bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of GABAA/Benzodiazepine Receptors on Clathrin‐Coated Vesicles from Rat Brain
Authors: Jalilian Tehrani Mohammad H. , Barnes Eugene M.
Published: December 2006

Abstract: To investigate the subcellular compartments that are involved in the endocytosis and intracellular trafficking of GABAA/benzodiazepine receptors, we have studied the distribution and properties of clonazepam‐displaceable binding of [3H]flunitrazepam to membrane fractions from rat brain. The microsomal fraction was subjected to density centrifugation and gel filtration to isolate clathrin‐coated vesicles. Homogeneity of the coated‐vesicle fraction was demonstrated by using electron microscopy and by analysis of clathrin subunits and clathrin light‐chain kinase. Vesicles exhibiting specific binding of [3H]flunitrazepam eluted from the sieving gel as a separate peak, which was coincident with that for coated vesicles. Scatchard analysis of equilibrium binding of [3H]flunitrazepam to coated vesicles yielded a KD value of 21 ± 4.7 nM and a Bmax value of 184 ± 28 fmol/mg. The KD value for coated vesicles was 12‐19‐fold that found with microsomal or crude synaptic membranes. This low‐affinity benzodiazepine receptor was not identified on any other subcellular fraction and thus appears to be a novel characteristic of coated vesicles. The Bmaxvalue for coated vesicles, expressed per milligram of protein, corresponded to 16 and 115% of that found for crude synaptic and microsomal membrane fractions, respectively. Because the trafficking of neurotransmitter receptors via clathrin‐coated vesicles is most likely to occur through endocytosis, the data suggest that an endocytotic pathway may be involved in the removal of GABAA/benzodiazepine receptors from the neuronal surfaces of the rat brain. This mechanism could play a role in receptor sequestration and down‐regulation that is produced by exposure to GABA and benzodiazepine agonists.
Elevated Stimulatory and Reduced Inhibitory G Protein α Subunits in Cerebellar Cortex of Patients with Dominantly Inherited Olivopontocerebellar Atrophy
Authors: Kish Stephen J. , Young L. Trevor , Li Peter P. , Siu Kin Po , Robitaille Yves , Ball Melvyn J. , Schut Lawrence , Warsh Jerry J.
Published: December 2006

Abstract: Although guanine nucleotide binding proteins (G proteins) are one of the critical components of signal transduction units for various membrane receptor‐mediated responses, little information is available regarding their status in brain of patients with neurodegenerative illnesses. We measured the immunoreactivity of G protein subunits (Gsα, Giα, Goα, Gq/11α, and Gβ) in autopsied cerebellar and cerebral cortices of 10 end‐stage patients with dominantly inherited olivopontocerebellar atrophy (OPCA) who all had severe loss of Purkinje cell neurons and climbing fiber afferents in cerebellar cortex. Compared with the controls, the long‐form Gsα (52‐kDa species) immunoreactivity was significantly elevated by 52% (p < 0.01) in the cerebellar cortex of the OPCA patients, whereas the Gi1α concentration was reduced by 35% (p < 0.02). No statistically significant differences were observed for Goα, Gi2α, Gβ1, Gβ2, or Gq/11α in cerebellar cortex or for any G protein subunit in the two examined cerebral cortical subdivisions (frontal and occipital). The cerebellar Gsα elevation could represent a compensatory response (e.g., sprouting, reactive synaptogenesis) by the remaining cerebellar neurons (granule cells?) to neuronal damage but also might contribute to the degenerative process, as suggested by the ability of Gsα, in some experimental preparations, to promote calcium flux. Further studies will be required to determine the actual functional consequences of the G protein changes in OPCA and whether the elevated Gsα is specific to OPCA cerebellum, because of its unique cellular pattern of morphological damage, or is found in brain of patients with other progressive neurodegenerative disorders.
Modulation of Neuropeptide FF Receptors by Guanine Nucleotides and Cations in Membranes of Rat Brain and Spinal Cord
Authors: Payza Kemal , Yang Hsiu‐Ying T.
Published: December 2006

Abstract: Using a radioligand binding assay, we examined ionic modulation and G protein coupling of neuropeptide FF(NPFF) receptors in membranes of rat brain and spinal cord. We found that NaCl (but not KCl or LiCl) and MgCl2 increased specific 125I‐YLFQPQRFamide (125I‐Y8Fa) binding to NPFF receptors in both tissues in a dose‐dependent manner, with optimal conditions being 60 mM NaCl and 1 mM MgCl2. Guanine nucleotides dose‐dependently inhibited specific 125I‐Y8Fa binding to rat brain and spinal cord membranes with maximal effects of 64 ± 6 and 71 ± 2%, respectively. The order of potency was nonhydrolyzable GTP analogues > GTP GDP > GMP, ATP. The guanine nucleotide inhibition was observed in the absence and presence of NaCl and MgCl2. The mechanism of inhibition in spinal cord membranes appeared to be a reduction in the number of NPFF receptors; in one experiment, control KD and Bmax values were 0.068 nM and 7.2 fmol/mg of protein, respectively, and with 0.1 μM guanylylimidodiphosphate the respective values were 0.081 nM and 4.9 fmol/mg, a 32% reduction in receptor number. Similar results were obtained with guanosine 5′‐0‐(3‐thiotriphosphate). Our data suggest that 125I‐Y8Fa binding sites in rat CNS are G protein‐coupled NPFF receptors regulated by GTP and cations.
Nine Residues Influence the Binding of α‐Bungarotoxin in α‐Subunit Region 185–200 of Human Muscle Acetylcholine Receptor
Authors: McCormick Daniel J. , Liebenow Jane A. , Griesmann Guy E. , Lennon Vanda A.
Published: December 2006

Abstract: Identification of residues in the skeletal muscle nicotinic acetylcholine receptor (AChR) that bind snake venom a‐neurotoxin antagonists of acetylcholine [e.g., α‐bungarotoxin (α‐BTx)] provides structural information about the neurotransmitter binding region of the receptor. Using synthetic peptides of the human AChR α‐subunit region 177–208, we previously localized a pharmacologically specific binding site for α‐BTx in segment 185–199. To define in more detail the residues that influence the binding of α‐BTx to this region, we prepared 16 peptide analogues of the α‐subunit segment 185–200, with the amino acid Lalanine sequentially replacing each native amino acid. Circular dichroism spectroscopy did not reveal changes in the secondary structure of the peptides except for the analogue in which Pro194 was substituted with alanine. This implies that any change in α‐BTx binding could be attributed to replacement of the native residue's side chain by alanine's methyl group, rather than to a change in the structure of the peptide. The influence of each substitution with alanine was determined by comparing the analogue to the parental sequence α 185–200 in solution‐phase competition with native human AChR for binding of 125I‐labeled α‐BTx. The binding of α‐BTx by analogue peptides with alanine substituted for Tyr190, Cys192, or Cys193 was greatly diminished. Binding of α‐BTx to peptides containing alanine replacements at Val188, Thr189, Pro194, Asp195, or Tyr198 was also reduced significantly (p < 0.003). An unanticipated finding was that substitution of alanine for Ser191 significantly increased α‐BTx binding (p < 0.003). The data imply that these nine amino acids influence the binding of the antagonist, α‐BTx, to the nicotinic acetylcholine receptor of human skeletal muscle, and confirm previous reports for certain contact residues for α‐BTX that were found in region α181‐200 of the Torpedo AChR.
Activation of Calcium‐Phospholipid‐Dependent Protein Kinase Enhances Benzodiazepine and Barbiturate Potentiation of the GABAA Receptor
Authors: Leidenheimer Nancy J. , Whiting Paul J. , Harris R. Adron
Published: December 2006

Abstract: The effect of calcium‐phospholipid‐dependent protein kinase (PKC) on GABAA receptor function was examined in Xenopus oocytes expressing recombinant human GABAA receptor using two‐electrode voltage‐clamp measurements. Phorbol 12‐myristate 13‐acetate (PMA), a potent activator of PKC, inhibited GABA‐gated chloride currents by ∼72% in oocytes expressing αlβ1γ2L subunit cDNAs. Phorbol 12‐monomyristate (PMM), a negative control analogue of PMA, did not alter GABAA receptor responses. To investigate whether activation of PKC could alter the modulatory responses of the receptor complex, the effect of PMA on benzodiazepine and barbiturate potentiation of GABA responses was assessed. In oocytes expressing αlβ1γ2s subunit cDNAs, diazepam (300 nM) potentiated GABA responses by ∼160%. Following PMA (5‐25 nM/) treatment, diazepam potentiation was significantly increased to 333%. No effect of the inactive phorbol ester PMM (25 nM) was observed on diazepam potentiation of GABA responses. PMA enhancement of diazepam potentiation of GABA responses was also observed in oocytes expressing αlβ1γ2Ssubunit cDNAs, indicating that the unique PKC site present in the Tγ2LL subunit is not required for observing the PMA effect. PMA (5‐25 nM) also enhanced pentobarbital potentiation of GABA responses. In oocytes expressing αlβ1γ2L subunit cDNAs, pentobarbital (25 μM) potentiated GABA receptor responses by ∼97%. Following treatment with PMA (5‐25 nM), pentobarbital potentiation of GABA responses increased to ∼ 156%. The present results suggest that protein phosphorylation may alter the coupling between the allosteric modulatory sites within the GABAA receptor complex.
Function of cardiac M3receptors
Authors: Wang H. , Lu Y. , Wang Z.
Published: December 2006

1 Since the initial identification of the M3subtype of muscarinic acetylcholine receptors (M3‐mAChR) in the heart, there have been increasing interest and advances in studies on the pathophysiological roles of M3‐mAChR in the heart. Recent studies from several laboratories have provided compelling and solid evidence in support of the important roles of M3‐mAChR in regulation and maintenance of cardiac function and in generation and progression of heart disease as well.

2 The functions of the cardiac M3‐mAChR revealed thus far include (i) M3‐mAChR regulation of heart rate and cardiac repolarization, (ii) modulation of inotropic effects, (iii) cytoprotection against ischaemic injuries of myocardium, (iv) regulation of cell‐to‐cell communication, and (v) participation in generation and maintenance of atrial fibrillation.

3 Signal transduction mechanisms underlying these pathophysiological functions have also been studied, which have allowed us to get insight into the following mechanistic aspects. (i) M3‐mAChR activates a delayed rectifying K+currentIKM3to participate in cardiac repolarization, negative chronotropic actions, and anti‐dysrhythmic (suppresses ischaemic dysrhythmias) as well as pro‐dysrhythmic (facilitates atrial fibrillation) actions. (ii) M3‐mAChR interacts with gap‐junctional channel connexin 43 to maintain cell–cell communication and excitation propagation. (iii) M3‐mAChR regulates intracellular phosphoinositide hydrolysis to improve cardiac contraction and haemodynamic function. (iv) M3‐mAChR activate anti‐apoptotic signalling molecules, enhances endogenous antioxidant capacity, and diminishes intracellular Ca2+overload, all of which contribute to protecting the heart against ischaemic injuries.

4 This article provides an overview of the potential roles of the M3‐mAChR in parasympathetic control of heart function under normal physiological conditions and in the setting of a variety of pathological processes including heart failure, myocardial ischaemia and dysrhythmias.
Teaching the Middle Ages on Film: Visual Narrative and the Historical Record
Authors: Driver Martha
Published: December 2006

This article provides an overview of some of the contentious issues concerning the role of film in historical studies of the Middle Ages. Is it appropriate to point out inaccuracies of detail in historical film? As a collective commercial enterprise, is a movie inherently limited in its portrayal of the past, and does this matter? How does film convention affect representation? Can movies err on the side of historical truth? What are the uses of purposeful or intentional anachronism? How have perceptions of movies changed with the advent of the paratext on DVD? How might movies with medieval themes be used effectively in the classroom? Responses to these and related questions are drawn from writings on film from 1915 to the present.
Effect of Cancer Screening and Desirable Health Behaviors on Functional Status, Self‐Rated Health, Health Service Use and Mortality
Authors: Fillenbaum Gerda G. , Burchett Bruce M. , Kuchibhatla Maragatha N. , Cohen Harvey J. , Blazer Dan G.
Published: December 2006

OBJECTIVES: To determine whether some health behaviors of older people (e.g., obtaining cancer screens) have a limited and others (e.g., exercise) have a broad association with population‐level health status 4 to 6 years later.

DESIGN: Longitudinal cohort.

SETTING: North Carolina five‐county urban and rural area.

PARTICIPANTS: Representative community residents aged 71 and older (Duke Established Populations for Epidemiologic Studies of the Elderly; African American, n=1,256; white, n=974) who provided information on cancer screening and health behaviors.

MEASUREMENTS: Demographics, health conditions, functional status, health service use, health insurance. Dependent measures were functional status and self‐rated health 4 years later, hospitalization within 4 years, and death within 6 years. Data were analyzed using descriptive statistics, multivariable logistic regression, and Cox proportional hazards.

RESULTS: In fully adjusted analyses, cancer screening had no significant protective association with functional status, self‐rated health, hospitalization, or death. Smoking was a risk factor for hospitalization (odds ratio (OR)=1.48, 95% confidence interval (CI)=1.07–2.05), and death (hazard rate (HR)=1.81, 95% CI=1.47–2.23). Sufficient food reduced hospitalization (OR=0.38, 95% CI=0.15–0.94) and mortality (HR=0.70, 95% CI=0.49–1.02). Regular exercise protected against poor mobility (OR=0.56, 95% CI=0.41–0.77), and poor self‐rated health (OR=0.61, 95% CI=0.45–0.82). Lower activity level increased the hazard of death (HR=1.18, 95% CI=1.03–1.36).

CONCLUSION: Disease‐specific screens are important at an individual level but, because of low incidence of condition and comorbidity, may not be associated with population‐level health 4 to 6 years later. Practice of health behaviors with a broader focus is associated, at a population level, with better functional status and self‐rated health and lower rates of hospitalization and death 4 to 6 years later.
Effects of Muscle Strength Training and Megestrol Acetate on Strength, Muscle Mass, and Function in Frail Older People
Authors: Sullivan Dennis H. , Roberson Paula K. , Smith Eugene S. , Price J. Allen , Bopp Melinda M.
Published: December 2006

OBJECTIVES: To determine the independent and combined effects of progressive resistance muscle strength training (PRMST) and megestrol acetate (MA) on strength, muscle mass, and function in older recuperative care patients.

DESIGN: Double‐blind, randomized, controlled intervention using a two‐by‐two factorial design and conducted between 1999 and 2001.

SETTING: University‐affiliated Department of Veterans Affairs hospital.

PARTICIPANTS: Twenty‐nine patients (mean age 79.4 ± 7.4, 90% white) aged 65 and older and had recent functional decline.

INTERVENTIONS: After randomization to one of four treatment groups (low‐resistance exercises plus 800 mg per day of MA or a placebo or high‐intensity PRMST plus 800 mg/d of MA or placebo), subjects received training and the drug or placebo for 12 weeks.

MEASUREMENTS: Change in muscle strength, mid‐thigh muscle area, and aggregate functional performance score as assessed using analysis of covariance.

RESULTS: Five subjects withdrew from the study before its completion. Based on intent‐to‐treat analyses, subjects who received high‐intensity PRMST and placebo experienced the greatest strength gains. The addition of MA was associated with worse outcomes than with high‐intensity exercise training alone, especially with regard to the leg exercises. Post hoc analysis demonstrated that subjects who received high‐intensity PRMST and placebo experienced significantly greater percentage increases in leg strength than subjects in either of the MA treatment groups (P<.05 for each comparison). There was also a significant negative effect of MA on physical function. In general, subjects who received MA experienced a deterioration in aggregate physical function scores, whereas the remaining subjects improved (−0.80±0.40 vs 0.48±0.41, P=.04). There was not a significant interaction between exercise and MA for any outcome.

CONCLUSION: High‐intensity PRMST is a safe and well‐tolerated exercise regimen for frail elderly patients. The addition of MA appears to blunt the beneficial effects of PRMST, resulting in less muscle strength and functional performance gains.
Combination Tibial Plateau Leveling Osteotomy and Cranial Closing Wedge Osteotomy of the Tibia for the Treatment of Cranial Cruciate Ligament‐Deficient Stifles with Excessive Tibial Plateau Angle
Authors: TALAAT MIRIAM B. , KOWALESKI MICHAEL P. , BOUDRIEAU RANDY J.
Published: December 2006

Objective— To describe a surgical technique, and outcome, for treatment of cranial cruciate ligament (CrCL) deficient stifle joints with excessive tibial plateau angle (TPA) by combined tibial plateau leveling osteotomy and cranial closing wedge osteotomy (TPLO/CCWO).

Study Design— Retrospective clinical study.

Animals— Fifteen client‐owned dogs (18 stifle joints).

Methods— Medical records of dogs that had TPLO/CCWO were reviewed. Pre‐ and postoperative TPA, CCWO technique, method of fixation and complications were recorded. In‐hospital re‐evaluation of limb function and length of time to radiographic healing was reviewed. Long‐term outcome was assessed by owner telephone interview.

Results— Mean pre‐ and postoperative TPA was 42° and 8°, respectively. The Slocum biradial saw was used to create the CCWO in 4 stifle joints (mean postoperative TPA, 16°) and a sagittal saw was used in 14 stifle joints (mean postoperative TPA, 5°). Postoperative surgical complications were documented in 77.8% of cases; including patellar tendon thickening (61.1%), and implant loosening or breakage (27.8%), seroma formation (11.1%), and local irritation (11.1%). A second surgical procedure was performed in one‐third of cases primarily to retrieve implants. Mean time to documented radiographic healing was 18 weeks. Final in‐hospital re‐evaluation of limb function (mean, 23 weeks postoperatively) was recorded as no lameness in 73.3% and mild lameness in 26.7%. All interviewed owners were satisfied with outcome and 90.9% reported marked improvement or a return to preinjury status.

Conclusions— Long‐term clinical outcome of TPLO/CCWO was very good in dogs with excessive TPA, with high owner satisfaction. Longer healing times and a higher complication rate were observed compared with TPLO alone.

Clinical Relevance— TPLO/CCWO of the tibia in stifle joints with excessive TPA allows for full correction of the TPA to 5° without eliminating buttress support of the tibial tuberosity.
Synthesis and Application of Stable Copper Oxide Nanoparticle Suspensions for Nanoparticulate Film Fabrication
Authors: Kida Tetsuya , Oka Takanori , Nagano Masamitsu , Ishiwata Yoichi , Zheng Xu‐Guang
Published: December 2006

Colloidal suspensions of copper oxide (CuO) nanoparticles were prepared by an alcothermal method, in which copper acetate was reacted with sodium hydroxide in the presence of acetic acid in ethanol at 78°C. The prepared suspension was stable for up to 1 month without stabilizers such as surfactants. Transmission electron microscopy analyses revealed that the suspension contained nanosized CuO particles of 5–10 nm size with a narrow size distribution. Nanoparticulate CuO films packed with grains smaller than 60 nm were fabricated on Si substrates by spin coating a suspension of CuO nanoparticles and subsequent heat treatment at 500°C.
Electrochemical Behavior of TiCN–Ni‐Based Cermets
Authors: Manoj Kumar B. V. , Balasubramaniam R. , Basu Bikramjit
Published: December 2006

The electrochemical behavior of TiCN–20 wt% Ni cermets containing different secondary carbides (10 wt% WC, NbC, TaC, and HfC) was investigated in freely aerated 0.2 mol/L sulfuric acid. A comparison has also been made with polarization behavior of pure Ni. All the materials (except HfC‐containing cermet) exhibited active–passive polarization behavior, characterized by two passive regions. The first passive region, obtained on polarizing past the zero current potential, was attributed to passive film formation due to TiCN, while the second passive film is presumably due to the presence of a Ni binder phase. The passivation behavior in the case of cermets containing various secondary carbides (WC, TaC, and NbC) was similar to baseline TiCN–20Ni cermets, while poor passivation behavior was observed in the case of TiCN–20Ni–10HfC. Efforts have been made to correlate the passivation behavior with the microstructural characteristics of sintered cermets.
Allele Frequency of D13S325 and D13S892 in Two Populations
Authors: Wang Zhuo , Wang Yanyun , Zhou Bin , Du Bin , Zhang Beilei , Zhang Gengqian , Jia Yi , Zhu Yinhua , Wei Ye Sheng , Zhang Lin
Published: December 2006

POPULATIONS: Chinese Han and Thai.
Introduction to the special issue on the role of nonfarm income in poverty reduction: evidence from Asia and East Africa
Authors: Otsuka Keijiro , Yamano Takashi
Published: December 2006

In this special issue, we present seven studies that collectively attempt to investigate the role of non‐farm income in long‐term and short‐term poverty reduction in Asia and Africa. The first four studies out of the seven use long‐term panel data over two decades in the Philippines, Thailand, Bangladesh, and India. These studies show drastic increases in non‐farm income shares and corresponding declines in poverty levels over time, especially in the Philippines and Thailand. Education levels of household members and returns to education also increased significantly in these countries. The remaining three studies use cross‐sectional and short‐term panel data from Ethiopia, Kenya, and Uganda. These African studies show high proportions of poor households and low shares of non‐farm income that are somewhat comparable to the situation in the 1980s described in the Asian studies. Without the Green Revolution that provided stable farm income and potential financial resources to invest in children' education in Asia, it is not clear if African farm households can follow the Asian examples.
Heart disease prevention in women: Promoting exercise
Authors: Perry Cindy K , Bennett Jill A.
Published: December 2006

Purpose: To reinforce the importance of exercise in reducing heart disease in women and to describe motivational interviewing (MI), an effective and efficient approach to promoting exercise with women in a brief office visit with a nurse practitioner (NP).

Data sources: Information was obtained from a literature review. Two brief examples from clinical practice are presented.

Conclusions: Although exercise can reduce the risk of heart disease in women, most women do not exercise enough to achieve a risk reduction. Although health promotion is a key goal of the NP, it can be difficult to incorporate in a busy practice. When time is limited, brief MI interactions can be effective in less than 10 min, and the results surpass those of the traditional advice to exercise.

Implications for practice: MI is an effective approach to exercise counseling that the NP can quickly learn and successfully conduct within the confines of a brief office visit.
Optical trapping for undergraduates
Authors: Appleyard D. C. , Vandermeulen K. Y. , Lee H. , Lang M. J.
Published: December 2006

The detailed design of a robust and inexpensive optical trap system is presented. The system features high-sensitivity back focal plane position detection, mechanically controlled specimen stage movement, and fluorescence imaging to provide broad experimental applications. Three educational experimental modules are described to cover basic concepts in optical trapping and biophysics at a level appropriate for undergraduate students.
Nucleocytoplasmic Shuttling of Bovine Papillomavirus E1 Helicase Downregulates Viral DNA Replication in S Phase
Authors: Hsu Chiung-Yueh , Mechali Francisca , Bonne-Andrea Catherine
Published: December 2006

The papillomavirus E1 protein is essential for the initiation of viral replication. We previously showed that the bovine papillomavirus E1 protein is unstable and becomes resistant to ubiquitin-mediated degradation when tightly bound to cyclin E-cyclin-dependent kinase 2 (Cdk2) before the start of DNA synthesis. However, neither the protection nor the targeted degradation of E1 appears to depend on its phosphorylation by Cdk. Here, we report that Cdk phosphorylation of E1 is also not a prerequisite for the initiation of viral DNA replication either in vitro or in vivo. Nevertheless, we found that phosphorylation of one Cdk site, Ser283, abrogates E1 replicative activity only in a cellular context. We show that this site-specific phosphorylation of E1 drives its export from the nucleus and promotes its continuous nucleocytoplasmic shuttling. In addition, we find that E1 shuttling occurs in S phase, when cyclin A-Cdk2 is activated. E1 interacts with the active cyclin A-Cdk2 complex and is phosphorylated on Ser283 by this kinase. These data suggest that the phosphorylation of E1 on Ser283 is a negative regulatory event that is involved in preventing the amplification of viral DNA during S phase. This finding reveals a novel facet of E1 regulation that could account for the variations of the viral replication capacity during different cell cycle phases, as well as in different stages of the viral cycle.
Identification of Linear Heparin-Binding Peptides Derived from Human Respiratory Syncytial Virus Fusion Glycoprotein That Inhibit Infectivity
Authors: Crim Roberta L. , Audet Susette A. , Feldman Steven A. , Mostowski Howard S. , Beeler Judy A.
Published: December 2006

It has been shown previously that the fusion glycoprotein of human respiratory syncytial virus (RSV-F) interacts with cellular heparan sulfate. Synthetic overlapping peptides derived from the F-protein sequence of RSV subtype A (strain A2) were tested for their ability to bind heparin using heparin-agarose affinity chromatography (HAAC). This evaluation identified 15 peptides representing eight linear heparin-binding domains (HBDs) located within F
1
and F
2
and spanning the protease cleavage activation site. All peptides bound to Vero and A549 cells, and binding was inhibited by soluble heparins and diminished by either enzymatic treatment to remove cell surface glycosaminoglycans or by treatment with sodium chlorate to decrease cellular sulfation. RSV-F HBD peptides were less likely to bind to glycosaminoglycan-deficient CHO-745 cells than parental CHO-K1 cells that express these molecules. Three RSV-F HBD peptides (F16, F26, and F55) inhibited virus infectivity; two of these peptides (F16 and F55) inhibited binding of virus to Vero cells, while the third (F26) did not. These studies provided evidence that two of the linear HBDs mapped by peptides F16 and F55 may mediate one of the first steps in the attachment of virus to cells while the third, F26, inhibited infectivity at a postattachment step, suggesting that interactions with cell surface glycosaminoglycans may play a role in infectivity of some RSV strains.
Viral Hijacking of Mitochondrial Lysyl-tRNA Synthetase
Authors: Kaminska Monika , Shalak Vyacheslav , Francin Mathilde , Mirande Marc
Published: December 2006

The primer for reverse transcription of the human immunodeficiency virus type 1 (HIV-1) genome is tRNA3Lys. During assembly of HIV-1 particles, tRNA3Lys is taken up from the host cell along with lysyl-tRNA synthetase (LysRS), the tRNA binding protein that specifically aminoacylates the different tRNALysisoacceptors. In humans, the cytoplasmic and mitochondrial species of LysRS are encoded by a single gene by means of alternative splicing. Here, we show that polyclonal antibodies directed to the full-length cytoplasmic enzyme equally recognized the two enzyme species. We raised antibodies against synthetic peptides that allowed discrimination between the two enzymes and found that mitochondrial LysRS is the only cellular source of LysRS detected in the virions. These results open new routes for understanding the molecular mechanisms involved in the specific packaging of tRNA3Lys into viral particles.
Inhibitory Effect of Gamma Interferon on BK Virus Gene Expression and Replication
Authors: Abend Johanna R. , Low Jonathan A. , Imperiale Michael J.
Published: December 2006

BK virus (BKV) is widely accepted to be the causative agent of polyomavirus nephropathy. In immunocompromised individuals, especially kidney transplant recipients, BKV can replicate in kidney epithelial cells, causing loss of renal function and eventual destruction of the graft. Advances in immunosuppressive therapies may be partially responsible for the increasing incidence of polyomavirus nephropathy among transplant recipients by more effectively eliminating components of the immune system, such as gamma interferon (IFN-γ)-producing lymphocytes, that keep BKV infections at a subclinical level. In this study, we investigated the role of IFN-γ in regulating lytic infection by BKV. Treatment with IFN-γ inhibited the expression of the viral early protein large tumor antigen (TAg) and the late protein VP1 in a dose-dependent manner. We detected 1.6- and 12-fold reductions in TAg transcripts at 48 and 96 h postinfection, respectively, with 250 U/ml IFN-γ, suggesting that IFN-γ-mediated inhibition occurs at the level of transcription. Furthermore, IFN-γ inhibited the level of viral progeny production as much as 50-fold at a multiplicity of infection (MOI) of 0.5 and 80-fold at an MOI of 0.1. The inhibitory effects of IFN-γ were similar for three different strains of BKV examined. These results indicate an important role for IFN-γ in regulating BKV lytic infection.
Comparison of the Influenza Virus-Specific Effector and Memory B-Cell Responses to Immunization of Children and Adults with Live Attenuated or Inactivated Influenza Virus Vaccines
Authors: Sasaki Sanae , Jaimes Maria C. , Holmes Tyson H. , Dekker Cornelia L. , Mahmood Kutubuddin , Kemble George W. , Arvin Ann M. , Greenberg Harry B.
Published: December 2006

Cellular immune responses to influenza virus infection and influenza virus vaccination have not been rigorously characterized. We quantified the effector and memory B-cell responses in children and adults after administration of either live attenuated (LAIV) or inactivated (TIV) influenza virus vaccines and compared these to antibody responses. Peripheral blood mononuclear cells were collected at days 0, 7 to 12, and 27 to 42 after immunization of younger children (6 months to 4 years old), older children (5 to 9 years old), and adults. Influenza virus-specific effector immunoglobulin A (IgA) and IgG circulating antibody-secreting cells (ASC) and stimulated memory B cells were detected using an enzyme-linked immunospot assay. Circulating influenza virus-specific IgG and IgA ASC were detected 7 to 12 days after TIV and after LAIV immunization. Seventy-nine percent or more of adults and older children had demonstrable IgG ASC responses, while IgA ASC responses were detected in 29 to 53% of the subjects. The IgG ASC response rate to LAIV immunization in adults was significantly higher than the response rate measured by standard serum antibody assays (26.3% and 15.8% by neutralization and hemagglutination inhibition assays, respectively). IgG ASC and serum antibody responses were relatively low in the younger children compared to older children and adults. TIV, but not LAIV, significantly increased the percentage of circulating influenza virus-specific memory B cells detected at 27 to 42 days after immunization in children and adults. In conclusion, although both influenza vaccines are effective, we found significant differences in the B-cell and antibody responses elicited after LAIV or TIV immunization in adults and older children and between young children and older age groups.
Solidification–stabilization of organic and inorganic contaminants using portland cement: a literature review
Authors: Paria Santanu , Yuet Pak K
Published: December 2006

The treatment of hazardous wastes using cement-based solidification–stabilization (S–S) is of increasing importance as an option for remediating contaminated sites. Indeed, among the various treatment techniques, S–S is one of the most widely used methods for treating inorganic wastes. To enhance the application of S–S and to further develop this technology for site remediation, particularly for organic contaminants, it is important to have a better understanding of the mechanisms involved in the process. The primary objective of this review is to survey the current knowledge in this subject, focusing on (i) cement chemistry, (ii) the effects of inorganic (heavy metals) and organic compounds on cement hydration, and (iii) the mechanisms of immobilization of different organic and inorganic compounds. For heavy metals, cement-based S–S technology has been shown to be effective in immobilizing the contaminants, even without any additives. In applying cement-based S–S for treating organic contaminants, the use of adsorbents such as organophilic clay and activated carbon, either as a pretreatment or as additives in the cement mix, can improve contaminant immobilization in the solidified–stabilized wastes. The concept of degradative solidification–stabilization, which combines chemical degradation with conventional solidification–stabilization, seems promising, although further study is required to assess its technical and economic feasibility.Key words: cement, contaminated soil, immobilization, organics, precipitation, adsorption.
Characterization of the human proliferating cell nuclear antigen physico-chemical properties: aspects of double trimer stability
Authors: Naryzhny Stanislav N. , DeSouza Leroi V. , Siu K.W. Michael , Lee Hoyun
Published: December 2006

Its toroidal structure allows the proliferating cell nuclear antigen (PCNA) to wrap around and move along the DNA fiber, thereby dramatically increasing the processivity of DNA polymerization. PCNA is also involved in the regulation of a wide spectrum of other biological functions, including epigenetic inheritance. We have recently reported that mammalian PCNA forms a double trimer complex, which may be critically important in coordinating DNA replication and other cellular functions. To gain a better understanding of the stability of PCNA complexes, we characterized the physico-chemical properties of the PCNA structure by in vivo and in vitro approaches. The data obtained by gel filtration and nondenaturing gel electrophoresis of native PCNA molecules confirm our previous observations, obtained using formaldehyde crosslinking, in which PCNA exists in the cell as a double trimer. We have also found that optimal pH (pH 6.5–7.5) is critical for the stability of the PCNA structure. The presence or absence of ATP, dithiothreitol, and Mg2+does not affect the stability of the PCNA trimer or double trimer. However, 0.02% SDS can effectively inhibit PCNA double trimer, but not single trimer, formation. Interestingly, glycerol and ammonium sulfate significantly destabilize both PCNA trimer and double trimer structures.
Inactivation mechanism of the β-ketoacyl-[acyl carrier protein] reductase of bacterial type-II fatty acid synthase by epigallocatechin gallate
Authors: Li Bing-Hui , Zhang Rui , Du Ya-Tao , Sun Ying-Hui , Tian Wei-Xi
Published: December 2006

Epigallocatechin gallate (EGCG), a major compound from green tea, reversibly inhibits β-ketoacyl-[acyl carrier protein] reductase (FabG) from Escherichia coli. In this study, we found that EGCG exhibited an atypical time-dependent inhibition of FabG, which possibly resulted from the EGCG-induced aggregation of FabG. It was observed that FabG inactivation and aggregation occurred nearly simultaneously, with a lag time that decreased with increasing EGCG concentration. These results suggest that some chemical reactions, required for aggregation and inactivation, occurred during the lag time. Since EGC was detected by HPLC after the incubation of EGCG with FabG, EGCG probably covalently modified FabG. These further results showed that 1 tetramer of FabG must be modified by several, possibly 4, EGCG molecules before the formation of FabG aggregates. FabG aggregation was a first-order reaction independent of protein concentration. Due to an initial lag time, the first-order rate of aggregation gradually increased, reaching a maximal and constant value. The effect of increasing concentration of EGCG on the first-order rate constant for aggregation indicated that EGCG bound to FabG by affinity labeling. Based on the results, we propose a mechanism for the interaction of EGCG with FabG:EGCG first binds reversibly to each subunit of FabG, followed by covalent modification and then aggregation of the 4 EGCG-modified subunits.
Purification and characterization of a nonpolymerizing long-pitch actin dimer
Authors: Sweeting Braden , Dawson John F.
Published: December 2006

Atomic resolution structures of filamentous actin have not been obtained owing to the self-association of actin under crystallization conditions. Obtaining short filamentous actin complexes of defined lengths is therefore a highly desirable goal. Here we report the production and isolation of a long-pitch actin dimer employing chemical crosslinking between wild-type actin and Q41C/C374A mutant actin. The Q41C/C374A mutant actin possessed altered polymerization properties, with a 2-fold reduction in the rate of elongation and an increased critical concentration relative to wild-type actin. The Q41C/C374A mutant actin also displayed an increase in the IC50for DNase I, a pointed-end actin-binding protein. The long-pitch dimer was bound by DNase I to prevent polymerization and purified. It was found that each actin dimer is bound by 2 DNase I molecules, 1 likely bound to each of the actin protomers. The long-pitch dimer bound by DNase I did not form short F actin structures, as assessed by the binding of rhodamine–phalloidin.
A SPACE EFFICIENT BIT-PARALLEL ALGORITHM FOR THE MULTIPLE STRING MATCHING PROBLEM
Authors: CANTONE DOMENICO , FARO SIMONE
Published: December 2006

Finite (nondeterministic) automata are very useful building blocks in the field of string matching. This is particularly true in the case of multiple pattern matching, where the use of factor-based automata can reduce substantially the number of computational steps when the patterns have large common factors.

Direct simulation of nondeterministic automata can be performed very efficiently using the bit-parallelism technique, though this is not necessarily true for factor-based automata.

In this paper we present an algorithm for the multiple string matching problem, based on the bit-parallel simulation of nondeterministic factor-based automata which satisfy a particular ordering condition. We also show how to enforce such condition by suitably modifying a minimal initial automaton, through equivalence preserving transformations. The resulting automaton turns out to be smaller than the corresponding maximal automata used by existing bit-parallel algorithms, as they do not take any advantage of common factors in patterns.
DYNAMIC ALLOCATION OF FINITE AUTOMATA STATES FOR FAST STRING RECOGNITION
Authors: NGASSAM ERNEST KETCHA , WATSON BRUCE W. , KOURIE DERRICK G.
Published: December 2006

The spatial and temporal locality of reference on which cache memory relies to minimize cache swaps, is exploited to design a new algorithm for finite automaton string recognition. It is shown that the algorithm, referred to as the Dynamic State Allocation algorithm outperforms the traditional table-driven algorithm for strings that tend to repeatedly access the same set of states, provided that the string is long enough to amortize the allocation cost. Further improvements on the algorithm result in even better performance.
BIT-PARALLEL COMPUTATION OF LOCAL SIMILARITY SCORE MATRICES WITH UNITARY WEIGHTS
Authors: HYYRÖ HEIKKI , NAVARRO GONZALO
Published: December 2006

Local similarity computation between two sequences permits detecting all the relevant alignments present between subsequences thereof. A well-known dynamic programming algorithm works in time O(mn), m and n being the lengths of the subsequences. The algorithm is rather slow when applied over many sequence pairs. In this paper we present the first bit-parallel computation of the score matrix, for a simplified choice of scores. If the computer word has w bits, then the resulting algorithm works in O(mn log min (m, n, w)/w) time, achieving up to 8-fold speedups in practice. Some DNA comparison applications use precisely the simplified scores we handle, and thus our algorithm is directly applicable. In others, our method could be used as a raw filter to discard most of the strings, so the classical algorithm can be focused only on the substring pairs that can yield relevant results.
From Suffix Trees to Suffix Vectors
Authors: Prieur Élise , Lecroq Thierry
Published: December 2006

We present a first formal setting for suffix vectors that are space economical alternative data structures to suffix trees. We give two linear algorithms for converting a suffix tree into a suffix vector and conversely. We enrich suffix vectors with formulas for counting the number of occurrences of repeated substrings. We also propose an alternative implementation for suffix vectors that should outperform the existing one.
FAST BROADCASTING WITH BYZANTINE FAULTS
Authors: PAQUETTE MICHEL , PELC ANDRZEJ
Published: December 2006

We construct and analyze a fast broadcasting algorithm working in the presence of Byzantine component faults. Such faults are particularly difficult to deal with, as faulty components may behave arbitrarily (even maliciously) as transmitters, by either blocking, rerouting, or altering transmitted messages in a way most detrimental to the broadcasting process. We assume that links and nodes of a communication network are subject to Byzantine failures, and that faults are distributed randomly and independently, with link failure probability p and node failure probability q, these parameters being constant and satisfying the inequality (1 - p)2(1 - q) > 1/2. A broadcasting algorithm, working in an n-node network, is called almost safe if the probability of its correctness is at least 1 - 1/n, for sufficiently large n. Thus the robustness of the algorithm grows with the size of the network. Our main result is the design and analysis of an almost safe broadcasting algorithm working in time O( log 2 n) and using O(n log n) messages in n-node networks. Under a stronger assumption on failure probability parameters, namely (1 - p)2(1 - q)2 > 1/2, our algorithm can be modified to work in time O( log 2 n/ log log n), also using O(n log n) messages. The novelty of our algorithm is that it can cope with the most difficult type of faults, potentially affecting all components of the network (both its links and nodes), and that it is simultaneously robust and efficient.
MINIMIZING TOTAL WEIGHTED COMPLETION TIME ON IDENTICAL PARALLEL BATCH MACHINES
Authors: LI SHUGUANG , LI GUOJUN , QI XINGQIN
Published: December 2006

We study the problem of scheduling n jobs with release dates on m identical parallel batch machines to minimize the total weighted completion time of the jobs. A batch machine with capacity B (B < n) is able to process a batch of up to B jobs simultaneously and the time needed is equal to the maximum processing time among the jobs in the batch. This model is motivated by applications in the manufacturing of integrated circuits. In this paper, we present a polynomial time approximation scheme (PTAS) for this problem.
A PRIORITY QUEUE WITH THE WORKING-SET PROPERTY
Authors: ELMASRY AMR
Published: December 2006

A new priority queue is introduced, for which the cost to insert a new item is constant and the cost to delete the item x with the minimum value is O( log kx), where kx, is the number of items that are inserted after x and are still in the heap when x is deleted. We achieve the above bounds in both the amortized case and the worst case.
THE COMPUTATIONAL COMPLEXITY OF AVOIDING FORBIDDEN SUBMATRICES BY ROW DELETIONS
Authors: WERNICKE SEBASTIAN , ALBER JOCHEN , GRAMM JENS , GUO JIONG , NIEDERMEIER ROLF
Published: December 2006

We initiate a systematic study of the ROW DELETION(B) problem on matrices: Given an input matrix A and a fixed "forbidden submatrix" B, the task is to remove a minimum number of rows from A such that no row or column permutation of B occurs as a submatrix in the resulting matrix. An application of this problem can be found, for instance, in the construction of perfect phylogenies. Establishing a strong connection to variants of the NP-complete HITTING SET problem, we describe and analyze structural properties of B that make ROW DELETION(B)NP-complete. On the positive side, the close relation with HITTING SET problems yields constant-factor polynomial-time approximation algorithms and fixed-parameter tractability results.
Cockroach Allergen Biology and Mitigation in the Indoor Environment
Authors: Gore J. Chad , Schal Coby
Published: December 2006

For nearly a half century, cockroaches have been recognized as a major cause of asthma morbidity in the urban, inner-city environment. Several cockroach-produced allergens have been identified and characterized, and a few have been produced as recombinant proteins. Recent research has moved beyond clinical, patient-based investigations to a more entomological perspective that addresses the production, physiological regulation, and developmental expression of cockroach allergens, thus providing insight into their functional biology and their relationship to current cockroach control strategies. Although successful removal of cockroach allergens from the infested environment has been difficult to accomplish with remedial sanitation, large-scale reductions in cockroach allergens below clinically relevant thresholds have recently been realized through suppression of cockroach populations. Here we review the current understanding of cockroach allergen biology and the demographics associated with human exposure and sensitization. We also critically evaluate allergen mitigation studies from an entomological perspective, highlighting disparities between successful and failed attempts to lessen the cockroach allergen burden in homes.