julilili42/papers huggingface dataset:
Photosynthetic redox regulation of the plastocyanin promoter in tobacco
2008-04-17

Persistent light quality gradients in dense plant populations induce imbalances in the distribution of excitation energy between the photosystems. Plants counteract such conditions by re‐adjusting the stoichiometry of photosystems, which involves control of photosynthesis gene expression both in chloroplasts and in the nucleus. Decisive control parameters are redox signals from the photosynthetic electron transport chain, one prominent is the plastoquinone (PQ) pool. In a recent study, a plastocyanin (PC)‐promoter::β‐glucuronidase reporter gene construct in tobacco demonstrated reversible redox regulation in response to varying light qualities. Here, northern and Western analyses demonstrate that this promoter regulation also accounts for the accumulation of the endogenous tobacco PetE gene transcripts and the protein amounts of the encoded PC. Hence, the reporter gene construct reflects the natural regulation of this nuclear gene in tobacco. In kinetic experiments, the response of the construct to either oxidation or reduction of the PQ pool was tested by defined light quality shifts. The construct displayed upregulation in response to a reduction signal and downregulation in response to an oxidation signal, both with a half‐time of about 24 h. The response was finished after 48 h. DCMU application abolished the upregulation in response to the reduction signal, indicating the dependence on thylakoid membrane electron transport. To study the redox‐responsive promoter region in more detail, several promoter deletion constructs were tested for their responsiveness. All constructs displayed a reversible response to light‐induced oxidation and reduction signals; however, a minimal promoter region localised between −168 to −79 bp upstream of the transcription start site was sufficient to confer this redox regulation. This indicates that photosynthetic redox signals act on distinct regions in the PC promoter in a manner independent from photoreceptors and upstream cis elements conferring high basic expression in the light.
Kinetics of Microbial and Chemical Reduction of Humic Substances: Implications for Electron Shuttling
2008-04-18

Humic substances (HS) are redox-active natural organic compounds and serve as electron shuttles between microorganisms and iron(III) minerals. Here we demonstrate that electron shuttling is possible only at concentrations of dissolved HS of at least 5-10 mg C/L. Although such concentrations can be found in many rivers, lakes, and even in some aquifers there are also many marine and freshwater systems with DOC < 5 mg C/L where consequently electron shuttling is not expected to happen. We found that in the case of HS concentrations which do not limit electron shuttling, Geobacter sulfurreducens transfers electrons to HS at least 27 times faster than to Fe(III)hydroxide. Microbially reduced HS transfer electrons to ferrihydrite at least 7 times faster than cells thereby first demonstrating that microbial mineral reduction via HS significantly accelerates Fe(III) mineral reduction and second that electron transfer from reduced HS to Fe(III) minerals represents the rate-limiting step in microbial Fe(III) mineral reduction via HS. Microbial reduction of HS transfers as many electrons to HS as chemical reduction with H2 indicating that all redox-active functional groups that can be reduced at a redox potential of -418 mV (Eh(0) of H2/H+ redox couple at pH 7) can also be reduced by microorganisms.
Temporal and spatial analyses disclose consequences of habitat fragmentation on the genetic diversity in capercaillie (Tetrao urogallus)
2008-04-18

Abstract As a result of habitat fragmentation, the capercaillie ( Tetrao urogallus ) population in the Black Forest mountain range in southwestern Germany has declined rapidly during the last decades and now persists in patchy isolated fragments. To study the effects of fragmentation, we quantified dispersal patterns by genotyping 213 individuals in four subpopulations. We used a landscape genetics approach to analyse individual genetic variation, and despite overall low genetic structure, we found strong indications for a major boundary separating the northern part of the Black Forest area from the other subpopulations. Males and females display different gene flow patterns across the landscape. Females tend to disperse across longer distances than do males. We additionally studied the effects of the population decline on genetic diversity during the last hundred years. Although the population has dramatically declined from over 4000 to 250 males over a few decades, genetic diversity was not affected in the same way. We found two haplotypes that were present only in historic samples but microsatellite markers revealed no significant reduction in genetic diversity. Among historic samples, genetic differentiation was very low, indicating that the current genetic structure is caused by recent habitat fragmentation. We argue that inferences about reduced genetic diversity are drawn cautiously and recommend sampling over different temporal scales.
Positron Emission Tomography/Computed Tomography and Whole-Body Magnetic Resonance Imaging in Staging of Advanced Nonsmall Cell Lung Cancer???Initial Results
2008-04-18

In the correct staging of advanced NSCLC, PET/CT has advantages in N-staging. This is of high relevance for therapy planning. WbMRI especially using volume interpolated breathhold examination sequences, has certain advantages in T-staging.
Selective Attention Increases the Dependency of Cortical Responses on Visual Motion Coherence in Man
2008-04-18

Attention improves visual discrimination and consequently allows to discern stimuli with low signal-to-noise ratios that otherwise would remain undetected. We used magnetoencephalography (MEG) to test whether neuromagnetic responses recorded from occipito-temporal cortex, reflecting the size of visual motion signals embedded in noise (motion coherence), would mirror the perceptual changes induced by attention. Attention directed to a given hemifield increased and decreased the coherence modulation of the MEG response over contralateral and ipsilateral visual cortex, respectively, indicating a change in the neuronal signal-to-noise ratio at the population level.
Distribution of muscarinic receptor subtype M3 in melanomas and their metastases
2008-04-18

Background: Muscarinic acetylcholine receptors (mR) are involved in the regulation of cancer cell motility and cancer progression. mR have been shown in melanoma cell lines and cryostat sections of melanomas. To substantiate the experimental data, here the correlation of mR‐expression with invasive growth was studied on the cellular level by comparison with HMB‐45 immunoreactivity. Methods: mR were detected by a M3 subtype‐specific polyclonal antibody in normal skin, benign compound nevi, primary melanomas [nodular type, nodular malignant melanoma (NMM)] and metastases, and were compared with HMB‐45 staining in parallel paraffin sections. Results: The general staining pattern of anti‐M3 and HMB‐45 was similar with accentuation of zones with infiltrative growth. On the cellular level, only a subpopulation of the HMB‐45 positive melanoma cells expressed mR. Immunoreactivity was encountered in 3 of 15 nevi, in 9 of 14 NMM and in 10 of 14 melanoma metastases. Polymorphonuclear granulocytes also exhibited strong reactivity for anti‐M3. Conclusion: mR‐expression is associated with invasive migration of melanomas.
The Alkaline-Peralkaline Tamazeght Complex, High Atlas Mountains, Morocco: Mineral Chemistry and Petrological Constraints for Derivation from a Compositionally Heterogeneous Mantle Source
2008-04-19

The Eocene Tamazeght complex, High Atlas Mountains, Morocco is a multiphase alkaline to peralkaline intrusive complex. A large variety of rock types (including pyroxenites, glimmerites, gabbroic to monzonitic rocks, feldspathoidal syenites, carbonatites and various dyke rocks) documents a progression from ultramafic to felsic magmatism. This study focuses on the silicate plutonic members and the genetic relationships between the various lithologies. Based on detailed petrographic and mineral chemical data we show that the various units crystallized under markedly different oxygen fugacity and silica activity conditions and demonstrate how these parameters influence both the phase assemblage and the detailed chemical evolution of the fractionating phases. Nepheline, olivine–clinopyroxene and hornblende–plagioclase thermometry indicate equilibration temperatures ≥800°C for all major rock types. Highly oxidized conditions (close to the hematite–magnetite buffer) are characteristic of the garnet-rich pyroxenites, ultrapotassic glimmerites and associated olivine-shonkinites. The parental magmas to these rocks evolved from low initial aSiO2 values of 0·1 to values of 0·5–0·8 during nepheline and alkali feldspar saturation. In contrast, the monzonitic rocks evolved from initially high aSiO2 values (up to 0·75) down to about 0·1 at intermediate values of oxygen fugacity (ΔFMQ = +2–5 to −1, where FMQ is the fayalite–magnetite–quartz buffer). For nepheline syenites and malignites, more reduced conditions (ΔFMQ = −2) and intermediate aSiO2 values (between 0·25 and 0·5) dominate. We conclude that fractional crystallization is not a likely mechanism to explain the large variety of lithologies present in the Tamazeght complex. It is more probable that successive melting of a compositionally heterogeneous mantle source region gave rise to several melt batches with distinct chemical and physico-chemical characteristics. Low-degree melts from a K-phase-bearing mantle domain resulted in the formation of ultrapotassic glimmerites, whereas garnet-rich pyroxenites and olivine-shonkinites may have originated from hybrid melts and partly from a pyroxene-dominated source. Less alkaline lithologies such as monzonites potentially reflect larger degrees of melting and the increased importance of a basaltic component, whereas nepheline syenites and malignites may be explained by lower degrees of melting and a more alkaline character for the parental melt of these rocks.
Anti-inflammatory medications for obstructive sleep apnea syndrome in children
2008-04-21

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: To assess the efficacy of anti‐inflammatory drugs for the treatment of obstructive sleep apnea syndrome in children.
Mosasaurs, Limpets or Diagenesis: How Placenticeras Shells Got Punctured
2008-04-22

Claimed mosasaur bites in Upper Cretaceous Placenticeras shells from the Western United States are reinterpreted as limpetmade pits that became punctured by compactional pressure and beveled during diagenesis.Die von Kauffman &amp; Kesling (1960) als Mosasaurier-Bisse gedeuteten Perforationen in oberkretazischen Ammonitengehäusen werden auf die Raspeltätikeit patellider Schnecken zurückgeführt. Diese besiedelten wahrscheinlich nekroplanktonische Gehäuse und lebten hauptsächlich von schalenbohrenden Algen. Erst diagenetische Prozesse haben das Durchbrechen der ursprünglichen Fressdellen sowie die Bördelung der Bruchränder bewirkt.doi:10.1002/mmng.19980010107
Re-discovery of a Supposedly Lost Muscle in Palaeognathous Birds and Its Phylogenetic Implications
2008-04-22

In four palaeognathous species dissected and in two species with section series, a true homologue of a M. geniohyoideus of other tetrapods was found. This muscle is innervated by the cranial nerve XII and extends from its origin on the mandibular symphysis caudally to its insertion on the ceratobranchiale. The muscle is sandwiched between the floor of the mouth and the M. intermandibularis. In none of the twelve neognathous species dissected, nor in the many descriptions in the literature was a muscle of this topographic configuration found. The presence of a M. geniohyoideus is part of the groundplan of birds in general, and is retained in palaeognaths as a plesiomorph feature. It is therefore not indicative of a monophyly of this group. In neognathous birds, the M. geniohyoideus was lost once or possibly twice. If it were lost once, namely in the stemgroup of the neognaths, this would be an autapomorphy of the group, corroborating its monophyly. However, it is also conceivable that the M. geniohyoideus was lost twice. Before this question can be resolved, more data, especially on the comparative functional morphology have to be gathered.
First‐trimester screening for trisomy 21 by free beta‐human chorionic gonadotropin and pregnancy‐associated plasma protein‐A: impact of maternal and pregnancy characteristics
2008-04-23

Abstract Objectives To use multiple regression analysis to define the contribution of maternal variables that influence the measured concentration of free beta‐human chorionic gonadotropin (β‐hCG) and pregnancy‐associated plasma protein‐A (PAPP‐A), and the interaction between these covariates, in first‐trimester biochemical screening for trisomy 21. Methods This was a multicenter study of prospective screening for trisomy 21 by a combination of fetal nuchal translucency thickness, and maternal serum free β‐hCG and PAPP‐A at 11 + 0 to 13 + 6 weeks of gestation. In the pregnancies subsequently found to have trisomy 21 and in those with no obvious chromosomal abnormality, we used multiple regression analysis to account for pregnancy characteristics that influence the measured concentrations of free β‐hCG and PAPP‐A. We fitted Gaussian distributions to the distribution of log multiples of the median (MoM) values in trisomy 21 and in unaffected pregnancies. Results There were 491 cases of trisomy 21 and 96 803 chromosomally normal pregnancies. Compared with values in Caucasian women, those who were parous, non‐smokers and those who conceived spontaneously, PAPP‐A was 57% higher in women of Afro‐Caribbean origin, 3% higher in South Asians, 9% higher in East Asians, 2% higher in nulliparous women, 17% lower in smokers and 10% lower in those conceiving by in‐vitro fertilization (IVF). Free β‐hCG was 12% higher in women of Afro‐Caribbean origin, 9% lower in South Asians, 8% higher in East Asians, 2% higher in nulliparous women, 4% lower in smokers and 9% higher in those conceiving by IVF. In screening for trisomy 21 by maternal age and serum free β‐hCG and PAPP‐A the estimated detection rate was 65% for a false‐positive rate of 5%. Conclusions In first‐trimester biochemical screening for trisomy 21 it is essential to adjust the measured values of free β‐hCG and PAPP‐A for maternal and pregnancy characteristics. Copyright © 2008 ISUOG. Published by John Wiley &amp; Sons, Ltd.
Genetic conservation of the GIL blood group determining aquaporin 3 gene in African and Caucasian populations
2008-04-23

BACKGROUND: The human GIL blood group is encoded by the aquaporin 3 (AQP3), a water‐glycerol channel present in human red cell (RBC) membranes. So far no molecular investigation of this gene has been performed in an African population. STUDY DESIGN AND METHODS: To analyze the genetic variability of the AQP3 gene in African and European persons, all exons including the boundaries to introns and the promoter region were sequenced. AQP3 mRNA levels in children affected by uncomplicated and by severe malarial anemia were determined by real‐time polymerase chain reaction (RT‐PCR). RESULTS: Two mutations in the promoter region and three synonymous mutations in the exons 1, 2, and 4 were found. The promoter polymorphisms, however, were not associated with the expression level of AQP3 measured in whole blood. Significant differences in AQP3 expression were found between malaria diseases severity groups (p = 0.017). CONCLUSION: AQP3 is a highly conserved gene. Although reticulocytes are highly abundant in malarial anemia, low AQP3 expression was observed. This may be a result of an impaired erythropoiesis.
CELL-SELEX: Novel Perspectives of Aptamer-Based Therapeutics
2008-04-24

Aptamers, single stranded DNA or RNA molecules, generated by a method called SELEX (systematic evolution of ligands by exponential enrichment) have been widely used in various biomedical applications. The newly developed Cell-SELEX (cell based-SELEX) targeting whole living cells has raised great expectations for cancer biology, -therapy and regenerative medicine. Combining nanobiotechnology with aptamers, this technology opens the way to more sophisticated applications in molecular diagnosis. This paper gives a review of recent developments in SELEX technologies and new applications of aptamers.
TheArabidopsisCOP9 signalosome is essential for G2 phase progression and genomic stability
2008-04-24

The COP9 signalosome (CSN) is required for the full activity of cullin-RING E3 ubiquitin ligases (CRLs) in eukaryotes. CSN exerts its function on CRLs by removing the ubiquitin-related NEDD8 conjugate from the cullin subunit of CRLs. CSN seems, thereby, to control CRL disassembly or CRL subunit stability. In Arabidopsis thaliana, loss of CSN function leads to constitutive photomorphogenic (cop) seedling development and a post-germination growth arrest. The underlying molecular cause of this growth arrest is currently unknown. Here, we show that Arabidopsis csn mutants are delayed in G2 phase progression. This cell cycle arrest correlates with the induction of the DNA damage response pathway and is suggestive of the activation of a DNA damage checkpoint. In support of this hypothesis, we detected gene conversion events in csn mutants that are indicative of DNA double-strand breaks. DNA damage is also apparent in mutants of the NEDD8 conjugation pathway and in mutants of the E3 ligase subunits CULLIN4, COP1 and DET1, which share phenotypes with csn mutants. In summary, our data suggest that Arabidopsis csn mutants undergo DNA damage, which might be the cause of the delay in G2 cell cycle progression.
Ancient associations of aquatic beetles and tank bromeliads in the Neotropical forest canopy
2008-04-24

Water reservoirs formed by the leaf axils of bromeliads are a highly derived system for nutrient and water capture that also house a diverse fauna of invertebrate specialists. Here we investigate the origin and specificity of bromeliad-associated insects using Copelatinae diving beetles (Dytiscidae). This group is widely distributed in small water bodies throughout tropical forests, but a subset of species encountered in bromeliad tanks is strictly specialized to this habitat. An extensive molecular phylogenetic analysis of Neotropical Copelatinae places these bromeliadicolous species in at least three clades nested within other Copelatus . One lineage is morphologically distinct, and its origin was estimated to reach back to 12–23 million years ago, comparable to the age of the tank habitat itself. Species of this clade in the Atlantic rainforest of southern Brazil and mountain ranges of northern Venezuela and Trinidad show marked phylogeographical structure with up to 8% mtDNA divergence, possibly indicating allopatric speciation. The other two invasions of bromeliad water tanks are more recent, and haplotype distributions within species are best explained by recent expansion into newly formed habitat. Hence, bromeliad tanks create a second stratum of aquatic freshwater habitat independent of that on the ground but affected by parallel processes of species and population diversification at various temporal scales, possibly reflecting the paleoclimatic history of neotropical forests.
EpiToolKit—a web server for computational immunomics
2008-04-24

Predicting the T-cell-mediated immune response is an important task in vaccine design and thus one of the key problems in computational immunomics. Various methods have been developed during the last decade and are available online. We present EpiToolKit, a web server that has been specifically designed to offer a problem-solving environment for computational immunomics. EpiToolKit offers a variety of different prediction methods for major histocompatibility complex class I and II ligands as well as minor histocompatibility antigens. These predictions are embedded in a user-friendly interface allowing refining, editing and constraining the searches conveniently. We illustrate the value of the approach with a set of novel tumor-associated peptides. EpiToolKit is available online at www.epitoolkit.org.
Expanding Assay Dynamics: A Combined Competitive and Direct Assay System for the Quantification of Proteins in Multiplexed Immunoassays
2008-04-24

Abstract Background: The concurrent detection and quantification of analytes that vary widely in concentration present a principal problem in multiplexed assay systems. Combining competitive and sandwich immunoassays permits coverage of a wide concentration range, and both highly abundant molecules and analytes present in low concentration can be quantified within the same assay. Methods: The use of different fluorescence readout channels allows the parallel use of a competitive system and a sandwich configuration. The 2 generated assay signals are combined and used to calculate the amount of analyte. The measurement range can be adjusted by varying the competitor concentration, and an extension of the assay system’s dynamic range is possible. Results: We implemented the method in a planar protein microarray–based autoimmune assay to detect autoantibodies against 13 autoantigens and to measure the concentration of a highly abundant protein, total human IgG, in one assay. Our results for autoantibody detection and IgG quantification agreed with results obtained with commercially available assays. The use of 2 readout channels in the protein microarray–based system reduced spot-to-spot variation and intraassay variation. Conclusions: By combining a direct immunoassay with a competitive system, analytes present in widely varying concentrations can be quantified within a single multiplex assay. Introducing a second readout channel for analyte quantification is an effective tool for spot-to-spot normalization and helps to lower intraassay variation.
Differential Sensitization of Afferent Neuronal Pathways During Postoperative Ileus in the Mouse Jejunum
2008-04-24

This study provides direct evidence from afferent nerve recordings that sensitivity to bradykinin, which stimulates predominantly spinal afferents, is augmented during postoperative ileus involving a COX-2 pathway. Vagal afferents were also sensitized because low-threshold mechanosensitivity and neuronal activation in the nTS were increased.