bluuebunny/crossref_metadata_2025 huggingface dataset:
Aegean Surface Circulation from a Satellite-Tracked Drifter Array
Authors: Olson Donald B. , Kourafalou Vassiliki H. , Johns William E. , Samuels Geoff , Veneziani Milena
Published: August 2007

A pilot experiment using an array of 45 drifters to explore the circulation in the north and central Aegean Sea is described. The global positioning system drifters with holey-sock drogues provide positions every hour with data recovery through the Argos system. The drifters were launched in four separate deployments over a 1-yr period. The resulting trajectories confirm the existence of a current around the rim of the basin consistent with a buoyancy plume created by the outflow of Black Sea waters through the Dardanelles (Strait of Çanakkale in Turkish). The degree to which this is augmented by an Ekman response to the dominant northerly winds is not obvious in the dataset owing to mesoscale dynamics that obscure the existence of any westward Ekman flow. The mesoscale eddy field involves anticylonic eddies in the current around the rim of the basin consistent with eddies with low-salinity-water cores. Cyclones are also seen, with the most prominent forming over deep regions in the basin topography. The array also documents the interaction of the currents with the straits through the Sporades and Cyclades island groups. These interactions are complicated by the nature of the mesoscale flow and in some trajectories suggest a Bernouilli acceleration in straits; in others the flow through the island groups appears to be more diffusive and involves deceleration and eddy motions. The rapid sampling by the drifters reveals an extremely nonlinear submesoscale eddy field in the basin with length scales less than 4 km and Rossby numbers of order 1. A better understanding of the dynamics of these features is of importance for understanding the circulation of the basin.
Global Patterns of Low-Mode Internal-Wave Propagation. Part II: Group Velocity
Authors: Alford Matthew H. , Zhao Zhongxiang
Published: August 2007

Using a set of 80 globally distributed time series of near-inertial and semidiurnal energy E and energy flux F computed from historical moorings, the group velocity ĉg ≡ FE−1 is estimated. For a single free wave, observed group speed |ĉg| should equal that expected from linear wave theory. For comparison, the latitude dependence of perceived group speed for perfectly standing waves is also derived. The latitudinal dependence of observed semidiurnal |ĉg| closely follows that expected for free waves at all latitudes, implying that 1) low-mode internal tides obey linear theory and 2) standing internal-tidal waves are rare in the deep ocean for latitudes equatorward of about 35°. At higher latitudes, standing waves cannot be easily distinguished from free waves using this method because their expected group speeds are similar. Near-inertial waves exhibit scattered |ĉg| values consistent with the passage of events generated at various latitudes, with implied frequencies ω ≈ 1.05–1.25 × f, as typically observed in frequency spectra.
Estuarine Boundary Layer Mixing Processes: Insights from Dye Experiments*
Authors: Chant Robert J. , Geyer Wayne R. , Houghton Robert , Hunter Elias , Lerczak James
Published: August 2007

A series of dye releases in the Hudson River estuary elucidated diapycnal mixing rates and temporal variability over tidal and fortnightly time scales. Dye was injected in the bottom boundary layer for each of four releases during different phases of the tide and of the spring–neap cycle. Diapycnal mixing occurs primarily through entrainment that is driven by shear production in the bottom boundary layer. On flood the dye extended vertically through the bottom mixed layer, and its concentration decreased abruptly near the base of the pycnocline, usually at a height corresponding to a velocity maximum. Boundary layer growth is consistent with a one-dimensional, stress-driven entrainment model. A model was developed for the vertical structure of the vertical eddy viscosity in the flood tide boundary layer that is proportional to u2*/N∞, where u* and N∞ are the bottom friction velocity and buoyancy frequency above the boundary layer. The model also predicts that the buoyancy flux averaged over the bottom boundary layer is equal to 0.06N∞u2* or, based on the structure of the boundary layer equal to 0.1NBLu2*, where NBL is the buoyancy frequency across the flood-tide boundary layer. Estimates of shear production and buoyancy flux indicate that the flux Richardson number in the flood-tide boundary layer is 0.1–0.18, consistent with the model indicating that the flux Richardson number is between 0.1 and 0.14. During ebb, the boundary layer was more stratified, and its vertical extent was not as sharply delineated as in the flood. During neap tide the rate of mixing during ebb was significantly weaker than on flood, owing to reduced bottom stress and stabilization by stratification. As tidal amplitude increased ebb mixing increased and more closely resembled the boundary layer entrainment process observed during the flood. Tidal straining modestly increased the entrainment rate during the flood, and it restratified the boundary layer and inhibited mixing during the ebb.
Injection moulding of alumina with partially water soluble binder system and solvent debinding kinetics
Authors: Bakan H. I.
Published: August 2007

A partially water soluble binder system was successfully derived and tested for injection moulding of alumina powder. The major binder of the binder system was comprised of poly(2-ethly-2-oxaline) and polyethylene glycol and these constituents formed the water soluble fraction of the system. The rheological properties of the feedstock were investigated systematically over a temperature range of 120 to 160°C and a shear rate range of 100 to 1000 s−1. Binder removal was accomplished using a two stage process. The water soluble constituents were removed by water leaching. The remaining binder constituents were removed by thermal pyrolysis. The solvent debinding kinetics of the water leaching process were studied as a function of temperature, ranging from 40 to 80°C. Solvent debinding is a two stage process consisting of dissolution and diffusion. In this study, dissolution was the rate limiting step during the first stage of water leaching over a leaching time of 90 min at 40°C. As the process proceeds, it is shown that diffusion becomes the rate limiting step.
AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip™ expression arrays with respect to SNPs
Authors: Kumari Sunita , Verma Lalit K , Weller Jennifer W
Published: August 2007

Background

Affymetrix gene expression arrays incorporate paired perfect match (PM) and mismatch (MM) probes to distinguish true signals from those arising from cross-hybridization events. A MM signal often shows greater intensity than a PM signal; we propose that one underlying cause is the presence of allelic variants arising from single nucleotide polymorphisms (SNPs). To annotate and characterize SNP contributions to anomalous probe binding behavior we have developed a software tool called AffyMAPSDetector.

Results

AffyMAPSDetector can be used to describe any Affymetrix expression GeneChip™ with respect to SNPs. When AffyMAPSDetector was run on GeneChip™ HG-U95Av2 against dbSNP-build-123, we found 7286 probes (belonging to 2,582 probesets) containing SNPs, out of which 325 probes contained at least one SNP at position 13. Against dbSNP-build-126, 8758 probes (belonging to 3,002 probesets) contained SNPs, of which 409 probes contained at least one SNP at position 13. Therefore, depending on the expressed allele, the MM probe can sometimes be the transcript complement. This information was used to characterize probe measurements reported in a published, well-replicated lung adenocarcinoma study. The total intensity distributions showed that the SNP-containing probes had a larger negative mean intensity difference (PM-MM) and greater range of the difference than did probes without SNPs. In the sample replicates, SNP-containing probes with reproducible intensity ratios were identified, allowing selection of SNP probesets that yielded unique sample signatures. At the gene expression level, use of the (MM-PM) value for SNP-containing probes resulted in different Presence/Absence calls for some genes. Such a change in status of the genes has the clear potential for influencing downstream clustering and classification results.

Conclusion

Output from this tool characterizes SNP-containing probes on GeneChip™ microarrays, thus improving our understanding of factors contributing to expression measurements. The pattern of SNP binding examined so far indicates distinct behavior of the SNP-containing probes and has the potential to help us identify new SNPs. Knowing which probes contain SNPs provides flexibility in determining whether to include or exclude them from gene-expression intensity calculations; selected sets of SNP-containing probes produce sample-unique signatures.

AffyMAPSDetector information is available at http://www.binf.gmu.edu/weller/BMC_bioinformatics/AffyMapsDetector/index.html
Haplotype-based score test for linkage in nuclear families
Authors: Nam Chung Mo , Kang Dae Ryong , Kim Jinheum
Published: August 2007

Background

To look for genetic linkage between angiotensin-I converting enzyme(ACE) gene and hypertension in a Korean adolescent cohort, we developed a powerful test using the covariances between marginal differences and their variances in a transmission/non-transmission table.

Results

We estimated haplotype frequencies using the parental and affected offspring's genotypes and then constructed a transmission/non-transmission table for the parental haplotypes transmitted to the offspring. We then proposed a test for checking the marginal homogeneity in the table. Because the cells in the table were dependent due to the uncertainty of the parental haplotypes, we adopted a randomization procedure to estimate the significance of the observed test statistic. Simulations show that our test performs well on a nominal level and has a monotone power, which increases as the relative risk increases. With our test, there was no evidence of genetic linkage between the ACE gene and hypertension in the Korean adolescent cohort.

Conclusion

We developed a score test for linkage and used simulations to demonstrate that our test performs well at a nominal level. Under some situations where the diversity of haplotypes is low, the proposed test gained a little power over the method based on only variances between marginal differences in a transmission/non-transmission table.
Alterations in transcript abundance of bovine oocytes recovered at growth and dominance phases of the first follicular wave
Authors: Ghanem Nasser , Hölker Michael , Rings Franca , Jennen Danyel , Tholen Ernst , Sirard Marc-André , Torner Helmut , Kanitz Wilhelm , Schellander Karl , Tesfaye Dawit
Published: August 2007

Background

Oocyte developmental competence is highly affected by the phase of ovarian follicular wave. Previous studies have shown that oocytes from subordinate follicles recovered at growth phase (day 3 after estrus) are developmentally more competent than those recovered at dominance phase (day 7 after estrus). However, the molecular mechanisms associated with these differences are not well elucidated. Therefore, the objective of this study was to investigate transcript abundance of bovine oocytes retrieved from small follicles at growth and dominance phases of the first follicular wave and to identify candidate genes related to oocyte developmental competence using cDNA microarray.

Results

Comparative gene expression analysis of oocytes from growth and dominance phases and subsequent data analysis using Significant Analysis of Microarray (SAM) revealed a total of 51 differentially regulated genes, including 36 with known function, 6 with unknown function and 9 novel transcripts. Real-time PCR has validated 10 transcripts revealed by microarray analysis and quantified 5 genes in cumulus cells derived from oocytes of both phases. The expression profile of 8 (80%) transcripts (ANAXA2, FL396, S100A10, RPL24, PP, PTTG1, MSX1 and BMP15) was in agreement with microarray data. Transcript abundance of five candidate genes in relation to oocyte developmental competence was validated using Brilliant Cresyl Blue (BCB) staining as an independent model. Furthermore, localization of mRNA and protein product of the candidate gene MSX1 in sections of ovarian follicles at days 0, 1, 3 and 7 of estrous cycle showed a clear fluorescent signal in both oocytes and cumulus cells with higher intensity in the former. Moreover, the protein product was detected in bovine oocytes and early cleavage embryos after fertilization with higher intensity around the nucleus.

Conclusion

This study has identified distinct sets of differentially regulated transcripts between bovine oocytes recovered from small follicles at growth and dominance phases of the first follicular wave. The validation with independent model supports our notion that many of the transcripts identified here may represent candidate genes associated with oocyte developmental competence. Further specific functional analysis will provide insights into the exact role of these transcripts in oocyte competence and early embryonic development.
Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region
Authors: Jiang Zhi J , Castoe Todd A , Austin Christopher C , Burbrink Frank T , Herron Matthew D , McGuire Jimmy A , Parkinson Christopher L , Pollock David D
Published: August 2007

Background

The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence.

Results

We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs.

Conclusion

Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria.
Evaluation of B-type Natriuretic Peptide for validation of a heart failure register in primary care
Authors: Bhatia Gurbir S , Sosin Michael D , Stubley Jane , Patel Jeetesh V , Hughes Elizabeth A , Gibbs Rebecca , Davis Russell C
Published: August 2007

Background

Diagnosing heart failure and left ventricular systolic dysfunction is difficult on clinical grounds alone. We sought to determine the accuracy of a heart failure register in a single primary care practice, and to examine the usefulness of b-type (or brain) natriuretic peptide (BNP) assay for this purpose.

Methods

A register validation audit in a single general practice in the UK was carried out. Of 217 patients on the heart failure register, 56 of 61 patients who had not been previously investigated underwent 12-lead electrocardiography and echocardiography within the practice site. Plasma was obtained for BNP assay from 45 subjects, and its performance in identifying echocardiographic abnormalities consistent with heart failure was assessed by analysing area under receiver operator characteristic (ROC) curves.

Results

30/217 were found to have no evidence to suggest heart failure on notes review and were probably incorrectly coded. 70/112 who were previously investigated were confirmed to have heart failure. Of those not previously investigated, 24/56 (42.9%) who attended for the study had echocardiographic left ventricular systolic dysfunction. A further 8 (14.3%) had normal systolic function, but had left ventricular hypertrophy or significant valve disease. Overall, echocardiographic features consistent with heart failure were found in only 102/203 (50.2%). BNP was poor at discriminating those with and without systolic dysfunction (area under ROC curve 0.612), and those with and without any significant echocardiographic abnormality (area under ROC curve 0.723).

Conclusion

In this practice, half of the registered patients did not have significant cardiac dysfunction. On-site echocardiography identifies patients who can be removed from the heart failure register. The use of BNP assay to determine which patients require echocardiography is not supported by these data.
Combined use of Amplified Fragment Length Polymorphism and IS6110 -RFLP in fingerprinting clinical isolates of Mycobacterium tuberculosis from Kerala, South India
Authors: Krishnan Manju Y , Radhakrishnan Indulakshmi , Joseph Biljo V , GK Madhavi Latha , Kumar R Ajay , Mundayoor Sathish
Published: August 2007

Background

DNA fingerprinting by IS6110-RFLP has shown a high incidence of Mycobacterium tuberculosis isolates having no and low copies of the insertion sequence in Kerala, South India. Amplified Fragment Length Polymorphism (AFLP) would scan the entire genome rather than a few repetitive elements, we thought that this technique would help us in differentiating the large reservoir of isolates from an endemic region. Here we evaluate the ability of Amplified Fragment Length Polymorphism (AFLP) to type clinical isolates.

Methods

Fifty clinical isolates of M. tuberculosis were analysed by conventional radioactive AFLP and IS6110- RFLP. M. bovis, M. bovis BCG and two non tuberculous mycobacteria were also analysed to see species specific differences generated by AFLP. Cluster analysis was performed using the AFLP profile that showed the maximum polymorphism within M. tuberculosis and this was compared to the number of copies of IS6110 insertions.

Results

For AFLP, out of ten primer pairs tested, the EO/MC pair generated maximum polymorphism among the clinical isolates of M. tuberculosis. The similarity between the isolates ranged between 88 and 99.5%. Majority (nearly 85%) of the 'low copy' IS6110 isolates clustered together, while the rest clustered irrespective of the copy numbers. AFLP could show rare differences between isolates of M. tuberculosis, M. bovis and M. bovis BCG. The AFLP profiles for non-tuberculous mycobacteria were highly different from those of M. tuberculosis.

Conclusion

Polymorphism generated by AFLP within the M. tuberculosis species is limited and hence AFLP alone seems to have limited use in fingerprinting the isolates in Kerala. The combined use of AFLP and IS6110-RFLP showed relatively better differentiation of 'high copy' IS6110 isolates, but failed to differentiate the 'low copy' isolates. However, the technique may be efficient in inter-species differentiation, and hence potentially useful in identifying and developing species- specific markers.
Absence of mutations in NR2E1 and SNX3in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes
Authors: Kumar Ravinesh A , Everman David B , Morgan Chad T , Slavotinek Anne , Schwartz Charles E , Simpson Elizabeth M
Published: August 2007

Background

A disruption of sorting nexin 3 (SNX3) on 6q21 was previously reported in a patient with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and t(6;13)(q21;q12) but no SNX3 mutations were identified in another sporadic case of MMEP, suggesting involvement of another gene. In this work, SNX3 was sequenced in three patients not previously studied for this gene. In addition, we test the hypothesis that mutations in the neighbouring gene NR2E1 may underlie MMEP and related phenotypes.

Methods

Mutation screening was performed in five patients: the t(6;13)(q21;q12) MMEP patient, three additional patients with possible MMEP or a related phenotype, and one patient with oligodactyly, ulnar aplasia, and a t(6;7)(q21;q31.2) translocation. We used sequencing to exclude SNX3 coding mutations in three patients not previously studied for this gene. To test the hypothesis that mutations in NR2E1 may contribute to MMEP or related phenotypes, we sequenced the entire coding region, complete 5' and 3' untranslated regions, consensus splice-sites, and evolutionarily conserved regions including core and proximal promoter in all five patients. Two-hundred and fifty control subjects were genotyped for any candidate mutation.

Results

We did not detect any synonymous nor nonsynonymous coding mutations of NR2E1 or SNX3. In one patient with possible MMEP, we identified a candidate regulatory mutation that has been reported previously in a patient with microcephaly but was not found in 250 control subjects examined here.

Conclusion

Our results do not support involvement of coding mutations in NR2E1 or SNX3 in MMEP or related phenotypes; however, we cannot exclude the possibility that regulatory NR2E1 or SNX3 mutations or deletions at this locus may underlie abnormal human cortical development in some patients.
Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes
Authors: Kaushal Ritesh , Woo Daniel , Pal Prodipto , Haverbusch Mary , Xi Huifeng , Moomaw Charles , Sekar Padmini , Kissela Brett , Kleindorfer Dawn , Flaherty Matthew , Sauerbeck Laura , Chakraborty Ranajit , Broderick Joseph , Deka Ranjan
Published: August 2007

Background

Apolipoprotein E (APOE) and elastin (ELN) are plausible candidate genes involved in the pathogenesis of stroke. We tested for association of variants in APOE and ELN with subarachnoid hemorrhage (SAH) in a population-based study. We genotyped 12 single nucleotide polymorphisms (SNPs) on APOE and 10 SNPs on ELN in a sample of 309 Caucasian individuals, of whom 107 are SAH cases and 202 are age-, race-, and gender-matched controls from the Greater Cincinnati/Northern Kentucky region. Associations were tested at genotype, allele, and haplotype levels. A genomic control analysis was performed to check for spurious associations resulting from population substructure.

Results

At the APOE locus, no individual SNP was associated with SAH after correction for multiple comparisons. Haplotype analysis revealed significant association of the major haplotype (Hap1) in APOE with SAH (p = 0.001). The association stemmed from both the 5' promoter and the 3' region of the APOE gene. APOE ε2 and ε 4 were not significantly associated with SAH. No association was observed for ELN at genotype, allele, or haplotype level and our study failed to confirm previous reports of ELN association with aneurysmal SAH.

Conclusion

This study suggests a role of the APOE gene in the etiology of aneurysmal SAH.
Predictors of health-related quality of life in type II diabetic patients in Greece
Authors: Papadopoulos Angelos A , Kontodimopoulos Nick , Frydas Aristidis , Ikonomakis Emmanuel , Niakas Dimitris
Published: August 2007

Background

Diabetes Mellitus (DM) is a major cause of morbidity and mortality affecting millions of people worldwide, while placing a noteworthy strain on public health funding. The aim of this study was to assess health-related quality of life (HRQOL) of Greek Type II DM patients and to identify significant predictors of the disease in this patient population.

Methods

The sample (N = 229, 52.8% female, 70.0 years mean age) lived in a rural community of Lesvos, an island in the northeast of the Aegean Archipelagos. The generic SF-36 instrument, administered by trainee physicians, was used to measure HRQOL. Scale scores were compared with non-parametric Mann-Whitney and Kruskal-Wallis tests and multivariate stepwise linear regression analyses were used to investigate the effect of sociodemographic and diabetes-related variables on HRQOL.

Results

The most important predictors of impaired HRQOL were female gender, diabetic complications, non-diabetic comorbidity and years with diabetes. Older age, lower education, being unmarried, obesity, hypertension and hyperlipidaemia were also associated with impaired HRQOL in at least one SF-36 subscale. Multivariate regression analyses produced models explaining significant portions of the variance in SF-36 subscales, especially physical functioning (R2 = 42%), and also showed that diabetes-related indicators were more important disease predictors, compared to sociodemographic variables.

Conclusion

The findings could have implications for health promotion in rural medical practice in Greece. In order to preserve a good HRQOL, it is obviously important to prevent diabetes complications and properly manage concomitant chronic diseases. Furthermore, the gender difference is interesting and requires further elucidation. Modifying screening methods and medical interventions or formulating educational programs for the local population appear to be steps in the correct direction.
Using system dynamics for collaborative design: a case study
Authors: Elf Marie , Putilova Mariya , von Koch Lena , Öhrn Kerstin
Published: August 2007

Background

In order to facilitate the collaborative design, system dynamics (SD) with a group modelling approach was used in the early stages of planning a new stroke unit. During six workshops a SD model was created in a multiprofessional group.

Aim

To explore to which extent and how the use of system dynamics contributed to the collaborative design process.

Method

A case study was conducted using several data sources.

Results

SD supported a collaborative design, by facilitating an explicit description of stroke care process, a dialogue and a joint understanding. The construction of the model obliged the group to conceptualise the stroke care and experimentation with the model gave the opportunity to reflect on care.

Conclusion

SD facilitated the collaborative design process and should be integrated in the early stages of the design process as a quality improvement tool.
Primary T-cells from human CD4/CCR5-transgenic rats support all early steps of HIV-1 replication including integration, but display impaired viral gene expression
Authors: Goffinet Christine , Michel Nico , Allespach Ina , Tervo Hanna-Mari , Hermann Volker , Kräusslich Hans-Georg , Greene Warner C , Keppler Oliver T
Published: August 2007

Background

In vivo studies on HIV-1 pathogenesis and testing of antiviral strategies have been hampered by the lack of an immunocompetent small animal model that is highly susceptible to HIV-1 infection. Since native rodents are non-permissive, we developed transgenic rats that selectively express the HIV-1 receptor complex, hCD4 and hCCR5, on relevant target cells. These animals display a transient low-level plasma viremia after HIV-1YU-2 infection, demonstrating HIV-1 susceptibility in vivo. However, unlike macrophages, primary CD4 T-cells from double-transgenic animals fail to support viral spread ex vivo. To identify quantitative limitations or absolute blocks in this rodent species, we quantitatively assessed the efficiency of key steps in the early phase of the viral replication cycle in a side-by-side comparison in infected cell lines and primary T-cells from hCD4/hCCR5-transgenic rats and human donors.

Results

Levels of virus entry, HIV-1 cDNA synthesis, nuclear import, and integration into the host genome were shown to be remarkably similar in cell lines and, where technically accessible, in primary T-cells from both species. In contrast, a profound impairment at the level of early HIV gene expression was disclosed at the single-cell level in primary rat T-cells and most other rat-derived cells. Macrophages were a notable exception, possibly reflecting the unique transcriptional milieu in this evolutionarily conserved target cell of all lentiviruses. Importantly, transient trans-complementation by ex vivo nucleofection with the Tat-interacting protein Cyclin T1 of human origin markedly elevated HIV gene expression in primary rat T-cells.

Conclusion

This is the first study that has quantitatively determined the efficiency of consecutive steps in the HIV-1 replication cycle in infected primary HIV target cells from a candidate transgenic small animal and compared it to human cells. Unlike cells derived from mice or rabbits, rat cells complete all of the early steps in the HIV-1 replication cycle, including provirus integration in vivo, with high efficiency. A deficiency in gene expression was disclosed at the single cell level and could be counteracted by the human pTEFb transcription complex factor Cyclin T1. Collectively, these results provide the basis for the advancement of this transgenic rat model through strategies aimed at boosting HIV-1 gene expression in primary rat CD4 T-cells, including human Cyclin T1 transgenesis.
Pathophysiology of ageing, longevity and age related diseases
Authors: Bürkle Alexander , Caselli Graziella , Franceschi Claudio , Mariani Erminia , Sansoni Paolo , Santoni Angela , Vecchio Giancarlo , Witkowski Jacek M , Caruso Calogero
Published: August 2007

On April 18, 2007 an international meeting on Pathophysiology of Ageing, Longevity and Age-Related Diseases was held in Palermo, Italy. Several interesting topics on Cancer, Immunosenescence, Age-related inflammatory diseases and longevity were discussed. In this report we summarize the most important issues. However, ageing must be considered an unavoidable end point of the life history of each individual, nevertheless the increasing knowledge on ageing mechanisms, allows envisaging many different strategies to cope with, and delay it. So, a better understanding of pathophysiology of ageing and age-related disease is essential for giving everybody a reasonable chance for living a long and enjoyable final part of the life.
Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region
Authors: Moratorio Gonzalo , Martínez Mariela , Gutiérrez María F , González Katiuska , Colina Rodney , López-Tort Fernando , López Lilia , Recarey Ricardo , Schijman Alejandro G , Moreno María P , García-Aguirre Laura , Manascero Aura R , Cristina Juan
Published: August 2007

Background

Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America.

Methods

Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program.

Results

Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region.

Conclusion

Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The coexistence of distinct type 1 HCV subpopulations is consistent with quasispecies dynamics, and suggests that multiple coexisting subpopulations may allow the virus to adapt to its human host populations.
Is untargeted educational outreach visiting delivered by pharmaceutical advisers effective in primary care? A pragmatic randomized controlled trial
Authors: Eccles Martin P , Steen Ian N , Whitty Paula M , Hall Lesley
Published: August 2007

Background

There is increasing evidence that clinical guidelines can lead to improvements in clinical care. However, they are not self-implementing. While educational outreach visits may improve prescribing behaviour, the effectiveness of routine delivery of these visits by existing pharmaceutical advisers is unknown.

Methods

Within a pragmatic randomized controlled trial, involving all general practices in two primary care trusts (PCTs), routine methods were used to distribute guidelines for the choice of antidepressants for the management of depression. Intervention practices were offered two visits (most accepted only one) by their PCT pharmaceutical adviser who had been trained in the techniques of outreach visiting. Intervention practices were visited regardless of whether they had prior problems with prescribing ('untargeted' visits). The intervention was evaluated using level three prescribing analysis and cost (PACT) data for antidepressant drugs for the six months during which the intervention was delivered and the subsequent twelve months.

Results

Across the 72 study practices there was no significant impact of the intervention on usage of any group of antidepressant drugs.

Conclusion

The routine use of untargeted educational outreach visiting delivered by existing pharmaceutical advisers may not be a worthwhile strategy.

Trial registration

ClinicalTrials.gov NCT00393536
Giant hepatocellular adenoma as cause of severe abdominal pain: a case report
Authors: Sandonato Luigi , Cipolla Calogero , Graceffa Giuseppa , Bartolotta Tommaso V. , Li Petri Sergio , Ciacio Oriana , Cannizzaro Fabio , Latteri Mario A.
Published: August 2007

The authors describe the case of a large hepatocellular adenoma diagnosed in a 30-year old woman who came to us complaining of acute pain in the upper abdominal quadrants. The patient had been taking an oral contraceptive pill for the last ten years. We present the clinical features, the diagnostic work-up and the treatment prescribed.
Diurnal secretion of growth hormone, cortisol, and dehydroepiandrosterone in pre- and perimenopausal women with active rheumatoid arthritis: a pilot case-control study
Authors: Blackman Marc R , Muniyappa Ranganath , Wilson Mildred , Moquin Barbara E , Baldwin Howard L , Wong Kelli A , Snyder Christopher , Magalnick Michael , Alli Shaan , Reynolds James , Steinberg Seth M , Goldbach-Mansky Raphaela
Published: August 2007

Rheumatoid arthritis (RA) is associated with neuroendocrine and immunologic dysfunction leading to rheumatoid cachexia. Although excess proinflammatory cytokines can decrease somatotropic axis activity, little is known about the effects of RA on growth hormone/insulin-like growth factor-1 (GH/IGF-I) axis function. We tested the hypothesis that patients with active RA exhibit decreased GH/IGF-I axis activity. To do so, we conducted a pilot case-control study at a clinical research center in 7 pre- and perimenopausal women with active RA and 10 age- and body mass index-matched healthy women. Participants underwent blood sampling every 20 minutes for 24 hours (8 a.m. to 8 a.m.), and sera were assayed for GH, cortisol, and dehydroepiandrosterone (DHEA). Sera obtained after overnight fasting were assayed for IGF-I, IGF-binding protein (IGFBP)-1, IGFBP-3, C-reactive protein (CRP), interleukin-6 (IL-6), glucose, insulin, and lipids. Body composition and bone mineral density were evaluated by DEXA (dual emission x-ray absorptiometry) scans. In patients with RA, mean disease duration was 7.6 ± 6.8 years, and erythrocyte sedimentation rate, CRP, and IL-6 were elevated. GH half-life was shorter than in control subjects (p = 0.0037), with no other significant group differences in GH deconvolution parameters or approximate entropy scores. IGF-I (p = 0.05) and IGFBP-3 (p = 0.058) were lower, whereas IGFBP-1 tended to be higher (p = 0.066), in patients with RA, with nonsignificantly increased 24-hour total GH production rates. There were no significant group differences in cortisol or DHEA secretion. Lean body mass was lower in patients with RA (p = 0.019), particularly in the legs (p = 0.01). Women with active RA exhibit a trend toward GH insensitivity and relatively diminished diurnal cortisol and DHEA secretion for their state of inflammation. Whether these changes contribute to rheumatoid cachexia remains to be determined.

Trial registration number

NCT00034060.
Characterization of a negative transcriptional element in the BRCA1 promoter
Authors: MacDonald Gwen , Stramwasser Melissa , Mueller Christopher R
Published: August 2007

Introduction

Decreased transcription of the BRCA1 gene has previously been observed to occur in sporadic breast tumours, making elucidation of the mechanisms regulating the expression of this gene important for our understanding of the etiology of the disease.

Methods

Transcriptional elements involved in the regulation of the BRCA1 promoter were analysed by co-transfection experiments into the human MCF-7 and T-47D breast cancer cell lines.

Results

We have identified a repressor element, referred to as the UP site, within the proximal BRCA1 promoter whose inactivation results in increased promoter activity. An E2F recognition element, previously suggested to mediate repression via E2F-6, is adjacent to the UP site and its inactivation also leads to increased BRCA1 expression. These two elements appear to form a composite repressor element whose combined effect is additive. The UP element is composed of two sequences, one of which binds the ubiquitously expressed ets family transcription factor GABP alpha/beta. This site is distinct from a previously identified GABP alpha/beta site, the RIBS element, though the RIBS site appears to be necessary for derepression of the promoter via mutations in the UP site. Knockdown of GABP alpha using an shRNA vector confirms that this protein is important for the function of both the RIBS and UP sites.

Conclusion

The identification of a repressor element in the BRCA1 promoter brings a new level of complexity to the regulation of BRCA1 expression. The elements characterized here may play a normal role in the integration of a variety of signals, including two different growth related pathways, and it is possible that loss of the ability to derepress the BRCA1 promoter during critical periods may contribute to breast transformation.
Air-pollutant chemicals and oxidized lipids exhibit genome-wide synergistic effects on endothelial cells
Authors: Gong Ke Wei , Zhao Wei , Li Ning , Barajas Berenice , Kleinman Michael , Sioutas Constantinos , Horvath Steve , Lusis Aldons J , Nel Andre , Araujo Jesus A
Published: August 2007

Background

Ambient air pollution is associated with increased cardiovascular morbidity and mortality. We have found that exposure to ambient ultrafine particulate matter, highly enriched in redox cycling organic chemicals, promotes atherosclerosis in mice. We hypothesize that these pro-oxidative chemicals could synergize with oxidized lipid components generated in low-density lipoprotein particles to enhance vascular inflammation and atherosclerosis.

Results

We have used human microvascular endothelial cells (HMEC) to study the combined effects of a model air pollutant, diesel exhaust particles (DEP), and oxidized 1-palmitoyl-2-arachidonyl-sn-glycero-3-phosphorylcholine (ox-PAPC) on genome-wide gene expression. We treated the cells in triplicate wells with an organic DEP extract, ox-PAPC at various concentrations, or combinations of both for 4 hours. Gene-expression profiling showed that both the DEP extract and ox-PAPC co-regulated a large number of genes. Using network analysis to identify coexpressed gene modules, we found three modules that were most highly enriched in genes that were differentially regulated by the stimuli. These modules were also enriched in synergistically co-regulated genes and pathways relevant to vascular inflammation. We validated this synergy in vivo by demonstrating that hypercholesterolemic mice exposed to ambient ultrafine particles exhibited significant upregulation of the module genes in the liver.

Conclusion

Diesel exhaust particles and oxidized phospholipids synergistically affect the expression profile of several gene modules that correspond to pathways relevant to vascular inflammatory processes such as atherosclerosis.
Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns
Authors: Szafranski Karol , Schindler Stefanie , Taudien Stefan , Hiller Michael , Huse Klaus , Jahn Niels , Schreiber Stefan , Backofen Rolf , Platzer Matthias
Published: August 2007

Background

Despite some degeneracy of sequence signals that govern splicing of eukaryotic pre-mRNAs, it is an accepted rule that U2-dependent introns exhibit the 3' terminal dinucleotide AG. Intrigued by anecdotal evidence for functional non-AG 3' splice sites, we carried out a human genome-wide screen.

Results

We identified TG dinucleotides functioning as alternative 3' splice sites in 36 human genes. The TG-derived splice variants were experimentally validated with a success rate of 92%. Interestingly, ratios of alternative splice variants are tissue-specific for several introns. TG splice sites and their flanking intron sequences are substantially conserved between orthologous vertebrate genes, even between human and frog, indicating functional relevance. Remarkably, TG splice sites are exclusively found as alternative 3' splice sites, never as the sole 3' splice site for an intron, and we observed a distance constraint for TG-AG splice site tandems.

Conclusion

Since TGs splice sites are exclusively found as alternative 3' splice sites, the U2 spliceosome apparently accomplishes perfect specificity for 3' AGs at an early splicing step, but may choose 3' TGs during later steps. Given the tiny fraction of TG 3' splice sites compared to the vast amount of non-viable TGs, cis-acting sequence signals must significantly contribute to splice site definition. Thus, we consider TG-AG 3' splice site tandems as promising subjects for studies on the mechanisms of 3' splice site selection.
Complexity, connectivity, and duplicability as barriers to lateral gene transfer
Authors: Wellner Alon , Lurie Mor N , Gophna Uri
Published: August 2007

Background

Lateral gene transfer is a major force in microbial evolution and a great source of genetic innovation in prokaryotes. Protein complexity has been claimed to be a barrier for gene transfer, due to either the inability of a new gene's encoded protein to become a subunit of an existing complex (lack of positive selection), or from a harmful effect exerted by the newcomer on native protein assemblages (negative selection).

Results

We tested these scenarios using data from the model prokaryote Escherichia coli. Surprisingly, the data did not support an inverse link between membership in protein complexes and gene transfer. As the complexity hypothesis, in its strictest sense, seemed valid only to essential complexes, we broadened its scope to include connectivity in general. Transferred genes are found to be less involved in protein-protein interactions, outside stable complexes, and this is especially true for genes recently transferred to the E. coli genome. Thus, subsequent to transfer, new genes probably integrate slowly into existing protein-interaction networks. We show that a low duplicability of a gene is linked to a lower chance of being horizontally transferred. Notably, many essential genes in E. coli are conserved as singletons across multiple related genomes, have high connectivity and a highly vertical phylogenetic signal.

Conclusion

High complexity and connectivity generally do not impede gene transfer. However, essential genes that exhibit low duplicability and high connectivity do exhibit mostly vertical descent.
smedinx-11is a planarian stem cell gap junction gene required for regeneration and homeostasis
Authors: Oviedo Néstor J. , Levin Michael
Published: August 2007

The largely unknown mechanisms that regulate adult stem cells probably involve signals from neighboring differentiated cells. Gap junction channels providing direct cell-cell communication via small molecules are a crucial component of morphogenesis and normal physiology. However, no specific gap junction protein has yet been functionally linked to adult/somatic stem cell behavior in vivo or to organ regeneration. We report the identification and characterization of smedinx-11 - an innexin gap junction channel gene expressed in the adult stem cells (neoblasts) of the planarian Schmidtea mediterranea. smedinx-11 RNAi treatment inhibits regeneration and abrogates neoblast maintenance. Moreover, smedinx-11 expression is enriched in an irradiation-sensitive subpopulation (`X2') and is required for proper expression of other stem cell-specific markers. Analyses of the smedinx-11 downregulation phenotype revealed a striking anterior-posterior neoblast gradient. Our data demonstrate a novel role for gap junction proteins and suggest gap junction-mediated signaling as a new and tractable control point for adult, somatic stem cell regulation.