bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean
Authors: Innes Roger W. , Ameline-Torregrosa Carine , Ashfield Tom , Cannon Ethalinda , Cannon Steven B. , Chacko Ben , Chen Nicolas W.G. , Couloux Arnaud , Dalwani Anita , Denny Roxanne , Deshpande Shweta , Egan Ashley N. , Glover Natasha , Hans Christian S. , Howell Stacy , Ilut Dan , Jackson Scott , Lai Hongshing , Mammadov Jafar , del Campo Sara Martin , Metcalf Michelle , Nguyen Ashley , O'Bleness Majesta , Pfeil Bernard E. , Podicheti Ram , Ratnaparkhe Milind B. , Samain Sylvie , Sanders Iryna , Ségurens Béatrice , Sévignac Mireille , Sherman-Broyles Sue , Thareau Vincent , Tucker Dominic M. , Walling Jason , Wawrzynski Adam , Yi Jing , Doyle Jeff J. , Geffroy Valérie , Roe Bruce A. , Maroof M.A. Saghai , Young Nevin D.
Published: October 2008

The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
Synchrotron powder diffraction characterization of the zeolite-based (p-N,N-dimethylnitroaniline–mordenite) guest–host phase
Authors: Porcher Florence , Borissenko Elena , Souhassou Mohamed , Takata Masaki , Kato Kenichi , Rodriguez-Carvajal Juan , Lecomte Claude
Published: October 2008

The crystal structure of a new phase consisting of the inclusion of the hyperpolarizable molecule p-N,N-dimethylnitroaniline (dimethyl-para-nitroaniline or dmpNA) in the large-pore zeolite mordenite (MOR) has been determined from high-resolution synchrotron powder diffraction at 300 and 90 K. The unit-cell parameters and space group at 300 K are similar to those of as-synthesized mordenite. The crystallographic study indicates that the MOR straight channels are almost fully loaded with molecules that are disordered over eight symmetry-related sites. As expected, the molecules are located in the large 12-membered ring channel, at the intersection with the secondary eight-membered channel with which they might form hydrogen bonds. The elongation axes (and then the dipole moments) of the molecules are slightly tilted (28.57°) from [001]. The configuration found suggests an interaction of dmpNA with framework O atoms through its methyl groups.
Isosymmetrical phase transition in α-YbV4O8
Authors: Friese Karen , Kanke Yasushi , Fitch Andy N. , Morgenroth Wolfgang , Grzechnik Andrzej
Published: October 2008

The structure of YbV4O8 is related to the CaFe2O4 structure type. VO6 octahedra form a three-dimensional framework with tunnels in which the Yb3+ ions are incorporated. Two different polymorphs α and β are known and differ mainly in the arrangement of the Yb ions within the framework. We studied the structure and magnetic properties of α-YbV4O8 as a function of temperature. At approximately 70 K α-YbV4O8 undergoes a first-order isosymmetrical phase transition (P21/n → P21/n). While in the high-temperature α phase the three V3+ and one V4+ are disordered over the four symmetrically independent octahedral sites, in the low-temperature α′ phase complete charge ordering is observed. The transition is accompanied by a paramagnetic–paramagnetic anomaly in the magnetic susceptibility data which can be interpreted on the basis of spin-gap formation. The transition mechanism in the α polymorph is very similar to that observed earlier in the β polymorph at 185 K.
Effects of texture on surface attachment of spawning‐run sea lampreys Petromyzon marinus: a quantitative analysis
Authors: Adams R. D. , Reinhardt U. G.
Published: October 2008

Adult sea lamprey Petromyzon marinus attachment strength by the oral sucker was quantified. Surfaces with shallow, rounded discontinuities into which the oral fimbriae could be folded yielded the strongest seal and some fish could control their mouths to improve ‘suction’. Narrow grooves of 1 mm width and 3 mm depth prevented P. marinus from creating a lasting attachment.
Variability in the mating calls of the Lusitanian toadfish Halobatrachus didactylus: cues for potential individual recognition
Authors: Amorim M. C. P. , Vasconcelos R. O.
Published: October 2008

The mating sounds (boatwhistles) of nesting batrachoidid Halobatrachus didactylus males were recorded in the Tagus Estuary from piers. Thirteen males with 16 boatwhistles per fish were analysed for 20 acoustic features. All variables showed larger between‐male than within‐male variation and differed significantly among individuals. Discriminant function analyses (DFA) considering seven of these variables assigned 90–100% of boatwhistles to the correct individual, depending on the number of males and number of sounds per male included in the model. The acoustic features that consistently best discriminated individuals were the dominant frequency of the middle tonal segment of the boatwhistle (P2) and dominant frequency modulation, followed by P2 pulse period, amplitude modulation and sound duration. These results suggest the possibility of individual recognition based on acoustic cues.
Temporal patterns of growth in larval cohorts of the Japanese sardine Sardinops melanostictus in a coastal nursery area
Authors: Plaza G. , Ishida M. , Aoyama D.
Published: October 2008

Growth patterns of larval sardine Sardinops melanostictus were studied in a coastal nursery area, in southern Japan for four monthly hatch cohorts of larvae (November, December, January and February) for the 2003–2004 and 2004–2005 seasons. Laird–Gompertz models were fitted to each cohort using both total length (LT)‐at‐age at capture and mean LT‐at‐age data derived from backcalculations. In both approaches, the absolute daily growth rates (GR) and absolute daily growth rates at the inflection point (GXO) were estimated. In parallel, individual growth rates (GI) were derived from backcalculated LT (LB). Growth showed the following general common patterns irrespective of hatch month, season and methods: (1) significant Laird–Gompertz fits, (2) asymptotic growth, (3) a decrease in GR after the inflexion point, except for February for the 2003–2004 season that showed an apparent constant growth pattern, (4) six in eight cohorts showed GXO ranging from 0·8 to 1·2 mm day−1 and (5) a decreasing tendency of GI from 1·75 to 0·24 mm day−1, from first feeding through the first month of larval life. The contrasting pattern between the 2003–2004 and the 2004–2005 seasons were: (1) allometric v. logarithmic (ln) LT and otolith radius relationships, (2) low GXOv. high GXO, (3) high GRv. low GR when growth turned asymptotic, (4) low GXOv. high GXO when monthly hatch cohorts were combined and (5) LB and GI not differing among monthly hatch cohorts. The differences in growth patterns and growth rates between seasons seemed to be linked to the influx of warmer and oligotrophic waters of the Kuroshio Current that triggered an increase of 3° C in the coastal area for the 2003–2004 seasons. In the overall context, however, the high GXO, within cohorts and seasons reported in the current study, suggests that either sea surface temperature (SST) or food availability, or both are in the optimal range of preferences for S. melanostictus larvae. Consequently, nearshore coastal areas seem to be playing an important role as a nursery area for the larval stage of this species.
Effects of different capture techniques on the physiological condition of bonefishAlbula vulpesevaluated using field diagnostic tools
Authors: Cooke S. J. , Suski C. D. , Danylchuk S. E. , Danylchuk A. J. , Donaldson M. R. , Pullen C. , Bulté G. , O’toole A. , Murchie K. J. , Koppelman J. B. , Shultz A. D. , Brooks E. , Goldberg T. L.
Published: October 2008

A study was conducted on bonefishAlbula vulpesin The Bahamas to assess the utility of portable physiological diagnostic tools (i‐STAT analyser with E3+ ion and haematology cartridge, ACCU‐CHEK glucose meter and Lactate Pro lactate meter) for field physiology applications in remote locations. Physiological values derived from portable diagnostic tools were significantly related to values obtained from standard laboratory techniques [glucose (r2= 0·96), packed cell volume (PCV;r2= 0·33), Na+(r2= 0·28), K+(r2= 0·71) and Cl−(r2= 0·15)]. Actual values (i.e.intercepts), however, tended to deviate slightly between the two techniques. Nonetheless, these tools showed promise for documenting relative differences among fishes experimentally exposed to treatments inducing different levels of ‘stress’. These tools were then used to characterize the effects of different capture techniques on the stress response ofA. vulpes.Albula vulpescaptured in seines and then temporarily held in pens were physiologically sampled between 1 and 45 min postcapture to evaluate postcapture stress dynamics. Blood glucose and lactate as well as PCV and haemoglobin (Hb) increased rapidly after capture but stabilized at maximal values byc.20 min postcapture. When angled, largerA. vulpestook longer to exhaust and land than did smaller individuals. In addition, there was a positive relationship between the magnitude of increase in lactate and the duration of the angling event, implying that anglers can reduce stress by minimizing the duration of the fight. Fish sampled before and after a simulated angling treatment displayed clear increases in blood lactate, K+, PCV and Hb, providing some of the first data on how individualA. vulpesrespond to angling stress. In summary, this study revealed that techniques are now available for conducting field physiological studies onA. vulpesand possibly other species in remote locales, and that haematological and biochemical indicators of physiological disturbance vary with the intensity of the angling event.
Measurement of blood volume in the elasmobranch fish Scyliorhinus canicula following acute and long‐term salinity transfers
Authors: Good J. P. , Wells A. , Hazon N.
Published: October 2008

A technique using 51chromium‐labelled erythrocytes was used to measure blood volume in Scyliorhinus canicula following long‐term and acute salinity transfers. Basal whole‐blood volume was 5·6 ± 0·2 ml 100 g−1 (mean ±s.e.), this increased (6·3 ± 0·2 ml 100 g−1) following +14 day acclimation to 80% sea water (SW) and decreased (4·6 ± 0·2 ml 100 g−1) following acclimation to 120% SW. These changes were shown to be primarily due to changes in plasma volume, with no significant changes in extrapolated red‐cell volume being demonstrated. Blood volume was also measured in the same animals during 10 h acute transfer to 100% SW. Plasma volume in S. canicula during acclimation from 80% SW was significantly reduced (4·5 ± 0·3 ml 100 g−1) after 6 h of transfer to 100% SW. Blood volume in animals during acclimation from 120% SW was significantly increased (4·8 ± 0·2 ml 100 g−1) after 4 h of acute transfer. The osmoregulatory implications of these different timeframes during hyposaline and hypersaline transfer are discussed, along with the importance of this in vivo technique as context for in vitro studies with haemo‐dynamic stimuli.
Growth, maturity and fecundity of female spotted wolffish Anarhichas minor in Icelandic waters
Authors: Gunnarsson Á. , Hjörleifsson E. , Thórarinsson K. , Marteinsdóttir G.
Published: October 2008

Fecundity, maturity and growth of spotted wolffish Anarhichas minor were studied in Icelandic waters. A total of 477 female A. minor were sampled. The time from the onset of the cortical alveolus stage until spawning was on average 5 years. The total length (LT50) and age (A50) at 50% maturity for spawning fish was 827 mm and 9·1 years. Observed average annual growth was 65 mm for A. minor at the age range 5–10 years. Spawning fish grew faster than fish at the cortical alveolus stage. Growth and maturity of A. minor in Iceland appeared to be similar to growth and maturity of A. minor in the Barents Sea. The fecundity of Barents Sea fish was, however, higher than Icelandic fish.
Parthenogenesis in a large‐bodied requiem shark, the blacktip Carcharhinus limbatus
Authors: Chapman D. D. , Firchau B. , Shivji M. S.
Published: October 2008

Genetic evidence is provided for parthenogenesis in a large‐bodied shark, the blacktip Carcharhinus limbatus, from the speciose and commercially important family Carcharhinidae, the first verified case of asexual development in this lineage and only the second for any chondrichthyan. The parthenogenetic embryo exhibited elevated homozygosity relative to its mother, indicating that automictic parthenogenesis is the most likely mechanism. Although this finding shows that parthenogenesis is more common and widespread in sharks than previously realized and supports the early existence of parthenogenetic abilities in vertebrates, the adaptive significance of automixis in these ancient fishes remains unclear.
Otolith formation, microstructure and daily increment validation in juvenile perch Perca fluviatilis
Authors: Kristensen P. B. , Closs G. P. , Lokman P. M. , Grønkjær P.
Published: October 2008

The otoliths of laboratory‐reared larval and juvenile perch Perca fluviatilis of known age were analysed to determine the age of otolith formation and validate the formation of daily increments. There was a linear relationship between number of increments and age in days post‐hatching, although by 82 days post‐hatching daily increment counts underestimated actual age by an average of 5 days. Otolith dimensions in relation to standard length indicated allometric growth of otoliths until completion of yolk absorption, and isometric growth thereafter, up to 82 days post‐hatching.
Autumnal shift from diurnal to nocturnal peaking feeding activity of Rutilus rutilus in boreal lake littoral zones
Authors: Hautala A.
Published: October 2008

The possibility that the feeding activity of roach Rutilus rutilus shows an autumnal shift towards hours of lower light intensity in shallow and illuminated habitats in temperate watercourses as a consequence of relatively increasing daytime predation risk was tested in a littoral zone of a large boreal lake using trapping experiments. Autumnal feeding activity of R. rutilus first showed a striking shift from day to twilight when water temperature fell from 20 to 10° C, and a low but steady night activity prevailed in late autumn, when temperature had fallen to 5° C and the length of the night had increased. The size of the captured littoral R. rutilus also increased throughout the autumn. Both shifts may be linked to increasing daytime predation risk and decreasing food demand and availability.
Acoustic ontogeny of a teleost
Authors: Horne J. K.
Published: October 2008

The influence of growth on the intensity and variability of acoustic echoes from individuals and groups of a teleosts was quantified using Donaldson trout (rainbow–steelhead hybrid) Oncorhynchus mykiss. Fish growth was linear in total length (LT) and quadratic in mass. Dorsal swimbladder area increased exponentially with LT. Allometric growth ratio (i.e. k) values of swimbladder length linearly increased with LT. Average swimbladder volumes occupied 3–6% of fish body volume and increased exponentially with LT. The aspect angle that resulted in the maximum average acoustic intensity from the group shifted from 80 to 86° through the experimental period. Mean echo intensities increased at both 38 and 120 kHz as mean LT increased. Predicted echo intensities at 38 kHz exceeded that at 120 kHz at LT <150 mm but were less than that predicted at 120 kHz at LT >280 mm. Generalized additive mixed models using LT, swimbladder angles and lateral elongation ratios of fish bodies were better predictors of echo intensities than LT alone.
Foraging rates and substratum selection in foraging activity of checkered snapper Lutjanus decussatus (Lutjanidae) in an Okinawan coral reef
Authors: Nanami A. , Yamada H.
Published: October 2008

The activity patterns and substratum selection for foraging of checkered snapper Lutjanus decussatus were observed. The foraging rate of small‐sized individuals (<150 mm in total length, LT) was significantly greater than that of large‐sized individuals (≥150 mm LT). There was significant positive use of live branching corals, whereas negative use of coral rubble, rocks and sand for both small‐sized and large‐sized individuals.
Crystal structure of Methanococcus jannaschii TATA box‐binding protein
Authors: Adachi Naruhiko , Senda Miki , Natsume Ryo , Senda Toshiya , Horikoshi Masami
Published: October 2008

As the archaeal transcription system consists of a eukaryotic‐type transcription apparatus and bacterial‐type regulatory transcription factors, analyses of the molecular interface between the transcription apparatus and regulatory transcription factors are critical to reveal the evolutionary change of the transcription system. TATA box‐binding protein (TBP), the central components of the transcription apparatus are classified into three groups: eukaryotic, archaeal‐I and archaeal‐II TBPs. Thus, comparative functional analysis of these three groups of TBP is important for the study of the evolution of the transcription system. Here, we present the first crystal structure of an archaeal‐II TBP from Methanococcus jannaschii. The highly conserved and group‐specific conserved surfaces of TBP bind to DNA and TFIIB/TFB, respectively. The phylogenetic trees of TBP and TFIIB/TFB revealed that they evolved in a coupled manner. The diversified surface of TBP is negatively charged in the archaeal‐II TBP, which is completely different from the case of eukaryotic and archaeal‐I TBPs, which are positively charged and biphasic, respectively. This difference is responsible for the diversification of the regulatory functions of TBP during evolution.
Hyperglycemia induces oxidative and nitrosative stress and increases renal functional impairment in Nrf2‐deficient mice
Authors: Yoh Keigyou , Hirayama Aki , Ishizaki Kazusa , Yamada Akiko , Takeuchi Masayoshi , Yamagishi Sho‐ichi , Morito Naoki , Nakano Takako , Ojima Masami , Shimohata Homare , Itoh Ken , Takahashi Satoru , Yamamoto Masayuki
Published: October 2008

The transcription factor Nrf2 regulates the expression of antioxidant genes. Hyperglycemia‐induced oxidative stress is involved in the pathogenesis of diabetes and its complications. However, little is known about the protective role of Nrf2 in diabetes. To gain insight into the protective role of Nrf2 in diabetes we treated Nrf2 knockout (Nrf2 KO) mice with streptozotocin (STZ). The STZ Nrf2 KO mice did not develop renal hyperfiltration, which was observed in the STZ‐treated wild‐type (STZ WT) mice, but renal function gradually deteriorated over the 10‐week observation period. Urinary excretion of nitric oxide metabolites and the occurrence of 8‐nitroguanosine, which was detected in glomerular lesions, were increased in STZ Nrf2 KO mice during the early stages after treatment. In vivo electron paramagnetic resonance analysis revealed an accelerated rate of decay of the 3‐carbamoyl‐2,2,5,5‐tetramethylpyrrolidine‐1‐oxyl spin probe signal in STZ Nrf2 KO mice. The addition of superoxide dismutase prolonged the half‐life of the signal, which suggested that increased oxygen radical formation occurred in the STZ Nrf2 KO mice. These results suggested that hyperglycemia increased oxidative and nitrosative stress and accelerated renal injury in the Nrf2 KO mice and that Nrf2 serves as a defense factor against some diabetic complications.
N‐acetyltransferase ARD1‐NAT1 regulates neuronal dendritic development
Authors: Ohkawa Noriaki , Sugisaki Shunichiro , Tokunaga Eri , Fujitani Kazuko , Hayasaka Takahiro , Setou Mitsutoshi , Inokuchi Kaoru
Published: October 2008

ARD1 and NAT1 constitute an N‐acetyltransferase complex where ARD1 holds the enzymatic activity of the complex. The ARD1–NAT1 complex mediates N‐terminal acetylation of nascent polypeptides that emerge from ribosomes after translation. ARD1 may also acetylate the internal lysine residues of proteins. Although ARD1 and NAT1 have been found in the brain, the physiological role and substrates of the ARD1–NAT1 complex in neurons remain unclear. Here we investigated role of N‐acetyltransferase activity in the process of neuronal development. Expression of ARD1 and NAT1 increased during dendritic development, and both proteins colocalized with microtubules in dendrites. The ARD1–NAT1 complex displayed acetyltransferase activity against a purified microtubule fraction in vitro. Inhibition of the complex limited the dendritic extension of cultured neurons. These findings suggest that the ARD1–NAT1 complex has acetyltransferase activity against microtubules in dendrites. Regulation by acetyltransferase activity is a novel mechanism that is required for dendritic arborization during neuronal development.
Nuclear inner membrane fusion facilitated by yeast Jem1p is required for spindle pole body fusion but not for the first mitotic nuclear division during yeast mating
Authors: Nishikawa Shuh‐ichi , Hirata Aiko , Endo Toshiya
Published: October 2008

During mating of budding yeast, Saccharomyces cerevisiae, two haploid nuclei fuse to produce a diploid nucleus. The process of nuclear fusion requires two J proteins, Jem1p in the endoplasmic reticulum (ER) lumen and Sec63p, which forms a complex with Sec71p and Sec72p, in the ER membrane. Zygotes of mutants defective in the functions of Jem1p or Sec63p contain two haploid nuclei that were closely apposed but failed to fuse. Here we analyzed the ultrastructure of nuclei in jem1Δ and sec71Δ mutant zygotes using electron microscope with the freeze‐substituted fixation method. Three‐dimensional reconstitution of nuclear structures from electron microscope serial sections revealed that Jem1p facilitates nuclear inner‐membrane fusion and spindle pole body (SPB) fusion while Sec71p facilitates nuclear outer‐membrane fusion. Two haploid SPBs that failed to fuse could duplicate, and mitotic nuclear division of the unfused haploid nuclei started in jem1Δ and sec71Δ mutant zygotes. This observation suggests that nuclear inner‐membrane fusion is required for SPB fusion, but not for SPB duplication in the first mitotic cell division.
Dental and anaesthetic management of children with dystrophic epidermolysis bullosa
Authors: LINDEMEYER ROCHELLE , WADENYA ROSE , MAXWELL LYNNE
Published: October 2008

Background.  Epidermolysis bullosa (EB) is a genetic disease associated with fragility and bullous lesions of the skin and mucous membranes. There are various patterns of inheritance and histopathology. The disease is associated with systemic and oral manifestations, among which may be dental decay necessitating oral rehabilitation. General anaesthesia is frequently required for oral rehabilitation in children with dystrophic EB. Paediatric dentists should be aware of the implications of dystrophic EB for dental and anaesthetic management.

Case report.  Two siblings with moderate to severe systemic and oral manifestations of dystrophic EB requiring extensive oral rehabilitation for rampant decay are described, including special anaesthetic techniques required for airway management and maintenance of skin integrity.

Conclusion.  Dystrophic EB is a rare genetic disorder in which vesiculobullous lesions occur with erosions and scarring of cutaneous and extracutaneous surfaces in the oral cavity. Poor oral hygiene results from efforts to avoid mucosal trauma, resulting in decay. The comprehensive care of children with dystrophic EB impacts not only dental management but anaesthesia administration as well.
Psychometric validation of the Chinese version of the Illness Perception Questionnaire‐Revised for patients with hypertension
Authors: Chen Shiah‐Lian , Tsai Jen‐Chen , Lee Wen‐Lieng
Published: October 2008

Title.  Psychometric validation of the Chinese version of the Illness Perception Questionnaire‐Revised for patients with hypertension.

Aim.  This paper is a report of a study to evaluate the psychometric properties of the Chinese version of the Illness Perception Questionnaire‐Revised using the technique of confirmatory factor analysis.

Background.  The Illness Perception Questionnaire‐Revised is the most commonly used instrument for assessing patients’ views of illness, and there is good evidence for the psychometric properties of the English version. However, there is inconsistency in the literature about how scores of the Illness Perception Questionnaire‐Revised should be used.

Method.  A cross‐sectional survey was conducted in three teaching hospitals in central Taiwan. The Chinese Illness Perception Questionnaire‐Revised was administered to a purposive sample of 358 patients with hypertension in 2005–2006.

Results.  Confirmatory factor analysis provided evidence of satisfactory factorial validity, convergent validity and discriminant validity of the Chinese Illness Perception Questionnaire‐Revised. Internal consistency was supported by adequate Cronbach’s alphas (ranging 0·67–0·87) and composite reliability (0·57–0·88). The factor structures of the identity and cause subscales were found to be an acceptable fit to the data. The findings of model evaluations supported the seven‐factor structure, after removal of six poorly fitting items. Second‐order analysis indicated two factors (control and negative illness representation) representing latent constructs underlying the factors of personal control, treatment control, consequence, timeline‐cyclic and emotional representation.

Conclusion.  The Chinese Illness Perception Questionnaire‐Revised is a reliable and valid instrument for the measurement of illness perceptions in patients with hypertension.
Collision fatality of raptors in wind farms does not depend on raptor abundance
Authors: De Lucas Manuela , Janss Guyonne F. E. , Whitfield D. P. , Ferrer Miguel
Published: October 2008

The number of wind farms is increasing worldwide. Despite their purported environmental benefits, wind energy developments are not without potential adverse impacts on the environment, and the current pace and scale of development proposals, combined with a poor understanding of their impacts, is a cause for concern.

Avian mortality through collision with moving rotor blades is one of the main adverse impacts of wind farms, yet long‐term studies are rare. We analyse bird fatalities in relation to bird abundance, and test several factors which have been hypothesized to be associated with bird mortality.

Bird abundance was compared with collision fatality records to identify species‐specific death risk. Failure time analysis incorporated censored mortality data in which the time of event occurrence (collision) was not known. The analysis was used to test null hypotheses of homogeneity in avian mortality distribution according to several factors.

There was no clear relationship between species mortality and species abundance, although all large‐bird collision victims were raptors and griffon vulture Gyps fulvus was most frequently killed. Bird mortality and bird abundance varied markedly among seasons, but mortality was not highest in the season with highest bird abundance. Mortality rates of griffon vultures did not differ significantly between years.

Bird collision probability depended on species, turbine height (taller = more victims) and elevation above sea level (higher = more victims), implicating species‐specific and topographic factors in collision mortality. There was no evidence of an association between collision probability and turbine type or the position of a turbine in a row.

Synthesis and applications. Bird abundance and bird mortality through collision with wind turbines were not closely related; this result challenges a frequent assumption of wind‐farm assessment studies. Griffon vulture was the most frequently killed species, and species‐specific flight behaviour was implicated. Vultures collided more often when uplift wind conditions were poor, such as on gentle slopes, when thermals were weak, and when turbines were taller at higher elevations. New wind installations and/or repowering of older wind farms with griffon vulture populations nearby, should avoid turbines on the top of hills with gentle slopes.
Forecasting the potential distribution of the invasive tunicate Didemnum vexillum
Authors: Herborg Leif‐Matthias , O’Hara Patrick , Therriault Thomas W.
Published: October 2008

Invasive species are a major threat to global biodiversity and their introduction can have significant economic consequences. The invasive tunicate Didemnum vexillum is a notorious invader with significant negative impacts on cultured shellfish and natural benthic communities, including commercially important ones.

We conducted an expert survey, identifying the five most important transport vectors for D. vexillum along the west coast of North America. We determined the spatially explicit vector density for all vectors in order to identify introduction hotspots. Additionally, we developed an environmental niche model based on 46 occurrence points and nine environmental variables to identify areas suitable for D. vexillum.

Spatial distribution of the most important transport vectors (slow‐moving vessels, aquaculture, fishing vessels, small vessels, and large commercial vessels) identified several hotspots with high vector densities. These proved to be a very good predictor of current D. vexillum occurrence in British Columbia (BC). Ecological niche modelling (Genetic Algorithm for Rule‐set Prediction) predicted suitable environments in southern BC, parts of central BC and along the east coast of the Queen Charlotte Islands. Independent validation of the model based on the current distribution in BC indicated good predictive accuracy. Additional analytical steps confirmed that no environmental variable dominated the predictions and we identified ranges of environmental conditions predicted suitable by the model.

We identified areas of high establishment probability for D. vexillum by combining the vector model and environmental niche model. Parts of central BC, the west coast of Vancouver Island and the Strait of Georgia are areas where D. vexillum is most likely to establish.

Synthesis and applications. Spatially explicit predictions of the potential distribution of biological invaders are crucial for informing risk assessments, development of management strategies, and resource allocation. While most studies only focus on one step in the invasion process, we successfully combined the likelihood of introduction and establishment. Results from this study are informing the canadian risk assessment of invasive tunicates, guiding current monitoring efforts, and providing a basis for potential intervention/mediation measures.
Insect seed predators and environmental change
Authors: Lewis Owen T. , Gripenberg Sofia
Published: October 2008

The seed‐to‐seedling transition may be a critical stage in determining the dynamics of plant populations. Insects which kill seeds either before or after dispersal can influence the population dynamics of individual plant species, and ultimately, plant diversity and assemblage composition.

We discuss the potential for insect seed predators to maintain diversity in plant assemblages and to structure their composition, with a particular focus on diverse tropical forest habitats. We suggest that our ability to understand the functional effects of insect seed predators is hampered by a shortage of unbiased information on (i) their responses to the density of prey seeds at different spatial scales, and (ii) their host plant specificity.

Density‐dependence and its implications may be best assessed using manipulative field experiments. Such approaches can reveal how insect seed predators respond behaviourally and demographically to the density of individual host species and multiple host species across a range of spatial scales.

Host specificity and its implications may be best addressed through quantitative food web approaches previously applied largely to host–parasitoid interactions. Food webs will allow ecologists to assess the likely importance of indirect interactions such as apparent competition and apparent mutualism in structuring plant assemblages, and the functional consequences of adding or removing individual resource or consumer species.

Fully quantifying the wider effects of seed predators will require studies that better integrate seed stage‐specific demographic information, and which quantify the long‐term effects of variations in seed predation rates for plant recruitment.

Synthesis and applications. Compared to other functionally important insect groups such as pollinators, seed predators have received relatively little attention in the context of the functioning and sustainability of agro‐ecosystems and the consequences of global environmental change for ecological communities. A fuller understanding of the ecology of insect seed predator–plant interactions will be valuable to conservation and management in a range of natural and agricultural systems. For example, seed predator community ecology is relevant to predicting the consequences of deliberately or unintentionally introducing novel resource or consumer species; the process of habitat recovery following local disturbances; and managing the effects of pest or beneficial seed predators in agricultural crops. Furthermore, patterns of insect seed predation on a larger scale are likely to be highly sensitive to global environmental change drivers such as climate change and systematic habitat modification and fragmentation, with implications for the structure and organization of ecological communities more widely.
Living with a relative who has a spinal cord injury: a grounded theory approach
Authors: Chen Hsiao‐Yu , Boore Jennifer R P
Published: October 2008

Aims.  This paper reports a study which explored family carers’ experiences of taking care of a relative who has a spinal cord injury.

Background.  Spinal cord injury is one of the most disastrous injuries a person may experience. Although one family member experiences the injury, the entire family is affected. In Taiwan, family carers carry the primary responsibility of providing care on a 24‐hour basis during the rehabilitation hospitalisation. However, very limited research exists regarding their experiences.

Design.  This qualitative study has a cross‐sectional and descriptive‐explorative design.

Method.  Grounded theory was used to explore the psychosocial implications for family carer who has a relative with spinal cord injury.

Data collection and analysis.  Data were collected through in‐depth, tape‐recorded, semi‐structured interviews and observation of a group discussion and two religious activities in a rehabilitation hospital in Taiwan. Fifteen family carers participated in this study comprising eight individual interviews and seven participating in the group discussion. Data collection and analysis occurred concurrently.

Results.  The findings resulted in the core category ‘living with a relative who has a spinal cord injury’ and identified the experience of taking care of a relative who has a spinal cord injury. Three stages, including four categories: stage 1 ‘A catastrophic life event’; stage 2 ‘Confronting challenges’; and stage 3 ‘Family resilience’ or ‘Family breakdown’.

Conclusions.  This study shows that family carers experience a catastrophic life event, they have to confront challenges and the positive consequence is family resilience, the negative consequence is family breakdown.

Relevance to clinical practice.  Knowing how prospective family carers view their own situation and what they need is essential to provide effective nursing care for the family that has been changed dramatically by a spinal cord injury.
Registered nurses’ use of research findings in the care of older people
Authors: Boström Anne‐Marie , Kajermo Kerstin Nilsson , Nordström Gun , Wallin Lars
Published: October 2008

Aims.  To describe registered nurses’ reported use of research in the care of older people and to examine associations between research use and factors related to the elements: the communication channels, the adopter and the social system.

Background.  Research use among registered nurses working in hospital settings has been reported in many studies. Few studies, however, have explored the use of research among registered nurses working in the care of older people.

Design.  A cross‐sectional survey.

Methods.  In eight municipalities, all registered nurses (n = 210) working in older people care were invited to participate (response rate 67%). The Research Utilisation Questionnaire was adopted. Questions concerning the work organisation and research‐related resources were sent to the Community Chief Nurse at each municipality. Descriptive statistics and logistic regression were applied.

Results.  The registered nurses reported a relatively low use of research findings in daily practice, despite reporting a positive attitude to research. The registered nurses reported lack of access to research reports at the work place and that they had little support from unit managers and colleagues. Registered nurses working in municipalities with access to research‐related resources reported more use of research than registered nurses without resources. The factors ‘Access to research findings at work place’, ‘Positive attitudes to research’ and ‘Nursing programme at university level’ were significantly associated with research use.

Conclusions.  There is a great potential to increase registered nurses’ use of research findings in the care of older people. Factors which were linked to the communication channels and the adopter were associated with research use.

Relevance to clinical practice.  Strategies to enhance research use should focus on access to and adequate training in using information sources, increased knowledge on research methodology and nursing science and a supportive organisation.
Clinical indicators of ineffective airway clearance in children with congenital heart disease
Authors: Da Silva Viviane Martins , De Oliveira Lopes Marcos Venícios , De Araujo Thelma Leite , Ciol Marcia Aparecida , De Carvalho Emília Campos
Published: October 2008

Aims and objectives.  To analyse the sensitivity and specificity of clinical indicators of ineffective airway clearance in children with congenital heart disease and to identify the indicators that have high predictive power.

Background.  The precise establishment of nursing diagnoses has been found to be one of the factors contributing to higher quality of care and cost reduction in healthcare institutions. The use of indicators to diagnose ineffective airway clearance could improve care of children with congenital heart disease.

Design.  Longitudinal study.

Methods.  Participants consisted of 45 children, ≤1 year of age, with congenital heart disease, who had not had definitive or palliative surgical correction. Six assessments were made at 2‐day intervals. Each clinical indicator was defined based on previously established operational criteria. Sensitivity, specificity and positive and negative predictive values of each indicator were calculated based on a model for the longitudinal data.

Results.  A nursing diagnosis of ineffective airway clearance was made in 31% of patients on the first assessment, rising to 71% on the last assessment, for a 40% increase. Sensitivity was highest for Changes in Respiratory Rates/Rhythms (0·99), followed by Adventitious Breath Sounds (0·97), Sputum Production (0·85) and Restlessness (0·53). Specificity was higher for Sputum Production (0·92), followed by Restlessness (0·73), Adventitious Breath Sounds (0·70) and Changes in Respiratory Rates/Rhythms (0·17). The best positive predictive values occurred for Sputum Production (0·93) and Adventitious Breath Sounds (0·80).

Conclusions.  Adventitious Breath Sounds followed by Sputum Production were the indicators that had the best overall sensitivity and specificity as well as the highest positive predictive values.

Relevance to clinical practice.  The use of simple indicators in nursing diagnoses can improve identification of ineffective airway clearance in children with congenital heart disease, thus leading to early treatment of the problem and better care for these children.
Cell–cell communication in filamentous cyanobacteria
Authors: Haselkorn Robert
Published: October 2008

Although cytoplasmic bridges between adjacent cells in the filaments of nitrogen‐fixing cyanobacteria have been known for decades, the existence also of a continuous periplasm along the filaments raised the possibility that alternative modes of communication between cells could be utilized. The latter hypothesis was investigated by using GFP fusions to proteins whose expression is cell‐specific and engineered to be transported into the periplasm. Two groups have recently obtained contradictory results, one supporting periplasmic transport of GFP from cell to cell, the other not. A third effort, involving members of the first group, used a smaller, soluble fluorophore and found rapid communication via the cytoplasmic bridges between cells. The dilemma of periplasmic diffusion remains unresolved.
Existence of periplasmic barriers preventing green fluorescent protein diffusion from cell to cell in the cyanobacterium Anabaena sp. strain PCC 7120
Authors: Zhang Li‐Chen , Chen Yi‐Fei , Chen Wen‐Li , Zhang Cheng‐Cai
Published: October 2008

When deprived of combined nitrogen, the filamentous cyanobacterium Anabaena PCC 7120 relies on intercellular cooperation involving two cell types: nitrogen‐fixing heterocysts and photosynthetic vegetative cells. Heterocysts send fixed nitrogen to vegetative cells over long distances along the filament, receiving a reduced carbon source from them. These intercellular exchanges might involve a continuous periplasm along the filament or cytoplasm‐to‐cytoplasm conduits or both. In the present study, the green fluorescent protein (GFP) was fused to a twin‐arginine translocation signal sequence, which exported GFP to the periplasm of either a heterocyst using the heterocyst‐specific promoters PhepA and PpatB or to the periplasm of vegetative cells using the vegetative cell‐specific promoter PrbcL. Using the techniques of FRAP (fluorescence recovery after photobleaching) and FLIP (fluorescence loss in photobleaching), we found no evidence for intercellular diffusion of GFP through the periplasm, either from a heterocyst to vegetative cells or vice versa, or among vegetative cells. GFP could diffuse within the periplasm of the producing cell, but the diffusion stopped at the cell border. GFP diffusion could occur between two dividing cells before septum closure. This study indicates that barriers exist at the periplasmic space to prevent free GFP diffusion across cell border along the filament.
Transfection of haloarchaea by the DNAs of spindle and round haloviruses and the use of transposon mutagenesis to identify non‐essential regions
Authors: Porter Kate , Dyall‐Smith Michael L.
Published: October 2008

Spindle‐shaped halovirus His2 and spherical halovirus SH1 represent ecologically dominant virus morphotypes in high‐salt environments. Both have linear dsDNA genomes with inverted terminal repeat sequences and terminal proteins, and probably replicate using protein priming. As a first step towards conventional genetic analyses on these viruses, we show that purified viral DNAs can transfect host cells. Intact terminal proteins were essential for this process. Despite the narrow host ranges of these viruses, at least under laboratory conditions, their DNAs were able to transfect a wide range of haloarchaeal species, demonstrating that the cytoplasms of diverse haloarchaea possess all the factors necessary for viral DNA synthesis and virion assembly. Transposon mutagenesis of viral DNAs was then used in conjunction with transfection to produce recombinant viruses, and to then map the insertion sites to identify non‐essential genes. The inserts in 34 His2 mutants were mapped precisely, and most clustered in a few, specific regions, particularly in the inverted terminal repeats and near the ends of ORFs. The results are consistent with the small genome size and densely packed, often overlapping ORFs that are transcribed as long operons. This study is the first demonstration of transfection and transposon mutagenesis in protein‐primed archaeal viruses.
A novel streptococcal integrative conjugative element involved in iron acquisition
Authors: Heather Zoe , Holden Matthew T. G. , Steward Karen F. , Parkhill Julian , Song Lijiang , Challis Gregory L. , Robinson Carl , Davis‐Poynter Nicholas , Waller Andrew S.
Published: October 2008

In this study, we determined the function of a novel non‐ribosomal peptide synthetase (NRPS) system carried by a streptococcal integrative conjugative element (ICE), ICESe2. The NRPS shares similarity with the yersiniabactin system found in the high‐pathogenicity island of Yersinia sp. and is the first of its kind to be identified in streptococci. We named the NRPS product ‘equibactin’ and genes of this locus eqbA–N. ICESe2, although absolutely conserved in Streptococcus equi, the causative agent of equine strangles, was absent from all strains of the closely related opportunistic pathogen Streptococcus zooepidemicus. Binding of EqbA, a DtxR‐like regulator, to the eqbB promoter was increased in the presence of cations. Deletion of eqbA resulted in a small‐colony phenotype. Further deletion of the irp2 homologue eqbE, or the genes eqbH, eqbI and eqbJ encoding a putative ABC transporter, or addition of the iron chelator nitrilotriacetate, reversed this phenotype, implicating iron toxicity. Quantification of 55Fe accumulation and sensitivity to streptonigrin suggested that equibactin is secreted by S. equi and that the eqbH, eqbI and eqbJ genes are required for its associated iron import. In agreement with a structure‐based model of equibactin synthesis, supplementation of chemically defined media with salicylate was required for equibactin production.