bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mn2+-adenosine nucleotide complexes in the presence of the nitrogenase iron-protein: detection of conformational rearrangements directly at the nucleotide binding site by EPR and 2D-ESEEM (two-dimensional electron spin-echo envelope modulation spectroscopy)
Authors: Petersen Jan , Gessner Christof , Fisher Karl , Mitchell Claire J. , Lowe David J. , Lubitz Wolfgang 
Published: October 2005

Both ATP and a bivalent nucleotide-bound metal activator, normally Mg2+, are required for nitrogenase activity. EPR and ESEEM (electron spin-echo envelope modulation) measurements have been carried out on adenosine nucleotides in which the Mg2+ ion that is usually bound is replaced by Mn2+ in the presence of Kp2 (nitrogenase Fe-protein from Klebsiella pneumoniae). The Mn2+ zero-field splitting parameters have been determined from the EPR-spectrum to be |D|=0.0125 cm−1 with a rhombicity λ=E/D=0.31 by direct diagonalization of the complete spin Hamiltonian. ESEEM spectra of the Fe-protein with MnADP and MnATP both show an ESEEM line pair with one signal component at about 3.6 MHz and a relatively broad resonance at 8 MHz originating from a superhyperfine coupling to a 31P nuclear spin from one or more directly co-ordinated phospho group(s) of the nucleotide. A pronounced resonance overlapping the low-frequency component of the 31P-signal at about 3.5 MHz is attributed to an interaction of Mn2+ with univalent 23Na nuclei. ESEEM lines at frequencies &lt;3.5 MHz have been ascribed to interactions with 14N nuclei. Differences in the 14N features that depend on the type of nucleotide are consistent with substantial conformational rearrangements at the nucleotide-binding site upon hydrolysis. In addition, four-pulse HYSCORE (hyperfine sublevel correlation spectroscopy) experiments not only confirm the three-pulse ESEEM results, but also achieve significantly better spectral deconvolution, especially of the 31P-couplings, and demonstrate that the nucleotide is at least a unidentate ligand of Mn2+. Moreover it was also possible to identify peaks from an 14N interaction more clearly; these most probably arise from outer-sphere interactions with nitrogen atom(s) of non-co-ordinated residues which are affected by conformational rearrangements upon nucleotide hydrolysis. In addition, different redox states of the [4Fe-4S] cluster of the Fe-protein show disparate conformations of the metal–nucleotide co-ordination environment, demonstrating that also the cluster site communicates with the nucleotide binding site.
Functional analysis of the promoter of the mitochondrial phosphate carrier human gene: identification of activator and repressor elements and their transcription factors
Authors: Iacobazzi Vito , Infantino Vittoria , Costanzo Paola , Izzo Paola , Palmieri Ferdinando 
Published: October 2005

The phosphate carrier (PiC) catalyses the import of phosphate into mitochondria where it is needed for ATP synthesis. We have analysed the 5′-flanking region of the human PiC gene and found that it has a single transcriptional initiation site and lacks a TATA box. Through deletion analysis of the −1213/−25 nt region, we identified an activation domain (−223/−25) and an inhibition domain (−1017/−814). The most effective promoter activity in transfected HeLa cells corresponded to the region containing putative binding sites for Sp1 (−163/−142; where Sp1 stands for stimulating protein-1) and CREB (−138/−116; where CREB stands for cAMP-response-element-binding protein). These DNA sequences were active in gel-shift assays in the presence of HeLa cell nuclear extracts or recombinant Sp1 and CREB respectively. Forskolin increased PiC promoter activity via the CREB site. Both footprinting and transfection of deletion constructs of the inhibition region (−1017/−814) showed that PiC silencer activity extends over 25 nt (−943/−919), which specifically binds two proteins present in HeLa cell nuclear extracts. These transcription factors were purified by DNA affinity, analysed by MS and identified as p54nrb/NonO (nuclear RNA binding protein) and PSF (protein-associated splicing factor). The PiC silencer region cloned in front of the ferritin promoter conferred a strong inhibition to the heterologous promoter. These findings may provide insight into control of PiC gene expression in different cell types and under different growth conditions. To our knowledge, this is the first study to analyse the regulation of the PiC gene expression in any cell.
Synaptic vesicle chips to assay botulinum neurotoxins
Authors: Ferracci Géraldine , Miquelis Raymond , Kozaki Shunji , Seagar Michael , Lévêque Christian 
Published: October 2005

BoNTs (botulinum neurotoxins), considered to be the most toxic of all biological substances, inhibit neurotransmission through proteolytic cleavage of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins [VAMP (vesicle-associated membrane protein, or synaptobrevin), SNAP-25 (25 kDa synaptosome-associated protein) or syntaxin]. Expansion in the use of BoNTs as therapeutic and cosmetic agents, and the potential threat they constitute as biological weapons, underlines the need for rapid and sensitive in vitro assays. Here, we present new automatized bioassays to detect VAMP cleavage by BoNT/B and F. Western blotting and SPR (surface plasmon resonance) methods revealed that BoNT/B and F totally cleave their substrate on immunoisolated SVs (synaptic vesicles). Real-time monitoring of the immunocapture of native SVs from crude lysates on SPR sensor chips enabled the detection of picogram amounts of different SV proteins. Pre-incubation of a membrane fraction containing SVs with BoNT specifically inhibited capture by anti-VAMP antibodies, and amounts as low as 0.1 pg of BoNT/B were detected. This automated SPR assay is approx. 200 times more sensitive, and 25 times more rapid, than the in vivo BoNT/B test currently used. Moreover, the method can be performed using a few thousand cultured neurons and constitutes a new screening assay for inhibitors. Our data indicate that native VAMP is an optimal substrate for in vitro BoNT assays that can be monitored by SPR.
Amino-acid limitation induces transcription from the human C/EBPβ gene via an enhancer activity located downstream of the protein coding sequence
Authors: Chen Chin , Dudenhausen Elizabeth , Chen Hong , Pan Yuan-Xiang , Gjymishka Altin , Kilberg Michael S. 
Published: October 2005

For animals, dietary protein is critical for the nutrition of the organism and, at the cellular level, protein nutrition translates into amino acid availability. Amino acid deprivation triggers the AAR (amino acid response) pathway, which causes enhanced transcription from specific target genes. The present results show that C/EBPβ (CCAAT/enhancer-binding protein β) mRNA and protein content were increased following the deprivation of HepG2 human hepatoma cells of a single amino acid. Although there was a modest increase in mRNA half-life following histidine limitation, the primary mechanism for the elevated steady-state mRNA was increased transcription. Transient transfection documented that C/EBPβ genomic fragments containing the 8451 bp 5′ upstream of the transcription start site did not contain amino-acid-responsive elements. However, deletion analysis of the genomic region located 3′ downstream of the protein coding sequence revealed that a 93 bp fragment contained an amino-acid-responsive activity that functioned as an enhancer. Exogenous expression of ATF4 (activating transcription factor 4), known to activate other genes through amino acid response elements, caused increased transcription from reporter constructs containing the C/EBPβ enhancer in cells maintained in complete amino acid medium. Chromatin immunoprecipitation demonstrated that RNA polymerase II is bound at the C/EBPβ promoter and at the 93 bp regulatory region in vivo, whereas ATF4 binds to the enhancer region only. Immediately following amino acid removal, the kinetics of binding for ATF4, ATF3, and C/EBPβ itself to the 93 bp regulatory region were similar to those observed for the amino-acid-responsive asparagine synthetase gene. Collectively the findings show that expression of C/EBPβ, which contributes to the regulation of amino-acid-responsive genes, is itself controlled by amino acid availability through transcription.
Attempts to characterize the NBD heterodimer of MRP1: transient complex formation involves Gly771 of the ABC signature sequence but does not enhance the intrinsic ATPase activity
Authors: Ramaen Odile , Sizun Christina , Pamlard Olivier , Jacquet Eric , Lallemand Jean-Yves 
Published: October 2005

MRP1 (multidrug-resistance-associated protein 1; also known as ABCC1) is a member of the human ABC (ATP-binding cassette) transporter superfamily that confers cell resistance to chemotherapeutic agents. Considering the structural and functional similarities to the other ABC proteins, the interaction between its two NBDs (nucleotide-binding domains), NBD1 (N-terminal NBD) and NBD2 (C-terminal NBD), is proposed to be essential for the regulation of the ATP-binding/ATP-hydrolysis cycle of MRP1. We were interested in the ability of recombinant NBD1 and NBD2 to interact with each other and to influence ATPase activity. We purified NBD1 (Asn642–Ser871) and NBD2 (Ser1286–Val1531) as soluble monomers under native conditions. We measured extremely low intrinsic ATPase activity of NBD1 (10−5 s−1) and NBD2 (6×10−6 s−1) and no increase in the ATP-hydrolysis rate could be detected in an NBD1+NBD2 mixture, with concentrations up to 200 μM. Despite the fact that both monomers bind ATP, no stable NBD1·NBD2 heterodimer could be isolated by gel-filtration chromatography or native-PAGE, but we observed some significant modifications of the heteronuclear single-quantum correlation NMR spectrum of 15N-NBD1 in the presence of NBD2. This apparent NBD1·NBD2 interaction only occurred in the presence of Mg2+ and ATP. Partial sequential assignment of the NBD1 backbone resonances shows that residue Gly771 of the LSGGQ sequence is involved in NBD1·NBD2 complex formation. This is the first NMR observation of a direct interaction between the ABC signature and the opposite NBD. Our study also reveals that the NBD1·NBD2 heterodimer of MRP1 is a transient complex. This labile interaction is not sufficient to induce an ATPase co-operativity of the NBDs and suggests that other structures are required for the ATPase activation mechanism.
The caspase-3 cleavage product of the plasma membrane Ca2+-ATPase 4b is activated and appropriately targeted
Authors: Pászty Katalin , Antalffy Géza , Penheiter Alan R. , Homolya László , Padányi Rita , Iliás Attila , Filoteo Adelaida G. , Penniston John T. , Enyedi Ágnes 
Published: October 2005

The calmodulin-activated transporter hPMCA4 (human plasma membrane Ca2+-ATPase isoform 4) is a target for cleavage by caspase-3 during apoptosis. We have demonstrated that caspase-3 generates a 120 kDa fragment of this pump which lacks the complete autoinhibitory sequence [Paszty, Verma, Padanyi, Filoteo, Penniston and Enyedi (2002) J. Biol. Chem. 277, 6822–6829]. In the present study we analysed further the characteristics of the fragment of hPMCA4b produced by caspase-3. We did this by overexpressing the caspase-3 cleavage product of hPMCA4b in COS-7 and MDCKII (Madin–Darby canine kidney II) cells. This technique made it possible to clearly define the properties of this fragment, and we showed that it is constitutively active, as it forms a phosphoenzyme intermediate and has high Ca2+ transport activity in the absence of calmodulin. When this fragment of hPMCA4b was stably expressed in MDCKII cell clones, it was targeted without degradation to the basolateral plasma membrane. In summary, our studies emphasize that the caspase-3 cleavage product of hPMCA4b is constitutively active, and that the C-terminus is not required for proper targeting of hPMCA4b to the plasma membrane. Also, for the first time, we have generated cell clones that stably express a constitutively active PMCA.
Endothelial nitric oxide synthase Glu298→Asp polymorphism, carotid atherosclerosis and intima-media thickness in a general population sample
Authors: Wolff Birger , Braun Claudia , Schlüter Christina , Grabe Hans J. , Popowski Katrin , Völzke Henry , Lüdemann Jan , John Ulrich , Cascorbi Ingolf 
Published: October 2005

The Glu298→Asp (E298D; 894G→T) polymorphism of eNOS (endothelial nitric oxide synthase) has been related with cardiovascular disease. In the present study, we investigated the association of Glu298→Asp with atherosclerotic plaques in different carotid vessel segments and with carotid IMT (intima-media thickness). The Glu298→Asp eNOS polymorphism was determined by 5′-exonuclease assay among 2448 participants of the SHIP (Study of Health in Pomerania). Mean and maximum common carotid IMT, as well as carotid atherosclerosis, were measured by high-resolution ultrasound. The Asp/Asp298 genotype was associated with an increased risk of atherosclerotic plaques at the level of the common carotid arteries [multivariate odds ratio, 1.57 and 95% CI (confidence interval), 1.05–2.34; P=0.025], but not in the carotid bifurcations or internal or external carotid arteries. Glu298→Asp genotype was not associated with carotid IMT in the whole sample. However, the Asp/Asp298 genotype was independently associated with both higher mean [adjusted increase by 0.046 mm (95% CI, 0.013–0.078); P=0.006] and maximum carotid IMT [0.137 mm (95% CI, 0.064–0.209); P&lt;0.001] in the low-risk group of subjects without carotid atherosclerosis. In conclusion, the Asp/Asp298 genotype is associated with atherosclerosis in the common carotid arteries and, in a low-risk group, also with carotid IMT. This suggests that the association of the Glu298→Asp genotype with atherosclerosis in the carotid arteries is site-specific and is modified by overall cardiovascular risk.
Inhibition of human endothelial cell nitric oxide synthesis by advanced glycation end-products but not glucose: relevance to diabetes
Authors: Xu Biao , Ji Yong , Yao Kang , Cao Yue-Xin , Ferro Albert 
Published: October 2005

Endothelial dysfunction, with decreased NO (nitric oxide) biosynthesis, may play a pathophysiological role in diabetic vasculopathy. The aim of the present study was to determine the relative contributions of glucose and AGE (advanced glycation end-product) accumulation in suppressing NOS-3 (the endothelial isoform of NO synthase). Cultured HUVECs (human umbilical vein endothelial cells) were incubated with different concentrations of glucose, unmodified albumin or AGE-modified albumin for different times. NOS activity was measured from the conversion of L-[3H]arginine into L-[3H]citrulline, and the expression, serine phosphorylation and O-glycosylation of NOS-3 were determined by Western blotting. High (25 mmol/l) glucose, for up to 12 days of incubation, had no effect on the activity or expression of NOS-3, nor on its degree of serine phosphorylation or O-glycosylation, compared with physiological (5 mmol/l) glucose. By contrast, AGE-modified albumin exerted a concentration- and time-dependent suppression of NOS-3 expression in HUVECs at a range of concentrations (0–200 mg/l) found in diabetic plasma; this was evident after 24 h, whereas inhibition of NOS activity was seen after only 3 h incubation with AGE-modified albumin, consistent with our previous observations of rapid suppression of NOS-3 serine phosphorylation and NOS-3 activity by AGE-modified albumin. In conclusion, AGE-modified albumin suppresses NOS-3 activity in HUVECs through two mechanisms: one rapid, involving suppression of its serine phosphorylation, and another slower, involving a decrease in its expression. We also conclude that, in the context of the chronic hyperglycaemia in diabetes, the effects of AGEs on endothelial NO biosynthesis are considerably more important than those of glucose.
Poverty reduction strategy papers: Now who calls the shots?
Authors: Fraser Alastair 
Published: October 2005

This paper argues that Poverty Reduction Strategy Papers (PRSPs) can be understood as a technology of ‘social control’, which seeks to shape domestic political space. Despite widespread recognition that the World Bank and the IMF continue to impose orthodox policy conditions on debt relief and loans to African countries, many suggest the requirement in PRSPs for civil society ‘participation’ introduces a progressive element that could, in time, subvert the logic of coercion. In contrast, this paper suggests that it is precisely through participation that international Non-Governmental Organisations (NGOs) and bilateral donors are working with the IFIs** to secure ever more intimate supervision of African political communities. Thus, if the answer to Hanlon's (1991) rhetorical question ‘who calls the shots?’ under structural adjustment was ‘the IFIs’, the answer under PRSPs is ‘an uneasy coalition of NGOs, donors and the IFIs’. These groups share an agenda of securing consent to liberal systems of political and economic management. Through the PRSP and related processes they divide the labour required to manufacture consent, seeking to build ‘reform coalitions’ by transforming the objectives and nature of states, bureaucracies, social and political movements and, at their most ambitious, populations. In the process they imperil African sovereignty, self-determination and hopes for substantive democracy.
** Editor's Note: International financial institutions (IFIs) are public banks, using taxpayer money to invest in countries outside their borders, often in the name of fostering economic development, at home or abroad. Many of these IFIs are also large backers of fossil fuel projects around the world. They include both multilateral and bilateral development banks and export credit agencies.
Representation formulae and inequalities for solutions of a class of second order partial differential equations
Authors: D’Ambrosio Lorenzo , Mitidieri Enzo , Pohozaev Stanislav 
Published: October 2005

LetLLbe a possibly degenerate second order differential operator and letΓη=d2−Q\Gamma _\eta =d^{2-Q}be its fundamental solution atη\eta; hereddis a suitable distance. In this paper we study necessary and sufficient conditions for the weak solutions of−Lu≥f(ξ,u)≥0-Lu\ge f(\xi ,u)\ge 0onRN{\mathbb {R}}^Nto satisfy the representation formula\[(R)u(η)≥∫RNΓηf(ξ,u)dξ.(\mbox R)\qquad \qquad \qquad \qquad \qquad u(\eta )\ge \int _{\mathbb {R}^N} \Gamma _\eta f(\xi ,u) \,d\xi .\qquad \qquad \qquad \qquad \qquad \qquad\]We prove that (R) holds providedf(ξ,⋅)f(\xi ,\cdot )is superlinear, without any assumption on the behavior ofuuat infinity. On the other hand, ifuusatisfies the condition\[lim infR→∞−∫R≤d(ξ)≤2R|u(ξ)|dξ=0,\liminf _{R\rightarrow \infty } {-\!\!\!\!\!\!\int }_{R\le d(\xi )\le 2R}|u(\xi )|d\xi =0,\]then (R) holds with no growth assumptions onf(ξ,⋅)f(\xi ,\cdot ).
On the Andrews-Stanley refinement of Ramanujan’s partition congruence modulo 5 and generalizations
Authors: Berkovich Alexander , Garvan Frank 
Published: October 2005

In a recent study of sign-balanced, labelled posets, Stanley introduced a new integral partition statistic

s
r
a
n
k

(
π
)
=

O

(
π
)
−

O

(

π
′

)
,

\begin{equation*} \mathrm {srank}(\pi ) = {\mathcal O}(\pi ) - {\mathcal O}(\pi ’), \end{equation*}

where

O

(
π
)

{\mathcal O}(\pi )

denotes the number of odd parts of the partition

π
\pi

and

π
′

\pi ’

is the conjugate of

π
\pi

. In a forthcoming paper, Andrews proved the following refinement of Ramanujan’s partition congruence mod

5
5

:

p
0

(
5
n
+
4
)

a
m
p
;
≡

p
2

(
5
n
+
4
)
≡
0

(
mod

5
)
,
p
(
n
)

a
m
p
;
=

p
0

(
n
)
+

p
2

(
n
)
,

\begin{align*} p_0(5n+4) &\equiv p_2(5n+4) \equiv 0 \pmod {5}, p(n) &= p_0(n) + p_2(n), \end{align*}

where

p
i

(
n
)

p_i(n)

(

i
=
0
,
2

i=0,2

) denotes the number of partitions of

n
n

with

s
r
a
n
k

≡
i

(
mod

4
)

\mathrm {srank}\equiv i\pmod {4}

and

p
(
n
)

p(n)

is the number of unrestricted partitions of

n
n

. Andrews asked for a partition statistic that would divide the partitions enumerated by

p
i

(
5
n
+
4
)

p_i(5n+4)

(

i
=
0
,
2

i=0,2

) into five equinumerous classes. In this paper we discuss three such statistics: the ST-crank, the

2
2

-quotient-rank and the

5
5

-core-crank. The first one, while new, is intimately related to the Andrews-Garvan (1988) crank. The second one is in terms of the

2
2

-quotient of a partition. The third one was introduced by Garvan, Kim and Stanton in 1990. We use it in our combinatorial proof of the Andrews refinement. Remarkably, the Andrews result is a simple consequence of a stronger refinement of Ramanujan’s congruence mod

5
5

. This more general refinement uses a new partition statistic which we term the BG-rank. We employ the BG-rank to prove new partition congruences modulo

5
5

. Finally, we discuss some new formulas for partitions that are

5
5

-cores and discuss an intriguing relation between

3
3

-cores and the Andrews-Garvan crank.
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium
Authors: Tan Yongxi , Shi Leming , Hussain Saber M. , Xu Jun , Tong Weida , Frazier John M. , Wang Charles 
Published: October 2005

Abstract
Motivation: DNA microarrays can provide information about the expression levels of thousands of genes simultaneously at the transcriptomic level, while conventional cell viability and cytotoxicity measurement methods provide information about the biological functions at the cellular level. Integrating these data at different levels provides a promising approach for evaluating or predicting how cells respond to chemical exposure. It is important to investigate the multi-scale biological system in a systematic way to better understand the gene regulation networks and signal transduction pathways involved in the cellular responses to environmental factors.
Results: Primary rat hepatocytes were exposed to cadmium acetate at 0, 1.25 and 2 μM. mRNA expression profiles at 0, 3, 6, 12 and 24 h were measured using the Affymetrix RatTox U34 GeneChip® arrays. Simultaneously, cytotoxicity was assessed by lactase dehydrogenase leakage assay. Gene expression profiles at different time points were used to evaluate cytotoxicity at subsequent time points using partial least squares, and it was found that gene expression profiles at 0 h had the best prediction accuracy for the cytotoxicity observed at 12 h. Some biomarkers whose expression profiles showed strong relationship with cytotoxicity were identified and the underlying pathways were reconstructed to illustrate how hepatocytes respond to cadmium exposure. Permutation studies were also applied to assess the reliability of the predictive models.
Availability: Matlab source code is available upon request and DNA microarray data are available at GEO ().
Contact: cwang61@ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.