bluuebunny/crossref_metadata_2025 huggingface dataset:
The Complete Genome Sequence of
Bacillus thuringiensis
Al Hakam
Authors: Challacombe Jean F. , Altherr Michael R. , Xie Gary , Bhotika Smriti S. , Brown Nancy , Bruce David , Campbell Connie S. , Campbell Mary L. , Chen Jin , Chertkov Olga , Cleland Cathy , Dimitrijevic Mira , Doggett Norman A. , Fawcett John J. , Glavina Tijana , Goodwin Lynne A. , Green Lance D. , Han Cliff S. , Hill Karen K. , Hitchcock Penny , Jackson Paul J. , Keim Paul , Kewalramani Avinash Ramesh , Longmire Jon , Lucas Susan , Malfatti Stephanie , Martinez Diego , McMurry Kim , Meincke Linda J. , Misra Monica , Moseman Bernice L. , Mundt Mark , Munk A. Christine , Okinaka Richard T. , Parson-Quintana B. , Reilly Lee Philip , Richardson Paul , Robinson Donna L. , Saunders Elizabeth , Tapia Roxanne , Tesmer Judith G. , Thayer Nina , Thompson Linda S. , Tice Hope , Ticknor Lawrence O. , Wills Patti L. , Gilna Paul , Brettin Thomas S.
Published: March 2007

Bacillus thuringiensis
is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev.
62:
775-806, 1998). Here we report the finished, annotated genome sequence of
B. thuringiensis
Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol.
69:
2755-2764, 2003).
In Vitro Studies of the Uridylylation of the Three P
II
Protein Paralogs from
Rhodospirillum rubrum
: the Transferase Activity of
R. rubrum
GlnD Is Regulated by α-Ketoglutarate and Divalent Cations but Not by Glutamine
Authors: Jonsson Anders , Nordlund Stefan
Published: March 2007

P
II
proteins have been shown to be key players in the regulation of nitrogen fixation and ammonia assimilation in bacteria. The mode by which these proteins act as signals is by being in either a form modified by UMP or the unmodified form. The modification, as well as demodification, is catalyzed by a bifunctional enzyme encoded by the
glnD
gene. The regulation of this enzyme is thus of central importance. In
Rhodospirillum rubrum
, three P
II
paralogs have been identified. In this study, we have used purified GlnD and P
II
proteins from
R. rubrum
, and we show that for the uridylylation activity of
R. rubrum
GlnD, α-ketoglutarate is the main signal, whereas glutamine has no effect. This is in contrast to, e.g., the
Escherichia coli
system. Furthermore, we show that all three P
II
proteins are uridylylated, although the efficiency is dependent on the cation present. This difference may be of importance in understanding the effects of the P
II
proteins on the different target enzymes. Furthermore, we show that the deuridylylation reaction is greatly stimulated by glutamine and that Mn

2
+

is required.
Characterization of
Sinorhizobium meliloti
Triose Phosphate Isomerase Genes
Authors: Poysti Nathan J. , Oresnik Ivan J.
Published: March 2007

A Tn
5
mutant strain of
Sinorhizobium meliloti
with an insertion in
tpiA
(systematic identifier SMc01023), a putative triose phosphate isomerase (TPI)-encoding gene, was isolated. The
tpiA
mutant grew more slowly than the wild type on rhamnose and did not grow with glycerol as a sole carbon source. The genome of
S. meliloti
wild-type Rm1021 contains a second predicted TPI-encoding gene,
tpiB
(SMc01614). We have constructed mutations and confirmed that both genes encode functional TPI enzymes.
tpiA
appears to be constitutively expressed and provides the primary TPI activity for central metabolism.
tpiB
has been shown to be required for growth with erythritol. TpiB activity is induced by growth with erythritol; however, basal levels of TpiB activity present in
tpiA
mutants allow for growth with gluconeogenic carbon sources. Although
tpiA
mutants can be complemented by
tpiB, tpiA
cannot substitute for mutations in
tpiB
with respect to erythritol catabolism. Mutations in
tpiA
or
tpiB
alone do not cause symbiotic defects; however, mutations in both
tpiA
and
tpiB
caused reduced symbiotic nitrogen fixation.
Probing the Essential Catalytic Residues and Substrate Affinity in the Thermoactive
Bacillus stearothermophilus
US100
l
-Arabinose Isomerase by Site-Directed Mutagenesis
Authors: Rhimi Moez , Juy Michel , Aghajari Nushin , Haser Richard , Bejar Samir
Published: March 2007

The
l
-arabinose isomerase (
l
-AI) from
Bacillus stearothermophilus
US100 is characterized by its high thermoactivity and catalytic efficiency. Furthermore, as opposed to the majority of
l
-arabinose isomerases, this enzyme requires metallic ions for its thermostability rather than for its activity. These features make US100
l
-AI attractive as a template for industrial use. Based on previously solved crystal structures and sequence alignments, we identified amino acids that are putatively important for the US100
l
-AI isomerization reaction. Among these, E306, E331, H348, and H447, which correspond to the suggested essential catalytic amino acids of the
l
-fucose isomerase and the
l
-arabinose isomerase from
Escherichia coli
, are presumed to be the active-site residues of US100
l
-AI. Site-directed mutagenesis confirmed that the mutation of these residues resulted in totally inactive proteins, thus demonstrating their critical role in the enzyme activity. A homology model of US100
l
-AI was constructed, and its analysis highlighted another set of residues which may be crucial for the recognition and processing of substrates; hence, these residues were subjected to mutagenesis studies. The replacement of the D308, F329, E351, and H446 amino acids with alanine seriously affected the enzyme activities, and suggestions about the roles of these residues in the catalytic mechanism are given. The mutation F279Q strongly increased the enzyme's affinity for
l
-fucose and decreased the affinity for
l
-arabinose compared to that of the wild-type enzyme, showing the implication of this amino acid in substrate recognition.
Regulation of Arsenate Resistance in
Desulfovibrio desulfuricans
G20 by an
arsRBCC
Operon and an
arsC
Gene
Authors: Li Xiangkai , Krumholz Lee R.
Published: March 2007

Desulfovibrio desulfuricans
G20 grows and reduces 20 mM arsenate to arsenite in lactate-sulfate media. Sequence analysis and experimental data show that
D. desulfuricans
G20 has one copy of
arsC
and a complete
arsRBCC
operon in different locations within the genome. Two mutants of strain G20 with defects in arsenate resistance were generated by nitrosoguanidine mutagenesis. The
arsRBCC
operons were intact in both mutant strains, but each mutant had one point mutation in the single
arsC
gene. Mutants transformed with either the
arsC1
gene or the
arsRBCC
operon displayed wild-type arsenate resistance, indicating that the two
arsC
genes were equivalently functional in the sulfate reducer. The
arsC1
gene and
arsRBCC
operon were also cloned into
Escherichia coli
DH5α independently, with either DNA fragment conferring increased arsenate resistance. The recombinant
arsRBCC
operon allowed growth at up to 50 mM arsenate in LB broth. Quantitative PCR analysis of mRNA products showed that the single
arsC1
was constitutively expressed, whereas the operon was under the control of the
arsR
repressor protein. We suggest a model for arsenate detoxification in which the product of the single
arsC1
is first used to reduce arsenate. The arsenite formed is then available to induce the
arsRBCC
operon for more rapid arsenate detoxification.
Exact moment of tendon of pectoralis major muscle rupture captured on video: Figure 1
Authors: Pochini Alberto Castro , Ejnisman Benno , Andreoli Carlos Vicente , Monteiro Gustavo Cara , Fleury Anna Maria , Faloppa Flavio , Cohen Moises , Albertoni Walter Manna
Published: March 2007

A powerlifting athlete ruptured his left tendon of the pectoralis major muscle while attempting to lift 160 kg in a Brazilian bench press championship. The injury seemed to occur in the concentric phase of exercise; however, the more common mechanism of rupture is during the eccentric phase. The tendon was reinserted to the humerus 3 weeks later with screws and washers. The athlete returned to competitive activities after 5 months. One year later he lifted 170 kg and won the national championship.
Calculation of Protein-Ligand Binding Affinities
Authors: Gilson Michael K. , Zhou Huan-Xiang
Published: March 2007

Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.
Bilayer Thickness and Membrane Protein Function: An Energetic Perspective
Authors: Andersen Olaf S. , Koeppe Roger E.
Published: March 2007

The lipid bilayer component of biological membranes is important for the distribution, organization, and function of bilayer-spanning proteins. This regulation is due to both specific lipid-protein interactions and general bilayer-protein interactions, which modulate the energetics and kinetics of protein conformational transitions, as well as the protein distribution between different membrane compartments. The bilayer regulation of membrane protein function arises from the hydrophobic coupling between the protein's hydrophobic domains and the bilayer hydrophobic core, which causes protein conformational changes that involve the protein/bilayer boundary to perturb the adjacent bilayer. Such bilayer perturbations, or deformations, incur an energetic cost, which for a given conformational change varies as a function of the bilayer material properties (bilayer thickness, intrinsic lipid curvature, and the elastic compression and bending moduli). Protein function therefore is regulated by changes in bilayer material properties, which determine the free-energy changes caused by the protein-induced bilayer deformation. The lipid bilayer thus becomes an allosteric regulator of membrane function.
Living with Noisy Genes: How Cells Function Reliably with Inherent Variability in Gene Expression
Authors: Maheshri Narendra , O’Shea Erin K.
Published: March 2007

Within a population of genetically identical cells there can be significant variation, or noise, in gene expression. Yet even with this inherent variability, cells function reliably. This review focuses on our understanding of noise at the level of both single genes and genetic regulatory networks, emphasizing comparisons between theoretical models and experimental results whenever possible. To highlight the importance of noise, we particularly emphasize examples in which a stochastic description of gene expression leads to a qualitatively different outcome than a deterministic one.
Physics of Proteins
Authors: Banavar Jayanth R. , Maritan Amos
Published: March 2007

Globular proteins are a key component of the network of life. Over many decades much experimental data on proteins have been gathered, yet theoretical progress has been somewhat limited. We show that the results accumulated over the years inexorably lead to a unified framework for understanding proteins. The framework predicts the existence of a fixed menu of folds determined by geometry, clarifies the role of the amino acid sequence in selecting the native-state structure from this menu, and explains the propensity for amyloid formation. The experimental data and the new approach reveal an astonishing simplicity underlying the protein problem.
High-Resolution, Single-Molecule Measurements of Biomolecular Motion
Authors: Greenleaf William J. , Woodside Michael T. , Block Steven M.
Published: March 2007

Many biologically important macromolecules undergo motions that are essential to their function. Biophysical techniques can now resolve the motions of single molecules down to the nanometer scale or even below, providing new insights into the mechanisms that drive molecular movements. This review outlines the principal approaches that have been used for high-resolution measurements of single-molecule motion, including centroid tracking, fluorescence resonance energy transfer, magnetic tweezers, atomic force microscopy, and optical traps. For each technique, the principles of operation are outlined, the capabilities and typical applications are examined, and various practical issues for implementation are considered. Extensions to these methods are also discussed, with an eye toward future application to outstanding biological problems.
ACh-induced relaxations of rabbit small mesenteric arteries: role of arachidonic acid metabolites and K+
Authors: Zhang David X. , Gauthier Kathryn M. , Chawengsub Yuttana , Campbell William B.
Published: March 2007

ACh-induced endothelium-dependent relaxation in rabbit small mesenteric arteries is resistant to N-nitro-l-arginine (l-NA) and indomethacin but sensitive to high K+, indicating the relaxations are mediated by endothelium-derived hyperpolarizing factors (EDHFs). The identity of the EDHFs in this vascular bed remains undefined. Small mesenteric arteries pretreated with l-NA and indomethacin were contracted with phenylephrine. ACh (10−10 to 10−6 M) caused concentration-dependent relaxations that were shifted to the right by lipoxygenase inhibition and the Ca2+-activated K+ channel inhibitors apamin (100 nM) or charybdotoxin (100 nM) and eliminated by the combination of apamin plus charybdotoxin. Relaxations to ACh were also blocked by a combination of barium (200 μM) and apamin but not barium plus charybdotoxin. Addition of K+ (10.9 mM final concentration) to the preconstricted arteries elicited small relaxations. K+ addition before ACh restored the charybdotoxin-sensitive component of relaxations to ACh. K+ (10.9 mM) also relaxed endothelium-denuded arteries, and the relaxations were inhibited by barium but not by charybdotoxin and apamin. With the use of whole cell patch-clamp analysis, ACh (10−7 M) stimulated voltage-dependent outward K+ current from endothelial cells, which was inhibited by charybdotoxin, indicating K+ efflux. Arachidonic acid (10−7 to 10−4 M) induced concentration-related relaxations that were inhibited by apamin but not by charybdotoxin and barium. Addition of arachidonic acid after K+ (10.9 mM) resulted in more potent relaxations to arachidonic acid compared with control without K+ (5.9 mM). These findings suggest that, in rabbit mesenteric arteries, ACh-induced, l-NA- and indomethacin-resistant relaxation is mediated by endothelial cell K+ efflux and arachidonic acid metabolites, and a synergism exists between these two separate mechanisms.
Restoration of CREB function is linked to completion and stabilization of adaptive cardiac hypertrophy in response to exercise
Authors: Watson Peter A. , Reusch Jane E. B. , McCune Sylvia A. , Leinwand Leslie A. , Luckey Stephen W. , Konhilas John P. , Brown David A. , Chicco Adam J. , Sparagna Genevieve C. , Long Carlin S. , Moore Russell L.
Published: March 2007

Potential regulation of two factors linked to physiological outcomes with left ventricular (LV) hypertrophy, resistance to apoptosis, and matching of metabolic capacity, by the transcription factor cyclic-nucleotide regulatory element binding protein (CREB), was examined in the two models of physiological LV hypertrophy: involuntary treadmill running of female Sprague-Dawley rats and voluntary exercise wheel running in female C57Bl/6 mice. Comparative studies were performed in the models of pathological LV hypertrophy and failure: the spontaneously hypertension heart failure (SHHF) rat and the hypertrophic cardiomyopathy (HCM) transgenic mouse, a model of familial idiopathic cardiomyopathy. Activating CREB serine-133 phosphorylation was decreased early in remodeling in response to both physiological (decreased 50–80%) and pathological (decreased 60–80%) hypertrophic stimuli. Restoration of LV CREB phosphorylation occurred concurrent with completion of physiological hypertrophy (94% of sedentary control), but remained decreased (by 90%) during pathological hypertrophy. In all models of hypertrophy, CREB phosphorylation/activation demonstrated strong positive correlations with 1) expression of the anti-apoptotic protein bcl-2 (a CREB-dependent gene) and subsequent reductions in the activation of caspase 9 and caspase 3; 2) expression of peroxisome proliferator-activated receptor-γ coactivator-1 (PGC-1; a major regulator of mitochondrial content and respiratory capacity), and 3) LV mitochondrial respiratory rates and mitochondrial protein content. Exercise-induced increases in LV mitochondrial respiratory capacity were commensurate with increases observed in LV mass, as previously reported in the literature. Exercise training of SHHF rats and HCM mice in LV failure improved cardiac phenotype, increased CREB activation (31 and 118%, respectively), increased bcl-2 content, improved apoptotic status, and enhanced PGC-1 content and mitochondrial gene expression. Adenovirus-mediated expression of constitutively active CREB in neonatal rat cardiac recapitulated exercise-induced upregulation of PGC-1 content and mitochondrial oxidative gene expression. These data support a model wherein CREB contributes to physiological hypertrophy by enhancing expression of genes important for efficient oxidative capacity and resistance to apoptosis.
Syntheses and crystal structures of trigonal rare-earth dioxymonocyanamides, Ln2O2CN2 (Ln=Dy, Ho, Er, Tm, Yb)
Authors: Li Min , Yuan Wenxia , Wang Jingfang , Gu Cong , Zhao Huaizhou
Published: March 2007

Trigonal rare-earth dioxymonocyanamides
Ln2O2CN2
(Ln=Dy, Ho, Er, Tm, Yb) were synthesized by the modified solid-state metathesis (SSM) method, in which
Ln2O3 and melamine
C3N6H6 were mixed and heated at 850 °C in vacuumed silica ampoules. Possible chemical reaction pathways are proposed. X-ray diffraction (XRD) patterns of
Ln2O2CN2 were refined using the Rietveld method. Compounds
Ln2O2CN2 crystallize in the trigonal system with space group P3m1, Z=1, and cell parameters of a and c varying from 3.7267(1) to 3.6407(1) Å and from 8.1848(3) to 8.1152(3) Å, respectively, as Ln atoms change from Dy to Yb. These compounds have stacking structures of
Ln2O22+ and
CN22− layers, similar to those of previously reported compounds
Ln2O2CN2
(Ln=Ce, Pr, Nd, Sm, Eu, Gd). The presence of
CN22− ions has been confirmed by infrared spectroscopy, with two characteristic peaks in the vicinity of 651 and 2075 cm−1.
X-ray powder diffraction characterization of the elusive tetraphosphine Si(CH2PPh2)4 silane
Authors: Masciocchi Norberto , Galli Simona , Bogza Mona , Blümel Janet
Published: March 2007

X-ray powder diffraction data for the tetraphosphinic
Si(CH2PPh2)4 silane are reported. Its crystal and molecular structures were determined by simulated annealing and full-profile Rietveld refinement methods.
Si(CH2PPh2)4 was found to have tetragonal symmetry with P-421c space group. The lattice parameters were determined to be a=17.211(2) Å, c=7.553(1) Å, V=2237.5(5) Å3. The crystal structure was found to contain isolated
Si(CH2PPh2)4 molecules. In each
Si(CH2PPh2)4 molecule, the central Si atom was fixed at the −4 symmetric position bearing four
CH2PPh2 branches. This environment was confirmed by
31P CP/MAS NMR measurements. Thermo-diffractometric measurements in the 20–120 °C range were also used to estimate the linear and volumetric thermal expansion coefficients (∂ ln V/∂T=1.8×10−4 K−1), typical for very “soft” materials.
Automatic calibration of powder diffraction experiments using two-dimensional detectors
Authors: Rajiv P. , Hinrichsen B. , Dinnebier R. , Jansen M. , Joswig M.
Published: March 2007

Calibration of powder diffraction experiments using area detectors is essential to extract high quality one-dimensional powder diffraction pattern. Precise calibration necessitates a sensible characterization of the Debye-Scherrer rings formed on the detector plane. An algorithm, designed and developed to automate this process, is described in this paper. All the parameters required for an experimental calibration are extracted using robust pattern recognition techniques. Several image preprocessing methods are employed, reducing the computational cost but retaining high signal quality. A modified version of a one-dimensional Hough transformation is used to determine the final parameters of the ellipses. After extraction, the parameters are optimized using nonlinear least squares fit. The presented algorithm is insensitive to image artefacts and was successfully applied to a large number of calibration images. The performance of the algorithm is demonstrated by the comparison of results obtained from the presented automatic calibration method and an existing manual method.
Internal Fixation of Juvenile Osteochondritis Dissecans Lesions of the Knee
Authors: Kocher Mininder S. , Czarnecki Joseph J. , Andersen Jason S. , Micheli Lyle J.
Published: March 2007

Background

Operative techniques for the management of juvenile osteochondritis dissecans lesions of the knee include drilling, internal fixation, fragment removal, and chondral resurfacing.

Purpose

To evaluate the functional and radiographic outcome of internal fixation of juvenile osteochondritis dissecans lesions of the knee.

Study Design

Case series; Level of evidence, 4.

Methods

The study design was a retrospective case series. Twenty-six knees in 24 skeletally immature patients underwent internal fixation of osteochondritis dissecans lesions. Mean follow-up was 4.25 years (range, 2-14.75 years). Mean patient age was 14.7 years (range, 11-16 years). There were 13 boys and 11 girls. Lesions were graded per the Ewing and Voto classification, with 9 stage II lesions (fissured), 11 stage III lesions (partially attached), and 6 stage IV lesions (detached). Methods of internal fixation included variable pitch screws (n = 11), bioabsorbable tacks (n = 10), partially threaded cannulated screws (n = 3), and bioabsorbable pins (n = 3). Mean follow-up was 4.25 years (range, 2.0-14.75 years).

Results

Healing occurred in 22 of 26 lesions (healing rate, 84.6%). There was no significant difference in healing rate for lesion location, fixation method, or lesion grade. In fact, all 6 stage IV (detached) lesions healed. The mean postoperative Lysholm score was 85.8, mean postoperative International Knee Documentation Committee score was 82.6, and mean postoperative Tegner activity level was 7.4. Mean time to healing was 6 months. Eight patients underwent additional procedures: 4 for nonunion, 1 for hemarthrosis, and 3 for elective screw removal.

Conclusion

Given the relatively high healing rate, good functional outcome, and low complication rate, the authors advocate internal fixation of unstable juvenile osteochondritis dissecans lesions of the knee, even for detached lesions and in patients with a history of surgery for the osteochondritis dissecans lesion.
Avoiding Allograft Length Mismatch during Anterior Cruciate Ligament Reconstruction
Authors: Brown John A. , Brophy Robert H. , Franco John , Marquand Allyson , Solomon Thomas C. , Watanabe Diane , Mandelbaum Bert R.
Published: March 2007

Background

Given the increasing use of allografts in anterior cruciate ligament reconstruction, selection of appropriate-sized grafts may help individual surgeons as well as the efficiency of the overall system for graft distribution.

Hypothesis

Recipient patient height can predict the desired length for the tendinous portion of a patellar bone-tendon-bone allograft in anterior cruciate ligament reconstruction.

Study Design

Cohort study (Prognosis); Level of evidence, 2.

Methods

A series of 414 knees in 392 consecutive patients undergoing magnetic resonance imaging evaluation of knee pain were enrolled in the study. Data collected from magnetic resonance imaging included patella and patellar tendon length and intra-articular length of the anterior cruciate ligament. Patient age, height, weight, and gender were recorded. Linear regression analysis assessed the correlation between patient height and intra-articular length of the anterior cruciate ligament as well as patellar tendon length. The effect of variance in age, weight, and gender on anterior cruciate ligament intra-articular length was also measured.

Results

A strong positive correlation was found between intra-articular length of the anterior cruciate ligament and patient height (Pearson r = 0.73; P < .001). Anterior cruciate ligament length (y, in millimeters) as a function of height (x, in inches) can be expressed as y = 1.17x — 41.29. As a function of height (x, in centimeters), anterior cruciate ligament length (y, in millimeters) can be expressed as y = 0.4606x — 41.29. Age, gender, and weight did not significantly influence this relationship. A weak positive association was found between patient height and patellar tendon length.

Conclusion

Patient height can predict the desired length of the tendinous portion of a patellar bone-tendon-bone allograft. An addition of 10 mm is made to the predicted anterior cruciate ligament length to allow for aperture tibial and femoral fixation. Patellar bone-tendon-bone allografts can be requested based on recipient patient height as follows: 5 ft, 0 in to 5 ft, 6 in: tendinous length/total length, 45 mm/95 mm; 5 ft, 7 in to 6 ft, 1 in: 50 mm/100 mm; >6 ft, 1 in: 55 mm/105 mm.
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database
Authors: Tung Chi-Hua , Huang Jhang-Wei , Yang Jinn-Moon
Published: March 2007

We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (κ, α) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity.
TTX-sensitive and TTX-insensitive control of spontaneous gut motility in the developing zebrafish (Danio rerio) larvae
Authors: Holmberg Anna , Olsson Catharina , Hennig Grant W.
Published: March 2007

Spontaneous regular gut motility in zebrafish begins around 4 days post fertilisation (d.p.f.) and is modulated by release of acetylcholine and nitric oxide. The role of intrinsic or extrinsic innervation for initiating and propagating the spontaneous contractions, however, is not well understood. By creating spatiotemporal maps, we could examine spontaneous motility patterns in zebrafish larvae in vivo at 4 and 7 d.p.f. in more detail. Tetrodotoxin (TTX) was added to elucidate the importance of nervous control. Anterograde and retrograde contraction waves originated in the same region,just posterior to the intestinal bulb. This area correlates well with the distribution of Hu (human neuronal protein C/D)-immunoreactive nerve cell bodies. Whereas numerous immunoreactive nerve cells were present in the mid and distal intestine at both 4 and 7 d.p.f., fewer cells were seen anterior to the origin of contractions. The overall frequency of contractions(1.16±0.15 cycles min–1, N=14 at 4 d.p.f.;1.05±0.09 cycles min–1, N=13 at 7 d.p.f.) and the interval between individual anterograde contraction waves (54.8±7.9 s at 4 d.p.f., N=14; 56.9±4.4 s, N=13 at 7 d.p.f.)did not differ between the two stages but the properties of the contractions were altered. The distance travelled by each wave increased from 591.0±43.8 μm at 4 d.p.f. (N=14) to 719.9±33.2 μm at 7 d.p.f. (N=13). By contrast, the velocity decreased from 4 d.p.f.(49.5±5.5 μm s–1, N=12) to 7 d.p.f.(27.8±3.6 μm s–1, N=13). At 4 d.p.f., TTX did not affect any of the parameters whereas at 7 d.p.f. anterograde frequency(control 1.07±0.12 cycles min–1, N=8; TTX 0.55±0.13 cycles min–1, N=8) and distance travelled (control 685.1±45.9 μm, N=8; TTX 318.7±88.7 μm, N=6) were decreased. In conclusion, enteric or extrinsic innervation does not seem to be necessary to initiate spontaneous contractions of the gut in zebrafish larvae. However, later in development,nerves have an increasingly important role as modulators of intestinal activity.)
Variation in salinity tolerance, gill Na+/K+-ATPase,Na+/K+/2Cl– cotransporter and mitochondria-rich cell distribution in three salmonids Salvelinus namaycush, Salvelinus fontinalis and Salmo salar
Authors: Hiroi Junya , McCormick Stephen D.
Published: March 2007

We compared seawater tolerance, gill Na+/K+-ATPase and Na+/K+/2Cl– cotransporter (NKCC)abundance, and mitochondria-rich cell (MRC) morphology of three salmonids,lake trout Salvelinus namaycush, brook trout Salvelinus fontinalis and Atlantic salmon Salmo salar. They were transferred directly from 0 p.p.t. (parts per thousand; freshwater) to 30 p.p.t. seawater, or transferred gradually from 0 to 10, 20 and 30 p.p.t. at 1-week intervals and kept in 30 p.p.t. for 3 weeks. The survival rates of lake trout, brook trout and Atlantic salmon were 80%, 50% and 100% following direct transfer, and 80%, 100% and 100% during gradual transfer, respectively. Plasma Na+, K+ and Cl– concentrations in surviving lake trout increased rapidly and remained at high levels in 30 p.p.t. of both direct and gradual transfer, whereas those in brook trout showed a transient increase following direct transfer but did not change significantly during gradual transfer. Only minor changes in plasma ions were observed in Atlantic salmon smolts in both direct and gradual transfer. These results suggest that lake trout retains some degree of euryhalinity and that brook trout possesses intermediate euryhalinity between lake trout and Atlantic salmon smolts. Gill Na+/K+-ATPase activity of lake trout and brook trout increased in seawater, whereas that of Atlantic salmon smolts was already upregulated in freshwater and remained high after seawater exposure. NKCC abundance was upregulated in parallel with gill Na+/K+-ATPase activity in each species. Immunocytochemistry with anti-Na+/K+-ATPaseα-subunit and anti-NKCC revealed that the two ion transporters were colocalized on the basolateral membrane of gill MRCs. Immunopositive MRCs were distributed on both primary filaments and secondary lamellae in all three species kept in freshwater; following transfer to seawater this pattern did not change in lake trout and brook trout but lamellar MRCs disappeared in Atlantic salmon. Previous studies on several teleost species have suggested that filament and lamellar MRCs would be involved in seawater and freshwater acclimation, respectively. However, our results in lake trout and brook trout suggest that lamellar MRCs could be also functional during seawater acclimation.
Male sex pheromone release and female mate choice in a butterfly
Authors: Andersson Johan , Borg-Karlson Anna-Karin , Vongvanich Namphung , Wiklund Christer
Published: March 2007

In butterflies female mate choice is influenced by both visual and olfactory cues, the latter of which are important at close range. Males of the green-veined butterfly, Pieris napi, are known to release citral(mixture of geranial and neral, 1:1), but its role(s) and conditions of release are not known. Here, we show that male P. napi release citral when interacting with conspecific males, conspecific females, heterospecific males and also when alone. The amount of citral released correlated strongly with male flight activity, which explained more than 70% of the variation. This suggests that males do not exercise control over turning release on or off, but rather that citral is emitted as a passive physical process during flight. Electroantennogram experiments showed that female antennal response was ten times more sensitive to citral than male response. Females expressed acceptance behavior when exposed to models made with freshly excised male wings or those treated with citral following chemical extraction, but not to ones with extracted wings only. Hence, these behavioral and electrophysiological tests provide strong evidence that citral is a signal from the male directed to the female during courtship, and that it functions as a male sex pheromone.
Does the metabolic rate–flight speed relationship vary among geometrically similar birds of different mass?
Authors: Bundle Matthew W. , Hansen Kacia S. , Dial Kenneth P.
Published: March 2007

Based on aerodynamic considerations, the energy use–flight speed relationship of all airborne animals and aircraft should be U-shaped. However,measures of the metabolic rate–flight speed relationship in birds have been available since Tucker's pioneering experiments with budgerigars nearly forty years ago, but this classic work remains the only study to have found a clearly U-shaped metabolic power curve. The available data suggests that the energetic requirements for flight within this species are unique, yet the metabolic power curve of the budgerigar is widely considered representative of birds in general. Given these conflicting results and the observation that the budgerigar's mass is less than 50% of the next smallest species to have been studied, we asked whether large and small birds have metabolic power curves of different shapes. To address this question we measured the rates of oxygen uptake and wingbeat kinematics in budgerigars and cockatiels flying within a variable-speed wind tunnel. These species are close phylogenetic relatives,have similar flight styles, wingbeat kinematics, and are geometrically similar but have body masses that differ by a factor of two. In contrast to our expectations, we found the metabolic rate–flight speed relationship of both species to be acutely U-shaped. We also found that neither budgerigars nor cockatiels used their normal intermittent flight style while wearing a respirometric mask. We conclude that species size differences alone do not explain the previously unique metabolic power curve of the budgerigar;however, due to the absence of comparable data we cannot evaluate whether the mask-related kinematic response we document influences the metabolic rate–flight speed relationship of these parrots, or whether the energetics of flight differ between this and other avian clades.)
Modulation of mandibular loading and bite force in mammals during mastication
Authors: Ross Callum F. , Dharia Ruchi , Herring Susan W. , Hylander William L. , Liu Zi-Jun , Rafferty Katherine L. , Ravosa Matthew J. , Williams Susan H.
Published: March 2007

Modulation of force during mammalian mastication provides insight into force modulation in rhythmic, cyclic behaviors. This study uses in vivo bone strain data from the mandibular corpus to test two hypotheses regarding bite force modulation during rhythmic mastication in mammals: (1)that bite force is modulated by varying the duration of force production, or(2) that bite force is modulated by varying the rate at which force is produced. The data sample consists of rosette strain data from 40 experiments on 11 species of mammals, including six primate genera and four nonprimate species: goats, pigs, horses and alpacas. Bivariate correlation and multiple regression methods are used to assess relationships between maximum(ϵ1) and minimum (ϵ2) principal strain magnitudes and the following variables: loading time and mean loading rate from 5% of peak to peak strain, unloading time and mean unloading rate from peak to 5% of peak strain, chew cycle duration, and chew duty factor. Bivariate correlations reveal that in the majority of experiments strain magnitudes are significantly (P<0.001) correlated with strain loading and unloading rates and not with strain loading and unloading times. In those cases when strain magnitudes are also correlated with loading times,strain magnitudes are more highly correlated with loading rate than loading time. Multiple regression analyses reveal that variation in strain magnitude is best explained by variation in loading rate. Loading time and related temporal variables (such as overall chew cycle time and chew duty factor) do not explain significant amounts of additional variance. Few and only weak correlations were found between strain magnitude and chew cycle time and chew duty factor. These data suggest that bite force modulation during rhythmic mastication in mammals is mainly achieved by modulating the rate at which force is generated within a chew cycle, and less so by varying temporal parameters. Rate modulation rather than time modulation may allow rhythmic mastication to proceed at a relatively constant frequency, simplifying motor control computation.)
Young Adults' Reactions to Grandparent Painful Self-Disclosure: The Influence of Grandparent Sex and Overall Motivations for Communication
Authors: Barker Valerie
Published: March 2007

This study examined young adult grandchildren's self-reports about the influence of grandparent sex on perceived grandparent painful self-disclosure (PSD) as well as their reactions to grandparent dyad PSD. Perceived grandmother and grandfather motivations for overall communication were assessed as mediators of young adult grandchildren's discomfort with grandparent dyad PSD. Findings show that participants perceived PSD more in their interactions with their maternal grandmothers compared to their maternal grandfathers. These young adult grandchildren were less likely to report discomfort if they perceived grandparents to be communicating overall for the purposes of positive affect, or identity, but more likely to feel discomfort if they perceived grandparents to be communicating for the purpose of control.
Cultural Barriers to Care: Inverting the Problem
Authors: Tripp-Reimer Toni , Choi Eunice , Kelley Lisa Skemp , Enslein Janet C.
Published: March 2007

In Brief

In working with diverse populations, health practitioners often view patients’ culture as a barrier to care. Inverting this problem by viewing the barriers as arising from the culture of biomedicine provides greater direction for practice. Integral to the delivery of culturally appropriate diabetes care are practitioner competencies in specific areas of cultural knowledge, as well as specific skills in intercultural communication, tripartite cultural assessment, selecting among levels of intensity of cultural interventions (neutral, sensitive, innovative, or transformative), adapting patient education, and developing community partnerships.
Psychosocial Barriers to Diabetes Self-Management and Quality of Life
Authors: Glasgow Russell E. , Toobert Deborah J. , Gillette Cynthia D.
Published: March 2007

In Brief

Diabetes self-management can be difficult and frustrating for both patients and practitioners. Information is needed about which barriers present the greatest obstacles for which types of patients, and from this, practical, cost-effective interventions need to be developed. This article reviews existing research on psychosocial and interpersonal barriers to diabetes self-management and quality of life. It also presents new data on a self-efficacy-based barriers instrument and makes recommendations for future research.
Select Vitamins and Minerals in the Management of Diabetes
Authors: O’Connell Belinda S.
Published: March 2007

In Brief

The use of vitamin, mineral, and other complementary nutrition-based therapies has increased dramatically in the United States. Many health care providers are also beginning to explore the use of these therapies in their practices. For those of us who work in conventional health care settings, this is a new venture. But for many of our patients who have been self-medicating with supplements, it is not. This article reviews how micronutrient requirements are determined and summarizes current recommendations for supplementation and the most pertinent research on the use of key vitamins and minerals in diabetes management.
Is Massage Useful in the Management of Diabetes? A Systematic Review
Authors: Ezzo Jeanette , Donner Thomas , Nickols Diane , Cox Mary
Published: March 2007

In Brief

Massage is among the fastest growing complementary therapies used in the United States. This article systematically reviews the available evidence on potential benefits and adverse effects of massage for people with diabetes. Massage at injection sites may increase insulin absorption. In addition, uncontrolled studies suggest that massage may have a positive effect on blood glucose levels and symptoms of diabetic neuropathy. However, randomized, placebo-controlled studies are needed to confirm any short- and long-term benefits of massage as a complementary treatment for diabetes and to further define an optimal massage treatment.
Group Medical Appointments in Diabetes Care: Is There a Future?
Authors: Weinger Katie
Published: March 2007

In Brief

New models are emerging for using patient groups in the medical care of diabetes. Most include a diabetes education component. Several of these models have demonstrated improved glycemic outcomes during randomized trials. However, determining which component of these care delivery systems is responsible for any realized clinical improvement is difficult. Thus, more well-designed, randomized, controlled studies and more details on applying group techniques to medical appointments are necessary to understand the health and cost-effectiveness outcomes of group medical appointments.
Thiazolidinediones: Potential Link Between Insulin Resistance and Cardiovascular Disease
Authors: Aroda Vanita R. , Henry Robert R.
Published: March 2007

The thiazolidinediones are a unique class of oral antidiabetic agents that has been shown to directly reduce insulin resistance at sites of insulin action, specifically adipose tissue, skeletal muscle, and the liver. By reducing insulin resistance, these drugs influence many of the modifiable cardiovascular risk factors associated with the insulin resistance syndrome, also known as the cardiovascular dysmetabolic syndrome. Such cardiovascular factors are involved in the development of atherosclerosis and include dyslipidemia, hypertension, microalbuminuria, impaired vascular reactivity, and impaired fibrinolysis. Whether these effects of the thiazolidinediones translate to a reduced incidence of cardiovascular events in people with type 2 diabetes remains to be seen.
The Impact of Bariatric Surgery on Severely Obese Patients With Diabetes
Authors: Eisenberg Daniel , Bell Robert L.
Published: March 2007

In Brief

Obesity and diabetes are two often interrelated and escalating health problems. For patients with clinically severe obesity and diabetes, surgery provides the best option for the cure of both disease processes. The resolution of diabetes may not result from weight loss alone, but instead may be caused by (surgical) alateration of the enteroinsular axis.
Family Conflict and Diabetes Management in Youth: Clinical Lessons From Child Development and Diabetes Research
Authors: Anderson Barbara J.
Published: March 2007

In Brief

This articles focuses on family conflict and parenting behavior and their link to self-esteem, treatment adherence, and glycemic control in children and adolescents with type 1 diabetes. From the diabetes literature and normal child development research, the concept of “authoritative parenting” seems especially applicable to the coping tasks facing parents and youth around the management of type 1 diabetes. Research on general family conflict, diabetes-specific family conflict, and child development are discussed with respect to the translation of findings to assist health care providers and parents.
Views From Within and Beyond: Illness Narratives of African-American Men With Type 2 Diabetes
Authors: Liburd Leandris C. , Namageyo-Funa Apophia , Jack Leonard , Gregg Edward
Published: March 2007

In Brief The management and impact of type 2 diabetes on the sense of self, lifestyle, and significant others of African-American men is not well understood. This article reports on a study to examine perceptions of managing and coping with diabetes among African-American men and summarizes its findings regarding the distribution of clinical biomarkers, participants'perceptions of the cause of their diabetes, its impact on masculinity, use of home remedies for diabetes care, and the degree to which effective coping skills and social support are engaged and available.
Managing Diabetes in Correctional Facilities
Authors: Edwards Linda L.
Published: March 2007

In Brief Managing diabetes in correctional facilities brings challenges unique to the setting in addition to those encountered in community practice. Although national standards of care have been available to guide medical care of diabetes for many years, efforts to adapt these guidelines to the needs of correctional facilities are relatively new. This article focuses on the challenges of implementing clinical practice recommendations for diabetes in the corrections environment.
A National Study of the Certified Diabetes Educator: Report on a Job Analysis Conducted by the National Certification Board for Diabetes Educators
Authors: Zrebiec John
Published: March 2007

Purpose. The job analysis described in this report was conducted by the National Certification Board for Diabetes Educators (NCBDE) in order to 1) provide a basis for documenting the continuing validity of the Certification Examination for Diabetes Educators, 2) define new areas that should be assessed in future certification examinations, and 3)ensure that the content of certification examinations is job related.

Methods. The study involved developing a diabetes educator job task list and survey, distributing 1,100 surveys, and analyzing survey responses from a multidisciplinary and geographically representative sample of certified diabetes educators.

Results. Three hundred and thirty-nine surveys were suitable for analysis, with relevant demographic subgroups adequately represented. Based on survey data, an examination matrix and detailed content outline was constructed that will be used by NCBDE to assemble future test forms.

Conclusions. Certification examination specifications were developed directly related to the important activities that diabetes educators perform. Future forms of the certification examination will continue to be matched to job-related, criterion-referenced test specifications and will have strong evidence of content validity. Future forms of the exam will contain 200 items at specified cognitive levels, with a representative sampling of tasks within three core areas from the detailed content outline.