bluuebunny/crossref_metadata_2025 huggingface dataset:
Breakpoints of gross deletions coincide with non-B DNA conformations
Authors: Bacolla Albino , Jaworski Adam , Larson Jacquelynn E. , Jakupciak John P. , Chuzhanova Nadia , Abeysinghe Shaun S. , O'Connell Catherine D. , Cooper David N. , Wells Robert D.
Published: September 2004

Genomic rearrangements are a frequent source of instability, but the mechanisms involved are poorly understood. A 2.5-kbp poly(purine·pyrimidine) sequence from the human
PKD1
gene, known to form non-B DNA structures, induced long deletions and other instabilities in plasmids that were mediated by mismatch repair and, in some cases, transcription. The breakpoints occurred at predicted non-B DNA structures. Distance measurements also indicated a significant proximity of alternating purine-pyrimidine and oligo(purine·pyrimidine) tracts to breakpoint junctions in 222 gross deletions and translocations, respectively, involved in human diseases. In 11 deletions analyzed, breakpoints were explicable by non-B DNA structure formation. We conclude that alternative DNA conformations trigger genomic rearrangements through recombination-repair activities.
Hyper-inducible expression system for streptomycetes
Authors: Herai Sachio , Hashimoto Yoshiteru , Higashibata Hiroki , Maseda Hideaki , Ikeda Haruo , Ōmura Satoshi , Kobayashi Michihiko
Published: September 2004

Streptomycetes produce useful enzymes and a wide variety of secondary metabolites with potent biological activities (e.g., antibiotics, immunosuppressors, pesticides, etc.). Despite their importance in the pharmaceutical and agrochemical fields, there have been no reports for practical expression systems in streptomycetes. Here, we developed a “P

nitA

-NitR” system for regulatory gene expression in streptomycetes based on the expression mechanism of
Rhodococcus rhodochrous
J1 nitrilase, which is highly induced by an inexpensive and safe inducer, ε-caprolactam. Heterologous protein expression experiments demonstrated that the system allowed suppressed basal expression and hyper-inducible expression, yielding target protein levels of as high as ≈40% of all soluble protein. Furthermore, the system functioned in important streptomycete strains. Thus, the P

nitA

-NitR system should be a powerful tool for improving the productivity of various useful products in streptomycetes.
The Los Alamos hepatitis C sequence database
Authors: Kuiken Carla , Yusim Karina , Boykin Laura , Richardson Russell
Published: September 2004

Motivation: The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide.

Results: The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of ∼280 visits per day from distinct IP addresses.

Availability: The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org

Contact:  hcv-info@lanl.gov
SNPP: automating large-scale SNP genotype data management
Authors: Zhao Lan-Juan , Li Miao-Xin , Guo Yan-Fang , Xu Fu-Hua , Li Jin-Long , Deng Hong-Wen
Published: September 2004

Summary: To manage high-throughput single nucleotide polymorphism (SNP) genotyping data efficiently, we developed a dynamic general database management system—SNPP (SNP Processor). It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.

Availability:  http://orclinux.creighton.edu/snpp/

Contact:  lanjuanzhao@creighton.edu
A simple and fast secondary structure prediction method using hidden neural networks
Authors: Lin Kuang , Simossis Victor A. , Taylor Willam R. , Heringa Jaap
Published: September 2004

Motivation: In this paper, we present a secondary structure prediction method YASPIN that unlike the current state-of-the-art methods utilizes a single neural network for predicting the secondary structure elements in a 7-state local structure scheme and then optimizes the output using a hidden Markov model, which results in providing more information for the prediction.

Results: YASPIN was compared with the current top-performing secondary structure prediction methods, such as PHDpsi, PROFsec, SSPro2, JNET and PSIPRED. The overall prediction accuracy on the independent EVA5 sequence set is comparable with that of the top performers, according to the Q3, SOV and Matthew's correlations accuracy measures. YASPIN shows the highest accuracy in terms of Q3 and SOV scores for strand prediction.

Availability: YASPIN is available on-line at the Centre for Integrative Bioinformatics website (http://ibivu.cs.vu.nl/programs/yaspinwww/) at the Vrije University in Amsterdam and will soon be mirrored on the Mathematical Biology website (http://www.mathbio.nimr.mrc.ac.uk) at the NIMR in London.

Contact:  kxlin@nimr.mrc.ac.uk
RALEE—RNA ALignment Editor in Emacs
Authors: Griffiths-Jones Sam
Published: September 2004

Summary: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS.

Availability: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples.

Contact:  sgj@sanger.ac.uk
RDP2: recombination detection and analysis from sequence alignments
Authors: Martin D. P. , Williamson C. , Posada D.
Published: September 2004

Summary: RDP2 is a Windows 95/XP program that examines nucleotide sequence alignments and attempts to identify recombinant sequences and recombination breakpoints using 10 published recombination detection methods, including GENECONV, BOOTSCAN, MAXIMUM χ2, CHIMAERA and SISTER SCANNING. The program enables fast automated analysis of large alignments (up to 300 sequences containing 13 000 sites), and interactive exploration, management and verification of results with different recombination detection and tree drawing methods.

Availability: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html)

Contact:  darren@science.uct.ac.za

Supplementary information: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded from the RDP2 website.
Predicting protein functions with message passing algorithms
Authors: Leone Michele , Pagnani Andrea
Published: September 2004

Motivation: In the last few years, a growing interest in biology has been shifting toward the problem of optimal information extraction from the huge amount of data generated via large-scale and high-throughput techniques. One of the most relevant issues has recently emerged that of correctly and reliably predicting the functions of a given protein with that of functions exploiting information coming from the whole network of proteins physically interacting with the functionally undetermined one. In the present work, we will refer to an ‘observed’ protein as the one present in the protein–protein interaction networks published in the literature.

Methods: The method proposed in this paper is based on a message passing algorithm known as Belief Propagation, which accepts the network of protein's physical interactions and a catalog of known protein's functions as input, and returns the probabilities for each unclassified protein of having one chosen function. The implementation of the algorithm allows for fast online analysis, and can easily be generalized into more complex graph topologies taking into account hypergraphs, i.e. complexes of more than two interacting proteins.

Results: Benchmarks of our method are the two Saccharomyces cerevisiae protein–protein interaction networks and the Database of Interacting Proteins. The validity of our approach is successfully tested against other available techniques.

Contact:  leone@isiosf.isi.it

Supplementary information:  http://isiosf.isi.it/~pagnani
Delayed administration may improve entacapone effects in parkinsonian patients non‐responding to the drug
Authors: Brusa L. , Bassi A. , Lunardi G. , Fedele E. , Peppe A. , Stefani A. , Pasqualetti P. , Stanzione P. , Pierantozzi M.
Published: September 2004

Background:  Entacapone is a COMT inhibitor used in Parkinson's disease (PD) patients, as an adjunctive therapy to l‐dopa in order to prolong its bioavailability and thus its clinical effect. However, previous studies reported entacapone‐induced l‐dopa to have lower Cmax and delayed tmax values, coupled with a delayed onset of the clinical effect, possibly suggesting an interference between the two drugs. The aim of our study was to evaluate whether a delayed entacapone administration in association with standard l‐dopa/carbidopa, may in some subjects improve the entacapone effects on l‐dopa AUC and thus on the clinical ‘on time’ duration.

Methods:  Twenty‐eight idiopathic advanced PD patients were blindly evaluated in three different test days, following administration of carbidopa/l‐dopa or carbidopa/l‐dopa plus co‐administered entacapone or plus entacapone administered with 30 min of delay.

Results:  The AUC, the ‘on time’ and UPDRS score of the whole group were improved by both modalities of entacapone administration. An ex post analysis showed that the delayed entacapone administration produced a significant improvement in a subgroup of 10 non‐responding patients to the co‐administration.

Conclusion:  We suggest that the delayed administration should be attempted in the subjects not improved by entacapone co‐administration.
SP-A1 and SP-A2 variants differentially enhance association ofPseudomonas aeruginosawith rat alveolar macrophages
Authors: Mikerov Anatoly N. , Umstead Todd M. , Huang Weixiong , Liu Wenlei , Phelps David S. , Floros Joanna
Published: September 2004

Chronic airway inflammation caused by Pseudomonas aeruginosa is an important feature of cystic fibrosis (CF). Surfactant protein A (SP-A) enhances phagocytosis of P. aeruginosa. Two genes, SP-A1 and SP-A2, encode human SP-A. We hypothesized that genetically determined differences in the activity of SP-A1 and SP-A2 gene products exist. To test this, we studied association of a nonmucoid P. aeruginosa strain (ATCC 39018) with rat alveolar macrophages in the presence or absence of insect cell-expressed human SP-A variants. We used two trios, each consisting of SP-A1, SP-A2, and their coexpressed SP-A1/SP-A2 variants. We tested the 6A2and 6A4alleles (for SP-A1), the 1A0and 1A alleles (for SP-A2), and their respective coexpressed SP-A1/SP-A2 gene products. After incubation of alveolar macrophages with P. aeruginosa in the presence of the SP-A variants at 37°C for 1 h, the cell association of bacteria was assessed by light microscopy analysis. We found 1) depending on SP-A concentration and variant, SP-A2 variants significantly increased the cell association more than the SP-A1 variants (the phagocytic index for SP-A1 was ∼52–95% of the SP-A2 activity); 2) coexpressed variants at certain concentrations were more active than single gene products; and 3) the phagocytic index for SP-A variants was ∼18–41% of the human SP-A from bronchoalveolar lavage. We conclude that human SP-A variants in vitro enhance association of P. aeruginosa with rat alveolar macrophages differentially and in a concentration-dependent manner, with SP-A2 variants having a higher activity compared with SP-A1 variants.
Distal angiogenesis: a new concept for lung vascular morphogenesis
Authors: Parera Marta Canis , van Dooren Marieke , van Kempen Marjon , de Krijger Ronald , Grosveld Frank , Tibboel Dick , Rottier Robbert
Published: September 2004

Although several molecular players have been described that play a role during the early phases of lung development, it is still unknown how the vasculature develops in relation to the airways. Two opposing models describe development of lung vasculature: one suggests that both vasculogenesis and angiogenesis are involved, whereas the second describes vasculogenesis as the primary mechanism. Therefore, we examined the development of the murine pulmonary vasculature through a morphological analysis from the onset of lung development [9.5 days postcoital (dpc)] until the pseudoglandular stage (13.5 dpc). We analyzed fetal lungs of Tie2-LacZ transgenic mice as well as serial sections of wild-type lungs stained with endothelial-specific antibodies (Flk-1, Fli-1, and PECAM-1). Embryos were processed with intact blood circulation to maintain the integrity of the vasculature; hence individual vessels could be identified with accuracy through serial section analysis. Furthermore, circulating primitive erythrocytes, formed exclusively by the blood islands in the yolk sac, are trapped in vessels during fixation, which proves the connection with the embryonic circulation. We report that from the first morphological sign of lung development, a clear vascular network exists that is in contact with the embryonic circulation. We propose distal angiogenesis as a new concept for early pulmonary vascular morphogenesis. In this model, capillary networks surround the terminal buds and expand by formation of new capillaries from preexisting vessels as the lung bud grows. The fact that at an early embryonic stage a complete vascular network exists may be important for the general understanding of embryonic development.
Regulation of TGF-β1-induced connective tissue growth factor expression in airway smooth muscle cells
Authors: Xie Shaoping , Sukkar Maria B. , Issa Razao , Oltmanns Ute , Nicholson Andrew G. , Chung Kian Fan
Published: September 2004

Transforming growth factor (TGF)-β may play an important role in airway remodeling, and the fibrogenic effect of TGF-β may be mediated through connective tissue growth factor (CTGF) release. We investigated the role of MAPKs and phosphatidylinositol 3-kinase (PI3K) and the effects of inflammatory cytokines on TGF-β-induced CTGF expression in human airway smooth muscle cells (ASMC). We examined whether Smad signal was involved in the regulatory mechanisms. TGF-β1 induced a time- and concentration-dependent expression of CTGF gene and protein as analyzed by real-time RT-PCR and Western blot. Inhibition of ERK and c- jun NH2-terminal kinase (JNK), but not of p38 MAPK and PI3K, blocked the effect of TGF-β1 on CTGF mRNA and protein expression and on Smad2/3 phosphorylation. T helper lymphocyte 2-derived cytokines, IL-4 and IL-13, attenuated TGF-β1-stimulated mRNA and protein expression of CTGF and inhibited TGF-β1-stimulated ERK1/2 and Smad2/3 activation in ASMC. The proinflammatory cytokines tumor necrosis factor-α and IL-1β reduced TGF-β1-stimulated mRNA expression of CTGF but did not inhibit TGF-β-induced Smad2/3 phosphorylation. TGF-β1-stimulated CTGF expression is mediated by mechanisms involving ERK and JNK pathways and is downregulated by IL-4 and IL-13 through modulation of Smad and ERK signals.
Regulation of pulmonary venous tone in response to muscarinic receptor activation
Authors: Ding Xueqin , Murray Paul A.
Published: September 2004

We investigated cellular mechanisms that mediate or modulate the vascular response to muscarinic receptor activation (ACh) in pulmonary veins (PV). Isometric tension was measured in isolated canine PV rings with endothelium (E+) and without endothelium (E−). Tension and intracellular Ca2+concentration ([Ca2+]i) were measured simultaneously in fura-2-loaded E− PV strips. In the absence of preconstriction, ACh (0.01–10 μM) caused dose-dependent contraction in E+ and E− rings. ACh contraction was potentiated by removing the endothelium or by nitric oxide (NO) synthase inhibition ( N-nitro-l-arginine methyl ester, P = 0.001). Cyclooxygenase inhibition (indomethacin) reduced ACh contraction in both E+ and E− PV rings ( P = 0.013 and P = 0.037, respectively). ACh contraction was attenuated by inhibitors of voltage-operated Ca2+channels (nifedipine, P < 0.001), inositol-1,4,5-trisphosphate (IP3)-mediated Ca2+release (2-aminoethoxydiphenyl borate, P = 0.001), PKC (bisindolylmaleimide I, P = 0.001), Rho-kinase (Y-27632, P = 0.002), and tyrosine kinase (TK; tyrphostin 47, P = 0.015) in E− PV rings. ACh (1 μM) caused a leftward shift in the [Ca2+]i-tension relationship ( P = 0.015), i.e., ACh increased myofilament Ca2+sensitivity. Inhibition of PKC, Rho-kinase, and TK attenuated the ACh-induced increase in myofilament Ca2+sensitivity ( P < 0.001, P < 0.001, and P = 0.024, respectively). These findings indicate that in canine PV, ACh contraction is modulated by NO and partially mediated by metabolites of the cyclooxygenase pathway and involves Ca2+influx through voltage-operated Ca2+channels and IP3-mediated Ca2+release. In addition, ACh induces increased myofilament Ca2+sensitivity, which requires the PKC, Rho-kinase, and TK pathways.
Important role for Rac1 in regulating reactive oxygen species generation and pulmonary arterial smooth muscle cell growth
Authors: Patil Sandip , Bunderson Melisa , Wilham Jason , Black Stephen M.
Published: September 2004

Vascular NADPH oxidases have been shown to be a major source of reactive oxygen species (ROS). Recent studies have also implicated ROS in the proliferation of vascular smooth muscle cells. However, the components required for activation of the NADPH oxidase complex have not been clearly elucidated. Here we demonstrate that ROS generation in ovine pulmonary arterial smooth muscle cells (PASMCs) requires the activation of Rac1, implicating this protein as an important subunit of the NADPH oxidase complex. Our results, using a geranylgeranyl transferase inhibitor (GGTI-287), demonstrated a dose-dependent inhibition of Rac1 activity and ROS production. This was associated with an inhibition of PASMC proliferation with an arrest at G2/M. The inhibition of Rac1 by GGTI-287 led us to more specifically target Rac1 to investigate its role in the generation of ROS and cellular proliferation. To accomplish this, we utilized a dominant negative Rac1 (N17Rac1) and a constitutively active Rac1 (V12Rac1). These two forms of Rac1 were transiently expressed in PASMCs using adenovirus-mediated gene transfer. N17Rac1 expression resulted in decreased cellular Rac1 activity, whereas V12Rac1 infection showed increased activity. Compared with controls, the V12Rac1-expressing cells had higher levels of ROS production and increased proliferation, whereas the N17Rac1-expressing cells had decreased ROS generation and proliferation and cell cycle arrest at G2/M. However, the inhibition of cell growth produced by N17Rac1 overexpression could be overcome if cells were co-incubated with the Cu,Zn superoxide dismutase inhibitor DETC. These results indicate the importance of Rac1 in ROS generation and proliferation of vascular smooth muscle cells.
Positive end-expiratory pressure prevents lung mechanical stress caused by recruitment/derecruitment
Authors: Farias Luciana L. , Faffe Débora S. , Xisto Débora G. , Santana Maria Cristina E. , Lassance Roberta , Prota Luiz Felipe M. , Amato Marcelo B. , Morales Marcelo M. , Zin Walter A. , Rocco Patricia R. M.
Published: September 2004

This study tests the hypotheses that a recruitment maneuver per se yields and/or intensifies lung mechanical stress. Recruitment maneuver was applied to a model of paraquat-induced acute lung injury (ALI) and to healthy rats with (ATEL) or without (CTRL) previous atelectasis. Recruitment was done by using 40-cmH2O continuous positive airway pressure for 40 s. Rats were, then, ventilated for 1 h at zero end-expiratory pressure (ZEEP) or positive end-expiratory pressure (PEEP; 5 cmH2O). Atelectasis was generated by inflating a sphygmomanometer around the thorax. Additional groups did not undergo recruitment but were ventilated for 1 h under ZEEP. Lung resistive and viscoelastic pressures and static elastance were computed before and immediately after recruitment, and at the end of 1 h of ventilation. Lungs were prepared for histology. Type III procollagen (PCIII) mRNA expression in lung tissue was analyzed by RT-PCR. Lung mechanics improved after recruitment in the CTRL and ALI groups. One hour of ventilation at ZEEP increased alveolar collapse, static elastance, and lung resistive and viscoelastic pressures. Alveolar collapse was similar in ATEL and ALI, and recruitment opened the alveoli in both groups. ALI showed higher PCIII expression than ATEL or CTRL groups. One hour of ventilation at ZEEP did not increase PCIII expression but augmented it significantly in the three groups when applied after recruitment. However, PEEP ventilation after recruitment avoided any increment in PCIII expression in all groups. In conclusion, recruitment followed by ZEEP was more deleterious in ALI than in mechanical ATEL, although ZEEP alone did not elevate PCIII expression. Ventilation with 5-cmH2O PEEP prevented derecruitment and aborted the increase in PCIII expression.
Muscle blood flow response to contraction: influence of venous pressure
Authors: Valic Zoran , Buckwalter John B. , Clifford Philip S.
Published: September 2004

The skeletal muscle pump is thought to be at least partially responsible for the immediate muscle hyperemia seen with exercise. We hypothesized that increases in venous pressure within the muscle would enhance the effectiveness of the muscle pump and yield greater postcontraction hyperemia. In nine anesthetized beagle dogs, arterial inflow and venous outflow of a single hindlimb were measured with ultrasonic transit-time flow probes in response to 1-s tetanic contractions evoked by electrical stimulation of the sciatic nerve. Venous pressure in the hindlimb was manipulated by tilting the upright dogs to a 30° angle in the head-up or head-down positions. The volume of venous blood expelled during contractions was 2.2 ± 0.2, 1.6 ± 0.2, and 1.4 ± 0.2 ml with the head-up, horizontal, and head-down positions, respectively. Although altering hindlimb venous pressure influenced venous expulsion during contraction, the increase in arterial inflow was similar regardless of position. Moreover, the volume of blood expelled was a small fraction of the cumulative arterial volume after the contraction. These results suggest that the muscle pump is not a major contributor to the hyperemic response to skeletal muscle contraction.
Exercise training increases oxidative capacity and attenuates exercise-induced ultrastructural damage in skeletal muscle of aged horses
Authors: Kim Jeong-su , Hinchcliff Kenneth W. , Yamaguchi Mamoru , Beard Laurie A. , Markert Chad D. , Devor Steven T.
Published: September 2004

Exercise training improves functional capacity in aged individuals. Whether such training reduces the severity of exercise-induced muscle damage is unknown. The purpose of the present study was to determine the effect of 10 wk of treadmill exercise training on skeletal muscle oxidative capacity and exercise-induced ultrastructural damage in six aged female Quarter horses (>23 yr of age). The magnitude of ultrastructural muscle damage induced by an incremental exercise test before and after training was determined by electron microscopic examination of samples of triceps, semimembranosus, and masseter (control) muscles. Maximal aerobic capacity increased 22% after 10 wk of exercise training. The percentage of type IIa myosin heavy chain increased in semimembranosus muscle, whereas the percentage of type IIx myosin heavy chain decreased in triceps muscle. After training, triceps muscle showed significant increases in activities of both citrate synthase and 3-hydroxyacyl-CoA-dehydrogenase. Attenuation of exercise-induced ultrastructural muscle damage occurred in the semimembranosus muscle at both the same absolute and the same relative workloads after the 10-wk conditioning period. We conclude that aged horses adapt readily to intense aerobic exercise training with improvements in endurance, whole body aerobic capacity, and muscle oxidative capacity, and heightened resistance to exercise-induced ultrastructural muscle cell damage. However, adaptations may be muscle-group specific.
Androgen receptor CAG repeat polymorphism is associated with fat-free mass in men
Authors: Walsh Sean , Zmuda Joseph M. , Cauley Jane A. , Shea Patrick R. , Metter E. Jeffrey , Hurley Ben F. , Ferrell Robert E. , Roth Stephen M.
Published: September 2004

The human androgen receptor (AR) gene contains a CAG (glutamine) repeat polymorphism in exon 1 that is inversely associated with transcriptional activity of the AR. We studied the association of AR CAG repeat length, fat-free mass (FFM), and testosterone in two independent cohorts: 294 Caucasian men, aged 55–93 yr, from the Study of Osteoporotic Risk in Men (STORM), and 202 Caucasian volunteers (112 men and 90 women), aged 19–90 yr, from the Baltimore Longitudinal Study of Aging (BLSA). Subjects were genotyped to determine the number of AR CAG repeats and grouped as carrying either <22 or ≥22 repeats. Whole body soft tissue composition was measured by dual-energy X-ray absorptiometry. Men with greater CAG repeat number exhibited significantly greater total FFM than those with fewer CAG repeats in both cohorts (STORM: 59.2 ± 0.3 vs. 58.0 ± 0.4 kg, P = 0.02; BLSA: 57.2 ± 1.1 vs. 53.8 ± 1.1 kg, P = 0.04). Similar results were observed for total FFM normalized to height. No differences were seen in women in the BLSA cohort. In the BLSA cohort, serum testosterone levels were higher in subjects with greater repeat number ( P = 0.003). This same pattern approached significance in the STORM cohort ( P = 0.07). In conclusion, the androgen receptor CAG repeat polymorphism is associated with FFM in men in two independent cohorts. Additional studies are needed to confirm this observation and to clarify the mechanisms involved.
Influence of amplitude cancellation on the simulated surface electromyogram
Authors: Keenan Kevin G. , Farina Dario , Maluf Katrina S. , Merletti Roberto , Enoka Roger M.
Published: September 2004

The purpose of the study was to quantify the influence of selected motor unit properties and patterns of activity on amplitude cancellation in the simulated surface electromyogram (EMG). The study involved computer simulations of a motor unit population with physiologically defined recruitment and rate coding characteristics that activated muscle fibers whose potentials were recorded on the skin over the muscle. Amplitude cancellation was quantified as the percent difference in signal amplitude when motor unit potentials were summed before and after rectification. The simulations involved varying the level of activation for the motor unit population, the recording configuration, the upper limit of motor unit recruitment, peak discharge rates, the amount of motor unit synchronization, muscle fiber length, the thickness of the subcutaneous tissue, and the motor unit properties that change with advancing age. The results confirmed a previous experimental report (Day SJ and Hulliger M, J Neurophysiol 86: 2144–2158, 2001) that amplitude cancellation in the surface EMG can reach 62% at maximal activation. A decrease in the range of amplitudes of the motor unit potentials, as can occur during fatiguing contractions, increased amplitude cancellation up to ∼85%. Differences in the amount of amplitude cancellation were observed across all simulated conditions, and resulted in substantial changes in the absolute magnitude of the EMG signal. The most profound factors influencing amplitude cancellation were the number of active motor units and the duration of the action potentials. The effects of amplitude cancellation were minimal (<5%) when the EMG amplitude was normalized to maximal values, with the exception of variations in peak discharge rate and recruitment range, which resulted in differences up to 17% in the normalized EMG signal across conditions. These results indicate the amount of amplitude cancellation that can occur in various experimental conditions and its influence on absolute and relative measures of EMG amplitude.
Intravenous adenosine and dyspnea in humans
Authors: Burki Nausherwan K. , Dale Wheeler J. , Lee Lu-Yuan
Published: September 2004

Intravenous adenosine for the treatment of supraventricular tachycardia is reported to cause bronchospasm and dyspnea and to increase ventilation in humans, but these effects have not been systematically studied. We therefore compared the effects of 10 mg of intravenous adenosine with placebo in 21 normal subjects under normoxic conditions and evaluated the temporal sequence of the effects of adenosine on ventilation, dyspnea, and heart rate. The study was repeated in 11 of these subjects during hyperoxia. In all subjects, adenosine resulted in the development of dyspnea, assessed by handgrip dynamometry, without any significant change ( P > 0.1) in lung resistance as measured by the interrupter technique. There were significant increases ( P < 0.05) in ventilation and heart rate in response to adenosine. The dyspneic response occurred slightly before the ventilatory or heart rate responses in every subject, but the timing of the dyspneic, ventilatory, and heart rate responses was not significantly different when the group data were analyzed (18.9 ± 5.8, 20.3 ± 5.5, and 19.7 ± 4.5 s, respectively). During hyperoxia, adenosine resulted in similar effects, with no significant differences in the magnitude of the ventilatory response; however, compared with the normoxic state, the intensity of the dyspneic response was significantly ( P < 0.05) reduced, whereas the heart rate response increased significantly ( P < 0.05). These data indicate that intravenous adenosine-induced dyspnea is not associated with bronchospasm in normal subjects. The time latency of the response indicates that the dyspnea is probably not a consequence of peripheral chemoreceptor or brain stem respiratory center stimulation, suggesting that it is most likely secondary to stimulation of receptors in the lungs, most likely vagal C fibers.
Sulfide consumption by mussel gill mitochondria is not strictly tied to oxygen reduction: measurements using a novel polarographic sulfide sensor
Authors: Kraus David W. , Doeller Jeannette E.
Published: September 2004

Some organisms that survive in environments rich in hydrogen sulfide possess specific metabolic pathways for sulfide oxidation and subsequent use of reducing equivalents in oxidative phosphorylation, a process called chemolithoheterotrophy. This process is dependent on ambient oxygen partial pressure and environmental sulfide exposure. To define accurately the kinetics of sulfide metabolism and its dependence on cellular conditions, we have developed a polarographic sulfide sensor (PSS) to measure sulfide concentrations directly and continuously under physiological conditions.

The ribbed mussel Geukensia demissa, an inhabitant of sulfide-rich coastal sediments, consumes sulfide in a chemolithoheterotrophic metabolic strategy. Gill mitochondria use sulfide as respiratory substrate for ATP production, and sulfide consumption is sufficiently rapid and so kinetically complex that only continuous real-time detection captures these events. Under normoxic conditions, oxygen and sulfide consumption are matched. Under hypoxic to anoxic conditions, however, sulfide consumption continues without commensurate oxygen consumption, and these results can be duplicated at higher oxygen conditions by selective blockade of terminal oxidases. These metabolic capabilities depend on prior environmental sulfide exposure, which suggests substantial mitochondrial metabolic plasticity. The recent finding that endogenous sulfide is a critical cell signaling molecule in all organisms suggests that the metabolic pathways that tightly control cellular sulfide levels are widespread. Sensors that accurately report sulfide concentrations under physiologically relevant conditions are valuable tools with which to explore the expanding role of sulfide in biological systems.
Producing H2‐rich gas from simulated biogas and applying the gas to a 50w PEFC stack
Authors: Xu Guangwen , Chen Xin , Honda Kazunori , Zhang Zhan‐Guo
Published: September 2004

Since 2000, a technical program was developed to convert biogas into hydrogen‐rich gas, and to demonstrate the possibility of applying the acquired hydrogenous gas to the polymer electrolyte fuel cell (PEFC). The gas conversion was accomplished in two steps, successively, in a desulfurizer that removes the hydrogen sulfide in biogas and in a hydrogen‐rich gas producer that converts the desulfurized biogas into hydrogen‐rich gas containing CO less than the PEFC‐tolerable value of 10 ppm. The gas producer consisted of four catalytic reactors, in succession, a steam reformer, two water‐gas‐shift reactors, and a selective CO oxidizer. Determining the necessary conditions for all such reactors and the applicability of the produced hydrogen‐rich gas to a 50‐watt model PEFC stack is examined. Experiments were conducted using clean model biogas over commercial catalysts. A successful production of the PEFC‐usable hydrogen‐rich gas was fulfilled, and the gas showed a composition of about 70 vol. % H2, 30 vol. % CO2, and residual CH4 (<1.0 vol. %). Directly applying the gas to the downstream model PEFC stack generated stable powers higher than 50 watts, provided the equivalent hydrogen feed was sufficient. Nonetheless, the CO2 in the gas obviously reduced the stack performance. Compared to the case running on pure hydrogen, the stack exhibited not only a lower voltage (power) at a given current, but also a smaller limit current that restricts the maximal output from the stack at each specified hydrogen feed rate. © 2004 American Institute of Chemical Engineers AIChE J, 50: 2467–2480, 2004
A case of Adams–Oliver syndrome with associated brain and pulmonary involvement: Further evidence of vascular pathology?
Authors: Piazza Anthony Joseph , Blackston Dwain , Sola Augusto
Published: September 2004

We report on a case of Adams–Oliver syndrome (AOS) with typical skin and limb defects along with the unique findings of pulmonary hypertension and central nervous system (CNS) involvement. Adams–Oliver syndrome has a wide spectrum of physical anomalies ranging from characteristic aplasia cutis congenita (ACC), transverse limb defects, and cutis marmorata telangiectica to extensive lethal anomalies. While pulmonary hypertension is usually not associated with AOS, the abnormal endothelial regulation of vascular tone seen in the pulmonary vasculature may enhance current pathophysiologic concepts of vascular abnormalities in AOS. There is accumulating evidence of significant CNS defects in AOS. This infant had hypoplastic corpus callosum and focal findings in the periventricular white matter. Evaluation for pulmonary hypertension and CNS anomalies in patients suspected to have AOS, can help identify those who are at risk for acute morbidities and associated developmental delays. © 2004 Wiley‐Liss, Inc.
Recreating the biological pacemaker
Authors: Rosen Michael R. , Robinson Richard B. , Brink Peter , Cohen Ira S.
Published: September 2004

In recent years, several groups have reported a variety of strategies for developing biological pacemakers whose ultimate function would be to supplement/replace electronic pacemakers. Strategies have included gene therapy using naked plasmids or viral vectors and cell therapy for which both adult human mesenchymal stem cells (hMSCs) and human embryonic stem cells have been employed. This article reviews the various approaches and summarizes our own research in which the pacemaker gene, HCN2, is administered via viral vector or in an hMSC platform to produce pacemaker function in the intact canine heart. © 2004 Wiley‐Liss, Inc.
Functional imaging of the embryonic pacemaking and cardiac conduction system over the past 150 years: Technologies to overcome the challenges
Authors: Rothenberg Florence , Efimov Igor R. , Watanabe Michiko
Published: September 2004

Early analyses of cardiac pacemaking and conduction system (CPCS) development relied on classic histology and visual inspection of the beating heart. Current techniques that facilitate delineation of the CPCS include the use of specific antibody markers and transgenic mouse lines specifically expressing reporter genes. Assaying the function of tiny embryonic hearts required an increase in the level of spatial and temporal resolution. Current methods for such analyses include the use of intracellular and extracellular microelectrodes, echocardiography, rapid optical imaging using fluorescent dyes, and most recently optical coherence tomography. This review will focus on methods developed to investigate the functional emergence of the embryonic cardiac conduction system. Where appropriate, the methods used to delineate the anatomic pathways will also be discussed. The combination of techniques to capture both morphological and functional data from the CPCS will further improve with continued interdisciplinary collaboration. © 2004 Wiley‐Liss, Inc.
Transitions in ventricular activation revealed by two‐dimensional optical mapping
Authors: Chuck Emil Thomas , Meyers Kathleen , France David , Creazzo Tony L. , Morley Gregory E.
Published: September 2004

While cardiac function in the mature heart is dependent on a properly functioning His‐Purkinje system, the early embryonic tubular heart efficiently pumps blood without a distinct specialized conduction system. Although His‐Purkinje system precursors have been identified using immunohistological techniques in the looped heart, little is known whether these precursors function electrically. To address this question, we used high‐resolution optical mapping and fluorescent dyes with two CCD cameras to describe the motion‐corrected activation patterns of 76 embryonic chick hearts from tubular stages (stage 10) to mature septated hearts (stage 35). Ventricular activation in the tubular looped heart (stages 10–17) using both calcium‐sensitive fluo‐4 and voltage‐sensitive di‐4‐ANEPPS shows sequentially uniform propagation. In late looped hearts (stages 18–22), domains of the dorsal and lateral ventricle are preferentially activated before spreading to the remaining myocardium and show alternating regions of fast and slow propagation. During stages 22–26, action potentials arise from the dorsal ventricle. By stages 27–29, action potential breakthrough is also observed at the right ventricle apex. By stage 31, activation of the heart proceeds from foci at the apex and dorsal surface of the heart. The breakthrough foci correspond to regions where putative conduction system precursors have been identified immunohistologically. To date, our study represents the most detailed electrophysiological characterization of the embryonic heart between the looped and preseptated stages and suggests that ventricular activation undergoes a gradual transformation from sequential to a mature pattern with right and left epicardial breakthroughs. Our investigation suggests that cardiac conduction system precursors may be electrophysiologically distinct and mature gradually throughout cardiac morphogenesis in the chick. © 2004 Wiley‐Liss, Inc.
Nature, significance, and mechanisms of electrical heterogeneities in ventricle
Authors: Poelzing Steven , Rosenbaum David S.
Published: September 2004

Previously, dispersion of repolarization (DOR) has been extensively linked to the development of arrhythmias and sudden cardiac death. The electrical heterogeneities that cause DOR between transmural myocyte layers have been reported in a wide variety of animals and humans. The underlying causes of transmural electrical heterogeneities are in part due to heterogeneous functional expression of proteins responsible for ion handling. Recently, we found that electrophysiologic heterogeneities between subepicardial and midmyocardial cells can form a substrate for reentrant ventricular arrhythmias. However, cell‐to‐cell coupling through gap junctions is expected to attenuate transmural heterogeneities between cell types spanning the ventricular wall. In this article we review a hypothesis that regional uncoupling resulting from expression patterns of gap junctions across the ventricular wall underlies DOR, and DOR can be amplified under disease conditions which remodel gap junctions. We find the principle gap junction protein, connexin43 (Cx43), is selectively reduced in the subepicardium (by 24%) compared to deeper layers of normal canine left ventricle. Additionally, the greatest DOR occurs within the subepicardial‐midmyocardial interface, precisely where Cx43 expression is reduced. The present data suggests that ion channel and gap junction heterogeneities act in conjunction to form and maintain transmural DOR. Importantly, both ion channel and gap junction remodeling occurs during many disease states such as heart failure. Importantly, in the absence of ion channel remodeling, pharmacological uncoupling increases transmural DOR, particularly within the epicardial‐midmyocardial interface, to values observed in heart failure. Therefore, these data suggest that heterogeneous Cx43 expression produces functionally significant electrophysiologic heterogeneities across the ventricular wall and may be a mechanism for promoting DOR which underlie arrhythmias in heart failure. © 2004 Wiley‐Liss, Inc.
GATA‐6 gene enhancer contains nested regulatory modules for primary myocardium and the embedded nascent atrioventricular conduction system
Authors: Adamo Richard F. , Guay Catherine L. , Edwards Angela V. , Wessels Andy , Burch John B.E.
Published: September 2004

The cGATA‐6 gene is flanked by an enhancer that selectively marks the atrioventricular conduction system (AVCS) in transgenic mice. This enhancer reads anterior/posterior and medial/lateral positional information very early in the cardiogenic program and remains active in progressively more restricted regions of primary myocardium leading up to the emergence of a histologically distinct AVCS. We undertook to parse this enhancer to resolve how the respective AVCS‐specific transcription program is regulated at the molecular level. We determined that this AVCS enhancer includes a 102 bp module that is sufficient to restrict expression to primary nonchamber myocardium. This offers a novel tool to analyze the early molecular delineation of primary and chamber myocardium, which subsequently give rise to components of the central and peripheral conduction system, respectively. Furthermore, we show that this 102 bp module in turn contains a nested 47 bp core module that has the potential to direct expression specifically to the AVCS domain of primary myocardium, albeit with low efficiency. Accordingly, we show that a GATA site and a GC‐rich site in the 102 bp region bolster the activity of the nested 47 bp AVCS core region even within the context of the parental 1,478 bp enhancer. These are the first functional elements to be reported for a cardiac conduction system‐specific control region. © 2004 Wiley‐Liss, Inc.
The muscular network of the sheep right atrium and frequency‐dependent breakdown of wave propagation
Authors: Berenfeld Omer , Zaitsev Alexey V.
Published: September 2004

The complex branching structure of the right atrium (RA) muscular network may provide the substrate for complex patterns of propagation during atrial fibrillation (AF). As AF results in some cases from stable sources in the left atrium (LA) with fibrillatory conduction toward the RA, we hypothesize that periodic input to the RA at an exceedingly high frequency results in disorganized wave propagation associated with the complex structure of the RA. Optical mapping was performed in isolated coronary‐perfused sheep RA. Rhythmic pacing of Bachmann's bundle allowed well‐controlled and realistic conditions for LA‐driven RA. Pacing at increasingly higher frequencies led to increasing delays in activation distal to major branching sites of the Crista terminalis and pectinate bundles, culminating in spatially distributed intermittent blockade at and above ∼ 6.5 Hz. At this breakdown frequency, the dominant frequencies of the RA response activity became spatially nonuniform. Such frequency‐dependent changes were independent of action potential duration. Rather, the spatial boundaries between proximal and distal frequencies correlated well with branch sites of the pectinate musculature. Thus, there exists a breakdown frequency in the sheep RA below which activity is periodic throughout the atrium and above which it is fibrillation‐like, consistent with the ideas that during AF, high‐frequency activation initiated in the LA undergoes fibrillatory conduction toward the RA, and that sink‐to‐source mismatch effect at branch points of the Crista terminalis and pectinate muscles is important in determining the complexity of the arrhythmia. © 2004 Wiley‐Liss, Inc.
Developmental transitions in electrical activation patterns in chick embryonic heart
Authors: Sedmera David , Reckova Maria , Bigelow Michael R. , Dealmeida Angela , Stanley Chiffvon P. , Mikawa Takashi , Gourdie Robert G. , Thompson Robert P.
Published: September 2004

The specialized conduction tissue network mediates coordinated propagation of electrical activity through the adult vertebrate heart. Following activation of the atria, the activation wave is slowed down in the atrioventricular canal or node, then spreads rapidly into the left and right ventricles via the His‐Purkinje system (HPS). This results in the ventricle being activated from the apex toward the base and is thought to represent HPS function. The development of mature HPS function in embryogenesis follows significant phases of cardiac morphogenesis. Initially, cardiac impulse propagates in a slow, linear, and isotropic fashion from the sinus venosus at the most caudal portion of the tubular heart. Although the speed of impulse propagation gradually increases, ventricular activation in the looped heart still follows the direction of blood flow. Eventually, the immature base‐to‐apex sequence of ventricular activation undergoes an apparent reversal, maturing to apex‐to‐base pattern. The embryonic chick heart has been studied intensively by both electrophysiological and morphological techniques, and the morphology of its conduction system (which is similar to mammals) is well characterized. One interesting but seldom studied feature is the anterior septal branch (ASB), which came sharply to focus (together with the rest of the ventricular conduction system) in our birthdating studies. Using an optical mapping approach, we show that ASB serves to activate ventricular surface between stages 16 and 25, predating the functionality of the His bundle/bundle branches. Heart morphogenesis and conduction system formation are thus linked, and studying the abnormal activation patterns could further our understanding of pathogenesis of congenital heart disease. © 2004 Wiley‐Liss, Inc.