lines of
Zea mays
significantly lost their gene collinearity and also differed
in the regulation of each remaining gene set. Furthermore, when inbreds were
reciprocally crossed, hybrids exhibited an unexpected shift of expression
patterns so that “overdominance” instead of “dominance
complementation” of allelic and nonallelic gene expression occurred. The
same interval also differed in length (360 vs. 263 kb). Segmental
rearrangements led to sequence changes, which were further enhanced by the
insertion of different transposable elements. Changes in gene order affected
not only
z1C
genes but also three unrelated genes. However, the
orthologous interval between two subspecies of rice (not rice cultivars) was
conserved in length and gene order, whereas changes between two maize inbreds
were as drastic as changes between maize and sorghum. Given that chromosomes
could conceivably consist of intervals of haplotypes that are highly diverged,
one could envision endless breeding opportunities because of their linear
arrangement along a chromosome and their expression potential in hybrid
combinations (“binary” systems). The implication of such a
hypothesis for heterosis is discussed.
Identification of myotubularin as the lipid phosphatase catalytic subunit associated with the 3-phosphatase adapter protein, 3-PAP
Authors: Nandurkar Harshal H. , Layton Meredith , Laporte Jocelyn , Selan Carly , Corcoran Lisa , Caldwell Kevin K. , Mochizuki Yasuhiro , Majerus Philip W. , Mitchell Christina A.
Published: July 2003

Myotubularin is a dual-specific phosphatase that dephosphorylates
phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bisphosphate.
Mutations in myotubularin result in the human disease X-linked myotubular
myopathy, characterized by persistence of muscle fibers that retain an
immature phenotype. We have previously reported the identification of the
3-phosphatase adapter protein (3-PAP), a catalytically inactive member of the
myotubularin gene family, which coprecipitates lipid phosphatidylinositol
3-phosphate-3-phosphatase activity from lysates of human platelets. We have
now identified myotubularin as the catalytically active 3-phosphatase subunit
interacting with 3-PAP. A 65-kDa polypeptide, coprecipitating with endogenous
3-PAP, was purified from SDS/PAGE, subjected to trypsin digestion, and
analyzed by collision-induced dissociation tandem MS. Three peptides derived
from human myotubularin were identified. Association between 3-PAP and
myotubularin was confirmed by reciprocal coimmunoprecipitation of both
endogenous and recombinant proteins expressed in K562 cells. Recombinant
myotubularin localized to the plasma membrane, causing extensive filopodia
formation. However, coexpression of 3-PAP with myotubularin led to attenuation
of the plasma membrane phenotype, associated with myotubularin relocalization
to the cytosol. Collectively these studies indicate 3-PAP functions as an
“adapter” for myotubularin, regulating myotubularin intracellular
location and thereby altering the phenotype resulting from myotubularin
overexpression.
CD1d-restricted T cells regulate dendritic cell function and antitumor immunity in a granulocyte–macrophage colony-stimulating factor-dependent fashion
Authors: Gillessen Silke , Naumov Yuri N. , Nieuwenhuis Edward E. S. , Exley Mark A. , Lee Frederick S. , Mach Nicolas , Luster Andrew D. , Blumberg Richard S. , Taniguchi Masaru , Balk Steven P. , Strominger Jack L. , Dranoff Glenn , Wilson S. Brian
Published: July 2003

CD1d-restricted T cells contribute to tumor protection, but their precise roles remain unclear. Here we show that tumor cells engineered to secrete granulocyte–macrophage colony-stimulating factor induce the expansion of CD1d-restricted T cells through a mechanism that involves CD1d and macrophage inflammatory protein 2 expression by CD8α–, CD11c+dendritic cells (DCs). The antitumor immunity stimulated by vaccination with irradiated, granulocyte-macrophage colony-stimulating factor-secreting tumor cells was abrogated in CD1d- and Jα281-deficient mice, revealing a critical role for CD1d-restricted T cells in this response. The loss of antitumor immunity was associated with impaired tumorinduced T helper 2 cytokine production, although IFN-γ secretion and cytotoxicity were preserved. DCs from immunized CD1d-deficient mice showed compromised maturation and function. Together, these results delineate a role for CD1d-restricted T cell–DC cross talk in the shaping of antitumor immunity.
Community assembly and invasion: An experimental test of neutral versus niche processes
Authors: Fargione Joseph , Brown Cynthia S. , Tilman David
Published: July 2003

A species-addition experiment showed that prairie grasslands have a
structured, nonneutral assembly process in which resident species inhibit, via
resource consumption, the establishment and growth of species with similar
resource use patterns and in which the success of invaders decreases as
diversity increases. In our experiment, species in each of four functional
guilds were introduced, as seed, into 147 prairie–grassland plots that
previously had been established and maintained to have different compositions
and diversities. Established species most strongly inhibited introduced
species from their own functional guild. Introduced species attained lower
abundances when functionally similar species were abundant and when
established species left lower levels of resources unconsumed, which occurred
at lower species richness. Residents of the C4 grass functional guild, the
dominant guild in nearby native grasslands, reduced the major limiting
resource, soil nitrate, to the lowest levels in midsummer and exhibited the
greatest inhibitory effect on introduced species. This simple mechanism of
greater competitive inhibition of invaders that are similar to established
abundant species could, in theory, explain many of the patterns observed in
plant communities.
Chirality sensing by
Escherichia coli
topoisomerase IV and the mechanism of type II topoisomerases
Authors: Stone Michael D. , Bryant Zev , Crisona Nancy J. , Smith Steven B. , Vologodskii Alexander , Bustamante Carlos , Cozzarelli Nicholas R.
Published: July 2003

Escherichia coli
topoisomerase (Topo) IV is an essential type II
Topo that removes DNA entanglements created during DNA replication. Topo IV
relaxes (+) supercoils much faster than (–) supercoils, promoting
replication while sparing the essential (–) supercoils. Here, we
investigate the mechanism underlying this chiral preference. Using DNA binding
assays and a single-molecule DNA braiding system, we show that Topo IV
recognizes the chiral crossings imposed by the left-handed superhelix of a (+)
supercoiled DNA, rather than global topology, twist deformation, or local
writhe. Monte Carlo simulations of braid, supercoil, and catenane
configurations demonstrate how a preference for a single-crossing geometry
during strand passage can allow Topo IV to perform its physiological
functions. Single-enzyme braid relaxation experiments also provide a direct
measure of the processivity of the enzyme and offer insight into its
mechanochemical cycle.
Impaired degradation of inhibitory subunit of NF-κB (IκB) and β-catenin as a result of targeted disruption of the β-
TrCP1
gene
Authors: Nakayama Keiko , Hatakeyama Shigetsugu , Maruyama Shun-ichiro , Kikuchi Akira , Onoé Kazunori , Good Robert A. , Nakayama Keiichi I.
Published: July 2003

β-TrCP1 (also known as Fbw1a or FWD1) is the F-box protein component
of an Skp1/Cul1/F-box (SCF)-type ubiquitin ligase complex. Although
biochemical studies have suggested that β-TrCP1 targets inhibitory
subunit of NF-κB(IκB) proteins and β-catenin for
ubiquitylation, the physiological role of β-TrCP1 in mammals has remained
unclear. We have now generated mice deficient in β-TrCP1 and shown that
the degradation of IκBα and IκBβ is reproducibly, but
not completely, impaired in the cells of these animals. The nuclear
translocation and DNA-binding activity of NF-κB as well as the ability
of this transcription factor to activate a luciferase reporter gene were also
inhibited in β-TrCP1
–
/
–
cells compared with those apparent in wild-type cells. The subcellular
localization of β-catenin was altered markedly in
β-TrCP1
–
/
–
cells.
Furthermore, the rate of proliferation was reduced and both cell size and the
percentage of polyploid cells were increased in embryonic fibroblasts derived
from β-TrCP1
–
/
–
mice pared
with the corresponding wild-type cells. These results suggest that
β-TrCP1 contributes to, but is not absolutely required for, the
degradation of IκB and β-catenin and the consequent regulation of
the NF-κB and Wnt signaling pathways, respectively. In addition, they
implicate β-TrCP1 in the maintenance of ploidy during cell-cycle
progression.
Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations
Authors: Dressman Devin , Yan Hai , Traverso Giovanni , Kinzler Kenneth W. , Vogelstein Bert
Published: July 2003

Many areas of biomedical research depend on the analysis of uncommon
variations in individual genes or transcripts. Here we describe a method that
can quantify such variation at a scale and ease heretofore unattainable. Each
DNA molecule in a collection of such molecules is converted into a single
magnetic particle to which thousands of copies of DNA identical in sequence to
the original are bound. This population of beads then corresponds to a
one-to-one representation of the starting DNA molecules. Variation within the
original population of DNA molecules can then be simply assessed by counting
fluorescently labeled particles via flow cytometry. This approach is called
BEAMing on the basis of four of its principal components (beads, emulsion,
amplification, and magnetics). Millions of individual DNA molecules can be
assessed in this fashion with standard laboratory equipment. Moreover,
specific variants can be isolated by flow sorting and used for further
experimentation. BEAMing can be used for the identification and quantification
of rare mutations as well as to study variations in gene sequences or
transcripts in specific populations or tissues.
Anti-nerve growth factor Ab abrogates macrophage-mediated HIV-1 infection and depletion of CD4+T lymphocytes in hu-SCID mice
Authors: Garaci Enrico , Aquaro Stefano , Lapenta Caterina , Amendola Alessandra , Spada Massimo , Covaceuszach Sonia , Perno Carlo-Federico , Belardelli Filippo
Published: July 2003

Infection by HIV-1 causes persistent, long-term high virus production in macrophages. Major evidence, both in humans and in primate models, shows the crucial role of macrophages in sustaining virus production and in mediating a cytopathic effect on bystander CD4+T lymphocytes and neuronal cells. In the present study, we used severe combined immunodeficient (SCID) mice engrafted with human peripheral blood lymphocytes (hu-PBL-SCID mice) to investigate thein vivoeffect of HIV-1-infected macrophages on virus spread and CD4+T lymphocyte depletion, and the ability of a mAb against nerve growth factor (NGF, a neurokine essential for the survival of HIV-1-infected macrophages) to suppress the pathogenetic events mediated by infected macrophages. Injection of mice with as few as 500 HIV-exposed macrophages causes (i) complete depletion of several millions of autologous CD4+T lymphocytes, (ii) sustained HIV viremia, and (iii) spreading of HIV-1 DNA in mouse lymphoid organs. In contrast,in vivotreatment with an anti-NGF Ab completely abrogates all effects mediated by HIV-infected macrophages. Taken together, the results demonstrate the remarkable power of macrophages in sustainingin vivoHIV-1 infection, and that such a phenomenon can be specifically abrogated by an anti-NGF Ab. This may open new perspectives of experimental approaches aimed at selectively eliminating persistently infected macrophages from the bodies of HIV-infected patients.
A microscopic view of ion conduction through the K+ channel
Authors: Bernèche Simon , Roux Benoît
Published: July 2003

Recent results from x-ray crystallography and molecular dynamics free-energy simulations have revealed the existence of a number of specific cation-binding sites disposed along the narrow pore of the K+channel fromStreptomyces lividans(KcsA), suggesting that K+ions might literally “hop” in single file from one binding site to the next as permeation proceeds. In support of this view, it was found that the ion configurations correspond to energy wells of similar depth and that ion translocation is opposed only by small energy barriers. Although such features of the multiion potential energy surface are certainly essential for achieving a high throughput rate, diffusional and dissipative dynamical factors must also be taken into consideration to understand how rapid conduction of K+is possible. To elucidate the mechanism of ion conduction, we established a framework theory enabling the direct simulation of nonequilibrium fluxes by extending the results of molecular dynamics over macroscopically long times. In good accord with experimental measurements, the simulated maximum conductance of the channel at saturating concentration is on the order of 550 and 360 pS for outward and inward ions flux, respectively, with a unidirectional flux-ratio exponent of 3. Analysis of the ion-conduction process reveals a lack of equivalence between the cation-binding sites in the selectivity filter.
Host-derived sialic acid is incorporated into
Haemophilus influenzae
lipopolysaccharide and is a major virulence factor in experimental otitis media
Authors: Bouchet Valérie , Hood Derek W. , Li Jianjun , Brisson Jean-Robert , Randle Gaynor A. , Martin Adèle , Li Zhong , Goldstein Richard , Schweda Elke K. H. , Pelton Stephen I. , Richards James C. , Moxon E. Richard
Published: July 2003

Otitis media, a common and often recurrent bacterial infection of
childhood, is a major reason for physician visits and the prescription of
antimicrobials.
Haemophilus influenzae
is the cause of ≈20% of
episodes of bacterial otitis media, but most strains lack the capsule, a
factor known to play a critical role in the virulence of strains causing
invasive
H. influenzae
disease. Here we show that in
capsule-deficient (nontypeable) strains, sialic acid, a terminal residue of
the core sugars of
H. influenzae
lipopolysaccharide (LPS), is a
critical virulence factor in the pathogenesis of experimental otitis media in
chinchillas. We used five epidemiologically distinct
H. influenzae
isolates, representative of the genetic diversity of strains causing otitis
media, to inoculate the middle ear of chinchillas. All animals developed acute
bacterial otitis media that persisted for up to 3 wk, whereas isogenic sialic
acid-deficient mutants (disrupted sialyltransferase or CMP-acetylneuraminic
acid synthetase genes) were profoundly attenuated. MS analysis indicated that
WT bacteria used to inoculate animals lacked any sialylated LPS glycoforms. In
contrast, LPS of
ex vivo
organisms recovered from chinchilla middle
ear exudates was sialylated. We conclude that sialylated LPS glycoforms play a
key role in pathogenicity of nontypeable
H. influenzae
and depend on
scavenging the essential precursors from the host during the infection.
Determining the basis of channel-tetramerization specificity by x-ray crystallography and a sequence-comparison algorithm: Family values (FamVal)
Authors: Nanao Max H. , Zhou Wei , Pfaffinger Paul J. , Choe Senyon
Published: July 2003

We have developed a semiempirical algorithm called Family Values (FamVal),
which identifies residues that encode functional specificity in a protein
sequence. Given a multiple sequence alignment (MSA) grouped into functionally
distinct subfamilies, FamVal calculates a specificity score for each subfamily
at every amino acid position of an MSA. This algorithm was used to predict
specificity-encoding positions within the tetramerization assembly (T1) domain
of voltage-gated potassium (Kv) channel subfamilies Kv3 and Kv4. The
importance of one such position (Arg to Ala at MSA position 93) was confirmed
by
in vitro
pull-down assays. The structural basis of this assembly
discrimination was elucidated by determining the crystal structure of the Kv4
T1 domain and comparing it to the Kv3 T1 domain.
The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis
Authors: Dey Anup , Chitsaz Farideh , Abbasi Asim , Misteli Tom , Ozato Keiko
Published: July 2003

Previous
in vitro
studies showed that the bromodomain binds to
acetyllysines on histone tails, leading to the proposal that the domain is
involved in deciphering the histone code. However, there is little
in
vivo
evidence supporting the binding of bromodomains to acetylated
chromatin in the native environment. Brd4 is a member of the BET family that
carries two bromodomains. It associates with mitotic chromosomes, a feature
characteristic of the family. Here, we studied the interaction of Brd4 with
chromatin in living cells by photobleaching. Brd4 was mobile and interacted
with chromatin with a rapid “on and off” mode of binding. This
interaction required both bromodomains. Indicating a preferential interaction
with acetylated chromatin, Brd4 became less mobile upon increased chromatin
acetylation caused by a histone deacetylase inhibitor. Providing biochemical
support, salt solubility of Brd4 was markedly reduced upon increased histone
acetylation. This change also required both bromodomains. In peptide binding
assays, Brd4 avidly bound to di- and tetraacetylated histone H4 and
diacetylated H3, but weakly or not at all to mono- and unacetylated H3 and H4.
By contrast, it did not bind to unacetylated H4 or H3. Further, Brd4
colocalized with acetylated H4 and H3 in noncentromeric regions of mitotic
chromosomes. This colocalization also required both bromodomains. These
observations indicate that Brd4 specifically recognizes acetylated histone
codes, and this recognition is passed onto the chromatin of newly divided
cells.
Response of a deterministic epidemiological system to a stochastically varying environment
Authors: Truscott J. E. , Gilligan C. A.
Published: July 2003

Fluctuations in the natural environment introduce variability into the biological systems that exist within them. In this paper, we develop a model for the influence of random fluctuations in the environment on a simple epidemiological system. The model describes the infection of a dynamic host population by an environmentally sensitive pathogen and is based on the infection of sugar beet plants by the endoparasitic slime-mold vector
Polymyxa betae
. The infection process is switched on only when the temperature is above a critical value. We discuss some of the problems inherent in modeling such a system and analyze the resulting model by using asymptotic techniques to generate closed-form solutions for the mean and variance of the net amount of new inoculum produced within a season. In this way, the variance of temperature profile can be linked with that of the inoculum produced in a season and hence the risk of disease. We also examine the connection between the model developed in this paper and discrete Markov-chain models for weather.
Printing chemical libraries on microarrays for fluid phase nanoliter reactions
Authors: Gosalia Dhaval N. , Diamond Scott L.
Published: July 2003

Chemical compounds within individual nanoliter droplets of glycerol were
microarrayed onto glass slides at 400 spots/cm
2
. Using aerosol
deposition, subsequent reagents and water were metered into each reaction
center to rapidly assemble diverse multicomponent reactions without
crosscontamination or the need for surface linkage. This proteomics technique
allowed the kinetic profiling of protease mixtures, protease–substrate
interactions, and high-throughput screening reactions. An inhibitor of
caspases 2, 4, and 6 was identified by using a 352-compound combinatorial
library microarrayed in quadruplicates on 100 slides and screened against
caspases 2, 4, and 6, as well as thrombin and chymotrypsin. From one printing
run that consumes <1 nanomole of each compound, large combinatorial
libraries can be subjected to numerous separation-free homogeneous assays at
volumes 10
3
–10
4
smaller than current
high-throughput methods.
Direct observation of protonation reactions during the catalytic cycle of cytochrome
c
oxidase
Authors: Nyquist Rebecca M. , Heitbrink Dirk , Bolwien Carsten , Gennis Robert B. , Heberle Joachim
Published: July 2003

Cytochrome
c
oxidase, the terminal protein in the respiratory
chain, converts oxygen into water and helps generate the electrochemical
gradient used in the synthesis of ATP. The catalytic action of cytochrome
c
oxidase involves electron transfer, proton transfer, and
O
2
reduction. These events trigger specific molecular changes at
the active site, which, in turn, influence changes throughout the protein,
including alterations of amino acid side chain orientations, hydrogen bond
patterns, and protonation states. We have used IR difference spectroscopy to
investigate such modulations for the functional intermediate states E,
R
2
,P
m
, and F. These spectra reveal deprotonation of its
key glutamic acid E286 in the E and in the P
m
states. The
consecutive deprotonation and reprotonation of E286 twice within one catalytic
turnover illustrates the role of this residue as a proton shuttle. In
addition, the spectra point toward deprotonation of a redox-active tyrosine,
plausibly Y288, in the F intermediate. Structural insights into the molecular
mechanism of catalysis based on the subtle molecular changes observed with IR
difference spectroscopy are discussed.
Voxel-based analysis of MRI reveals anterior cingulate gray-matter volume reduction in posttraumatic stress disorder due to terrorism
Authors: Yamasue H. , Kasai K. , Iwanami A. , Ohtani T. , Yamada H. , Abe O. , Kuroki N. , Fukuda R. , Tochigi M. , Furukawa S. , Sadamatsu M. , Sasaki T. , Aoki S. , Ohtomo K. , Asukai N. , Kato N.
Published: July 2003

MRI studies using the manual tracing method have shown a smaller-than-normal hippocampal volume in patients with posttraumatic stress disorder (PTSD). However, these studies have yielded inconsistent results, and brain structures other than the hippocampus have not been well investigated. A recently developed, fully automated method called voxel-based morphometry enables an exploration of structural changes throughout the brain by applying statistical parametric mapping to high-resolution MRI. Here we first used this technology in patients with PTSD. Participants were 9 victims of the Tokyo subway sarin attack with PTSD and 16 matched victims of the same traumatic event without PTSD. The voxel-based morphometry showed a significant gray-matter volume reduction in the left anterior cingulate cortex (ACC) in trauma survivors with PTSD compared with those without PTSD. The severity of the disorder was negatively correlated with the gray-matter volume of the left ACC in PTSD subjects. There were no significant differences in other gray-matter regions or any of the white-matter regions between two groups. The present study demonstrates evidence for structural abnormalities of ACC in patients with PTSD. Together with previous functional neuroimaging studies showing a dysfunction of this region, the present findings provide further support for the important role of ACC, which is pivotally involved in attention, emotional regulation, and conditioned fear, in the pathology of PTSD.
Natural selection of more designable folds: A mechanism for thermophilic adaptation
Authors: England Jeremy L. , Shakhnovich Boris E. , Shakhnovich Eugene I.
Published: July 2003

An open question of great interest in biophysics is whether variations in
structure cause protein folds to differ in the number of amino acid sequences
that can fold to them stably, i.e., in their designability. Recently, we have
shown that a novel quantitative measure of a fold's tertiary topology, called
its contact trace, strongly correlates with the fold's designability. Here, we
investigate the relationship between a fold's contact trace and its relative
frequency of usage in mesophilic vs. thermophilic eubacteria. We observe that
thermophilic organisms exhibit a bias toward using folds of higher contact
trace when compared with mesophiles. We establish this difference both for the
distributions of folds at the whole-proteome level and also through more
focused structural comparisons of orthologous proteins. Our findings suggest
that thermophilic adaptation in bacterial genomes occurs in part through
natural selection of more designable folds, pointing to designability as a key
component of protein fitness.
Resolving intermediates in biological proton-coupled electron transfer: A tyrosyl radical prior to proton movement
Authors: Faller Peter , Goussias Charilaos , Rutherford A. William , Un Sun
Published: July 2003

The coupling of proton chemistry with redox reactions is important in many
enzymes and is central to energy transduction in biology. However, the
mechanistic details are poorly understood. Here, we have studied tyrosine
oxidation, a reaction in which the removal of one electron from the amino acid
is linked to the release of its phenolic proton. Using the unique
photochemical properties of photosystem II, it was possible to oxidize the
tyrosine at 1.8 K, a temperature at which proton and protein motions are
limited. The state formed was detected by high magnetic field EPR as a
high-energy radical intermediate trapped in an unprecedentedly electropositive
environment. Warming of the protein allows this state to convert to a relaxed,
stable form of the radical. The relaxation event occurs at 77 K and seems to
involve proton migration and only a very limited movement of the protein.
These reactions represent a stabilization process that prevents the
back-reaction and determines the reactivity of the radical.
Solitary chemoreceptor cells in the nasal cavity serve as sentinels of respiration
Authors: Finger Thomas E. , Böttger Bärbel , Hansen Anne , Anderson Karl T. , Alimohammadi Hessamedin , Silver Wayne L.
Published: July 2003

Inhalation of irritating substances leads to activation of the trigeminal
nerve, triggering protective reflexes that include apnea or sneezing.
Receptors for trigeminal irritants are generally assumed to be located
exclusively on free nerve endings within the nasal epithelium, requiring that
trigeminal irritants diffuse through the junctional barrier at the epithelial
surface to activate receptors. We find, in both rats and mice, an extensive
population of chemosensory cells that reach the surface of the nasal
epithelium and form synaptic contacts with trigeminal afferent nerve fibers.
These chemosensory cells express T2R “bitter-taste” receptors and
α-gustducin, a G protein involved in chemosensory transduction.
Functional studies indicate that bitter substances applied to the nasal
epithelium activate the trigeminal nerve and evoke changes in respiratory
rate. By extending to the surface of the nasal epithelium, these chemosensory
cells serve to expand the repertoire of compounds that can activate trigeminal
protective reflexes. The trigeminal chemoreceptor cells are likely to be
remnants of the phylogenetically ancient population of solitary chemoreceptor
cells found in the epithelium of all anamniote aquatic vertebrates.
Feynman diagrams and Wick products associated withq-Fock space
Authors: Effros Edward G. , Popa Mihai
Published: July 2003

It is shown that if one keeps track of crossings, Feynman diagrams can be used to compute theq-Wick products and usual operator products in terms of each other.
Dissection of the triple tryptophan electron transfer chain in
Escherichia coli
DNA photolyase: Trp382 is the primary donor in photoactivation
Authors: Byrdin Martin , Eker André P. M. , Vos Marten H. , Brettel Klaus
Published: July 2003

In
Escherichia coli
photolyase, excitation of the FAD cofactor in
its semireduced radical state (FADH
•
) induces an electron
transfer over ≈15 Å from tryptophan W306 to the flavin. It has been
suggested that two additional tryptophans are involved in an electron transfer
chain FADH
•
← W382 ← W359 ← W306. To test this
hypothesis, we have mutated W382 into redox inert phenylalanine. Ultrafast
transient absorption studies showed that, in WT photolyase, excited
FADH
•
decayed with a time constant τ ≈ 26 ps to fully
reduced flavin and a tryptophan cation radical. In W382F mutant photolyase,
the excited flavin was much longer lived (τ ≈ 80 ps), and no
significant amount of product was detected. We conclude that, in WT
photolyase, excited FADH
•
is quenched by electron transfer
from W382. On a millisecond scale, a product state with extremely low yield
(≈0.5% of WT) was detected in W382F mutant photolyase. Its spectral and
kinetic features were similar to the fully reduced flavin/neutral tryptophan
radical state in WT photolyase. We suggest that, in W382F mutant photolyase,
excited FADH
•
is reduced by W359 at a rate that competes only
poorly with the intrinsic decay of excited FADH
•
(τ ≈
80 ps), explaining the low product yield. Subsequently, the W359 cation
radical is reduced by W306. The rate constants of electron transfer from W382
to excited FADH
•
in WT and from W359 to excited
FADH
•
in W382F mutant photolyase were estimated and related to
the donor–acceptor distances.
Biogenesis of lysosome-related organelles complex 3 (BLOC-3): A complex containing the Hermansky–Pudlak syndrome (HPS) proteins HPS1 and HPS4
Authors: Nazarian Ramin , Falcón-Pérez Juan M. , Dell'Angelica Esteban C.
Published: July 2003

Hermansky–Pudlak syndrome (HPS) defines a group of autosomal
recessive disorders characterized by deficiencies in lysosome-related
organelles such as melanosomes and platelet-dense granules. Several
HPS
genes encode proteins of unknown function including HPS1, HPS3,
and HPS4. Here we have identified and characterized endogenous HPS3 and HPS4
proteins from HeLa cells. Both proteins were found in soluble and
membrane-associated forms. Sedimentation-velocity and coimmunoprecipitation
experiments revealed that HPS4 but not HPS3 associates with HPS1 in a complex,
which we term biogenesis of lysosome-related organelles complex 3 (BLOC-3).
Mutant fibroblasts deficient in either HPS1 or HPS4 displayed abnormal
localization of lysosomes and late endosomes, which were less concentrated at
the juxtanuclear region in mutant cells than in control fibroblasts. The
coat-color phenotype of young homozygous double-mutant mice deficient in
subunits of BLOC-3 (HPS1) and BLOC-1 (pallidin) was indistinguishable from
that of BLOC-1 single mutants. Taken together, these observations suggest that
HPS1 and HPS4 are components of a protein complex that regulates the
intracellular localization of lysosomes and late endosomes and may function in
a BLOC-1-dependent pathway for melanosome biogenesis.
Increased cell proliferation and neurogenesis in the adult human Huntington's disease brain
Authors: Curtis Maurice A. , Penney Ellen B. , Pearson Andree G. , van Roon-Mom Willeke M. C. , Butterworth Niqi J. , Dragunow Michael , Connor Bronwen , Faull Richard L. M.
Published: July 2003

Neurogenesis has recently been observed in the adult human brain,
suggesting the possibility of endogenous neural repair. However, the
augmentation of neurogenesis in the adult human brain in response to neuronal
cell loss has not been demonstrated. This study was undertaken to investigate
whether neurogenesis occurs in the subependymal layer (SEL) adjacent to the
caudate nucleus in the human brain in response to neurodegeneration of the
caudate nucleus in Huntington's disease (HD). Postmortem control and HD human
brain tissue were examined by using the cell cycle marker proliferating cell
nuclear antigen (PCNA), the neuronal marker βIII-tubulin, and the glial
cell marker glial fibrillary acidic protein (GFAP). We observed a significant
increase in cell proliferation in the SEL in HD compared with control brains.
Within the HD group, the degree of cell proliferation increased with
pathological severity and increasing CAG repeats in the HD gene. Most
importantly, PCNA
+
cells were shown to coexpress βIII-tubulin
or GFAP, demonstrating the generation of neurons and glial cells in the SEL of
the diseased human brain. Our results provide evidence of increased progenitor
cell proliferation and neurogenesis in the diseased adult human brain and
further indicate the regenerative potential of the human brain.
A ring of eight conserved negatively charged amino acids doubles the conductance of BK channels and prevents inward rectification
Authors: Brelidze Tinatin I. , Niu Xiaowei , Magleby Karl L.
Published: July 2003

Large-conductance Ca
2+
–voltage-activated K
+
channels (BK channels) control many key physiological processes, such as
neurotransmitter release and muscle contraction. A signature feature of BK
channels is that they have the largest single channel conductance of all
K
+
channels. Here we examine the mechanism of this large
conductance. Comparison of the sequence of BK channels to lower-conductance
K
+
channels and to a crystallized bacterial K
+
channel
(MthK) revealed that BK channels have a ring of eight negatively charged
glutamate residues at the entrance to the intracellular vestibule. This ring
of charge, which is absent in lower-conductance K
+
channels, is
shown to double the conductance of BK channels for outward currents by
increasing the concentration of K
+
in the vestibule through an
electrostatic mechanism. Removing the ring of charge converts BK channels to
inwardly rectifying channels. Thus, a simple electrostatic mechanism
contributes to the large conductance of BK channels.
Structure of a photosystem II supercomplex isolated from
Prochloron didemni
retaining its chlorophyll
a/b
light-harvesting system
Authors: Bibby Thomas S. , Nield Jon , Chen Min , Larkum Anthony W. D. , Barber James
Published: July 2003

Prochlorophytes are a class of cyanobacteria that do not use
phycobiliproteins as light-harvesting systems, but contain chlorophyll (Chl)
a
/
b
-binding Pcb proteins. Recently it was shown that Pcb
proteins form an 18-subunit light-harvesting antenna ring around the
photosystem I (PSI) trimeric reaction center complex of the prochlorophyte
Prochlorococcus marinus
SS120. Here we have investigated whether the
symbiotic prochlorophyte
Prochloron didemni
also contains the same
supermolecular complex. Using cells isolated directly from its ascidian host,
we found no evidence for the presence of the Pcb–PSI supercomplex.
Instead we have identified and characterized a supercomplex composed of
photosystem II (PSII) and Pcb proteins. We show that 10-Pcb subunits associate
with the PSII dimeric reaction center core to form a giant complex having an
estimated
M
r
of 1,500 kDa with dimensions of 210 ×
290 Å. Five-Pcb subunits flank each long side of the dimer and assuming
each binds 13 Chl molecules, increase the antenna size of PSII by ≈200%.
Fluorescence emission studies indicate that energy transfer occurs efficiently
from the Pcb antenna. Modeling using the x-ray structure of cyanobacterial
PSII suggests that energy transfer to the PSII reaction center is via the Chls
bound to the CP47 and CP43 proteins.
Foreign-language experience in infancy: Effects of short-term exposure and social interaction on phonetic learning
Authors: Kuhl Patricia K. , Tsao Feng-Ming , Liu Huei-Mei
Published: July 2003

Infants acquire language with remarkable speed, although little is known about the mechanisms that underlie the acquisition process. Studies of the phonetic units of language have shown that early in life, infants are capable of discerning differences among the phonetic units of all languages, including native- and foreign-language sounds. Between 6 and 12 mo of age, the ability to discriminate foreign-language phonetic units sharply declines. In two studies, we investigate the necessary and sufficient conditions for reversing this decline in foreign-language phonetic perception. In Experiment 1, 9-mo-old American infants were exposed to native Mandarin Chinese speakers in 12 laboratory sessions. A control group also participated in 12 language sessions but heard only English. Subsequent tests of Mandarin speech perception demonstrated that exposure to Mandarin reversed the decline seen in the English control group. In Experiment 2, infants were exposed to the same foreign-language speakers and materials via audiovisual or audio-only recordings. The results demonstrated that exposure to recorded Mandarin, without interpersonal interaction, had no effect. Between 9 and 10 mo of age, infants show phonetic learning from live, but not prerecorded, exposure to a foreign language, suggesting a learning process that does not require long-term listening and is enhanced by social interaction.
Identification of an activator protein required for the induction of
fruA
, a gene essential for fruiting body development in
Myxococcus xanthus
Authors: Ueki Toshiyuki , Inouye Sumiko
Published: July 2003

Myxococcus xanthus
exhibits social behavior and multicellular
development. FruA is an essential transcription factor for fruiting body
development in
M. xanthus
. In the present study, the upstream
promoter region was found to be necessary for the induction of
fruA
expression during development. A cis-acting element required for the induction
was identified and was located between nucleotides –154 and –107
with respect to the transcription initiation site. In addition, it was found
that two binding sites exist within this element of the
fruA
promoter. By using DNA affinity column chromatography containing the
cis-acting element, a
fruA
promoter-binding protein was purified. The
purified protein was shown by N-terminal sequence analysis to be identical to
MrpC, a protein identified previously by transposon insertion mutagenesis as
an essential locus for fruiting body development [Sun, H. & Shi, W. (2001)
J. Bacteriol.
183, 4786–4795]. Furthermore,
fruA
mRNA
was not detectable in the
mrpC
::
km
strain, demonstrating
that MrpC is essential for
fruA
expression. Moreover, mutational
analysis of the binding sites for MrpC in the
fruA
promoter indicates
that binding of MrpC activates transcription of
fruA in vivo
. This
report provides evidence for a direct molecular interaction involved in
temporally regulated gene expression in
M. xanthus
.
Activation of yeast Snf1 and mammalian AMP-activated protein kinase by upstream kinases
Authors: Hong Seung-Pyo , Leiper Fiona C. , Woods Angela , Carling David , Carlson Marian
Published: July 2003

The Snf1/AMP-activated protein kinase (AMPK) family plays fundamental roles
in cellular responses to metabolic stress in eukaryotes. In humans, AMPK
regulates lipid and glucose metabolism and has been implicated in such
metabolic disorders as diabetes and obesity and in cardiac abnormalities. Snf1
and AMPK are the downstream components of kinase cascades, but the upstream
kinase(s) have remained elusive. We have here identified three yeast kinases,
Pak1p, Tos3p, and Elm1p, that activate Snf1 kinase
in vivo
. Triple
deletion of the cognate genes causes a Snf
–
mutant phenotype
and abolishes Snf1 catalytic activity. All three kinases phosphorylate
recombinant Snf1p on the activation-loop threonine. Moreover, Tos3p
phosphorylates mammalian AMPK on the equivalent residue and activates the
enzyme, suggesting functional conservation of the upstream kinases between
yeast and mammals. We further show that the closely related mammalian LKB1
kinase, which is associated with Peutz–Jeghers cancer-susceptibility
syndrome, phosphorylates and activates AMPK
in vitro
. Thus, the
identification of the yeast upstream kinases should facilitate identification
of the corresponding, physiologically important mammalian upstream
kinases.
Engineering disulfide bridges to dissect antimicrobial and chemotactic activities of human β-defensin 3
Authors: Wu Zhibin , Hoover David M. , Yang De , Boulègue Cyril , Santamaria Fanny , Oppenheim Joost J. , Lubkowski Jacek , Lu Wuyuan
Published: July 2003

Human defensins form a family of small, cationic, and Cys-rich antimicrobial proteins that play important roles in innate immunity against invading microbes. They also function as effective immune modulators in adaptive immunity by selectively chemoattracting T lymphocytes and immature dendritic cells. On the basis of sequence homology and the connectivity of six conserved Cys residues, human defensins are classified into α and β families. Structures of several β-defensins have recently been characterized, confirming the disulfide connectivity conserved within the family, i.e., Cys1–Cys5, Cys2–Cys4, and Cys3–Cys6. We found that human β-defensin 3 (hBD3), a recently described member of the growing β family, did not fold preferentially into a native conformationin vitrounder various oxidative conditions. Using the orthogonal protection of Cys1–Cys5and of Cys1–Cys6, we chemically synthesized six topological analogs of hBD3 with predefined disulfide connectivities, including the (presumably) native β pairing. Unexpectedly, all differently folded hBD3 species exhibited similar antimicrobial activity againstEscherichia coli, whereas a wide range of chemotactic activities was observed with these analogs for monocytes and cells transfected by the chemokine receptor CCR6. Furthermore, whereas substitution of all Cys residues by α-aminobutyric acid completely abolished the chemotactic activity of hBD3, the bactericidal activity remained unaffected in the absence of any disulfide bridge. Our findings demonstrate that disulfide bonding in hBD3, although required for binding and activation of receptors for chemotaxis, is fully dispensable for its antimicrobial function, thus shedding light on the mechanisms of action for human β-defensins and the design of novel peptide antibiotics.