bluuebunny/crossref_metadata_2025 huggingface dataset:
Unravelling the effects of soil properties on water infiltration: segmented quantile regression on a large data set from arid south-west Africa
Authors: Mills A. J. , Fey M. V. , Gröngröft A. , Petersen A. , Medinski T. V.
Published: November 2006

Relationships were sought between infiltrability and the properties of hundreds of surface soils (pedoderms) sampled across Namibia and western South Africa. Infiltrability was determined using a laboratory method, calibrated against a rainfall simulator, which measures the passage of a suspension of soil in distilled water through a small column packed with the same soil. Other properties determined were EC, pH, water-soluble cations and anions, ammonium acetate-extractable cations, organic C, total N, a 7-fraction particle size distribution, water-dispersible silt and clay, and clay mineral composition. Our objective was to ascertain whether general principles pertaining to infiltrability can be deduced from an analysis of a wide diversity of soils. To achieve this we compared correlation analysis, generalised linear models (GLMs), and generalised additive models (GAMs) with a segmented quantile regression approach, in which parametric regression lines were fitted to the 0.9 and 0.1 quantile values of equal subpopulations based on the x variable. Quantile regression demarcated relational envelopes enclosing four-fifths of the data points. The envelopes revealed ranges for soil properties over which infiltrability is potentially maximal (spread over a wide range) or predictably minimal (confined to small values). The r2 value of the 0.9 quantile regression line was taken as an index of reliability in being able to predict limiting effects on infiltrability associated with a variety of soil properties. Prediction of infiltration was most certain from textural properties, especially the content of water-dispersible silt (r2 = 0.96, n = 581), water-dispersible clay (0.88, n = 581), very fine sand (0.86, n = 174), and medium sand (0.84, n = 174). Chemical properties such as EC, sodium status, organic C content, and clay mineralogy were less clearly related to infiltrability than was texture. The role of fine-particle dispersion in blocking pores was highlighted by the stronger prediction in all statistical analyses provided by the water-dispersible as opposed to total content of silt and clay. All the statistical analyses revealed a probable skeletal role of medium and fine sand fractions in shaping pores and a plasmic (mobile) role of finer fractions in blocking pores. A noteworthy discovery was an apparent switch in role from skeletal to plasmic at a particle diameter of about 0.1 mm (i.e. between fine and very fine sand).
Soil factors that influence the fruiting of Tuber melanosporum (black truffle)
Authors: García-Montero L. G. , Casermeiro M. A. , Hernando J. , Hernando I.
Published: November 2006

Although soil is one of the factors in the biology of Tuber melanosporum (black truffle of Périgord), which has been the subject of much study, there are few quantitative analyses relating to its effects on carpophore production. The aim of this work is to establish the statistical relationship between T. melanosporum productivity in 20 soil surface horizons and their conventional soil properties (granulometric texture, pH, calcareous fractions, organic carbon, total nitrogen, exchangeable cations). The study area is situated in the centre of the Iberian Peninsula under a Mediterranean climate. Statistical analysis shows that the collective influence of these conventional soil features is low, as principal component analysis explains only 27% of the variance in T. melanosporum production. However, a high percentage of active limestone (calcium carbonate extractable with ammonium oxalate) accounts for 40% of the variance in T. melanosporum production. Active limestone is very important to T. melanosporum because it regulates soil pH and exchangeable Ca2+ availability and participates in the organisation and maintenance of the soil structure; it also plays a role in the truffle’s nutrition. These results obtained for active limestone may be of use in truffle cultivation.
Nitrification activity in acid soils of north-eastern Victoria, Australia, as affected by liming and phosphorus fertilisation
Authors: Islam A. , White R. E. , Chen D.
Published: November 2006

A short-term nitrification assay (SNA) was used to measure the activity of soil nitrifiers and their response to pH change in acid pasture soils (pH 4.8–5.3 in water) at the sites of Maindample and Ruffy in north-eastern Victoria, Australia. Changes in soil pH associated with lime applications in the field resulted in a change in the optimum pH (pHopt) of the nitrifying organisms in the range 4.93–6.94. Nitrification in these soils was predominantly autotrophic, and rates increased from 0.18 to 0.93 μg NO3–-N/g.h with increasing pH. The strong positive correlation between field soil pH and the respective pHopt values suggested that the indigenous nitrifier population had adapted to the change in soil pH. SNA measurements within 6 months of lime application to Maindample soil showed that the soil nitrifying organisms had rapidly adapted to the pH change. However, the residual effect of lime on nitrifier activity was long-lasting (up to 8 years) and may involve more than a simple effect on soil pH. Repeat application of lime further enhanced nitrification activity on an already elevated activity, but only if sufficient time was allowed (>3 years) after the earlier application. Phosphate applications to these soils did not affect the general pH response in nitrifier activity. Both soils had considerable capacity for nitrification, even at pHs much lower than the commonly accepted range for autotrophic nitrifiers.
Zinc binding to the HCCH motif of HIV-1 virion infectivity factor induces a conformational change that mediates protein–protein interactions
Authors: Paul Indrani , Cui Jian , Maynard Ernest L.
Published: November 2006

Virion infectivity factor (Vif) is an accessory protein encoded by HIV-1 and is critical for viral infection of the host CD4
+
T cell population. Vif induces ubiquitination and subsequent degradation of Apo3G, a cytosolic cytidine deaminase that otherwise targets the retroviral genome. Interaction of Vif with the cellular Cullin5-based E3 ubiquitin ligase requires a conserved BC box and upstream residues that are part of the conserved H-(Xaa)
5
-C-(Xaa)
17–18
-C-(Xaa)
3–5
-H (HCCH) motif. The HCCH motif is involved in stabilizing the Vif–Cullin 5 interaction, but the exact role of the conserved His and Cys residues remains elusive. In this report, we find that full-length HIV-1 Vif, as well as a HCCH peptide, is capable of binding to zinc with high specificity. Zinc binding induces a conformational change that leads to the formation of large protein aggregates. EDTA reversed aggregation and regenerated the apoprotein conformation. Cysteine modification studies with the HCCH peptide suggest that C114 is critical for stabilizing the fold of the apopeptide, and that C133 is located in a solvent-exposed region with no definite secondary structure. Selective alkylation of C133 reduced metal-binding specificity of the HCCH peptide, allowing cobalt to bind with rates comparable to that with zinc. This study demonstrates that the HCCH motif of HIV-1 Vif is a unique metal-binding domain capable of mediating protein–protein interactions in the presence of zinc and adds to a growing list of examples in which metal ion binding induces protein misfolding and/or aggregation.
Smad4 cooperates with lymphoid enhancer-binding factor 1/T cell-specific factor to increase c-
myc
expression in the absence of TGF-β signaling
Authors: Lim S. Kyun , Hoffmann F. Michael
Published: November 2006

The c-
myc
protooncogene is a key regulator of cell proliferation whose expression is reduced in normal epithelial cells in response to the growth inhibitory cytokine TGF-β. Smad4 mediates this inhibitory effect of TGF-β by forming a complex with Smad3, E2F4/5, and p107 at the TGF-β inhibitory element (TIE) element on the c-
myc
promoter. In contrast, cell proliferation and c-
myc
expression are increased in response to Wnt ligands; this effect is mediated through the lymphoid enhancer-binding factor 1/T cell-specific factor (LEF/TCF) family of transcription factors on the c-
myc
promoter LEF/TCF-binding elements (TBE1 and TBE2). We report that a peptide aptamer designed to inhibit the binding between Smad4 and LEF/TCF reduced c-
myc
expression and the growth rate of HepG2 cells. Further analysis demonstrated that, in the absence of TGF-β, Smad4 was bound to the positive regulatory element TBE1 from the c-
myc
promoter and activated c-
myc
promoter activity. Smad4 binding to the positive TBE1 c-
myc
element was reduced by TGF-β, consistent with Smad4's inhibitory role on c-
myc
expression in response to TGF-β. Reduction of Smad4 levels by RNAi knockdown also reduced c-
myc
expression levels and sensitized hepatocytes to cell death by serum deprivation. Two tumor-derived mutant Smad4 proteins that fail to mediate TGF-β responses were still competent to cooperate with LEF1 to activate the c-
myc
promoter. These results support a previously unreported TGF-β-independent function for Smad4 in cooperating with LEF/TCF to activate c-
myc
expression.
Silencing leaf sorbitol synthesis alters long-distance partitioning and apple fruit quality
Authors: Teo Gianni , Suzuki Yasuo , Uratsu Sandie L. , Lampinen Bruce , Ormonde Nichole , Hu William K. , DeJong Ted M. , Dandekar Abhaya M.
Published: November 2006

Sorbitol and sucrose are major products of photosynthesis distributed in apple trees (Malus domesticaBorkh. cv. “Greensleeves”) that affect quality in fruit. Transgenic apple plants were silenced or up-regulated for sorbitol-6-phosphate dehydrogenase by using the CaMV35S promoter to define the role of sorbitol distribution in fruit development. Transgenic plants with suppressed sorbitol-6-phosphate dehydrogenase compensated by accumulating sucrose and starch in leaves, and morning and midday net carbon assimilation rates were significantly lower. The sorbitol to sucrose ratio in leaves was reduced by ≈90% and in phloem exudates by ≈75%. The fruit accumulated more glucose and less fructose, starch, and malic acid, with no overall differences in weight and firmness. Sorbitol dehydrogenase activity was reduced in silenced fruit, but activities of neutral invertase, vacuolar invertase, cell wall-bound invertase, fructose kinase, and hexokinase were unaffected. Analyses of transcript levels and activity of enzymes involved in carbohydrate metabolism throughout fruit development revealed significant differences in pathways related to sorbitol transport and breakdown. Together, these results suggest that sorbitol distribution plays a key role in fruit carbon metabolism and affects quality attributes such as sugar–acid balance and starch accumulation.
Premature arrest of the male flower meristem precedes sexual dimorphism in the dioecious plant
Silene latifolia
Authors: Zluvova Jitka , Nicolas Michaël , Berger Adeline , Negrutiu Ioan , Monéger Françoise
Published: November 2006

Most dioecious plant species are believed to derive from hermaphrodite ancestors. The regulatory pathways that have been modified during evolution of the hermaphrodite ancestors and led to the emergence of dioecious species still remain unknown.
Silene latifolia
is a dioecious plant species harboring XY sex chromosomes. To identify the molecular mechanisms involved in female organ suppression in male flowers of
S. latifolia
, we looked for genes potentially involved in the establishment of floral organ and whorl boundaries. We identified homologs of
Arabidopsis thaliana
SHOOTMERISTEMLESS
(
STM
) and
CUP SHAPED COTYLEDON
(
CUC
)
1
and
CUC2
genes in
S. latifolia
. Our phylogenetic analyses suggest that we identified true orthologs for both types of genes. Detailed expression analyses showed a conserved expression pattern for these genes between
S. latifolia
and
A. thaliana
, suggesting a conserved function of the corresponding proteins. Comparative
in situ
hybridization experiments between male, female, and hermaphrodite individuals reveal that these genes show a male-specific pattern of expression before any morphological difference become apparent. Our results make
SlSTM
and
SlCUC
strong candidates for being involved in sex determination in
S. latifolia
.
Topographical complexity of multidimensional energy landscapes
Authors: Rylance Gareth J. , Johnston Roy L. , Matsunaga Yasuhiro , Li Chun-Biu , Baba Akinori , Komatsuzaki Tamiki
Published: November 2006

A scheme for visualizing and quantifying the complexity of multidimensional energy landscapes and multiple pathways is presented employing principal component-based disconnectivity graphs and the Shannon entropy of relative “sizes” of superbasins. The principal component-based disconnectivity graphs incorporate a metric relationship between the stationary points of the system, which enable us to capture not only the actual assignment of the superbasins but also the size of each superbasin in the multidimensional configuration space. The landscape complexity measure quantifies the degree of topographical complexity of a multidimensional energy landscape and tells us at which energy regime branching of the main path becomes significant, making the system more likely to be kinetically trapped in local minima. The path complexity measure quantifies the difficulty encountered by the system to reach a connected local minimum by the path in question, implying that the more significant the branching points along the path the more difficult it is to end up in the desired local minimum. As an illustrative example, we apply this analysis to two kinds of small model protein systems exhibiting a highly frustrated and an ideal funnel-like energy landscape.
Prediction of active nodes in the transcriptional network of neural tube patterning
Authors: Kioussi Chrissa , Shih Hung-Ping , Loflin John , Gross Michael K.
Published: November 2006

A transcriptional network governs patterning in the developing spinal cord. As the developmental program runs, the levels of sequence-specific DNA-binding transcription factors (SSTFs) in each progenitor cell type change to ultimately define a set of postmitotic populations with combinatorial codes of expressed SSTFs. A network description of the neural tube (NT) transcriptional patterning process will require definition of nodes (SSTFs and target enhancers) and edges (interactions between nodes). There are 1,600 SSTF nodes in a given mammalian genome. To limit the complexity of a network description, it will be useful to discriminate between active and passive SSTF nodes. We define active SSTF nodes as those that are differentially expressed within the system. Our system, the developing NT, was partitioned into two pools of genetically defined populations by using flow sorting. Microarray comparisons across the partition led to an estimate of 500–700 active SSTF nodes in the transcriptional network of the developing NT. These included most of the 66 known SSTFs assembled from review articles and recent reports on NT patterning. Empirical cutoffs based on the performance of knowns were used to identify 188 further active SSTFs nodes that performed similarly. The general utility and limitations of the population-partitioning paradigm are discussed.
Attenuation of signaling pathways stimulated by pathologically activated FGF-receptor 2 mutants prevents craniosynostosis
Authors: Eswarakumar V. P. , Özcan F. , Lew E. D. , Bae J. H. , Tomé F. , Booth C. J. , Adams D. J. , Lax I. , Schlessinger J.
Published: November 2006

Craniosynostosis, the fusion of one or more of the sutures of the skull vault before the brain completes its growth, is a common (1 in 2,500 births) craniofacial abnormality, ≈20% of which occurrences are caused by gain-of-function mutations in FGF receptors (FGFRs). We describe a genetic and pharmacological approach for the treatment of a murine model system of Crouzon-like craniosynostosis induced by a dominant mutation in Fgfr2c. Using genetically modified mice, we demonstrate that premature fusion of sutures mediated by Crouzon-like activated Fgfr2c mutant is prevented by attenuation of signaling pathways by selective uncoupling between the docking protein Frs2α and activated Fgfr2c, resulting in normal skull development. We also demonstrate that attenuation of Fgfr signaling in a calvaria organ culture with an Fgfr inhibitor prevents premature fusion of sutures without adversely affecting calvaria development. These experiments show that attenuation of FGFR signaling by pharmacological intervention could be applied for the treatment of craniosynostosis or other severe bone disorders caused by mutations in FGFRs that currently have no treatment.
Dendritic spines linearize the summation of excitatory potentials
Authors: Araya Roberto , Eisenthal Kenneth B. , Yuste Rafael
Published: November 2006

In mammalian cortex, most excitatory inputs occur on dendritic spines, avoiding dendritic shafts. Although spines biochemically isolate inputs, nonspiny neurons can also implement biochemical compartmentalization; so, it is possible that spines have an additional function. We have recently shown that the spine neck can filter membrane potentials going into and out of the spine. To investigate the potential function of this electrical filtering, we used two-photon uncaging of glutamate and compared the integration of electrical signals in spines vs. dendritic shafts from basal dendrites of mouse layer 5 pyramidal neurons. Uncaging potentials onto spines summed linearly, whereas potentials on dendritic shafts reduced each other's effect. Linear integration of spines was maintained regardless of the amplitude of the response, distance between spines (as close as <2 μm), distance of the spines to the soma, dendritic diameter, or spine neck length. Our findings indicate that spines serve as electrical isolators to prevent input interaction, and thus generate a linear arithmetic of excitatory inputs. Linear integration could be an essential feature of cortical and other spine-laden circuits.
Distant touch hydrodynamic imaging with an artificial lateral line
Authors: Yang Yingchen , Chen Jack , Engel Jonathan , Pandya Saunvit , Chen Nannan , Tucker Craig , Coombs Sheryl , Jones Douglas L. , Liu Chang
Published: November 2006

Nearly all underwater vehicles and surface ships today use sonar and vision for imaging and navigation. However, sonar and vision systems face various limitations, e.g., sonar blind zones, dark or murky environments, etc. Evolved over millions of years, fish use the lateral line, a distributed linear array of flow sensing organs, for underwater hydrodynamic imaging and information extraction. We demonstrate here a proof-of-concept artificial lateral line system. It enables a distant touch hydrodynamic imaging capability to critically augment sonar and vision systems. We show that the artificial lateral line can successfully perform dipole source localization and hydrodynamic wake detection. The development of the artificial lateral line is aimed at fundamentally enhancing human ability to detect, navigate, and survive in the underwater environment.
Spin motion at and near orbital resonance in storage rings
with Siberian Snakes I: at orbital resonance
Authors: Barber D P , Vogt M
Published: November 2006

In this paper, and in a sequel, we invoke the invariant spin field to provide an
in-depth study of spin motion at and near low order orbital resonances in a simple
model for the effects of vertical betatron motion in a storage ring with Siberian
Snakes. This leads to a clear understanding, within the model, of the behaviour of
the beam polarization at and near so-called snake resonances in proton storage
rings.
Inhibition of Release of Vasoactive and Inflammatory Mediators in Airway and Vascular Tissues and Macrophages by a Chinese Herbal Medicine Formula for Allergic Rhinitis
Authors: Lenon George Binh , Li Chun Guang , Xue Charlie Changli , Thien Francis Chung Kong , Story David Frederick
Published: November 2006

Herbal therapies are being used increasingly for the treatment of allergic rhinitis. The aim of this study was to investigate the possible pharmacological actions and cellular targets of a Chinese herbal formula (RCM‐101), which was previously shown to be effective in reducing seasonal allergic rhinitis symptoms in a randomized, placebo‐controlled clinical trial. Rat and guinea pig isolated tissues (trachea and aorta) were used to study the effects of RCM‐101 on responses to various mediators. Production of leukotriene B4 in porcine neutrophils and of prostaglandin E2 and nitric oxide (NO) in Raw 264.7 cells were also measured. In rat and guinea pig tracheal preparations, RCM‐101 inhibited contractile responses to compound 48/80 but not those to histamine (guinea pig preparations) or serotonin (rat preparations). Contractile responses of guinea pig tracheal preparations to carbachol and leukotriene C4, and relaxant responses to substance P and prostaglandin E2 were not affected by RCM‐101. In rat aortic preparations, precontracted with phenylephrine, endothelium‐dependent relaxant responses to acetylcholine and endothelium‐independent relaxant responses to sodium nitroprusside were not affected by RCM‐101. However, RCM‐101 inhibited relaxations to l‐arginine in endothelium‐denuded rat aortic preparations, which had been pre‐incubated with lipopolysaccharide. RCM‐101 did not affect leukotriene B4 formation in isolated porcine neutrophils, induced by the calcium ionophore A23187; however, it inhibited prostaglandin E2 and NO production in lipopolysaccharide‐stimulated murine macrophages (Raw 264.7 cells).The findings indicate that RCM‐101 may have multiple inhibitory actions on the release and/or synthesis of inflammatory mediators involved in allergic rhinitis.
Three Case Reports to Illustrate Clinical Applications in the Use of Erythrocyte Transketolase
Authors: Lonsdale Derrick
Published: November 2006

Non‐caloric nutrients (NCN) are extremely numerous and it is more than obvious that they work in a team relationship. These vitally important interactions are, for the most part, poorly understood. These brief case reports illustrate this in the therapeutic use of thiamin in a clinical setting. The initially abnormal erythrocyte transketolase activity (TKA) and/or the thiamin pyrophosphate effect (TPPE), indicating intracellular cofactor deficiency, usually improves with thiamin administration. Biochemical correction of the abnormality is, however, invariably dependent on the provision of other NCN, especially magnesium. In two patients reported here, this correction required several infusions containing magnesium and other NCN administered intravenously. In a third patient, hemoconcentration associated with an abnormal TPPE was normalized after administration of nutrients that included thiamin and magnesium.
Aortic Arch Laceration: A Lethal Complication After Percutaneous Tracheostomy
Authors: Ayoub Omar M. , Griffiths Mansel V.
Published: November 2006

Percutaneous dilatational tracheostomy (PDT) is not a new technique. However, it was not until Ciaglia introduced a simple technique using a needle, catheter, and guidewire that it became a possible alternative to open surgical tracheotomy. PDT is not performed blindly but with the assistance of fiberoptic endoscopy. However, even with fiberoptic endoscopic control, PDT can give rise to serious complications similar to those encountered with open surgical tracheostomy. We present an uncommon complication of percutaneous tracheostomy, a case of aortic arch laceration. We discuss the anatomy of the pretracheal space and how to avoid such a lethal complication.
Pneumococcal Peptidoglycan‐Polysaccharides Induce the Expression of Interleukin‐8 in Airway Epithelial Cells by way of Nuclear Factor‐κB, Nuclear Factor Interleukin‐6, or Activation Protein‐1 Dependent Mechanisms
Authors: Tsuchiya Katsuyuki , Toyama Katsuhiro , Tsuprun Vladimir , Hamajima Yuki , Kim Youngki , Ondrey Frank G. , Lin Jizhen
Published: November 2006

Cell envelope compounds of bacteria trigger immune and inflammatory reactions by way of chemokines/cytokines. In this study, we demonstrated that pneumococcal peptidoglycan‐polysaccharides (PGPS) induced the production of interleukin (IL)‐8 by way of nuclear factor (NF)‐κB, nuclear factor interleukin (NF‐IL)6, and activation protein (AP)‐1 dependent mechanisms in the human bronchial epithelial cells (NL‐20) in a dose‐ and time‐dependent manner in vitro, and the mutation of either the NF‐κB, NF‐IL6, or AP‐1 binding sites in the promoter of IL‐8 abrogated the IL‐8 transcriptional activity. In a similar way, lipopolysaccharides induced the promoter activation of IL‐8 in NL‐20. However, the PGPS‐induced IL‐8 promoter activation in rodent middle ear epithelial cells required NF‐κB and NF‐IL6 but not AP‐1.
Endoscopic Surgery for Sinonasal Invasive Aspergillosis in Bone Marrow Transplantation Patients
Authors: Eliashar Ron , Resnick Igor B. , Goldfarb Abraham , Wohlgelernter Jay , Gross Menachem
Published: November 2006

Objectives/Hypothesis: Sinonasal invasive aspergillosis (IA) is an aggressive fungal infection with high mortality rates. It commonly develops in immunocompromised patients, often after bone marrow transplantation (BMT). Aggressive surgical debridement by an external approach has been considered a central element of treatment. We describe our experience in endoscopic management of IA in BMT patients in a retrospective study.

Methods: Charts of BMT patients with IA in the past 5 years were reviewed. Demographic data, primary disease, comorbidities, signs and symptoms, blood test results, preparation for surgery, surgical technique, and outcome were recorded.

Results: Fourteen BMT patients, age ranging from 3 to 56 years, had sinonasal IA. The primary disease was acute myelogenous leukemia in 6, acute lymphoblastic leukemia in 3, chronic myeloblastic leukemia in one, severe combined immunodeficiency disease in 2, and myelodysplastic syndrome in 2 patients. Diagnosis was made by physical examination, biopsy, culture, and computed tomography scan. Treatment, including aggressive endoscopic debridement, a systemic antifungal medication, and local irrigations of amphotericin‐B enabled eradication of IA in all patients. Seven patients required two or more operations. None required orbital exenteration or craniotomy. Six patients died of the primary illness or of comorbidities with no evidence of residual disease. Eight patients are alive.

Conclusion: Early detection of IA in BMT patients enables aggressive treatment before the disease spreads into the orbit or brain. Proper preoperative preparation facilitates safe endoscopic surgery in patients with severe bleeding tendencies. Although sinonasal IA is lethal, endoscopic surgery is feasible and efficient, enabling excellent local control.
An Analysis of Surgical Complications, Morbidity, and Cost Calculation in Patients Undergoing Multimodal Treatment for Operable Oropharyngeal Carcinoma
Authors: Preuss Simon F. , Quante Gero , Semrau Robert , Mueller Rolf‐Peter , Klussmann Jens Peter , Guntinas‐Lichius Orlando
Published: November 2006

Objective/Hypothesis: Tumor control and survival are considered the most important measures of treatment efficacy for patients with primary oropharyngeal squamous cell carcinoma. Furthermore, multimodal treatment protocols should be judged by their complication rates, morbidity, and therapy costs.

Study Design: The results of a combined approach of primary surgery and neck dissection with postoperative radio)chemo)therapy were analyzed in retrospective chart review.

Methods: Two hundred eleven patients' records were analyzed for surgical complications, therapeutic morbidity, and treatment costs.

Results: The rate of postoperative hemorrhage was 4.7%. We observed no fatal complications. Ten percent of our patients required nutrition through percutaneous endoscopic gastrostomy (PEG). Twelve percent of all patients required long‐term tracheostomy. The rates of PEG and tracheostomy were significantly higher in patients operated by the transcervical approach. The costs for the combined approach ranged from 10,587 euros ($13,377) to 24,531 euros ($30,996).

Conclusions: The presented multimodal approach provides a low rate of surgical complications and a tolerable morbidity. Considering the excellent oncologic results, this extensive and more cost‐intensive multimodal approach is justified for patients with oropharyngeal cancer.
Specific interactions by the N‐terminal arm inhibit self‐association of the AraC dimerization domain
Authors: Weldon John E. , Schleif Robert F.
Published: November 2006

Deletion of the regulatory N‐terminal arms of the AraC protein from its dimerization domain fragments increases the susceptibility of the dimerization domain to form a series of higher order polymers by indefinite self‐association. We investigated how the normal presence of the arm inhibits this self‐association. One possibility is that arms can act as an entropic bristles to interfere with the approach of other macromolecules, thereby decreasing collision frequencies. We examined the repulsive effect of flexible arms by measuring the rate of trypsin cleavage of a specially constructed ubiquitin‐arm protein. Adding an arm to ubiquitin or increasing its length produced only a modest repulsive effect. This suggests that arms such as the N‐terminal arm of AraC do not reduce self‐association by entropic exclusion. We consequently tested the hypothesis that the arm on AraC reduces self‐association by binding to the core of the dimerization domain even in the absence of arabinose. The behaviors of dimerization domain mutants containing deletions or alterations in the N‐terminal arms substantiate this hypothesis. Apparently, interactions between the N‐terminal arm and the dimerization domain core position the arm to interfere with the protein–protein contacts necessary for self‐association.
New algorithms and an in silico benchmark for computational enzyme design
Authors: Zanghellini Alexandre , Jiang Lin , Wollacott Andrew M. , Cheng Gong , Meiler Jens , Althoff Eric A. , Röthlisberger Daniela , Baker David
Published: November 2006

The creation of novel enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Here we describe two new algorithms for enzyme design that employ hashing techniques to allow searching through large numbers of protein scaffolds for optimal catalytic site placement. We also describe an in silico benchmark, based on the recapitulation of the active sites of native enzymes, that allows rapid evaluation and testing of enzyme design methodologies. In the benchmark test, which consists of designing sites for each of 10 different chemical reactions in backbone scaffolds derived from 10 enzymes catalyzing the reactions, the new methods succeed in identifying the native site in the native scaffold and ranking it within the top five designs for six of the 10 reactions. The new methods can be directly applied to the design of new enzymes, and the benchmark provides a powerful in silico test for guiding improvements in computational enzyme design.
Enhanced cell‐free protein expression by fusion with immunoglobulin Cκ domain
Authors: Palmer Elizabeth , Liu Hong , Khan Farid , Taussig Michael J. , He Mingyue
Published: November 2006

While cell‐free systems are increasingly used for protein expression in structural and functional studies, several proteins are difficult to express or expressed only at low levels in cell‐free lysates. Here, we report that fusion of the human immunoglobulin κ light chain constant domain (Cκ) at the C terminus of four representative proteins dramatically improved their production in the Escherichia coli S30 system, suggesting that enhancement of cell‐free protein expression by Cκ fusion will be widely applicable.
Identifying protein construct variants with increased crystallization propensity––A case study
Authors: Malawski Guido A. , Hillig Roman C. , Monteclaro Felipe , Eberspaecher Uwe , Schmitz Arndt A.P. , Crusius Kerstin , Huber Martina , Egner Ursula , Donner Peter , Müller‐Tiemann Beate
Published: November 2006

This study describes an efficient multiparallel automated workflow of cloning, expression, purification, and crystallization of a large set of construct variants for isolated protein domains aimed at structure determination by X‐ray crystallography. This methodology is applied to MAPKAP kinase 2, a key enzyme in the inflammation pathway and thus an attractive drug target. The study reveals a distinct subset of truncation variants with improved crystallization properties. These constructs distinguish themselves by increased solubility and stability during a parallel automated multistep purification process including removal of the recombinant tag. High‐throughput protein melting point analysis characterizes this subset of constructs as particularly thermostable. Both parallel purification screening and melting point determination clearly identify residue 364 as the optimal C terminus for the kinase domain. Moreover, all three constructs that ultimately crystallized feature this C terminus. At the N terminus, only three amino acids differentiate a noncrystallizing from a crystallizing construct. This study addresses the very common issues associated with difficult to crystallize proteins, those of solubility and stability, and the crucial importance of particular residues in the formation of crystal contacts. A methodology is suggested that includes biophysical measurements to efficiently identify and produce construct variants of isolated protein domains which exhibit higher crystallization propensity.
Altered immune function of monocytes in different stages of patients with acute on chronic liver failure
Authors: Xing T , Li L , Cao H , Huang J
Published: November 2006

The aim of this study was to investigate the characteristics of the immune function of monocytes in different stages of the patients with acute on chronic liver failure (ACLF). Human leucocyte antigen (HLA)-DR and Toll-like receptor 4 (TLR-4) expression on monocytes in early and late stages of acute on chronic liver failure were detected by flow cytometry. The secretion function of monocytes was measured by cytometric bead array. Compared with healthy controls, the levels of HLA-DR expression on monocytes in patients with chronic hepatitis B, liver cirrhosis and acute on chronic liver failure were gradually decreased, especially in the late stage of acute on chronic liver failure (P < 0·001). TLR-4 expression on monocytes in patients with liver cirrhosis and acute on chronic liver failure were higher than the healthy controls. The concentrations of interleukin (IL)-1β, tumour necrosis factor (TNF)-α and IL-12p70 in early-stage ACLF were significantly higher compared with healthy controls and lower in late-stage ACLF (P < 0·01, 0·05). However, a significantly lower amount of IL-10 was found on monocytes in early-stage ACLF than that of late-stage ACLF and healthy controls (P < 0·01). Monocyte HLA-DR expression in patients who died was significantly lower compared with patients who survived in the early and late stages of ACLF (P < 0·01). The dynamic detection of HLA-DR expression or cytokines secreted from monocytes could contribute to the estimation of the status of the immune function of patients with acute on chronic liver failure.
Proinflammatory cytokine synthesis by mucosal fibroblasts from mouse colitis is enhanced by interferon-γ-mediated up-regulation of CD40 signalling
Authors: De L Karlson T , Whiting C V , Bland P W
Published: November 2006

Gut mesenchymal fibroblasts form complex phenotypical and functional populations. They participate actively in homeostatic maintenance of the extracellular matrix, epithelial barrier function, repair mechanisms and leucocyte migration. In inflammation, they become activated, change matrix expression and synthesize proinflammatory mediators. Subpopulations of mucosal fibroblasts express CD40 and the aim of this study was to define its role in their proinflammatory function. Stable primary fibroblast lines derived from normal mouse colon and inflamed colon from CD4+ CD45RBhigh-transplanted SCID mice were used as models to explore the role of mucosal fibroblast CD40 in the inflammatory process. Phenotype correlated with in situ fibroblast phenotype in the tissues of origin. Lines from both sources co-expressed CD40 and Thy1·2 independently of α-smooth muscle actin. A subpopulation of CD40+ fibroblasts from normal colon expressed CD40 at high levels and expression was enhanced by interferon (IFN)-γ treatment, whereas all CD40+ fibroblasts from colitis expressed at low levels and expression was unaffected by IFN-γ treatment. Despite lower-level expression of CD40 by cells from colitis, they secreted constitutively interleukin (IL)-6 and C-C chemokine (CCL)2. Ligation of CD40 enhanced secretion of these mediators and induced secretion of CCL3. CD40 in cells from colitis was more responsive to ligation than CD40 on cells from normal tissue and this sensitivity was amplified selectively by the action of IFN-γ. We conclude that the inflammatory milieu in colitis induces long-lasting changes in phenotype and proinflammatory function in colonic fibroblasts. In particular, proinflammatory signalling from fibroblast CD40 is amplified synergistically by the Th1 effector T cell cytokine, IFN-γ.
The impact of interleukin-6 promoter −597/−572/−174genotype on interleukin-6 production after lipopolysaccharide stimulation
Authors: Müller-Steinhardt M , Ebel B , Härtel C
Published: November 2006

Interleukin (IL)-6 is a pleiotropic cytokine, produced by different cells. There is accumulating evidence that IL-6 promoter polymorphisms impact substantially on various diseases and we identified kidney transplant recipients carrying the IL-6 GGG/GGG −597/−572/−174genotype to have superior graft survival. To prove a functional impact on gene expression, we analysed systematically IL-6 production in healthy individuals with respect to the IL-6 −597/−572/−174genotype. IL-6 was determined in 100 healthy blood donors at protein and mRNA levels upon specific stimulation in monocytes and T lymphocytes under whole blood conditions. GGG/GGG individuals showed a lower IL-6 secretion upon lipopolysaccharide (LPS)-stimulation versus all others (P = 0·039). This link was even stronger when −597 and −174GG genotypes were reanalysed separately (P = 0·008, P = 0·017). However, we found neither a difference at the mRNA level or percentage of CD14+ cells nor after T cell stimulation. We found evidence for the IL-6 −597/−572/−174genotype to affect IL-6 synthesis, i.e. lower levels of IL-6 protein upon LPS-stimulation in GGG/GGG individuals. Further studies are needed in kidney transplant recipients to investigate the potential link between the GGG/GGG genotype and graft survival. In line with this, determination of the genetic risk profiles might be promising to improve the transplant outcome in the individual patient.
Rheumatoid factor induction in murine models of liver injury
Authors: Nowak U , Gill K , Skamene E , Newkirk M M
Published: November 2006

Alcoholic liver disease and hepatitis C are associated with the production of autoantibodies such as rheumatoid factors (RF), which bind to IgG and can aid in host defence, but are also associated with pathological conditions such as rheumatoid arthritis. Because little is known about the role of RF in liver disease, we characterized the RF production that either occurred spontaneously in response to alcohol consumption or was induced by injection of an Escherichia coli glycolipoprotein in C57Bl/6 mice. Whereas severe liver damage was induced by carbon tetrachloride (CCl4), minimal damage was caused by chronic alcohol consumption. Liver damage was monitored by measurements of serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Circulating RF was induced in response to chronic alcohol consumption; the latter probably involved Toll-like receptor ligation. In contrast, CCl4-induced damage was not associated with RF induction. However, concurrent treatment with an E. coli glycolipoprotein macromolecule that induced RF, protected against CCL4-induced liver damage as measured by a highly significant decrease (P = 0·008) at 4 weeks in AST and ALT. RF induced by E. coli glycolipoprotein correlated with ‘protection’ from liver damage, indicating that the RF autoimmune response does not necessarily exacerbate liver disease.
Critical evaluation of three indirect assays for quantifying phytosiderophores released by the roots of Poaceae
Authors: Reichman S. M. , Parker D. R.
Published: November 2006

Indirect assays are commonly used to measure phytosiderophore (PS) concentrations in the root exudates of grasses. The Cu‐mobilizing, Cu‐CAS and Fe‐binding assays are three commonly used assays but there have been few published attempts to validate or calibrate them rigorously. Thus, we undertook to compare, validate and, where appropriate, to improve and/or optimize each assay. Ethylenediamine‐N,N′‐diacetic acid (EDDA) and N‐2‐hydroxyethylethylenediamine‐N,N′,N′‐triacetic acid (HEDTA) bracket deoxymugineic acid for binding strength with both Fe and Cu and were thus used as model ligands. For the Cu‐mobilizing assay, reasonable regressions (as R2) were obtained between measured and known ligand concentrations for all resin combinations tested. However, the relationship was non‐stoichiometric; less than 5% of the ligand present was recovered as a Cu‐complex. Testing of the Cu‐CAS assay yielded good 1:1 stoichiometric relationships (slopes of 0.97 and 1.08 for EDDA and HEDTA, respectively) with little scatter (R2= 0.97). However, the limits of quantification were approximately 30 μm, which is greater than concentrations generally found in root‐exudate collections. Thus, the Cu‐CAS assay is best suited to situations where large concentrations of PSs are expected. Results from the original Fe‐binding assay indicated a lack of linearity and considerable scatter (R2= 0.57 for EDDA; R2= 0.28 for HEDTA). Thus, as published, use of the original Fe‐binding assay is not recommended. The effects of filter paper, FeCl3 reagent concentration and increase in the reduction time were tested and a revised Fe‐binding assay developed with both good stoichiometry and great precision (R2≥ 0.99). We suggest the use of the revised Fe‐binding assay in most situations where PS concentration would be expected to be < 30 μm.
Lead sorption to selected Portuguese soils
Authors: Trancoso M. A. , Correiados Santos M. M. , Gonçalves M. L. S
Published: November 2006

We studied the interaction of lead with seven Portuguese soils with different physical and chemical properties in order to elucidate more fully the behaviour of Pb in soil. We studied these adsorption phenomena by voltammetric titrations with differential pulse polarography (DPP) at different pH (6.0–7.2) and ionic strengths, I (0.010–0.50 m) in order to clarify some of the factors that might control soil sorption capacity for Pb. From the voltammetric data, average formation constants, , and binding capacity, Cc, have been estimated according to a surface complexation model based on Scatchard and van den Berg–R?zic methods. Linear Scatchard and van den Berg–R?zic plots (r≥ 0.99) indicated that the results can be interpreted according to the existence of just one predominant active site for Pb(II) adsorption. The values from both procedures () agreed in all cases (r= 0.938, n= 66, P < 0.001). The same happened with Cc values that were statistically equivalent (r= 0.9998; n= 66; P < 0.001). The Cc values were found to depend on the pH and I, as well as on the soil properties. Either Langmuir or Freundlich isotherms fitted the experimental data well (r > 0.90, P < 0.05). The lead binding capacities were strongly and significantly correlated (P < 0.05) with pH, cation exchange capacity, organic carbon, loss‐on‐ignition, total Al2O3 content, extractable forms of Al and pyrophosphate extractable Fe, [Fep]. From a forward, stepwise regression model we concluded that [Al2O3], [Pb′] (concentration of labile lead in solution), [Fep], pH and I are able to explain more than 99.7% of the variation in lead sorption in our soils. The soils’ surface groups with special affinity to Pb(II) are in the inorganic fraction associated with aluminium.
From Plinthic Acrisols to Plinthosols and Gleysols: iron and groundwater dynamics in the tertiary sediments of the upper Amazon basin
Authors: Fritsch E. , Herbillon A. J. , Do Nascimento N. R. , Grimaldi M , Melfi A. J.
Published: November 2006

Topography has been reported to be the major factor ruling the spatial distribution of Acrisols, Plinthosols and Gleysols on the seasonally flooded, low elevation plateaux of the upper Amazon basin occupied by Tertiary (Iça & Solimões) sediments. In this study, detailed morphological and mineralogical investigations conducted in a representative 25‐ha site were combined with hydro‐geochemical data to relate the vertical and lateral soil differentiations observed to the hydro‐geological history of that part of the basin. As a result of the uplift of the Andes, several cuts in the extensive Tertiary marshlands have formed, at first, slightly incised plateaux of low elevation. There, weathering under hot and humid climates would have generated a reddish, freely drained and bioturbated topsoil layer and the vertical differentiation in subsoil sediments of a plinthite over an iron‐depleted mottled clay. The second episode of soil differentiation is linked to the replacement of the forest by a savannah under the drier climates of the late Pleistocene, which favours surface runoff and the infill of the incisions by fine particles. This infill, combined with the return to the present humid climate, has then enabled the local groundwater to rise on the plateaux and to generate episaturation at the topsoil/subsoil transition close to the depressions. Nowadays, ferrous iron is released from the partly iron‐depleted topsoil weathering front at high water levels during the rainy seasons. It moves from footslope to low‐lying positions and from top to bottom in the soil profile according to the groundwater dynamics. The present general trend is thus to the lateral export of iron at high water levels due to subsurface and overland flows, its vertical transfer during the recession of the groundwater and accumulation in a nodular plinthite. In the latter, ferrous iron is adsorbed onto its softest iron masses where it feeds the neoformation of ferrihydrite that rapidly dehydrates into haematite.
Bacteria can control stoichiometry and nutrient limitation of phytoplankton
Authors: DANGER M. , OUMAROU C. , BENEST D. , LACROIX G.
Published: November 2006

The chemical composition of primary producers, which occupy the base of food webs, is highly variable over space and time. Determining the causes of these variations is crucial to the understanding of ecosystem functioning.

By differentially stocking and recycling nutrients, heterotrophic organisms such as bacteria may change the nature of the factor that limits algal growth, thus influencing algal chemical composition.

We tested this hypothesis by growing a green alga, Scenedesmus obliquus (Turpin) Kützing, along a phosphorus gradient in the presence or absence of a bacterial community.

We first confirmed that the limiting factor affects the chemical composition of phytoplankton. We then observed that the bacteria switched the nutrient that limited algal growth, from nitrogen to phosphorus in high N : P media. This generated considerable variation in algal stoichiometry.

We propose that the bacterial compartment may have a greater influence on the structure and functioning of aquatic ecosystems than previously believed.