bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field observations of extended locomotor activity at sub‐optimal body temperatures in a diurnal heliothermic lizard (Tiliqua rugosa)
Authors: Kerr Gregory D. , Bull C. Michael 
Published: September 2004

AbstractThe behavioural response of the sleepy lizard Tiliqua rugosa to an extended drought was examined in spring and summer 2002. Observations of the behaviour and use of microhabitat by radio‐tagged lizards for spring in 2000–2002 showed that the lizards in 2002 suffered decreased body mass and increased mortality, were less active, showed reduced mating behaviour and increased use of burrows when compared with the more normal wetter years of 2000 and 2001. The lizards lost significant mass owing to dehydration and starvation. An ‘onboard’ data logger recorded lizard stride frequency and body temperature continuously for 4 months on 11 lizards during the drought of 2002. The normally diurnal heliothermic sleepy lizards responded to rare rainfall events during the drought whenever they occurred, day or night, by emerging from burrows or other shelters for extended periods of activity with sub‐optimal body temperatures as low as 8.5°C. They moved more often, and with higher stride frequencies during periods of rain than during dry periods, both overnight and during the day. As a consequence of this extended activity under physiological stress, the lizards were able to respond to naturally occurring transient opportunities for food and water that would not have been available if they were only active at optimal body temperatures. In an area where freestanding water is rarely available, the lizards were able to access limited water by licking substrate. They also gained water and perhaps nutrition by consuming the temporarily rehydrated thalli of the free‐living terrestrial cyanobacterium Nostoc commune. Such behaviour enabled lizards to regain much of the mass lost before the rainfall and probably enabled many lizards to survive until more normal food sources became available. These rare events may have a significant effect on the shaping of the sleepy lizards phenotypic capacities outside routine day‐to‐day activities.
RLP, a novel Ras-like protein, is an immediate-early transforming growth factor-β (TGF-β) target gene that negatively regulates transcriptional activity induced by TGF-β
Authors: PIEK Ester , van DINTHER Maarten , PARKS W. Tony , SALLEE John M. , BÖTTINGER Erwin P. , ROBERTS Anita B. , ten DIJKE Peter 
Published: September 2004

We have described previously the use of microarray technology to identify novel target genes of TGF-β (transforming growth factor-β) signalling in mouse embryo fibroblasts deficient in Smad2 or Smad3 [Yang, Piek, Zavadil, Liang, Xie, Heyer, Pavlidis, Kucherlapati, Roberts and Böttinger (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 10269–10274]. Among the TGF-β target genes identified, a novel gene with sequence homology to members of the Ras superfamily was identified, which we have designated as RLP (Ras-like protein). RLP is a Smad3-dependent immediate-early TGF-β target gene, its expression being induced within 45 min. Bone morphogenetic proteins also induce expression of RLP, whereas epidermal growth factor and phorbol ester PMA suppress TGF-β-induced expression of RLP. Northern-blot analysis revealed that RLP was strongly expressed in heart, brain and kidney, and below the detection level in spleen and skeletal muscles. At the protein level, RLP is approx. 30% homologous with members of the Ras superfamily, particularly in domains characteristic for small GTPases. However, compared with prototypic Ras, RLP contains a modified P-loop, lacks the consensus G2 loop and the C-terminal prenylation site and harbours amino acid substitutions at positions that render prototypic Ras oncogenic. However, RLP does not have transforming activity, does not affect phosphorylation of mitogen-activated protein kinase and is unable to bind GTP or GDP. RLP was found to associate with certain subtypes of the TGF-β receptor family, raising the possibility that RLP plays a role in TGF-β signal transduction. Although RLP did not interact with Smads and did not affect TGF-β receptor-induced Smad2 phosphorylation, it inhibited TGF-β-induced transcriptional reporter activation, suggesting that it is a novel negative regulator of TGF-β signalling.
Association study of the I/D polymorphism and plasma angiotensin-converting enzyme (ACE) as risk factors for stent restenosis
Authors: RIBICHINI Flavio , FERRERO Valeria , MATULLO Giuseppe , FEOLA Mauro , VADO Antonello , CAMILLA Terenzio , GUARRERA Simonetta , CARTURAN Sonia , VASSANELLI Corrado , USLENGHI Eugenio , PIAZZA Alberto 
Published: September 2004

The ID (insertion/deletion) polymorphism of the ACE (angiotensin-converting enzyme) gene controls plasma ACE levels. Both have been correlated with ISR (in-stent restenosis) in preliminary analyses, but not confirmed in larger studies. In the present study, baseline and 6-month quantitative coronary analysis were performed in 897 patients who had stent implantation and the ID polymorphism genotyped. Plasma ACE levels were measured in 848 patients (95%). Restenosis rates among genotypes were 31.2% DD, 25.5% ID and 28.8% II (not significant). Plasma ACE levels were significantly higher in restenotic patients compared with patients without restenosis (30.7±18.6 units/l compared with 22.8±12.8 units/l; P=0.0001) and a strong independent predictor of ISR [OR (odds ratio)=3.70; 95% CI (confidence interval), 2.40–5.71; P&lt;0.0001], except in diabetics. In the subgroup of diabetics and patients with AMI (acute myocardial infarction), the DD genotypes actually had a lower risk of ISR than the II genotypes (diabetics, OR=0.16; 95% CI, 0.04–0.69; P=0.014; and patients with AMI, OR=0.21; 95% CI, 0.061–0.749; P=0.016). After exclusion of diabetics and patients with AMI, ISR rates for genotypes in 632 patients were 31.7% DD, 24.3% ID and 17.6% II (P=0.02; DD compared with non-DD OR=1.57; 95% CI, 1.09–2.25). The association between the D allele and ISR observed in selected populations does not hold with a larger sample size. Other than sample size, clinical variables can modulate the association between ID polymorphism and ISR. Plasma ACE level is a risk factor for ISR, independently of the ID genotype.
Invasive measurements of pulse wave velocity correlate with the degree of aortic valve calcification and severity associated with matrix metalloproteinases in elderly patients with aortic valve stenosis
Authors: LIU Ping-Yen , TSAI Wei-Chuan , LIN Chih-Chan , HSU Chih-Hsin , HAUNG Yao-Yi , CHEN Jyh-Hong 
Published: September 2004

The aim of the present study was to assess the association between invasive PWV (pulse wave velocity), serum levels of MMPs (matrix metalloproteinases) and the echocardiographic severity and calcification score of degenerative AS (aortic stenosis). We enrolled 30 patients (16 males; age, 61.3±8.2 years) diagnosed with degenerative AS and an additional 30 age- and sex-matched control patients. Invasive PWV methods with a pigtail catheter and double-channel recording were performed in both groups in our catheterization laboratory. We scored the severity of calcification at the AV (aortic valve) during two-dimensional echocardiography. The association between the trans-valvular pressure gradient, the severity of calcification of the AV and the value of PWV were analysed. We also analysed the serum levels of MMP-9, MMP-3 and TIMP-1 (tissue inhibitor of metalloproteinases-1) in these patients. In the group with degenerative AS, mean AV pressure gradients (56.0 compared with 9.5 mmHg; P&lt;0.001) and calcified AV scoring (3.3±1.2 compared with 2.1±0.9; P&lt;0.001) were higher than in the control group. In addition, PWV was faster in the group with degenerative AS (15.5±3.8 compared with 8.0±2.7 m/s; P=0.001). After being adjusted for age, sex, mean blood pressure and left ventricular function, both the AV pressure gradient and the severity of calcification were strongly correlated with PWV (R=0.706, P&lt;0.0001, and R=0.561, P=0.03 respectively). In addition, the serum levels of MMP-9, MMP-3 and TIMP-1 were all significantly higher and correlated with PWV in the group with AS (all P&lt;0.05). With higher serum levels of MMPs and their inhibitors, we found that this invasive measurement of PWV was associated strongly with the pressure gradient and calcification of AV. More advanced degenerative changes in AV was probably associated with more severe aortic arteriosclerosis.
Carotid artery stiffening does not explain baroreflex impairment in pre-eclampsia
Authors: MERSICH Beatrix , RIGÓ János , LÉNÁRD Zsuzsanna , STUDINGER Péter , VISONTAI Zsuzsanna , KOLLAI Mark 
Published: September 2004

Stiffening of the barosensory vessel wall in hypertension has been suggested to play a role in the associated baroreflex impairment. The carotid distensibility–BRS (baroreflex sensitivity) relationship, however, has not been studied in pre-eclampsia, a condition where hypertension is spontaneously reversible. Twelve normotensive pregnant women and 12 patients with pre-eclampsia matched for maternal age and week of gestation were studied in the third trimester and 3 months postpartum. Carotid artery diastolic diameter and pulsatile distension was measured by echo-wall tracking and carotid pulse pressure by applanation tonometry, and the carotid distensibility coefficient was calculated. Spontaneous BRS was determined by the sequence and spectral methods from 10 min continuous recording of ECG and finger arterial blood pressure. In the third trimester, carotid distensibility was lower in patients with pre-eclampsia than in normotensive pregnant women (2.47±0.17 compared with 4.08±0.16×10−3/mmHg); postpartum, it increased moderately in patients, but remained below normotensive values (3.25±0.12 compared with 4.25±0.19×10−3/mmHg). In the third trimester, both patients and healthy pregnant women had equally low BRS values; postpartum, the various BRS indices increased markedly (by 60–190%) and to the same level in both groups. No correlation was found between changes in carotid artery distensibility and those in BRS from the third trimester to postpartum period in patients and healthy pregnant women. The lack of association between changes in carotid distensibility and BRS suggest that stiffening of the carotid artery in pre-eclampsia is not responsible for baroreflex dysfunction.
Stepwise detection of recombination breakpoints in sequence alignments
Authors: Graham Jinko , McNeney Brad , Seillier-Moiseiwitsch Françoise 
Published: September 2004

Abstract
Motivation: We propose a stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints.
Results: We illustrate the approach by analyses of a simulated dataset and alignments of real data from HIV-1 and human chromosome 7. The presented simulation results compare the statistical properties of one-step and two-step procedures. More breakpoints are found with a two-step procedure than with a single application of a given method, particularly for higher recombination rates. At higher recombination rates, the additional breakpoints were located at the cost of only a slight increase in the number of falsely declared breakpoints. However, a large proportion of breakpoints still go undetected.
Availability: A makefile and C source code for phylogenetic profiling and the maximum χ2 method, tested with the gcc compiler on Linux and WindowsXP, are available at http://stat-db.stat.sfu.ca/stepwise/
Contact: jgraham@stat.sfu.ca
Average protein density is a molecular‐weight‐dependent function
Authors: Fischer Hannes , Polikarpov Igor , Craievich Aldo F. 
Published: September 2004

AbstractThe mass density of proteins is a relevant basic biophysical quantity. It is also a useful input parameter, for example, for three‐dimensional structure determination by protein crystallography and studies of protein oligomers in solution by analytic ultracentrifugation. We have performed a critical analysis of published, theoretical, and experimental investigations about this issue and concluded that the average density of proteins is not a constant as often assumed. For proteins with a molecular weight below 20 kDa, the average density exhibits a positive deviation that increases for decreasing molecular weight. A simple molecular‐weight‐depending function is proposed that provides a more accurate estimate of the average protein density.
Improved pKa calculations through flexibility based sampling of a water‐dominated interaction scheme
Authors: Warwicker Jim 
Published: September 2004

AbstractIonizable groups play critical roles in biological processes. Computation of pKas is complicated by model approximations and multiple conformations. Calculated and experimental pKas are compared for relatively inflexible active‐site side chains, to develop an empirical model for hydration entropy changes upon charge burial. The modification is found to be generally small, but large for cysteine, consistent with small molecule ionization data and with partial charge distributions in ionized and neutral forms. The hydration model predicts significant entropic contributions for ionizable residue burial, demonstrated for components in the pyruvate dehydrogenase complex. Conformational relaxation in a pH‐titration is estimated with a mean‐field assessment of maximal side chain solvent accessibility. All ionizable residues interact within a low protein dielectric finite difference (FD) scheme, and more flexible groups also access water‐mediated Debye‐Hückel (DH) interactions. The DH method tends to match overall pH‐dependent stability, while FD can be more accurate for active‐site groups. Tolerance for side chain rotamer packing is varied, defining access to DH interactions, and the best fit with experimental pKas obtained. The new (FD/DH) method provides a fast computational framework for making the distinction between buried and solvent‐accessible groups that has been qualitatively apparent from previous work, and pKa calculations are significantly improved for a mixed set of ionizable residues. Its effectiveness is also demonstrated with computation of the pH‐dependence of electrostatic energy, recovering favorable contributions to folded state stability and, in relation to structural genomics, with substantial improvement (reduction of false positives) in active‐site identification by electrostatic strain.
Selectivity and specificity of substrate binding in methionyl‐tRNA synthetase
Authors: Datta Deepshikha , Vaidehi Nagarajan , Zhang Deqiang , Goddard William A. 
Published: September 2004

AbstractThe accuracy of in vivo incorporation of amino acids during protein biosynthesis is controlled to a significant extent by aminoacyl‐tRNA synthetases (aaRS). This paper describes the application of the HierDock computational method to study the molecular basis of amino acid binding to the Escherichia coli methionyl tRNA synthetase (MetRS). Starting with the protein structure from the MetRS cocrystal, the HierDock calculations predict the binding site of methionine in MetRS to a root mean square deviation in coordinates (CRMS) of 0.55 Å for all the atoms, compared with the crystal structure. The MetRS conformation in the cocrystal structure shows good discrimination between cognate and the 19 noncognate amino acids. In addition, the calculated binding energies of a set of five methionine analogs show a good correlation (R2 = 0.86) to the relative free energies of binding derived from the measured in vitro kinetic parameters, Km and kcat. Starting with the crystal structure of MetRS without the methionine (apo‐MetRS), the putative binding site of methionine was predicted. We demonstrate that even the apo‐MetRS structure shows a preference for binding methionine compared with the 19 other natural amino acids. On comparing the calculated binding energies of the 20 natural amino acids for apo‐MetRS with those for the cocrystal structure, we observe that the discrimination against the noncognate substrate increases dramatically in the second step of the physical binding process associated with the conformation change in the protein.
High‐throughput automated refolding screening of inclusion bodies
Authors: Vincentelli Renaud , Canaan Stéphane , Campanacci Valérie , Valencia Christel , Maurin Damien , Frassinetti Frédéric , Scappucini‐Calvo Loréna , Bourne Yves , Cambillau Christian , Bignon Christophe 
Published: September 2004

AbstractOne of the main stumbling blocks encountered when attempting to express foreign proteins in Escherichia coli is the occurrence of amorphous aggregates of misfolded proteins, called inclusion bodies (IB). Developing efficient protein native structure recovery procedures based on IB refolding is therefore an important challenge. Unfortunately, there is no “universal” refolding buffer: Experience shows that refolding buffer composition varies from one protein to another. In addition, the methods developed so far for finding a suitable refolding buffer suffer from a number of weaknesses. These include the small number of refolding formulations, which often leads to negative results, solubility assays incompatible with high‐throughput, and experiment formatting not suitable for automation. To overcome these problems, it was proposed in the present study to address some of these limitations. This resulted in the first completely automated IB refolding screening procedure to be developed using a 96‐well format. The 96 refolding buffers were obtained using a fractional factorial approach. The screening procedure is potentially applicable to any nonmembrane protein, and was validated with 24 proteins in the framework of two Structural Genomics projects. The tests used for this purpose included the use of quality control methods such as circular dichroism, dynamic light scattering, and crystallogenesis. Out of the 24 proteins, 17 remained soluble in at least one of the 96 refolding buffers, 15 passed large‐scale purification tests, and five gave crystals.
Regulation of carotenoid biosynthesis in plants: evidence for a key role of hydroxymethylbutenyl diphosphate reductase in controlling the supply of plastidial isoprenoid precursors
Authors: Botella‐Pavía Patricia , Besumbes Óscar , Phillips Michael A. , Carretero‐Paulet Lorenzo , Boronat Albert , Rodríguez‐Concepción Manuel 
Published: September 2004

SummaryCarotenoids are isoprenoid pigments that function as photoprotectors, precursors of the hormone abscisic acid (ABA), colorants and nutraceuticals. A major problem for the metabolic engineering of high carotenoid levels in plants is the limited supply of their isoprenoid precursor geranylgeranyl diphosphate (GGPP), formed by condensation of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) units usually synthesized by the methylerythritol phosphate (MEP) pathway in plastids. Our earlier work with three of the seven MEP pathway enzymes suggested that the first reaction of the pathway catalyzed by deoxyxylulose 5‐phosphate synthase (DXS) is limiting for carotenoid biosynthesis during tomato (Lycopersicon esculentum) fruit ripening. Here we investigate the contribution of the enzyme hydroxymethylbutenyl diphoshate reductase (HDR), which simultaneously synthesizes IPP and DMAPP in the last step of the pathway. A strong upregulation of HDR gene expression was observed in correlation with carotenoid production during both tomato fruit ripening and Arabidopsis thaliana seedling deetiolation. Constitutive overexpression of the tomato cDNA encoding HDR in Arabidopsis did not increase carotenoid levels in etioplasts. By contrast, light‐grown transgenic plants showed higher carotenoid levels and an enhanced seed dormancy phenotype suggestive of increased ABA levels. The analysis of double transgenic Arabidopsis plants overproducing both the enzyme taxadiene synthase (which catalyzes the production of the non‐native isoprenoid taxadiene from GGPP) and either HDR or DXS showed a twofold stronger effect of HDR in increasing taxadiene levels. Together, the data support a major role for HDR in controlling the production of MEP‐derived precursors for plastid isoprenoid biosynthesis.
Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome
Authors: Schrader Jarmo , Moyle Richard , Bhalerao Rupali , Hertzberg Magnus , Lundeberg Joakim , Nilsson Peter , Bhalerao Rishikesh P. 
Published: September 2004

SummaryThe establishment of the dormant state in meristems involves considerable physiological and metabolic alterations necessary for surviving unfavourable growth conditions. However, a global molecular analysis of dormancy in meristems has been hampered by the difficulty in isolating meristem cells. We used cryosectioning to isolate purified cambial meristem cells from the woody plant Populus tremula during active growth and dormancy. These samples were used to generate meristem‐specific cDNA libraries and for cDNA microarray experiments to define the global transcriptional changes underlying cambial dormancy. The results indicate a significant reduction in the complexity of the cambial transcriptome in the dormant state. Although cell division is terminated in the dormant cambium, the cell cycle machinery appears to be maintained in a skeletal state as suggested by the continued presence of transcripts for several cell cycle regulators. The downregulation of PttPIN1 and PttPIN2 transcripts explains the reduced basipetal polar auxin transport during dormancy. The induction of a member of the SINA family of ubiquitin ligases implicated in auxin signalling indicates a potential mechanism for modulation of auxin sensitivity during cambial dormancy. The metabolic alterations during dormancy are mirrored in the induction of genes involved in starch breakdown and the glyoxysomal cycle. Interestingly, the induction of RGA1 like gene suggests modification of gibberellin signalling in cambial dormancy. The induction of genes such as poplar orthologues of FIE and HAP2 indicates a potential role for these global regulators of transcription in orchestrating extensive changes in gene expression during dormancy.
Plastid transformation reveals that moss tRNAArg‐CCG is not essential for plastid function
Authors: Sugiura Chika , Sugita Mamoru 
Published: September 2004

SummaryThree distinct arginine tRNA genes, trnR‐CCG, trnR‐ACG, and trnR‐UCU, are present in the plastid genome of bryophytes, whereas only the latter two trnR genes are present in the major vascular plants, except for black pine. trnR‐CCG is located between rbcL and accD in the moss Physcomitrella patens and it was previously believed to be functional in plastids. However, no trnR‐CCG transcript has been detected by Northern hybridization, and the codon usage of CGG is quite low in plastid protein‐coding sequences. This raises the possibility that trnR‐CCG is non‐functional. To investigate this possibility, we integrated a foreign gene into the trnR‐CCG coding region via homologous recombination, and constructed stable plastid trnR‐CCG knock‐out moss transformants. The trnR‐CCG knock‐out transformants grew normally, indicating that the P. patenstrnR‐CCG gene is not essential for plastid function.