bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil Water Content Determination by Karl Fischer Titration
Authors: Zellis M. K. , Bell J. S. , Prunty Lyle
Published: July 2010

Karl Fischer (KF) titration is a specific analysis for water content. We hypothesized that it may be useful in soils where volatiles besides water are present, since oven drying (OD) determines total volatile components, not water content specifically. We examined KF titration as a technique for soil water content determination. Two soils (a quartz sand separate and Barnes loam [fine‐loamy, mixed Udic Haploboroll]) were prepared with varying known amounts of water (0–240 g kg−1) and a non‐aqueous‐phase liquid (NAPL), either octane or toluene (0–128 g kg−1), then analyzed for water content using both the OD and KF methods. The experimental matrix included all six possible combinations of two soils × three liquids. Soil water contents determined by the calibrated KF method (wc) compared favorably to those determined by OD (wo). Slopes for the six wc vs. wo regressions ranged from 0.980 to 1.009 while intercepts ranged from −0.6 to 7.8 g kg−1. Mean r2 was 0.97 with a range of 0.93 to 0.99. The sand with octane and sand with toluene mixtures had intercepts of 6.1 ± 2.5 and 7.8 ± 5.4 g kg−1 (95% confidence intervals), respectively. All other intercept confidence intervals included zero. Plots of the data show essentially a 1:1 correspondence of wc to wo. Variability was greater when toluene was present, possibly because of toluene's higher vapor pressure.
Cold storage of a tropical soil decreases nitrification potential
Authors: Verchot Louis V.
Published: July 2010

Recommendations for soil handling when determining microbial attributes often include cold storage in the interim between collecting and executing an assay, even if the storage period is likely to be short. Cold storage may not be appropriate for isothermic tropical soils where microbial communities are not adapted to low temperatures. The objective of this experiment was to determine the effects of a short period of cold storage on nitrifying bacterial activity in an Oxisol from eastern Amazonia. Soil samples were collected from primary forest, active pasture, and secondary forest in eastern Amazonia; half were stored at 4°C for 5 d and the other half were incubated immediately. Nitrification potential was determined using a slurry incubation assay. Cold storage reduced the absolute value obtained from the nitrification potential incubationsHowever, relative ranking of the ecosystems was the same for stored and fresh samples. Therefore, storage for short periods at room temperature may be the best treatment for tropical soils. However, when the objective is to obtain a relative index of nitrification, cold storage may simply reduce the sensitivity of the method.
Particulate Organic Matter Composition and Pythium Damping‐Off of Cucumber
Authors: Stone A.G. , Traina S.J. , Hoitink H.A.J.
Published: July 2010

Organic matter–mediated root rot suppression is unpredictable in field soils. This study was conducted to determine whether particulate organic matter (POM) composition and content were related to Pythium damping‐off (DO) incidence in a sand amended with sawdust‐bedded dairy manure compost (15% compost:85% sand, v/v) incubated in pots for 506 d. Suppressive and conducive POM composition was then related to literature values for agricultural and forest soil POM fractions. The suppressive potential of the substrate was determined with a Cucumis sativus L. (cucumber)/Pythium ultimum DO bioassay. Particulate organic matter composition was determined spectroscopically. The compost‐amended sand supported suppression of DO for a period of ∼1 yr. Suppression was sustained by the degradation of the less decomposed coarse and mid‐sized POM fractions. After these fractions stabilized in mass, suppression was lost. Plant constituents were highly degraded during composting before amendment to sand. Compost‐derived POM composition changed little as suppression was supported for 1 yr. In contrast, aromatic and aliphatic contents and alkyl‐ and O‐alkyl C declined as suppression was lost. Suppressive POM was similar in composition to forest soil organic horizons and soil unprotected light fraction (ULF), suggesting that the least‐decomposed soil physical fractions may be the only fractions compositionally capable of supporting suppression of DO in field soils.
Enhancing the Mineralizable Nitrogen Pool Through Substrate Diversity in Long Term Cropping Systems
Authors: Sanchez Jose E. , Willson Thomas C. , Kizilkaya Kadir , Parker Elaine , Harwood Richard R.
Published: July 2010

The development of sustainable N management systems requires a better understanding of the contribution of on‐farm resources to the active N pool size and its mineralization. This study explores the effect of substrate diversity on improving N supply through mineralization. A “diverse system”, consisting of a corn (Zea maysL.)‐corn–soybean (Glycine maxL.)‐wheat (Triticum aestivumL.) rotation with cover crops and fertilized with composted manure was compared with a corn monoculture with conventional fertilizers. Nitrogen mineralization was measured in situ and in laboratory incubations as was the ability of each soil to mineralize added compost and red clover (Trifolium pratense) residue in the 6th and 7th yr of rotation. Net mineralized N in the diverse system was 90 and 40% higher than that in the monoculture at 70 and 150 d of laboratory incubations respectively. Comparable response was found in situ where a 70% higher net mineralization was observed in the diverse system at 70 d. The 70‐ and 150‐d mineralizable N pools increased over time, but the ability of soil organisms to break down additional substrate did not change as a result of system diversity. At 150 d of laboratory incubation, a synergistic effect was observed when 5 Mg ha−1of compost plus 5 Mgha−1of clover was added to either soil. The combination of the two organic materials mineralized more N than the sum of their individual mineralization results. A more diverse cropping system may increase the soil's capacity to supply N to a growing crop while maintaining desirable levels of soil organic matter. This is essential for the overall long‐term productivity and sustainability of agricultural systems.
Comparison of Labile Soil Organic Matter Fractionation Techniques
Authors: McLauchlan Kendra K. , Hobbie Sarah E.
Published: July 2010

Labile soil organic carbon (SOCL), soil organic carbon with a relatively short turnover time, is an important source of energy for the belowground portion of ecosystems and is sensitive to land management changes. Many techniques exist to differentiate and quantify labile SOC, but rarely have these been directly compared. Here we compare the results of four common chemical, physical, and biological methods of empirically measuring labile SOC with soils taken from 33 restored grasslands that differ in length of time since cessation of agriculture. Among sites, microbial biomass C, acid‐hydrolyzable C, the amount of C respired after 12 d of a laboratory incubation, and light fraction carbon (LFC) were all positively correlated with one another, although there were large differences in the sizes of the pools estimated with each method. Acid‐hydrolyzable C consistently provided the largest estimate and 12‐d incubations the smallest estimate of labile SOC. The quantity of labile SOC obtained by fitting respiration data from a laboratory incubation with a two‐pool model with separate decay constants for each pool was also positively correlated with the three measures of labile soil C not derived from respiration data, although this technique was sensitive to whether the decay constant of the recalcitrant pool was constrained or not. All methods showed increases in labile SOC pools with increases in total soil organic carbon (SOCT) pools, although the rate of change varied between techniques. The size of stable aggregates correlated positively with hydrolyzable C and SOCT, supporting the idea that aggregates may physically protect soil C from decomposition, although the degree to which this C is labile is unclear.
Patience and action pays: a comparative analysis of WSS reforms in three East African cities
Authors: Mugisha Silver , Brown Ato
Published: July 2010

There have been significant efforts in the last 15 years to improve performance in water supply and sewerage services (WSS) operations of most cities in Africa. This has called for a number of reforms. WSS utilities in the three East African capital cities have been among the list that has undertaken such reform. Consequently, a number of legislative, institutional and managerial reforms, all aimed at creating good enabling environments to drive performance, have been undertaken. This paper outlines some of these reforms in WSS operations of the three capital cities of Kampala, Nairobi and Dar es Salaam. We present, amongst other things, the key reform drivers, reforms undertaken, achievements and underlying success factors. We conclude that there is need to synergise the use of incentives, strong leadership, managerial autonomy and accountability as important buttresses for successful reforms. In doing all this, political support and, indeed, support from other stakeholders is important. We also note that reforms need time, adequate stakeholder mapping and incorporation of significant local capacity development to be fully effective.
Progressionism in the 1850s: Lyell, Owen, Mantell and the Elgin fossil reptile Leptopleuron (Telerpeton)
Authors: BENTON MICHAEL J.
Published: July 2010

The advanced fossil reptile Leptopleuron (Telerpeton), collected in 1851 from supposedly Old Red Sandstone rocks near Elgin, northern Scotland, was regarded by Charles Lyell as good evidence for his anti-progressionist views. The specimen was sent to London to be described by Richard Owen, who published a brief account of it. Gideon Mantell then published a longer description of the same specimen, apparently at the request of its discoverer. The general opinion, then and now, has been that Owen acted badly, as he apparently did in other cases, because of his personal enmity towards both Lyell and Mantell. However, new evidence from previously unpublished archive materials shows that Lyell urged the ailing Mantell to produce a description at speed, in full knowledge that Owen was also doing so. Leptopleuron was almost the last piece of evidence that Lyell proposed as evidence against progressionism, and he was happy to accept its true Triassic age by 1860, by which time he was a progressionist and grudging evolutionist.
Miller's Gardeners Dictionary: some inconsistencies between editions
Authors: TJADEN W. L.
Published: July 2010

SUMMARY

Some unexplained changes in Philip Miller's statements on certain amaryllid species occur between the first four folio editions and later editions of the Gardeners Dictionary. His later editions made mistakes absent from his earlier ones. Miller expected too much of Linnaeus. He misread him on one species (Amaryllis belladonna) and misled him on another (A. reginae). Miller also stated that a drawing and a pamphlet had been prepared by James Douglas on the latter species: neither have been found. Finally, the earliest descriptions of the Cape Belladonna Lily, by G. B. Ferrari are discussed.
Walking the swards: medical education and the rise and spread of the botanical field class
Authors: ALLEN D. E.
Published: July 2010

Physic gardens expressly for teaching medical students to recognise herbs in the living state originated in northern Italy in 1543 and became a facility to which Europe's leading universities increasingly aspired. In default of one, the practice arose of taking students into the countryside instead; but that depended on there being a teacher who was also a keen field botanist. In the seventeenth century Paris, London and Edinburgh replaced Montpellier and Basle as the principal centres of this more informal approach, which eventually had one or two commercial imitators as well. When stricter qualifications governing medical practice in Britain induced a great expansion of medical schools there after 1815 student excursions were taken in Scotland to new heights of popularity and ambitiousness. Having originated in a need to protect future practitioners from being duped by their suppliers, field classes ended up by generating the publication of floras, a market for botanical collecting equipment and, above all, a simpler model for local associations of naturalists which liberated them from an inherited organisational straitjacket.
“A most glorious country”: Charles Darwin and North Wales, especially his 1831 geological tour
Authors: LUCAS PETER
Published: July 2010

Darwin's tour with Adam Sedgwick in 1831, the last of some 14 Welsh visits before the Beagle voyage, divides into three periods: a week, mostly with Sedgwick, from 5 August; a middle period ending by 20 August, when Sedgwick left Anglesey; and a final period during which Darwin spent some days in Barmouth, reaching Shrewsbury on 29 August. His activities are well documented, for the first period, through both men's geological notes and, for the last, in the journal of the Lowe brothers (showing Darwin reaching Barmouth from Ffestiniog on 23 August and parting from Robert Lowe on 29 August). For the middle period the circumstantial evidence points to Anglesey: whether Darwin's writings show any first hand knowledge of the island needs further examination. Robert Lowe was one of Darwin's most gifted contemporaries; his „early hero-worship” enhances the conventional picture of Darwin on the eve of the voyage. After his return to North Wales in 1842, to investigate the effects of glacial action, Darwin saw the tour as illustrating the futility of observations outside of any adequate theoretical framework.
Catalytic Asymmetric Intramolecular Cascade Reaction for the Construction of Functionalized Benzobicyclo[4.3.0] Skeletons. Remote Control of Enantioselectivity
Authors: Wang Qing‐Gang , Zhu Shou‐Fei , Ye Long‐Wu , Zhou Chang‐Yue , Sun Xiu‐Li , Tang Yong , Zhou Qi‐Lin
Published: July 2010

A catalytic asymmetric version of the intramolecular ylide annulation has been developed which affords high ee values and diastereoselectivities and which further shows that spirobiindane‐based chiral phosphines can be excellent organocatalysts. Both optically active benzobicyclo[4.3.0] compounds 2 and 2′ with three continuous stereogenic centers could be obtained as major products selectively under neutral and mild conditions just by a choice of an additive.
Novel Ladder π‐Conjugated Materials—Sila‐Pentathienoacenes: Synthesis, Structure, and Electronic Properties
Authors: Wan Jun‐Hua , Fang Wei‐Fen , Li Zhi‐Fang , Xiao Xu‐Qiong , Xu Zheng , Deng Yuan , Zhang Li‐Hong , Jiang Jian‐Xiong , Qiu Hua‐Yu , Wu Lian‐Bin , Lai Guo‐Qiao
Published: July 2010

A novel series of ladder π‐conjugated materials—sila‐pentathienoacenes (Si‐PTA) are synthesized and characterized. Crystal structures of the compounds show that the length of alkyl chains substituting on the thiophene ring has a significant influence on molecular packing. A densely packed structure with an interfacial distance of about 3.66 Å between the adjacent molecules is observed for the compound with shorter alkyl chains. However, a large interfacial distance (7.99 Å) is obtained for another compound because of the insertion of long alkyl chains between two planes. The investigation of the optical and electrochemical properties shows that the silylene bridge incorporated into the pentathienoacene framework exerts a clear effect on the electronic properties by the σ*–π* conjugation. Although only a slight enhancement is observed for the HOMO levels, with respect to that of pentathienoacene, the LUMO levels are significantly lowered. The observed electronic properties are consistent with the theoretical calculations.
Synthesis of β‐Methoxyacrylate Natural Products Based on Box‐PdII‐Catalyzed Intermolecular Methoxycarbonylation of Alkynoles
Authors: Motodate Satoshi , Kobayashi Takuya , Fujii Mikio , Mochida Tomoyuki , Kusakabe Taichi , Katoh Shigeki , Akita Hiroyuki , Kato Keisuke
Published: July 2010

Bis(oxazoline)‐palladium(II) catalyzed carbonylation of homopropargyl alcohols afforded acyclic methoxyacrylate 2 and 6‐membered lactone 3a, 3b, 3d, 3e, 3f, 3g, 3h, 3i, 3j, 3k in good combined yield. In the case of propargyl alcohols, 5‐membered lactones 3p, 3q, 16 were obtained in moderate yields. The one‐pot synthesis of kawa lactones 3a, 3r, 3s and formal synthesis of dihydroxycystothiazole A and dihydroxycystothiazole C are presented. To elucidate the stereochemistry of (+)‐annularin G and (−)‐annularin H, the first asymmetric syntheses of these natural products were achieved.
Transient expression of antibodies in suspension plant cell suspension cultures is enhanced when co‐transformed with the tomato bushy stunt virus p19 viral suppressor of gene silencing
Authors: Boivin Eric B. , Lepage Étienne , Matton Daniel P. , De Crescenzo Gregory , Jolicoeur Mario
Published: July 2010

Two distinct transient expression approaches were compared with assess the impact of the viral suppressor p19 on a recombinant protein production performed in Nicotiana benthamiana suspension culture. A parental N. benthamiana cell line was transiently transformed with either an Agrobacterium containing a gene construct for a murine IgG1 (R514) or concurrently with two Agrobacteria containing R514 or p19. In addition, a stably transformed N. benthamiana cell line that constitutively expresses p19 was transformed with R514‐containing Agrobacterium. The parental N. benthamiana cell line that had been co‐cultivated with both p19 and R514 achieved the highest yield of IgG1 (1.06 mg IgG1/kg FW; 0.024% TSP) compared with that obtained without p19 (0.61 mg IgG1/kg FW; 0.014% TSP). The N. benthamiana cell line that had been stably transformed with p19 only reached 0.25 mg IgG1/kg FW (0.009% TSP) when co‐cultured with R514‐containing Agrobacterium. Dual agroinfiltration of N. benthamiana leaves with p19 and R514 was also performed to assess for Agrobacteria efficiencies and 147.7 mg IgG1/kg FW were obtained. Therefore, our results demonstrate that transient co‐transformation of plant cell suspension culture with two transformation vectors is feasible and that the use of the viral suppressor of silencing p19 significantly raises the production of the protein of interest. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010
Applied Biotransformations in Green Solvents
Authors: Hernáiz María J. , Alcántara Andrés R. , García José I. , Sinisterra José V.
Published: July 2010

The definite interest in implementing sustainable industrial technologies has impelled the use of biocatalysts (enzymes or cells), leading to high chemo‐, regio‐ and stereoselectivities under mild conditions. As usual substrates are not soluble in water, the employ of organic solvents is mandatory. We will focus on different attempts to combine the valuable properties of green solvents with the advantages of using biocatalysts for developing cleaner synthetic processes.
The molecular pathogenesis of hereditary ovarian carcinoma
Authors: Norquist Barbara M. , Garcia Rochelle L. , Allison Kimberly H. , Jokinen Chris H. , Kernochan Lauren E. , Pizzi Catherine C. , Barrow Bethany J. , Goff Barbara A. , Swisher Elizabeth M.
Published: July 2010

BACKGROUND:

BRCA1 or BRCA2 (BRCA1/2)‐mutated ovarian carcinomas may originate in the fallopian tube. The authors of this report investigated alterations in BRCA1/2 tubal epithelium to define the molecular pathogenesis of these carcinomas.

METHODS:

Tubal epithelium was evaluated from 31 BRCA1/2 mutation carriers with gynecologic carcinomas (BRCA CA), 89 mutation carriers who underwent risk‐reducing salpingo‐oophorectomy (RRSO), and 87 controls. Ki‐67 expression and p53 foci (≥10 of 12 consecutive staining cells) were scored by 2 investigators who were blinded to patient designations. Expression levels of p27 and p21 were evaluated within p53 foci. Loss of heterozygosity at the BRCA1/2 mutation site was evaluated in microdissected p53 foci and tubal neoplasms.

RESULTS:

Background tubal proliferation as measured by Ki‐67 staining was increased in the BRCA1 RRSO group (P = .005) compared with the control group. Women who had BRCA1/2 mutations had more p53 foci identified per tubal segment than women in the control group (P = .02). Levels of p27 were decreased in 12 of 28 p53 foci from women with BRCA1 mutations and in 0 of 16 p53 foci from controls (P = .002). There was no loss of the wild type BRCA1/2 allele in 5 tested p53 foci. Tubal neoplasia lost the wild type allele in 6 of 6 foci (P = .002).

CONCLUSIONS:

The current results suggested a model of tubal carcinogenesis in women with BRCA1/2 mutations. Increased proliferation occurred globally in at‐risk tubal epithelium. A mutation in the tumor protein p53 gene TP53 with clonal proliferation and loss of p27 occurred before neoplastic proliferation. Loss of the wild type BRCA1/2 allele occurred with neoplastic proliferation and before invasion. Cancer 2010. © 2010 American Cancer Society.
The X1s Method for Accurate Bond Dissociation Energies
Authors: Wu Jianming , Ying Zhang Igor , Xu Xin
Published: July 2010

Previously, we have put forward the X1 method that combines B3LYP with neural network correction for an accurate yet efficient prediction of thermochemistry. Without paying additional computational cost, X1 reduces B3LYP’s mean absolute deviation (MAD) for a set of 92 bond dissociation energies (BDEs) from 5.5 to 2.4 kcal mol−1. In this work, we extend X1 and propose the X1s method by including the spin change from molecules to atoms during atomization as an additional descriptor. X1s further reduces the MAD for BDEs to 1.4 kcal mol−1, thus showing substantial improvement.
Procedural learning and dyslexia
Authors: Nicolson R. I. , Fawcett A. J. , Brookes R. L. , Needle J.
Published: July 2010

Three major ‘neural systems’, specialized for different types of information processing, are the sensory, declarative, and procedural systems. It has been proposed (Trends Neurosci.,30(4), 135–141) that dyslexia may be attributable to impaired function in the procedural system together with intact declarative function. We provide a brief overview of the increasing evidence relating to the hypothesis, noting that the framework involves two main claims: first that ‘neural systems’ provides a productive level of description avoiding the underspecificity of cognitive descriptions and the overspecificity of brain structural accounts; and second that a distinctive feature of procedural learning is its extended time course, covering from minutes to months. In this article, we focus on the second claim. Three studies—speeded single word reading, long‐term response learning, and overnight skill consolidation—are reviewed which together provide clear evidence of difficulties in procedural learning for individuals with dyslexia, even when the tasks are outside the literacy domain. The educational implications of the results are then discussed, and in particular the potential difficulties that impaired overnight procedural consolidation would entail. It is proposed that response to intervention could be better predicted if diagnostic tests on the different forms of learning were first undertaken. Copyright © 2010 John Wiley & Sons, Ltd.
Interaction of phonological awareness and ‘magnocellular’ processing during normal and dyslexic reading: behavioural and fMRI investigations
Authors: Heim Stefan , Grande Marion , Pape‐Neumann Julia , van Ermingen Muna , Meffert Elisabeth , Grabowska Anna , Huber Walter , Amunts Katrin
Published: July 2010

We investigated whether phonological deficits are a consequence of magnocellular processing deficits in dyslexic and control children. In Experiment 1, children were tested for reading ability, phonological awareness, visuo‐magnocellular motion perception, and attention shifting (sometimes considered as magnocellular function). A two‐step cluster analysis of the behavioural scores revealed four clusters of children. Phonological awareness was correlated with attention (cluster ♯1) or motion detection (cluster ♯2), whereas attention and motion detection were correlated in cluster ♯3. In cluster ♯4, all variables were uncorrelated. In Experiment 2, the same variables plus auditory discrimination were tested with fMRI in a sub‐sample of Experiment 1. Although dyslexics had reduced activation in visual or auditory cortex during motion detection or auditory discrimination, respectively, they had increased right frontal activation in areas 44 and 45 in all ‘magnocellular’ (including auditory) tasks. In contrasts, during phonological decisions, there was higher activation for good readers than dyslexics in left areas 44 and 45. Together, the two experiments give insight into the interplay of phonological and magnocellular processing during reading. Distinct left versus right frontal effects reveal partly different underlying neural mechanisms. These data contradict the view that phonological processing deficits in dyslexia necessarily result from impaired magnocellular functioning. Copyright © 2010 John Wiley & Sons, Ltd.
Formal Total Synthesis of (–)‐Raphidecursinol B
Authors: Kumar Das Sanjit , Kumar Das Sajal , Panda Gautam
Published: July 2010

An efficient enantioselective formal total synthesis of antimalarial natural product (–)‐raphidecursinol B along with its all stereoisomers is described from commercially available 3,4,5‐trimethoxybenzaldehyde using the Sharpless asymmetric dihydroxylation, regioselective α‐tosylation, epoxide opening and Mitsunobu reaction as the key reaction steps.
2‐Substituted Benzo[b]furans from (E)‐1,2‐Dichlorovinyl Ethers and Organoboron Reagents: Scope and Mechanistic Investigations into the One‐Pot Suzuki Coupling/Direct Arylation
Authors: Geary Laina M. , Hultin Philip G.
Published: July 2010

2‐Substituted benzo[b]furans can easily be assembled from simple phenols, boronic acids or other organoboron reagents, and trichloroethylene. The overall process requires only two synthetic steps, with the key step being a one‐pot sequential Suzuki cross‐coupling/direct arylation reaction. The method tolerates many useful functional groups and does not require the installation of any other activating functionality. The modular nature of the process permits the rapid synthesis of many analogues using essentially the same chemistry, of particular value in drug development. Results of kinetic isotope effect studies and investigations into the regioselectivity of the process indicate that the direct arylation step most likely does not involve an electrophilic palladation. The most likely mechanism lies somewhere on the continuum between a C–H bond metathesis and an assisted palladation or concerted metallation‐deprotonation pathway.
What differs in visual recognition of handwritten vs. printed letters? An fMRI study
Authors: Longcamp Marieke , Hlushchuk Yevhen , Hari Riitta
Published: July 2010

In models of letter recognition, handwritten letters are considered as a particular font exemplar, not qualitatively different in their processing from printed letters. Yet, some data suggest that recognizing handwritten letters might rely on distinct processes, possibly related to motor knowledge. We applied functional magnetic resonance imaging to compare the neural correlates of perceiving handwritten letters vs. standard printed letters. Statistical analysis circumscribed to frontal brain regions involved in hand‐movement triggering and execution showed that processing of handwritten letters is supported by a stronger activation of the left primary motor cortex and the supplementary motor area. At the whole‐brain level, additional differences between handwritten and printed letters were observed in the right superior frontal, middle occipital, and parahippocampal gyri, and in the left inferior precentral and the fusiform gyri. The results are suggested to indicate embodiment of the visual perception of handwritten letters. Hum Brain Mapp, 2011. © 2010 Wiley‐Liss, Inc.
Multicentre validation of a prognostic index for overall survival in chronic lymphocytic leukaemia
Authors: Bulian Pietro , Tarnani Michela , Rossi Davide , Forconi Francesco , Del Poeta Giovanni , Bertoni Francesco , Zucca Emanuele , Montillo Marco , Pozzato Gabriele , Deaglio Silvia , D'Arena Giovanni , Efremov Dimitar , Marasca Roberto , Lauria Francesco , Gattei Valter , Gaidano Gianluca , Laurenti Luca
Published: July 2010

We wish to validate in a multicentric CLL population a nomogram and a risk score recently developed to predict overall survival (OS). Complete records from 1037 CLL patients were retrospectively collected to estimate OS and time to treatment (TTT). Cox models were used to test the independence of age, β‐2‐microglobulin, absolute lymphocyte count (ALC), sex, Rai stage and number of involved lymph node regions (LNR). Accuracy of prognostic models was tested with the concordance index (c‐index). Median follow‐up was 5.5 years, with 151 deaths and 475 treated patients. Median OS was not reached (65% survival rate at 13.9 years), median TTT was 6 years. We confirmed the ability of the prognostic score to predict OS and TTT in three risk groups, with results comparable with those reported in the original report. However, ALC and Rai stage were not independent predictors, whereas the Binet staging system, which incorporates LNR variable, showed independent predictive power; furthermore, both 5‐ and 10‐year OS estimates from nomogram were lower compared to real data. When separately analysed, the impact of therapy on OS was not selected as independent predictor of OS in our series. According to these results, we proposed a simpler four‐variable model (age, sex, Binet staging, β‐2‐microglobulin) and a new nomogram. This model had a c‐index of 0.78 versus 0.76 of the six‐variable model (p = 0.043), showing better predictive accuracy. External validation and refinement are needed on independent data sets, possibly from cancer registry patients' series. Copyright © 2010 John Wiley & Sons, Ltd.
Cell‐penetrating chitosan/doxorubicin/TAT conjugates for efficient cancer therapy
Authors: Lee Jue‐Yeon , Choi Young‐Suk , Suh Jin‐Sook , Kwon Young‐Min , Yang Victor C. , Lee Seung‐Jin , Chung Chong‐Pyoung , Park Yoon‐Jeong
Published: July 2010

In this study, a cell‐penetrating peptide, the transactivating transcriptional factor (TAT) domain from HIV, was linked to a chitosan/doxorubicin (chitosan/DOX) conjugate to form a chitosan/DOX/TAT hybrid. The synthesized chitosan/DOX/TAT conjugate showed a different intracellular distribution pattern from a conjugate without TAT. Unlike both free DOX and the conjugate without TAT, the chitosan/DOX/TAT conjugate was capable of efficient cell entry. The chitosan/DOX/TAT conjugate was found to be highly cytotoxic, with an IC50 value of approximately 480 nM, 2 times less than that of chitosan/DOX (980 nM). The chitosan/DOX/TAT provided decreases in tumor volume of 77.4 and 57.5% compared to free DOX and chitosan/DOX, respectively, in tumor‐bearing mice. Therefore, this study suggests that TAT‐mediated chitosan/DOX conjugate delivery is effective in slowing tumor growth.
Impact of diabetes mellitus on incidence of hepatocellular carcinoma in chronic hepatitis C patients treated with interferon‐based antiviral therapy
Authors: Hung Chao‐Hung , Lee Chuan‐Mo , Wang Jing‐Houng , Hu Tsung‐Hui , Chen Chien‐Hung , Lin Chih‐Yun , Lu Sheng‐Nan
Published: July 2010

There is strong evidence linking chronic hepatitis C virus (HCV) infection and Type 2 diabetes mellitus (DM). Recent studies have suggested that DM is associated with increased risk of developing hepatocellular carcinoma (HCC). The aim of our cohort study was to assess whether DM influence the incidence of HCC in chronic hepatitis C patients treated with interferon (IFN)‐based antiviral therapy. A total of 1,470 chronic hepatitis C patients treated with IFN or pegylated‐IFN plus ribavirin therapy were enrolled. Of them, 253 (17%) patients had DM at entry. Evaluation of HCC incidence was performed by Kaplan–Meier method and Cox proportional hazards analysis. Patients with baseline DM were significantly older and had higher body mass index, serum transaminase levels and fibrosis scores and lower platelet counts compared to non‐DM subjects. Sustained virological response (SVR) was achieved in 160 (63%) of DM and 867 (71%) of non‐DM patients (p = 0.008). During a median follow‐up period of 4.3 years, HCC developed in 21 (8.3%) of DM and 66 (5.4%) of non‐DM patients (p = 0.017). However, DM was not an independent covariate by Cox proportional hazards analysis. In a subgroup analysis, DM (hazard ratio, 4.32; 95% confidence interval, 1.23–15.25; p = 0.023) was an independent predictor of HCC in the SVR patients without baseline cirrhosis, despite a low HCC incidence. In conclusion, DM has a selective impact on HCC development among chronic hepatitis C patients after IFN‐based therapy. DM may increase the HCC risk in chronic hepatitis C without cirrhosis after eradication of HCV.
A water soluble parthenolide analog suppresses in vivo tumor growth of two tobacco‐associated cancers, lung and bladder cancer, by targeting NF‐κB and generating reactive oxygen species
Authors: Shanmugam Rajasubramaniam , Kusumanchi Praveen , Appaiah Hitesh , Cheng Liang , Crooks Peter , Neelakantan Sundar , Peat Tyler , Klaunig James , Matthews William , Nakshatri Harikrishna , Sweeney Christopher J.
Published: July 2010

Dimethylaminoparthenolide (DMAPT) is a water soluble parthenolide analog with preclinical activity in hematologic malignancies. Using non–small lung cancer (NSCLC) cell lines (A549 and H522) and an immortalized human bronchial epithelial cell line (BEAS2B) and TCC cell lines (UMUC‐3, HT‐1197 and HT‐1376) and a bladder papilloma (RT‐4), we aimed to characterize DMAPT's anticancer activity in tobacco‐associated neoplasms. Flow cytometric, electrophoretic mobility gel shift assays (EMSA), and Western blot studies measured generation of reactive oxygen species (ROS), inhibition of NFκB DNA binding, and changes in cell cycle distribution and apoptotic proteins. DMAPT generated ROS with subsequent JNK activation and also decreased NFκB DNA binding and antiapoptotic proteins, TRAF‐2 and XIAP. DMAPT‐induced apoptotic cell death and altered cell cycle distribution with upregulation of p21 and p73 levels in a cell type–dependent manner. DMAPT suppressed cyclin D1 in BEAS2B. DMAPT retained NFκB and cell cycle inhibitory activity in the presence of the tobacco carcinogen nitrosamine ketone, 4(methylnitrosamino)‐1‐(3–pyridyl)‐1‐butanone (NNK). Using a BrdU accumulation assay, 5–20 μM of DMAPT was shown to inhibit cellular proliferation of all cell lines by more than 95%. Oral dosing of DMAPT suppressed in vivo A549 and UMUC‐3 subcutaneous xenograft growth by 54% (p = 0.015) and 63% (p < 0.01), respectively, and A549 lung metastatic volume by 28% (p = 0.043). In total, this data demonstrates DMAPT's novel anticancer properties in both early and late stage tobacco‐associated neoplasms as well as its significant in vivo activity. The data provides support for the conduct of clinical trials in TCC and NSCLC.
Notch as a molecular switch in neural stem cells
Authors: Zhou Zhi‐Dong , Kumari Udhaya , Xiao Zhi‐Cheng , Tan Eng‐King
Published: July 2010

Notch signaling pathway, originally discovered in Drosophila, impinges on a wide array of cellular processes including cell proliferation, cell differentiation, and cell apoptosis. Recent accumulating evidences implicated the important roles of Notch signal pathway in different aspects of stem cell biology of neural stem cell (NSC). In vivo and in vitro studies illustrated that Notch signal pathway could promote gliogenesis, inhibit premature neurogenesis, and be involved in self‐renew of NSC. This short review summarizes the roles of the Notch signaling pathway on gliogenesis, neurogenesis, and self‐renew of NSC and their underlying molecular mechanisms. © 2010 IUBMB IUBMB Life, 62(8): 618–623, 2010.
Hypoxia regulates the ferrous iron uptake and reactive oxygen species level via divalent metal transporter 1 (DMT1) Exon1B by hypoxia‐inducible factor‐1
Authors: Wang Dan , Wang Li‐Hong , Zhao Yu , Lu Ya‐Peng , Zhu Li
Published: July 2010

Hypoxia has been shown to increase the expression of a variety of proteins involved in iron homeostasis, including ceruloplasmin, transferrin, and transferring receptor. Divalent metal transporter 1 (DMT1) is a transmembrane protein that is important in divalent metal ion transport, in particular iron. Although previous studies have provided that DMT1 exon1A is regulated by hypoxia, little is known about the relationship between DMT1 exon1B and hypoxia. Hypoxia‐inducible factor 1 (HIF‐1) is a transcription factor which is stabilized when mammalian cells are subjected to hypoxia. In this study, we have identified a functional hypoxia‐response element (HRE) at position of −327 to −323 (‐ACGTG‐) in DMT1 exon1B promoter using a combination of bioinformatics and biological approaches. Both the total cellular iron and ferrous uptake increased after hypoxia, decreased after DMT1 RNA interference. Reactive oxygen species (ROS) were also changed by +iron responsive element (IRE) DMT1 exon1B overexpression. These findings implicated DMT1 exon1B was a target gene for HIF‐1. Hypoxia might affect cellular iron uptake through regulating the expression of DMT1. When iron was present in excess, cells might be damaged by the ROS production. © 2010 IUBMB IUBMB Life, 62(8): 629–636, 2010.
Calcium channel blocker use and risk of Parkinson's disease
Authors: Simon Kelly Claire , Gao Xiang , Chen Honglei , Schwarzschild Michael A. , Ascherio Alberto
Published: July 2010

We investigated whether the use of calcium channel blockers (CCBs) was associated with a reduced risk of Parkinson's disease (PD) in two large prospective cohorts: the Nurses' Health Study (NHS) and Health Professionals' Follow‐Up Study (HPFS). Cox proportional hazards models were used to estimate relative risks (RRs) and 95% confidence intervals (CIs) to assess the association between use of CCBs and risk of PD adjusting for potential confounders. We identified 514 incident cases of PD during follow‐up. No association between baseline use of CCBs (RR = 1.18, 95% CI: 0.73–1.92), frequency of use or duration of use of CCBs and PD risk was observed (P > 0.2 for all). These findings do not support a role for CCBs in providing neuroprotection against development of PD. © 2010 Movement Disorder Society
A proton NMR study on the hydration of normal versus psoriatic stratum corneum: linking distinguishable reservoirs to anatomical structures
Authors: Laule Cornelia , Tahir Sumia , Chia Charmaine L. L. , Vavasour Irene M. , Kitson Neil , MacKay Alex L.
Published: July 2010

The NMR behaviour of normal and psoriatic stratum corneum (SC) was investigated as a function of hydration with the aim of obtaining a better understanding of the role of water in the SC structure. Time domain NMR techniques were employed to identify the signal from water and that from nonaqueous components of the SC, such as lipids and proteins. The signals were investigated as a function of water content. The free induction decay was separated into mobile signal (from water and mobile lipids) and solid signal (from protein and 'solid' lipids). Spin–spin relaxation (T2) measurements further separated the mobile domains within the SC. The results suggested that, when water is added to dry SC, it first enters the corneocytes; then, at a hydration of 0.24–0.33 g H2O/g SC (normal SC) or 0.12–0.24 g H2O/g SC (psoriatic SC), water begins to accumulate in hydrated lipid regions. Water was found to exchange between these two domains on the time scale of a few hundred milliseconds. When compared with normal SC, psoriatic SC had a looser corneocyte structure, a larger mobile lipid component at low hydration and a smaller capacity for corneocyte water. Copyright © 2010 John Wiley & Sons, Ltd.
Determination of the X‐ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography
Authors: Banigan James R. , Mandal Kalyaneswar , Sawaya Michael R. , Thammavongsa Vilasak , Hendrickx Antoni P. A. , Schneewind Olaf , Yeates Todd O. , Kent Stephen B. H.
Published: July 2010

The 50‐residue snake venom protein L‐omwaprin and its enantiomer D‐omwaprin were prepared by total chemical synthesis. Radial diffusion assays were performed against Bacillus megaterium and Bacillus anthracis; both L‐ and D‐omwaprin showed antibacterial activity against B. megaterium. The native protein enantiomer, made of L‐amino acids, failed to crystallize readily. However, when a racemic mixture containing equal amounts of L‐ and D‐omwaprin was used, diffraction quality crystals were obtained. The racemic protein sample crystallized in the centrosymmetric space group P21/c and its structure was determined at atomic resolution (1.33 Å) by a combination of Patterson and direct methods based on the strong scattering from the sulfur atoms in the eight cysteine residues per protein. Racemic crystallography once again proved to be a valuable method for obtaining crystals of recalcitrant proteins and for determining high‐resolution X‐ray structures by direct methods.
Helicity of short E‐R/K peptides
Authors: Sommese Ruth F. , Sivaramakrishnan Sivaraj , Baldwin Robert L. , Spudich James A.
Published: July 2010

Understanding the secondary structure of peptides is important in protein folding, enzyme function, and peptide‐based drug design. Previous studies of synthetic Ala‐based peptides (>12 a.a.) have demonstrated the role for charged side chain interactions involving Glu/Lys or Glu/Arg spaced three (i, i + 3) or four (i, i + 4) residues apart. The secondary structure of short peptides (<9 a.a.), however, has not been investigated. In this study, the effect of repetitive Glu/Lys or Glu/Arg side chain interactions, giving rise to E‐R/K helices, on the helicity of short peptides was examined using circular dichroism. Short E‐R/K–based peptides show significant helix content. Peptides containing one or more E‐R interactions display greater helicity than those with similar E‐K interactions. Significant helicity is achieved in Arg‐based E‐R/K peptides eight, six, and five amino acids long. In these short peptides, each additional i + 3 and i + 4 salt bridge has substantial contribution to fractional helix content. The E‐R/K peptides exhibit a strongly linear melt curve indicative of noncooperative folding. The significant helicity of these short peptides with predictable dependence on number, position, and type of side chain interactions makes them an important consideration in peptide design.
Non‐3D domain swapped crystal structure of truncated zebrafish alphaA crystallin
Authors: Laganowsky A. , Eisenberg D.
Published: July 2010

In previous work on truncated alpha crystallins (Laganowsky et al., Protein Sci 2010; 19:1031–1043), we determined crystal structures of the alpha crystallin core, a seven beta‐stranded immunoglobulin‐like domain, with its conserved C‐terminal extension. These extensions swap into neighboring cores forming oligomeric assemblies. The extension is palindromic in sequence, binding in either of two directions. Here, we report the crystal structure of a truncated alphaA crystallin (AAC) from zebrafish (Danio rerio) revealing C‐terminal extensions in a non three‐dimensional (3D) domain swapped, “closed” state. The extension is quasi‐palindromic, bound within its own zebrafish core domain, lying in the opposite direction to that of bovine AAC, which is bound within an adjacent core domain (Laganowsky et al., Protein Sci 2010; 19:1031–1043). Our findings establish that the C‐terminal extension of alpha crystallin proteins can be either 3D domain swapped or non‐3D domain swapped. This duality provides another molecular mechanism for alpha crystallin proteins to maintain the polydispersity that is crucial for eye lens transparency.
Oligomerization state and supramolecular structure of the HIV‐1 Vpu protein transmembrane segment in phospholipid bilayers
Authors: Lu Jun‐Xia , Sharpe Simon , Ghirlando Rodolfo , Yau Wai‐Ming , Tycko Robert
Published: July 2010

HIV‐1 Vpu is an 81‐residue protein with a single N‐terminal transmembrane (TM) helical segment that is involved in the release of new virions from host cell membranes. Vpu and its TM segment form ion channels in phospholipid bilayers, presumably by oligomerization of TM helices into a pore‐like structure. We describe measurements that provide new constraints on the oligomerization state and supramolecular structure of residues 1–40 of Vpu (Vpu1–40), including analytical ultracentrifugation measurements to investigate oligomerization in detergent micelles, photo‐induced crosslinking experiments to investigate oligomerization in bilayers, and solid‐state nuclear magnetic resonance measurements to obtain constraints on intermolecular contacts between and orientations of TM helices in bilayers. From these data, we develop molecular models for Vpu TM oligomers. The data indicate that a variety of oligomers coexist in phospholipid bilayers, so that a unique supramolecular structure can not be defined. Nonetheless, since oligomers of various sizes have similar intermolecular contacts and orientations, molecular models developed from our data are most likely representative of Vpu TM oligomers that exist in host cell membranes.
Structural and functional characterization of Salmonella enterica serovar Typhimurium YcbL: An unusual Type II glyoxalase
Authors: Stamp Anna L. , Owen Paul , El Omari Kamel , Nichols Charles E. , Lockyer Michael , Lamb Heather K. , Charles Ian G. , Hawkins Alastair R. , Stammers David K.
Published: July 2010

YcbL has been annotated as either a metallo‐β‐lactamase or glyoxalase II (GLX2), both members of the zinc metallohydrolase superfamily, that contains many enzymes with a diverse range of activities. Here, we report crystallographic and biochemical data for Salmonella enterica serovar Typhimurium YcbL that establishes it as GLX2, which differs in certain structural and functional properties compared with previously known examples. These features include the insertion of an α‐helix after residue 87 in YcbL and truncation of the C‐terminal domain, which leads to the loss of some recognition determinants for the glutathione substrate. Despite these changes, YcbL has robust GLX2 activity. A further difference is that the YcbL structure contains only a single bound metal ion rather than the dual site normally observed for GLX2s. Activity assays in the presence of various metal ions indicate an increase in activity above basal levels in the presence of manganous and ferrous ions. Thus, YcbL represents a novel member of the GLX2 family.