bluuebunny/crossref_metadata_2025 huggingface dataset:
The synthesis of some mechanistic probes for sialic acid processing enzymes and the labeling of a sialidase fromTrypanosoma rangeli
Authors: Watts Andrew G , Withers Stephen G
Published: January 2005

Sialyl hydrolases, trans-sialidases, and sialyl transferases are biologically important enzymes that are responsible for the incorporation and removal of sialic acid residues, which decorate many cell surface glycocongugates. Two fluorinated sialic acid derivatives have been synthesized as mechanism-based inactivators, to probe the catalytic mechanisms through which sialidases and trans-sialidases operate. Both compounds are known to be covalent inactivators of a trans-sialidase from Trypanosoma cruzi. Here, 3-fluorosialosyl fluoride has been found to covalently label the catalytic nucleophile of a sialidase from T. rangeli, and the residue involved is shown to be Tyr346 within the sequence DENSGYSSVL. This is the first demonstration that sialidases operate through a covalent glycosyl-enzyme intermediate, strongly suggesting a common catalytic mechanism amongst all members of the sialidase superfamily. CMP-3-fluoro sialic acid is a competitive inhibitor of sialyl transferases and was synthesized via a two-step enzymatic process from commercially available N-acetyl mannosamine, 3-fluoropyruvic acid, and cytidine triphosphate in around 84% yield.Key words: sialidase, mechanism, labeling, nucleophile, inhibitor.
Molecular modeling utilizing purple acid phosphatase biomimetic models
Authors: Paes Lilian W , Faria Roberto B , Machuca-Herrera Juan O , Neves Ademir , Machado Sérgio P
Published: January 2005

Purple acid phosphatases (PAPs) constitute a new class of metalloenzymes that catalyze the hydrolysis of certain phosphate esters, including nucleoside di- and triphosphates and aryl phosphates, under acidic conditions. To provide some insight into these metalloenzymes we have performed quantum chemical and molecular mechanics calculations based on the mixed-valence [FeIIFeIII(BPBPMP)(OAc)2]+model complex (1) (H2BPBPMP = 2-bis[{(2-pyridylmethyl)-aminomethyl}-6-{(2-hydroxybenzyl)-(2-pyridylmethyl)}-aminomethyl]-4-methylphenol). The geometric and the vibrational parameters calculated by molecular mechanics show that the force fields established in this work reproduce the binuclear iron core with µ-phenoxo or µ-alkoxo and di-µ-acetate bridges presented in the PAPs model complexes. The atomic orbital analysis of the SOMO contributions indicated that the FeIIIatom and the terminal phenolate are involved in the phenolate to FeIIIcharge transfer electronic transition in 1 as argued from electronic spectroscopic data in the PAPs. Key words: mixed-valence FeIIFeIIIcomplex, purple acid phosphatases, molecular modeling.
Group IV phosphinimide amide complexes
Authors: Hollink Emily , Wei Pingrong , Stephan Douglas W
Published: January 2005

Complexes of formula TiCp(NPR3)(NMe2)2 (R = t-Bu 1, Ph 2) were prepared via salt metathesis of TiCp(NPR3)Cl2 with a slight excess of LiNMe2. The species Ti(NP-t-Bu3)(NMe2)3 (3) was obtained as a by-product. The related derivative ZrCp(NP-t-Bu3)(NMe2)2 (4) was also prepared. Reaction of TiCp(NP-t-Bu3)Cl2 with LiNHC6H3(2,6-i-Pr2) afforded TiCp(NP-t-Bu3)(NHC6H3(2,6-i-Pr2))Cl (5) and Ti(NP-t-Bu3)(NHC6H3(2,6-i-Pr2))3 (6). In a similar manner, the Zr analogs ZrCp(NP-t-Bu3)(NHC6H3(2,6-i-Pr2))Me (7) and ZrCp(NP-t-Bu3)(NHC6H3(2,6-i-Pr2))2 (8) were also prepared. X-ray structural data for compounds 5, 6, and 8 are reported. Reactivity of these phosphinimideamide derivatives was explored. While these species do not yield imide derivatives upon thermolysis, reaction of 5 with excess AlMe3 afforded TiCp(NP-t-Bu3)Me2 while reaction with 1 equiv. of AlMe3 gave TiCp(NP-t-Bu3)MeCl (9) and Al2(m-NHC6H3(2,6-i-Pr2))2Me4 (10). Key words: titanium, zirconium, phosphinimide, amide, ligand metathesis.
Effects of chronic inhibition of inducible nitric oxide synthase in hyperthyroid rats
Authors: Rodríguez-Gómez Isabel , Wangensteen Rosemary , Moreno Juan Manuel , Chamorro Virginia , Osuna Antonio , Vargas Félix
Published: January 2005

We hypothesized that nitric oxide generated by inducible nitric oxide synthase (iNOS) may contribute to the homeostatic role of this agent in hyperthyroidism and may, therefore, participate in long-term control of blood pressure (BP). The effects of chronic iNOS inhibition by oral aminoguanidine (AG) administration on BP and morphological and renal variables in hyperthyroid rats were analyzed. The following four groups ( n = 8 each) of male Wistar rats were used: control group and groups treated with AG (50 mg·kg−1·day−1, via drinking water), thyroxine (T4, 50 μg·rat−1·day−1), or AG + T4. All treatments were maintained for 3 wk. Tail systolic BP and heart rate (HR) were recorded weekly. Finally, we measured BP (mmHg) and HR in conscious rats and morphological, plasma, and renal variables. T4administration produced a small BP (125 ± 2, P < 0.05) increase vs. control (115 ± 2) rats. AG administration to normal rats did not modify BP (109 ± 3) or any other hemodynamic variable. However, coadministration of T4and AG produced a marked increase in BP (140 ± 3, P < 0.01 vs. T4). Pulse pressure and HR were increased in both T4- and T4+ AG -treated groups without differences between them. Plasma NOx (μmol/l) were increased in the T4group (10.02 ± 0.15, P < 0.05 vs. controls 6.1 ± 0.10), and AG reduced this variable in T4-treated rats (6.81 ± 0.14, P < 0.05 vs. T4) but not in normal rats (5.78 ± 0.20). Renal and ventricular hypertrophy and proteinuria of hyperthyroid rats were unaffected by AG treatment. In conclusion, the results of the present paper indicate that iNOS activity may counterbalance the prohypertensive effects of T4.
TGF-β impairs renal autoregulation via generation of ROS
Authors: Sharma Kumar , Cook Anthony , Smith Matt , Valancius Cathryn , Inscho Edward W.
Published: January 2005

Impaired autoregulation in chronic kidney disease can result in elevation of glomerular capillary pressure and progressive glomerular damage; however, the factors linking chronic glomerular disorders to impaired autoregulation have not been identified. We tested the hypothesis that the cytokine most closely associated with progressive glomerular disease, transforming growth factor (TGF)-β, may also attenuate autoregulation. Kidneys from normal rats were prepared for videomicroscopy, using the blood-perfused juxtamedullary nephron technique. Autoregulatory responses were measured under control conditions and during superfusion with TGF-β1(10 ng/ml). Control afferent arteriolar diameter averaged 18.4 ± 1 μm and significantly decreased to 16.3 ± 0.9 and 13.2 ± 0.8 μm at perfusion pressures of 130 and 160 mmHg, respectively. In the presence of TGF-β1, autoregulatory responses were completely blocked. In similar experiments performed using PDGF-BB (10 ng/ml) and HGF (25 ng/ml), the normal autoregulatory response was not affected. In vitro studies, using isolated preglomerular vascular smooth muscle cells, revealed that exposure to TGF-β1stimulated a rapid increase in reactive oxygen species (ROS) that was inhibited by NADPH oxidase inhibitors. In situ studies, with dihydroethidium staining, revealed a marked increase in renal vessel ROS production on exposure to TGF-β1. Pretreatment of the juxtamedullary afferent arterioles with tempol, a ROS scavenger, or with apocynin, a NADPH oxidase inhibitor, prevented the impaired autoregulation induced by TGF-β1. These data reveal a novel hemodynamic pathway by which TGF-β could lead to progressive glomerular injury by impairing normal renal microvascular function.
Infants with univentricular heart have reduced heart rate and blood pressure responses to side motion and altered responses to head-up tilt
Authors: Kirjavainen Turkka , Viskari Suvi , Pitkänen Olli , Jokinen Eero
Published: January 2005

Cardiovascular control was studied in infants with univentricular heart (UVH). Side motion tests and 45-s 45° head-up tilt tests were performed in 11 control and 9 UVH infants at the age of 13 ± 3.2 wk. In addition, heart rate (HR) reactions to spontaneous arousals and HR variability during slow-wave sleep (SWS) were determined. All UVH infants had been hypoxic for several weeks, and during the sleep study the mean arterial oxyhemoglobin saturation was 82 ± 5%. Tests were done at night during SWS, confirmed by polysomnographic recording. Continuous beat-to-beat blood pressure (BP) was measured. In the side-motion tests, control infants consistently showed a transient increase in HR and BP. This response was markedly reduced in all of the UVH infants ( P < 0.0001). In tilt tests, the UVH infants showed normal BP responses, but, although a sustained 2.0% decrease in HR was observed in the controls, the UVH infants presented with a sustained 2.6% mean HR increase ( P = 0.005). The UVH infants also showed attenuated HR acceleration during spontaneous arousals ( P = 0.01), but HR variability did not differ significantly from the controls. In conclusion, UVH infants with chronic hypoxia exhibit defective vestibulosympathetic pathways, as expressed by an absence of acute HR and BP reactivity to side motion. HR reactions to postural challenge and spontaneous arousal are also altered. Autonomic function abnormalities in these infants are suggested to be secondary to hypoxia.
Electromyographic Activity of Dorsal Neck Muscles in Squirrel Monkeys During Rotations in an Upright or Upside Down Posture
Authors: Killian J. Eric , Baker James F.
Published: January 2005

Electromyographic (EMG) activity was recorded from occipitoscapularis, semispinalis, and splenius neck muscles in five alert squirrel monkeys during 0.25-Hz rotations about horizontal axes oriented at 22.5° intervals, including pitch, roll, and intermediate axes. The animals were oriented in either upright or upside down posture. In the upright posture, all monkeys exhibited compensatory EMG activity with maximal activation during rotations about axes between pitch in the pitch forward direction and contralaterally directed roll. Response timing varied across animals with EMG peaks ranging from near pitch forward head velocity to near pitch forward head position. When the head was upside down, response dynamics and directionality were altered to varying degrees in different monkeys. The greatest change in response to head inversion was seen in the monkey that had response phases closest to head position, the least in the animal with phases closest to head velocity. The monkey with EMG response peaks closest to position phase showed nearly 180° inversion of responses when the head was upside down, suggesting that in this monkey a righting reflex mediated by utricular signals was activated in the upside down posture. The monkey with EMG response peaks closest to velocity phase may have lacked a righting response and exhibited only a canal-mediated compensatory vestibulocervical reflex in both upright and upside down postures. The results suggest that reflex contraction of neck muscles in response to passive head rotation includes an interplay of compensatory and righting responses that varies from animal to animal.
Pursuit—Vestibular Interactions in Brain Stem Neurons During Rotation and Translation
Authors: Meng Hui , Green Andrea M. , Dickman J. David , Angelaki Dora E.
Published: January 2005

Under natural conditions, the vestibular and pursuit systems work synergistically to stabilize the visual scene during movement. How translational vestibular signals [translational vestibuloocular reflex (TVOR)] are processed in the premotor pathways for slow eye movements continues to remain a challenging question. To further our understanding of how premotor neurons contribute to this processing, we recorded neural activities from the prepositus and rostral medial vestibular nuclei in macaque monkeys. Vestibular neurons were tested during 0.5-Hz rotation and lateral translation (both with gaze stable and during VOR cancellation tasks), as well as during smooth pursuit eye movements. Data were collected at two different viewing distances, 80 and 20 cm. Based on their responses to rotation and pursuit, eye-movement–sensitive neurons were classified into position–vestibular–pause (PVP) neurons, eye–head (EH) neurons, and burst–tonic (BT) cells. We found that approximately half of the type II PVP and EH neurons with ipsilateral eye movement preference were modulated during TVOR cancellation. In contrast, few of the EH and none of the type I PVP cells with contralateral eye movement preference modulated during translation in the absence of eye movements; nor did any of the BT neurons change their firing rates during TVOR cancellation. Of the type II PVP and EH neurons that modulated during TVOR cancellation, cell firing rates increased for either ipsilateral or contralateral displacement, a property that could not be predicted on the basis of their rotational or pursuit responses. In contrast, under stable gaze conditions, all neuron types, including EH cells, were modulated during translation according to their ipsilateral/contralateral preference for pursuit eye movements. Differences in translational response sensitivities for far versus near targets were seen only in type II PVP and EH cells. There was no effect of viewing distance on response phase for any cell type. When expressed relative to motor output, neural sensitivities during translation (although not during rotation) and pursuit were equivalent, particularly for the 20-cm viewing distance. These results suggest that neural activities during the TVOR were more motorlike compared with cell responses during the rotational vestibuloocular reflex (RVOR). We also found that neural responses under stable gaze conditions could not always be predicted by a linear vectorial addition of the cell activities during pursuit and VOR cancellation. The departure from linearity was more pronounced for the TVOR under near-viewing conditions. These results extend previous observations for the neural processing of otolith signals within the premotor circuitry that generates the RVOR and smooth pursuit eye movements.
Assessing natural variations in gene expression in humans by comparing with monozygotic twins using microarrays
Authors: Sharma Anu , Sharma Vineet K. , Horn-Saban Shirley , Lancet Doron , Ramachandran Srinivasan , Brahmachari Samir K.
Published: January 2005

Quantitative variation in gene expression in humans is the outcome of various factors, including differences in genetic background, gender, age, and environment. However, the extent of the influence of these factors on gene expression is not clear. We attempted to address this issue by carrying out gene expression profiling in blood leukocytes with 13 individuals (including 5 pairs of monozygotic twins) on 10,000 genes using HG-U95Av2 oligonucleotide microarrays. The proportion of differentially expressed genes between monozygotic twins was low (up to 1.76%). Most of the variations belonged to the least variable category. These genes, exhibiting “random variations,” did not show clear preference to any functional class, although “signaling and communication” and “immune and related functions” generally topped the list. The extent of variation in gene expression increased in comparisons between unrelated individuals (up to 14.13%). Most of the genes (89%) exhibiting random variations in twins also varied in expression in unrelated individuals. As with twins, signaling and communication topped the list, and substantial variations were observed in all three categories: least variable, moderately variable, and most variable. An important outcome of this study was that the housekeeping genes were nearly insensitive to random variations but appeared to be more susceptible to genetic differences. However, the highly expressed housekeeping genes exhibited low variation and appeared to be insensitive to all known factors. Gene expression profiling in monozygotic twins can provide useful data for the assessment of natural variation in gene expression in humans.
Population Pharmacokinetics of Erythropoietin in Critically Ill Subjects
Authors: Chakraborty Abhijit , Natarajan Jaya , Guilfoyle Mary , Morgan Nancy , Vercammen Els , Cheung Wing
Published: January 2005

The effects of various covariate factors on the pharmacokinetics of erythropoietin (EPO) in subjects who are critically ill and admitted to an intensive care unit were evaluated. Nonlinear mixed‐effects modeling was used to analyze the data from 48 patients receiving subcutaneous doses of 40 000 IU/wk epoetin alfa enrolled in a randomized, double‐blind, placebo‐controlled, multicenter study. The pharmacokinetics of EPO follows a 1‐compartment disposition model with first‐order absorption and an endogenous input rate. For a patient weighing 70 kg, the typical apparent clearance (CL/F) and apparent volume of distribution (V/F) were estimated to be 1.86 L/h and 27.8 L. The interindividual variability in CL/F and V/F was estimated to be 57.2% and 83.8%. CL/F and V/F of EPO increased with body weight, as described by the following relation: CL/F = (CL/F)std*(W/Wstd)0.75, and V/F = (V/F)std*(W/Wstd)1.37, where W is individual weight, and Wstd is the median weight of the study population. There was a 46% drop in exposure of EPO from the first to the subsequent dosing events. The endogenous EPO production rate was found to decrease progressively with the course of the study. In addition, the modeled endogenous EPO production rate increased with body weight. The net effect of this increase on the endogenous plasma EPO levels may not be significant because EPO clearance was found to increase with body weight. All other factors investigated (eg, Sequential Organ Failure Assessment [SOFA] scores and APACHE II scores) had no significant effect on EPO pharmacokinetics. The typical population estimate of CL/F of EPO was close to previously reported values in healthy volunteers.
Pharmacokinetics of Anthocyanidin‐3‐Glycosides Following Consumption of Hibiscus sabdariffa L. Extract
Authors: Frank Thomas , Janßen Marlies , Netzel Michael , Straß Gabriele , Kler Adolf , Kriesl Erwin , Bitsch Irmgard
Published: January 2005

Pharmacokinetic parameters of several dietary anthocyanins following consumption of Hibiscus sabdariffa L. extract were determined in 6 healthy volunteers. Subjects were given a single oral dose of 150 mL of Hibiscus sabdariffa L. extract yielding 62.6 mg of cyanidin‐3‐sambubioside, 81.6 mg of delphindin‐3‐sambubioside, and 147.4 mg of total anthocyanins (calculated as cyanidin equivalents). Within 7 hours, the urinary excretion of cyanidin‐3‐sambubioside, delphinidin‐3‐sambubioside, and total anthocyanins (ie, the sum of all quantifiable anthocyanidin glycosides) was 0.016%, 0.021%, and 0.018% of the administered doses, respectively. Maximum excretion rates were determined at 1.5 to 2.0 hours after intake. The dose‐normalized plasma area under the curve estimates were 0.076, 0.032, and 0.050 ng•h/mL/mg for cyanidin‐3‐sambubioside, delphinidin‐3‐sambubioside, and total anthocyanins, respectively. The dose‐normalized Cmax estimates were 0.036, 0.015, and 0.023 ng/mL/mg in the same sequence. They were reached each at 1.5 hours (median) after intake. The geometric means of t1/2 were 2.18, 3.34, and 2.63 hours for cyanidin‐3‐sambubioside, delphinidin‐3‐sambubioside, and total anthocyanins, respectively. The urinary excretion of intact anthocyanins was fast and appeared to be monoexponential. To evaluate the contribution of anthocyanins to the health‐protecting effects of Hibiscus sabdariffa L. extract, it will be necessary to perform further studies on both the intact glycosides and their in vivo metabolites or conjugates in human plasma and urine.
Comparison of the Oropharyngeal Deposition of Inhaled Ciclesonide and Fluticasone Propionate in Patients With Asthma
Authors: Richter Kai , Kanniess Frank , Biberger Christian , Nave Ruediger , Magnussen Helgo
Published: January 2005

Ciclesonide is a novel inhaled corticosteroid that is converted in the lungs to its active metabolite, desisobutyryl‐ciclesonide (des‐CIC). The aim of this study was to compare the deposition of ciclesonide, as well as its conversion to des‐CIC, in the oropharyngeal cavity with fluticasone propionate (FP) following inhalation via hydrofluoroalkane‐propelled metered‐dose inhalers (HFA‐MDIs). Eighteen asthmatics inhaled ciclesonide 800 μg followed by FP 1000 μg or vice versa in an open, randomized, 2‐treatment, 2‐sequence study design. The oropharynx was washed out immediately and at 15, 30, 45, and 60 minutes after inhalation. Samples were analyzed for ciclesonide, des‐CIC, and FP using liquid chromatography with tandem mass‐spectrometric detection. Concentrationtime curves and area under the concentration‐time curve (AUC) were calculated for each drug. Ciclesonide and FP were recovered in almost all samples. Within 60 minutes after inhalation, the amounts of both ciclesonide and FP decreased sharply, and low residual levels were detected after 30 minutes. des‐CIC was detected in relatively low concentrations, with maximum concentration 30 minutes following inhalation. The AUC0–60 min for ciclesonide (250.4 nmol•h/L) and des‐CIC (37.8 nmol•h/L) were found to be significantly lower compared with FP (636.2 nmol•h/L, P <.001). Approximately 50% less ciclesonide and 90% less metabolite were present in the oropharynx compared with FP. Less than 20% of the residual ciclesonide in the oropharynx was metabolized to des‐CIC. These findings indicate that oropharyngeal deposition of ciclesonide is only half that of FP following inhalation from an HFA‐MDI. Furthermore, there is little activation of ciclesonide to its active metabolite in the oropharynx, suggesting a decreased likelihood of inhaled ciclesonide‐associated oropharyngeal side effects.
Small and Medium-sized Enterprises Involved in Technology Transfer to China
Authors: Marcotte Claude , Niosi Jorge
Published: January 2005

Technology transfer is a frequent component of foreign direct investment and cross-border cooperative agreements. Little is known concerning the comparative effectiveness of technology transfer accomplished by small and medium-sized enterprises (SMEs) in developing countries. The goal of this study is to compare small and large organizations on measures of learning accomplished by their respective partners during technology transfer. Twenty-eight Canadian manufacturing firms involved in technology transfer to China were surveyed and seven case studies were conducted in China. Learning in recipient firms was not significantly associated with the size of their Canadian transferors. The case study results revealed other factors that seemed to influence learning.
Age-Related Changes in Gait and Obstacle Avoidance Capabilities in Older Adults: A Review
Authors: Kovacs Christopher R.
Published: January 2005

Walking is a fundamental motor skill that significantly affects the level of independence in older adults today. Changes in gait and obstacle avoidance strategies have been well documented in the literature, and falling has been shown to be one of the most significant health care concerns in the elderly population today. Falls are a major contributor to the increasing morbidity rates seen in the older population, and in many cases, alterations in gait or stepping ability have played a significant role. This reviewexamines the specific changes seen in gait and obstacle avoidance in the elderly population and some of the underlying changes seen in sensory capability that play a role in safe and efficient ambulation in older adults. Normal gait (unassisted ambulation) will be presented, followed by an examination of the literature that has examined changes in performance factors associated with gait and obstacle avoidance strategies.
The social capital of European welfare states: the crowding out hypothesis revisited
Authors: van Oorschot Wim , Arts Wil
Published: January 2005

A recurrent critique on the welfare state is that it crowds out social capital (networks, trust and norms). However, the empirical evidence on the crowding out hypothesis is still scarce, findings are sometimes contradictory, and there is variation in the measurement of social capital. In this article we explore the crowding out hypothesis on the basis of data from the European Values Survey wave 1999/2000 for 23 European countries. Compared to (the few) other comparative studies on the hypothesis, our study contains more recent data and for a larger number of countries. Instead of focusing on a single dimension of social capital, we use an eight-scale measurement model of social capital; we explore the relationship between welfare (regime type, social spending) and social capital at both country and individual level, and we control for confounding factors. At the aggregate country level we found no evidence at all in favour of the hypothesis. At the individual level we found that it does matter for people’s social capital in which type and size of welfare state they live. However, there is only evidence for a crowding out effect in case of people’s trustworthiness. With regard to other forms of social capital, there is at best mixed evidence, but mostly our findings contradict the crowding out hypothesis altogether.
Human somatic PTPN11 mutations induce hematopoietic-cell hypersensitivity to granulocyte-macrophage colony-stimulating factor
Authors: Chan Rebecca J. , Leedy Melissa B. , Munugalavadla Veerendra , Voorhorst Cara S. , Li Yanjun , Yu Menggang , Kapur Reuben
Published: January 2005

Juvenile myelomonocytic leukemia (JMML) is a lethal disease of young children characterized by hypersensitivity of hematopoietic progenitors to granulocyte-macrophage colony-stimulating factor (GM-CSF). Mutations in PTPN11, which encodes the protein tyrosine phosphatase Shp-2, are common in JMML. We hypothesized that PTPN11 mutations induce hypersensitivity of hematopoietic progenitors to GM-CSF and confer increased GM-CSF–stimulated phospho–extracellular signal-regulated kinase (Erk) levels. To test this hypothesis, the wild-type (WT) and 3 mutant Ptpn11 cDNAs (E76K, D61V, and D61Y) were transduced into murine bone marrow cells to examine GM-CSF–stimulated granulocyte-macrophage colony-forming unit (CFU-GM) growth, macrophage progenitor proliferation, and activation of the Ras signaling pathway. Expression of the Shp-2 mutants induced progenitor cell hypersensitivity to GM-CSF compared with cells transduced with vector alone or WT Shp-2. Macrophage progenitors expressing the Shp-2 mutants displayed both basal and GM-CSF–stimulated hyperproliferation compared with cells transduced with vector alone or WT Shp-2. Consistently, macrophage progenitors transduced with the Shp-2 mutants demonstrated constitutively elevated phospho-Erk levels and sustained activation of phospho-Erk following GM-CSF stimulation compared with vector alone or WT Shp-2. These data support the hypothesis that PTPN11 mutations induce hematopoietic progenitor hypersensitivity to GM-CSF due to hyperactivation of the Ras signaling axis and provide a basis for the GM-CSF signaling pathway as a target for rational drug design in JMML.
TRAIL counteracts the proadhesive activity of inflammatory cytokines in endothelial cells by down-modulating CCL8 and CXCL10 chemokine expression and release
Authors: Secchiero Paola , Corallini Federica , di Iasio Maria Grazia , Gonelli Arianna , Barbarotto Elisa , Zauli Giorgio
Published: January 2005

Exposure of endothelial cells to recombinant tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) induced a modest (2-fold) increase of HL-60 cell adhesion as compared to TNF-α (40-fold) or interleukin 1β (IL-1β; 20-fold). However, pretreatment of endothelial cultures with TRAIL determined a significant reduction of the proadhesive activity induced by both TNF-α and IL-1β. Unexpectedly, the antiadhesive activity of TRAIL was not due to interference with the nuclear factor κB (NF-κB)-mediated up-regulation of surface intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), and E-selectin adhesion molecules in response to inflammatory cytokines. In searching for the molecular mechanism underlying this biologic activity of TRAIL, a cDNA microarray analysis was performed. TRAIL pretreatment variably down-modulated the mRNA steady-state levels of several TNF-α-induced chemokines, and, in particular, it abrogated the TNF-α-mediated up-regulation of CCL8 and CXCL10. Of note, the addition of optimal concentrations of recombinant CCL8 plus CXCL10 to endothelial cultures completely restored the proadhesive activity of TNF-α. Moreover, experiments performed with agonistic anti-TRAIL receptor antibodies demonstrated that both TRAIL-R1 and TRAIL-R2 contributed, although at different levels, to TRAIL-induced chemokine modulation. Taken together, our data suggest that TRAIL might play an important role in modulating leukocyte/endothelial cell adhesion by selectively down-regulating CCL8 and CXCL10 chemokines.
Human lung cancer cells express functionally active Toll-like receptor 9
Authors: Droemann Daniel , Albrecht Dirk , Gerdes Johannes , Ulmer Artur J , Branscheid Detlev , Vollmer Ekkehard , Dalhoff Klaus , Zabel Peter , Goldmann Torsten
Published: January 2005

Background

CpG-oligonucleotides (CpG-ODN), which induce signaling through Toll-like receptor 9 (TLR9), are currently under investigation as adjuvants in therapy against infections and cancer. CpG-ODN function as Th-1 adjuvants and are able to activate dendritic cells. In humans TLR9 has been described to be strongly expressed in B-lymphocytes, monocytes, plasmacytoid dendritic cells and at low levels in human respiratory cells. We determined whether a direct interaction of bacterial DNA with the tumor cells themselves is possible and investigated the expression and function of TLR9 in human malignant solid tumors and cell lines. TLR9 expression by malignant tumor cells, would affect treatment approaches using CpG-ODN on the one hand, and, on the other hand, provide additional novel information about the role of tumor cells in tumor-immunology.

Methods

The expression of TLR9 in HOPE-fixed non-small lung cancer, non-malignant tissue and tumor cell lines was assessed using immunohistochemistry, confocal microscopy, in situ hybridization, RT-PCR and DNA-sequencing. Apoptosis and chemokine expression was detected by FACS analysis and the Bio-Plex system.

Results

We found high TLR9 signal intensities in the cytoplasm of tumor cells in the majority of lung cancer specimens as well as in all tested tumor cell lines. In contrast to this non-malignant lung tissues showed only sporadically weak expression. Stimulation of HeLa and A549 cells with CpG-ODN induced secretion of monocyte chemoattractant protein-1 and reduction of spontaneous and tumor necrosis factor-alpha induced apoptosis.

Conclusions

Here we show that TLR9 is expressed in a selection of human lung cancer tissues and various tumor cell lines. The expression of functionally active TLR9 in human malignant tumors might affect treatment approaches using CpG-ODN and shows that malignant cells can be regarded as active players in tumor-immunology.
Involvement of RhoA-mediated Ca2+ sensitization in antigen-induced bronchial smooth muscle hyperresponsiveness in mice
Authors: Chiba Yoshihiko , Ueno Ayako , Shinozaki Koji , Takeyama Hisao , Nakazawa Shuji , Sakai Hiroyasu , Misawa Miwa
Published: January 2005

Background

It has recently been suggested that RhoA plays an important role in the enhancement of the Ca2+ sensitization of smooth muscle contraction. In the present study, a participation of RhoA-mediated Ca2+ sensitization in the augmented bronchial smooth muscle (BSM) contraction in a murine model of allergic asthma was examined.

Methods

Ovalbumin (OA)-sensitized BALB/c mice were repeatedly challenged with aerosolized OA and sacrificed 24 hours after the last antigen challenge. The contractility and RhoA protein expression of BSMs were measured by organ-bath technique and immunoblotting, respectively.

Results

Repeated OA challenge to sensitized mice caused a BSM hyperresponsiveness to acetylcholine (ACh), but not to high K+-depolarization. In α-toxin-permeabilized BSMs, ACh induced a Ca2+ sensitization of contraction, which is sensitive to Clostridium botulinum C3 exoenzyme, indicating that RhoA is implicated in this Ca2+ sensitization. Interestingly, the ACh-induced, RhoA-mediated Ca2+ sensitization was significantly augmented in permeabilized BSMs of OA-challenged mice. Moreover, protein expression of RhoA was significantly increased in the hyperresponsive BSMs.

Conclusion

These findings suggest that the augmentation of Ca2+ sensitizing effect, probably via an up-regulation of RhoA protein, might be involved in the enhanced BSM contraction in antigen-induced airway hyperresponsiveness.
Dynamic changes of serum SARS-Coronavirus IgG, pulmonary function and radiography in patients recovering from SARS after hospital discharge
Authors: Xie Lixin , Liu Youning , Fan Baoxing , Xiao Yueyong , Tian Qing , Chen Liangan , Zhao Hong , Chen Weijun
Published: January 2005

Objective

The intent of this study was to examine the recovery of individuals who had been hospitalized for severe acute respiratory syndrome (SARS) in the year following their discharge from the hospital. Parameters studied included serum levels of SARS coronavirus (SARS-CoV) IgG antibody, tests of lung function, and imaging data to evaluate changes in lung fibrosis. In addition, we explored the incidence of femoral head necrosis in some of the individuals recovering from SARS.

Methods

The subjects of this study were 383 clinically diagnosed SARS patients in Beijing, China. They were tested regularly for serum levels of SARS-CoV IgG antibody and lung function and were given chest X-rays and/or high resolution computerized tomography (HRCT) examinations at the Chinese PLA General Hospital during the 12 months that followed their release from the hospital. Those individuals who were found to have lung diffusion abnormities (transfer coefficient for carbon monoxide [DLCO] < 80% of predicted value [pred]) received regular lung function tests and HRCT examinations in the follow-up phase in order to document the changes in their lung condition. Some patients who complained of joint pain were given magnetic resonance imaging (MRI) examinations of their femoral heads.

Findings

Of all the subjects, 81.2% (311 of 383 patients) tested positive for serum SARS-CoV IgG. Of those testing positive, 27.3% (85 of 311 patients) were suffering from lung diffusion abnormities (DLCO < 80% pred) and 21.5% (67 of 311 patients) exhibited lung fibrotic changes. In the 12 month duration of this study, all of the 40 patients with lung diffusion abnormities who were examined exhibited some improvement of lung function and fibrosis detected by radiography. Of the individuals receiving MRI examinations, 23.1% (18 of 78 patients) showed signs of femoral head necrosis.

Interpretation

The lack of sero-positive SARS-CoV in some individuals suggests that there may have been some misdiagnosed cases among the subjects included in this study. Of those testing positive, the serum levels of SARS-CoV IgG antibody decreased significantly during the 12 months after hospital discharge. Additionally, we found that the individuals who had lung fibrosis showed some spontaneous recovery. Finally, some of the subjects developed femoral head necrosis.
Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations
Authors: Gurunathan Rajalakshmi , Van Emden Bernard , Panchanathan Sethuraman , Kumar Sudhir
Published: January 2005

Background

Modern developmental biology relies heavily on the analysis of embryonic gene expression patterns. Investigators manually inspect hundreds or thousands of expression patterns to identify those that are spatially similar and to ultimately infer potential gene interactions. However, the rapid accumulation of gene expression pattern data over the last two decades, facilitated by high-throughput techniques, has produced a need for the development of efficient approaches for direct comparison of images, rather than their textual descriptions, to identify spatially similar expression patterns.

Results

The effectiveness of the Binary Feature Vector (BFV) and Invariant Moment Vector (IMV) based digital representations of the gene expression patterns in finding biologically meaningful patterns was compared for a small (226 images) and a large (1819 images) dataset. For each dataset, an ordered list of images, with respect to a query image, was generated to identify overlapping and similar gene expression patterns, in a manner comparable to what a developmental biologist might do. The results showed that the BFV representation consistently outperforms the IMV representation in finding biologically meaningful matches when spatial overlap of the gene expression pattern and the genes involved are considered. Furthermore, we explored the value of conducting image-content based searches in a dataset where individual expression components (or domains) of multi-domain expression patterns were also included separately. We found that this technique improves performance of both IMV and BFV based searches.

Conclusions

We conclude that the BFV representation consistently produces a more extensive and better list of biologically useful patterns than the IMV representation. The high quality of results obtained scales well as the search database becomes larger, which encourages efforts to build automated image query and retrieval systems for spatial gene expression patterns.
Visualization of comparative genomic analyses by BLAST score ratio
Authors: Rasko David A , Myers Garry SA , Ravel Jacques
Published: January 2005

Background

The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis.

Results

The BLAST Score Ratio (BSR) approach, implemented in a Perl script, classifies all putative peptides within three genomes using a measure of similarity based on the ratio of BLAST scores. The output of the BSR analysis enables global visualization of the degree of proteome similarity between all three genomes. Additional output enables the genomic synteny (conserved gene order) between each genome pair to be assessed. Furthermore, we extend this synteny analysis by overlaying BSR data as a color dimension, enabling visualization of the degree of similarity of the peptides being compared.

Conclusions

Combining the degree of similarity, synteny and annotation will allow rapid identification of conserved genomic regions as well as a number of common genomic rearrangements such as insertions, deletions and inversions. The script and example visualizations are available at: http://www.microbialgenomics.org/BSR/.
Differences in codon bias cannot explain differences in translational power among microbes
Authors: Dethlefsen Les , Schmidt Thomas M
Published: January 2005

Background

Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. One factor known to affect translational power is biased use of synonymous codons. The correlation within an organism between expression level and degree of codon bias among genes of Escherichia coli and other bacteria capable of rapid growth is commonly attributed to selection for high translational power. Conversely, the absence of such a correlation in some slowly growing microbes has been interpreted as the absence of selection for translational power. Because codon bias caused by translational selection varies between rapidly growing and slowly growing microbes, we investigated whether observed differences in translational power among microbes could be explained entirely by differences in the degree of codon bias. Although the data are not available to estimate the effect of codon bias in other species, we developed an empirically-based mathematical model to compare the translation rate of E. coli to the translation rate of a hypothetical strain which differs from E. coli only by lacking codon bias.

Results

Our reanalysis of data from the scientific literature suggests that translational power can differ by a factor of 5 or more between E. coli and slowly growing microbial species. Using empirical codon-specific in vivo translation rates for 29 codons, and several scenarios for extrapolating from these data to estimates over all codons, we find that codon bias cannot account for more than a doubling of the translation rate in E. coli, even with unrealistic simplifying assumptions that exaggerate the effect of codon bias. With more realistic assumptions, our best estimate is that codon bias accelerates translation in E. coli by no more than 60% in comparison to microbes with very little codon bias.

Conclusions

While codon bias confers a substantial benefit of faster translation and hence greater translational power, the magnitude of this effect is insufficient to explain observed differences in translational power among bacterial and archaeal species, particularly the differences between slowly growing and rapidly growing species. Hence, large differences in translational power suggest that the translational apparatus itself differs among microbes in ways that influence translational performance.
EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments
Authors: Gelly Jean-Christophe , Chiche Laurent , Gracy Jérôme
Published: January 2005

Background

Structure-dependent substitution matrices increase the accuracy of sequence alignments when the 3D structure of one sequence is known, and are successful e.g. in fold recognition. We propose a new automated method, EvDTree, based on a decision tree algorithm, for automatic derivation of amino acid substitution probabilities from a set of sequence-structure alignments. The main advantage over other approaches is an unbiased automatic selection of the most informative structural descriptors and associated values or thresholds. This feature allows automatic derivation of structure-dependent substitution scores for any specific set of structures, without the need to empirically determine best descriptors and parameters.

Results

Decision trees for residue substitutions were constructed for each residue type from sequence-structure alignments extracted from the HOMSTRAD database. For each tree cluster, environment-dependent substitution profiles were derived. The resulting structure-dependent substitution scores were assessed using a criterion based on the mean ranking of observed substitution among all possible substitutions and in sequence-structure alignments. The automatically built EvDTree substitution scores provide significantly better results than conventional matrices and similar or slightly better results than other structure-dependent matrices. EvDTree has been applied to small disulfide-rich proteins as a test case to automatically derive specific substitutions scores providing better results than non-specific substitution scores. Analyses of the decision tree classifications provide useful information on the relative importance of different structural descriptors.

Conclusions

We propose a fully automatic method for the classification of structural environments and inference of structure-dependent substitution profiles. We show that this approach is more accurate than existing methods for various applications. The easy adaptation of EvDTree to any specific data set opens the way for class-specific structure-dependent substitution scores which can be used in threading-based remote homology searches.
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases
Authors: Srdanovic Marko , Schenk Ulf , Schwieger Michael , Campagne Fabien
Published: January 2005

Background

Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO) persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships.

Results

Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications.

Conclusions

The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends.
Regulation of cell cycle by the anaphase spindle midzone
Authors: Murata-Hori Maki , Sluder Greenfield , Wang Yu-li
Published: January 2005

Abstract1

Background

A number of proteins accumulate in the spindle midzone and midbody of dividing animal cells. Besides proteins essential for cytokinesis, there are also components essential for interphase functions, suggesting that the spindle midzone and/or midbody may play a role in regulating the following cell cycle.

Results

We microsurgically severed NRK epithelial cells during anaphase or telophase, such that the spindle midzone/midbody was associated with only one of the daughter cells. Time-lapse recording of cells severed during early anaphase indicated that the cell with midzone underwent cytokinesis-like cortical contractions and progressed normally through the interphase, whereas the cell without midzone showed no cortical contraction and an arrest or substantial delay in the progression of interphase. Similar microsurgery during telophase showed a normal progression of interphase for both daughter cells with or without the midbody. Microsurgery of anaphase cells treated with cytochalasin D or nocodazole indicated that interphase progression was independent of cortical ingression but dependent on microtubules.

Conclusions

We conclude that the mitotic spindle is involved in not only the separation of chromosomes but also the regulation of cell cycle. The process may involve activation of components in the spindle midzone that are required for the cell cycle, and/or degradation of components that are required for cytokinesis but may interfere with the cell cycle.