bluuebunny/crossref_metadata_2025 huggingface dataset:
Flour, starch and composite breadmaking quality of various cassava clones
Authors: Eggleston Gillian , Omoaka Paulyn E , Arowshegbe Aduni U
Published: October 2006

Bread was made using a straight‐dough baking process from a local soft wheat flour partially substituted at four levels with flour from nine different cassava (Manihot esculenta, Crantz) clones. The physicochemical properties of the blended flouts, including starch quality, were determined and related to dough rheology, bread volume and crumb characteristics. Breadmaking quality at substitution levels of 100 and 200 g kg−1 of mixed flour was reliably predicted from the cassava flour diastatic activity only. Flours with relatively high diastatic activities, ie above ∼ 145 mg of maltose, had deleterious breadmaking effects. Baking absorption effects were more critical at substitution levels of 300 and 400 g kg−1. Cassava flour diastatic activity was highly dependent on the moisture contents of the respective tuberous roots, and affected the extent of starch gelatinisation in the breadcrumbs.
A critical introduction to mathematical modelling of the aerobic deterioration of silage
Authors: Ruxton G D , Gibson G J
Published: October 2006

The last 3 years have seen the publication of a number of papers featuring mathematical models of the aerobic deterioration silage. Here, we provide an overview of this work. A brief summary is given of the reasons why quantitative understanding of the mechanisms behind aerobic deterioration is of interest. We discuss the use of modelling as an investigative tool, considering the modelling approaches which have been used and the limitations of these approaches. The previous publications in this field are considered chronologically. We describe each in depth, highlighting the assumptions they embody and their relation to each other. A highly‐simplified model is used to demonstrate shortcomings common to all the models described previously. The paper concludes by discussing the most interesting questions yet to be answered in this field and suggests some possible strategies for tackling them.
Effect of alkali halides on α‐chymotrypsin activity in the plastein reaction
Authors: Lozano Pedro , Combes Didier
Published: October 2006

The influence of different alkali halides (LiF, LiCl. LiBr, NaF, NaCl, NaBr, KF, KCl and KBr) on α‐chymotrypsin‐catalysed plastein synthesis has been studied in aqueous medium at different substrate concentrations. The results showed an enhancing effect on the plastein synthesis enzyme action by the presence of salts, proportional to salt concentration, which was decreased when the substrate concentration was increased. Additionally, these facts allowed the ions to be classified as a function of their activation power (F− > Cl− > Br−: K+ > Na+ > Li+), which was in agreement with the interpretation of the Hofmeister lyotropic series. The influence of the several phenomena produced by the presence of salts in the plastein reaction, such as, salt‐substrate interactions and water activity, as well as the presence of deactivated enzyme was also analysed. The obtained results showed that the substrate concentration is the most important factor, and the activating effect of salts could be simultaneously involved with both a structural change on the substrate conformation and a reduction of water activity into the reaction media, enhancing the catalytic capability of the α‐chymotrypsin towards a peptide synthesis action.
Effects of levels of fat, surimi from sardine (Sardina pilchardus) and heat processing on thermal gelation of meat batters
Authors: Colmenero Francisco JiméNez , Cavestany Marta , Carballo José
Published: October 2006

The object of the study was to analyse the Theological behaviour occurring during heat‐induced gelation (measured by thermal scanning rigidity monitor) of meat batters containing various proportions of fat (48, 106, 147 and 208 g kg−1) and sardine surimi (0, 100, 200 and 300 g kg−1 fish protein added with respect to total protein present) and subjected to different heat treatments (A, heating from 14 to 76†C at a rate of 1†C min−1; B, gradual temperature increase at a rate of 1†C min−1 up to 40†C, maintenance at this temperature for 30 min, then heating from 40 to 76†C at 1†C min−1; C, samples kept at 4†C for 20 h and then heated in the same way as process A). The results indicate that differences in levels of fat content significantly affect the gelation patterns of pork batters, gels being stiffer the higher the fat content and the lower the water content. A highly significant correlation (r = 0.78, P < 0.01) has been established between fat content and maximum values of G, which occur at the final experimental temperature of 76†C. In contrast, in general, neither addition of surimi nor variation in the heat treatment applied has any major effect on the gelation process in the system as formulated.
Survey on biogenic amines in Egyptian foods: Sausage
Authors: Shalaby A R
Published: October 2006

A survey was conducted to determine the biogenic amine contents of Egyptian dry sausage. Histamine was found in 46% of the tested samples with an average of 5.25 mg kg−1, while putrescine and cadaverine were found in 96 and 94% of the tested samples, respectively. The corresponding average concentrations were 38.62 and 19.20 mg kg−1. Tyramine was found in 78% of the tested samples and tryptamine was found in 68% of the tested sausage, while 18% of the tested sausage samples were found to contain phenylethylamine. The average concentrations of 19.25, 12.70 and 33.25 mg kg−1 were obtained for tyramine, tryptamine and phenylethylamine, respectively. The polyamines, spermine and spermidine, were found in 54 and 44% of the tested samples, with an average of 1.75 and 2.30 mg kg−1, respectively.
Behaviour of tannic acid from various commercial sources towards redox, metal complexing and protein precipitation assays of tannins
Authors: Makkar Harinder P S , Becker Klaus
Published: October 2006

Tannic acid is the most commonly used standard for quantitation of tannins. Tannic acid from five commercial sources (Merck, Sigma, Aldrich, Fluka and Apin chemical companies) was tested towards a redox (Folin‐Ciocalteu method) and a metal complexing (ferric chloride method) assay, and three protein precipitation assays. Tannic acid from various commercial sources behaved differently towards these tannin assays showing that (i) tannic acid preparation differed from source to source, and (ii) tannic acid from different sources as a standard results in different tannin values for a given sample. It is suggested that the source of tannic acid used as a standard should be stated, and the assay values obtained by different workers should be compared with caution.
Thought suppression mediates the relationship between negative mood and PTSD in sexually assaulted women
Authors: Rosenthal M. Zachary , Cheavens Jennifer S. , Lynch Thomas R. , Follette Victoria
Published: October 2006

Sexually victimized individuals often report chronic attempts to avoid unpleasant internal experiences (e.g., thoughts, emotions, memories) as a means of affect regulation. The aim of this study was to expand upon previous findings by examining the relationships among negative mood, thought suppression, and posttraumatic stress disorder (PTSD) in a sample of adult women with a history of sexual assault after age 14 and assault‐related intrusions in the past week. Chronic thought suppression partially mediated the relationship between negative mood and PTSD symptom severity after covarying the use of worry to control unpleasant thoughts. Findings extend previous studies and suggest that chronic thought suppression may help explain the link between negative mood and PTSD.
Impaired long‐term potentiation–like plasticity of the trigeminal blink reflex circuit in Parkinson's disease
Authors: Battaglia Fortunato , Ghilardi Maria Felice , Quartarone Angelo , Bagnato Sergio , Girlanda Paolo , Hallett Mark
Published: October 2006

We investigated the hypothesis that Parkinsons's disease (PD) is associated with abnormal plasticity of the neuronal circuits mediating blink reflex. We induced long‐term potentiation (LTP)‐like plasticity in trigeminal wide dynamic range neurons of the blink reflex circuit by pairing an high‐frequency train of electrical stimuli over the right supraorbital nerve (SO) coincident with the R2 response elicited by a preceding SO stimulus. The facilitation of the R2 response after the induction protocol was markedly decreased in patients relative to controls. Treatment with dopaminergic drugs normalized the LTP‐like plasticity of the R2 response. We conclude that nigrostriatal denervation disrupts LTP‐like plasticity in the trigeminal reflex circuit. © 2006 Movement Disorder Society
Long‐term benefit to pallidal deep brain stimulation in a case of dystonia secondary to pantothenate kinase‐associated neurodegeneration
Authors: Krause Martin , Fogel Wolfgang , Tronnier Volker , Pohle Sabine , Hörtnagel Konstanze , Thyen Ute , Volkmann Jens
Published: October 2006

Pantothenate kinase‐associated neurodegeneration (PKAN) is a rare autosomal recessive disorder with onset in childhood and rapid progression. There is no causative and insufficient symptomatic drug therapy. Deep brain stimulation (DBS) of the internal pallidum (GPi) has been reported to improve motor function. Most case reports, however, are limited to short observational periods. The impact of DBS on the progression and life expectancy in PKAN is unknown. We present a 5‐year outcome and video documentation of bilateral GPi‐DBS of an adolescent patient suffering from genetically defined PKAN. © 2006 Movement Disorder Society
Potassium sensitivity test (PST) as a measurement of treatment efficacy of painful bladder syndrome/interstitial cystitis: A prospective study with cyclosporine A and pentosan polysulfate sodium
Authors: Sairanen Jukka , Tammela Teuvo L. J. , Leppilahti Mikael , Onali Markku , Forsell Tapio , Ruutu Mirja
Published: October 2006

Aims

Potassium sensitivity test (PST) has been used as an optional tool in diagnosing painful bladder syndrome/interstitial cystitis (PBS/IC). The role of PST in the follow‐up of patients with PBS/IC is elusive. We performed PST before and after treatment of PBS/IC with cyclosporine A (CyA) or pentosan polysulfate sodium (PPS), to test whether the result of repeated PST correlates with alleviation of PBS/IC‐related symptoms.

Materials and Methods

Sixty‐four patients who participated in a randomized clinical study comparing CyA and PPS in the treatment of PBS/IC were recruited to the present study. Patients underwent 0.4 M PST before and after 6 months of treatment. The primary end point was a change from positive PST to negative among patients who responded to both treatments determined by global response assessment (GRA).

Results

Potassium sensitivity test (PST) was more likely to change from positive to negative among patients who responded to their treatment according to GRA (P < 0.001). The PST change follows the clinical course (ICSI score, voiding frequency, VAS score), which was more beneficial in the CyA‐treated patients.

Conclusions

Potassium sensitivity test (PST) reflects symptom severity of PBS/IC patients. Change of pre‐treatment positive PST to negative correlates well with clinical alleviation of PBS/IC‐related symptoms. In patients with persistent symptoms it may be painful and does not offer additional information. Thus, we do not recommend PST to be used as a routine clinical test in monitoring of PBS/IC treatment efficacy. Neurourol. Urodynam. 26:267–270, 2007. © 2006 Wiley‐Liss, Inc.
Clinical experience with urethral retro‐resistance pressure measurement: A prospective pre‐ and postoperative evaluation in women with stress urinary incontinence
Authors: Tunn Ralf , Marschke Juliane , Wildt Bettina , Gauruder‐Burmester Annett
Published: October 2006

Aims

To identify possible correlations of urethral retro‐resistance pressure (URP) with clinically and urodynamically proven stress urinary incontinence (SUI) and the outcome of anti‐incontinence surgery.

Materials and Methods

URP was measured using the Monitorr® system in women with clinically and urodynamically proven SUI without prolapse before and after anti‐incontinence surgery (colposuspension n = 8, tension‐free vaginal tape n = 6, tension‐free transobturator tape n = 34).

Results

Forty‐eight women (mean age 61.8 ± 8.9 years) were evaluated preoperatively and on average 10 weeks postoperatively. Mean URP was 75.6 ± 20.8 cm H2O preoperatively versus 75.4 ± 17.9 cm H2O postoperatively (P = 0.898). The type of anti‐incontinence surgery performed had no significant effect on postoperative URP. While no association was found between age and URP (P = 0.35), there was a positive correlation between URP and body mass index (BMI; r = 0.49, P = 0.0004). There was no correlation of URP with the preoperative pad test (P = 0.17) and urethral closure pressure at rest (P = 0.51). Finally, URP did not correlate significantly with the preserved length of the continence zone (0‐1/3‐2/3‐3/3) as determined by the urethral stress profile (P = 0.37–0.72) or with the objective cure rate (negative pad test).

Conclusions

Preoperative URP does not correlate with SUI in all women, has no predictive value, and does not correlate with the outcome of anti‐incontinence surgery. However, there seems to be an association with biomechanical factors such as obesity, which may open up a new area of application for URP measurement in urogynecologic diagnosis. Neurourol. Urodynam. 26:262–266, 2007. © 2006 Wiley‐Liss, Inc.
Clinical ultrashort echo time imaging of bone and other connective tissues
Authors: Robson Matthew D. , Bydder Graeme M.
Published: October 2006

The background underpinning the clinical use of ultrashort echo time, SPRITE and other pulse sequences for imaging bone and other connective tissues with short T2 is reviewed. Features of the basic physics relevant to UTE imaging are described, including the consequences when the radiofrequency pulse duration is of the order of T2 so that rotation of tissue magnetization into the transverse plane is incomplete. Consequences of the broad linewidth of short T2 components are also discussed, including partial saturation by off‐resonance fat suppression pulses as well as those used in multislice and multiecho imaging. The need for rapid data acquisition of the order of T2 is explained. The basic two‐dimensional UTE pulse sequence with its half excitation pulse and radial imaging from the centre of k‐space is described, together with options that suppress fat and/or reduce the signal from long T2 components. The basic features of SPRITE and other sequences with very short TE are described. Image interpretation is discussed. Clinical features of the imaging of cortical bone, tendons, ligaments, menisci, periosteum and the spine are illustrated. The source of the short T2 signal in these tissues is predominantly collagen and water tightly bound to collagen. Short T2 components in all of these tissues are detectible and may show high signals. Possible future developments are outlined, as are technical limitations of clinical magnetic resonance systems. Copyright © 2006 John Wiley & Sons, Ltd.
Advances in MR imaging of the skin
Authors: Bittoun Jacques , Querleux Bernard , Darrasse Luc
Published: October 2006

MR imaging of the skin is challenging because of the small size of the structures to be visualized. By increasing the gradient amplitude and/or duration, skin layers can be visualized with a voxel size of the order of 20 µm, clearly the smallest obtained for in vivo images in a whole‐body imager. Currently, the gradient strength of most commercial systems enables acquisition of such a small voxel size, and the main difficulty has thus become to achieve sufficient detection sensitivity. The signal‐to‐noise ratio (SNR) can be increased either by increasing the magnetic field strength or by minimizing noise with small coils; cooling copper coils or superconducting coils can enhance the SNR by a factor of 3 or more. MR imaging, because of the large number of parameters it is able to measure, can provide more than the microscopic architecture of the skin: physical parameters such as relaxation times, magnetization transfer or diffusion, and chemical parameters such as the water and fat contents or phosphorus metabolism. In spite of the amount of information they have provided to date, MR imaging and spectroscopy have had limited clinical applications, mainly because cutaneous pathologies are easily accessible to the naked eye and surgery. However, MR technologies indeed represent powerful research tools to study normal and diseased skin. Copyright © 2006 John Wiley & Sons, Ltd.
Preparation of monodisperse fluorescent core–shell polymer microspheres with functional groups in the shell layer by two‐stage distillation–precipitation polymerization
Authors: Qi Donglai , Yang Xinlin , Huang Wenqiang
Published: October 2006

Monodisperse crosslinked core–shell micrometer‐sized microspheres bearing a brightly blue fluorescent dye, carbazole, and containing various functional groups in the shell layers were prepared by a two‐stage distillation–precipitation polymerization in acetonitrile in the absence of any stabilizer. Commercial divinylbenzene (DVB), containing 80 vol.% of DVB, was polymerized by distillation–precipitation in acetonitrile without any stabilizer using 2,2′‐azobisisobutyronitrile (AIBN) as the initiator for the first stage of polymerization which resulted in monodisperse polyDVB microspheres used as the core. Several functional monomers, including 2‐hydroxyethyl methacrylate and acrylonitrile together with N‐vinylcarbazole blue fluorescent comonomer, were incorporated into the shell layers with AIBN as initiator during the second stage of polymerization. The resultant core–shell polymer microspheres were characterized using scanning electron microscopy, Fourier transform infrared spectroscopy, UV‐visible spectroscopy and fluorescence spectroscopy. Copyright © 2006 Society of Chemical Industry
An all‐atom, distance‐dependent scoring function for the prediction of protein–DNA interactions from structure
Authors: Robertson Timothy A. , Varani Gabriele
Published: October 2006

We have developed an all‐atom statistical potential function for the prediction of protein–DNA interactions from their structures, and show that this method outperforms similar, lower‐resolution statistical potentials in a series of decoy discrimination experiments. The all‐atom formalism appears to capture details of atomic interactions that are missed by the lower‐resolution methods, with the majority of the discriminatory power arising from its description of short‐range atomic contacts. We show that, on average, the method is able to identify 90% of near‐native docking decoys within the best‐scoring 10% of structures in a given decoy set, and it compares favorably with an optimized physical potential function in a test of structure‐based identification of DNA binding‐sequences. These results demonstrate that all‐atom statistical functions specific to protein–DNA interactions can achieve great discriminatory power despite the limited size of the structural database. They also suggest that the statistical scores may soon be able to achieve accuracy on par with more complex, physical potential functions. Proteins 2007. © 2006 Wiley‐Liss, Inc.
The location and characterisation of the O‐linked glycans of the human insulin receptor
Authors: Sparrow Lindsay G. , Gorman Jeffrey J. , Strike Phillip M. , Robinson Christine P. , McKern Neil M. , Epa V. Chandana , Ward Colin W.
Published: October 2006

O‐linked glycosylation is a post‐translational and post‐folding event involving exposed S/T residues at β‐turns or in regions with extended conformation. O‐linked sites are difficult to predict from sequence analyses compared to N‐linked sites. Here we compare the results of chemical analyses of isolated glycopeptides with the prediction using the neural network prediction method NetOGlyc3.1, a procedure that has been reported to correctly predict 76% of O‐glycosylated residues in proteins. Using the heavily glycosylated human insulin receptor as the test protein six sites of mucin‐type O‐glycosylation were found at residues T744, T749, S757, S758, T759, and T763 compared to the three sites (T759 and T763‐ correctly, T756‐ incorrectly) predicted by the neural network method. These six sites occur in a 20 residue segment that begins nine residues downstream from the start of the insulin receptor β‐chain. This region which also includes N‐linked glycosylation sites at N742 and N755, is predicted to lack secondary structure and is followed by residues 765–770, the known linear epitope for the monoclonal antibody 18–44. Proteins 2007. © 2006 Wiley‐Liss, Inc.
IR spectral and structural studies of 4‐aminobenzenesulfonamide (sulfanilamide)‐d0, ‐d4, and ‐15N, as well as their azanions: Combined DFT B3LYP/experimental approach
Authors: Popova Angelina D. , Georgieva Miglena. K. , Petrov Ognyan. I. , Petrova Katya. V. , Velcheva Evelina. A.
Published: October 2006

The infrared (IR) spectra of sulfanilamide 1 and of its azanion (counter ion Na+) 2 have been measured in dimethyl sulfoxide (DMSO) solutions. The density functional theory (DFT) B3LYP 6‐31++G(d,p) computations performed adequately describe the experimental spectroscopic data, including the corresponding frequency isotopic shifts. In agreement between theory and experiment, the conversion of sulfanilamide 1 into azanion 2 results in strong frequency decreases of the asymmetrical and symmetrical vibrations of the SO2 group: predicted 122 cm−1, measured 140 cm−1 in solution (total values), as well as in other essential IR spectral changes. According to the computations, the strongest changes in the steric structure take place at and next to the azanionic center. The new (azanionic) charge is distributed, as follows: 0.08e−, 0.23e−, and 0.12e− are delocalized over the amino, phenylene, and sulfonic groups, respectively, and 0.57e− of it remain localized at the azanionic center. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Is Mars alive?
Authors: Allen Mark , Sherwood Lollar Barbara , Runnegar Bruce , Oehler Dorothy Z. , Lyons James R. , Manning Craig E. , Summers Michael E.
Published: October 2006

Mars long has been considered a cold, dead planet. However, recent reports of methane in the Martian atmosphere [Formisano et al., 2004; Krasnopolsky et al., 2004; Mumma et al., 2004] suggest that methane currently is being produced, since its calculated atmospheric lifetime of 400 years or less [Nair et al., 2005] requires a constant resupply. Possible subsurface sources for this resupply are geological, or even microbiological, in nature. So the question is: Is Mars alive, biologically or geologically speaking?

If either geological or microbiological sources of methane on Mars can be confirmed, there will be profound implications for astrobiology and the U.S. space program. If the existence of active microbiology were established, it would not be surprising if NASA reorganized its mission plan to follow‐up on such a discovery. Additionally, current geological processes that result in the formation of methane would be in locations that are warm and wet, and thus likely habitable. If key nutrients such as nitrogen and phosphorus—in addition to liquid water—also were available, such locations could support life, and not necessarily just methane‐producing organisms.
Nonspecific binding to structured RNA and preferential unwinding of an exposed helix by the CYT-19 protein, a DEAD-box RNA chaperone
Authors: Tijerina Pilar , Bhaskaran Hari , Russell Rick
Published: October 2006

We explore the interactions of CYT-19, a DExD/H-box protein that functions in folding of group I RNAs, with a well characterized misfolded species of the
Tetrahymena
ribozyme. Consistent with its function, CYT-19 accelerates refolding of the misfolded RNA to its native state. Unexpectedly, CYT-19 performs another reaction much more efficiently; it unwinds the 6-bp P1 duplex formed between the ribozyme and its oligonucleotide substrate. Furthermore, CYT-19 performs this reaction 50-fold more efficiently than it unwinds the same duplex free in solution, suggesting that it forms additional interactions with the ribozyme, most likely using a distinct RNA binding site from the one responsible for unwinding. This site can apparently bind double-stranded RNA, as attachment of a simple duplex adjacent to P1 recapitulates much of the activation provided by the ribozyme. Unwinding the native P1 duplex does not accelerate refolding of the misfolded ribozyme, implying that CYT-19 can disrupt multiple contacts on the RNA, consistent with its function in folding of multiple RNAs. Further experiments showed that the P1 duplex unwinding activity is virtually the same whether the ribozyme is misfolded or native but is abrogated by formation of tertiary contacts between the P1 duplex and the body of the ribozyme. Together these results suggest a mechanism for CYT-19 and other general DExD/H-box RNA chaperones in which the proteins bind to structured RNAs and efficiently unwind loosely associated duplexes, which biases the proteins to disrupt nonnative base pairs and gives the liberated strands an opportunity to refold.
Day-to-day dynamics of experience–cortisol associations in a population-based sample of older adults
Authors: Adam Emma K. , Hawkley Louise C. , Kudielka Brigitte M. , Cacioppo John T.
Published: October 2006

In 156 older adults, day-to-day variations in cortisol diurnal rhythms were predicted from both prior-day and same-day experiences, to examine the temporal ordering of experience–cortisol associations in naturalistic environments. Diary reports of daily psychosocial, emotional, and physical states were completed at bedtime on each of three consecutive days. Salivary cortisol levels were measured at wakeup, 30 min after awakening, and at bedtime each day. Multilevel growth curve modeling was used to estimate diurnal cortisol profiles for each person each day. The parameters defining those profiles (wakeup level, diurnal slope, and cortisol awakening response) were predicted simultaneously from day-before and same-day experiences. Prior-day feelings of loneliness, sadness, threat, and lack of control were associated with a higher cortisol awakening response the next day, but morning awakening responses did not predict experiences of these states later the same day. Same-day, but not prior-day, feelings of tension and anger were associated with flatter diurnal cortisol rhythms, primarily because of their association with higher same-day evening cortisol levels. Although wakeup cortisol levels were not predicted by prior-day levels of fatigue and physical symptoms, low wakeup cortisol predicted higher levels of fatigue and physical symptoms later that day. Results are consistent with a dynamic and transactional function of cortisol as both a transducer of psychosocial and emotional experience into physiological activation and an influence on feelings of energy and physical well-being.
A backbone-based theory of protein folding
Authors: Rose George D. , Fleming Patrick J. , Banavar Jayanth R. , Maritan Amos
Published: October 2006

Under physiological conditions, a protein undergoes a spontaneous disorder ⇌ order transition called “folding.” The protein polymer is highly flexible when unfolded but adopts its unique native, three-dimensional structure when folded. Current experimental knowledge comes primarily from thermodynamic measurements in solution or the structures of individual molecules, elucidated by either x-ray crystallography or NMR spectroscopy. From the former, we know the enthalpy, entropy, and free energy differences between the folded and unfolded forms of hundreds of proteins under a variety of solvent/cosolvent conditions. From the latter, we know the structures of ≈35,000 proteins, which are built on scaffolds of hydrogen-bonded structural elements, α-helix and β-sheet. Anfinsen showed that the amino acid sequence alone is sufficient to determine a protein's structure, but the molecular mechanism responsible for self-assembly remains an open question, probably the most fundamental open question in biochemistry. This perspective is a hybrid: partly review, partly proposal. First, we summarize key ideas regarding protein folding developed over the past half-century and culminating in the current mindset. In this view, the energetics of side-chain interactions dominate the folding process, driving the chain to self-organize under folding conditions. Next, having taken stock, we propose an alternative model that inverts the prevailing side-chain/backbone paradigm. Here, the energetics of backbone hydrogen bonds dominate the folding process, with preorganization in the unfolded state. Then, under folding conditions, the resultant fold is selected from a limited repertoire of structural possibilities, each corresponding to a distinct hydrogen-bonded arrangement of α-helices and/or strands of β-sheet.
Changing green leaf volatile biosynthesis in plants: An approach for improving plant resistance against both herbivores and pathogens
Authors: Shiojiri Kaori , Kishimoto Kyutaro , Ozawa Rika , Kugimiya Soichi , Urashimo Soichi , Arimura Genichiro , Horiuchi Junichiro , Nishioka Takaaki , Matsui Kenji , Takabayashi Junji
Published: October 2006

Green leaf volatiles (GLVs) are commonly emitted by green plants, and their production is drastically enhanced when they are under biotic stress. To clarify the ecological function of naturally emitted GLVs, we studied the response of
Arabidopsis
, whose GLV biosynthesis had been modified, when subjected to herbivory or a pathogenic infection. There was a significant increase in GLV production after herbivory by cabbage white butterfly larvae and pathogen (gray mold) infection in hydroperoxide lyase (HPL) sense
Arabidopsis
compared with WT controls. The
HPL
sense modification resulted in the plant being more attractive to the parasitic wasp
Cotesia glomerata
, leading to higher mortality of the herbivores. The
HPL
sense modification also resulted in greater inhibition of growth of the fungus. By contrast,
HPL
antisense
Arabidopsis
produced fewer GLVs, attracted fewer parasitoids, and was more susceptible to the pathogens than the WT control. These data show that (
i
) one of the ecological functions of GLV biosynthesis related to resistance against both herbivores and pathogens, and (
ii
) the genetic modification of GLV biosynthesis could be a unique approach for improving plant resistance against such biotic stresses.
Template disruptions and failure of double Holliday junction dissolution during double-strand break repair in
Drosophila BLM
mutants
Authors: Johnson-Schlitz Dena , Engels William R.
Published: October 2006

Previous biochemical studies of the
BLM
gene product have shown its ability in conjunction with topoisomerase IIIα to resolve double Holliday structures through a process called “dissolution.” This process could prevent crossing over during repair of double-strand breaks. We report an analysis of the
Drosophila
BLM
gene,
DmBlm
, in the repair of double-strand breaks in the premeiotic germ line of
Drosophila
males. With a repair reporter construct, Rr3, and other genetic tools, we show that
DmBlm
mutants are defective for homologous repair but show a compensating increase in single-strand annealing. Increases of 40- to 50-fold in crossing over and flanking deletions also were seen. Perhaps most significantly, the template used for homologous repair in
DmBlm
mutants is itself subject to deletions and complex rearrangements. These template disruptions are indicative of failure to resolve double Holliday junctions. These findings, along with the demonstration that a weak allele of topoisomerase IIIα has some of the same defects as
DmBlm
, support the dissolution model. Finally, an analysis of
DmBlm
mutants in conjunction with
mus81
or
spnA
(
Rad51
) reveals a second function of
BLM
distinct from the repair of induced double-strand breaks and possibly related to maintenance of replication forks.
Universal scaling for polymer chain scission in turbulence
Authors: Vanapalli Siva A. , Ceccio Steven L. , Solomon Michael J.
Published: October 2006

We report that previous polymer chain scission experiments in strong flows, long analyzed according to accepted laminar flow scission theories, were in fact affected by turbulence. We reconcile existing anomalies between theory and experiment with the hypothesis that the local stress at the Kolmogorov scale generates the molecular tension leading to polymer covalent bond breakage. The hypothesis yields a universal scaling for polymer scission in turbulent flows. This surprising reassessment of over 40 years of experimental data simplifies the theoretical picture of polymer dynamics leading to scission and allows control of scission in commercial polymers and genomic DNA.
A Ras-induced conformational switch in the Ras activator Son of sevenless
Authors: Freedman Tanya S. , Sondermann Holger , Friedland Gregory D. , Kortemme Tanja , Bar-Sagi Dafna , Marqusee Susan , Kuriyan John
Published: October 2006

The Ras-specific guanine nucleotide-exchange factors Son of sevenless (Sos) and Ras guanine nucleotide-releasing factor 1 (RasGRF1) transduce extracellular stimuli into Ras activation by catalyzing the exchange of Ras-bound GDP for GTP. A truncated form of RasGRF1 containing only the core catalytic Cdc25 domain is sufficient for stimulating Ras nucleotide exchange, whereas the isolated Cdc25 domain of Sos is inactive. At a site distal to the catalytic site, nucleotide-bound Ras binds to Sos, making contacts with the Cdc25 domain and with a Ras exchanger motif (Rem) domain. This allosteric Ras binding stimulates nucleotide exchange by Sos, but the mechanism by which this stimulation occurs has not been defined. We present a crystal structure of the Rem and Cdc25 domains of Sos determined at 2.0-Å resolution in the absence of Ras. Differences between this structure and that of Sos bound to two Ras molecules show that allosteric activation of Sos by Ras occurs through a rotation of the Rem domain that is coupled to a rotation of a helical hairpin at the Sos catalytic site. This motion relieves steric occlusion of the catalytic site, allowing substrate Ras binding and nucleotide exchange. A structure of the isolated RasGRF1 Cdc25 domain determined at 2.2-Å resolution, combined with computational analyses, suggests that the Cdc25 domain of RasGRF1 is able to maintain an active conformation in isolation because the helical hairpin has strengthened interactions with the Cdc25 domain core. These results indicate that RasGRF1 lacks the allosteric activation switch that is crucial for Sos activity.
Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer
Authors: Fang Chong , Senes Alessandro , Cristian Lidia , DeGrado William F. , Hochstrasser Robin M.
Published: October 2006

The tertiary interactions between amide-I vibrators on the separate helices of transmembrane helix dimers were probed by ultrafast 2D vibrational photon echo spectroscopy. The 2D IR approach proves to be a useful structural method for the study of membrane-bound structures. The 27-residue human erythrocyte protein Glycophorin A transmembrane peptide sequence: KKITLIIF
G
79
VMAGVIGTILLISW
G
94
IKK was labeled at
G
79
and
G
94
with
13
C

16
O or
13
C

18
O. The isotopomers and their 50:50 mixtures formed helical dimers in SDS micelles whose 2D IR spectra showed components from homodimers when both helices had either
13
C

16
O or
13
C

18
O substitution and a heterodimer when one had
13
C

16
O substitution and the other had
13
C

18
O substitution. The cross-peaks in the pure heterodimer 2D IR difference spectrum and the splitting of the homodimer peaks in the linear IR spectrum show that the amide-I mode is delocalized across a pair of helices. The excitation exchange coupling in the range 4.3–6.3 cm
−1
arises from through-space interactions between amide units on different helices. The angle between the two Gly
79
amide-I transition dipoles, estimated at 103° from linear IR spectroscopy and 110° from 2D IR spectroscopy, combined with the coupling led to a structural picture of the hydrophobic interface that is remarkably consistent with results from NMR on helix dimers. The helix crossing angle in SDS is estimated at 45°. Two-dimensional IR spectroscopy also sets limits on the range of geometrical parameters for the helix dimers from an analysis of the coupling constant distribution.
Diffusion tensor imaging and magnetic resonance spectroscopy of the brain in a patient with sturge-weber syndrome
Authors: Sijens P. E. , Gieteling E. W. , Meiners L. C. , Sival D. A. , Potze J. H. , Irwan R. , Oudkerk M.
Published: October 2006

Quantitative brain MR spectroscopy (MRS) and diffusion tensor imaging (DTI) were used to characterize one patient with Sturge-Weber syndrome. Choline increases and N-acetylaspartate decreases were observed in pathologic frontal gray matter tissue compared to contralateral unaffected brain tissue without any change in the diffusion tensor imaging parameters (fractional anisotropy, apparent diffusion coefficient). The N-acetylaspartate decreases and/or choline increases observed here and in eight previously described Sturge-Weber patients probably reflect neuronal loss or dysfunction and demyelination as a result of recurrent seizures.
Bronchial stump fistula: treatment with covered, retrievable, expandable, hinged stents—preliminary clinical experience
Authors: Li Yong-Dong , Han Xin-Wei , Li Ming-Hua , Wu Gang
Published: October 2006

Purpose: To evaluate the preliminary clinical efficacy and retrievability of a covered, retrievable, metallic hinged stent in the treatment of bronchial stump fistula (BPF).

Material and Methods: Between April 2003 and March 2005, eight patients with bronchial stump fistula after pneumonectomy or lobectomy were treated with two types of covered, retrievable, metallic hinged stents. Type A stent was placed in six patients and type B in two under fluoroscopic guidance. The stent was removed with a retrieval set when BPF was healed or complications occurred.

Results: Stent placement in the bronchial tree was technically successful in all patients, without procedure-related complications. Immediate closure of the BPF was achieved in all patients after the procedure. Stents were removed from all patients but one. Removal of the stents was difficult in two patients due to tissue hyperplasia. Patients were followed for 4–16 months. Placement of the stents remained stable in all patients except one due to severe cough. Permanent closure of BPF was achieved in seven (87.5%) of eight patients.

Conclusion: Use of a covered, retrievable, expandable, metallic hinged stent is a simple, safe, and effective procedure for the closure of bronchial stump fistula. Retrieval of the stent seems feasible.
Bleeding pulmonary artery pseudoaneurysm secondary to squamous cell lung cancer: computed tomography findings and endovascular management
Authors: Akpinar E. , Turkbey B. , Canyigit M. , Peynircioglu B. , Hazirolan T. , Pamuk A. G. , Cil B. E.
Published: October 2006

A case of bleeding pulmonary artery pseudoaneurysm secondary to squamous cell lung cancer is reported. The patient presented with massive hemoptysis, diagnosis was made with multidetector computed tomography, and the pseudoaneurysm was successfully embolized with platinum coils. Hemoptysis ceased following the procedure.
Cine magnetic resonance imaging of the small bowel: comparison of different oral contrast media
Authors: Asbach P. , Breitwieser C. , Diederichs G. , Eisele S. , Kivelitz D. , Taupitz M. , Zeitz M. , Hamm B. , Klessen C.
Published: October 2006

Purpose: To evaluate several substances regarding small bowel distension and contrast on balanced steady-state free precession (bSSFP) cine magnetic resonance (MR) images.

Material and Methods: Luminal contrast was evaluated in 24 volunteers after oral application of two different contrast agent groups leading to either bright lumen (pineapple, blueberry juice) or dark lumen (tap water, orange juice) on T1-weighted images. Bowel distension was evaluated in 30 patients ingesting either methylcellulose or mannitol solution for limiting intestinal absorption. Fifteen patients with duodeno-jejunal intubation served as the control. Quantitative evaluation included measurement of luminal signal intensities and diameters of four bowel segments, qualitative evaluation assessed luminal contrast and distension on a five-point scale.

Results: Quantitative and qualitative evaluation of the four contrast agents revealed no significant differences regarding luminal contrast on bSSFP images. Quantitative evaluation revealed significantly lower ( P<0.05) small bowel distension for three out of four segments (qualitative evaluation: two out of four segments) for methylcellulose in comparison to the control. Mannitol was found to be equal to the control.

Conclusion: Oral ingestion of tap water or orange juice in combination with mannitol is recommended for cine MR imaging of the small bowel regarding luminal contrast and small bowel distension on bSSFP sequences.
eIF4E is a central node of an RNA regulon that governs cellular proliferation
Authors: Culjkovic Biljana , Topisirovic Ivan , Skrabanek Lucy , Ruiz-Gutierrez Melisa , Borden Katherine L.B.
Published: October 2006

This study demonstrates that the eukaryotic translation initiation factor eIF4E is a critical node in an RNA regulon that impacts nearly every stage of cell cycle progression. Specifically, eIF4E coordinately promotes the messenger RNA (mRNA) export of several genes involved in the cell cycle. A common feature of these mRNAs is a structurally conserved, ∼50-nucleotide element in the 3′ untranslated region denoted as an eIF4E sensitivity element. This element is sufficient for localization of capped mRNAs to eIF4E nuclear bodies, formation of eIF4E-specific ribonucleoproteins in the nucleus, and eIF4E-dependent mRNA export. The roles of eIF4E in translation and mRNA export are distinct, as they rely on different mRNA elements. Furthermore, eIF4E-dependent mRNA export is independent of ongoing RNA or protein synthesis. Unlike the NXF1-mediated export of bulk mRNAs, eIF4E-dependent mRNA export is CRM1 dependent. Finally, the growth-suppressive promyelocytic leukemia protein (PML) inhibits this RNA regulon. These data provide novel perspectives into the proliferative and oncogenic properties of eIF4E.
Activation of p38α/β MAPK in myogenesis via binding of the scaffold protein JLP to the cell surface protein Cdo
Authors: Takaesu Giichi , Kang Jong-Sun , Bae Gyu-Un , Yi Min-Jeong , Lee Clement M. , Reddy E. Premkumar , Krauss Robert S.
Published: October 2006

The p38 mitogen-activated protein kinase (MAPK) pathway plays an important role in cell differentiation, but the signaling mechanisms by which it is activated during this process are largely unknown. Cdo is an immunoglobulin superfamily member that functions as a component of multiprotein cell surface complexes to promote myogenesis. In this study, we report that the Cdo intracellular region interacts with JLP, a scaffold protein for the p38α/β MAPK pathway. Cdo, JLP, and p38α/β form complexes in differentiating myoblasts, and Cdo and JLP cooperate to enhance levels of active p38α/β in transfectants. Primary myoblasts from Cdo−/− mice, which display a defective differentiation program, are deficient in p38α/β activity, and the expression of an activated form of MKK6 (an immediate upstream activator of p38) rescues the ability of Cdo−/− cells to differentiate. These results document a novel mechanism of signaling during cell differentiation: the interaction of a MAPK scaffold protein with a cell surface receptor.
A role for IRF3-dependent RXRα repression in hepatotoxicity associated with viral infections
Authors: Chow Edward K. , Castrillo Antonio , Shahangian Arash , Pei Liming , O'Connell Ryan M. , Modlin Robert L. , Tontonoz Peter , Cheng Genhong
Published: October 2006

Viral infections and antiviral responses have been linked to several metabolic diseases, including Reye's syndrome, which is aspirin-induced hepatotoxicity in the context of a viral infection. We identify an interferon regulatory factor 3 (IRF3)–dependent but type I interferon–independent pathway that strongly inhibits the expression of retinoid X receptor α (RXRα) and suppresses the induction of its downstream target genes, including those involved in hepatic detoxification. Activation of IRF3 by viral infection in vivo greatly enhances bile acid– and aspirin-induced hepatotoxicity. Our results provide a critical link between the innate immune response and host metabolism, identifying IRF3-mediated down-regulation of RXRα as a molecular mechanism for pathogen-associated metabolic diseases.
Conserved F84 and P86 residues in αB‐crystallin are essential to effectively prevent the aggregation of substrate proteins
Authors: Santhoshkumar Puttur , Sharma K. Krishna
Published: October 2006

Previously, we have shown that residues 73–92 (sequence DRFSVNLDVKHFSPEELKVK) in αB‐crystallin are involved in preventing the formation of light scattering aggregates by substrate proteins. In this study, we made single substitutions of three conserved amino acid residues (H83 → A, F84 → G, and P86 → A) and a nonconserved amino acid residue (K90 → C) in the functional region of αB‐crystallin and evaluated their role in anti‐aggregation activity. Mutation of conserved residues led to changes in intrinsic tryptophan intensity, bis‐ANS binding, and in the secondary and tertiary structures. The H83A mutation led to a twofold increase in molar mass, while the other mutants did not produce significant changes in the molar mass when compared to that of wild‐type protein. The chaperone‐like activity of the H83A mutant was enhanced by 15%–20%, and the chaperone‐like activity of F84G and P86A mutants was reduced by 50%–65% when compared to the chaperone‐like activity of wild‐type αB‐crystallin. The substitution of the nonconserved residue (K90 → C) did not induce an appreciable change in the structure and function of the mutant protein. Fluorescence resonance energy transfer (FRET) assay demonstrated that destabilized ADH interacted near the K90 region in αB‐crystallin. The data show that F84 and P86 residues are essential for αB‐crystallin to effectively prevent the aggregation of substrate proteins. This study further supports the involvement of the residues in the 73–92 region of αB‐crystallin in substrate protein binding and chaperone‐like action.
Declines in the abundance of Chaetodon butterflyfishes following extensive coral depletion
Authors: Pratchett M. S. , Wilson S. K. , Baird A. H.
Published: October 2006

This study documented temporal variation in the abundance of butterflyfishes (Chaetodontidae) at Trunk Reef, on the central Great Barrier Reef, Australia, from May 2000 to March 2005. During this period, live coral cover declined by >90%, mostly due to severe coral bleaching. There were no short‐term changes (within 4 months) in the abundance of butterflyfishes following initial declines in live coral cover. Surveys conducted in 2005, however, revealed significant declines in the abundance of Chaetodon baronessa, Chaetodon lunulatus, Chaetodon trifascialis, Chaetodon plebeius and Chaetodon rainfordi, all of which are obligate hard‐coral feeders. In contrast, there was no significant change in the abundance of Chaetodon auriga, Chaetodon aureofasciatus, Chaetodon citrinellus, Chaetodon melannotus or Chaetodon vagabundus, which are much less reliant on scleractinian coral for food. Clearly, extensive coral depletion, such as that caused by severe coral bleaching, can have a major effect on the abundance of butterflyfishes. Specific responses of butterflyfishes varied according to their reliance on hard corals for food and their ability to utilize alternate prey types.