bluuebunny/crossref_metadata_2025 huggingface dataset:
Fundamental importance of Na+–Ca2+ exchange for the pacemaking mechanism in guinea‐pig sino‐atrial node
Authors: Sanders Luke , Rakovic Stevan , Lowe Matthew , Mattick Paul A. D. , Terrar Derek A.
Published: January 2006

Na+–Ca2+ exchange (NCX) current has been suggested to play a role in cardiac pacemaking, particularly in association with Ca2+ release from the sarcoplasmic reticulum (SR) that occurs just before the action potential upstroke. The present experiments explore in more detail the contribution of NCX to pacemaking. Na+–Ca2+ exchange current was inhibited by rapid switch to low‐Na+ solution (with Li+ replacing Na+) within the time course of a single cardiac cycle to avoid slow secondary effects. Rapid switch to low‐Na+ solution caused immediate cessation of spontaneous action potentials. ZD7288 (3 μm), to block If (funny current) channels, slowed but did not stop the spontaneous activity, and tetrodotoxin (10 μm), to block Na+ channels, had little effect, but in the presence of either of these agents, rapid switch to low‐Na+ solution again caused immediate cessation of spontaneous action potentials. Spontaneous electrical activity was also stopped following loading of the cells with the Ca2+ chelators BAPTA and EGTA, and by exposure to the NCX inhibitor KB‐R7943 (5 μm). When rapid switch to low‐Na+ solution caused cessation of spontaneous activity, this was found (using confocal microscopy, with fluo‐4 as the Ca2+ probe) to be accompanied by an initial fall in cytosolic [Ca2+], with subsequent appearance of Ca2+ waves. Inhibition of SR Ca2+ uptake with cyclopiazonic acid (CPA, 30 μm) slowed but did not stop spontaneous activity. Rapid switch to low‐Na+ solution in the presence of CPA caused abolition of spontaneous Ca2+ transients and a progressive rise in cytosolic [Ca2+]. With ratiometric fluorescence methods (indo‐5F as the Ca2+ probe), the minimum level of [Ca2+] between beats was found to be approximately 225 nm, and abolition of beating with nifedipine, acetylcholine or adenosine caused a fall in cytosolic [Ca2+] below this level. These observations support the hypothesis that NCX current is essential for normal pacemaker activity under the conditions of our experiments. A continuous depolarizing influence of current through the NCX protein might result from maintained electrogenic NCX (with 3:1 stoichiometry, supported by a cytosolic [Ca2+] that normally does not fall below 225 nm between beats) and/or from a novel, recently suggested role of the NCX protein to allow a Na+ leak pathway.
Static and dynamic γ‐motor output to ankle flexor muscles during locomotion in the decerebrate cat
Authors: Taylor A. , Durbaba R. , Ellaway P. H. , Rawlinson S.
Published: January 2006

In locomotion, the flexor muscles of the leg are mainly concerned with the relatively constant task of raising the foot, whereas the extensors have the more variable task of support and propulsion at different speeds. This suggests that the way in which the fusimotor system works may differ between the two muscle groups. Observations previously made of the static and dynamic γ‐motor firing patterns in the ankle extensor medial gastrocnemius (MG) have therefore been repeated in the flexor tibialis anterior (TA). One or more single γ‐motor axons, dissected from a small filament of TA nerve, were recorded simultaneously with a number of single spindle afferents in dorsal rootlets. Cats were decerebrated and locomoted spontaneously on a treadmill. Identification of each γ‐motor axon depended on relating the changes in firing caused by midbrain stimulation to the changes in static and dynamic behaviour of the spindle afferents in response to repetitive ramp and hold stretches. Static γ axons all showed a smooth modulation in frequency, increasing in phase with muscle shortening, superimposed on a minimum frequency of about 20–30 impulses s−1. Dynamic γ axons showed interrupted firing with the frequency rising abruptly from zero at the onset of shortening, and falling again to zero shortly after the onset of lengthening. The frequency during the active periods was relatively constant, even when movement amplitudes varied. The basic similarity in the static and dynamic gamma discharge patterns for the two muscles suggests that the strategy of γ‐motor control is common to both flexors and extensors. The static γ pattern is thought to be a ‘temporal template’ of the expected movement, effectively expanding the dynamic response range of the spindles in active movements. The dynamic γ pattern sensitizes the primary afferents to detect the onset of muscle lengthening and to detect departures from the intended movement trajectory.
Displacement of Natural Ventilation in an Enclosure With a Convective/Radiative Heat Source and Nonadiabatic Envelopes
Authors: Gao Jun , Zhao Jia-ning , Gao Fu-sheng
Published: January 2006

This paper studies the real case of naturally ventilated space with a convective/radiative heat source and nonadiabatic envelopes. The real envelopes and heat source are introduced into a simple two-layer model of the displacement of natural ventilation, and then contribute to achieving a newly developed one: the “Thermal and airFlow Natural Ventilation” (TFNV) model. The TFNV model divides a whole space into two vertical zones of different temperatures and defines air temperature in the lower zone higher than in outdoor air. Comparisons of the predictions by the TFNV model and Computational Fluid Dynamics (CFD) simulation show good agreement. It is found that the TFNV model simplifies the multilevel stratifications in such a real case of naturally ventilated space into an ideal two-layer thermal stratification. Through a procedure for the TFNV model, fundamental guidelines for well-designed real naturally ventilated buildings are then discussed in this paper. Two notable points are presented, first, improving natural ventilation by increasing the effective area of openings and second, designing displacement of natural ventilation based on a desired interface height.
An Independent-Flow-Field Model for a SDOF Nonlinear Structural System–Part II: Analysis of Complex Responses
Authors: Lin Huan , Yim Solomon C. S.
Published: January 2006

Complex responses observed in an experimental, nonlinear, moored structural system subjected to nearly periodic wave excitations are examined and compared to the simulations of a newly proposed independent-flow-field (IFF) model in this paper. Variations in wave heights are approximated by additive random perturbations to the dominant periodic component. Simulations show good agreement with the experimental results in both time and frequency domains. Noise effects on the experimental results, including bridging and transition phenomena, are investigated and interpreted by comparing to the simulations of its deterministic counterpart. Possible causes of a chaoticlike experimental result as previously observed are also inferred.
Floating Installation Marine System Vulnerability: Global Alert
Authors: Smith Andrew L. , Young Eoin H. S. , Morris Peter G. , English Max
Published: January 2006

The owners and operators of FPSO’s and FSU’s need to be advised of the risks posed by the uncontrolled flooding of machinery spaces, with regard to the safety of on-board personnel and the vessel itself. The UK Health and Safety Executive has drawn these concerns to the attention of the Classification Societies and the International Association of Classification Societies. A Safety Notice detailing the marine flooding hazards and recommended actions to be taken was issued in December 2003. The global potential for these incidents is highlighted because the methods of operating floating installations differ significantly from those of trading ships and flooding incidents are more frequent than major process accident scenarios.
Hydrogen Production by Solar Reforming of Natural Gas: A Comparison Study of Two Possible Process Configurations
Authors: Möller Stephan , Kaucic Dario , Sattler Christian
Published: January 2006

Solar steam reforming of natural gas (NG) is a possibility to lower the cost for introducing renewable hydrogen production technologies to the market by a combination of fossil fuel and solar energy. It comprises the production of hydrogen from NG and steam that acts as a chemical storage for hydrogen and solar energy as the renewable energy source to heat up the system and set free the hydrogen. Using the solar reformer technology fuel savings of up to 40% compared to a conventional plant are expected. The CO2 emissions can be reduced accordingly. The cost study shows that hydrogen produced by solar reforming might cost between 4.5 and 4.7ct€∕kWh (LHV of H2) today. Therefore, it is only about 20% more expensive than conventionally produced hydrogen. Rising prices for NG will result in favorable conditions for the solar technology.
Elastic Collisions with Two Moving Objects Made Simple
Authors: Funk Deb
Published: January 2006

We are all familiar with head-on elastic collisions. They conserve energy and momentum according to the formulas: Conservation of Energy: ½ v12 + ½ v22 = ½ V12 + ½ V22 and Conservation of Momentum: m1v1 + m2v2 = m1V1 + m2V2. Many texts expect the student to solve these two formulas simultaneously to find the final velocity of the two objects after the collision. Other books give the students the formulas to find the velocity of each car after the collision. These formulas are derived from the laws of conservation of energy and momentum with the additional but very limiting parameter that v2 = 0 (i.e., you must hit a stationary object). The formulas are: V1 = (m1 − m2)v1m1 + m2 and V2 = (2m1)v1m1 + m2. The problem is that not every object that is struck is stationary. Stationary objects are just easier targets.
Lenz's Law Magic Trick
Authors: Ruiz Michael J.
Published: January 2006

The demonstration of Lenz's law by dropping a powerful magnet down a nonmagnetic metal pipe has become a classic lecture-hall demonstration.1,2 An inexpensive version is packaged as a professional magic trick3 called “Newton's Nightmare.” Combining sleight-of-hand with a demonstration of Lenz's law is a surefire way to heighten student interest. The subsequent student discussion motivated by a desire to understand the magic trick can lead to a memorable physics lesson. This paper will discuss Lenz's law magic and review literature that reveals the subtlety of the physics.
When Is a Capacitor NOT a Capacitor?
Authors: Ray Biswajit
Published: January 2006

This paper presents a simple yet effective experiment-based exercise that leads students to develop a circuit model for real capacitors. Additionally, this exercise drives home the point that characteristics of commonly used electrical components are heavily dependent on operating frequency. In this context a concise discussion of equivalent-series-resistance and equivalent-series-inductance for capacitors is presented.
Transient Homologous Chromosome Pairing Marks the Onset of X Inactivation
Authors: Xu Na , Tsai Chia-Lun , Lee Jeannie T.
Published: January 2006

Mammalian X inactivation turns off one female X chromosome to enact dosage compensation between XX and XY individuals. X inactivation is known to be regulated in cis by
Xite, Tsix
, and
Xist
, but in principle the two Xs must also be regulated in trans to ensure mutually exclusive silencing. Here, we demonstrate that interchromosomal pairing mediates this communication. Pairing occurs transiently at the onset of X inactivation and is specific to the X-inactivation center. Deleting
Xite
and
Tsix
perturbs pairing and counting/choice, whereas their autosomal insertion induces de novo X-autosome pairing. Ectopic X-autosome interactions inhibit endogenous X-X pairing and block the initiation of X-chromosome inactivation. Thus,
Tsix
and
Xite
function both in cis and in trans. We propose that
Tsix
and
Xite
regulate counting and mutually exclusive choice through X-X pairing.
Native Cell Wall Organization Shown by Cryo-Electron Microscopy Confirms the Existence of a Periplasmic Space in
Staphylococcus aureus
Authors: Matias Valério R. F. , Beveridge Terry J.
Published: January 2006

The current perception of the ultrastructure of gram-positive cell envelopes relies mainly on electron microscopy of thin sections and on sample preparation. Freezing of cells into a matrix of amorphous ice (i.e., vitrification) results in optimal specimen preservation and allows the observation of cell envelope boundary layers in their (frozen) hydrated state. In this report, cryo-transmission electron microscopy of frozen-hydrated sections of
Staphylococcus aureus
D
2
C was used to examine cell envelope organization. A bipartite wall was positioned above the plasma membrane and consisted of a 16-nm low-density inner wall zone (IWZ), followed by a 19-nm high-density outer wall zone (OWZ). Observation of plasmolyzed cells, which were used to artificially separate the membrane from the wall, showed membrane vesicles within the space associated with the IWZ in native cells and a large gap between the membrane and OWZ, suggesting that the IWZ was devoid of a cross-linked polymeric cell wall network. Isolated wall fragments possessed only one zone of high density, with a constant level of density throughout their thickness, as was previously seen with the OWZs of intact cells. These results strongly indicate that the IWZ represents a periplasmic space, composed mostly of soluble low-density constituents confined between the plasma membrane and OWZ, and that the OWZ represents the peptidoglycan-teichoic acid cell wall network with its associated proteins. Cell wall differentiation was also seen at the septum of dividing cells. Here, two high-density zones were sandwiched between three low-density zones. It appeared that the septum consisted of an extension of the IWZ and OWZ from the outside peripheral wall, plus a low-density middle zone that separated adjacent septal cross walls, which could contribute to cell separation during division.
Distribution and Genetic Diversity of the ABC Transporter Lipoproteins PiuA and PiaA withinStreptococcus pneumoniaeand Related Streptococci
Authors: Whalan Rachael H. , Funnell Simon G. P. , Bowler Lucas D. , Hudson Michael J. , Robinson Andrew , Dowson Christopher G.
Published: January 2006

Streptococcus pneumoniaeis a major cause of morbidity and mortality worldwide. The existence of approximately 90 antigenically distinct capsular serotypes has greatly complicated the development of an effective pneumococcal vaccine. Virulence-associated proteins common and conserved among all capsular types now represent the best strategy to combat pneumococcal infections. PiuA and PiaA are the lipoprotein components of two pneumococcal iron ABC transporters and are required for full virulence in mouse models of infection. Here we describe a study of the distribution and genetic diversity of PiuA and PiaA within typical and atypicalS. pneumoniae,Streptococcus oralis, andStreptococcus mitisstrains. The genes encoding both PiuA and PiaA were present in all typical pneumococci tested, (covering 20 and 27 serotypes, respectively). ThepiuAgene was highly conserved within the typical pneumococci (0.3% nucleotide divergence), but was also present in “atypical” pneumococci and the closely related speciesS. mitisandS. oralis, showing up to 10.4% nucleotide divergence and 7.5% amino acid divergence from the typical pneumococcal alleles. Conversely, thepiaAgene was found to be specific to typical pneumococci, 100% conserved, and absent from the oral streptococci, including isolates ofS. mitisknown to possess pneumolysin and autolysin. These are desirable qualities for a vaccine candidate and as a diagnostic tool forS. pneumoniae.
Biochemical Analysis of Lpt3, a Protein Responsible forPhosphoethanolamine Addition to Lipooligosaccharide ofPathogenic
Neisseria
Authors: O'Connor Ellen T. , Piekarowicz Andrzej , Swanson Karen V. , Griffiss J. McLeod , Stein Daniel C.
Published: January 2006

The
inner core of neisserial lipooligosaccharide (LOS) contains heptose
residues that can be decorated by phosphoethanolamine (PEA). PEA
modification of heptose II (HepII) can occur at the 3, 6, or 7
position(s). We used a genomic DNA sequence of
lpt3
, derived
from
Neisseria meningitidis
MC58, to search the genomic
sequence of
N. gonorrhoeae
FA1090 and identified a homolog of
lpt3
in
N. gonorrhoeae
. A PCR amplicon containing
lpt3
was amplified from F62ΔLgtA, cloned, mutagenized,
and inserted into the chromosome of
N. gonorrhoeae
strain
F62ΔLgtA, producing strain
F62ΔLgtAlpt3::Tn
5
. LOS isolated
from this strain lost the ability to bind monoclonal antibody (MAb)
2-1-L8. Complementation of this mutation by genetic removal of the
transposon insertion restored MAb 2-1-L8 binding. Mass spectrometry
analysis of LOS isolated from the F62ΔLgtA indicated that this
strain contained two PEA modifications on its LOS.
F62ΔLgtAlpt3::Tn
5
lacked a PEA
modification on its LOS, a finding consistent with the hypothesis that
lpt3
encodes a protein mediating PEA addition onto gonococcal
LOS. The DNA encoding
lpt3
was cloned into an expression
vector and Lpt3 was purified. Purified Lpt3 was able to mediate the
addition of PEA to LOS isolated from
F62ΔLgtAlpt3::Tn
5
.
Segregation of the Replication Terminus of the TwoVibrio choleraeChromosomes
Authors: Srivastava Preeti , Fekete Richard A. , Chattoraj Dhruba K.
Published: January 2006

Genome duplication and segregation normally are completed before cell division in all organisms. The temporal relation of duplication and segregation, however, can vary in bacteria. Chromosomal regions can segregate towards opposite poles as they are replicated or can stay cohered for a considerable period before segregation. The bacteriumVibrio choleraehas two differently sized circular chromosomes, chromosome I (chrI) and chrII, of about 3 and 1 Mbp, respectively. The two chromosomes initiate replication synchronously, and the shorter chrII is expected to complete replication earlier than the longer chrI. A question arises as to whether the segregation of chrII also is completed before that of chrI. We fluorescently labeled the terminus regions of chrI and chrII and followed their movements during the bacterial cell cycle. The chrI terminus behaved similarly to that of theEscherichia colichromosome in that it segregated at the very end of the cell division cycle: cells showed a single fluorescent focus even when the division septum was nearly complete. In contrast, the single focus representing the chrII terminus could divide at the midcell position well before cell septation was conspicuous. There were also cells where the single focus for chrII lingered at midcell until the end of a division cycle, like the terminus of chrI. The single focus in these cells overlapped with the terminus focus for chrI in all cases. It appears that there could be coordination between the two chromosomes through the replication and/or segregation of the terminus region to ensure their segregation to daughter cells.
Overexpression of Genes of the Cell Wall Stimulon in Clinical Isolates ofStaphylococcus aureusExhibiting Vancomycin-Intermediate-S. aureus-Type Resistance to Vancomycin
Authors: McAleese Fionnuala , Wu Shang Wei , Sieradzki Krzysztof , Dunman Paul , Murphy Ellen , Projan Steven , Tomasz Alexander
Published: January 2006

Custom-designed gene chips (Affymetrix) were used to determine genetic relatedness and gene expression profiles inStaphylococcus aureusisolates with increasing MICs of vancomycin that were recovered over a period of several weeks from the blood and heart valve of a patient undergoing extensive vancomycin therapy. The isolates were found to be isogenic as determined by the GeneChip based genotyping approach and thus represented a unique opportunity to study changes in gene expression that may contribute to the vancomycin resistance phenotype. No differences in gene expression were detected between the parent strain, JH1, and JH15, isolated from the nares of a patient contact. Few expression changes were observed between blood and heart valve isolates with identical vancomycin MICs. A large number of genes had altered expression in the late stage JH9 isolate (MIC = 8 μg/ml) compared to JH1 (MIC = 1 μg/ml). Most genes with altered expression were involved in housekeeping functions or cell wall biosynthesis and regulation. The sortase-encoding genes,srtAandsrtB, as well as several surface protein-encoding genes were downregulated in JH9. Two hypothetical protein-encoding genes, SAS016 and SA2343, were dramatically overexpressed in JH9. Interestingly, 27 of the genes with altered expression in JH9 grown in drug-free medium were found to be also overexpressed when the parental strain JH1 was briefly exposed to inhibitory concentrations of vancomycin, and more than half (17 of 27) of the genes with altered expression belonged to determinants that were proposed to form part of a general cell wall stress stimulon (S. Utaida et al., Microbiology 149:2719-2732, 2003).
Regulation and Physiologic Significance of the Agmatine Deiminase System of
Streptococcus mutans
UA159
Authors: Griswold Ann R. , Jameson-Lee Max , Burne Robert A.
Published: January 2006

We previously demonstrated that
Streptococcus mutans
expresses a functional agmatine deiminase system (AgDS) encoded by the agmatine-inducible
aguBDAC
operon (A. R. Griswold, Y. Y. Chen, and R. A. Burne, J. Bacteriol.
186:
1902-1904, 2004). The AgDS yields ammonia, CO
2
, and ATP while converting agmatine to putrescine and is proposed to augment the acid resistance properties and pathogenic potential of
S. mutans
. To initiate a study of
agu
gene regulation, the
aguB
transcription initiation site was identified by primer extension and a putative σ
70
-like promoter was mapped 5′ to
aguB
. Analysis of the genome database revealed an open reading frame (SMU.261c) encoding a putative transcriptional regulator located 239 bases upstream of
aguB
. Inactivation of SMU.261c decreased AgD activity by sevenfold and eliminated agmatine induction. AgD was also found to be induced by certain environmental stresses, including low pH and heat, implying that the AgDS may also be a part of a general stress response pathway of this organism. Interestingly, an AgDS-deficient strain was unable to grow in the presence of 20 mM agmatine, suggesting that the AgDS converts a growth-inhibitory substance into products that can enhance acid tolerance and contribute to the competitive fitness of the organism at low pH. The capacity to detoxify and catabolize agmatine is likely to have major ramifications on oral biofilm ecology.
ohrR
and
ohr
Are the Primary Sensor/Regulator and Protective Genes against Organic Hydroperoxide Stress in
Agrobacterium tumefaciens
Authors: Chuchue Tatsanee , Tanboon Weerachai , Prapagdee Benjaphorn , Dubbs James M. , Vattanaviboon Paiboon , Mongkolsuk Skorn
Published: January 2006

The genes involved in organic hydroperoxide protection in
Agrobacterium tumefaciens
were functionally evaluated. Gene inactivation studies and functional analyses have identified
ohr
, encoding a thiol peroxidase, as the gene primarily responsible for organic hydroperoxide protection in
A. tumefaciens
. An
ohr
mutant was sensitive to organic hydroperoxide killing and had a reduced capacity to metabolize organic hydroperoxides.
ohr
is located next to, and is divergently transcribed from,
ohrR
, encoding a sensor and transcription regulator of organic hydroperoxide stress. Transcription of both
ohr
and
ohrR
was induced by exposure to organic hydroperoxides but not by exposure to other oxidants. This induction required functional
ohrR
. The results of gel mobility shift and DNase I footprinting assays with purified OhrR, combined with in vivo promoter deletion analyses, confirmed that OhrR regulated both
ohrR
and
ohr
by binding to a single OhrR binding box that overlapped the
ohrR
and
ohr
promoters.
ohrR
and
ohr
are both required for the establishment of a novel cumene hydroperoxide-induced adaptive response. Inactivation or overexpression of other Prx family genes (
prx1
,
prx2
,
prx3
,
bcp1
, and
bcp2
) did not affect either the resistance to, or the ability to degrade, organic hydroperoxide. Taken together, the results of biochemical, gene regulation and physiological studies support the role of
ohrR
and
ohr
as the primary system in sensing and protecting
A. tumefaciens
from organic hydroperoxide stress.
Domains Required for Transcriptional Activation Show Conservation in the Mga Family of Virulence Gene Regulators
Authors: Vahling Cheryl M. , McIver Kevin S.
Published: January 2006

Mga, or the multigene regulator of the group A streptococcus (GAS) (
Streptococcus pyogenes
), is a transcriptional regulator of virulence genes important for colonization and immune evasion. All serotypes of the GAS possess one of two divergent
mga
alleles (
mga-1
or
mga-2
), and orthologues of Mga have also been identified in other pathogenic streptococci. To date, the only functional motifs established within Mga are two amino-terminal DNA-binding domains (HTH-3 and HTH-4). To uncover novel domains, a random mutagenesis screen using an M6 Mga (
mga-1
) was undertaken to find mutations leading to a defect in transcriptional activation of the Mga-regulated
emm
gene. In addition to mutations in the established DNA-binding domains, the screen also revealed mutations in a region conserved among several Mga orthologues. Alanine scanning helped resolve the boundaries of this
c
onserved
M
ga
d
omain (CMD-1) spanning from residues 10 to 15 of the protein, with the two flanking amino acid residues likely involved in protein stability. Transcriptional reporter analyses demonstrated the importance of CMD-1 for activation of P
emm
and autoactivation of P
mga
in the serotype M6 Mga. Mutational analyses showed that both CMD-1 and HTH-4 are also necessary for activation of the promoter target P
mrp
in a divergent serotype M4 Mga (
mga-2
), suggesting a conserved functionality. However, in contrast to M6, the M4 Mga mutants did not show a defect in autoregulation. Mutation of similar conserved residues in the Mga-like regulator DmgB from
S. dysgalactiae
subsp.
dysgalactiae
showed that CMD-1 and HTH-4 are critical for transcriptional activation in this orthologue, implying that a common mechanism of virulence gene activation may exist for members of the Mga family of regulators.
The
yjeB
(
nsrR
) Gene of
Escherichia coli
Encodes a Nitric Oxide-Sensitive Transcriptional Regulator
Authors: Bodenmiller Diane M. , Spiro Stephen
Published: January 2006

Microarray studies of the
Escherichia coli
response to nitric oxide and nitrosative stress have suggested that additional transcriptional regulators of this response remain to be characterized. We identify here the product of the
yjeB
gene as a negative regulator of the transcription of the
ytfE
,
hmpA
and
ygbA
genes, all of which are known to be upregulated by nitrosative stress. Transcriptional fusions to the promoters of these genes were expressed constitutively in a
yjeB
mutant, indicating that all three are targets for repression by YjeB. An inverted repeat sequence that overlaps the −10 element of all three promoters is proposed to be a binding site for the YjeB protein. A similar inverted repeat sequence was identified in the
tehA
promoter, which is also known to be sensitive to nitrosative stress. The
ytfE
,
hmpA
,
ygbA
, and
tehA
promoters all caused derepression of a
ytfE
-
lacZ
transcriptional fusion when present in the cell in multiple copies, presumably by a repressor titration effect, suggesting the presence of functional YjeB binding sites in these promoters. However, YjeB regulation of
tehA
was weak, as judged by the activity of a
tehA
-
lacZ
fusion, perhaps because YjeB repression of
tehA
is masked by other regulatory mechanisms. Promoters regulated by YjeB could be derepressed by iron limitation, which is consistent with an iron requirement for YjeB activity. The YjeB protein is a member of the Rrf2 family of transcriptional repressors and shares three conserved cysteine residues with its closest relatives. We propose a regulatory model in which the YjeB repressor is directly sensitive to nitrosative stress. On the basis of similarity to the nitrite-responsive repressor NsrR from
Nitrosomonas europaea
, we propose that the
yjeB
gene of
E. coli
be renamed
nsrR
.
Anatomy of the Replication Origin of Plasmid ColE2-P9
Authors: Yagura Masaru , Nishio Shin-ya , Kurozumi Hideki , Wang Cheng-fu , Itoh Tateo
Published: January 2006

The plasmid ColE2-P9 origin is a 32-bp region which is specifically recognized by the plasmid-specified Rep protein to initiate DNA replication. We analyzed the structural and functional organization of the ColE2 origin by using various derivatives carrying deletions and single-base-pair substitutions. The origin may be divided into three subregions: subregion I, which is important for stable binding of the Rep protein; subregion II, which is important for binding of the Rep protein and for initiation of DNA replication; and subregion III, which is important for DNA replication but apparently not for binding of the Rep protein. The Rep protein might recognize three specific DNA elements in subregions I and II. The relative transformation frequency of the autonomously replicating plasmids carrying deletions in subregion I is lower, and nevertheless the copy numbers of these plasmids in host bacteria are higher than those of the wild-type plasmid. Efficient and stable binding of the Rep protein to the origin might be important for the replication efficiency to be at the normal (low) level. Subregion II might be essential for interaction with the catalytic domain of the Rep protein for primer RNA synthesis. The 8-bp sequence across the border of subregions II and III, including the primer sequence, is conserved in the (putative) origins of many plasmids, the putative Rep proteins of which are related to the ColE2-P9 Rep protein. Subregion III might be required for a step that is necessary after Rep protein binding has taken place.
Effect and Mechanism of Total Saponin of Dioscorea on Animal Experimental Hyperuricemia
Authors: Chen Guang-Liang , Wei Wei , Xu Shu-Yun
Published: January 2006

In this study, we investigated the effects and mechanisms of Total Saponin of Dioscorea (TSD) on animal experimental hyperuricemia. Mouse and rat hyperuricemic models were made by orally administering yeast extract paste once a day (30 and 20 g/kg, respectively), for 7 days. Yeast would disturb normal purine metabolism by increasing xanthine oxidase (XOD) activity and generating large quantities of uric acid. This model is similar to human hyperuricemia, which is induced by high-protein diets, due to a purine and nucleic acid metabolic disturbance. Another mouse hyperuricemia model was generated by intraperitoneal injection once with uric acid 250 mg/kg or potassium oxonate 300 mg/kg. Potassium oxonate, a urate oxidase inhibitor, can raise the serum uric acid level by inhibiting the decomposition of uric acid. Likewise, injecting uric acid can also increase serum uric acid concentration. The concentration of uric acid in serum or urine was detected by the phosphotungstic acid method, and the activity of XOD was assayed by a test kit. The results showed that TSD (240, 120 and 60 mg/kg, ig) could significantly lower the level of serum uric acid in hyperuricemic mice. TSD (120 and 60 mg/kg, ig) could also lower the level of serum uric acid in hyperuricemic rats, reduce the activity of XOD in the serum and liver of hyperuricemic rats, and increase the level of urine uric acid concentration as well as 24-hour total uric acid excretion. In conclusion, TSD possesses a potent anti-hyperuricemic effect on hyperuricemic animals, and the mechanism may be relevant in accelerating the excretion and decreasing the production of uric acid.
Therapeutic Effects and Molecular Mechanisms of Ginkgo Biloba Extract on Liver Fibrosis in Rats
Authors: Liu Shi-Quan , Yu Jie-Ping , Chen Hong-Lei , Luo He-Sheng , Chen Shi-Ming , Yu Hong-Gang
Published: January 2006

Oxidative stress can be implicated as a cause of liver fibrosis. In this sense, Ginkgo Biloba Extract (EGB), an antioxidant, may be beneficial in restraining liver fibrosis. The aim of this study was to evaluate the effects of EGB on experimental liver fibrosis. Rat liver fibrosis was induced by intraperitoneal injection of carbon tetrachloride ( CCl4) twice a week for 8 weeks. Three groups of rats received EGB (0.25, 0.5 and 1.0 g/kg, respectively) by stomach everyday. CCl4administration induced liver fibrosis, which was inhibited by EGB in a dose-dependent manner. The histopathologic score of fibrosis, liver function and the levels of plasma hyaluronic acid (HA) and laminin (LN) were significantly improved in rats treated with CCl4+ EGB , compared with those treated with CCl4only ( p < 0.01 or p < 0.05). The activities of superoxide dismutase (SOD) and glutathione pero xidase (GSH-Px) were notably elevated, while malondialdehyde (MDA) content was significantly decreased in the rats treated with CCl4+ EGB ( p < 0.01 or p < 0.05). Inhibition of hepatic stellate cell (HSC) activation and nuclear factor kappaBP65(NF-κBP65) expression was demonstrated in the livers of EGB-treated rats. The activation of NF-κB was significantly suppressed in EGB-treated rats determined by electrophoretic mobility shift assay (EMSA). Furthermore, EGB reduced expressions of transforming growth factor-β1(TGF-β1) and collagen I mRNA. In conclusion, EGB is able to ameliorate liver injury and prevent rats from CCl4-induced liver fibrosis by suppressing oxidative stress. This process may be related to inhibiting the induction of NF-κB on HSC activation and the expression of TGF-β1.
IMPLEMENTING THE MODEL EVOLUTION CALCULUS
Authors: BAUMGARTNER PETER , FUCHS ALEXANDER , TINELLI CESARE
Published: January 2006

Darwin is the first implementation of the Model Evolution Calculus by Baumgartner and Tinelli. The Model Evolution Calculus lifts the DPLL procedure to first-order logic. Darwin is meant to be a fast and clean implementation of the calculus, showing its effectiveness and providing a base for further improvements and extensions.

Based on a brief summary of the Model Evolution Calculus, we describe in the main part of the paper Darwin's proof procedure and its data structures and algorithms, discussing the main design decisions and features that influence Darwin's performance. We also report on practical experiments carried out with problems from the CASC-J2 system competition and parts of the TPTP Problem Library, and compare the results with those of other state-of-the-art theorem provers.
THINGS TO KNOW WHEN IMPLEMENTING LPO
Authors: LÖCHNER BERND
Published: January 2006

The Lexicographic Path Ordering (LPO) poses an interesting problem to the implementor: How to achieve a version that is both efficient and correct? The method of program transformation helps us to develop an efficient version step-by-step, making clear the essential ideas, while retaining correctness. By theoretical analysis we show that the worst-case behavior is thereby changed from exponential to polynomial. Detailed measurements show the practical improvements of the different variants. They allow us to assess experimentally various optimizations suggested for LPO.
HYDROGEN ISOTOPIC (D/H) COMPOSITION OF ORGANIC MATTER DURING DIAGENESIS AND THERMAL MATURATION
Authors: Schimmelmann Arndt , Sessions Alex L. , Mastalerz Maria
Published: January 2006

Changes in the D/H ratio of sedimentary organic matter (SOM) during thermal maturation have been difficult to interpret because the effects of hydrogen exchange and kinetic fractionations are confounded in natural samples. Recent analytical developments have significantly improved our understanding of the responsible mechanisms. In this paper, we review experimental and field data that document a progressive increase in the D/H ratio of most organic hydrogen at the bulk and molecular levels, and suggest that the transfer of hydrogen from water to organic matter is the most important mechanism leading to those changes. SOM and water in natural petroleum systems approach a pseudoequilibrium D/H fractionation of about −80 to −110‰. D/H ratios of organic hydrogen can preserve quantitative information about paleoclimate throughout diagenesis, and some qualitative information through catagenesis.
Gene deletion of MK2 inhibits TNF-α and IL-6 and protects against cerulein-induced pancreatitis
Authors: Tietz Anne Barbara , Malo Antje , Diebold Joachim , Kotlyarov Alexey , Herbst Andreas , Kolligs Frank T. , Brandt-Nedelev Barbara , Halangk Walter , Gaestel Matthias , Göke Burkhard , Schäfer Claus
Published: January 2006

Inflammatory effects contribute to the pathogenesis of pancreatitis. Clearly, proinflammatory cytokines like TNF-α and IL-6 are involved in this process and the associated systemic complications. The MAPKAPK-2 (MK2) signaling pathway is involved in cytokine gene expression. Therefore, we hypothesized that blockade of this pathway inhibits the expression of proinflammatory cytokines and thereby protects against pancreatitis. To investigate this, we used an in vivo mouse model with a homozygous deletion of the MK2 gene. Pancreatitis was induced by injection of cerulein. The severity was determined by measuring serum lipase, pancreatic trypsin activation, pancreatic edema, and morphological changes by quantitative scoring of histological sections. Systemic inflammation was evaluated by measuring myeloperoxidase activity in lung tissue. Serum levels of TNF-α and IL-6 were measured using an ELISA, and mRNA levels were identified using RT-PCR and subsequent quantitative PCR analysis. Pancreatitis in animals with deletion of the MK2 gene is less severe and accompanied with reduced serum levels of TNF-α and IL-6. Pancreatic mRNA levels revealed a fourfold reduction of IL-6 mRNA expression in MK2 −/− mice. Effects were associated with suppression of pancreatic trypsin activity and reduced acinar cell injury. In summary, these data show that gene deletion of MK2 ameliorates cerulein-induced pancreatitis. TNF-α and IL-6 signaling is mediated by the MK2 pathway and therefore crucial for the regulatory inflammatory processes. TNF-α expression is supposably regulated by a posttranscriptional mechanism, whereas IL-6 expression is most likely regulated by transcriptional effects.
Mechanisms underlying the anti-inflammatory actions of boswellic acid derivatives in experimental colitis
Authors: Anthoni C. , Laukoetter M. G. , Rijcken E. , Vowinkel T. , Mennigen R. , Müller S. , Senninger N. , Russell J. , Jauch J. , Bergmann J. , Granger D. N. , Krieglstein C. F.
Published: January 2006

Recent clinical trials of the gum resin of Boswellia serrata have shown promising results in patients with ulcerative colitis. The objective of this study was to determine whether a semisynthetic form of acetyl-11-keto-β-boswellic acid (sAKBA), the most potent anti-inflammatory component of the resin, also confers protection in experimental murine colitis induced by dextran sodium sulfate (DSS) to compare its effects with those standard medications of ulcerative colitis like steroids and to examine whether leukocyte-endothelial cell adhesion is a major target of action of sAKBA. Clinical measurements of disease activity and histology were used to assess disease progression, and intravital microscopy was employed to monitor the adhesion of leukocytes and platelets in postcapillary venules of the inflamed colon. sAKBA treatment significantly blunted disease activity as assessed both grossly and by histology. Similarly, the recruitment of adherent leukocytes and platelets into inflamed colonic venules was profoundly reduced in mice treated with sAKBA. Because previous studies in the DSS model have shown that P-selectin mediates these blood cell-endothelial cell interactions, the expression of P-selectin in the colonic microcirculation was monitored using the dual-radiolabeled antibody technique. The treatment of established colitis with sAKBA largely prevented the P-selectin upregulation normally associated with DSS colitis. All of the protective responses observed with sAKBA were comparable to that realized in mice treated with a corticosteroid. Our findings demonstrated an anti-inflammatory effect of sAKBA and indicated that P-selectin-mediated recruitment of inflammatory cells is a major site of action for this novel anti-inflammatory agent.
Activation of cardiac AMP-activated protein kinase by LKB1 expression or chemical hypoxia is blunted by increased Akt activity
Authors: Soltys Carrie-Lynn M. , Kovacic Suzanne , Dyck Jason R. B.
Published: January 2006

AMP-activated protein kinase (AMPK) plays a major role in the regulation of cardiac energy substrate utilization and can be negatively regulated by Akt activation in the heart. It has recently been shown that Akt directly phosphorylates AMPKα1/α2 on Ser485/491 in vitro and prevents the AMPK kinase (AMPKK) LKB1 from phosphorylating AMPKα at its primary activation site, Thr172 (S Horman, D Vertommen, R Heath, D Neumann, V Mouton, A Woods, U Schlattner, T Wallimann, D Carling, L Hue, and MH Rider. J Biol Chem 281: 5335–5340, 2006). To determine whether this is also the case in the cardiac myocyte, neonatal rat cardiac myocytes (NRCM) were infected with a recombinant adenovirus expressing a constitutively active mutant of Akt1 (myrAkt1) and then with or without adenoviruses expressing the active LKB1 complex. Expression of myrAkt1 blunted LKB1-induced phosphorylation of AMPKα at Thr172, which resulted in a dramatic decrease in phosphorylation of AMPK's target, acetyl CoA-carboxylase. This decrease in AMPK activity was associated with prior Akt1-dependent phosphorylation of AMPKα1/α2 at Ser485/491. To investigate whether Akt1 activation was also able to prevent other AMPKKs from phosphorylating AMPKα, we subjected NRCM to chemical hypoxia and noted a marked increase in phosphorylation of AMPKα at Thr172, despite no change in LKB1 activity. NRCM expressing myrAkt1 demonstrated increased phosphorylation of AMPKα1/α2 at Ser485/491 and a complete inhibition of chemical hypoxia-induced phosphorylation of AMPKα at Thr172. Taken together, our data show that activation of Akt1 is able to prevent activation of cardiac AMPK by LKB1 and at least one other AMPKK, likely by prior phosphorylation of AMPKα1/α2 at Ser485/491.
Cerebral autoregulation is preserved during orthostatic stress superimposed with systemic hypotension
Authors: Guo Hong , Tierney Nancy , Schaller Frederic , Raven Peter B. , Smith Scott A. , Shi Xiangrong
Published: January 2006

We sought to determine whether cerebral autoregulation (CA) is compromised during orthostatic stress superimposed with systemic hypotension. Transient systemic hypotension was produced by deflation of thigh cuffs previously inflated to suprasystolic pressure, combined with or without lower body negative pressure (LBNP). Cardiac output (CO) decreased from a baseline of 5.0 ± 0.5 l/min by −8.3 ± 1.7, −19.2 ± 2.0, and −30.6 ± 3.4% during LBNP of −15, −30, and −50 Torr, respectively. Mean arterial pressure (MAP) was maintained during LBNP, despite decreases in systolic and pulse pressures. Middle cerebral arterial blood flow velocity ( VMCA) decreased significantly from a baseline of 64 ± 3 to 58 ± 4 cm/s (−9.7 ± 2.4%) at −50 Torr of LBNP. The reduction in VMCA was associated with a decrease in regional cerebral O2 saturation. However, the percent decrease in VMCA was markedly less than that of CO. This suggests that the magnitude of the change in VMCA (an index of cerebral blood flow) is less than would be predicted, given the decrease in CO. Transient systemic hypotension decreased MAP by −21 ± 2, −24 ± 2, −28 ± 3, and −26 ± 3% at rest and during LBNP of −15, −30, and −50 Torr, respectively. Likewise, this acute hypotension resulted in decreases in VMCA of −20 ± 2, −21 ± 2, −24 ± 25, and −19 ± 2% and regional cerebral O2 saturation of −5 ± 1, −6 ± 1, −6 ± 1, and −7 ± 2% at rest and during LBNP of −15, −30, and −50 Torr, respectively. Complete recovery of VMCA to baseline values following transient hypotension (ranging from 5 to 8 s) occurred significantly earlier compared with MAP (from 10 to 12 s). No subjects experienced syncope during acute hypotension. We conclude that CA is preserved during LBNP, superimposed with transient systemic hypotension, despite the decrease in VMCA associated with sustained central hypovolemia in normal healthy individuals. This preserved CA is vital for the prevention of orthostatic syncope.
Soleus aponeurosis strain distribution following chronic unloading in humans: an in vivo MR phase-contrast study
Authors: Lee Hae-Dong , Finni Taija , Hodgson John A. , Lai Alex M. , Edgerton V. Reggie , Sinha Shantanu
Published: January 2006

The in vivo strain properties of human skeletal muscle-tendon complexes are poorly understood, particularly following chronic periods of reduced load bearing. We studied eight healthy volunteers who underwent 4 wk of unilateral lower limb suspension (ULLS) to induce chronic unloading. Before and after the ULLS, maximum isometric ankle plantar flexion torque was determined by using a magnetic resonance (MR)-compatible dynamometry. Volumes of the triceps surae muscles and strain distribution of the soleus aponeurosis and the Achilles tendon at a constant submaximal plantar flexion (20% pre-maximal voluntary contraction) were measured by using MRI and velocity-encoded, phase-contrast MRI techniques. Following ULLS, volumes of the soleus and the medial gastrocnemius and the maximum isometric ankle plantar flexion (maximum voluntary contraction) decreased by 5.5 ± 1.9, 7.5 ± 2.7, and 48.1 ± 6.1%, respectively. The strain of the aponeurosis along the length of the muscle before the ULLS was 0.3 ± 0.3%, ranging from −1.5 to 2.7% in different locations of the aponeurosis. Following ULLS, the mean strain was −6.4 ± 0.3%, ranging from −1.6 to 1.3%. The strain distribution of the midregion of the aponeurosis was significantly influenced by the ULLS, whereas the more distal component showed no consistent changes. Achilles tendon strain was not affected by the ULLS. These results raise the issue as to whether these changes in strain distribution affect the functional properties of the triceps surae and whether the probability of strain injuries within the triceps surae increases following chronic unloading in those regions of this muscle complex in which unusual strains occur.