bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colicin E3 cleavage of 16S rRNA impairs decoding and accelerates tRNA translocation on Escherichia coli ribosomes
Authors: Lancaster Lorna E. , Savelsbergh Andreas , Kleanthous Colin , Wintermeyer Wolfgang , Rodnina Marina V. 
Published: May 2008

SummaryThe cytotoxin colicin E3 targets the 30S subunit of bacterial ribosomes and specifically cleaves 16S rRNA at the decoding centre, thereby inhibiting translation. Although the cleavage site is well known, it is not clear which step of translation is inhibited. We studied the effects of colicin E3 cleavage on ribosome functions by analysing individual steps of protein synthesis. We find that the cleavage affects predominantly the elongation step. The inhibitory effect of colicin E3 cleavage originates from the accumulation of sequential impaired decoding events, each of which results in low occupancy of the A site and, consequently, decreasing yield of elongating peptide. The accumulation leads to an almost complete halt of translation after reading of a few codons. The cleavage of 16S rRNA does not impair monitoring of codon–anticodon complexes or GTPase activation during elongation‐factor Tu‐dependent binding of aminoacyl‐tRNA, but decreases the stability of the codon–recognition complex and slows down aminoacyl‐tRNA accommodation in the A site. The tRNA–mRNA translocation is faster on colicin E3‐cleaved than on intact ribosomes and is less sensitive to inhibition by the antibiotic viomycin.
PigZ, a TetR/AcrR family repressor, modulates secondary metabolism via the expression of a putative four‐component resistance‐nodulation‐cell‐division efflux pump, ZrpADBC, in Serratia sp. ATCC 39006
Authors: Gristwood Tamzin , Fineran Peter C. , Everson Lee , Salmond George P. C. 
Published: May 2008

SummaryThe Gram‐negative enterobacterium, Serratia sp. ATCC 39006 synthesizes several secondary metabolites, including prodigiosin (Pig) and a carbapenem antibiotic (Car). A complex hierarchical network of regulatory proteins control Pig and Car production. In this study we characterize a TetR family regulator, PigZ, which represses transcription of a divergently transcribed putative resistance‐nodulation‐cell‐division (RND) efflux pump, encoded by zrp (PigZ repressed pump) ADBC, via direct binding to the zrpA‐pigZ intergenic region. Unusually, this putative RND pump contains two predicted membrane fusion proteins (MFPs), ZrpA and ZrpD. A mutation in pigZ resulted in multiple phenotypic changes, including exoenzyme production, motility and differential regulation of Pig and Car production. A polar suppressor mutation, within zrpA, restored all tested phenotypes to parental strain levels, indicating that the changes observed are due to the increase in expression of ZrpADBC in the absence of the repressor, PigZ. Genomic deletions of zrpA and zrpD indicate that the MFP ZrpD, but not ZrpA, is essential for activity of the putative pump. Bioinformatic analysis revealed that putative RND efflux pumps encoding two MFP components are not uncommon, particularly among plant‐associated, Gram‐negative bacteria. In addition, based on phylogenetic analysis, we propose that these pairs of MFPs consist of two distinct subtypes.
Structure and functional properties of the Bacillus subtilis transcriptional repressor Rex
Authors: Wang Ellen , Bauer Mikael C. , Rogstam Annika , Linse Sara , Logan Derek T. , Von Wachenfeldt Claes 
Published: May 2008

SummaryThe transcription factor Rex has been implicated in regulation of the expression of genes important for fermentative growth and for growth under conditions of low oxygen tension in several Gram‐positive bacteria. Rex senses the redox poise of the cell through changes in the NADH/NAD+ ratio. The crystal structures of two essentially identical Rex proteins, from Thermus aquaticus and T. thermophilus, have previously been determined in complex with NADH. Here we present the crystal structure of the Rex protein from Bacillus subtilis, as well as extensive studies of its affinity for nucleotides and DNA, using surface plasmon resonance, isothermal titration calorimetry and electrophoretic mobility shift assays. We show that Rex has a very high affinity for NADH but that its affinity for NAD+ is 20 000 times lower. However, the NAD+ affinity is increased by a factor of 30 upon DNA binding, suggesting that there is a positive allosteric coupling between DNA binding and NAD+ binding. The crystal structures of two pseudo‐apo forms (from crystals soaked with NADH and cocrystallized with ATP) show a very different conformation from the previously determined Rex:NADH complexes, in which the N‐terminal domains are splayed away from the dimer core. A mechanism is proposed whereby conformational changes in a C‐terminal domain‐swapped helix mediate the transition from a flexible DNA binding form to a locked NADH‐bound form incapable of binding DNA.
Variants of CARD15, TNFA and PTPN22 and susceptibility to Crohn’s disease in the Czech population: high frequency of the CARD15 1007fs
Authors: Hradsky O. , Lenicek M. , Dusatkova P. , Bronsky J. , Nevoral J. , Valtrova V. , Kotalova R. , Szitanyi P. , Petro R. , Starzykova V. , Bortlik M. , Vitek L. , Lukas M. , Cinek O. 
Published: May 2008

AbstractCrohn’s disease (CD) has been shown to be associated with the variants in the CARD15 gene as well as in other genes involved in the immune response. The frequencies of the variants profoundly differ among populations and so does the associated risk. We examined the associations of variants in the CARD15, TNFA and PTPN22 genes with pediatric‐onset and adult‐onset CD in the Czech population. Genotype, phenotype and allelic frequencies were compared between 345 patients with CD (136 pediatric‐onset and 209 adult‐onset patients) and 501 unrelated healthy controls. At least one minor allele of the CARD15 gene was carried by 46% patients and only 21% control subjects (OR = 3.2, 95% CI 2.4–4.4). In a multiple logistic regression model, the strongest association with CD was found for the 1007fs variant (OR = 4.6, 95% CI 3.0–7.0), followed by p.G908R (OR = 2.9, 95% CI 1.5–5.7) and p.R702W (OR = 1.7, 95% CI 1.0–2.9), while no independent association was found for the remaining variants in the CARD15 gene (p.268S, p.955I and p.289S), for the p.R620W variant in the PTPN22 gene or for the g.−308G>A variant in the TNFA gene. The age at CD onset was strongly modified by positivity for the 1007fs allele: it was present in 42% pediatric‐onset and only 25% adult‐onset patients. In conclusion, we report a high frequency of the minor allele of the CARD15 1007fs polymorphism in the Czech population and a strong effect of this allele on the age at disease onset.
Peptides: the cornerstone of HLA‐B27 biology and pathogenetic role in spondyloarthritis
Authors: Marcilla M. , López de Castro J. A. 
Published: May 2008

AbstractThe association of human leukocyte antigen (HLA)‐B27 to ankylosing spondylitis is one of the strongest between a major histocompatibility complex molecule and a disease. Yet, the basis for this association remains unknown. Several hypotheses, each based on a particular feature of HLA‐B27, guide much of the current research on the pathogenesis of this disease, but none has yet satisfactorily explained its mechanism and the differential association of B27 subtypes to it. In this review, the pathogenetic role of HLA‐B27 will be analyzed from a global perspective of its biology, emphasizing the interdependency of multiple molecular features and the likely influence of disease‐modifying gene products. From this perspective, peptide binding emerges as the cornerstone of all other biological properties.
Is the intrinsic potassium content of forages an important factor in intake regulation of dairy cows?
Authors: Leiber F. , Wettstein H.‐R. , Kreuzer M. 
Published: May 2008

SummaryHay from intensively managed grassland with high nutrient density and digestibility containing 29 g potassium/kg dry matter (DM) and hay from an alpine pasture, clearly lower in energy, digestibility and potassium (12 g/kg DM) were offered as sole feeds to 18 lactating dairy cows following a change‐over arrangement within three periods of 21 days each (schedule either alpine‐lowland‐alpine or lowland‐alpine‐lowland hay). Faeces and urine were quantitatively collected over 7 days. Dry matter intake was similar and neutral detergent fibre (NDF) intake was higher with alpine than with lowland hay (1.57 kg/100 kg vs. 1.43 kg/100 kg body weight). Potassium intake was approximately three times lower with alpine than with lowland hay. Urinary water output was closely correlated with potassium intake. It was also correlated with DM intake but only in animals receiving lowland hay, while it remained independent from intake when alpine hay was fed. Plasma osmolality was lower when alpine hay was fed. As energy requirements were not covered with either diet, the lower NDF intake with lowland hay was assumed to have been caused by higher ruminal osmolality because of the higher intrinsic potassium concentrations of this hay type. Further studies are necessary to determine potassium levels critical for feed intake.
Thalassiocyclus pankensis sp. nov., a new diatom from the Panke Swamp, northern Japan (Bacillariophyta)
Authors: Tanaka Hiroyuki , Nagumo Tamotsu 
Published: May 2008

SUMMARY Thalassiocyclus pankensis sp. nov. is described from Panke Swamp (Panke‐numa) located in Horonobe Town, Hokkaido, northern Japan. The species is characterized by a strong transversely undulate central area of the valve face with one to three fultoportulae on the elevated part and one fultoportula on the depressed part. The external valve face has costate radial interfascicles and very wide fascicles on the marginal area. Thickened openings of mantle fultoportulae are located at the end of interfascicles with roofed board spines. The cingulum consists of five bands. The new species is compared to the only other species belonging to genus Thalassiocyclus, T. lucens (Hustedt) Håkansson & Mahood. Thalassiocyclus pankensis is the second species in the genus Thalassiocyclus and also the first report of a Thalassiocyclus species in Japan.
Research Note: Molecular phylogenetic affiliations of Dissodinium pseudolunula, Pheopolykrikos hartmannii, Polykrikos cf. schwartzii and Polykrikos kofoidii to Gymnodinium sensu stricto species (Dinophyceae)
Authors: Kim Keun‐Yong , Iwataki Mitsunori , Kim Chang‐Hoon 
Published: May 2008

SUMMARYPartial large subunit ribosomal DNA (LSU rDNA) sequences of Dissodinium pseudolunula Swift ex Elbrächter et Drebes, Pheopolykrikos hartmannii (Zimmermann) Matsuoka et Fukuyo, Polykrikos cf. schwartzii Bütschli and Polykrikos kofoidii Chatton were analyzed to reveal their phylogenetic status. The four athecate dinoflagellate species fell within the clade of Gymnodinium sensu G. Hansen et Moestrup supported by high likelihood values without apparent phylogenetic relationships to neither Gymnodinium species nor each other. Their genetic affiliations to typical Gymnodinium species were morphologically supported by the loop‐shaped apical grooves in Pheopolykrikos and Polykrikos species and the Gymnodinium‐like motile stage at least once during pleomorphic life cycles in D. pseudolunula and Ph. hartmannii.
Seasonal variation in the biomass, quantity and quality of agar from Gelidiella acerosa (Forsskal) Feldmann et Hamel (Gelidiales, Rhodophyta) from the Gulf of Mannar Marine Biosphere Reserve, India
Authors: Ganesan Meenakshisundaram , Reddy Chennur R.K. , Eswaran Karuppanan , Jha Bhavanath 
Published: May 2008

SUMMARYThe Gulf of Mannar on the southeast coast of India, which has recently been declared as biosphere reserve, is the main harvesting place of Gelidiella acerosa for the Indian agar industry. The biomass harvested from natural stocks was estimated to be over 10 000 tonnes dry weight (DW) in the last two decades and is a serious cause of concern on long term sustainability of this valuable resource from this region. The present study reports the seasonal variation in the biomass and agar yield and quality from G. acerosa in four different habitats such as Rameswaram (rocky intertidal), Ervadi (lower intertidal), Sethukarai (subtidal) and Krusadai Island (lagoon reef area). A maximum biomass of 260 ± 26 g DW m−2 was recorded from Ervadi, whereas Sethukarai showed the highest percentage cover (69.83 ± 4.83%) and density (208.20 ± 30.16 plants m−2). Biomass, percentage cover and density were lowest in Rameswaram and significantly lower (P < 0.001) than the other three stations. A single peak in biomass was observed with autumn maxima in Ervadi and Rameswaram and southwest monsoon maxima in Sethukarai and Krusaidai Island. Length of G. acerosa was maximum (9.65 ± 0.25 cm) in Ervadi and the branch index value was maximum (24.70 ± 4.01 br−1 g−1 DW) for Rameswaram. Agar yield (37.24 ± 7.59%) and gel strength (448.66 ± 6.50 g/cm2) were higher in Sethukarai plants. The agar yields attained a peak in the northeast monsoon and decreased in summer, whereas a reverse trend was observed for gel strength. Evidently, agar yield showed a strong negative correlation with gel strength (P < 0.0001) and gelling (P < 0.0001) and melting temperatures (P < 0.01). The single annual peak in biomass observed in the present study, as compared with two peaks reported earlier, are attributed to the continuous overharvesting that would have had an effect on the overall annual biomass production. The findings of this study reveal that a single harvest during the autumn months (January to March) could yield optimum biomass with moderate agar and that would be the best for sustainable usage and conservation of this resource from this region.
New red alga Meristotheca imbricata (Solieriaceae, Gigartinales) from Japan
Authors: Faye Etienne Jean , Kogame Kazuhiro , Shimada Satoshi , Kawaguchi Shigeo , Masuda Michio 
Published: May 2008

SUMMARYA new red alga Meristotheca imbricata Faye et Masuda (Solieriaceae, Gigartinales) was described on the basis of specimens collected from southern Japan. Although this species might have been for a long time included in the concept of M. coacta Okamura, until recently a very poorly known alga, it is distinguished from the latter by the following features: (i) each thallus consists of one primary blade and several secondary blades, the latter arising from the apical or subapical portion of terminal segments of the primary blade; (ii) the individual blades are repeatedly dichotomously divided into linear segments of which margins are neither undulate nor crispate, and are fleshy, imbricate, frequently anastomosing and often acervate; (iii) each tetrasporangial initial is attached by a basal pit‐connection to the parental cell, and the position of the pit‐connection changes from basal to lateral by inward growth of the tetrasporangium; and (iv) the carpogonial branches sometimes have a one‐celled sterile lateral.
Alpha–beta diversity in trap‐nesting wasps (Hymenoptera: Aculeata) in Southern Brazil
Authors: Buschini Maria Luisa Tunes , Woiski Thiago Demetrius 
Published: May 2008

AbstractThis study was carried out at the Parque Municipal das Araucárias, in the municipality of Guarapuava, state of Paraná, southern Brazil. The aims of the present study were to access the spectrum of wasp species inhabiting trap‐nests in three habitats, to record their richness and diversity and elucidate the process responsible for their composition and abundance and to investigate if there is difference in their diversity between Brazilian tropical and subtropical regions. A total of 1097 nests, belonging to 21 species of solitary wasps, were collected. Of these, nine belonged to the family Vespidae (42.86%), six to Pompilidae (28.57%), four to Crabronidae (19.05%) and two to Sphecidae (9.52%). Crabronidae was the most abundant family in the samplings, with a total of 927 collected nests (84.3%). The environment that presented the greatest species diversity, richness and evenness was the grassland areas. Using the Bray–Curtis coefficient (beta diversity), the greatest similarity, in relation to species abundance, occurred between swamp and grasslands. In contrast, the araucaria forest was the habitat with the greatest dissimilarity, a result corroborated by the correspondence analysis.
Patterns of intervention for renal lesions in von Hippel‐Lindau disease
Authors: Matin Surena F. , Ahrar Kamran , Wood Christopher G. , Daniels Molly , Jonasch Eric 
Published: May 2008

OBJECTIVETo review the records of patients at our centre with von Hippel‐Lindau (VHL) disease, to determine the incidence of renal cell carcinoma (RCC) and patterns of intervention using minimally invasive therapies.PATIENTS AND METHODSPatients with genetically confirmed VHL were evaluated in a multidisciplinary clinical care centre established in 2003. Patients were preferentially offered percutaneous radiofrequency ablation (RFA). Cystic tumours were considered contraindications to RFA, as were larger tumours or extensive multifocality with tumours of >3 cm. These patients had either open partial nephrectomy (OPN) or, in unsalvageable cases, radical nephrectomy.RESULTSOf 38 patients with VHL, 16 (42%) were found to have RCC; two with small tumours are under observation. Fourteen of the 16 have had a total of 25 renal interventions, none of whom has progressed to end‐stage renal disease. OPN was performed in 15 (60%) cases, including those who had had multiple bilateral procedures; RFA was used in five (20%) cases. After median follow‐up of 41 months, local recurrence was detected in 33%; the metastasis‐free survival rate was 93.3% and overall survival 87.5%.CONCLUSIONSOf patients with VHL, 88% with renal involvement require interventions for their kidneys. OPN is the primary method used, and was successful both as a primary and secondary procedure in 60% of cases. In only 20% was RFA possible due to limitations of current technology. The introduction of protocol‐based targeted therapies holds the promise of reducing the number of interventions required for treating VHL.
Retrospective outcome analysis of one‐stage penile urethroplasty using a flap or graft in a homogeneous series of patients
Authors: Barbagli Guido , Morgia Guiseppe , Lazzeri Massimo 
Published: May 2008

OBJECTIVETo compare the results of a one‐stage penile flap or graft urethroplasty.PATIENTS AND METHODSSixty‐three patients had a penile urethroplasty using one‐stage techniques; 18 (29%) had a one‐stage flap urethroplasty and 45 (71%) a one‐stage urethroplasty using skin (23) or oral mucosal (22) grafts. The clinical outcome was considered a failure when any instrumentation was needed after surgery.RESULTSThe mean follow‐up was 55 months; of the 63 procedures, 48 (76%) were successful and 15 (24%) failures. Of 18 patients who had a one‐stage flap urethroplasty, 12 (67%) were successful and six (33%) were failures; of the 45 who had one‐stage graft urethroplasty, 36 (80%) were successful and nine (20%) were failures; of 23 penile skin grafts, 18 (78%) were successful and five (22%) were failures; and of 22 oral mucosal grafts, 18 (82%) were successful and four (18%) were failures.CONCLUSIONSThe use of grafts for one‐stage penile urethroplasty gave a higher success rate (80%) than flaps (67%). The difference in the success rate between oral mucosal grafts (82%) and skin grafts (78%) was not clinically significant.
A randomized clinical trial of suspension technique for improving early recovery of urinary continence after radical retropubic prostatectomy
Authors: Noguchi Masanori , Kakuma Tatsuyuki , Suekane Shigetaka , Nakashima Osamu , Mohamed Elnisr Rashed , Matsuoka Kei 
Published: May 2008

OBJECTIVETo evaluate, in a prospective, single‐blind, randomized trial, the safety and efficacy of a suspension technique for improving early recovery of continence after radical retropubic prostatectomy (RRP).PATIENTS AND METHODSWe randomly assigned 60 men with clinically localized prostate cancer to RRP; 30 were treated with the suspension technique and the remaining 30 were not. All patients had RRP by the same surgeon followed by early catheter removal on the third day after RRP. The primary outcome measures were the interval to recovery of continence, and the positive margin rates. The continence status was evaluated by a third party using validated questionnaires at baseline before RRP and at 4 and 7 days, and 2 weeks, 1, 3, 6 and 12 months after RRP.RESULTSThe suspension technique resulted in significantly greater continence rates at 1, 3 and 6 months after RRP of 53% vs 20%, 73% vs 47% and 100% vs 83%. Kaplan‐Meier curves also showed that patients in the suspension group had a significantly earlier recovery of continence than in the no‐suspension group; the median (95% confidence interval) interval for recovery was 31 (12–74) days in the suspension group and 90 (65–150) days in the no‐suspension group (log rank test, P = 0.002). The groups had no significant differences in their histological status.CONCLUSIONSThe suspension technique had a significant effect on the earlier recovery of urinary continence within 6 months after RRP, without compromising the oncological outcome of RRP.
The development of a rat model of erectile dysfunction after radical prostatectomy: preliminary findings
Authors: Kaufmann Oskar , Claro Joaquim , Cury Jose , Andrade Enrico , Longo Beatriz , Aguiar Wilson , Mello Luiz , Srougi Miguel 
Published: May 2008

OBJECTIVETo develop a rat model of erectile dysfunction (ED) after cavernous nerve injury.MATERIALS AND METHODSGiven the great similarity between the anatomical structure of the cavernous nerve in rats and humans, 24 rats underwent dissections and the cavernous nerves were identified with the aid of an operating microscope. Then the rats were randomized into two groups: sham‐operated controls and a bilateral cavernous nerve section group. At 3 months after surgery, the rats were evaluated for their response to an apomorphine challenge.RESULTSThe erectile response after an apomorphine challenge was normal in all the control rats, while there were no erections in the bilateral injured group.CONCLUSIONThe rat major autonomic ganglion and its cavernous nerve can be identified with the aid of a microscope. Rats are inexpensive and easy to handle, thus a good animal for developing an ED model of cavernous nerve injury. In the present study, the rats with cavernous nerve injury lost erectile capacity in a reliable and reproducible fashion. Because of the great similarity between the cavernous nerve of rats and humans, one may consider this technique as a reliable experimental model for studying ED after radical prostatectomy.
The ipsilateral cortico‐spinal tract is activated after hemiparetic stroke
Authors: Misawa S. , Kuwabara S. , Matsuda S. , Honma K. , Ono J. , Hattori T. 
Published: May 2008

Background and purpose: The presence of a projection from the primary motor cortex to the ipsilateral muscles has been established in human, but whether this pathway contributes to functional recovery after stroke is unclear. We investigated whether the ipsilateral tract is activated in hemiparetic stroke.Methods: Motor‐evoked potentials (MEPs) were simultaneously recorded from the bilateral trapezius or abductor digiti minimi (ADM) muscles after magnetic stimulation to the motor cortex in 40 acute stroke patients.Results: At rest, ipsilateral trapezius MEPs were recordable in none of the 24 normal controls, and in 38% of the patients after stimulation to the non‐affected hemisphere (P < 0.001). With voluntary contraction, ipsilateral trapezius MEPs were elicited in 21% of the normal controls and 73% of the patients (P < 0.001). Ipsilateral ADM MEPs were rarely recordable in both controls (0%) and patients (3%). The presence of ipsilateral trapezius MEPs was associated with less severe paresis in the trapezius (P = 0.04) and deltoid (P = 0.07), but not in the more distal muscles.Conclusions: The ipsilateral cortico‐spinal tract is acutely facilitated after stroke in the trunk or proximal muscles, but not in the hand muscles. Activation of such pathway appears to partly compensate motor dysfunction of the trunk/proximal muscles.