bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of storage temperature and container type on the vigour of Welsh onion seeds with low moisture content
Authors: Yanping Yin , Rongqi Gao , Qingquan Sun , Shengfu Li
Published: September 2002

Summary. The vigour of Welsh onion
(Allium fistulosum L.) seeds with low moisture content
was determined after exposure to different storage temperatures and container
types. As the storage period was prolonged, the effects of storage temperature
and container type on seed vigour became more pronounced. Storage temperature
had a greater effect on seed vigour than container types, and the effect of
the latter was subject to the storage temperature. When the seeds were stored
in the same type of container, several indices of the seed vigour declined as
the storage temperature increased. A highly significant positive correlation
was evident between dehydrogenase activity and the percentage germination of
the seed. Improving storage conditions could prolong seed longevity. If the
seeds, in which the moisture content has been reduced to less than 6%,
are stored airtight, the percentage germination will be about 85% after
storage for 2 years at room temperature or after 3-year storage at 6°C. If
the seeds are stored at –6°C, the percentage germination will range
from 86 to 91% after 3-year storage, regardless of the storage
container types in this study. These data are very important for the seed
storage and germplasm conservation of Welsh onion.
Waddington's canalization revisited: Developmental stability and evolution
Authors: Siegal Mark L. , Bergman Aviv
Published: September 2002

Most species maintain abundant genetic variation and experience a range of environmental conditions, yet phenotypic variation is low. That is, development is robust to changes in genotype and environment. It has been claimed that this robustness, termed canalization, evolves because of long-term natural selection for optimal phenotypes. We show that the developmental process, here modeled as a network of interacting transcriptional regulators, constrains the genetic system to produce canalization, even without selection toward an optimum. The extent of canalization, measured as the insensitivity to mutation of a network's equilibrium state, depends on the complexity of the network, such that more highly connected networks evolve to be more canalized. We argue that canalization may be an inevitable consequence of complex developmental–genetic processes and thus requires no explanation in terms of evolution to suppress phenotypic variation.
Heterologous desensitization of opioid receptors by chemokines inhibits chemotaxis and enhances the perception of pain
Authors: Szabo Imre , Chen Xiao-Hong , Xin Li , Adler Martin W. , Howard O. M. Z. , Oppenheim Joost J. , Rogers Thomas J.
Published: September 2002

The chemokines use G protein-coupled receptors to regulate the migratory and proadhesive responses of leukocytes. Based on observations that G protein-coupled receptors undergo heterologous desensitization, we have examined the ability of chemokines to also influence the perception of pain by cross-desensitizing opioid G protein-coupled receptors functionin vitroandin vivo. We find that the chemotactic activities of both μ- and δ-opioid receptors are desensitized following activation of the chemokine receptors CCR5, CCR2, CCR7, and CXCR4 but not of the CXCR1 or CXCR2 receptors. Furthermore, we also find that pretreatment with RANTES/CCL5, the ligand for CCR1, and CCR5 or SDF-1α/CXCL12, the ligand for CXCR4, followed by opioid administration into the periaqueductal gray matter of the brain results in an increased rat tail flick response to a painful stimulus. Because chemokine administration into the periaqueductal gray matter inhibits opioid-induced analgesia, we propose that the activation of proinflammatory chemokine receptors down-regulates the analgesic functions of opioid receptors, and this enhances the perception of pain at inflammatory sites.
C-terminal domain phosphatase-like family members (AtCPLs) differentially regulateArabidopsis thalianaabiotic stress signaling, growth, and development
Authors: Koiwa Hisashi , Barb Adam W. , Xiong Liming , Li Fang , McCully Michael G. , Lee Byeong-ha , Sokolchik Irina , Zhu Jianhua , Gong Zhizhong , Reddy Muppala , Sharkhuu Altanbadralt , Manabe Yuzuki , Yokoi Shuji , Zhu Jian-Kang , Bressan Ray A. , Hasegawa Paul M.
Published: September 2002

Cold, hyperosmolarity, and abscisic acid (ABA) signaling induceRD29Aexpression, which is an indicator of the plant stress adaptation response. Two nonallelicArabidopsis thaliana(ecotype C24) T-DNA insertional mutations,cpl1andcpl3, were identified based on hyperinduction ofRD29Aexpression that was monitored by using the luciferase (LUC) reporter gene (RD29A:LUC) imaging system. Genetic linkage analysis and complementation data established that the recessivecpl1andcpl3mutations are caused by T-DNA insertions inAtCPL1(ArabidopsisC-terminal domain phosphatase-like) andAtCPL3, respectively. Gel assays using recombinant AtCPL1 and AtCPL3 detected innate phosphatase activity like other members of the phylogenetically conserved family that dephosphorylate the C-terminal domain of RNA polymerase II (RNAP II).cpl1mutation causesRD29A:LUChyperexpression and transcript accumulation in response to cold, ABA, and NaCl treatments, whereas thecpl3mutation mediates hyperresponsiveness only to ABA. Northern analysis confirmed thatLUCtranscript accumulation also occurs in response to these stimuli.cpl1plants accumulate biomass more rapidly and exhibit delayed flowering relative to wild type whereascpl3plants grow more slowly and flower earlier than wild-type plants. Hence AtCPL1 and AtCPL3 are negative regulators of stress responsive gene transcription and modulators of growth and development. These results suggest that C-terminal domain phosphatase regulation of RNAP II phosphorylation status is a focal control point of complex processes like plant stress responses and development. AtCPL family members apparently have both unique and overlapping transcriptional regulatory functions that differentiate the signal output that determines the plant response.
Numerical operator calculus in higher dimensions
Authors: Beylkin Gregory , Mohlenkamp Martin J.
Published: September 2002

When an algorithm in dimension one is extended to dimensiond, in nearly every case its computational cost is taken to the powerd. This fundamental difficulty is the single greatest impediment to solving many important problems and has been dubbed thecurse of dimensionality. For numerical analysis in dimensiond, we propose to use a representation for vectors and matrices that generalizes separation of variables while allowing controlled accuracy. Basic linear algebra operations can be performed in this representation using one-dimensional operations, thus bypassing the exponential scaling with respect to the dimension. Although not all operators and algorithms may be compatible with this representation, we believe that many of the most important ones are. We prove that the multiparticle Schrödinger operator, as well as the inverse Laplacian, can be represented very efficiently in this form. We give numerical evidence to support the conjecture that eigenfunctions inherit this property by computing the ground-state eigenfunction for a simplified Schrödinger operator with 30 particles. We conjecture and provide numerical evidence that functions of operators inherit this property, in which case numerical operator calculus in higher dimensions becomes feasible.
A clogged gutter mechanism for protease inhibitors
Authors: Radisky Evette S. , Koshland Daniel E.
Published: September 2002

A classical peptide inhibitor of serine proteases that is hydrolyzed ≈10
7
times more slowly than a good substrate is shown to form an acyl–enzyme intermediate rapidly. Despite this quick first step, further reaction is slowed dramatically because of tight and oriented binding of the cleaved peptide, preventing acyl–enzyme hydrolysis and favoring the reverse reaction. Moreover, this mechanism appears to be common to a large class of tight-binding serine protease inhibitors that mimic good substrates. The arrest of enzymatic reaction at the intermediate stage allowed us to determine that the consensus nucleophilic attack angle is close to 90° in the reactive Michaelis complexes.
Dissection of the c-Kit signaling pathway in mouse primordial germ cells by retroviral-mediated gene transfer
Authors: De Miguel Maria P. , Cheng Linzhao , Holland Eric C. , Federspiel Mark J. , Donovan Peter J.
Published: September 2002

Establishment of the mammalian germ line is a prerequisite for fertility of the adult animal but we know surprisingly little about the molecular mechanisms regulating germ-line development in mammals. Signaling from the c-Kit receptor tyrosine kinase is essential for primordial germ cell (PGC) growth both
in vivo
and
in vitro
. Many downstream effectors of the c-Kit signaling pathway have been identified in other cell types but how these molecules control PGC survival and proliferation are unknown. Determination of the c-Kit effectors acting in PGCs has been hampered by the lack of effective methods to easily manipulate gene expression in these cells. We overcame this problem by testing the efficacy of retroviral-mediated gene transfer for manipulating gene expression in mammalian germ cells. We found that PGCs can be successfully infected with a variety of types of retroviruses. We used this method to demonstrate an important role for the AKT kinase in regulating PGC growth. Such technology for manipulating gene expression in PGCs will allow many of the molecular mechanisms regulating germ cell growth, behavior, and differentiation to be comprehensively analyzed.
Two sequence motifs from HIF-1α bind to the DNA-binding site of p53
Authors: Hansson Lars O. , Friedler Assaf , Freund Stefan , Rüdiger Stefan , Fersht Alan R.
Published: September 2002

There is evidence that hypoxia-inducible factor-1α (HIF-1α) interacts with the tumor suppressor p53. To characterize the putative interaction, we mapped the binding of the core domain of p53 (p53c) to an array of immobilized HIF-1α-derived peptides and found two peptide-sequence motifs that bound to p53c with micromolar affinity in solution. One sequence was adjacent to and the other coincided with the two proline residues of the oxygen-dependent degradation domain (P402 and P564) that act as switches for the oxygen-dependent regulation of HIF-1α. The binding affinity was independent of the hydroxylation state of P564. We found from NMR spectroscopy that these sequence motifs bind to the DNA-binding site of p53c. Because the two sequences are homologous and separated by 120 residues, and one is in a largely unstructured transactivation domain, we speculate that each sequence motif in HIF-1α binds to a different subunit of the p53 tetramer, leading to very tight binding. The binding data support the proposal that p53 provides a route for the degradation in hypoxic tumor cells of HIF-1α that is not hydroxylated at the two proline residues.
Cross-cultural evidence of cognitive adaptations for social exchange among the Shiwiar of Ecuadorian Amazonia
Authors: Sugiyama Lawrence S. , Tooby John , Cosmides Leda
Published: September 2002

On the basis of evolutionary game theory, it was hypothesized that humans have an evolved cognitive specialization for reasoning about social exchange, including a subroutine for detecting cheaters. This hypothesis led to a specific prediction: Although humans are known to be poor at detecting potential violations of conditional rules in general, they should nevertheless detect them easily when the rule involves social exchange and looking for violations corresponds to looking for cheaters. This prediction was subsequently confirmed by numerous tests. Evolutionary analyses further predict that: (i) in humans, complex adaptations will be distributed in a species-typical fashion; and (ii) aspects of cognitive organization relevant to performing the evolved function of an adaptation should be more buffered against environmental and cultural variation than function-irrelevant aspects. Here we report experiments testing whether social exchange reasoning exhibits these properties of adaptations. Existing tests of conditional reasoning were adapted for nonliterate experimental subjects and were administered to Shiwiar hunter–horticulturalists of the Ecuadorian Amazon. As predicted, Shiwiar subjects were as highly proficient at cheater detection as subjects from developed nations. Indeed, the frequency of cheater-relevant choices among Shiwiar hunter-horticulturalists was indistinguishable from that of Harvard undergraduates. Also as predicted, cultural variation was confined to those aspects of reasoning that are irrelevant to social exchange algorithms functioning as an evolutionarily stable strategy. Finally, Shiwiar subjects displayed the same low performance on descriptive conditionals as subjects from developed nations. Taken together, these findings support the hypotheses that social exchange algorithms are species-typical and that their evolutionarily stable strategy (ESS)-relevant subroutines are developmentally buffered against cultural variation.
Intracellular gene transfer: Reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochromecoxidase
Authors: Daley Daniel O. , Clifton Rachel , Whelan James
Published: September 2002

Subunit 2 of cytochromecoxidase (Cox2) in legumes offers a rare opportunity to investigate factors necessary for successful gene transfer of a hydrophobic protein that is usually mitochondrial-encoded. We found that changes in local hydrophobicity were necessary to allow import of this nuclear-encoded protein into mitochondria. All legume species containing both a mitochondrial and nuclear encoded Cox2 displayed a similar pattern, with a large decrease in hydrophobicity evident in the first transmembrane region of the nuclear encoded protein compared with the organelle-encoded protein. Mitochondrial-encoded Cox2 could not be imported into mitochondria under the direction of the mitochondrial targeting sequence that readily supports the import of nuclear encoded Cox2. Removal of the first transmembrane region promotes import ability of the mitochondrial-encoded Cox2. Changing just two amino acids in the first transmembrane region of mitochondrial-encoded Cox2 to the corresponding amino acids in the nuclear encoded Cox2 also promotes import ability, whereas changing the same two amino acids in the nuclear encoded Cox2 to what they are in the mitochondrial-encoded copy prevents import. Therefore, changes in amino acids in the mature protein were necessary and sufficient for gene transfer to allow import under the direction of an appropriate signal to achieve the functional topology of Cox2.
KRIT1
, a gene mutated in cerebral cavernous malformation, encodes a microtubule-associated protein
Authors: Gunel Murat , Laurans Maxwell S. H. , Shin Dana , DiLuna Michael L. , Voorhees Jennifer , Choate Keith , Nelson-Williams Carol , Lifton Richard P.
Published: September 2002

Mutations in Krev1 interaction trapped gene 1 (
KRIT1
) cause cerebral cavernous malformation, an autosomal dominant disease featuring malformation of cerebral capillaries resulting in cerebral hemorrhage, strokes, and seizures. The biological functions of
KRIT1
are unknown. We have investigated KRIT1 expression in endothelial cells by using specific anti-KRIT1 antibodies. By both microscopy and coimmunoprecipitation, we show that KRIT1 colocalizes with microtubules. In interphase cells, KRIT1 is found along the length of microtubules. During metaphase, KRIT1 is located on spindle pole bodies and the mitotic spindle. During late phases of mitosis, KRIT1 localizes in a pattern indicative of association with microtubule plus ends. In anaphase, the plus ends of the interpolar microtubules show strong KRIT1 staining and, in late telophase, KRIT1 stains the midbody remnant most strongly; this is the site of cytokinesis where plus ends of microtubules from dividing cells overlap. These results establish that KRIT1 is a microtubule-associated protein; its location at plus ends in mitosis suggests a possible role in microtubule targeting. These findings, coupled with evidence of interaction of KRIT1 with Krev1 and integrin cytoplasmic domain-associated protein-1 alpha (ICAP1 α), suggest that KRIT1 may help determine endothelial cell shape and function in response to cell–cell and cell–matrix interactions by guiding cytoskeletal structure. We propose that the loss of this targeting function leads to abnormal endothelial tube formation, thereby explaining the mechanism of formation of cerebral cavernous malformation (CCM) lesions.
Amplitude envelope onsets and developmental dyslexia: A new hypothesis
Authors: Goswami Usha , Thomson Jennifer , Richardson Ulla , Stainthorp Rhona , Hughes Diana , Rosen Stuart , Scott Sophie K.
Published: September 2002

A core difficulty in developmental dyslexia is the accurate specification and neural representation of speech. We argue that a likely perceptual cause of this difficulty is a deficit in the perceptual experience of rhythmic timing. Speech rhythm is one of the earliest cues used by infants to discriminate syllables and is determined principally by the acoustic structure of amplitude modulation at relatively low rates in the signal. We show significant differences between dyslexic and normally reading children, and between young early readers and normal developers, in amplitude envelope onset detection. We further show that individual differences in sensitivity to the shape of amplitude modulation account for 25% of the variance in reading and spelling acquisition even after controlling for individual differences in age, nonverbal IQ, and vocabulary. A possible causal explanation dependent on perceptual-center detection and the onset-rime representation of syllables is discussed.
Cerebral energetics and spiking frequency: The neurophysiological basis of fMRI
Authors: Smith Arien J. , Blumenfeld Hal , Behar Kevin L. , Rothman Douglas L. , Shulman Robert G. , Hyder Fahmeed
Published: September 2002

Functional MRI (fMRI) is widely assumed to measure neuronal activity, but no satisfactory mechanism for this linkage has been identified. Here we derived the changes in the energetic component from the blood oxygenation level-dependent (BOLD) fMRI signal and related it to changes in the neuronal spiking frequency in the activated voxels. Extracellular recordings were used to measure changes in cerebral spiking frequency (Δν/ν) of a neuronal ensemble during forepaw stimulation in the α-chloralose anesthetized rat. Under the same conditions localized changes in brain energy metabolism (ΔCMR
O2
/CMR
O2
) were obtained from BOLD fMRI data in conjunction with measured changes in cerebral blood flow (ΔCBF/CBF), cerebral blood volume (ΔCBV/CBV), and transverse relaxation rates of tissue water (T

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and T
2
) by MRI methods at 7T. On stimulation from two different depths of anesthesia ΔCMR
O2
/CMR
O2
≈ Δν/ν. Previous
13
C magnetic resonance spectroscopy studies, under similar conditions, had shown that ΔCMR
O2
/CMR
O2
was proportional to changes in glutamatergic neurotransmitter flux (ΔV
cyc
/V
cyc
). These combined results show that ΔCMR
O2
/CMR
O2
≈ ΔV
cyc
/V
cyc
≈ Δν/ν, thereby relating the energetic basis of brain activity to neuronal spiking frequency and neurotransmitter flux. Because ΔCMR
O2
/CMR
O2
had the same high spatial and temporal resolutions of the fMRI signal, these results show how BOLD imaging, when converted to ΔCMR
O2
/CMR
O2
, responds to localized changes in neuronal spike frequency.
Total neuroenergetics support localized brain activity: Implications for the interpretation of fMRI
Authors: Hyder Fahmeed , Rothman Douglas L. , Shulman Robert G.
Published: September 2002

In α-chloralose-anesthetized rats, changes in the blood oxygenation level-dependent (BOLD) functional MRI (fMRI) signal (ΔS/S), and the relative spiking frequency of a neuronal ensemble (Δν/ν) were measured in the somatosensory cortex during forepaw stimulation from two different baselines. Changes in cerebral oxygen consumption (ΔCMR
O2
/CMR
O2
) were derived from the BOLD signal (at 7T) by independent determinations in cerebral blood flow (ΔCBF/CBF) and volume (ΔCBV/CBV). The spiking frequency was measured by extracellular recordings in layer 4. Changes in all three parameters (CMR
O2
, ν, and S) were greater from the lower baseline (i.e., deeper anesthesia). For both baselines, ΔCMR
O2
/CMR
O2
and Δν/ν were approximately one order of magnitude larger than ΔS/S. The final values of CMR
O2
and ν reached during stimulation were approximately the same from both baselines. If only increments were required to support functions then their magnitudes should be independent of the baseline. In contrast, if particular magnitudes of activity were required, then sizes of increments should inversely correlate with the baseline (being larger from a lower baseline). The results show that particular magnitudes of activity support neural function. The disregard of baseline activity in fMRI experiments by differencing removes a large and necessary component of the total activity. Implications of these results for understanding brain function and fMRI experiments are discussed.
Enhanced microtubule-dependent trafficking and p53 nuclear accumulation by suppression of microtubule dynamics
Authors: Giannakakou Paraskevi , Nakano Michel , Nicolaou Kyriacos C. , O'Brate Aurora , Yu Jian , Blagosklonny Mikhail V. , Greber Urs F. , Fojo Tito
Published: September 2002

The tumor suppressor protein p53 localizes to microtubules (MT) and, in response to DNA damage, is transported to the nucleus via the MT minus-end-directed motor protein dynein. Dynein is also responsible for MT-mediated nuclear targeting of adenovirus type 2 (Ad2). Here we show that treatment with low concentrations of MT-targeting compounds (MTCs) that do not disrupt the MT network but are known to suppress MT dynamics enhanced p53 nuclear accumulation, and the activation of the p53-downstream target genes. p53 nuclear accumulation required binding of MTCs to MTs and enhanced the induction of p53-up-regulated modulator of apoptosis (PUMA) mRNA and apoptosis on challenging cells with the DNA-damaging drug adriamycin. Low concentrations of MTCs enhanced the rate of movement of fluorescent Ad2 to the nucleus and increased the nuclear targeting efficiency of Ad2. We propose that suppression of MT dynamics by low concentrations of MTCs enhances MT-dependent trafficking toward the minus ends of MTs and facilitates nuclear targeting.
Transplanting allosteric control of enzyme activity by protein–protein interactions: Coupling a regulatory site to the conserved catalytic core
Authors: Pawlyk Aaron C. , Pettigrew Donald W.
Published: September 2002

Glycerol kinase from
Escherichia coli
, but not
Haemophilus influenzae
, is inhibited allosterically by phosphotransferase system protein IIA
Glc
. The primary structures of these related kinases contain 501 amino acids, differing at 117. IIA
Glc
inhibition is transplanted from
E. coli
glycerol kinase into
H. influenzae
glycerol kinase by interconverting only 11 of the differences: 8 residues that interact with IIA
Glc
at the allosteric binding site and 3 residues in the conserved ATPase catalytic core that do not interact with IIA
Glc
but the solvent accessible surface of which decreases when it binds. The three core residues are crucial for coupling the allosteric site to the conserved catalytic core of the enzyme. The site of the coupling residues identifies a regulatory locus in the sugar kinase/heat shock protein 70/actin superfamily and suggests relations between allosteric regulation and the active site closure that characterizes the family. The location of the coupling residues provides empirical validation of a computational model that predicts a coupling pathway between the IIA
Glc
-binding site and the active site [Luque, I. & Freire, E. (2000)
Proteins Struct. Funct. Genet.
Suppl. 4, 63–71]. The requirement for changes in core residues to couple the allosteric and active sites and switching from inhibition to activation by a single amino acid change are consistent with a postulated mechanism for molecular evolution of allosteric regulation.
Hybrid
Tamarix
widespread in U.S. invasion and undetected in native Asian range
Authors: Gaskin John F. , Schaal Barbara A.
Published: September 2002

Biological invasions are drastically altering natural habitats and threatening biodiversity on both local and global levels. In one of the United States' worst invasions, Eurasian
Tamarix
plant species have spread rapidly to dominate over 600,000 riparian and wetland hectares. The largest
Tamarix
invasion consists of
Tamarix chinensis
and
Tamarix ramosissima
, two morphologically similar species. To clarify the identity, origins, and population structuring of this invasion, we analyzed DNA sequence data from an intron of a nuclear gene, phosphoenolpyruvate carboxylase (
PepC
). This intron proved to be highly variable at the population level, and the 269 native and invasive specimens yielded 58 haplotypes, from which we constructed a gene genealogy. Only four of these haplotypes were common to both the U.S. and Eurasia. Surprisingly, we found that the most common plant in this U.S. invasion is a hybrid combination of two species-specific genotypes that were geographically isolated in their native Eurasian range. Less extensive hybrids exist in the invasion, involving combinations of
T. ramosissima
and
T. chinensis
with
Tamarix parviflora
and
Tamarix gallica
. The presence of potentially novel hybrids in the U.S. illustrates how importation of exotics can alter population structures of species and contribute to invasions.
Mismatch-targeted transposition of Mu: A new strategy to map genetic polymorphism
Authors: Yanagihara Katsuhiko , Mizuuchi Kiyoshi
Published: September 2002

Phage Mu DNA transposes to duplex target DNA sites with limited sequence specificity. Here we demonstrate that Mu transposition exhibits a strong target site preference for all single-nucleotide mismatches. This finding has implications for the mechanism of transposition and provides a powerful tool for genomic research. A single mismatch could be detected as a preferred target of Mu transposition in the presence of 300,000-fold excess of nonmismatched sites. We demonstrate the detection of both heterozygous and homozygous mutations in the cystic fibrosis transmembrane conductance regulator gene and single nucleotide polymorphism in HLA region by Mu transposition mismatch analysis procedure.
Concentration fluctuations in a mesoscopic oscillating chemical reaction system
Authors: Qian Hong , Saffarian Saveez , Elson Elliot L.
Published: September 2002

Under sustained pumping, kinetics of macroscopic nonlinear biochemical reaction systems far from equilibrium either can be in a stationary steady state or can execute sustained oscillations about a fixed mean. For a system of two dynamic species X and Y, the concentrations
n
x
and
n
y
will be constant or will repetitively trace a closed loop in the (
n
x
,
n
y
) phase plane, respectively. We study a mesoscopic system with
n
x
and
n
y
very small; hence the occurrence of random fluctuations modifies the deterministic behavior and the law of mass action is replaced by a stochastic model. We show that
n
x
and
n
y
execute cyclic random walks in the (
n
x
,
n
y
) plane whether or not the deterministic kinetics for the corresponding macroscopic system represents a steady or an oscillating state. Probability distributions and correlation functions for
n
x
(
t
) and
n
y
(
t
) show quantitative but not qualitative differences between states that would appear as either oscillating or steady in the corresponding macroscopic systems. A diffusion-like equation for probability
P
(
n
x
,
n
y
,
t
) is obtained for the two-dimensional Brownian motion in the (
n
x
,
n
y
) phase plane. In the limit of large
n
x
,
n
y
, the deterministic nonlinear kinetics derived from mass action is recovered. The nature of large fluctuations in an oscillating nonequilibrium system and the conceptual difference between “thermal stochasticity” and “temporal complexity” are clarified by this analysis. This result is relevant to fluorescence correlation spectroscopy and metabolic reaction networks.
Urokinase plasminogen activator receptor: Prognostic biomarker for endometrial cancer
Authors: Memarzadeh Sanaz , Kozak Katherine R. , Chang Lisbeth , Natarajan Sathima , Shintaku Peter , Reddy Srinivasa T. , Farias-Eisner Robin
Published: September 2002

Endometrial adenocarcinoma is the most common gynecologic malignancy in the United States. However, reliable diagnostic or prognostic tumor markers have not been identified for endometrial cancer. In this study, we examined whether urokinase plasminogen activator receptor (UPAR), a glycosyl-phosphatidylinositol-linked membrane protein, is a candidate diagnostic or prognostic marker for patients with cancer of the endometrium. Sixty-five surgically excised, formalin-fixed endometrial tissue specimens were accessioned through the Department of Pathology Registry at the University of California, Los Angeles, and analyzed for UPAR expression by using immunohistochemical techniques. A retrospective review was also performed to determine stage and histopathologic grade of disease, recurrence, and mortality. No expression of UPAR protein was present in seven patients with benign neoplasia of the endometrium. UPAR protein expression highly correlated with stage of disease (ungrouped Spearman correlation = 0.625,
P
< 0.0001): 40% of patients with stage I, 66% of patients with stage II, 100% of patients with stage III, and 85% with stage IV demonstrated the highest level of UPAR expression. Moreover, high UPAR expression positively correlated with grade of disease (ungrouped Spearman correlation = 0.71,
P
< 0.0001): 29% of grade 1 specimens, 57% of grade 2, and over 90% of specimens with grade 3, the majority representing uterine papillary serous carcinoma and mixed malignant mesodermal tumor. Finally, UPAR protein expression also positively correlated with rate of recurrence and mortality in patients with adenocarcinoma of the endometrium (ungrouped
P
= 0.034). Our data suggest that UPAR is a useful prognostic marker for biologically aggressive forms of endometrial cancer.
Structure of decay-accelerating factor bound to echovirus 7: A virus-receptor complex
Authors: He Yongning , Lin Feng , Chipman Paul R. , Bator Carol M. , Baker Timothy S. , Shoham Menachem , Kuhn Richard J. , Medof M. Edward , Rossmann Michael G.
Published: September 2002

Echoviruses are enteroviruses that belong to
Picornaviridae
. Many echoviruses use decay-accelerating factor (DAF) as their cellular receptor. DAF is a glycosylphosphatidyl inositol-anchored complement regulatory protein found on most cell surfaces. It functions to protect cells from complement attack. The cryo-electron microscopy reconstructions of echovirus 7 complexed with DAF show that the DAF-binding regions are located close to the icosahedral twofold axes, in contrast to other enterovirus complexes where the viral canyon is the receptor binding site. This novel receptor binding position suggests that DAF is important for the attachment of viral particles to host cells, but probably not for initiating viral uncoating, as is the case with canyon-binding receptors. Thus, a different cell entry mechanism must be used for enteroviruses that bind DAF.
A hemocyanin from the Onychophora and the emergence of respiratory proteins
Authors: Kusche Kristina , Ruhberg Hilke , Burmester Thorsten
Published: September 2002

The velvet worms (Onychophora) are considered living fossils and are closely related to the Euarthropoda. Onychophora possess a tracheal system for respiratory function, but oxygen-transport proteins have been considered unnecessary. Here, we show that the hemolymph of the
Epiperipatus
sp. (Onychophora: Peripatidae) contains an arthropod-type hemocyanin, demonstrating that such protein exists outside the Euarthropoda. Thus, the evolution of oxygen carriers preceded the divergence of the Onychophora and Euarthropoda and was most likely linked to the evolution of an efficient circulatory system in a low-oxygen environment. The cDNA of the
Epiperipatus
hemocyanin subunit comprises 2,287 bp and encodes for a protein of 641 aa (73.6 kDa). Phylogenetic analyses of the arthropod hemocyanin sequences show that the Onychophora form a robust sister-group of the Euarthropoda, whereas the monophyly of the Tracheata is not supported.
Previously uncharacterized genes in the UV- and MMS-induced DNA damage response in yeast
Authors: Hanway Denise , Chin Jodie K. , Xia Gang , Oshiro Guy , Winzeler Elizabeth A. , Romesberg Floyd E.
Published: September 2002

A competitive growth assay has been used to identify yeast genes involved in the repair of UV- or MMS-induced DNA damage. A collection of 2,827 yeast strains was analyzed in which each strain has a single ORF replaced with a cassette containing two unique sequence tags, allowing for its detection by hybridization to a high-density oligonucleotide array. The hybridization data identify a high percentage of the deletion strains present in the collection that were previously characterized as being sensitive to the DNA-damaging agents. The assay, and subsequent analysis, has been used to identify six genes not formerly known to be involved in the damage response, whose deletion renders the yeast sensitive to UV or MMS treatment. The recently identified genes include three uncharacterized ORFs, as well as genes that encode protein products implicated in ubiquitination, gene silencing, and transport across the mitochondrial membrane. Epistatsis analysis of four of the genes was performed to determine the DNA damage repair pathways in which the protein products function.
Effects of aging on central and peripheral mammalian clocks
Authors: Yamazaki Shin , Straume Marty , Tei Hajime , Sakaki Yoshiyuki , Menaker Michael , Block Gene D.
Published: September 2002

Circadian organization changes with age, but we do not know the extent to which age-related changes are the result of alterations in the central pacemakers, the peripheral oscillators, or the coupling mechanisms that hold the system together. By using transgenic rats with a
luciferase
(
luc
) reporter, we assessed the effects of aging on the rhythm of expression of the
Period 1
(
Per1
) gene in the suprachiasmatic nucleus (SCN) and in peripheral tissues. Young (2 months) and aged (24–26 months)
Per1-luc
transgenic rats, entrained to light–dark cycles, were killed, and tissues were removed and cultured.
Per1-luc
expression was measured from 10 tissues. In the SCN, the central mammalian pacemaker,
Per1-luc
expression was robustly rhythmic for more than 7 weeks in culture. The only difference between SCN rhythmicity in young and old rats was a small but significant age-related shortening of the free-running period. Circadian rhythmicity in some peripheral tissues was unaffected by aging, whereas rhythmicity in other tissues was either phase advanced relative to the light cycle or absent. Those tissues that were arrhythmic could be induced to oscillate by application of forskolin, suggesting that they retained the capacity to oscillate but were not being appropriately driven
in vivo
. Overall, the results provide new insights into the effects of aging on the mammalian circadian system. Aging seems to affect rhythms in some but not in all tissues and may act primarily on interactions among circadian oscillators, perhaps attenuating the ability of the SCN to drive damped oscillators in the periphery.
Mitochondrial DNA and the origins of the domestic horse
Authors: Jansen Thomas , Forster Peter , Levine Marsha A. , Oelke Hardy , Hurles Matthew , Renfrew Colin , Weber Jürgen , Olek Klaus
Published: September 2002

The place and date of the domestication of the horse has long been a matter for debate among archaeologists. To determine whether horses were domesticated from one or several ancestral horse populations, we sequenced the mitochondrial D-loop for 318 horses from 25 oriental and European breeds, including American mustangs. Adding these sequences to previously published data, the total comes to 652, the largest currently available database. From these sequences, a phylogenetic network was constructed that showed that most of the 93 different mitochondrial (mt)DNA types grouped into 17 distinct phylogenetic clusters. Several of the clusters correspond to breeds and/or geographic areas, notably cluster A2, which is specific to Przewalski's horses, cluster C1, which is distinctive for northern European ponies, and cluster D1, which is well represented in Iberian and northwest African breeds. A consideration of the horse mtDNA mutation rate together with the archaeological timeframe for domestication requires at least 77 successfully breeding mares recruited from the wild. The extensive genetic diversity of these 77 ancestral mares leads us to conclude that several distinct horse populations were involved in the domestication of the horse.
Ubiquitin ligase-associated protein SGT1 is required for host and nonhost disease resistance in plants
Authors: Peart Jack R. , Lu Rui , Sadanandom Ari , Malcuit Isabelle , Moffett Peter , Brice David C. , Schauser Leif , Jaggard Daniel A. W. , Xiao Shunyuan , Coleman Mark J. , Dow Max , Jones Jonathan D. G. , Shirasu Ken , Baulcombe David C.
Published: September 2002

Homologues of the yeast ubiquitin ligase-associated protein SGT1 are required for disease resistance in plants mediated by nucleotide-binding site/leucine-rich repeat (NBS-LRR) proteins. Here, by silencing
SGT1
in
Nicotiana benthamiana
, we extend these findings and demonstrate that SGT1 has an unexpectedly general role in disease resistance. It is required for resistance responses mediated by NBS-LRR and other R proteins in which pathogen-derived elicitors are recognized either inside or outside the host plant cell. A requirement also exists for SGT1 in nonhost resistance in which all known members of a host species are resistant against every characterized isolate of a pathogen. Our findings show that silencing
SGT1
affects diverse types of disease resistance in plants and support the idea that R protein-mediated and nonhost resistance may involve similar mechanisms.
Brain monoglyceride lipase participating in endocannabinoid inactivation
Authors: Dinh T. P. , Carpenter D. , Leslie F. M. , Freund T. F. , Katona I. , Sensi S. L. , Kathuria S. , Piomelli D.
Published: September 2002

The endogenous cannabinoids (endocannabinoids) are lipid molecules that may mediate retrograde signaling at central synapses and other forms of short-range neuronal communication. The monoglyceride 2-arachidonoylglycerol (2-AG) meets several criteria of an endocannabinoid substance: (
i
) it activates cannabinoid receptors; (
ii
) it is produced by neurons in an activity-dependent manner; and (
iii
) it is rapidly eliminated. 2-AG inactivation is only partially understood, but it may occur by transport into cells and enzymatic hydrolysis. Here we tested the hypothesis that monoglyceride lipase (MGL), a serine hydrolase that converts monoglycerides to fatty acid and glycerol, participates in 2-AG inactivation. We cloned MGL by homology from a rat brain cDNA library. Its cDNA sequence encoded for a 303-aa protein with a calculated molecular weight of 33,367 daltons. Northern blot and
in situ
hybridization analyses revealed that MGL mRNA is heterogeneously expressed in the rat brain, with highest levels in regions where CB
1
cannabinoid receptors are also present (hippocampus, cortex, anterior thalamus, and cerebellum). Immunohistochemical studies in the hippocampus showed that MGL distribution has striking laminar specificity, suggesting a presynaptic localization of the enzyme. Adenovirus-mediated transfer of MGL cDNA into rat cortical neurons increased MGL expression and attenuated
N
-methyl-D-aspartate/carbachol-induced 2-AG accumulation in these cells. No such effect was observed on the accumulation of anandamide, another endocannabinoid lipid. The results suggest that hydrolysis by means of MGL is a primary mechanism for 2-AG inactivation in intact neurons.
Mutations in the
DNAH11
(axonemal heavy chain dynein type 11) gene cause one form of situs inversus totalis and most likely primary ciliary dyskinesia
Authors: Bartoloni Lucia , Blouin Jean-Louis , Pan Yanzhen , Gehrig Corinne , Maiti Amit K. , Scamuffa Nathalie , Rossier Colette , Jorissen Mark , Armengot Miguel , Meeks Maggie , Mitchison Hannah M. , Chung Eddie M. K. , Delozier-Blanchet Celia D. , Craigen William J. , Antonarakis Stylianos E.
Published: September 2002

Primary ciliary dyskinesia (PCD; MIM 242650) is an autosomal recessive disorder of ciliary dysfunction with extensive genetic heterogeneity. PCD is characterized by bronchiectasis and upper respiratory tract infections, and half of the patients with PCD have situs inversus (Kartagener syndrome). We characterized the transcript and the genomic organization of the axonemal heavy chain dynein type 11 (
DNAH1
1) gene, the human homologue of murine
Dnah11
or
lrd
, which is mutated in the
iv
/
iv
mouse model with situs inversus. To assess the role of
DNAH11
, which maps on chromosome 7p21, we searched for mutations in the 82 exons of this gene in a patient with situs inversus totalis, and probable Kartagener syndrome associated with paternal uniparental disomy of chromosome 7 (patUPD7). We identified a homozygous nonsense mutation (R2852X) in the
DNAH11
gene. This patient is remarkable because he is also homozygous for the F508del allele of the cystic fibrosis transmembrane conductance regulator (
CFTR
) gene. Sequence analysis of the
DNAH11
gene in an additional 6 selected PCD sibships that shared
DNAH11
alleles revealed polymorphic variants and an R3004Q substitution in a conserved position that might be pathogenic. We conclude that mutations in the coding region of
DNAH11
account for situs inversus totalis and probably a minority of cases of PCD.
Comprehensive analysis of gene expression in
Nicotiana tabacum
leaves acclimated to oxidative stress
Authors: Vranová Eva , Atichartpongkul Sopapan , Villarroel Raimundo , Van Montagu Marc , Inzé Dirk , Van Camp Wim
Published: September 2002

The molecular mechanisms by which plants acclimate to oxidative stress are poorly understood. To identify the processes involved in acclimation, we performed a comprehensive analysis of gene expression in
Nicotiana tabacum
leaves acclimated to oxidative stress. Combining mRNA differential display and cDNA array analysis, we estimated that at least 95 genes alter their expression in tobacco leaves acclimated to oxidative stress, of which 83% are induced and 17% repressed. Sequence analysis of 53 sequence tags revealed that, in addition to antioxidant genes, genes implicated in abiotic and biotic stress defenses, cellular protection and detoxification, energy and carbohydrate metabolism,
de novo
protein synthesis, and signal transduction showed altered expression. Expression of most of the genes was enhanced, except for genes associated with photosynthesis and light-regulated processes that were repressed. During acclimation, two distinct groups of coregulated genes (“early-” and “late-response” gene regulons) were observed, indicating the presence of at least two different gene induction pathways. These two gene regulons also showed differential expression patterns on an oxidative stress challenge. Expression of “late-response” genes was augmented in the acclimated leaf tissues, whereas expression of “early-response” genes was not. Together, our data suggest that acclimation to oxidative stress is a highly complex process associated with broad gene expression adjustments. Moreover, our data indicate that in addition to defense gene induction, sensitization of plants for potentiated gene expression might be an important factor in oxidative stress acclimation.
De novo
determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy
Authors: Rienstra Chad M. , Tucker-Kellogg Lisa , Jaroniec Christopher P. , Hohwy Morten , Reif Bernd , McMahon Michael T. , Tidor Bruce , Lozano-Pérez Tomás , Griffin Robert G.
Published: September 2002

The three-dimensional structure of the chemotactic peptide
N-
formyl-
l
-Met-
l
-Leu-
l
-Phe-OH was determined by using solid-state NMR (SSNMR). The set of SSNMR data consisted of 16
13
C–
15
N distances and 18 torsion angle constraints (on 10 angles), recorded from uniformly
13
C,
15
N- and
15
N-labeled samples. The peptide's structure was calculated by means of simulated annealing and a newly developed protocol that ensures that all of conformational space, consistent with the structural constraints, is searched completely. The result is a high-quality structure of a molecule that has thus far not been amenable to single-crystal diffraction studies. The extensions of the SSNMR techniques and computational methods to larger systems appear promising.
Altered glycan-dependent signaling induces insulin resistance and hyperleptinemia
Authors: McClain Donald A. , Lubas William A. , Cooksey Robert C. , Hazel Mark , Parker Glendon J. , Love Dona C. , Hanover John A.
Published: September 2002

Insulin resistance and β cell toxicity are key features of type 2 diabetes. One leading hypothesis suggests that these abnormalities result from excessive flux of nutrients through the UDP–hexosamine biosynthetic pathway leading to “glucose toxicity.” How the products of the hexosamine pathway mediate these effects is not known. Here, we show that transgenic overexpression of an enzyme using UDP-GlcNAc to modify proteins with O-GlcNAc produces the type 2 diabetic phenotype. Even modest overexpression of an isoform of O-GlcNAc transferase, in muscle and fat, leads to insulin resistance and hyperleptinemia. These data support the proposal that O-linked GlcNAc transferase participates in a hexosamine-dependent signaling pathway that is linked to insulin resistance and leptin production.
Up-regulation of plasma membrane-associated ganglioside sialidase (Neu3) in human colon cancer and its involvement in apoptosis suppression
Authors: Kakugawa Yoichiro , Wada Tadashi , Yamaguchi Kazunori , Yamanami Hideaki , Ouchi Kiyoaki , Sato Ikuro , Miyagi Taeko
Published: September 2002

Human plasma membrane-associated sialidase (Neu3) is unique in specifically hydrolyzing gangliosides, thought to participate in cell differentiation and transmembrane signaling, thereby playing crucial roles in the regulation of cell surface functions. We have discovered levels of mRNA for this sialidase to be increased in restricted cases of human colon cancer by 3- to 100-fold compared with adjacent nontumor mucosa (
n
= 32), associated with significant elevation in sialidase activity in tumors (
n
= 50).
In situ
hybridization showed the sialidase expression in epithelial elements of adenocarcinomas. In cultured human colon cancer cells, the sialidase level was down-regulated in the process of differentiation and apoptosis induced by sodium butyrate, whereas lysosomal sialidase (Neu1) was up-regulated. Transfection of the sialidase gene into colon cancer cells inhibited apoptosis and was accompanied by increased Bcl-2 and decreased caspase expression. Colon cancer exhibited a marked accumulation of lactosylceramide, a possible sialidase product, and addition of the glycolipid to the culture reduced apoptotic cells during sodium butyrate treatment. These results indicate that high expression of the sialidase in cancer cells leads to protection against programmed cell death, probably modulation of gangliosides. This finding provides a possible sialidase target for diagnosis and therapy of colon cancer.