bluuebunny/crossref_metadata_2025 huggingface dataset:
Viscous flow in smectic A liquid crystals
Authors: DeGennes P. G.
Published: February 2004

Smectics A are fluid, layered, materials which obey Darcy's law for flow normal to the layers, and an equation of the Navier-Stokes type in the other two directions. The slow motions of various solid bodies inside a smectic are discussed, assuming that the layers are not distorted around the solid at rest. The flow pattern depends on a dimensionless parameter κL = S where L is the size of the object and κ−1 is a characteristic length of the smectic fluid. Only the limit S ≫ 1 is considered. Depending on the shape of the object and on the direction of motion, either a velocity field confined to the smectic planes, but not very different from the Stokes flow in viscous fluids, or a “permeation layer” of thickness δ ∼ κ−1/2L1/2 is found. In the latter case the drag is strongly enhanced. The idea of a permeation layer is also applied to a discussion of the undulation mode of a smectic sample between fixed plates, which has recently been studied by inelastic scattering of light.
Resonant oscillations of a porous plate in an electrically conducting rotating viscous fluid
Authors: Debnath Lokenath
Published: February 2004

An unsteady analysis is made of the nontorsionally generated hydromagnetic flow in a semiinfinite expanse of an electrically conducting rotating viscous fluid bounded by an infinite nonconducting porous plate with uniform suction or blowing in the presence of a transverse uniform magnetic field. The structure of the steady and the unsteady velocity distributions and the associated hydromagnetic multiple boundary layers are investigated including the case of blowing and resonant oscillations. Both the steady and the unsteady velocity fields describe the general features of the hydromagnetic boundary layer flows in the rotating fluid including the effects of uniform suction or blowing for all frequencies of oscillations of the plate. Unlike the hydrodynamic situation for the case of blowing and resonance, the hydromagnetic steady-state solution satisfies the boundary condition at infinity and the associated boundary layers are confined to the plate. The inherent difficulty involved in the purely hydrodynamic problem associated with the case of blowing and the resonant frequency has been resolved in this paper by the addition of the magnetic field.
Control of density correlations in laser-heated plasma
Authors: Steiger A. D. , Woods C. H.
Published: February 2004

The excitation of plasma density perturbations of selected wavenumber spectra by two oppositely directed short-wavelength laser beams and the simultaneous interaction with these perturbations of a long-wavelength laser beam whose frequency is comparable to the electron Langmuir frequency is analyzed. Perturbations of the plasma density having a spatial period equal to one-half the wavelength of the short-wavelength beams are produced at zero frequency, and at the ion-acoustic frequency. The third beam excites the oscillating two-stream instability and the ion-acoustic decay instability, so that these initial perturbations will grow rapidly and dominate the density fluctuation spectrum. The present scheme may be useful in avoiding superthermal electrons that are typically produced when radiation from a single beam is absorbed and long-wavelength density fluctuations become significant.
Energy input into a gas enclosed Z-pinch
Authors: Manheimer Wallace M.
Published: February 2004

In a gas-enclosed Z-pinch experiment, energy is coupled from an external circuit by rapid buildup of a confining field. From the basic energetics, one can calculate the necessary current rise times for maintenance of equilibrium as a thermonuclear pinch is being formed. If the rise time is too slow, the Ohmic heating of the plasma will be fast compared with the buildup of the confining field, and it will blow out; if too fast, the confining field will build up before the plasma can heat appreciably. In the early phase of heating, very short rise times are needed (nanoseconds) so that the initial tendency of the plasma is to blow outward.
Stability of a shear layer in a viscous fluid
Authors: Roberts B.
Published: February 2004

It is pointed out that a transformation used in a shear flow problem arising in magnetohydrodynamics may also be used in other shear flow problems. This is illustrated by considering the stability of a thermally stratified flow.
Investigation by electro-ultrafiltration on N and P distribution in rhizosphere and bulk soil of field-grown corn
Authors: Arienzo Michele , Meo Vincenzo Di , Adamo Paola , Violante Pietro
Published: February 2004

The distribution of available levels of N and P in rhizosphere and bulk soils of field-grown corn (Zea mays cv. Forban 300) in response to N, P, K fertiliser supply was investigated by electro-ultrafiltration (EUF). This technique allowed 3 operationally defined nutrient fractions to be extracted: soluble and immediately available (EUF-I), available (EUF-II), and retained reserve (EUF-III). For nitrogen, the NO3– and NH4+ forms were measured in the EUF extracts. The investigation was carried out providing N, N+P, N+K, and N+K+P. The results indicated that only at 40 days after sowing (DAS), rhizosphere soil was significantly less alkaline than bulk soil and characterised by higher organic carbon levels that increased with crop age. The slightly more acidic environment of the rhizosphere at 40 DAS seemed to be related to the lower levels of EUF-N-NH4+ fractions of rhizosphere soil (0.1–3.2 mg NH4+/kg) relative to bulk soil (0.5–4.9 mg NH4+/kg), with more significant differences observed for the soluble NH4+ pool, EUF-I, and when N was combined with P (N+P) or K (N+K). The extensive nitrification of NH4+ and the initially greater availability of NO3– accounted for the larger extraction of NO3– in the EUF-I-NO3– fraction at 40 DAS. The levels of labile extracted NO3– were ~8 times greater than EUF-II and EUF-III fractions, with significantly higher values of 27.4 (rhizosphere soil) and 18.8 mg NO3–/kg (bulk soil) for the N+P treatment. Due to plant uptake, at 40 DAS the EUF-I-NO3– fraction of rhizosphere soil was also the only pool significantly (P�< 0.05) lower than bulk soil, with differences that for N+P treatment were in excess of 45%. Later, at 60–120 DAS, during maximum corn nutrient demand, the levels of all of the EUF-N-NO3– fractions became higher in bulk soil. The pool of labile P, EUF-I-P, was higher in the rhizosphere soil and related to pH lowering, which occurred especially at 40 DAS and fell below the adequate level indicated by the ratio EUF-II-P/EUF-I-P. The use of the EUF methodology allowed a rough estimate of the amounts of different available nutrients of the studied soil as well as of their relationships with soil properties. Issues of rhizosphere sampling in situ were considered and discussed.
Analysis of turbulent flow patterns of soil water under field conditions using Burgers equation and porous suction-cup samplers
Authors: Su Ninghu , Watt Jim P. C. , Vincent Keith W. , Close Murray E. , Mao Renzhao
Published: February 2004

This paper presents results using the Burgers equation in spherical coordinates for the investigation of soil water dynamics around porous cup samplers under field conditions. The analysis reveals that the yield (V) of the porous suction-cup sampler is a power function of inflow duration (T) and source moisture strength (A). It also shows that the shock front velocity and moving boundary of the front are both power functions of A and time. The analysis further demonstrates that the asymptotic shock front velocity derived from a similarity solution is the same for different versions of Burgers equation, indicating the validity of different versions of Burgers equation for the same flow patterns. The observation using time domain reflectometry shows that a moisture shock was induced around the sampler following application of a vacuum, which justifies the application of Burgers equation. The values of A were derived using field data to determine the location and the front velocity of the shock.
Silver ion desorption kinetics from iron oxides and soil organic matter: effect of adsorption period
Authors: Li Jian , Rate Andrew W. , Gilkes Robert J.
Published: February 2004

In order to have a better understanding of the mobility and bioavailability of silver in the environment, it is important to investigate the desorption behaviour of silver from some environmentally relevant soil components. Four single soil constituents (charcoal, humic acid, ferrihydrite, goethite) were chosen to investigate the rate of desorption of silver ions. The effect of reaction period between silver and the soil constituents on subsequent desorption was also investigated. A significant proportion of Ag+ sorbed by Fe oxides, humic acid, and charcoal cannot readily be desorbed back into solution. For goethite and humic acid, a longer contact period between Ag+ and the adsorbing phase caused subsequent slower rates of desorption, and a smaller proportion of adsorbed Ag+ was desorbed back into solution. Two-site and log-normal equations, assuming the desorption reaction was first-order, gave excellent fits to experimental data, except for Ag+ desorption from charcoal, in which case the kinetic experimental data fitted to a 1-site model better. The parameters obtained from the modelling provide information regarding the possible changes in metal–oxide binding and metal–humic acid complexing mechanisms, and these changes can be interpreted as a re-arrangement of Ag ions to sites with slower desorption reaction rates. All the reaction sites on charcoal have very similar desorption rates (rate constants), and these sites are relatively slow to desorb Ag. Fe oxides, and humic acid and charcoal could be very important sinks for Ag. The longer the Ag interacts with soils in environment, the less mobile Ag becomes, and the less toxic and bioavailable it will be to living organisms.
Herbicide loss in runoff: effects of herbicide properties, slope, and rainfall intensity
Authors: Müller K. , Trolove M. , James T. K. , Rahman A.
Published: February 2004

Runoff potential of 5 herbicides (acetochlor, atrazine, hexazinone, pendimethalin, and terbuthylazine) was evaluated in a small-scale study under simulated rainfall on a cultivated Hamilton clay loam soil. At 24 h after herbicide application, rainfall events of different intensities were simulated to 0.5-m2 field plots with 20% (70, 88, and 111 mm/h) and 30% (60, 70, and 80 mm/h) slope, respectively. The objective of this study was to compare the behaviour of pesticides covering a range of properties under identical hydrodynamic conditions. Sediment amounts and herbicide concentrations were determined in the runoff samples. As the transported sediment amounts were not sufficient for chemical analyses, herbicide residues attached to sediment were estimated using Kd values determined locally for the soil. Whereas pendimethalin concentrations followed no noticeable pattern, the concentrations for the other herbicides were highest in the first runoff samples, and decreased exponentially with further rain. Results show that herbicides were primarily transported in their dissolved form with the exception of pendimethalin. Slope affected cumulative runoff, sediment, and herbicide losses significantly (P < 0.05). The impact of increased rainfall intensity on runoff initiation followed a similar trend, but herbicide losses from plots exposed to different intensities were not always significant. Losses dissolved in runoff from plots with 20% slope were ≤1% of the applied herbicide, whereas on plots with 30% slope the maximum recorded loss was 65%. Here, losses for all herbicides ranged between 1 and 7% at 60 mm/h and 8 and 65% at 80 mm/h. Exports of herbicides with moderate solubility were negatively correlated with their Kd values and their water solubility.
Demographics of tiger quoll (Dasyurus maculatus maculatus) populations in south-eastern Australia
Authors: Belcher C. A.
Published: February 2004

The tiger quoll is a large marsupial carnivore that occurs in forested habitat in south-eastern Australia. Three tiger quoll populations were trapped for up to six years and data on population parameters, including size, structure, sex ratio, adult : subadult ratio, weight, breeding characteristics, age and longevity were recorded for each population. Sex ratios (♂ : ♀) varied from 5 : 1 to 0 : 1. Population size and age structure reflected previous mortality events and social organisation traits, with all populations showing signs of instability due to disturbance events. Males did not reach full adult weight until three years of age and females until two years. Mean adult male weight was 2.81 kg ± 0.50 (s.d.) (range 2.0–4.2 kg) and mean adult female weight was 1.73 kg ± 0.22 (s.d.) (range 1.2–2.1 kg). Most females did not breed before two years of age and were recorded breeding up to four years of age. A proportion of females did not appear to breed in consecutive years. Matings were estimated to have occurred between late June and early August and births between mid-July and late August. Pouch litter size varied from 4 to 6 with a mean of 5.38 ± 0.65 (s.d.). The adult to juvenile ratio suggests that the mean number of young weaned per female is probably as low as one or two. Monitoring of four females found that the average number of young weaned was three with a range of 2–4. The maximum age recorded was five years. Population declines were found to correlate with 1080 poison baiting programmes, but not with selective logging.
The outer plastid envelope protein Oep16: Role as precursor translocase in import of protochlorophyllide oxidoreductase A
Authors: Reinbothe Steffen , Quigley Françoise , Springer Armin , Schemenewitz Andreas , Reinbothe Christiane
Published: February 2004

A 16-kDa plastid envelope protein was identified by chemical crosslinking that interacts with the precursor of NADPH:protochlorophyllide oxdidoreductase A (pPORA) during its posttranslational import into isolated barley chloroplasts. Protein purification and subsequent protein sequencing showed that the 16-kDa protein is an ortholog of a previously identified outer plastid envelope protein, Oep16. A protein of identical size was present in barley etioplasts and interacted with pPORA. Similar 16-kDa protein-dependent crosslink products of pPORA were detected in wheat, pea, and
Arabidopsis
chloroplasts. Database analyses revealed that the 16-kDa protein belongs to a family of preprotein and amino acid transporters found in free-living bacteria and endosymbiotic mitochondria and chloroplasts. Antibodies raised against the 16-kDa protein inhibited import of pPORA, highlighting its role in protein import.
Identification and analysis of plasticity-induced late-response genes
Authors: Hong Suk Jin , Li Huiwu , Becker Kevin G. , Dawson Valina L. , Dawson Ted M.
Published: February 2004

The excitatory neurotransmitter, glutamate, activatesN-methyl-d-aspartate (NMDA) receptors to induce long-lasting synaptic changes through alterations in gene expression. It is believed that these long-lasting changes contribute to learning and memory, drug tolerance, and ischemic preconditioning. To identify NMDA-induced late-response genes, we used a powerful gene-identification method, differential analysis of primary cDNA library expression (DAzLE), and cDNA microarray from primary cortical neurons. We report here that a variety of genes, which we have named plasticity-induced genes (PLINGs), are up-regulated with differential expression patterns after NMDA receptor activation, indicating that there is a broad and dynamic range of long-lasting neuronal responses that occur through NMDA receptor activation. Our results provide a molecular dissection of the activity-dependent long-lasting neuronal responses induced by NMDA receptor activation.
A revised view of sensory cortical parcellation
Authors: Wallace Mark T. , Ramachandran Ramnarayan , Stein Barry E.
Published: February 2004

Traditional cortical parcellation schemes have emphasized the presence of sharply defined visual, auditory, and somatosensory domains populated exclusively by modality-specific neurons (i.e., neurons responsive to sensory stimuli from a single sensory modality). However, the modality-exclusivity of this scheme has recently been challenged. Observations in a variety of species suggest that each of these domains is subject to influences from other senses. Using the cerebral cortex of the rat as a model, the present study systematically examined the capability of individual neurons in visual, auditory, and somatosensory cortex to be activated by stimuli from other senses. Within the major modality-specific domains, the incidence of inappropriate (i.e., nonmatching) and/or multisensory neurons was very low. However, at the borders between each of these domains a concentration of multisensory neurons was found whose modality profile matched the representations in neighboring cortices and that were able to integrate their cross-modal inputs to give rise to enhanced and/or depressed responses. The results of these studies are consistent with some features of both the traditional and challenging views of cortical organization, and they suggest a parcellation scheme in which modality-specific cortical domains are separated from one another by transitional multisensory zones.
Starch granule initiation is controlled by a heteromultimeric isoamylase in potato tubers
Authors: Bustos Regla , Fahy Brendan , Hylton Christopher M. , Seale Robert , Nebane N. Miranda , Edwards Anne , Martin Cathie , Smith Alison M.
Published: February 2004

Starch granule initiation is not understood, but recent evidence implicates a starch debranching enzyme, isoamylase, in the control of this process. Potato tubers contain isoamylase activity attributable to a heteromultimeric protein containing Stisa1 and Stisa2, the products of two of the three isoamylase genes of potato. To discover whether this enzyme is involved in starch granule initiation, activity was reduced by expression of antisense RNA for Stisa1 or Stisa2. Transgenic tubers accumulated a small amount of a soluble glucan, similar in structure to the phytoglycogen of cereal,
Arabidopsis
, and
Chlamydomonas
mutants lacking isoamylase. The major effect, however, was on the number of starch granules. Transgenic tubers accumulated large numbers of tiny granules not seen in normal tubers. These data indicate that the heteromultimeric isoamylase functions during starch synthesis to suppress the initiation of glucan molecules in the plastid stroma that would otherwise crystallize to nucleate new starch granules.
Replication of plant RNA virus genomes in a cell-free extract of evacuolated plant protoplasts
Authors: Komoda Keisuke , Naito Satoshi , Ishikawa Masayuki
Published: February 2004

The replication of eukaryotic positive-strand RNA virus genomes occurs through a complex process involving multiple viral and host proteins and intracellular membranes. Here we report a cell-free system that reproduces this process
in vitro
. This system uses a membrane-containing extract of uninfected plant protoplasts from which the vacuoles had been removed by Percoll gradient centrifugation. We demonstrate that the system supported translation, negative-strand RNA synthesis, genomic RNA replication, and subgenomic RNA transcription of tomato mosaic virus and two other plant positive-strand RNA viruses. The RNA synthesis, which depended on translation of the genomic RNA, produced virus-related RNA species similar to those that are generated
in vivo
. This system will aid in the elucidation of the mechanisms of genome replication in these viruses.
Mimicking live flavivirus immunization with a noninfectious RNA vaccine
Authors: Kofler Regina M. , Aberle Judith H. , Aberle Stephan W. , Allison Steven L. , Heinz Franz X. , Mandl Christian W.
Published: February 2004

Flaviviruses are human pathogens of world-wide medical importance. They have recently received much additional attention because of their spread to new regions (such as West Nile virus to North America), highlighting their potential as newly emerging disease agents. Using tick-borne encephalitis virus, we have developed and evaluated in mice a new genetic vaccine based on self-replicating but noninfectious RNA. This RNA contains all of the necessary genetic information for establishing its replication machinery in the host cell, thus mimicking a natural infection. However, genetic modifications in the region encoding the capsid protein simultaneously prevent the assembly of infectious virus particles and promote the secretion of noninfectious subviral particles that elicit neutralizing antibodies. These characteristics demonstrate that a new generation of flavivirus vaccines can be designed that stimulate the same spectrum of innate and specific immune responses as a live vaccine but have the safety features of an inactivated vaccine.
Identification of plastid envelope proteins required for import of protochlorophyllide oxidoreductase A into the chloroplast of barley
Authors: Reinbothe Steffen , Quigley Françoise , Gray John , Schemenewitz Andreas , Reinbothe Christiane
Published: February 2004

Chloroplasts synthesize an abundance of different tetrapyrrole compounds. Among them are chlorophyll and its precursor protochlorophyllide (Pchlide), which accumulate in light- and dark-grown plants, respectively. Pchlide is converted to chlorophyllide by virtue of the NADPH:Pchlide oxidoreductase (POR), which, in angiosperms, is the only known light-dependent enzyme of the chlorophyll biosynthetic pathway. In etiolated barley plants, two closely related POR proteins exist termed PORA and PORB, which are nuclear gene products. Here we identified plastid envelope proteins that interact with the cytosolic PORA precursor (pPORA) during its posttranslational chloroplast import. We demonstrate that pPORA interacts with several previously unreported components. Among them is a Pchlide
a
oxygenase, which provides Pchlide
b
as import substrate for pPORA, and a tyrosine aminotransferase thought to be involved in the synthesis of photoprotective vitamin E. Two other constituents were found to be orthologs of the GTP-binding proteins Toc33/34 and of the outer plastid envelope protein Oep16.
Association of rat8 with Fyn protein kinase via lipid rafts is required for rat mammary cell differentiationin vitro
Authors: Zucchi I. , Prinetti A. , Scotti M. , Valsecchi V. , Valaperta R. , Mento E. , Reinbold R. , Vezzoni P. , Sonnino S. , Albertini A. , Dulbecco R.
Published: February 2004

We previously identified rat8 in the pathway involved in epithelial cell differentiation that occurs in the rat mammary gland at pregnancy when tubules and alveoli are formed.rat8, which encodes an IFN-inducible membrane protein, is the rat homologue of the mouse genefragilis. By differential detergent extraction and isopycnic sucrose density gradients, we show that rat8 protein is associated to lipid membrane domains together with Lyn and Fyn, members of the Src tyrosine kinase family. We also show that recruitment of rat8 to lipid membrane domains is a necessary step in mammary epithelial cell differentiation. Immunoprecipitation analysis, performed with an anti-Fyn protein antibody, shows that rat8 was present in the Fyn immunoprecipitate. Antisense oligonucleotides, used to inhibit Fyn protein expression, block mammary cell differentiation. Taken together, these results suggest that the functional interaction, via lipid membrane domains, of rat8 and Fyn proteins is required for mammary cell differentiation. Therefore,rat8, likefragilis, may be involved in developmental decisions and the demarcation of a subset of cells in the mammary gland that cause epithelial cells to develop into a network of tubuloalveolar structures involved in secretion.
Chronic restraint stress up-regulates GLT-1 mRNA and protein expression in the rat hippocampus: Reversal by tianeptine
Authors: Reagan Lawrence P. , Rosell Daniel R. , Wood Gwendolyn E. , Spedding Michael , Muñoz Carmen , Rothstein Jeffrey , McEwen Bruce S.
Published: February 2004

Excitatory amino acids play a key role in stress-induced remodeling of dendrites in the hippocampus as well as in suppression of neurogenesis in the dentate gyrus. The regulation of extracellular glutamate levels has been suggested as a potential mechanism through which repeated stress causes dendritic remodeling of CA3 pyramidal neurons. Accordingly, the current study examined the distribution and regulation of the glia glutamate transporter GLT-1 and the recently identified GLT isoform, GLT-1b, in the hippocampus of rats subjected to chronic restraint stress (CRS). We also examined the ability of the antidepressant tianeptine, which blocks CRS-induced dendritic remodeling, to modulate CRS-mediated changes in GLT-1 and GLT-1b expression. CRS increased GLT-1 mRNA expression in the dentate gyrus and CA3 region of Ammon's horn, increases that were inhibited by tianeptine. CRS more selectively increased GLT-1 protein levels in the subregion where dendritic remodeling is most prominent, namely the CA3 region, increases that were also inhibited by tianeptine administration. In contrast, GLT-1b mRNA expression was not modulated in the hippocampus in any of these groups, but CRS increased GLT-1b protein levels in all hippocampal subfields examined, increases that were unaffected by tianeptine treatment. These results point to the importance of understanding the mechanism for the differential and subregional regulation of GLT-1 isoforms in neuronal and glial compartments in the hippocampus as a basis for understanding the effects of chronic stress on structural plasticity as well as the neuroprotective properties of agents such as tianeptine.
B cell development and immunoglobulin transcription in Oct-1-deficient mice
Authors: Wang Victoria E. H. , Tantin Dean , Chen Jianzhu , Sharp Phillip A.
Published: February 2004

The POU domain transcription factors Oct-1 and Oct-2 interact with the octamer element, a motif conserved within Ig promoters and enhancers, and mediate transcription from the Ig loci. Inactivation of Oct-2 by gene targeting results in normal B cell development and Ig transcription. To study the role of Oct-1 in these processes, the lymphoid compartment of RAG-1–/–animals was reconstituted with Oct-1-deficient fetal liver hematopoietic cells. Recipient mice develop B cells with levels of surface Ig expression comparable with wild type, although at slightly reduced numbers. These B cells transcribe Ig normally, respond to antigenic stimulation, undergo class switching, and use a normal repertoire of light chain variable segments. However, recipient mice show slight reductions in serum IgM and IgA. Thus, the Oct-1 protein is dispensable for B cell development and Ig transcription.
A 9,000-year record of Chagas' disease
Authors: Aufderheide Arthur C. , Salo Wilmar , Madden Michael , Streitz John , Buikstra Jane , Guhl Felipe , Arriaza Bernardo , Renier Colleen , Wittmers Lorentz E. , Fornaciari Gino , Allison Marvin
Published: February 2004

Tissue specimens from 283 principally spontaneously (naturally) desiccated human mummies from coastal and low valley sites in northern Chile and southern Peru were tested with a DNA probe directed at a kinetoplast DNA segment of
Trypanosoma cruzi
. The time interval spanned by the eleven major cultural groups represented in the sample ranged from ≈9,000 years B.P. (7050 B.C.) to approximately the time of the Spanish conquest, ≈450 B.P. (≈1500 A.D.). Forty-one percent of the tissue extracts, amplified by the PCR reacted positively (i.e., hybridized) with the probe. Prevalence patterns demonstrated no statistically significant differences among the individual cultural groups, nor among subgroups compared on the basis of age, sex, or weight of specimen tested. These results suggest that the sylvatic (animal-infected) cycle of Chagas' disease was probably well established at the time that the earliest humans (members of the Chinchorro culture) first peopled this segment of the Andean coast and inadvertently joined the many other mammal species acting as hosts for this parasite.
Breakdown of Bell's theorem for certain objective local parameter spaces
Authors: Hess Karl , Philipp Walter
Published: February 2004

We show that the known proofs of Bell's inequalities contain algebraic manipulations that are not appropriate within the syntax of Kolmogorov's axioms for probability theory without detailed justification. Such justification can be achieved by a variant of the techniques used in Bell-type proofs but only for a subclass of objective local parameter spaces. It cannot be achieved for an extended parameter space that is still objective local and that includes instrument parameters correlated by both time and setting dependencies.
The mouse olfactory receptor gene family
Authors: Godfrey Paul A. , Malnic Bettina , Buck Linda B.
Published: February 2004

In mammals, odor detection in the nose is mediated by a diverse family of olfactory receptors (ORs), which are used combinatorially to detect different odorants and encode their identities. The OR family can be divided into subfamilies whose members are highly related and are likely to recognize structurally related odorants. To gain further insight into the mechanisms underlying odor detection, we analyzed the mouse OR gene family. Exhaustive searches of a mouse genome database identified 913 intact OR genes and 296 OR pseudogenes. These genes were localized to 51 different loci on 17 chromosomes. Sequence comparisons showed that the mouse OR family contains 241 subfamilies. Subfamily sizes vary extensively, suggesting that some classes of odorants may be more easily detected or discriminated than others. Determination of subfamilies that contain ORs with identified ligands allowed tentative functional predictions for 19 subfamilies. Analysis of the chromosomal locations of members of each subfamily showed that many OR gene loci encode only one or a few subfamilies. Furthermore, most subfamilies are encoded by a single locus, suggesting that different loci may encode receptors for different types of odorant structural features. Comparison of human and mouse OR subfamilies showed that the two species have many, but not all, subfamilies in common. However, mouse subfamilies are usually larger than their human counterparts. This finding suggests that humans and mice recognize many of the same odorant structural motifs, but mice may be superior in odor sensitivity and discrimination.
Cofilin peptide homologs interfere with immunological synapse formation and T cell activation
Authors: Eibert Sybille M. , Lee Kyeong-Hee , Pipkorn Rüdiger , Sester Urban , Wabnitz Guido H. , Giese Thomas , Meuer Stefan C. , Samstag Yvonne
Published: February 2004

The formation of supramolecular activation clusters within the immunological synapse, crucial for sustained signaling and T lymphocyte activation, requires costimulation-dependent reorganization of the actin cytoskeleton. Here we have identified the actin-remodeling protein cofilin as a key player in this process. Cell-permeable peptides that block costimulation-induced cofilin/F-actin interactions in untransformed human T lymphocytes impair receptor capping and immunological synapse formation at the interface between T cells and antigen-presenting cells. As a consequence, T cell activation, as measured by cytokine production and proliferation, is inhibited.
Identification of a prostate cancer susceptibility locus on chromosome 7q11–21 in Jewish families
Authors: Friedrichsen Danielle M. , Stanford Janet L. , Isaacs Sarah D. , Janer Marta , Chang Bao-li , Deutsch Kerry , Gillanders Elizabeth , Kolb Suzanne , Wiley Katherine E. , Badzioch Michael D. , Zheng S. Lilly , Walsh Patrick C. , Jarvik Gail P. , Hood Leroy , Trent Jeffrey M. , Isaacs William B. , Ostrander Elaine A. , Xu Jianfeng
Published: February 2004

Results from over a dozen prostate cancer susceptibility genome-wide scans, encompassing some 1,500 hereditary prostate cancer families, indicate that prostate cancer is an extremely heterogeneous disease with multiple loci contributing to overall susceptibility. In an attempt to reduce locus heterogeneity, we performed a genomewide linkage scan for prostate cancer susceptibility genes with 36 Jewish families, which represent a stratification of hereditary prostate cancer families with potentially increased locus homogeneity. The 36 Jewish families represent a combined dataset of 17 Jewish families from the Fred Hutchinson Cancer Research Center-based Prostate Cancer Genetic Research Study dataset and 19 Ashkenazi Jewish families collected at Johns Hopkins University. All available family members, including 94 affected men, were genotyped at markers distributed across the genome with an average interval of <10 centimorgans. Nonparametric multipoint linkage analyses were the primary approach, although parametric analyses were performed as well. Our strongest signal was a significant linkage peak at 7q11–21, with a nonparametric linkage (NPL) score of 3.01 (
P
= 0.0013). Simulations indicated that this corresponds to a genomewide empirical
P
= 0.006. All other regions had NPL
P
values ≥0.02. After genotyping additional markers within the 7q11–21 peak, the NPL score increased to 3.35 (
P
= 0.0004) at D7S634 with an allele-sharing logarithm of odds of 3.12 (
P
= 0.00007). These studies highlight the utility of analyzing defined sets of families with a common origin for reducing locus heterogeneity problems associated with studying complex traits.
The promyelocytic leukemia zinc finger protein down-regulates apoptosis and expression of the proapoptotic BID protein in lymphocytes
Authors: Parrado Antonio , Robledo Macarena , Moya-Quiles M. Rosa , Marín Luis A. , Chomienne Christine , Padua Rose Ann , Álvarez-López M. Rocío
Published: February 2004

The promyelocytic leukemia zinc finger (
PLZF
) gene, involved in rare cases of acute promyelocytic leukemia, encodes a Krüppel-type zinc finger transcription factor. It has been reported that PLZF affects myeloid cell growth, differentiation, and apoptosis. However, the function of PLZF in the lymphoid compartment, where PLZF is also expressed, remains largely unknown. To investigate a potential relationship between PLZF expression in lymphocytes and programmed cell death, an inducible model of stable clones of the lymphoid Jurkat cell line was created by using the tet-off system. Although induction of PLZF expression by itself did not produce changes in the basal levels of apoptosis, PLZF had a significant anti-apoptotic effect in Jurkat cells cultured in conditions of serum starvation, as measured by annexin V staining and terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling. In addition, retarded loss of mitochondrial transmembrane potential was observed in the PLZF-expressing clones, suggesting that PLZF protects from cell death through a mitochondrial-dependent mechanism. To identify apoptosis-related targets of PLZF, a screen for differential expression identified BID, a proapoptotic member of the Bcl2 family, as significantly down-regulated by PLZF. Furthermore, a high-affinity PLZF-binding site element was identified upstream of the
BID
transcriptional start site, as assessed by electrophoretic mobility-shift assays. These results suggest that BID is a target of PLZF repression and a candidate gene to mediate the PLZF-induced resistance to apoptosis.
Cholesterol feeding of mice expressing cholesterol 7α-hydroxylase increases bile acid pool size despite decreased enzyme activity
Authors: Tiemann Michaela , Han Zhihua , Soccio Raymond , Bollineni Jaya , Shefer Sarah , Sehayek Ephraim , Breslow Jan L.
Published: February 2004

Dietary cholesterol regulation of cholesterol 7α-hydroxylase (Cyp7a1), the rate-limiting enzyme in the classical pathway of bile acid synthesis, has been implicated in plasma cholesterol responsiveness. In the current study, the effects of 0.0% and 0.5% cholesterol diets were examined in Cyp7a1 knockout (KO), heterozygous Cyp7a1 KO (Het), and human Cyp7a1 transgenic mice on the mouse Cyp7a1 KO background (Tg+KO). We confirmed previous findings that dietary cholesterol increased mouse Cyp7a1 activity in Het mice but decreased human Cyp7a1 activity in Tg+KO mice. However, in both Het and Tg+KO mice, dietary cholesterol increased bile acid pool size (36% and 72%, respectively) and fecal bile acid excretion (2.2- and 3.6-fold, respectively). The expression of cholesterol 27-hydroxylase (Cyp27), the major enzyme of the alternative pathway of bile acid synthesis, was not significantly different in cholesterol-fed KO, Het, or Tg+KO mice. Furthermore, dietary cholesterol had comparable effects on total plasma cholesterol and non-high-density lipoprotein cholesterol in KO, Het, and Tg+KO mice. Thus, in Tg+KO mice, dietary cholesterol regulates bile acid pool size, fecal bile acid excretion, and plasma cholesterol independently of Cyp7a1 activity. These results challenge the notion that dietary cholesterol regulation of Cyp7a1 is a major determinant of plasma cholesterol responsiveness.
Expansion and contraction of the hepatitis B virus transcriptional template in infected chimpanzees
Authors: Wieland Stefan F. , Spangenberg Hans Christian , Thimme Robert , Purcell Robert H. , Chisari Francis V.
Published: February 2004

We have previously shown that hepatitis B virus (HBV) replication is controlled by noncytolytic mechanisms that depend primarily on the effector functions of the CD8
+
T cell response, especially the production of IFN-γ in the liver. The mechanisms that control the nuclear pool of viral covalently closed circular DNA (cccDNA) transcriptional template of HBV, which must be eliminated to eradicate infection, have been difficult to resolve. To examine those mechanisms, we quantitated intrahepatic HBV cccDNA levels in acutely infected chimpanzees whose virological, immunological, and pathological features were previously described. Our results demonstrate that the elimination kinetics of the cccDNA are more rapid than the elimination of HBV antigen-positive hepatocytes during the early phase of viral clearance, and they coincide with the influx of small numbers of IFN-γ producing CD8
+
T cells into the liver. In contrast, terminal clearance of the cccDNA is associated with the peak of liver disease and hepatocellular turnover and with a surge of IFN-γ producing CD8
+
T cells in the liver. Collectively, these results suggest that cccDNA clearance is a two-step process mediated by the cellular immune response. The first step reduces the pool of cccDNA molecules noncytolytically, probably by eliminating their relaxed circular DNA precursors and perhaps by destabilizing them. The second step enhances this process by destroying infected hepatocytes and triggering their turnover. Surprisingly, despite this multipronged response, traces of cccDNA persist indefinitely in the liver, likely providing a continuous antigenic stimulus that confers lifelong immunity.
Cyclin-dependent kinase 5 regulates dopaminergic and glutamatergic transmission in the striatum
Authors: Chergui Karima , Svenningsson Per , Greengard Paul
Published: February 2004

Dopaminergic and glutamatergic neurotransmissions in the striatum play an essential role in motor- and reward-related behaviors. Dysfunction of these neurotransmitter systems has been found in Parkinson's disease, schizophrenia, and drug addiction. Cyclin-dependent kinase 5 (CDK5) negatively regulates postsynaptic signaling of dopamine in the striatum. This kinase also reduces the behavioral effects of cocaine. Here we demonstrate that, in addition to a postsynaptic role, CDK5 negatively regulates dopamine release in the striatum. Inhibitors of CDK5 increase evoked dopamine release in a way that is additive to that of cocaine. This presynaptic action of CDK5 also regulates glutamatergic transmission. Indeed, inhibition of CDK5 increases the activity and phosphorylation of
N
-methyl-
d
-aspartate receptors, and these effects are reduced by a dopamine D1 receptor antagonist. Using mice with a point mutation of the CDK5 site of the postsynaptic protein DARPP-32 (dopamine- and cAMP-regulated phosphoprotein, molecular mass of 32 kDa), in the absence or in the presence of a dopamine D1 receptor antagonist, we provide evidence that CDK5 inhibitors potentiate dopaminergic transmission at both presynaptic and postsynaptic locations. These findings, together with the known ability of CDK5 inhibitors to prevent degeneration of dopaminergic neurons, suggest that this class of compounds could potentially be used as a novel treatment for disorders associated with dopamine deficiency, such as Parkinson's disease.
Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells
Authors: Scacheri Peter C. , Rozenblatt-Rosen Orit , Caplen Natasha J. , Wolfsberg Tyra G. , Umayam Lowell , Lee Jeffrey C. , Hughes Christina M. , Shanmugam Kalai Selvi , Bhattacharjee Arindam , Meyerson Matthew , Collins Francis S.
Published: February 2004

RNA interference (RNAi) mediated by short interfering RNAs (siRNAs) is a widely used method to analyze gene function. To use RNAi knockdown accurately to infer gene function, it is essential to determine the specificity of siRNA-mediated RNAi. We have assessed the specificity of 10 different siRNAs corresponding to the
MEN1
gene by examining the expression of two additional genes,
TP53
(p53) and
CDKN1A
(p21), which are considered functionally unrelated to menin but are sensitive markers of cell state.
MEN1
RNA and corresponding protein levels were all reduced after siRNA transfection of HeLa cells, although the degree of inhibition mediated by individual siRNAs varied. Unexpectedly, we observed dramatic and significant changes in protein levels of p53 and p21 that were unrelated to silencing of the target gene. The modulations in p53 and p21 levels were not abolished on titration of the siRNAs, and similar results were obtained in three other cell lines; in none of the cell lines tested did we see an effect on the protein levels of actin. These data suggest that siRNAs can induce nonspecific effects on protein levels that are siRNA sequence dependent but that these effects may be difficult to detect until genes central to a pivotal cellular response, such as p53 and p21, are studied. We find no evidence that activation of the double-stranded RNA-triggered IFN-associated antiviral pathways accounts for these effects, but we speculate that partial complementary sequence matches to off-target genes may result in a micro-RNA-like inhibition of translation.
Mode of inheritance of the polymorphic esterases in Myzus persicae (Hemiptera: Aphididae) in Japan
Authors: Shigehara T. , Takada H.
Published: February 2004

Crossing experiments were conducted with 43 different parental clones of Myzus persicae (Sulzer) to clarify the genetic bases of esterase variations detected by electrophoresis. A total of 468 F1 clones obtained were analysed for variants at six polymorphic esterase loci, including one associated with resistance to organophosphorus insecticides (RAE). In addition, the effect of six different host plants on the activity of esterases was examined. The inheritance of variants at two loci could be explained by two-allele models, and that at three other loci by three-allele models, while segregation ratios at the RAE locus suggested a cumulative effect of the multiple genes. An interdependent assortment was found between two loci. The activity of the esterases detected in the alimentary canal was affected by the host plant. By combining the variants at the six polymorphic esterase loci with those in body colour, a total of 2592 colour-esterase forms were distinguishable. Thus esterases could be useful as genetic markers to study the genotypic composition and its dynamics of M. persicaepopulations.
Habitat-related mtDNA polymorphism in the stored-bean pest Callosobruchus chinensis (Coleoptera: Bruchidae)
Authors: Tuda M. , Wasano N. , Kondo N. , Horng S.-B. , Chou L.-Y. , Tateishi Y.
Published: February 2004

The genetic diversity of populations of the azuki bean beetle, Callosobruchus chinensis (Linnaeus) from natural, pre-harvest and post-harvest sites, was investigated to understand population structure and gene flow. A 522-bp fragment of the mitochondrial gene COI was sequenced for eight populations of C. chinensisfrom Japan, Korea and Taiwan collected from different habitats. Six haplotypes were detected, one of which, U1, occurred most frequently and widely. The following hypotheses were tested as a cause of the wide distribution of haplotype U1; (i) topographical separation (by national boundaries), (ii) host plant species, and (iii) habitat type (natural, pre-harvest crop, or post-harvest storage). Categorization of collection sites by country or by host species did not yield differences in the occurrence of haplotype U1, but habitat type did. Populations utilizing cultivated post-harvest hosts that were mass stored were highly likely to be the common haplotype, whereas host plants in natural habitats away from agriculture were utilized by populations with locally characteristic haplotypes. Sampling of commercial beans for quarantine and export purposes indicated that gene flow in C. chinensis was largely unidirectional into Japan at the present time.
Seedling and adult plant resistance to Sitobion avenae (Hemiptera: Aphididae) in Triticum monococcum (Poaceae), an ancestor of wheat
Authors: Migui S.M. , Lamb R.J.
Published: February 2004

Cereal aphids are important pests of wheat, Triticum aestivum L. and Triticum durum Desf. Crop resistance is a desirable method for managing cereal aphids in central North America, where the dominant crop, spring-sown wheat, has a low value per unit area. A diploid ancestor of wheat, Triticum monococcum L., is reported to be partially resistant to Sitobion avenae (Fabricius), the most damaging cereal aphid in the region. To identify potential sources of resistance, 42 accessions of T. monococcum and three cultivated wheats were infested with aphids, seedlings for six days and adult plants for 21 days. Overall resistance was estimated by the biomass loss of foliage and spikes in relation to uninfested control plants. Antibiosis was estimated by the gain in biomass of aphids during infestation, and tolerance was estimated as a biomass conversion ratio, overall resistance divided by antibiosis. A few T. monococcum accessions exhibited partial resistance. No relationship was found between seedling and adult plant resistance: the former exhibited primarily antibiosis and the latter primarily tolerance. Two accessions with antibiosis reduced aphid biomass by 60% compared with commercial wheats. Tolerance was correlated with growth potential, and was useful only in accessions with high growth potential. Four accessions exhibited tolerance levels at least 30% greater than commercial wheats. Highly susceptible accessions also were identified, which would be useful for investigating the inheritance of antibiosis and tolerance.