bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and characterization of 23 polymorphic microsatellite markers for diversity and stock analysis in tiger shrimp (Penaeus monodon)
Authors: PAN YU‐WEN , CHOU HSIN‐HUNG , YOU EN‐MIN , YU HON‐TSEN
Published: August 2004

The tiger shrimp (Penaeus monodon) is an important marine crustacean in terms of biological diversity and aquaculture resource. The shrimp is widespread across the Indo‐Pacific region and shows apparent genetic differentiation among geographical populations. It is common practice to transport female brooders between different countries to seed the shrimp farms, posing potential problems of unwanted population admixture. We developed 23 polymorphic microsatellites for P. monodon (average HE = 0.936) and these microsatellites were applicable for studying population differentiation, identifying valid stocks and tagging nonindigenous farmed shrimps.
Identification and characterization of 10 microsatellite primers for the calanoid freshwater copepods Eudiaptomus gracilis and E. graciloides using enriched genomic libraries
Authors: ZELLER MARTINA , REUSCH THORSTEN B. H.
Published: August 2004

The calanoid copepods Eudiaptomus gracilis and Eudiaptomus graciloides are widespread among European lakes. We constructed enriched genomic libraries for both species in order to isolate and characterise microsatellite markers. The obtained 7 polymorphic microsatellite‐loci for E. gracilis and 3 for E. graciloides are the first for any freshwater copepod. They display an expected heterozygosity ranging from 0.60 to 0.96 and 0.63 to 0.94 and observed heterozygosity ranging from 0.53 to 0.87 and 0.57 to 0.87, respectively. We were not able to cross‐amplify the isolated loci across species, indicating long divergence among both congeneric species despite morphological similarity.
Isolation and characterization of microsatellite loci from Acacia nilotica ssp. indica (Mimosaceae)
Authors: WARDILL T. J. , SCOTT K. D. , GRAHAM G. C. , ZALUCKI M. P.
Published: August 2004

Five microsatellite loci are presented for prickly acacia, Acacia nilotica ssp. indica (Benth.) Brenan, an introduced weed of national significance in Australia. These microsatellite loci were obtained through the construction of an enriched library and their use will enable us to determine the genetic origin and extent of genetic diversity of this weed in Australia.
Identification and characterization of microsatellite DNA markers developed in an endangered cyprinid of the Mekong River, the seven‐line barb (Probarbus jullieni Sauvage, 1880)
Authors: SUKUMASAVIN N. , NAKAJIMA M. , TANIGUCHI N.
Published: August 2004

Microsatellite markers for an endangered cyprinid species of the Mekong River, the seven‐line barb (Probarbus jullieni Sauvage, 1880) were developed from the wild caught samples using (GT)15 probe. The number of alleles per locus ranged from seven to 16. The expected heterozygosities ranged from 0.47 to 0.91. Also, these primers were successfully amplified in the two closely related species, P. labeamajor and P. labeaminor. These markers have proven to be very useful for the population genetic structure study in this species and other related cyprinids.
Development of VNTR markers for two Fusarium graminearum clade species
Authors: SUGA H. , GALE L. R. , KISTLER H. C.
Published: August 2004

Using a bioinformatics approach, we developed 10 variable number of tandem repeat (VNTR) markers for Fusarium graminearum and Fusarium asiaticum useful for population genetic studies. Repeat sequences in the genome sequence of F. graminearum were identified by a tandem repeat finding program. Length polymorphisms at 54 loci were examined for five strains each from the United States, Italy and China. From these 54 loci, 10 were selected based on polymorphisms detected across species, ease of scoring, and their dispersed location in the genome.
Improved noninvasive genotyping method: application to brown bear (Ursus arctos) faeces
Authors: BELLEMAIN E. , TABERLET P.
Published: August 2004

We redesigned new microsatellite primers and one sex‐specific primer for amplification of faecal DNA from brown bears (Ursus arctos). We also combined a semi‐nested polymerase chain reaction (PCR) with a newly developed multiplex preamplification method in order to increase the quality of the amplified DNA fragments. In comparison with a conventional PCR approach, the genotyping error rate was substantially reduced and the amplification rate was increased. This new approach could be transposed to other species where conventional PCR methods experience low success due to limited DNA concentration and/or quality.
Isolation of six microsatellite markers from the pea aphid, Acyrthosiphon pisum (Homoptera, Aphididae)
Authors: KUROKAWA TAROH , YAO IZUMI , AKIMOTO SHIN‐ICHI , HASEGAWA EISUKE
Published: August 2004

Using the magnetic particles method, we isolated six polymorphic microsatellite loci from the pea aphid, Acyrthosiphon pisum (Harris), which feeds on a wide range of legume species. The isolated loci were polymorphic, with three to six alleles in 40 aphids. Expected heterozygosities ranged from 0.12 to 0.65. These loci can be used to quantify clonal diversity and compare genetic population structure between sexual and asexual populations.
Characterization and cross‐species amplification of microsatellite loci in the plant pathogenic fungus Leptosphaeria maculans
Authors: HAYDEN HELEN L. , WILSON LEANNE M. , COZIJNSEN ANTON J. , HOWLETT BARBARA J.
Published: August 2004

Seven polymorphic microsatellite markers suitable for population genetic studies and genetic mapping were developed for Leptosphaeria maculans, a fungal pathogen of canola (Brassica napus). Polymorphism was evaluated using 14 isolates from diverse geographical locations. Each locus had either two or three alleles. Cross‐species amplification was observed for almost all loci in L. biglobosa ‘brassicae’ and L. maculans ‘lepidii’.
Microsatellite markers in coast redwood (Sequoia sempervirens)
Authors: BRUNO D. , BRINEGAR C.
Published: August 2004

Five polymorphic microsatellite markers are described for coast redwood, a hexaploid conifer. Dinucleotide (three), trinucleotide (one) and tetranucleotide (one) repeat loci were isolated from a genomic plasmid library and amplified in a test population of 25 second‐growth redwoods. There were three to 11 alleles per locus and observed heterozygosities ranged from 0.00 to 0.80. The nonheterozygous locus (a CTTA repeat) is probably of chloroplast origin and may have potential as a marker for paternal inheritance.
Characterization and isolation of DNA microsatellite primers in the spiny dogfish (Squalus acanthias)
Authors: McCAULEY LINDA , GOECKER COURTNEY , PARKER PAUL , RUDOLPH TOM , GOETZ FREDERICK , GERLACH GABRIELE
Published: August 2004

The North Atlantic spiny dogfish (Squalus acanthias) population has been declining since the 1980s. Proper management of this population is essential as dogfish are prone to rapid collapse based on the unique biology of this species. We characterized eight microsatellite loci for spiny dogfish to use in determining the genetic structure of this species along the Atlantic coast of the USA.
Characterization of six microsatellite primers for the grey fox (Urocyon cinereoargenteus)
Authors: WESTON JULIE L. , SCHABLE NANCY A. , GLENN TRAVIS C.
Published: August 2004

We describe polymerase chain reaction (PCR) primers and conditions to amplify one dinucleotide and five tetranucleotide microsatellite DNA loci isolated from the grey fox (Urocyon cinereoargenteus). The PCR primers were tested on nine to 12 individuals collected from the Department of Energy's Savannah River site (Aiken, SC, USA). The grey fox microsatellite primers developed had three to 10 alleles per locus that yielded observed heterozygosities ranging from 0.222 to 0.889.
Delayed Restenosis after Gamma Brachytherapy for In‐Stent Restenosis
Authors: HIROSE MAKOTO , KOBAYASHI YOSHIO , MOSES JEFFREY W.
Published: August 2004

Intracoronary brachytherapy is a promising modality for inhibition of in‐stent restenosis. However, there is a concern of late progression after brachytherapy. This case report describes delayed restenosis after brachytherapy.
The Cutting Balloon for In‐Stent Restenosis:
Authors: BEJARANO JORGE
Published: August 2004

Extraordinary advances have been made in the prevention, medical treatment, and the surgical and percutaneous intervention of coronary artery disease. However, despite the vast contribution of coronary artery stenting, coronary artery disease remains a major health problem. The massive treatment of symptomatic coronary artery disease with non‐drug‐eluting stents in the past, accounts for a large incidence of in‐stent restenosis (ISR). We know today that in the following days after coronary artery angioplasty, new layers of intimal cells, called neo‐intima, scaffold the endothelium forming a rubbery membrane. Numerous attempts have been made, and are still ongoing, to prevent the formation or to remove the neo‐intima with suboptimal results and cost‐effectiveness. Drug‐eluting stents seem to be the most promising approach to date, however, the high cost of these devices may limit their use. In the mean time, new cases of ISR present to our cardiology practices. Because of its lower cost and identical technique to a regular balloon, the cutting balloon has emerged in numerous observational studies, and in a few randomized studies as a practical alternative to treat ISR. Although a few randomized studies have compared angioplasty with the cutting balloon versus angioplasty with a regular balloon, there are no randomized or economic studies comparing this device to excimer laser or intracoronary radiation in the treatment of this complication of coronary stenting. We reviewed the most prominent studies to date, on the performance of the cutting balloon in the treatment of ISR.
Catheter‐Induced Dissection of the Left Main Coronary Artery With and Without Extension to the Aortic Root:
Authors: AWADALLA HANY , SALLOUM JOSEPH G. , SMALLING RICHARD W. , SDRINGOLA STEFANO
Published: August 2004

Catheter‐induced left main coronary artery dissection is quite rare. We describe two cases of iatrogenic left main coronary artery dissection. In the first case, the aortic root was involved in the dissection process, and stenting of the entry point did not halt the progression of dissection. In the second case, the dissection did not involve the aortic root.
Long‐Term Results of Endovascular Exclusion of Extracranial Internal Carotid Artery Aneurysms and Dissecting Aneurysm
Authors: BERGERON Patrice , KHANOYAN Patrick , MEUNIER Jean‐Pierre , GRAZIANI Jean‐Noël , GAY Joel
Published: August 2004

Objectives: Surgery remains the standard option to treat symptomatic or complicated aneurysms of the extracranial internal carotid arteries (EICA). When located more distally to the EICA, surgery appears to be very invasive and disabling. Endovascular treatment of high aneurysmal EICA has been poorly reported. We report our experience in this particular field.

Methods: We treated five EICA endovascularly, using covered stents and stentgrafts in four patients, two males and two females. One male was treated bilaterally. The average age was 59.2 years (39–80). Three patients were symptomatic (two transient ischemic attack and one stroke). Patients were followed by duplex scan, CT scan, or angio MR.

Results: Protecting devices were used in two cases. No in‐hospital complication was observed. During follow‐up (3.6 ± 1.3 years), no adverse event was observed and all devices remained patent at duplex scan and angiography. One early endoleak was observed and treated with covered stent extension. No sign of in‐stent stenosis was observed. All the aneurysmal sacs thrombosed.

Conclusion: Covered stents and stentgrafts allow a less invasive approach to treat highly located internal carotid aneurysms. Larger series are needed to assess the role of covered stents in treating aneurysmal EICA as first choice.
Spontaneous Spiral Dissection of a LIMA–LAD Bypass Graft:
Authors: WONG PHILIP , RUBENSTEIN MARK , INGLESSIS IGNACIO , POMERANTSEV EUGENE , FERRELL MARGARET , LEINBACH ROBERT
Published: August 2004

We describe an unusual case of spontaneous spiral dissection of a LIMA–LAD bypass graft presenting with an acute coronary syndrome. This complex lesion was treated percutaneously with multiple coronary stents.
Transactional Communication Disturbances in Families of Male Schizophrenics
Authors: WILD CYNTHIA M. , SHAPIRO LINDA N. , GOLDENBERG LOUISE
Published: August 2004

Criteria were developed for scoring the interaction of families (mother, father, son) of schizophrenics, psychiatrically hospitalized nonschizophrenic controls, and normal controls, on transactional Attention Difficulties, Closure Difficulties, Problem‐Solving Efficiency, and Dominance. These variables were scored by observers watching the interaction, from tapes, and from transcripts of the sessions. Tape‐scoring was the most efficient and effective in discriminating the three groups. Mothers', couples' (mother and father), and families' total Amorphous Attention Difficulties scores were higher in the schizophrenic than in the normal control group; but families of both hospitalized and normal controls were distinguished from families of schizophrenics only when mothers' Amorphous Difficulties and fathers' Closure Difficulties were considered together. The groups were similar on Problem‐Solving Efficiency. Fathers of schizophrenics were most Dominant, both within their families and compared with fathers in the other two groups.
Predictability, Failure, and Guilt in Suicide: A Personal Account
Authors: WETHERILL PHYLLIS S.
Published: August 2004

The lifetime medical, social and psychiatric history of a young man who took his life at age twenty‐one is presented as his mother observed and recorded it. The predictability of the suicide is discussed; questions are raised about personal and professional responsibility and guilt.
“Enmeshment” and the Too Richly Cross‐Joined System
Authors: HOFFMAN LYNN
Published: August 2004

This paper traces out a connection between Minuchin's concept of an “enmeshed” family and Ashby's discussion of the problems inherent in a system in which all the parts are tightly interlocked. Adaptiveness to change in such a system will depend on the possibility for the joins between parts to become temporarily inactive. This observation supports maneuvers in family therapy that emphasize the creation of boundaries between subsystems, differentiating individuals from one another, and blocking customary sequences of interaction.
An Application of Balance Theory to Family Treatment
Authors: COHEN CARL I. , CORWIN JUNE
Published: August 2004

The formulations of Heider's Balance Theory are reviewed. An application of Balance Theory to the diagnosis and treatment of family dysfunction is demonstrated.
Treatment of Temper Tantrums by a Paradoxical Intervention
Authors: HARE‐MUSTIN RACHEL T.
Published: August 2004

In the present case, a paradoxical intervention was employed in the treatment of a 4‐year‐old boy for temper tantrums. Temper tantrums, which had been a daily occurrence, disappeared entirely after the second session. A follow‐up at nine months indicated there had been no further tantrums.
Adoption: Legal Resolution or Legal Fraud?
Authors: ANDREWS ROBERTA G.
Published: August 2004

Adoption, long considered a binding social contract, is under attack because it separates the adopted from their biological family. The attitudes and practices of secrecy by the courts, agencies, and adoptive families have intensified the adoptees' feelings of being different and cut off from their roots. In a changing climate of greater openness about sensitive subjects, less tension in discussing adoption can be a significant prophylactic factor. In this sense, adopted people, collectively and individually, are making a meaningful contribution to a complex area of human relations. However, if adoption records are unsealed by legislative acts, the primary needs of the adoptive and biological parents can be undermined by the needs of the adopted adult.
Relabeling and Reframing Reconsidered: The Beneficial Effects of a Pathological Label
Authors: GRUNEBAUM HENRY , CHASIN RICHARD
Published: August 2004

Traditional labeling theory usually contends that pathological labels contribute to pathology and benign labels help alleviate it. However, it is likely that the role of pathological labels as the cause of pathology has been overstated and over‐generalized. Family therapists have probably overused the practice of substituting a benign label for a pathological label—relabeling. In fact, there are many families in which a pathological label applied to one family member may have beneficial impact on the family system, including that member. Five such cases are presented, and labeling theory is reviewed. Definitions of the terms reframing and relabeling are suggested, and the differing implications of diagnosis and labeling theory are discussed.
UK patients with primary Sjögren's syndrome are at increased risk from clinical depression
Authors: Stevenson H. A. , Jones M. E. , Rostron J. L. , Longman L. P. , Field E. A.
Published: August 2004

Objective:  This study was undertaken to assess the presence and degree of anxiety and depression in a group of UK patients with primary Sjögren's syndrome (1°SS).

Design:  Cross‐sectional.

Setting:  Department of Oral Medicine, Liverpool University Dental Hospital.

Subjects:  Eighty adult patients; 40 diagnosed with 1°SS according to the revised European Criteria and 40 age/gender‐matched controls with no history of chronic illness.

Intervention:  Hospital Anxiety and Depression Scale (HADS), a self‐administered questionnaire designed to evaluate the presence and degree of anxiety and depression in a clinical setting.

Main outcome measures:  Age, gender, Hospital Anxiety and Depression Scale (HADS).

Results:  Forty patients with 1°SS and 40/age/gender‐matched controls completed the HADS. Scores for anxiety in both the 1°SS and control groups showed no statistically significant difference. Patients with 1°SS had statistically significant higher, mean HADS scores for depression than the controls. There was an increased prevalence of ‘definite’ clinical depression in the 1°SS group.

Conclusion:  Patients with 1°SS appear to be at increased risk from clinical depression. Early recognition and appropriate intervention is therefore essential to reduce the negative impact of depression on the patient's quality of life and outcome of their disease.
Association between functional dental state and dietary intake of Chinese vegetarian old age home residents
Authors: Kwok Timothy , Yu Charles N.F. , Hui Hing W. , Kwan Mandy , Chan Veronica
Published: August 2004

Objective:  To examine the association between dental functional status and dietary intakes of Chinese vegetarian old age home residents.

Subjects and methods:  A cross‐sectional survey was performed in a group of 76 older vegetarian Chinese women living in an old age home. Oral examination was performed by a dental surgeon. Sixty‐eight of them had a 24‐hour food record by direct observation, analysed by a Chinese food composition table. Nutritional status was measured by Body Mass Index (BMI), and the functional status by modified Barthel Index (BI).

Results:  Forty‐two subjects (55.3%) were edentulous; 59 subjects (77.6%) had chewing difficulties; 35 subjects (46%) had poor dental functional status defined by having five or less functional teeth unit (FTU). When compared with those older people with better dental functional status, the poor dental functional status group was more likely to have chewing difficulties, tolerate soft diet only, and be functionally dependent (BI < 15/20). Poor dental functional status was associated with lower mean daily fibre intake, but not with intakes of macronutrients and micronutrients, after adjustment by BI categories.

Conclusion:  Poor dental functional status is associated with impaired chewing and lower fibre intake in Chinese vegetarian old age home residents, but it is not associated with reduced intakes of macronutrients or micronutrients.
Regulation of human airway ciliary beat frequency by intracellular pH
Authors: Sutto Zoltan , Conner Gregory E. , Salathe Matthias
Published: August 2004

pHi affects a number of cellular functions, but the influence of pHi on mammalian ciliary beat frequency (CBF) is not known. CBF and pHi of single human tracheobronchial epithelial cells in submerged culture were measured simultaneously using video microscopy (for CBF) and epifluorescence microscopy with the pH‐sensitive dye BCECF. Baseline CBF and pHi values in bicarbonate‐free medium were 7.2 ± 0.2 Hz and 7.49 ± 0.02, respectively (n= 63). Alkalization by ammonium pre‐pulse to pHi 7.78 ± 0.02 resulted in a 2.2 ± 0.1 Hz CBF increase (P < 0.05). Following removal of NH4Cl, pHi decreased to 7.24 ± 0.02 and CBF to 5.8 ± 0.1 Hz (P < 0.05). Removal of extracellular CO2 to change pHi resulted in similar CBF changes. Pre‐activation of cAMP‐dependent protein kinase (10 μm forskolin), broad inhibition of protein kinases (100 μm H‐7), inhibition of PKA (10 μm H‐89), nor inhibition of phosphatases (10 μm cyclosporin + 1.5 μm okadaic acid) changed pHi‐mediated changes in CBF, nor were they due to [Ca2+]i changes. CBF of basolaterally permeabilized human tracheobronchial cells, re‐differentiated at the air–liquid interface, was 3.9 ± 0.3, 5.7 ± 0.4, 7.0 ± 0.3 and 7.3 ± 0.3 Hz at basolateral i.e., intracellular pH of 6.8, 7.2, 7.6 and 8.0, respectively (n= 18). Thus, intracellular alkalization stimulates, while intracellular acidification attenuates human airway CBF. Since phosphorylation and [Ca2+]i changes did not seem to mediate pHi‐induced CBF changes, pHi may directly act on the ciliary motile machinery.
Resource Letter RPS-1: Research in problem solving
Authors: Hsu Leonardo , Brewe Eric , Foster Thomas M. , Harper Kathleen A.
Published: August 2004

This Resource Letter provides a guide to the literature on research in problem solving, especially in physics. The references were compiled with two audiences in mind: physicists who are (or might become) engaged in research on problem solving, and physics instructors who are interested in using research results to improve their students’ learning of problem solving. In addition to general references, journal articles and books are cited for the following topics: cognitive aspects of problem solving, expert-novice problem-solver characteristics, problem solving in mathematics, alternative problem types, curricular interventions, and the use of computers in problem solving.
Computer simulations, exact trajectories, and the gravitational N-body problem
Authors: Hayes Wayne
Published: August 2004

Many physical systems of current interest are chaotic, which means that numerical errors in their simulation are exponentially magnified with the passage of time. This could mean that a numerical solution of a chaotic system is the result of nothing but magnified noise, which calls into question the value of such simulations. Although this fact has been well known for a long time, its impact on the validity of simulations is not well understood. The study of shadowing may provide an answer. A shadow is an exact trajectory of a chaotic map or ordinary differential equation that remains close to an approximate solution for a nontrivial duration of time. If it can be shown that a numerical solution has a shadow, then the validity of the solution is strong, in the sense that it can be viewed as an experimental observation of the shadow, which is an exact solution. We present a discussion of shadowing, including an algorithm to find shadows, using the gravitational N-body problem as an example.
What makes bowling balls hook?
Authors: Frohlich Cliff
Published: August 2004

This article presents exact equations of motion for a rotating bowling ball in a form that explicitly separates contributions due to nonequal principal moments of inertia, center-of-mass offset, and friction between the ball and lane. A computer program that solves the equations demonstrates that all of these factors are important for a realistic analysis of bowling. These factors significantly affect how much balls hook, that is, deflect sideways and approach the pins at an oblique angle. Simulations that approximate real bowling conditions indicate that the largest contribution comes from variable friction along the lane, that is, bowling lanes are generally prepared so that lane friction is higher by a factor of 2 or more along the last one-third of the ball’s trajectory. The analysis supports most (but not all) of the guidelines that bowlers have developed for predicting ball performance.
Wigner quasi-probability distribution for the infinite square well: Energy eigenstates and time-dependent wave packets
Authors: Belloni M. , Doncheski M. A. , Robinett R. W.
Published: August 2004

We calculate and visualize the Wigner quasi-probability distribution for the position and momentum, PW(n)(x,p), for the energy eigenstates of the infinite square well. We evaluate the time-dependent Wigner distribution, PW(x,p;t), for Gaussian wave packet solutions of this system, and illustrate the short-term semi-classical time dependence and the longer-term revival and fractional revival behavior. Our results indicate how the Wigner distribution can be used to examine the highly correlated dynamical position-momentum structure of quantum states. In particular, this tool provides an excellent way of demonstrating the patterns of highly correlated Schrödinger-cat-like “mini-packets” which appear at fractional multiples of the exact revival time.
Modeling and propagation of near-field diffraction patterns: A more complete approach
Authors: Gillen Glen D. , Guha Shekhar
Published: August 2004

We discuss the origins and regions of validity of various near-field diffraction models. The complete Rayleigh–Sommerfeld model is found to accurately represent intensity distributions for axial distances up to and including the location of the aperture, a region where commonly used models fail. We show that near-field diffraction theory can be applied to the refraction of light at an interface between two different media yielding results that demonstrate the validity of Snell’s law in the presence of diffraction. Calculations using near-field diffraction and Fourier optics are compared to experimentally measured intensity distributions.
Hybrid Cars Now, Fuel Cell Cars Later
Authors: Demirdöven Nurettin , Deutch John
Published: August 2004

We compare the energy efficiency of hybrid and fuel cell vehicles as well as conventional internal combustion engines. Our analysis indicates that fuel cell vehicles using hydrogen from fossil fuels offer no significant energy efficiency advantage over hybrid vehicles operating in an urban drive cycle. We conclude that priority should be placed on hybrid vehicles by industry and government.
Modulation of Hematopoietic Stem Cell Homing and Engraftment by CD26
Authors: Christopherson Kent W. , Hangoc Giao , Mantel Charlie R. , Broxmeyer Hal E.
Published: August 2004

Hematopoietic stem cell homing and engraftment are crucial to transplantation efficiency, and clinical engraftment is severely compromised when donor-cell numbers are limiting. The peptidase CD26 (DPPIV/dipeptidylpeptidase IV) removes dipeptides from the amino terminus of proteins. We present evidence that endogenous CD26 expression on donor cells negatively regulates homing and engraftment. By inhibition or deletion of CD26, it was possible to increase greatly the efficiency of transplantation. These results suggest that hematopoietic stem cell engraftment is not absolute, as previously suggested, and indicate that improvement of bone marrow transplant efficiency may be possible in the clinic.
Sample Dimensions Influence Strength and Crystal Plasticity
Authors: Uchic Michael D. , Dimiduk Dennis M. , Florando Jeffrey N. , Nix William D.
Published: August 2004

When a crystal deforms plastically, phenomena such as dislocation storage, multiplication, motion, pinning, and nucleation occur over the submicron-to-nanometer scale. Here we report measurements of plastic yielding for single crystals of micrometer-sized dimensions for three different types of metals. We find that within the tests, the overall sample dimensions artificially limit the length scales available for plastic processes. The results show dramatic size effects at surprisingly large sample dimensions. These results emphasize that at the micrometer scale, one must define both the external geometry and internal structure to characterize the strength of a material.
Discovery of Symbiotic Nitrogen-Fixing Cyanobacteria in Corals
Authors: Lesser Michael P. , Mazel Charles H. , Gorbunov Maxim Y. , Falkowski Paul G.
Published: August 2004

Colonies of the Caribbean coral
Montastraea cavernosa
exhibit a solar-stimulated orange-red fluorescence that is spectrally similar to a variety of fluorescent proteins expressed by corals. The source of this fluorescence is phycoerythrin in unicellular, nonheterocystis, symbiotic cyanobacteria within the host cells of the coral. The cyanobacteria coexist with the symbiotic dinoflagellates (zooxanthellae) of the coral and express the nitrogen-fixing enzyme nitrogenase. The presence of this prokaryotic symbiont in a nitrogen-limited zooxanthellate coral suggests that nitrogen fixation may be an important source of this limiting element for the symbiotic association.
The Soft Sector in Physics
Authors: Wong Gerard C. L.
Published: August 2004

Structured Fluids
Polymers, Colloids, Surfactants. by Thomas A. Witten with Philip A. Pincus. Oxford University Press, Oxford, 2004. 230 pp. $74.50, £39.95. ISBN 0-19-852688-1.

The authors use a scaling approach to provide a unified, pedagogical introduction to fluids containing polyatomic structures such as polymer molecules or colloidal grains ("soft condensed matter").
Visual Pattern Recognition in
Drosophila
Is Invariant for Retinal Position
Authors: Tang Shiming , Wolf Reinhard , Xu Shuping , Heisenberg Martin
Published: August 2004

Vision relies on constancy mechanisms. Yet, these are little understood, because they are difficult to investigate in freely moving organisms. One such mechanism, translation invariance, enables organisms to recognize visual patterns independent of the region of their visual field where they had originally seen them. Tethered flies (
Drosophila melanogaster
) in a flight simulator can recognize visual patterns. Because their eyes are fixed in space and patterns can be displayed in defined parts of their visual field, they can be tested for translation invariance. Here, we show that flies recognize patterns at retinal positions where the patterns had not been presented before.
Stabilization Wedges: Solving the Climate Problem for the Next 50 Years with Current Technologies
Authors: Pacala S. , Socolow R.
Published: August 2004

Humanity already possesses the fundamental scientific, technical, and industrial know-how to solve the carbon and climate problem for the next half-century. A portfolio of technologies now exists to meet the world's energy needs over the next 50 years and limit atmospheric CO
2
to a trajectory that avoids a doubling of the preindustrial concentration. Every element in this portfolio has passed beyond the laboratory bench and demonstration project; many are already implemented somewhere at full industrial scale. Although no element is a credible candidate for doing the entire job (or even half the job) by itself, the portfolio as a whole is large enough that not every element has to be used.
SOS Response Induction by ß-Lactams and Bacterial Defense Against Antibiotic Lethality
Authors: Miller Christine , Thomsen Line Elnif , Gaggero Carina , Mosseri Ronen , Ingmer Hanne , Cohen Stanley N.
Published: August 2004

The SOS response aids bacterial propagation by inhibiting cell division during repair of DNA damage. We report that inactivation of the
ftsI
gene product, penicillin binding protein 3, by either β-lactam antibiotics or genetic mutation induces SOS in
Escherichia coli
through the DpiBA two-component signal transduction system. This event, which requires the SOS-promoting
recA
and
lexA
genes as well as
dpiA
, transiently halts bacterial cell division, enabling survival to otherwise lethal antibiotic exposure. Our findings reveal defective cell wall synthesis as an unexpected initiator of the bacterial SOS response, indicate that β-lactam antibiotics are extracellular stimuli of this response, and demonstrate a novel mechanism for mitigation of antimicrobial lethality.
Phospholipid Scramblase 1 Potentiates the Antiviral Activity of Interferon
Authors: Dong Beihua , Zhou Quansheng , Zhao Ji , Zhou Aimin , Harty Ronald N. , Bose Santanu , Banerjee Amiya , Slee Roger , Guenther Jeanna , Williams Bryan R. G. , Wiedmer Therese , Sims Peter J. , Silverman Robert H.
Published: August 2004

Phospholipid scramblase 1 (PLSCR1) is an interferon (IFN)- and growth factor-inducible, calcium-binding protein that either inserts into the plasma membrane or binds DNA in the nucleus depending on its state of palmyitoylation. In certain hematopoietic cells, PLSCR1 is required for normal maturation and terminal differentiation from progenitor cells as regulated by select growth factors, where it promotes recruitment and activation of Src kinases. PLSCR1 is a substrate of Src (and Abl) kinases, and transcription of the PLSCR1 gene is regulated by the same growth factor receptor pathways in which PLSCR1 potentiates afferent signaling. The marked transcriptional upregulation of PLSCR1 by IFNs led us to explore whether PLSCR1 plays an analogous role in cellular responses to IFN, with specific focus on antiviral activities. Accordingly, human cells in which PLSCR1 expression was decreased with short interfering RNA were rendered relatively insensitive to the antiviral activity of IFNs, resulting in higher titers of vesicular stomatitis virus (VSV) and encephalomyocarditis virus. Similarly, VSV replicated to higher titers in mousePLSCR1−/−embryonic fibroblasts than in identical cells transduced to express PLSCR1. PLSCR1 inhibited accumulation of primary VSV transcripts, similar to the effects of IFN against VSV. The antiviral effect of PLSCR1 correlated with increased expression of a subset of IFN-stimulated genes (ISGs), including ISG15, ISG54, p56, and guanylate binding proteins. Our results suggest that PLSCR1, which is itself an ISG-encoded protein, provides a mechanism for amplifying and enhancing the IFN response through increased expression of a select subset of potent antiviral genes.
Palindrome Regeneration by Template Strand-Switching Mechanism at the Origin of DNA Replication of Porcine Circovirus via the Rolling-Circle Melting-Pot Replication Model
Authors: Cheung Andrew K.
Published: August 2004

Palindromic sequences (inverted repeats) flanking the origin of DNA replication with the potential of forming single-stranded stem-loop cruciform structures have been reported to be essential for replication of the circular genomes of many prokaryotic and eukaryotic systems. In this study, mutant genomes of porcine circovirus with deletions in the origin-flanking palindrome and incapable of forming any cruciform structures invariably yielded progeny viruses containing longer and more stable palindromes. These results suggest that origin-flanking palindromes are essential for termination but not for initiation of DNA replication. Detection of template strand switching in the middle of an inverted repeat strand among the progeny viruses demonstrated that both the minus genome and a corresponding palindromic strand served as templates simultaneously during DNA biosynthesis and supports the recently proposed rolling-circle “melting-pot” replication model. The genome configuration presented by this model, a four-stranded tertiary structure, provides insights into the mechanisms of DNA replication, inverted repeat correction (or conversion), and illegitimate recombination of any circular DNA molecule with an origin-flanking palindrome.
Inhibition of Hepatitis C Virus-Like Particle Binding to Target Cells by Antiviral Antibodies in Acute and Chronic Hepatitis C
Authors: Steinmann Daniel , Barth Heidi , Gissler Bettina , Schürmann Peter , Adah Mohammed I. , Gerlach J. Tilman , Pape Gerd R. , Depla Erik , Jacobs Dirk , Maertens Geert , Patel Arvind H. , Inchauspé Geneviève , Liang T. Jake , Blum Hubert E. , Baumert Thomas F.
Published: August 2004

Hepatitis C virus (HCV) is a leading cause of chronic viral hepatitis worldwide. The study of antibody-mediated virus neutralization has been hampered by the lack of an efficient and high-throughput cell culture system for the study of virus neutralization. The HCV structural proteins have been shown to assemble into noninfectious HCV-like particles (HCV-LPs). Similar to serum-derived virions, HCV-LPs bind and enter human hepatocytes and hepatoma cell lines. In this study, we developed an HCV-LP-based model system for a systematic functional analysis of antiviral antibodies from patients with acute or chronic hepatitis C. We demonstrate that cellular HCV-LP binding was specifically inhibited by antiviral antibodies from patients with acute or chronic hepatitis C in a dose-dependent manner. Using a library of homologous overlapping envelope peptides covering the entire HCV envelope, we identified an epitope in the N-terminal E2 region (SQKIQLVNTNGSWHI; amino acid positions 408 to 422) as one target of human antiviral antibodies inhibiting cellular particle binding. Using a large panel of serum samples from patients with acute and chronic hepatitis C, we demonstrated that the presence of antibodies with inhibition of binding activity was not associated with viral clearance. In conclusion, antibody-mediated inhibition of cellular HCV-LP binding represents a convenient system for the functional characterization of human anti-HCV antibodies, allowing the mapping of envelope neutralization epitopes targeted by naturally occurring antiviral antibodies.
Global Effects of Human Papillomavirus Type 18 E6/E7 in an Organotypic Keratinocyte Culture System
Authors: Garner-Hamrick Peggy A. , Fostel J. M. , Chien Wei-Ming , Banerjee N. Sanjib , Chow Louise T. , Broker Thomas R. , Fisher Chris
Published: August 2004

The effects of human papillomavirus type 18 (HPV-18) E6 and E7 proteins on global patterns of host gene expression in primary human keratinocytes grown in organotypic raft culture system were assessed. Primary human keratinocytes were infected with retroviruses that express the wild-type HPV-18 E6 and E7 genes from the native differentiation-dependent HPV enhancer-promoter. Total RNA was isolated from raft cultures and used to generate probes for querying Affymetrix U95A microarrays, which contain >12,500 human gene sequences. Quadruplicate arrays of each E6/E7-transduced and empty vector-transduced samples were analyzed by 16 pairwise comparisons. Transcripts altered in ≥12 comparisons were selected for further analysis. With this approach, HPV-18 E6/E7 expression significantly altered the expression of 1,381 genes. A large increase in transcripts associated with DNA and RNA metabolism was observed, with major increases noted for transcription factors, splicing factors, and DNA replication elements, among others. Multiple genes associated with protein translation were downregulated. In addition, major alterations were found in transcripts associated with the cell cycle and cell differentiation. Our study provides a systematic description of transcript changes brought about by HPV-18 E6/E7 in a physiologically relevant model and should furnish a solid source of information to guide future studies.
Subcellular Localization and Calcium and pH Requirements for Proteolytic Processing of the Hendra Virus Fusion Protein
Authors: Pager Cara Theresia , Wurth Mark Allen , Dutch Rebecca Ellis
Published: August 2004

Proteolytic cleavage of the Hendra virus fusion (F) protein results in the formation of disulfide-linked F
1
and F
2
subunits, with cleavage occurring after residue K
109
in the sequence GDVK↓L. This unusual cleavage site and efficient propagation of Hendra virus in a furin-deficient cell line indicate that the Hendra F protein is not cleaved by furin, the protease responsible for proteolytic activation of many viral fusion proteins. To identify the subcellular site of Hendra F processing, Vero cells transfected with pCAGGS-Hendra F or pCAGGS-SV5 F were metabolically labeled and chased in the absence and presence of inhibitors of exocytosis. The addition of carbonyl-cyanide-3-chlorophenylhydrazone, monensin, brefeldin A, or NaF-AlCl
3
or incubation of cells at 20°C all inhibited processing of the Hendra F protein, suggesting that cleavage of Hendra F occurs either in secretory vesicles budding from the
trans
-Golgi network or at the cell surface. In contrast to proteolytic cleavage of the simian virus 5 (SV5) F protein by the Ca
2+
-dependent protease furin, proteolytic cleavage of the Hendra F protein was not significantly inhibited by decreases in Ca
2+
levels following incubation with EGTA or A23187. However, in the presence of weak amines and H
+
V-ATPase inhibitors, known to raise intracellular pH, cleavage of Hendra F protein was inhibited while processing of the SV5 F protein was not significantly affected. The subcellular location, sensitivity to pH changes, and decreased Ca
2+
requirement suggest that the protease responsible for cleavage of Hendra F protein differs from proteases previously shown to be involved in the processing of other viral glycoproteins.
Glycosylation of Immunodominant Linear Epitopes in the Carboxy-Terminal Region of the Caprine Arthritis-Encephalitis Virus Surface Envelope Enhances Vaccine-Induced Type-Specific and Cross-Reactive Neutralizing Antibody Responses
Authors: Trujillo J. D. , Kumpula-McWhirter N. M. , Hötzel K. J. , Gonzalez M. , Cheevers W. P.
Published: August 2004

This study evaluated type-specific and cross-reactive neutralizing antibodies induced by immunization with modified surface glycoproteins (SU) of the 63 isolate of caprine arthritis-encephalitis lentivirus (CAEV-63). Epitope mapping of sera from CAEV-infected goats localized immunodominant linear epitopes in the carboxy terminus of SU. Two modified SU (SU-M and SU-T) and wild-type CAEV-63 SU (SU-W) were produced in vaccinia virus and utilized to evaluate the effects of glycosylation or the deletion of immunodominant linear epitopes on neutralizing antibody responses induced by immunization. SU-M contained two N-linked glycosylation sites inserted into the target epitopes by R539S and E542N mutations. SU-T was truncated at 518A, upstream from the target epitopes, by introduction of termination codons at 519Y and 521Y. Six yearling Saanen goats were immunized subcutaneously with 30 μg of SU-W, SU-M, or SU-T in Quil A adjuvant and boosted at 3, 7, and 16 weeks. SU antibody titers determined by indirect enzyme-linked immunosorbent assay demonstrated anamnestic responses after each boost. Wild-type and modified SU-induced type-specific CAEV-63 neutralizing antibodies and cross-reactive neutralizing antibodies against CAEV-Co, a virus isolate closely related to CAEV-63, and CAEV-1g5, an isolate geographically distinct from CAEV-63, were determined. Immunization with SU-T resulted in altered recognition of SU linear epitopes and a 2.8- to 4.6-fold decrease in neutralizing antibody titers against CAEV-63, CAEV-Co, and CAEV-1g5 compared to titers of SU-W-immunized goats. In contrast, immunization with SU-M resulted in reduced recognition of glycosylated epitopes and a 2.4- to 2.7-fold increase in neutralizing antibody titers compared to titers of SU-W-immunized goats. Thus, the glycosylation of linear immunodominant nonneutralization epitopes, but not epitope deletion, is an effective strategy to enhance neutralizing antibody responses by immunization.
Unique Features of Hepatitis C Virus Capsid Formation Revealed by De Novo Cell-Free Assembly
Authors: Klein Kevin C. , Polyak Stephen J. , Lingappa Jaisri R.
Published: August 2004

The assembly of hepatitis C virus (HCV) is poorly understood, largely due to the lack of mammalian cell culture systems that are easily manipulated and produce high titers of virus. This problem is highlighted by the inability of the recently established HCV replicon systems to support HCV capsid assembly despite high levels of structural protein synthesis. Here we demonstrate that up to 80% of HCV core protein synthesized de novo in cell-free systems containing rabbit reticulocyte lysate or wheat germ extracts assembles into HCV capsids. This contrasts with standard primate cell culture systems, in which almost no core assembles into capsids. Cell-free HCV capsids, which have a sedimentation value of ≈100S, have a buoyant density (1.28 g/ml) on cesium chloride similar to that of HCV capsids from other systems. Capsids produced in cell-free systems are also indistinguishable from capsids isolated from HCV-infected patient serum when analyzed by transmission electron microscopy. Using these cell-free systems, we show that HCV capsid assembly is independent of signal sequence cleavage, is dependent on the N terminus but not the C terminus of HCV core, proceeds at very low nascent chain concentrations, is independent of intact membrane surfaces, and is partially inhibited by cultured liver cell lysates. By allowing reproducible and quantitative assessment of viral and cellular requirements for capsid formation, these cell-free systems make a mechanistic dissection of HCV capsid assembly possible.
Evidence of Unique Genotypes of
Beak and Feather Disease Virus
in Southern Africa
Authors: Heath Livio , Martin Darren P. , Warburton Louise , Perrin Mike , Horsfield William , Kingsley Chris , Rybicki Edward P. , Williamson Anna-Lise
Published: August 2004

Psittacine beak and feather disease (PBFD), caused by
Beak and feather disease virus
(BFDV), is the most significant infectious disease in psittacines. PBFD is thought to have originated in Australia but is now found worldwide; in Africa, it threatens the survival of the indigenous endangered Cape parrot and the vulnerable black-cheeked lovebird. We investigated the genetic diversity of putative BFDVs from southern Africa. Feathers and heparinized blood samples were collected from 27 birds representing 9 psittacine species, all showing clinical signs of PBFD. DNA extracted from these samples was used for PCR amplification of the putative BFDV coat protein (CP) gene. The nucleotide sequences of the CP genes of 19 unique BFDV isolates were determined and compared with the 24 previously described sequences of BFDV isolates from Australasia and America. Phylogenetic analysis revealed eight BFDV lineages, with the southern African isolates representing at least three distinctly unique genotypes; 10 complete genome sequences were determined, representing at least one of every distinct lineage. The nucleotide diversity of the southern African isolates was calculated to be 6.4% and is comparable to that found in Australia and New Zealand. BFDVs in southern Africa have, however, diverged substantially from viruses found in other parts of the world, as the average distance between the southern African isolates and BFDV isolates from Australia ranged from 8.3 to 10.8%. In addition to point mutations, recombination was found to contribute substantially to the level of genetic variation among BFDVs, with evidence of recombination in all but one of the genomes analyzed.