bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dual altered peptide ligand down‐regulates myasthenogenic T cell responses and reverses experimental autoimmune myasthenia gravis via up‐regulation of Fas–FasL‐mediated apoptosis
Authors: Aruna Badiga Venkata , Ben‐David Hava , Sela Michael , Mozes Edna 
Published: June 2006

SummaryMyasthenia gravis (MG) and experimental autoimmune MG (EAMG) are T cell‐dependent, antibody‐mediated autoimmune diseases. A dual altered peptide ligand (APL) that is composed of the tandemly arranged two single amino acid analogues of two myasthenogenic peptides, p195–212 and p259–271, was demonstrated to down‐regulate in vitro and in vivo MG‐associated autoreactive responses. The aims of this study were to investigate the possible role of Fas–FasL‐mediated apoptosis in the down‐regulatory mechanism of the dual APL. We demonstrate here the effect of the dual APL on expression of key molecules involved in the Fas–FasL pathway, in a p195–212‐specific T cell line, in mice immunized with Torpedo acetylcholine receptor and in mice afflicted with EAMG (induced with the latter). In vitro and in vivo results show that the dual APL up‐regulated expression of Fas and FasL on the CD4 cells. Expression of the pro‐apoptotic molecules, caspase 8 and caspase 3, was significantly up‐regulated, while anti‐apoptotic cFLIP and Bcl‐2 were down‐regulated upon treatment with the dual APL. The dual APL also increased phosphorylation of the mitogen‐activated protein kinases, c‐Jun‐NH2‐terminal kinase and p‐38, known to play a role in the regulation of FasL expression. Further, in the T cell line incubated with the dual APL as well as in mice of the SJL inbred strain immunized with the myasthenogenic peptide and treated concomitantly with the dual APL, the percentage of apoptotic cells increased. Results strongly indicate that up‐regulation of apoptosis via the Fas–FasL pathway is one of the mechanisms by which the dual APL reverses EAMG manifestations in C57BL/6 mice.
Real‐time quadrupole mass spectrometer analysis of gas in borehole fluid samples acquired using the U‐tube sampling methodology
Authors: FREIFELD B. M. , TRAUTZ R. C. 
Published: June 2006

AbstractSampling of fluids in deep boreholes is challenging because of the necessity of minimizing external contamination and maintaining sample integrity during recovery. The U‐tube sampling methodology was developed to collect large volume, multiphase samples at in situ pressures. As a permanent or semi‐permanent installation, the U‐tube can be used for rapidly acquiring multiple samples or it may be installed for long‐term monitoring applications. The U‐tube was first deployed in Liberty County, TX to monitor crosswell CO2 injection as part of the Frio CO2 sequestration experiment. Analysis of gases (dissolved or separate phase) was performed in the field using a quadrupole mass spectrometer, which served as the basis for determining the arrival of the CO2 plume. The presence of oxygen and argon in elevated concentrations, along with reduced methane concentration, indicates sample alteration caused by the introduction of surface fluids during borehole completion. Despite producing the well to eliminate non‐native fluids, measurements demonstrate that contamination persists until the immiscible CO2 injection swept formation fluid into the observation wellbore.
Colorectal Cancer Screening in the Elderly Population: Disparities by Dual Medicare–Medicaid Enrollment Status
Authors: Koroukian Siran M. , Xu Fang , Dor Avi , Cooper Gregory S. 
Published: June 2006

Objectives. To assess the disparities in colorectal cancer (CRC) screening between elderly dual Medicare–Medicaid enrollees (or duals), the most vulnerable subgroup of the Medicare population, and nonduals.Data Sources/Study Setting. The 1999 Medicare Denominator File, the Medicare Outpatient Standard Analytic Files, and Physician Supplier Part B files. In addition, the 1998 Area Resource File was used as a source for county‐level attributes.Data Collection/Extraction Methods. CRC screening procedures for 1999—fecal occult blood test (FOBT), flexible sigmoidoscopy (FLEX), colonoscopy with FOBT and/or FLEX (COL‐WFF), and colonoscopy only (COL‐ONLY)—were extracted from claim records, using diagnostic and procedure codes. Duals (n=2.5 million) and nonduals (n=20.2 million) receiving their care through the fee‐for‐service system were identified from the Denominator file. Hierarchical logistic regression analysis was conducted to adjust for individual‐ and county‐level characteristics.Principal Findings. Compared with nonduals, duals were disproportionately represented by female, older‐old, and minority individuals (respectively 74.4 versus 58.5 percent; 19.3 versus 10.8 percent; 35.7 versus 8.0 percent), and CRC screening was significantly lower in duals than in nonduals (5.1 versus 12.2 percent for FOBT adjusted odds ratio [AOR]: 0.48, 95 percent confidence interval [CI]: 0.45–0.51); 0.7 versus 1.9 percent for FLEX, (AOR: 0.55, 95 percent CI: 0.49–0.61); 0.4 versus 0.8 percent for COL‐WFF (AOR: 0.60, 95 percent CI: 0.54–0.67); and 1.8 versus 2.5 percent for COL‐ONLY (AOR: 0.85, 95 percent CI: 0.80–0.89); p<.001 for all comparisons.Conclusions. Duals are significantly less likely than nonduals to undergo CRC screening, even after adjusting for individual‐ and county‐level covariates. Future studies should evaluate the contribution of comorbidity and low socioeconomic status to these disparities.
Feline head and neck squamous cell carcinoma: a natural model for the human disease and development of a mouse model
Authors: Tannehill‐Gregg S. H. , Levine A. L. , Rosol T. J. 
Published: June 2006

AbstractHead and neck squamous cell carcinoma (H/N SCC) is a devastating disease in humans and cats, and shares similar features between the two species. The large population of pet cats inthe United States, along with the high incidence of oral SCC in the cat, makes the cat an attractive candidate as a natural model for the human disease. There are similarities in pathology, progression, outcome, resistance to treatment, possible aetiologies and p53 expression, and we discuss the benefits of the cat as a natural model. We describe the development of a nude mouse xenograft model of feline oral SCC using the SCCF1 cell line transfected with a luciferase expression construct.In vivotumour growth and metastasis were measured using serial bioluminescent imaging, and tumours grew best in the subcutis. The cat and nude mouse models will be useful to investigate the pathogenesis and the molecular basis of H/N SCC, and for preclinical drug screening.
Reflexive Interdisciplinary Research: The Making of a Research Programme on the Rural Economy and Land Use
Authors: Lowe Philip , Phillipson Jeremy 
Published: June 2006

AbstractThis paper provides an account of the origins and formation of the UK Research Councils’ Rural Economy and Land Use (RELU) programme and its approach to promoting interdisciplinary working between social and natural scientists. The programme is set in the context of broader developments in science policy, including a policy discourse centred upon sustainable development and the knowledge economy and associated demands for greater accountability in science. Interdisciplinarity promises research that will be more relevant and responsive to public needs and concerns. In describing the provenance of the RELU programme, therefore, the paper seeks to lay out the different stages in its initiation and design to show how, to varying degrees, these were open to external scrutiny and influence. The process of developing the programme illustrates that it is not straightforward to make research agendas and funding more transparent and accountable. It also provides insights into the challenges that interdisciplinarity and accountability present to established science institutions.
Landscape as a Focus for Integrating Human and Environmental Processes
Authors: Matthews Robin , Selman Paul 
Published: June 2006

AbstractThe landscape has long been an important object of rural policy, particularly in terms of protecting scenic areas. Increasingly, however, landscape is seen as a multifunctional and holistic entity, which provides a framework for the governance and interdisciplinary study of spatial units. A central dilemma in the maintenance of cultural landscapes is that the historical practices which produced them are often obsolete, and new social and economic forces may fail to reproduce their valued properties. Sustainable development strategies therefore seek to instil ‘virtuous’ circles in cultural landscapes, linking society and economy to environmental service functions and land uses, in order to generate mutually reinforcing feedback loops resulting in socially preferred outcomes. We explore ways of investigating these linkages as a basis for future rural research and policy. We conceptualise cultural landscapes as ‘socio‐ecological systems’ (SESs), and consider their capacity for resilience and stability. Noting that resilient systems are characterised, not by simple equilibria, but by ‘basins of attraction’, we argue the need to understand the ways in which SESs stabilise within a particular basin, or move to an alternative. In particular, we reflect on the dynamics of ‘adaptive cycles’ that may lead to changes in system state. Finally, we discuss the development of appropriate models as tools for investigating whether a landscape is trending towards stability within a ‘vicious’ or a ‘virtuous’ circle, and evaluating potential interventions to alter this trajectory.
Roads Alter the Colonization Dynamics of a Keystone Herbivore in Neotropical Savannas1
Authors: Vasconcelos Heraldo L. , Vieira‐Neto Ernane H. M. , Mundim Fabiane M. , Bruna Emilio M. 
Published: June 2006

ABSTRACTRoads can facilitate the establishment and spread of both native and exotic species. Nevertheless, the precise mechanisms facilitating this expansion are rarely known. We tested the hypothesis that dirt roads are favorable landing and nest initiation sites for founding‐queens of the leaf‐cutter ant Atta laevigata. For 2 yr, we compared the number of attempts to found new nests (colonization attempts) in dirt roads and the adjacent vegetation in a reserve of cerrado (tree‐dominated savanna) in southeastern Brazil. The number of colonization attempts in roads was 5 to 10 times greater than in the adjacent vegetation. Experimental transplants indicate that founding‐queens are more likely to establish a nest on bare soil than on soil covered with leaf‐litter, but the amount of litter covering the ground did not fully explain the preference of queens for dirt roads. Queens that landed on roads were at higher risk of predation by beetles and ants than those that landed in the adjacent vegetation. Nevertheless, greater predation in roads was not sufficient to offset the greater number of colonization attempts in this habitat. As a consequence, significantly more new colonies were established in roads than in the adjacent vegetation. Our results suggest that disturbance caused by the opening of roads could result in an increased Atta abundance in protected areas of the Brazilian Cerrado.
Arthropod Abundance, Canopy Structure, and Microclimate in a Bornean Lowland Tropical Rain Forest1
Authors: Dial Roman J. , Ellwood Martin D. F. , Turner Edward C. , Foster William A. 
Published: June 2006

ABSTRACTThis study applies a novel, vertically stratified fogging protocol to document arthropod abundance, density, and biomass across a vertical gradient in a primary, lowland dipterocarp forest canopy in Borneo. We fogged arthropods at 5 m vertical intervals and 20 m horizontal intervals along six full‐canopy transects and measured leaf surface areas along the same transects. The results show that arthropod biomass in the aboveground regions was 23.6 kg/ha, the abundance was 23.9 million individuals/ha, and the density on leaf surfaces was 280 individuals/m2 leaf area. All three numbers are five to ten times higher than estimated by previous surveys of tropical lowland rain forest canopies using mass‐collection techniques. Arthropod abundance and biomass were analyzed in relation to canopy structure, composition, vapor pressure deficit (VPD), photosynthetic photon flux density (PPFD), and height. Using stepwise regression we found that 13 of 14 arthropod groups had significant positive relationships with one‐sided leaf area, 11 had significant negative relationships with VPD, 3 had significant relationships with height, and none showed positive relationships with light. Classifying the 14 taxa based on their responses to leaf area and VPD created three groups that corresponded roughly to the biology of these taxa. This study suggests that the biomass and abundance, and perhaps therefore—by extrapolation—the biodiversity, of tropical canopy arthropods may be very much higher than previously estimated.
Preliminary Evidence of the Importance of ENSO in Modifying Food Availability for White‐tailed Deer in a Mexican Tropical Dry Forest1
Authors: Mandujano Salvador 
Published: June 2006

ABSTRACTThe influence of El Niño/Southern Oscillation (ENSO) on rainfall and its possible effect on availability of food for white‐tailed deer (Odocoileus virginianus) in a tropical dry forest in the Pacific coast of Mexico was studied. From 1977 to 2003 there were three significant El Niño and La Niña events. During El Niño years rainfall decreased during the wet season ( June to October) and increased during the dry season (November to May), with the opposite effect during La Niña years. Plant diversity was monitored in permanent plots during the wet and dry seasons of 1989–1993. The results provide evidence that ENSO events affect deer food availability, particularly in the dry season.
PopF1 and PopF2, Two Proteins Secreted by the Type III Protein Secretion System of
Ralstonia solanacearum
, Are Translocators Belonging to the HrpF/NopX Family
Authors: Meyer Damien , Cunnac Sébastien , Guéneron Mareva , Declercq Céline , Van Gijsegem Frédérique , Lauber Emmanuelle , Boucher Christian , Arlat Matthieu 
Published: June 2006

ABSTRACT

Ralstonia solanacearum
GMI1000 is a gram-negative plant pathogen which contains an
hrp
gene cluster which codes for a type III protein secretion system (TTSS). We identified two novel Hrp-secreted proteins, called PopF1 and PopF2, which display similarity to one another and to putative TTSS translocators, HrpF and NopX, from
Xanthomonas
spp. and rhizobia, respectively. They also show similarities with TTSS translocators of the YopB family from animal-pathogenic bacteria. Both
popF1
and
popF2
belong to the HrpB regulon and are required for the interaction with plants, but PopF1 seems to play a more important role in virulence and hypersensitive response (HR) elicitation than PopF2 under our experimental conditions. PopF1 and PopF2 are not necessary for the secretion of effector proteins, but they are required for the translocation of AvrA avirulence protein into tobacco cells. We conclude that PopF1 and PopF2 are type III translocators belonging to the HrpF/NopX family. The
hrpF
gene of
Xanthomonas campestris
pv.
campestris
partially restored HR-inducing ability to
popF1 popF2
mutants of
R. solanacearum
, suggesting that translocators of
R. solanacearum
and
Xanthomonas
are functionally conserved. Finally,
R. solanacearum
strain UW551, which does not belong to the same phylotype as GMI1000, also possesses two putative translocator proteins. However, although one of these proteins is clearly related to PopF1 and PopF2, the other seems to be different and related to NopX proteins, thus showing that translocators might be variable in
R. solanacearum
.
Uracil Salvage Pathway in
Lactobacillus plantarum
: Transcription and Genetic Studies
Authors: Arsène-Ploetze Florence , Nicoloff Hervé , Kammerer Benoît , Martinussen Jan , Bringel Françoise 
Published: June 2006

ABSTRACT

The uracil salvage pathway in
Lactobacillus plantarum
was demonstrated to be dependent on the
upp-pyrP
gene cluster. PyrP was the only high-affinity uracil transporter since a
pyrP
mutant no longer incorporated low concentrations of radioactively labeled uracil and had increased resistance to the toxic uracil analogue 5-fluorouracil. The
upp
gene encoded a uracil phosphoribosyltransferase (UPRT) enzyme catalyzing the conversion of uracil and 5-phosphoribosyl-α-1-pyrophosphate to UMP and pyrophosphate. Analysis of mutants revealed that UPRT is a major cell supplier of UMP synthesized from uracil provided by preformed nucleic acid degradation. In a mutant selection study, seven independent
upp
mutants were isolated and all were found to excrete low amounts of pyrimidines to the growth medium. Pyrimidine-dependent transcription regulation of the biosynthetic pyrimidine
pyrR1-B-C-Aa1-Ab1-D-F-E
operon was impaired in the
upp
mutants. Despite the fact that
upp
and
pyrP
are positioned next to each other on the chromosome, they are not cotranscribed. Whereas
pyrP
is expressed as a monocistronic message, the
upp
gene is part of the
lp
_
2376-glyA-upp
operon. The
lp
_
2376
gene encodes a putative protein that belongs to the conserved protein family of translation modulators such as Sua5, YciO, and YrdC. The
glyA
gene encodes a putative hydroxymethyltransferase involved in C
1
unit charging of tetrahydrofolate, which is required in the biosynthesis of thymidylate, pantothenate, and purines. Unlike
upp
transcription,
pyrP
transcription is regulated by exogenous pyrimidine availability, most likely by the same mechanism of transcription attenuation as that of the
pyr
operon.
The Conjugative Transposon Tn
5397
Has a Strong Preference for Integration into Its
Clostridium difficile
Target Site
Authors: Wang Hongmei , Smith Margaret C. M. , Mullany Peter 
Published: June 2006

ABSTRACT

Tn
5397
is a conjugative transposon, originally isolated from
Clostridium difficile
. The Tn
5397
transposase TndX is related to the phage-encoded serine integrases and the
Clostridium perfringens
Tn
4451
transposase TnpX. TndX is required for the insertion and excision of the transposon. Tn
5397
inserts at one locus,

attB
Cd

, in
C. difficile
but at multiple sites in
Bacillus subtilis
. Apart from a conserved 5′ GA dinucleotide at the recombination site, there appears to be little sequence conservation between the known target sites. To test the target site preference of Tn
5397
,

attB
Cd

was introduced into the
B. subtilis
genome. When Tn
5397
was transferred into this strain, 100% of the 50 independent transconjugants tested had Tn
5397
inserted into

attB
Cd

. This experiment was repeated using a 50-bp

attB
Cd

with no loss of target preference. The mutation of the 5′ GA to 5′ TC in the

attB
Cd

target site caused a switch in the polarity of insertion of Tn
5397
, which is consistent with this dinucleotide being at the crossover site and in keeping with the mechanism of other serine recombinases. Tn
5397
could also transpose into 50-bp sequences encoding the end joints
attL
and
attR
but, surprisingly, could not recombine into the circular joint of Tn
5397
,
attTn
. Purified TndX was shown to bind specifically to 50-bp

attB
Cd

,
attL
,
attR
,
attTn
, and

attB
Bs

3
with relative binding affinities
attTn
≈
attR
>
attL
>

attB
Cd

>

attB
Bs

3
. We conclude that TndX has a strong preference for

attB
Cd

over other potential recombination sites in the
B. subtilis
genome and therefore behaves as a site-specific recombinase.
A Pair of Iron-Responsive Genes Encoding Protein Kinases with a Ser/Thr Kinase Domain and a His Kinase Domain Are Regulated by NtcA in the CyanobacteriumAnabaenasp. Strain PCC 7120
Authors: Cheng Yong , Li Jian-Hong , Shi Lei , Wang Li , Latifi Amel , Zhang Cheng-Cai 
Published: June 2006

ABSTRACTThe filamentous cyanobacteriumAnabaenasp. strain PCC 7120 can fix N2when combined nitrogen is not available in the growth medium. It has a family of 13 genes encoding proteins with both a Ser/Thr kinase domain and a His kinase domain. The function of these enzymes is unknown. Two of them are encoded bypkn41(alr0709) andpkn42(alr0710). These two genes are separated by only 72 bp on the chromosome, and our results indicate that they are cotranscribed. The expression ofpkn41andpkn42is induced by iron deprivation irrespective of the nature of the nitrogen source. Mutants inactivating eitherpkn41,pkn42, or both grow similarly to the wild type under normal conditions, but their growth is impaired either in the presence of an iron chelator or under conditions of nitrogen fixation and iron limitation, two situations where the demand for iron is particularly strong. Consistent with these results, these mutants display lower iron content than the wild type and a higher level of expression fornifJ1andnifJ2, which encode pyruvate:ferredoxin oxidoreductases. BothnifJ1andnifJ2are known to be induced by iron limitation. NtcA, a global regulatory factor for different metabolic pathways, binds to the putative promoter region ofpkn41, and the induction ofpkn41in response to iron limitation no longer occurs in anntcAmutant. Our results suggest thatntcAnot only regulates the expression of genes involved in nitrogen and carbon metabolism but also coordinates iron acquisition and nitrogen metabolism by activating the expression ofpkn41andpkn42.
In silico identification of putative promoter motifs of White Spot Syndrome Virus
Authors: Marks Hendrik , Ren Xin-Ying , Sandbrink Hans , van Hulten Mariëlle CW , Vlak Just M 
Published: June 2006

Abstract

Background
White Spot Syndrome Virus, a member of the virus family Nimaviridae, is a large dsDNA virus infecting shrimp and other crustacean species. Although limited information is available on the mode of transcription, previous data suggest that WSSV gene expression occurs in a coordinated and cascaded fashion. To search in silico for conserved promoter motifs (i) the abundance of all 4 through 8 nucleotide motifs in the upstream sequences of WSSV genes relative to the complete genome was determined, and (ii) a MEME search was performed in the upstream sequences of either early or late WSSV genes, as assigned by microarray analysis. Both methods were validated by alignments of empirically determined 5' ends of various WSSV mRNAs.

Results
The collective information shows that the upstream region of early WSSV genes, containing a TATA box and an initiator, is similar to Drosophila RNA polymerase II core promoter sequences, suggesting utilization of the cellular transcription machinery for generating early transcripts. The alignment of the 5' ends of known well-established late genes, including all major structural protein genes, identified a degenerate motif (ATNAC) which could be involved in WSSV late transcription. For these genes, only one contained a functional TATA box. However, almost half of the WSSV late genes, as previously assigned by microarray analysis, did contain a TATA box in their upstream region.

Conclusion
The data may suggest the presence of two separate classes of late WSSV genes, one exploiting the cellular RNA polymerase II system for mRNA synthesis and the other generating messengers by a new virus-induced transcription mechanism.