bluuebunny/crossref_metadata_2025_split 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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.
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.
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

AbstractWe 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

SUMMARYSpontaneous 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

SUMMARY
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

SUMMARYIn 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

SUMMARYBased 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.)