bluuebunny/crossref_metadata_2025 huggingface dataset:
Activity budgets of the agile wallaby, Macropus agilis
Authors: Stirrat Simon C.
Published: March 2004

The activity budgets of agile wallabies were investigated in the wet season and dry season in the wet–dry tropics. In the dry season and in clear weather in the wet season the wallabies were essentially nocturnal, foraging throughout the night in open areas and resting during the day in monsoon rainforest patches. The day was clearly partitioned into active and inactive periods, with activity coordination (behaviour synchrony) being high during the night and day and low in the transition between these foraging and resting periods. In overcast weather activity coordination was lower throughout the day. The day was not partitioned into active and inactive periods and the wallabies were observed foraging in the open at all times of day. However, they foraged for no longer over 24 hours than in clear weather when foraging was mainly a nocturnal activity. The wallabies spent more time foraging, moved greater distances while foraging, were less vigilant, and rested and groomed less in the dry season when forage quality was poor.
The helminth parasites of Melomys cervinipes (Rodentia : Muridae : Hydromyinae)
Authors: Smales L. R. , Heinrich B. , McKillup S. C.
Published: March 2004

Melomys cervinipes Gould is one of four melomys species native to Australia. There have been no systematic surveys of parasite distribution and prevalence, or parasite community structure, for any species of Melomys. We present a comprehensive summary of the parasites of M. cervinipes by location in Queensland and northern New South Wales from published records, examination of museum specimens and data from an intensive sampling of hosts from four localities within central Queensland. An updated list prepared on the basis of these data and other published records is included.New host records include one cestode (Riallietina celebensis), one trematode (Platynosomum australiense) and 21 nematodes. Trichostrongyloid nematodes (Odilia spp.) were the dominant helminth group, with Odilia melomyos (Mawson, 1960) and O. mackerrasae (Mawson, 1960) being the core components of the helminth community. The structure of this community, with endemic and cosmopolitan elements, appears to have developed through both coevolution of hosts and parasites and host-switching events. Multidimensional scaling analysis of parasites from four central Queensland localities suggests considerable differences in community composition on a relatively small spatial scale. An island locality had a significantly different community structure and greater species diversity than nearby mainland sites. These results emphasise the importance of comparative studies of parasites among localities, and especially between island and mainland communities.
Amyloid β peptide load is correlated with increased β-secretase activity in sporadic Alzheimer's disease patients
Authors: Li Rena , Lindholm Kristina , Yang Li-Bang , Yue Xu , Citron Martin , Yan Riqiang , Beach Thomas , Sue Lucia , Sabbagh Marwan , Cai Huaibin , Wong Philip , Price Donald , Shen Yong
Published: March 2004

Whether elevated β-secretase (BACE) activity is related to plaque formation or amyloid β peptide (Aβ) production in Alzheimer's disease (AD) brains remains inconclusive. Here, we report that we used sandwich enzyme-linked immunoabsorbent assay to quantitate various Aβ species in the frontal cortex of AD brains homogenized in 70% formic acid. We found that most of the Aβ species detected in rapidly autopsied brains (<3 h) with sporadic AD were Aβ1-xand Aβ1-42, as well as Aβx-42. To establish a linkage between Aβ levels and BACE, we examined BACE protein, mRNA expression and enzymatic activity in the same brain region of AD brains. We found that both BACE mRNA and protein expression is elevatedin vivoin the frontal cortex. The elevation of BACE enzymatic activity in AD is correlated with brain Aβ1-xand Aβ1-42production. To examine whether BACE elevation was due to mutations in the BACE-coding region, we sequenced the entire ORF region of the BACE gene in these same AD and nondemented patients and performed allelic association analysis. We found no mutations in the ORF of the BACE gene. Moreover, we found few changes of BACE protein and mRNA levels in Swedish mutated amyloid precursor protein-transfected cells. These findings demonstrate correlation between Aβ loads and BACE elevation and also suggest that as a consequence, BACE elevation may lead to increased Aβ production and enhanced deposition of amyloid plaques in sporadic AD patients.
Frontostriatal deficits in fragile X syndrome: Relation to
FMR1
gene expression
Authors: Menon V. , Leroux J. , White C. D. , Reiss A. L.
Published: March 2004

Fragile X syndrome (fraX) is the most common known cause of inherited developmental disability. fraX is associated with a CGG expansion in the
FMR1
gene on the long arm of the X chromosome. Behavioral deficits, including problems with impulse control and distractibility, are common in fraX. We used functional brain imaging with a Go/NoGo task to examine the neural substrates of response inhibition in females with fraX (ages 10-22) and age- and gender-matched typically developing subjects. Although subjects with fraX had significantly lower IQ scores, as a group their performance on the Go/NoGo task was equivalent to that of the typically developing group. However, females with fraX showed abnormal activation patterns in several cortical and subcortical regions, with significantly reduced activation in the supplementary motor area, anterior cingulate and midcingulate cortex, basal ganglia, and hippocampus. An important finding of our study is that neural responses in the right ventrolateral prefrontal cortex (PFC) and the left and right striatum were correlated with the level of
FMR1
gene expression. Our findings support the hypothesis that frontostriatal regions typically associated with response inhibition are dysfunctional in females with fraX. In addition to task-related activation deficits, reduced levels of “deactivation” were observed in the ventromedial PFC, and, furthermore, these reductions were correlated with the level of
FMR1
gene expression. The ventromedial PFC is a key node in a “default mode” network that monitors mental and physiological states; we suggest that self-monitoring processes may be aberrant in fraX.
Microscopic observations reveal that fusogenic peptides induce liposome shrinkage prior to membrane fusion
Authors: Nomura Fumimasa , Inaba Takehiko , Ishikawa Satoshi , Nagata Miki , Takahashi Sho , Hotani Hirokazu , Takiguchi Kingo
Published: March 2004

To study the mechanisms involved in membrane fusion, we visualized the fusion process of giant liposomes in real time by optical dark-field microscopy. To induce membrane fusion, we used (i) influenza hemagglutinin peptide (HA), a 20-aa peptide derived from the N-terminal fusion peptide region of the HA2 subunit, and (ii) two synthetic analogue peptides of HA, a negatively (E5) and positively (K5) charged analogue. We were able to visualize membrane fusion caused by E5 or by K5 alone, as well as by the mixture of these two peptides. The HA peptide however, did not induce membrane fusion, even at an acidic pH, which has been described as the optimal condition for the fusion of large unilamellar vesicles. Surprisingly, before membrane fusion, the shrinkage of liposomes was always observed. Our results suggest that a perturbation of lipid bilayers, which probably resulted from alterations in the bending folds of membranes, is a critical factor in fusion efficiency.
Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain
Authors: Karanicolas John , Brooks Charles L.
Published: March 2004

Because of the association of β-sheet formation with the initiation and propagation of amyloid diseases, model systems have been sought to further our understanding of this process. WW domains have been proposed as one such model system. Whereas the folding of the WW domains from human Yes-associated protein (YAP) and Pin have been shown to obey single-exponential kinetics, the folding of the WW domain from formin-binding protein (FBP) 28 has been shown to proceed via biphasic kinetics. From an analysis of free-energy landscapes from atomic-level molecular dynamics simulations, the biphasic folding kinetics observed in the FBP WW domain may be traced to the ability of this WW domain to adopt two slightly different forms of packing in its hydrophobic core. This conformational change is propagated along the peptide backbone and affects the position of a tryptophan residue shown in other WW domains to play a key role in binding. The WW domains of Pin and YAP do not support more than one type of packing each, leading to monophasic folding kinetics. The ability of the FBP WW domain to assume two different types of packing may, in turn, explain the capacity of this WW domain to bind two classes of ligand, a property that is not shared by other WW domains. These findings lead to the hypothesis that lability with respect to conformations separated by an observable barrier as a requirement for function is incompatible with the ability of a protein to fold via single-exponential kinetics.
Isolation and characterization of a digoxin transporter and its rat homologue expressed in the kidney
Authors: Mikkaichi Tsuyoshi , Suzuki Takehiro , Onogawa Tohru , Tanemoto Masayuki , Mizutamari Hiroya , Okada Masahiro , Chaki Tatsuji , Masuda Satohiro , Tokui Taro , Eto Nobuaki , Abe Michiaki , Satoh Fumitoshi , Unno Michiaki , Hishinuma Takanori , Inui Ken-ichi , Ito Sadayoshi , Goto Junichi , Abe Takaaki
Published: March 2004

Digoxin, which is one of the most commonly prescribed drugs for the treatment of heart failure, is mainly eliminated from the circulation by the kidney. P-glycoprotein is well characterized as a digoxin pump at the apical membrane of the nephron. However, little is known about the transport mechanism at the basolateral membrane. We have isolated an organic anion transporter (OATP4C1) from human kidney. Human OATP4C1 is the first member of the organic anion transporting polypeptide (OATP) family expressed in human kidney. The isolated cDNA encodes a polypeptide of 724 aa with 12 transmembrane domains. The genomic organization consists of 13 exons located on chromosome 5q21. Its rat counterpart, Oatp4c1, is also isolated from rat kidney. Human OATP4C1 transports cardiac glycosides (digoxin,
K
m
= 7.8 μM and ouabain,
K
m
= 0.38 μM), thyroid hormone (triiodothyronine,
K
m
= 5.9 μM and thyroxine), cAMP, and methotrexate in a sodium-independent manner. Rat Oatp4c1 also transports digoxin (
K
m
= 8.0 μM) and triiodothyronine (
K
m
= 1.9 μM). Immunohistochemical analysis reveals that rat Oatp4c1 protein is localized at the basolateral membrane of the proximal tubule cell in the kidney. These data suggest that human OATP4C1/rat Oatp4c1 might be a first step of the transport pathway of digoxin and various compounds into urine in the kidney.
Geography, biogeography, and why some countries are rich and others are poor
Authors: Hibbs Douglas A. , Olsson Ola
Published: March 2004

The most important event in human economic history before the industrial revolution was the Neolithic transition from a nomadic hunter-gatherer lifestyle to sedentary agriculture, beginning ≈10,000 years ago. The transition made possible the human population explosion, the rise of non-food-producing specialists, and the acceleration of technological progress that led eventually to the industrial revolution. But the transition occurred at different times in different regions of the world, with big consequences for the present-day economic conditions of populations indigenous to each region. In this article, we show that differences in biogeographic initial conditions and in geography largely account for the different timings of the Neolithic transition and, thereby, ultimately help account for the 100-fold differences among the prosperity of nations today. The effects of biogeography and geography on the wealth of nations are partly mediated by the quality of present-day institutions but also are partly independent of institutional quality.
Solution structure of dengue virus capsid protein reveals another fold
Authors: Ma Lixin , Jones Christopher T. , Groesch Teresa D. , Kuhn Richard J. , Post Carol Beth
Published: March 2004

Dengue virus is responsible for ≈50–100 million infections, resulting in nearly 24,000 deaths annually. The capsid (C) protein of dengue virus is essential for specific encapsidation of the RNA genome, but little structural information on the C protein is available. We report the solution structure of the 200-residue homodimer of dengue 2 C protein. The structure provides, to our knowledge, the first 3D picture of a flavivirus C protein and identifies a fold that includes a large dimerization surface contributed by two pairs of helices, one of which has characteristics of a coiled-coil. NMR structure determination involved a secondary structure sorting approach to facilitate assignment of the intersubunit nuclear Overhauser effect interactions. The dimer of dengue C protein has an unusually high net charge, and the structure reveals an asymmetric distribution of basic residues over the surface of the protein. Nearly half of the basic residues lie along one face of the dimer. In contrast, the conserved hydrophobic region forms an extensive apolar surface at a dimer interface on the opposite side of the molecule. We propose a model for the interaction of dengue C protein with RNA and the viral membrane that is based on the asymmetric charge distribution of the protein and is consistent with previously reported results.
Structural availability influences the capacity of autoantigenic epitopes to induce a widespread lupus-like autoimmune response
Authors: McClain Micah T. , Lutz Carol S. , Kaufman Kenneth M. , Faig Ofer Z. , Gross Timothy F. , James Judith A.
Published: March 2004

A subset of lupus patients with severe nephritis and anti-nRNP reactivity produces autoantibodies primarily against two major epitopes of the nRNP A (also known as U1A) protein. These sequences span amino acids 44-56 (A3) and amino acids 103-115 (A6). These two epitopes represent structurally different regions of the protein, as both epitopes are located on the surface, but the A6 epitope is functionally maskedin vivoby binding between nRNP A and the U1 RNA. Rabbits were immunized with either the A3 or A6 peptides constructed on a branching polylysine backbone. Rabbits immunized with each of these peptides first developed antibodies directed against the peptide of immunization. With boosting, the immune response of rabbits immunized with the A3 peptide spread to other common antigenic regions of nRNP A. These regions of nRNP A bound by A3 immunized rabbits are very similar to common epitopes in human systemic lupus erythematosus. These A3 immunized rabbits also develop antibodies to common antigenic regions of nRNP 70K, nRNP C, Sm B/B′, and Sm D1 proteins, as well as clinical symptoms of systemic lupus erythematosus such as leukopenia and renal insufficiency. On the other hand, rabbits immunized with the A6 peptide only develop antibodies to the peptide of immunization. Anti-A3, but not anti-A6, antibodies are capable of immunoprecipitating native small nuclear ribonucleoprotein complexes. Immunization with the A3 peptide of nRNP A (a surface epitope), but not the A6 peptide (masked), induces an extensive, varied immune response against multiple small nuclear ribonucleoprotein autoantigens similar to that seen in human systemic lupus erythematosus.
High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal
Authors: Aguilar Andres , Roemer Gary , Debenham Sally , Binns Matthew , Garcelon David , Wayne Robert K.
Published: March 2004

The San Nicolas Island fox (
Urocyon littoralis dickeyi
) is genetically the most monomorphic sexually reproducing animal population yet reported and has no variation in hypervariable genetic markers. Such low levels of variation imply lower resistance to pathogens, reduced fitness, and problems in distinguishing kin from non-kin. In vertebrates, the MHC contains genes that influence disease resistance and kin recognition and may be under intense balancing selection in some populations. Hence, genetic variation at the MHC might persist despite the extreme monomorphism shown by neutral markers. We examine variation of five loci within the MHC of San Nicolas Island foxes and find remarkably high levels of variation. Further, we show by simulation that genetic monomorphism at neutral loci and high MHC variation could arise only through an extreme population bottleneck of <10 individuals, ≈10–20 generations ago, accompanied by unprecedented selection coefficients of >0.5 on MHC loci. These results support the importance of balancing selection as a mechanism to maintain variation in natural populations and expose the difficulty of using neutral markers as surrogates for variation in fitness-related loci.
The cardiovascular physiologic actions of urocortin II: Acute effects in murine heart failure
Authors: Bale Tracy L. , Hoshijima Masahiko , Gu Yusu , Dalton Nancy , Anderson Keith R. , Lee Kuo-Fen , Rivier Jean , Chien Kenneth R. , Vale Wylie W. , Peterson Kirk L.
Published: March 2004

Corticotropin-releasing factor (CRF) and its paralogues urocortin (Ucn)I, -II, and -III signal by activating their receptors, CRF receptors (CRFR)1 and -2, to maintain homeostasis through endocrine, autonomic, and behavioral responses. CRFR2 is found in cardiomyocytes and in endothelial and smooth muscle cells of the systemic vasculature. Echocardiography and cardiac catheterization were used in mice to assess the physiologic effects of i.v. UcnII and CRFR2 deficiency on left ventricular function and the systemic vasculature. UcnII treatment augmented heart rate, exhibited potent inotropic and lusitropic actions on the left ventricle, and induced a downward shift of the diastolic pressure-volume relation. UcnII also reduced systemic arterial pressure, associated with a lowering of systemic arterial elastance (end-systolic pressure/stroke volume) and systemic vascular resistance. CRFR2-deficient mice showed no alteration in cardiac contractility or blood pressure in response to UcnII administration, suggesting that the effects of UcnII are specific to CRFR2 function. Pretreatment with a β-adrenergic receptor antagonist, esmalol, had no effect on the inotropic or lusitropic effects of UcnII
in vivo
, indicating that its actions are independent of β-adrenergic receptors. Single i.v. bolus administration of UcnII to a heart failure model (muscle-specific LIM protein-deficient mice) produced significant enhancement of inotropic and lusitropic effects on left ventricular function and improved cardiac output. These results demonstrate the potent cardiovascular physiologic actions of UcnII in both wild-type and cardiomyopathic mice and support a potential beneficial use of this peptide in therapy of congestive heart failure.
Differential tumor necrosis factor receptor 2-mediated editing of virus-specific CD8+effector T cells
Authors: Turner Stephen J. , La Gruta Nicole L. , Stambas John , Diaz Gabriela , Doherty Peter C.
Published: March 2004

Much of the CD8+T cell response in H2bmice with influenza pneumonia is directed at the nucleoprotein366-374(NP366) and acid polymerase224-233(PA224) peptides presented by the H2DbMHC class I glycoprotein. These DbNP366- and DbPA224-specific T cell populations are readily analyzed by staining with tetrameric complexes of MHC+peptide (tetramers) or by cytokine production subsequent toin vitrostimulation with the cognate peptides. The DbPA224-specific CD8+effector T cells make more tumor necrosis factor (TNF) α than the comparable CD8+DbNP366+set, a difference reflected in the greater sensitivity of the CD8+DbPA224+population to TNF receptor (TNFR) 2-mediated apoptosis under conditions ofin vitroculture. Freshly isolated CD8+DbNP366+and CD8+DbPA224+T cells from influenza-infected TNFR2-/-mice produce higher levels of IFN-γ and TNF-α afterin vitrostimulation with peptide, although the avidity of the T cell receptor-epitope interaction does not change. Increased numbers of both CD8+DbPA224+and CD8+DbNP366+T cells were recovered from the lungs (but not the spleens) of secondarily challenged TNFR2-/-mice, a pattern that correlates with the profiles of TNFR expression in the TNFR2+/+controls. Thus, it seems that TNFR2-mediated editing of influenza-specific CD8+T cells functions to limit the numbers of effectors that have localized to the site of pathology in the lung but does not modify the size of the less activated responder T cell populations in the spleen. Therefore, the massive difference in magnitude for the secondary, although not the primary, response to these DbNP366and DbPA224epitopes cannot be considered to reflect differential TNFR2-mediated T cell editing.
The role of the allosteric B site in the fumarase reaction
Authors: Rose Irwin A. , Weaver Todd M.
Published: March 2004

The role of a malate binding site in a concavity external to the more deeply situated active site has been a major mystery of the fumarase reaction. The malate, within 12 Å of the active site, was bound by hydrogen bonds to two main-chain amides and to two basic residues, H129 and R126. Mutation of the His of this so-called B site of
Escherichia coli
fumarase had little effect on the overall initial rate kinetics of the enzyme, which has obscured an understanding of the critical role of the site. Contrary to the WT enzyme, which is rate-limited in the recycling of free enzyme isoforms that follows product release, the enzyme with both basic residues modified is rate-limited in the product release step itself. A loss of complexity in the mutated, but still functional, step is indicated by a greatly reduced sensitivity of its rate to changes in temperature. Unlike the inhibition by glycerol shown with normal enzyme and attributed to a viscogenic effect on the recycling rate, the product-release step of the B-site mutants is accelerated by glycerol, suggestive of a structural effect on the 12-Å space between the A and B sites. It is proposed that the “extra” malate represents a stage in the transfer of substrate and product between the solvent and the “buried” active site of the enzyme.
Codon usage between genomes is constrained by genome-wide mutational processes
Authors: Chen Swaine L. , Lee William , Hottes Alison K. , Shapiro Lucy , McAdams Harley H.
Published: March 2004

Analysis of genome-wide codon bias shows that only two parameters effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms. The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. Both of these parameters may be calculated from intergenic sequences. Therefore, genome-wide codon bias in eubacteria and archaea may be predicted from intergenic sequences that are not translated. When these two parameters are calculated for genes from nonmammalian eukaryotic organisms, genes from the same organism again have similar values, and genome-wide codon bias may also be predicted from intergenic sequences. In mammals, genes from the same organism are similar only in the second parameter, because GC content varies widely among isochores. Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences.
Biological glass fibers: Correlation between optical and structural properties
Authors: Aizenberg Joanna , Sundar Vikram C. , Yablon Andrew D. , Weaver James C. , Chen Gang
Published: March 2004

Biological systems have, through the course of time, evolved unique solutions for complex optical problems. These solutions are often achieved through a sophisticated control of fine structural features. Here we present a detailed study of the optical properties of basalia spicules from the glass sponge
Euplectella aspergillum
and reconcile them with structural characteristics. We show these biosilica fibers to have a distinctive layered design with specific compositional variations in the glass/organic composite and a corresponding nonuniform refractive index profile with a high-index core and a low-index cladding. The spicules can function as single-mode, few-mode, or multimode fibers, with spines serving as illumination points along the spicule shaft. The presence of a lens-like structure at the end of the fiber increases its light-collecting efficiency. Although free-space coupling experiments emphasize the similarity of these spicules to commercial optical fibers, the absence of any birefringence, the presence of technologically inaccessible dopants in the fibers, and their improved mechanical properties highlight the advantages of the low-temperature synthesis used by biology to construct these remarkable structures.
The tumor suppressor LKB1 kinase directly activates AMP-activated kinase and regulates apoptosis in response to energy stress
Authors: Shaw Reuben J. , Kosmatka Monica , Bardeesy Nabeel , Hurley Rebecca L. , Witters Lee A. , DePinho Ronald A. , Cantley Lewis C.
Published: March 2004

AMP-activated protein kinase (AMPK) is a highly conserved sensor of cellular energy status found in all eukaryotic cells. AMPK is activated by stimuli that increase the cellular AMP/ATP ratio. Essential to activation of AMPK is its phosphorylation at Thr-172 by an upstream kinase, AMPKK, whose identity in mammalian cells has remained elusive. Here we present biochemical and genetic evidence indicating that the LKB1 serine/threonine kinase, the gene inactivated in the Peutz-Jeghers familial cancer syndrome, is the dominant regulator of AMPK activation in several mammalian cell types. We show that LKB1 directly phosphorylates Thr-172 of AMPKα
in vitro
and activates its kinase activity. LKB1-deficient murine embryonic fibroblasts show nearly complete loss of Thr-172 phosphorylation and downstream AMPK signaling in response to a variety of stimuli that activate AMPK. Reintroduction of WT, but not kinase-dead, LKB1 into these cells restores AMPK activity. Furthermore, we show that LKB1 plays a biologically significant role in this pathway, because LKB1-deficient cells are hypersensitive to apoptosis induced by energy stress. On the basis of these results, we propose a model to explain the apparent paradox that LKB1 is a tumor suppressor, yet cells lacking LKB1 are resistant to cell transformation by conventional oncogenes and are sensitive to killing in response to agents that elevate AMP. The role of LKB1/AMPK in the survival of a subset of genetically defined tumor cells may provide opportunities for cancer therapeutics.
Presynaptic homeostasis at CNS nerve terminals compensates for lack of a key Ca
2+
entry pathway
Authors: Piedras-Rentería Erika S. , Pyle Jason L. , Diehn Max , Glickfeld Lindsey L. , Harata Nobutoshi C. , Cao Yuqing , Kavalali Ege T. , Brown Patrick O. , Tsien Richard W.
Published: March 2004

At central synapses, P/Q-type Ca
2+
channels normally provide a critical Ca
2+
entry pathway for neurotransmission. Nevertheless, we found that nerve terminals lacking α
1A
(Ca
V
2.1), the pore-forming subunit of P/Q-type channels, displayed a remarkable preservation of synaptic function. Two consistent physiological changes reflective of synaptic homeostasis were observed in cultured hippocampal neurons derived from α
1A
(-/-) mice. First, the presynaptic response to an ionophore-mediated Ca
2+
elevation was 50% greater, indicating an enhanced Ca
2+
sensitivity of the release machinery. Second, basal miniature excitatory postsynaptic current frequency in α
1A
(-/-) neurons was increased 2-fold compared with WT neurons and occluded the normal response of presynaptic terminals to cAMP elevation, suggesting that the compensatory mechanism in α
1A
(-/-) synapses and the modulation of presynaptic function by PKA might share a final common pathway. We used cDNA microarray analysis to identify molecular changes underlying homeostatic regulation in the α
1A
(-/-) hippocampus. The 40,000 entries in our custom-made array included likely targets of presynaptic homeostasis, along with many other transcripts, allowing a wide-ranging examination of gene expression. The developmental pattern of changes in transcript levels relative to WT was striking; mRNAs at 5 and 11 days postnatal showed little deviation, but clear differences emerged by 22 days. Many of the transcripts that differed significantly in abundance corresponded to known genes that could be incorporated within a logical pattern consistent with the modulation of presynaptic function. Changes in endocytotic proteins, signal transduction kinases, and candidates for Ca
2+
-sensing molecules were consistent with implications of the direct physiological experiments.
Delay accuracy in bat sonar is related to the reciprocal of normalized echo bandwidth, or
Q
Authors: Simmons James A. , Neretti Nicola , Intrator Nathan , Altes Richard A. , Ferragamo Michael J. , Sanderson Mark I.
Published: March 2004

Big brown bats (
Eptesicus fuscus
) emit wideband, frequency-modulated biosonar sounds and perceive the distance to objects from the delay of echoes. Bats remember delays and patterns of delay from one broadcast to the next, and they may rely on delays to perceive target scenes. While emitting a series of broadcasts, they can detect very small changes in delay based on their estimates of delay for successive echoes, which are derived from an auditory time/frequency representation of frequency-modulated sounds. To understand how bats perceive objects, we need to know how information distributed across the time/frequency surface is brought together to estimate delay. To assess this transformation, we measured how alteration of the frequency content of echoes affects the sharpness of the bat's delay estimates from the distribution of errors in a psychophysical task for detecting changes in delay. For unrestricted echo frequency content and high echo signal-to-noise ratio, bats can detect extremely small changes in delay of about 10 ns. When echo bandwidth is restricted by filtering out low or high frequencies, the bat's delay acuity declines in relation to the reciprocal of relative echo bandwidth, expressed as
Q
, which also is the relative width of the target impulse response in cycles rather than time. This normalized-time dimension may be efficient for target classification if it leads to target shape being displayed independent of size. This relation may originate from cochlear transduction by parallel frequency channels with active amplification, which creates the auditory time/frequency representation itself.
Inhibition of neuronal phenotype by PTEN in PC12 cells
Authors: Musatov Sergei , Roberts Jill , Brooks Andrew I. , Pena John , Betchen Simone , Pfaff Donald W. , Kaplitt Michael G.
Published: March 2004

The mechanisms of neuronal differentiation in PC12 cells are still not completely understood. Here, we report that the tumor suppressor PTEN has a profound effect on differentiation by affecting several pathways involved in nerve growth factor (NGF) signaling. When overexpressed in PC12 cells, PTEN (phosphatase and tensin homologue deleted on chromosome ten) blocked neurite outgrowth induced by NGF. In addition, these cells failed to demonstrate the transient mitogenic response to NGF, as well as subsequent growth arrest. Consistent with these observations was a finding that PTEN significantly inhibits NGF-mediated activation of the members of mitogen-activated protein kinase kinase (MEK)/mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)/AKT signaling pathways, crucial for these processes. While exploring possible mechanisms of PTEN effects on NGF signaling, we discovered a significant down-regulation of both high-affinity (TrkA) and low-affinity (p75) NGF receptors in PTEN-overexpressing clones. Subsequent microarray analysis of several independent clonal isolates revealed a myriad of neuronal genes to be affected by PTEN. All of these changes were validated by quantitative PCR. Of particular interest were the genes for the key enzymes of the dopamine synthesis pathway, receptors for different neurotransmitters, and neuron-specific cytoskeleton proteins, among others. Some, but not all effects could be reproduced by pharmacological inhibitors of PI3K and/or MAPK, suggesting that PTEN may influence some genes by mechanisms independent of these signaling pathways. Our findings may shed new light on the role of this tumor suppressor during normal brain development and suggest a previously uncharacterized mechanism of PTEN action in neuron-like cells.
Missing self-recognition of Ocil/Clr-b by inhibitory NKR-P1 natural killer cell receptors
Authors: Carlyle James R. , Jamieson Amanda M. , Gasser Stephan , Clingan Christopher S. , Arase Hisashi , Raulet David H.
Published: March 2004

The NKR-P1 family of C-type lectin-like receptors are expressed on natural killer (NK) cells and NKT cells. We report the cloning and characterization of a cognate ligand for the inhibitory mouse NK receptors (NKR)-P1B and NKR-P1D (CD161b/d). The NKR-P1B/D ligand is osteoclast inhibitory lectin (Ocil), also known as Clr-b, a member of a previously cloned group of C-type lectin-related (Clr) proteins linked to the NKR-P1 receptors in the mouse NK gene complex (NKC). Expression of Ocil/Clr-b on mouse tumor cell lines inhibits NK cell-mediated killing. Inhibition is blocked with a new mAb (4A6) specific for Ocil/Clr-b. By using 4A6 mAb, we demonstrate that Ocil/Clr-b is displayed at high levels on nearly all hematopoietic cells, with the exception of erythrocytes, in a pattern that is similar to that of class I MHC molecules. Remarkably, Ocil/Clr-b is frequently down-regulated on mouse tumor cell lines, indicating a role for this receptor-ligand system in a new form of “missing self-recognition” of tumor cells.
Vitamin C controls the cystic fibrosis transmembrane conductance regulator chloride channel
Authors: Fischer Horst , Schwarzer Christian , Illek Beate
Published: March 2004

Vitamin C (l-ascorbate) is present in the respiratory lining fluid of human lungs, and local deficits occur during oxidative stress. Here we report a unique function of vitamin C on the cystic fibrosis (CF) transmembrane conductance regulator (CFTR), a cAMP-dependent Cl channel that regulates epithelial surface fluid secretion. Vitamin C (100 μM) induced the openings of CFTR Cl channels by increasing its average open probability from 0 to 0.21 ± 0.08, without a detectable increase in intracellular cAMP levels. Exposure of the apical airway surface to vitamin C stimulated the transepithelial Cl secretion to 68% of forskolin-stimulated currents. The average half-maximal stimulatory constant was 36.5 ± 2.9 μM, which corresponds to physiological concentrations. When vitamin C was instilled into the nasal epithelium of human subjects, it effectively activated Cl transportin vivo. In CF epithelia, previous treatment of the underlying trafficking defect with trimethylamine oxide or expression of WT CFTR restored the activation of Cl transport by vitamin C. Sodium dependency and phloretin sensitivity, as well as the expression of transcripts for sodium-dependent vitamin C transporter (SVCT)-1 and SVCT2, support a model in which an apical vitamin C transporter is central for relaying the effect of vitamin C to CFTR. We conclude that cellular vitamin C is a biological regulator of CFTR-mediated Cl secretion in epithelia. The pool of vitamin C in the respiratory tract represents a potential nutraceutical and pharmaceutical target for the complementary treatment of sticky airway secretions by enhancing epithelial fluid secretion.
Toll-like receptor 3-mediated activation of NF-κB and IRF3 diverges at Toll-IL-1 receptor domain-containing adapter inducing IFN-β
Authors: Jiang Zhengfan , Mak Tak W. , Sen Ganes , Li Xiaoxia
Published: March 2004

We have previously shown that double-stranded RNA-triggered, Toll-like receptor 3 (TLR3)-mediated signaling is independent of MyD88, IRAK4, and IRAK. Instead, TRAF6, TAK1, and TAB2 are recruited to TLR3 on poly(I·C) stimulation. TRAF6-TAK1-TAB2 are then translocated to the cytosol where TAK1 is phosphorylated and activated, leading to the activation of IκB kinase and NFκB. The present study addressed two important questions: (
i
) How are TRAF6, TAK1, and TAB2 recruited to TLR3? (
ii
) Are TRAF6, TAK1, and TAB2 also required for TLR3-mediated IRF3 activation? Recently, a novel Toll-IL-1 receptor (TIR)-containing adapter, TIR domain-containing adapter inducing IFN-β (TRIF), was shown to play a critical role in TLR3-mediated activation of NF-κB and IRF3. We found that TLR3 recruits TRAF6 via adapter TRIF through a TRAF6-binding sequence in TRIF (PEEMSW, amino acids 250-255). Mutation of this TRAF6-binding sequence abolished the interaction of TRIF with TRAF6, but not with TLR3. Interestingly, mutation of the TRAF6-binding site of TRIF only abolished its ability to activate NF-κB but not IRF3, suggesting that TLR3-mediated activation of NF-κB and IRF3 might bifurcate at TRIF. In support of this finding, we showed that DN-TRAF6 and DN-TAK1 blocked poly(I·C)-induced NF-κB but not IRF3 activation. Furthermore, whereas poly(I·C)-induced NF-κB activation is completely abolished inTRAF6-/- MEFs, the signal-induced activation of IRF3 is TRAF6 independent. In conclusion, TRIF recruits TRAF6-TAK1-TAB2 to TLR3 through its TRAF6-binding site, which is required for NF-κB but not IRF3 activation. Therefore, double-stranded RNA-induced TLR3/TRIF-mediated NF-κB and IRF3 activation diverge at TRIF.
Identification of p53 regulators by genome-wide functional analysis
Authors: Huang Qihong , Raya Angel , DeJesus Paul , Chao Sheng-Hao , Quon Kim C. , Caldwell Jeremy S. , Chanda Sumit K. , Izpisua-Belmonte Juan C. , Schultz Peter G.
Published: March 2004

The p53 tumor-suppressor protein is a critical mediator of cellular growth arrest and the induction of apoptosis. To identify proteins involved in the modulation of p53 transcriptional activity, a gain-of-function cellular screen was carried out with an arrayed matrix of ≈20,000 cDNAs. Nine genes previously unknown to be involved in regulating p53 activity were identified. Overexpression of seven of these genes (
Hey1
,
Hes1
,
TFAP4
,
Osr1
,
NR2F2
,
SFRS10
, and
FLJ11339
) resulted in up-regulation of p53 activity; overexpression of two genes (
M17S2
and
cathepsin B
) resulted in down-regulation of p53 activity in mammalian cells. HES1, HEY1, and TFAP4, which are members of the basic helix–loop–helix transcription family, and OSR1 were shown to activate p53 through repression of HDM2 transcription. Ectopic expression of these basic helix–loop–helix transcription factors in both zebrafish and avian developmental systems activated p53 and induced apoptosis
in vivo
, resulting in a phenotype similar to that of p53 overexpression. Furthermore,
ras
- and
myc
-mediated transformation of mouse embryonic fibroblasts was abrogated by expression of HEY1 in a p53-dependent manner. These results suggest that these transcription factors are members of an evolutionarily conserved network that governs p53 function.
Venezuelan kindreds reveal that genetic and environmental factors modulate Huntington's disease age of onset
Authors:   The U.S.–Venezuela Collaborative Research Project*, Wexler Nancy S.
Published: March 2004

Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by a triplet (CAG) expansion mutation. The length of the triplet repeat is the most important factor in determining age of onset of HD, although substantial variability remains after controlling for repeat length. The Venezuelan HD kindreds encompass 18,149 individuals spanning 10 generations, 15,409 of whom are living. Of the 4,384 immortalized lymphocyte lines collected, 3,989 DNAs were genotyped for their HD alleles, representing a subset of the population at greatest genetic risk. There are 938 heterozygotes, 80 people with variably penetrant alleles, and 18 homozygotes. Analysis of the 83 kindreds that comprise the Venezuelan HD kindreds demonstrates that residual variability in age of onset has both genetic and environmental components. We created a residual age of onset phenotype from a regression analysis of the log of age of onset on repeat length. Familial correlations (correlation ± SE) were estimated for sibling (0.40 ± 0.09), parent-offspring (0.10 ± 0.11), avuncular (0.07 ± 0.11), and cousin (0.15 ± 0.10) pairs, suggesting a familial origin for the residual variance in onset. By using a variance-components approach with all available familial relationships, the additive genetic heritability of this residual age of onset trait is 38%. A model, including shared sibling environmental effects, estimated the components of additive genetic (0.37), shared environment (0.22), and nonshared environment (0.41) variances, confirming that ≈40% of the variance remaining in onset age is attributable to genes other than the HD gene and 60% is environmental.
Intestinal inflammation in mice deficient in
Tir8
, an inhibitory member of the IL-1 receptor family
Authors: Garlanda Cecilia , Riva Federica , Polentarutti Nadia , Buracchi Chiara , Sironi Marina , De Bortoli Maida , Muzio Marta , Bergottini Raffaella , Scanziani Eugenio , Vecchi Annunciata , Hirsch Emilio , Mantovani Alberto
Published: March 2004

TIR8, also known as single Ig IL-1-related receptor, is a member of the IL-1 receptor/Toll-like receptor (TLR) superfamily, which acts as an intracellular decoy for components of the signaling pathway. Here we report that
Tir8
has a unique pattern of expression, which includes mucosal tissues and dendritic cells (DC).
Tir8
-deficient DC showed increased cytokine production in response to TLR agonists (lipopolysaccharide, CpG oligodeoxynucleotides).
Tir8
-deficient mice had normal susceptibility to systemic lipopolysaccharide toxicity and to i.p. or s.c. inflammation. However,
Tir8
-deficient mice were more susceptible to intestinal inflammation. Thus, TIR8 represents a negative pathway of regulation of the IL-1 receptor/TLR system, expressed in epithelial cells and DC, crucial for tuning inflammation in the gastrointestinal tract.
Inactivation of a
Pseudomonas aeruginosa
quorum-sensing signal by human airway epithelia
Authors: Chun Carlene K. , Ozer Egon A. , Welsh Michael J. , Zabner Joseph , Greenberg E. P.
Published: March 2004

Mammalian airways protect themselves from bacterial infection by using multiple defense mechanisms including antimicrobial peptides, mucociliary clearance, and phagocytic cells. We asked whether airways might also target a key bacterial cell-cell communication system, quorum-sensing. The opportunistic pathogen
Pseudomonas aeruginosa
uses two quorum-sensing molecules,
N
-(3-oxododecanoyl)-
l
-homoserine lactone (3OC12-HSL) and
N
-butanoyl-
l
-homoserine lactone (C4-HSL), to control production of extracellular virulence factors and biofilm formation. We found that differentiated human airway epithelia inactivated 3OC12-HSL. Inactivation was selective for acyl-HSLs with certain acyl side chains, and C4-HSL was not inactivated. In addition, the capacity for inactivation varied widely in different cell types. 3OC12-HSL was inactivated by a cell-associated activity rather than a secreted factor. These data suggest that the ability of human airway epithelia to inactivate quorum-sensing signal molecules could play a role in the innate defense against bacterial infection.
Overexpression of acid-sensing ion channel 1a in transgenic mice increases acquired fear-related behavior
Authors: Wemmie John A. , Coryell Matthew W. , Askwith Candice C. , Lamani Ejvis , Leonard A. Soren , Sigmund Curt D. , Welsh Michael J.
Published: March 2004

The acid-sensing ion channel 1a (ASIC1a) is abundantly expressed in the amygdala complex and other brain regions associated with fear. Studies of mice with a disruptedASIC1gene suggested that ASIC1a may contribute to learned fear. To test this hypothesis, we generated mice overexpressing human ASIC1a by using the pan-neuronal synapsin 1 promoter. Transgenic ASIC1a interacted with endogenous mouse ASIC1a and was distributed to the synaptosomal fraction of brain. Transgenic expression of ASIC1a also doubled neuronal acid-evoked cation currents. The amygdala showed prominent expression, and overexpressing ASIC1a enhanced fear conditioning, an animal model of acquired anxiety. These data raise the possibility that ASIC1a and H+-gated currents may contribute to the development of abnormal fear and to anxiety disorders in humans.
Expression and activation of the farnesoid X receptor in the vasculature
Authors: Bishop-Bailey David , Walsh Desmond T. , Warner Timothy D.
Published: March 2004

The farnesoid X receptor/bile acid receptor (FXR) is a recently discovered member of the nuclear hormone superfamily. FXR ligands have been proposed as targets in cardiovascular disease, regulating cholesterol metabolism and bile acid transport and metabolism in the liver and gastrointestinal tract. When we used a human cardiovascular tissue array, we found that FXR is expressed in a variety of normal and pathological human tissue. Particularly high levels of FXR were found in the vasculature and in a number of different metastatic cancers, as well as the previously identified target tissues of the liver, small intestine, and kidney.
In vitro
, FXR is present in rat and human vascular smooth muscle cells. When treated with a range of FXR ligands, vascular smooth muscle cells undergo apoptosis in a manner that correlates with the ligands' ability to activate FXR. Furthermore, FXR activators induce mRNA for the FXR target genes, phospholipid transfer protein, and the small heterodimer partner. FXR therefore is a functional protein in the vasculature that may provide a direct target for the treatment of proliferative and dyslipidaemic diseases.
Structural mechanism for affinity maturation of an anti-lysozyme antibody
Authors: Cauerhff Ana , Goldbaum Fernando A. , Braden Bradford C.
Published: March 2004

In the immune response against a typical T cell-dependent protein antigen, the affinity maturation process is fast and is associated with the early class switch from IgM to IgG. As such, a comprehension of the molecular basis of affinity maturation could be of great importance in biomedical and biotechnological applications. Affinity maturation of anti-protein antibodies has been reported to be the result of small structural changes, mostly confined to the periphery of the antigen-combining site. However, little is understood about how these small structural changes account for the increase in the affinity toward the antigen. Herein, we present the three-dimensional structure of the Fab fragment from BALB/c mouse mAb F10.6.6 in complex with the antigen lysozyme. This antibody was obtained from a long-term exposure to the antigen. mAb F10.6.6, and the previously described antibody D44.1, are the result of identical or nearly identical somatic recombination events. However, different mutations in the framework and variable regions result in an ≈103higher affinity for the F10.6.6 antibody. The comparison of the three-dimensional structures of these Fab-lysozyme complexes reveals that the affinity maturation produces a fine tuning of the complementarity of the antigen-combining site toward the epitope, explaining at the molecular level how the immune system is able to increase the affinity of an anti-protein antibody to subnanomolar levels.