bluuebunny/crossref_metadata_2025_split huggingface dataset:
Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin
Authors: Brandsdal Bjørn O. , Smalås Arne O. , Åqvist Johan 
Published: June 2006

AbstractSerine proteinases and their protein inhibitors belong to one of the most comprehensively studied models of protein–protein interactions. It is well established that the narrow trypsin specificity is caused by the presence of a negatively charged aspartate at the specificity pocket. X‐ray crystallography as well as association measurements revealed, surprisingly, that BPTI with glutamatic acid as the primary binding (P1) residue was able to bind to trypsin. Previous free energy calculations showed that there was a substantially unfavorable binding free energy associated with accommodation of ionized P1 Glu at the S1‐site of trypsin. In this study, the binding of P1 Glu to trypsin has been systematically investigated in terms of the protonation states of P1 Glu and Asp189, the orientation of Gln192, as well as the possible presence of counterions using the linear interaction energy (LIE) approach and the free energy perturbation (FEP) method. Twenty‐four conceivable binding arrangements were evaluated and quantitative agreement with experiments is obtained when the P1 Glu binds in its protonated from. The results suggest that P1 Glu is one of the variants of BPTI that inhibit trypsin strongest at low pH, contrary to the specificity profile of trypsin, suggesting a new regulation mechanism of trypsin‐like enzymes. Proteins 2006. © 2006 Wiley‐Liss, Inc.
The planar conformation of a strained proline ring: A QM/MM study
Authors: Donnini Serena , Groenhof Gerrit , Wierenga Rik K. , Juffer André H. 
Published: June 2006

AbstractQM and QM/MM energy calculations have been carried out on an atomic resolution structure of liganded triosephosphate isomerase (TIM) that has an active site proline (Pro168) in a planar conformation. The origin of the planarity of this proline has been identified. Steric interactions between the atoms of the proline ring and a tyrosine ring (Tyr166) on one side of the proline prevent the ring from adopting the up pucker (χ1 is approximately −30°), while the side chain of a nearby alanine (Ala171) forbids the down pucker (χ1 is approximately +30°). To obtain a proline conformation that is in agreement with the experimentally observed planar state, a quantum system of sufficient size is required and should at least include the nearby side chains of Tyr166, Ala171, and Glu129 to provide enough stabilization. It is argued that the current force fields for structure optimization do not describe strained protein fragments correctly. The proline is part of a catalytic loop that closes upon ligand binding. Comparison of the proline conformation in different TIM X‐ray structures, indicates that in the closed conformation of TIM the proline is planar or nearly planar, while in the open conformation it is down puckered. This suggests that the planarity possibly plays a role in the overall catalytic cycle of TIM, presumable acting as a reservoir of energy that becomes available upon loop opening. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Soil application of azadirachtin and 3‐tigloyl‐azadirachtol to control western flower thrips, Frankliniella occidentalis (Thysanoptera: Thripidae): translocation and persistence in bean plants
Authors: Thoeming Gunda , Draeger Gerald , Poehling Hans‐Michael 
Published: June 2006

AbstractTo study the systemic effects of active neem ingredients, the substrate of bean plants was treated with a 170 g kg−1 azadirachtin (NeemAzal‐U; Trifolio‐M GmbH, Lahnau, Germany, registration pending). This product was used at a dose rate of 10 mg AZA (azadirachtin a) and 1.2 mg 3‐tigloyl‐azadirachtol (azadirachtin b) per treated bean plant. Afterwards, the translocation and persistence of AZA and 3‐tigloyl‐azadirachtol and the effects on western flower thrips, Frankliniella occidentalis (Pergande), were studied. Residues of AZA and 3‐tigloyl‐azadirachtol from substrates with different contents of organic matter [pure culture substrate (CS), CS–sand mixture] and from various plant parts were quantified by high‐performance liquid chromatography‐mass spectrometry (HPLC‐MS). The dissipation trends of AZA and 3‐tigloyl‐azadirachtol were similar within the same substrates. A slower decline of both active ingredients was measured with CS than with CS–sand mixture. Residue analysis of the bean plants showed that only small proportions of the initial amounts of AZA and 3‐tigloyl‐azadirachtol applied to the substrate were present in the plant (0.3‐8.1%). Variable amounts of residues of the active components in relation to plant parts and time of analysis indicated a different translocation pattern for the two active ingredients. Higher residues of the active ingredients were found in roots and stems after neem application using CS, whereas higher residues were found in leaves after CS–sand mixture treatments. Mortality of F. occidentalis after NeemAzal‐U soil applications reached up to 95% on CS–sand mixture, compared with 86% in CS. Copyright © 2006 Society of Chemical Industry
Pycnogenol® protects against Ionizing radiation as shown in the intestinal mucosa of rats exposed to X‐rays
Authors: de Moraes Ramos Flávia Maria , Schönlau Frank , Novaes Pedro Duarte , Manzi Flávio Ricardo , Bóscolo Frab Norberto , de Almeida Solange Maria 
Published: June 2006

AbstractX‐rays and gamma radiation delivered to the abdominal region for cancer treatment encompasses severe damage to the intestinal mucosa, which significantly impairs a patient's quality of life. To a great extent the deleterious effects of x‐radiation originate from radiolysis‐induced reactive oxygen species. The well‐researched powerful antioxidant Pycnogenol® was administered orally to rats prior to x‐irradiation with 15 Gy. Histological sections of the intestines showed a dramatically better condition of the mucosal layers compared with the irradiated control animals administered water without Pycnogenol®. Pycnogenol® treatment significantly preserved the height and number of villi as well as the glandular layer and a diminished number of congested vases were present. No intestinal alterations were seen in control animals receiving Pycnogenol® in the absence of radiation. It is concluded that Pycnogenol® provides significant protection from ionizing radiation damage. Copyright © 2006 John Wiley & Sons, Ltd.
Improving upon the ZORA Hamiltonian
Authors: Sadlej Andrzej J. 
Published: June 2006

AbstractThe metric perturbation method is used to derive what is called the normalized zeroth‐order regular approximation (ZORA) Hamiltonian. This Hamiltonian, although derived in a different way, turns out to be equivalent to the infinite‐order regular approximation (IORA) operator of Dyall and van Lenthe. The normalized ZORA Hamiltonian is analyzed in terms of its expansion with respect to the leading order of the fine structure constant. Through the leading second‐order in the fine structure constant, the normalized ZORA Hamiltonian recovers all terms of what is known as the first‐order regular approximation (FORA). The relation of the regular approximation to methods based on the Douglas–Kroll transformation is discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Effect of moderate ethanol dose on dopamine uptake in rat nucleus accumbens in vivo
Authors: Jones Sara R. , Mathews Tiffany A. , Budygin Evgeny A. 
Published: June 2006

AbstractThe present study was designed to evaluate the effects of a moderate dose of ethanol (1 g/kg) on dopamine (DA) dynamics in rat nucleus accumbens (NAc) using fast‐scan cyclic voltammetry. Voltammetric recordings were made every 100 ms at a carbon fiber microelectrode, positioned in the NAc core. Acute ethanol did not significantly alter DA uptake parameters (KmandVmax), but amplitudes of the DA signals were decreased after the drug in both freely moving and anesthetized rats. Therefore, the present in vivo voltammetry results suggest that DA uptake changes are not involved in ethanol‐induced increases in extracellular DA concentrations. Synapse 60:251–255, 2006. © 2006 Wiley‐Liss, Inc.
Enhanced locomotor activity in adult rats with neonatal administration of N‐omega‐nitro‐L‐arginine
Authors: Mejorada Alejandro , Aguilar‐Alonso Patricia , León‐Chavez Bertha Alicia , Flores Gonzalo 
Published: June 2006

AbstractNitric oxide (NO) is a neuronal messenger molecule that plays important roles in the development, maintenance, and functional modifications of brain circuits. We investigated whether the NO levels at different postnatal day (P) periods of the brain develop interference with the locomotion in a novel environment during the postpuberal age (P60). First, using the determination of the nitrite accumulation, we evaluated whether treatment with the NO‐synthase inhibitor N‐nitro‐L‐arginine (L‐NNA) during different neonatal ages (P1 to P3, P4 to P6, and P7 to P9) affected the levels of NO activity in different regions in the neonatal brain of the rat. We then evaluated whether the locomotor activity in the adult rat (P60) is affected by the blocking of the neonatal NO‐activity during a specific period of the development of the nervous system. Neonatal rats with L‐NNA administration at P4 to P6 and P7 to P9 show a significant decrease in the levels of NO activity in all the brain regions. However, the blocking of NO synthesis during the neonatal period between P4 to P6 produced an increase in the locomotion after puberty. These data suggest that during a specific step in the development of the brain, the NO levels may play a critical role in the structures that control the spontaneous locomotion in a novel environment after puberty. Synapse 60:264–270, 2006. © 2006 Wiley‐Liss, Inc.
Surgical management of retraction pockets of the pars tensa with cartilage and perichondrial grafts
Authors: Spielmann P , Mills R 
Published: June 2006

Stable, self-cleansing retraction pockets of the pars tensa are common incidental findings and require no treatment. In other cases, recurrent discharge occurs and there may also be associated conductive hearing loss. In a minority of cases, cholesteatoma may develop.This paper presents the results of surgery using a graft composed of cartilage and perichondrium for retraction pockets involving the posterior half of the tympanic membrane, as well as early results using a larger graft designed to manage retraction of the entire tympanic membrane. Data on 51 patients with posterior retraction pockets are presented. Forty-two (82 per cent) patients had no aural discharge one year following surgery and the tympanic membrane was not retracted in 43 (84 per cent). The larger ‘Mercedes-Benz’ graft was used in four patients and the results obtained suggested that it may prove a successful technique for extensive retraction pockets.
Emergency cardiopulmonary bypass for impassable airway
Authors: Tyagi I , Goyal A , Syal R , Agarwal S K , Tewari P 
Published: June 2006

Introduction: Some medical emergencies need compromised airway management as the first measure. Most of these cases are first seen by an ENT surgeon, whose proper evaluation and timely intervention can prove decisive. Knowledge of alternatives for airway management can prove life-saving, although these may require the active involvement of other specialities.Case reports: Two patients, a 27-year-old man and a 31-year-old woman, presented in respiratory distress with cyanosis. Each had a pedunculated mass in the lower trachea above the carina, with about 90 per cent tracheal lumen obstruction. They were managed successfully with femorofemoral cardiopulmonary bypass and restoration of airway.Conclusion: Femorofemoral cardiopulmonary bypass can be a relatively safe option which gains time for airway management in such conditions. Knowledge of this procedure among ENT surgeons can lead to timely intervention, in properly selected cases, which can save valuable time.
Salvage radiotherapy for patients with increasing prostate-specific antigen levels after radical prostatectomy: evaluation of the role of retrograde urethrography
Authors: Buskirk S. J. , Kraft K. J. , Witt N. J. , Scheuer A. K. , Gianforti B. L. , DeGuzman M. L. , Hunter C. A. , Guida M. , Serago C. F. , Schild S. E. , Collie A. C. 
Published: June 2006

Purpose: To evaluate the role of retrograde urethrography in treatment planning for salvage external beam radiotherapy in patients with increasing prostate-specific antigen levels after radical prostatectomy.Methods and Materials: From July 1988 to December 2002, 173 consecutive patients received external beam radiotherapy for increasing prostate-specific antigen levels after radical prostatectomy. All 173 simulation films were reviewed, and retrograde urethrography was performed in 148 patients (86%). The distance between the line connecting the lower poles of the ischial tuberosities and site of abrupt narrowing of contrast material was measured in all 148 patients. This distance was compared with that measured in 148 consecutive patients with intact prostates who had retrograde urethrography while undergoing treatment planning for definitive radiotherapy.Results: The mean (median) distance from the line connecting the lower poles of the ischial tuberosities to the abrupt narrowing seen in the urethrogram in patients with increasing prostate-specific antigen levels was 1.54cm (1.50cm) compared with 1.73cm (1.80cm) in those with intact prostates (p = 0.0145).Conclusion: Retrograde urethrography is important in treatment planning for salvage radiotherapy of the prostate bed after radical prostatectomy to adequately treat the apex of the prostate bed.
Superrigidity for irreducible lattices and geometric splitting
Authors: Monod Nicolas 
Published: June 2006

We prove general superrigidity results for actions of irreducible lattices on CAT

(
0
)

(0)

spaces, first in terms of the ideal boundary, and then for the intrinsic geometry (also for infinite-dimensional spaces). In particular, one obtains a new and self-contained proof of Margulis’ superrigidity theorem for uniform irreducible lattices in non-simple groups. The proofs rely on simple geometric arguments, including a splitting theorem which can be viewed as an infinite-dimensional (and singular) generalization of the Lawson-Yau/Gromoll-Wolf theorem. Appendix A gives a very elementary proof of commensurator superrigidity; Appendix B proves that all our results also hold for certain non-uniform lattices.
Ecology of Antibiotic Resistance Genes: Characterization of Enterococci from Houseflies Collected in Food Settings
Authors: Macovei Lilia , Zurek Ludek 
Published: June 2006

ABSTRACT

In this project, enterococci from the digestive tracts of 260 houseflies (
Musca domestica
L.) collected from five restaurants were characterized. Houseflies frequently (97% of the flies were positive) carried enterococci (mean, 3.1 × 10
3
CFU/fly). Using multiplex PCR, 205 of 355 randomly selected enterococcal isolates were identified and characterized. The majority of these isolates were
Enterococcus faecalis
(88.2%); in addition, 6.8% were
E. faecium
, and 4.9% were
E. casseliflavus. E. faecalis
isolates were phenotypically resistant to tetracycline (66.3%), erythromycin (23.8%), streptomycin (11.6%), ciprofloxacin (9.9%), and kanamycin (8.3%). Tetracycline resistance in
E. faecalis
was encoded by
tet
(M) (65.8%),
tet
(O) (1.7%), and
tet
(W) (0.8%). The majority (78.3%) of the erythromycin-resistant
E. faecalis
isolates carried
erm
(B). The conjugative transposon Tn
916
and members of the Tn
916/
Tn
1545
family were detected in 30.2% and 34.6% of the identified isolates, respectively.
E. faecalis
carried virulence genes, including a gelatinase gene (
gelE
; 70.7%), an aggregation substance gene (
asa1
; 33.2%), an enterococcus surface protein gene (
esp
; 8.8%), and a cytolysin gene (
cylA
; 8.8%). Phenotypic assays showed that 91.4% of the isolates with the
gelE
gene were gelatinolytic and that 46.7% of the isolates with the
asa1
gene aggregated. All isolates with the
cylA
gene were hemolytic on human blood. This study showed that houseflies in food-handling and -serving facilities carry antibiotic-resistant and potentially virulent enterococci that have the capacity for horizontal transfer of antibiotic resistance genes to other bacteria.
New Recombinant
Escherichia coli
Strain Tailored for the Production of Poly(3-Hydroxybutyrate) from Agroindustrial By-Products
Authors: Nikel Pablo I. , de Almeida Alejandra , Melillo Evelia C. , Galvagno Miguel A. , Pettinari M. Julia 
Published: June 2006

ABSTRACT

A recombinant
E. coli
strain (K24K) was constructed and evaluated for poly(3-hydroxybutyrate) (PHB) production from whey and corn steep liquor as main carbon and nitrogen sources. This strain bears the
pha
biosynthetic genes from
Azotobacter
sp. strain FA8 expressed from a T5 promoter under the control of the lactose operator. K24K does not produce the lactose repressor, ensuring constitutive expression of genes involved in lactose transport and utilization. PHB was efficiently produced by the recombinant strain grown aerobically in fed-batch cultures in a laboratory scale bioreactor on a semisynthetic medium supplemented with the agroindustrial by-products. After 24 h, cells accumulated PHB to 72.9% of their cell dry weight, reaching a volumetric productivity of 2.13 g PHB per liter per hour. Physical analysis of PHB recovered from the recombinants showed that its molecular weight was similar to that of PHB produced by
Azotobacter
sp. strain FA8 and higher than that of the polymer from
Cupriavidus necator
and that its glass transition temperature was approximately 20°C higher than those of PHBs from the natural producer strains.
Necrotrophic Growth of
Legionella pneumophila
Authors: Temmerman R. , Vervaeren H. , Noseda B. , Boon N. , Verstraete W. 
Published: June 2006

ABSTRACT

This study examined whether
Legionella pneumophila
is able to thrive on heat-killed microbial cells (necrotrophy) present in biofilms or heat-treated water systems. Quantification by means of plate counting, real-time PCR, and flow cytometry demonstrated necrotrophic growth of
L. pneumophila
in water after 96 h, when at least 100 dead cells are available to one
L. pneumophila
cell. Compared to the starting concentration of
L. pneumophila
, the maximum observed necrotrophic growth was 1.89 log units for real-time PCR and 1.49 log units for plate counting. The average growth was 1.57 ± 0.32 log units (
n
= 5) for real-time PCR and 1.14 ± 0.35 log units (
n
= 5) for plate counting. Viability staining and flow cytometry showed that the fraction of living cells in the
L. pneumophila
population rose from the initial 54% to 82% after 96 h. Growth was measured on heat-killed
Pseudomonas putida
,
Escherichia coli
,
Acanthamoeba castellanii
,
Saccharomyces boulardii
, and a biofilm sample. Gram-positive organisms did not result in significant growth of
L. pneumophila
, probably due to their robust cell wall structure. Although necrotrophy showed lower growth yields compared to replication within protozoan hosts, these findings indicate that it may be of major importance in the environmental persistence of
L. pneumophila
. Techniques aimed at the elimination of protozoa or biofilm from water systems will not necessarily result in a subsequent removal of
L. pneumophila
unless the formation of dead microbial cells is minimized.
Yersiniabactin Production by
Pseudomonas syringae
and
Escherichia coli
, and Description of a Second Yersiniabactin Locus Evolutionary Group
Authors: Bultreys Alain , Gheysen Isabelle , de Hoffmann Edmond 
Published: June 2006

ABSTRACT

The siderophore and virulence factor yersiniabactin is produced by
Pseudomonas syringae
. Yersiniabactin was originally detected by high-pressure liquid chromatography (HPLC); commonly used PCR tests proved ineffective. Yersiniabactin production in
P. syringae
correlated with the possession of
irp1
located in a predicted yersiniabactin locus. Three similarly divergent yersiniabactin locus groups were determined: the
Yersinia pestis
group, the
P. syringae
group, and the
Photorhabdus luminescens
group; yersiniabactin locus organization is similar in
P. syringae
and
P. luminescens
. In
P. syringae
pv. tomato DC3000, the locus has a high GC content (63.4% compared with 58.4% for the chromosome and 60.1% and 60.7% for adjacent regions) but it lacks high-pathogenicity-island features, such as the insertion in a tRNA locus, the integrase, and insertion sequence elements. In
P. syringae
pv. tomato DC3000 and pv. phaseolicola 1448A, the locus lies between homologues of Psyr_2284 and Psyr_2285 of
P. syringae
pv. syringae B728a, which lacks the locus. Among tested pseudomonads, a PCR test specific to two yersiniabactin locus groups detected a locus in genospecies 3, 7, and 8 of
P. syringae
, and DNA hybridization within
P. syringae
also detected a locus in the pathovars phaseolicola and glycinea. The PCR and HPLC methods enabled analysis of nonpathogenic
Escherichia coli
. HPLC-proven yersiniabactin-producing
E. coli
lacked modifications found in
irp1
and
irp2
in the human pathogen CFT073, and it is not clear whether CFT073 produces yersiniabactin. The study provides clues about the evolution and dispersion of yersiniabactin genes. It describes methods to detect and study yersiniabactin producers, even where genes have evolved.
New Lineage of Filamentous, Spore-Forming, Gram-Positive Bacteria from Soil
Authors: Cavaletti Linda , Monciardini Paolo , Bamonte Ruggiero , Schumann Peter , Rohde Manfred , Sosio Margherita , Donadio Stefano 
Published: June 2006

ABSTRACT

A novel bacterial strain that was isolated from an Italian soil and was designated SOSP1-21
T
forms branched mycelia in solid and liquid media and has a filamentous morphology similar to that of some genera belonging to the
Actinobacteria
. Electron microscopy showed that this organism has a grape-like appearance, resulting from interlacing of spores originating from sporophoric hyphae. Ten strains that are morphologically related to SOSP1-21
T
were recovered from soil. Phylogenetic analyses of 16S rRNA gene segments confirmed the relatedness of these strains to SOSP1-21
T
and indicated that the newly isolated strains form separate clades in a deeply branching lineage. The closest matches for the 16S rRNA sequences of all the strains (around 79% identity) were matches with representatives of the
Chloroflexi
, although the affiliation with this division was not supported by high bootstrap values. The strains are mesophilic aerobic heterotrophs and are also capable of growing under microaerophilic conditions. They all stain gram positive. Strain SOSP1-21
T
contains ornithine, alanine, glutamic acid, serine, and glycine as the peptidoglycan amino acids. In addition, an unusual level of C16:1 2OH (30%) was found in the cellular fatty acids. The G+C content of SOSP1-21
T
genomic DNA is 53.9%, and MK-9(H
2
) was the only menaquinone detected. All these data suggest that SOSP1-21
T
and the related strains may constitute a new division of filamentous, spore-forming, gram-positive bacteria. We propose the name
Ktedobacter racemifer
gen. nov., sp. nov. for strain SOSP1-21
T
.